[med-svn] [unanimity] 01/02: Imported Upstream version 2.0.2+20160812+ds
Afif Elghraoui
afif at moszumanska.debian.org
Wed Dec 7 07:10:07 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch draft-packaging
in repository unanimity.
commit d9039ac110499ce344f948fdbef5314cd3149f20
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Fri Aug 12 22:40:31 2016 -0700
Imported Upstream version 2.0.2+20160812+ds
---
.clang-format | 13 +
.gitignore | 2 +
.gitmodules | 12 +
CHANGELOG.md | 24 +
CMakeLists.txt | 52 +
LICENSE | 34 +
README.md | 44 +
circle.yml | 39 +
cmake/uny-ccache.cmake | 8 +
cmake/uny-codecoverage.cmake | 197 +
cmake/uny-compilerflags.cmake | 64 +
cmake/uny-config.cmake | 10 +
cmake/uny-dependencies.cmake | 62 +
cmake/uny-findpythonpath.cmake | 39 +
cmake/uny-gitsha1.cmake | 20 +
cmake/uny-releasewithassert.cmake | 6 +
.../.gitignore | 1 +
.../Makefile | 225 +
doc/ConsensusCore2-DesignAndImplementation/conf.py | 335 +
.../index.rst | 142 +
.../make.bat | 281 +
doc/DEVELOPER.md | 45 +
doc/INSTALL.md | 55 +
doc/PBCCS.md | 156 +
doc/TODO.md | 6 +
doc/img/unanimity.png | Bin 0 -> 2408 bytes
include/pacbio/Version.h.in | 65 +
include/pacbio/align/AffineAlignment.h | 86 +
include/pacbio/align/AlignConfig.h | 80 +
include/pacbio/align/BandedAligner.h | 582 +
include/pacbio/align/ChainScorer.h | 204 +
include/pacbio/align/ChainSeeds.h | 696 +
include/pacbio/align/ChainSeedsConfig.h | 105 +
include/pacbio/align/FilterSeeds.h | 123 +
include/pacbio/align/FindSeeds.h | 260 +
include/pacbio/align/FindSeedsConfig.h | 69 +
include/pacbio/align/HomopolymerHasher.h | 103 +
include/pacbio/align/LinearAlignment.h | 60 +
include/pacbio/align/PairwiseAlignment.h | 110 +
include/pacbio/align/SeedScorer.h | 254 +
include/pacbio/align/SparseAlignment.h | 176 +
include/pacbio/ccs/ChainSeeds.h | 51 +
include/pacbio/ccs/Consensus.h | 684 +
include/pacbio/ccs/SparseAlignment.h | 283 +
include/pacbio/ccs/Whitelist.h | 123 +
include/pacbio/chimera/ChimeraLabel.h | 127 +
include/pacbio/chimera/ChimeraLabeler.h | 710 +
include/pacbio/chimera/ChimeraResultWriter.h | 81 +
include/pacbio/consensus/AbstractIntegrator.h | 160 +
include/pacbio/consensus/AbstractMatrix.h | 67 +
include/pacbio/consensus/Coverage.h | 57 +
include/pacbio/consensus/EasyReadScorer.h | 69 +
include/pacbio/consensus/Evaluator.h | 111 +
include/pacbio/consensus/ModelConfig.h | 104 +
include/pacbio/consensus/ModelSelection.h | 54 +
include/pacbio/consensus/MonoMolecularIntegrator.h | 82 +
.../pacbio/consensus/MultiMolecularIntegrator.h | 80 +
include/pacbio/consensus/Mutation.h | 121 +
include/pacbio/consensus/Polish.h | 76 +
include/pacbio/consensus/PolishResult.h | 64 +
include/pacbio/consensus/Template.h | 195 +
include/pacbio/data/ChemistryMapping.h | 72 +
include/pacbio/data/ChemistryTriple.h | 78 +
include/pacbio/data/Interval.h | 174 +
include/pacbio/data/IntervalTree.h | 168 +
include/pacbio/data/Read.h | 112 +
include/pacbio/data/ReadId.h | 73 +
include/pacbio/data/Sequence.h | 49 +
include/pacbio/data/State.h | 63 +
include/pacbio/data/StrandType.h | 48 +
include/pacbio/data/SubreadResultCounter.h | 74 +
include/pacbio/denovo/PoaConsensus.h | 100 +
include/pacbio/denovo/PoaGraph.h | 127 +
include/pacbio/denovo/RangeFinder.h | 93 +
include/pacbio/denovo/SparsePoa.h | 162 +
include/pacbio/exception/CCSExceptions.h | 59 +
include/pacbio/exception/ModelError.h | 72 +
include/pacbio/exception/StateError.h | 78 +
include/pacbio/io/Utility.h | 73 +
include/pacbio/log/Logging.h | 406 +
include/pacbio/parallel/WorkQueue.h | 190 +
include/pacbio/util/ExecUtils.h | 61 +
include/pacbio/util/Timer.h | 59 +
scripts/cram | 9 +
scripts/makeChangeLog.py | 31 +
scripts/task_pbccs_ccs | 218 +
setup.py | 161 +
src/AbstractIntegrator.cpp | 203 +
src/CMakeLists.txt | 118 +
src/ChainSeeds.cpp | 319 +
src/ChemistryMapping.cpp | 94 +
src/ChemistryTriple.cpp | 87 +
src/Consensus.cpp | 61 +
src/Coverage.cpp | 125 +
src/EasyReadScorer.cpp | 67 +
src/Evaluator.cpp | 212 +
src/EvaluatorImpl.cpp | 244 +
src/EvaluatorImpl.h | 95 +
src/Interval.cpp | 62 +
src/JsonHelpers.h | 77 +
src/ModelConfig.cpp | 65 +
src/ModelFactory.cpp | 150 +
src/ModelFactory.h | 124 +
src/ModelFormFactory.cpp | 99 +
src/ModelFormFactory.h | 108 +
src/ModelSelection.cpp | 130 +
src/MonoMolecularIntegrator.cpp | 187 +
src/MultiMolecularIntegrator.cpp | 140 +
src/Mutation.cpp | 156 +
src/Polish.cpp | 345 +
src/Read.cpp | 102 +
src/ReadId.cpp | 68 +
src/Recursor.cpp | 50 +
src/Recursor.h | 801 +
src/Sequence.cpp | 98 +
src/SparsePoa.cpp | 226 +
src/SubreadResultCounter.cpp | 140 +
src/Template.cpp | 467 +
src/Timer.cpp | 61 +
src/Utility.cpp | 137 +
src/align/AffineAlignment.cpp | 234 +
src/align/AlignConfig.cpp | 58 +
src/align/LinearAlignment.cpp | 272 +
src/align/PairwiseAlignment.cpp | 329 +
src/main/ChimeraLabeler.cpp | 78 +
src/main/ccs.cpp | 658 +
src/matrix/ScaledMatrix.cpp | 99 +
src/matrix/ScaledMatrix.h | 149 +
src/matrix/SparseMatrix.cpp | 126 +
src/matrix/SparseMatrix.h | 190 +
src/matrix/SparseVector.h | 227 +
src/models/MarginalModelForm.cpp | 232 +
src/models/P6C4NoCovModel.cpp | 251 +
src/models/PwSnrAModelForm.cpp | 283 +
src/models/PwSnrModelForm.cpp | 284 +
src/models/S_P1C1Beta_Model.cpp | 216 +
src/models/S_P1C1v1_Model.cpp | 395 +
src/models/S_P1C1v2_Model.cpp | 396 +
src/models/SnrModelForm.cpp | 272 +
src/poa/BoostGraph.h | 43 +
src/poa/POA-NOTES.txt | 140 +
src/poa/PoaAlignmentMatrix.cpp | 128 +
src/poa/PoaAlignmentMatrix.h | 121 +
src/poa/PoaConsensus.cpp | 105 +
src/poa/PoaGraph.cpp | 103 +
src/poa/PoaGraphImpl.cpp | 453 +
src/poa/PoaGraphImpl.h | 267 +
src/poa/PoaGraphTraversals.cpp | 459 +
src/poa/RangeFinder.cpp | 251 +
src/poa/VectorL.h | 113 +
swig/Alignment.i | 17 +
swig/CMakeLists.txt | 61 +
swig/ConsensusCore2.i | 96 +
swig/Coverage.i | 14 +
swig/Evaluator.i | 9 +
swig/Integrator.i | 17 +
swig/Matrix.i | 12 +
swig/ModelConfig.i | 12 +
swig/Mutation.i | 9 +
swig/Poa.i | 11 +
swig/Polish.i | 8 +
swig/Read.i | 15 +
swig/State.i | 6 +
swig/Template.i | 11 +
swig/Version.i | 11 +
swig/numpy.i | 3161 +++
tests/CMakeLists.txt | 67 +
tests/cram/0passes.t | 11 +
tests/cram/100zmws.t | 411 +
tests/cram/100zmws_byStrand.t | 813 +
tests/cram/43385286.t | 8 +
tests/cram/nozfilter.t | 8 +
tests/cram/tiny.t | 28 +
tests/data/0passes.bam | Bin 0 -> 1142 bytes
tests/data/100zmws.bam | Bin 0 -> 864304 bytes
tests/data/43385286.bam | Bin 0 -> 3320 bytes
tests/data/Malformed.json | 0
tests/data/chimera_extensive.fasta | 503 +
tests/data/chimera_minimal.fasta | 220 +
..._c100564852550000001823085912221377_s1_X0.fasta | 109 +
tests/data/mapping.xml | 142 +
tests/data/params/SP1C1Beta.json | 208 +
tests/data/params/SP1C1v1.json | 1012 +
tests/data/params/SP1C1v2.json | 1026 +
tests/data/test.fastq | 40 +
tests/data/tiny.bam | Bin 0 -> 35094 bytes
tests/python/test_tool_contract.py | 61 +
tests/unit/ChimeraTest.cpp | 97 +
tests/unit/Mutations.cpp | 67 +
tests/unit/Mutations.h | 46 +
tests/unit/RandomDNA.cpp | 60 +
tests/unit/RandomDNA.h | 42 +
tests/unit/TestAlignment.cpp | 370 +
tests/unit/TestChemistry.cpp | 50 +
tests/unit/TestConsensus.cpp | 96 +
tests/unit/TestCoverage.cpp | 94 +
tests/unit/TestData.h.in | 47 +
tests/unit/TestIntegrator.cpp | 375 +
tests/unit/TestInterval.cpp | 249 +
tests/unit/TestLoadModels.cpp | 235 +
tests/unit/TestMutationEnumerator.cpp | 124 +
tests/unit/TestPoaConsensus.cpp | 603 +
tests/unit/TestPolish.cpp | 90 +
tests/unit/TestSequence.cpp | 52 +
tests/unit/TestSparseAlign.cpp | 163 +
tests/unit/TestSparsePoa.cpp | 299 +
tests/unit/TestSparseVector.cpp | 101 +
tests/unit/TestTemplate.cpp | 338 +
tests/unit/TestUtility.cpp | 74 +
tests/unit/TestUtility.h | 44 +
tests/unit/TestWhitelist.cpp | 80 +
third-party/cpp-optparse-fix-warnings.patch | 19 +
third-party/cpp-optparse/Makefile | 21 +
third-party/cpp-optparse/OptionParser.cpp | 577 +
third-party/cpp-optparse/OptionParser.h | 367 +
third-party/cpp-optparse/README | 51 +
third-party/cpp-optparse/test.cpp | 153 +
third-party/gmock-1.7.0/gmock-gtest-all.cc | 11443 +++++++++++
third-party/gmock-1.7.0/gmock/gmock.h | 14198 +++++++++++++
third-party/gmock-1.7.0/gmock_main.cc | 54 +
third-party/gmock-1.7.0/gtest/gtest.h | 20061 +++++++++++++++++++
tools/Darwin/clang-format | Bin 0 -> 2490044 bytes
tools/Linux/clang-format | Bin 0 -> 2754467 bytes
tools/check-formatting | 33 +
tools/format-all | 8 +
tools/git-clang-format | 485 +
tools/win32/clang-format.exe | Bin 0 -> 1315328 bytes
227 files changed, 82707 insertions(+)
diff --git a/.clang-format b/.clang-format
new file mode 100644
index 0000000..1519f35
--- /dev/null
+++ b/.clang-format
@@ -0,0 +1,13 @@
+BasedOnStyle: Google
+BreakBeforeBraces: Mozilla
+
+AllowShortLoopsOnASingleLine: false
+AccessModifierOffset: -4
+BreakConstructorInitializersBeforeComma: true
+ColumnLimit: 100
+IndentWidth: 4
+PointerAlignment: Left
+TabWidth: 4
+
+ReflowComments: false # protect ASCII art in comments
+KeepEmptyLinesAtTheStartOfBlocks: true
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..68fc691
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+.DS_Store
+/build
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..fae5e39
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,12 @@
+[submodule "third-party/htslib"]
+ path = third-party/htslib
+ url = https://github.com/PacificBiosciences/htslib
+ branch = pb
+[submodule "third-party/pbbam"]
+ path = third-party/pbbam
+ url = https://github.com/PacificBiosciences/pbbam
+ branch = master
+[submodule "third-party/seqan"]
+ path = third-party/seqan
+ url = https://github.com/PacificBiosciences/seqan.git
+ branch = master
\ No newline at end of file
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..870750f
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,24 @@
+# UNANIMITY - CHANGELOG
+
+## [2.0.2]
+
+### Added
+ - Fix index errors in the Hirschberg aligner
+ - Added a cleaner interface for AddRead/GetTemplate
+
+## [2.0.1]
+
+### Added
+ - Add new ReleaseWithAssert CMAKE_BUILD_TYPE
+ - Bump version (to cc2 + ccs)
+ - Unify CCS and CC2 versioning under unanimity
+ - Cleanup python/swig generation
+ - Cleanup version handling
+
+## [0.0.1]
+
+### Added
+ - Unify code base, refactor directory structure
+ - Add pbccs, ConsensusCore2, pbsparse, and pbchimera
+ - Code coverage report
+ - Initial framework including pbbam, htslib, pbcopper
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..96ed9fe
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,52 @@
+##############################################
+# CMake build script for the UNANIMITY library
+##############################################
+
+cmake_policy(SET CMP0048 NEW)
+project(UNANIMITY VERSION 2.0.2 LANGUAGES CXX C)
+cmake_minimum_required(VERSION 3.2)
+
+set(ROOT_PROJECT_NAME ${PROJECT_NAME} CACHE STRING "root project name")
+
+# Build type
+IF(NOT CMAKE_BUILD_TYPE)
+ SET(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: Debug Release Profile RelWithDebInfo ReleaseWithAssert" FORCE)
+ENDIF(NOT CMAKE_BUILD_TYPE)
+
+# Build-time options
+option(UNY_build_bin "Build binaries." ON)
+option(UNY_build_tests "Build UNANIMITY's unit tests." ON)
+option(UNY_inc_coverage "Include UNANIMITY's coverage script." OFF)
+option(UNY_use_ccache "Build UNANIMITY using ccache, if available." ON)
+
+# Main project paths
+set(UNY_RootDir ${UNANIMITY_SOURCE_DIR})
+set(UNY_IncludeDir ${UNY_RootDir}/include)
+set(UNY_SourceDir ${UNY_RootDir}/src)
+set(UNY_SwigDir ${UNY_RootDir}/swig)
+set(UNY_TestsDir ${UNY_RootDir}/tests)
+set(UNY_ThirdPartyDir ${UNY_RootDir}/third-party)
+
+# Project configuration
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake ${CMAKE_MODULE_PATH})
+
+# Fixed order, do not sort or shuffle
+include(uny-ccache)
+include(uny-compilerflags)
+include(uny-releasewithassert)
+include(uny-dependencies)
+include(uny-gitsha1)
+include(uny-config)
+
+# Build library
+add_subdirectory(${UNY_SourceDir})
+
+# Build tests
+if(UNY_build_tests)
+ add_subdirectory(${UNY_TestsDir})
+endif()
+
+# Swig
+if (PYTHON_SWIG)
+ add_subdirectory(${UNY_SwigDir})
+endif()
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..0e38eca
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,34 @@
+Copyright (c) 2016, Pacific Biosciences of California, Inc.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted (subject to the limitations in the
+disclaimer below) provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of Pacific Biosciences nor the names of its
+ contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGE.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..721bced
--- /dev/null
+++ b/README.md
@@ -0,0 +1,44 @@
+<p align="center">
+ <img src="doc/img/unanimity.png" alt="unanimity logo"/>
+</p>
+<h1 align="center">Unanimity</h1>
+<p align="center">C++ library and its applications to generate and process accurate consensus sequences</p>
+
+***
+## Documentation
+
+ - [Getting Started](doc/INSTALL.md)
+ - Projects
+ - Available
+ - Consensus Core
+ - [Circular Consensus Calling `ccs`](doc/PBCCS.md)
+ - Work in Progress
+ - Genomic Consensus Calling `gcpp`
+ - Viral Haplotype Phasing `eden`
+ - Planned
+ - Minor Variant Calling
+ - [Developer environment](doc/DEVELOPER.md)
+ - [PacBio open source license](LICENSE)
+
+## Quick Tools Overview
+
+### [Circular Consensus Calling](doc/PBCCS.md)
+
+`ccs` takes multiple reads of the same SMRTbell sequence and combines
+them, employing a statistical model, to produce one high quality consensus sequence.
+
+### [Genomic Consensus Calling](doc/GCPP.md)
+
+`gcpp` will replace the current python [GenomicConsensus](https://github.com/PacificBiosciences/GenomicConsensus), until then please use the existing solution.
+
+### Minor Variant Calling
+
+This tool will be able to precisely call single-nucleotide variants from consensus data.
+
+### [Viral Haplotype Phasing](doc/EDEN.md)
+
+`eden` will leverage CCS reads to identify low-frequency haplotypes within polyploid samples.
+
+## Help
+
+Issues? Bugs? Please create a github issue.
diff --git a/circle.yml b/circle.yml
new file mode 100644
index 0000000..8a3072f
--- /dev/null
+++ b/circle.yml
@@ -0,0 +1,39 @@
+machine:
+ python:
+ version: 2.7.9
+dependencies:
+ cache_directories:
+ - "_deps/cmake-3.3.0-Linux-x86_64"
+ - "_deps/boost_1_60_0"
+ - "_deps/swig-3.0.8"
+ pre:
+ - curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash
+ - sudo apt-get install git-lfs=1.1.0
+ - if [ ! -d _deps ] ; then mkdir _deps ; fi # Create a directory for dependencies, These are static, cache them.
+ - pushd _deps ; if [ ! -d cmake-3.3.0-Linux-x86_64 ] ; then wget --no-check-certificate https://www.cmake.org/files/v3.3/cmake-3.3.0-Linux-x86_64.tar.gz ; tar xzf cmake-3.3.0-Linux-x86_64.tar.gz ; fi
+ - pushd _deps ; if [ ! -d boost_1_60_0 ] ; then wget https://downloads.sourceforge.net/project/boost/boost/1.60.0/boost_1_60_0.tar.bz2 ; tar xjf boost_1_60_0.tar.bz2 ; fi
+ - pushd _deps ; if [ ! -f swig-3.0.8/bin/swig ] ; then rm -fr swig-3.0.8* ; mkdir dl ; pushd dl ; wget https://downloads.sourceforge.net/project/swig/swig/swig-3.0.8/swig-3.0.8.tar.gz ; tar xzf swig-3.0.8.tar.gz ; pushd swig-3.0.8 ; ./configure --prefix $(readlink -f ../../swig-3.0.8) ; make ; make install ; fi
+ - pushd _deps ; git clone https://github.com/PacificBiosciences/PacBioTestData.git
+ - pip install --upgrade pip
+ - pip install numpy cython h5py pysam cram nose
+ - pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcommand.git
+ - pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcore.git
+ - pushd _deps/PacBioTestData ; git lfs pull && make python
+ - mkdir _rev_deps # Create a directory for reverse-dependencies, ie things that depend on us. These are not static, do not cache them.
+ # Build ConsensusCore
+ - pushd _deps ; git clone https://github.com/PacificBiosciences/ConsensusCore.git
+ - pushd _deps/ConsensusCore ; python setup.py install --boost=$(readlink -f ../../_deps/boost_1_60_0) --swig=$(readlink -f ../../_deps/swig-3.0.8/bin/swig)
+ - pushd _rev_deps ; git clone https://github.com/PacificBiosciences/GenomicConsensus.git
+ - git submodule update --init --remote
+ override:
+ - CMAKE_BUILD_TYPE=ReleaseWithAssert CMAKE_COMMAND=$(readlink -f _deps/cmake-3.3.0-Linux-x86_64/bin/cmake) Boost_INCLUDE_DIRS=$(readlink -f _deps/boost_1_60_0) SWIG_COMMAND=$(readlink -f _deps/swig-3.0.8/bin/swig) VERBOSE=1 pip install --verbose --upgrade --no-deps .
+ - python -c "import ConsensusCore2 ; print ConsensusCore2.__version__"
+ - pushd _rev_deps/GenomicConsensus ; pip install --upgrade --no-deps --verbose .
+ - pushd _rev_deps/GenomicConsensus ; make check # Test GC
+test:
+ pre:
+ - mkdir _build
+ - pushd _build ; $(readlink -f ../_deps/cmake-3.3.0-Linux-x86_64/bin/cmake) -DBoost_INCLUDE_DIRS=$(readlink -f ../_deps/boost_1_60_0) -DCMAKE_BUILD_TYPE=ReleaseWithAssert ..
+ override:
+ - pushd _build ; make
+ - pushd _build ; make check
diff --git a/cmake/uny-ccache.cmake b/cmake/uny-ccache.cmake
new file mode 100644
index 0000000..56e88f3
--- /dev/null
+++ b/cmake/uny-ccache.cmake
@@ -0,0 +1,8 @@
+
+if(UNY_use_ccache)
+ find_program(CCACHE_FOUND ccache)
+ if(CCACHE_FOUND)
+ set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE ccache)
+ set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK ccache)
+ endif()
+endif()
diff --git a/cmake/uny-codecoverage.cmake b/cmake/uny-codecoverage.cmake
new file mode 100644
index 0000000..d115248
--- /dev/null
+++ b/cmake/uny-codecoverage.cmake
@@ -0,0 +1,197 @@
+# Copyright (c) 2012 - 2015, Lars Bilke
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this
+# list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+# this list of conditions and the following disclaimer in the documentation
+# and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its contributors
+# may be used to endorse or promote products derived from this software without
+# specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+#
+#
+# 2012-01-31, Lars Bilke
+# - Enable Code Coverage
+#
+# 2013-09-17, Joakim Söderberg
+# - Added support for Clang.
+# - Some additional usage instructions.
+#
+# USAGE:
+
+# 0. (Mac only) If you use Xcode 5.1 make sure to patch geninfo as described here:
+# http://stackoverflow.com/a/22404544/80480
+#
+# 1. Copy this file into your cmake modules path.
+#
+# 2. Add the following line to your CMakeLists.txt:
+# INCLUDE(CodeCoverage)
+#
+# 3. Set compiler flags to turn off optimization and enable coverage:
+# SET(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
+# SET(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
+#
+# 3. Use the function SETUP_TARGET_FOR_COVERAGE to create a custom make target
+# which runs your test executable and produces a lcov code coverage report:
+# Example:
+# SETUP_TARGET_FOR_COVERAGE(
+# my_coverage_target # Name for custom target.
+# test_driver # Name of the test driver executable that runs the tests.
+# # NOTE! This should always have a ZERO as exit code
+# # otherwise the coverage generation will not complete.
+# coverage # Name of output directory.
+# )
+#
+# 4. Build a Debug build:
+# cmake -DCMAKE_BUILD_TYPE=Debug ..
+# make
+# make my_coverage_target
+#
+#
+
+# Check prereqs
+FIND_PROGRAM( GCOV_PATH gcov )
+FIND_PROGRAM( LCOV_PATH lcov )
+FIND_PROGRAM( GENHTML_PATH genhtml )
+FIND_PROGRAM( GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/tests)
+
+IF(NOT GCOV_PATH)
+ MESSAGE(FATAL_ERROR "gcov not found! Aborting...")
+ENDIF() # NOT GCOV_PATH
+
+IF(NOT CMAKE_COMPILER_IS_GNUCXX)
+ # Clang version 3.0.0 and greater now supports gcov as well.
+
+ IF(NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+ MESSAGE(FATAL_ERROR "Compiler is not GNU gcc! Aborting...")
+ ENDIF()
+ENDIF() # NOT CMAKE_COMPILER_IS_GNUCXX
+
+SET(CMAKE_CXX_FLAGS_COVERAGE
+ "-g -O0 --coverage -fprofile-arcs -ftest-coverage"
+ CACHE STRING "Flags used by the C++ compiler during coverage builds."
+ FORCE )
+SET(CMAKE_C_FLAGS_COVERAGE
+ "-g -O0 --coverage -fprofile-arcs -ftest-coverage"
+ CACHE STRING "Flags used by the C compiler during coverage builds."
+ FORCE )
+SET(CMAKE_EXE_LINKER_FLAGS_COVERAGE
+ ""
+ CACHE STRING "Flags used for linking binaries during coverage builds."
+ FORCE )
+SET(CMAKE_SHARED_LINKER_FLAGS_COVERAGE
+ ""
+ CACHE STRING "Flags used by the shared libraries linker during coverage builds."
+ FORCE )
+MARK_AS_ADVANCED(
+ CMAKE_CXX_FLAGS_COVERAGE
+ CMAKE_C_FLAGS_COVERAGE
+ CMAKE_EXE_LINKER_FLAGS_COVERAGE
+ CMAKE_SHARED_LINKER_FLAGS_COVERAGE )
+
+IF ( NOT (CMAKE_BUILD_TYPE STREQUAL "Debug" OR CMAKE_BUILD_TYPE STREQUAL "Coverage"))
+ MESSAGE( WARNING "Code coverage results with an optimized (non-Debug) build may be misleading" )
+ENDIF() # NOT CMAKE_BUILD_TYPE STREQUAL "Debug"
+
+
+# Param _targetname The name of new the custom make target
+# Param _testrunner The name of the target which runs the tests.
+# MUST return ZERO always, even on errors.
+# If not, no coverage report will be created!
+# Param _outputname lcov output is generated as _outputname.info
+# HTML report is generated in _outputname/index.html
+# Optional fourth parameter is passed as arguments to _testrunner
+# Pass them in list form, e.g.: "-j;2" for -j 2
+FUNCTION(SETUP_TARGET_FOR_COVERAGE _targetname _testrunner _outputname)
+
+ IF(NOT LCOV_PATH)
+ MESSAGE(FATAL_ERROR "lcov not found! Aborting...")
+ ENDIF() # NOT LCOV_PATH
+
+ IF(NOT GENHTML_PATH)
+ MESSAGE(FATAL_ERROR "genhtml not found! Aborting...")
+ ENDIF() # NOT GENHTML_PATH
+
+ SET(coverage_info "${CMAKE_BINARY_DIR}/${_outputname}.info")
+ SET(coverage_cleaned "${coverage_info}.cleaned")
+
+ SEPARATE_ARGUMENTS(test_command UNIX_COMMAND "${_testrunner}")
+
+ # Setup target
+ ADD_CUSTOM_TARGET(${_targetname}
+
+ # Cleanup lcov
+ ${LCOV_PATH} --directory . --zerocounters
+
+ # Run tests
+ COMMAND ${test_command} ${ARGV3}
+
+ # Capturing lcov counters and generating report
+ COMMAND ${LCOV_PATH} --directory . --capture --output-file ${coverage_info}
+ COMMAND ${LCOV_PATH} --remove ${coverage_info} 'tests/*' '/usr/*' 'third-party/*' --output-file ${coverage_cleaned}
+ COMMAND ${GENHTML_PATH} -o ${_outputname} ${coverage_cleaned}
+ COMMAND ${CMAKE_COMMAND} -E remove ${coverage_info} ${coverage_cleaned}
+
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+ COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
+ )
+
+ # Show info where to find the report
+ ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
+ COMMAND ;
+ COMMENT "Open ./${_outputname}/index.html in your browser to view the coverage report."
+ )
+
+ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE
+
+# Param _targetname The name of new the custom make target
+# Param _testrunner The name of the target which runs the tests
+# Param _outputname cobertura output is generated as _outputname.xml
+# Optional fourth parameter is passed as arguments to _testrunner
+# Pass them in list form, e.g.: "-j;2" for -j 2
+FUNCTION(SETUP_TARGET_FOR_COVERAGE_COBERTURA _targetname _testrunner _outputname)
+
+ IF(NOT PYTHON_EXECUTABLE)
+ MESSAGE(FATAL_ERROR "Python not found! Aborting...")
+ ENDIF() # NOT PYTHON_EXECUTABLE
+
+ IF(NOT GCOVR_PATH)
+ MESSAGE(FATAL_ERROR "gcovr not found! Aborting...")
+ ENDIF() # NOT GCOVR_PATH
+
+ ADD_CUSTOM_TARGET(${_targetname}
+
+ # Run tests
+ ${_testrunner} ${ARGV3}
+
+ # Running gcovr
+ COMMAND ${GCOVR_PATH} -x -r ${CMAKE_SOURCE_DIR} -e '${CMAKE_SOURCE_DIR}/tests/' -o ${_outputname}.xml
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+ COMMENT "Running gcovr to produce Cobertura code coverage report."
+ )
+
+ # Show info where to find the report
+ ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
+ COMMAND ;
+ COMMENT "Cobertura code coverage report saved in ${_outputname}.xml."
+ )
+
+ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE_COBERTURA
\ No newline at end of file
diff --git a/cmake/uny-compilerflags.cmake b/cmake/uny-compilerflags.cmake
new file mode 100644
index 0000000..f5ede27
--- /dev/null
+++ b/cmake/uny-compilerflags.cmake
@@ -0,0 +1,64 @@
+
+include(CheckCXXCompilerFlag)
+
+# shared CXX flags for all source code & tests
+set(UNY_FLAGS "-std=c++11 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable")
+
+# gperftools support
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
+ set(UNY_LINKER_FLAGS "${UNY_LINKER_FLAGS} -Wl,-no_pie")
+endif(CMAKE_BUILD_TYPE STREQUAL "Debug")
+
+# static linking
+IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
+ set(UNY_LINKER_FLAGS "${UNY_LINKER_FLAGS} -static-libgcc -static-libstdc++")
+ENDIF()
+
+# NOTE: quash clang warnings w/ Boost
+check_cxx_compiler_flag("-Wno-unused-local-typedefs" HAS_NO_UNUSED_LOCAL_TYPEDEFS)
+if(HAS_NO_UNUSED_LOCAL_TYPEDEFS)
+ set(UNY_FLAGS "${UNY_FLAGS} -Wno-unused-local-typedefs")
+endif()
+
+# Cannot use this until pbbam complies
+# if (CMAKE_COMPILER_IS_GNUCXX)
+# set(UNY_FLAGS "${UNY_FLAGS} -Werror=suggest-override")
+# endif()
+
+# Coverage settings
+if (UNY_inc_coverage)
+ set(UNY_COV_FLAGS "${UNY_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+
+# Extra testing that will lead to longer compilation times!
+if (SANITIZE)
+ # AddressSanitizer is a fast memory error detector
+ set(UNY_SANITY_FLAGS "${UNY_SANITY_FLAGS} -fsanitize=address -fno-omit-frame-pointer -fno-optimize-sibling-calls")
+
+ # Clang Thread Safety Analysis is a C++ language extension which warns about
+ # potential race conditions in code.
+ set(UNY_SANITY_FLAGS "${UNY_SANITY_FLAGS} -Wthread-safety")
+
+ # ThreadSanitizer is a tool that detects data races
+ set(UNY_SANITY_FLAGS "${UNY_SANITY_FLAGS} -fsanitize=thread")
+
+ # MemorySanitizer is a detector of uninitialized reads.
+ set(UNY_SANITY_FLAGS "${UNY_SANITY_FLAGS} -fsanitize=memory")
+
+ # UndefinedBehaviorSanitizer is a fast undefined behavior detector.
+ set(UNY_SANITY_FLAGS "${UNY_SANITY_FLAGS} -fsanitize=undefined")
+endif()
+
+# shared CXX flags for src & tests
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${UNY_FLAGS}")
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${UNY_COV_FLAGS} ${UNY_SANITY_FLAGS}")
+SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${UNY_LINKER_FLAGS}")
+
+
+# Set additionally needed linker flags
+if(APPLE)
+ set(PRE_LINK -force_load)
+elseif(UNIX)
+ SET(PRE_LINK -Wl,-whole-archive)
+ SET(POST_LINK -Wl,-no-whole-archive)
+endif()
\ No newline at end of file
diff --git a/cmake/uny-config.cmake b/cmake/uny-config.cmake
new file mode 100644
index 0000000..d60010a
--- /dev/null
+++ b/cmake/uny-config.cmake
@@ -0,0 +1,10 @@
+# Config generation
+
+find_git_sha1(UNANIMITY_GIT_SHA1)
+
+file (STRINGS "${UNY_RootDir}/CHANGELOG.md" UNANIMITY_CHANGELOG)
+
+configure_file(
+ ${UNY_IncludeDir}/pacbio/Version.h.in
+ ${CMAKE_BINARY_DIR}/generated/pacbio/Version.h
+)
diff --git a/cmake/uny-dependencies.cmake b/cmake/uny-dependencies.cmake
new file mode 100644
index 0000000..6721d96
--- /dev/null
+++ b/cmake/uny-dependencies.cmake
@@ -0,0 +1,62 @@
+
+# External libraries
+
+# Get static libraries
+SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+
+# pbcopper
+# if (NOT pbcopper)
+# add_subdirectory(${UNY_ThirdPartyDir}/pbcopper external/pbcopper/build)
+# endif()
+
+# Boost
+if(NOT Boost_INCLUDE_DIRS)
+ find_package(Boost REQUIRED)
+endif()
+
+# only require if NOT called from pip install
+if (NOT PYTHON_SWIG)
+ # Threads
+ if (NOT Threads)
+ find_package(Threads REQUIRED)
+ endif()
+
+ # ZLIB
+ if (NOT ZLIB_INCLUDE_DIRS OR NOT ZLIB_LIBRARIES)
+ find_package(ZLIB REQUIRED)
+ endif()
+
+ # htslib
+ if(NOT HTSLIB_INCLUDE_DIRS OR
+ NOT HTSLIB_LIBRARIES)
+ find_package(htslib
+ PATHS ${UNY_ThirdPartyDir}/htslib
+ REQUIRED)
+ endif()
+
+ # pbbam
+ if (NOT PacBioBAM_INCLUDE_DIRS OR
+ NOT PacBioBAM_LIBRARIES)
+ set(PacBioBAM_build_docs OFF CACHE INTERNAL "" FORCE)
+ set(PacBioBAM_build_tests OFF CACHE INTERNAL "" FORCE)
+ set(PacBioBAM_build_tools OFF CACHE INTERNAL "" FORCE)
+ add_subdirectory(${UNY_ThirdPartyDir}/pbbam external/pbbam/build)
+ if (TARGET htslib)
+ add_dependencies(pbbam htslib)
+ endif()
+ endif()
+
+ # cpp-optparse sources
+ if (NOT CPPOPTPARSE_CPP)
+ set(CPPOPTPARSE_CPP ${UNY_ThirdPartyDir}/cpp-optparse/OptionParser.cpp CACHE INTERNAL "" FORCE)
+ endif()
+
+ if (NOT CPPOPTPARSE_IncludeDir)
+ set(CPPOPTPARSE_IncludeDir ${UNY_ThirdPartyDir}/cpp-optparse CACHE INTERNAL "" FORCE)
+ endif()
+
+ # seqan headers
+ if (NOT SEQAN_INCLUDE_DIRS)
+ set(SEQAN_INCLUDE_DIRS ${UNY_ThirdPartyDir}/seqan/include CACHE INTERNAL "" FORCE)
+ endif()
+endif()
diff --git a/cmake/uny-findpythonpath.cmake b/cmake/uny-findpythonpath.cmake
new file mode 100644
index 0000000..9a5d751
--- /dev/null
+++ b/cmake/uny-findpythonpath.cmake
@@ -0,0 +1,39 @@
+
+if (__find_python_inc)
+ return()
+endif()
+set(__find_python_inc YES)
+
+function(find_python_inc _PYTHON_INC)
+ # find the executable
+ if (NOT PYTHON_EXECUTABLE)
+ find_package(PythonInterp REQUIRED)
+ endif()
+ # find the include directory
+ execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
+ "from __future__ import print_function; import distutils.sysconfig; print(distutils.sysconfig.get_python_inc(), end='')"
+ RESULT_VARIABLE PYTHON_INCLUDE_SUCCESS
+ OUTPUT_VARIABLE PYTHON_INCLUDE_DIRS)
+ # check for success
+ if (NOT PYTHON_INCLUDE_SUCCESS EQUAL 0 OR
+ NOT PYTHON_INCLUDE_DIRS)
+ message(FATAL_ERROR "${_PYTHON_INC} needs to be set manually")
+ endif()
+ # set the output variables
+ set(${_PYTHON_INC} "${PYTHON_INCLUDE_DIRS}" PARENT_SCOPE)
+endfunction()
+
+function(find_numpy_inc _NUMPY_INC)
+ if (NOT PYTHON_EXECUTABLE)
+ find_package(PythonInterp REQUIRED)
+ endif()
+ execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
+ "from __future__ import print_function; import numpy; print(numpy.get_include(), end='')"
+ RESULT_VARIABLE NUMPY_INCLUDE_SUCCESS
+ OUTPUT_VARIABLE NUMPY_INCLUDE_DIRS)
+ if (NOT NUMPY_INCLUDE_SUCCESS EQUAL 0 OR
+ NOT NUMPY_INCLUDE_DIRS)
+ message(FATAL_ERROR "NUMPY_INCLUDE_DIRS needs to be set manually")
+ endif()
+ set(${_NUMPY_INC} "${NUMPY_INCLUDE_DIRS}" PARENT_SCOPE)
+endfunction()
diff --git a/cmake/uny-gitsha1.cmake b/cmake/uny-gitsha1.cmake
new file mode 100644
index 0000000..8a25e7a
--- /dev/null
+++ b/cmake/uny-gitsha1.cmake
@@ -0,0 +1,20 @@
+
+if(__find_git_sha1)
+ return()
+endif()
+set(__find_git_sha1 YES)
+
+function(find_git_sha1 _GIT_SHA1)
+ find_package(Git QUIET REQUIRED)
+ execute_process(COMMAND
+ "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=*"
+ WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+ RESULT_VARIABLE res
+ OUTPUT_VARIABLE out
+ ERROR_QUIET
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+ if (NOT res EQUAL 0)
+ message(FATAL_ERROR "Could not determine git sha1 via `git describe --always --dirty=*`")
+ endif()
+ set(${_GIT_SHA1} "${out}" PARENT_SCOPE)
+endfunction()
diff --git a/cmake/uny-releasewithassert.cmake b/cmake/uny-releasewithassert.cmake
new file mode 100644
index 0000000..a41dbd4
--- /dev/null
+++ b/cmake/uny-releasewithassert.cmake
@@ -0,0 +1,6 @@
+string(REGEX REPLACE "[/-][dD][^/-]*NDEBUG" "" CMAKE_C_FLAGS_RELEASEWITHASSERT_INIT "${CMAKE_C_FLAGS_RELEASE_INIT}")
+string(REGEX REPLACE "[/-][dD][^/-]*NDEBUG" "" CMAKE_CXX_FLAGS_RELEASEWITHASSERT_INIT "${CMAKE_CXX_FLAGS_RELEASE_INIT}")
+set(CMAKE_C_FLAGS_RELEASEWITHASSERT "${CMAKE_C_FLAGS_RELEASEWITHASSERT_INIT}" CACHE STRING "C flags for release with assert builds.")
+set(CMAKE_CXX_FLAGS_RELEASEWITHASSERT "${CMAKE_CXX_FLAGS_RELEASEWITHASSERT_INIT}" CACHE STRING "C++ flags for release with assert builds.")
+set(CMAKE_EXE_LINKER_FLAGS_RELEASEWITHASSERT "" CACHE STRING "Linker flags for release with assert builds.")
+mark_as_advanced(CMAKE_CXX_FLAGS_RELEASEWITHASSERT CMAKE_C_FLAGS_RELEASEWITHASSERT)
\ No newline at end of file
diff --git a/doc/ConsensusCore2-DesignAndImplementation/.gitignore b/doc/ConsensusCore2-DesignAndImplementation/.gitignore
new file mode 100644
index 0000000..e35d885
--- /dev/null
+++ b/doc/ConsensusCore2-DesignAndImplementation/.gitignore
@@ -0,0 +1 @@
+_build
diff --git a/doc/ConsensusCore2-DesignAndImplementation/Makefile b/doc/ConsensusCore2-DesignAndImplementation/Makefile
new file mode 100644
index 0000000..98d0163
--- /dev/null
+++ b/doc/ConsensusCore2-DesignAndImplementation/Makefile
@@ -0,0 +1,225 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = _build
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " singlehtml to make a single large HTML file"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " applehelp to make an Apple Help Book"
+ @echo " devhelp to make HTML files and a Devhelp project"
+ @echo " epub to make an epub"
+ @echo " epub3 to make an epub3"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
+ @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+ @echo " text to make text files"
+ @echo " man to make manual pages"
+ @echo " texinfo to make Texinfo files"
+ @echo " info to make Texinfo files and run them through makeinfo"
+ @echo " gettext to make PO message catalogs"
+ @echo " changes to make an overview of all changed/added/deprecated items"
+ @echo " xml to make Docutils-native XML files"
+ @echo " pseudoxml to make pseudoxml-XML files for display purposes"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+ @echo " coverage to run coverage check of the documentation (if enabled)"
+ @echo " dummy to check syntax errors of document sources"
+
+.PHONY: clean
+clean:
+ rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/ConsensusCore2DesignandImplementation.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/ConsensusCore2DesignandImplementation.qhc"
+
+.PHONY: applehelp
+applehelp:
+ $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+ @echo
+ @echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+ @echo "N.B. You won't be able to view it unless you put it in" \
+ "~/Library/Documentation/Help or install it in your application" \
+ "bundle."
+
+.PHONY: devhelp
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/ConsensusCore2DesignandImplementation"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/ConsensusCore2DesignandImplementation"
+ @echo "# devhelp"
+
+.PHONY: epub
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: epub3
+epub3:
+ $(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
+ @echo
+ @echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
+
+.PHONY: latex
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+ "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: latexpdfja
+latexpdfja:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through platex and dvipdfmx..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: text
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+texinfo:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+ @echo "Run \`make' in that directory to run these through makeinfo" \
+ "(use \`make info' here to do that automatically)."
+
+.PHONY: info
+info:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo "Running Texinfo files through makeinfo..."
+ make -C $(BUILDDIR)/texinfo info
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+.PHONY: gettext
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+ $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+ @echo "Testing of coverage in the sources finished, look at the " \
+ "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+ $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+ @echo
+ @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+ $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+ @echo
+ @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+.PHONY: dummy
+dummy:
+ $(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
+ @echo
+ @echo "Build finished. Dummy builder generates no files."
diff --git a/doc/ConsensusCore2-DesignAndImplementation/conf.py b/doc/ConsensusCore2-DesignAndImplementation/conf.py
new file mode 100644
index 0000000..0114124
--- /dev/null
+++ b/doc/ConsensusCore2-DesignAndImplementation/conf.py
@@ -0,0 +1,335 @@
+# -*- coding: utf-8 -*-
+#
+# ConsensusCore2: Design and Implementation documentation build configuration file, created by
+# sphinx-quickstart on Wed Jul 27 09:09:44 2016.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+ 'sphinx.ext.todo',
+ 'sphinx.ext.mathjax',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The encoding of source files.
+#
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'ConsensusCore2: Design and Implementation'
+copyright = u'2016, David Alexander, Nigel Delaney, Lance Hepler, Armin Töpfer'
+author = u'David Alexander, Nigel Delaney, Lance Hepler, Armin Töpfer'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'0.1'
+# The full version, including alpha/beta/rc tags.
+release = u'0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#
+# today = ''
+#
+# Else, today_fmt is used as the format for a strftime call.
+#
+# today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#
+# add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.
+# "<project> v<release> documentation" by default.
+#
+# html_title = u'ConsensusCore2: Design and Implementation v0.1'
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#
+# html_logo = None
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#
+# html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#
+# html_extra_path = []
+
+# If not None, a 'Last updated on:' timestamp is inserted at every page
+# bottom, using the given strftime format.
+# The empty string is equivalent to '%b %d, %Y'.
+#
+# html_last_updated_fmt = None
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+#
+# html_domain_indices = True
+
+# If false, no index is generated.
+#
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
+# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh'
+#
+# html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# 'ja' uses this config value.
+# 'zh' user can custom change `jieba` dictionary path.
+#
+# html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#
+# html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'ConsensusCore2DesignandImplementationdoc'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+ # The paper size ('letterpaper' or 'a4paper').
+ #
+ # 'papersize': 'letterpaper',
+
+ # The font size ('10pt', '11pt' or '12pt').
+ #
+ # 'pointsize': '10pt',
+
+ # Additional stuff for the LaTeX preamble.
+ #
+ # 'preamble': '',
+
+ # Latex figure (float) alignment
+ #
+ # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+# author, documentclass [howto, manual, or own class]).
+latex_documents = [
+ (master_doc, 'ConsensusCore2DesignandImplementation.tex', u'ConsensusCore2: Design and Implementation Documentation',
+ u'David Alexander, Nigel Delaney, Lance Hepler, Armin Töpfer', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+#
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#
+# latex_appendices = []
+
+# If false, no module index is generated.
+#
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ (master_doc, 'consensuscore2designandimplementation', u'ConsensusCore2: Design and Implementation Documentation',
+ [author], 1)
+]
+
+# If true, show URL addresses after external links.
+#
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ (master_doc, 'ConsensusCore2DesignandImplementation', u'ConsensusCore2: Design and Implementation Documentation',
+ author, 'ConsensusCore2DesignandImplementation', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+#
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#
+# texinfo_no_detailmenu = False
diff --git a/doc/ConsensusCore2-DesignAndImplementation/index.rst b/doc/ConsensusCore2-DesignAndImplementation/index.rst
new file mode 100644
index 0000000..7d7dc44
--- /dev/null
+++ b/doc/ConsensusCore2-DesignAndImplementation/index.rst
@@ -0,0 +1,142 @@
+
+``ConsensusCore2``: design and implementation
+===========================================
+
+Authors: David Alexander, Nigel Delaney, Lance Hepler, Armin Töpfer
+Last modified: July 27, 2016
+
+
+Motivation
+----------
+
+PacBio raw reads are highly error prone compared to short read
+technologies. Confident inference about the underlying DNA sequence
+can only be made on the basis of multiple observations---either
+multiple read passes of the insert from a single ZMW, or multiple
+reads otherwise determined to correspond to a common genomic region
+(for example, because they map to the same window of the reference).
+The problem of identifying the most plausible underlying DNA sequence,
+based on multiple observations, is termed *consensus*.
+
+Consensus is trivial for short read platforms because errors are
+predominantly *mismatch errors*; in such a world one can confidently
+call consensus by perfoming a multiple alignment and voting in each
+column.
+
+The consensus problem is more challenging for PacBio reads because the
+predominant error type is insertions and deletions, especially in
+homopolymer sequence. While heuristic approaches based on multiple
+alignment are possible even in this context, we have found better
+results by taking the approach of modeling consenus in a probabilistic
+framework, asking the question "what is the probability that an
+underlying *template* sequence T generated an observed read sequence
+R?", and then using the model :math:`\Pr(R \mid T)` to answer the
+multi-read consensus problem via maximum likelihood---the consensus
+sequence then mathematically defined as :math:`\arg\max_T \Pr(T \mid
+\mathbf{R})`, where :math:`\mathbf{R}` represents the vector of
+multiple reads.
+
+Such a likelihood model is implemented using standard techniques from
+the hidden Markov model (HMM) literature. The likelihood model is
+made tractable by approximating full dynamic programming using
+banding, and, critically, the maximum likelihood search is made
+tractable using a greedy search and a core routine using a
+forward-backward identity that enables fast (:math:`O(1)`)
+recalculation of the likelihood when the template is mutated pointwise
+from :math:`T` to :math:`T+\mu`.
+
+The consensus problem has multiple guises, as we have mentioned. In
+the *circular consensus sequence* application (*CCS*), multiple
+successive reads from of a single circularized DNA insert template (a
+*SMRTbell*) are gathered and used as evidence for a more confident
+consensus sequence for the molecule. In *genomic consensus*, reads
+from many molecules are mapped to a reference genome or a "draft"
+assembly, then a consensus sequence is generated for the genome by
+aggregating together the reads mapping to each genomic region. In the
+context of a reference genome, this application is referred to as
+*resequencing* and while a consensus sequence is produced, the goal is
+typically to identify *variants*---positions evidencing variation from
+the reference genome. In the context of a "draft" assembly, the
+application is referred to as "polishing" and the goal is simply to
+produce the most accurate sequence of the genome as possible.
+
+[add picture here]
+
+Additionally, the mathematical model of :math:`Pr(T \mid \mathbf{R})`
+has immediate applications even beyond the single-template consensus
+problem. It presents the natural framework for comparing hypotheses
+about single or even mutliple underlying template sequences, giving
+rise to elegant approaches for variant calling and confidence
+estimation, as well as haplotype phasing. The latter problem is
+
+
+History
+-------
+
+An initial consensus model (names `Quiver` in 2012) was originated in
+the original CCS implementation (ca. 2010) and proved capable of
+generating consensus sequences with accuracy near Q25 provided enough
+evidence---enough "passes" of the insert DNA. The initial codebase
+was in C# with some routines in C/C++. In 2012-2013, the core of the
+Quiver consensus algorithm was exported to a C++ library,
+`ConsensusCore`, which provided SWIG bindings to higher-level host
+languages (Python and C#, in chief), enabling use from other
+applications . The C# algorithm implementation was replaced by calls
+to the `ConsensusCore` library; simultaneously, a Python application
+(``GenomicConsenus``) was developed for applications in genome
+assembly polishing, yielding very successful results: over Q50 (and in
+some cases, over Q60) accuracy achieved on bacterial genome
+assemblies.
+
+The arrival of the ``GenomicConsensus" application coincided roughly
+with the initial development of HGAP (the Hierarchical Genome Assembly
+Program), thus offering fast end-to-end genome assembly with
+exceptionally high quality results, establishing PacBio as a player in
+the fields of "sequence finishing" and microbiology in 2013.
+Throughput improvements would
+
+Analyses of CCS results using the Quiver model showed evidence that
+CCS was far from a solved problem. First of all, the accuracy of CCS
+results were found to fall short of the accuracy from multi-molecule
+consensus sequences with comparable "coverage" in multiple controlled
+experiments. Perhaps more troubling, it was observed that consensus
+accuracy "saturated", failing to increase beyond a certain point when
+
+
+The Arrow model
+---------------
+
+Differences from Quiver...
+
+
+
+Implementation
+--------------
+
+Draft consensus by partial-order alignment
+``````````````````````````````````````````
+
+The essence: calculating, and re-calculating, likelihood
+````````````````````````````````````````````````````````
+
+Numerical aspects
+`````````````````
+
+Scaling vs log-domain math.
+
+The counterweights.
+
+
+Setup for calling consensus: the `Integrator` classes
+`````````````````````````````````````````````````````
+
+
+Model lookup
+````````````
+
+
+Model parameter lookup
+``````````````````````
+
+Training
+````````
diff --git a/doc/ConsensusCore2-DesignAndImplementation/make.bat b/doc/ConsensusCore2-DesignAndImplementation/make.bat
new file mode 100644
index 0000000..4b1a5c3
--- /dev/null
+++ b/doc/ConsensusCore2-DesignAndImplementation/make.bat
@@ -0,0 +1,281 @@
+ at ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set I18NSPHINXOPTS=%SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+ set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+ set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+ :help
+ echo.Please use `make ^<target^>` where ^<target^> is one of
+ echo. html to make standalone HTML files
+ echo. dirhtml to make HTML files named index.html in directories
+ echo. singlehtml to make a single large HTML file
+ echo. pickle to make pickle files
+ echo. json to make JSON files
+ echo. htmlhelp to make HTML files and a HTML help project
+ echo. qthelp to make HTML files and a qthelp project
+ echo. devhelp to make HTML files and a Devhelp project
+ echo. epub to make an epub
+ echo. epub3 to make an epub3
+ echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+ echo. text to make text files
+ echo. man to make manual pages
+ echo. texinfo to make Texinfo files
+ echo. gettext to make PO message catalogs
+ echo. changes to make an overview over all changed/added/deprecated items
+ echo. xml to make Docutils-native XML files
+ echo. pseudoxml to make pseudoxml-XML files for display purposes
+ echo. linkcheck to check all external links for integrity
+ echo. doctest to run all doctests embedded in the documentation if enabled
+ echo. coverage to run coverage check of the documentation if enabled
+ echo. dummy to check syntax errors of document sources
+ goto end
+)
+
+if "%1" == "clean" (
+ for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+ del /q /s %BUILDDIR%\*
+ goto end
+)
+
+
+REM Check if sphinx-build is available and fallback to Python version if any
+%SPHINXBUILD% 1>NUL 2>NUL
+if errorlevel 9009 goto sphinx_python
+goto sphinx_ok
+
+:sphinx_python
+
+set SPHINXBUILD=python -m sphinx.__init__
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.http://sphinx-doc.org/
+ exit /b 1
+)
+
+:sphinx_ok
+
+
+if "%1" == "html" (
+ %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+ goto end
+)
+
+if "%1" == "dirhtml" (
+ %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+ goto end
+)
+
+if "%1" == "singlehtml" (
+ %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+ goto end
+)
+
+if "%1" == "pickle" (
+ %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the pickle files.
+ goto end
+)
+
+if "%1" == "json" (
+ %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the JSON files.
+ goto end
+)
+
+if "%1" == "htmlhelp" (
+ %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+ goto end
+)
+
+if "%1" == "qthelp" (
+ %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+ echo.^> qcollectiongenerator %BUILDDIR%\qthelp\ConsensusCore2DesignandImplementation.qhcp
+ echo.To view the help file:
+ echo.^> assistant -collectionFile %BUILDDIR%\qthelp\ConsensusCore2DesignandImplementation.ghc
+ goto end
+)
+
+if "%1" == "devhelp" (
+ %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished.
+ goto end
+)
+
+if "%1" == "epub" (
+ %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The epub file is in %BUILDDIR%/epub.
+ goto end
+)
+
+if "%1" == "epub3" (
+ %SPHINXBUILD% -b epub3 %ALLSPHINXOPTS% %BUILDDIR%/epub3
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The epub3 file is in %BUILDDIR%/epub3.
+ goto end
+)
+
+if "%1" == "latex" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "latexpdf" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ cd %BUILDDIR%/latex
+ make all-pdf
+ cd %~dp0
+ echo.
+ echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "latexpdfja" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ cd %BUILDDIR%/latex
+ make all-pdf-ja
+ cd %~dp0
+ echo.
+ echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "text" (
+ %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The text files are in %BUILDDIR%/text.
+ goto end
+)
+
+if "%1" == "man" (
+ %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The manual pages are in %BUILDDIR%/man.
+ goto end
+)
+
+if "%1" == "texinfo" (
+ %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+ goto end
+)
+
+if "%1" == "gettext" (
+ %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+ goto end
+)
+
+if "%1" == "changes" (
+ %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.The overview file is in %BUILDDIR%/changes.
+ goto end
+)
+
+if "%1" == "linkcheck" (
+ %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+ goto end
+)
+
+if "%1" == "doctest" (
+ %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+ goto end
+)
+
+if "%1" == "coverage" (
+ %SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Testing of coverage in the sources finished, look at the ^
+results in %BUILDDIR%/coverage/python.txt.
+ goto end
+)
+
+if "%1" == "xml" (
+ %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The XML files are in %BUILDDIR%/xml.
+ goto end
+)
+
+if "%1" == "pseudoxml" (
+ %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+ goto end
+)
+
+if "%1" == "dummy" (
+ %SPHINXBUILD% -b dummy %ALLSPHINXOPTS% %BUILDDIR%/dummy
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. Dummy builder generates no files.
+ goto end
+)
+
+:end
diff --git a/doc/DEVELOPER.md b/doc/DEVELOPER.md
new file mode 100644
index 0000000..b958606
--- /dev/null
+++ b/doc/DEVELOPER.md
@@ -0,0 +1,45 @@
+# Developer environment
+
+## Clang-format pre commit hook
+
+### What?
+The intention here is to get source code formatting automatically
+checked and guaranteed before checkin.
+
+### Why?
+- Automate style-guide compliance to avoid squabbles
+- Post-checkin reformatting binges mess up history. It's best to get
+ it right from the get-go.
+
+
+### How?
+See the tools:
+ - `tools/check-formatting --staged` for fast style-checking of
+ changed files, in a git commit/push hook;
+ - `tools/check-formatting --all` for slower style-checking of everything
+ - `tools/format-all`to format everything
+
+To enable the checking as a pre-commit hook, place the following in
+`.git/hooks/pre-commit` (and make that file executable):
+
+```sh
+#!/bin/bash
+./tools/check-formatting --staged
+```
+
+### Tips
+- We should *not* reformat bundled third-party code as it will make it
+ difficult to diff with upstream. Put such code in a subdirectory
+ with its own .clang-format file containing: "BasedOnStyle: None" to
+ disable formatting.
+
+- If clang-format mangles something (for example, a comment block with
+ ASCII art or significant whitespace), you can protect a block using
+ `// clang-format off` and then `// clang-format on`.
+
+* What are these binaries?
+ The `clang-format` binaries that are checked in are static builds of
+ clang-format v3.9 from https://github.com/angular/clang-format.
+ They are bundled because the LLVM toolchain has a reputation for
+ rapid change and incompatibility. We want to guarantee that devs
+ are using the same version as CI is.
diff --git a/doc/INSTALL.md b/doc/INSTALL.md
new file mode 100644
index 0000000..443c1e7
--- /dev/null
+++ b/doc/INSTALL.md
@@ -0,0 +1,55 @@
+*Note: all are welcome to build our software from source, but official
+ support is only provided for official builds provided by PacBio
+ (the SMRT Analysis suite)*
+
+ ***
+
+### Individual tools: use `pitchfork`
+
+The easiest way to build is to use the `pitchfork` build tool, which
+automates dependency fetching/resolution:
+
+ ```sh
+ git clone https://github.com/PacificBiosciences/pitchfork && \
+ cd pitchfork && \
+ make pbccs
+ ```
+
+### All tools: manually
+
+Building from scratch requires system-wide installed boost (>=1.5.8),
+cmake (3.2), and a c++11 compiler (>=gcc-5.3.0, clang):
+
+ ```sh
+ git clone https://github.com/PacificBiosciences/unanimity && \
+ cd unanimity && \
+ git submodule update --init --remote && \
+ mkdir build && \
+ cd build && \
+ cmake -DCMAKE_INSTALL_PREFIX=~/bin .. && \
+ make -j install && \
+ ~/bin/ccs
+ ```
+
+### Individual tools: manually
+
+Invoke the different `make` targets, currently available
+
+ ```sh
+ $ make pbccs
+ ```
+
+### Install ConsensusCore2 python library for GenomicConsensus
+
+Building from scratch requires system-wide installed boost (>=1.5.8),
+cmake (3.2), python 2.x, and a c++11 compiler (>=gcc-5.3.0, clang):
+
+ ```sh
+ git clone https://github.com/PacificBiosciences/unanimity && \
+ cd unanimity && \
+ git submodule update --init --remote && \
+ pip install numpy cython h5py pysam cram nose && \
+ pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcommand.git && \
+ pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcore.git && \
+ pip install --upgrade --no-deps .
+ ```
\ No newline at end of file
diff --git a/doc/PBCCS.md b/doc/PBCCS.md
new file mode 100644
index 0000000..32cc6c2
--- /dev/null
+++ b/doc/PBCCS.md
@@ -0,0 +1,156 @@
+<h1 align="center">
+ pbccs - Generate Accurate Consensus Sequences from a Single SMRTbell
+</h1>
+
+<p align="center">
+ <img src="http://www.evolvedmicrobe.com/CCS.png" alt="Image of SMRTbell"/>
+</p>
+
+### Input
+
+The ccs program needs a .subreads.bam file containing the subreads for each SMRTbell sequenced. Older versions of the PacBio RS software outputted data in bas.h5 files, while the new software outputs BAM files. If you have a bas.h5 file from the older software, you will need to convert it into a BAM. This can be done with the tool bax2bam which simply needs the name of any bas.h5 files to convert and the prefix of the output file. Assuming your original file is named mydata.bas.h5, y [...]
+
+ bax2bam -o mynewbam mydata.1.bax.h5 mydata.2.bax.h5 mydata.3.bax.h5
+
+
+### Running CCS
+
+CCS can be run at the command line as follows:
+
+ ccs [OPTIONS] OUTPUT FILES...
+
+An example command would be:
+
+ ccs --minLength=100 myCCS.bam myData.subreads.bam
+
+The CCS program can be run with a variety of options described below.
+
+
+| Option | Example (Defaults) | Explanation [...]
+| -------------------------- | --------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- [...]
+| Output File Name | myResult.bam | This argument is the first argument that comes after the named arguments shown below. [...]
+| Input Files | myData.subreads.bam | The end of the CCS command following the named arguments and the output file name is the name of one, or more, subread.bam files to be processed. [...]
+| Version Number | --version | Prints the version number [...]
+| Report File Name | --reportFile=ccs_report.txt | The report file contains a result tally of the outcomes for all ZMWs that were processed. If the filename is not given the report is outputted to the text file ccs_report.txt In addition to the count of successfully produced consensus sequences, this file lists how many ZMWs failed various data quality filters (SNR too low, not enough full passes, etc.) and is useful for diagnosing unexpected drops in yield.| [...]
+| Minimum SNR | --minSnr=3.75 | This filter removes data that is likely to contain deletions. SNR is a measure of the strength of signal for all 4 channels (A, C, G, T) used to detect basepair incorporation. The SNR can vary depending on where in the ZMW a SMRTbell stochastochastically lands when loading occurs. SMRTbells that land near the edge and away from the center of the ZMW have a less intense signal, and as a result can contain sequences with more [...]
+| Minimum Read Score | ----minReadScore=0.75 | Sets a minimum value for the predicted quality of any subread used for CCS. Note that this filters the input to CCS (the subread quality must be above this value), whereas the --minPredictedAccuracy option filters the output (the predicted consensus sequence must be above a certain predicted accuracy).|
+| Minimum Length | --minLength=10 | Sets a minimum length requirement for the median size of insert reads in order to generate a consensus sequence. If the targeted template is known to be a particular size range, this can filter out alternative DNA templates. [...]
+| Maximum Length | --maxLength=7000 | Sets a maximum length for both subreads that will be processed as well as the consensus sequence that will be generated. For robust results while avoiding unnecessary computation on unusual data, this can be set to ~20% above the largest expected insert size. [...]
+| Minimum Number of Passes | --minPasses=3 | Sets a minimum number of passes for a ZMW to be emitted. This is the number of full passes. Full passes must have an adapter hit before and after the insert sequence and so does not include any partial passes at the start and end of the sequencing reaction. Additionally, the full pass count does not include any reads that were dropped by the Z-Filter. [...]
+| Minimum Predicted Accuracy | --minPredictedAccuracy=0.9 | The minimum predicted accuracy of a read. CCS generates an accuracy prediction for each read, defined as the expected percentage of matches in an alignment of the consensus sequence to the true read. A value of 0.99 indicates that only reads expected to be 99% accurate are emitted. [...]
+| Minimum Z Score | --minZScore=-3.5 | The minimum Z-Score for a subread to be included in the consensus generating process. For more information, see the "What are Z-Scores" section below. [...]
+| Maximum Dropped Fraction | --maxDropFraction=0.34 | The maximum number of subreads that can be dropped before the entire ZMW is discarded. Subreads that appear very unlikely given the initial template (low Z-score), are discarded before generating the consensus sequence as part of an initial quality filter. Typically, very few reads should be discarded but if a high proportion are, then the entire ZMW is dropped. [...]
+| ZMWs to Process | --zmws=0-100000000000 | If the consensus sequence for only a subset of ZMWs is required, they can be specified here. ZMWs an be specified either by range (--zmws=1-2000) by values (--zmws=5,10,20), or by both (--zmws=5-10,35,1000-2000). Simply use a comma separated list with no spaces. [...]
+| Number of Threads to Use | --numThreads=0 | How many threads to use while processing. By default, ccs will use as many threads as there are available cores to minimize processing time, but fewer threads can be specified here. [...]
+| Log File | --logFile=mylog.txt | The name of a log file to use, if none is given the logging information is printed to STDERR. [...]
+| Log level verbosity | --logLevel=INFO | How much log data to produce? By setting --logLevel=DEBUG, you can obtain detailed information on what ZMWs were dropped during processing, as well as any errors which may have appeared. [...]
+| Disable Polishing | --noPolish | After constructing the initial template, do not proceed with the polishing steps. This is significantly faster, but generates less accurate data with no RQ or QUAL values associated with each base. [...]
+| Analyze strands separately | --byStrand | Separately generate a consensus sequence from the forward and reverse strands. Useful for identifying heteroduplexes formed during sample preparation. [...]
+| Overwrite output file | --force | When you don't care it already exists. [...]
+
+
+### Output
+
+When the ccs program finishes, it outputs a BAM file with one entry for each consensus sequence derived from a ZMW. BAM is a general file format for storing sequence data, which is described fully by the SAM/BAM working group [here](https://samtools.github.io/hts-specs/SAMv1.pdf). The CCS output format is a version of this general format, where the consensus sequence is represented by the "Query Sequence" and several tags have been added to provide additional meta information.
+
+An example BAM entry for a consensus as seen by [samtools](http://samtools.sourceforge.net/) is shown below.
+
+```
+ m141008_060349_42194_c100704972550000001823137703241586_s1_p0/63/ccs 4 * 0 255 * * 0 0 CCCGGGGATCCTCTAGAATGC ~~~~~~~~~~~~~~~~~~~~~ RG:Z:83ba013f np:i:35 rq:i:999 rs:B:i,37,0,0,1,0 sn:B:f,11.3175,6.64119,11.6261,14.5199 za:f:2.25461 zm:i:63 zs:B:f,-1.57799,3.41424,2.96088,2.76274,3.65339,2.89414,2.446,3.04751,2.35529,3.65944,2.76774,4.119,1.67981,1.66385,3.59421,2.32752,4.17803,-0.00353378,nan,0.531571,2.21918 [...]
+
+ ```
+
+ A description of each of the common separated fields is given below.
+
+| Name | Definition |
+| ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| Query Name | Movie Name / ZMW # /ccs |
+| FLAG | Required by format but meaningless in this context. Always set to indicate the read is unmapped (4) |
+| Reference Name | Required by format but meaningless in this context. Always set to '*' |
+| Mapping Start | Required by format but meaningless in this context. Always set to '0' |
+| Mapping Quality | Required by format but meaningless in this context. Always set to '255' |
+| CIGAR | Required by format but meaningless in this context. Always set to '*' |
+| RNEXT | Required by format but meaningless in this context. Always set to '*' |
+| PNEXT | Required by format but meaningless in this context. Always set to '0' |
+| TLEN | Required by format but meaningless in this context. Always set to '0' |
+| Consensus Sequence | This is the consensus sequence generated. |
+| Quality Values | This is the per-base parameteric quality metric. For more information see the "interpretting QUALs" section. |
+| RG Tag | This is the read group identifier. |
+| bc Tag | This is a 2-entry array of upstream-provided barcode calls for this ZMW. |
+| bq Tag | This is the quality of the barcode call. (optional, depends on barcoded inputs) |
+| np Tag | The number of full passes that went into the subread. (optional, depends on barcoded inputs) |
+| rq Tag | The predicted read quality. |
+| rs Tag | An array of counts for the effect of adding each subread. The first element indicates the number of success and the remaining indicate the number of failures. This is a comma separated list of the number of reads Successfully Added, Failed to Converge in likelihood, Failed the Z Filtering, Failed to pass the pre-POA size filtering, or were excluded for another reason. |
+| za Tag | The average Z-score for all reads successfully added. |
+| zm Tag | The ZMW hole number. |
+| zs Tag | This is a comma separated list of the Z-scores for each subread when compared to the initial candidate template. A "nan" value indicates that the subread was not added. |
+
+## Interpretting QUAL values
+
+The QUAL value of a read is a measure of the posterior likelihood of an error at a particular position. Increasing QUAL values are associated with a decreasing probability of error. For the case of Indels and homopolymers, it is there is ambiguity as to which QUAL value is associated with the error probability. Shown below are different types of alignment errors, with a '*' indicating which sequence BP should be associated with the alignment error.
+
+### Mismatch
+
+```
+ *
+ ccs: ACGTATA
+ ref: ACATATA
+
+```
+
+### Deletion
+
+```
+ *
+ ccs: AC-TATA
+ ref: ACATATA
+
+```
+
+### Insertion
+
+```
+ *
+ ccs: ACGTATA
+ ref: AC-TATA
+
+```
+
+### Homopolymer Insertion or Deletion
+Indels should always be left-aligned and the error probability is only given for the first base in a homopolymer.
+
+```
+ * *
+ ccs: ACGGGGTATA ccs: AC-GGGTATA
+ ref: AC-GGGTATA ref: ACGGGGTATA
+
+```
+
+
+## What are Z-Scores?
+
+Z-score filtering is a way to remove outliers and contaminating data from the CCS dataset prior to consensus generation, a crucial step for any analysis. For example, in the second world war the U.S. Navy tried to gauge the accuracy of a newly developed optical range finder by having a few hundred sailors practice on a known target. The mean accuracy was quite poor, but after realizing that 20% of people cannot view sterotypically, these individuals could be excluded, leading to much h [...]
+
+The Z-score for a subread is a metric which quantifies how well it doesn't fit the model or assumptions of CCS scoring. In CCS, an initial template sequence is proposed, and then further refined using data in the templates. The initial template is usually quite close to the final consensus sequence, and at this stage ccs will evaluate how likely each read is based on the candidate template. The likelihood of a read for a template is summarized by it's Z-score, which asymptotically is [...]
+
+Subreads with very low Z-scores are very unlikely to have been produced according to the CCS model, and so represent outliers. For example, the plot below shows the Z-scores for several subreads. With a -5 cutoff, we can see that one subread is excluded from the data.
+
+
+
+
+## CCS Yield Report
+
+After ccs runs, a report is generated that specifies the number of ZMWs that successfully produced consensus sequences, as well as a count of how many ZMWs did not produce a consensus sequence for various reasons. The entries in this report, as well as parameters that can be set to change to increase of decrease the number of ZMWs that pass various filters, are explained in the table below.
+
+| ZMW result | Parameter(s) affecting result | Description |
+|--------------------------------------|---------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Below SNR threshold | --minSnr | ZMW had at least one channel's SNR below the minimum threshold. |
+| No usable subreads | --minReadScore, --minLength, --maxLength | The ZMW had no usable subreads, either there were no subreads, or all the subreads were below the minimum quality threshold or were above/below the specified length thresholds. |
+| Insert size too long | --maxLength | The consensus sequence was above the maximum length threshold. Note that if all the input subreads were already above this threshold, they would all have been excluded leading to "No usable subreads." |
+| Insert size too small | --minLength | The consensus sequence was below the miminum length threshold. Note that if all the input subreads were already below this threshold, they would all have been excluded leading to "No usable subreads." |
+| Not enough full passes | --minPasses | There were not enough subreads that had an adapter at the start and end of the subread (a "full pass"). |
+| Too many unusable subreads | --minZScore, --maxDropFraction | The ZMW had too many subreads that could not be used. A read can be unusable if it appears too unlikely given the initial template (low Z-score), or rarely, if a numerical rounding error occurs during processing. |
+| CCS did not converge | None | The consensus sequence did not converge after the maximum number of allowed rounds of polishing. |
+| CCS below minimum predicted accuracy | --minPredictedAccuracy | Each CCS read has a predicted level of accuracy associated with it, reads that are below the minimum specified threshold are removed. |
+| Unknown error during processing | None | These should not occur. |
+
diff --git a/doc/TODO.md b/doc/TODO.md
new file mode 100644
index 0000000..98d7abd
--- /dev/null
+++ b/doc/TODO.md
@@ -0,0 +1,6 @@
+ * models compiled into separate static lib for -Wl,-whole-archive-ness
+ * more comments and documentation overall
+ * merge Mono-/Multi-MolecularIntegrators, use map of (SNRs + Models) -> Template
+ * template-ify Evaluator, Template for ModelConfig, get rid of unique_ptr-ing, EvaluatorFactory
+ * SparsePoa isn't actually sparse, makeAlignmentColumn isn't using the provided beginRow/endRow
+ * Add more random tests of assumed invariants (e.g. mutating each position of a homopolymer should be identical)
diff --git a/doc/img/unanimity.png b/doc/img/unanimity.png
new file mode 100644
index 0000000..4544166
Binary files /dev/null and b/doc/img/unanimity.png differ
diff --git a/include/pacbio/Version.h.in b/include/pacbio/Version.h.in
new file mode 100644
index 0000000..430b5e4
--- /dev/null
+++ b/include/pacbio/Version.h.in
@@ -0,0 +1,65 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Armin Töpfer
+
+#pragma once
+
+#include <string>
+
+namespace PacBio {
+namespace {
+constexpr char UnyVersion[] = "@UNANIMITY_VERSION@";
+constexpr char UnyGitSha1[] = "@UNANIMITY_GIT_SHA1@";
+constexpr char UnyChangelog[] = "${UNANIMITY_CHANGELOG}";
+constexpr size_t UnyVersionMajor = @UNANIMITY_VERSION_MAJOR@;
+constexpr size_t UnyVersionMinor = @UNANIMITY_VERSION_MINOR@;
+constexpr size_t UnyVersionPatch = @UNANIMITY_VERSION_PATCH@;
+}
+
+std::string UnanimityVersion()
+{ return UnyVersion; }
+
+std::string UnanimityGitSha1()
+{ return UnyGitSha1; }
+
+std::string UnanimityChangelog()
+{
+ std::string changelog(UnyChangelog);
+ std::replace(changelog.begin(), changelog.end(), ';', '\n');
+ return changelog;
+}
+
+} // ::PacBio
diff --git a/include/pacbio/align/AffineAlignment.h b/include/pacbio/align/AffineAlignment.h
new file mode 100644
index 0000000..4b27154
--- /dev/null
+++ b/include/pacbio/align/AffineAlignment.h
@@ -0,0 +1,86 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+//
+// Support for pairwise alignment with an affine gap penalty.
+//
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+namespace PacBio {
+namespace Align {
+
+class PairwiseAlignment;
+
+struct AffineAlignmentParams
+{
+ float MatchScore;
+ float MismatchScore;
+ float GapOpen;
+ float GapExtend;
+ float PartialMatchScore;
+
+ AffineAlignmentParams(float matchScore, float mismatchScore, float gapOpen, float gapExtend,
+ float partialMatchScore = 0);
+};
+
+AffineAlignmentParams DefaultAffineAlignmentParams();
+AffineAlignmentParams IupacAwareAffineAlignmentParams();
+
+//
+// Affine gap-penalty alignment.
+//
+PairwiseAlignment* AlignAffine(
+ const std::string& target, const std::string& query,
+ AffineAlignmentParams params = DefaultAffineAlignmentParams()); // NOLINT
+
+//
+// Affine gap-penalty alignment with partial awareness of IUPAC ambiguous bases---
+// half-penalizes partial mismatches. For example: (M = IUPAC A/C)
+// T->A = -1,
+// T->M = -1,
+// A->M = -0.5
+//
+PairwiseAlignment* AlignAffineIupac(
+ const std::string& target, const std::string& query,
+ AffineAlignmentParams params = IupacAwareAffineAlignmentParams()); // NOLINT
+
+} // namespace Align
+} // namespace PacBio
diff --git a/include/pacbio/align/AlignConfig.h b/include/pacbio/align/AlignConfig.h
new file mode 100644
index 0000000..d3e849b
--- /dev/null
+++ b/include/pacbio/align/AlignConfig.h
@@ -0,0 +1,80 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#pragma once
+
+#include <cstdint>
+
+namespace PacBio {
+namespace Align {
+
+//
+// Scoring params for Needleman-Wunsch or Smith-Waterman style aligners
+//
+struct AlignParams
+{
+ int Match;
+ int Mismatch;
+ int Insert;
+ int Delete;
+
+ AlignParams(int match, int mismatch, int insert, int delete_);
+
+ // Edit distance params
+ static AlignParams Default();
+};
+
+enum struct AlignMode : uint8_t
+{
+ GLOBAL = 0, // Global in both sequences
+ SEMIGLOBAL = 1, // Global in query, local in target
+ LOCAL = 2 // Local in both sequences
+};
+
+struct AlignConfig
+{
+ AlignParams Params;
+ AlignMode Mode;
+
+ AlignConfig(AlignParams params, AlignMode mode);
+
+ // Default corresponds to global alignment mode, edit distance params
+ static AlignConfig Default();
+};
+
+} // namespace Align
+} // namespace PacBio
diff --git a/include/pacbio/align/BandedAligner.h b/include/pacbio/align/BandedAligner.h
new file mode 100644
index 0000000..8635f07
--- /dev/null
+++ b/include/pacbio/align/BandedAligner.h
@@ -0,0 +1,582 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Programmer: Brett Bowman
+
+#pragma once
+
+#include <algorithm>
+#include <exception>
+
+#include <seqan/journaled_set/score_biaffine.h>
+#include <seqan/seeds.h>
+
+namespace PacBio {
+namespace Align {
+
+class BandedAligner
+{
+
+public: // Derived types and values
+ typedef seqan::Dna TAlphabet;
+ typedef seqan::String<TAlphabet> TString;
+ typedef seqan::StringSet<TString> TStringSet;
+
+ typedef seqan::Seed<seqan::Simple> TSeed;
+ typedef seqan::String<TSeed> TSeedChain;
+ typedef std::pair<size_t, TSeedChain> THit;
+
+ typedef seqan::AlignConfig<true, true, true, true> TAlignConfig;
+ typedef seqan::Align<TString, seqan::ArrayGaps> TAlign;
+ typedef std::pair<TAlign, seqan::AlignmentStats> TAlignPair;
+ typedef seqan::Row<TAlign>::Type TRow;
+ typedef seqan::Iterator<TRow>::Type TRowIter;
+ typedef seqan::Score<long, seqan::BiAffine> TScoringScheme;
+
+public: // structors
+ // Default constructor
+ BandedAligner(const TStringSet& references, const size_t flankingBuffer = 50,
+ const size_t minMatchLength = 5, const size_t minQueryLength = 50,
+ const size_t bandExtension = 15)
+ : references_(references)
+ , flankingBuffer_(flankingBuffer)
+ , minQueryLength_(minQueryLength)
+ , minMatchLength_(minMatchLength)
+ , bandExtension_(bandExtension)
+ {
+ using namespace seqan;
+
+ // Sanity-check the two arguments with hard range requirements
+ if (minMatchLength_ < 1) throw std::invalid_argument("minMatchLength must be >= 1");
+ if (bandExtension_ < 1) throw std::invalid_argument("bandExtension must be >= 1");
+
+ // NOTE: BLASR uses inverted scores, i.e. (-5, 6, 4, 5)
+ //scoringScheme_ = TScoringScheme(5, -6, -4, -4, -5, -5);
+ }
+
+ // Move constructor
+ BandedAligner(BandedAligner&& src) = default;
+ // Copy constructor
+ BandedAligner(const BandedAligner& src) = default;
+ // Move assignment operator
+ BandedAligner& operator=(BandedAligner&& rhs) = default;
+ // Copy assignment operator
+ BandedAligner& operator=(const BandedAligner& rhs) = default;
+ // Destructor
+ ~BandedAligner() = default;
+
+public: // non-modifying methods
+ /// Using the seed-chain as a guide, align the banded region of probable
+ /// similarity between the query and the reference sequence and return
+ /// the alignment.
+ ///
+ /// Roughly equivalent to BLASR's SDPAlign
+ ///
+ /// \param region A seed for storing the final alignment region
+ /// \param query The query sequence in which the seeds were found
+ /// \param hit A pair with the reference sequence index and the
+ /// chain of seeds
+ ///
+ /// \return TAlignPair an Alignment/Stats pair object
+ TAlignPair AlignHit(TSeed& region, const TString& query, const THit& hit)
+ {
+ using namespace seqan;
+
+ // Initialize the object we will return
+ TAlignPair pair;
+ resize(rows(pair.first), 2);
+
+ // Extract the input data for easier access
+ const TString& reference = references_[hit.first];
+ const TSeedChain& seedChain = hit.second;
+
+ // Identify the window around the seeded region in the query to align
+ size_t queryStart = beginPositionH(front(seedChain));
+ size_t queryMinStart =
+ ((queryStart <= flankingBuffer_) ? 0 : (queryStart - flankingBuffer_));
+ size_t queryStartDiff = queryStart - queryMinStart;
+ size_t queryEnd = endPositionH(back(seedChain));
+ size_t queryMaxEnd = std::min(length(query), queryEnd + flankingBuffer_);
+ size_t queryEndDiff = queryMaxEnd - queryEnd;
+
+ // Identify the window around the seeded region in the reference to align
+ size_t refStart = beginPositionV(front(seedChain));
+ size_t refMinStart = ((refStart <= flankingBuffer_) ? 0 : (refStart - flankingBuffer_));
+ size_t refStartDiff = refStart - refMinStart;
+ size_t refEnd = endPositionV(back(seedChain));
+ size_t refMaxEnd = std::min(length(reference), refEnd + flankingBuffer_);
+ size_t refEndDiff = refMaxEnd - refEnd;
+
+ // Given the size of the flanking regions around both sides of the anchors,
+ // what is the maximum amount of buffer we can safely take from both?
+ size_t startDiff = std::min(queryStartDiff, refStartDiff);
+ size_t endDiff = std::min(queryEndDiff, refEndDiff);
+
+ // If the maximum size allow for the left-side flanks is different
+ // from what we previously calculated, recalculate
+ size_t queryAlignStart = queryMinStart;
+ if (startDiff != queryStartDiff) queryAlignStart += queryStartDiff - startDiff;
+
+ size_t refAlignStart = refMinStart;
+ if (startDiff != refStartDiff) refAlignStart += refStartDiff - startDiff;
+
+ // Ditto the right-side flanks
+ size_t queryAlignEnd = queryMaxEnd;
+ if (endDiff != queryEndDiff) queryAlignEnd -= queryEndDiff - endDiff;
+
+ size_t refAlignEnd = refMaxEnd;
+ if (endDiff != refEndDiff) refAlignEnd -= refEndDiff - endDiff;
+
+ // Extract infixes from sequences and set them as our alignment targets
+ const auto queryInfix = infix(query, queryAlignStart, queryAlignEnd);
+ const auto refInfix = infix(reference, refAlignStart, refAlignEnd);
+ assignSource(row(pair.first, 0), queryInfix);
+ assignSource(row(pair.first, 1), refInfix);
+
+ if (queryAlignStart == 0 && refAlignStart == 0) {
+ // If both of our subsequences start at the beginning,
+ // we can use the seedChain as-is
+ bandedChainAlignment(pair.first, seedChain, scoringScheme_, alignConfig_,
+ bandExtension_);
+ } else if (queryAlignStart > 10) {
+ // Otherwise we need to left-shift the values in the seed chain
+ const TSeedChain& shiftedChain =
+ ShiftSeedChain(seedChain, queryAlignStart, refAlignStart);
+ bandedChainAlignment(pair.first, shiftedChain, scoringScheme_, alignConfig_,
+ bandExtension_);
+ } else {
+ // There appears to be a bug with bandedChainAlignment, where by it
+ // will fail to align with default values for the bandExtension_
+ // if the seed chain starts too close to the beginning of the
+ // query sequence. This is a temporary hack to work around that.
+ const TSeedChain& shiftedChain =
+ ShiftSeedChain(seedChain, queryAlignStart, refAlignStart);
+ bandedChainAlignment(pair.first, shiftedChain, scoringScheme_, alignConfig_, 10);
+ }
+
+ // Clip the alignment to the region with a good similarity
+ ClipAlignment(&pair);
+
+ // Now that the edges of the alignment are finalized we can calculate the region
+ SetAlignmentRegion(pair.first, queryAlignStart, refAlignStart, ®ion);
+
+ // Return the final alignment
+ return pair;
+ }
+
+private: // Private non-modifying functions
+ /// The existing banded alignment algorithm provided by seqan crashes
+ /// if given any overlapping seeds, while Lance's seed-chaining algorithm
+ /// is both non-global and significantly faster. In order to use the former
+ /// with the later, it is first necessary to trim such overlaps from the data.
+ ///
+ /// Overlaps represent small repeat regions, usually homopolymers, whose
+ /// edges are deliniated by the edges of the overlap. So by swapping the
+ /// overlapping start/end positions, we are effectively trimming the seeds
+ /// back to the non-repetitive region and allowing the banded aligner to
+ /// find the optimal path through the repeat.
+ ///
+ /// \param chain A seed-set of kmer matchs between the sequences
+ void TrimOverlappingSeeds(TSeedChain* chain)
+ {
+ using namespace seqan;
+
+ // SeqAn doesn't support "->at()", so we de-reference here
+ TSeedChain& chainRef = *chain;
+
+ // If each pair of adjacent seeds, I and J ...
+ for (size_t j = 1; j < length(chainRef); ++j) {
+ size_t i = j - 1;
+
+ // ... if they over lap in either dimension ...
+ if (endPositionH(chainRef[i]) > beginPositionH(chainRef[j]) ||
+ endPositionV(chainRef[i]) > beginPositionV(chainRef[j])) {
+ // ... swap their start and end positions in both dimensions
+ size_t maxPosV = endPositionV(chainRef[i]);
+ setEndPositionV(chainRef[i], beginPositionV(chainRef[j]));
+ setBeginPositionV(chainRef[j], maxPosV);
+
+ size_t maxPosH = endPositionH(chainRef[i]);
+ setEndPositionH(chainRef[i], beginPositionH(chainRef[j]));
+ setBeginPositionH(chainRef[j], maxPosH);
+ }
+ }
+ }
+
+ /// When identifying seeds from a seed chain that need to be removed
+ /// for whatever reason, we don't want to do so immediately lest we
+ /// confuse our indices. Instead we set the horizonal (query) length
+ /// to zero, to be removed afterward.
+ ///
+ /// \param chain A seed-set of kmer matchs between the sequences
+ ///
+ /// \return int The number of seeds so removed
+ int RemoveZeroLengthSeeds(TSeedChain* chain)
+ {
+ using namespace seqan;
+
+ // SeqAn doesn't support "->at()", so we de-reference here
+ TSeedChain& chainRef = *chain;
+
+ int size = length(chainRef);
+ int curr = 0;
+
+ for (int i = 0; i < size; ++i) {
+ // If end is greater than beginning, its a still-valid seed.
+ // Copy it to our current counter-position and increment
+ if (endPositionH(chainRef[i]) > beginPositionH(chainRef[i])) {
+ chainRef[curr] = chainRef[i];
+ curr++;
+ }
+ }
+
+ // Erase the last "curr" seeds, which are now all duplicates
+ for (int i = size - 1; i >= curr; --i)
+ erase(chainRef, i);
+
+ // Shrink the container to fit the new smaller dataset
+ shrinkToFit(chainRef);
+ return size - curr;
+ }
+
+ /// The existing banded alignment algorithm provided by seqan crashes
+ /// if given any overlapping seeds, while Lance's seed-chaining algorithm
+ /// is both non-global and significantly faster. In order to use the former
+ /// with the later, it is first necessary to remove any seeds entirely
+ /// "contained" seeds from the seed chain.
+ ///
+ /// \param chain A seed-set of kmer matchs between the sequences
+ ///
+ /// \return int The number of seeds so removed
+ int RemoveContainedSeeds(TSeedChain* chain)
+ {
+ using namespace seqan;
+
+ // SeqAn doesn't support "->at()", so we de-reference here
+ TSeedChain& chainRef = *chain;
+
+ for (int m = length(chainRef) - 1; m > 0; --m) {
+ int n = m - 1;
+ bool mergeFound = false;
+ while (mergeFound == false && n >= 0) {
+ if ((beginPositionH(chainRef[n]) < beginPositionH(chainRef[m]) &&
+ endPositionH(chainRef[n]) >= endPositionH(chainRef[m])) ||
+ (beginPositionV(chainRef[n]) < beginPositionV(chainRef[m]) &&
+ endPositionV(chainRef[n]) >= endPositionV(chainRef[m]))) {
+ setEndPositionH(chainRef[m], beginPositionH(chainRef[m]));
+ mergeFound = true;
+ }
+ n--;
+ }
+ }
+
+ // Remove zero-length seeds and return the count
+ int numRemoved = RemoveZeroLengthSeeds(&chainRef);
+ return numRemoved;
+ }
+
+ /// The existing banded chain alignment algorithm in SeqAn is global,
+ /// whereas we want local alignments around our seed chains. We can use
+ /// infixes of the sequences we want to work around this, but we have to
+ /// adjust the start positions of our seeds accordingly so they are correct
+ /// relative to the start of the infix.
+ ///
+ /// \param input A seed-set of kmer matchs between the sequences
+ /// \param leftShift Number of horizontal bases to shift the seeds
+ /// \param upShift Number of vertical bases to shift the seeds
+ ///
+ /// \return TSeedChain A copy of input with the starting locations
+ TSeedChain ShiftSeedChain(const TSeedChain& input, const size_t leftShift, const size_t upShift)
+ {
+ using namespace seqan;
+ TSeedChain output;
+
+ for (size_t i = 0; i < length(input); ++i) {
+ const TSeed& seed = input[i];
+ const size_t queryStart = beginPositionH(seed) - leftShift;
+ const size_t refStart = beginPositionV(seed) - upShift;
+ const size_t size = seedSize(seed);
+ appendValue(output, TSeed(queryStart, refStart, size));
+ }
+
+ return output;
+ }
+
+ /// Clip the alignment down to the highest accuracy core region
+ /// longer than minQueryLength and update the stats object in
+ /// the pair accordingly.
+ ///
+ /// \param pair An Alignment/Stats pair object
+ ///
+ /// \return int An error flag - 0 if successful, 1 if failure
+ void ClipAlignment(TAlignPair* pair)
+ {
+ using namespace seqan;
+
+ // Traverse the ends of the alignment for minimal match anchors
+ TRow& queryRow = row(pair->first, 0);
+ TRow& refRow = row(pair->first, 1);
+ int alignStart = FindLeftSideMinMatch(queryRow, refRow);
+ int alignEnd = FindRightSideMinMatch(queryRow, refRow);
+
+ // If the alignment start or end positions don't make sense,
+ // this is probably a garbage alignment. Compute the
+ // alignment stats as-is and abandon clipping.
+ if (alignStart < 0 || alignEnd < 0) {
+ computeAlignmentStats(pair->second, pair->first, scoringScheme_);
+ return;
+ }
+
+ // Clip the alignment to the ends of the range and compute our stats
+ setClippedBeginPosition(queryRow, alignStart);
+ setClippedEndPosition(queryRow, alignEnd);
+ setClippedBeginPosition(refRow, alignStart);
+ setClippedEndPosition(refRow, alignEnd);
+ computeAlignmentStats(pair->second, pair->first, scoringScheme_);
+
+ // If the initial alignment is short, we succeeded but do not have room
+ // for refinement - exit here.
+ if (LengthInSequence(queryRow, alignStart, alignEnd) <= minQueryLength_) return;
+
+ // Otherwise we need to clear our clipping ahead of refinement
+ clearClipping(queryRow);
+ clearClipping(refRow);
+
+ // Declare looping variables
+ AlignmentStats newLeftStats, newRightStats;
+ int newAlignStart, newAlignEnd;
+
+ while (true) {
+ // Clear the alignment stats from the previous iteration
+ clear(newLeftStats);
+ clear(newRightStats);
+
+ // Calculate the next valid start and end position for the alignment
+ newAlignStart = FindLeftSideMinMatch(queryRow, refRow, alignStart + minMatchLength_);
+ newAlignEnd = FindRightSideMinMatch(queryRow, refRow, alignEnd - minMatchLength_);
+
+ if (LengthInSequence(queryRow, newAlignStart, alignEnd) > minQueryLength_) {
+ // If the alignment length in the query is long enough to be valid,
+ // calculate the accuracy of the new start with the old end
+ setClippedBeginPosition(queryRow, newAlignStart);
+ setClippedEndPosition(queryRow, alignEnd);
+ setClippedBeginPosition(refRow, newAlignStart);
+ setClippedEndPosition(refRow, alignEnd);
+ computeAlignmentStats(newLeftStats, pair->first, scoringScheme_);
+ clearClipping(queryRow);
+ clearClipping(refRow);
+ }
+
+ if (LengthInSequence(queryRow, alignStart, newAlignEnd) > minQueryLength_) {
+ // If the alignment length in the query is long enough to be valid,
+ // calculate the accuracy of the old start with the new end
+ setClippedBeginPosition(queryRow, alignStart);
+ setClippedEndPosition(queryRow, newAlignEnd);
+ setClippedBeginPosition(refRow, alignStart);
+ setClippedEndPosition(refRow, newAlignEnd);
+ computeAlignmentStats(newRightStats, pair->first, scoringScheme_);
+ clearClipping(queryRow);
+ clearClipping(refRow);
+ }
+
+ if (newLeftStats.alignmentIdentity > newRightStats.alignmentIdentity &&
+ newLeftStats.alignmentIdentity >
+ pair->second.alignmentIdentity + minAccuracyImprovement_) {
+ // If the new align-start produces a better alignment than the end,
+ // and the improvement is non-trivial, keep it
+ alignStart = newAlignStart;
+ pair->second = newLeftStats;
+ } else if (newRightStats.alignmentIdentity > newLeftStats.alignmentIdentity &&
+ newRightStats.alignmentIdentity >
+ pair->second.alignmentIdentity + minAccuracyImprovement_) {
+ // If the new align-end produces a better alignment than the start,
+ // and the improvement is non-trivial, keep it
+ alignEnd = newAlignEnd;
+ pair->second = newRightStats;
+ } else {
+ // If both possible new positions are invalid or inferior, we
+ // assume that the previous clipping was optimal
+ setClippedBeginPosition(queryRow, alignStart);
+ setClippedEndPosition(queryRow, newAlignEnd);
+ setClippedBeginPosition(refRow, alignStart);
+ setClippedEndPosition(refRow, newAlignEnd);
+ break;
+ }
+ }
+
+ return;
+ }
+
+ /// Compare two aligned sequences and, counting in from the left-end, find
+ /// the first position where they match for at least minMatchLength_ bases.
+ ///
+ /// \param queryRow The first row to compare
+ /// \param refRow The second row to compare
+ /// \param startPos Optional position to begin the search
+ ///
+ /// \return int The position in the row the match begins
+ int FindLeftSideMinMatch(const TRow& queryRow, const TRow& refRow, const size_t startPos = 0)
+ {
+ size_t matchCount = 0;
+ for (size_t i = startPos; i < seqan::length(queryRow); ++i) {
+ // If either row is a gap, reset the counter
+ if (IsGap(refRow[i]) || IsGap(queryRow[i])) {
+ matchCount = 0;
+ continue;
+ }
+
+ // If the aligned characters aren't gaps but still don't match,
+ // it's a subsitution error
+ if (queryRow[i] != refRow[i]) {
+ matchCount = 0;
+ continue;
+ }
+
+ // If we made it this far it's a match - increment the counter
+ matchCount++;
+
+ // If we've seen enough matches in a row, return our position
+ if (matchCount >= minMatchLength_) {
+ return i - minMatchLength_ + 1;
+ }
+ }
+
+ // If we made it this far, something went wrong - return an error
+ return -1;
+ }
+
+ /// Compare two aligned sequences and, counting in from the right-end, find
+ /// the first position where they match for at least minMatchLength_ bases.
+ ///
+ /// \param queryRow The first row to compare
+ /// \param refRow The second row to compare
+ /// \param startPos Optional position to begin the search
+ ///
+ /// \return int The position in the alignment the match ends
+ int FindRightSideMinMatch(const TRow& queryRow, const TRow& refRow, size_t startPos = 0)
+ {
+ // If not specified, default to starting at the right end
+ if (startPos == 0) startPos = seqan::length(queryRow) - 1;
+
+ size_t matchCount = 0;
+ for (int i = startPos; i >= 0; --i) {
+ // If either row is a gap, reset the counter
+ if (IsGap(refRow[i]) || IsGap(queryRow[i])) {
+ matchCount = 0;
+ continue;
+ }
+
+ // If the aligned characters aren't gaps but still don't match,
+ // it's a subsitution error
+ if (queryRow[i] != refRow[i]) {
+ matchCount = 0;
+ continue;
+ }
+
+ // If we made it this far it's a match - increment the counter
+ matchCount++;
+
+ // If we've seen enough matches in a row, return our position
+ if (matchCount >= minMatchLength_) {
+ return i + minMatchLength_;
+ }
+ }
+
+ // If we made it this far, something went wrong - return an error
+ return -1;
+ }
+
+ /// Since our alignments are local (i.e. relative to the position of the
+ /// infixes used) we need to calculate and store their global position
+ /// in a useful way. This function recycles SeqAn's build in SimpleSeed
+ /// class to do just that.
+ ///
+ /// \param region The TSeed object to store the alignment location in
+ /// \param align The alignment object for which to record it's location
+ /// \param queryAlignStart The number of bases trimmed from the infix
+ /// that became the first alignment row
+ /// \param refAlignStart The number of bases trimmed from the infix
+ /// that became the second alignment row
+ ///
+ void SetAlignmentRegion(const TAlign& align, const size_t queryAlignStart,
+ const size_t refAlignStart, TSeed* region)
+ {
+ using namespace seqan;
+ setBeginPositionH(*region, queryAlignStart + beginPosition(row(align, 0)));
+ setEndPositionH(*region, queryAlignStart + endPosition(row(align, 0)));
+ setBeginPositionV(*region, refAlignStart + beginPosition(row(align, 1)));
+ setEndPositionV(*region, refAlignStart + endPosition(row(align, 1)));
+ }
+
+ /// We wish to only consider alignments that cover at least a certain
+ /// span in the query.
+ ///
+ /// \param row The sequence in which we wish to know the alignment span
+ /// \param alignStart The start position, with respect to the alignment
+ /// \param alignEnd The end position, with respect to the alignment
+ //
+ /// \return size_t The distance between the alignment start and end,
+ /// with respect to the sequence provided
+ inline size_t LengthInSequence(const TRow& row, const int alignStart, const int alignEnd)
+ {
+ using namespace seqan;
+
+ return toSourcePosition(row, alignEnd) - toSourcePosition(row, alignStart);
+ }
+
+ /// Is a given character counted as a gap or not?
+ ///
+ /// \param base The character in question
+ /// \return bool Whether the input is a gap character
+ inline bool IsGap(const char base) { return base == gapValue_; }
+
+private: // User-defined member variables
+ const TStringSet& references_;
+ const size_t flankingBuffer_;
+ const size_t minQueryLength_;
+ const size_t minMatchLength_;
+ const size_t bandExtension_;
+
+private: // Class-defined memeber variables
+ static constexpr float minAccuracyImprovement_ = 3.0f;
+
+ // These aren't static since C doesn't allow static function calls
+ const TScoringScheme scoringScheme_ = TScoringScheme(5, -6, -4, -4, -5, -5);
+ const TAlignConfig alignConfig_ = TAlignConfig();
+ const char gapValue_ = seqan::gapValue<char>();
+};
+
+} // Align
+} // PacBio
diff --git a/include/pacbio/align/ChainScorer.h b/include/pacbio/align/ChainScorer.h
new file mode 100644
index 0000000..86fcd41
--- /dev/null
+++ b/include/pacbio/align/ChainScorer.h
@@ -0,0 +1,204 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Programmer: Brett Bowman
+
+#pragma once
+
+#include <seqan/index.h>
+#include <seqan/seeds.h>
+
+#include "SeedScorer.h"
+
+namespace PacBio {
+namespace Align {
+
+template <typename TConfig>
+class ChainScorer
+{
+
+public: // Template types and values
+ typedef typename TConfig::IndexType TIndexSpec;
+ typedef typename TConfig::ShapeType TShapeSpec;
+ size_t Size = TConfig::Size;
+
+public: // Derived types and values
+ typedef seqan::Dna TAlphabet;
+ typedef seqan::String<TAlphabet> TString;
+ typedef seqan::Index<seqan::StringSet<TString>, TIndexSpec> TIndex;
+
+ // Equivalent to BLASR's "T_Tuple"
+ typedef seqan::Shape<TAlphabet, TShapeSpec> TShape;
+ // Equivalent to BLASR's "MatchPos"
+ typedef seqan::Seed<seqan::Simple> TSeed;
+ // Equivalent to BLASR's "LongestIncreasingSubsequence"
+ typedef seqan::String<TSeed> TSeedChain;
+ typedef std::pair<size_t, TSeedChain> THit;
+
+public: // structors
+ // Default constructor
+ ChainScorer(const TIndex& index, const size_t kmerSize)
+ : index_(index)
+ , shape_(seqan::indexShape(index))
+ , kmerSize_(kmerSize)
+ , seedScorer_(index, kmerSize)
+ {
+ using namespace seqan;
+
+ // Store the size of the reference as a float for calculating frequencies
+ referenceSize_ = static_cast<float>(length(getFibre(index_, QGram_RawText()))) / 2.0f;
+ }
+
+ // Move constructor
+ ChainScorer(ChainScorer&& src) = delete;
+ // Copy constructor
+ ChainScorer(const ChainScorer& src) = delete;
+ // Move assignment operator
+ ChainScorer& operator=(ChainScorer&& rhs) = delete;
+ // Copy assignment operator
+ ChainScorer& operator=(const ChainScorer& rhs) = delete;
+ // Destructor
+ ~ChainScorer() = default;
+
+public: // non-modifying methods
+ /// Score a given seed-set found that matches the reference index, returning
+ /// a score that approximates it's log-likehood.
+ ///
+ /// Equivalent to BLASR's ComputeLISPValue function.
+ ///
+ /// \param query The query sequence in which the hits were found
+ /// \param chain A seed-set of matching positions between the query and references
+ /// \return float
+ float operator()(const TString& query, const THit& hit)
+ {
+ float score = defaultScore_;
+
+ // Count the number of seeds in the chain
+ const size_t& referenceIdx = hit.first;
+ const TSeedChain& chain = hit.second;
+ size_t chainLength = seqan::length(chain);
+
+ if (chainLength <= 0) {
+ // If there are no seeds in this chain, we shouldn't be here
+ return defaultScore_;
+ } else if (chainLength == 1) {
+ // If we have 1 seed and we can score it, return that value
+ if (seedScorer_(query, chain[0], referenceIdx, score)) {
+ return score;
+ } else {
+ return defaultScore_;
+ }
+ } else // If the chain has more than 1-seed, score it differently
+ {
+ /*std::cout << 0 << " "
+ << seqan::beginPositionH(chain[0]) << " "
+ << seqan::endPositionH(chain[0]) << " "
+ << seqan::endPositionH(chain[0]) - seqan::beginPositionH(chain[0]) << " "
+ //<< seqan::beginPositionH(seqan::back(chain)) << " "
+ //<< seqan::endPositionH(seqan::back(chain)) << " "
+ << CountOccurrences(query, chain[0], referenceIdx) << std::endl;*/
+ // If we can score the first seed, use that as the base value
+ if (seedScorer_(query, chain[0], referenceIdx, score)) {
+ // Iterate over each seed in the chain past the first
+ for (size_t i = 1; i < chainLength; ++i) {
+ /*std::cout << i << " "
+ << seqan::beginPositionH(chain[i]) << " "
+ << seqan::endPositionH(chain[i]) << " "
+ << seqan::endPositionH(chain[i]) - seqan::beginPositionH(chain[i]) << " "
+ //<< seqan::beginPositionH(seqan::back(chain)) << " "
+ //<< seqan::endPositionH(seqan::back(chain)) << " "
+ << CountOccurrences(query, chain[i], referenceIdx) << std::endl;*/
+ float seedFrequency = GetFrequency(query, chain[i], referenceIdx);
+ score += std::log(seedFrequency);
+ }
+ } else {
+ return defaultScore_;
+ }
+ }
+ // Return the calculated pValue
+ return score;
+ }
+
+ /// Calculate the expected frequency of a Kmer in
+ ///
+ /// Equivalent to BLASR's qLambda calcultion from LISPValueImpl.hpp
+ ///
+ /// \param query The sequence from which a substring will be counted
+ /// \param seed A seed with the start-position of the Kmer
+ /// \return float The frequency of the occurrence of the seed in the
+ /// reference
+ float GetFrequency(const TString& query, const TSeed& seed, const size_t& referenceIdx)
+ {
+ return CountOccurrences(query, seed, referenceIdx) / referenceSize_;
+ }
+
+ /// \param query The sequence from which a substring will be counted
+ /// \param seed A seed with the start-position of the Kmer start position
+ /// \return the number of occurences
+ size_t CountOccurrences(const TString& query, const TSeed& seed, const size_t& referenceIdx)
+ {
+ using namespace seqan;
+
+ size_t occurrences = 0;
+ if (LengthH(seed) == Size) {
+ hash(shape_, begin(query) + beginPositionH(seed));
+ for (const auto o : getOccurrences(index_, shape_))
+ if (getValueI1(o) == referenceIdx) occurrences += 1;
+ return occurrences;
+ } else {
+ hash(shape_, begin(query) + beginPositionH(seed));
+ for (const auto o : getOccurrences(index_, shape_))
+ if (getValueI1(o) == referenceIdx) occurrences += 1;
+ return occurrences;
+ }
+ }
+
+ size_t LengthH(const TSeed& seed)
+ {
+ using namespace seqan;
+
+ return endPositionH(seed) - beginPositionH(seed);
+ }
+
+private: // data
+ TIndex index_;
+ TShape shape_;
+ size_t kmerSize_;
+ float referenceSize_;
+ SeedScorer<TConfig> seedScorer_;
+ float defaultScore_ = 1.0f;
+};
+}
+} // ::PacBio::Align
diff --git a/include/pacbio/align/ChainSeeds.h b/include/pacbio/align/ChainSeeds.h
new file mode 100644
index 0000000..e88bbb7
--- /dev/null
+++ b/include/pacbio/align/ChainSeeds.h
@@ -0,0 +1,696 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler, Brett Bowman
+
+#pragma once
+
+#include <algorithm>
+#include <queue>
+#include <set>
+
+#include <boost/optional.hpp>
+#include <boost/optional/optional_io.hpp>
+
+#include <seqan/seeds.h>
+#include <seqan/sequence.h>
+
+#include <pacbio/align/ChainSeedsConfig.h>
+
+namespace PacBio {
+namespace Align {
+
+// H is query, V is reference
+
+namespace {
+
+/// Calculate number of bases between a seed and the diagonal
+/// axis of the matrix it's in as extended outward from the
+/// upper-left-hand corner of the matrix toward the lower right.
+/// High numbers are closer to the upper-right, negative numbers
+/// closer to the lower-left.
+///
+/// \param seed The seed whose diagonal is desired.
+///
+/// \return long The distance from the seed's upper-left corner and
+/// the diagonal axis of the matrix.
+long Diagonal(const seqan::Seed<seqan::Simple>& seed)
+{
+ size_t v = beginPositionV(seed);
+ size_t h = beginPositionH(seed);
+
+ if (v > h) return -static_cast<long>(v - h);
+
+ return static_cast<long>(h - v);
+}
+
+/// Compare seeds for sorting, first in the horizontal (query)
+/// dimension, then in the vertical (reference) dimension.
+///
+/// \param lhs The left-hand side seed to compare
+/// \param rhs The right-hand side seed to compare
+///
+/// \return bool Whether the left seed preceeds the right seed
+bool HVCompare(const seqan::Seed<seqan::Simple>& lhs, const seqan::Seed<seqan::Simple>& rhs)
+{
+ unsigned leftH = beginPositionH(lhs), rightH = beginPositionH(rhs);
+
+ if (leftH < rightH) return true;
+
+ if (leftH == rightH) return endPositionV(lhs) < endPositionV(rhs);
+
+ return false;
+}
+
+/// Compare seeds for sorting, first in the vertical (reference)
+/// dimension, then in the horizontal (query) dimension.
+///
+/// \param lhs The left-hand side seed to compare
+/// \param rhs The right-hand side seed to compare
+///
+/// \return bool Whether the left seed preceeds the right seed
+bool VHCompare(const seqan::Seed<seqan::Simple>& lhs, const seqan::Seed<seqan::Simple>& rhs)
+{
+ unsigned leftV = beginPositionV(lhs), rightV = beginPositionV(rhs);
+
+ if (leftV < rightV) return true;
+
+ if (leftV == rightV) return endPositionH(lhs) < endPositionH(rhs);
+
+ return false;
+}
+
+/// Compare seeds for sorting, by whether one seed is higher or
+/// lower than another in the sparse matrix of their alignment,
+/// according to their diagonals. Seeds near the upper-right
+/// corner are said to preceed seeds closer to the lower-left.
+///
+/// \param lhs The left-hand seed to compare
+/// \param rhs The right-hand seed to compare
+///
+/// \return bool Whether the left seed preceeds the right seed
+bool DiagonalCompare(const seqan::Seed<seqan::Simple>& lhs, const seqan::Seed<seqan::Simple>& rhs)
+{
+ int leftD = beginDiagonal(lhs), rightD = beginDiagonal(rhs);
+
+ if (leftD == rightD) return beginPositionH(lhs) < beginPositionH(rhs);
+
+ return leftD < rightD;
+}
+
+/// Score the possible linkage of two seeds based on 3 criteria:
+/// (A) The number of bases in the shortest seed
+/// (B) The number of bases between the two seeds
+/// (C) The size of the difference between their diagonals
+/// each with it's own weight(s).
+///
+/// \param lhs The left-hand side seed to link
+/// \param rhs The right-hand side seed to link
+/// \param matchScore The reward for each base within the seeds.
+/// (Value should be > 0).
+/// \param mismatchScore The penalty for each base between the seeds.
+/// (Value should be <= 0)
+/// \param insertionScore The penalty for each difference in between the
+/// diagonals, if Left > Right. (Value should be < 0)
+/// \param deletionScore The penalty for each difference in between the
+/// diagonals, if Right > Left. (Value should be < 0)
+///
+/// \return long The score associated with the linkage
+long LinkScore(const seqan::Seed<seqan::Simple>& lhs, const seqan::Seed<seqan::Simple>& rhs,
+ const ChainSeedsConfig config)
+{
+ using namespace std;
+
+ long lH = static_cast<long>(beginPositionH(lhs));
+ long lV = static_cast<long>(beginPositionV(lhs));
+ long rH = static_cast<long>(beginPositionH(rhs));
+ long rV = static_cast<long>(beginPositionV(rhs));
+ long k = min(static_cast<long>(seedSize(lhs)), static_cast<long>(seedSize(rhs)));
+ long fwd = min(lH - rH, lV - rV);
+
+ // matchReward = # of anchor bases * matchScore;
+ long matches = k - max(0l, k - fwd);
+ long matchReward = matches * config.matchScore;
+
+ // nonMatchPenalty = # of non-anchor, on-diagonal bases * nonMatchPenalty
+ long nonMatches = fwd - matches;
+ long nonMatchScorePenalty = nonMatches * config.nonMatchPenalty;
+
+ // Ignore any linkage over a certain size, no matter the score
+ if (nonMatches > config.maxSeedGap) return -1;
+
+ // indelPenalty = difference in the seed diagonals * indelScore
+ long diagL = Diagonal(lhs);
+ long diagR = Diagonal(rhs);
+ long drift = diagL - diagR;
+ long indelScorePenalty = 0;
+ if (drift > 0)
+ indelScorePenalty = drift * config.insertionPenalty;
+ else if (drift < 0)
+ indelScorePenalty = -drift * config.deletionPenalty;
+
+ return matchReward + indelScorePenalty + nonMatchScorePenalty;
+}
+
+///
+/// A Sparse Dynamic Programming hit. A wrapper around SeqAn's Seed class
+/// with an additional field for storing it's index in the original seed set.
+///
+/// TODO (bbowman): Can I replace this struct with just Seeds by using the
+/// build in SeedScore field and setter/getters?
+///
+struct SDPHit : public seqan::Seed<seqan::Simple>
+{
+ size_t Index;
+
+ SDPHit(const seqan::Seed<seqan::Simple>& seed, const size_t index)
+ : seqan::Seed<seqan::Simple>(seed), Index(index)
+ {
+ }
+
+ ///
+ ///
+ /// \return bool Whether this s
+ bool operator<(const SDPHit& other) const { return DiagonalCompare(*this, other); }
+};
+
+/// Compare two seeds (SDPHits) according to their original indices in
+/// their source seedSet
+///
+/// \param lhs The left-hand side seed to compare
+/// \param rhs The right-hand side seed to compare
+///
+/// \return bool Whether the original index of LHS is less than RHS
+bool IndexCompare(const SDPHit& lhs, const SDPHit& rhs) { return lhs.Index < rhs.Index; }
+
+///
+/// A column in the Sparse Dynamic Programming matrix. A wrapper around the above
+/// SDPHit struct to give it a column field and a comparison operator that uses it.
+///
+/// TODO (bbowman): Can I replace this struct with just SDPHits or just Seeds, since
+/// we get the Column from SeqAn function endPositionH() function
+/// anyway?
+///
+struct SDPColumn
+{
+ boost::optional<SDPHit> Seed;
+ size_t Column;
+
+ SDPColumn(size_t column, const boost::optional<SDPHit> seed = boost::none)
+ : Seed(seed), Column(column)
+ {
+ }
+
+ bool operator<(const SDPColumn& other) const { return Column < other.Column; }
+};
+
+///
+///
+/// \param seeds A vector of the SDPHits, sorted by their position in the
+/// horizontal (query)
+/// \param sweepSet
+///
+/// \return vector<optional<SDPHits>> For each seed in the input vector, the
+/// first index that is visible to it's left, if any.
+std::vector<boost::optional<SDPHit>> ComputeVisibilityLeft(const std::vector<SDPHit>& seeds,
+ std::set<SDPHit>& sweepSet)
+{
+ using namespace seqan;
+ using namespace std;
+ using boost::optional;
+
+ vector<optional<SDPHit>> visible(seeds.size(), boost::none); // Output
+
+ auto toRemove = seeds.begin();
+ for (auto it = seeds.begin(); it != seeds.end();) {
+ const size_t col = beginPositionH(*it);
+ const auto start = it;
+
+ // Advance the iterator to the end of the current column in our
+ // column-sorted vector of seeds
+ for (; it != seeds.end() && col == beginPositionH(*it); ++it) {
+ // For each seed, record in the output vector, record the first
+ // seed after it in the sweepSet (if any). Since the sweepSet
+ // only contains seeds from previous columns and is sorted by
+ // their diagonals, this means the seeds found in this way will
+ // all (A) Start to the left and (B) Start on a higher diagonal
+ auto succ = sweepSet.upper_bound(*it);
+ if (succ != sweepSet.end()) {
+ visible[it->Index] = *succ;
+ }
+ }
+
+ // Add all seeds to the sweepSet that start in the current column
+ sweepSet.insert(start, it);
+
+ // Remove all seeds from the sweepSet that end before the current column
+ for (; toRemove != seeds.end() && endPositionH(*toRemove) < col; ++toRemove) {
+ sweepSet.erase(*toRemove);
+ }
+ }
+
+ // clear the sweepSet after use
+ sweepSet.clear();
+
+ return visible;
+}
+
+///
+/// A possible chain of SDP seeds. A simple struct for wrapping the
+/// three pieces of information we need to filter and possibly
+/// reconstruct a chain that we've found:
+/// (A) The reference sequence where the chain was found
+/// (B) The terminal seed in the chain
+/// (C) The chain's score
+///
+struct ChainHit
+{
+ size_t seedSetIdx;
+ size_t endIndex;
+ long score;
+};
+
+//
+// Functor for sorting ChainHits by score
+//
+class ChainHitCompare
+{
+public:
+ bool operator()(const ChainHit& lhs, const ChainHit& rhs) { return lhs.score > rhs.score; }
+};
+
+/// Though we expect to receive the Seeds we'll be chaining in a tree-like
+/// SeedSet, we need them and their scores in well-ordered vectors to
+/// perform the actual chaining ourselves. This function is a simple
+/// helper for abstracting away that process.
+///
+/// \param seedSet The collection of seeds to be chained
+/// \param seeds The vector of SDPHit objects that will actually be chained
+/// \param scores The vector of scores to initialize with default per-seed scores
+void InitializeSeedsAndScores(const seqan::SeedSet<seqan::Seed<seqan::Simple>>& seedSet,
+ std::vector<SDPHit>* seeds, std::vector<long>* scores)
+{
+ size_t i = 0;
+ for (auto it = begin(seedSet); it != end(seedSet); ++it, ++i) {
+ seeds->push_back(SDPHit(*it, i));
+ scores->at(i) = seedSize(*it);
+ }
+}
+
+/// Search a SeedSet for the best numCandidates sets of locally-chainable
+/// seeds according to some scoring criteria. Seed chains are scored based
+/// on their length and penalized according to the distance between them and
+/// how far apart their diagonals are. Final scores for a chain must be above
+/// some minScore threshold to be reported.
+///
+/// Roughly equivalent to BLASR's SDPAlign
+///
+/// TODO (bbowman): I shouldn't report partial and complete chains of the same seeds
+/// TODO (bbowman): Figure out why my penalties need to be lower than BLASR's
+/// for similar results
+///
+/// \param chains A vector of SeedSets to store and return collections of
+/// locally chained seeds in.
+/// \param seedSet The SeedSet to search for chains in
+/// \param numCandidates The maximum number of chains to report
+/// \param minScore The minimum score to require from a reported chain
+/// \param match Score to add to each matching base in each seed
+/// \param nonmatch Penalty for each non-aligned base between seeds
+/// along whichever dimension they are closest together
+/// \param insertion Penalty for each base along the diagonal that
+/// separates two seeds, if the 'upstream' seed is on
+/// a higher diagonal than the 'downstream' seed.
+/// \param deletion Penalty for each base along the diagonal that
+/// separates two seeds, if the 'upstream' seed is on
+/// a lower diagonal than the 'downstream' seed.
+void __attribute__((__unused__))
+ChainSeedsImpl(std::priority_queue<ChainHit, std::vector<ChainHit>, ChainHitCompare>* chainHits,
+ std::vector<boost::optional<size_t>>* chainPred, std::vector<SDPHit>* seeds,
+ std::vector<long>& scores, const size_t seedSetIdx, const ChainSeedsConfig& config)
+{
+ using namespace std;
+ using namespace seqan;
+
+ // compute visibility left, requires H-sorted seeds
+ std::set<SDPHit> sweepSet;
+ sort(seeds->begin(), seeds->end(), HVCompare);
+ auto visible = ComputeVisibilityLeft(*seeds, sweepSet);
+
+ // compute the visibility above, requires V-sorted seeds
+ sort(seeds->begin(), seeds->end(), VHCompare);
+ auto toRemove = seeds->begin();
+ std::set<SDPColumn> colSet;
+
+ auto zScore = [&scores](const SDPHit& seed) {
+ return scores[seed.Index] + beginPositionH(seed) + beginPositionV(seed);
+ };
+
+ for (auto it = seeds->begin(); it != seeds->end();) {
+ const size_t row = beginPositionV(*it);
+ const auto start = it;
+
+ for (; it != seeds->end() && row == beginPositionV(*it); ++it) {
+ long bestScore = -numeric_limits<long>::max();
+ boost::optional<SDPHit> bestSeed = boost::none;
+
+ // find the previous column and best fragment from it
+ {
+ SDPColumn col(beginPositionH(*it));
+ auto pred = colSet.lower_bound(col);
+
+ if (pred != colSet.begin()) {
+ pred = prev(pred);
+ long s = scores[pred->Seed->Index] + LinkScore(*it, *(pred->Seed), config);
+
+ if (s > bestScore) {
+ bestScore = s;
+ bestSeed = pred->Seed;
+ }
+ }
+ }
+
+ // search visible fragments (above)
+ {
+ auto visa = sweepSet.lower_bound(*it);
+
+ if (visa != sweepSet.begin()) {
+ visa = prev(visa);
+ long s = scores[visa->Index] + LinkScore(*it, *visa, config);
+
+ if (s > bestScore) {
+ bestScore = s;
+ bestSeed = *visa;
+ }
+ }
+ }
+
+ // search visible fragments (left)
+ if (auto visl = visible[it->Index]) {
+ long s = scores[visl->Index] + LinkScore(*it, *visl, config);
+
+ if (s > bestScore) {
+ bestScore = s;
+ bestSeed = visl;
+ }
+ }
+
+ if (bestSeed && bestScore >= config.minScore) {
+ scores[it->Index] = bestScore;
+ chainPred->at(it->Index) = bestSeed->Index;
+
+ if (chainHits->size() < config.numCandidates) {
+ chainHits->push({seedSetIdx, it->Index, bestScore});
+ } else if (bestScore > chainHits->top().score) {
+ chainHits->pop();
+ chainHits->push({seedSetIdx, it->Index, bestScore});
+ }
+ } else if (scores[it->Index] >= config.minScore) {
+ // PLEASE NOTE: these have already been done at creation time
+ // scores[it->Index] = seedSize(*it);
+ // chainPred[it->Index] = boost::none;
+ //
+
+ if (chainHits->size() < config.numCandidates) {
+ chainHits->push({seedSetIdx, it->Index, bestScore});
+ } else if (bestScore > chainHits->top().score) {
+ chainHits->pop();
+ chainHits->push({seedSetIdx, it->Index, bestScore});
+ }
+ }
+ }
+
+ sweepSet.insert(start, it);
+
+ // remove all seeds from the sweepSet with end position less than the current row,
+ // and ensure the colSet invariant is kept:
+ // that all columns greater than our current
+ for (; toRemove != seeds->end() && endPositionV(*toRemove) < row; ++toRemove) {
+ SDPColumn col(endPositionH(*toRemove), boost::make_optional(*toRemove));
+
+ auto it = colSet.find(col);
+
+ // update the column if it doesn't exist
+ // or if its score is less than the fragment we're removing from consideration
+ if (it == colSet.end() || zScore(*(it->Seed)) < zScore(*toRemove)) {
+ // insert the updated column, get successor
+ it = next(colSet.insert(col).first);
+
+ // keep removing columns long as the scores are less than
+ while (it != colSet.end() && zScore(*(it->Seed)) < zScore(*toRemove)) {
+ it = colSet.erase(it);
+ }
+ }
+
+ sweepSet.erase(*toRemove);
+ }
+ }
+
+ // seeds need to be sorted by Index to ... index into it properly
+ sort(seeds->begin(), seeds->end(), IndexCompare);
+}
+
+/// Search a SeedSet for the best numCandidates sets of locally-chainable
+/// seeds according to some scoring criteria. Seed chains are scored based
+/// on their length and penalized according to the distance between them and
+/// how far apart their diagonals are. Final scores for a chain must be above
+/// some minScore threshold to be reported.
+///
+/// Roughly equivalent to BLASR's SDPAlign
+///
+/// \param chains A vector of SeedSets to store and return collections of
+/// locally chained seeds in.
+/// \param seedSet The SeedSet to search for chains in
+/// \param numCandidates The maximum number of chains to report
+/// \param minScore The minimum score to require from a reported chain
+/// \param match Score to add to each matching base in each seed
+/// \param nonmatch Penalty for each non-aligned base between seeds
+/// along whichever dimension they are closest together
+/// \param insertion Penalty for each base along the diagonal that
+/// separates two seeds, if the 'upstream' seed is on
+/// a higher diagonal than the 'downstream' seed.
+/// \param deletion Penalty for each base along the diagonal that
+/// separates two seeds, if the 'upstream' seed is on
+/// a lower diagonal than the 'downstream' seed.
+void __attribute__((__unused__))
+ChainSeeds(std::vector<seqan::String<seqan::Seed<seqan::Simple>>>* chains,
+ const seqan::SeedSet<seqan::Seed<seqan::Simple>>& seedSet,
+ const ChainSeedsConfig& config)
+{
+ using namespace seqan;
+ using namespace std;
+
+ // Initialize the work-horse vectors we will actually work with
+ priority_queue<ChainHit, vector<ChainHit>, ChainHitCompare> chainHits;
+ vector<boost::optional<size_t>> chainPred(length(seedSet), boost::none);
+ vector<SDPHit> seeds;
+ vector<long> scores(length(seedSet), 0L);
+ InitializeSeedsAndScores(seedSet, &seeds, &scores);
+
+ // Call the main function
+ ChainSeedsImpl(&chainHits, &chainPred, &seeds, scores, 0, config);
+
+ // Empty and resize the result vector
+ chains->clear();
+ chains->resize(chainHits.size());
+
+ // Pop our results from our queue and convert them into Seed Chains / Sets
+ int i = chainHits.size() - 1;
+ while (!chainHits.empty()) {
+ const auto hit = chainHits.top();
+ //std::cout << "b(" << hit.reference << ", " << hit.endIndex << ", " << hit.score << ")" << std::endl;
+
+ // While there are additional links in the chain, append them
+ boost::optional<size_t> chainEnd = hit.endIndex;
+ while (chainEnd) {
+ appendValue(chains->at(i), seeds[*chainEnd]);
+ chainEnd = chainPred[*chainEnd];
+ }
+
+ // We appended seeds back-to-front, so reverse the current order in place
+ reverse(chains->at(i));
+
+ chainHits.pop();
+ --i;
+ }
+}
+
+/// Search a SeedSet for the best numCandidates sets of locally-chainable
+/// seeds according to some scoring criteria. Seed chains are scored based
+/// on their length and penalized according to the distance between them and
+/// how far apart their diagonals are. Final scores for a chain must be above
+/// some minScore threshold to be reported.
+///
+/// Roughly equivalent to BLASR's SDPAlign
+///
+/// \param chains A vector of SeedSets to store and return collections of
+/// locally chained seeds in.
+/// \param seedSet The SeedSet to search for chains in
+/// \param numCandidates The maximum number of chains to report
+/// \param minScore The minimum score to require from a reported chain
+/// \param match Score to add to each matching base in each seed
+/// \param nonmatch Penalty for each non-aligned base between seeds
+/// along whichever dimension they are closest together
+/// \param insertion Penalty for each base along the diagonal that
+/// separates two seeds, if the 'upstream' seed is on
+/// a higher diagonal than the 'downstream' seed.
+/// \param deletion Penalty for each base along the diagonal that
+/// separates two seeds, if the 'upstream' seed is on
+/// a lower diagonal than the 'downstream' seed.
+void __attribute__((__unused__))
+ChainSeeds(std::vector<seqan::SeedSet<seqan::Seed<seqan::Simple>>>* chains,
+ const seqan::SeedSet<seqan::Seed<seqan::Simple>>& seedSet,
+ const ChainSeedsConfig& config)
+{
+ using namespace seqan;
+ using namespace std;
+
+ // Initialize the work-horse vectors we will actually work with
+ priority_queue<ChainHit, vector<ChainHit>, ChainHitCompare> chainHits;
+ vector<boost::optional<size_t>> chainPred(length(seedSet), boost::none);
+ vector<SDPHit> seeds;
+ vector<long> scores(length(seedSet), 0L);
+ InitializeSeedsAndScores(seedSet, &seeds, &scores);
+
+ // Call the main function
+ ChainSeedsImpl(&chainHits, &chainPred, &seeds, scores, 0, config);
+
+ // Empty and resize the result vector
+ chains->clear();
+ chains->resize(chainHits.size());
+
+ // Pop our results from our queue and convert them into Seed Chains / Sets
+ int i = chainHits.size() - 1;
+ while (!chainHits.empty()) {
+ const auto hit = chainHits.top();
+
+ // While there are additional links in the chain, append them
+ boost::optional<size_t> chainEnd = hit.endIndex;
+ while (chainEnd) {
+ Seed<Simple> seed = seeds[*chainEnd];
+ addSeed(chains->at(i), seed, Single());
+ chainEnd = chainPred[*chainEnd];
+ }
+
+ chainHits.pop();
+ --i;
+ }
+}
+
+/// Search a SeedSet for the best numCandidates sets of locally-chainable
+/// seeds according to some scoring criteria. Seed chains are scored based
+/// on their length and penalized according to the distance between them and
+/// how far apart their diagonals are. Final scores for a chain must be above
+/// some minScore threshold to be reported.
+///
+/// Roughly equivalent to BLASR's SDPAlign
+///
+/// \param chains A vector of SeedSets to store and return collections of
+/// locally chained seeds in.
+/// \param seedSet The SeedSet to search for chains in
+/// \param numCandidates The maximum number of chains to report
+/// \param minScore The minimum score to require from a reported chain
+/// \param match Score to add to each matching base in each seed
+/// \param nonmatch Penalty for each non-aligned base between seeds
+/// along whichever dimension they are closest together
+/// \param insertion Penalty for each base along the diagonal that
+/// separates two seeds, if the 'upstream' seed is on
+/// a higher diagonal than the 'downstream' seed.
+/// \param deletion Penalty for each base along the diagonal that
+/// separates two seeds, if the 'upstream' seed is on
+/// a lower diagonal than the 'downstream' seed.
+void __attribute__((unused))
+ChainSeeds(std::vector<std::pair<size_t, seqan::SeedSet<seqan::Seed<seqan::Simple>>>>* chains,
+ const std::map<size_t, seqan::SeedSet<seqan::Seed<seqan::Simple>>> seedSets,
+ const ChainSeedsConfig config)
+{
+ using namespace seqan;
+ using namespace std;
+
+ // The queue will accumulat results across SeedSets
+ priority_queue<ChainHit, vector<ChainHit>, ChainHitCompare> chainHits;
+
+ // Our vectors of seeds and chain-links need to persist for eventual
+ // use reconstructing our chains, so we initialize them as
+ // vectors-of-vectors here, 1 per seedSet we will analyze
+ size_t numSeedSets = seedSets.size();
+ vector<vector<boost::optional<size_t>>> chainPred(numSeedSets);
+ vector<vector<SDPHit>> seeds(numSeedSets);
+
+ // We also need to record which seedSet came from which reference
+ vector<size_t> references(numSeedSets);
+
+ // Iterate over the multiple SeedSets once to search for chains
+ int i = 0;
+ for (auto it = seedSets.begin(); it != seedSets.end(); ++it, ++i) {
+ // Extract the contents of our K/V pair
+ references[i] = it->first;
+ const auto& seedSet = it->second;
+
+ // Initialize the work-horse vectors we will actually work with
+ chainPred[i] = vector<boost::optional<size_t>>(length(seedSet), boost::none);
+ vector<long> scores(length(seedSet), 0L);
+ InitializeSeedsAndScores(seedSet, &seeds[i], &scores);
+
+ // Call the main function on the current seedSet
+ ChainSeedsImpl(&chainHits, &chainPred[i], &seeds[i], scores, i, config);
+ }
+
+ // Empty and resize the result vector
+ chains->clear();
+ chains->resize(chainHits.size());
+
+ // Pop our results from our queue and convert them into Seed Chains / Sets
+ int j = chainHits.size() - 1;
+ while (!chainHits.empty()) {
+ // Take our next hit and extract the relevant indices ...
+ const auto hit = chainHits.top();
+ chains->at(j).first = references[hit.seedSetIdx];
+
+ // While there are additional links in the chain, append them
+ boost::optional<size_t> chainEnd = hit.endIndex;
+ while (chainEnd) {
+ Seed<Simple> seed = seeds[hit.seedSetIdx][*chainEnd];
+ addSeed(chains->at(j).second, seed, Single());
+ chainEnd = chainPred[hit.seedSetIdx][*chainEnd];
+ }
+
+ chainHits.pop();
+ --j;
+ }
+}
+
+} // anonymous namespace
+}
+} // PacBio::Align
diff --git a/include/pacbio/align/ChainSeedsConfig.h b/include/pacbio/align/ChainSeedsConfig.h
new file mode 100644
index 0000000..749aff6
--- /dev/null
+++ b/include/pacbio/align/ChainSeedsConfig.h
@@ -0,0 +1,105 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Brett Bowman
+
+#pragma once
+
+namespace PacBio {
+namespace Align {
+
+// Default values for struct fields
+static const size_t NUM_CANDIDATES = 10;
+static const long MIN_SCORE = 18;
+static const int MATCH_SCORE = 5;
+static const int NON_MATCH_PENALTY = 0;
+static const int INSERTION_PENALTY = -4;
+static const int DELETION_PENALTY = -8;
+static const int MAX_SEED_GAP = 200;
+
+/// A simple struct for represting a complete specialization for an
+/// implementation of the Baker-Giancarlo SDP algorithm. Templating
+/// around this struct allows us to greatly reduce the number of
+/// parameters that need to be thrown around.
+///
+struct ChainSeedsConfig
+{
+ // Default constructor
+ ChainSeedsConfig(const size_t numCandidatesArg, const long minScoreArg, const int matchScoreArg,
+ const int nonMatchPenaltyArg, const int insertionPenaltyArg,
+ const int deletionPenaltyArg, const int maxSeedGapArg)
+ : numCandidates(numCandidatesArg)
+ , minScore(minScoreArg)
+ , matchScore(matchScoreArg)
+ , nonMatchPenalty(nonMatchPenaltyArg)
+ , insertionPenalty(insertionPenaltyArg)
+ , deletionPenalty(deletionPenaltyArg)
+ , maxSeedGap(maxSeedGapArg)
+ {
+ }
+
+ // Abbreviated constructors
+ ChainSeedsConfig(const size_t numCandidatesArg)
+ : numCandidates(numCandidatesArg)
+ , minScore(MIN_SCORE)
+ , matchScore(MATCH_SCORE)
+ , nonMatchPenalty(NON_MATCH_PENALTY)
+ , insertionPenalty(INSERTION_PENALTY)
+ , deletionPenalty(DELETION_PENALTY)
+ , maxSeedGap(MAX_SEED_GAP)
+ {
+ }
+
+ ChainSeedsConfig()
+ : numCandidates(NUM_CANDIDATES)
+ , minScore(MIN_SCORE)
+ , matchScore(MATCH_SCORE)
+ , nonMatchPenalty(NON_MATCH_PENALTY)
+ , insertionPenalty(INSERTION_PENALTY)
+ , deletionPenalty(DELETION_PENALTY)
+ , maxSeedGap(MAX_SEED_GAP)
+ {
+ }
+
+ size_t numCandidates;
+ long minScore;
+ int matchScore;
+ int nonMatchPenalty;
+ int insertionPenalty;
+ int deletionPenalty;
+ int maxSeedGap;
+};
+}
+} // PacBio::Align
diff --git a/include/pacbio/align/FilterSeeds.h b/include/pacbio/align/FilterSeeds.h
new file mode 100644
index 0000000..e0e9afb
--- /dev/null
+++ b/include/pacbio/align/FilterSeeds.h
@@ -0,0 +1,123 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Brett Bowman
+
+#pragma once
+
+#include <functional>
+#include <map>
+#include <queue>
+#include <utility>
+#include <vector>
+
+#include <seqan/align.h>
+#include <seqan/basic.h>
+#include <seqan/index.h>
+#include <seqan/seeds.h>
+#include <seqan/sequence.h>
+
+namespace PacBio {
+namespace Align {
+
+/// Count the number of seeds in a container. Additionally,
+/// if the MERGESEEDS pre-processing directive is on, adjust
+/// the count for the fact that each individual seed may be
+/// a composite of multiple smaller seeds.
+///
+/// \param seeds Any container-type of seeds that supports
+/// range-based iteration.
+template <size_t TSize, typename TContainer>
+size_t CountSeeds(const TContainer& seeds)
+{
+ using namespace seqan;
+
+ size_t count = length(seeds);
+
+#ifdef MERGESEEDS
+ for (const auto& seed : seeds) {
+ count += seedSize(seed) - TSize;
+ }
+#endif
+
+ return count;
+}
+
+/// Count the number of seeds in a container. Additionally,
+/// if the MERGESEEDS pre-processing directive is on, adjust
+/// the count for the fact that each individual seed may be
+/// a composite of multiple smaller seeds.
+///
+/// \param seeds A map of Int<-->SeedSet pairs, linking the index
+/// of the reference sequence to the seeds found within.
+/// \param size_t The number of top hits to retain and report
+template <size_t TSize>
+void FilterSeeds(std::map<size_t, seqan::SeedSet<seqan::Seed<seqan::Simple>>>* seeds,
+ const size_t nBest)
+{
+ using namespace std;
+
+ // If we already have fewer
+ if (seeds->size() <= nBest) return;
+
+ // keep a priority queue of the biggest hits,
+ // sorted ascendingly. Bump the least value if a new one is bigger.
+ priority_queue<size_t, std::vector<size_t>, std::greater<size_t>> best;
+
+ for (const auto& kv : *seeds) {
+ size_t nSeeds = CountSeeds<TSize>(kv.second);
+
+ if (best.size() < nBest) {
+ best.push(nSeeds);
+ } else if (nSeeds > best.top()) {
+ best.pop();
+ best.push(nSeeds);
+ }
+ }
+
+ // Erase all SeedSets with fewer seeds that the smallest
+ // item that made it into the queue.
+ size_t minSize = best.top();
+ for (auto it = seeds->begin(); it != seeds->end();) {
+ if (CountSeeds<TSize>(it->second) < minSize) {
+ it = seeds.erase(it);
+ } else {
+ ++it;
+ }
+ }
+}
+
+} // Align
+} // PacBio
diff --git a/include/pacbio/align/FindSeeds.h b/include/pacbio/align/FindSeeds.h
new file mode 100644
index 0000000..65dc2ec
--- /dev/null
+++ b/include/pacbio/align/FindSeeds.h
@@ -0,0 +1,260 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler, Brett Bowman
+
+#pragma once
+
+#include <map>
+#include <vector>
+
+#include <seqan/basic.h>
+#include <seqan/index.h>
+#include <seqan/seeds.h>
+#include <seqan/sequence.h>
+
+#include <pacbio/align/ChainSeeds.h>
+#include <pacbio/align/FindSeedsConfig.h>
+#include <pacbio/align/HomopolymerHasher.h>
+
+/*
+ * This file contains a few minimal wrapper functions around the index types
+ * provided by SeqAn for finding K-mer seeds between some query sequence
+ * and some reference sequence or index.
+ *
+ * NOTE: Though these functions should in theory work with any index type
+ * supported by SeqAn, they have only been extensively tested with the QGram
+ * index specialization. Use other types at your own risk.
+ *
+ * In addition to the templating around the TConfig, of which more details
+ * are in FindSeedConfig.h, there are two pre-processor directives that
+ * can be used to further customize the code, described below. Speed costs
+ * associated with either are highly application-specific, so we recommend
+ * testing both for each new application.
+ *
+ * MERGESEEDS: There are two common specializations of the addSeeds function
+ * that we use to add a K-mer hit to a SeedSet - Single() and Merge().
+ * By default FindSeeds uses Single(), which is the fastest method
+ * because it does no chaining at all. Alternatively, we can use the
+ * Merge() function from SeqAn, which combines seeds that precisely
+ * overlap with each other but is slightly slower. The advantage of
+ * Merge() is that the resulting SeedSets are smaller, so down-stream
+ * processes that require for sorting and iterating may be greatly
+ * expedited. Enable this directive to use Merge() instead of Single().
+ *
+ * FILTERHOMOPOLYMERS: By default, FindSeeds treats all K-mer seeds it finds
+ * as equal. However if the sequences might contain large homopolymers,
+ * or if there is a large number of sequences in the the reference /
+ * index, it may be faster in the long run to spend some CPU cycles
+ * checking whether a K-mer is a homopolymer before searching the index
+ * for it. Enable this directive to enable that filter.
+ */
+
+namespace PacBio {
+namespace Align {
+
+/// Unsigned-integer safe subtraction - returns either the difference
+/// between the arguments or zero, whichever is larger.
+///
+/// \param size The first integer, or minuend
+/// \param k The second interger, or the subtrahend
+///
+/// \return size_t The difference
+inline size_t SafeSubtract(size_t size, size_t k) { return size > k ? size - k : 0; }
+
+/// Find all matching seeds between two DNA sequences
+///
+/// \param seeds The SeedSet object to store the results in
+/// \param seq1 The first, or query, sequence
+/// \param seq2 The second, or reference, sequence
+template <typename TConfig>
+void FindSeeds(seqan::SeedSet<seqan::Seed<seqan::Simple>>* seeds, const seqan::DnaString& seq1,
+ const seqan::DnaString& seq2)
+{
+ using namespace seqan;
+
+ typedef Shape<Dna, typename TConfig::ShapeType> TShape;
+
+ Index<DnaString, typename TConfig::IndexType> index(seq1);
+ TShape shape = indexShape(index);
+
+#ifdef FILTERHOMOPOLYMERS
+ HomopolymerHasher<TShape> isHomopolymer(shape);
+#endif
+
+ auto start = begin(seq2);
+ size_t end = SafeSubtract(length(seq2) + 1, TConfig::Size);
+
+ hashInit(shape, start);
+ for (size_t i = 0; i < end; i++) {
+ hashNext(shape, start + i);
+#ifdef FILTERHOMOPOLYMERS
+ if (isHomopolymer(hashNext(shape, start + i))) continue;
+#endif
+
+ auto hits = getOccurrences(index, shape);
+
+ for (const auto& hit : hits) {
+ Seed<Simple> seed(hit, i, TConfig::Size);
+
+#ifdef MERGESEEDS
+ if (!addSeed(*seeds, seed, 0, Merge()))
+#endif
+ {
+ addSeed(*seeds, seed, Single());
+ }
+ }
+ }
+}
+
+/// Find all matching seeds between a DNA index and the sequences
+/// represented in some supplied index of the type specified in TConfig.
+/// Since some index types, most notably the QGram index, can store seeds
+/// from multiple references, the return value has to be a map of seed sets
+/// rather than a single one.
+///
+/// \param seeds A map of integers-SeedSet pairs for storing results
+/// \param index The index of of the various
+/// \param seq The query sequence
+template <typename TConfig>
+void FindSeeds(
+ std::map<size_t, seqan::SeedSet<seqan::Seed<seqan::Simple>>>* seeds,
+ const seqan::Index<seqan::StringSet<seqan::DnaString>, typename TConfig::IndexType>& index,
+ const seqan::DnaString& seq)
+{
+ using namespace seqan;
+ using namespace std;
+
+ typedef Shape<Dna, typename TConfig::ShapeType> TShape;
+
+ TShape shape = indexShape(index);
+
+#ifdef FILTERHOMOPOLYMERS
+ HomopolymerHasher<TShape> isHomopolymer(shape);
+#endif
+
+ auto start = begin(seq);
+ size_t end = SafeSubtract(length(seq) + 1, TConfig::Size);
+
+ hashInit(shape, start);
+
+ for (size_t i = 0; i < end; i++) {
+ hashNext(shape, start + i);
+
+#ifdef FILTERHOMOPOLYMERS
+ if (isHomopolymer(hashNext(shape, start + i))) continue;
+#endif
+
+ auto hits = getOccurrences(index, shape);
+
+ for (const auto& hit : hits) {
+ size_t rIdx = getValueI1(hit);
+
+ size_t j = getValueI2(hit);
+ Seed<Simple> seed(i, j, TConfig::Size);
+
+#ifdef MERGESEEDS
+ if (!addSeed(seeds->operator[](rIdx), seed, 0, Merge()))
+#endif
+ {
+ addSeed(seeds->operator[](rIdx), seed, Single());
+ }
+ }
+ }
+}
+
+/// Find all matching seeds between a DNA index and the sequences
+/// represented in some supplied index of the type specified in TConfig.
+/// Since some index types, most notably the QGram index, can store seeds
+/// from multiple references, the return value has to be a map of seed sets
+/// rather than a single one. In addition the query sequence may itself
+/// be in the index, in which case we pass in it's known index so we do
+/// not count it.
+///
+/// \param seeds A map of integers-SeedSet pairs for storing results
+/// \param index The index of of the various
+/// \param seq The query sequence
+/// \param qIdx The index of the query in the ... index, so it can be ignored
+template <typename TConfig>
+void FindSeeds(
+ std::map<size_t, seqan::SeedSet<seqan::Seed<seqan::Simple>>>* seeds,
+ const seqan::Index<seqan::StringSet<seqan::DnaString>, typename TConfig::IndexType>& index,
+ const seqan::DnaString& seq, const size_t qIdx)
+{
+ using namespace seqan;
+ using namespace std;
+
+ typedef Shape<Dna, typename TConfig::ShapeType> TShape;
+
+ TShape shape = indexShape(index);
+
+#ifdef FILTERHOMOPOLYMERS
+ HomopolymerHasher<TShape> isHomopolymer(shape);
+#endif
+
+ auto start = begin(seq);
+ size_t end = SafeSubtract(length(seq) + 1, TConfig::Size);
+
+ hashInit(shape, start);
+
+ for (size_t i = 0; i < end; i++) {
+ hashNext(shape, start + i);
+
+#ifdef FILTERHOMOPOLYMERS
+ if (isHomopolymer(hashNext(shape, start + i))) continue;
+#endif
+
+ auto hits = getOccurrences(index, shape);
+
+ for (const auto& hit : hits) {
+ size_t rIdx;
+
+ if ((rIdx = getValueI1(hit)) == qIdx) continue;
+
+ size_t j = getValueI2(hit);
+ Seed<Simple> seed(i, j, TConfig::Size);
+
+#ifdef MERGESEEDS
+ if (!addSeed(seeds->operator[](rIdx), seed, 0, Merge()))
+#endif
+ {
+ addSeed(seeds->operator[](rIdx), seed, Single());
+ }
+ }
+ }
+}
+
+} // Align
+} // PacBio
diff --git a/include/pacbio/align/FindSeedsConfig.h b/include/pacbio/align/FindSeedsConfig.h
new file mode 100644
index 0000000..ce8f75b
--- /dev/null
+++ b/include/pacbio/align/FindSeedsConfig.h
@@ -0,0 +1,69 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <seqan/align.h>
+#include <seqan/basic.h>
+#include <seqan/index.h>
+#include <seqan/seeds.h>
+#include <seqan/sequence.h>
+
+namespace PacBio {
+namespace Align {
+
+/// A simple struct for represting a complete specialization for a SeqAn index
+/// such that template-ifying code around different indices can be done around
+/// a single, simple parameter.
+///
+/// TODO (lhepler) : investigate default values other than 10
+///
+/// \param size_t The length of the K-mer or Q-Gram used by the index.
+/// By default 10.
+/// \param TShape The SeqAn shape specialization. By default Ungapped.
+/// \param TIndex The SeqAn index specialization. By default Q-Gram.
+template <size_t TSize = 10, typename TShape = seqan::UngappedShape<TSize>,
+ typename TIndex = seqan::IndexQGram<TShape>>
+struct FindSeedsConfig
+{
+ typedef TIndex IndexType;
+ typedef TShape ShapeType;
+ static const size_t Size = TSize;
+};
+
+} // Align
+} // PacBio
diff --git a/include/pacbio/align/HomopolymerHasher.h b/include/pacbio/align/HomopolymerHasher.h
new file mode 100644
index 0000000..55ef2c3
--- /dev/null
+++ b/include/pacbio/align/HomopolymerHasher.h
@@ -0,0 +1,103 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler, Brett Bowman
+
+#pragma once
+
+#include <vector>
+
+#include <seqan/basic.h>
+
+namespace PacBio {
+namespace Align {
+
+template <typename TShape>
+class HomopolymerHasher
+{
+
+public: // Structors
+ // Default constructor
+ HomopolymerHasher(TShape& shape) { Initialize(shape); }
+
+ // Move constructor
+ HomopolymerHasher(HomopolymerHasher&& src) = delete;
+ // Copy constructor
+ HomopolymerHasher(const HomopolymerHasher& src) = delete;
+ // Move assignment operator
+ HomopolymerHasher& operator=(HomopolymerHasher&& rhs) = delete;
+ // Copy assignment operator
+ HomopolymerHasher& operator=(const HomopolymerHasher& rhs) = delete;
+ // Destructor
+ ~HomopolymerHasher() = default;
+
+private: // Internal class methods
+ /// Initialize the hasher object by creating all possible
+ /// homopolymer templates that fill the shape used by the
+ /// index and saves them for later used by
+ ///
+ /// \param shape The Q-gram shape used in the index
+ void Initialize(const TShape& shape)
+ {
+ using namespace seqan;
+
+ const char dna[4] = {'A', 'C', 'G', 'T'};
+
+ for (size_t i = 0; i < 4; i++) {
+ DnaString s = std::string(length(shape), dna[i]);
+ hashes[i] = seqan::hash(shape, begin(s));
+ }
+ }
+
+public: // Main Function
+ /// Given the hash of a Q-Gram, check whether it matches the
+ /// pattern of one of the stored hashes for known homopolymers.
+ /// If so return True, otherwise False.
+ ///
+ /// \param h The Q-Gram hash of the query sequence
+ inline bool operator()(const unsigned h) const
+ {
+ if (h == hashes[0] || h == hashes[1] || h == hashes[2] || h == hashes[3]) return true;
+
+ return false;
+ }
+
+private: // Class variables
+ unsigned hashes[4];
+
+}; // class HomopolymerHasher
+
+} // namespace Align
+} // namespace PacBio
diff --git a/include/pacbio/align/LinearAlignment.h b/include/pacbio/align/LinearAlignment.h
new file mode 100644
index 0000000..88b9595
--- /dev/null
+++ b/include/pacbio/align/LinearAlignment.h
@@ -0,0 +1,60 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+//
+// Linear-space basic alignment following Hirschberg
+//
+
+#pragma once
+
+#include <string>
+
+#include <pacbio/align/PairwiseAlignment.h>
+
+namespace PacBio {
+namespace Align {
+
+class PairwiseAlignment;
+
+PairwiseAlignment* AlignLinear(const std::string& target, const std::string& query,
+ AlignConfig config = AlignConfig::Default());
+
+PairwiseAlignment* AlignLinear(const std::string& target, const std::string& query, int* score,
+ AlignConfig config = AlignConfig::Default());
+
+} // namespace Align
+} // namespace PacBio
diff --git a/include/pacbio/align/PairwiseAlignment.h b/include/pacbio/align/PairwiseAlignment.h
new file mode 100644
index 0000000..621c96d
--- /dev/null
+++ b/include/pacbio/align/PairwiseAlignment.h
@@ -0,0 +1,110 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Authors: David Alexander, Lance Hepler
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include <pacbio/align/AlignConfig.h>
+
+namespace PacBio {
+namespace Align {
+namespace {
+
+// Utility functions common to implementations of aligners
+
+inline int Max3(int a, int b, int c) { return std::max((a), std::max((b), (c))); }
+inline int ArgMax3(int a, int b, int c)
+{
+ if (a >= b && a >= c)
+ return 0;
+ else if (b >= c)
+ return 1;
+ else
+ return 2;
+}
+
+} // anonymous namespace
+
+/// \brief A pairwise alignment
+class PairwiseAlignment
+{
+private:
+ std::string target_;
+ std::string query_;
+ std::string transcript_;
+
+public:
+ // target string, including gaps; usually the "reference"
+ std::string Target() const;
+
+ // query string, including gaps; usually the "read"
+ std::string Query() const;
+
+ // transcript as defined by Gusfield pg 215.
+ std::string Transcript() const;
+
+public:
+ float Accuracy() const;
+ int Matches() const;
+ int Errors() const;
+ int Mismatches() const;
+ int Insertions() const;
+ int Deletions() const;
+ int Length() const;
+
+public:
+ PairwiseAlignment(const std::string& target, const std::string& query);
+
+ static PairwiseAlignment* FromTranscript(const std::string& transcript,
+ const std::string& unalnTarget,
+ const std::string& unalnQuery);
+};
+
+PairwiseAlignment* Align(const std::string& target, const std::string& query, int* score,
+ AlignConfig config = AlignConfig::Default());
+
+PairwiseAlignment* Align(const std::string& target, const std::string& query,
+ AlignConfig config = AlignConfig::Default());
+
+// These calls return an array, same len as target, containing indices into the query string.
+std::vector<int> TargetToQueryPositions(const std::string& transcript);
+std::vector<int> TargetToQueryPositions(const PairwiseAlignment& aln);
+
+} // namespace Align
+} // namespace PacBio
diff --git a/include/pacbio/align/SeedScorer.h b/include/pacbio/align/SeedScorer.h
new file mode 100644
index 0000000..70e7788
--- /dev/null
+++ b/include/pacbio/align/SeedScorer.h
@@ -0,0 +1,254 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Programmer: Brett Bowman
+
+#pragma once
+
+#include <stdbool.h>
+
+#include <seqan/index.h>
+#include <seqan/seeds.h>
+
+namespace PacBio {
+namespace Align {
+
+template <typename TConfig>
+class SeedScorer
+{
+
+public: // Template types and values
+ typedef typename TConfig::IndexType IndexType;
+ typedef typename TConfig::ShapeType ShapeType;
+ size_t Size = TConfig::Size;
+
+public: // Derived types and values
+ typedef seqan::Index<seqan::StringSet<seqan::DnaString>, IndexType> TIndex;
+ typedef seqan::Finder<TIndex> TFinder;
+ typedef seqan::Dna TAlphabet;
+ typedef typename seqan::ValueSize<TAlphabet>::Type TAlphabetSize;
+ // Equivalent to BLASR's "T_Tuple"
+ typedef seqan::Shape<seqan::Dna, ShapeType> TShape;
+ // Equivalent to BLASR's "MatchPos"
+ typedef seqan::Seed<seqan::Simple> TSeed;
+
+public: // structors
+ SeedScorer(const TIndex& index, const size_t kmerSize)
+ : index_(index)
+ , shape_(seqan::indexShape(index))
+ , kmerFinder_(index)
+ , kmerSize_(kmerSize)
+ , alphabetSize_(seqan::ValueSize<seqan::Dna>::VALUE)
+ {
+ }
+
+ // Move constructor
+ SeedScorer(SeedScorer&& src) = delete;
+ // Copy constructor
+ SeedScorer(const SeedScorer& src) = delete;
+ // Move assignment operator
+ SeedScorer& operator=(SeedScorer&& rhs) = delete;
+ // Copy assignment operator
+ SeedScorer& operator=(const SeedScorer& rhs) = delete;
+ // Destructor
+ ~SeedScorer() = default;
+
+public: // non-modifying methods
+ /// Score a given seed found that matches the reference index, returning
+ /// a number approximating it's log-likehood.
+ ///
+ /// Equivalent to BLASR's PMatch function.
+ ///
+ /// \param seed The position and length of the query
+ /// \param query The query sequence being
+ /// \param pValue The number of occurences
+ /// \return bool Flag whether the scoring succeeded
+ bool operator()(const seqan::DnaString& query, const TSeed& seed, const size_t referenceIdx,
+ float& score)
+ {
+ // Default
+ score = 1.0f;
+
+ // If the count is 0, something when wrong - return failure;
+ size_t count = CountOccurrences(query, seed, referenceIdx);
+ //std::cout << beginPositionH(seed) << " " << endPositionH(seed) << " " << count << std::endl;
+ //std::cout << seqan::infix(query, beginPositionH(seed), endPositionH(seed)) << std::endl;
+ if (count == 0) return false;
+
+ // If the match is shorter than our Kmer-size, just assume we will
+ // always find a match (e.g. return 0, since it's Log(1.0))
+ size_t currSeedSize = seqan::seedSize(seed);
+ if (currSeedSize < kmerSize_) {
+ score = 0.0f;
+ return true;
+ }
+
+ /*std::cout << "S " << 0 << " "
+ << seqan::beginPositionV(seed) << " "
+ << seqan::endPositionV(seed) << " "
+ << seqan::endPositionV(seed) - seqan::beginPositionH(seed) << " "
+ << count << " "
+ << score << std::endl;*/
+
+ // Iterate over each successor seed in the match
+ for (size_t i = 1; i <= currSeedSize - kmerSize_; ++i) {
+ //std::cout << "i:" << i << " " << seqan::beginPositionH(seed) << " " << currSeedSize << " " << Size << std::endl;
+ size_t nextShapeCount = 0;
+ size_t nextPossibleCount =
+ CountPossibleSuccessors(query, seed, i, referenceIdx, nextShapeCount);
+
+ /*std::cout << "S " << i << " "
+ << seqan::beginPositionV(seed) << " "
+ << seqan::endPositionV(seed) << " "
+ << seqan::endPositionV(seed) - seqan::beginPositionV(seed) << " "
+ //<< CountOccurrences(query, seed, referenceIdx) << " "
+ << nextShapeCount << " "
+ << nextPossibleCount << " "
+ << score << std::endl;*/
+
+ // There is no background distribution available for this
+ // sequence context, therefore no way to evaluate p-value.
+ if (nextPossibleCount == 0) return false;
+
+ // Add the log-probability of seeing this particule successor to
+ // the running sum of the pValue
+ score += std::log((nextShapeCount / static_cast<float>(nextPossibleCount)));
+ }
+
+ // Return success
+ return true;
+ }
+
+ /// Count the number of times the possible successor Kmers to a given
+ /// seed are found,
+ ///
+ /// Equivalent to BLASR's SumRightShiftMarginalTupleCounts function.
+ ///
+ /// \param TSeed the position and length of the query
+ /// \return size_t the total occurrences of all possible successors
+ size_t CountPossibleSuccessors(const seqan::DnaString& query, const TSeed& seed,
+ const size_t offset, const size_t referenceIdx,
+ size_t& nextShapeCount)
+ {
+ // Initialize return values
+ nextShapeCount = 0;
+ size_t nextPossibleCount = 0;
+
+ // Calculate the relative
+ size_t beginPos = seqan::beginPositionH(seed) + offset;
+ size_t endPos = beginPos + kmerSize_;
+
+ // Pull-out pointers to the successor string and it's N-1 root
+ seqan::DnaString referenceString = seqan::infix(query, beginPos, endPos);
+ seqan::DnaString rootString = seqan::prefix(referenceString, kmerSize_ - 1);
+ //std::cout << referenceString << " "
+ // << rootString << std::endl;
+
+ // Count the number of occurrences of all possible successor strings
+ for (TAlphabetSize i = 0; i < alphabetSize_; ++i) {
+ seqan::DnaString testString = rootString;
+ seqan::append(testString, alphabet_[i]);
+ size_t testStringCount = CountOccurrences(testString, referenceIdx);
+ //std::cout << referenceString << " "
+ // << rootString << " "
+ // << alphabet_[i] << " "
+ // << testString << " "
+ // << testStringCount << std::endl;
+
+ // Add the count for the current testString to the running total
+ nextPossibleCount += testStringCount;
+
+ // If the test successor is equal to the actual successor, save it.
+ if (testString == referenceString) nextShapeCount = testStringCount;
+ }
+
+ // Return the sum of the counts of all possible successor strings
+ // the count for the actual successor is returned via reference.
+ return nextPossibleCount;
+ }
+
+ /// Count the number of times a given sequence is found in the index,
+ /// usually representing all Kmers found in a reference.
+ ///
+ /// Equivalent to BLASR's GetTupleCount function.
+ ///
+ /// \param query The sequence whose occurrences are to be counted
+ /// \return the number of occurences
+ size_t CountOccurrences(const seqan::DnaString& query, const size_t referenceIdx)
+ {
+ using namespace seqan;
+
+ //std::cout << "CO " << query << " " << referenceIdx << std::endl;
+ size_t occurrences = 0;
+ clear(kmerFinder_);
+ while (find(kmerFinder_, query)) {
+ //std::cout << position(kmerFinder_) << std::endl;
+ if (getValueI1(position(kmerFinder_)) == referenceIdx) occurrences += 1;
+ }
+ //std::cout << "CO " << query << " " << referenceIdx << " " << occurrences << std::endl;
+ return occurrences;
+ }
+
+ /// Count the number of times a given subtring sequence is found in the
+ /// index, usually representing all Kmers found in a reference.
+ ///
+ /// Equivalent to BLASR's GetTupleCount function.
+ ///
+ /// \param query The sequence from which a substring will be counted
+ /// \param seed A seed with the start-position of the Kmer start position
+ /// \return the number of occurences
+ size_t CountOccurrences(const seqan::DnaString& query, const TSeed& seed,
+ const size_t referenceIdx)
+ {
+ using namespace seqan;
+
+ size_t occurrences = 0;
+ hash(shape_, begin(query) + beginPositionH(seed));
+ for (const auto o : getOccurrences(index_, shape_)) {
+ if (getValueI1(o) == referenceIdx) occurrences += 1;
+ }
+ return occurrences;
+ }
+
+private: // data
+ TIndex index_;
+ TShape shape_;
+ TFinder kmerFinder_;
+ size_t kmerSize_;
+ TAlphabetSize alphabetSize_;
+ char alphabet_[4] = {'A', 'C', 'G', 'T'};
+};
+}
+} // ::PacBio::Align
diff --git a/include/pacbio/align/SparseAlignment.h b/include/pacbio/align/SparseAlignment.h
new file mode 100644
index 0000000..c975f26
--- /dev/null
+++ b/include/pacbio/align/SparseAlignment.h
@@ -0,0 +1,176 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Brett Bowman
+
+#pragma once
+
+#include <vector>
+
+#include <seqan/align.h>
+#include <seqan/basic.h>
+#include <seqan/index.h>
+#include <seqan/seeds.h>
+#include <seqan/sequence.h>
+
+#include <pacbio/align/ChainSeeds.h>
+#include <pacbio/align/FindSeeds.h>
+#include <pacbio/align/FindSeedsConfig.h>
+
+namespace PacBio {
+namespace Align {
+
+namespace {
+
+/// \brief Generate an full alignment for two sequences, given their shared seeds
+///
+/// \tparam TAlignConfig The style global/local alignment to perform
+/// \tparam TScoring The alignment scoring scheme to use
+///
+/// \param[in] seq1 The query sequence as a DnaString
+/// \param[in] seq2 The reference sequence as a DnaString
+/// \param[in] seeds The seeds shared by the query and reference
+/// \param[in] scoring The alignment scoring configuration
+/// \param[in] config The alignment type configuration
+///
+/// \returns The full banded alignment between the two sequences
+///
+template <typename TAlignConfig, typename TScoring>
+const seqan::Align<seqan::DnaString, seqan::ArrayGaps> SeedsToAlignment(
+ const seqan::DnaString& seq1, const seqan::DnaString& seq2,
+ const seqan::SeedSet<seqan::Seed<seqan::Simple>>& seeds, const TScoring& scoring,
+ const TAlignConfig& config)
+{
+ using namespace seqan;
+
+ String<Seed<Simple>> chain;
+ chainSeedsGlobally(chain, seeds, SparseChaining());
+
+ seqan::Align<DnaString, ArrayGaps> alignment;
+ resize(rows(alignment), 2);
+ assignSource(row(alignment, 0), seq1);
+ assignSource(row(alignment, 1), seq2);
+
+ bandedChainAlignment(alignment, chain, scoring, config);
+
+ return alignment;
+}
+
+/// \brief Generate an SDP alignment from two sequences
+///
+/// \tparam TSize The size of the seeds to look for
+///
+/// \param[in] seq1 The query sequence as a DnaString
+/// \param[in] seq2 The reference sequence as a DnaString
+///
+/// \returns The SDP alignment as a SeedString
+///
+template <size_t TSize>
+const seqan::String<seqan::Seed<seqan::Simple>> SparseAlign(const seqan::DnaString& seq1,
+ const seqan::DnaString& seq2)
+{
+ using namespace seqan;
+
+ typedef FindSeedsConfig<TSize> TConfig;
+ ChainSeedsConfig chainConfig;
+
+ SeedSet<Seed<Simple>> seeds;
+ FindSeeds<TConfig>(&seeds, seq1, seq2);
+
+ std::vector<String<Seed<Simple>>> chains;
+ String<Seed<Simple>> chain;
+ ChainSeeds(&chains, seeds, chainConfig);
+
+ if (chains.size() == 0) return chain;
+
+ return chains[0];
+}
+
+/// \brief Generate an SDP alignment from the best orientation of two sequences
+///
+/// \param[in] seq1 The query sequence as a DnaString
+/// \param[in] seq2 The reference sequence as a DnaString
+///
+/// \returns A flag for the best orientation found, and the SDP alignment
+/// from that orientation as a SeedString, in an std::pair
+///
+const std::pair<size_t, seqan::String<seqan::Seed<seqan::Simple>>> BestSparseAlign(
+ const seqan::DnaString& seq1, const seqan::DnaString& seq2)
+{
+ using namespace seqan;
+
+ //TODO(bbowman) Clean this up, pronto
+ DnaString seq2_str(seq2);
+ reverseComplement(seq2_str);
+ const std::string seq2rc(toCString(CharString(seq2_str)));
+
+ const auto& fwd = SparseAlign<10>(seq1, seq2);
+ const auto& rev = SparseAlign<10>(seq1, seq2rc);
+
+ if (length(fwd) > length(rev)) return std::make_pair(0, fwd);
+ return std::make_pair(1, rev);
+}
+
+/// \brief Generate an SDP alignment from two sequences and hide the
+/// SeqAn library dependencies
+///
+/// \param[in] seq1 The query sequence as an std::string
+/// \param[in] seq2 The reference sequence as a std::string
+///
+/// \returns A vector of pairs, representing Kmer start positions
+/// that match in the query and reference sequences
+///
+template <size_t TSize>
+const std::vector<std::pair<size_t, size_t>> SparseAlign(const std::string& seq1,
+ const std::string& seq2)
+{
+ using namespace seqan;
+ using namespace std;
+
+ DnaString a = seq1, b = seq2;
+ auto chain = SparseAlign<TSize>(a, b);
+
+ vector<pair<size_t, size_t>> result;
+
+ for (const auto& s : chain) {
+ result.push_back(make_pair(beginPositionH(s), beginPositionV(s)));
+ }
+
+ return result;
+}
+
+} // Anonymous namespace
+}
+} // ::PacBio::Align
diff --git a/include/pacbio/ccs/ChainSeeds.h b/include/pacbio/ccs/ChainSeeds.h
new file mode 100644
index 0000000..689b851
--- /dev/null
+++ b/include/pacbio/ccs/ChainSeeds.h
@@ -0,0 +1,51 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <seqan/seeds.h>
+#include <seqan/sequence.h>
+
+namespace PacBio {
+namespace CCS {
+
+void ChainSeeds(seqan::String<seqan::Seed<seqan::Simple>>& chain,
+ const seqan::SeedSet<seqan::Seed<seqan::Simple>>& seedSet,
+ const int matchReward = 3);
+
+} // namespace CCS
+} // namespace PacBio
diff --git a/include/pacbio/ccs/Consensus.h b/include/pacbio/ccs/Consensus.h
new file mode 100644
index 0000000..d2a5110
--- /dev/null
+++ b/include/pacbio/ccs/Consensus.h
@@ -0,0 +1,684 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <algorithm>
+#include <cmath>
+#include <functional>
+#include <memory>
+#include <numeric>
+#include <stdexcept>
+#include <string>
+#include <tuple>
+#include <vector>
+
+#include <boost/optional.hpp>
+
+#include <OptionParser.h>
+
+#include <pacbio/consensus/MonoMolecularIntegrator.h>
+#include <pacbio/consensus/Polish.h>
+#include <pacbio/data/State.h>
+#include <pacbio/data/StrandType.h>
+#include <pacbio/denovo/PoaConsensus.h>
+
+#include <pbbam/Accuracy.h>
+#include <pbbam/LocalContextFlags.h>
+
+#include <pacbio/data/ReadId.h>
+#include <pacbio/data/SubreadResultCounter.h>
+#include <pacbio/denovo/SparsePoa.h>
+#include <pacbio/log/Logging.h>
+#include <pacbio/util/Timer.h>
+
+namespace PacBio {
+namespace CCS {
+
+using Accuracy = PacBio::BAM::Accuracy;
+using Interval = PacBio::Data::Interval;
+using LocalContextFlags = PacBio::BAM::LocalContextFlags;
+using QualityValues = PacBio::Consensus::QualityValues;
+using ReadId = PacBio::Data::ReadId;
+using Read = PacBio::Data::Read;
+using MappedRead = PacBio::Data::MappedRead;
+using SNR = PacBio::Data::SNR;
+using State = PacBio::Data::State;
+using StrandType = PacBio::Data::StrandType;
+using SubreadResultCounter = PacBio::Data::SubreadResultCounter;
+using Timer = PacBio::Util::Timer;
+using PoaAlignmentSummary = PacBio::Poa::PoaAlignmentSummary;
+using SparsePoa = PacBio::Poa::SparsePoa;
+using AlignConfig = PacBio::Align::AlignConfig;
+using AlignMode = PacBio::Align::AlignMode;
+
+namespace OptionNames {
+// constexpr auto MaxPoaCoverage = "maxPoaCoverage";
+constexpr auto MaxLength = "maxLength";
+constexpr auto MinLength = "minLength";
+constexpr auto MinPasses = "minPasses";
+constexpr auto MinPredictedAccuracy = "minPredictedAccuracy";
+constexpr auto MinZScore = "minZScore";
+constexpr auto MaxDropFraction = "maxDropFraction";
+constexpr auto NoPolish = "noPolish";
+constexpr auto MinReadScore = "minReadScore";
+constexpr auto MinSnr = "minSnr";
+constexpr auto ByStrand = "byStrand";
+} // namespace OptionNames
+
+struct ConsensusSettings
+{
+ size_t MaxPoaCoverage;
+ size_t MaxLength;
+ size_t MinLength;
+ size_t MinPasses;
+ double MinPredictedAccuracy;
+ double MinZScore;
+ double MaxDropFraction;
+ bool ByStrand;
+ bool NoPolish;
+ double MinReadScore;
+ double MinSNR;
+
+ ConsensusSettings(const optparse::Values& options);
+
+ static void AddOptions(optparse::OptionParser* const parser)
+ {
+ const std::string em = "--";
+ // TODO(lhepler) implement alignment to POA
+ // parser->add_option(em +
+ // OptionNames::MaxPoaCoverage).type("int").set_default(1024).help("Maximum number of
+ // subreads to use when building POA. Default = %default");
+ parser->add_option(em + OptionNames::MaxLength)
+ .type("int")
+ .set_default(7000)
+ .help("Maximum length of subreads to use for generating CCS. Default = %default");
+ parser->add_option(em + OptionNames::MinLength)
+ .type("int")
+ .set_default(10)
+ .help("Minimum length of subreads to use for generating CCS. Default = %default");
+ parser->add_option(em + OptionNames::MinPasses)
+ .type("int")
+ .set_default(3)
+ .help("Minimum number of subreads required to generate CCS. Default = %default");
+ parser->add_option(em + OptionNames::MinPredictedAccuracy)
+ .type("float")
+ .set_default(0.90)
+ .help("Minimum predicted accuracy in [0, 1]. Default = %default");
+ parser->add_option(em + OptionNames::MinZScore)
+ .type("float")
+ .set_default(-3.5)
+ .help("Minimum z-score to use a subread. NaN disables this filter. Default = %default");
+ parser->add_option(em + OptionNames::MaxDropFraction)
+ .type("float")
+ .set_default(0.34)
+ .help(
+ "Maximum fraction of subreads that can be dropped before giving up. Default = "
+ "%default");
+ parser->add_option(em + OptionNames::MinSnr)
+ .type("float")
+ .set_default(
+ 3.75) // See https://github.com/PacificBiosciences/pbccs/issues/86 for a more
+ // detailed discussion of this default.
+ .help("Minimum SNR of input subreads. Default = %default");
+ parser->add_option(em + OptionNames::MinReadScore)
+ .type("float")
+ .set_default(0.75)
+ .help("Minimum read score of input subreads. Default = %default");
+ parser->add_option(em + OptionNames::ByStrand)
+ .action("store_true")
+ .help("Generate a consensus for each strand. Default = false");
+ parser->add_option(em + OptionNames::NoPolish)
+ .action("store_true")
+ .help(
+ "Only output the initial template derived from the POA (faster, less accurate). "
+ "Default = false");
+ }
+};
+
+template <typename TId>
+struct ReadType
+{
+ TId Id;
+ std::string Seq;
+ std::vector<uint8_t> IPD;
+ std::vector<uint8_t> PulseWidth;
+ LocalContextFlags Flags;
+ Accuracy ReadAccuracy;
+ // TODO (move SNR and Chemistry here, eventually)
+ // SNR SignalToNoise;
+ // std::string Chemistry;
+};
+
+template <typename TId, typename TRead>
+struct ChunkType
+{
+ TId Id;
+ std::vector<TRead> Reads;
+ SNR SignalToNoise;
+ std::string Chemistry;
+ boost::optional<std::tuple<int16_t, int16_t, uint8_t>> Barcodes;
+};
+
+struct ConsensusType
+{
+ Consensus::PolishResult polishResult;
+ ReadId Id;
+ boost::optional<StrandType> Strand;
+ std::string Sequence;
+ QualityValues QVs;
+ size_t NumPasses;
+ double PredictedAccuracy;
+ double AvgZScore;
+ std::vector<double> ZScores;
+ std::vector<int32_t> StatusCounts;
+ SNR SignalToNoise;
+ float ElapsedMilliseconds;
+ boost::optional<std::tuple<int16_t, int16_t, uint8_t>> Barcodes;
+};
+
+template <typename TConsensus>
+class ResultType : public std::vector<TConsensus>
+{
+public:
+ size_t Success;
+ size_t PoorSNR;
+ size_t NoSubreads;
+ size_t TooLong;
+ size_t TooShort;
+ size_t TooFewPasses;
+ size_t TooManyUnusable;
+ size_t NonConvergent;
+ size_t PoorQuality;
+ size_t ExceptionThrown;
+ SubreadResultCounter SubreadCounter;
+
+ ResultType()
+ : Success{0}
+ , PoorSNR{0}
+ , NoSubreads{0}
+ , TooLong{0}
+ , TooShort{0}
+ , TooFewPasses{0}
+ , TooManyUnusable{0}
+ , NonConvergent{0}
+ , PoorQuality{0}
+ , ExceptionThrown{0}
+ , SubreadCounter{}
+ {
+ }
+
+ ResultType<TConsensus>& operator+=(const ResultType<TConsensus>& other)
+ {
+ Success += other.Success;
+ PoorSNR += other.PoorSNR;
+ NoSubreads += other.NoSubreads;
+ TooLong += other.TooLong;
+ TooShort += other.TooShort;
+ TooManyUnusable += other.TooManyUnusable;
+ TooFewPasses += other.TooFewPasses;
+ NonConvergent += other.NonConvergent;
+ PoorQuality += other.PoorQuality;
+ ExceptionThrown += other.ExceptionThrown;
+ SubreadCounter += other.SubreadCounter;
+ return *this;
+ }
+
+ size_t Total() const
+ {
+ return (Success + PoorSNR + NoSubreads + TooShort + TooManyUnusable + TooFewPasses +
+ NonConvergent + PoorQuality + ExceptionThrown);
+ }
+};
+
+namespace { // anonymous
+
+template <typename T>
+float Median(std::vector<T>* vs)
+{
+ const size_t n = vs->size();
+ std::sort(vs->begin(), vs->end());
+ if (n % 2 == 1) return static_cast<float>(vs->at(n / 2));
+ return 0.5 * (vs->at(n / 2 - 1) + vs->at(n / 2));
+}
+
+template <typename TRead>
+std::vector<const TRead*> FilterReads(const std::vector<TRead>& reads,
+ const ConsensusSettings& settings,
+ SubreadResultCounter* resultCounter)
+{
+ // This is a count of subreads removed for bing too short, or too long.
+ std::vector<const TRead*> results;
+
+ if (reads.empty()) return results;
+
+ std::vector<size_t> lengths;
+ size_t longest = 0;
+
+ // get the lengths for all full-length subreads
+ for (const auto& read : reads) {
+ longest = std::max(longest, read.Seq.length());
+ if ((read.Flags & BAM::ADAPTER_BEFORE) && (read.Flags & BAM::ADAPTER_AFTER) &&
+ read.ReadAccuracy >= settings.MinReadScore)
+ lengths.emplace_back(read.Seq.length());
+ }
+
+ // nonexistent median is just the greatest observed length
+ const float median = lengths.empty() ? static_cast<float>(longest) : Median(&lengths);
+ size_t maxLen = std::min(2 * static_cast<size_t>(median), settings.MaxLength);
+
+ // if it's too short, return nothing
+ if (median < static_cast<float>(settings.MinLength)) {
+ resultCounter->FilteredBySize += reads.size();
+ return results;
+ }
+ results.reserve(reads.size());
+
+ for (const auto& read : reads) {
+ // if the median exists, then this filters stuff,
+ // otherwise it's twice the longest read and is always true
+
+ if (read.ReadAccuracy < settings.MinReadScore) {
+ resultCounter->BelowMinQual += 1;
+ results.emplace_back(nullptr);
+ } else if (read.Seq.length() < maxLen) {
+ results.emplace_back(&read);
+ } else {
+ resultCounter->FilteredBySize += 1;
+ results.emplace_back(nullptr);
+ }
+ }
+
+ // TODO(lhepler): incorporate per-subread quality here
+ // End-to-end reads take priority, hence the lexicographical sort;
+ // always take the read with the least deviation from the median.
+ // In the case of no median, longer reads are prioritized.
+ const auto lexForm = [median](const TRead* read) {
+ const float l = static_cast<float>(read->Seq.length());
+ const float v = std::min(l / median, median / l);
+
+ if (read->Flags & BAM::ADAPTER_BEFORE && read->Flags & BAM::ADAPTER_AFTER)
+ return std::make_tuple(v, 0.0f);
+
+ return std::make_tuple(0.0f, v);
+ };
+
+ std::stable_sort(results.begin(), results.end(),
+ [&lexForm](const TRead* lhs, const TRead* rhs) {
+ if (lhs == nullptr)
+ return false;
+ else if (rhs == nullptr)
+ return true;
+
+ return lexForm(lhs) > lexForm(rhs);
+ });
+
+ return results;
+}
+
+template <typename TRead>
+boost::optional<MappedRead> ExtractMappedRead(const TRead& read, const PacBio::Data::SNR& snr,
+ const std::string& chem,
+ const PoaAlignmentSummary& summary,
+ const size_t poaLength,
+ const ConsensusSettings& settings,
+ SubreadResultCounter* resultCounter)
+{
+ constexpr size_t kStickyEnds = 7;
+
+ size_t readStart = summary.ExtentOnRead.Left();
+ size_t readEnd = summary.ExtentOnRead.Right();
+ size_t tplStart = summary.ExtentOnConsensus.Left();
+ size_t tplEnd = summary.ExtentOnConsensus.Right();
+
+ // if we're ADAPTER_BEFORE and _AFTER and mapped nearly end-to-end,
+ // just make it end to end (but for each side, respectively)
+ if (summary.ReverseComplementedRead) {
+ if (read.Flags & BAM::ADAPTER_BEFORE && (poaLength - tplEnd) <= kStickyEnds)
+ tplEnd = poaLength;
+ if (read.Flags & BAM::ADAPTER_AFTER && tplStart <= kStickyEnds) tplStart = 0;
+ } else {
+ if (read.Flags & BAM::ADAPTER_BEFORE && tplStart <= kStickyEnds) tplStart = 0;
+ if (read.Flags & BAM::ADAPTER_AFTER && (poaLength - tplEnd) <= kStickyEnds)
+ tplEnd = poaLength;
+ }
+
+ if (readStart > readEnd || readEnd - readStart < settings.MinLength) {
+ resultCounter->FilteredBySize += 1;
+ PBLOG_DEBUG << "Skipping read " << read.Id << ", too short (<" << settings.MinLength << ')';
+ return boost::none;
+ } else if (readEnd - readStart > settings.MaxLength) {
+ resultCounter->FilteredBySize += 1;
+ PBLOG_DEBUG << "Skipping read " << read.Id << ", too long (>" << settings.MaxLength << ')';
+ return boost::none;
+ }
+
+ MappedRead mappedRead(
+ Read(read.Id, read.Seq.substr(readStart, readEnd - readStart),
+ std::vector<uint8_t>(read.IPD.begin() + readStart, read.IPD.begin() + readEnd),
+ std::vector<uint8_t>(read.PulseWidth.begin() + readStart,
+ read.PulseWidth.begin() + readEnd),
+ snr, chem),
+ summary.ReverseComplementedRead ? StrandType::REVERSE : StrandType::FORWARD, tplStart,
+ tplEnd, (tplStart == 0) ? true : false, (tplEnd == poaLength) ? true : false);
+
+ return boost::make_optional(mappedRead);
+}
+
+#if 0
+template<typename TRead>
+bool ReadAccuracyDescending(const std::pair<size_t, const TRead*>& a,
+ const std::pair<size_t, const TRead*>& b)
+{
+ return a.second->ReadAccuracy > b.second->ReadAccuracy;
+}
+#endif
+
+} // namespace anonymous
+
+template <typename TRead>
+std::string PoaConsensus(const std::vector<const TRead*>& reads,
+ std::vector<SparsePoa::ReadKey>* readKeys,
+ std::vector<PoaAlignmentSummary>* summaries, const size_t maxPoaCov)
+{
+ SparsePoa poa;
+ size_t cov = 0;
+
+#if 0
+ // create a vector of indices into the original reads vector,
+ // sorted by the ReadAccuracy in descending order
+ std::vector<std::pair<size_t, const TRead*>> sorted;
+
+ for (size_t i = 0; i < reads.size(); ++i)
+ sorted.emplace_back(std::make_pair(i, reads[i]));
+
+ std::sort(sorted.begin(), sorted.end(), ReadAccuracyDescending<TRead>);
+#endif
+
+ // initialize readKeys and resize
+ readKeys->clear();
+ // readKeys->resize(sorted.size());
+
+ for (const auto read : reads) {
+ SparsePoa::ReadKey key = (read == nullptr) ? -1 : poa.OrientAndAddRead(read->Seq);
+ // SparsePoa::ReadKey key = poa.OrientAndAddRead(read.second->Seq);
+ // readKeys->at(read.first) = key;
+ readKeys->emplace_back(key);
+ if (key >= 0 && (++cov) >= maxPoaCov) break;
+ }
+
+ // at least 50% of the reads should cover
+ // TODO(lhepler) revisit this minimum coverage equation
+ const size_t minCov = (cov < 5) ? 1 : (cov + 1) / 2 - 1;
+ return poa.FindConsensus(minCov, &(*summaries))->Sequence;
+}
+
+// pass unique_ptr by reference to satisfy finickyness wrt move semantics in <future>
+// but then take ownership here with a local unique_ptr
+template <typename TChunk>
+ResultType<ConsensusType> Consensus(std::unique_ptr<std::vector<TChunk>>& chunksRef,
+ const ConsensusSettings& settings)
+{
+ using namespace PacBio::Consensus;
+
+ auto chunks(std::move(chunksRef));
+ ResultType<ConsensusType> result;
+
+ if (!chunks) return result;
+ // We should only be dealing with chunks of size 1
+ if (chunks->size() != 1) {
+ throw std::runtime_error("CCS chunk was of size != 1");
+ }
+ const auto& chunk = chunks->at(0);
+
+ try {
+ Timer timer;
+
+ // Do read level SNR filtering first
+ auto& snr = chunk.SignalToNoise;
+ auto minSNR = std::min(std::min(snr.A, snr.C), std::min(snr.G, snr.T));
+ if (minSNR < settings.MinSNR) {
+ result.SubreadCounter.ZMWBelowMinSNR += chunk.Reads.size();
+ result.PoorSNR += 1;
+ return result;
+ }
+
+ auto reads = FilterReads(chunk.Reads, settings, &result.SubreadCounter);
+
+ if (reads.empty() || // Check if subread are present
+ std::accumulate(reads.begin(), reads.end(), 0, std::plus<bool>()) == 0) {
+ result.NoSubreads += 1;
+ PBLOG_DEBUG << "Skipping " << chunk.Id << ", no high quality subreads available";
+ return result;
+ }
+
+ // If it is not possible to exceed the minPasses requirement, we will bail here before
+ // generating the POA, filling the matrices and performing all the other checks
+ size_t possiblePasses = 0;
+ size_t activeReads = 0;
+ for (size_t i = 0; i < reads.size(); ++i) {
+ if (reads[i] != nullptr) {
+ activeReads += 1;
+ if (reads[i]->Flags & BAM::ADAPTER_BEFORE && reads[i]->Flags & BAM::ADAPTER_AFTER) {
+ possiblePasses += 1;
+ }
+ }
+ }
+
+ if (possiblePasses < settings.MinPasses) {
+ result.TooFewPasses += 1;
+ result.SubreadCounter.ZMWNotEnoughSubReads += activeReads;
+ PBLOG_DEBUG << "Skipping " << chunk.Id << ", not enough possible passes ("
+ << possiblePasses << '<' << settings.MinPasses << ')';
+ return result;
+ }
+
+ std::vector<SparsePoa::ReadKey> readKeys;
+ std::vector<PoaAlignmentSummary> summaries;
+ std::string poaConsensus =
+ PoaConsensus(reads, &readKeys, &summaries, settings.MaxPoaCoverage);
+
+ if (poaConsensus.length() < settings.MinLength) {
+ result.TooShort += 1;
+ result.SubreadCounter.Other += activeReads;
+ PBLOG_DEBUG << "Skipping " << chunk.Id << ", initial consensus too short (<"
+ << settings.MinLength << ')';
+ } else if (poaConsensus.length() > settings.MaxLength) {
+ result.TooLong += 1;
+ result.SubreadCounter.Other += activeReads;
+ PBLOG_DEBUG << "Skipping " << chunk.Id << ", initial consensus too long (>"
+ << settings.MaxLength << ')';
+ } else {
+ if (settings.NoPolish) {
+ const size_t len = poaConsensus.length();
+ // generate dummy QVs, will use 20
+ // TODO(lhepler): should we use different values for delQVs, insQVs, and subQVs?
+ QualityValues qvs{std::vector<int>(len, 20), std::vector<int>(len, 20),
+ std::vector<int>(len, 20), std::vector<int>(len, 20)};
+ result.Success += 1;
+ result.SubreadCounter.Success += activeReads;
+ result.emplace_back(ConsensusType{
+ PolishResult(), chunk.Id, boost::none, poaConsensus, qvs, possiblePasses, 0, 0,
+ std::vector<double>(1), result.SubreadCounter.ReturnCountsAsArray(),
+ chunk.SignalToNoise, timer.ElapsedMilliseconds(), chunk.Barcodes});
+ } else {
+ const auto mkConsensus = [&](const boost::optional<StrandType> strand) {
+ // give this consensus attempt a name we can refer to
+ std::string chunkName(chunk.Id);
+ if (strand && *strand == StrandType::FORWARD) chunkName += " [fwd]";
+ if (strand && *strand == StrandType::REVERSE) chunkName += " [rev]";
+
+ try {
+ // setup the arrow integrator
+ IntegratorConfig cfg(settings.MinZScore, 12.5);
+ MonoMolecularIntegrator ai(poaConsensus, cfg, chunk.SignalToNoise,
+ chunk.Chemistry);
+ const size_t nReads = readKeys.size();
+ size_t nPasses = 0, nDropped = 0;
+
+ // If this ZMW could possibly pass, add the reads to the integrator
+ for (size_t i = 0; i < nReads; ++i) {
+ // skip unadded reads
+ if (readKeys[i] < 0) continue;
+
+ if (auto mr = ExtractMappedRead(*reads[i], chunk.SignalToNoise,
+ chunk.Chemistry, summaries[readKeys[i]],
+ poaConsensus.length(), settings,
+ &result.SubreadCounter)) {
+ // skip reads not belonging to this strand, if we're --byStrand
+ if (strand && mr->Strand != *strand) continue;
+ auto status = ai.AddRead(*mr);
+ // increment the status count
+ result.SubreadCounter.AddResult(status);
+ if (status == State::VALID &&
+ reads[i]->Flags & BAM::ADAPTER_BEFORE &&
+ reads[i]->Flags & BAM::ADAPTER_AFTER) {
+ nPasses += 1;
+ } else if (status != State::VALID) {
+ nDropped += 1;
+ PBLOG_DEBUG << "Skipping read " << mr->Name << ", " << status;
+ }
+ }
+ }
+
+ if (nPasses < settings.MinPasses) {
+ // Reassign all the successful reads to the other category
+ result.SubreadCounter.AssignSuccessToOther();
+ result.TooFewPasses += 1;
+ PBLOG_DEBUG << "Skipping " << chunkName
+ << ", insufficient number of passes (" << nPasses << '<'
+ << settings.MinPasses << ')';
+ return;
+ }
+
+ // this is hairy, but also relatively straightforward, so bear with me:
+ // if we're not doing strand-specific consensus, the total number of
+ // available reads is just nReads. If we're doing byStrand though,
+ // then the number of available reads is those that mapped to this
+ // strand, plus half of those that didn't map to the POA (we assume).
+ const size_t nAvail =
+ (!strand) ? nReads
+ : (std::count_if(
+ readKeys.cbegin(), readKeys.cend(),
+ [&](const SparsePoa::ReadKey key) {
+ return key >= 0 &&
+ summaries[key].ReverseComplementedRead ==
+ (*strand == StrandType::REVERSE);
+ }) +
+ std::count_if(
+ readKeys.cbegin(), readKeys.cend(),
+ [](const SparsePoa::ReadKey key) { return key < 0; }) /
+ 2);
+
+ const double fracDropped = static_cast<double>(nDropped) / nAvail;
+ if (fracDropped > settings.MaxDropFraction) {
+ result.TooManyUnusable += 1;
+ result.SubreadCounter.AssignSuccessToOther();
+ PBLOG_DEBUG << "Skipping " << chunkName
+ << ", too high a fraction of unusable subreads ("
+ << fracDropped << '>' << settings.MaxDropFraction << ')';
+ return;
+ }
+
+ const double zAvg = ai.AvgZScore();
+ const auto zScores = ai.ZScores();
+
+ // find consensus!!
+ const PolishResult polishResult = Polish(&ai, PolishConfig());
+
+ if (!polishResult.hasConverged) {
+ result.NonConvergent += 1;
+ result.SubreadCounter.AssignSuccessToOther();
+ PBLOG_DEBUG << "Skipping " << chunkName << ", failed to converge";
+ return;
+ }
+
+ // compute predicted accuracy
+ double predAcc = 0.0;
+ QualityValues qvs = ConsensusQVs(ai);
+ for (const int qv : qvs.Qualities) {
+ predAcc += pow(10.0, static_cast<double>(qv) / -10.0);
+ }
+ predAcc = 1.0 - predAcc / qvs.Qualities.size();
+
+ if (predAcc < settings.MinPredictedAccuracy) {
+ result.PoorQuality += 1;
+ result.SubreadCounter.AssignSuccessToOther();
+ PBLOG_DEBUG << "Skipping " << chunkName
+ << ", failed to meet minimum predicted accuracy ("
+ << predAcc << '<' << settings.MinPredictedAccuracy << ')';
+ return;
+ }
+
+ // return resulting sequence!!
+ result.Success += 1;
+ result.emplace_back(ConsensusType{
+ polishResult, chunk.Id, strand, std::string(ai), std::move(qvs),
+ nPasses, predAcc, zAvg, zScores,
+ result.SubreadCounter.ReturnCountsAsArray(), chunk.SignalToNoise,
+ timer.ElapsedMilliseconds(), chunk.Barcodes});
+ } catch (const std::exception& e) {
+ result.ExceptionThrown += 1;
+ PBLOG_ERROR << "Skipping " << chunkName << ", caught exception: '"
+ << e.what() << "\'";
+ }
+ };
+
+ if (settings.ByStrand) {
+ mkConsensus(StrandType::FORWARD);
+ mkConsensus(StrandType::REVERSE);
+ } else {
+ mkConsensus(boost::none);
+ }
+ }
+ }
+ } catch (const std::exception& e) {
+ result.ExceptionThrown += 1;
+ PBLOG_ERROR << "Skipping " << chunk.Id << ", caught exception: '" << e.what() << "\'";
+ } catch (...) {
+ // This should NEVER happen. Only here as a guard, if this is ever printed someone
+ // goofed
+ // up by throwing something that didn't derive from std::exception.
+ result.ExceptionThrown += 1;
+ PBLOG_ERROR << "Skipping " << chunk.Id << ", caught unknown exception type";
+ }
+
+ return result;
+}
+
+} // namespace CCS
+} // namespace PacBio
diff --git a/include/pacbio/ccs/SparseAlignment.h b/include/pacbio/ccs/SparseAlignment.h
new file mode 100644
index 0000000..e5a2093
--- /dev/null
+++ b/include/pacbio/ccs/SparseAlignment.h
@@ -0,0 +1,283 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <map>
+#include <queue>
+#include <utility>
+#include <vector>
+
+#include <boost/optional.hpp>
+
+#include <seqan/align.h>
+#include <seqan/basic.h>
+#include <seqan/index.h>
+#include <seqan/seeds.h>
+#include <seqan/sequence.h>
+
+#include <pacbio/ccs/ChainSeeds.h>
+#include <pacbio/exception/CCSExceptions.h>
+
+namespace PacBio {
+namespace CCS {
+namespace {
+
+inline size_t SafeSubtract(size_t size, size_t k) { return size > k ? size - k : 0; }
+template <typename TShape>
+class HpHasher
+{
+public:
+ HpHasher(TShape& shape)
+ {
+ using namespace seqan;
+ using std::string;
+
+ const char dna[4] = {'A', 'C', 'G', 'T'};
+
+ for (size_t i = 0; i < 4; i++) {
+ DnaString s = string(length(shape), dna[i]);
+ hashes[i] = hash(shape, begin(s));
+ }
+ }
+
+ inline bool operator()(const unsigned h) const
+ {
+ if (h == hashes[0] || h == hashes[1] || h == hashes[2] || h == hashes[3]) return true;
+
+ return false;
+ }
+
+private:
+ unsigned hashes[4];
+};
+
+} // anonymous namespace
+
+template <typename TConfig>
+void FindSeeds(seqan::SeedSet<seqan::Seed<seqan::Simple>>& seeds, const seqan::DnaString& seq1,
+ const seqan::DnaString& seq2)
+{
+ using namespace seqan;
+
+ typedef Shape<Dna, typename TConfig::ShapeType> TShape;
+
+ Index<DnaString, typename TConfig::IndexType> index(seq1);
+ TShape shape = indexShape(index);
+ HpHasher<TShape> isHomopolymer(shape);
+ auto start = begin(seq2);
+ size_t end = SafeSubtract(length(seq2) + 1, TConfig::Size);
+
+ hashInit(shape, start);
+
+ for (size_t j = 0; j < end; j++) {
+ if (isHomopolymer(hashNext(shape, start + j))) continue;
+
+ auto hits = getOccurrences(index, shape);
+
+ for (const auto& i : hits) {
+ Seed<Simple> seed(i, j, TConfig::Size);
+
+#ifdef MERGESEEDS
+ if (!addSeed(seeds, seed, 0, Merge()))
+#endif
+ {
+ addSeed(seeds, seed, Single());
+ }
+ }
+ }
+}
+
+template <typename TConfig>
+void FindSeeds(
+ std::map<size_t, seqan::SeedSet<seqan::Seed<seqan::Simple>>>& seeds,
+ const seqan::Index<seqan::StringSet<seqan::DnaString>, typename TConfig::IndexType>& index,
+ const seqan::DnaString& seq, const boost::optional<size_t> qIdx = boost::none)
+{
+ using namespace seqan;
+ using namespace std;
+
+ typedef Shape<Dna, typename TConfig::ShapeType> TShape;
+
+ TShape shape = indexShape(index);
+ HpHasher<TShape> isHomopolymer(shape);
+ auto start = begin(seq);
+ size_t end = SafeSubtract(length(seq) + 1, TConfig::Size);
+
+ hashInit(shape, start);
+
+ for (size_t i = 0; i < end; i++) {
+ if (isHomopolymer(hashNext(shape, start + i))) continue;
+
+ auto hits = getOccurrences(index, shape);
+
+ for (const auto& hit : hits) {
+ size_t rIdx = getValueI1(hit);
+
+ if (qIdx && rIdx == *qIdx) continue;
+
+ size_t j = getValueI2(hit);
+ Seed<Simple> seed(i, j, TConfig::Size);
+
+#ifdef MERGESEEDS
+ if (!addSeed(seeds[rIdx], seed, 0, Merge()))
+#endif
+ {
+ addSeed(seeds[rIdx], seed, Single());
+ }
+ }
+ }
+}
+
+template <size_t TSize, typename TContainer>
+size_t CountSeeds(const TContainer& seeds)
+{
+ using namespace seqan;
+
+ size_t count = length(seeds);
+
+#ifdef MERGESEEDS
+ for (const auto& seed : seeds) {
+ count += seedSize(seed) - TSize;
+ }
+#endif
+
+ return count;
+}
+
+template <size_t TSize>
+void FilterSeeds(std::map<size_t, seqan::SeedSet<seqan::Seed<seqan::Simple>>>& seeds,
+ const size_t nBest)
+{
+ using namespace std;
+
+ if (seeds.size() <= nBest) return;
+
+ // keep a priority queue of the biggest hits,
+ // sorted ascendingly. Bump the least value if a new one is bigger.
+ priority_queue<size_t, std::vector<size_t>, std::greater<size_t>> best;
+
+ for (const auto& kv : seeds) {
+ size_t nSeeds = CountSeeds<TSize>(kv.second);
+
+ if (best.size() < nBest) {
+ best.push(nSeeds);
+ } else if (nSeeds > best.top()) {
+ best.pop();
+ best.push(nSeeds);
+ }
+ }
+
+ size_t minSize = best.top();
+
+ for (auto it = seeds.begin(); it != seeds.end();) {
+ if (CountSeeds<TSize>(it->second) < minSize) {
+ it = seeds.erase(it);
+ } else {
+ ++it;
+ }
+ }
+}
+
+template <typename TAlignConfig, typename TScoring>
+seqan::Align<seqan::DnaString, seqan::ArrayGaps> SeedsToAlignment(
+ const seqan::DnaString& seq1, const seqan::DnaString& seq2,
+ const seqan::SeedSet<seqan::Seed<seqan::Simple>>& seeds, const TScoring& scoring,
+ const TAlignConfig& config)
+{
+ using namespace seqan;
+
+ String<Seed<Simple>> chain;
+ chainSeedsGlobally(chain, seeds, SparseChaining());
+
+ seqan::Align<DnaString, ArrayGaps> alignment;
+ resize(rows(alignment), 2);
+ assignSource(row(alignment, 0), seq1);
+ assignSource(row(alignment, 1), seq2);
+
+ bandedChainAlignment(alignment, chain, scoring, config);
+
+ return alignment;
+}
+
+// TODO (lhepler) : investigate default values other than 10
+template <size_t TSize = 10, typename TShape = seqan::UngappedShape<TSize>,
+ typename TIndex = seqan::IndexQGram<TShape>>
+struct FindSeedsConfig
+{
+ typedef TIndex IndexType;
+ typedef TShape ShapeType;
+ static const size_t Size = TSize;
+};
+
+template <size_t TSize>
+seqan::String<seqan::Seed<seqan::Simple>> SparseAlign(const seqan::DnaString& seq1,
+ const seqan::DnaString& seq2)
+{
+ using namespace seqan;
+
+ typedef FindSeedsConfig<TSize> TConfig;
+
+ SeedSet<Seed<Simple>> seeds;
+ FindSeeds<TConfig>(seeds, seq1, seq2);
+
+ String<Seed<Simple>> chain;
+ ChainSeeds(chain, seeds);
+
+ return chain;
+}
+
+template <size_t TSize>
+std::vector<std::pair<size_t, size_t>> SparseAlign(const std::string& seq1, const std::string& seq2)
+{
+ using namespace seqan;
+ using namespace std;
+
+ DnaString a = seq1, b = seq2;
+ auto chain = SparseAlign<TSize>(a, b);
+
+ vector<pair<size_t, size_t>> result;
+
+ for (const auto& s : chain) {
+ result.push_back(make_pair(beginPositionH(s), beginPositionV(s)));
+ }
+
+ return result;
+}
+
+} // namespace CCS
+} // namespace PacBio
diff --git a/include/pacbio/ccs/Whitelist.h b/include/pacbio/ccs/Whitelist.h
new file mode 100644
index 0000000..0d09b7c
--- /dev/null
+++ b/include/pacbio/ccs/Whitelist.h
@@ -0,0 +1,123 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <map>
+#include <stdexcept>
+#include <string>
+
+#include <boost/algorithm/string.hpp>
+#include <boost/optional.hpp>
+
+#include <pacbio/data/IntervalTree.h>
+
+namespace PacBio {
+namespace CCS {
+
+class Whitelist
+{
+public:
+ Whitelist(const std::string& spec) : all(false), globalZmws(boost::none)
+ {
+ // if we're all or *:*, then set all and break out
+ if (spec == "all" || spec == "*:*") {
+ all = true;
+ return;
+ }
+
+ std::vector<std::string> mspecs;
+ boost::split(mspecs, spec, boost::is_any_of(";"));
+
+ for (const auto& mspec : mspecs) {
+ // no craziness policy
+ if (mspec == "all" || mspec == "*:*" || globalZmws)
+ throw std::invalid_argument("invalid whitelist specification");
+
+ std::vector<std::string> parts;
+ boost::split(parts, mspec, boost::is_any_of(":"));
+
+ // only 1 part, it's a ZMW range
+ if (parts.size() == 1) {
+ if (movieZmws.empty()) {
+ globalZmws = PacBio::Data::IntervalTree::FromString(parts[0]);
+ continue;
+ }
+ }
+ // two parts, but *:_? again, it's just a ZMW range
+ else if (parts.size() == 2 && parts[0] == "*") {
+ if (movieZmws.empty()) {
+ globalZmws = PacBio::Data::IntervalTree::FromString(parts[1]);
+ continue;
+ }
+ }
+ // two parts, either _:_ or _:*?
+ // either grab a range from the movie or everything, respectively
+ else if (parts.size() == 2 && movieZmws.find(parts[0]) == movieZmws.end()) {
+ if (parts[1] == "*")
+ movieZmws[parts[0]] = boost::none;
+ else
+ movieZmws[parts[0]] = PacBio::Data::IntervalTree::FromString(parts[1]);
+
+ continue;
+ }
+
+ // anything else is bad, including resetting any range
+ throw std::invalid_argument("invalid whitelist specification");
+ }
+ }
+
+ bool Contains(const std::string& movieName, int32_t holeNumber) const
+ {
+ if (all) return true;
+
+ if (globalZmws) return globalZmws->Contains(holeNumber);
+
+ auto it = movieZmws.find(movieName);
+ if (it != movieZmws.end()) return !it->second || it->second->Contains(holeNumber);
+
+ return false;
+ }
+
+private:
+ bool all;
+ boost::optional<PacBio::Data::IntervalTree> globalZmws;
+ std::map<std::string, boost::optional<PacBio::Data::IntervalTree>> movieZmws;
+};
+
+} // namespace CCS
+} // namespace PacBio
diff --git a/include/pacbio/chimera/ChimeraLabel.h b/include/pacbio/chimera/ChimeraLabel.h
new file mode 100644
index 0000000..051b6f1
--- /dev/null
+++ b/include/pacbio/chimera/ChimeraLabel.h
@@ -0,0 +1,127 @@
+// Copyright (c) 2014, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Armin Töpfer
+
+#pragma once
+
+#include <stdbool.h>
+#include <string>
+
+namespace PacBio {
+namespace Chimera {
+
+///
+/// \brief Label that annotates a read for a single chimeric breakpoint
+///
+struct ChimeraLabel
+{
+ // Instance variables
+ std::string sequenceId;
+ bool chimeraFlag;
+ std::string leftParentId;
+ std::string rightParentId;
+ int32_t crossover;
+ double score;
+
+ // Default Constructor
+ ChimeraLabel(std::string sequenceIdArg, std::string leftParentArg, std::string rightParentArg,
+ int32_t crossoverArg, double scoreArg)
+ : sequenceId(sequenceIdArg)
+ , chimeraFlag(false)
+ , leftParentId(leftParentArg)
+ , rightParentId(rightParentArg)
+ , crossover(crossoverArg)
+ , score(scoreArg){};
+
+ // Name-Only or Place-Holder Constructor
+ explicit ChimeraLabel(std::string sequenceIdArg)
+ : sequenceId(sequenceIdArg)
+ , chimeraFlag(false)
+ , leftParentId("N/A")
+ , rightParentId("N/A")
+ , crossover(-1)
+ , score(-1.0f){};
+
+ // Empty or Dummy Constructor
+ ChimeraLabel()
+ : sequenceId("Dummy")
+ , chimeraFlag(false)
+ , leftParentId("N/A")
+ , rightParentId("N/A")
+ , crossover(-1)
+ , score(-1.0f){};
+
+ // Move constructor
+ ChimeraLabel(ChimeraLabel &&src) = default;
+ // Copy constructor is deleted!
+ ChimeraLabel(const ChimeraLabel &src) = default;
+ // Move assignment constructor
+ ChimeraLabel &operator=(ChimeraLabel &&rhs) = default;
+ // Copy assignment constructor is deleted!
+ ChimeraLabel &operator=(const ChimeraLabel &rhs) = default;
+ // Destructor
+ ~ChimeraLabel() = default;
+
+ friend std::ostream &operator<<(std::ostream &o, const ChimeraLabel &label)
+ {
+ // Stream the Sequence Id first
+ o << label.sequenceId << ",";
+
+ // Then a human-readable representation of the flag
+ if (label.chimeraFlag)
+ o << "True"
+ << ",";
+ else
+ o << "False"
+ << ",";
+
+ // The score is only meaningfully defined > 0
+ if (label.score >= 0.0f)
+ o << label.score << ",";
+ else
+ o << "NaN"
+ << ",";
+
+ // Finally the parents and the putative crossover
+ o << label.leftParentId << "," << label.rightParentId << "," << label.crossover;
+
+ // Return the stream reference
+ return o;
+ }
+};
+
+} // namespace Chimera
+} // namespace PacBio
diff --git a/include/pacbio/chimera/ChimeraLabeler.h b/include/pacbio/chimera/ChimeraLabeler.h
new file mode 100644
index 0000000..6e30541
--- /dev/null
+++ b/include/pacbio/chimera/ChimeraLabeler.h
@@ -0,0 +1,710 @@
+// Copyright (c) 2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Brett Bowman
+
+#pragma once
+
+#include <algorithm>
+#include <iostream>
+#include <limits>
+#include <set>
+#include <string>
+#include <vector>
+
+#include <seqan/graph_msa.h>
+#include <seqan/sequence.h>
+
+#include "ChimeraLabel.h"
+
+namespace PacBio {
+namespace Chimera {
+
+namespace {
+
+/// Seprates a string on a specified delimiter
+///
+/// \param s Input string
+/// \param delim Delimiter character
+///
+/// \return Vector of sub-strings of the input string
+static std::vector<std::string> Split(const std::string &s, char delim)
+{
+ std::vector<std::string> elems;
+ std::stringstream ss(s);
+ std::string item;
+ while (std::getline(ss, item, delim)) {
+ elems.push_back(item);
+ }
+ return elems;
+}
+
+} // Anonymous namespace
+
+///
+/// Chimera detector - this is an implementation of the UCHIME algorithm, with a
+/// few generalizations:
+/// Edgar, Robert C., et al. "UCHIME improves sensitivity and speed of chimera
+/// detection." Bioinformatics 27.16 (2011): 2194-2200.
+///
+/// Notes: We do full length alignments between the database and the test
+/// sequence, then find the best scoring splice site for each pair of database -
+/// test seq alignments
+/// This is probably not as scalable as doing chunkwise alignments and only
+/// considering the best alignment to each chunk, but it's presumably more
+/// sensitive...
+/// May need to speed this up (and lot's of other things) if the number of
+/// haplotypes gets very large.
+///
+class ChimeraLabeler
+{
+public: // structors
+ // Default constructor
+ explicit ChimeraLabeler(double minChimeraScoreArg = 1.0, size_t maxChimeraSupportArg = 100,
+ bool verboseArg = false)
+ : minChimeraScore(minChimeraScoreArg)
+ , maxChimeraSupport(maxChimeraSupportArg)
+ , beta(4)
+ , pseudocount(2.0)
+ , chunks(4)
+ , verbose(verboseArg){};
+ // Move constructor
+ ChimeraLabeler(ChimeraLabeler &&src) = delete;
+ // Copy constructor
+ ChimeraLabeler(const ChimeraLabeler &src) = delete;
+ // Move assignment constructor
+ ChimeraLabeler &operator=(ChimeraLabeler &&rhs) = delete;
+ // Copy assignment constructor
+ ChimeraLabeler &operator=(const ChimeraLabeler &rhs) = delete;
+ // Destructor
+ ~ChimeraLabeler() = default;
+
+private: // Type definitions
+ typedef seqan::Align<seqan::Dna5String, seqan::ArrayGaps> TAlign;
+ typedef seqan::Score<int32_t, seqan::Simple> TScore;
+ typedef seqan::Row<TAlign>::Type TRow;
+ typedef seqan::Iterator<TRow>::Type TRowIter;
+ typedef seqan::IterMakeConst<TRowIter>::Type TRowIterC;
+ enum orientation_t
+ {
+ A_B,
+ B_A,
+ NA
+ };
+
+private: // Instance variables
+ const double minChimeraScore;
+ const size_t maxChimeraSupport;
+ const size_t beta;
+ const double pseudocount;
+ const size_t chunks;
+ const bool verbose;
+ const TScore scoringScheme = TScore(2, -5, -3, -3);
+
+private: // State variables
+ std::vector<std::string> ids_;
+ std::vector<seqan::Dna5String> nonChimeras_;
+ size_t minSize_ = std::numeric_limits<size_t>::max();
+ size_t numAnalyzed_ = 0;
+
+public: // Modifying methods
+ /// \brief Clear and reset all stateful variables to default
+ ///
+ void clear()
+ {
+ ids_.clear();
+ nonChimeras_.clear();
+ minSize_ = std::numeric_limits<size_t>::max();
+ numAnalyzed_ = 0;
+ }
+
+ /// \brief Label a vector of sequence records as Chimeric or not.
+ /// Secondary entry-point.
+ ///
+ /// \param A vector of all of the sequence ids as strings
+ /// \param A vector of all of the sequences as strings
+ /// \param A vector of integers, representing the support for each sequence
+ ///
+ /// \return A set of labels representing the chimeric parents (if any) for
+ /// each input sequence
+ ///
+ std::vector<ChimeraLabel> LabelChimeras(const std::vector<std::string> &idList,
+ const std::vector<std::string> &seqList,
+ const std::vector<size_t> &sizeList)
+ {
+ std::vector<seqan::Dna5String> dnaStringList;
+ for (const auto &seq : seqList)
+ dnaStringList.emplace_back(seq);
+ return LabelChimeras(idList, dnaStringList, sizeList);
+ }
+
+ /// \brief Label a vector of sequence records as Chimeric or not.
+ /// Secondary entry-point.
+ ///
+ /// \param A vector of all of the sequence ids as strings
+ /// \param A vector of all of the sequences as strings
+ ///
+ /// \return A set of labels representing the chimeric parents (if any) for
+ /// each input sequence
+ ///
+ std::vector<ChimeraLabel> LabelChimeras(const std::vector<std::string> &idList,
+ const std::vector<std::string> &seqList)
+ {
+ std::vector<size_t> sizeList = ParseNumReads(idList);
+ std::vector<seqan::Dna5String> dnaStringList;
+ for (const auto &seq : seqList)
+ dnaStringList.emplace_back(seq);
+ return LabelChimeras(idList, dnaStringList, sizeList);
+ }
+
+ /// \brief Label a vector of sequence records as Chimeric or not.
+ /// Secondary entry-point.
+ ///
+ /// \param A vector of all the sequence ids as strings
+ /// \param A vector of all the sequences as Dna5Strings
+ ///
+ /// \return A set of labels representing the chimeric parents (if any) for
+ /// each input sequence
+ ///
+ std::vector<ChimeraLabel> LabelChimeras(const std::vector<std::string> &idList,
+ const std::vector<seqan::Dna5String> &seqList)
+ {
+ std::vector<size_t> sizeList = ParseNumReads(idList);
+ return LabelChimeras(idList, seqList, sizeList);
+ }
+
+ /// \brief Label a vector of sequence records as Chimeric or not.
+ /// Main entry-point.
+ ///
+ /// \param A vector of all the sequence ids as strings
+ /// \param A vector of all the sequences as Dna5Strings
+ /// \param A vector of integers, representing the support for each sequence
+ ///
+ /// \return A set of labels representing the chimeric parents (if any) for
+ /// each input sequence
+ ///
+ std::vector<ChimeraLabel> LabelChimeras(const std::vector<std::string> &ids,
+ const std::vector<seqan::Dna5String> &seqs,
+ const std::vector<size_t> &sizes)
+ {
+ // Declare the output vector now
+ std::vector<ChimeraLabel> output;
+
+ // Iterate over each Fasta record in order of their size
+ for (size_t i = 0; i < ids.size(); ++i) {
+ ChimeraLabel label = LabelChimera(ids[i], seqs[i], sizes[i]);
+ output.push_back(label);
+ }
+
+ return output;
+ }
+
+ /// \brief Label a vector of sequence records as Chimeric or not.
+ /// Main entry-point.
+ ///
+ /// \param The Id of the sequence as a string
+ /// \param The sequence itself
+ /// \param The support for the sequence, as an integer
+ ///
+ /// \return A label for whether and how the query is chimeric
+ ///
+ ChimeraLabel LabelChimera(const std::string &id, const seqan::Dna5String &sequence,
+ const size_t size)
+ {
+ ChimeraLabel label(id);
+
+ // Error-out if sequences are presented out of order
+ if (size > minSize_) throw std::runtime_error("Sequences analyzed out of order!");
+
+ // Declare containers for tracking non-Chimeric parents
+ std::vector<size_t> parentIds;
+
+ // The first two sequences do not have enough possible parents, and any
+ // records with a high enough number of supporting reads, assume real
+ if (ids_.size() < 2 || size > maxChimeraSupport) {
+ if (verbose)
+ std::cout << "consensus '" << id << "' is abundant, assumed real" << std::endl;
+#ifdef PBLOG_DEBUG
+ PBLOG_DEBUG << "consensus '" << id << "' is abundant, assumed real";
+#endif
+ // Create a default label for the assumed-non-chimeric read
+ AddNonChimera(id, sequence, size);
+ return label;
+ } else // Otherwise we align
+ {
+ // Find probable parents from the highest scoring SW templates
+ parentIds = FindParents(sequence);
+
+ // If there is only one high scoring parent, then the sequence
+ // probably represents a true allele and we keep it.
+ if (parentIds.size() == 1) {
+ if (verbose)
+ std::cout << "consensus '" << id
+ << "' has only one proposed parent, assumed real" << std::endl;
+#ifdef PBLOG_DEBUG
+ PBLOG_DEBUG << "consensus '" << id
+ << "' has only one proposed parent, assumed real";
+#endif
+ // Add a default label for the non-chimeric read
+ AddNonChimera(id, sequence, size);
+ return label;
+ } else // Otherwise we need to test it for chimerism
+ {
+ auto label = TestPossibleChimera(id, sequence, parentIds);
+
+ if (label.score > 0.0f) {
+ if (verbose) {
+ std::cout << "consensus '" << id << "' has a possible cross-over at "
+ << label.crossover << " with a score of " << label.score
+ << std::endl;
+ std::cout << "possible parents are '" << label.leftParentId << "' and '"
+ << label.rightParentId << "'" << std::endl;
+ }
+#ifdef PBLOG_DEBUG
+ PBLOG_DEBUG << "consensus '" << id << "' has a possible cross-over at "
+ << label.crossover << " with a score of " << label.score;
+ PBLOG_DEBUG << "possible parents are '" << label.leftParentId << "' and '"
+ << label.rightParentId << "'";
+#endif
+ } else {
+ if (verbose)
+ std::cout
+ << "consensus '" << id
+ << "' had no possible cross-overs with positive scores, assumed real"
+ << std::endl;
+#ifdef PBLOG_DEBUG
+ PBLOG_DEBUG
+ << "consensus '" << id
+ << "' has no possible cross-overs with positive scores, assumed real";
+#endif
+ }
+
+ // If the score is high enough, set the flag, otherwise we add it to our
+ // reference
+ if (label.score > minChimeraScore) {
+ label.chimeraFlag = true;
+ } else {
+ AddNonChimera(id, sequence, size);
+ }
+
+ return label;
+ }
+ }
+ }
+
+private: // non-modifying methods
+ /// \brief Add a non-chimeric sequence to th
+ ///
+ /// \param The sequence Id as a string
+ /// \param The sequence itself, as a Dna5String
+ /// \param It's level of coverage or support
+ ///
+ void AddNonChimera(const std::string &id, const seqan::Dna5String sequence, const size_t size)
+ {
+ ids_.push_back(id);
+ nonChimeras_.push_back(sequence);
+ AddReverseComplement(sequence);
+ minSize_ = std::min(size, minSize_);
+ }
+
+ /// \brief Add the reverse-complement of a Sequence to the references
+ ///
+ /// \param The sequence itself, as a Dna5String
+ ///
+ void AddReverseComplement(const seqan::Dna5String &sequence)
+ {
+ seqan::Dna5String revComSeq = sequence;
+ seqan::reverseComplement(revComSeq);
+ nonChimeras_.push_back(revComSeq);
+ }
+
+ /// \brief Find the most probable parents for a possible chimera
+ ///
+ /// \param A vector of all of the available sequences
+ /// \param A vector of indices of non-chimeric sequences in that vector
+ /// \param The index of the current sequence to be tested
+ ///
+ /// \return A set of indices representing the best scoring parents for the
+ /// various regions of the current sequences
+ ///
+ std::vector<size_t> FindParents(const seqan::Dna5String &sequence)
+ {
+ // Declare the output variable and the set we will build it from
+ std::vector<size_t> output;
+ std::set<size_t> parentIds;
+
+ // Initialize the pairwise-alignment object we will be reusing
+ TAlign align;
+ seqan::resize(rows(align), 2);
+
+ // Pre-calculate the size of each chunk
+ size_t chunkSize = seqan::length(sequence) / chunks;
+
+ // Iterate over each chunk, aligning it to all possible parents
+ for (size_t i = 0; i < chunks; ++i) {
+ // Initialize the alignment with the current sequence chunk
+ size_t chunkStart = i * chunkSize;
+ size_t chunkEnd = chunkStart + chunkSize;
+ const auto chunkSeq = infix(sequence, chunkStart, chunkEnd);
+ seqan::assignSource(seqan::row(align, 0), chunkSeq);
+
+ // Initialize loop variables;
+ size_t score = 0;
+ size_t maxScore = 0;
+ size_t maxParent = 0;
+
+ // iterate over each non-Chimeric sequence
+ for (size_t i = 0; i < nonChimeras_.size(); ++i) {
+ // Fill out the alignment with the current parents
+ seqan::assignSource(seqan::row(align, 1), nonChimeras_[i]);
+ score = seqan::localAlignment(align, scoringScheme);
+
+ // If the current parent is better than the best, keep it
+ if (score > maxScore) {
+ maxScore = score;
+ maxParent = i;
+ }
+ }
+
+ // Add the best parent for this chunk to the set
+ parentIds.insert(maxParent);
+ }
+
+ // Convert the set of parents to a vector for down-stream use
+ std::move(parentIds.begin(), parentIds.end(), std::back_inserter(output));
+ return output;
+ }
+
+ /// \brief Identify the highest-scoring chimeric explaination for a query
+ /// from a list of
+ ///
+ /// \param A pointer to a vector of sequences
+ /// \param A pointer to a vector of sequence ids
+ /// \param An unsigned int for the index of the query in the above vectors
+ /// \param A vector of unsigned ints for
+ ///
+ /// \return A ChimeraLabel for the highest-scoring chimeric explaination
+ /// for a given query
+ ///
+ ChimeraLabel TestPossibleChimera(const std::string &id, const seqan::Dna5String &sequence,
+ const std::vector<size_t> &possibleParents)
+ {
+ // First we align the query to all of the possible parents
+ // auto alignments = GetFullAlignments(sequences, index,
+ // possibleParents);
+ auto alignments = GetMultiSequenceAlignment(sequence, possibleParents);
+
+ // Initialize two Labels - one for the max and one for the loop variable
+ ChimeraLabel bestLabel(id);
+
+ // Loop variables for the names of the identified parents
+ std::string parentA;
+ std::string parentB;
+
+ // Iterate over all possible "Parent A"'s
+ for (size_t i = 1; i < possibleParents.size(); ++i) {
+ size_t parentAIdx = possibleParents[i];
+ parentA = ids_[parentAIdx / 2];
+
+ // Iterate over all possible "Parent B"'s
+ for (size_t j = 0; j < i; ++j) {
+ size_t parentBIdx = possibleParents[j];
+ parentB = ids_[parentBIdx / 2];
+
+ // For a given ParentA and ParentB, what is the maximum
+ // possible Chimera score?
+ ChimeraLabel label =
+ ScorePossibleChimera(alignments, id, parentA, parentB, i + 1, j + 1);
+
+ // Keep the highest scoring label
+ if (label.score > bestLabel.score && label.score > 0.0f)
+ bestLabel = std::move(label);
+ }
+ }
+
+ return bestLabel;
+ }
+
+ /// \brief Generate an MSA of a query sequence and all possible parents
+ ///
+ /// \param A pointer to a vector of possible sequences
+ /// \param An unsigned int for the index of the query in the vector of
+ /// sequences
+ /// \param A vector of unsigned ints for the indices of all possible parents
+ ///
+ /// \return a pointer to an MSA
+ ///
+ TAlign GetMultiSequenceAlignment(const seqan::Dna5String &sequence,
+ const std::vector<size_t> &parentIds)
+ {
+ // Initialize the alignment with the query sequence
+ TAlign align;
+ seqan::resize(rows(align), parentIds.size() + 1);
+ seqan::assignSource(seqan::row(align, 0), sequence);
+
+ // Successively add each parent to the alignment
+ for (size_t i = 1; i <= parentIds.size(); ++i) {
+ size_t parentIdx = parentIds[i - 1];
+ seqan::assignSource(seqan::row(align, i), nonChimeras_[parentIdx]);
+ }
+
+ // Perform the alignment operation and return
+ seqan::globalMsaAlignment(align, scoringScheme);
+ return align;
+ }
+
+ /// \brief Scan an MSA of sequences for all possible chimeric break-points
+ /// that could explain the query as a composite of the parents
+ ///
+ /// \param A pointer to an MSA of sequences
+ /// \param A string for the name of the Query
+ /// \param A string for the name of the first parent
+ /// \param A string for the name of the second parent
+ /// \param An unsigned int for the row-index of the first parent
+ /// \param An unsigned int for the row-index of the second parent
+ ///
+ /// \return A ChimeraLabel of the highest-scoring possible chimera
+ ///
+ ChimeraLabel ScorePossibleChimera(const TAlign &alignment, const std::string &queryId,
+ const std::string &parentAId, const std::string &parentBId,
+ const size_t firstIdx, const size_t secondIdx)
+ {
+ // Second, extract references to the rows we need to inspect
+ const TRow &queryRow = seqan::row(alignment, 0);
+ const TRow &parentA = seqan::row(alignment, firstIdx);
+ const TRow &parentB = seqan::row(alignment, secondIdx);
+
+ // Initialize const-iterators for each row
+ TRowIterC itQ = seqan::begin(queryRow);
+ TRowIterC itA = seqan::begin(parentA);
+ TRowIterC itB = seqan::begin(parentB);
+
+ // Initialize end-point for the const-iterators (since we're traversing
+ // an MSA all 3 iterators will terminate at the same point)
+ TRowIterC qEnd = seqan::end(queryRow);
+
+ // Count variables
+ size_t rightA = 0;
+ size_t rightB = 0;
+ size_t rightAbs = 0;
+ size_t leftA = 0;
+ size_t leftB = 0;
+ size_t leftAbs = 0;
+
+ // First we iterate once, counting up the total number of A/B/Abs votes
+ // to initialize the counts for the right-hand segment
+ for (; itQ != qEnd; ++itQ, ++itA, ++itB) {
+ // We can't trust our consensus around gaps for low-coverage reads
+ // so we skip them
+ if (seqan::isGap(itQ) || seqan::isGap(itA) || seqan::isGap(itB)) continue;
+
+ // Identical bases are useless for Chimera Detection - skip
+ if (*itQ == *itA && *itQ == *itB) continue;
+
+ // If we made it here, count the difference as a vote
+ if (*itA == *itB) {
+ ++rightAbs;
+ } else if (*itQ == *itA) {
+ ++rightA;
+ } else if (*itQ == *itB) {
+ ++rightB;
+ }
+ }
+
+ // Re-initialize iterators for each row
+ itQ = seqan::begin(queryRow);
+ itA = seqan::begin(parentA);
+ itB = seqan::begin(parentB);
+
+ // Initialize variables for the maximum chimera
+ double maxChimeraScore = 0.0f;
+ size_t maxChimeraCrossover = 0;
+ orientation_t maxChimeraOrientation = NA;
+
+ // And per-iteration variables
+ double abScore, baScore, chimeraScore;
+ size_t chimeraCrossover = 0;
+ orientation_t chimeraOrientation;
+
+ // Second time we iterate, we subtract from the right
+ for (; itQ != qEnd; ++itQ, ++itA, ++itB) {
+ // If the Query sequence is not at a gap, increment the
+ // tracking variable for the crossover postion
+ if (seqan::isGap(itQ))
+ continue;
+ else
+ ++chimeraCrossover;
+
+ // We can't trust our consensus around gaps for low-coverage reads
+ // so we skip them
+ if (seqan::isGap(itA) || seqan::isGap(itB)) continue;
+
+ // Identical bases are useless for Chimera Detection - skip
+ if (*itQ == *itA && *itQ == *itB) continue;
+
+ // If we made it here, count the differences as a vote
+ if (*itA == *itB) {
+ ++leftAbs;
+ --rightAbs;
+ } else if (*itQ == *itA) {
+ ++leftA;
+ --rightA;
+ } else if (*itQ == *itB) {
+ ++leftB;
+ --rightB;
+ }
+
+ // If we've exhausted the right-side votes, there are no more
+ // possible break points
+ if (rightA == 0 && rightB == 0) break;
+
+ // If haven't seen any left-side votes, we haven't reached any
+ // possible break points yet
+ if (leftA == 0 && leftB == 0) continue;
+
+ // If the Left leans A and the right leans B, test "AAABBB"
+ if (leftA > leftB && rightA < rightB) {
+ chimeraScore = ScoreBreakPoint(leftA, leftB, leftAbs, rightB, rightA, rightAbs);
+ chimeraOrientation = A_B;
+ } // If the Left leans B and the right leans A, test "BBBAAA"
+ else if (leftA < leftB && rightA > rightB) {
+ chimeraScore = ScoreBreakPoint(leftB, leftA, leftAbs, rightA, rightB, rightAbs);
+ chimeraOrientation = B_A;
+ } // If either left or right isn't clear, test both options
+ else {
+ abScore = ScoreBreakPoint(leftA, leftB, leftAbs, rightB, rightA, rightAbs);
+ baScore = ScoreBreakPoint(leftB, leftA, leftAbs, rightA, rightB, rightAbs);
+ if (abScore > baScore) {
+ chimeraScore = abScore;
+ chimeraOrientation = A_B;
+ } else {
+ chimeraScore = baScore;
+ chimeraOrientation = B_A;
+ }
+ }
+
+ // Keep the best chimera we've seen so far
+ if (chimeraScore > maxChimeraScore) {
+ maxChimeraScore = chimeraScore;
+ maxChimeraCrossover = chimeraCrossover;
+ maxChimeraOrientation = chimeraOrientation;
+ }
+ }
+
+ // Build and return an appropriately oriented ChimeraLabel
+ if (maxChimeraOrientation == A_B)
+ return ChimeraLabel(queryId, parentAId, parentBId, maxChimeraCrossover,
+ maxChimeraScore);
+ else
+ return ChimeraLabel(queryId, parentBId, parentAId, maxChimeraCrossover,
+ maxChimeraScore);
+ }
+
+public: // Public Static Methods
+ /// \brief Parse the number of reads supporting a sequence from it's Id
+ ///
+ /// \param The Id to be parsed as a string
+ ///
+ /// \return The support for that sequence, as an integer
+ ///
+ static size_t ParseNumReads(const std::string id)
+ {
+ const auto &parts = Split(id, '_');
+ const auto &numReadsString = parts[3].substr(8);
+ const size_t numReads = std::stoi(numReadsString);
+ return numReads;
+ }
+
+ /// \brief Parse the number of reads supporting a vector of sequences from
+ /// their Ids
+ ///
+ /// \param The vector of Ids to be parsed as strings
+ ///
+ /// \return The support for those sequences, as integers
+ ///
+ static std::vector<size_t> ParseNumReads(const std::vector<std::string> ids)
+ {
+ std::vector<size_t> retval;
+ for (size_t i = 0; i < ids.size(); ++i)
+ retval.emplace_back(ParseNumReads(ids[i]));
+ return retval;
+ }
+
+private: // Inlined methods
+ /// \brief Calculates the H-score for a chimeric alignment as per Edgar(2011)
+ ///
+ /// \param An unsigned int of votes for left-side similarity
+ /// \param An unsigned int of votes against left-side similarity
+ /// \param An unsigned int of votes neither for or against the left side
+ /// \param An unsigned int of votes for right-side similarity
+ /// \param An unsigned int of votes against right-side similarity
+ /// \param An unsigned int of votes neither for or against the right side
+ ///
+ /// \return A double representing the strength of the similarity between the
+ /// query
+ /// sequence and a hypothetical chimera composed of left and right
+ /// segments
+ /// taken from existing sequences
+ ///
+ inline double ScoreBreakPoint(const size_t leftYesVotes, const size_t leftNoVotes,
+ const size_t leftAbsVotes, const size_t rightYesVotes,
+ const size_t rightNoVotes, const size_t rightAbsVotes)
+ {
+ // Score the left and right segments independently
+ double leftScore = ScoreSegment(leftYesVotes, leftNoVotes, leftAbsVotes);
+ double rightScore = ScoreSegment(rightYesVotes, rightNoVotes, rightAbsVotes);
+
+ // Return their product
+ return leftScore * rightScore;
+ }
+
+ /// \brief Calculates the H-score for a pairwise alignment segment,
+ /// as per Edgar(2011)
+ ///
+ /// \param An unsigned int of votes for similarity
+ /// \param An unsigned int of votes against similarity
+ /// \param An unsigned int of votes neither for nor against
+ ///
+ /// \return A double representing the strength of the similarity between two
+ /// sequences
+ ///
+ inline double ScoreSegment(const size_t yesVotes, const size_t noVotes, const size_t absVotes)
+ {
+ return yesVotes / (beta * (noVotes + pseudocount) + absVotes);
+ }
+};
+
+} // namespace Chimera
+} // namespace PacBio
diff --git a/include/pacbio/chimera/ChimeraResultWriter.h b/include/pacbio/chimera/ChimeraResultWriter.h
new file mode 100644
index 0000000..ac2262d
--- /dev/null
+++ b/include/pacbio/chimera/ChimeraResultWriter.h
@@ -0,0 +1,81 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Brett Bowman
+
+#pragma once
+
+#include <vector>
+
+#include "ChimeraLabel.h"
+
+namespace PacBio {
+namespace Chimera {
+
+///
+/// \brief Write out to file a series ChimeraLabels in human-readable form
+///
+class ChimeraResultWriter
+{
+public:
+ ChimeraResultWriter(const std::string &csvFile) : csvWriter_(csvFile)
+ {
+ ValidateCsvFile(csvFile);
+ csvWriter_ << "SequenceId,IsChimera,ChimeraScore,"
+ << "ParentSequenceA,ParentSequenceB,CrossoverPosition" << std::endl;
+ }
+
+ void WriteResult(const ChimeraLabel &label) { csvWriter_ << label << std::endl; }
+ void WriteResults(const std::vector<ChimeraLabel> &labels)
+ {
+ for (const auto &label : labels)
+ WriteResult(label);
+ }
+
+private:
+ static void ValidateCsvFile(const std::string &filename)
+ {
+ const std::string ext = filename.substr(filename.find_last_of(".") + 1);
+
+ if (ext != "csv")
+ throw std::invalid_argument("invalid sequence file type, only CSVs supported");
+ }
+
+private:
+ std::ofstream csvWriter_;
+};
+
+} // namespace Chimera
+} // namespace PacBio
diff --git a/include/pacbio/consensus/AbstractIntegrator.h b/include/pacbio/consensus/AbstractIntegrator.h
new file mode 100644
index 0000000..6ed3fd8
--- /dev/null
+++ b/include/pacbio/consensus/AbstractIntegrator.h
@@ -0,0 +1,160 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <cmath>
+#include <cstdint>
+#include <functional>
+#include <iostream>
+#include <memory>
+#include <numeric>
+
+#include <pacbio/consensus/Evaluator.h>
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/data/State.h>
+#include <pacbio/exception/StateError.h>
+
+namespace PacBio {
+namespace Consensus {
+
+class AbstractMatrix;
+
+struct IntegratorConfig
+{
+ double MinZScore;
+ double ScoreDiff;
+
+ IntegratorConfig(double minZScore = -3.5, double scoreDiff = 12.5);
+};
+
+class AbstractIntegrator
+{
+public:
+ virtual ~AbstractIntegrator();
+
+ virtual size_t TemplateLength() const = 0;
+
+ virtual char operator[](size_t i) const = 0;
+ virtual operator std::string() const = 0;
+
+ virtual double LL(const Mutation& mut);
+ virtual double LL() const;
+
+ double AvgZScore() const;
+ std::vector<double> ZScores() const;
+
+ std::vector<std::pair<double, double>> NormalParameters() const;
+
+ virtual void ApplyMutation(const Mutation& mut) = 0;
+ virtual void ApplyMutations(std::vector<Mutation>* muts) = 0;
+
+ virtual PacBio::Data::State AddRead(const PacBio::Data::MappedRead& read) = 0;
+
+ // For debugging purposes
+ // (Note that these include results include all evaluators, even the inactive ones)
+ std::vector<double> LLs(const Mutation& mut);
+ std::vector<double> LLs() const;
+ std::vector<std::string> ReadNames() const;
+
+ std::vector<int> NumFlipFlops() const;
+ int MaxNumFlipFlops() const;
+
+ float MaxAlphaPopulated() const;
+ float MaxBetaPopulated() const;
+
+ std::vector<PacBio::Data::State> States() const;
+ std::vector<PacBio::Data::StrandType> StrandTypes() const;
+
+ const Evaluator& GetEvaluator(size_t idx) const;
+
+public:
+ // Abstract matrix access for SWIG and diagnostics
+ const AbstractMatrix& Alpha(size_t idx) const;
+ const AbstractMatrix& Beta(size_t idx) const;
+
+protected:
+ Mutation ReverseComplement(const Mutation& mut) const;
+
+ AbstractIntegrator(const IntegratorConfig& cfg);
+
+ // move constructor
+ AbstractIntegrator(AbstractIntegrator&&);
+
+ PacBio::Data::State AddRead(std::unique_ptr<AbstractTemplate>&& tpl,
+ const PacBio::Data::MappedRead& read);
+
+ IntegratorConfig cfg_;
+ std::vector<Evaluator> evals_;
+
+private:
+ /// Extract a feature vector from a vector of Evaluators for non-const functions.
+ template <typename T>
+ inline std::vector<T> TransformEvaluators(std::function<T(Evaluator&)> functor)
+ {
+ // TODO(atoepfer) How can we use const_cast to convert this?
+ std::vector<T> vec;
+ vec.reserve(evals_.size());
+ std::transform(evals_.begin(), evals_.end(), std::back_inserter(vec), functor);
+ return vec;
+ }
+
+ /// Extract a feature vector from a vector of Evaluators for const functions.
+ template <typename T>
+ inline std::vector<T> TransformEvaluators(std::function<T(const Evaluator&)> functor) const
+ {
+ std::vector<T> vec;
+ vec.reserve(evals_.size());
+ std::transform(evals_.begin(), evals_.end(), std::back_inserter(vec), functor);
+ return vec;
+ }
+};
+
+/// Accumulate all non inf or -inf doubles.
+inline double AccumulateNoInf(std::vector<double> input)
+{
+ const auto AddNoInf = [](double a, double b) { return a + (std::isinf(b) ? 0.0 : b); };
+ return std::accumulate(input.cbegin(), input.cend(), 0.0, AddNoInf);
+}
+
+/// Helper function to get maximal number from a vector.
+template <typename T>
+inline T MaxElement(const std::vector<T>& in)
+{
+ return *std::max_element(in.cbegin(), in.end());
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/consensus/AbstractMatrix.h b/include/pacbio/consensus/AbstractMatrix.h
new file mode 100644
index 0000000..dc67585
--- /dev/null
+++ b/include/pacbio/consensus/AbstractMatrix.h
@@ -0,0 +1,67 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+namespace PacBio {
+namespace Consensus {
+
+// AbstractMatrix is a superclass of the matrix types used in the arrow
+// banded dynamic programming. It exposes a minimal interface only
+// intended for diagnostic purposes (looking at a matrix from Python,
+// seeing how well the banding is working, ...). No matrix implementation
+// details are exposed---one can think of this as effectively an opaque
+// data type.
+class AbstractMatrix
+{
+public:
+ // Method SWIG clients can use to get a native matrix (e.g. Numpy)
+ // mat must be filled as a ROW major matrix, and the understanding
+ // is that the entries represent natural-logs of probabilities.
+ // N.B.: Needs int, not size_t dimensions, for SWIG/numpy
+ virtual void ToHostMatrix(double** mat, int* rows, int* cols) const = 0;
+
+public:
+ // Methods for inquiring about matrix occupancy.
+ virtual size_t UsedEntries() const = 0;
+ virtual float UsedEntriesRatio() const = 0;
+ virtual size_t AllocatedEntries() const = 0; // an entry may be allocated but not used
+
+public:
+ virtual ~AbstractMatrix() {}
+};
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/consensus/Coverage.h b/include/pacbio/consensus/Coverage.h
new file mode 100644
index 0000000..ed9ae58
--- /dev/null
+++ b/include/pacbio/consensus/Coverage.h
@@ -0,0 +1,57 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Authors: David Alexander, Lance Hepler
+
+#pragma once
+
+#include <utility>
+#include <vector>
+
+namespace PacBio {
+namespace Consensus {
+
+// These APIs are a little more awkward than I'd have liked---see
+// "winLen" instead of winEnd. Had to contort a bit to get SWIG
+// bindings working well.
+
+void CoverageInWindow(int tStartDim, int* tStart, int tEndDim, int* tEnd, int winStart, int winLen,
+ int* coverage);
+
+std::vector<std::pair<int, int>> CoveredIntervals(int minCoverage, int tStartDim, int* tStart,
+ int tEndDim, int* tEnd, int winStart, int winLen);
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/consensus/EasyReadScorer.h b/include/pacbio/consensus/EasyReadScorer.h
new file mode 100644
index 0000000..a4eee30
--- /dev/null
+++ b/include/pacbio/consensus/EasyReadScorer.h
@@ -0,0 +1,69 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#pragma once
+
+namespace PacBio {
+
+namespace Data {
+struct MappedRead;
+} // PacBio::Data
+
+namespace Consensus {
+
+class Evaluator;
+
+//
+// EasyReadScorer is a simplified means to get access to the evaluator
+// scoring machinery. This is suitable for experimental purposes,
+// not intended for use in production code.
+//
+class EasyReadScorer
+{
+
+public:
+ //
+ // This is a convenient means to build an evaluator---it will automatically
+ // look up the model, populate the template object, etc.
+ //
+ static Evaluator* MakeEvaluator(const std::string& tplString,
+ const PacBio::Data::MappedRead& mappedRead, double minZScore,
+ double scoreDiff);
+};
+
+} // PacBio::Consensus
+} // PacBio
diff --git a/include/pacbio/consensus/Evaluator.h b/include/pacbio/consensus/Evaluator.h
new file mode 100644
index 0000000..71e6125
--- /dev/null
+++ b/include/pacbio/consensus/Evaluator.h
@@ -0,0 +1,111 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <memory>
+#include <utility>
+#include <vector>
+
+#include <pacbio/consensus/Template.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/data/State.h>
+
+namespace PacBio {
+namespace Consensus {
+
+// forward declaration
+class EvaluatorImpl;
+class AbstractMatrix;
+
+class Evaluator
+{
+public:
+ Evaluator() = delete;
+ explicit Evaluator(PacBio::Data::State);
+ Evaluator(std::unique_ptr<AbstractTemplate>&& tpl, const PacBio::Data::MappedRead& mr,
+ double minZScore, double scoreDiff);
+
+ // copying is verboten
+ Evaluator(const Evaluator&) = delete;
+ Evaluator& operator=(const Evaluator&) = delete;
+
+ // move constructor
+ Evaluator(Evaluator&&);
+ // move assign operator
+ Evaluator& operator=(Evaluator&&);
+
+ ~Evaluator();
+
+ size_t Length() const; // TODO: is this used anywhere? If not, delete it.
+ PacBio::Data::StrandType Strand() const;
+
+ operator bool() const { return IsValid(); }
+ bool IsValid() const { return curState_ == PacBio::Data::State::VALID; }
+
+ operator std::string() const;
+ std::string ReadName() const;
+
+ double LL(const Mutation& mut);
+ double LL() const;
+
+ std::pair<double, double> NormalParameters() const;
+
+ double ZScore() const;
+
+ bool ApplyMutation(const Mutation& mut);
+ bool ApplyMutations(std::vector<Mutation>* muts);
+
+ PacBio::Data::State Status() const { return curState_; }
+ int NumFlipFlops() const;
+
+ void Release();
+
+public:
+ const AbstractMatrix& Alpha() const;
+ const AbstractMatrix& Beta() const;
+
+private:
+ void CheckZScore(const double minZScore, const std::string& model);
+
+ void Status(PacBio::Data::State nextState);
+
+private:
+ std::unique_ptr<EvaluatorImpl> impl_;
+ PacBio::Data::State curState_;
+};
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/consensus/ModelConfig.h b/include/pacbio/consensus/ModelConfig.h
new file mode 100644
index 0000000..db47f05
--- /dev/null
+++ b/include/pacbio/consensus/ModelConfig.h
@@ -0,0 +1,104 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <array>
+#include <cstdint>
+#include <map>
+#include <memory>
+#include <ostream>
+#include <stdexcept>
+#include <string>
+#include <vector>
+
+namespace PacBio {
+
+namespace Data {
+struct MappedRead;
+struct SNR;
+}
+
+namespace Consensus {
+namespace detail {
+
+extern uint8_t TranslationTable[256];
+
+} // namespace detail
+
+// fwd decl
+class AbstractRecursor;
+class AbstractTemplate;
+
+struct TemplatePosition
+{
+ char Base;
+ uint8_t Idx;
+ double Match;
+ double Branch;
+ double Stick;
+ double Deletion;
+};
+
+std::ostream& operator<<(std::ostream&, const TemplatePosition&);
+
+enum struct MoveType : uint8_t
+{
+ MATCH = 0,
+ BRANCH = 1,
+ STICK = 2,
+ DELETION = 3 // never used for covariate
+};
+
+enum struct MomentType : uint8_t
+{
+ FIRST = 0,
+ SECOND = 1
+};
+
+class ModelConfig
+{
+public:
+ virtual ~ModelConfig() {}
+ virtual std::unique_ptr<AbstractRecursor> CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const PacBio::Data::MappedRead& mr,
+ double scoreDiff) const = 0;
+ virtual std::vector<TemplatePosition> Populate(const std::string& tpl) const = 0;
+ virtual double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const = 0;
+};
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/consensus/ModelSelection.h b/include/pacbio/consensus/ModelSelection.h
new file mode 100644
index 0000000..da063ec
--- /dev/null
+++ b/include/pacbio/consensus/ModelSelection.h
@@ -0,0 +1,54 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <set>
+#include <string>
+
+namespace PacBio {
+namespace Consensus {
+
+std::set<std::string> SupportedModels();
+std::set<std::string> SupportedChemistries();
+
+bool OverrideModel(const std::string& model);
+bool UnOverrideModel();
+
+size_t LoadModels(const std::string& path);
+}
+}
diff --git a/include/pacbio/consensus/MonoMolecularIntegrator.h b/include/pacbio/consensus/MonoMolecularIntegrator.h
new file mode 100644
index 0000000..b9d521f
--- /dev/null
+++ b/include/pacbio/consensus/MonoMolecularIntegrator.h
@@ -0,0 +1,82 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <cstdint>
+#include <functional>
+#include <iostream>
+#include <memory>
+#include <set>
+
+#include <pacbio/consensus/AbstractIntegrator.h>
+#include <pacbio/consensus/Evaluator.h>
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/data/State.h>
+#include <pacbio/exception/StateError.h>
+
+namespace PacBio {
+namespace Consensus {
+
+class MonoMolecularIntegrator : public AbstractIntegrator
+{
+public:
+ MonoMolecularIntegrator(const std::string& tpl, const IntegratorConfig& cfg,
+ const PacBio::Data::SNR& snr, const std::string& model);
+
+ // move constructor
+ MonoMolecularIntegrator(MonoMolecularIntegrator&&);
+
+ size_t TemplateLength() const override;
+
+ char operator[](size_t i) const override;
+ operator std::string() const override;
+
+ double LL(const Mutation& mut) override;
+ inline double LL() const override { return AbstractIntegrator::LL(); }
+ void ApplyMutation(const Mutation& mut) override;
+ void ApplyMutations(std::vector<Mutation>* muts) override;
+
+ PacBio::Data::State AddRead(const PacBio::Data::MappedRead& read) override;
+
+protected:
+ std::string mdl_;
+ PacBio::Data::SNR snr_;
+ Template fwdTpl_;
+ Template revTpl_;
+};
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/consensus/MultiMolecularIntegrator.h b/include/pacbio/consensus/MultiMolecularIntegrator.h
new file mode 100644
index 0000000..a97dcf3
--- /dev/null
+++ b/include/pacbio/consensus/MultiMolecularIntegrator.h
@@ -0,0 +1,80 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <cstdint>
+#include <functional>
+#include <iostream>
+#include <memory>
+#include <set>
+
+#include <pacbio/consensus/AbstractIntegrator.h>
+#include <pacbio/consensus/Evaluator.h>
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/data/State.h>
+#include <pacbio/exception/StateError.h>
+
+namespace PacBio {
+namespace Consensus {
+
+class MultiMolecularIntegrator : public AbstractIntegrator
+{
+public:
+ MultiMolecularIntegrator(const std::string& tpl, const IntegratorConfig& cfg);
+
+ size_t TemplateLength() const override;
+
+ char operator[](size_t i) const override;
+ operator std::string() const override;
+
+ void ApplyMutation(const Mutation& mut) override;
+ void ApplyMutations(std::vector<Mutation>* muts) override;
+
+ PacBio::Data::State AddRead(const PacBio::Data::MappedRead& read) override;
+
+protected:
+ std::unique_ptr<AbstractTemplate> GetTemplate(const PacBio::Data::MappedRead& read);
+
+ std::string fwdTpl_;
+ std::string revTpl_;
+
+private:
+ friend struct std::hash<MultiMolecularIntegrator>;
+};
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/consensus/Mutation.h b/include/pacbio/consensus/Mutation.h
new file mode 100644
index 0000000..a965f2b
--- /dev/null
+++ b/include/pacbio/consensus/Mutation.h
@@ -0,0 +1,121 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <cstddef>
+#include <cstdint>
+#include <ostream>
+#include <string>
+#include <tuple>
+#include <vector>
+
+namespace PacBio {
+namespace Consensus {
+
+enum struct MutationType : uint8_t
+{
+ DELETION,
+ INSERTION,
+ SUBSTITUTION,
+ ANY_INSERTION,
+ ANY_SUBSTITUTION
+};
+
+// forward decl
+class ScoredMutation;
+
+class Mutation
+{
+public:
+ char Base;
+ MutationType Type;
+
+ Mutation(MutationType type, size_t start, char base = '-');
+
+ // TODO(lhepler): do we *really* need these?
+ bool IsDeletion() const;
+ bool IsInsertion() const;
+ bool IsSubstitution() const;
+ bool IsAnyInsertion() const;
+ bool IsAnySubstitution() const;
+
+ size_t Start() const;
+ size_t End() const;
+
+ int LengthDiff() const;
+
+ bool operator==(const Mutation& other) const;
+ operator std::string() const;
+
+ ScoredMutation WithScore(double score) const;
+
+ static bool SiteComparer(const Mutation& lhs, const Mutation& rhs)
+ {
+ // perform a lexicographic sort on End, Start, IsDeletion
+ const auto l = std::make_tuple(lhs.End(), lhs.Start(), lhs.IsDeletion());
+ const auto r = std::make_tuple(rhs.End(), rhs.Start(), rhs.IsDeletion());
+ return l < r;
+ }
+
+private:
+ size_t start_;
+};
+
+class ScoredMutation : public Mutation
+{
+public:
+ double Score;
+
+ static bool ScoreComparer(const ScoredMutation& lhs, const ScoredMutation& rhs)
+ {
+ return lhs.Score < rhs.Score;
+ }
+
+private:
+ ScoredMutation(const Mutation& mut, double score);
+
+ // so Mutation can access the constructor
+ friend class Mutation;
+};
+
+std::ostream& operator<<(std::ostream& out, MutationType type);
+std::ostream& operator<<(std::ostream& out, const Mutation& mut);
+std::ostream& operator<<(std::ostream& out, const ScoredMutation& smut);
+
+std::string ApplyMutations(const std::string& tpl, std::vector<Mutation>* muts);
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/consensus/Polish.h b/include/pacbio/consensus/Polish.h
new file mode 100644
index 0000000..5eedc1a
--- /dev/null
+++ b/include/pacbio/consensus/Polish.h
@@ -0,0 +1,76 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <tuple>
+#include <vector>
+
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/consensus/PolishResult.h>
+
+namespace PacBio {
+namespace Consensus {
+
+// forward declaration
+class AbstractIntegrator;
+
+struct PolishConfig
+{
+ size_t MaximumIterations;
+ size_t MutationSeparation;
+ size_t MutationNeighborhood;
+
+ PolishConfig(size_t iterations = 40, size_t separation = 10, size_t neighborhood = 20);
+};
+
+PolishResult Polish(AbstractIntegrator* ai, const PolishConfig& cfg);
+
+struct QualityValues
+{
+ std::vector<int> Qualities;
+ std::vector<int> DeletionQVs;
+ std::vector<int> InsertionQVs;
+ std::vector<int> SubstitutionQVs;
+};
+
+std::vector<int> ConsensusQualities(AbstractIntegrator& ai);
+
+QualityValues ConsensusQVs(AbstractIntegrator& ai);
+
+std::vector<Mutation> Mutations(const AbstractIntegrator& ai);
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/consensus/PolishResult.h b/include/pacbio/consensus/PolishResult.h
new file mode 100644
index 0000000..8e44f1a
--- /dev/null
+++ b/include/pacbio/consensus/PolishResult.h
@@ -0,0 +1,64 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <vector>
+
+namespace PacBio {
+namespace Consensus {
+
+/// This struct contains the results of AbstractIntegrator::Polish()
+struct PolishResult
+{
+ // Did Polish() converge?
+ bool hasConverged = false;
+ // How many mutations have been tested?
+ size_t mutationsTested = 0;
+ // How many mutations have been actually applied?
+ size_t mutationsApplied = 0;
+
+ // For each iteration in Polish(), get the max of all Evaluators to
+ // diagnose the worst performing one.
+ //
+ // Maximal ratio of populated alpha cells
+ std::vector<float> maxAlphaPopulated;
+ // Maximal ratio of populated beta cells
+ std::vector<float> maxBetaPopulated;
+ // Maximal number of flip flop events
+ std::vector<int> maxNumFlipFlops;
+};
+}
+} // ::PacBio::Consensus
\ No newline at end of file
diff --git a/include/pacbio/consensus/Template.h b/include/pacbio/consensus/Template.h
new file mode 100644
index 0000000..f4b0b8c
--- /dev/null
+++ b/include/pacbio/consensus/Template.h
@@ -0,0 +1,195 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <cstdint>
+#include <iostream>
+#include <memory>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include <boost/optional.hpp>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/exception/StateError.h>
+
+namespace PacBio {
+namespace Consensus {
+
+// fwd decl
+class AbstractRecursor;
+class ScaledMatrix;
+
+class AbstractTemplate
+{
+public:
+ virtual ~AbstractTemplate();
+
+ virtual size_t Length() const = 0;
+ virtual const TemplatePosition& operator[](size_t i) const = 0;
+
+ operator std::string() const;
+
+ // virtual mutations (for mutation testing purposes)
+ virtual bool IsMutated() const = 0;
+ virtual boost::optional<Mutation> Mutate(const Mutation& m) = 0;
+ virtual void Reset() = 0;
+
+ // actually apply mutations
+ virtual bool ApplyMutation(const Mutation& mut);
+ virtual bool ApplyMutations(std::vector<Mutation>* muts);
+
+ // access model configuration
+ virtual std::unique_ptr<AbstractRecursor> CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const PacBio::Data::MappedRead& mr,
+ double scoreDiff) const = 0;
+
+ virtual double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const = 0;
+
+ std::pair<double, double> NormalParameters() const;
+
+ // a sad but necessary release valve for MonoMolecularIntegrator Length()
+ size_t TrueLength() const;
+
+protected:
+ AbstractTemplate(size_t start, size_t end, bool pinStart, bool pinEnd);
+
+ bool InRange(size_t start, size_t end) const;
+
+ size_t start_;
+ size_t end_;
+ bool pinStart_;
+ bool pinEnd_;
+
+private:
+ std::pair<double, double> SiteNormalParameters(size_t i) const;
+};
+
+std::ostream& operator<<(std::ostream&, const AbstractTemplate&);
+
+class Template : public AbstractTemplate
+{
+public:
+ Template(const std::string& tpl, std::unique_ptr<ModelConfig>&& cfg);
+ Template(const std::string& tpl, std::unique_ptr<ModelConfig>&& cfg, size_t start, size_t end,
+ bool pinStart, bool pinEnd);
+
+ size_t Length() const override;
+ const TemplatePosition& operator[](size_t i) const override;
+
+ bool IsMutated() const override;
+ boost::optional<Mutation> Mutate(const Mutation& mut) override;
+ void Reset() override;
+
+ bool ApplyMutation(const Mutation& mut) override;
+
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const PacBio::Data::MappedRead& mr,
+ double scoreDiff) const override;
+
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const override;
+
+private:
+ std::unique_ptr<ModelConfig> cfg_;
+ std::vector<TemplatePosition> tpl_;
+ bool mutated_;
+ size_t mutStart_;
+ size_t mutEnd_;
+ int mutOff_;
+ TemplatePosition mutTpl_[2];
+
+ friend class VirtualTemplate;
+};
+
+class VirtualTemplate : public AbstractTemplate
+{
+public:
+ VirtualTemplate(const Template& master, size_t start, size_t end, bool pinStart, bool pinEnd);
+
+ size_t Length() const override;
+ const TemplatePosition& operator[](size_t i) const override;
+
+ bool IsMutated() const override;
+ boost::optional<Mutation> Mutate(const Mutation&) override;
+ void Reset() override {}
+ bool ApplyMutation(const Mutation& mut) override;
+
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const PacBio::Data::MappedRead& mr,
+ double scoreDiff) const override;
+
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const override;
+
+private:
+ Template const& master_;
+};
+
+// this needs to be here because the unique_ptr deleter for AbstractRecursor must know its size
+class AbstractRecursor
+{
+protected:
+ typedef ScaledMatrix M;
+
+public:
+ AbstractRecursor(std::unique_ptr<AbstractTemplate>&& tpl, const PacBio::Data::MappedRead& mr,
+ double scoreDiff);
+ virtual ~AbstractRecursor() {}
+ virtual size_t FillAlphaBeta(M& alpha, M& beta) const = 0;
+ virtual void FillAlpha(const M& guide, M& alpha) const = 0;
+ virtual void FillBeta(const M& guide, M& beta) const = 0;
+ virtual double LinkAlphaBeta(const M& alpha, size_t alphaColumn, const M& beta,
+ size_t betaColumn, size_t absoluteColumn) const = 0;
+ virtual void ExtendAlpha(const M& alpha, size_t beginColumn, M& ext,
+ size_t numExtColumns = 2) const = 0;
+ virtual void ExtendBeta(const M& beta, size_t endColumn, M& ext, int lengthDiff = 0) const = 0;
+ virtual double UndoCounterWeights(size_t nEmissions) const = 0;
+
+public:
+ std::unique_ptr<AbstractTemplate> tpl_;
+ PacBio::Data::MappedRead read_;
+
+protected:
+ double scoreDiff_; // reciprocal of "natural scale"
+};
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/include/pacbio/data/ChemistryMapping.h b/include/pacbio/data/ChemistryMapping.h
new file mode 100644
index 0000000..2635555
--- /dev/null
+++ b/include/pacbio/data/ChemistryMapping.h
@@ -0,0 +1,72 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <map>
+#include <string>
+
+#include <pacbio/data/ChemistryTriple.h>
+
+namespace PacBio {
+namespace Data {
+
+class ChemistryMapping
+{
+public:
+ ChemistryMapping(const std::string& mappingXML);
+
+ std::string MapTriple(const ChemistryTriple& triple, const std::string& fallback = "") const;
+
+private:
+ struct ChemistryComparer
+ {
+ bool operator()(const ChemistryTriple& a, const ChemistryTriple& b) const
+ {
+ if (a.BindingKit < b.BindingKit or a.SequencingKit < b.SequencingKit or
+ a.MajorVersion < b.MajorVersion or a.MinorVersion < b.MinorVersion) {
+ return true;
+ }
+ return false;
+ }
+ };
+
+ std::map<ChemistryTriple, std::string, ChemistryComparer> mapping;
+};
+
+} // namespace Data
+} // namespace PacBio
diff --git a/include/pacbio/data/ChemistryTriple.h b/include/pacbio/data/ChemistryTriple.h
new file mode 100644
index 0000000..ee32a1b
--- /dev/null
+++ b/include/pacbio/data/ChemistryTriple.h
@@ -0,0 +1,78 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <string>
+
+namespace PacBio {
+namespace Data {
+
+class ChemistryTriple
+{
+public:
+ unsigned BindingKit;
+ unsigned SequencingKit;
+ unsigned MajorVersion;
+ unsigned MinorVersion;
+
+ ChemistryTriple() : BindingKit{0}, SequencingKit{0}, MajorVersion{0}, MinorVersion{0} {}
+
+ ChemistryTriple(const std::string& bindingKit, const std::string& sequencingKit,
+ const std::string& changeListID);
+
+ static ChemistryTriple Null() { return ChemistryTriple(); }
+
+ bool IsNull() const
+ {
+ return BindingKit == 0 and SequencingKit == 0 and MajorVersion == 0 and MinorVersion == 0;
+ }
+
+ void SetNull()
+ {
+ BindingKit = 0;
+ SequencingKit = 0;
+ MajorVersion = 0;
+ MinorVersion = 0;
+ }
+
+ bool SetValues(const std::string& bindingKit, const std::string& sequencingKit,
+ const std::string& changeListID);
+};
+
+} // namespace Data
+} // namespace PacBio
diff --git a/include/pacbio/data/Interval.h b/include/pacbio/data/Interval.h
new file mode 100644
index 0000000..742895f
--- /dev/null
+++ b/include/pacbio/data/Interval.h
@@ -0,0 +1,174 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <algorithm>
+#include <cassert>
+#include <functional>
+#include <iosfwd>
+#include <stdexcept>
+#include <string>
+#include <tuple>
+#include <vector>
+
+#include <boost/algorithm/string.hpp>
+#include <boost/lexical_cast.hpp>
+
+namespace PacBio {
+namespace Data {
+
+class Interval
+{
+public:
+ inline Interval() : left{0}, right{0} { Validate(); }
+ inline Interval(const size_t l, const size_t r) : left{l}, right{r} { Validate(); }
+ inline void Reset(const size_t l, const size_t r)
+ {
+ left = l;
+ right = r;
+ Validate();
+ }
+
+ inline void Reset(const Interval& other)
+ {
+ left = other.Left();
+ right = other.Right();
+ Validate();
+ }
+
+ inline size_t Length() const { return right - left; }
+
+ inline size_t Left() const { return left; }
+ inline size_t Right() const { return right; }
+
+ // this also handles adjacency
+ inline bool Overlaps(const Interval& other) const
+ {
+ // if the left of one is in the range of the other
+ return (other.Left() <= left && left <= other.Right()) ||
+ (left <= other.Left() && other.Left() <= right);
+ }
+
+ inline bool Contains(const size_t value) const { return (left <= value) && (value < right); }
+
+ inline bool Covers(const Interval& other) const { return (Intersect(other) == other); }
+
+ inline Interval Intersect(const Interval& other) const
+ {
+ if (!Overlaps(other))
+ throw std::invalid_argument("interval to intersect does not overlap!");
+
+ return Interval(std::max(left, other.Left()), std::min(right, other.Right()));
+ }
+
+ inline Interval Union(const Interval& other) const
+ {
+ if (!Overlaps(other)) throw std::invalid_argument("interval to merge does not overlap!");
+
+ return Interval(std::min(left, other.Left()), std::max(right, other.Right()));
+ }
+
+ inline bool operator<(const Interval& other) const
+ {
+ if (left < other.Left()) return true;
+
+ if (left == other.Left()) return right < other.Right();
+
+ return false;
+ }
+
+ inline bool operator==(const Interval& other) const
+ {
+ return (left == other.Left() && right == other.Right());
+ }
+
+ inline bool operator!=(const Interval& other) const { return !(*this == other); }
+
+ inline Interval& operator++()
+ {
+ ++left;
+ return *this;
+ }
+
+ inline Interval operator++(int) { return Interval(left++, right); }
+
+ inline size_t operator*() const { return left; }
+
+ inline Interval begin() const { return Interval(left, right); }
+
+ inline Interval end() const { return Interval(right, right); }
+
+ inline operator std::tuple<size_t, size_t>() const { return std::make_tuple(left, right); }
+
+ inline operator std::tuple<size_t&, size_t&>()
+ {
+ return std::make_tuple(std::ref(left), std::ref(right));
+ }
+
+ operator std::string() const;
+
+ friend std::ostream& operator<<(std::ostream& os, const Interval& interval);
+
+ static Interval FromString(const std::string& str)
+ {
+ try {
+ std::vector<std::string> components;
+ boost::split(components, str, boost::is_any_of("-"));
+ if (components.size() == 1) {
+ size_t left = boost::lexical_cast<size_t>(components[0]);
+ return Interval(left, left + 1);
+ } else if (components.size() == 2) {
+ size_t left = boost::lexical_cast<size_t>(components[0]);
+ size_t right = boost::lexical_cast<size_t>(components[1]);
+ // if right < left, we have an invalid interval, fall through
+ if (left <= right) return Interval(left, right + 1);
+ }
+ } catch (...) {
+ }
+ throw std::invalid_argument("invalid Interval specification");
+ }
+
+private:
+ size_t left;
+ size_t right;
+
+ inline void Validate() const { assert(left <= right); }
+};
+
+} // namespace Data
+} // namespace PacBio
diff --git a/include/pacbio/data/IntervalTree.h b/include/pacbio/data/IntervalTree.h
new file mode 100644
index 0000000..81b0c6a
--- /dev/null
+++ b/include/pacbio/data/IntervalTree.h
@@ -0,0 +1,168 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <algorithm>
+#include <set>
+#include <string>
+#include <vector>
+
+#include <boost/algorithm/string.hpp>
+
+#include <pacbio/data/Interval.h>
+
+namespace PacBio {
+namespace Data {
+
+class IntervalTree
+{
+private:
+ struct WeakIntervalOrdering
+ {
+ bool operator()(const Interval& lhs, const Interval& rhs) const
+ {
+ return lhs.Left() < rhs.Left();
+ }
+ };
+
+ typedef std::multiset<Interval, WeakIntervalOrdering> StorageType;
+
+public:
+ typedef StorageType::iterator iterator;
+ typedef StorageType::const_iterator const_iterator;
+
+ inline void Insert(const Interval& interval)
+ {
+ auto it = storage.insert(interval);
+
+ // check to see if we overlap the previous element,
+ // if we do, start our merge loop from there
+ if (it != begin()) {
+ const_iterator prev = std::prev(it);
+
+ if (prev->Overlaps(*it)) it = prev;
+ }
+
+ while (it != end()) {
+ const_iterator nx = std::next(it);
+
+ if (nx != end() && it->Overlaps(*nx)) {
+ const Interval u = it->Union(*nx);
+ it = storage.erase(it);
+ it = storage.erase(it);
+ it = storage.insert(it, u);
+ } else
+ break;
+ }
+ }
+
+ inline IntervalTree Gaps() const
+ {
+ IntervalTree gaps;
+
+ for (auto it = begin(); it != end(); ++it) {
+ const_iterator nx = std::next(it);
+
+ if (nx == end()) break;
+
+ gaps.Insert(Interval(it->Right(), nx->Left()));
+ }
+
+ return gaps;
+ }
+
+ inline IntervalTree Gaps(const Interval& interval) const
+ {
+ auto left = begin();
+ auto right = end();
+
+ // if we're empty (left == right == end()) or we don't overlap the interval
+ // return just the provided interval
+ if (left == right || !interval.Overlaps(Interval(left->Left(), (--right)->Right()))) {
+ IntervalTree gaps;
+ gaps.Insert(interval);
+ return gaps;
+ }
+
+ IntervalTree gaps = Gaps();
+
+ if (interval.Left() < left->Left()) gaps.Insert(Interval(interval.Left(), left->Left()));
+
+ if (right->Right() < interval.Right())
+ gaps.Insert(Interval(right->Right(), interval.Right()));
+
+ return gaps;
+ }
+
+ inline bool Contains(const size_t value) const
+ {
+ const_iterator it = std::lower_bound(begin(), end(), Interval(value, value + 1));
+
+ if (it != begin()) it = std::prev(it);
+
+ for (; it != end() && it->Left() <= value; ++it) {
+ if (it->Contains(value)) return true;
+ }
+
+ return false;
+ }
+
+ inline iterator begin() { return storage.begin(); }
+ inline const_iterator begin() const { return storage.begin(); }
+ inline iterator end() { return storage.end(); }
+ inline const_iterator end() const { return storage.end(); }
+
+ inline size_t size() const { return storage.size(); }
+
+ static IntervalTree FromString(const std::string& str)
+ {
+ std::vector<std::string> components;
+ boost::split(components, str, boost::is_any_of(","));
+ IntervalTree tree;
+ for (const auto& component : components) {
+ tree.Insert(Interval::FromString(component));
+ }
+ return tree;
+ }
+
+private:
+ StorageType storage;
+};
+
+} // namespace Data
+} // namespace PacBio
diff --git a/include/pacbio/data/Read.h b/include/pacbio/data/Read.h
new file mode 100644
index 0000000..7cc5b70
--- /dev/null
+++ b/include/pacbio/data/Read.h
@@ -0,0 +1,112 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <algorithm>
+#include <cstdint>
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include <pacbio/data/StrandType.h>
+
+namespace PacBio {
+namespace Data {
+
+struct SNR
+{
+ double A;
+ double C;
+ double G;
+ double T;
+
+ SNR(double a, double c, double g, double t);
+ SNR(const std::vector<double>& snrs);
+
+ inline double operator[](const size_t i) const
+ {
+ if (i == 0) return A;
+ if (i == 1) return C;
+ if (i == 2) return G;
+ if (i == 3) return T;
+ throw std::invalid_argument("SNR out of bounds!");
+ }
+
+ inline bool operator==(const SNR& other) const
+ {
+ return other.A == A && other.C == C && other.G == G && other.T == T;
+ }
+
+ inline bool operator!=(const SNR& other) const { return !(*this == other); }
+};
+
+SNR ClampSNR(const SNR& val, const SNR& min, const SNR& max);
+
+struct Read
+{
+ Read(const std::string& name, const std::string& seq, const std::vector<uint8_t>& ipd,
+ const std::vector<uint8_t>& pw, const SNR& snr, const std::string& model);
+ Read(const Read& read) = default;
+ Read(Read&& read) = default;
+
+ std::string Name;
+ std::string Seq;
+ std::vector<uint8_t> IPD;
+ std::vector<uint8_t> PulseWidth;
+ SNR SignalToNoise;
+ std::string Model;
+
+ inline size_t Length() const { return Seq.length(); }
+};
+
+struct MappedRead : public Read
+{
+ MappedRead(const Read& read, StrandType strand, size_t templateStart, size_t templateEnd,
+ bool pinStart = false, bool pinEnd = false);
+ MappedRead(const MappedRead& read) = default;
+ MappedRead(MappedRead&& read) = default;
+
+ StrandType Strand;
+ size_t TemplateStart;
+ size_t TemplateEnd;
+ bool PinStart;
+ bool PinEnd;
+};
+
+std::ostream& operator<<(std::ostream&, const MappedRead&);
+
+} // namespace Data
+} // namespace PacBio
diff --git a/include/pacbio/data/ReadId.h b/include/pacbio/data/ReadId.h
new file mode 100644
index 0000000..c2703a5
--- /dev/null
+++ b/include/pacbio/data/ReadId.h
@@ -0,0 +1,73 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <iostream>
+#include <memory>
+#include <string>
+
+#include <boost/optional.hpp>
+
+#include <pacbio/data/Interval.h>
+
+namespace PacBio {
+namespace Data {
+
+struct ReadId
+{
+ std::shared_ptr<std::string> MovieName;
+ size_t HoleNumber;
+ boost::optional<Interval> ZmwInterval;
+
+ ReadId(const std::shared_ptr<std::string>& movieName, size_t holeNumber)
+ : MovieName(movieName), HoleNumber{holeNumber}, ZmwInterval{boost::none}
+ {
+ }
+
+ ReadId(const std::shared_ptr<std::string>& movieName, size_t holeNumber,
+ const Interval& interval)
+ : MovieName(movieName), HoleNumber{holeNumber}, ZmwInterval(interval)
+ {
+ }
+
+ operator std::string() const;
+ friend std::ostream& operator<<(std::ostream&, const ReadId&);
+};
+
+} // namespace Data
+} // namespace PacBio
diff --git a/include/pacbio/data/Sequence.h b/include/pacbio/data/Sequence.h
new file mode 100644
index 0000000..c80f987
--- /dev/null
+++ b/include/pacbio/data/Sequence.h
@@ -0,0 +1,49 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <string>
+
+namespace PacBio {
+namespace Data {
+
+char Complement(char base);
+std::string Complement(const std::string& input);
+std::string Reverse(const std::string& input);
+std::string ReverseComplement(const std::string& input);
+
+} // namespace Data
+} // namespace PacBio
diff --git a/include/pacbio/data/State.h b/include/pacbio/data/State.h
new file mode 100644
index 0000000..3919bf4
--- /dev/null
+++ b/include/pacbio/data/State.h
@@ -0,0 +1,63 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <iostream>
+
+namespace PacBio {
+namespace Data {
+
+enum struct State : uint8_t
+{
+ VALID = 0,
+ ALPHA_BETA_MISMATCH,
+ POOR_ZSCORE,
+ TEMPLATE_TOO_SMALL,
+ MANUALLY_RELEASED,
+
+ SIZE
+};
+
+static const char* StateName[] = {"VALID", "ALPHA/BETA MISMATCH", "POOR Z-SCORE",
+ "TEMPLATE TOO SMALL", "MANUALLY RELEASED"};
+
+inline std::ostream& operator<<(std::ostream& os, State result)
+{
+ os << PacBio::Data::StateName[static_cast<size_t>(result)];
+ return os;
+}
+}
+} //::PacBio::Data
\ No newline at end of file
diff --git a/include/pacbio/data/StrandType.h b/include/pacbio/data/StrandType.h
new file mode 100644
index 0000000..dd9ff7d
--- /dev/null
+++ b/include/pacbio/data/StrandType.h
@@ -0,0 +1,48 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+namespace PacBio {
+namespace Data {
+
+enum struct StrandType : uint8_t
+{
+ FORWARD,
+ REVERSE,
+ UNMAPPED
+};
+}
+} //::PacBio::Data
\ No newline at end of file
diff --git a/include/pacbio/data/SubreadResultCounter.h b/include/pacbio/data/SubreadResultCounter.h
new file mode 100644
index 0000000..6b8f8f7
--- /dev/null
+++ b/include/pacbio/data/SubreadResultCounter.h
@@ -0,0 +1,74 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <stdlib.h>
+#include <iostream>
+#include <vector>
+
+#include <pacbio/data/State.h>
+
+namespace PacBio {
+namespace Data {
+
+// A class to store and report on the results of what happens to subreads.
+class SubreadResultCounter
+{
+public:
+ int32_t Success;
+ int32_t AlphaBetaMismatch;
+ int32_t BelowMinQual;
+ int32_t FilteredBySize;
+ int32_t ZMWBelowMinSNR;
+ int32_t ZMWNotEnoughSubReads;
+ int32_t PoorZScore;
+ int32_t Other;
+
+ SubreadResultCounter();
+ std::vector<int32_t> ReturnCountsAsArray() const;
+ void AddResult(PacBio::Data::State);
+ /* Certain conditions may make reads that were on their
+ way to success go to the garbage bin, in this case we reassign
+ all the success reads to the other category */
+ void AssignSuccessToOther();
+ void CombineWithOtherResult(const SubreadResultCounter& other);
+ SubreadResultCounter& operator+=(const SubreadResultCounter& other);
+ void WriteResultsReport(std::ostream& report) const;
+ int32_t Total() const;
+};
+
+} // namespace Data
+} // namespace PacBio
diff --git a/include/pacbio/denovo/PoaConsensus.h b/include/pacbio/denovo/PoaConsensus.h
new file mode 100644
index 0000000..e719262
--- /dev/null
+++ b/include/pacbio/denovo/PoaConsensus.h
@@ -0,0 +1,100 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#pragma once
+
+#include <boost/utility.hpp>
+#include <climits>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include <pacbio/align/AlignConfig.h>
+#include <pacbio/denovo/PoaGraph.h>
+
+namespace PacBio {
+namespace Poa {
+
+class PoaGraph;
+class PoaGraphPath;
+class ScoredMutation;
+
+PacBio::Align::AlignConfig DefaultPoaConfig(
+ PacBio::Align::AlignMode mode = PacBio::Align::AlignMode::GLOBAL);
+
+/// \brief A multi-sequence consensus obtained from a partial-order alignment
+struct PoaConsensus : private boost::noncopyable
+{
+ const std::string Sequence;
+ PoaGraph Graph;
+ std::vector<PoaGraph::Vertex> Path;
+
+ PoaConsensus(const std::string& css, const PoaGraph& g,
+ const std::vector<PoaGraph::Vertex>& ConsensusPath);
+
+ // NB: this constructor exists to provide a means to avoid an unnecessary
+ // copy of the
+ // boost graph. If we had move semantics (C++11) we would be able to get by
+ // without
+ // this.
+ PoaConsensus(const std::string& css, const detail::PoaGraphImpl& g,
+ const std::vector<PoaGraph::Vertex>& ConsensusPath);
+
+ ~PoaConsensus();
+
+ static const PoaConsensus* FindConsensus(const std::vector<std::string>& reads);
+
+ static const PoaConsensus* FindConsensus(const std::vector<std::string>& reads,
+ const PacBio::Align::AlignConfig& config,
+ int minCoverage = -INT_MAX);
+
+ static const PoaConsensus* FindConsensus(const std::vector<std::string>& reads,
+ PacBio::Align::AlignMode mode,
+ int minCoverage = -INT_MAX);
+
+public:
+ // Additional accessors, which do things on the graph/graphImpl
+ // LikelyVariants
+
+public:
+ std::string ToGraphViz(int flags = 0) const;
+
+ void WriteGraphVizFile(std::string filename, int flags = 0) const;
+};
+
+} // namespace Poa
+} // namespace PacBio
diff --git a/include/pacbio/denovo/PoaGraph.h b/include/pacbio/denovo/PoaGraph.h
new file mode 100644
index 0000000..36a3751
--- /dev/null
+++ b/include/pacbio/denovo/PoaGraph.h
@@ -0,0 +1,127 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#pragma once
+
+#include <climits>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include <pacbio/align/AlignConfig.h>
+
+namespace PacBio {
+namespace Poa {
+
+// fwd decls
+namespace detail {
+
+class PoaGraphImpl;
+class SdpRangeFinder;
+
+} // namespace detail
+
+struct PoaConsensus;
+
+class PoaAlignmentMatrix
+{
+public:
+ virtual ~PoaAlignmentMatrix(){};
+ virtual float Score() const = 0;
+ virtual size_t NumRows() const = 0;
+ virtual size_t NumCols() const = 0;
+ virtual void Print() const = 0;
+};
+
+/// \brief An object representing a Poa (partial-order alignment) graph
+class PoaGraph
+{
+public:
+ typedef size_t Vertex;
+ typedef size_t ReadId;
+
+ static const Vertex NullVertex = (Vertex)-1;
+
+public: // Flags enums for specifying GraphViz output features
+ enum
+ {
+ COLOR_NODES = 0x1,
+ VERBOSE_NODES = 0x2
+ };
+
+public:
+ PoaGraph();
+ PoaGraph(const PoaGraph& other);
+ PoaGraph(const detail::PoaGraphImpl& o); // NB: this performs a copy
+ ~PoaGraph();
+
+ //
+ // Easy API
+ //
+ void AddRead(const std::string& sequence, const PacBio::Align::AlignConfig& config,
+ detail::SdpRangeFinder* rangeFinder = NULL,
+ std::vector<Vertex>* readPathOutput = NULL);
+
+ //
+ // API for more control
+ //
+ void AddFirstRead(const std::string& sequence, std::vector<Vertex>* readPathOutput = NULL);
+
+ PoaAlignmentMatrix* TryAddRead(const std::string& sequence,
+ const PacBio::Align::AlignConfig& config,
+ detail::SdpRangeFinder* rangeFinder = NULL) const;
+
+ void CommitAdd(PoaAlignmentMatrix* mat, std::vector<Vertex>* readPathOutput = NULL);
+
+ // ----------
+
+ size_t NumReads() const;
+
+ std::string ToGraphViz(int flags = 0, const PoaConsensus* pc = NULL) const;
+
+ void WriteGraphVizFile(const std::string& filename, int flags = 0,
+ const PoaConsensus* pc = NULL) const;
+
+ const PoaConsensus* FindConsensus(const PacBio::Align::AlignConfig& config,
+ int minCoverage = -INT_MAX) const;
+
+private:
+ detail::PoaGraphImpl* impl;
+};
+
+} // namespace Poa
+} // namespace PacBio
diff --git a/include/pacbio/denovo/RangeFinder.h b/include/pacbio/denovo/RangeFinder.h
new file mode 100644
index 0000000..121de5f
--- /dev/null
+++ b/include/pacbio/denovo/RangeFinder.h
@@ -0,0 +1,93 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <cstddef>
+#include <map>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include <pacbio/denovo/PoaGraph.h>
+
+namespace PacBio {
+namespace Poa {
+namespace detail {
+
+// an Anchor represents a point (cssPos, readPos)
+typedef std::pair<size_t, size_t> SdpAnchor;
+typedef std::vector<SdpAnchor> SdpAnchorVector;
+
+class PoaGraphImpl;
+
+// using PacBio::Consensus::PoaGraph;
+
+//
+// SdpRangeFinder objects are responsible for identifying the range
+// of read positions that we should seek to align to a POA vertex;
+// this implementation uses SDP to identify fairly narrow bands,
+// enabling sparse memory usage.
+//
+// This is an abstract class that will be inherited in a client
+// library that has access to an SDP method.
+//
+// RangeFinder state goes away on next call to InitRangeFinder. We could
+// have dealt with this using a factory pattern but bleh.
+//
+class SdpRangeFinder
+{
+private:
+ std::map<PoaGraph::Vertex, std::pair<int, int>> alignableReadIntervalByVertex_;
+
+public:
+ virtual ~SdpRangeFinder();
+
+ void InitRangeFinder(const PoaGraphImpl& poaGraph,
+ const std::vector<PoaGraph::Vertex>& consensusPath,
+ const std::string& consensusSequence, const std::string& readSequence);
+
+ // TODO: write contract
+ std::pair<int, int> FindAlignableRange(PoaGraph::Vertex v);
+
+protected:
+ // TODO: write contract
+ virtual SdpAnchorVector FindAnchors(const std::string& consensusSequence,
+ const std::string& readSequence) const = 0;
+};
+
+} // namespace detail
+} // namespace Poa
+} // namespace PacBio
diff --git a/include/pacbio/denovo/SparsePoa.h b/include/pacbio/denovo/SparsePoa.h
new file mode 100644
index 0000000..3ade174
--- /dev/null
+++ b/include/pacbio/denovo/SparsePoa.h
@@ -0,0 +1,162 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander, Lance Hepler
+
+#pragma once
+
+#include <memory>
+#include <string>
+#include <vector>
+
+#include <pacbio/denovo/RangeFinder.h>
+
+#include <pacbio/data/Interval.h>
+
+namespace PacBio {
+
+// fwd decls
+namespace Consensus {
+class ScoredMutation;
+} // namespace Consensus
+
+namespace Poa {
+// fwd decls
+class PoaGraph;
+
+using Interval = PacBio::Data::Interval;
+using PoaGraph = PacBio::Poa::PoaGraph;
+
+class SdpRangeFinder : public PacBio::Poa::detail::SdpRangeFinder
+{
+protected:
+ virtual PacBio::Poa::detail::SdpAnchorVector FindAnchors(
+ const std::string& consensusSequence, const std::string& readSequence) const final;
+};
+
+//
+// Details of how a read aligns to the POA graph
+//
+struct PoaAlignmentSummary
+{
+ bool ReverseComplementedRead;
+ Interval ExtentOnRead;
+ Interval ExtentOnConsensus;
+ float AlignmentScore;
+ float AlignmentIdentity;
+
+ PoaAlignmentSummary()
+ : ReverseComplementedRead{false}
+ , ExtentOnRead(0, 0)
+ , ExtentOnConsensus(0, 0)
+ , AlignmentScore{0}
+ , AlignmentIdentity{0}
+ {
+ }
+};
+
+struct PoaAlignmentOptions
+{
+ bool ClipBegin;
+ bool ClipEnd;
+};
+
+//
+// Partial order aligner with parsimonious memory usage
+//
+class SparsePoa
+{
+public:
+ // ReadKey: Integer key representing
+ // >= 0: a read in the POA graph
+ // -1: read could not be inserted into POA graph
+ using ReadKey = int;
+
+public:
+ SparsePoa();
+ ~SparsePoa();
+
+ //
+ // Add read, which must already have been oriented to be in the
+ // "forward" convention
+ //
+ ReadKey AddRead(const std::string& readSequence,
+ const PoaAlignmentOptions& alnOptions = PoaAlignmentOptions(),
+ float minScoreToAdd = 0);
+
+ //
+ // Find better orientation, (fwd or RC) and add as such
+ //
+ ReadKey OrientAndAddRead(const std::string& readSequence,
+ const PoaAlignmentOptions& alnOptions = PoaAlignmentOptions(),
+ float minScoreToAdd = 0);
+
+ //
+ // Walk the POA and get the optimal consensus path
+ //
+ std::shared_ptr<const PacBio::Poa::PoaConsensus> FindConsensus(
+ int minCoverage, std::vector<PoaAlignmentSummary>* summaries = NULL) const;
+
+ //
+ // Serialize the POA graph to std::string
+ //
+ std::string ToGraphViz(int flags = 0, const PacBio::Poa::PoaConsensus* pc = nullptr) const;
+
+ //
+ // Serialize the POA graph to a file
+ //
+ void WriteGraphVizFile(const std::string& filename, int flags = 0,
+ const PacBio::Poa::PoaConsensus* pc = nullptr) const;
+
+ //
+ // Clean up the POA graph, pruning minority paths, to speed up
+ // successive AddRead operations.
+ //
+ void PruneGraph(float minCoverageFraction);
+
+private:
+ void repCheck();
+
+private:
+ using Path = std::vector<PoaGraph::Vertex>;
+
+ PoaGraph* graph_;
+ std::vector<Path> readPaths_;
+ std::vector<bool> reverseComplemented_;
+ SdpRangeFinder* rangeFinder_;
+};
+
+} // namespace Poa
+} // namespace PacBio
diff --git a/include/pacbio/exception/CCSExceptions.h b/include/pacbio/exception/CCSExceptions.h
new file mode 100644
index 0000000..c62ff86
--- /dev/null
+++ b/include/pacbio/exception/CCSExceptions.h
@@ -0,0 +1,59 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <cstddef>
+#include <stdexcept>
+
+namespace PacBio {
+namespace Exception {
+
+class BadMappingXMLException : public std::runtime_error
+{
+public:
+ BadMappingXMLException(const std::string& msg) : std::runtime_error(msg) {}
+};
+
+class BadChemistryTriple : public std::runtime_error
+{
+public:
+ BadChemistryTriple(const std::string& msg) : std::runtime_error(msg) {}
+};
+
+} // namespace Exception
+} // namespace PacBio
diff --git a/include/pacbio/exception/ModelError.h b/include/pacbio/exception/ModelError.h
new file mode 100644
index 0000000..7ed8d37
--- /dev/null
+++ b/include/pacbio/exception/ModelError.h
@@ -0,0 +1,72 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <stdexcept>
+#include <string>
+
+namespace PacBio {
+namespace Exception {
+
+class ModelError : public std::runtime_error
+{
+public:
+ ModelError(const std::string& msg) : std::runtime_error(msg) {}
+};
+
+class ChemistryNotFound : public ModelError
+{
+public:
+ ChemistryNotFound(const std::string& name)
+ : ModelError(std::string("chemistry not found: '") + name + "'")
+ {
+ }
+};
+
+class DuplicateModel : public ModelError
+{
+public:
+ DuplicateModel(const std::string& name) : ModelError("duplicate model: '" + name + "'") {}
+};
+
+class MalformedModelFile : public ModelError
+{
+public:
+ MalformedModelFile() : ModelError("malformed model!") {}
+};
+
+} // namespace Exception
+} // namespace PacBio
diff --git a/include/pacbio/exception/StateError.h b/include/pacbio/exception/StateError.h
new file mode 100644
index 0000000..97057cf
--- /dev/null
+++ b/include/pacbio/exception/StateError.h
@@ -0,0 +1,78 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <stdexcept>
+#include <string>
+
+#include <pacbio/data/State.h>
+
+namespace PacBio {
+namespace Exception {
+
+class StateError : public std::runtime_error
+{
+public:
+ StateError(PacBio::Data::State state, const std::string& msg)
+ : std::runtime_error(msg), state_(state)
+ {
+ }
+
+ PacBio::Data::State WhatState() const { return state_; }
+ virtual const char* what() const noexcept override { return std::runtime_error::what(); }
+private:
+ PacBio::Data::State state_;
+};
+
+class TemplateTooSmall : public StateError
+{
+public:
+ TemplateTooSmall() : StateError(PacBio::Data::State::TEMPLATE_TOO_SMALL, "Template too short!")
+ {
+ }
+};
+
+class AlphaBetaMismatch : public StateError
+{
+public:
+ AlphaBetaMismatch()
+ : StateError(PacBio::Data::State::ALPHA_BETA_MISMATCH, "Alpha/beta mismatch!")
+ {
+ }
+};
+
+} // namespace Exception
+} // namespace PacBio
diff --git a/include/pacbio/io/Utility.h b/include/pacbio/io/Utility.h
new file mode 100644
index 0000000..3f86739
--- /dev/null
+++ b/include/pacbio/io/Utility.h
@@ -0,0 +1,73 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <memory>
+#include <string>
+#include <vector>
+
+#include <pbbam/DataSet.h>
+
+namespace PacBio {
+namespace IO {
+
+std::string AbsolutePath(const std::string& path);
+
+bool FileExists(const std::string& path);
+
+std::string FileExtension(const std::string& path);
+
+struct SnrInfo
+{
+ const float A;
+ const float C;
+ const float G;
+ const float T;
+
+ SnrInfo(float a, float c, float g, float t) : A(a), C(c), G(g), T(t) {}
+ // comes in TGAC from the instrument, usually
+ SnrInfo(float* snr) : SnrInfo(snr[2], snr[3], snr[1], snr[0]) {}
+ float Min() const { return std::min(std::min(A, C), std::min(G, T)); }
+};
+
+std::vector<std::string> FlattenFofn(const std::vector<std::string>& files);
+
+bool ValidBaseFeatures(const PacBio::BAM::DataSet& ds);
+
+} // namespace IO
+} // namespace PacBio
diff --git a/include/pacbio/log/Logging.h b/include/pacbio/log/Logging.h
new file mode 100644
index 0000000..b55a1b7
--- /dev/null
+++ b/include/pacbio/log/Logging.h
@@ -0,0 +1,406 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <chrono>
+#include <condition_variable>
+#include <csignal>
+#include <cstdlib>
+#include <ctime>
+#include <exception>
+#include <functional>
+#include <iomanip>
+#include <iostream>
+#include <map>
+#include <memory>
+#include <mutex>
+#include <queue>
+#include <sstream>
+#include <stdexcept>
+#include <string>
+#include <thread>
+#include <utility>
+
+namespace PacBio {
+namespace Logging {
+
+// borrowed a little from primary's SmartEnum
+class LogLevel
+{
+public:
+ LogLevel(const unsigned char value) : value_{value} {}
+ LogLevel(const std::string& value) : value_{FromString(value)} {}
+ enum : unsigned char
+ {
+ TRACE = 0,
+ DEBUG = 1,
+ INFO = 2,
+ NOTICE = 3,
+ WARN = 4,
+ ERROR = 5,
+ CRITICAL = 6,
+ FATAL = 7
+ };
+
+ operator unsigned char() const { return value_; }
+private:
+ inline static LogLevel FromString(const std::string& level)
+ {
+ if (level == "TRACE") return LogLevel::TRACE;
+ if (level == "DEBUG") return LogLevel::DEBUG;
+ if (level == "INFO") return LogLevel::INFO;
+ if (level == "NOTICE") return LogLevel::NOTICE;
+ if (level == "WARN") return LogLevel::WARN;
+ if (level == "ERROR") return LogLevel::ERROR;
+ if (level == "CRITICAL") return LogLevel::CRITICAL;
+ if (level == "FATAL") return LogLevel::FATAL;
+ throw std::invalid_argument("invalid log level");
+ }
+
+private:
+ unsigned char value_;
+};
+
+class LoggerConfig : public std::map<LogLevel, std::vector<std::reference_wrapper<std::ostream>>>
+{
+public:
+ LoggerConfig(const std::map<LogLevel, std::vector<std::reference_wrapper<std::ostream>>>& cfg)
+ : std::map<LogLevel, std::vector<std::reference_wrapper<std::ostream>>>(cfg)
+ {
+ }
+
+ LoggerConfig(
+ const std::map<std::string, std::vector<std::reference_wrapper<std::ostream>>>& cfg)
+ {
+ for (const auto& kv : cfg)
+ (*this)[kv.first] = kv.second;
+ }
+
+ LoggerConfig(std::ostream& os, const LogLevel level = LogLevel::INFO)
+ {
+ for (size_t i = static_cast<size_t>(level); i < 8; ++i)
+ (*this)[static_cast<LogLevel>(i)].push_back(os);
+ }
+
+ LoggerConfig(std::ostream& os, const std::string& level) : LoggerConfig(os, LogLevel(level)) {}
+};
+
+// necessary fwd decl
+class LogMessage;
+
+class Logger
+{
+public:
+ template <typename... Args>
+ Logger(Args&&... args)
+ : cfg_(std::forward<Args>(args)...), writer_(&Logger::MessageWriter, this)
+ {
+#ifdef NDEBUG
+ if (Handles(LogLevel::TRACE))
+ throw std::invalid_argument("one cannot simply log TRACE messages in release builds!");
+#endif
+ }
+
+ Logger(const Logger& logger) = delete;
+
+ ~Logger()
+ {
+ if (!writer_.joinable()) throw std::runtime_error("this logger is already dead!");
+
+ // place a terminal sentinel for MessageWriter to know it's done
+ {
+ std::lock_guard<std::mutex> g(m_);
+ queue_.emplace(std::unique_ptr<std::pair<LogLevel, std::ostringstream>>());
+ }
+ pushed_.notify_all();
+
+ // wait for everything to be flushed
+ {
+ std::unique_lock<std::mutex> lk(m_);
+ popped_.wait(lk, [this]() { return queue_.empty(); });
+ // endl implicitly flushes, so no need to call os_.flush() here
+ }
+
+ // join writer thread
+ writer_.join();
+ }
+
+ static inline Logger& Default(Logger* logger = nullptr)
+ {
+ static std::unique_ptr<Logger> logger_(new Logger(std::cerr));
+ if (logger) logger_.reset(logger);
+ return *logger_;
+ }
+
+private:
+ inline bool Handles(const LogLevel level) const
+ {
+ return cfg_.find(level) != cfg_.end() && !cfg_.at(level).empty();
+ }
+
+ inline Logger& operator<<(std::unique_ptr<std::pair<LogLevel, std::ostringstream>>&& ptr)
+ {
+ if (!writer_.joinable()) throw std::runtime_error("this logger is dead!");
+
+ {
+ std::lock_guard<std::mutex> g(m_);
+ queue_.emplace(
+ std::forward<std::unique_ptr<std::pair<LogLevel, std::ostringstream>>>(ptr));
+ }
+ pushed_.notify_all();
+ return *this;
+ }
+
+ void MessageWriter()
+ {
+ while (true) {
+ std::unique_ptr<std::pair<LogLevel, std::ostringstream>> ptr;
+
+ // wait on messages to arrive in the queue_, and pop them off
+ {
+ std::unique_lock<std::mutex> lk(m_);
+ pushed_.wait(lk, [&ptr, this]() {
+ if (queue_.empty()) return false;
+
+ ptr = std::move(queue_.front());
+ queue_.pop();
+
+ return true;
+ });
+ }
+
+ // if we've reached the null terminator, notify flush and stop
+ if (!ptr) {
+ popped_.notify_all();
+ break;
+ }
+
+ // otherwise, push the message onto os_
+ const LogLevel level = std::get<0>(*ptr);
+ if (cfg_.find(level) != cfg_.end())
+ for (const auto& os : cfg_.at(level))
+ os.get() << std::get<1>(*ptr).str() << std::endl;
+
+ // and notify flush we delivered a message to os_,
+ popped_.notify_all();
+ }
+ }
+
+private:
+ std::mutex m_;
+ LoggerConfig cfg_;
+ std::condition_variable popped_;
+ std::condition_variable pushed_;
+ std::queue<std::unique_ptr<std::pair<LogLevel, std::ostringstream>>> queue_;
+ std::thread writer_;
+
+ friend class LogMessage;
+};
+
+class LogMessage
+{
+public:
+ LogMessage(const char* file __attribute__((unused)),
+ const char* function __attribute__((unused)),
+ unsigned int line __attribute__((unused)), const LogLevel level, Logger& logger)
+ : logger_(logger)
+ {
+ using std::chrono::duration_cast;
+ using std::chrono::milliseconds;
+ using std::chrono::seconds;
+ using std::chrono::system_clock;
+
+ if (!logger_.Handles(level)) return;
+
+ ptr_.reset(new std::pair<LogLevel, std::ostringstream>(
+ std::piecewise_construct, std::forward_as_tuple(level), std::forward_as_tuple()));
+
+ static const char* delim = " -|- ";
+
+ // get the time, separated into seconds and milliseconds
+ const auto now = system_clock::now();
+ const auto secs = duration_cast<seconds>(now.time_since_epoch());
+ const auto time = system_clock::to_time_t(system_clock::time_point(secs));
+ const auto msec = duration_cast<milliseconds>(now.time_since_epoch() - secs).count();
+
+ // format the time and print out the log header to the ostringstream
+ // TODO(lhepler) make this std::put_time when we move to gcc-5
+ char buf[20];
+ std::strftime(buf, 20, "%Y%m%d %T.", std::gmtime(&time));
+
+ std::get<1>(*ptr_) << ">|> " << buf << std::setfill('0') << std::setw(3)
+ << std::to_string(msec) << delim << LogLevelRepr(level) << delim
+ << function
+#ifndef NDEBUG
+ << " at " << file << ':' << line
+#endif
+ << delim << std::hex << std::showbase << std::this_thread::get_id()
+ << std::noshowbase << std::dec << "||" << delim;
+ }
+
+ LogMessage(const LogMessage& msg) = delete;
+
+ ~LogMessage()
+ {
+ if (ptr_) logger_ << std::move(ptr_);
+ }
+
+ template <typename T>
+ inline LogMessage& operator<<(const T& t)
+ {
+ if (ptr_) std::get<1>(*ptr_) << t;
+ return *this;
+ }
+
+private:
+ static const char* LogLevelRepr(LogLevel level)
+ {
+ // by specification these are all of length 10
+ switch (level) {
+ case LogLevel::TRACE:
+ return "TRACE ";
+ case LogLevel::DEBUG:
+ return "DEBUG ";
+ case LogLevel::INFO:
+ return "INFO ";
+ case LogLevel::NOTICE:
+ return "NOTICE ";
+ case LogLevel::WARN:
+ return "WARN ";
+ case LogLevel::ERROR:
+ return "ERROR ";
+ case LogLevel::CRITICAL:
+ return "CRITICAL ";
+ case LogLevel::FATAL:
+ return "FATAL ";
+ default:
+ return "OTHER ";
+ }
+ }
+
+private:
+ std::unique_ptr<std::pair<LogLevel, std::ostringstream>> ptr_;
+ Logger& logger_;
+};
+
+// trace is disabled under Release builds (-DNDEBUG)
+#ifdef NDEBUG
+#define PBLOGGER_LEVEL(lg, lvl) \
+ if (PacBio::Logging::lvl != PacBio::Logging::LogLevel::TRACE) \
+ PacBio::Logging::LogMessage(__FILE__, __func__, __LINE__, PacBio::Logging::lvl, (lg))
+#else
+#define PBLOGGER_LEVEL(lg, lvl) \
+ PacBio::Logging::LogMessage(__FILE__, __func__, __LINE__, PacBio::Logging::lvl, (lg))
+#endif
+
+#define PBLOGGER_TRACE(lg) PBLOGGER_LEVEL(lg, LogLevel::TRACE)
+#define PBLOGGER_DEBUG(lg) PBLOGGER_LEVEL(lg, LogLevel::DEBUG)
+#define PBLOGGER_INFO(lg) PBLOGGER_LEVEL(lg, LogLevel::INFO)
+#define PBLOGGER_NOTICE(lg) PBLOGGER_LEVEL(lg, LogLevel::NOTICE)
+#define PBLOGGER_WARN(lg) PBLOGGER_LEVEL(lg, LogLevel::WARN)
+#define PBLOGGER_ERROR(lg) PBLOGGER_LEVEL(lg, LogLevel::ERROR)
+#define PBLOGGER_CRITICAL(lg) PBLOGGER_LEVEL(lg, LogLevel::CRITICAL)
+#define PBLOGGER_FATAL(lg) PBLOGGER_LEVEL(lg, LogLevel::FATAL)
+
+#define PBLOG_LEVEL(lvl) PBLOGGER_LEVEL(PacBio::Logging::Logger::Default(), lvl)
+
+#define PBLOG_TRACE PBLOG_LEVEL(LogLevel::TRACE)
+#define PBLOG_DEBUG PBLOG_LEVEL(LogLevel::DEBUG)
+#define PBLOG_INFO PBLOG_LEVEL(LogLevel::INFO)
+#define PBLOG_NOTICE PBLOG_LEVEL(LogLevel::NOTICE)
+#define PBLOG_WARN PBLOG_LEVEL(LogLevel::WARN)
+#define PBLOG_ERROR PBLOG_LEVEL(LogLevel::ERROR)
+#define PBLOG_CRITICAL PBLOG_LEVEL(LogLevel::CRITICAL)
+#define PBLOG_FATAL PBLOG_LEVEL(LogLevel::FATAL)
+
+inline void InstallSignalHandlers(Logger& logger = Logger::Default())
+{
+ using std::raise;
+ using std::signal;
+
+ static Logger& logger_ = logger;
+
+ std::set_terminate([]() {
+ if (auto eptr = std::current_exception()) {
+ try {
+ std::rethrow_exception(eptr);
+ } catch (const std::exception& e) {
+ PBLOGGER_FATAL(logger_) << "caught exception: \"" << e.what() << '"';
+ } catch (...) {
+ PBLOGGER_FATAL(logger_) << "caught unknown exception type";
+ }
+ }
+ // call the SIGABRT handler (below)
+ std::abort();
+ });
+ signal(SIGABRT, [](int) {
+ {
+ PBLOGGER_FATAL(logger_) << "caught SIGABRT";
+ }
+ logger_.~Logger();
+ signal(SIGABRT, SIG_DFL);
+ raise(SIGABRT);
+ });
+ signal(SIGINT, [](int) {
+ {
+ PBLOGGER_FATAL(logger_) << "caught SIGINT";
+ }
+ logger_.~Logger();
+ signal(SIGINT, SIG_DFL);
+ raise(SIGINT);
+ });
+ signal(SIGSEGV, [](int) {
+ {
+ PBLOGGER_FATAL(logger_) << "caught SIGSEGV";
+ }
+ logger_.~Logger();
+ signal(SIGSEGV, SIG_DFL);
+ raise(SIGSEGV);
+ });
+ signal(SIGTERM, [](int) {
+ {
+ PBLOGGER_FATAL(logger_) << "caught SIGTERM";
+ }
+ logger_.~Logger();
+ signal(SIGTERM, SIG_DFL);
+ raise(SIGTERM);
+ });
+}
+
+} // namespace Logging
+} // namespace PacBio
diff --git a/include/pacbio/parallel/WorkQueue.h b/include/pacbio/parallel/WorkQueue.h
new file mode 100644
index 0000000..f21ae7f
--- /dev/null
+++ b/include/pacbio/parallel/WorkQueue.h
@@ -0,0 +1,190 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <condition_variable>
+#include <exception>
+#include <future>
+#include <mutex>
+#include <queue>
+
+#include <boost/optional.hpp>
+
+namespace PacBio {
+namespace Parallel {
+
+template <typename T>
+class WorkQueue
+{
+private:
+ typedef boost::optional<std::packaged_task<T(void)>> TTask;
+ typedef boost::optional<std::future<T>> TFuture;
+
+public:
+ WorkQueue(const size_t size) : exc{nullptr}, sz{size}
+ {
+ for (size_t i = 0; i < size; ++i) {
+ threads.emplace_back(std::thread([this]() {
+ try {
+ while (auto task = PopTask()) {
+ (*task)();
+ }
+ } catch (...) {
+ {
+ std::lock_guard<std::mutex> g(m);
+ exc = std::current_exception();
+ }
+ popped.notify_all();
+ }
+ }));
+ }
+ }
+
+ ~WorkQueue()
+ {
+ for (auto& thread : threads) {
+ thread.join();
+ }
+
+ // wait to see if there's a final exception, throw if so..
+ {
+ std::lock_guard<std::mutex> g(m);
+ if (exc) std::rethrow_exception(exc);
+ }
+ }
+
+ template <typename F, typename... Args>
+ void ProduceWith(F&& f, Args&&... args)
+ {
+ std::packaged_task<T(void)> task{
+ std::bind(std::forward<F>(f), std::forward<Args>(args)...)};
+
+ {
+ std::unique_lock<std::mutex> lk(m);
+ popped.wait(lk, [&task, this]() {
+ if (exc) std::rethrow_exception(exc);
+
+ if (head.size() < sz) {
+ head.emplace(std::move(task));
+ return true;
+ }
+
+ return false;
+ });
+ }
+ pushed.notify_all();
+ }
+
+ template <typename F, typename... Args>
+ bool ConsumeWith(F&& cont, Args&&... args)
+ {
+ TFuture fut(boost::none);
+
+ {
+ std::unique_lock<std::mutex> lk(m);
+ popped.wait(lk, [&fut, this]() {
+ if (tail.empty()) return false;
+
+ if ((fut = std::move(tail.front()))) {
+ tail.pop();
+ }
+
+ return true;
+ });
+ }
+
+ try {
+ if (!fut) return false;
+
+ cont(std::forward<Args>(args)..., std::move(fut->get()));
+ return true;
+ } catch (...) {
+ {
+ std::lock_guard<std::mutex> g(m);
+ exc = std::current_exception();
+ }
+ popped.notify_all();
+ }
+ return false;
+ }
+
+ void Finalize()
+ {
+ {
+ std::lock_guard<std::mutex> g(m);
+ head.emplace(boost::none);
+ }
+ pushed.notify_all();
+ }
+
+private:
+ TTask PopTask()
+ {
+ TTask task(boost::none);
+
+ {
+ std::unique_lock<std::mutex> lk(m);
+ pushed.wait(lk, [&task, this]() {
+ if (head.empty()) return false;
+
+ if ((task = std::move(head.front()))) {
+ head.pop();
+ tail.emplace(task->get_future());
+ } else
+ tail.emplace(boost::none);
+
+ return true;
+ });
+ }
+ popped.notify_all();
+
+ return task;
+ }
+
+ std::vector<std::thread> threads;
+ std::queue<TTask> head;
+ std::queue<TFuture> tail;
+ std::condition_variable popped;
+ std::condition_variable pushed;
+ std::exception_ptr exc;
+ std::mutex m;
+ size_t sz;
+};
+
+} // namespace parallel
+} // namespace PacBio
diff --git a/include/pacbio/util/ExecUtils.h b/include/pacbio/util/ExecUtils.h
new file mode 100644
index 0000000..bb3fafb
--- /dev/null
+++ b/include/pacbio/util/ExecUtils.h
@@ -0,0 +1,61 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <cstdio>
+#include <cstdlib>
+
+#include <sys/ioctl.h>
+
+namespace PacBio {
+namespace Util {
+
+inline void SetColumns()
+{
+ struct winsize w;
+ ioctl(STDOUT_FILENO, TIOCGWINSZ, &w);
+ static char env[32];
+ unsigned short col_size = w.ws_col > 0 ? w.ws_col : 80;
+ int retval = snprintf(env, sizeof(env), "COLUMNS=%u", col_size);
+ if (retval >= 0 && static_cast<size_t>(retval) < sizeof(env)) {
+ putenv(env);
+ }
+}
+
+} // namespace Util
+} // namespace PacBio
diff --git a/include/pacbio/util/Timer.h b/include/pacbio/util/Timer.h
new file mode 100644
index 0000000..d992b85
--- /dev/null
+++ b/include/pacbio/util/Timer.h
@@ -0,0 +1,59 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <chrono>
+
+namespace PacBio {
+namespace Util {
+
+class Timer
+{
+public:
+ Timer();
+
+ float ElapsedMilliseconds() const;
+ float ElapsedSeconds() const;
+ void Restart();
+
+private:
+ std::chrono::time_point<std::chrono::steady_clock> tick;
+};
+
+} // namespace Util
+} // namespace PacBio
diff --git a/scripts/cram b/scripts/cram
new file mode 100755
index 0000000..2f232fe
--- /dev/null
+++ b/scripts/cram
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+# if we have cram already, use that
+if [[ -x "$(which cram)" ]]; then
+ exec cram "$@"
+fi
+
+CRAMDIR=$(dirname "${BASH_SOURCE[0]}")/../third-party/cram-0.7
+exec env PYTHONPATH=$CRAMDIR $CRAMDIR/scripts/cram "$@"
diff --git a/scripts/makeChangeLog.py b/scripts/makeChangeLog.py
new file mode 100644
index 0000000..5623b60
--- /dev/null
+++ b/scripts/makeChangeLog.py
@@ -0,0 +1,31 @@
+""" File to generate a CHANGELOG from git commits. This will parse the git log
+command and convert any commit with `**` in the title into a changelog event """
+
+cl = open("CHANGELOG", 'w')
+cl.write("Recent Program Changes:\n\n")
+
+import os
+from subprocess import *
+
+GIT_COMMIT_FIELDS = ['id', 'author_name', 'author_email', 'date', 'message']
+GIT_LOG_FORMAT = ['%H', '%an', '%ae', '%ad', '%s']
+
+p = Popen('git log --format="%s"' % GIT_LOG_FORMAT, shell=True, stdout=PIPE)
+(log, _) = p.communicate()
+log = log.strip().split("\n")
+
+log = [row.strip().replace("'","").split(",") for row in log]
+log = [dict(zip(GIT_COMMIT_FIELDS, row)) for row in log]
+
+for commit in log:
+ msg = commit["message"]
+ if msg.count("**") > 0:
+ dt = commit["date"].split(" ")
+ date = "-".join(dt[2:4])
+ msg = msg.replace("]","").replace("**","")
+ id = commit["id"][1:7]
+ cl.write("\t*" + " " + msg + " " + date + " " + id + "\n")
+
+cl.write("\n\nFile is automatically created by makeChangeLog.py\n\n\n")
+
+cl.close()
\ No newline at end of file
diff --git a/scripts/task_pbccs_ccs b/scripts/task_pbccs_ccs
new file mode 100755
index 0000000..7768e6f
--- /dev/null
+++ b/scripts/task_pbccs_ccs
@@ -0,0 +1,218 @@
+#!/usr/bin/env python
+
+# TODO replace this with native C++ implementation.
+
+"""
+Wrapper for 'ccs' executable to provide tool contract interface support (and
+incidentally, using DataSet XML as input). Note that this will *not* currently
+support chunking, since it access the individual .bam files en masse.
+"""
+
+import logging
+import re
+import os
+import sys
+
+from pbcommand.models import FileTypes, SymbolTypes, get_pbparser
+from pbcommand.models.report import Report, Attribute
+from pbcommand.cli import pbparser_runner
+from pbcommand.utils import setup_log
+from pbcommand.engine import run_cmd
+from pbcore.io import ConsensusReadSet, SubreadSet
+
+__version__ = "0.1"
+log = logging.getLogger(__name__)
+
+class Constants(object):
+ TOOL_ID = "pbccs.tasks.ccs"
+ TOOL_NAME = "ccs"
+ DRIVER_EXE = "task_pbccs_ccs --resolved-tool-contract "
+ CCS_EXE = os.environ.get("__PBTEST_CCS_EXE", "ccs")
+ #
+ MIN_SNR_ID = "pbccs.task_options.min_snr"
+ MIN_SNR_DEFAULT = 3.75
+ MIN_READ_SCORE_ID = "pbccs.task_options.min_read_score"
+ MIN_READ_SCORE_DEFAULT = 0.65
+ MAX_LENGTH_ID = "pbccs.task_options.max_length"
+ MAX_LENGTH_DEFAULT = 7000
+ MIN_LENGTH_ID = "pbccs.task_options.min_length"
+ MIN_LENGTH_DEFAULT = 10
+ MIN_PASSES_ID = "pbccs.task_options.min_passes"
+ MIN_PASSES_DEFAULT = 3
+ MIN_PREDICTED_ACCURACY_ID = "pbccs.task_options.min_predicted_accuracy"
+ MIN_PREDICTED_ACCURACY_DEFAULT = 0.9
+ MIN_ZSCORE_ID = "pbccs.task_options.min_zscore"
+ MIN_ZSCORE_DEFAULT = -5
+ MAX_DROP_FRAC_ID = "pbccs.task_options.max_drop_fraction"
+ MAX_DROP_FRAC_DEFAULT = 0.34
+ NO_POLISH_ID="pbccs.task_options.no_polish"
+ NO_POLISH_DEFAULT=False
+ BY_STRAND_ID="pbccs.task_options.by_strand"
+ BY_STRAND_DEFAULT=False
+ MODEL_PATH_ID="pbccs.task_options.model_path"
+ MODEL_PATH_DEFAULT=""
+ MODEL_SPEC_ID="pbccs.task_options.model_spec"
+ MODEL_SPEC_DEFAULT=""
+ #
+ REPORT_FIELDS = {
+ "CCS generated": "num_ccs_reads",
+ "Below SNR threshold": "num_below_snr_threshold",
+ "No usable subreads": "num_no_usable_subreads",
+ "Insert size too long": "num_insert_size_too_long",
+ "Insert size too small": "num_insert_size_too_small",
+ "Not enough full passes": "num_not_enough_full_passes",
+ "Too many unusable subreads": "num_too_many_unusable_subreads",
+ "CCS did not converge": "num_not_converged",
+ "CCS below minimum predicted accuracy": "num_below_min_accuracy",
+ }
+
+
+def args_runner(args):
+ raise NotImplementedError("Please call 'ccs' directly.")
+
+
+def resolved_tool_contract_runner(rtc):
+ """
+ Run the ccs binary from the resolved tool contract, and generate an XML
+ dataset around the resulting .bam file.
+ """
+ subreads_file = rtc.task.input_files[0]
+ # XXX checking to make sure we don't propagate nonsense
+ barcode_sets = set()
+ with SubreadSet(subreads_file) as ds_in:
+ for ext_res in ds_in.externalResources:
+ if ext_res.barcodes is not None:
+ barcode_sets.add(ext_res.barcodes)
+ if len(barcode_sets) > 1:
+ raise RuntimeError("The input SubreadSet contains multiple distinct "+
+ "BarcodeSets.")
+ output_file = rtc.task.output_files[0]
+ if output_file.endswith(".consensusreadset.xml"):
+ output_file = re.sub(".consensusreadset.xml", ".bam", output_file)
+ assert output_file.endswith(".bam")
+ report_file = rtc.task.output_files[1]
+ log.info("CCS_EXE = {e}".format(e=Constants.CCS_EXE))
+ args = [
+ Constants.CCS_EXE,
+ "--pbi",
+ "--force",
+ "--logLevel=DEBUG",
+ "--reportFile=%s" % report_file,
+ "--numThreads=%d" % rtc.task.nproc,
+ "--minSnr=%g" % rtc.task.options[Constants.MIN_SNR_ID],
+ "--minReadScore=%g" % rtc.task.options[Constants.MIN_READ_SCORE_ID],
+ "--maxLength=%d" % rtc.task.options[Constants.MAX_LENGTH_ID],
+ "--minLength=%d" % rtc.task.options[Constants.MIN_LENGTH_ID],
+ "--minPasses=%d" % rtc.task.options[Constants.MIN_PASSES_ID],
+ "--minZScore=%g" % rtc.task.options[Constants.MIN_ZSCORE_ID],
+ "--maxDropFraction=%g" % rtc.task.options[Constants.MAX_DROP_FRAC_ID],
+ "--minPredictedAccuracy=%g" % \
+ rtc.task.options[Constants.MIN_PREDICTED_ACCURACY_ID],
+ "--noPolish" if rtc.task.options[Constants.NO_POLISH_ID] else "",
+ "--byStrand" if rtc.task.options[Constants.BY_STRAND_ID] else "",
+ ("--modelPath=%s" % rtc.task.options[Constants.MODEL_PATH_ID]) if \
+ rtc.task.options[Constants.MODEL_PATH_ID] else "",
+ ("--modelSpec=%s" % rtc.task.options[Constants.MODEL_SPEC_ID]) if \
+ rtc.task.options[Constants.MODEL_SPEC_ID] else "",
+ subreads_file,
+ output_file
+ ]
+ log.info(" ".join(args))
+ result = run_cmd(
+ cmd=" ".join(args),
+ stdout_fh=sys.stdout,
+ stderr_fh=sys.stderr)
+ if result.exit_code != 0:
+ return result.exit_code
+ assert os.path.isfile(output_file)
+ ccs_ds = ConsensusReadSet(output_file, strict=True)
+ if len(barcode_sets) == 1:
+ for ext_res in ccs_ds.externalResources:
+ ext_res.barcodes = list(barcode_sets)[0]
+ ccs_ds.write(rtc.task.output_files[0])
+ ccs_ds.close()
+ return 0
+
+
+def get_parser():
+ p = get_pbparser(
+ tool_id=Constants.TOOL_ID,
+ version=__version__,
+ name=Constants.TOOL_NAME,
+ description=__doc__,
+ driver_exe=Constants.DRIVER_EXE,
+ nproc=SymbolTypes.MAX_NPROC,
+ default_level="INFO")
+ p.add_input_file_type(FileTypes.DS_SUBREADS, "subread_set",
+ "SubreadSet", "Subread DataSet or .bam file")
+ p.add_output_file_type(FileTypes.DS_CCS, "bam_output",
+ name="ConsensusReadSet",
+ description="Output DataSet XML file",
+ default_name="ccs")
+ p.add_output_file_type(FileTypes.TXT, "ccs_summary_txt",
+ name="CCS run summary",
+ description="Text report summarizing run statistics",
+ default_name="ccs_summary")
+ p.add_float(Constants.MIN_SNR_ID, "minSnr",
+ default=Constants.MIN_SNR_DEFAULT,
+ name="Minimum SNR",
+ description="Minimum SNR of input subreads")
+ p.add_float(Constants.MIN_READ_SCORE_ID, "minReadScore",
+ default=Constants.MIN_READ_SCORE_DEFAULT,
+ name="Minimum Read Score",
+ description="Minimum read score of input subreads")
+ p.add_int(Constants.MAX_LENGTH_ID, "maxLength",
+ default=Constants.MAX_LENGTH_DEFAULT,
+ name="Maximum Subread Length",
+ description="Maximum length of subreads to use for generating CCS")
+ p.add_int(Constants.MIN_LENGTH_ID, "minLength",
+ default=Constants.MIN_LENGTH_DEFAULT,
+ name="Minimum Subread Length",
+ description="Minimum length of subreads to use for generating CCS")
+ p.add_int(Constants.MIN_PASSES_ID, "minPasses",
+ default=Constants.MIN_PASSES_DEFAULT,
+ name="Minimum Number of Passes",
+ description="Minimum number of subreads required to generate CCS")
+ p.add_float(Constants.MIN_PREDICTED_ACCURACY_ID, "minPredictedAccuracy",
+ default=Constants.MIN_PREDICTED_ACCURACY_DEFAULT,
+ name="Minimum Predicted Accuracy",
+ description="Minimum predicted accuracy in [0, 1]")
+ p.add_float(Constants.MIN_ZSCORE_ID, "minZScore",
+ default=Constants.MIN_ZSCORE_DEFAULT,
+ name="Minimum Z Score",
+ description="Minimum Z score to use a subread")
+ p.add_float(Constants.MAX_DROP_FRAC_ID, "maxDropFraction",
+ default=Constants.MAX_DROP_FRAC_DEFAULT,
+ name="Maximum Dropped Fraction",
+ description="Maximum fraction of subreads that can be dropped before " +
+ "giving up")
+ p.add_boolean(Constants.NO_POLISH_ID, "noPolish",
+ default=Constants.NO_POLISH_DEFAULT,
+ name="No Polish CCS",
+ description="Only output the initial template derived from the POA")
+ p.add_boolean(Constants.BY_STRAND_ID, "byStrand",
+ default=Constants.BY_STRAND_DEFAULT,
+ name="By Strand CCS",
+ description="For each ZMW, generate two CCS sequences, one for each strand")
+ p.add_str(Constants.MODEL_PATH_ID, "modelPath",
+ default=Constants.MODEL_PATH_DEFAULT,
+ name="Model(s) Path",
+ description="Path to model parameter file(s)")
+ p.add_str(Constants.MODEL_SPEC_ID, "modelSpec",
+ default=Constants.MODEL_SPEC_DEFAULT,
+ name="Model Override",
+ description="Override default model selection with a provided model specification")
+ return p
+
+
+def main(argv=sys.argv):
+ return pbparser_runner(
+ argv=argv[1:],
+ parser=get_parser(),
+ args_runner_func=args_runner,
+ contract_runner_func=resolved_tool_contract_runner,
+ alog=log,
+ setup_log_func=setup_log)
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..5e2de22
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,161 @@
+
+from __future__ import print_function
+
+import os
+import os.path
+import re
+import sys
+
+from copy import copy
+from distutils.command.build_ext import build_ext
+from distutils.util import strtobool
+from setuptools import setup, Extension
+from shutil import copy2, rmtree
+from subprocess import Popen
+
+def ParseVersion():
+ thisDir = os.path.dirname(os.path.realpath(__file__))
+ cmakeLists = os.path.join(thisDir, "CMakeLists.txt")
+ regexp = re.compile(r'project\([^ ]+ VERSION (\d+\.\d+\.\d+) [^\)]+\)')
+ with open(cmakeLists) as handle:
+ for line in handle:
+ m = regexp.search(line)
+ if m:
+ return m.group(1)
+ raise RuntimeError("unable to find version string!")
+
+def which(program, env=os.environ):
+ def isExe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+ fpath, fname = os.path.split(program)
+ if fpath:
+ if isExe(program):
+ return program
+ else:
+ for path in env.get("PATH", "").split(os.pathsep):
+ path = path.strip("\"")
+ exe = os.path.join(path, program)
+ if isExe(exe):
+ return exe
+ return None
+
+class CMake(object):
+ def __init__(self, env=os.environ, verbose=False):
+ cmake = env.get("CMAKE_COMMAND", "cmake") or which("cmake", env)
+ if cmake is None:
+ raise RuntimeError("cannot find `cmake` command, "
+ "please populate CMAKE_COMMAND environment variable")
+ self.build = ["make"]
+ self.env = env
+ self.configure = [cmake]
+ self.definitions = dict()
+ self.generator = None
+
+ rpath = self.env.get("CMAKE_SKIP_RPATH", "")
+ try:
+ rpath = bool(strtobool(rpath))
+ except ValueError:
+ rpath = False
+ if rpath:
+ self.add_definition("CMAKE_SKIP_RPATH", "TRUE")
+
+ verbose = self.env.get("VERBOSE", "{0}".format(verbose))
+ try:
+ verbose = bool(strtobool(verbose))
+ except ValueError:
+ verbose = False
+ self.verbose = verbose
+
+ def add_definition(self, key, value):
+ self.definitions[key] = value
+
+ def add_definition_from_env(self, key, default=None):
+ value = self.env.get(key, default)
+ if value:
+ self.add_definition(key, value)
+
+ def set_build_type(self, buildType):
+ if buildType not in set(["Release", "Debug", "RelWithDebInfo"]):
+ raise ValueError("CMAKE_BUILD_TYPE must be in (Release, Debug, RelWithDebInfo)")
+ self.add_definition("CMAKE_BUILD_TYPE", buildType)
+
+ def set_generator(self, gen):
+ if gen not in set(["Default", "Ninja"]):
+ raise ValueError("valid generators must be in (default, ninja)")
+ if gen == "Default":
+ gen = None
+ self.build = ["make"]
+ if self.verbose:
+ self.build.append("VERBOSE=1")
+ elif gen == "Ninja":
+ self.ninja = self.env.get("NINJA_COMMAND", None) or which("ninja", self.env)
+ if not self.ninja:
+ raise RuntimeError("cannot find `ninja` command, "
+ "please populate NINJA_COMMAND environment variable")
+ self.build = [self.ninja]
+ if self.verbose:
+ self.build.append("-v")
+ self.generator = gen
+
+ def __call__(self, sourceDir, binaryDir, targets=[]):
+ configure = copy(self.configure)
+ if self.generator:
+ configure.append("-G{0}".format(self.generator))
+ for k, v in self.definitions.iteritems():
+ configure.append("-D{0}={1}".format(k, v))
+ configure.append(sourceDir)
+ print("Configuring with command `{0}`".format(" ".join(configure)), file=sys.stderr)
+ retcode = Popen(configure, cwd=binaryDir, env=self.env).wait()
+ if retcode != 0:
+ raise RuntimeError("failed to configure the project")
+ build = self.build + targets
+ print("Building with command `{0}`".format(" ".join(build)), file=sys.stderr)
+ retcode = Popen(build, cwd=binaryDir).wait()
+ if retcode != 0:
+ raise RuntimeError("failed to build the project")
+
+class MyBuildExt(build_ext):
+ def build_extension(self, ext):
+ destDir = os.path.dirname(self.get_ext_fullpath(ext.name))
+ thisDir = os.path.dirname(os.path.realpath(__file__))
+ try:
+ os.makedirs(self.build_temp)
+ os.makedirs(destDir)
+ except OSError:
+ pass
+ env = os.environ.copy()
+ cmake = CMake(env)
+ cmake.add_definition_from_env("Boost_INCLUDE_DIRS")
+ cmake.add_definition_from_env("PYTHON_INCLUDE_DIRS")
+ cmake.add_definition_from_env("SWIG_COMMAND")
+ cmake.add_definition_from_env("CMAKE_BUILD_TYPE", "RelWithDebInfo")
+ cmake.add_definition("PYTHON_SWIG", "1")
+ cmake.add_definition("UNY_build_tests", "0")
+ cmake.add_definition("UNY_build_bin", "0")
+ cmake.add_definition("PYTHON_EXECUTABLE", sys.executable)
+ cmake.set_generator("Ninja" if which("ninja", env) else "Default")
+ targets = ["_ConsensusCore2"]
+ try:
+ cmake(thisDir, self.build_temp, targets)
+ except RuntimeError:
+ # if this happens we're probably under pip and need to regenerate
+ rmtree(self.build_temp)
+ os.makedirs(self.build_temp)
+ cmake(thisDir, self.build_temp, targets)
+ for fname in ("_ConsensusCore2.so", "__init__.py"):
+ copy2(os.path.join(self.build_temp, "swig", "lib", fname), destDir)
+
+setup(
+ name="ConsensusCore2",
+ version=ParseVersion(),
+ author="PacificBiosciences",
+ author_email="devnet at pacb.com",
+ url="http://www.github.com/PacificBiosciences/ConsensusCore2",
+ description="A library for generating consensus sequences for PacBio data",
+ license="BSD",
+ ext_package="ConsensusCore2",
+ ext_modules=[Extension("_ConsensusCore2", [])],
+ install_requires=["numpy >= 1.6.0"],
+ setup_requires=["numpy >= 1.6.0"],
+ cmdclass={"build_ext": MyBuildExt}
+ )
diff --git a/src/AbstractIntegrator.cpp b/src/AbstractIntegrator.cpp
new file mode 100644
index 0000000..00adf87
--- /dev/null
+++ b/src/AbstractIntegrator.cpp
@@ -0,0 +1,203 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cassert>
+#include <cmath>
+#include <exception>
+#include <limits>
+#include <numeric>
+#include <utility>
+
+#include <pacbio/consensus/AbstractIntegrator.h>
+#include <pacbio/consensus/AbstractMatrix.h>
+
+#include <pacbio/data/Sequence.h>
+
+#include "ModelFactory.h"
+
+namespace PacBio {
+namespace Consensus {
+
+using namespace PacBio::Data;
+
+namespace {
+
+constexpr double NEG_DBL_INF = -std::numeric_limits<double>::infinity();
+constexpr int NEG_INT_INF = -std::numeric_limits<int>::infinity();
+constexpr float NEG_FLOAT_INF = -std::numeric_limits<float>::infinity();
+
+} // anonymous namespace
+
+IntegratorConfig::IntegratorConfig(const double minZScore, const double scoreDiff)
+ : MinZScore{minZScore}, ScoreDiff{scoreDiff}
+{
+ if (ScoreDiff < 0) {
+ throw std::runtime_error("Score diff must be > 0");
+ }
+}
+
+AbstractIntegrator::AbstractIntegrator(const IntegratorConfig& cfg) : cfg_{cfg} {}
+
+AbstractIntegrator::AbstractIntegrator(AbstractIntegrator&& ai)
+ : cfg_{ai.cfg_}, evals_{std::move(ai.evals_)}
+{
+}
+
+AbstractIntegrator::~AbstractIntegrator() {}
+
+Data::State AbstractIntegrator::AddRead(std::unique_ptr<AbstractTemplate>&& tpl,
+ const Data::MappedRead& read)
+{
+ // TODO(atoepfer) Why don't we add those reads and tag them as TEMPLATE_TOO_SMALL
+ // and effectively keep book about them? This logic should be
+ // in the Evaluator
+ if (read.TemplateEnd <= read.TemplateStart) throw std::invalid_argument("template span < 2!");
+
+ if (read.Length() < 2) throw std::invalid_argument("read span < 2!");
+
+ evals_.emplace_back(Evaluator(std::move(tpl), read, cfg_.MinZScore, cfg_.ScoreDiff));
+ return evals_.back().Status();
+}
+
+double AbstractIntegrator::LL(const Mutation& fwdMut) { return AccumulateNoInf(LLs(fwdMut)); }
+
+double AbstractIntegrator::LL() const { return AccumulateNoInf(LLs()); }
+
+std::vector<double> AbstractIntegrator::LLs(const Mutation& fwdMut)
+{
+ const Mutation revMut(ReverseComplement(fwdMut));
+
+ const auto functor = [&fwdMut, &revMut](Evaluator& eval) {
+ switch (eval.Strand()) {
+ case StrandType::FORWARD:
+ return eval.LL(fwdMut);
+ case StrandType::REVERSE:
+ return eval.LL(revMut);
+ case StrandType::UNMAPPED:
+ return NEG_DBL_INF;
+ default:
+ throw std::runtime_error("Unknown StrandType");
+ }
+ };
+
+ return TransformEvaluators<double>(functor);
+}
+
+std::vector<double> AbstractIntegrator::LLs() const
+{
+ const auto functor = [](const Evaluator& eval) { return eval.LL(); };
+ return TransformEvaluators<double>(functor);
+}
+
+std::vector<std::string> AbstractIntegrator::ReadNames() const
+{
+ return TransformEvaluators<std::string>([](const Evaluator& eval) { return eval.ReadName(); });
+}
+
+std::vector<int> AbstractIntegrator::NumFlipFlops() const
+{
+ return TransformEvaluators<int>([](const Evaluator& eval) { return eval.NumFlipFlops(); });
+}
+
+int AbstractIntegrator::MaxNumFlipFlops() const { return MaxElement<int>(NumFlipFlops()); }
+
+float AbstractIntegrator::MaxAlphaPopulated() const
+{
+ const auto functor = [](const Evaluator& eval) {
+ return (eval.IsValid() ? eval.Alpha().UsedEntriesRatio() : NEG_FLOAT_INF);
+ };
+ auto alphaPopulated = TransformEvaluators<float>(functor);
+ return MaxElement<float>(alphaPopulated);
+}
+
+float AbstractIntegrator::MaxBetaPopulated() const
+{
+ const auto functor = [](const Evaluator& eval) {
+ return (eval.IsValid() ? eval.Beta().UsedEntriesRatio() : NEG_FLOAT_INF);
+ };
+ auto betaPopulated = TransformEvaluators<float>(functor);
+ return MaxElement<float>(betaPopulated);
+}
+
+double AbstractIntegrator::AvgZScore() const
+{
+ double mean = 0.0, var = 0.0;
+ size_t n = 0;
+ for (const auto& eval : evals_) {
+ if (eval) {
+ double m, v;
+ std::tie(m, v) = eval.NormalParameters();
+ mean += m;
+ var += v;
+ ++n;
+ }
+ }
+ return (LL() / n - mean / n) / std::sqrt(var / n);
+}
+
+std::vector<double> AbstractIntegrator::ZScores() const
+{
+ return TransformEvaluators<double>([](const Evaluator& eval) { return eval.ZScore(); });
+}
+
+std::vector<std::pair<double, double>> AbstractIntegrator::NormalParameters() const
+{
+ return TransformEvaluators<std::pair<double, double>>(
+ [](const Evaluator& eval) { return eval.NormalParameters(); });
+}
+
+std::vector<Data::State> AbstractIntegrator::States() const
+{
+ return TransformEvaluators<Data::State>([](const Evaluator& eval) { return eval.Status(); });
+}
+
+std::vector<StrandType> AbstractIntegrator::StrandTypes() const
+{
+ return TransformEvaluators<StrandType>([](const Evaluator& eval) { return eval.Strand(); });
+}
+
+const Evaluator& AbstractIntegrator::GetEvaluator(size_t idx) const { return evals_[idx]; }
+
+const AbstractMatrix& AbstractIntegrator::Alpha(size_t idx) const { return evals_[idx].Alpha(); }
+
+const AbstractMatrix& AbstractIntegrator::Beta(size_t idx) const { return evals_[idx].Beta(); }
+
+Mutation AbstractIntegrator::ReverseComplement(const Mutation& mut) const
+{
+ return Mutation(mut.Type, TemplateLength() - mut.End(), Complement(mut.Base));
+}
+
+} // namespace Align
+} // namespace PacBio
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 0000000..5113729
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,118 @@
+# get all header files for IDE support
+file(GLOB_RECURSE UNY_HEADER "${UNY_IncludeDir}/*.h")
+file(GLOB_RECURSE UNY_HIDDEN_HEADER "*.h")
+# get sources for src/align
+file(GLOB UNY_ALIGN_CPP "align/*.cpp")
+# get sources for src/matrix
+file(GLOB UNY_MATRIX_CPP "matrix/*.cpp")
+# get sources for src/models
+file(GLOB UNY_MODELS_CPP "models/*.cpp")
+# get sources for src/poa
+file(GLOB UNY_POA_CPP "poa/*.cpp")
+
+# includes
+set(UNY_INCLUDE_DIRS
+ ${UNY_IncludeDir}
+ ${CMAKE_BINARY_DIR}/generated
+ ${Boost_INCLUDE_DIRS}
+ ${ZLIB_INCLUDE_DIRS}
+ ${HTSLIB_INCLUDE_DIRS}
+ ${SEQAN_INCLUDE_DIRS}
+ ${CPPOPTPARSE_IncludeDir}
+ ${PacBioBAM_INCLUDE_DIRS}
+ CACHE INTERNAL
+ "${PROJECT_NAME}: Include Directories"
+ FORCE
+)
+
+# add subset of sources that only contains cc2
+add_library(cc2 STATIC
+ ${UNY_ALIGN_CPP}
+ ${UNY_MATRIX_CPP}
+ ${UNY_MODELS_CPP}
+ ${UNY_POA_CPP}
+ AbstractIntegrator.cpp
+ Coverage.cpp
+ EasyReadScorer.cpp
+ Evaluator.cpp
+ EvaluatorImpl.cpp
+ ModelConfig.cpp
+ ModelFactory.cpp
+ ModelFormFactory.cpp
+ ModelSelection.cpp
+ MonoMolecularIntegrator.cpp
+ MultiMolecularIntegrator.cpp
+ Mutation.cpp
+ Polish.cpp
+ Read.cpp
+ Recursor.cpp
+ Sequence.cpp
+ Template.cpp
+)
+
+target_include_directories(cc2
+ PUBLIC ${UNY_INCLUDE_DIRS}
+)
+
+# add main library including everything
+add_library(unanimity STATIC
+ ${UNY_HEADER}
+ ${UNY_HIDDEN_HEADER}
+ ${CPPOPTPARSE_CPP}
+ ChainSeeds.cpp
+ ChemistryMapping.cpp
+ ChemistryTriple.cpp
+ Consensus.cpp
+ Interval.cpp
+ ReadId.cpp
+ SparsePoa.cpp
+ SubreadResultCounter.cpp
+ Timer.cpp
+ Utility.cpp
+)
+
+target_include_directories(unanimity
+ PUBLIC ${UNY_INCLUDE_DIRS}
+)
+
+set(UNY_LIBRARIES
+ ${PRE_LINK}
+ cc2
+ ${POST_LINK}
+ unanimity
+ ${ZLIB_LIBRARIES}
+ ${HTSLIB_LIBRARIES}
+ ${PacBioBAM_LIBRARIES}
+ CACHE INTERNAL
+ "${PROJECT_NAME}: Libraries"
+ FORCE
+)
+
+# add executables
+if (UNY_build_bin)
+ add_executable(ccs ${UNY_SourceDir}/main/ccs.cpp)
+
+ set_target_properties(ccs PROPERTIES
+ RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
+ )
+
+ target_include_directories(ccs
+ PUBLIC ${UNY_INCLUDE_DIRS}
+ )
+
+ target_link_libraries(ccs
+ ${UNY_LIBRARIES}
+ ${CMAKE_THREAD_LIBS_INIT}
+ ${CMAKE_DL_LIBS}
+ )
+
+ if (TARGET htslib)
+ add_dependencies(ccs htslib)
+ endif()
+
+ if (TARGET pbbam)
+ add_dependencies(ccs pbbam)
+ endif()
+
+ install(TARGETS ccs RUNTIME DESTINATION bin)
+endif()
diff --git a/src/ChainSeeds.cpp b/src/ChainSeeds.cpp
new file mode 100644
index 0000000..0f7a8b8
--- /dev/null
+++ b/src/ChainSeeds.cpp
@@ -0,0 +1,319 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <algorithm>
+#include <set>
+
+#include <boost/optional.hpp>
+
+#include <seqan/seeds.h>
+#include <seqan/sequence.h>
+
+#include <pacbio/ccs/ChainSeeds.h>
+
+namespace PacBio {
+namespace CCS {
+namespace {
+
+// H is query, V is reference
+
+long Diagonal(const seqan::Seed<seqan::Simple>& seed)
+{
+ size_t v = beginPositionV(seed);
+ size_t h = beginPositionH(seed);
+
+ if (v > h) return -static_cast<long>(v - h);
+
+ return static_cast<long>(h - v);
+}
+
+bool HVCompare(const seqan::Seed<seqan::Simple>& a, const seqan::Seed<seqan::Simple>& b)
+{
+ unsigned leftA = beginPositionH(a), leftB = beginPositionH(b);
+
+ if (leftA < leftB) return true;
+
+ if (leftA == leftB) return endPositionV(a) < endPositionV(b);
+
+ return false;
+}
+
+bool VHCompare(const seqan::Seed<seqan::Simple>& a, const seqan::Seed<seqan::Simple>& b)
+{
+ unsigned leftA = beginPositionV(a), leftB = beginPositionV(b);
+
+ if (leftA < leftB) return true;
+
+ if (leftA == leftB) return endPositionH(a) < endPositionH(b);
+
+ return false;
+}
+
+bool DiagonalCompare(const seqan::Seed<seqan::Simple>& a, const seqan::Seed<seqan::Simple>& b)
+{
+ int diagA = Diagonal(a), diagB = Diagonal(b);
+
+ if (diagA == diagB) return beginPositionH(a) < beginPositionH(b);
+
+ return diagA < diagB;
+}
+
+long LinkScore(const seqan::Seed<seqan::Simple>& a, const seqan::Seed<seqan::Simple>& b,
+ const int matchReward)
+{
+ using namespace std;
+
+ long aH = static_cast<long>(beginPositionH(a));
+ long aV = static_cast<long>(beginPositionV(a));
+ long bH = static_cast<long>(beginPositionH(b));
+ long bV = static_cast<long>(beginPositionV(b));
+ long k = min(static_cast<long>(seedSize(a)), static_cast<long>(seedSize(b)));
+
+ long diagA = Diagonal(a);
+ long diagB = Diagonal(b);
+ long fwd = min(aH - bH, aV - bV);
+ long indels = abs(diagA - diagB);
+ long matches = k - max(0L, k - fwd);
+ long mismatches = fwd - matches;
+
+ return matchReward * matches - indels - mismatches;
+}
+
+struct SDPHit : public seqan::Seed<seqan::Simple>
+{
+ size_t Index;
+
+ SDPHit(const seqan::Seed<seqan::Simple>& seed, const size_t index)
+ : seqan::Seed<seqan::Simple>(seed), Index(index)
+ {
+ }
+
+ bool operator<(const SDPHit& other) const { return DiagonalCompare(*this, other); }
+};
+
+bool IndexCompare(const SDPHit& a, const SDPHit& b) { return a.Index < b.Index; }
+struct SDPColumn
+{
+ boost::optional<SDPHit> Seed;
+ size_t Column;
+
+ SDPColumn(size_t column, const boost::optional<SDPHit> seed = boost::none)
+ : Seed(seed), Column(column)
+ {
+ }
+
+ bool operator<(const SDPColumn& other) const { return Column < other.Column; }
+};
+
+std::vector<boost::optional<SDPHit>> ComputeVisibilityLeft(const std::vector<SDPHit>& seeds,
+ std::set<SDPHit>& sweepSet)
+{
+ using namespace seqan;
+ using namespace std;
+
+ vector<boost::optional<SDPHit>> visible(seeds.size(), boost::none);
+ auto toRemove = seeds.begin();
+
+ for (auto it = seeds.begin(); it != seeds.end();) {
+ const size_t col = beginPositionH(*it);
+ const auto start = it;
+
+ for (; it != seeds.end() && col == beginPositionH(*it); ++it) {
+ auto succ = sweepSet.upper_bound(*it);
+
+ if (succ != sweepSet.end()) {
+ visible[it->Index] = *succ;
+ }
+ }
+
+ sweepSet.insert(start, it);
+
+ for (; toRemove != seeds.end() && endPositionH(*toRemove) < col; ++toRemove) {
+ sweepSet.erase(*toRemove);
+ }
+ }
+
+ // clear the sweepSet after use
+ sweepSet.clear();
+
+ return visible;
+}
+
+} // anonymous namespace
+
+void ChainSeeds(seqan::String<seqan::Seed<seqan::Simple>>& chain,
+ const seqan::SeedSet<seqan::Seed<seqan::Simple>>& seedSet, const int matchReward)
+{
+ using namespace seqan;
+ using namespace std;
+
+ vector<SDPHit> seeds;
+ vector<long> scores(length(seedSet), 0L);
+
+ // initialize our "SDPHits" vector (has fixed index)
+ {
+ size_t i = 0;
+
+ for (auto it = begin(seedSet); it != end(seedSet); ++it, ++i) {
+ seeds.push_back(SDPHit(*it, i));
+ scores[i] = seedSize(*it);
+ }
+ }
+
+ // compute visibility left, requires H-sorted seeds
+ std::set<SDPHit> sweepSet;
+ sort(seeds.begin(), seeds.end(), HVCompare);
+ auto visible = ComputeVisibilityLeft(seeds, sweepSet);
+
+ // compute the visibility above, requires V-sorted seeds
+ sort(seeds.begin(), seeds.end(), VHCompare);
+ auto toRemove = seeds.begin();
+ std::set<SDPColumn> colSet;
+
+ long bestChainScore = -numeric_limits<long>::max();
+ boost::optional<size_t> bestChainEnd = boost::none;
+ vector<boost::optional<size_t>> chainPred(seeds.size(), boost::none);
+
+ auto zScore = [&scores](const SDPHit& seed) {
+ return scores[seed.Index] + beginPositionH(seed) + beginPositionV(seed);
+ };
+
+ for (auto it = seeds.begin(); it != seeds.end();) {
+ const size_t row = beginPositionV(*it);
+ const auto start = it;
+
+ for (; it != seeds.end() && row == beginPositionV(*it); ++it) {
+ long bestScore = -numeric_limits<long>::max();
+ boost::optional<SDPHit> bestSeed = boost::none;
+
+ // find the previous column and best fragment from it
+ {
+ SDPColumn col(beginPositionH(*it));
+ auto pred = colSet.lower_bound(col);
+
+ if (pred != colSet.begin()) {
+ pred = prev(pred);
+ long s = scores[pred->Seed->Index] + LinkScore(*it, *(pred->Seed), matchReward);
+
+ if (s > bestScore) {
+ bestScore = s;
+ bestSeed = pred->Seed;
+ }
+ }
+ }
+
+ // search visible fragments (above)
+ {
+ auto visa = sweepSet.lower_bound(*it);
+
+ if (visa != sweepSet.begin()) {
+ visa = prev(visa);
+ long s = scores[visa->Index] + LinkScore(*it, *visa, matchReward);
+
+ if (s > bestScore) {
+ bestScore = s;
+ bestSeed = *visa;
+ }
+ }
+ }
+
+ // search visible fragments (left)
+ if (auto visl = visible[it->Index]) {
+ long s = scores[visl->Index] + LinkScore(*it, *visl, matchReward);
+
+ if (s > bestScore) {
+ bestScore = s;
+ bestSeed = visl;
+ }
+ }
+
+ if (bestSeed && bestScore > 0) {
+ scores[it->Index] = bestScore;
+ chainPred[it->Index] = bestSeed->Index;
+
+ if (bestScore > bestChainScore) {
+ bestChainScore = bestScore;
+ bestChainEnd = it->Index;
+ }
+ } else {
+ // PLEASE NOTE: these have already been done at creation time
+ // scores[it->Index] = seedSize(*it);
+ // chainPred[it->Index] = boost::none;
+ }
+ }
+
+ sweepSet.insert(start, it);
+
+ // remove all seeds from the sweepSet with end position less than the current row,
+ // and ensure the colSet invariant is kept:
+ // that all columns greater than our current
+ for (; toRemove != seeds.end() && endPositionV(*toRemove) < row; ++toRemove) {
+ SDPColumn col(endPositionH(*toRemove), boost::make_optional(*toRemove));
+
+ auto it = colSet.find(col);
+
+ // update the column if it doesn't exist
+ // or if its score is less than the fragment we're removing from consideration
+ if (it == colSet.end() || zScore(*(it->Seed)) < zScore(*toRemove)) {
+ // insert the updated column, get successor
+ it = next(colSet.insert(col).first);
+
+ // keep removing columns long as the scores are less than
+ while (it != colSet.end() && zScore(*(it->Seed)) < zScore(*toRemove)) {
+ it = colSet.erase(it);
+ }
+ }
+
+ sweepSet.erase(*toRemove);
+ }
+ }
+
+ // seeds need to be sorted by Index to ... index into it properly
+ sort(seeds.begin(), seeds.end(), IndexCompare);
+ clear(chain);
+
+ while (bestChainEnd) {
+ appendValue(chain, seeds[*bestChainEnd]);
+ bestChainEnd = chainPred[*bestChainEnd];
+ }
+
+ // reverse the chain order in place
+ reverse(chain);
+}
+
+} // namespace CCS
+} // namespace PacBio
diff --git a/src/ChemistryMapping.cpp b/src/ChemistryMapping.cpp
new file mode 100644
index 0000000..e56bee0
--- /dev/null
+++ b/src/ChemistryMapping.cpp
@@ -0,0 +1,94 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <boost/foreach.hpp>
+#include <boost/property_tree/ptree.hpp>
+#include <boost/property_tree/xml_parser.hpp>
+
+#include <pacbio/data/ChemistryMapping.h>
+#include <pacbio/data/ChemistryTriple.h>
+#include <pacbio/exception/CCSExceptions.h>
+#include <pacbio/io/Utility.h>
+
+using namespace std;
+
+namespace PacBio {
+namespace Data {
+
+using namespace PacBio::IO;
+using namespace PacBio::Exception;
+
+ChemistryMapping::ChemistryMapping(const std::string& mappingXML)
+{
+ using boost::property_tree::ptree;
+ using boost::property_tree::xml_parser::read_xml;
+
+ ptree pt;
+
+ if (!FileExists(mappingXML)) throw BadMappingXMLException("File does not exist: " + mappingXML);
+
+ read_xml(mappingXML, pt);
+
+ try {
+ mapping[ChemistryTriple::Null()] =
+ pt.get<string>("MappingTable.DefaultSequencingChemistry");
+
+ BOOST_FOREACH (ptree::value_type& v, pt.get_child("MappingTable")) {
+ if (v.first.compare("Mapping") == 0) {
+ ChemistryTriple entry(v.second.get<string>("BindingKit"),
+ v.second.get<string>("SequencingKit"),
+ v.second.get<string>("SoftwareVersion"));
+ mapping[entry] = v.second.get<string>("SequencingChemistry");
+ }
+ }
+ } catch (...) {
+ throw BadMappingXMLException("Could not parse mapping xml!");
+ }
+}
+
+string ChemistryMapping::MapTriple(const ChemistryTriple& triple, const std::string& fallback) const
+{
+ try {
+ return mapping.at(triple);
+ } catch (const out_of_range& e) {
+ if (fallback.empty()) throw;
+ return fallback;
+ }
+}
+
+} // namespace Data
+} // namespace PacBio
diff --git a/src/ChemistryTriple.cpp b/src/ChemistryTriple.cpp
new file mode 100644
index 0000000..121471b
--- /dev/null
+++ b/src/ChemistryTriple.cpp
@@ -0,0 +1,87 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <boost/lexical_cast.hpp>
+#include <boost/xpressive/xpressive.hpp>
+
+#include <pacbio/data/ChemistryTriple.h>
+#include <pacbio/exception/CCSExceptions.h>
+
+using namespace std;
+
+namespace PacBio {
+namespace Data {
+
+using namespace PacBio::Exception;
+
+ChemistryTriple::ChemistryTriple(const std::string& bindingKit, const std::string& sequencingKit,
+ const std::string& changeListID)
+{
+ if (!SetValues(bindingKit, sequencingKit, changeListID)) {
+ throw BadChemistryTriple("unparsable ChemistryTriple(" + bindingKit + ", " + sequencingKit +
+ ", " + changeListID + ")");
+ }
+}
+
+bool ChemistryTriple::SetValues(const std::string& bindingKit, const std::string& sequencingKit,
+ const std::string& changeListID)
+{
+ using namespace boost::xpressive;
+
+ using boost::lexical_cast;
+
+ try {
+ BindingKit = lexical_cast<unsigned>(bindingKit);
+ SequencingKit = lexical_cast<unsigned>(sequencingKit);
+
+ smatch what;
+ // sregex::compile("^(\\d+)\\.(\\d+)");
+ sregex re = bos >> (s1 = +_d) >> '.' >> (s2 = +_d);
+
+ if (regex_search(changeListID.begin(), changeListID.end(), what, re)) {
+ MajorVersion = lexical_cast<unsigned>(what[1]);
+ MinorVersion = lexical_cast<unsigned>(what[2]);
+ return true;
+ }
+ } catch (const boost::bad_lexical_cast& e) {
+ }
+
+ return false;
+}
+
+} // namespace Data
+} // namespace PacBio
diff --git a/src/Consensus.cpp b/src/Consensus.cpp
new file mode 100644
index 0000000..a74e0f8
--- /dev/null
+++ b/src/Consensus.cpp
@@ -0,0 +1,61 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <limits>
+
+#include <pacbio/ccs/Consensus.h>
+
+namespace PacBio {
+namespace CCS {
+
+ConsensusSettings::ConsensusSettings(const optparse::Values& options)
+ : MaxPoaCoverage{std::numeric_limits<size_t>::max()}
+ , MaxLength{options.get(OptionNames::MaxLength)}
+ , MinLength{options.get(OptionNames::MinLength)}
+ , MinPasses{options.get(OptionNames::MinPasses)}
+ , MinPredictedAccuracy{options.get(OptionNames::MinPredictedAccuracy)}
+ , MinZScore{options.get(OptionNames::MinZScore)}
+ , MaxDropFraction{options.get(OptionNames::MaxDropFraction)}
+ , ByStrand{options.get(OptionNames::ByStrand)}
+ , NoPolish{options.get(OptionNames::NoPolish)}
+ , MinReadScore{static_cast<float>(options.get(OptionNames::MinReadScore))}
+ , MinSNR{static_cast<double>(options.get(OptionNames::MinSnr))}
+{
+}
+
+} // namespace CCS
+} // namespace PacBio
diff --git a/src/Coverage.cpp b/src/Coverage.cpp
new file mode 100644
index 0000000..eefdf74
--- /dev/null
+++ b/src/Coverage.cpp
@@ -0,0 +1,125 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <algorithm>
+#include <cassert>
+#include <utility>
+#include <vector>
+
+#include <pacbio/consensus/Coverage.h>
+
+namespace PacBio {
+namespace Consensus {
+
+void CoverageInWindow(int tStartDim, int *tStart, int tEndDim, int *tEnd, int winStart, int winLen,
+ int *coverage)
+{
+ using std::max;
+ using std::min;
+
+ assert(tStartDim == tEndDim);
+
+ int nReads = tStartDim;
+ int winEnd = winStart + winLen;
+ std::fill_n(coverage, winLen, 0);
+ for (int read = 0; read < nReads; read++) {
+ int tStart_ = tStart[read];
+ int tEnd_ = tEnd[read];
+ for (int pos = max(tStart_, winStart); pos < min(tEnd_, winEnd); pos++) {
+ coverage[pos - winStart] += 1;
+ }
+ }
+}
+
+constexpr int CHUNK_SIZE = 10000;
+
+std::vector<std::pair<int, int>> CoveredIntervals(int minCoverage, int tStartDim, int *tStart,
+ int tEndDim, int *tEnd, int winStart, int winLen)
+{
+ assert(tStartDim == tEndDim);
+ // assert(isSorted(tStart)); // find out how to get this ... it's C++11
+
+ // Approach: divide into chunks, find coverage in each chunk,
+ // then scan for covered windows ... careful to anneal windows
+ // spanning chunk boundaries. We also rely on the sortedness of the
+ // tStart to restrict our attention to
+
+ int winEnd = winStart + winLen;
+ int coverage[CHUNK_SIZE];
+ int currentIntervalStart = -1;
+ std::vector<std::pair<int, int>> intervals;
+
+ int startRowInChunk = 0;
+ for (int chunkStart = winStart; chunkStart < winEnd; chunkStart += CHUNK_SIZE) {
+ int chunkEnd = std::min(chunkStart + CHUNK_SIZE, winEnd);
+
+ // We compute a conservative guess of the rows that are involved in
+ // this chunk. Not every row in the range [startRowInChunk, endRowInChunk)
+ // actually overlaps the chunk, but no rows not in that range intersect the chunk.
+ // startRowInChunk is computed by scanning from where it was for the last chunk.
+ // This is the best we can do within pulling in the nBackRead stuff.
+ int endRowInChunk = std::lower_bound(tStart, tStart + tStartDim, chunkEnd) - tStart;
+ for (; ((startRowInChunk < endRowInChunk) & (tEnd[startRowInChunk] < chunkStart));
+ startRowInChunk++)
+ ;
+
+ CoverageInWindow((endRowInChunk - startRowInChunk), tStart + startRowInChunk,
+ (endRowInChunk - startRowInChunk), tEnd + startRowInChunk, chunkStart,
+ CHUNK_SIZE, coverage);
+ int j = 0;
+ while (j < (chunkEnd - chunkStart)) {
+ if (coverage[j] >= minCoverage) {
+ if (currentIntervalStart == -1) {
+ currentIntervalStart = chunkStart + j;
+ }
+ } else {
+ if (currentIntervalStart != -1) {
+ intervals.push_back(std::make_pair(currentIntervalStart, chunkStart + j));
+ currentIntervalStart = -1;
+ }
+ }
+ j++;
+ }
+ }
+ if (currentIntervalStart != -1) {
+ intervals.push_back(std::make_pair(currentIntervalStart, winEnd));
+ }
+ return intervals;
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/EasyReadScorer.cpp b/src/EasyReadScorer.cpp
new file mode 100644
index 0000000..e1fe6a2
--- /dev/null
+++ b/src/EasyReadScorer.cpp
@@ -0,0 +1,67 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include "ModelFactory.h"
+
+#include <pacbio/consensus/EasyReadScorer.h>
+#include <pacbio/consensus/Evaluator.h>
+#include <pacbio/consensus/Template.h>
+#include <pacbio/data/Read.h>
+
+#include <memory>
+#include <string>
+
+namespace PacBio {
+namespace Consensus {
+
+class ModelConfig;
+
+Evaluator* EasyReadScorer::MakeEvaluator(const std::string& tplString,
+ const PacBio::Data::MappedRead& mappedRead,
+ double minZScore, double scoreDiff)
+{
+ // Make a "ModelConfig"
+ std::unique_ptr<ModelConfig> cfg =
+ ModelFactory::Create(mappedRead.Model, mappedRead.SignalToNoise);
+ // make a "template" object
+ std::unique_ptr<AbstractTemplate> tpl(new Template(tplString, std::move(cfg)));
+
+ return new Evaluator(std::move(tpl), mappedRead, minZScore, scoreDiff);
+}
+
+} // PacBio::Consensus
+} // PacBio
diff --git a/src/Evaluator.cpp b/src/Evaluator.cpp
new file mode 100644
index 0000000..e7508ab
--- /dev/null
+++ b/src/Evaluator.cpp
@@ -0,0 +1,212 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cmath>
+#include <memory>
+#include <string>
+
+#include <pacbio/consensus/Evaluator.h>
+#include <pacbio/exception/StateError.h>
+
+#include "EvaluatorImpl.h"
+
+using namespace PacBio::Data;
+using namespace PacBio::Exception;
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+constexpr double NEG_DBL_INF = -std::numeric_limits<double>::infinity();
+constexpr int NEG_INT_INF = -std::numeric_limits<int>::infinity();
+constexpr float NEG_FLOAT_INF = -std::numeric_limits<float>::infinity();
+constexpr size_t EXTEND_BUFFER_COLUMNS = 8;
+
+} // anonymous namespace
+
+Evaluator::Evaluator(const State state) : impl_{nullptr}, curState_{state}
+{
+ if (curState_ == State::VALID)
+ throw std::invalid_argument("cannot initialize a dummy Evaluator with VALID state");
+}
+
+Evaluator::Evaluator(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ const double minZScore, const double scoreDiff)
+ : impl_{nullptr}, curState_{State::VALID}
+{
+ try {
+ impl_.reset(
+ new EvaluatorImpl(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff));
+
+ CheckZScore(minZScore, mr.Model);
+ } catch (const StateError& e) {
+ Status(e.WhatState());
+ }
+}
+
+Evaluator::Evaluator(Evaluator&& eval) : impl_{std::move(eval.impl_)}, curState_{eval.curState_} {}
+
+Evaluator& Evaluator::operator=(Evaluator&& eval)
+{
+ impl_ = move(eval.impl_);
+ curState_ = eval.curState_;
+ return *this;
+}
+
+Evaluator::~Evaluator() {}
+
+size_t Evaluator::Length() const
+{
+ if (IsValid()) return impl_->recursor_->tpl_->Length();
+ return 0;
+}
+
+StrandType Evaluator::Strand() const
+{
+ if (IsValid()) return impl_->recursor_->read_.Strand;
+ return StrandType::UNMAPPED;
+}
+
+std::string Evaluator::ReadName() const
+{
+ if (IsValid()) return impl_->ReadName();
+ return "*Inactive evaluator*";
+}
+
+double Evaluator::LL(const Mutation& mut)
+{
+ if (IsValid()) return impl_->LL(mut);
+ return NEG_DBL_INF;
+}
+
+double Evaluator::LL() const
+{
+ if (IsValid()) return impl_->LL();
+ return NEG_DBL_INF;
+}
+
+std::pair<double, double> Evaluator::NormalParameters() const
+{
+ if (IsValid()) return impl_->NormalParameters();
+ return std::make_pair(NEG_DBL_INF, NEG_DBL_INF);
+}
+
+double Evaluator::ZScore() const
+{
+ if (IsValid()) return impl_->ZScore();
+ return NEG_DBL_INF;
+}
+
+int Evaluator::NumFlipFlops() const
+{
+ if (IsValid()) return impl_->NumFlipFlops();
+ return NEG_INT_INF;
+}
+
+bool Evaluator::ApplyMutation(const Mutation& mut)
+{
+ bool mutApplied = false;
+ if (IsValid()) {
+ try {
+ mutApplied = impl_->ApplyMutation(mut);
+ } catch (const StateError& e) {
+ Status(e.WhatState());
+ }
+ }
+ return mutApplied;
+}
+
+bool Evaluator::ApplyMutations(std::vector<Mutation>* muts)
+{
+ bool mutsApplied = false;
+ if (IsValid()) {
+ try {
+ mutsApplied = impl_->ApplyMutations(muts);
+ } catch (const StateError& e) {
+ Status(e.WhatState());
+ }
+ }
+ return mutsApplied;
+}
+
+void Evaluator::Status(State nextState)
+{
+ // Allow transition from VALID to anything and
+ // from anything to DISABLED
+ if (curState_ == State::VALID)
+ curState_ = nextState;
+ else
+ std::cerr << "Log this behaviour and return" << std::endl;
+
+ if (curState_ != State::VALID) impl_.reset(nullptr);
+}
+
+void Evaluator::Release() { Status(State::MANUALLY_RELEASED); }
+
+const AbstractMatrix& Evaluator::Alpha() const
+{
+ if (IsValid()) {
+ return impl_->Alpha();
+ } else {
+ return ScaledMatrix::Null();
+ }
+}
+
+const AbstractMatrix& Evaluator::Beta() const
+{
+ if (IsValid()) {
+ return impl_->Beta();
+ } else {
+ return ScaledMatrix::Null();
+ }
+}
+
+void Evaluator::CheckZScore(const double minZScore, const std::string& model)
+{
+ // the zscore filter is disabled under the following conditions
+ // - unsupported model
+ for (const auto& m : {"S/P1-C1", "S/P2-C2/prospective-compatible"})
+ if (model.find(m) != std::string::npos) return;
+
+ // - threshold undefined or too low
+ if (std::isnan(minZScore) || minZScore <= -100.0) return;
+
+ const double zScore = impl_->ZScore();
+ // TODO(lhepler): re-enable this check when the zscore bits are working again
+ // assert(std::isfinite(zScore));
+ if (!std::isfinite(zScore) || zScore < minZScore) Status(State::POOR_ZSCORE);
+}
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/EvaluatorImpl.cpp b/src/EvaluatorImpl.cpp
new file mode 100644
index 0000000..88f918b
--- /dev/null
+++ b/src/EvaluatorImpl.cpp
@@ -0,0 +1,244 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cmath>
+
+#include <boost/optional.hpp>
+
+#include "EvaluatorImpl.h"
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+namespace { // anonymous
+
+constexpr size_t EXTEND_BUFFER_COLUMNS = 8;
+
+#if 0
+std::ostream& operator<<(std::ostream& out, const std::pair<size_t, size_t>& x)
+{
+ return out << '(' << x.first << ", " << x.second << ')';
+}
+
+void WriteMatrix(const ScaledMatrix& mat)
+{
+ std::cerr << std::pair<size_t, size_t>(mat.Rows(), mat.Columns()) << std::endl;
+
+ for (size_t j = 0; j < mat.Columns(); ++j)
+ std::cerr << " " << mat.UsedRowRange(j);
+ std::cerr << std::endl;
+
+ std::cerr << "lg: ";
+ for (size_t j = 0; j < mat.Columns(); ++j)
+ std::cerr << "\t" << std::fixed << std::setprecision(3) << mat.GetLogScale(j);
+ std::cerr << std::endl;
+
+ std::cerr << "lgS: ";
+ double lgS = 0.0;
+ for (size_t j = 0; j < mat.Columns(); ++j)
+ std::cerr << "\t" << std::fixed << std::setprecision(3) << (lgS += mat.GetLogScale(j));
+ std::cerr << std::endl;
+
+ for (size_t i = 0; i < mat.Rows(); ++i)
+ {
+ for (size_t j = 0; j < mat.Columns(); ++j)
+ {
+ std::cerr << "\t" << std::fixed << std::setprecision(3) << std::log(mat.Get(i, j)) + mat.GetLogScale(j);
+ }
+ std::cerr << std::endl;
+ }
+}
+#endif
+
+} // namespace anonymous
+
+EvaluatorImpl::EvaluatorImpl(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ const double scoreDiff)
+ : recursor_{tpl->CreateRecursor(std::move(tpl), mr, scoreDiff)}
+ , alpha_(mr.Length() + 1, recursor_->tpl_->Length() + 1, ScaledMatrix::FORWARD)
+ , beta_(mr.Length() + 1, recursor_->tpl_->Length() + 1, ScaledMatrix::REVERSE)
+ , extendBuffer_(mr.Length() + 1, EXTEND_BUFFER_COLUMNS, ScaledMatrix::FORWARD)
+{
+ numFlipFlops_ = recursor_->FillAlphaBeta(alpha_, beta_);
+}
+
+std::string EvaluatorImpl::ReadName() const { return recursor_->read_.Name; }
+
+double EvaluatorImpl::LL(const Mutation& mut_)
+{
+ // apply the virtual mutation
+ boost::optional<Mutation> mut(recursor_->tpl_->Mutate(mut_));
+
+ // if the resulting template is 0, simulate TEMPLATE_TOO_SMALL (removal)
+ if (recursor_->tpl_->Length() == 0) {
+ recursor_->tpl_->Reset();
+ return 0.0;
+ }
+
+ // if the mutation didn't hit this read, just return the ll as-is
+ if (!mut) return LL();
+
+ size_t betaLinkCol = 1 + mut->End();
+ size_t absoluteLinkColumn = 1 + mut->End() + mut->LengthDiff();
+
+ double score;
+
+ bool atBegin = mut->Start() < 3;
+ bool atEnd = (mut->End() + 3) > beta_.Columns();
+
+ if (!atBegin && !atEnd) {
+ const size_t extendLength = 2;
+ size_t extendStartCol;
+
+ if (mut->Type == MutationType::DELETION) {
+ // Future thought: If we revise the semantic of Extra,
+ // we can remove the extend and just link alpha and
+ // beta directly.
+ extendStartCol = mut->Start() - 1;
+ } else {
+ extendStartCol = mut->Start();
+ assert(extendLength <= EXTEND_BUFFER_COLUMNS);
+ }
+ extendBuffer_.SetDirection(ScaledMatrix::FORWARD);
+ recursor_->ExtendAlpha(alpha_, extendStartCol, extendBuffer_, extendLength);
+ score = recursor_->LinkAlphaBeta(extendBuffer_, extendLength, beta_, betaLinkCol,
+ absoluteLinkColumn) +
+ alpha_.GetLogProdScales(0, extendStartCol);
+ } else if (!atBegin && atEnd) {
+ //
+ // Extend alpha to end
+ //
+ size_t extendStartCol = mut->Start() - 1;
+ assert(recursor_->tpl_->Length() + 1 > extendStartCol);
+ size_t extendLength = recursor_->tpl_->Length() - extendStartCol + 1;
+
+ extendBuffer_.SetDirection(ScaledMatrix::FORWARD);
+ recursor_->ExtendAlpha(alpha_, extendStartCol, extendBuffer_, extendLength);
+ score = std::log(extendBuffer_(recursor_->read_.Length(), extendLength - 1)) +
+ alpha_.GetLogProdScales(0, extendStartCol) +
+ extendBuffer_.GetLogProdScales(0, extendLength);
+ } else if (atBegin && !atEnd) {
+ // If the mutation occurs at positions 0 - 2
+ size_t extendLastCol = mut->End();
+ // We duplicate this math inside the function
+ size_t extendLength = 1 + mut->End() + mut->LengthDiff();
+
+ extendBuffer_.SetDirection(ScaledMatrix::REVERSE);
+ recursor_->ExtendBeta(beta_, extendLastCol, extendBuffer_, mut->LengthDiff());
+ score = std::log(extendBuffer_(0, 0)) +
+ beta_.GetLogProdScales(extendLastCol + 1, beta_.Columns()) +
+ extendBuffer_.GetLogProdScales(0, extendLength);
+ } else {
+ assert(atBegin && atEnd);
+ /* This should basically never happen...
+ and is a total disaster if it does. The basic idea is that
+ FillAlpha and FillBeta use the real "template" while we test
+ mutations using "virtual" template positions and the Extend/Link
+ methods. Trying to call FillAlpha to calculate the likelihood of a
+ virtual
+ mutation is therefore going to fail, as it calculates using the
+ "real" template.
+ throw TooSmallTemplateException();
+ */
+
+ //
+ // Just do the whole fill
+ //
+ ScaledMatrix alphaP(recursor_->read_.Length() + 1, recursor_->tpl_->Length() + 1,
+ ScaledMatrix::FORWARD);
+ recursor_->FillAlpha(ScaledMatrix::Null(), alphaP);
+ score = std::log(alphaP(recursor_->read_.Length(), recursor_->tpl_->Length())) +
+ alphaP.GetLogProdScales();
+ }
+
+ // reset the virtual mutation
+ recursor_->tpl_->Reset();
+
+ return score + recursor_->UndoCounterWeights(recursor_->read_.Length());
+}
+
+double EvaluatorImpl::LL() const
+{
+ return std::log(beta_(0, 0)) + beta_.GetLogProdScales() +
+ recursor_->UndoCounterWeights(recursor_->read_.Length());
+}
+
+std::pair<double, double> EvaluatorImpl::NormalParameters() const
+{
+ return recursor_->tpl_->NormalParameters();
+}
+
+double EvaluatorImpl::ZScore() const
+{
+ double mean, var;
+ std::tie(mean, var) = NormalParameters();
+ return (LL() - mean) / std::sqrt(var);
+}
+
+inline void EvaluatorImpl::Recalculate()
+{
+ size_t I = recursor_->read_.Length() + 1;
+ size_t J = recursor_->tpl_->Length() + 1;
+ alpha_.Reset(I, J);
+ beta_.Reset(I, J);
+ extendBuffer_.Reset(I, EXTEND_BUFFER_COLUMNS);
+ recursor_->FillAlphaBeta(alpha_, beta_);
+}
+
+bool EvaluatorImpl::ApplyMutation(const Mutation& mut)
+{
+ if (recursor_->tpl_->ApplyMutation(mut)) {
+ Recalculate();
+ return true;
+ }
+ return false;
+}
+
+bool EvaluatorImpl::ApplyMutations(std::vector<Mutation>* muts)
+{
+ if (recursor_->tpl_->ApplyMutations(muts)) {
+ Recalculate();
+ return true;
+ }
+ return false;
+}
+
+const AbstractMatrix& EvaluatorImpl::Alpha() const { return alpha_; }
+
+const AbstractMatrix& EvaluatorImpl::Beta() const { return beta_; }
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/EvaluatorImpl.h b/src/EvaluatorImpl.h
new file mode 100644
index 0000000..28524d8
--- /dev/null
+++ b/src/EvaluatorImpl.h
@@ -0,0 +1,95 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <memory>
+#include <utility>
+#include <vector>
+
+#include <pacbio/consensus/Evaluator.h>
+#include <pacbio/consensus/Template.h>
+#include <pacbio/data/Read.h>
+
+#include "Recursor.h"
+#include "matrix/ScaledMatrix.h"
+
+namespace PacBio {
+namespace Consensus {
+
+class EvaluatorImpl
+{
+public:
+ EvaluatorImpl(std::unique_ptr<AbstractTemplate>&& tpl, const PacBio::Data::MappedRead& mr,
+ double scoreDiff = 12.5);
+
+ std::string ReadName() const;
+
+ double LL(const Mutation& mut);
+ double LL() const;
+
+ // TODO: Comments are nice! Explain what this is about---ZScore calculation?
+ std::pair<double, double> NormalParameters() const;
+
+ double ZScore() const;
+
+ bool ApplyMutation(const Mutation& mut);
+ bool ApplyMutations(std::vector<Mutation>* muts);
+
+ int NumFlipFlops() const { return numFlipFlops_; }
+
+public:
+ const AbstractMatrix& Alpha() const;
+ const AbstractMatrix& Beta() const;
+
+private:
+ void Recalculate();
+
+private:
+ std::unique_ptr<AbstractRecursor>
+ recursor_; // TODO: does this need to be a pointer? is it always non-null?
+ // are we making it a UP just so we can do a fwd decl and still have
+ // RAII semantics?
+ ScaledMatrix alpha_;
+ ScaledMatrix beta_;
+ ScaledMatrix extendBuffer_;
+
+ int numFlipFlops_;
+
+ friend class Evaluator;
+};
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/Interval.cpp b/src/Interval.cpp
new file mode 100644
index 0000000..920d19e
--- /dev/null
+++ b/src/Interval.cpp
@@ -0,0 +1,62 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <iostream>
+#include <sstream>
+#include <string>
+
+#include <pacbio/data/Interval.h>
+
+using namespace std;
+
+namespace PacBio {
+namespace Data {
+
+Interval::operator string() const
+{
+ stringstream ss;
+ ss << *this;
+ return ss.str();
+}
+
+ostream& operator<<(ostream& os, const Interval& interval)
+{
+ return os << '[' << interval.Left() << ", " << interval.Right() << ')';
+}
+
+} // namespace Data
+} // namespace PacBio
diff --git a/src/JsonHelpers.h b/src/JsonHelpers.h
new file mode 100644
index 0000000..5542deb
--- /dev/null
+++ b/src/JsonHelpers.h
@@ -0,0 +1,77 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <boost/property_tree/ptree.hpp>
+
+namespace PacBio {
+namespace Consensus {
+template <size_t I>
+void ReadMatrix(double (&mat)[I], const boost::property_tree::ptree& pt)
+{
+ if (pt.size() != I) throw std::invalid_argument("bad size (1D)");
+ size_t i = 0;
+ for (const auto& item : pt) {
+ mat[i] = item.second.get_value<double>();
+ ++i;
+ }
+}
+
+template <size_t I, size_t J>
+void ReadMatrix(double (&mat)[I][J], const boost::property_tree::ptree& pt)
+{
+ if (pt.size() != I) throw std::invalid_argument("bad size (2D)");
+ size_t i = 0;
+ for (const auto& item : pt) {
+ ReadMatrix<J>(mat[i], item.second);
+ ++i;
+ }
+}
+
+template <size_t I, size_t J, size_t K>
+void ReadMatrix(double (&mat)[I][J][K], const boost::property_tree::ptree& pt)
+{
+ if (pt.size() != I) throw std::invalid_argument("bad size (3D)");
+ size_t i = 0;
+ for (const auto& item : pt) {
+ ReadMatrix<J, K>(mat[i], item.second);
+ ++i;
+ }
+}
+}
+}
diff --git a/src/ModelConfig.cpp b/src/ModelConfig.cpp
new file mode 100644
index 0000000..c5f74a0
--- /dev/null
+++ b/src/ModelConfig.cpp
@@ -0,0 +1,65 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cassert>
+#include <cstdint>
+
+#include <pacbio/consensus/ModelConfig.h>
+
+namespace PacBio {
+namespace Consensus {
+namespace detail {
+
+// for converting Aa->0, Cc->1, Gg->2, Tt->3, _->4
+uint8_t TranslationTable[256] = {
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4};
+
+} // namespace detail
+
+std::ostream& operator<<(std::ostream& out, const TemplatePosition& pos)
+{
+ return out << "TemplatePosition(" << pos.Base << ", " << pos.Match << ", " << pos.Branch << ", "
+ << pos.Stick << ", " << pos.Deletion << ')';
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/ModelFactory.cpp b/src/ModelFactory.cpp
new file mode 100644
index 0000000..cfd1000
--- /dev/null
+++ b/src/ModelFactory.cpp
@@ -0,0 +1,150 @@
+// Copyright (c) 2015-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <set>
+#include <stdexcept>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include <boost/optional.hpp>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/exception/StateError.h>
+
+#include "ModelFactory.h"
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+using ChemistryNotFound = PacBio::Exception::ChemistryNotFound;
+
+size_t Count(const std::string& str, const std::string& delim)
+{
+ size_t count = 0;
+ size_t start = 0;
+
+ while ((start = str.find(delim, start)) != std::string::npos) {
+ ++count;
+ start += delim.length();
+ }
+
+ return count;
+}
+}
+
+std::unique_ptr<ModelConfig> ModelFactory::Create(const std::string& name, const SNR& snr)
+{
+ boost::optional<std::string> model(boost::none);
+
+ if (!(model = ModelOverride()))
+ if (!(model = Resolve(name))) throw ChemistryNotFound(name);
+
+ const auto& tbl = CreatorTable();
+ const auto it = tbl.find(*model);
+
+ if (it == tbl.end()) throw ChemistryNotFound(name);
+
+ return it->second->Create(snr);
+}
+
+std::unique_ptr<ModelConfig> ModelFactory::Create(const PacBio::Data::Read& read)
+{
+ return Create(read.Model, read.SignalToNoise);
+}
+
+bool ModelFactory::Register(const std::string& name, std::unique_ptr<ModelCreator>&& ctor)
+{
+ return CreatorTable()
+ .insert(std::make_pair(name, std::forward<std::unique_ptr<ModelCreator>>(ctor)))
+ .second;
+}
+
+boost::optional<std::string> ModelFactory::Resolve(const std::string& name)
+{
+ const std::vector<std::string> forms = {"PwSnr", "PwSnrA", "Snr", "Marginal"};
+ const std::vector<std::string> origins = {"FromFile", "Compiled"};
+ const auto& tbl = CreatorTable();
+ const size_t nParts = Count(name, "::") + 1;
+
+ if (nParts == 3) {
+ if (tbl.find(name) != tbl.end()) return name;
+ }
+
+ else if (nParts == 2) {
+ for (const auto& origin : origins) {
+ const std::string model = name + "::" + origin;
+ if (tbl.find(model) != tbl.end()) return model;
+ }
+ }
+
+ else if (nParts == 1) {
+ for (const auto& form : forms) {
+ for (const auto& origin : origins) {
+ const std::string model = name + "::" + form + "::" + origin;
+ if (tbl.find(model) != tbl.end()) return model;
+ }
+ }
+ }
+
+ return boost::none;
+}
+
+std::set<std::string> ModelFactory::SupportedModels()
+{
+ const auto& tbl = CreatorTable();
+ std::set<std::string> result;
+ for (const auto& item : tbl)
+ result.insert(item.first);
+ return result;
+}
+
+std::map<std::string, std::unique_ptr<ModelCreator>>& ModelFactory::CreatorTable()
+{
+ static std::map<std::string, std::unique_ptr<ModelCreator>> tbl;
+ return tbl;
+}
+
+boost::optional<std::string>& ModelOverride()
+{
+ static boost::optional<std::string> ovr = boost::none;
+ return ovr;
+}
+
+} // Consensus
+} // PacBio
diff --git a/src/ModelFactory.h b/src/ModelFactory.h
new file mode 100644
index 0000000..377a185
--- /dev/null
+++ b/src/ModelFactory.h
@@ -0,0 +1,124 @@
+// Copyright (c) 2015-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <map>
+#include <memory>
+#include <set>
+#include <string>
+
+#include <boost/optional.hpp>
+
+#include <pacbio/data/Read.h>
+#include <pacbio/exception/ModelError.h>
+
+namespace PacBio {
+
+// forward declarations
+namespace Data {
+struct SNR;
+}
+
+namespace Consensus {
+
+// forward declarations
+class ModelConfig;
+
+using SNR = PacBio::Data::SNR;
+
+// this pattern is based on
+// http://blog.fourthwoods.com/2011/06/04/factory-design-pattern-in-c/
+
+// An abstract class with a single abstract method, Create, for
+// instantiating a concrete model given the discriminative SNR
+class ModelCreator
+{
+public:
+ virtual ~ModelCreator() {}
+ virtual std::unique_ptr<ModelConfig> Create(const SNR&) const = 0;
+};
+
+// A static class containing the map of parameterized models that need
+// only SNR to become concrete, with methods to create such models,
+// register models, resolve models, and list available models
+class ModelFactory
+{
+public:
+ static std::unique_ptr<ModelConfig> Create(const std::string& name, const SNR&);
+ static std::unique_ptr<ModelConfig> Create(const PacBio::Data::Read& read);
+ static bool Register(const std::string& name, std::unique_ptr<ModelCreator>&& ctor);
+ static boost::optional<std::string> Resolve(const std::string& name);
+ static std::set<std::string> SupportedModels();
+
+private:
+ static std::map<std::string, std::unique_ptr<ModelCreator>>& CreatorTable();
+};
+
+// The concrete form of ModelCreator, which registers a compiled-in
+// model with the ModelFactory and implements the aforementioned
+// Create method for instantiating a concrete model given an SNR
+template <typename T>
+class ModelCreatorImpl : public ModelCreator
+{
+public:
+ ModelCreatorImpl<T>() {}
+ ModelCreatorImpl<T>(const std::set<std::string>& names)
+ {
+ for (const std::string& name : names)
+ if (!ModelFactory::Register(name + "::Compiled",
+ std::unique_ptr<ModelCreator>(new ModelCreatorImpl<T>())))
+ throw PacBio::Exception::DuplicateModel(name);
+ }
+
+ virtual std::unique_ptr<ModelConfig> Create(const SNR& snr) const
+ {
+ return std::unique_ptr<ModelConfig>(new T(snr));
+ }
+};
+
+// An accessor to a global parameter for overriding the model
+boost::optional<std::string>& ModelOverride();
+
+#define REGISTER_MODEL(cls) \
+private: \
+ static const ModelCreatorImpl<cls> creator_
+
+#define REGISTER_MODEL_IMPL(cls) const ModelCreatorImpl<cls> cls::creator_(cls::Names())
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/ModelFormFactory.cpp b/src/ModelFormFactory.cpp
new file mode 100644
index 0000000..0d7056f
--- /dev/null
+++ b/src/ModelFormFactory.cpp
@@ -0,0 +1,99 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <map>
+#include <string>
+#include <utility>
+
+#include <boost/property_tree/json_parser.hpp>
+#include <boost/property_tree/ptree.hpp>
+
+#include <pacbio/exception/ModelError.h>
+
+#include "ModelFactory.h"
+#include "ModelFormFactory.h"
+
+namespace PacBio {
+namespace Consensus {
+
+using ModelError = PacBio::Exception::ModelError;
+
+std::map<std::string, ModelFormCreator*>& ModelFormFactory::CreatorTable()
+{
+ static std::map<std::string, ModelFormCreator*> tbl;
+ return tbl;
+}
+
+bool ModelFormFactory::LoadModel(const std::string& path)
+{
+ using boost::property_tree::ptree;
+ using boost::property_tree::read_json;
+
+ ptree pt;
+
+ try {
+ read_json(path, pt);
+ // verify we're looking at consensus model parameters
+ std::string version = pt.get<std::string>("ConsensusModelVersion");
+ if (version != "3.0.0") return false;
+ } catch (boost::property_tree::ptree_error) {
+ return false;
+ }
+
+ const std::string chemistry = pt.get<std::string>("ChemistryName");
+ const std::string form = pt.get<std::string>("ModelForm");
+
+ const auto tbl = CreatorTable();
+ const auto it = tbl.find(form);
+
+ if (it == tbl.end()) return false;
+
+ const std::string name = chemistry + "::" + form + "::" + "FromFile";
+
+ try {
+ return ModelFactory::Register(name, it->second->LoadParams(pt));
+ } catch (ModelError& e) {
+ return false;
+ }
+}
+
+bool ModelFormFactory::Register(const std::string& form, ModelFormCreator* ctor)
+{
+ return CreatorTable().insert(std::make_pair(form, ctor)).second;
+}
+}
+}
diff --git a/src/ModelFormFactory.h b/src/ModelFormFactory.h
new file mode 100644
index 0000000..08551a0
--- /dev/null
+++ b/src/ModelFormFactory.h
@@ -0,0 +1,108 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#pragma once
+
+#include <map>
+#include <memory>
+#include <string>
+
+#include <boost/property_tree/ptree.hpp>
+
+#include "ModelFactory.h"
+
+namespace PacBio {
+namespace Consensus {
+
+// this pattern is based on
+// http://blog.fourthwoods.com/2011/06/04/factory-design-pattern-in-c/
+
+// An abstract class defining a single abstract method, LoadParams, for
+// parameterizing a model form yielding a ModelCreator that can be
+// used to instantiate a concrete model given an SNR (see ModelCreator)
+class ModelFormCreator
+{
+public:
+ virtual ~ModelFormCreator() {}
+ virtual std::unique_ptr<ModelCreator> LoadParams(
+ const boost::property_tree::ptree& pt) const = 0;
+};
+
+// A static factory class that holds onto all available model forms,
+// with methods to: get the static map of ModelFormCreators accessible
+// by their form name; to register a form within said map; and to load
+// a model parameter file, find its model form, and insert a
+// parameterized model into the ModelFactory where it is discoverable
+// by the rest of the library
+class ModelFormFactory
+{
+public:
+ static bool LoadModel(const std::string& path);
+ static bool Register(const std::string& form, ModelFormCreator* ctor);
+
+private:
+ static std::map<std::string, ModelFormCreator*>& CreatorTable();
+};
+
+// The concrete version of the ModelFormCreator, which registers
+// a model form with the ModelFormFactory, and implements the
+// aforementioned abstract method LoadParams to yield a ModelCreator
+// given a property_tree full of parameters
+template <typename T>
+class ModelFormCreatorImpl : public ModelFormCreator
+{
+public:
+ ModelFormCreatorImpl<T>(const std::string& form)
+ {
+ if (!ModelFormFactory::Register(form, this))
+ throw std::runtime_error("duplicate model form inserted into form factory!");
+ }
+
+ virtual std::unique_ptr<ModelCreator> LoadParams(const boost::property_tree::ptree& pt) const
+ {
+ return std::unique_ptr<ModelCreator>(new T(pt));
+ }
+};
+
+#define REGISTER_MODELFORM(cls) \
+private: \
+ static const ModelFormCreatorImpl<cls> creator_
+
+#define REGISTER_MODELFORM_IMPL(cls) const ModelFormCreatorImpl<cls> cls::creator_(cls::Name())
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/ModelSelection.cpp b/src/ModelSelection.cpp
new file mode 100644
index 0000000..660bf19
--- /dev/null
+++ b/src/ModelSelection.cpp
@@ -0,0 +1,130 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <set>
+#include <string>
+#include <vector>
+
+#include <dirent.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+
+#include <pacbio/consensus/ModelSelection.h>
+
+#include "ModelFactory.h"
+#include "ModelFormFactory.h"
+
+namespace PacBio {
+namespace Consensus {
+
+std::set<std::string> SupportedModels() { return ModelFactory::SupportedModels(); }
+
+std::set<std::string> SupportedChemistries()
+{
+ std::set<std::string> chems;
+ for (const auto& model : SupportedModels())
+ chems.insert(model.substr(0, model.find_first_of(':')));
+ return chems;
+}
+
+bool OverrideModel(const std::string& name)
+{
+ boost::optional<std::string> model(boost::none);
+
+ if (!(model = ModelFactory::Resolve(name))) return false;
+
+ ModelOverride() = *model;
+ return true;
+}
+
+bool UnOverrideModel()
+{
+ ModelOverride() = boost::none;
+ return true;
+}
+
+bool LoadModelFromFile(const std::string& path)
+{
+ struct stat st;
+ if (stat(path.c_str(), &st) != 0 || !S_ISREG(st.st_mode)) return false;
+ return ModelFormFactory::LoadModel(path);
+}
+
+size_t LoadModelsFromDirectory(const std::string& dirPath)
+{
+ struct stat st;
+ if (stat(dirPath.c_str(), &st) != 0) return false;
+ if (!S_ISDIR(st.st_mode)) return false;
+
+ DIR* dp = opendir(dirPath.c_str());
+ if (dp == nullptr) return false;
+
+ // iterate through .json files in directory,
+ // loading any into ModelFactory
+ bool ret = true;
+ size_t nModels = 0;
+ struct dirent* ep;
+ while ((ep = readdir(dp)) != nullptr) {
+ std::string path = dirPath + '/' + ep->d_name;
+ if (path.substr(path.find_last_of('.')) != ".json") continue;
+ if (!(ret &= (stat(path.c_str(), &st) == 0))) break;
+ if (S_ISREG(st.st_mode)) {
+ if ((ret &= LoadModelFromFile(path)))
+ ++nModels;
+ else
+ break;
+ }
+ }
+
+ closedir(dp);
+
+ return nModels;
+}
+
+size_t LoadModels(const std::string& path)
+{
+ struct stat st;
+ if (stat(path.c_str(), &st) != 0)
+ return 0;
+ else if (S_ISDIR(st.st_mode))
+ return LoadModelsFromDirectory(path);
+ else if (S_ISREG(st.st_mode))
+ return LoadModelFromFile(path) ? 1 : 0;
+ return 0;
+}
+}
+}
diff --git a/src/MonoMolecularIntegrator.cpp b/src/MonoMolecularIntegrator.cpp
new file mode 100644
index 0000000..99a0496
--- /dev/null
+++ b/src/MonoMolecularIntegrator.cpp
@@ -0,0 +1,187 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cassert>
+#include <cmath>
+#include <limits>
+#include <utility>
+
+#include <pacbio/consensus/MonoMolecularIntegrator.h>
+#include <pacbio/data/Sequence.h>
+
+#include "ModelFactory.h"
+
+using namespace PacBio::Data;
+using namespace PacBio::Exception;
+
+namespace PacBio {
+namespace Consensus {
+
+MonoMolecularIntegrator::MonoMolecularIntegrator(const std::string& tpl,
+ const IntegratorConfig& cfg, const SNR& snr,
+ const std::string& model)
+ : AbstractIntegrator(cfg)
+ , mdl_{model}
+ , snr_{snr}
+ , fwdTpl_(tpl, ModelFactory::Create(mdl_, snr_))
+ , revTpl_(::PacBio::Data::ReverseComplement(tpl), ModelFactory::Create(mdl_, snr_))
+{
+}
+
+MonoMolecularIntegrator::MonoMolecularIntegrator(MonoMolecularIntegrator&& mmi)
+ : AbstractIntegrator(std::move(mmi))
+ , mdl_{mmi.mdl_}
+ , snr_{mmi.snr_}
+ , fwdTpl_{std::move(mmi.fwdTpl_)}
+ , revTpl_{std::move(mmi.revTpl_)}
+{
+}
+
+State MonoMolecularIntegrator::AddRead(const MappedRead& read)
+{
+ if (read.Model != mdl_) throw std::invalid_argument("invalid model for integrator!");
+ if (read.SignalToNoise != snr_) throw std::invalid_argument("invalid SNR for integrator!");
+
+ try {
+ if (read.Strand == StrandType::FORWARD)
+ return AbstractIntegrator::AddRead(
+ std::unique_ptr<AbstractTemplate>(new VirtualTemplate(
+ fwdTpl_, read.TemplateStart, read.TemplateEnd, read.PinStart, read.PinEnd)),
+ read);
+
+ else if (read.Strand == StrandType::REVERSE)
+ return AbstractIntegrator::AddRead(
+ std::unique_ptr<AbstractTemplate>(new VirtualTemplate(
+ revTpl_, TemplateLength() - read.TemplateEnd,
+ TemplateLength() - read.TemplateStart, read.PinEnd, read.PinStart)),
+ read);
+ } catch (const TemplateTooSmall& e) {
+ return State::TEMPLATE_TOO_SMALL;
+ }
+
+ throw std::invalid_argument("read is unmapped!");
+}
+
+size_t MonoMolecularIntegrator::TemplateLength() const { return fwdTpl_.TrueLength(); }
+
+char MonoMolecularIntegrator::operator[](const size_t i) const { return fwdTpl_[i].Base; }
+
+MonoMolecularIntegrator::operator std::string() const
+{
+ std::string result;
+
+ result.resize(fwdTpl_.Length());
+
+ for (size_t i = 0; i < fwdTpl_.Length(); ++i)
+ result[i] = fwdTpl_[i].Base;
+
+ return result;
+}
+
+double MonoMolecularIntegrator::LL(const Mutation& fwdMut)
+{
+ const Mutation revMut(ReverseComplement(fwdMut));
+ fwdTpl_.Mutate(fwdMut);
+ revTpl_.Mutate(revMut);
+ const double ll = AbstractIntegrator::LL(fwdMut);
+ fwdTpl_.Reset();
+ revTpl_.Reset();
+ return ll;
+}
+
+void MonoMolecularIntegrator::ApplyMutation(const Mutation& fwdMut)
+{
+ const Mutation revMut(ReverseComplement(fwdMut));
+
+ fwdTpl_.ApplyMutation(fwdMut);
+ revTpl_.ApplyMutation(revMut);
+
+ for (auto& eval : evals_) {
+ if (eval.Strand() == StrandType::FORWARD)
+ eval.ApplyMutation(fwdMut);
+ else if (eval.Strand() == StrandType::REVERSE)
+ eval.ApplyMutation(revMut);
+ }
+
+ assert(fwdTpl_.Length() == revTpl_.Length());
+
+#ifndef NDEBUG
+ std::string fwd;
+ std::string rev;
+
+ for (size_t i = 0; i < TemplateLength(); ++i) {
+ fwd.push_back(fwdTpl_[i].Base);
+ rev.push_back(revTpl_[i].Base);
+ }
+
+#endif
+
+ assert(fwd == ::PacBio::Data::ReverseComplement(rev));
+}
+
+void MonoMolecularIntegrator::ApplyMutations(std::vector<Mutation>* fwdMuts)
+{
+ std::vector<Mutation> revMuts;
+
+ for (auto it = fwdMuts->crbegin(); it != fwdMuts->crend(); ++it)
+ revMuts.emplace_back(ReverseComplement(*it));
+
+ fwdTpl_.ApplyMutations(fwdMuts);
+ revTpl_.ApplyMutations(&revMuts);
+
+ for (auto& eval : evals_) {
+ if (eval.Strand() == StrandType::FORWARD)
+ eval.ApplyMutations(fwdMuts);
+ else if (eval.Strand() == StrandType::REVERSE)
+ eval.ApplyMutations(&revMuts);
+ }
+
+ assert(fwdTpl_.Length() == revTpl_.Length());
+
+#ifndef NDEBUG
+ std::string fwd;
+ std::string rev;
+
+ for (size_t i = 0; i < TemplateLength(); ++i) {
+ fwd.push_back(fwdTpl_[i].Base);
+ rev.push_back(revTpl_[i].Base);
+ }
+#endif
+
+ assert(fwd == ::PacBio::Data::ReverseComplement(rev));
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/MultiMolecularIntegrator.cpp b/src/MultiMolecularIntegrator.cpp
new file mode 100644
index 0000000..eb104c5
--- /dev/null
+++ b/src/MultiMolecularIntegrator.cpp
@@ -0,0 +1,140 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cassert>
+#include <cmath>
+#include <limits>
+#include <utility>
+
+#include <pacbio/consensus/MultiMolecularIntegrator.h>
+#include <pacbio/data/Sequence.h>
+
+#include "ModelFactory.h"
+
+using namespace PacBio::Data;
+using namespace PacBio::Exception;
+
+namespace PacBio {
+namespace Consensus {
+
+MultiMolecularIntegrator::MultiMolecularIntegrator(const std::string& tpl,
+ const IntegratorConfig& cfg)
+ : AbstractIntegrator(cfg), fwdTpl_{tpl}, revTpl_{::PacBio::Data::ReverseComplement(tpl)}
+{
+}
+
+State MultiMolecularIntegrator::AddRead(const PacBio::Data::MappedRead& read)
+{
+ try {
+ return AbstractIntegrator::AddRead(GetTemplate(read), read);
+ } catch (const TemplateTooSmall& e) {
+ return State::TEMPLATE_TOO_SMALL;
+ }
+}
+
+size_t MultiMolecularIntegrator::TemplateLength() const { return fwdTpl_.length(); }
+
+char MultiMolecularIntegrator::operator[](const size_t i) const { return fwdTpl_[i]; }
+
+MultiMolecularIntegrator::operator std::string() const { return fwdTpl_; }
+
+void MultiMolecularIntegrator::ApplyMutation(const Mutation& fwdMut)
+{
+ const Mutation revMut(ReverseComplement(fwdMut));
+
+ std::vector<Mutation> fwdMuts = {fwdMut};
+ std::vector<Mutation> revMuts = {revMut};
+
+ fwdTpl_ = ::PacBio::Consensus::ApplyMutations(fwdTpl_, &fwdMuts);
+ revTpl_ = ::PacBio::Consensus::ApplyMutations(revTpl_, &revMuts);
+
+ for (auto& eval : evals_) {
+ if (eval.Strand() == StrandType::FORWARD)
+ eval.ApplyMutation(fwdMut);
+ else if (eval.Strand() == StrandType::REVERSE)
+ eval.ApplyMutation(revMut);
+ }
+
+ assert(fwdTpl_.length() == revTpl_.length());
+ assert(fwdTpl_ == ::PacBio::Data::ReverseComplement(revTpl_));
+}
+
+void MultiMolecularIntegrator::ApplyMutations(std::vector<Mutation>* fwdMuts)
+{
+ std::vector<Mutation> revMuts;
+
+ for (auto it = fwdMuts->crbegin(); it != fwdMuts->crend(); ++it)
+ revMuts.emplace_back(ReverseComplement(*it));
+
+ fwdTpl_ = ::PacBio::Consensus::ApplyMutations(fwdTpl_, fwdMuts);
+ revTpl_ = ::PacBio::Consensus::ApplyMutations(revTpl_, &revMuts);
+
+ for (auto& eval : evals_) {
+ if (eval.Strand() == StrandType::FORWARD)
+ eval.ApplyMutations(fwdMuts);
+ else if (eval.Strand() == StrandType::REVERSE)
+ eval.ApplyMutations(&revMuts);
+ }
+
+ assert(fwdTpl_.length() == revTpl_.length());
+ assert(fwdTpl_ == ::PacBio::Data::ReverseComplement(revTpl_));
+}
+
+std::unique_ptr<AbstractTemplate> MultiMolecularIntegrator::GetTemplate(
+ const PacBio::Data::MappedRead& read)
+{
+ const size_t len = read.TemplateEnd - read.TemplateStart;
+
+ if (read.Strand == StrandType::FORWARD) {
+ const size_t start = read.TemplateStart;
+ const size_t end = read.TemplateEnd;
+
+ return std::unique_ptr<AbstractTemplate>(new Template(fwdTpl_.substr(start, len),
+ ModelFactory::Create(read), start,
+ end, read.PinStart, read.PinEnd));
+ } else if (read.Strand == StrandType::REVERSE) {
+ const size_t start = revTpl_.size() - read.TemplateEnd;
+ const size_t end = revTpl_.size() - read.TemplateStart;
+
+ return std::unique_ptr<AbstractTemplate>(new Template(revTpl_.substr(start, len),
+ ModelFactory::Create(read), start,
+ end, read.PinEnd, read.PinStart));
+ }
+
+ throw std::invalid_argument("read is unmapped!");
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/Mutation.cpp b/src/Mutation.cpp
new file mode 100644
index 0000000..5fc353f
--- /dev/null
+++ b/src/Mutation.cpp
@@ -0,0 +1,156 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <algorithm>
+#include <cassert>
+#include <sstream>
+#include <stdexcept>
+
+#include <pacbio/consensus/Mutation.h>
+
+namespace PacBio {
+namespace Consensus {
+
+Mutation::Mutation(MutationType type, size_t start, char base)
+ : Base{base}, Type{type}, start_{start}
+{
+ assert(Type == MutationType::DELETION || Type == MutationType::ANY_INSERTION ||
+ Type == MutationType::ANY_SUBSTITUTION || Base == 'A' || Base == 'C' || Base == 'G' ||
+ Base == 'T');
+}
+
+bool Mutation::IsDeletion() const { return Type == MutationType::DELETION; }
+bool Mutation::IsInsertion() const { return Type == MutationType::INSERTION; }
+bool Mutation::IsSubstitution() const { return Type == MutationType::SUBSTITUTION; }
+bool Mutation::IsAnyInsertion() const { return Type == MutationType::ANY_INSERTION; }
+bool Mutation::IsAnySubstitution() const { return Type == MutationType::ANY_SUBSTITUTION; }
+
+size_t Mutation::Start() const { return start_; }
+
+size_t Mutation::End() const
+{
+ if (Type == MutationType::INSERTION || Type == MutationType::ANY_INSERTION) return start_;
+
+ // if (Type == MutationType::SUBSTITUTION ||
+ // Type == MutationType::ANY_SUBSTITUTION ||
+ // Type == MutationType::DELETION)
+ return start_ + 1;
+}
+
+int Mutation::LengthDiff() const
+{
+ if (Type == MutationType::SUBSTITUTION || Type == MutationType::ANY_SUBSTITUTION) return 0;
+
+ if (Type == MutationType::INSERTION || Type == MutationType::ANY_INSERTION) return 1;
+
+ // Type == deletion
+ return -1;
+}
+
+bool Mutation::operator==(const Mutation& other) const
+{
+ return Type == other.Type && Base == other.Base && start_ == other.start_;
+}
+
+Mutation::operator std::string() const
+{
+ std::stringstream ss;
+ ss << (*this);
+ return ss.str();
+}
+
+ScoredMutation Mutation::WithScore(double score) const { return ScoredMutation(*this, score); }
+
+ScoredMutation::ScoredMutation(const Mutation& mut, double score) : Mutation(mut), Score{score} {}
+
+std::ostream& operator<<(std::ostream& out, const MutationType type)
+{
+ out << "MutationType::";
+ switch (type) {
+ case MutationType::DELETION:
+ out << "DELETION";
+ break;
+ case MutationType::INSERTION:
+ out << "INSERTION";
+ break;
+ case MutationType::SUBSTITUTION:
+ out << "SUBSTITUTION";
+ break;
+ case MutationType::ANY_INSERTION:
+ out << "ANY_INSERTION";
+ break;
+ case MutationType::ANY_SUBSTITUTION:
+ out << "ANY_SUBSTITUTION";
+ break;
+ default:
+ throw std::invalid_argument("invalid MutationType");
+ }
+ return out;
+}
+
+std::ostream& operator<<(std::ostream& out, const Mutation& mut)
+{
+ return out << "Mutation(" << mut.Type << ", " << mut.Start() << ", '" << mut.Base << "')";
+}
+
+std::ostream& operator<<(std::ostream& out, const ScoredMutation& smut)
+{
+ return out << "ScoredMutation(" << static_cast<Mutation>(smut) << ", '" << smut.Score << "')";
+}
+
+std::string ApplyMutations(const std::string& oldTpl, std::vector<Mutation>* const muts)
+{
+ std::sort(muts->begin(), muts->end(), Mutation::SiteComparer);
+ std::vector<Mutation>::const_reverse_iterator it;
+
+ if (muts->empty() || oldTpl.empty()) return oldTpl;
+
+ // TODO(lhepler) make this algorithm not (n^2)
+ std::string newTpl(oldTpl);
+
+ for (it = muts->crbegin(); it != muts->crend(); ++it) {
+ if (it->IsDeletion())
+ newTpl.erase(newTpl.begin() + it->Start());
+ else if (it->IsInsertion())
+ newTpl.insert(newTpl.begin() + it->Start(), it->Base);
+ else if (it->IsSubstitution())
+ newTpl[it->Start()] = it->Base;
+ }
+
+ return newTpl;
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/Polish.cpp b/src/Polish.cpp
new file mode 100644
index 0000000..8e92552
--- /dev/null
+++ b/src/Polish.cpp
@@ -0,0 +1,345 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <algorithm>
+#include <cmath>
+#include <functional>
+#include <iterator>
+#include <limits>
+#include <list>
+#include <set>
+#include <string>
+#include <tuple>
+#include <vector>
+
+#include <boost/optional.hpp>
+
+#include <pacbio/consensus/AbstractIntegrator.h>
+#include <pacbio/consensus/Polish.h>
+
+using namespace std;
+
+namespace PacBio {
+namespace Consensus {
+
+PolishConfig::PolishConfig(const size_t iterations, const size_t separation,
+ const size_t neighborhood)
+ : MaximumIterations(iterations)
+ , MutationSeparation(separation)
+ , MutationNeighborhood(neighborhood)
+{
+}
+
+void Mutations(vector<Mutation>* muts, const AbstractIntegrator& ai, const size_t start,
+ const size_t end)
+{
+ constexpr auto bases = "ACGT";
+ constexpr size_t nbases = 4;
+
+ if (start == end) return;
+
+ char last = (start > 0) ? ai[start - 1] : '\0';
+
+ for (size_t i = start; i < end; ++i) {
+ const char curr = ai[i];
+
+ // insertions come before deletion/substitutions at site i, their End()
+ // is i < i + 1
+ for (size_t j = 0; j < nbases; ++j) {
+ // if it's not a homopolymer insertion, or it's the first base of
+ // one..
+ if (bases[j] != last)
+ muts->emplace_back(Mutation(MutationType::INSERTION, i, bases[j]));
+ }
+
+ // if we're the first in the homopolymer, we can delete
+ if (curr != last) muts->emplace_back(Mutation(MutationType::DELETION, i));
+
+ for (size_t j = 0; j < nbases; ++j) {
+ if (bases[j] != curr)
+ muts->emplace_back(Mutation(MutationType::SUBSTITUTION, i, bases[j]));
+ }
+
+ last = curr;
+ }
+
+ // if we are at the end, make sure we're not performing a terminal
+ // homopolymer insertion
+ for (size_t j = 0; j < nbases; ++j)
+ if (bases[j] != last) muts->emplace_back(Mutation(MutationType::INSERTION, end, bases[j]));
+}
+
+vector<Mutation> Mutations(const AbstractIntegrator& ai, const size_t start, const size_t end)
+{
+ vector<Mutation> muts;
+ Mutations(&muts, ai, start, end);
+ return muts;
+}
+
+vector<Mutation> Mutations(const AbstractIntegrator& ai)
+{
+ return Mutations(ai, 0, ai.TemplateLength());
+}
+
+vector<Mutation> BestMutations(list<ScoredMutation>* scoredMuts, const size_t separation)
+{
+ vector<Mutation> result;
+
+ // TODO handle 0-separation correctly
+ if (separation == 0) throw invalid_argument("nonzero separation required");
+
+ while (!scoredMuts->empty()) {
+ const auto& mut =
+ *max_element(scoredMuts->begin(), scoredMuts->end(), ScoredMutation::ScoreComparer);
+
+ result.emplace_back(mut);
+
+ const size_t start = (separation < mut.Start()) ? mut.Start() - separation : 0;
+ const size_t end = mut.End() + separation;
+
+ scoredMuts->remove_if(
+ [start, end](const ScoredMutation& m) { return start <= m.End() && m.Start() < end; });
+ }
+
+ return result;
+}
+
+vector<Mutation> NearbyMutations(vector<Mutation>* applied, vector<Mutation>* centers,
+ const AbstractIntegrator& ai, const size_t neighborhood)
+{
+ const size_t len = ai.TemplateLength();
+ const auto clamp = [len](const int i) { return max(0, min<int>(len, i)); };
+
+ vector<Mutation> result;
+
+ if (centers->empty()) return result;
+
+ sort(applied->begin(), applied->end(), Mutation::SiteComparer);
+ sort(centers->begin(), centers->end(), Mutation::SiteComparer);
+
+ const auto mutRange = [clamp, neighborhood](const Mutation& mut, const int diff) {
+ const int start = diff + mut.Start() - neighborhood;
+ const int end = diff + mut.End() + neighborhood;
+ return pair<size_t, size_t>(clamp(start), clamp(end));
+ };
+
+ // find the ranges
+ auto ait = applied->cbegin();
+ auto cit = centers->cbegin();
+ int lengthDiff = 0;
+
+ for (; ait != applied->cend() && ait->End() <= cit->Start(); ++ait)
+ lengthDiff += ait->LengthDiff();
+
+ vector<pair<size_t, size_t>> ranges = {mutRange(*cit, lengthDiff)};
+ size_t currEnd = ranges.back().second;
+
+ // increment to the next centerpoint and continue
+ for (++cit; cit != centers->cend(); ++cit) {
+ size_t nextStart, nextEnd;
+
+ for (; ait != applied->cend() && ait->End() <= cit->Start(); ++ait)
+ lengthDiff += ait->LengthDiff();
+
+ tie(nextStart, nextEnd) = mutRange(*cit, lengthDiff);
+
+ // if the next range touches the last one, just extend the last one
+ if (nextStart <= currEnd)
+ ranges.back().second = nextEnd;
+ else {
+ ranges.emplace_back(make_pair(nextStart, nextEnd));
+ currEnd = nextEnd;
+ }
+ }
+
+ for (const auto& range : ranges)
+ Mutations(&result, ai, range.first, range.second);
+
+ return result;
+}
+
+PolishResult Polish(AbstractIntegrator* ai, const PolishConfig& cfg)
+{
+ vector<Mutation> muts = Mutations(*ai);
+ hash<string> hashFn;
+ size_t oldTpl = hashFn(*ai);
+ set<size_t> history = {oldTpl};
+
+ PolishResult result;
+
+ for (size_t i = 0; i < cfg.MaximumIterations; ++i) {
+ // find the best mutations given our parameters
+ {
+ const double LL = ai->LL();
+ list<ScoredMutation> scoredMuts;
+
+ for (const auto& mut : muts) {
+ const double ll = ai->LL(mut);
+ if (ll > LL) scoredMuts.emplace_back(mut.WithScore(ll));
+ ++result.mutationsTested;
+ }
+
+ // take best mutations in separation window, apply them
+ muts = BestMutations(&scoredMuts, cfg.MutationSeparation);
+ }
+
+ // convergence!!
+ if (muts.empty()) {
+ result.hasConverged = true;
+ return result;
+ }
+
+ const size_t newTpl = hashFn(ApplyMutations(*ai, &muts));
+
+ const auto diagnostics = [&result](AbstractIntegrator* ai) {
+ result.maxAlphaPopulated.emplace_back(ai->MaxAlphaPopulated());
+ result.maxBetaPopulated.emplace_back(ai->MaxBetaPopulated());
+ result.maxNumFlipFlops.emplace_back(ai->MaxNumFlipFlops());
+ };
+
+ if (history.find(newTpl) != history.end()) {
+ /* Cyclic behavior guard - Dave A. found some edge cases where the
+ template was mutating back to an earlier version. This is a bad
+ and should be rare. He found that by applying the single best
+ mutation you could avoid the loop. (That is if adding Muts X + Y
+ made removing muts X + Y beneficial, then you can break that
+ inifinite loop by just applying X or Y, as presumably this removes
+ the interaction between them that leads to the cycling behavior.
+ This step is just a heuristic work around that was found. */
+ ai->ApplyMutation(muts.front());
+ oldTpl = hashFn(*ai);
+ ++result.mutationsApplied;
+
+ diagnostics(ai);
+
+ // get the mutations for the next round
+ vector<Mutation> applied = {muts.front()};
+ muts = NearbyMutations(&applied, &muts, *ai, cfg.MutationNeighborhood);
+ } else {
+ ai->ApplyMutations(&muts);
+ oldTpl = newTpl;
+ result.mutationsApplied += muts.size();
+
+ diagnostics(ai);
+
+ // get the mutations for the next round
+ muts = NearbyMutations(&muts, &muts, *ai, cfg.MutationNeighborhood);
+ }
+
+ // keep track of which templates we've seen
+ history.insert(oldTpl);
+ }
+
+ return result;
+}
+
+namespace { // anonymous
+
+int ProbabilityToQV(double probability)
+{
+ if (probability < 0.0 || probability > 1.0)
+ throw invalid_argument("invalid value: probability not in [0,1]");
+ else if (probability == 0.0)
+ probability = numeric_limits<double>::min();
+
+ return static_cast<int>(round(-10.0 * log10(probability)));
+}
+
+inline int ScoreSumToQV(const double scoreSum)
+{
+ return ProbabilityToQV(1.0 - 1.0 / (1.0 + scoreSum));
+}
+
+} // anonymous namespace
+
+vector<int> ConsensusQualities(AbstractIntegrator& ai)
+{
+ vector<int> quals;
+ quals.reserve(ai.TemplateLength());
+ const double LL = ai.LL();
+ for (size_t i = 0; i < ai.TemplateLength(); ++i) {
+ double scoreSum = 0.0;
+ for (const auto& m : Mutations(ai, i, i + 1)) {
+ // skip mutations that start beyond the current site (e.g. trailing insertions)
+ if (m.Start() > i) continue;
+ // TODO (lhepler): this is dumb, but untestable mutations,
+ // aka insertions at ends, cause all sorts of weird issues
+ const double score = ai.LL(m) - LL;
+ // this really should never happen
+ if (score >= 0.0) continue;
+ scoreSum += exp(score);
+ }
+ quals.emplace_back(ScoreSumToQV(scoreSum));
+ }
+ return quals;
+}
+
+QualityValues ConsensusQVs(AbstractIntegrator& ai)
+{
+ const size_t len = ai.TemplateLength();
+ vector<int> quals, delQVs, insQVs, subQVs;
+ quals.reserve(len);
+ delQVs.reserve(len);
+ insQVs.reserve(len);
+ subQVs.reserve(len);
+ const double LL = ai.LL();
+ for (size_t i = 0; i < len; ++i) {
+ double qualScoreSum = 0.0, delScoreSum = 0.0, insScoreSum = 0.0, subScoreSum = 0.0;
+ for (const auto& m : Mutations(ai, i, i + 1)) {
+ // skip mutations that start beyond the current site (e.g. trailing insertions)
+ if (m.Start() > i) continue;
+ const double score = ai.LL(m) - LL;
+ // this really should never happen
+ if (score >= 0.0) continue;
+ const double expScore = exp(score);
+ qualScoreSum += expScore;
+ if (m.IsDeletion())
+ delScoreSum += expScore;
+ else if (m.IsInsertion())
+ insScoreSum += expScore;
+ else if (m.IsSubstitution())
+ subScoreSum += expScore;
+ }
+ quals.emplace_back(ScoreSumToQV(qualScoreSum));
+ delQVs.emplace_back(ScoreSumToQV(delScoreSum));
+ insQVs.emplace_back(ScoreSumToQV(insScoreSum));
+ subQVs.emplace_back(ScoreSumToQV(subScoreSum));
+ }
+ // TODO(lhepler): discuss InsQV being len + 1 to capture trailing insertion
+ return QualityValues{move(quals), move(delQVs), move(insQVs), move(subQVs)};
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/Read.cpp b/src/Read.cpp
new file mode 100644
index 0000000..882eaf0
--- /dev/null
+++ b/src/Read.cpp
@@ -0,0 +1,102 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cassert>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/data/Read.h>
+
+namespace PacBio {
+namespace Data {
+
+SNR::SNR(const double a, const double c, const double g, const double t) : A(a), C(c), G(g), T(t) {}
+
+SNR::SNR(const std::vector<double>& snrs) : A(snrs[0]), C(snrs[1]), G(snrs[2]), T(snrs[3])
+{
+ assert(snrs.size() == 4);
+}
+
+namespace {
+
+double clamp(double val, double lo, double hi) { return std::min(std::max(val, lo), hi); }
+
+} // namespace
+
+SNR ClampSNR(const SNR& val, const SNR& lo, const SNR& hi)
+{
+ return SNR(clamp(val.A, lo.A, hi.A), clamp(val.C, lo.C, hi.C), clamp(val.G, lo.G, hi.G),
+ clamp(val.T, lo.T, hi.T));
+}
+
+Read::Read(const std::string& name, const std::string& seq, const std::vector<uint8_t>& ipd,
+ const std::vector<uint8_t>& pw, const SNR& snr, const std::string& model)
+ : Name{name}, Seq{seq}, IPD{ipd}, PulseWidth{pw}, SignalToNoise{snr}, Model{model}
+{
+}
+
+MappedRead::MappedRead(const Read& read, StrandType strand, size_t templateStart,
+ size_t templateEnd, bool pinStart, bool pinEnd)
+ : Read(read)
+ , Strand{strand}
+ , TemplateStart{templateStart}
+ , TemplateEnd{templateEnd}
+ , PinStart{pinStart}
+ , PinEnd{pinEnd}
+{
+}
+
+std::ostream& operator<<(std::ostream& os, const MappedRead& mr)
+{
+ os << "MappedRead(Read(\"" << mr.Name << "\", \"" << mr.Seq << "\", \"" << mr.Model << "\"), ";
+ switch (mr.Strand) {
+ case StrandType::FORWARD:
+ os << "StrandType_FORWARD, ";
+ break;
+ case StrandType::REVERSE:
+ os << "StrandType_REVERSE, ";
+ break;
+ case StrandType::UNMAPPED:
+ os << "StrandType_UNMAPPED, ";
+ break;
+ default:
+ throw std::runtime_error("Unsupported Strand");
+ }
+ os << mr.TemplateStart << ", " << mr.TemplateEnd << ", ";
+ os << mr.PinStart << ", " << mr.PinEnd << ")";
+ return os;
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/ReadId.cpp b/src/ReadId.cpp
new file mode 100644
index 0000000..c26b62c
--- /dev/null
+++ b/src/ReadId.cpp
@@ -0,0 +1,68 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <iostream>
+#include <sstream>
+#include <string>
+
+#include <pacbio/data/ReadId.h>
+
+using namespace std;
+
+namespace PacBio {
+namespace Data {
+
+ReadId::operator std::string() const
+{
+ stringstream ss;
+ ss << *this;
+ return ss.str();
+}
+
+ostream& operator<<(ostream& os, const ReadId& id)
+{
+ os << *(id.MovieName) << '/' << id.HoleNumber;
+
+ if (id.ZmwInterval) {
+ os << '/' << id.ZmwInterval->Left() << '_' << id.ZmwInterval->Right();
+ }
+
+ return os;
+}
+
+} // namespace Data
+} // namespace PacBio
diff --git a/src/Recursor.cpp b/src/Recursor.cpp
new file mode 100644
index 0000000..bb08d79
--- /dev/null
+++ b/src/Recursor.cpp
@@ -0,0 +1,50 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include "Recursor.h"
+
+namespace PacBio {
+namespace Consensus {
+
+AbstractRecursor::AbstractRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const PacBio::Data::MappedRead& mr, const double scoreDiff)
+ : tpl_{std::forward<std::unique_ptr<AbstractTemplate>>(tpl)}
+ , read_{mr}
+ , scoreDiff_{exp(scoreDiff)}
+{
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/Recursor.h b/src/Recursor.h
new file mode 100644
index 0000000..9932151
--- /dev/null
+++ b/src/Recursor.h
@@ -0,0 +1,801 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander, Lance Hepler
+
+#pragma once
+
+#include <algorithm>
+#include <climits>
+#include <memory>
+#include <utility>
+
+#include <pacbio/consensus/Template.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/exception/StateError.h>
+
+#include "matrix/ScaledMatrix.h"
+
+namespace PacBio {
+namespace Consensus {
+
+// AbstractRecursor is in Template.h
+
+// TODO(lhepler) comment about use of CRTP
+template <typename Derived>
+class Recursor : public AbstractRecursor
+{
+public:
+ // \brief Construct a Recursor from a Template and a MappedRead,
+ // The scoreDiff here is passed in negative logScale and converted
+ // to the appropriate divisor.
+ Recursor(std::unique_ptr<AbstractTemplate>&& tpl, const PacBio::Data::MappedRead& mr,
+ double scoreDiff = 12.5);
+
+ /// \brief Fill the alpha and beta matrices.
+ /// This routine will fill the alpha and beta matrices, ensuring
+ /// that the score computed from the alpha and beta recursions are
+ /// identical, refilling back-and-forth if necessary.
+ size_t FillAlphaBeta(M& alpha, M& beta) const;
+
+ /**
+ Fill in the alpha matrix. This matrix has the read run along the rows, and
+ the template run along the columns. The first row and column do not correspond
+ to a template position. Therefore the match represented at position (i,j)
+ corresponds to a match between template positions (i+1, j+1).
+
+ The alpha matrix is the "Forward" matrix used in the forward/backward
+ algorithm.
+ The i,j position of the matrix represents the probability of all paths up
+ to the point where the ith read position and jth template have been
+ "emitted."
+ The matrix is calculated recursively by examining all possible transitions
+ into (i,j), and calculating the probability we were in the previous state,
+ times the probability of a transition into (i,j) times the probability of
+ emitting the observation that corresponds to (i,j). All probabilities are
+ calculated and stored as LOG values.
+
+ Note that in doing this calculation, in order to work with di-nucleotide
+ contexts, we require that the first and last transition be a match. In other words the
+ start and end of the read and template are "pinned" to each other.
+
+ //TODO: Verify memory is initialized to 0!
+
+ @param guide An object that helps inform how to select the size of "bands"
+ for the banded algorithm used. This is typically the beta matrix if we are
+ "repopulating" the matrix.
+ @param alpha The matrix to be filled.
+ */
+
+ void FillAlpha(const M& guide, M& alpha) const;
+
+ /**
+ Fill the Beta matrix, the backwards half of the forward-backward algorithm.
+ This represents the probability that starting from the (i,j) state, the
+ combined probability of transitioning out and following all paths through to the
+ end. That is, we need to calculate transition from state and emit from next
+ state for each
+
+ In combination with the Alpha matrix, this allows us to calculate all paths
+ that pass through the (i,j) element, as exp(Alpha(i,j) + Beta(i,j))
+
+ All probabilities stored in the matrix are stored as NON-LOGGED
+ probabilities.
+
+ @param e The evaluator, such as QvEvaluator
+ @param M the guide matrix for banding (this needs more documentation)
+ @param beta The Beta matrix, stored as either a DenseMatrix or a
+ SparseMatrix.
+ */
+
+ void FillBeta(const M& guide, M& beta) const;
+
+ /// \brief Calculate the recursion score by "linking" partial alpha and/or
+ /// beta matrices.
+ double LinkAlphaBeta(const M& alpha, size_t alphaColumn, const M& beta, size_t betaColumn,
+ size_t absoluteColumn) const;
+
+ void ExtendAlpha(const M& alpha, size_t beginColumn, M& ext, size_t numExtColumns = 2) const;
+
+ void ExtendBeta(const M& beta, size_t endColumn, M& ext, int lengthDiff = 0) const;
+
+private:
+ std::pair<size_t, size_t> RowRange(size_t j, const M& matrix) const;
+
+ /// \brief Reband alpha and beta matrices.
+ /// This routine will reband alpha and beta to the convex hull
+ /// of the maximum path through each and the inputs for column j.
+ bool RangeGuide(size_t j, const M& guide, const M& matrix, size_t* beginRow,
+ size_t* endRow) const;
+ // The RangeGuide function determines the minimum score by dividing out scoreDiff_
+
+private:
+ std::vector<uint8_t> emissions_;
+};
+
+namespace { // anonymous
+
+typedef std::pair<size_t, size_t> Interval;
+
+// TODO(dalexander): put these into a RecursorConfig struct
+// TODO(anybody): Hmmm... not sure what the heck to do about these...
+constexpr int MAX_FLIP_FLOPS = 5;
+constexpr double ALPHA_BETA_MISMATCH_TOLERANCE = 0.001;
+constexpr double REBANDING_THRESHOLD = 0.04;
+
+constexpr uint8_t kDefaultBase = 0; // corresponding to A, usually
+constexpr TemplatePosition kDefaultTplPos = TemplatePosition{'A', kDefaultBase, 1, 0, 0, 0};
+
+inline Interval RangeUnion(const Interval& range1, const Interval& range2)
+{
+ return Interval(std::min(range1.first, range2.first), std::max(range1.second, range2.second));
+}
+
+inline Interval RangeUnion(const Interval& range1, const Interval& range2, const Interval& range3,
+ const Interval& range4)
+{
+ return RangeUnion(RangeUnion(range1, range2), RangeUnion(range3, range4));
+}
+
+inline double Combine(const double a, const double b) { return a + b; }
+} // namespace anonymous
+
+template <typename Derived>
+void Recursor<Derived>::FillAlpha(const M& guide, M& alpha) const
+{
+ // We are pinning, so should never go all the way to the end of the
+ // read/template
+ // But our matrix indexing is one off the model/outcome indexing
+ // so the match in (1,1) corresponds to a pairing between
+ // Model[0]/Outcome[0]
+ size_t I = read_.Length();
+ size_t J = tpl_->Length();
+
+ assert(alpha.Rows() == I + 1 && alpha.Columns() == J + 1);
+ assert(guide.IsNull() || (guide.Rows() == alpha.Rows() && guide.Columns() == alpha.Columns()));
+
+ // Initial condition, we always start with a match
+ alpha.StartEditingColumn(0, 0, 1);
+ alpha.Set(0, 0, 1.0);
+ alpha.FinishEditingColumn<false>(0, 0, 1);
+ // End initial conditions
+
+ size_t hintBeginRow = 1, hintEndRow = 1;
+ auto prevTransProbs = kDefaultTplPos;
+ uint8_t prevTplBase = prevTransProbs.Idx;
+
+ for (size_t j = 1; j < J; ++j) // Note due to offset with reads and otherwise, this is ugly-ish
+ {
+ // Load up the transition parameters for this context
+
+ auto currTransProbs = (*tpl_)[j - 1];
+ auto currTplBase = currTransProbs.Idx;
+ this->RangeGuide(j, guide, alpha, &hintBeginRow, &hintEndRow);
+
+ size_t i;
+ double thresholdScore = 0.0;
+ double maxScore = 0.0;
+ double score = 0.0;
+ alpha.StartEditingColumn(j, hintBeginRow, hintEndRow);
+
+ auto nextTplBase = (*tpl_)[j].Idx;
+
+ size_t beginRow = hintBeginRow, endRow;
+ // Recursively calculate [Probability in last state] * [Probability
+ // transition to new state] * [Probability of emission]
+ for (i = beginRow; i < I && (score >= thresholdScore || i < hintEndRow); ++i) {
+ // TODO: Terrible hack right now to emit this guy as teh IQV
+ const uint8_t curReadEm = emissions_[i - 1];
+ double thisMoveScore = 0.0;
+ score = 0.0;
+ // Match:
+ /* Important! Note that because we require the initial state to be
+ a match,
+ when i = 1 and j = 1 the match transition probability must be 1,
+ since no other options
+ are allowed. Similarly, the probability for the match
+ probability to the end base should be 1.
+
+ Note that for the first "match" between a read and template, we
+ have no choice but to
+ hard code it to 1, as there is no defined transition probability
+ for a dinucleotide context.
+
+ *********** EDGE_CONDITION ************
+ */
+ if (i > 0 && j > 0) {
+ thisMoveScore = alpha(i - 1, j - 1) * prevTransProbs.Match *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::MATCH, curReadEm, prevTplBase, currTplBase);
+ score = Combine(score, thisMoveScore);
+ }
+
+ if (i > 1) {
+ // Branch, due to pinning, can't "insert" first or last read base
+ thisMoveScore = alpha(i - 1, j) * currTransProbs.Branch *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::BRANCH, curReadEm, currTplBase, nextTplBase);
+ score = Combine(score, thisMoveScore);
+
+ // Stick
+ thisMoveScore = alpha(i - 1, j) * currTransProbs.Stick *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::STICK, curReadEm, currTplBase, nextTplBase);
+ score = Combine(score, thisMoveScore);
+ }
+
+ // Deletion, due to pinning, can't "delete" first or last template bp
+ if (j > 1) {
+ thisMoveScore = alpha(i, j - 1) * prevTransProbs.Deletion;
+ score = Combine(score, thisMoveScore);
+ }
+
+ // Save score
+ alpha.Set(i, j, score);
+
+ if (score > maxScore) {
+ maxScore = score;
+ thresholdScore = maxScore / scoreDiff_;
+ }
+ }
+ endRow = i;
+ prevTransProbs = currTransProbs;
+ prevTplBase = currTplBase;
+ // Now, revise the hints to tell the caller where the mass of the
+ // distribution really lived in this column.
+ hintEndRow = endRow;
+ for (i = beginRow; i < endRow && alpha(i, j) < thresholdScore; ++i)
+ ;
+ hintBeginRow = i;
+
+ // Don't rescale until we finish updating the hint.
+ alpha.FinishEditingColumn<true>(j, beginRow, endRow, maxScore);
+ }
+
+ /* Now fill out the probability in the last pinned position.
+ * We require that we end in a match.
+ * search for the term EDGE_CONDITION to find a comment with more
+ * information */
+ {
+ auto currTplBase = (*tpl_)[J - 1].Idx;
+ assert(J < 2 || prevTplBase == (*tpl_)[J - 2].Idx);
+ // end in the homopolymer state for now.
+ auto likelihood = alpha(I - 1, J - 1) *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::MATCH, emissions_[I - 1], prevTplBase, currTplBase);
+ alpha.StartEditingColumn(J, I, I + 1);
+ alpha.Set(I, J, likelihood);
+ alpha.FinishEditingColumn<false>(J, I, I + 1);
+ }
+}
+
+template <typename Derived>
+void Recursor<Derived>::FillBeta(const M& guide, M& beta) const
+{
+ size_t I = read_.Length();
+ size_t J = tpl_->Length();
+
+ assert(beta.Rows() == I + 1 && beta.Columns() == J + 1);
+ assert(guide.IsNull() || (guide.Rows() == beta.Rows() && guide.Columns() == beta.Columns()));
+
+ // Setup initial condition, at the end we are one
+ beta.StartEditingColumn(J, I, I + 1);
+ beta.Set(I, J, 1.0);
+ beta.FinishEditingColumn<false>(J, I, I + 1);
+
+ // Totally arbitray decision here...
+ size_t hintBeginRow = I, hintEndRow = I;
+
+ // Recursively calculate [Probability transition to next state] *
+ // [Probability of emission at that state] * [Probability from that state]
+ for (size_t j = J - 1; j > 0; --j) {
+ const auto nextTplPos = (*tpl_)[j];
+ const auto nextTplBase = nextTplPos.Idx;
+ const auto currTransProbs = (*tpl_)[j - 1];
+
+ this->RangeGuide(j, guide, beta, &hintBeginRow, &hintEndRow);
+
+ beta.StartEditingColumn(j, hintBeginRow, hintEndRow);
+
+ size_t i;
+ double score = 0.0;
+ double thresholdScore = 0.0;
+ double maxScore = 0.0;
+
+ size_t endRow = hintEndRow;
+ for (i = endRow > 0 ? endRow - 1 : 0; // Since we stop if i <= 0, do not allow i to be neg
+ i > 0 && (score >= thresholdScore || i >= hintBeginRow); --i) {
+ const uint8_t nextReadEm = emissions_[i];
+ double thisMoveScore = 0.0;
+ score = 0.0;
+
+ // Match
+ if (i + 1 < I) {
+ thisMoveScore = beta(i + 1, j + 1) * currTransProbs.Match *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::MATCH, nextReadEm, currTransProbs.Idx, nextTplBase);
+ score = Combine(score, thisMoveScore);
+ } else if (i + 1 == I && j + 1 == J) {
+ thisMoveScore = beta(i + 1, j + 1) *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::MATCH, nextReadEm, currTransProbs.Idx, nextTplBase);
+ score = Combine(score, thisMoveScore);
+ }
+
+ // Branch, can only transition to an insertion for the 2nd to last read base and before
+ if (0 < i && i < I) {
+ thisMoveScore = beta(i + 1, j) * currTransProbs.Branch *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::BRANCH, nextReadEm, currTransProbs.Idx, nextTplBase);
+ score = Combine(score, thisMoveScore);
+
+ // Stick, can only transition to an insertion for the 2nd to last read base
+ thisMoveScore = beta(i + 1, j) * currTransProbs.Stick *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::STICK, nextReadEm, currTransProbs.Idx, nextTplBase);
+ score = Combine(score, thisMoveScore);
+ }
+
+ // Deletion
+ if (0 < j && j < J) {
+ thisMoveScore = beta(i, j + 1) * currTransProbs.Deletion;
+ score = Combine(score, thisMoveScore);
+ }
+
+ // Save score
+ beta.Set(i, j, score);
+
+ if (score > maxScore) {
+ maxScore = score;
+ thresholdScore = maxScore / scoreDiff_;
+ }
+ }
+
+ size_t beginRow = i + 1;
+ // DumpBetaMatrix(beta);
+ // Now, revise the hints to tell the caller where the mass of the
+ // distribution really lived in this column.
+
+ hintBeginRow = beginRow;
+ for (i = endRow; i > beginRow && beta(i - 1, j) < thresholdScore; --i)
+ ;
+ hintEndRow = i;
+
+ // Don't rescale until we update the hints
+ beta.FinishEditingColumn<true>(j, beginRow, endRow, maxScore);
+ }
+
+ /* Now to fill the top row which must be a match
+ * search for the term EDGE_CONDITION to find a comment with more
+ * information */
+ {
+ beta.StartEditingColumn(0, 0, 1);
+ auto match_emission_prob = static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::MATCH, emissions_[0], kDefaultBase, (*tpl_)[0].Idx);
+ beta.Set(0, 0, match_emission_prob * beta(1, 1));
+ beta.FinishEditingColumn<false>(0, 0, 1);
+ }
+}
+
+/// Calculate the recursion score by "stitching" together partial
+/// alpha and beta matrices. alphaColumn, betaColumn, and
+/// absoluteColumn all refer to the same logical position in the
+/// template, but may have different values if, for instance,
+/// alpha here is a sub-range of the columns of the full alpha
+/// matrix. Columns betaColumn and betaColumn + 1 of beta will be
+/// read; columns alphaColumn - 1 and alphaColumn - 2 of alpha
+/// will be read.
+template <typename Derived>
+double Recursor<Derived>::LinkAlphaBeta(const M& alpha, size_t alphaColumn, const M& beta,
+ size_t betaColumn, size_t absoluteColumn) const
+{
+ const size_t I = read_.Length();
+
+ assert(alphaColumn > 1 && absoluteColumn > 1);
+ assert(absoluteColumn <= tpl_->Length());
+
+ size_t usedBegin, usedEnd;
+ std::tie(usedBegin, usedEnd) =
+ RangeUnion(alpha.UsedRowRange(alphaColumn - 2), alpha.UsedRowRange(alphaColumn - 1),
+ beta.UsedRowRange(betaColumn), beta.UsedRowRange(betaColumn + 1));
+
+ double v = 0.0, thisMoveScore;
+
+ const auto currTplParams = (*tpl_)[absoluteColumn - 1];
+ const auto prevTplParams = (*tpl_)[absoluteColumn - 2];
+
+ for (size_t i = usedBegin; i < usedEnd; i++) {
+ if (i < I) {
+ const uint8_t readEm = emissions_[i];
+ // Match
+ thisMoveScore = alpha(i, alphaColumn - 1) * prevTplParams.Match *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::MATCH, readEm, prevTplParams.Idx, currTplParams.Idx) *
+ beta(i + 1, betaColumn);
+ v = Combine(v, thisMoveScore);
+ }
+
+ // Delete
+ thisMoveScore = alpha(i, alphaColumn - 1) * prevTplParams.Deletion * beta(i, betaColumn);
+ v = Combine(v, thisMoveScore);
+ }
+
+ return (std::log(v) + alpha.GetLogProdScales(0, alphaColumn) +
+ beta.GetLogProdScales(betaColumn, beta.Columns()));
+}
+
+/**
+ This method extends that Alpha matrix into a temporary matrix given by
+ ext. It extends the region [beginColumn, beginColumn + numExtColumns)
+
+ Note that this method is used EXCLUSIVELY for testing mutations, and so
+ we don't get the actual parameters and positions from the template, but we
+ get them after a "virtual" mutation has been applied.
+
+ All new data is placed in the extension matrix. The guesses for start/end
+ rows in the banding are determined by evaluating neighbors of each position.
+ @param <#parameter#>
+ @returns <#retval#>
+ */
+template <typename Derived>
+void Recursor<Derived>::ExtendAlpha(const M& alpha, size_t beginColumn, M& ext,
+ size_t numExtColumns) const
+{
+ assert(numExtColumns >= 2); // We have to fill at least one
+ assert(alpha.Rows() == read_.Length() + 1 &&
+ ext.Rows() == read_.Length() + 1); // The read never mutates
+
+ // The new template may not be the same length as the old template.
+ // Just make sure that we have anough room to fill out the extend buffer
+ assert(beginColumn + 1 < tpl_->Length() + 1);
+ assert(ext.Columns() >= numExtColumns);
+ assert(beginColumn >= 2);
+ // Due to pinning at the end, moves are only possible if less than these
+ // positions.
+ size_t maxLeftMovePossible = tpl_->Length();
+ size_t maxDownMovePossible = read_.Length();
+
+ // completely fill the rectangle bounded by the min and max
+ size_t beginRow, endRow;
+ std::tie(beginRow, endRow) = alpha.UsedRowRange(beginColumn);
+ for (size_t j = 1; j + beginColumn < alpha.Columns() && j <= numExtColumns; ++j)
+ endRow = std::max(alpha.UsedRowRange(j + beginColumn).second, endRow);
+
+ for (size_t extCol = 0; extCol < numExtColumns; extCol++) {
+ size_t j = beginColumn + extCol;
+
+ ext.StartEditingColumn(extCol, beginRow, endRow);
+
+ size_t i;
+ double score = 0.0;
+ double max_score = score;
+ // Grab values that will be useful for the whole column
+ auto currTplParams = (*tpl_)[j - 1];
+ auto currTplBase = currTplParams.Idx;
+ TemplatePosition prevTplParams = kDefaultTplPos;
+ if (j > 1) {
+ prevTplParams = (*tpl_)[j - 2];
+ }
+ uint8_t nextTplBase = -1; // This value is never being used, but it silences notorious gcc
+ if (j != maxLeftMovePossible) {
+ nextTplBase = (*tpl_)[j].Idx;
+ }
+
+ for (i = beginRow; i < endRow; i++) {
+ const uint8_t currReadEm = emissions_[i - 1];
+ double thisMoveScore = 0.0;
+
+ // Match
+ if (i > 0 && j > 0) {
+ double prev = extCol == 0 ? alpha(i - 1, j - 1) : ext(i - 1, extCol - 1);
+ if (i < maxDownMovePossible && j < maxLeftMovePossible) {
+ thisMoveScore =
+ prev * prevTplParams.Match *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::MATCH, currReadEm, prevTplParams.Idx, currTplParams.Idx);
+ } else if (i == maxDownMovePossible && j == maxLeftMovePossible) {
+ thisMoveScore =
+ prev *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::MATCH, currReadEm, prevTplParams.Idx, currTplParams.Idx);
+ }
+ score = thisMoveScore;
+ }
+
+ // Branch
+ if (i > 1 && i < maxDownMovePossible && j != maxLeftMovePossible) {
+ thisMoveScore = ext(i - 1, extCol) * currTplParams.Branch *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::BRANCH, currReadEm, currTplBase, nextTplBase);
+ score = Combine(score, thisMoveScore);
+ }
+
+ // Stick
+ if (i > 1 && i < maxDownMovePossible && j != maxLeftMovePossible) {
+ thisMoveScore = ext(i - 1, extCol) * currTplParams.Stick *
+ static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::STICK, currReadEm, currTplBase, nextTplBase);
+ score = Combine(score, thisMoveScore);
+ }
+
+ // Delete
+ if (j > 1 && j < maxLeftMovePossible && i != maxDownMovePossible) {
+ double prev = extCol == 0 ? alpha(i, j - 1) : ext(i, extCol - 1);
+ thisMoveScore = prev * prevTplParams.Deletion;
+ score = Combine(score, thisMoveScore);
+ }
+ ext.Set(i, extCol, score);
+ if (score > max_score) max_score = score;
+ }
+ assert(i == endRow);
+ ext.FinishEditingColumn<true>(extCol, beginRow, endRow, max_score);
+ }
+}
+
+// Semantic: After ExtendBeta(B, j), we have
+// ext(:, numExtColumns-1) = B'(:,j)
+// ext(:, numExtColumns-2) = B'(:,j-1) ...
+//
+// Note: lastColumn is the numerically largest column number that
+// will be filled, but it is filled first since beta fill is done
+// backwards.
+//
+// Accesses B(:, ..(j+2))
+
+/* Note this is a very confusing routine in order to avoid recomputing and
+ additional memory allocations. This routine tries to stick on a beta matrix
+ to the original and back trace to the 0,0 position of this extension matrix.
+ matrix from the original. Note that the original beta
+ matrix is indexed by the original template positions, while the template
+ bases and parameters are now indexed according the the "virtual" template
+ to which mutations have been applied.
+ */
+// @param lastColumn - Where we
+template <typename Derived>
+void Recursor<Derived>::ExtendBeta(const M& beta, size_t lastColumn, M& ext, int lengthDiff) const
+{
+ size_t I = read_.Length();
+ size_t J = tpl_->Length();
+
+ // How far back do we have to go until we are at the zero (first) column?
+ // we always go all the way back.
+ size_t numExtColumns = 1 + lengthDiff + lastColumn;
+ int firstColumn = 0 - lengthDiff;
+ int lastExtColumn = numExtColumns - 1;
+
+ // The new template may not be the same length as the old template.
+ // Just make sure that we have enough room to fill out the extend buffer
+ assert(lastColumn + 1 <= J);
+ assert(lastColumn < 4); // Since we are only testing mutations of size 1,
+ // and the check prior for a beginning mutation is
+ // < 3, max = 2 + 1 = 3
+ assert(ext.Columns() >= numExtColumns);
+ assert(beta.Rows() == I + 1 && ext.Rows() == I + 1);
+ assert(abs(lengthDiff) < 2);
+
+ // completely fill the rectangle bounded by the min and max
+ int beginRow, endRow;
+ if (lastColumn + 1 < beta.Columns())
+ std::tie(beginRow, endRow) = beta.UsedRowRange(lastColumn + 1);
+ else
+ std::tie(beginRow, endRow) = beta.UsedRowRange(lastColumn);
+ for (size_t j = 0; j <= lastColumn && j <= numExtColumns; ++j)
+ beginRow = std::min(static_cast<int>(beta.UsedRowRange(lastColumn - j).first), beginRow);
+
+ for (int j = lastColumn; j + numExtColumns - lastColumn > 0; j--) {
+ /* Convert from old template to new template coordinates.
+ lengthDiff will be 0 for substitution, -1 for deletion and +1 for
+ insertion
+ */
+ size_t jp = j + lengthDiff;
+ // What is the current extension column we are adding data into.
+ size_t extCol = lastExtColumn - (lastColumn - j);
+
+ ext.StartEditingColumn(extCol, beginRow, endRow);
+
+ // Load up useful values referenced throughout the column.
+ auto nextTplParams = (*tpl_)[jp];
+ auto nextTplBase = nextTplParams.Idx;
+
+ TemplatePosition currTplParams = kDefaultTplPos;
+ if (jp > 0) currTplParams = (*tpl_)[jp - 1];
+ double max_score = 0.0;
+
+ for (int i = endRow - 1; i >= beginRow; i--) {
+ assert(i < static_cast<int>(I));
+ assert(j < static_cast<int>(J));
+ uint8_t nextReadEm = emissions_[i];
+ double score = 0.0;
+
+ if (0 < i && firstColumn < j) {
+ bool extColIsLastExtColumn = static_cast<int>(extCol) == lastExtColumn;
+ // Match
+ const double matchNext =
+ extColIsLastExtColumn ? beta(i + 1, j + 1) : ext(i + 1, extCol + 1);
+ // First and last have to start with an emission
+ const double matchScore =
+ matchNext * currTplParams.Match *
+ static_cast<const Derived*>(this)->EmissionPr(MoveType::MATCH, nextReadEm,
+ currTplParams.Idx, nextTplBase);
+ score = Combine(score, matchScore);
+
+ // Branch
+ const double branchScore =
+ ext(i + 1, extCol) * currTplParams.Branch *
+ static_cast<const Derived*>(this)->EmissionPr(MoveType::BRANCH, nextReadEm,
+ currTplParams.Idx, nextTplBase);
+ score = Combine(score, branchScore);
+
+ // Stick
+ const double stickScore =
+ ext(i + 1, extCol) * currTplParams.Stick *
+ static_cast<const Derived*>(this)->EmissionPr(MoveType::STICK, nextReadEm,
+ currTplParams.Idx, nextTplBase);
+ score = Combine(score, stickScore);
+
+ // Deletion
+ double const delNext = extColIsLastExtColumn ? beta(i, j + 1) : ext(i, extCol + 1);
+ double const deletionScore = delNext * currTplParams.Deletion;
+ score = Combine(score, deletionScore);
+ }
+
+ ext.Set(i, extCol, score);
+ if (score > max_score) max_score = score;
+ }
+ ext.FinishEditingColumn<true>(extCol, beginRow, endRow, max_score);
+ }
+
+ // fill out the (0, 0) entry of the matrix
+ {
+ ext.StartEditingColumn(0, 0, 1);
+ const double match_trans_prob = (lastExtColumn == 0) ? beta(1, lastColumn + 1) : ext(1, 1);
+ const double match_emission_prob = static_cast<const Derived*>(this)->EmissionPr(
+ MoveType::MATCH, emissions_[0], kDefaultBase, (*tpl_)[0].Idx);
+ ext.Set(0, 0, match_trans_prob * match_emission_prob);
+ ext.FinishEditingColumn<false>(0, 0, 1);
+ }
+}
+
+template <typename Derived>
+Recursor<Derived>::Recursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const PacBio::Data::MappedRead& mr, const double scoreDiff)
+ : AbstractRecursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff)
+ , emissions_{Derived::EncodeRead(read_)}
+{
+}
+
+template <typename Derived>
+size_t Recursor<Derived>::FillAlphaBeta(M& a, M& b) const
+{
+ if (tpl_->Length() == 0) throw std::runtime_error("template length is 0, invalid state!");
+
+ FillAlpha(M::Null(), a);
+ FillBeta(a, b);
+
+ size_t I = read_.Length();
+ size_t J = tpl_->Length();
+ int flipflops = 0;
+ size_t maxSize =
+ std::max(100ul, static_cast<size_t>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1)));
+
+ // if we use too much space, do at least one more round
+ // to take advantage of rebanding
+ if (a.UsedEntries() >= maxSize || b.UsedEntries() >= maxSize) {
+ FillAlpha(b, a);
+ FillBeta(a, b);
+ FillAlpha(b, a);
+ flipflops += 3;
+ }
+
+ const double unweight = UndoCounterWeights(read_.Length());
+ double alphaV, betaV;
+ while (flipflops <= MAX_FLIP_FLOPS) {
+ alphaV = std::log(a(I, J)) + a.GetLogProdScales() + unweight;
+ betaV = std::log(b(0, 0)) + b.GetLogProdScales() + unweight;
+
+ if (std::abs(1.0 - alphaV / betaV) <= ALPHA_BETA_MISMATCH_TOLERANCE) break;
+
+ if (flipflops % 2 == 0)
+ FillAlpha(b, a);
+ else
+ FillBeta(a, b);
+
+ ++flipflops;
+ }
+
+ if (std::abs(1.0 - alphaV / betaV) > ALPHA_BETA_MISMATCH_TOLERANCE || !std::isfinite(betaV))
+ throw PacBio::Exception::AlphaBetaMismatch();
+
+ return flipflops;
+}
+
+template <typename Derived>
+inline Interval Recursor<Derived>::RowRange(size_t j, const M& matrix) const
+{
+ int beginRow, endRow;
+ std::tie(beginRow, endRow) = matrix.UsedRowRange(j);
+ int maxRow = beginRow;
+ double maxScore = matrix(maxRow, j);
+ int i;
+
+ for (i = beginRow + 1; i < endRow; i++) {
+ double score = matrix(i, j);
+
+ if (score > maxScore) {
+ maxRow = i;
+ maxScore = score;
+ }
+ }
+
+ double thresholdScore = maxScore / scoreDiff_;
+
+ for (i = beginRow; i < maxRow && matrix(i, j) < thresholdScore; i++)
+ ;
+ beginRow = i;
+
+ for (i = endRow - 1; i >= maxRow && matrix(i, j) < thresholdScore; i--)
+ ;
+ endRow = i + 1;
+
+ return Interval(beginRow, endRow);
+}
+
+template <typename Derived>
+inline bool Recursor<Derived>::RangeGuide(size_t j, const M& guide, const M& matrix,
+ size_t* beginRow, size_t* endRow) const
+{
+ bool useGuide = !(guide.IsNull() || guide.IsColumnEmpty(j));
+ bool useMatrix = !(matrix.IsNull() || matrix.IsColumnEmpty(j));
+
+ if (!useGuide && !useMatrix) {
+ return false;
+ }
+
+ Interval interval(*beginRow, *endRow);
+ if (useGuide) {
+ interval = RangeUnion(RowRange(j, guide), interval);
+ }
+
+ if (useMatrix) {
+ interval = RangeUnion(RowRange(j, matrix), interval);
+ }
+
+ std::tie(*beginRow, *endRow) = interval;
+
+ return true;
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/Sequence.cpp b/src/Sequence.cpp
new file mode 100644
index 0000000..09a53df
--- /dev/null
+++ b/src/Sequence.cpp
@@ -0,0 +1,98 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <stdexcept>
+#include <string>
+
+#include <pacbio/data/Sequence.h>
+
+namespace PacBio {
+namespace Data {
+
+char Complement(char base)
+{
+ switch (base) {
+ case 'A':
+ return 'T';
+ case 'a':
+ return 't';
+ case 'C':
+ return 'G';
+ case 'c':
+ return 'g';
+ case 'G':
+ return 'C';
+ case 'g':
+ return 'c';
+ case 'T':
+ return 'A';
+ case 't':
+ return 'a';
+ case '-':
+ return '-';
+ default:
+ throw std::invalid_argument("invalid base!");
+ }
+}
+
+std::string Complement(const std::string& input)
+{
+ std::string output;
+ output.reserve(input.length());
+ for (const char b : input)
+ output.push_back(Complement(b));
+ return output;
+}
+
+std::string Reverse(const std::string& input)
+{
+ std::string output;
+ output.reserve(input.length());
+ for (auto it = input.crbegin(); it != input.crend(); ++it)
+ output.push_back(*it);
+ return output;
+}
+
+std::string ReverseComplement(const std::string& input)
+{
+ std::string output;
+ output.reserve(input.length());
+ for (auto it = input.crbegin(); it != input.crend(); ++it)
+ output.push_back(Complement(*it));
+ return output;
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/SparsePoa.cpp b/src/SparsePoa.cpp
new file mode 100644
index 0000000..10067c5
--- /dev/null
+++ b/src/SparsePoa.cpp
@@ -0,0 +1,226 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <iostream>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include <pacbio/align/AlignConfig.h>
+#include <pacbio/data/Sequence.h>
+#include <pacbio/denovo/PoaConsensus.h>
+#include <pacbio/denovo/PoaGraph.h>
+
+#include <pacbio/ccs/SparseAlignment.h>
+#include <pacbio/denovo/SparsePoa.h>
+#include <pacbio/log/Logging.h>
+
+using PacBio::Poa::detail::SdpAnchorVector;
+using PacBio::Align::AlignConfig;
+using PacBio::Align::AlignMode;
+using PacBio::Poa::DefaultPoaConfig;
+using PacBio::Poa::PoaConsensus;
+using PacBio::Poa::PoaGraph;
+using PacBio::Data::ReverseComplement;
+
+namespace PacBio {
+namespace Poa {
+
+typedef PoaGraph::Vertex Vertex;
+
+SdpAnchorVector SdpRangeFinder::FindAnchors(const std::string& consensusSequence,
+ const std::string& readSequence) const
+{
+ return CCS::SparseAlign<6>(consensusSequence, readSequence);
+}
+
+SparsePoa::SparsePoa()
+ : graph_(new PoaGraph())
+ , readPaths_()
+ , reverseComplemented_()
+ , rangeFinder_(new SdpRangeFinder())
+{
+}
+
+SparsePoa::~SparsePoa()
+{
+ delete graph_;
+ delete rangeFinder_;
+}
+
+SparsePoa::ReadKey SparsePoa::AddRead(const std::string& readSequence,
+ const PoaAlignmentOptions& /* alnOptions */,
+ float minScoreToAdd)
+{
+ AlignConfig config = DefaultPoaConfig(AlignMode::LOCAL);
+ Path outputPath;
+ ReadKey key = -1;
+
+ if (graph_->NumReads() == 0) {
+ graph_->AddFirstRead(readSequence, &outputPath);
+ readPaths_.push_back(outputPath);
+ reverseComplemented_.push_back(false);
+ key = graph_->NumReads() - 1;
+ } else {
+ auto c = graph_->TryAddRead(readSequence, config, rangeFinder_);
+
+ if (c->Score() >= minScoreToAdd) {
+ graph_->CommitAdd(c, &outputPath);
+ readPaths_.push_back(outputPath);
+ reverseComplemented_.push_back(false);
+ key = graph_->NumReads() - 1;
+ }
+
+ delete c;
+ }
+
+ return key;
+}
+
+SparsePoa::ReadKey SparsePoa::OrientAndAddRead(const std::string& readSequence,
+ const PoaAlignmentOptions& /* alnOptions */,
+ float minScoreToAdd)
+{
+ AlignConfig config = DefaultPoaConfig(AlignMode::LOCAL);
+ Path outputPath;
+ ReadKey key;
+
+ if (graph_->NumReads() == 0) {
+ graph_->AddFirstRead(readSequence, &outputPath);
+ readPaths_.push_back(outputPath);
+ reverseComplemented_.push_back(false);
+ key = graph_->NumReads() - 1;
+ } else {
+ auto c1 = graph_->TryAddRead(readSequence, config, rangeFinder_);
+ auto c2 = graph_->TryAddRead(ReverseComplement(readSequence), config, rangeFinder_);
+
+ if (c1->Score() >= c2->Score() && c1->Score() >= minScoreToAdd) {
+ graph_->CommitAdd(c1, &outputPath);
+ readPaths_.push_back(outputPath);
+ reverseComplemented_.push_back(false);
+ key = graph_->NumReads() - 1;
+ } else if (c2->Score() >= c1->Score() && c2->Score() >= minScoreToAdd) {
+ graph_->CommitAdd(c2, &outputPath);
+ readPaths_.push_back(outputPath);
+ reverseComplemented_.push_back(true);
+ key = graph_->NumReads() - 1;
+ } else {
+ key = -1;
+ }
+
+ delete c1;
+ delete c2;
+ }
+ return key;
+}
+
+std::shared_ptr<const PoaConsensus> SparsePoa::FindConsensus(
+ int minCoverage, std::vector<PoaAlignmentSummary>* summaries) const
+{
+ AlignConfig config = DefaultPoaConfig(AlignMode::LOCAL);
+ std::shared_ptr<const PoaConsensus> pc(graph_->FindConsensus(config, minCoverage));
+ std::string css = pc->Sequence;
+
+ if (summaries != NULL) {
+ summaries->clear();
+
+ // digest the consensus path consensus into map(vtx, pos)
+ // the fold over the readPaths
+ std::map<Vertex, size_t> cssPosition;
+
+ int i = 0;
+ for (Vertex v : pc->Path) {
+ cssPosition[v] = i;
+ i++;
+ }
+
+ for (size_t readId = 0; readId < graph_->NumReads(); readId++) {
+ size_t readS = 0, readE = 0;
+ size_t cssS = 0, cssE = 0;
+ bool foundStart = false;
+
+ const std::vector<Vertex>& readPath = readPaths_[readId];
+
+ for (size_t readPos = 0; readPos < readPath.size(); readPos++) {
+ Vertex v = readPath[readPos];
+ if (cssPosition.find(v) != cssPosition.end()) {
+ if (!foundStart) {
+ cssS = cssPosition[v];
+ readS = readPos;
+ foundStart = true;
+ }
+
+ cssE = cssPosition[v] + 1;
+ readE = readPos + 1;
+ }
+ }
+
+ Interval readExtent(readS, readE);
+ Interval cssExtent(cssS, cssE);
+
+ PoaAlignmentSummary summary;
+ summary.ReverseComplementedRead = reverseComplemented_[readId];
+ summary.ExtentOnRead = readExtent;
+ summary.ExtentOnConsensus = cssExtent;
+
+ (*summaries).push_back(summary);
+ }
+ }
+
+ return pc;
+}
+
+std::string SparsePoa::ToGraphViz(int flags, const PoaConsensus* pc) const
+{
+ return graph_->ToGraphViz(flags, pc);
+}
+
+void SparsePoa::WriteGraphVizFile(const std::string& filename, int flags,
+ const PoaConsensus* pc) const
+{
+ graph_->WriteGraphVizFile(filename, flags, pc);
+}
+
+void SparsePoa::PruneGraph(float /* minCoverageFraction */) {}
+void SparsePoa::repCheck()
+{
+ assert(graph_->NumReads() == readPaths_.size());
+ assert(graph_->NumReads() == reverseComplemented_.size());
+}
+
+} // namespace CCS
+} // namespace PacBio
diff --git a/src/SubreadResultCounter.cpp b/src/SubreadResultCounter.cpp
new file mode 100644
index 0000000..7e057c2
--- /dev/null
+++ b/src/SubreadResultCounter.cpp
@@ -0,0 +1,140 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <pacbio/data/SubreadResultCounter.h>
+#include <stdexcept>
+
+using namespace PacBio::Data;
+
+std::vector<int32_t> SubreadResultCounter::ReturnCountsAsArray() const
+{
+ std::vector<int32_t> results{Success, AlphaBetaMismatch, BelowMinQual,
+ PoorZScore, FilteredBySize, Other};
+ return results;
+}
+
+void SubreadResultCounter::AddResult(State result)
+{
+ switch (result) {
+ case State::ALPHA_BETA_MISMATCH:
+ AlphaBetaMismatch++;
+ break;
+ case State::POOR_ZSCORE:
+ PoorZScore++;
+ break;
+ case State::SIZE:
+ FilteredBySize++;
+ break;
+ case State::VALID:
+ Success++;
+ break;
+ default:
+ throw std::runtime_error("Unexpected State");
+ break;
+ }
+}
+
+int32_t SubreadResultCounter::Total() const
+{
+ return (AlphaBetaMismatch + Success + BelowMinQual + FilteredBySize + Other + PoorZScore +
+ ZMWBelowMinSNR + ZMWNotEnoughSubReads);
+}
+
+SubreadResultCounter::SubreadResultCounter()
+ : Success{0}
+ , AlphaBetaMismatch{0}
+ , BelowMinQual{0}
+ , FilteredBySize{0}
+ , ZMWBelowMinSNR{0}
+ , ZMWNotEnoughSubReads{0}
+ , PoorZScore{0}
+ , Other{0}
+
+{
+}
+
+void SubreadResultCounter::WriteResultsReport(std::ostream& report) const
+{
+ using namespace std;
+ double total = static_cast<float>(Total());
+
+ report << "Subread Yield" << endl;
+
+ report << "Success - Used for CCS," << Success << "," << 100.0 * Success / total << '%' << endl;
+
+ report << "Failed -- Below SNR threshold," << ZMWBelowMinSNR << ","
+ << 100.0 * ZMWBelowMinSNR / total << '%' << endl;
+
+ report << "Failed -- Alpha/Beta mismatch," << AlphaBetaMismatch << ","
+ << 100.0 * AlphaBetaMismatch / total << '%' << endl;
+
+ report << "Failed -- Below minimum quality," << BelowMinQual << ","
+ << 100.0 * BelowMinQual / total << '%' << endl;
+
+ report << "Failed -- Filtered by size," << FilteredBySize << ","
+ << 100.0 * FilteredBySize / total << '%' << endl;
+
+ report << "Failed -- Z-Score too low," << PoorZScore << "," << 100.0 * PoorZScore / total << '%'
+ << endl;
+
+ report << "Failed -- From ZMW with too few passes," << ZMWNotEnoughSubReads << ","
+ << 100.0 * ZMWNotEnoughSubReads / total << '%' << endl;
+
+ report << "Failed -- Other," << Other << "," << 100.0 * Other / total << '%' << endl;
+}
+
+void SubreadResultCounter::AssignSuccessToOther()
+{
+ Other += Success;
+ Success = 0;
+}
+
+void SubreadResultCounter::CombineWithOtherResult(const SubreadResultCounter& other)
+{
+ Success += other.Success;
+ AlphaBetaMismatch += other.AlphaBetaMismatch;
+ BelowMinQual += other.BelowMinQual;
+ FilteredBySize += other.FilteredBySize;
+ Other += other.Other;
+ PoorZScore += other.PoorZScore;
+ ZMWBelowMinSNR += other.ZMWBelowMinSNR;
+ ZMWNotEnoughSubReads += other.ZMWNotEnoughSubReads;
+}
+
+SubreadResultCounter& SubreadResultCounter::operator+=(const SubreadResultCounter& other)
+{
+ CombineWithOtherResult(other);
+ return *this;
+}
diff --git a/src/Template.cpp b/src/Template.cpp
new file mode 100644
index 0000000..830a4a4
--- /dev/null
+++ b/src/Template.cpp
@@ -0,0 +1,467 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cassert>
+#include <cmath>
+#include <sstream>
+#include <stdexcept>
+
+#include <pacbio/consensus/Template.h>
+#include <pacbio/exception/StateError.h>
+
+namespace PacBio {
+namespace Consensus {
+
+using TemplateTooSmall = PacBio::Exception::TemplateTooSmall;
+
+AbstractTemplate::AbstractTemplate(const size_t start, const size_t end, const bool pinStart,
+ const bool pinEnd)
+ : start_{start}, end_{end}, pinStart_{pinStart}, pinEnd_{pinEnd}
+{
+ assert(start_ <= end_);
+
+ // Templates that are below two bases are not allowed.
+ // This exception will get propagted up the chain up to the Integrator
+ // constructor or Integrator::AddRead.
+ if (end_ - start_ < 2) throw TemplateTooSmall();
+}
+
+AbstractTemplate::~AbstractTemplate() {}
+AbstractTemplate::operator std::string() const
+{
+ std::stringstream ss;
+ for (size_t i = 0; i < Length(); ++i)
+ ss << (*this)[i].Base;
+ return ss.str();
+}
+
+bool AbstractTemplate::ApplyMutation(const Mutation& mut)
+{
+ const bool mutApplied = InRange(mut.Start(), mut.End());
+
+ // update the end_ mapping if...
+ // we're pinned at the end (and we're not trying to delete nonexistent bases), or
+ // we're before the end of our mapping, or
+ // TODO(lhepler) I HAVE NO IDEA WHY I PUT THIS HERE ARGH
+ if ((pinEnd_ && (end_ > 0 || mut.LengthDiff() > 0)) || mut.Start() < end_ ||
+ mut.End() <= start_)
+ end_ += mut.LengthDiff();
+
+ // update the start_ mapping if...
+ // we're NOT pinned at the start, or
+ // the mutation comes before the start mapping.
+ if (!pinStart_ && mut.End() <= start_) start_ += mut.LengthDiff();
+
+ assert(start_ <= end_);
+
+ return mutApplied;
+}
+
+bool AbstractTemplate::ApplyMutations(std::vector<Mutation>* const muts)
+{
+ bool mutsApplied = false;
+
+ // make sure the mutations are sorted by site: End() then Start()
+ std::sort(muts->begin(), muts->end(), Mutation::SiteComparer);
+
+ for (auto it = muts->crbegin(); it != muts->crend(); ++it)
+ mutsApplied |= ApplyMutation(*it);
+
+ return mutsApplied;
+}
+
+std::pair<double, double> AbstractTemplate::NormalParameters() const
+{
+ double mean = 0.0, var = 0.0;
+ /* Brute forcing this for clarity of code as I don't think this is limiting.
+ Should profiling show this is a problem, we can use the fact that there are only
+ 8 possible dinucleotide contexts and so we can multiply instead of performing repeated
+ addition.
+ e.g. A + B + A + A + B = 3 * A + 2 * B, so we could avoid the nested add step */
+
+ // Now sum up the mean and variance
+ for (size_t i = 0; (i + 1) < Length(); ++i) {
+ double m, v;
+ std::tie(m, v) = SiteNormalParameters(i);
+ mean += m;
+ /* Add the variance, note that the sites are independent so
+ Var (A + B) = Var(A) + Var(B) as Cov(A,B) = 0 */
+ var += v; // Add the variance (note sites are indpe
+ }
+ return std::make_pair(mean, var);
+}
+
+size_t AbstractTemplate::TrueLength() const { return end_ - start_; }
+
+/* See PBEP #4 for a write-up of this code and an explanation of the algorithm.
+
+ The R script below can be used to validate the moments are calculated correctly by
+ comparing to a brute-force simulation
+
+ # Sample Parameters
+ p_m = 0.95583140484751283
+ p_d = 0.00097238955012494488
+ p_b = 0.029256323818866534
+ p_s = 0.013939881783495679
+ eps = 0.00505052456472967
+
+ # Expected Results
+ mean = -0.27568172991312162
+ var = 1.019204780302317
+
+ pmE = p_m / (p_m + p_d)
+ exitLL <- function() {
+ if (runif(1) < pmE) {
+ if (runif(1) < eps) {
+ return( log(p_m) + log(eps) + log(1/3))
+ } else {
+ return(log(p_m) + log(1-eps))
+ }
+ } else {
+ return(log(p_d))
+ }
+ }
+
+ insertLL <- function() {
+ LL <- 0
+ pbI = p_b / (p_b + p_s)
+ while (runif(1) < (p_b + p_s)) {
+ if (runif(1) < pbI) {
+ LL <- LL + log(p_b)
+ } else {
+ LL <- LL + log(p_s) + log(1/3)
+ }
+ }
+ return(LL)
+ }
+
+ getSamp <- function() {
+ return(insertLL() + exitLL())
+ }
+ res = replicate(5000000, getSamp())
+ mean(res)
+ var(res)
+*/
+std::pair<double, double> AbstractTemplate::SiteNormalParameters(const size_t i) const
+{
+ const auto params = (*this)[i];
+ // TODO: This is a bit unsafe, we should understand context and have this conversion in one
+ // place (or really just move directly to using .Idx without bit shifting
+ const uint8_t prev = (i == 0) ? 0 : (*this)[i - 1].Idx; // default base : A
+ const uint8_t curr = params.Idx;
+
+ const double p_m = params.Match, l_m = std::log(p_m), l2_m = l_m * l_m;
+ const double p_d = params.Deletion, l_d = std::log(p_d), l2_d = l_d * l_d;
+ const double p_b = params.Branch, l_b = std::log(p_b), l2_b = l_b * l_b;
+ const double p_s = params.Stick, l_s = std::log(p_s), l2_s = l_s * l_s;
+
+ // First moment expectations (zero terms used for clarity)
+ const double E_M = ExpectedLLForEmission(MoveType::MATCH, prev, curr, MomentType::FIRST);
+ const double E_D = 0.0;
+ const double E_B = ExpectedLLForEmission(MoveType::BRANCH, prev, curr, MomentType::FIRST);
+ const double E_S = ExpectedLLForEmission(MoveType::STICK, prev, curr, MomentType::FIRST);
+
+ // Calculate first moment
+ const double E_MD = (l_m + E_M) * p_m / (p_m + p_d) + (l_d + E_D) * p_d / (p_m + p_d);
+ const double E_I = (l_b + E_B) * p_b / (p_b + p_s) + (l_s + E_S) * p_s / (p_b + p_s);
+ const double E_BS = E_I * (p_s + p_b) / (p_m + p_d);
+ const double mean = E_MD + E_BS;
+
+ // Calculate second momment
+ // Key expansion used repeatedly here: (A + B)^2 = A^2 + 2AB + B^2
+ const double E2_M = ExpectedLLForEmission(MoveType::MATCH, prev, curr, MomentType::SECOND);
+ const double E2_S = ExpectedLLForEmission(MoveType::STICK, prev, curr, MomentType::SECOND);
+ const double E2_B = ExpectedLLForEmission(MoveType::BRANCH, prev, curr, MomentType::SECOND);
+ const double E2_MD =
+ (l2_m + 2 * l_m * E_M + E2_M) * p_m / (p_m + p_d) + l2_d * p_d / (p_m + p_d);
+ const double E2_I = (l2_b + 2 * E_B * l_b + E2_B) * p_b / (p_b + p_s) +
+ (l2_s + 2 * E_S * l_s + E2_S) * p_s / (p_b + p_s);
+ const double E2_BS = E2_I * (p_s + p_b) / (p_m + p_d);
+ const double moment2 = E2_BS + 2 * E_BS * E_MD + E2_MD;
+ const double var = moment2 - mean * mean;
+ return std::make_pair(mean, var);
+}
+
+std::ostream& operator<<(std::ostream& os, const AbstractTemplate& tpl)
+{
+ os << std::string(tpl);
+ return os;
+}
+
+Template::Template(const std::string& tpl, std::unique_ptr<ModelConfig>&& cfg)
+ : Template(tpl, std::forward<std::unique_ptr<ModelConfig>>(cfg), 0, tpl.length(), true, true)
+{
+}
+
+Template::Template(const std::string& tpl, std::unique_ptr<ModelConfig>&& cfg, const size_t start,
+ const size_t end, const bool pinStart, const bool pinEnd)
+ : AbstractTemplate(start, end, pinStart, pinEnd)
+ , cfg_(std::forward<std::unique_ptr<ModelConfig>>(cfg))
+ , tpl_{cfg_->Populate(tpl)}
+ , mutated_{false}
+ , mutOff_{0}
+{
+ assert(end_ - start_ == tpl_.size());
+ assert(!pinStart_ || start_ == 0);
+ // cannot test this unfortunately =(
+ // assert(!pinEnd_ || end_ == tpl_.size());
+}
+
+boost::optional<Mutation> Template::Mutate(const Mutation& mut)
+{
+ Reset();
+
+ if (Length() == 0 && mut.LengthDiff() < 1) return boost::none;
+ if (!InRange(mut.Start(), mut.End())) return boost::none;
+
+ const uint8_t idx = detail::TranslationTable[static_cast<uint8_t>(mut.Base)];
+ if (mut.Type != MutationType::DELETION && idx > 3)
+ throw std::invalid_argument("invalid character in template!");
+
+ mutStart_ = mut.Start() - start_;
+ mutEnd_ = mut.End() - start_;
+
+ if (mut.Type == MutationType::INSERTION) {
+ if (mutStart_ > 0) mutTpl_[0] = cfg_->Populate({tpl_[mutStart_ - 1].Base, mut.Base})[0];
+
+ if (mutStart_ < tpl_.size())
+ mutTpl_[1] = cfg_->Populate({mut.Base, tpl_[mutStart_].Base})[0];
+ else
+ mutTpl_[1] = TemplatePosition{mut.Base, idx, 1.0, 0.0, 0.0, 0.0};
+ } else if (mut.Type == MutationType::SUBSTITUTION) {
+ if (mutStart_ > 0) mutTpl_[0] = cfg_->Populate({tpl_[mutStart_ - 1].Base, mut.Base})[0];
+
+ if (mutStart_ + 1 < tpl_.size())
+ mutTpl_[1] = cfg_->Populate({mut.Base, tpl_[mutStart_ + 1].Base})[0];
+ else
+ mutTpl_[1] = TemplatePosition{mut.Base, idx, 1.0, 0.0, 0.0, 0.0};
+ } else if (mut.Type == MutationType::DELETION) {
+ // if there's a predecessor, fill it
+ if (mutStart_ > 0) {
+ if (mutStart_ + 1 < tpl_.size())
+ mutTpl_[0] =
+ cfg_->Populate({tpl_[mutStart_ - 1].Base, tpl_[mutStart_ + 1].Base})[0];
+ else
+ mutTpl_[0] = TemplatePosition{
+ tpl_[mutStart_ - 1].Base, tpl_[mutStart_ - 1].Idx, 1.0, 0.0, 0.0, 0.0};
+ }
+
+ // if there's a successor, the params for the mutant position
+ // are equiv to the next position in the original tpl
+ if (mutStart_ + 1 < tpl_.size()) mutTpl_[1] = tpl_[mutStart_ + 1];
+ } else
+ throw std::invalid_argument(
+ "invalid mutation type! must be DELETION, INSERTION, or "
+ "SUBSTITUTION");
+
+ mutOff_ = mut.LengthDiff();
+ mutated_ = true;
+
+ // Either the length is 0 or an operation had been applied
+ assert(Length() == 0 ||
+ ((*this)[Length() - 1].Match == 1.0 && (*this)[Length() - 1].Branch == 0.0 &&
+ (*this)[Length() - 1].Stick == 0.0 && (*this)[Length() - 1].Deletion == 0.0));
+
+ return Mutation(mut.Type, mutStart_, mut.Base);
+}
+
+void Template::Reset()
+{
+ mutOff_ = 0;
+ mutated_ = false;
+}
+
+bool Template::ApplyMutation(const Mutation& mut)
+{
+ if (mutated_)
+ throw std::runtime_error(
+ "cannot ApplyMutation to an already mutated Template, call Reset first");
+
+ const uint8_t idx = detail::TranslationTable[static_cast<uint8_t>(mut.Base)];
+ if (mut.Type != MutationType::DELETION && idx > 3)
+ throw std::invalid_argument("invalid character in template!");
+
+ bool mutApplied = false;
+
+ if (Length() == 0 && mut.LengthDiff() < 1) goto finish;
+ if (!InRange(mut.Start(), mut.End())) goto finish;
+
+ {
+ const size_t i = mut.Start() - start_;
+
+ if (mut.Type == MutationType::INSERTION) {
+ if (i > 0) tpl_[i - 1] = cfg_->Populate({tpl_[i - 1].Base, mut.Base})[0];
+
+ if (i < tpl_.size())
+ tpl_.insert(tpl_.begin() + i, cfg_->Populate({mut.Base, tpl_[i].Base})[0]);
+ else
+ tpl_.emplace_back(TemplatePosition{mut.Base, idx, 1.0, 0.0, 0.0, 0.0});
+ } else if (mut.Type == MutationType::SUBSTITUTION) {
+ if (i > 0) tpl_[i - 1] = cfg_->Populate({tpl_[i - 1].Base, mut.Base})[0];
+
+ if (i + 1 < tpl_.size())
+ tpl_[i] = cfg_->Populate({mut.Base, tpl_[i + 1].Base})[0];
+ else
+ tpl_[i] = TemplatePosition{mut.Base, idx, 1.0, 0.0, 0.0, 0.0};
+ } else if (mut.Type == MutationType::DELETION) {
+ tpl_.erase(tpl_.begin() + i);
+
+ if (i > 0) {
+ if (i < tpl_.size())
+ tpl_[i - 1] = cfg_->Populate({tpl_[i - 1].Base, tpl_[i].Base})[0];
+ else
+ tpl_[i - 1] =
+ TemplatePosition{tpl_[i - 1].Base, tpl_[i - 1].Idx, 1.0, 0.0, 0.0, 0.0};
+ }
+ } else
+ throw std::invalid_argument(
+ "invalid mutation type! must be DELETION, INSERTION, or "
+ "SUBSTITUTION");
+
+ mutApplied = true;
+ }
+
+finish:
+ // update the start_ and end_ mappings
+ AbstractTemplate::ApplyMutation(mut);
+
+ assert(tpl_.size() == end_ - start_);
+ assert(Length() == 0 ||
+ ((*this)[Length() - 1].Match == 1.0 && (*this)[Length() - 1].Branch == 0.0 &&
+ (*this)[Length() - 1].Stick == 0.0 && (*this)[Length() - 1].Deletion == 0.0));
+
+ assert(!pinStart_ || start_ == 0);
+
+ if (Length() < 2) throw TemplateTooSmall();
+
+ return mutApplied;
+}
+
+VirtualTemplate::VirtualTemplate(const Template& master, const size_t start, const size_t end,
+ const bool pinStart, const bool pinEnd)
+ : AbstractTemplate(start, end, pinStart, pinEnd), master_(master)
+{
+ assert(!pinStart_ || start_ == 0);
+ assert(!pinEnd_ || end_ == master_.tpl_.size());
+}
+
+bool VirtualTemplate::ApplyMutation(const Mutation& mut)
+{
+ assert(!pinStart_ || start_ == 0);
+ const bool mutApplied = AbstractTemplate::ApplyMutation(mut);
+ assert(!pinStart_ || start_ == 0);
+ return mutApplied;
+}
+
+size_t Template::Length() const { return tpl_.size() + mutOff_; }
+
+size_t VirtualTemplate::Length() const
+{
+ if (IsMutated()) return end_ - start_ + master_.mutOff_;
+
+ return end_ - start_;
+}
+
+// inline function impls
+bool AbstractTemplate::InRange(const size_t start, const size_t end) const
+{
+ if ((pinStart_ || start_ < end) && (pinEnd_ || start < end_)) return true;
+ return false;
+}
+
+const TemplatePosition& Template::operator[](size_t i) const
+{
+ // if no mutation, or everything up to the base before mutStart_, just return
+ // what we have
+ if (!IsMutated() || i + 1 < mutStart_) return tpl_[i];
+
+ // if we're beyond the mutation position, take the appropriate base
+ else if (i > mutStart_)
+ return tpl_[i - mutOff_];
+
+ // otherwise if we're the base before mutStart_, 0, else 1 of our mutated tpl
+ // params
+ return mutTpl_[i == mutStart_];
+}
+
+bool Template::IsMutated() const { return mutated_; }
+
+std::unique_ptr<AbstractRecursor> Template::CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const PacBio::Data::MappedRead& mr,
+ double scoreDiff) const
+{
+ return cfg_->CreateRecursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr,
+ scoreDiff);
+}
+double Template::ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const
+{
+ return cfg_->ExpectedLLForEmission(move, prev, curr, moment);
+}
+
+const TemplatePosition& VirtualTemplate::operator[](const size_t i) const
+{
+ if (master_.IsMutated() && !pinStart_ && master_.mutEnd_ <= start_)
+ return master_[start_ + i + master_.mutOff_];
+ return master_[start_ + i];
+}
+
+bool VirtualTemplate::IsMutated() const
+{
+ return master_.IsMutated() && InRange(master_.mutStart_, master_.mutEnd_);
+}
+
+boost::optional<Mutation> VirtualTemplate::Mutate(const Mutation& mut)
+{
+ if (!master_.IsMutated()) throw std::runtime_error("virtual template badness");
+ if (!InRange(mut.Start(), mut.End())) return boost::optional<Mutation>(boost::none);
+ return boost::optional<Mutation>(Mutation(mut.Type, mut.Start() - start_, mut.Base));
+}
+
+std::unique_ptr<AbstractRecursor> VirtualTemplate::CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const PacBio::Data::MappedRead& mr,
+ double scoreDiff) const
+{
+ return master_.CreateRecursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr,
+ scoreDiff);
+}
+double VirtualTemplate::ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const
+{
+ return master_.ExpectedLLForEmission(move, prev, curr, moment);
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/Timer.cpp b/src/Timer.cpp
new file mode 100644
index 0000000..f43ca94
--- /dev/null
+++ b/src/Timer.cpp
@@ -0,0 +1,61 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <chrono>
+
+#include <pacbio/util/Timer.h>
+
+using std::chrono::steady_clock;
+using std::chrono::milliseconds;
+
+namespace PacBio {
+namespace Util {
+
+Timer::Timer() { Restart(); }
+
+float Timer::ElapsedMilliseconds() const
+{
+ auto tock = steady_clock::now();
+ return std::chrono::duration_cast<milliseconds>(tock - tick).count();
+}
+
+float Timer::ElapsedSeconds() const { return ElapsedMilliseconds() / 1000; }
+
+void Timer::Restart() { tick = steady_clock::now(); }
+
+} // namespace CCS
+} // namespace PacBio
diff --git a/src/Utility.cpp b/src/Utility.cpp
new file mode 100644
index 0000000..b409aa1
--- /dev/null
+++ b/src/Utility.cpp
@@ -0,0 +1,137 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <climits>
+#include <cstdlib>
+#include <fstream>
+
+#include <sys/stat.h>
+
+#include <boost/algorithm/string.hpp>
+
+#include <pacbio/io/Utility.h>
+
+using namespace std;
+
+namespace PacBio {
+namespace IO {
+
+string AbsolutePath(const string& path)
+{
+ char buf[PATH_MAX + 1];
+ char* res = realpath(path.c_str(), buf);
+
+ if (res != nullptr) {
+ string abspath(res);
+ return abspath;
+ }
+
+ return path;
+}
+
+bool FileExists(const string& path)
+{
+ struct stat buffer;
+ return stat(path.c_str(), &buffer) == 0;
+}
+
+string FileExtension(const string& path)
+{
+ size_t fileStart = path.find_last_of("/");
+
+ if (fileStart == string::npos) fileStart = 0;
+
+ // increment beyond the '/'
+ ++fileStart;
+
+ size_t extStart = path.substr(fileStart, path.length() - fileStart).find_last_of(".");
+
+ if (extStart == string::npos) return "";
+
+ // increment beyond '.'
+ ++extStart;
+
+ return path.substr(fileStart + extStart, path.length() - fileStart - extStart);
+}
+
+void FlattenFofn(vector<string>& res, const string& file)
+{
+ using boost::algorithm::iends_with;
+ using boost::algorithm::trim;
+
+ if (iends_with(file, ".fofn")) {
+ ifstream fofn(file);
+ string line;
+ while (getline(fofn, line)) {
+ trim(line);
+ FlattenFofn(res, line);
+ }
+ } else if (iends_with(file, ".bam"))
+ res.push_back(file);
+ else
+ throw invalid_argument("not a .fofn or .bam file!");
+}
+
+vector<string> FlattenFofn(const vector<string>& files)
+{
+ vector<string> res;
+
+ for (const auto& file : files) {
+ FlattenFofn(res, file);
+ }
+
+ return res;
+}
+
+bool ValidBaseFeatures(const PacBio::BAM::DataSet& ds)
+{
+ for (const auto& bam : ds.BamFiles()) {
+ for (const auto& rg : bam.Header().ReadGroups()) {
+ // P6-C4 and S/P1-C1/beta do not require covariates besides SNR
+ if (rg.SequencingChemistry() == "P6-C4" || rg.SequencingChemistry() == "S/P1-C1/beta")
+ continue;
+ // everything else requires IPD and PulseWidth
+ else if (!rg.HasBaseFeature(PacBio::BAM::BaseFeature::IPD) ||
+ !rg.HasBaseFeature(PacBio::BAM::BaseFeature::PULSE_WIDTH))
+ return false;
+ }
+ }
+ return true;
+}
+
+} // namespace CCS
+} // namespace PacBio
diff --git a/src/align/AffineAlignment.cpp b/src/align/AffineAlignment.cpp
new file mode 100644
index 0000000..4dcf9fb
--- /dev/null
+++ b/src/align/AffineAlignment.cpp
@@ -0,0 +1,234 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Authors: David Alexander, Lance Hepler
+
+#include <algorithm>
+#include <cassert>
+#include <cfloat>
+#include <string>
+#include <vector>
+
+#include <boost/numeric/ublas/matrix.hpp>
+#include <boost/numeric/ublas/matrix_proxy.hpp>
+
+#include <pacbio/align/AffineAlignment.h>
+#include <pacbio/align/PairwiseAlignment.h>
+#include <pacbio/data/Sequence.h>
+// #include <pacbio/consensus/Utils.h>
+
+namespace PacBio {
+namespace Align {
+
+using namespace PacBio::Data;
+
+namespace {
+
+class IupacAware;
+class Standard;
+
+static float MAX4(float a, float b, float c, float d)
+{
+ return std::max(std::max(a, b), std::max(c, d));
+}
+
+inline bool IsIupacPartialMatch(char iupacCode, char b)
+{
+ assert(iupacCode != b);
+
+ switch (iupacCode) {
+ case 'R':
+ return (b == 'A' || b == 'G');
+ case 'Y':
+ return (b == 'C' || b == 'T');
+ case 'S':
+ return (b == 'G' || b == 'C');
+ case 'W':
+ return (b == 'A' || b == 'T');
+ case 'K':
+ return (b == 'G' || b == 'T');
+ case 'M':
+ return (b == 'A' || b == 'C');
+ default:
+ return false;
+ }
+}
+
+template <typename C>
+inline float MatchScore(char t, char q, float matchScore, float mismatchScore,
+ float partialMatchScore);
+
+template <>
+inline float MatchScore<Standard>(char t, char q, float matchScore, float mismatchScore,
+ float partialMatchScore)
+{
+ return (t == q ? matchScore : mismatchScore);
+}
+
+template <>
+inline float MatchScore<IupacAware>(char t, char q, float matchScore, float mismatchScore,
+ float partialMatchScore)
+{
+ if (t == q) {
+ return matchScore;
+ } else if (IsIupacPartialMatch(t, q)) {
+ return partialMatchScore;
+ } else if (IsIupacPartialMatch(q, t)) {
+ return partialMatchScore;
+ } else {
+ return mismatchScore;
+ } // NOLINT
+}
+
+template <class C>
+PairwiseAlignment* AlignAffineGeneric(const std::string& target, const std::string& query,
+ AffineAlignmentParams params)
+{
+ // Implementation follows the textbook "two-state" affine gap model
+ // description from Durbin et. al
+ using boost::numeric::ublas::matrix;
+
+ int I = query.length();
+ int J = target.length();
+ matrix<float> M(I + 1, J + 1);
+ matrix<float> GAP(I + 1, J + 1);
+
+ // Initialization
+ M(0, 0) = 0;
+ GAP(0, 0) = -FLT_MAX;
+ for (int i = 1; i <= I; ++i) {
+ M(i, 0) = -FLT_MAX;
+ GAP(i, 0) = params.GapOpen + (i - 1) * params.GapExtend;
+ }
+ for (int j = 1; j <= J; ++j) {
+ M(0, j) = -FLT_MAX;
+ GAP(0, j) = params.GapOpen + (j - 1) * params.GapExtend;
+ }
+
+ // Main part of the recursion
+ for (int i = 1; i <= I; ++i) {
+ for (int j = 1; j <= J; ++j) {
+ float matchScore = MatchScore<C>(target[j - 1], query[i - 1], params.MatchScore,
+ params.MismatchScore, params.PartialMatchScore);
+ M(i, j) = std::max(M(i - 1, j - 1), GAP(i - 1, j - 1)) + matchScore;
+ GAP(i, j) = MAX4(M(i, j - 1) + params.GapOpen, GAP(i, j - 1) + params.GapExtend,
+ M(i - 1, j) + params.GapOpen, GAP(i - 1, j) + params.GapExtend);
+ }
+ }
+
+ // Perform the traceback
+ const int MATCH_MATRIX = 1;
+ const int GAP_MATRIX = 2;
+
+ std::string raQuery, raTarget;
+ int i = I, j = J;
+ int mat = (M(I, J) >= GAP(I, J) ? MATCH_MATRIX : GAP_MATRIX);
+ int iPrev, jPrev, matPrev;
+ while (i > 0 || j > 0) {
+ if (mat == MATCH_MATRIX) {
+ matPrev = (M(i - 1, j - 1) >= GAP(i - 1, j - 1) ? MATCH_MATRIX : GAP_MATRIX);
+ iPrev = i - 1;
+ jPrev = j - 1;
+ raQuery.push_back(query[iPrev]);
+ raTarget.push_back(target[jPrev]);
+ } else {
+ assert(mat == GAP_MATRIX);
+ float s[4];
+ s[0] = (j > 0 ? M(i, j - 1) + params.GapOpen : -FLT_MAX);
+ s[1] = (j > 0 ? GAP(i, j - 1) + params.GapExtend : -FLT_MAX);
+ s[2] = (i > 0 ? M(i - 1, j) + params.GapOpen : -FLT_MAX);
+ s[3] = (i > 0 ? GAP(i - 1, j) + params.GapExtend : -FLT_MAX);
+ int argMax = std::max_element(s, s + 4) - s;
+
+ matPrev = ((argMax == 0 || argMax == 2) ? MATCH_MATRIX : GAP_MATRIX);
+ if (argMax == 0 || argMax == 1) {
+ iPrev = i;
+ jPrev = j - 1;
+ raQuery.push_back('-');
+ raTarget.push_back(target[jPrev]);
+ } else {
+ iPrev = i - 1;
+ jPrev = j;
+ raQuery.push_back(query[iPrev]);
+ raTarget.push_back('-');
+ }
+ }
+
+ // Go to previous square
+ i = iPrev;
+ j = jPrev;
+ mat = matPrev;
+ }
+
+ assert(raQuery.length() == raTarget.length());
+ return new PairwiseAlignment(Reverse(raTarget), Reverse(raQuery));
+}
+
+} // anonymous namespace
+
+AffineAlignmentParams::AffineAlignmentParams(float matchScore, float mismatchScore, float gapOpen,
+ float gapExtend, float partialMatchScore)
+ : MatchScore(matchScore)
+ , MismatchScore(mismatchScore)
+ , GapOpen(gapOpen)
+ , GapExtend(gapExtend)
+ , PartialMatchScore(partialMatchScore)
+{
+}
+
+AffineAlignmentParams DefaultAffineAlignmentParams()
+{
+ return AffineAlignmentParams(0, -1.0, -1.0, -0.5, 0);
+}
+
+AffineAlignmentParams IupacAwareAffineAlignmentParams()
+{
+ return AffineAlignmentParams(0, -1.0, -1.0, -0.5, -0.25);
+}
+
+PairwiseAlignment* AlignAffine(const std::string& target, const std::string& query,
+ AffineAlignmentParams params)
+{
+ return AlignAffineGeneric<Standard>(target, query, params);
+}
+
+PairwiseAlignment* AlignAffineIupac(const std::string& target, const std::string& query,
+ AffineAlignmentParams params)
+{
+ return AlignAffineGeneric<IupacAware>(target, query, params);
+}
+
+} // namespace Align
+} // namespace PacBio
diff --git a/src/align/AlignConfig.cpp b/src/align/AlignConfig.cpp
new file mode 100644
index 0000000..7f24eeb
--- /dev/null
+++ b/src/align/AlignConfig.cpp
@@ -0,0 +1,58 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Authors: David Alexander, Lance Hepler
+
+#include <pacbio/align/AlignConfig.h>
+
+namespace PacBio {
+namespace Align {
+
+AlignParams::AlignParams(int match, int mismatch, int insert, int delete_)
+ : Match(match), Mismatch(mismatch), Insert(insert), Delete(delete_)
+{
+}
+
+AlignParams AlignParams::Default() { return AlignParams(0, -1, -1, -1); }
+
+AlignConfig::AlignConfig(AlignParams params, AlignMode mode) : Params(params), Mode(mode) {}
+
+AlignConfig AlignConfig::Default()
+{
+ return AlignConfig(AlignParams::Default(), AlignMode::GLOBAL);
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/align/LinearAlignment.cpp b/src/align/LinearAlignment.cpp
new file mode 100644
index 0000000..24cd856
--- /dev/null
+++ b/src/align/LinearAlignment.cpp
@@ -0,0 +1,272 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Authors: David Alexander, Lance Hepler
+
+//
+// This is the basic Hirschberg algo, not the affine variation by Myers and Miller.
+// The tricky part of this code is that we use the a single array to store portions
+// of two rows in the alignment matrices.
+//
+// Straightforward notes here: http://globin.cse.psu.edu/courses/fall2001/DP.pdf ;
+// taken from "Recent Developments in Linear-Space Alignment Methods: A Survey".
+// I follow them pretty closely except for the semiglobal alignment mode implemented
+// here.
+//
+// For the affine (Gotoh) variation, not yet implemented, see Myers & Miller 1988
+//
+
+#include <algorithm>
+#include <cassert>
+#include <string>
+#include <vector>
+
+#include <boost/numeric/ublas/io.hpp>
+#include <boost/numeric/ublas/matrix.hpp>
+#include <boost/numeric/ublas/vector.hpp>
+
+#include <pacbio/align/LinearAlignment.h>
+#include <pacbio/align/PairwiseAlignment.h>
+// #include <pacbio/consensus/Utils.h>
+
+//#define DEBUG_LINEAR_ALIGNMENT
+
+#ifdef DEBUG_LINEAR_ALIGNMENT
+#include <iostream>
+using std::cout;
+using std::endl;
+#endif // DEBUG_LINEAR_ALIGNMENT
+
+namespace PacBio {
+namespace Align {
+namespace {
+
+namespace ublas = boost::numeric::ublas;
+
+int INSERT_SCORE = -2;
+int DELETE_SCORE = -2;
+int MISMATCH_SCORE = -1;
+int MATCH_SCORE = +2;
+
+const AlignParams params(MATCH_SCORE, MISMATCH_SCORE, INSERT_SCORE, DELETE_SCORE);
+const AlignConfig config(params, AlignMode::GLOBAL);
+
+//
+// Get transcript of NW alignment taking
+// target[j1..j2] into query[i1..i2] (one-based indexing)
+// used for trivial base cases.
+//
+std::string NWTranscript(const std::string& target, int j1, int j2, const std::string& query,
+ int i1, int i2, int* score)
+{
+ // If j1 > j2 or i1 > i2, the respective subtarget or subquery is empty,
+ // ergo we have pure insertions or deletions.
+ assert((i2 - i1 >= -1) && (j2 - j1 >= -1));
+
+ // implement this inline later
+ std::string T = target.substr(j1 - 1, j2 - j1 + 1);
+ std::string Q = query.substr(i1 - 1, i2 - i1 + 1);
+ PairwiseAlignment* aln = Align(T, Q, score, config);
+ std::string X = aln->Transcript();
+ delete aln;
+ return X;
+}
+
+#ifndef NDEBUG
+bool CheckTranscript(const std::string& transcript, const std::string& unalnTarget,
+ const std::string& unalnQuery)
+{
+ PairwiseAlignment* pa = PairwiseAlignment::FromTranscript(transcript, unalnTarget, unalnQuery);
+ if (pa == NULL) {
+ return false;
+ } else {
+ delete pa;
+ return true;
+ }
+}
+#endif // NDEBUG
+
+//
+// Hirschberg recursion:
+// Find optimal transcript taking target[j1..j2] into query[i1..i2] (one-based indices)
+// Operates by divide-and-conquer, finding midpoint (m, j*) and recursing on halves, then joining.
+// Notes:
+//
+// | Alignment | L | L_1 | L_2 |
+// | Path | (0,0) ~> (I,J) | (0,0) ~> (m, j*) | (m, j*) ~> (I, J) |
+// | T, Q | T[1..J], Q[1..I] | T[1..j*], Q[1..m] | T[j*+1..J], Q[m+1..I] |
+// | Transcript | X | X_1 | X_2 |
+//
+// target on horizontal, query on vertical
+// i refers to query; j refers to target
+// this gives better balanced recursion in the (common) semiglobal case
+//
+std::string OptimalTranscript(const std::string& target, int j1, int j2, const std::string& query,
+ int i1, int i2, ublas::vector<int>& buf1, ublas::vector<int>& buf2,
+ int* score = NULL)
+{
+#ifndef NDEBUG
+ std::string subtarget = target.substr(j1 - 1, j2 - j1 + 1);
+ std::string subquery = query.substr(i1 - 1, i2 - i1 + 1);
+#endif
+
+#ifdef DEBUG_LINEAR_ALIGNMENT
+ cout << "Called OptimalTranscript("
+ << "T[" << j1 << ".." << j2 << "], "
+ << "Q[" << i1 << ".." << i2 << "]) "
+ << " " << target << " " << query << " "
+ << "(" << subtarget << ", " << subquery << ")" << endl;
+#endif
+
+ std::string x, x1, x2;
+ int segmentScore;
+ const AlignParams& params = config.Params;
+
+ //
+ // Base case
+ //
+ if ((j2 - j1 < 1) || (i2 - i1 < 1)) {
+ x = NWTranscript(target, j1, j2, query, i1, i2, &segmentScore);
+ }
+
+ //
+ // Recursive case
+ //
+ else {
+ assert(buf1.size() == target.size() + 1);
+ assert(buf2.size() == target.size() + 1);
+
+ ublas::vector<int>& Sm = buf1; // S-
+ ublas::vector<int>& Sp = buf2; // S+
+
+ int mid = (i1 + i2) / 2;
+
+ //
+ // Score forward, i1 upto mid
+ // ( T[j1..j2] vs Q[i1..m] )
+ //
+ Sm(j1 - 1) = 0;
+ for (int j = j1; j <= j2; j++) {
+ Sm(j) = Sm(j - 1) + params.Delete;
+ }
+ for (int i = i1; i <= mid; i++) {
+ int s, c;
+ s = Sm(j1 - 1);
+ c = Sm(j1 - 1) + params.Insert;
+ Sm(j1 - 1) = c;
+ for (int j = j1; j <= j2; j++) {
+ char t = target[j - 1];
+ char q = query[i - 1];
+ c = Max3(Sm(j) + params.Insert, s + (t == q ? params.Match : params.Mismatch),
+ c + params.Delete);
+ s = Sm(j);
+ Sm(j) = c;
+ }
+ }
+
+ //
+ // Score backwards, i2 downto mid
+ // ( T[j1..j2] vs Q[m+1..i2] )
+ //
+ Sp(j2) = 0;
+ for (int j = j2 - 1; j >= j1 - 1; j--) {
+ Sp(j) = Sp(j + 1) + params.Delete;
+ }
+ for (int i = i2 - 1; i >= mid; i--) {
+ int s, c;
+ s = Sp(j2);
+ c = Sp(j2) + params.Delete;
+ Sp(j2) = c;
+ for (int j = j2 - 1; j >= j1 - 1; j--) {
+ char t = target[j]; // j + 1 - 1
+ char q = query[i]; // i + 1 - 1
+ c = Max3(Sp(j) + params.Insert, s + (t == q ? params.Match : params.Mismatch),
+ c + params.Delete);
+ s = Sp(j);
+ Sp(j) = c;
+ }
+ }
+
+ //
+ // Find where optimal path crosses the mid row
+ //
+ ublas::vector<int> sum = Sm + Sp;
+ int j = std::max_element(sum.begin() + j1 - 1, sum.begin() + j2 + 1) - sum.begin();
+ segmentScore = sum[j];
+
+ int segment1Score, segment2Score;
+ x1 = OptimalTranscript(target, j1, j, query, i1, mid, buf1, buf2, &segment1Score);
+ x2 = OptimalTranscript(target, j + 1, j2, query, mid + 1, i2, buf1, buf2, &segment2Score);
+ assert(segmentScore == segment1Score + segment2Score);
+ x = x1 + x2;
+ }
+
+ // Check 1: transcript has to take target[j1..j2] into query[i1..i2]
+ assert(CheckTranscript(x, subtarget, subquery));
+
+// Check 2: same score as basic N/W?
+#ifndef NDEBUG
+ int peerScore;
+ PairwiseAlignment* peerAlignment = Align(subtarget, subquery, &peerScore, config);
+ assert(peerScore == segmentScore);
+ delete peerAlignment;
+#endif
+
+ if (score != NULL) {
+ *score = segmentScore;
+ }
+ return x;
+}
+
+} // anonymous namespace
+
+PairwiseAlignment* AlignLinear(const std::string& target, const std::string& query, int* score,
+ AlignConfig config)
+{
+ int J = target.length();
+ ublas::vector<int> buf1(J + 1), buf2(J + 1);
+ std::string x =
+ OptimalTranscript(target, 1, target.length(), query, 1, query.length(), buf1, buf2, score);
+ return PairwiseAlignment::FromTranscript(x, target, query);
+}
+
+PairwiseAlignment* AlignLinear(const std::string& target, const std::string& query,
+ AlignConfig config)
+{
+ return AlignLinear(target, query, NULL, config);
+}
+
+} // namespace Align
+} // namespace PacBio
diff --git a/src/align/PairwiseAlignment.cpp b/src/align/PairwiseAlignment.cpp
new file mode 100644
index 0000000..07848db
--- /dev/null
+++ b/src/align/PairwiseAlignment.cpp
@@ -0,0 +1,329 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <algorithm>
+#include <string>
+#include <vector>
+
+#include <boost/numeric/ublas/matrix.hpp>
+
+#include <pacbio/align/PairwiseAlignment.h>
+#include <pacbio/data/Sequence.h>
+// #include <pacbio/consensus/Utils.hpp>
+
+namespace PacBio {
+namespace Align {
+
+using namespace PacBio::Data;
+
+std::string PairwiseAlignment::Target() const { return target_; }
+
+std::string PairwiseAlignment::Query() const { return query_; }
+
+float PairwiseAlignment::Accuracy() const { return ((float)(Matches())) / Length(); }
+
+std::string PairwiseAlignment::Transcript() const { return transcript_; }
+
+int PairwiseAlignment::Matches() const
+{
+ return std::count(transcript_.begin(), transcript_.end(), 'M');
+}
+
+int PairwiseAlignment::Errors() const { return Length() - Matches(); }
+
+int PairwiseAlignment::Mismatches() const
+{
+ return std::count(transcript_.begin(), transcript_.end(), 'R');
+}
+
+int PairwiseAlignment::Insertions() const
+{
+ return std::count(transcript_.begin(), transcript_.end(), 'I');
+}
+
+int PairwiseAlignment::Deletions() const
+{
+ return std::count(transcript_.begin(), transcript_.end(), 'D');
+}
+
+int PairwiseAlignment::Length() const { return target_.length(); }
+
+PairwiseAlignment::PairwiseAlignment(const std::string& target, const std::string& query)
+ : target_(target), query_(query), transcript_(target_.length(), 'Z')
+{
+ if (target_.length() != query_.length()) {
+ throw std::invalid_argument("target length must equal query length");
+ }
+ for (unsigned int i = 0; i < target_.length(); i++) {
+ char t = target_[i];
+ char q = query_[i];
+ char tr;
+
+ if (t == '-' && q == '-') {
+ throw std::invalid_argument("invalid target and query transcript");
+ } else if (t == q) {
+ tr = 'M';
+ } else if (t == '-') {
+ tr = 'I';
+ } else if (q == '-') {
+ tr = 'D';
+ } else {
+ tr = 'R';
+ } // NOLINT
+
+ transcript_[i] = tr;
+ }
+}
+
+PairwiseAlignment* Align(const std::string& target, const std::string& query, int* score,
+ AlignConfig config)
+{
+ using boost::numeric::ublas::matrix;
+
+ const AlignParams& params = config.Params;
+ if (config.Mode != AlignMode::GLOBAL) {
+ throw std::invalid_argument("Only AlignMode::GLOBAL alignment supported at present");
+ }
+
+ int I = query.length();
+ int J = target.length();
+ matrix<int> Score(I + 1, J + 1);
+
+ Score(0, 0) = 0;
+ for (int i = 1; i <= I; i++) {
+ Score(i, 0) = i * params.Insert;
+ }
+ for (int j = 1; j <= J; j++) {
+ Score(0, j) = j * params.Delete;
+ }
+ for (int i = 1; i <= I; i++) {
+ for (int j = 1; j <= J; j++) {
+ bool isMatch = (query[i - 1] == target[j - 1]);
+ Score(i, j) = Max3(Score(i - 1, j - 1) + (isMatch ? params.Match : params.Mismatch),
+ Score(i - 1, j) + params.Insert, Score(i, j - 1) + params.Delete);
+ }
+ }
+ if (score != NULL) {
+ *score = Score(I, J);
+ }
+
+ // Traceback, build up reversed aligned query, aligned target
+ std::string raQuery, raTarget;
+ int i = I, j = J;
+ while (i > 0 || j > 0) {
+ int move;
+ if (i == 0) {
+ move = 2; // only deletion is possible
+ } else if (j == 0) {
+ move = 1; // only insertion is possible
+ } else {
+ bool isMatch = (query[i - 1] == target[j - 1]);
+ move = ArgMax3(Score(i - 1, j - 1) + (isMatch ? params.Match : params.Mismatch),
+ Score(i - 1, j) + params.Insert, Score(i, j - 1) + params.Delete);
+ }
+ // Incorporate:
+ if (move == 0) {
+ i--;
+ j--;
+ raQuery.push_back(query[i]);
+ raTarget.push_back(target[j]);
+ }
+ // Insert:
+ else if (move == 1) {
+ i--;
+ raQuery.push_back(query[i]);
+ raTarget.push_back('-');
+ }
+ // Delete:
+ else if (move == 2) {
+ j--;
+ raQuery.push_back('-');
+ raTarget.push_back(target[j]);
+ }
+ }
+
+ return new PairwiseAlignment(Reverse(raTarget), Reverse(raQuery));
+}
+
+PairwiseAlignment* Align(const std::string& target, const std::string& query, AlignConfig config)
+{
+ return Align(target, query, NULL, config);
+}
+
+//
+// Code for lifting target coordinates into query coordinates.
+//
+
+static bool addsToTarget(char transcriptChar)
+{
+ return (transcriptChar == 'M' || transcriptChar == 'R' || transcriptChar == 'D');
+}
+
+static int targetLength(const std::string& alignmentTranscript)
+{
+ return std::count_if(alignmentTranscript.begin(), alignmentTranscript.end(), addsToTarget);
+}
+
+#ifndef NDEBUG
+static bool addsToQuery(char transcriptChar)
+{
+ return (transcriptChar == 'M' || transcriptChar == 'R' || transcriptChar == 'I');
+}
+
+static int queryLength(const std::string& alignmentTranscript)
+{
+ return std::count_if(alignmentTranscript.begin(), alignmentTranscript.end(), addsToQuery);
+}
+#endif // !NDEBUG
+
+// TargetPositionsInQuery:
+// * Returns a vector of targetLength(transcript) + 1, which,
+// roughly speaking, indicates the positions in the query string of the
+// the characters in the target, as induced by an alignment with the
+// given transcript string.
+// * More precisely, given an alignment (T, Q, X) (x=transcript),
+// letting T[s, e) denote any slice of T,
+// - [s',e') denote the subslice of indices of Q aligned to T[s, e),
+// - ntp = NewTargetPositions(X)
+// we have
+// [s', e') = [ntp(s), ntp(e))
+//
+// * Ex:
+// MMM -> 0123
+// DMM -> 0012, MMD -> 0122, MDM -> 0112
+// IMM -> 123, MMI -> 013, MIM -> 023
+// MRM, MIDM, MDIM -> 0123
+std::vector<int> TargetToQueryPositions(const std::string& transcript)
+{
+ std::vector<int> ntp;
+ ntp.reserve(targetLength(transcript) + 1);
+
+ int targetPos = 0;
+ int queryPos = 0;
+ for (const char c : transcript) {
+ if (c == 'M' || c == 'R') {
+ ntp.push_back(queryPos);
+ targetPos++;
+ queryPos++;
+ } else if (c == 'D') {
+ ntp.push_back(queryPos);
+ targetPos++;
+ } else if (c == 'I') {
+ queryPos++;
+ } else {
+ throw std::runtime_error("unreachable");
+ }
+ }
+ ntp.push_back(queryPos);
+
+ assert((int)ntp.size() == targetLength(transcript) + 1);
+ assert(ntp[targetLength(transcript)] == queryLength(transcript));
+ return ntp;
+}
+
+std::vector<int> TargetToQueryPositions(const PairwiseAlignment& aln)
+{
+ return TargetToQueryPositions(aln.Transcript());
+}
+
+// Build the alignment given the unaligned sequences and the transcript
+// Returns NULL if transcript does not map unalnTarget into unalnQuery.
+PairwiseAlignment* PairwiseAlignment::FromTranscript(const std::string& transcript,
+ const std::string& unalnTarget,
+ const std::string& unalnQuery)
+{
+ std::string alnTarget;
+ std::string alnQuery;
+ int tPos, qPos;
+ int tLen, qLen;
+
+ tLen = unalnTarget.length();
+ qLen = unalnQuery.length();
+ tPos = 0;
+ qPos = 0;
+ for (const char x : transcript) {
+ if (tPos > tLen || qPos > qLen) {
+ return NULL;
+ }
+
+ char t = (tPos < tLen ? unalnTarget[tPos] : '\0');
+ char q = (qPos < qLen ? unalnQuery[qPos] : '\0');
+
+ switch (x) {
+ case 'M':
+ if (t != q) {
+ return NULL;
+ }
+ alnTarget.push_back(t);
+ alnQuery.push_back(q);
+ tPos++;
+ qPos++;
+ break;
+ case 'R':
+ if (t == q) {
+ return NULL;
+ }
+ alnTarget.push_back(t);
+ alnQuery.push_back(q);
+ tPos++;
+ qPos++;
+ break;
+ case 'I':
+ alnTarget.push_back('-');
+ alnQuery.push_back(q);
+ qPos++;
+ break;
+ case 'D':
+ alnTarget.push_back(t);
+ alnQuery.push_back('-');
+ tPos++;
+ break;
+ default:
+ return NULL;
+ }
+ }
+ // Didn't consume all of one of the strings
+ if (tPos != tLen || qPos != qLen) {
+ return NULL;
+ }
+
+ // Provide another constructor to inject transcript? Calculate transcript on the fly?
+ return new PairwiseAlignment(alnTarget, alnQuery);
+}
+
+} // namespace Align
+} // namespace PacBio
diff --git a/src/main/ChimeraLabeler.cpp b/src/main/ChimeraLabeler.cpp
new file mode 100644
index 0000000..f80f456
--- /dev/null
+++ b/src/main/ChimeraLabeler.cpp
@@ -0,0 +1,78 @@
+// Copyright (c) 2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Brett Bowman
+
+#include <seqan/seq_io.h>
+
+#include "pacbio/chimera/ChimeraLabeler.h"
+#include "pacbio/chimera/ChimeraResultWriter.h"
+
+using namespace PacBio::Chimera;
+
+int main(int argc, char const **argv)
+{
+ using namespace seqan;
+
+ if (argc != 2) return 1; // Invalid number of arguments.
+
+ // Get the input file
+ std::string inputFile(argv[1]);
+ SeqFileIn inputHandle(inputFile.c_str());
+
+ // Parse the records
+ StringSet<CharString> ids;
+ StringSet<Dna5String> seqs;
+ readRecords(ids, seqs, inputHandle);
+
+ // Declare the vectors we'll use to actually perform the Chimera-labeling
+ std::vector<std::string> idList;
+ std::vector<Dna5String> seqList;
+
+ for (size_t i = 0; i < length(ids); ++i) {
+ idList.push_back(toCString(static_cast<CharString>(ids[i])));
+ seqList.push_back(static_cast<Dna5String>(seqs[i]));
+ }
+
+ // Label the Records
+ ChimeraLabeler chimeraLabeler(1.0f, 100, true);
+ auto labels = chimeraLabeler.LabelChimeras(idList, seqList);
+
+ // Display the results
+ ChimeraResultWriter csvWriter("temp.csv");
+ csvWriter.WriteResults(labels);
+
+ return 0;
+}
diff --git a/src/main/ccs.cpp b/src/main/ccs.cpp
new file mode 100644
index 0000000..17114d7
--- /dev/null
+++ b/src/main/ccs.cpp
@@ -0,0 +1,658 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <algorithm>
+#include <fstream>
+#include <functional>
+#include <iostream>
+#include <iterator>
+#include <map>
+#include <memory>
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include <boost/algorithm/string/join.hpp>
+#include <boost/numeric/conversion/cast.hpp>
+#include <boost/optional.hpp>
+
+#include <OptionParser.h>
+
+#include <pbbam/BamWriter.h>
+#include <pbbam/EntireFileQuery.h>
+#include <pbbam/PbiBuilder.h>
+#include <pbbam/PbiFilterQuery.h>
+#include <pbbam/ReadGroupInfo.h>
+
+#include <pacbio/ccs/Consensus.h>
+#include <pacbio/ccs/Whitelist.h>
+#include <pacbio/consensus/ModelSelection.h>
+#include <pacbio/data/Interval.h>
+#include <pacbio/data/ReadId.h>
+#include <pacbio/io/Utility.h>
+#include <pacbio/log/Logging.h>
+#include <pacbio/parallel/WorkQueue.h>
+#include <pacbio/util/ExecUtils.h>
+
+#include <pacbio/Version.h>
+
+using namespace std;
+using namespace PacBio::BAM;
+using namespace PacBio::CCS;
+using namespace PacBio::Data;
+using namespace PacBio::Poa;
+using namespace PacBio::Align;
+using namespace PacBio::Consensus;
+using namespace PacBio::Parallel;
+using namespace PacBio::Util;
+using namespace PacBio::IO;
+using namespace PacBio::Logging;
+
+using boost::none;
+using boost::numeric_cast;
+using boost::optional;
+using optparse::OptionParser;
+
+// these strings are part of the BAM header, they CANNOT contain newlines
+#define DESCRIPTION "Generate circular consensus sequences (ccs) from subreads."
+
+namespace PacBio {
+namespace CCS {
+namespace OptionNames {
+constexpr auto ForceOutput = "force";
+constexpr auto PbIndex = "pbi";
+constexpr auto Zmws = "zmws";
+constexpr auto ReportFile = "reportFile";
+constexpr auto NumThreads = "numThreads";
+constexpr auto LogFile = "logFile";
+constexpr auto LogLevel = "logLevel";
+constexpr auto RichQVs = "richQVs";
+constexpr auto ModelPath = "modelPath";
+constexpr auto ModelSpec = "modelSpec";
+} // namespace OptionNames
+} // namespace CCS
+} // namespace PacBio
+
+typedef ReadType<ReadId> Subread;
+typedef ChunkType<ReadId, Subread> Chunk;
+typedef ResultType<ConsensusType> Results;
+
+const auto CircularConsensus = &PacBio::CCS::Consensus<Chunk>;
+
+inline std::string QVsToASCII(const std::vector<int>& qvs)
+{
+ std::string result;
+ result.reserve(qvs.size());
+
+ for (const int qv : qvs) {
+ result.push_back(static_cast<char>(std::min(std::max(0, qv), 93) + 33));
+ }
+
+ return result;
+}
+
+void WriteBamRecords(BamWriter& ccsBam, unique_ptr<PbiBuilder>& ccsPbi, Results& counts,
+ const bool richQVs, Results&& results)
+{
+ counts += results;
+
+ for (const auto& ccs : results) {
+ BamRecordImpl record;
+ TagCollection tags;
+ stringstream name;
+
+ // some defaults values
+ record.Bin(0)
+ .InsertSize(0)
+ .MapQuality(255)
+ .MatePosition(-1)
+ .MateReferenceId(-1)
+ .Position(-1)
+ .ReferenceId(-1)
+ .Flag(0)
+ .SetMapped(false);
+
+ name << *(ccs.Id.MovieName) << '/' << ccs.Id.HoleNumber << "/ccs";
+
+ if (ccs.Strand && *(ccs.Strand) == StrandType::FORWARD) name << "/fwd";
+ if (ccs.Strand && *(ccs.Strand) == StrandType::REVERSE) name << "/rev";
+
+ vector<float> snr = {
+ static_cast<float>(ccs.SignalToNoise.A), static_cast<float>(ccs.SignalToNoise.C),
+ static_cast<float>(ccs.SignalToNoise.G), static_cast<float>(ccs.SignalToNoise.T)};
+
+ tags["RG"] = MakeReadGroupId(*(ccs.Id.MovieName), "CCS");
+ tags["zm"] = static_cast<int32_t>(ccs.Id.HoleNumber);
+ tags["np"] = static_cast<int32_t>(ccs.NumPasses);
+ tags["rq"] = static_cast<float>(ccs.PredictedAccuracy);
+ tags["sn"] = snr;
+
+ // deletion, insertion, and substitution QVs
+ if (richQVs) {
+ tags["dq"] = QVsToASCII(ccs.QVs.DeletionQVs);
+ tags["iq"] = QVsToASCII(ccs.QVs.InsertionQVs);
+ tags["sq"] = QVsToASCII(ccs.QVs.SubstitutionQVs);
+ }
+
+ // TODO(lhepler) maybe remove one day
+ tags["za"] = static_cast<float>(ccs.AvgZScore);
+ vector<float> zScores;
+ for (const double z : ccs.ZScores)
+ zScores.emplace_back(static_cast<float>(z));
+ tags["zs"] = zScores;
+ tags["rs"] = ccs.StatusCounts;
+
+ if (ccs.Barcodes) {
+ int16_t first, second;
+ uint8_t quality;
+ tie(first, second, quality) = *ccs.Barcodes;
+ vector<uint16_t> bcs{numeric_cast<uint16_t>(first), numeric_cast<uint16_t>(second)};
+ tags["bc"] = bcs;
+ tags["bq"] = static_cast<int32_t>(quality);
+ }
+
+#if DIAGNOSTICS
+ tags["ms"] = ccs.ElapsedMilliseconds;
+ tags["mt"] = static_cast<int32_t>(ccs.polishResult.mutationsTested);
+ tags["ma"] = static_cast<int32_t>(ccs.polishResult.mutationsApplied);
+ tags["ap"] = ccs.polishResult.maxAlphaPopulated;
+ tags["bp"] = ccs.polishResult.maxBetaPopulated;
+ tags["ff"] = ccs.polishResult.maxNumFlipFlops;
+#endif
+
+ record.Name(name.str())
+ .SetSequenceAndQualities(ccs.Sequence, QVsToASCII(ccs.QVs.Qualities))
+ .Tags(tags);
+
+ int64_t offset;
+ ccsBam.Write(record, &offset);
+
+ if (ccsPbi) ccsPbi->AddRecord(record, offset);
+ }
+ ccsBam.TryFlush();
+}
+
+Results BamWriterThread(WorkQueue<Results>& queue, unique_ptr<BamWriter>&& ccsBam,
+ unique_ptr<PbiBuilder>&& ccsPbi, const bool richQVs)
+{
+ Results counts;
+ while (queue.ConsumeWith(WriteBamRecords, ref(*ccsBam), ref(ccsPbi), ref(counts), richQVs))
+ ;
+ return counts;
+}
+
+void WriteFastqRecords(ofstream& ccsFastq, Results& counts, Results&& results)
+{
+ counts += results;
+ for (const auto& ccs : results) {
+ ccsFastq << '@' << *(ccs.Id.MovieName) << '/' << ccs.Id.HoleNumber << "/ccs";
+
+ if (ccs.Strand && *(ccs.Strand) == StrandType::FORWARD) ccsFastq << "/fwd";
+ if (ccs.Strand && *(ccs.Strand) == StrandType::REVERSE) ccsFastq << "/rev";
+
+ ccsFastq << " np:i:" << ccs.NumPasses << " rq:f:" << ccs.PredictedAccuracy;
+
+ if (ccs.Barcodes) {
+ int16_t first, second;
+ uint8_t quality;
+ tie(first, second, quality) = *ccs.Barcodes;
+ ccsFastq << " bc:B:S," << first << ',' << second << " bq:i:" << quality;
+ }
+
+ ccsFastq << '\n';
+ ccsFastq << ccs.Sequence << '\n';
+ ccsFastq << "+\n";
+ ccsFastq << QVsToASCII(ccs.QVs.Qualities) << '\n';
+ }
+
+ ccsFastq.flush();
+}
+
+Results FastqWriterThread(WorkQueue<Results>& queue, const string& fname)
+{
+ ofstream ccsFastq(fname);
+ Results counts;
+ while (queue.ConsumeWith(WriteFastqRecords, ref(ccsFastq), ref(counts)))
+ ;
+ return counts;
+}
+
+BamHeader PrepareHeader(const OptionParser& parser, int argc, char** argv, const DataSet& ds)
+{
+ using boost::algorithm::join;
+
+ ProgramInfo program(parser.prog() + "-" + PacBio::UnanimityVersion());
+ program.Name(parser.prog())
+ .CommandLine(parser.prog() + " " + join(vector<string>(argv + 1, argv + argc), " "))
+ .Description(DESCRIPTION)
+ .Version(PacBio::UnanimityVersion());
+
+ BamHeader header;
+ header.PacBioBamVersion("3.0.1").SortOrder("unknown").Version("1.5").AddProgram(program);
+
+ for (const auto& bam : ds.BamFiles()) {
+ for (const auto& rg : bam.Header().ReadGroups()) {
+ if (rg.ReadType() != "SUBREAD")
+ parser.error("invalid input file, READTYPE must be SUBREAD");
+
+ ReadGroupInfo readGroup(rg.MovieName(), "CCS");
+ readGroup.BindingKit(rg.BindingKit())
+ .SequencingKit(rg.SequencingKit())
+ .BasecallerVersion(rg.BasecallerVersion())
+ .FrameRateHz(rg.FrameRateHz());
+
+ if (rg.HasBarcodeData()) {
+ readGroup.BarcodeData(rg.BarcodeFile(), rg.BarcodeHash(), rg.BarcodeCount(),
+ rg.BarcodeMode(), rg.BarcodeQuality());
+ }
+
+ header.AddReadGroup(readGroup);
+ }
+ }
+
+ return header;
+}
+
+size_t ThreadCount(int n)
+{
+ const int m = thread::hardware_concurrency();
+
+ if (n < 1) return max(1, m + n);
+
+ return min(m, n);
+}
+
+void WriteResultsReport(ostream& report, const Results& counts)
+{
+ size_t total = counts.Total();
+
+ report << fixed << setprecision(2);
+
+ report << "ZMW Yield" << endl;
+
+ report << "Success -- CCS generated," << counts.Success << "," << 100.0 * counts.Success / total
+ << '%' << endl;
+
+ report << "Failed -- Below SNR threshold," << counts.PoorSNR << ","
+ << 100.0 * counts.PoorSNR / total << '%' << endl;
+
+ report << "Failed -- No usable subreads," << counts.NoSubreads << ","
+ << 100.0 * counts.NoSubreads / total << '%' << endl;
+
+ report << "Failed -- Insert size too long," << counts.TooLong << ","
+ << 100.0 * counts.TooShort / total << '%' << endl;
+
+ report << "Failed -- Insert size too small," << counts.TooShort << ","
+ << 100.0 * counts.TooShort / total << '%' << endl;
+
+ report << "Failed -- Not enough full passes," << counts.TooFewPasses << ","
+ << 100.0 * counts.TooFewPasses / total << '%' << endl;
+
+ report << "Failed -- Too many unusable subreads," << counts.TooManyUnusable << ","
+ << 100.0 * counts.TooManyUnusable / total << '%' << endl;
+
+ report << "Failed -- CCS did not converge," << counts.NonConvergent << ","
+ << 100.0 * counts.NonConvergent / total << '%' << endl;
+
+ report << "Failed -- CCS below minimum predicted accuracy," << counts.PoorQuality << ","
+ << 100.0 * counts.PoorQuality / total << '%' << endl;
+
+ report << "Failed -- Unknown error during processing," << counts.ExceptionThrown << ","
+ << 100.0 * counts.ExceptionThrown / total << '%' << endl;
+ report << endl << endl;
+
+ // Now output the per-subread yield report.
+ counts.SubreadCounter.WriteResultsReport(report);
+}
+
+int main(int argc, char** argv)
+{
+ using boost::algorithm::join;
+ using boost::make_optional;
+
+ SetColumns();
+
+ // args and options
+ //
+ //
+ // clang-format off
+ // clang messes with the way the arg to version() is formatted..
+ auto parser =
+ OptionParser()
+ .usage("usage: %prog [OPTIONS] INPUT OUTPUT")
+ .version("%prog " + PacBio::UnanimityVersion() + " (commit " + PacBio::UnanimityGitSha1() + ")" +
+ "\nunanimity " + PacBio::UnanimityVersion() + " (commit " + PacBio::UnanimityGitSha1() + ")" +
+ "\nCopyright (c) 2014-2016 Pacific Biosciences, Inc.\nLicense: 3-BSD")
+ .description(DESCRIPTION
+ "\nAdditional documentation: http://github.com/PacificBiosciences/unanimity");
+ // clang-format on
+ //
+ const vector<string> logLevels = {"TRACE", "DEBUG", "INFO", "NOTICE",
+ "WARN", "ERROR", "CRITICAL", "FATAL"};
+ const string em = "--";
+
+ parser.add_option(em + OptionNames::ForceOutput)
+ .action("store_true")
+ .help("Overwrite OUTPUT file if present.");
+ parser.add_option(em + OptionNames::PbIndex)
+ .action("store_true")
+ .help("Generate a .pbi file for the OUTPUT file.");
+ parser.add_option(em + OptionNames::Zmws)
+ .help(
+ "Generate CCS for the provided comma-separated holenumber ranges only. Default = all");
+
+ ConsensusSettings::AddOptions(&parser);
+
+ parser.add_option(em + OptionNames::RichQVs)
+ .action("store_true")
+ .help("Emit dq, iq, and sq \"rich\" quality tracks. Default = false");
+ parser.add_option(em + OptionNames::ReportFile)
+ .set_default("ccs_report.txt")
+ .help("Where to write the results report. Default = %default");
+ parser.add_option("-M", em + OptionNames::ModelPath)
+ .help("Path to a model file or directory containing model files. Default = none");
+ parser.add_option("-m", em + OptionNames::ModelSpec)
+ .help("Name of chemistry or model to use, overriding default selection. Default = none");
+ parser.add_option(em + OptionNames::NumThreads)
+ .type("int")
+ .set_default(0)
+ .help("Number of threads to use, 0 means autodetection. Default = %default");
+ parser.add_option(em + OptionNames::LogFile).help("Log to a file, instead of STDERR.");
+ parser.add_option(em + OptionNames::LogLevel)
+ .choices(logLevels.begin(), logLevels.end())
+ .set_default("INFO")
+ .help("Set log level. Default = %default");
+
+ const auto options = parser.parse_args(argc, argv);
+ const auto files = parser.args();
+
+ const ConsensusSettings settings(options);
+
+ const bool richQVs = options.get(OptionNames::RichQVs);
+ const bool forceOutput = options.get(OptionNames::ForceOutput);
+ const bool pbIndex = options.get(OptionNames::PbIndex);
+ const size_t nThreads = ThreadCount(options.get(OptionNames::NumThreads));
+ const size_t chunkSize = 1;
+
+ // handle --zmws
+ //
+ //
+ optional<Whitelist> whitelist(none);
+ const string wlspec(options.get(OptionNames::Zmws));
+ try {
+ if (!wlspec.empty()) whitelist = Whitelist(wlspec);
+ } catch (...) {
+ parser.error("option --zmws: invalid specification: '" + wlspec + "'");
+ }
+
+ // input validation
+ //
+ //
+ if (files.size() < 1)
+ parser.error("missing INPUT and OUTPUT");
+ else if (files.size() < 2)
+ parser.error("missing OUTPUT");
+ else if (files.size() > 2)
+ parser.error("too many arguments for INPUT and OUTPUT");
+
+ // pop first file off the list, is OUTPUT file
+ const string inputFile = files.front();
+ const string outputFile = files.back();
+
+ // verify input file exists
+ if (!FileExists(inputFile)) parser.error("INPUT: file does not exist: '" + inputFile + "'");
+
+ // verify output file does not already exist
+ if (FileExists(outputFile) && !forceOutput)
+ parser.error("OUTPUT: file already exists: '" + outputFile + "'");
+
+ if (settings.ByStrand && settings.NoPolish)
+ parser.error("option --byStrand: incompatible with --noPolish");
+
+ // logging
+ //
+ //
+ ofstream logStream;
+ {
+ string logLevel(options.get(OptionNames::LogLevel));
+ string logFile(options.get(OptionNames::LogFile));
+
+ if (!logFile.empty()) {
+ logStream.open(logFile);
+ Logger::Default(new Logger(logStream, logLevel));
+ } else {
+ Logger::Default(new Logger(cerr, logLevel));
+ }
+ InstallSignalHandlers();
+ }
+
+ // load models from file or directory
+ //
+ //
+ {
+ string modelPath(options.get(OptionNames::ModelPath));
+ if (!modelPath.empty()) {
+ PBLOG_INFO << "Loading model parameters from: '" << modelPath << "'";
+ if (!LoadModels(modelPath)) {
+ PBLOG_FATAL << "Failed to load models from: " << modelPath;
+ exit(-1);
+ }
+ }
+ }
+
+ // start processing chunks!
+ //
+ //
+ const auto avail = SupportedChemistries();
+
+ PBLOG_DEBUG << "Found consensus models for: (" << join(avail, ", ") << ')';
+
+ DataSet ds(inputFile);
+
+ // test that all input chemistries are supported
+ {
+ set<string> used;
+ string modelSpec(options.get(OptionNames::ModelSpec));
+ if (!modelSpec.empty()) {
+ PBLOG_INFO << "Overriding model selection with: '" << modelSpec << "'";
+ if (!(OverrideModel(modelSpec) && used.insert(modelSpec).second)) {
+ PBLOG_FATAL << "Failed to find specified model: " << modelSpec;
+ exit(-1);
+ }
+ } else {
+ try {
+ used = ds.SequencingChemistries();
+ } catch (InvalidSequencingChemistryException& e) {
+ PBLOG_FATAL << e.what();
+ exit(-1);
+ }
+
+ vector<string> unavail;
+
+ set_difference(used.begin(), used.end(), avail.begin(), avail.end(),
+ back_inserter(unavail));
+
+ if (!unavail.empty()) {
+ PBLOG_FATAL << "Unsupported chemistries found: (" << join(unavail, ", ") << "), "
+ << "supported chemistries are: (" << join(avail, ", ") << ")";
+ exit(-1);
+ }
+ }
+ PBLOG_DEBUG << "Using consensus models for: (" << join(used, ", ") << ')';
+ }
+
+ if (!ValidBaseFeatures(ds)) {
+ PBLOG_FATAL << "Missing base features: IPD or PulseWidth";
+ exit(-1);
+ }
+
+ const auto filter = PbiFilter::FromDataSet(ds);
+ unique_ptr<internal::IQuery> query(nullptr);
+ if (filter.IsEmpty())
+ query.reset(new EntireFileQuery(ds));
+ else
+ query.reset(new PbiFilterQuery(filter, ds));
+
+ WorkQueue<Results> workQueue(nThreads);
+ future<Results> writer;
+
+ const string outputExt = FileExtension(outputFile);
+ if (outputExt == "bam") {
+ unique_ptr<BamWriter> ccsBam(
+ new BamWriter(outputFile, PrepareHeader(parser, argc, argv, ds)));
+ const std::string pbiFileName = outputFile + ".pbi";
+ unique_ptr<PbiBuilder> ccsPbi(pbIndex ? new PbiBuilder(pbiFileName) : nullptr);
+ writer = async(launch::async, BamWriterThread, ref(workQueue), move(ccsBam), move(ccsPbi),
+ richQVs);
+
+ // Prepare dataset
+ const std::string desc =
+ "Points to the ccs bam file generated by pbccs " + PacBio::UnanimityVersion();
+ const std::string name = "ccs bam";
+ const std::string metatype = "PacBio.DataSet.ConsensusReadSet";
+ DataSet ccsSet(DataSet::TypeEnum::CONSENSUS_READ);
+ ExternalResource resource(metatype, outputFile);
+ resource.Name(name).Description(desc);
+
+ if (pbIndex) {
+ FileIndex pbi("PacBio.Index.PacBioIndex", pbiFileName);
+ resource.FileIndices().Add(pbi);
+ }
+
+ ccsSet.ExternalResources().Add(resource);
+
+ // File path without .bam suffix
+ const auto outputPrefix = outputFile.substr(0, outputFile.size() - 4);
+ // Save dataset
+ std::ofstream ccsOut(outputPrefix + ".consensusreadset.xml");
+ ccsSet.SaveToStream(ccsOut);
+ } else if (outputExt == "fastq" || outputExt == "fq")
+ writer = async(launch::async, FastqWriterThread, ref(workQueue), ref(outputFile));
+ else
+ parser.error("OUTPUT: invalid file extension: '" + outputExt + "'");
+
+ unique_ptr<vector<Chunk>> chunk(new vector<Chunk>());
+ map<string, shared_ptr<string>> movieNames;
+ optional<int32_t> holeNumber(none);
+ bool skipZmw = false;
+ optional<tuple<int16_t, int16_t, uint8_t>> barcodes(none);
+
+ for (const auto& read : *query) {
+ const string movieName = read.MovieName();
+
+ if (movieNames.find(movieName) == movieNames.end())
+ movieNames[movieName] = make_shared<string>(movieName);
+
+ // check if we've started a new ZMW
+ if (!holeNumber || *holeNumber != read.HoleNumber()) {
+ if (chunk && chunk->size() >= chunkSize) {
+ workQueue.ProduceWith(CircularConsensus, move(chunk), settings);
+ chunk.reset(new vector<Chunk>());
+ }
+ holeNumber = read.HoleNumber();
+ auto snr = read.SignalToNoise();
+
+ // barcodes
+ if (read.HasBarcodes() && read.HasBarcodeQuality()) {
+ int16_t first, second;
+ uint8_t quality = read.BarcodeQuality();
+ tie(first, second) = read.Barcodes();
+ barcodes = make_tuple(first, second, quality);
+ } else {
+ barcodes = none;
+ }
+
+ if (whitelist && !whitelist->Contains(movieName, *holeNumber))
+ skipZmw = true;
+ else {
+ skipZmw = false;
+ chunk->emplace_back(Chunk{ReadId(movieNames[movieName], *holeNumber),
+ vector<Subread>(), SNR(snr[0], snr[1], snr[2], snr[3]),
+ read.ReadGroup().SequencingChemistry(), barcodes});
+ }
+ }
+
+ if (skipZmw) continue;
+
+ // check that barcode matches the previous ones, or else...
+ if (barcodes && (!read.HasBarcodes() || !read.HasBarcodeQuality() ||
+ read.BarcodeForward() != get<0>(*barcodes) ||
+ read.BarcodeReverse() != get<1>(*barcodes) ||
+ read.BarcodeQuality() != get<2>(*barcodes))) {
+ PBLOG_FATAL << "invalid data: \"bc\" or \"bq\" tag did not agree between subreads!";
+ exit(-1);
+ }
+
+ vector<uint8_t> ipd;
+ if (read.HasIPD())
+ ipd = read.IPD().Encode();
+ else
+ ipd = vector<uint8_t>(read.Sequence().length(), 0);
+
+ vector<uint8_t> pw;
+ if (read.HasPulseWidth())
+ pw = read.PulseWidth().Encode();
+ else
+ pw = vector<uint8_t>(read.Sequence().length(), 0);
+
+ chunk->back().Reads.emplace_back(
+ Subread{ReadId(movieNames[movieName], *holeNumber,
+ Interval(read.QueryStart(), read.QueryEnd())),
+ read.Sequence(), std::move(ipd), std::move(pw), read.LocalContextFlags(),
+ read.ReadAccuracy()});
+ }
+
+ // run the remaining tasks
+ if (chunk && !chunk->empty()) workQueue.ProduceWith(CircularConsensus, move(chunk), settings);
+
+ // wait for the queue to be done
+ workQueue.Finalize();
+
+ // wait for the writer thread and get the results counter
+ // then add in the snr/minPasses counts and write the report
+ auto counts = writer.get();
+ const string reportFile(options.get(OptionNames::ReportFile));
+
+ if (reportFile == "-")
+ WriteResultsReport(cout, counts);
+ else {
+ ofstream stream(reportFile);
+ WriteResultsReport(stream, counts);
+ }
+
+ return 0;
+}
diff --git a/src/matrix/ScaledMatrix.cpp b/src/matrix/ScaledMatrix.cpp
new file mode 100644
index 0000000..46aec38
--- /dev/null
+++ b/src/matrix/ScaledMatrix.cpp
@@ -0,0 +1,99 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <algorithm>
+#include <cmath>
+#include <iomanip>
+
+#include "ScaledMatrix.h"
+
+namespace PacBio {
+namespace Consensus {
+
+ScaledMatrix::ScaledMatrix(size_t rows, size_t cols, Direction dir)
+ : SparseMatrix(rows, cols), logScalars_(cols, 0.0), dir_{dir}
+{
+}
+
+ScaledMatrix::ScaledMatrix(const ScaledMatrix& other)
+ : SparseMatrix(other), logScalars_(other.logScalars_)
+{
+}
+
+void ScaledMatrix::Reset(size_t rows, size_t cols)
+{
+ std::vector<double>(cols, 0.0).swap(logScalars_);
+ SparseMatrix::Reset(rows, cols);
+}
+
+ScaledMatrix::Direction ScaledMatrix::SetDirection(const Direction dir)
+{
+ const Direction res = dir_;
+ dir_ = dir;
+ std::fill(logScalars_.begin(), logScalars_.end(), 0.0);
+ return res;
+}
+
+std::ostream& operator<<(std::ostream& os, const ScaledMatrix& mat)
+{
+ os << "MATRIX (" << mat.Rows() << ", " << mat.Columns() << ") BEGIN" << std::endl;
+ os << std::fixed << std::setprecision(4);
+ for (size_t i = 0; i < mat.Rows(); ++i) {
+ os << ' ';
+ for (size_t j = 0; j < mat.Columns(); ++j) {
+ os << ' ' << std::setw(9) << std::log(mat.Get(i, j)) + mat.GetLogScale(j);
+ }
+ os << std::endl;
+ }
+ os << "END" << std::endl;
+ return os;
+}
+
+void ScaledMatrix::ToHostMatrix(double** mat, int* rows, int* cols) const
+{
+ const double nan = std::numeric_limits<double>::quiet_NaN();
+ *mat = new double[Rows() * Columns()];
+ *rows = Rows();
+ *cols = Columns();
+ for (size_t i = 0; i < Rows(); i++) {
+ for (size_t j = 0; j < Columns(); j++) {
+ (*mat)[i * Columns() + j] =
+ IsAllocated(i, j) ? std::log(Get(i, j)) + GetLogScale(j) : nan;
+ }
+ }
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/matrix/ScaledMatrix.h b/src/matrix/ScaledMatrix.h
new file mode 100644
index 0000000..2a37758
--- /dev/null
+++ b/src/matrix/ScaledMatrix.h
@@ -0,0 +1,149 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <algorithm>
+#include <cmath>
+#include <iostream>
+#include <numeric>
+#include <vector>
+
+#include "SparseMatrix.h"
+
+namespace PacBio {
+namespace Consensus {
+
+class ScaledMatrix : public SparseMatrix
+{
+public:
+ enum Direction
+ {
+ FORWARD,
+ REVERSE
+ };
+
+public: // constructor/destructor
+ ScaledMatrix(size_t rows, size_t cols, Direction dir);
+ ScaledMatrix(const ScaledMatrix& other);
+ ~ScaledMatrix(void) override = default;
+
+public:
+ void Reset(size_t rows, size_t cols) override;
+ Direction SetDirection(Direction dir);
+
+public: // nullability
+ static const ScaledMatrix& Null();
+
+public: // information about entries filled by column
+ template <bool maxProvided>
+ void FinishEditingColumn(size_t j, size_t usedBegin, size_t usedEnd, double max_val = 0.0);
+
+public: // Scaling and normalization
+ double GetLogScale(size_t j) const;
+ double GetLogProdScales(size_t s, size_t e) const;
+ double GetLogProdScales() const;
+
+public: // Convenient matrix access for SWIG
+ void ToHostMatrix(double** mat, int* rows, int* cols) const override;
+
+private:
+ std::vector<double> logScalars_;
+ Direction dir_;
+};
+
+std::ostream& operator<<(std::ostream&, const ScaledMatrix&);
+
+inline const ScaledMatrix& ScaledMatrix::Null()
+{
+ static ScaledMatrix* nullObj = new ScaledMatrix(0, 0, FORWARD);
+ return *nullObj;
+}
+
+template <bool maxProvided>
+inline void ScaledMatrix::FinishEditingColumn(const size_t j, const size_t usedBegin,
+ const size_t usedEnd, double max_val)
+{
+ // get the constant to scale by
+ if (!maxProvided) {
+ max_val = 0.0;
+ for (size_t i = usedBegin; i < usedEnd; ++i) {
+ max_val = std::max(max_val, SparseMatrix::Get(i, j));
+ }
+ }
+
+ // cumsum stuff
+ double last = 0.0;
+ if (dir_ == FORWARD && j > 0)
+ last = logScalars_[j - 1];
+ else if (dir_ == REVERSE && j + 1 < Columns())
+ last = logScalars_[j + 1];
+
+ // set it
+ if (max_val != 0.0 && max_val != 1.0) {
+ for (size_t i = usedBegin; i < usedEnd; ++i) {
+ SparseMatrix::Set(i, j, SparseMatrix::Get(i, j) / max_val);
+ }
+ logScalars_[j] = last + std::log(max_val);
+ } else {
+ logScalars_[j] = last;
+ }
+
+ SparseMatrix::FinishEditingColumn(j, usedBegin, usedEnd);
+}
+
+inline double ScaledMatrix::GetLogScale(size_t j) const { return logScalars_[j]; }
+
+inline double ScaledMatrix::GetLogProdScales(size_t beginColumn, size_t endColumn) const
+{
+ double f, l;
+ if (dir_ == FORWARD) {
+ f = (beginColumn > 0) ? logScalars_[beginColumn - 1] : 0.0;
+ l = (endColumn > 0) ? logScalars_[endColumn - 1] : 0.0;
+ return l - f;
+ } // else dir_ == REVERSE
+ f = logScalars_[beginColumn];
+ l = (endColumn < Columns()) ? logScalars_[endColumn] : 0.0;
+ return f - l;
+}
+
+inline double ScaledMatrix::GetLogProdScales() const
+{
+ if (dir_ == FORWARD) return logScalars_.back();
+ return logScalars_.front();
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/matrix/SparseMatrix.cpp b/src/matrix/SparseMatrix.cpp
new file mode 100644
index 0000000..5590aeb
--- /dev/null
+++ b/src/matrix/SparseMatrix.cpp
@@ -0,0 +1,126 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include "SparseMatrix.h"
+
+namespace PacBio {
+namespace Consensus {
+
+SparseMatrix::SparseMatrix(const size_t rows, const size_t cols)
+ : columns_(cols)
+ , nCols_(cols)
+ , nRows_(rows)
+ , columnBeingEdited_(std::numeric_limits<size_t>::max())
+ , usedRanges_(cols, std::make_pair(0, 0))
+{
+}
+
+SparseMatrix::SparseMatrix(const SparseMatrix& other)
+ : columns_(other.nCols_)
+ , nCols_(other.nCols_)
+ , nRows_(other.nRows_)
+ , columnBeingEdited_(other.columnBeingEdited_)
+ , usedRanges_(other.usedRanges_)
+{
+ for (size_t j = 0; j < nCols_; j++)
+ if (other.columns_[j])
+ columns_[j] = std::unique_ptr<SparseVector>(new SparseVector(*other.columns_[j]));
+}
+
+SparseMatrix::~SparseMatrix() {}
+
+void SparseMatrix::Reset(const size_t rows, const size_t cols)
+{
+ std::vector<std::unique_ptr<SparseVector>>(cols).swap(columns_);
+ nCols_ = cols;
+ nRows_ = rows;
+ std::vector<std::pair<size_t, size_t>>(cols, std::make_pair(0, 0)).swap(usedRanges_);
+ columnBeingEdited_ = std::numeric_limits<size_t>::max();
+}
+
+size_t SparseMatrix::UsedEntries() const
+{
+ // use column ranges
+ size_t filledEntries = 0;
+ for (size_t col = 0; col < Columns(); ++col) {
+ size_t start, end;
+ std::tie(start, end) = UsedRowRange(col);
+ filledEntries += (end - start);
+ }
+ return filledEntries;
+}
+
+float SparseMatrix::UsedEntriesRatio() const
+{
+ const float filled = static_cast<float>(UsedEntries());
+ const float size = static_cast<float>(Rows() * Columns());
+ return filled / size;
+}
+
+size_t SparseMatrix::AllocatedEntries() const
+{
+ size_t sum = 0;
+ for (size_t j = 0; j < nCols_; j++) {
+ sum += (columns_[j] != NULL ? columns_[j]->AllocatedEntries() : 0);
+ }
+ return sum;
+}
+
+void SparseMatrix::ToHostMatrix(double** mat, int* rows, int* cols) const
+{
+ const double nan = std::numeric_limits<double>::quiet_NaN();
+ *mat = new double[Rows() * Columns()];
+ *rows = static_cast<int>(Rows());
+ *cols = static_cast<int>(Columns());
+ for (size_t i = 0; i < Rows(); i++) {
+ for (size_t j = 0; j < Columns(); j++) {
+ (*mat)[i * Columns() + j] = IsAllocated(i, j) ? Get(i, j) : nan;
+ }
+ }
+}
+
+void SparseMatrix::CheckInvariants(size_t column) const
+{
+#ifndef NDEBUG
+ for (size_t j = 0; j < nCols_; j++) {
+ if (columns_[j] != NULL) columns_[j]->CheckInvariants();
+ }
+#endif
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/matrix/SparseMatrix.h b/src/matrix/SparseMatrix.h
new file mode 100644
index 0000000..cb9cf4d
--- /dev/null
+++ b/src/matrix/SparseMatrix.h
@@ -0,0 +1,190 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#pragma once
+
+#include <algorithm>
+#include <cassert>
+#include <memory>
+#include <utility>
+#include <vector>
+
+#include <pacbio/consensus/AbstractMatrix.h>
+#include "SparseVector.h"
+
+namespace PacBio {
+namespace Consensus {
+
+class SparseMatrix : public AbstractMatrix
+{
+public: // Constructor, destructor
+ SparseMatrix(size_t rows, size_t cols);
+ SparseMatrix(const SparseMatrix& other);
+ virtual ~SparseMatrix();
+
+public:
+ virtual void Reset(size_t rows, size_t cols);
+
+public: // Nullability
+ static const SparseMatrix& Null();
+ bool IsNull() const;
+
+public: // Size information
+ size_t Rows() const;
+ size_t Columns() const;
+
+public: // Information about entries filled by column
+ void StartEditingColumn(size_t j, size_t hintBegin, size_t hintEnd);
+ void FinishEditingColumn(size_t j, size_t usedBegin, size_t usedEnd);
+ std::pair<size_t, size_t> UsedRowRange(size_t j) const;
+ bool IsColumnEmpty(size_t j) const;
+ size_t UsedEntries() const override;
+ float UsedEntriesRatio() const override;
+ size_t AllocatedEntries() const override; // an entry may be allocated but not used
+
+public: // Accessors
+ const double& operator()(size_t i, size_t j) const;
+ bool IsAllocated(size_t i, size_t j) const;
+ double Get(size_t i, size_t j) const;
+ void Set(size_t i, size_t j, double v);
+ void ClearColumn(size_t j);
+
+public:
+ void ToHostMatrix(double** mat, int* rows, int* cols) const override;
+
+private:
+ static double* EmptyCell();
+
+private:
+ void CheckInvariants(size_t column) const;
+
+private:
+ std::vector<std::unique_ptr<SparseVector>> columns_;
+ size_t nCols_;
+ size_t nRows_;
+ size_t columnBeingEdited_;
+ std::vector<std::pair<size_t, size_t>> usedRanges_;
+};
+
+//
+// Nullability
+//
+inline const SparseMatrix& SparseMatrix::Null()
+{
+ static SparseMatrix* nullObj = new SparseMatrix(0, 0);
+ return *nullObj;
+}
+
+inline bool SparseMatrix::IsNull() const { return (Rows() == 0 && Columns() == 0); }
+
+//
+// Size information
+//
+inline size_t SparseMatrix::Rows() const { return nRows_; }
+inline size_t SparseMatrix::Columns() const { return nCols_; }
+
+//
+// Entry range queries per column
+//
+inline void SparseMatrix::StartEditingColumn(size_t j, size_t hintBegin, size_t hintEnd)
+{
+ assert(columnBeingEdited_ == std::numeric_limits<size_t>::max());
+ columnBeingEdited_ = j;
+ if (columns_[j] != NULL) {
+ columns_[j]->ResetForRange(hintBegin, hintEnd);
+ } else {
+ columns_[j] = std::unique_ptr<SparseVector>(new SparseVector(Rows(), hintBegin, hintEnd));
+ }
+}
+
+inline void SparseMatrix::FinishEditingColumn(size_t j, size_t usedRowsBegin, size_t usedRowsEnd)
+{
+ assert(columnBeingEdited_ == j);
+ usedRanges_[j] = std::make_pair(usedRowsBegin, usedRowsEnd);
+ CheckInvariants(columnBeingEdited_);
+ columnBeingEdited_ = std::numeric_limits<size_t>::max();
+}
+
+inline std::pair<size_t, size_t> SparseMatrix::UsedRowRange(size_t j) const
+{
+ assert(j < usedRanges_.size());
+ return usedRanges_[j];
+}
+
+inline bool SparseMatrix::IsColumnEmpty(size_t j) const
+{
+ assert(j < usedRanges_.size());
+ size_t begin, end;
+ std::tie(begin, end) = usedRanges_[j];
+ return begin >= end;
+}
+
+//
+// Accessors
+//
+inline const double& SparseMatrix::operator()(size_t i, size_t j) const
+{
+ if (columns_[j] == NULL) {
+ static const double emptyCell = 0.0;
+ return emptyCell;
+ } else {
+ return (*columns_[j])(i);
+ }
+}
+
+inline bool SparseMatrix::IsAllocated(size_t i, size_t j) const
+{
+ return columns_[j] != NULL && columns_[j]->IsAllocated(i);
+}
+
+inline double SparseMatrix::Get(size_t i, size_t j) const { return (*this)(i, j); }
+
+inline void SparseMatrix::Set(size_t i, size_t j, double v)
+{
+ assert(columnBeingEdited_ == j);
+ columns_[j]->Set(i, v);
+}
+
+inline void SparseMatrix::ClearColumn(size_t j)
+{
+ usedRanges_[j] = std::make_pair(0, 0);
+ columns_[j]->Clear();
+ CheckInvariants(j);
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/matrix/SparseVector.h b/src/matrix/SparseVector.h
new file mode 100644
index 0000000..6cf738d
--- /dev/null
+++ b/src/matrix/SparseVector.h
@@ -0,0 +1,227 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#pragma once
+
+#include <algorithm>
+#include <cassert>
+#include <cstring>
+#include <utility>
+#include <vector>
+
+namespace PacBio {
+namespace Consensus {
+
+class SparseVector
+{
+public: // Constructor, destructor
+ SparseVector(size_t logicalLength, size_t beginRow, size_t endRow);
+ SparseVector(const SparseVector& other);
+ ~SparseVector() = default;
+
+ // Ensures there is enough allocated storage to
+ // hold entries for at least [beginRow, endRow) (plus padding);
+ // clears existing entries.
+ void ResetForRange(size_t beginRow, size_t endRow);
+
+public:
+ const double& operator()(size_t i) const;
+ bool IsAllocated(size_t i) const;
+ double Get(size_t i) const;
+ void Set(size_t i, double v);
+ void Clear();
+
+public:
+ size_t AllocatedEntries() const;
+ void CheckInvariants() const;
+
+private:
+ // Expand the range of rows for which we have backing storage,
+ // while preserving contents. The arguments will become the
+ // new allocated bounds, so caller should add padding if desired
+ // before calling.
+ void ExpandAllocated(size_t newAllocatedBegin, size_t newAllocatedEnd);
+
+private:
+ // the "logical" length of the vector, of which only
+ // a subset of entries are actually allocated
+ size_t logicalLength_;
+
+ // row numbers in the abstraction we are presenting
+ size_t allocatedBeginRow_;
+ size_t allocatedEndRow_;
+
+ // the storage
+ std::vector<double> storage_;
+
+ // analytics
+ size_t nReallocs_;
+};
+
+namespace { // anonymous
+
+constexpr size_t PADDING = 8;
+constexpr double SHRINK_THRESHOLD = 0.8;
+
+} // anonymous namespace
+
+inline SparseVector::SparseVector(size_t logicalLength, size_t beginRow, size_t endRow)
+ : logicalLength_(logicalLength)
+ , allocatedBeginRow_((beginRow > PADDING) ? beginRow - PADDING : 0)
+ , allocatedEndRow_(std::min(endRow + PADDING, logicalLength_))
+ , storage_(allocatedEndRow_ - allocatedBeginRow_, 0.0)
+ , nReallocs_(0)
+{
+ assert(beginRow <= endRow && endRow <= logicalLength);
+ CheckInvariants();
+}
+
+inline SparseVector::SparseVector(const SparseVector& other)
+ : logicalLength_(other.logicalLength_)
+ , allocatedBeginRow_(other.allocatedBeginRow_)
+ , allocatedEndRow_(other.allocatedEndRow_)
+ , storage_(other.storage_)
+ , nReallocs_(0)
+{
+ CheckInvariants();
+}
+
+inline void SparseVector::ResetForRange(size_t beginRow, size_t endRow)
+{
+ // Allows reuse. Destructive.
+ CheckInvariants();
+ assert(beginRow <= endRow && endRow <= logicalLength_);
+ size_t newAllocatedBegin = (beginRow > PADDING) ? beginRow - PADDING : 0;
+ size_t newAllocatedEnd = std::min(endRow + PADDING, logicalLength_);
+ if ((newAllocatedEnd - newAllocatedBegin) > (allocatedEndRow_ - allocatedBeginRow_)) {
+ storage_.resize(newAllocatedEnd - newAllocatedBegin);
+ nReallocs_++;
+ Clear();
+ } else if ((newAllocatedEnd - newAllocatedBegin) <
+ static_cast<size_t>(SHRINK_THRESHOLD * (allocatedEndRow_ - allocatedBeginRow_))) {
+ // use swap trick to free allocated but unused memory,
+ // see:
+ // http://stackoverflow.com/questions/253157/how-to-downsize-stdvector
+ std::vector<double>(newAllocatedEnd - newAllocatedBegin, 0.0).swap(storage_);
+ nReallocs_++;
+ } else {
+ Clear();
+ }
+ allocatedBeginRow_ = newAllocatedBegin;
+ allocatedEndRow_ = newAllocatedEnd;
+ CheckInvariants();
+}
+
+inline void SparseVector::ExpandAllocated(size_t newAllocatedBegin, size_t newAllocatedEnd)
+{
+ // Expands allocated storage while preserving the contents.
+ CheckInvariants();
+ assert(newAllocatedBegin <= newAllocatedEnd && newAllocatedEnd <= logicalLength_);
+ assert(newAllocatedBegin <= allocatedBeginRow_ && newAllocatedEnd >= allocatedEndRow_);
+ // Resize the underlying storage.
+ storage_.resize(newAllocatedEnd - newAllocatedBegin);
+ // Use memmove to robustly relocate the old data (handles overlapping
+ // ranges).
+ // Data is at:
+ // storage[0 ... (end - begin) )
+ // Must be moved to:
+ // storage[(begin - newBegin) ... (end - newBegin)]
+ memmove(&storage_[allocatedBeginRow_ - newAllocatedBegin], &storage_[0],
+ (allocatedEndRow_ - allocatedBeginRow_) * sizeof(double)); // NOLINT
+ // "Zero"-fill the allocated but unused space.
+ std::fill(storage_.begin(), storage_.begin() + (allocatedBeginRow_ - newAllocatedBegin), 0.0);
+ std::fill(storage_.begin() + (allocatedEndRow_ - newAllocatedBegin), storage_.end(), 0.0);
+ // Update pointers.
+ allocatedBeginRow_ = newAllocatedBegin;
+ allocatedEndRow_ = newAllocatedEnd;
+ nReallocs_++;
+ CheckInvariants();
+}
+
+inline bool SparseVector::IsAllocated(size_t i) const
+{
+ assert(i < logicalLength_);
+ return i >= allocatedBeginRow_ && i < allocatedEndRow_;
+}
+
+inline const double& SparseVector::operator()(size_t i) const
+{
+ if (IsAllocated(i)) {
+ return storage_[i - allocatedBeginRow_];
+ } else {
+ static const double emptyCell_ = 0.0;
+ return emptyCell_;
+ }
+}
+
+inline double SparseVector::Get(size_t i) const { return (*this)(i); }
+
+inline void SparseVector::Set(size_t i, double v)
+{
+ using std::max;
+ using std::min;
+
+ CheckInvariants();
+ assert(i < logicalLength_);
+ if (!IsAllocated(i)) {
+ size_t newBeginRow = min((i > PADDING) ? i - PADDING : 0, allocatedBeginRow_);
+ size_t newEndRow = min(max(i + PADDING, allocatedEndRow_), logicalLength_);
+ ExpandAllocated(newBeginRow, newEndRow);
+ }
+ storage_[i - allocatedBeginRow_] = v;
+ CheckInvariants();
+}
+
+inline void SparseVector::Clear() { std::fill(storage_.begin(), storage_.end(), 0.0); }
+
+inline size_t SparseVector::AllocatedEntries() const
+{
+ // We want the real memory usage. std::vector is holding some memory back
+ // from us.
+ return storage_.capacity();
+}
+
+inline void SparseVector::CheckInvariants() const
+{
+ assert(allocatedBeginRow_ < logicalLength_);
+ assert(allocatedEndRow_ <= logicalLength_);
+ assert(allocatedBeginRow_ <= allocatedEndRow_);
+ assert((allocatedEndRow_ - allocatedBeginRow_) <= storage_.size());
+}
+
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/models/MarginalModelForm.cpp b/src/models/MarginalModelForm.cpp
new file mode 100644
index 0000000..896a20c
--- /dev/null
+++ b/src/models/MarginalModelForm.cpp
@@ -0,0 +1,232 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <cassert>
+#include <cmath>
+#include <memory>
+#include <stdexcept>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/exception/ModelError.h>
+
+#include "../JsonHelpers.h"
+#include "../ModelFactory.h"
+#include "../ModelFormFactory.h"
+#include "../Recursor.h"
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+using MalformedModelFile = PacBio::Exception::MalformedModelFile;
+
+constexpr size_t CONTEXT_NUMBER = 8;
+constexpr size_t OUTCOME_NUMBER = 4;
+
+// fwd decl
+class MarginalModelCreator;
+
+class MarginalModel : public ModelConfig
+{
+public:
+ MarginalModel(const MarginalModelCreator* params, const SNR& snr);
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr, double scoreDiff) const;
+ std::vector<TemplatePosition> Populate(const std::string& tpl) const;
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const;
+
+private:
+ const MarginalModelCreator* params_;
+ double counterWeight_;
+};
+
+class MarginalRecursor : public Recursor<MarginalRecursor>
+{
+public:
+ MarginalRecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff, const MarginalModelCreator* params, double counterWeight);
+
+ static std::vector<uint8_t> EncodeRead(const MappedRead& read);
+ double EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr) const;
+ double UndoCounterWeights(size_t nEmissions) const;
+
+private:
+ const MarginalModelCreator* params_;
+ double counterWeight_;
+ double nLgCounterWeight_;
+};
+
+class MarginalModelCreator : public ModelCreator
+{
+ REGISTER_MODELFORM(MarginalModelCreator);
+ friend class MarginalModel;
+ friend class MarginalRecursor;
+
+public:
+ static std::string Name() { return "Marginal"; }
+ MarginalModelCreator(const boost::property_tree::ptree& pt);
+ virtual std::unique_ptr<ModelConfig> Create(const SNR& snr) const
+ {
+ return std::unique_ptr<ModelConfig>(new MarginalModel(this, snr));
+ };
+
+private:
+ double emissionPmf_[3][CONTEXT_NUMBER][OUTCOME_NUMBER];
+ double transitionPmf_[CONTEXT_NUMBER][4];
+ double counterWeight_;
+};
+
+REGISTER_MODELFORM_IMPL(MarginalModelCreator);
+
+MarginalModel::MarginalModel(const MarginalModelCreator* params, const SNR& snr) : params_{params}
+{
+ counterWeight_ = params_->counterWeight_;
+}
+
+std::unique_ptr<AbstractRecursor> MarginalModel::CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff) const
+{
+ return std::unique_ptr<AbstractRecursor>(
+ new MarginalRecursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff,
+ params_, counterWeight_));
+}
+
+std::vector<TemplatePosition> MarginalModel::Populate(const std::string& tpl) const
+{
+ std::vector<TemplatePosition> result;
+
+ if (tpl.empty()) return result;
+
+ result.reserve(tpl.size());
+
+ // calculate transition probabilities
+ uint8_t prev = detail::TranslationTable[static_cast<uint8_t>(tpl[0])];
+ if (prev > 3) throw std::invalid_argument("invalid character in template!");
+
+ for (size_t i = 1; i < tpl.size(); ++i) {
+ const uint8_t curr = detail::TranslationTable[static_cast<uint8_t>(tpl[i])];
+ if (curr > 3) throw std::invalid_argument("invalid character in template!");
+ const uint8_t ctx = ((prev == curr) << 2) | curr;
+ const auto& params = params_->transitionPmf_[ctx];
+ result.emplace_back(TemplatePosition{
+ tpl[i - 1], prev,
+ params[0], // match
+ params[1], // branch
+ params[2], // stick
+ params[3] // deletion
+ });
+ prev = curr;
+ }
+ result.emplace_back(TemplatePosition{tpl.back(), prev, 1.0, 0.0, 0.0, 0.0});
+
+ return result;
+}
+
+double MarginalModel::ExpectedLLForEmission(const MoveType move, const uint8_t prev,
+ const uint8_t curr, const MomentType moment) const
+{
+ const uint8_t ctx = ((prev == curr) << 2) | curr;
+ double expectedLL = 0;
+ for (size_t i = 0; i < OUTCOME_NUMBER; i++) {
+ double curProb = params_->emissionPmf_[static_cast<uint8_t>(move)][ctx][i];
+ double lgCurProb = std::log(curProb);
+ if (moment == MomentType::FIRST)
+ expectedLL += curProb * lgCurProb;
+ else if (moment == MomentType::SECOND)
+ expectedLL += curProb * (lgCurProb * lgCurProb);
+ }
+ return expectedLL;
+}
+
+MarginalRecursor::MarginalRecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff, const MarginalModelCreator* params,
+ double counterWeight)
+ : Recursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff)
+ , params_{params}
+ , counterWeight_{counterWeight}
+ , nLgCounterWeight_{-std::log(counterWeight_)}
+{
+}
+
+std::vector<uint8_t> MarginalRecursor::EncodeRead(const MappedRead& read)
+{
+ std::vector<uint8_t> result;
+ result.reserve(read.Length());
+
+ for (const char bp : read.Seq) {
+ const uint8_t em = detail::TranslationTable[static_cast<uint8_t>(bp)];
+ if (em > 3) throw std::invalid_argument("invalid character in read!");
+ result.emplace_back(em);
+ }
+
+ return result;
+}
+
+double MarginalRecursor::EmissionPr(MoveType move, uint8_t emission, uint8_t prev,
+ uint8_t curr) const
+{
+ assert(move != MoveType::DELETION);
+ const uint8_t ctx = ((prev == curr) << 2) | curr;
+ return params_->emissionPmf_[static_cast<uint8_t>(move)][ctx][emission] * counterWeight_;
+}
+
+double MarginalRecursor::UndoCounterWeights(const size_t nEmissions) const
+{
+ return nLgCounterWeight_ * nEmissions;
+}
+
+MarginalModelCreator::MarginalModelCreator(const boost::property_tree::ptree& pt)
+{
+ try {
+ ReadMatrix<3, CONTEXT_NUMBER, OUTCOME_NUMBER>(emissionPmf_,
+ pt.get_child("EmissionParameters"));
+ ReadMatrix<CONTEXT_NUMBER, 4>(transitionPmf_, pt.get_child("TransitionParameters"));
+ counterWeight_ = pt.get<double>("CounterWeight");
+ } catch (std::invalid_argument& e) {
+ throw MalformedModelFile();
+ } catch (boost::property_tree::ptree_error) {
+ throw MalformedModelFile();
+ }
+}
+
+} // namespace anonymous
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/models/P6C4NoCovModel.cpp b/src/models/P6C4NoCovModel.cpp
new file mode 100644
index 0000000..3ae9287
--- /dev/null
+++ b/src/models/P6C4NoCovModel.cpp
@@ -0,0 +1,251 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cassert>
+#include <cmath>
+#include <memory>
+#include <stdexcept>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/data/Read.h>
+
+#include "../ModelFactory.h"
+#include "../Recursor.h"
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+constexpr double kEps = 0.00505052456472967;
+constexpr double kCounterWeight = 1.894736842105264607;
+
+class P6C4NoCovModel : public ModelConfig
+{
+ REGISTER_MODEL(P6C4NoCovModel);
+
+public:
+ static std::set<std::string> Names() { return {"P6-C4::Snr"}; }
+ P6C4NoCovModel(const SNR& snr);
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr, double scoreDiff) const;
+ std::vector<TemplatePosition> Populate(const std::string& tpl) const;
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const;
+
+private:
+ SNR snr_;
+};
+
+REGISTER_MODEL_IMPL(P6C4NoCovModel);
+
+// TODO(lhepler) comments regarding the CRTP
+class P6C4NoCovRecursor : public Recursor<P6C4NoCovRecursor>
+{
+public:
+ P6C4NoCovRecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff);
+ static inline std::vector<uint8_t> EncodeRead(const MappedRead& read);
+ static inline double EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr);
+ virtual double UndoCounterWeights(size_t nEmissions) const;
+};
+
+double P6C4NoCovParams[4][2][3][4] = {
+ { // A
+ {// NA
+ {2.35936060895653, -0.463630601682986, 0.0179206897766131, -0.000230839937063052},
+ {3.22847830625841, -0.0886820214931539, 0.00555981712798726, -0.000137686231186054},
+ {-0.101031042923432, -0.0138783767832632, -0.00153408019582419, 7.66780338484727e-06}},
+ {// AA
+ {3.76122480667588, -0.536010820176981, 0.0275375059387171, -0.000470200724345621},
+ {3.57517725358548, -0.0257545295375707, -0.000163673803286944, 5.3256984681724e-06},
+ {0.858421613302247, -0.0276654216841666, -8.85549766507732e-05, -4.85355908595337e-05}}},
+ { // C
+ {// NC
+ {5.956054206161, -1.71886470811695, 0.153315470604752, -0.00474488595513198},
+ {3.89418464416296, -0.174182841558867, 0.0171719290275442, -0.000653629721359769},
+ {2.40532887070852, -0.652606650098156, 0.0688783864119339, -0.00246479494650594}},
+ {// CC
+ {5.66725538674764, -1.10462196933913, 0.0879811093908922, -0.00259393800835979},
+ {4.11682756767018, -0.124758322644639, 0.00659795177909886, -0.000361914629195461},
+ {3.17103818507405, -0.729020290806687, 0.0749784690396837, -0.00262779517495421}}},
+ { // G
+ {// NG
+ {3.53508304630569, -0.788027301381263, 0.0469367803413207, -0.00106221924705805},
+ {2.85440184222226, 0.166346531056167, -0.0166161828155307, 0.000439492705370092},
+ {0.238188180807376, 0.0589443522886522, -0.0123401045958974, 0.000336854126836293}},
+ {// GG
+ {3.81920778703052, -0.540309003502589, 0.0389569264893982, -0.000901245733796236},
+ {3.31322216145728, 0.123514009118836, -0.00807401406655071, 0.000230843924466035},
+ {2.06006877520527, -0.451486652688621, 0.0375212898173045, -0.000937676250926241}}},
+ { // T
+ {// NT
+ {5.36199280681367, -1.46099908985536, 0.126755291030074, -0.0039102734460725},
+ {3.41597143103046, -0.066984162951578, 0.0138944877787003, -0.000558939998921912},
+ {1.37371376794871, -0.246963827944892, 0.0209674231346363, -0.000684856715039738}},
+ {// TT
+ {5.39308368236762, -1.32931568057267, 0.107844580241936, -0.00316462903462847},
+ {4.21031404956015, -0.347546363361823, 0.0293839179303896, -0.000893802212450644},
+ {2.33143889851302, -0.586068444099136, 0.040044954697795, -0.000957298861394191}}}};
+
+// For P6-C4 we cap SNR at 20.0 (19.0 for C); as the training set only went that
+// high; extrapolation beyond this cap goes haywire because of the higher-order
+// terms in the regression model. See bug 31423.
+P6C4NoCovModel::P6C4NoCovModel(const SNR& snr)
+ : snr_(ClampSNR(snr, SNR(0, 0, 0, 0), SNR(20, 19, 20, 20)))
+{
+}
+
+std::vector<TemplatePosition> P6C4NoCovModel::Populate(const std::string& tpl) const
+{
+ std::vector<TemplatePosition> result;
+
+ if (tpl.empty()) return result;
+
+ uint8_t prev = detail::TranslationTable[static_cast<uint8_t>(tpl[0])];
+ if (prev > 3) throw std::invalid_argument("invalid character in sequence!");
+
+ for (size_t i = 1; i < tpl.size(); ++i) {
+ const uint8_t curr = detail::TranslationTable[static_cast<uint8_t>(tpl[i])];
+ if (curr > 3) throw std::invalid_argument("invalid character in sequence!");
+ const bool hp = tpl[i - 1] == tpl[i]; // NA -> 0, AA -> 1
+ const auto params = P6C4NoCovParams[curr][hp];
+ const double snr = snr_[curr], snr2 = snr * snr, snr3 = snr2 * snr;
+ double tprobs[3];
+ double sum = 1.0;
+
+ for (size_t j = 0; j < 3; ++j) {
+ double xb =
+ params[j][0] + snr * params[j][1] + snr2 * params[j][2] + snr3 * params[j][3];
+ xb = std::exp(xb);
+ tprobs[j] = xb;
+ sum += xb;
+ }
+
+ for (size_t j = 0; j < 3; ++j)
+ tprobs[j] /= sum;
+
+ result.emplace_back(TemplatePosition{
+ tpl[i - 1], prev,
+ tprobs[1], // match
+ 1.0 / sum, // branch
+ tprobs[2], // stick
+ tprobs[0] // deletion
+ });
+
+ prev = curr;
+ }
+
+ result.emplace_back(TemplatePosition{tpl.back(), prev, 1.0, 0.0, 0.0, 0.0});
+
+ return result;
+}
+
+std::unique_ptr<AbstractRecursor> P6C4NoCovModel::CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff) const
+{
+ return std::unique_ptr<AbstractRecursor>(
+ new P6C4NoCovRecursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff));
+}
+
+double P6C4NoCovModel::ExpectedLLForEmission(const MoveType move, const uint8_t prev,
+ const uint8_t curr, const MomentType moment) const
+{
+ const double lgThird = -std::log(3.0);
+ if (move == MoveType::MATCH) {
+ constexpr double probMatch = 1.0 - kEps;
+ constexpr double probMismatch = kEps;
+ const double lgMatch = std::log(probMatch);
+ const double lgMismatch = lgThird + std::log(probMismatch);
+ if (moment == MomentType::FIRST)
+ return probMatch * lgMatch + probMismatch * lgMismatch;
+ else if (moment == MomentType::SECOND)
+ return probMatch * (lgMatch * lgMatch) + probMismatch * (lgMismatch * lgMismatch);
+ } else if (move == MoveType::BRANCH)
+ return 0.0;
+ else if (move == MoveType::STICK) {
+ if (moment == MomentType::FIRST)
+ return lgThird;
+ else if (moment == MomentType::SECOND)
+ return lgThird * lgThird;
+ }
+ throw std::invalid_argument("invalid move!");
+}
+
+P6C4NoCovRecursor::P6C4NoCovRecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff)
+ : Recursor<P6C4NoCovRecursor>(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr,
+ scoreDiff)
+{
+}
+
+std::vector<uint8_t> P6C4NoCovRecursor::EncodeRead(const MappedRead& read)
+{
+ std::vector<uint8_t> result;
+
+ for (const char bp : read.Seq) {
+ const uint8_t em = detail::TranslationTable[static_cast<uint8_t>(bp)];
+ if (em > 3) throw std::invalid_argument("invalid character in read!");
+ result.emplace_back(em);
+ }
+
+ return result;
+}
+
+double P6C4NoCovRecursor::EmissionPr(MoveType move, const uint8_t emission, const uint8_t prev,
+ const uint8_t curr)
+{
+ assert(move != MoveType::DELETION);
+
+ // probability of a mismatch
+ constexpr double tbl[3][2] = {
+ // 0 (match), 1 (mismatch)
+ {1.0 - kEps, kEps / 3.0}, // MATCH
+ {1.0, 0.0}, // BRANCH
+ {0.0, 1.0 / 3.0} // STICK
+ };
+
+ return tbl[static_cast<uint8_t>(move)][curr != emission] * kCounterWeight;
+}
+
+double P6C4NoCovRecursor::UndoCounterWeights(const size_t nEmissions) const
+{
+ return -std::log(kCounterWeight) * nEmissions;
+}
+
+} // namespace anonymous
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/models/PwSnrAModelForm.cpp b/src/models/PwSnrAModelForm.cpp
new file mode 100644
index 0000000..3d6c73d
--- /dev/null
+++ b/src/models/PwSnrAModelForm.cpp
@@ -0,0 +1,283 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <cassert>
+#include <cmath>
+#include <memory>
+#include <stdexcept>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/exception/ModelError.h>
+
+#include "../JsonHelpers.h"
+#include "../ModelFactory.h"
+#include "../ModelFormFactory.h"
+#include "../Recursor.h"
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+using MalformedModelFile = PacBio::Exception::MalformedModelFile;
+
+template <typename T>
+inline T clip(const T val, const T range[2])
+{
+ return std::max(range[0], std::min(val, range[1]));
+}
+
+constexpr size_t OUTCOME_NUMBER = 12;
+constexpr size_t CONTEXT_NUMBER = 16;
+
+// fwd decl
+class PwSnrAModelCreator;
+
+class PwSnrAModel : public ModelConfig
+{
+public:
+ PwSnrAModel(const PwSnrAModelCreator* params, const SNR& snr);
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr, double scoreDiff) const;
+ std::vector<TemplatePosition> Populate(const std::string& tpl) const;
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const;
+
+private:
+ double CalculateExpectedLLForEmission(const size_t move, const uint8_t row,
+ const size_t moment) const;
+
+ const PwSnrAModelCreator* params_;
+ SNR snr_;
+ double ctxTrans_[CONTEXT_NUMBER][4];
+ double cachedEmissionExpectations_[CONTEXT_NUMBER][3][2];
+ double counterWeight_;
+};
+
+class PwSnrARecursor : public Recursor<PwSnrARecursor>
+{
+public:
+ PwSnrARecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff,
+ const PwSnrAModelCreator* params, double counterWeight);
+
+ static std::vector<uint8_t> EncodeRead(const MappedRead& read);
+ double EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr) const;
+ double UndoCounterWeights(size_t nEmissions) const;
+
+private:
+ const PwSnrAModelCreator* params_;
+ double counterWeight_;
+ double nLgCounterWeight_;
+};
+
+class PwSnrAModelCreator : public ModelCreator
+{
+ REGISTER_MODELFORM(PwSnrAModelCreator);
+ friend class PwSnrAModel;
+ friend class PwSnrARecursor;
+
+public:
+ static std::string Name() { return "PwSnrA"; }
+ PwSnrAModelCreator(const boost::property_tree::ptree& pt);
+ virtual std::unique_ptr<ModelConfig> Create(const SNR& snr) const
+ {
+ return std::unique_ptr<ModelConfig>(new PwSnrAModel(this, snr));
+ };
+
+private:
+ double snrRanges_[2];
+ double emissionPmf_[3][CONTEXT_NUMBER][OUTCOME_NUMBER];
+ double transitionParams_[CONTEXT_NUMBER][3][4];
+ double counterWeight_;
+};
+
+REGISTER_MODELFORM_IMPL(PwSnrAModelCreator);
+
+inline double PwSnrAModel::CalculateExpectedLLForEmission(const size_t move, const uint8_t row,
+ const size_t moment) const
+{
+ double expectedLL = 0;
+ for (size_t i = 0; i < OUTCOME_NUMBER; i++) {
+ double curProb = params_->emissionPmf_[move][row][i];
+ double lgCurProb = std::log(curProb);
+ if (moment == static_cast<uint8_t>(MomentType::FIRST))
+ expectedLL += curProb * lgCurProb;
+ else if (moment == static_cast<uint8_t>(MomentType::SECOND))
+ expectedLL += curProb * (lgCurProb * lgCurProb);
+ }
+ return expectedLL;
+}
+
+PwSnrAModel::PwSnrAModel(const PwSnrAModelCreator* params, const SNR& snr)
+ : params_{params}, snr_(snr)
+{
+ const double snr1 = clip(snr_.A, params_->snrRanges_), snr2 = snr1 * snr1, snr3 = snr2 * snr1;
+ for (size_t ctx = 0; ctx < CONTEXT_NUMBER; ++ctx) {
+ double sum = 1.0;
+
+ // cached transitions
+ ctxTrans_[ctx][0] = 1.0;
+ for (size_t j = 0; j < 3; ++j) {
+ double xb = params_->transitionParams_[ctx][j][0] +
+ params_->transitionParams_[ctx][j][1] * snr1 +
+ params_->transitionParams_[ctx][j][2] * snr2 +
+ params_->transitionParams_[ctx][j][3] * snr3;
+ xb = std::exp(xb);
+ ctxTrans_[ctx][j + 1] = xb;
+ sum += xb;
+ }
+ for (size_t j = 0; j < 4; ++j)
+ ctxTrans_[ctx][j] /= sum;
+
+ // cached expectations
+ for (size_t move = 0; move < 3; ++move)
+ for (size_t moment = 0; moment < 2; ++moment)
+ cachedEmissionExpectations_[ctx][move][moment] =
+ CalculateExpectedLLForEmission(move, ctx, moment);
+ }
+
+ counterWeight_ = params_->counterWeight_;
+}
+
+std::unique_ptr<AbstractRecursor> PwSnrAModel::CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff) const
+{
+ return std::unique_ptr<AbstractRecursor>(
+ new PwSnrARecursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff,
+ params_, counterWeight_));
+}
+
+std::vector<TemplatePosition> PwSnrAModel::Populate(const std::string& tpl) const
+{
+ std::vector<TemplatePosition> result;
+
+ if (tpl.empty()) return result;
+
+ result.reserve(tpl.size());
+
+ // calculate transition probabilities
+ uint8_t prev = detail::TranslationTable[static_cast<uint8_t>(tpl[0])];
+ if (prev > 3) throw std::invalid_argument("invalid character in template!");
+
+ for (size_t i = 1; i < tpl.size(); ++i) {
+ const uint8_t curr = detail::TranslationTable[static_cast<uint8_t>(tpl[i])];
+ if (curr > 3) throw std::invalid_argument("invalid character in template!");
+ const auto row = (prev << 2) | curr;
+ const auto params = ctxTrans_[row];
+ result.emplace_back(TemplatePosition{
+ tpl[i - 1], prev,
+ params[0], // match
+ params[1], // branch
+ params[2], // stick
+ params[3] // deletion
+ });
+ prev = curr;
+ }
+ result.emplace_back(TemplatePosition{tpl.back(), prev, 1.0, 0.0, 0.0, 0.0});
+
+ return result;
+}
+
+double PwSnrAModel::ExpectedLLForEmission(const MoveType move, const uint8_t prev,
+ const uint8_t curr, const MomentType moment) const
+{
+ const size_t row = (prev << 2) | curr;
+ return cachedEmissionExpectations_[row][static_cast<uint8_t>(move)]
+ [static_cast<uint8_t>(moment)];
+}
+
+PwSnrARecursor::PwSnrARecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff, const PwSnrAModelCreator* params,
+ double counterWeight)
+ : Recursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff)
+ , params_{params}
+ , counterWeight_{counterWeight}
+ , nLgCounterWeight_{-std::log(counterWeight_)}
+{
+}
+
+std::vector<uint8_t> PwSnrARecursor::EncodeRead(const MappedRead& read)
+{
+ std::vector<uint8_t> result;
+
+ result.reserve(read.Length());
+
+ for (size_t i = 0; i < read.Length(); ++i) {
+ if (read.PulseWidth[i] < 1U) throw std::runtime_error("invalid PulseWidth in read!");
+ const uint8_t pw = std::min(2, read.PulseWidth[i] - 1);
+ const uint8_t bp = detail::TranslationTable[static_cast<uint8_t>(read.Seq[i])];
+ if (bp > 3) throw std::invalid_argument("invalid character in read!");
+ const uint8_t em = (pw << 2) | bp;
+ if (em > 11) throw std::runtime_error("read encoding error!");
+ result.emplace_back(em);
+ }
+
+ return result;
+}
+
+double PwSnrARecursor::EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr) const
+{
+ assert(move != MoveType::DELETION);
+ const auto row = (prev << 2) | curr;
+ return params_->emissionPmf_[static_cast<uint8_t>(move)][row][emission] * counterWeight_;
+}
+
+double PwSnrARecursor::UndoCounterWeights(const size_t nEmissions) const
+{
+ return nLgCounterWeight_ * nEmissions;
+}
+
+PwSnrAModelCreator::PwSnrAModelCreator(const boost::property_tree::ptree& pt)
+{
+ try {
+ ReadMatrix<2>(snrRanges_, pt.get_child("SnrRanges"));
+ ReadMatrix<3, CONTEXT_NUMBER, OUTCOME_NUMBER>(emissionPmf_,
+ pt.get_child("EmissionParameters"));
+ ReadMatrix<CONTEXT_NUMBER, 3, 4>(transitionParams_, pt.get_child("TransitionParameters"));
+ counterWeight_ = pt.get<double>("CounterWeight");
+ } catch (std::invalid_argument& e) {
+ throw MalformedModelFile();
+ } catch (boost::property_tree::ptree_error) {
+ throw MalformedModelFile();
+ }
+}
+
+} // namespace anonymous
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/models/PwSnrModelForm.cpp b/src/models/PwSnrModelForm.cpp
new file mode 100644
index 0000000..4b5d470
--- /dev/null
+++ b/src/models/PwSnrModelForm.cpp
@@ -0,0 +1,284 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <cassert>
+#include <cmath>
+#include <memory>
+#include <stdexcept>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/exception/ModelError.h>
+
+#include "../JsonHelpers.h"
+#include "../ModelFactory.h"
+#include "../ModelFormFactory.h"
+#include "../Recursor.h"
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+using MalformedModelFile = PacBio::Exception::MalformedModelFile;
+
+template <typename T>
+inline T clip(const T val, const T range[2])
+{
+ return std::max(range[0], std::min(val, range[1]));
+}
+
+constexpr size_t OUTCOME_NUMBER = 12;
+constexpr size_t CONTEXT_NUMBER = 16;
+
+// fwd decl
+class PwSnrModelCreator;
+
+class PwSnrModel : public ModelConfig
+{
+public:
+ PwSnrModel(const PwSnrModelCreator* params, const SNR& snr);
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr, double scoreDiff) const;
+ std::vector<TemplatePosition> Populate(const std::string& tpl) const;
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const;
+
+private:
+ double CalculateExpectedLLForEmission(const size_t move, const uint8_t row,
+ const size_t moment) const;
+
+ const PwSnrModelCreator* params_;
+ SNR snr_;
+ double ctxTrans_[CONTEXT_NUMBER][4];
+ double cachedEmissionExpectations_[CONTEXT_NUMBER][3][2];
+ double counterWeight_;
+};
+
+class PwSnrRecursor : public Recursor<PwSnrRecursor>
+{
+public:
+ PwSnrRecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff,
+ const PwSnrModelCreator* params, double counterWeight);
+
+ static std::vector<uint8_t> EncodeRead(const MappedRead& read);
+ double EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr) const;
+ double UndoCounterWeights(size_t nEmissions) const;
+
+private:
+ const PwSnrModelCreator* params_;
+ double counterWeight_;
+ double nLgCounterWeight_;
+};
+
+class PwSnrModelCreator : public ModelCreator
+{
+ REGISTER_MODELFORM(PwSnrModelCreator);
+ friend class PwSnrModel;
+ friend class PwSnrRecursor;
+
+public:
+ static std::string Name() { return "PwSnr"; }
+ PwSnrModelCreator(const boost::property_tree::ptree& pt);
+ virtual std::unique_ptr<ModelConfig> Create(const SNR& snr) const
+ {
+ return std::unique_ptr<ModelConfig>(new PwSnrModel(this, snr));
+ };
+
+private:
+ double snrRanges_[4][2];
+ double emissionPmf_[3][CONTEXT_NUMBER][OUTCOME_NUMBER];
+ double transitionParams_[CONTEXT_NUMBER][3][4];
+ double counterWeight_;
+};
+
+REGISTER_MODELFORM_IMPL(PwSnrModelCreator);
+
+inline double PwSnrModel::CalculateExpectedLLForEmission(const size_t move, const uint8_t row,
+ const size_t moment) const
+{
+ double expectedLL = 0;
+ for (size_t i = 0; i < OUTCOME_NUMBER; i++) {
+ double curProb = params_->emissionPmf_[move][row][i];
+ double lgCurProb = std::log(curProb);
+ if (moment == static_cast<uint8_t>(MomentType::FIRST))
+ expectedLL += curProb * lgCurProb;
+ else if (moment == static_cast<uint8_t>(MomentType::SECOND))
+ expectedLL += curProb * (lgCurProb * lgCurProb);
+ }
+ return expectedLL;
+}
+
+PwSnrModel::PwSnrModel(const PwSnrModelCreator* params, const SNR& snr) : params_{params}, snr_(snr)
+{
+ for (size_t ctx = 0; ctx < CONTEXT_NUMBER; ++ctx) {
+ const uint8_t bp = ctx & 3; // (equivalent to % 4)
+ const double snr1 = clip(snr_[bp], params_->snrRanges_[bp]), snr2 = snr1 * snr1,
+ snr3 = snr2 * snr1;
+ double sum = 1.0;
+
+ // cached transitions
+ ctxTrans_[ctx][0] = 1.0;
+ for (size_t j = 0; j < 3; ++j) {
+ double xb = params_->transitionParams_[ctx][j][0] +
+ params_->transitionParams_[ctx][j][1] * snr1 +
+ params_->transitionParams_[ctx][j][2] * snr2 +
+ params_->transitionParams_[ctx][j][3] * snr3;
+ xb = std::exp(xb);
+ ctxTrans_[ctx][j + 1] = xb;
+ sum += xb;
+ }
+ for (size_t j = 0; j < 4; ++j)
+ ctxTrans_[ctx][j] /= sum;
+
+ // cached expectations
+ for (size_t move = 0; move < 3; ++move)
+ for (size_t moment = 0; moment < 2; ++moment)
+ cachedEmissionExpectations_[ctx][move][moment] =
+ CalculateExpectedLLForEmission(move, ctx, moment);
+ }
+
+ counterWeight_ = params_->counterWeight_;
+}
+
+std::unique_ptr<AbstractRecursor> PwSnrModel::CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff) const
+{
+ return std::unique_ptr<AbstractRecursor>(
+ new PwSnrRecursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff,
+ params_, counterWeight_));
+}
+
+std::vector<TemplatePosition> PwSnrModel::Populate(const std::string& tpl) const
+{
+ std::vector<TemplatePosition> result;
+
+ if (tpl.empty()) return result;
+
+ result.reserve(tpl.size());
+
+ // calculate transition probabilities
+ uint8_t prev = detail::TranslationTable[static_cast<uint8_t>(tpl[0])];
+ if (prev > 3) throw std::invalid_argument("invalid character in template!");
+
+ for (size_t i = 1; i < tpl.size(); ++i) {
+ const uint8_t curr = detail::TranslationTable[static_cast<uint8_t>(tpl[i])];
+ if (curr > 3) throw std::invalid_argument("invalid character in template!");
+ const uint8_t row = (prev << 2) | curr;
+ const auto& params = ctxTrans_[row];
+ result.emplace_back(TemplatePosition{
+ tpl[i - 1], prev,
+ params[0], // match
+ params[1], // branch
+ params[2], // stick
+ params[3] // deletion
+ });
+ prev = curr;
+ }
+ result.emplace_back(TemplatePosition{tpl.back(), prev, 1.0, 0.0, 0.0, 0.0});
+
+ return result;
+}
+
+double PwSnrModel::ExpectedLLForEmission(const MoveType move, const uint8_t prev,
+ const uint8_t curr, const MomentType moment) const
+{
+ const size_t row = (prev << 2) | curr;
+ return cachedEmissionExpectations_[row][static_cast<uint8_t>(move)]
+ [static_cast<uint8_t>(moment)];
+}
+
+PwSnrRecursor::PwSnrRecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff, const PwSnrModelCreator* params,
+ double counterWeight)
+ : Recursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff)
+ , params_{params}
+ , counterWeight_{counterWeight}
+ , nLgCounterWeight_{-std::log(counterWeight_)}
+{
+}
+
+std::vector<uint8_t> PwSnrRecursor::EncodeRead(const MappedRead& read)
+{
+ std::vector<uint8_t> result;
+
+ result.reserve(read.Length());
+
+ for (size_t i = 0; i < read.Length(); ++i) {
+ if (read.PulseWidth[i] < 1U) throw std::runtime_error("invalid PulseWidth in read!");
+ const uint8_t pw = std::min(2, read.PulseWidth[i] - 1);
+ const uint8_t bp = detail::TranslationTable[static_cast<uint8_t>(read.Seq[i])];
+ if (bp > 3) throw std::invalid_argument("invalid character in read!");
+ const uint8_t em = (pw << 2) | bp;
+ if (em > 11) throw std::runtime_error("read encoding error!");
+ result.emplace_back(em);
+ }
+
+ return result;
+}
+
+double PwSnrRecursor::EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr) const
+{
+ assert(move != MoveType::DELETION);
+ const uint8_t row = (prev << 2) | curr;
+ return params_->emissionPmf_[static_cast<uint8_t>(move)][row][emission] * counterWeight_;
+}
+
+double PwSnrRecursor::UndoCounterWeights(const size_t nEmissions) const
+{
+ return nLgCounterWeight_ * nEmissions;
+}
+
+PwSnrModelCreator::PwSnrModelCreator(const boost::property_tree::ptree& pt)
+{
+ try {
+ ReadMatrix<4, 2>(snrRanges_, pt.get_child("SnrRanges"));
+ ReadMatrix<3, CONTEXT_NUMBER, OUTCOME_NUMBER>(emissionPmf_,
+ pt.get_child("EmissionParameters"));
+ ReadMatrix<CONTEXT_NUMBER, 3, 4>(transitionParams_, pt.get_child("TransitionParameters"));
+ counterWeight_ = pt.get<double>("CounterWeight");
+ } catch (std::invalid_argument& e) {
+ throw MalformedModelFile();
+ } catch (boost::property_tree::ptree_error) {
+ throw MalformedModelFile();
+ }
+}
+
+} // namespace anonymous
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/models/S_P1C1Beta_Model.cpp b/src/models/S_P1C1Beta_Model.cpp
new file mode 100644
index 0000000..f453665
--- /dev/null
+++ b/src/models/S_P1C1Beta_Model.cpp
@@ -0,0 +1,216 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cassert>
+#include <cmath>
+#include <memory>
+#include <stdexcept>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/data/Read.h>
+
+#include "../ModelFactory.h"
+#include "../Recursor.h"
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+class S_P1C1Beta_Model : public ModelConfig
+{
+ REGISTER_MODEL(S_P1C1Beta_Model);
+
+public:
+ static std::set<std::string> Names() { return {"S/P1-C1/beta::Marginal"}; }
+ S_P1C1Beta_Model(const SNR& snr);
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr, double scoreDiff) const;
+ std::vector<TemplatePosition> Populate(const std::string& tpl) const;
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const;
+
+private:
+ SNR snr_;
+};
+
+REGISTER_MODEL_IMPL(S_P1C1Beta_Model);
+
+class S_P1C1Beta_Recursor : public Recursor<S_P1C1Beta_Recursor>
+{
+public:
+ S_P1C1Beta_Recursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff);
+ static inline std::vector<uint8_t> EncodeRead(const MappedRead& read);
+ static inline double EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr);
+ virtual double UndoCounterWeights(size_t nEmissions) const;
+};
+
+constexpr double emissionPmf[3][8][4] = {
+ {
+ // matchPmf
+ {0.980417570, 0.011537479, 0.005804964, 0.002239987}, // AA
+ {0.026122324, 0.972937583, 0.000367796, 0.000572296}, // CC
+ {0.002544283, 0.002239375, 0.962042375, 0.033173967}, // GG
+ {0.000509814, 0.001489097, 0.094228328, 0.903772761}, // TT
+ {0.979840156, 0.012582917, 0.005185205, 0.002391722}, // NA
+ {0.015528755, 0.984439781, 7.91000E-07, 3.07000E-05}, // NC
+ {0.002667013, 0.002095727, 0.961571053, 0.033666207}, // NG
+ {0.000506358, 0.001057035, 0.116124340, 0.882312267} // NT
+ },
+ {
+ // branchPmf
+ {1, 0, 0, 0}, // AA
+ {0, 1, 0, 0}, // CC
+ {0, 0, 1, 0}, // GG
+ {0, 0, 0, 1}, // TT
+ {1, 0, 0, 0}, // NA
+ {0, 1, 0, 0}, // NC
+ {0, 0, 1, 0}, // NG
+ {0, 0, 0, 1} // NT
+ },
+ {
+ // stickPmf
+ {0.000000000, 0.254503401, 0.574809968, 0.170686631}, // AA
+ {0.399446202, 0.000000000, 0.510664061, 0.089889737}, // CC
+ {0.505214805, 0.188597323, 0.000000000, 0.306187872}, // GG
+ {0.361855644, 0.132870306, 0.505274050, 0.000000000}, // TT
+ {0.000000000, 0.210676350, 0.615161689, 0.174161960}, // NA
+ {0.357451562, 0.000000000, 0.473482915, 0.169065523}, // NC
+ {0.577147745, 0.169785817, 0.000000000, 0.253066438}, // NG
+ {0.446834358, 0.144605809, 0.408559833, 0.000000000} // NT
+ }};
+
+constexpr double transProbs[8][4] = {
+ // Match, Branch, Stick, Delete
+ {0.888913751, 0.021169653, 0.034937054, 0.054979542}, // AA
+ {0.835822697, 0.036126801, 0.091992041, 0.036058461}, // CC
+ {0.886427657, 0.022596867, 0.039619893, 0.051355584}, // GG
+ {0.821252207, 0.072798639, 0.068161389, 0.037787765}, // TT
+ {0.857630366, 0.072058988, 0.036435296, 0.033875351}, // NA
+ {0.846000625, 0.032981179, 0.076759732, 0.044258463}, // NC
+ {0.881462348, 0.042444137, 0.039293952, 0.036799562}, // NG
+ {0.879087800, 0.022178294, 0.057073518, 0.041660389} // NT
+};
+
+S_P1C1Beta_Model::S_P1C1Beta_Model(const SNR& snr) : snr_(snr) {}
+std::vector<TemplatePosition> S_P1C1Beta_Model::Populate(const std::string& tpl) const
+{
+ std::vector<TemplatePosition> result;
+
+ if (tpl.empty()) return result;
+
+ uint8_t prev = detail::TranslationTable[static_cast<uint8_t>(tpl[0])];
+ if (prev > 3) throw std::invalid_argument("invalid character in sequence!");
+
+ for (size_t i = 1; i < tpl.size(); ++i) {
+ const uint8_t curr = detail::TranslationTable[static_cast<uint8_t>(tpl[i])];
+ if (curr > 3) throw std::invalid_argument("invalid character in sequence!");
+ const bool hpAdd = tpl[i - 1] == tpl[i] ? 0 : 4;
+ const auto params = transProbs[curr + hpAdd];
+ result.emplace_back(TemplatePosition{
+ tpl[i - 1], prev,
+ params[0], // match
+ params[1], // branch
+ params[2], // stick
+ params[3] // deletion
+ });
+ prev = curr;
+ }
+
+ result.emplace_back(TemplatePosition{tpl.back(), prev, 1.0, 0.0, 0.0, 0.0});
+
+ return result;
+}
+
+std::unique_ptr<AbstractRecursor> S_P1C1Beta_Model::CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff) const
+{
+ return std::unique_ptr<AbstractRecursor>(new S_P1C1Beta_Recursor(
+ std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff));
+}
+
+double S_P1C1Beta_Model::ExpectedLLForEmission(const MoveType move, const uint8_t prev,
+ const uint8_t curr, const MomentType moment) const
+{
+ const uint8_t hpAdd = prev == curr ? 0 : 4;
+ const uint8_t row = curr + hpAdd;
+ double expectedLL = 0;
+ for (size_t i = 0; i < 4; i++) {
+ double curProb = emissionPmf[static_cast<uint8_t>(move)][row][i];
+ double lgCurProb = std::log(curProb);
+ if (moment == MomentType::FIRST)
+ expectedLL += curProb * lgCurProb;
+ else if (moment == MomentType::SECOND)
+ expectedLL += curProb * (lgCurProb * lgCurProb);
+ }
+ return expectedLL;
+}
+
+S_P1C1Beta_Recursor::S_P1C1Beta_Recursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr, double scoreDiff)
+ : Recursor<S_P1C1Beta_Recursor>(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr,
+ scoreDiff)
+{
+}
+
+std::vector<uint8_t> S_P1C1Beta_Recursor::EncodeRead(const MappedRead& read)
+{
+ std::vector<uint8_t> result;
+
+ for (const char bp : read.Seq) {
+ const uint8_t em = detail::TranslationTable[static_cast<uint8_t>(bp)];
+ if (em > 3) throw std::invalid_argument("invalid character in read!");
+ result.emplace_back(em);
+ }
+
+ return result;
+}
+
+double S_P1C1Beta_Recursor::EmissionPr(MoveType move, const uint8_t emission, const uint8_t prev,
+ const uint8_t curr)
+{
+ assert(move != MoveType::DELETION);
+ const uint8_t hpAdd = prev == curr ? 0 : 4;
+ // Which row do we want?
+ const uint8_t row = curr + hpAdd;
+ return emissionPmf[static_cast<uint8_t>(move)][row][emission];
+}
+
+double S_P1C1Beta_Recursor::UndoCounterWeights(const size_t nEmissions) const { return 0; }
+} // namespace anonymous
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/models/S_P1C1v1_Model.cpp b/src/models/S_P1C1v1_Model.cpp
new file mode 100644
index 0000000..7c8d3bc
--- /dev/null
+++ b/src/models/S_P1C1v1_Model.cpp
@@ -0,0 +1,395 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <cassert>
+#include <cmath>
+#include <memory>
+#include <stdexcept>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/data/Read.h>
+
+#include "../ModelFactory.h"
+#include "../Recursor.h"
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+constexpr double kCounterWeight = 15.0;
+constexpr size_t OUTCOME_NUMBER = 12;
+constexpr size_t CONTEXT_NUMBER = 16;
+
+class S_P1C1v1_Model : public ModelConfig
+{
+ REGISTER_MODEL(S_P1C1v1_Model);
+
+public:
+ static std::set<std::string> Names() { return {"S/P1-C1.1::PwSnrA"}; }
+ S_P1C1v1_Model(const SNR& snr);
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr, double scoreDiff) const;
+ std::vector<TemplatePosition> Populate(const std::string& tpl) const;
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const;
+
+private:
+ SNR snr_;
+ double ctxTrans_[CONTEXT_NUMBER][4];
+ double cachedEmissionExpectations_[CONTEXT_NUMBER][3][2];
+};
+
+REGISTER_MODEL_IMPL(S_P1C1v1_Model);
+
+// TODO(lhepler) comments regarding the CRTP
+class S_P1C1v1_Recursor : public Recursor<S_P1C1v1_Recursor>
+{
+public:
+ S_P1C1v1_Recursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff);
+ static inline std::vector<uint8_t> EncodeRead(const MappedRead& read);
+ static inline double EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr);
+ virtual double UndoCounterWeights(size_t nEmissions) const;
+};
+
+constexpr double emissionPmf[3][CONTEXT_NUMBER][OUTCOME_NUMBER] = {
+ {// matchPmf
+ {0.0516695237, 0.000856759021, 0.000805765869, 6.40098033e-05, 0.0735681929, 0.000490647727,
+ 0.00171763848, 1.66588276e-05, 0.864949369, 0.00298262543, 0.0027926093, 6.28389773e-05},
+ {0.00543436007, 0.011889156, 0.000101241451, 0.000115879948, 0.0161576112, 0.0379073447,
+ 0.00013138862, 0.000162963331, 0.0238359857, 0.903407615, 0.000310425863, 0.00051517498},
+ {0.00078327569, 8.9195486e-05, 0.0213823858, 0.00233242884, 0.00122583139, 2.26787869e-05,
+ 0.0797753558, 0.0023406575, 0.000536349203, 0.000218984243, 0.881882162, 0.00937678742},
+ {0.000153647232, 0.00010627987, 0.0103924584, 0.0168897121, 0.000528420929, 0.000114998697,
+ 0.034445993, 0.0461495153, 0.000202642175, 0.000688915405, 0.0797339416, 0.810568344},
+ {0.0217684866, 0.000615574217, 0.00123796174, 0.000194115893, 0.0630331228, 0.000312092976,
+ 0.00217859654, 1.70111886e-05, 0.905859233, 0.00150065174, 0.0030195303, 0.00023882051},
+ {0.043036651, 0.0109154406, 0.000137917521, 6.63118913e-05, 0.0135411051, 0.0336696383,
+ 3.68321175e-05, 9.7192835e-05, 0.0198015123, 0.878552904, 1.95554178e-05, 9.54805479e-05},
+ {0.00018454615, 1.51427373e-05, 0.00855522704, 0.00108940771, 0.000328562866, 1.41858457e-05,
+ 0.0341491789, 0.00128003844, 0.00124774351, 0.000256778116, 0.944704089, 0.00815078658},
+ {0.000244636834, 5.95364998e-05, 0.0103025634, 0.0176534311, 0.000417091732, 3.89027835e-05,
+ 0.0347137702, 0.0495173978, 0.000658139356, 0.000481549284, 0.0798548882, 0.80602469},
+ {0.0120953705, 0.000297201253, 0.000336831573, 0.000109810239, 0.0339973245, 0.000295424749,
+ 0.000821327226, 7.0554379e-05, 0.947447668, 0.00298212225, 0.00115060424, 0.000366663193},
+ {0.00202072785, 0.0061102332, 0.000138730316, 8.82424379e-05, 0.00783346136, 0.0193899073,
+ 0.000128803697, 5.1853045e-05, 0.0145084431, 0.948899725, 0.000308586587, 0.00049984933},
+ {0.0362076945, 3.82567383e-05, 0.00699047085, 0.000843806016, 0.00025900091, 2.74289133e-05,
+ 0.0275479876, 0.00133679409, 0.00089127495, 0.000135756189, 0.918742407, 0.00694931573},
+ {0.000148143946, 5.09628138e-05, 0.00492091587, 0.00825067123, 3.34491844e-05, 1.52215475e-05,
+ 0.0185009947, 0.0282098475, 0.000211194, 0.000843725462, 0.0534485418, 0.885335084},
+ {0.0233179774, 0.000994145372, 0.000594429081, 3.30759279e-05, 0.061000414, 0.00042148067,
+ 0.00179973978, 7.98899e-05, 0.906095769, 0.00277286156, 0.00269906625, 0.000153458766},
+ {0.00252578813, 0.0058253842, 2.66040065e-05, 8.55149972e-05, 0.00783559799, 0.020356316,
+ 0.000125999422, 9.67021798e-05, 0.0145272461, 0.948105104, 0.000231890377, 0.000228741056},
+ {0.000344291837, 1.71744233e-05, 0.0093318888, 0.00101109441, 0.000518176918, 2.49752238e-05,
+ 0.0364757971, 0.00118973194, 0.00131474596, 0.000128603181, 0.942187364, 0.00743159244},
+ {0.0286354873, 0.000348696974, 0.00669477573, 0.00817040337, 0.00263533574, 0.000832163375,
+ 0.0187454532, 0.0241172554, 0.0272027554, 0.0261244204, 0.0786962737, 0.777776291}},
+
+ {// branchPmf
+ {0.337545783, 0.000189833088, 0.000189833088, 0.000189833088, 0.167897832, 0.000189833088,
+ 0.000189833088, 0.000189833088, 0.491898721, 0.000189833088, 0.000189833088, 0.000189833088},
+ {0.000455211501, 0.10721842, 0.000455211501, 0.000455211501, 0.000455211501, 0.0880290507,
+ 0.000455211501, 0.000455211501, 0.000455211501, 0.798379568, 0.000455211501, 0.000455211501},
+ {0.000139076929, 0.000139076929, 0.277526154, 0.000139076929, 0.000139076929, 0.000139076929,
+ 0.164738707, 0.000139076929, 0.000139076929, 0.000139076929, 0.555788062, 0.000139076929},
+ {0.000340988677, 0.000340988677, 0.000340988677, 0.107667327, 0.000340988677, 0.000340988677,
+ 0.000340988677, 0.11481587, 0.000340988677, 0.000340988677, 0.000340988677, 0.772742962},
+ {0.15792522, 4.71456125e-05, 4.71456125e-05, 4.71456125e-05, 0.141752834, 4.71456125e-05,
+ 4.71456125e-05, 4.71456125e-05, 0.699661908, 4.71456125e-05, 4.71456125e-05, 4.71456125e-05},
+ {8.48749074e-05, 0.0356794691, 8.47792483e-05, 8.47792483e-05, 8.50080149e-05, 0.0463288295,
+ 8.47792483e-05, 8.47792483e-05, 8.85882375e-05, 0.916800659, 8.47792483e-05, 8.47792483e-05},
+ {7.09844065e-05, 7.09844065e-05, 0.228163146, 7.09844065e-05, 7.09844065e-05, 7.09844065e-05,
+ 0.125258165, 7.09844065e-05, 7.09844065e-05, 7.09844065e-05, 0.645584908, 7.09844065e-05},
+ {0.000294417195, 0.000294417195, 0.000294417195, 0.0762864785, 0.000294417195, 0.000294417195,
+ 0.000294417195, 0.115945928, 0.000294417195, 0.000294417195, 0.000294417195, 0.803645753},
+ {0.116533833, 5.79322675e-05, 5.79322675e-05, 5.79322675e-05, 0.0942835568, 5.79322675e-05,
+ 5.79322675e-05, 5.79322675e-05, 0.788371558, 5.79322675e-05, 5.79322675e-05, 5.79322675e-05},
+ {0.000156684083, 0.0527691682, 0.000156684083, 0.000156684083, 0.000156684083, 0.0520229677,
+ 0.000156684083, 0.000156684083, 0.000156684083, 0.893014287, 0.000156684083, 0.000156684083},
+ {0.000167018487, 0.000165322717, 0.312421562, 0.000165322717, 0.000165401501, 0.000165322717,
+ 0.133726114, 0.000165322717, 0.000165734487, 0.000165322717, 0.55153562, 0.000165322717},
+ {0.000203462057, 0.000203462057, 0.000203462057, 0.0471982179, 0.000203462057, 0.000203462057,
+ 0.000203462057, 0.049201974, 0.000203462057, 0.000203462057, 0.000203462057, 0.900751339},
+ {0.119585426, 6.14072028e-05, 6.14072028e-05, 6.14072028e-05, 0.116129123, 6.14072028e-05,
+ 6.14072028e-05, 6.14072028e-05, 0.76342575, 6.14072028e-05, 6.14072028e-05, 6.14072028e-05},
+ {0.000110720498, 0.0349410744, 0.000110720498, 0.000110720498, 0.000110720498, 0.0453942421,
+ 0.000110720498, 0.000110720498, 0.000110720498, 0.918114596, 0.000110720498, 0.000110720498},
+ {7.09455464e-05, 7.09455464e-05, 0.186570455, 7.09455464e-05, 7.09455464e-05, 7.09455464e-05,
+ 0.11383208, 7.09455464e-05, 7.09455464e-05, 7.09455464e-05, 0.698604227, 7.09455464e-05},
+ {5.44400066e-05, 4.58781747e-05, 4.58781747e-05, 0.0513058841, 4.58791482e-05, 4.58781747e-05,
+ 4.58781747e-05, 0.081923538, 4.95222541e-05, 4.58781747e-05, 4.58781747e-05, 0.866116077}},
+
+ {// stickPmf
+ {0.000154038684, 0.0291154091, 0.423444453, 0.0352058932, 0.000154038684, 0.0176086145,
+ 0.149856392, 0.0151919119, 0.000154038684, 0.0916984378, 0.168808535, 0.067838043},
+ {0.13839578, 9.92440537e-05, 0.329722566, 0.0318555909, 0.0371088704, 9.92440537e-05,
+ 0.148457457, 0.0195393534, 0.112987247, 9.92440537e-05, 0.103583418, 0.0775557653},
+ {0.39242986, 0.0361688498, 0.00033884198, 0.138030777, 0.0355767848, 0.0102554086,
+ 0.00033884198, 0.054319306, 0.0665562733, 0.0785778949, 0.00033884198, 0.185374109},
+ {0.265583401, 0.0323250154, 0.267620652, 0.000144990997, 0.0553401869, 0.0100214732,
+ 0.12586624, 0.000144990997, 0.081077577, 0.0457693156, 0.115236212, 0.000144990997},
+ {8.86069101e-05, 0.0224045604, 0.391863179, 0.0374698777, 8.86069101e-05, 0.014879736,
+ 0.127064528, 0.0148023081, 8.86069101e-05, 0.199043674, 0.127110897, 0.0646523839},
+ {0.132279199, 5.64661147e-05, 0.321806183, 0.0323685244, 0.0725530116, 4.63524839e-05,
+ 0.160579431, 0.0137370025, 0.108005126, 4.69523474e-05, 0.116162938, 0.0421336554},
+ {0.320519663, 0.0239698473, 0.00011228542, 0.0412339441, 0.124873594, 0.0131178903,
+ 0.00011228542, 0.0214946836, 0.139243924, 0.223216618, 0.00011228542, 0.091431553},
+ {0.236440465, 0.0125729978, 0.174982446, 0.000114967022, 0.072742801, 0.0157082833,
+ 0.107504931, 0.000114967022, 0.0812575292, 0.199021401, 0.0988494102, 0.000114967022},
+ {0.000172377278, 0.0252780963, 0.441347929, 0.0431573519, 0.000172377278, 0.0109779693,
+ 0.122083706, 0.01370133, 0.000172377278, 0.112156842, 0.126224513, 0.103693244},
+ {0.11616354, 4.4550521e-05, 0.38730196, 0.0316267288, 0.048597637, 4.4550521e-05, 0.217316542,
+ 0.0147582454, 0.0443979757, 4.4550521e-05, 0.0941246042, 0.0453563631},
+ {0.351437251, 0.0237786623, 0.00123104756, 0.0609100017, 0.132002208, 0.0127583294,
+ 0.000288446433, 0.0203701885, 0.1316581, 0.080542757, 0.000252892079, 0.18353973},
+ {0.298492049, 0.0269851185, 0.29827165, 0.000200099143, 0.102490322, 0.0117983684, 0.121179733,
+ 0.000200099143, 0.0770158895, 0.0380659958, 0.0241000812, 0.000200099143},
+ {0.000141627536, 0.01777018, 0.301881108, 0.0226933622, 0.000141627536, 0.0109104656,
+ 0.114187821, 0.0163453226, 0.000141627536, 0.102595478, 0.208037711, 0.204445531},
+ {0.132859004, 7.16119861e-05, 0.2406106, 0.0231724181, 0.057038948, 7.16119861e-05,
+ 0.0925183577, 0.0141944935, 0.0659598334, 7.16119861e-05, 0.125422694, 0.247650755},
+ {0.355614563, 0.0234102543, 0.000187722927, 0.0564654303, 0.109173536, 0.0154941999,
+ 0.000187722927, 0.0155496293, 0.106690121, 0.0539175558, 0.000187722927, 0.262182928},
+ {0.152511749, 0.0105044023, 0.228700197, 9.13331245e-05, 0.0553648837, 0.00620728656,
+ 0.191510525, 7.33906221e-05, 0.048230451, 0.0444486569, 0.261928846, 7.37812688e-05}}};
+
+constexpr double transProbs[16][3][4] = {
+ // Fit for context: AA
+ {{-11.8402163277545, 4.12000773672109, -0.661725654820908, 0.0337357107347639},
+ {-3.10509518253287, 0.275600076181856, -0.101980967380149, 0.00728037713082447},
+ {8.79817734479091, -4.80619827278369, 0.668699377698361, -0.0323014351665758}},
+ // Fit for context: AC
+ {{3.76105501880563, -3.52354687054574, 0.518155785867385, -0.0259189282231727},
+ {1.14984691288476, -1.86148610164711, 0.282410704404651, -0.0137482001748907},
+ {8.87581132716677, -6.06418672877366, 0.934174708128712, -0.047710831271599}},
+ // Fit for context: AG
+ {{-3.5155637685456, 0.445157302722387, -0.0895426643665516, 0.00489266836530986},
+ {-2.13069399948839, -0.350350414444882, 0.00136462130313272, 0.000872314444289463},
+ {8.18160747215397, -4.75181353430953, 0.663320066629866, -0.0312212296436783}},
+ // Fit for context: AT
+ {{-0.791966407223805, -1.1076552938185, 0.121601533987201, -0.00531175337455805},
+ {-0.881444261440707, -0.731399892071115, 0.05057749339712, 9.31173789284391e-05},
+ {1.41263899033538, -2.13869979708684, 0.29554287522677, -0.0139759898505845}},
+ // Fit for context: CA
+ {{-3.26897975135237, 0.486468075687521, -0.0760370712635174, 0.00388977870825071},
+ {-1.35534562252107, -0.638577072165448, 0.0728422429297584, -0.0017528458186216},
+ {1.44591127557233, -1.35648438299165, 0.109211078325847, -0.00258389758690641}},
+ // Fit for context: CC
+ {{-3.06858725937395, 0.180650646816408, -0.0144155236738455, -0.000689002527617641},
+ {-6.84579191173796, 2.25516178646427, -0.339242808398693, 0.0163235455182541},
+ {0.960878124005925, -1.79437153365345, 0.26563747809023, -0.0132138048710256}},
+ // Fit for context: CG
+ {{-2.94152963474479, 0.229999854263155, -0.0481872379951125, 0.00285101023017463},
+ {0.869169888335733, -1.64839041486039, 0.219451593119437, -0.00974508815102731},
+ {3.06149815060729, -2.70884449310353, 0.353919865598604, -0.0152760395255156}},
+ // Fit for context: CT
+ {{0.713137277702561, -1.70038938696478, 0.195497764255509, -0.006277117941137},
+ {0.547238286104262, -1.18712111898372, 0.10016377902078, 0.000101142585729921},
+ {12.8142966669109, -7.60356150884139, 1.14279549736876, -0.0556464549926148}},
+ // Fit for context: GA
+ {{-4.04796366671756, 0.995050162374295, -0.176460865193268, 0.0098125020081521},
+ {-2.84979586974211, -0.0156903140508224, -0.0289509861158852, 0.00249431280742574},
+ {3.58059555038287, -2.82647199241841, 0.361847788449807, -0.0165539653343998}},
+ // Fit for context: GC
+ {{-0.349844213146088, -1.43550809248254, 0.203825919576521, -0.00916693940279327},
+ {1.63175479730304, -2.09434440700094, 0.344467568084574, -0.0177539882113115},
+ {-0.575918177053267, -1.5981774767604, 0.220590706766665, -0.0105341908671507}},
+ // Fit for context: GG
+ {{-2.7885490831891, 0.0219683824222214, -0.0434630049972039, 0.00405333456781744},
+ {1.88946633862993, -2.07810257475806, 0.259413174779754, -0.0120217530655737},
+ {1.69364885624261, -1.79573141305228, 0.241169169566732, -0.0114709227454174}},
+ // Fit for context: GT
+ {{-3.5677104673935, 0.358289552435854, -0.0789736924123636, 0.0036044786219107},
+ {-6.64088518072203, 2.07297640845549, -0.400256333112317, 0.0235022424593019},
+ {4.80925899732482, -3.74080441862834, 0.510449289512398, -0.0219234011000643}},
+ // Fit for context: TA
+ {{-2.64069119760436, 0.38549684716509, -0.0816358329471849, 0.00533873493972419},
+ {1.9113212271993, -2.61336018392704, 0.462996555125255, -0.0271165824050175},
+ {0.238605182625403, -0.457118176718339, -0.0792840976069514, 0.00934498149921929}},
+ // Fit for context: TC
+ {{-0.392997656904618, -0.971016641524484, 0.103185513110187, -0.00226499422687784},
+ {-5.41259348922946, 1.37988834568899, -0.223433285481649, 0.0121196778796477},
+ {0.756454968716176, -2.18832755353204, 0.294407264252205, -0.0125416902322882}},
+ // Fit for context: TG
+ {{-3.13537076489306, 0.356196913405038, -0.0801078852726234, 0.00556755944444425},
+ {0.0417901722734827, -1.44128792816831, 0.193288926462961, -0.00976454902739811},
+ {2.9482632980712, -2.38567585927352, 0.272478951901359, -0.0102457478965403}},
+ // Fit for context: TT
+ {{-2.23386221240998, -0.150165813792347, 0.0503325945637299, -0.00444264897626409},
+ {1.66643125707819, -2.11840547506457, 0.345196264109573, -0.0190747089705634},
+ {-1.9903454046927, -0.489297962270134, 0.0503913801733079, -0.00174698908180932}}};
+
+inline double CalculateExpectedLLForEmission(const size_t move, const uint8_t row,
+ const size_t moment)
+{
+ double expectedLL = 0;
+ for (size_t i = 0; i < OUTCOME_NUMBER; ++i) {
+ const double curProb = emissionPmf[move][row][i];
+ const double lgCurProb = std::log(curProb);
+ if (moment == static_cast<uint8_t>(MomentType::FIRST))
+ expectedLL += curProb * lgCurProb;
+ else if (moment == static_cast<uint8_t>(MomentType::SECOND))
+ expectedLL += curProb * (lgCurProb * lgCurProb);
+ }
+ return expectedLL;
+}
+
+S_P1C1v1_Model::S_P1C1v1_Model(const SNR& snr) : snr_(snr)
+{
+ // Generate cached transistion probabilities
+
+ double snr1 = snr_.A;
+ // Adjust as necessary to clamp to bounds of SNRs observe during training
+ if (snr1 < 4.0) {
+ snr1 = 4.0;
+ } else if (snr1 > 10.65) {
+ snr1 = 10.65;
+ }
+
+ const double snr2 = snr1 * snr1, snr3 = snr2 * snr1;
+ for (size_t ctx = 0; ctx < CONTEXT_NUMBER; ++ctx) {
+ double sum = 1.0;
+ ctxTrans_[ctx][0] = 1.0;
+ for (size_t j = 0; j < 3; ++j) {
+ double xb = transProbs[ctx][j][0] + snr1 * transProbs[ctx][j][1] +
+ snr2 * transProbs[ctx][j][2] + snr3 * transProbs[ctx][j][3];
+ xb = std::exp(xb);
+ ctxTrans_[ctx][j + 1] = xb;
+ sum += xb;
+ }
+ for (size_t j = 0; j < 4; ++j)
+ ctxTrans_[ctx][j] /= sum;
+ }
+
+ // Generate cached emission expectations
+ // TODO: These are identical for all instances, either we should enrich the model or avoid doing
+ // this in a context dependent way
+ for (size_t ctx = 0; ctx < CONTEXT_NUMBER; ++ctx)
+ for (size_t move = 0; move < 3; ++move)
+ for (size_t moment = 0; moment < 2; ++moment)
+ cachedEmissionExpectations_[ctx][move][moment] =
+ CalculateExpectedLLForEmission(move, ctx, moment);
+}
+
+std::unique_ptr<AbstractRecursor> S_P1C1v1_Model::CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff) const
+{
+ return std::unique_ptr<AbstractRecursor>(
+ new S_P1C1v1_Recursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff));
+}
+
+std::vector<TemplatePosition> S_P1C1v1_Model::Populate(const std::string& tpl) const
+{
+ std::vector<TemplatePosition> result;
+
+ if (tpl.empty()) return result;
+
+ result.reserve(tpl.size());
+
+ // Calculate probabilities in all 16 Contexts
+ uint8_t prev = detail::TranslationTable[static_cast<uint8_t>(tpl[0])];
+ if (prev > 3) throw std::invalid_argument("invalid character in template!");
+
+ for (size_t i = 1; i < tpl.size(); ++i) {
+ const uint8_t curr = detail::TranslationTable[static_cast<uint8_t>(tpl[i])];
+ if (curr > 3) throw std::invalid_argument("invalid character in template!");
+ const auto row = (prev << 2) | curr;
+ const auto params = ctxTrans_[row];
+ result.emplace_back(TemplatePosition{
+ tpl[i - 1], prev,
+ params[0], // match
+ params[1], // branch
+ params[2], // stick
+ params[3] // deletion
+ });
+ prev = curr;
+ }
+ result.emplace_back(TemplatePosition{tpl.back(), prev, 1.0, 0.0, 0.0, 0.0});
+
+ return result;
+}
+
+double S_P1C1v1_Model::ExpectedLLForEmission(const MoveType move, const uint8_t prev,
+ const uint8_t curr, const MomentType moment) const
+{
+ const size_t row = (prev << 2) | curr;
+ return cachedEmissionExpectations_[row][static_cast<uint8_t>(move)]
+ [static_cast<uint8_t>(moment)];
+}
+
+S_P1C1v1_Recursor::S_P1C1v1_Recursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff)
+ : Recursor<S_P1C1v1_Recursor>(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr,
+ scoreDiff)
+{
+}
+
+std::vector<uint8_t> S_P1C1v1_Recursor::EncodeRead(const MappedRead& read)
+{
+ std::vector<uint8_t> result;
+
+ result.reserve(read.Length());
+
+ for (size_t i = 0; i < read.Length(); ++i) {
+ if (read.PulseWidth[i] < 1U) throw std::runtime_error("invalid PulseWidth in read!");
+ const uint8_t pw = std::min(2, read.PulseWidth[i] - 1);
+ const uint8_t bp = detail::TranslationTable[static_cast<uint8_t>(read.Seq[i])];
+ if (bp > 3) throw std::invalid_argument("invalid character in read!");
+ const uint8_t em = (pw << 2) | bp;
+ if (em > 11) throw std::runtime_error("read encoding error!");
+ result.emplace_back(em);
+ }
+
+ return result;
+}
+
+double S_P1C1v1_Recursor::EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr)
+{
+ assert(move != MoveType::DELETION);
+ const auto row = (prev << 2) | curr;
+ return emissionPmf[static_cast<uint8_t>(move)][row][emission] * kCounterWeight;
+}
+
+double S_P1C1v1_Recursor::UndoCounterWeights(const size_t nEmissions) const
+{
+ return -std::log(kCounterWeight) * nEmissions;
+}
+} // namespace anonymous
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/models/S_P1C1v2_Model.cpp b/src/models/S_P1C1v2_Model.cpp
new file mode 100644
index 0000000..9db4328
--- /dev/null
+++ b/src/models/S_P1C1v2_Model.cpp
@@ -0,0 +1,396 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <cassert>
+#include <cmath>
+#include <memory>
+#include <stdexcept>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/data/Read.h>
+
+#include "../ModelFactory.h"
+#include "../Recursor.h"
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+template <typename T>
+inline T clip(const T val, const T range[2])
+{
+ return std::max(range[0], std::min(val, range[1]));
+}
+
+constexpr double kCounterWeight = 20.0;
+constexpr size_t nOutcomes = 12;
+constexpr size_t nContexts = 16;
+
+class S_P1C1v2_Model : public ModelConfig
+{
+ REGISTER_MODEL(S_P1C1v2_Model);
+
+public:
+ static std::set<std::string> Names() { return {"S/P1-C1.2::PwSnr"}; }
+ S_P1C1v2_Model(const SNR& snr);
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr, double scoreDiff) const;
+ std::vector<TemplatePosition> Populate(const std::string& tpl) const;
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const;
+
+private:
+ SNR snr_;
+ double ctxTrans_[nContexts][4];
+ double cachedEmissionExpectations_[nContexts][3][2];
+};
+
+REGISTER_MODEL_IMPL(S_P1C1v2_Model);
+
+// TODO(lhepler) comments regarding the CRTP
+class S_P1C1v2_Recursor : public Recursor<S_P1C1v2_Recursor>
+{
+public:
+ S_P1C1v2_Recursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff);
+ static inline std::vector<uint8_t> EncodeRead(const MappedRead& read);
+ static inline double EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr);
+ virtual double UndoCounterWeights(size_t nEmissions) const;
+};
+
+constexpr double snrRanges[4][2] = {{4.000641, 9.799212}, // A
+ {5.654043, 17.958242}, // C
+ {4.000119, 9.744069}, // G
+ {5.751278, 14.595276}}; // T
+
+constexpr double emissionPmf[3][nContexts][nOutcomes] = {
+ {// matchPmf
+ {0.050560033, 0.00144763859, 0.000163177865, 2.0867935e-05, 0.0726032734, 0.000842439402,
+ 0.000271423794, 8.43974963e-06, 0.869290866, 0.00413508802, 0.000521750699, 0.000118837204},
+ {0.00462830888, 0.0139517191, 0.000101186697, 5.67650713e-05, 0.0160684007, 0.0406243136,
+ 0.000138793033, 5.62552642e-05, 0.0190043135, 0.904879566, 0.000174480994, 0.000295282359},
+ {0.000175052112, 2.26892306e-05, 0.0196019025, 0.00400244294, 0.000509824298, 9.75492549e-06,
+ 0.0802293256, 0.00408560015, 0.000147604012, 0.000331175767, 0.872713612, 0.0181486146},
+ {8.73952452e-05, 6.17770545e-05, 0.00903033597, 0.018502656, 0.000200885068, 9.75016622e-05,
+ 0.0351722645, 0.0517276852, 0.000352994508, 0.000385742081, 0.0644170155, 0.819947012},
+ {0.0198831161, 0.000961303214, 0.000144597389, 4.67305367e-05, 0.0638168971, 0.000837850222,
+ 0.000558459661, 3.99576048e-05, 0.910672574, 0.00217152562, 0.000648278718, 0.000202152294},
+ {0.0410273877, 0.0126381834, 5.80888114e-05, 4.64404749e-05, 0.0138647592, 0.0380978485,
+ 2.49507103e-05, 4.31344748e-05, 0.0155899299, 0.878541588, 1.74872929e-05, 3.0599793e-05},
+ {8.32672171e-05, 2.20656741e-05, 0.00834519645, 0.00156910057, 0.000172765793, 2.1418975e-05,
+ 0.0356742714, 0.00212721578, 0.000622484386, 0.000230268885, 0.933599375, 0.0175160384},
+ {3.86341223e-05, 6.93599568e-05, 0.0106638632, 0.0194476326, 2.80847249e-05, 6.80203472e-05,
+ 0.0350317359, 0.0561405145, 0.000248220527, 0.000735245812, 0.064117019, 0.813389881},
+ {0.01055129, 0.000606336462, 0.000106046244, 6.17777656e-05, 0.0340550092, 0.000538619497,
+ 0.000266054642, 9.96327513e-06, 0.948832735, 0.00433935042, 0.000343332891, 0.000270289762},
+ {0.00199646998, 0.0070224845, 6.10929446e-05, 5.77297092e-05, 0.0076668946, 0.0217966053,
+ 9.74216351e-05, 1.5916467e-05, 0.011502371, 0.949283502, 0.000259732895, 0.000225420187},
+ {0.0363913971, 5.18879484e-05, 0.00586382213, 0.00119694109, 7.89913825e-05, 1.4820869e-05,
+ 0.0288807762, 0.00180293314, 0.000312950446, 0.000119941063, 0.909704767, 0.0155609746},
+ {1.64569235e-05, 4.43086063e-05, 0.00453413579, 0.0102359104, 5.18293729e-05, 6.02931756e-05,
+ 0.0180114607, 0.0306943017, 0.000153656166, 0.000607235317, 0.0413053796, 0.894264433},
+ {0.0214236803, 0.00145057122, 0.000196790896, 7.29502814e-05, 0.0617915495, 0.000820733636,
+ 0.00047074373, 5.43281455e-05, 0.908393448, 0.0044080379, 0.000772738613, 0.000118585931},
+ {0.00254794588, 0.00714226772, 5.36718881e-05, 5.4246971e-05, 0.00790636565, 0.0227387232,
+ 3.97346769e-05, 4.53241014e-05, 0.0116566568, 0.947447228, 0.000175142411, 0.000173810276},
+ {8.63087551e-05, 2.68932315e-05, 0.00961793262, 0.00169384557, 7.28762914e-05, 7.4200117e-06,
+ 0.037210596, 0.00195177916, 0.000458586001, 0.000265371391, 0.933488709, 0.0151035143},
+ {0.0297329186, 0.000570699243, 0.00648572858, 0.00907544748, 0.00299260939, 0.000974535227,
+ 0.0194331272, 0.0272735285, 0.0264500987, 0.0267971751, 0.0666750407, 0.783525197}},
+ {// branchPmf
+ {0.271862342, 0.000108958984, 0.000108958984, 0.000108958984, 0.160747222, 0.000108958984,
+ 0.000108958984, 0.000108958984, 0.56586501, 0.000108958984, 0.000108958984, 0.000108958984},
+ {0.000253399313, 0.0805474032, 0.000253399313, 0.000253399313, 0.000253399313, 0.11493698,
+ 0.000253399313, 0.000253399313, 0.000253399313, 0.800968026, 0.000253399313, 0.000253399313},
+ {9.96116186e-05, 9.96116186e-05, 0.295921139, 9.96116186e-05, 9.96116186e-05, 9.96116186e-05,
+ 0.156000597, 9.96116186e-05, 9.96116186e-05, 9.96116186e-05, 0.546683702, 9.96116186e-05},
+ {0.000266389696, 0.000266389696, 0.000266389696, 0.106949539, 0.000266389696, 0.000266389696,
+ 0.000266389696, 0.117892594, 0.000266389696, 0.000266389696, 0.000266389696, 0.771428411},
+ {0.158494227, 3.22815102e-05, 3.22815102e-05, 3.22815102e-05, 0.135246183, 3.22815102e-05,
+ 3.22815102e-05, 3.22815102e-05, 0.705807649, 3.22815102e-05, 3.22815102e-05, 3.22815102e-05},
+ {5.63990004e-05, 0.0396234254, 5.4605313e-05, 5.4605313e-05, 5.47353715e-05, 0.0555789327,
+ 5.4605313e-05, 5.4605313e-05, 5.64103869e-05, 0.904029439, 5.4605313e-05, 5.4605313e-05},
+ {4.80816837e-05, 4.80816837e-05, 0.214977302, 4.80816837e-05, 4.80816837e-05, 4.80816837e-05,
+ 0.123027519, 4.80816837e-05, 4.80816837e-05, 4.80816837e-05, 0.661322035, 4.80816837e-05},
+ {0.00019927387, 0.00019927387, 0.00019927387, 0.101763692, 0.00019927387, 0.00019927387,
+ 0.00019927387, 0.111141255, 0.00019927387, 0.00019927387, 0.00019927387, 0.784305219},
+ {0.126620811, 3.77512454e-05, 3.77512454e-05, 3.77512454e-05, 0.0949253706, 3.77512454e-05,
+ 3.77512454e-05, 3.77512454e-05, 0.777925301, 3.77512454e-05, 3.77512454e-05, 3.77512454e-05},
+ {8.34845269e-05, 0.0522147481, 8.34845269e-05, 8.34845269e-05, 8.34845269e-05, 0.0565042132,
+ 8.34845269e-05, 8.34845269e-05, 8.34845269e-05, 0.890112255, 8.34845269e-05, 8.34845269e-05},
+ {0.000110815138, 0.000110427066, 0.329742326, 0.000110427066, 0.000113945866, 0.000110427066,
+ 0.140289483, 0.000110427066, 0.000117423649, 0.000110427066, 0.528411309, 0.000110427066},
+ {0.000131337002, 0.000131337002, 0.000131337002, 0.0390710366, 0.000131337002, 0.000131337002,
+ 0.000131337002, 0.0617348823, 0.000131337002, 0.000131337002, 0.000131337002, 0.897355363},
+ {0.121151783, 3.91167535e-05, 3.91167535e-05, 3.91167535e-05, 0.121341222, 3.91167535e-05,
+ 3.91167535e-05, 3.91167535e-05, 0.75695936, 3.91167535e-05, 3.91167535e-05, 3.91167535e-05},
+ {6.4451422e-05, 0.030096713, 6.4451422e-05, 6.4451422e-05, 6.4451422e-05, 0.0520326862,
+ 6.4451422e-05, 6.4451422e-05, 6.4451422e-05, 0.916968281, 6.4451422e-05, 6.4451422e-05},
+ {4.34265926e-05, 4.34265926e-05, 0.172479716, 4.34265926e-05, 4.34265926e-05, 4.34265926e-05,
+ 0.113044043, 4.34265926e-05, 4.34265926e-05, 4.34265926e-05, 0.713868268, 4.34265926e-05},
+ {3.16836313e-05, 2.73694388e-05, 2.73694388e-05, 0.04721317, 2.77977828e-05, 2.73694388e-05,
+ 2.73694388e-05, 0.078916509, 3.46399946e-05, 2.73694388e-05, 2.73694388e-05, 0.873475136}},
+ {// stickPmf
+ {0.000103010778, 0.0380995742, 0.426353247, 0.0339918103, 0.000103010778, 0.0211011476,
+ 0.126299789, 0.0147406207, 0.000103010778, 0.111827288, 0.148961708, 0.0778007297},
+ {0.142966063, 6.82261622e-05, 0.318828309, 0.0291750067, 0.0612651332, 6.82261622e-05,
+ 0.132226999, 0.0222891262, 0.108765546, 6.82261622e-05, 0.107092044, 0.0768459636},
+ {0.435501353, 0.0281061159, 0.00022795498, 0.112842372, 0.0386560686, 0.0153571105,
+ 0.00022795498, 0.0531675523, 0.0885281789, 0.0680543734, 0.00022795498, 0.157963236},
+ {0.277671243, 0.0199532671, 0.279545911, 9.68193392e-05, 0.0672566924, 0.0113474679,
+ 0.103986414, 9.68193392e-05, 0.0874665425, 0.0477403036, 0.104257603, 9.68193392e-05},
+ {6.26766712e-05, 0.0248510469, 0.399492811, 0.0373275328, 6.26766712e-05, 0.00916381627,
+ 0.119657428, 0.0131950955, 6.26766712e-05, 0.212819044, 0.124778109, 0.0582137031},
+ {0.125185057, 3.47389275e-05, 0.306433733, 0.0308523177, 0.0774246347, 3.52102425e-05,
+ 0.149641423, 0.0134852162, 0.129457219, 3.45901197e-05, 0.128579834, 0.0386692545},
+ {0.314712978, 0.0245469889, 7.44182399e-05, 0.0329602878, 0.124756147, 0.0144931638,
+ 7.44182399e-05, 0.0161076306, 0.157254073, 0.222533644, 7.44182399e-05, 0.0920397407},
+ {0.234807777, 0.0143254662, 0.196699446, 7.60379939e-05, 0.0813954759, 0.0105264534,
+ 0.0840430032, 7.60379939e-05, 0.112867722, 0.174110565, 0.0906157878, 7.60379939e-05},
+ {0.000114280663, 0.0243444281, 0.457199123, 0.0381081135, 0.000114280663, 0.0162510324,
+ 0.124731361, 0.0167679501, 0.000114280663, 0.107039005, 0.107835264, 0.106809478},
+ {0.118927574, 3.10562894e-05, 0.343802957, 0.0333522609, 0.0496397906, 3.10562894e-05,
+ 0.195022097, 0.0163660717, 0.0539508263, 3.10562894e-05, 0.125648942, 0.0630410307},
+ {0.335673887, 0.0267972214, 0.00093244908, 0.0455030532, 0.129837105, 0.0126090082,
+ 0.000180646254, 0.0192047603, 0.142185037, 0.0744691665, 0.000164140614, 0.211647424},
+ {0.299454906, 0.0203545133, 0.270281208, 0.000115353453, 0.10064444, 0.00705182304,
+ 0.114896506, 0.000115353453, 0.100554091, 0.0384270526, 0.0474126337, 0.000115353453},
+ {7.92484966e-05, 0.0190180551, 0.262244947, 0.019509475, 7.92484966e-05, 0.0113606249,
+ 0.0949860067, 0.0183237604, 7.92484966e-05, 0.106081588, 0.21160129, 0.256240265},
+ {0.125916528, 4.15946843e-05, 0.209865333, 0.0203882413, 0.0577305702, 4.15946843e-05,
+ 0.0904461035, 0.018649162, 0.0587107584, 4.15946843e-05, 0.129821536, 0.28813901},
+ {0.33820122, 0.0210315415, 0.000104202635, 0.0409843175, 0.118326009, 0.0105217011,
+ 0.000104202635, 0.0250824494, 0.10336307, 0.0371536554, 0.000104202635, 0.304502416},
+ {0.148349765, 0.0127413602, 0.22312407, 4.96955324e-05, 0.0595806675, 0.00463335009,
+ 0.177668167, 4.83714586e-05, 0.0574131588, 0.0412555016, 0.274858141, 4.85075474e-05}}};
+
+constexpr double transProbs[nContexts][3][4] = {
+ {// AA
+ {5.85956362, -4.41463293, 0.683309462, -0.0346718671},
+ {7.06499623, -4.40259797, 0.607137416, -0.027878395},
+ {1.73648922, -0.935476496, 0.0264529997, 0.00196800649}},
+ {// AC
+ {2.68872981, -1.33398847, 0.0860003242, -0.00189734598},
+ {3.55997286, -1.60728992, 0.130435583, -0.00340039547},
+ {4.95711278, -1.98021021, 0.144128237, -0.00360784403}},
+ {// AG
+ {-3.23979278, 0.356138788, -0.0870220245, 0.00546284744},
+ {2.5291947, -2.13705602, 0.206929395, -0.00511956903},
+ {2.20068033, -0.996606761, -0.00278577326, 0.00492497905}},
+ {// AT
+ {-1.15847683, -0.771986547, 0.0645814917, -0.0018601879},
+ {-2.78585757, 0.178618309, -0.0499252647, 0.00257301448},
+ {3.08433285, -1.67474855, 0.14589205, -0.00469624396}},
+ {// CA
+ {-0.451942513, -0.575360527, 0.0401324889, 0.000694689568},
+ {0.58830656, -1.53028855, 0.204160977, -0.00810273241},
+ {2.35067779, -1.31686514, 0.0730142817, -1.00923273e-05}},
+ {// CC
+ {-7.2469072, 1.26130953, -0.111198017, 0.0031739936},
+ {-5.43347752, 0.980596171, -0.0930509844, 0.00284106343},
+ {-4.62125702, 0.536176189, -0.0532120198, 0.00156457856}},
+ {// CG
+ {-1.85080654, -0.271149887, 0.0233007441, -0.000158657488},
+ {3.74845392, -2.86890561, 0.378280475, -0.0155172951},
+ {5.12582688, -3.00674655, 0.342928086, -0.0137785283}},
+ {// CT
+ {1.59462161, -1.32139342, 0.112979516, -0.00350654749},
+ {-2.66688067, 0.149169695, -0.0394165557, 0.00221529117},
+ {3.35981388, -1.6812294, 0.144580211, -0.00463679475}},
+ {// GA
+ {1.94929663, -1.87204746, 0.262415331, -0.0114952071},
+ {0.776645323, -1.57584288, 0.170612002, -0.00429563295},
+ {9.14677248, -5.01761335, 0.672305833, -0.031991748}},
+ {// GC
+ {10.8094257, -3.57210251, 0.294531042, -0.0079448247},
+ {-1.6188921, -0.212323741, 0.0145898135, -0.000189460808},
+ {0.516468575, -0.980880476, 0.0607592136, -0.00125531492}},
+ {// GG
+ {-1.967728, -0.522486336, 0.0601164523, -0.00183881474},
+ {3.12610849, -2.59191292, 0.325979211, -0.0138882827},
+ {3.05491681, -2.21846076, 0.287404314, -0.0128841407}},
+ {// GT
+ {-5.79447669, 0.996639643, -0.120105223, 0.00438200289},
+ {7.06158739, -2.93404754, 0.268804061, -0.00798584198},
+ {6.70262773, -2.87567511, 0.264224627, -0.00821191872}},
+ {// TA
+ {-7.07222018, 2.94211219, -0.543110434, 0.0320758432},
+ {-0.220904721, -0.873637208, 0.06909082, 0.000725498815},
+ {3.06972721, -1.54851697, 0.0802862366, 0.00176909841}},
+ {// TC
+ {2.13319889, -1.20882369, 0.0954386191, -0.00244438603},
+ {-2.18846256, 0.022602406, -0.0121265739, 0.000696342338},
+ {-5.49462196, 0.733656731, -0.098767722, 0.00362214647}},
+ {// TG
+ {0.459855955, -1.41666334, 0.205580055, -0.00922652629},
+ {1.40013661, -1.69751326, 0.165896712, -0.00352395246},
+ {3.64491162, -2.25206115, 0.23605282, -0.00926403736}},
+ {// TT
+ {-4.66331239, 0.6977867, -0.0659908318, 0.00212194439},
+ {-0.800912389, -0.311917271, 0.00243369751, 0.000960389041},
+ {6.01995449, -2.74903881, 0.271552639, -0.00905647598}}};
+
+inline double CalculateExpectedLLForEmission(const size_t move, const uint8_t row,
+ const size_t moment)
+{
+ double expectedLL = 0;
+ for (size_t i = 0; i < nOutcomes; i++) {
+ double curProb = emissionPmf[move][row][i];
+ double lgCurProb = std::log(curProb);
+ if (moment == static_cast<uint8_t>(MomentType::FIRST))
+ expectedLL += curProb * lgCurProb;
+ else if (moment == static_cast<uint8_t>(MomentType::SECOND))
+ expectedLL += curProb * (lgCurProb * lgCurProb);
+ }
+ return expectedLL;
+}
+
+S_P1C1v2_Model::S_P1C1v2_Model(const SNR& snr) : snr_(snr)
+{
+ for (size_t ctx = 0; ctx < nContexts; ++ctx) {
+ const uint8_t bp = ctx & 3; // (equivalent to % 4)
+ const double snr1 = clip(snr_[bp], snrRanges[bp]), snr2 = snr1 * snr1, snr3 = snr2 * snr1;
+ double sum = 1.0;
+
+ // cached transitions
+ ctxTrans_[ctx][0] = 1.0;
+ for (size_t j = 0; j < 3; ++j) {
+ double xb = transProbs[ctx][j][0] + snr1 * transProbs[ctx][j][1] +
+ snr2 * transProbs[ctx][j][2] + snr3 * transProbs[ctx][j][3];
+ xb = std::exp(xb);
+ ctxTrans_[ctx][j + 1] = xb;
+ sum += xb;
+ }
+ for (size_t j = 0; j < 4; ++j)
+ ctxTrans_[ctx][j] /= sum;
+
+ // cached expectations
+ for (size_t move = 0; move < 3; ++move)
+ for (size_t moment = 0; moment < 2; ++moment)
+ cachedEmissionExpectations_[ctx][move][moment] =
+ CalculateExpectedLLForEmission(move, ctx, moment);
+ }
+}
+
+std::unique_ptr<AbstractRecursor> S_P1C1v2_Model::CreateRecursor(
+ std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff) const
+{
+ return std::unique_ptr<AbstractRecursor>(
+ new S_P1C1v2_Recursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff));
+}
+
+std::vector<TemplatePosition> S_P1C1v2_Model::Populate(const std::string& tpl) const
+{
+ std::vector<TemplatePosition> result;
+
+ if (tpl.empty()) return result;
+
+ result.reserve(tpl.size());
+
+ // calculate transition probabilities
+ uint8_t prev = detail::TranslationTable[static_cast<uint8_t>(tpl[0])];
+ if (prev > 3) throw std::invalid_argument("invalid character in template!");
+
+ for (size_t i = 1; i < tpl.size(); ++i) {
+ const uint8_t curr = detail::TranslationTable[static_cast<uint8_t>(tpl[i])];
+ if (curr > 3) throw std::invalid_argument("invalid character in template!");
+ const auto row = (prev << 2) | curr;
+ const auto params = ctxTrans_[row];
+ result.emplace_back(TemplatePosition{
+ tpl[i - 1], prev,
+ params[0], // match
+ params[1], // branch
+ params[2], // stick
+ params[3] // deletion
+ });
+ prev = curr;
+ }
+ result.emplace_back(TemplatePosition{tpl.back(), prev, 1.0, 0.0, 0.0, 0.0});
+
+ return result;
+}
+
+double S_P1C1v2_Model::ExpectedLLForEmission(const MoveType move, const uint8_t prev,
+ const uint8_t curr, const MomentType moment) const
+{
+ const size_t row = (prev << 2) | curr;
+ return cachedEmissionExpectations_[row][static_cast<uint8_t>(move)]
+ [static_cast<uint8_t>(moment)];
+}
+
+S_P1C1v2_Recursor::S_P1C1v2_Recursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff)
+ : Recursor<S_P1C1v2_Recursor>(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr,
+ scoreDiff)
+{
+}
+
+std::vector<uint8_t> S_P1C1v2_Recursor::EncodeRead(const MappedRead& read)
+{
+ std::vector<uint8_t> result;
+
+ result.reserve(read.Length());
+
+ for (size_t i = 0; i < read.Length(); ++i) {
+ if (read.PulseWidth[i] < 1U) throw std::runtime_error("invalid PulseWidth in read!");
+ const uint8_t pw = std::min(2, read.PulseWidth[i] - 1);
+ const uint8_t bp = detail::TranslationTable[static_cast<uint8_t>(read.Seq[i])];
+ if (bp > 3) throw std::invalid_argument("invalid character in read!");
+ const uint8_t em = (pw << 2) | bp;
+ if (em > 11) throw std::runtime_error("read encoding error!");
+ result.emplace_back(em);
+ }
+
+ return result;
+}
+
+double S_P1C1v2_Recursor::EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr)
+{
+ assert(move != MoveType::DELETION);
+ const auto row = (prev << 2) | curr;
+ return emissionPmf[static_cast<uint8_t>(move)][row][emission] * kCounterWeight;
+}
+
+double S_P1C1v2_Recursor::UndoCounterWeights(const size_t nEmissions) const
+{
+ return -std::log(kCounterWeight) * nEmissions;
+}
+} // namespace anonymous
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/models/SnrModelForm.cpp b/src/models/SnrModelForm.cpp
new file mode 100644
index 0000000..2475fa6
--- /dev/null
+++ b/src/models/SnrModelForm.cpp
@@ -0,0 +1,272 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <cassert>
+#include <cmath>
+#include <memory>
+#include <stdexcept>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/exception/ModelError.h>
+
+#include "../JsonHelpers.h"
+#include "../ModelFactory.h"
+#include "../ModelFormFactory.h"
+#include "../Recursor.h"
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+namespace {
+
+using MalformedModelFile = PacBio::Exception::MalformedModelFile;
+
+template <typename T>
+inline T clip(const T val, const T range[2])
+{
+ return std::max(range[0], std::min(val, range[1]));
+}
+
+constexpr size_t CONTEXT_NUMBER = 8;
+
+// fwd decl
+class SnrModelCreator;
+
+class SnrModel : public ModelConfig
+{
+public:
+ SnrModel(const SnrModelCreator* params, const SNR& snr);
+ std::unique_ptr<AbstractRecursor> CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr, double scoreDiff) const;
+ std::vector<TemplatePosition> Populate(const std::string& tpl) const;
+ double ExpectedLLForEmission(MoveType move, uint8_t prev, uint8_t curr,
+ MomentType moment) const;
+
+private:
+ const SnrModelCreator* params_;
+ SNR snr_;
+ double ctxTrans_[CONTEXT_NUMBER][4];
+ double counterWeight_;
+};
+
+class SnrRecursor : public Recursor<SnrRecursor>
+{
+public:
+ SnrRecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr, double scoreDiff,
+ const SnrModelCreator* params, double counterWeight);
+
+ static std::vector<uint8_t> EncodeRead(const MappedRead& read);
+ double EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr) const;
+ double UndoCounterWeights(size_t nEmissions) const;
+
+private:
+ const SnrModelCreator* params_;
+ double counterWeight_;
+ double nLgCounterWeight_;
+};
+
+class SnrModelCreator : public ModelCreator
+{
+ REGISTER_MODELFORM(SnrModelCreator);
+ friend class SnrModel;
+ friend class SnrRecursor;
+
+public:
+ static std::string Name() { return "Snr"; }
+ SnrModelCreator(const boost::property_tree::ptree& pt);
+ virtual std::unique_ptr<ModelConfig> Create(const SNR& snr) const
+ {
+ return std::unique_ptr<ModelConfig>(new SnrModel(this, snr));
+ };
+
+private:
+ double snrRanges_[4][2];
+ double emissionPmf_[3][2];
+ double transitionParams_[CONTEXT_NUMBER][3][4];
+ double substitutionRate_;
+ double counterWeight_;
+};
+
+REGISTER_MODELFORM_IMPL(SnrModelCreator);
+
+SnrModel::SnrModel(const SnrModelCreator* params, const SNR& snr) : params_{params}, snr_(snr)
+{
+ for (size_t ctx = 0; ctx < CONTEXT_NUMBER; ++ctx) {
+ const uint8_t bp = ctx & 3; // (equivalent to % 4)
+ const double snr1 = clip(snr_[bp], params_->snrRanges_[bp]), snr2 = snr1 * snr1,
+ snr3 = snr2 * snr1;
+ double sum = 1.0;
+
+ // cached transitions
+ ctxTrans_[ctx][0] = 1.0;
+ for (size_t j = 0; j < 3; ++j) {
+ double xb = params_->transitionParams_[ctx][j][0] +
+ params_->transitionParams_[ctx][j][1] * snr1 +
+ params_->transitionParams_[ctx][j][2] * snr2 +
+ params_->transitionParams_[ctx][j][3] * snr3;
+ xb = std::exp(xb);
+ ctxTrans_[ctx][j + 1] = xb;
+ sum += xb;
+ }
+ for (size_t j = 0; j < 4; ++j)
+ ctxTrans_[ctx][j] /= sum;
+ }
+
+ counterWeight_ = params_->counterWeight_;
+}
+
+std::unique_ptr<AbstractRecursor> SnrModel::CreateRecursor(std::unique_ptr<AbstractTemplate>&& tpl,
+ const MappedRead& mr,
+ double scoreDiff) const
+{
+ return std::unique_ptr<AbstractRecursor>(
+ new SnrRecursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff,
+ params_, counterWeight_));
+}
+
+std::vector<TemplatePosition> SnrModel::Populate(const std::string& tpl) const
+{
+ std::vector<TemplatePosition> result;
+
+ if (tpl.empty()) return result;
+
+ result.reserve(tpl.size());
+
+ // calculate transition probabilities
+ uint8_t prev = detail::TranslationTable[static_cast<uint8_t>(tpl[0])];
+ if (prev > 3) throw std::invalid_argument("invalid character in template!");
+
+ for (size_t i = 1; i < tpl.size(); ++i) {
+ const uint8_t curr = detail::TranslationTable[static_cast<uint8_t>(tpl[i])];
+ if (curr > 3) throw std::invalid_argument("invalid character in template!");
+ const uint8_t row = ((prev == curr) << 2) | curr;
+ const auto& params = ctxTrans_[row];
+ result.emplace_back(TemplatePosition{
+ tpl[i - 1], prev,
+ params[0], // match
+ params[1], // branch
+ params[2], // stick
+ params[3] // deletion
+ });
+ prev = curr;
+ }
+ result.emplace_back(TemplatePosition{tpl.back(), prev, 1.0, 0.0, 0.0, 0.0});
+
+ return result;
+}
+
+double SnrModel::ExpectedLLForEmission(const MoveType move, const uint8_t prev, const uint8_t curr,
+ const MomentType moment) const
+{
+ const double lgThird = -std::log(3.0);
+ if (move == MoveType::MATCH) {
+ const double probMismatch = params_->substitutionRate_;
+ const double probMatch = 1.0 - probMismatch;
+ const double lgMatch = std::log(probMatch);
+ const double lgMismatch = lgThird + std::log(probMismatch);
+ if (moment == MomentType::FIRST)
+ return probMatch * lgMatch + probMismatch * lgMismatch;
+ else if (moment == MomentType::SECOND)
+ return probMatch * (lgMatch * lgMatch) + probMismatch * (lgMismatch * lgMismatch);
+ } else if (move == MoveType::BRANCH)
+ return 0.0;
+ else if (move == MoveType::STICK) {
+ if (moment == MomentType::FIRST)
+ return lgThird;
+ else if (moment == MomentType::SECOND)
+ return lgThird * lgThird;
+ }
+ throw std::invalid_argument("invalid move!");
+}
+
+SnrRecursor::SnrRecursor(std::unique_ptr<AbstractTemplate>&& tpl, const MappedRead& mr,
+ double scoreDiff, const SnrModelCreator* params, double counterWeight)
+ : Recursor(std::forward<std::unique_ptr<AbstractTemplate>>(tpl), mr, scoreDiff)
+ , params_{params}
+ , counterWeight_{counterWeight}
+ , nLgCounterWeight_{-std::log(counterWeight_)}
+{
+}
+
+std::vector<uint8_t> SnrRecursor::EncodeRead(const MappedRead& read)
+{
+ std::vector<uint8_t> result;
+ result.reserve(read.Length());
+
+ for (const char bp : read.Seq) {
+ const uint8_t em = detail::TranslationTable[static_cast<uint8_t>(bp)];
+ if (em > 3) throw std::invalid_argument("invalid character in read!");
+ result.emplace_back(em);
+ }
+
+ return result;
+}
+
+double SnrRecursor::EmissionPr(MoveType move, uint8_t emission, uint8_t prev, uint8_t curr) const
+{
+ assert(move != MoveType::DELETION);
+
+ return params_->emissionPmf_[static_cast<uint8_t>(move)][curr != emission] * counterWeight_;
+}
+
+double SnrRecursor::UndoCounterWeights(const size_t nEmissions) const
+{
+ return nLgCounterWeight_ * nEmissions;
+}
+
+SnrModelCreator::SnrModelCreator(const boost::property_tree::ptree& pt)
+ : emissionPmf_{{0.0, 0.0}, {1.0, 0.0}, {0.0, 1.0 / 3.0}}
+{
+ try {
+ ReadMatrix<4, 2>(snrRanges_, pt.get_child("SnrRanges"));
+ ReadMatrix<CONTEXT_NUMBER, 3, 4>(transitionParams_, pt.get_child("TransitionParameters"));
+ substitutionRate_ = pt.get<double>("SubstitutionRate");
+ emissionPmf_[0][0] = 1.0 - substitutionRate_;
+ emissionPmf_[0][1] = substitutionRate_ / 3.0;
+ counterWeight_ = pt.get<double>("CounterWeight");
+ } catch (std::invalid_argument& e) {
+ throw MalformedModelFile();
+ } catch (boost::property_tree::ptree_error) {
+ throw MalformedModelFile();
+ }
+}
+
+} // namespace anonymous
+} // namespace Consensus
+} // namespace PacBio
diff --git a/src/poa/BoostGraph.h b/src/poa/BoostGraph.h
new file mode 100644
index 0000000..719879a
--- /dev/null
+++ b/src/poa/BoostGraph.h
@@ -0,0 +1,43 @@
+#pragma once
+
+#include <boost/config.hpp>
+#include <boost/graph/adjacency_list.hpp>
+#include <boost/static_assert.hpp>
+#include <boost/type_traits.hpp>
+
+namespace boost {
+enum vertex_info_t
+{
+ vertex_info = 424
+}; // a unique #
+BOOST_INSTALL_PROPERTY(vertex, info);
+} // namespace boost
+
+namespace PacBio {
+namespace Poa {
+namespace detail {
+
+/* using boost::adjacency_list; */
+/* using boost::graph_traits; */
+/* using boost::property; */
+/* using boost::property_map; */
+
+using namespace boost;
+
+struct PoaNode;
+
+// BGL is intimidating, and it *deserves* your hatred. But it's
+// the only game in town!
+typedef property<vertex_info_t, PoaNode, property<vertex_index_t, size_t> > vertex_property_t;
+typedef adjacency_list<setS, listS, bidirectionalS, vertex_property_t> BoostGraph;
+
+// Descriptor types used internally
+typedef graph_traits<BoostGraph>::edge_descriptor ED;
+typedef graph_traits<BoostGraph>::vertex_descriptor VD;
+
+typedef property_map<BoostGraph, vertex_info_t>::type VertexInfoMap;
+typedef property_map<BoostGraph, vertex_index_t>::type index_map_t;
+static const VD null_vertex = graph_traits<BoostGraph>::null_vertex();
+}
+}
+}
diff --git a/src/poa/POA-NOTES.txt b/src/poa/POA-NOTES.txt
new file mode 100644
index 0000000..2050e3d
--- /dev/null
+++ b/src/poa/POA-NOTES.txt
@@ -0,0 +1,140 @@
+Notes on the POA implementation
+===============================
+
+Lineage
+-------
+
+The POA is an implementation of the partial order aligner of Lee,
+Grasso, Sharlow (2002).
+
+Our original implementations were done in F# then C# by Pat Marks.
+These was limited to global alignment and couldn't cope with large
+sequences due to memory limitations---there was no capability to do
+banded alignment. I ported the C# implementation to C++ in
+ConsenusCore for use in Quiver.
+
+All of these implementations are in the same spirit, and the only
+principle difference between them and the description in the Lee paper
+is that our implementations do not maintain the equality relations
+determined by aligned residues (bases). I see this as a bit of a
+limitation which forces our hand in some ways. It would be nice to
+have this information.
+
+
+Details of current implementation
+---------------------------------
+
+Basically, we maintain a graph that reads can be aligned against; the
+aligned read can then be inserted into the graph. At any point a
+"consensus" of the graph can be retrieved. Information about each
+vertex is contained in a PoaNode struct.
+
+Unlike Pat's implementation, I chose *not* to retain "read pointer"
+information (readId, readPosition) in each PoaNode, because I was
+concerned that this would bloat the graph data, and in particular
+would add considerably to the memory consumption of Quiver. I work
+around this limitation as I will describe shortly.
+
+The ConsensusCore POA implementation is totally sufficient for
+Quiver's purposes but not sufficient for LAAMM, where very long reads
+can be added to the POA and naive Smith-Waterman approaches are memory
+inefficient. To support sparse-memory usage, the ConsensusCore
+exposes an API that allows plug-in banding... the client needs only
+provide an "SdpRangeFinder" implementation that identifies SDP anchors
+to be used in determining the subrange of each read that should be
+aligned. This code was left "pluggable" so that we would not need to
+add a dependency on SDP algorithms in ConsensusCore. LAAMM implements
+an SdpRangeFinder based on Seqan.
+
+The other "pluggable" aspect is that the read extent information is
+not maintained at all by the ConsensusCore POA; rather, when the
+client inserts a read to the graph, it can get the path of vertices
+the read traces. It can then, later, see how this path intersects the
+consensus path, to determine extents. (It has not escaped my notice
+that the extents should really be based on the "aligned residue"
+equivalence relation, which we do not maintain, but in practice this
+is probably fine).
+
+I am on the fence about adding readpointers into the base
+graph---perhaps templated out, so Quiver doesn't get bloated. It
+seems a more direct way of encoding the information, if we could do it
+compactly enough.
+
+
+Notes on coverage, minCoverage
+------------------------------
+
+In LOCAL or SEMIGLOBAL uses of the POA (so, CCS and LAAMM, but not
+Quiver), reads may represent only a portion of the template---they do
+not go end-to-end. For these modes we need to maintain some
+information about
+
+Each POA node knows how many reads it represents (pass through the
+vertex, basically). We also maintain information about the total
+effective width of the graph at any point "the coverage" (known as
+SpanningReads in this codebase). Formally, we can think of the
+coverage of a vertex as the number of reads that pass through this
+vertex, plus any other reads which pass through at least one ancestor
+and at least one descendant of this vertex. Pat implements coverage
+exactly from this definition, using the readpointers in his POA. The
+ConsensusCore POA, since it does not maintain the readpointers, can't
+do this, so instead we use a different approach ("tagSpan" approach)
+where, when each read is added, we incremement the spanning coverage
+for all vertices "covered" by the read. This approach may be
+suboptimal, and we should explore that.
+
+The coverage information is only important in determining consensus.
+Briefly, we calculate the consensus by looking for a path maximizing a
+score determined as a sum of vertex scores, where each vertex score is
+determined as
+
+ (2 * numReads[v] - coverage[v] - epsilon)
+
+so that if a vertex represents less than half of the coverage at its
+position, its score for inclusion in the POA consensus will be
+negative (discouraging inclusion in the consensus).
+
+`minCoverage` is a parameter to some of the API methods which From the
+API user's point of view, `minCoverage` represents a lower-bound
+estimate of the "basal" level of coverage over the span of the
+template under consideration. It is used to
+
+Given minCoverage, the vertex score becomes
+
+ (2 * numReads[v] - max(coverage[v], minCoverage) - epsilon)
+
+so minCoverage bounds the computed coverage from below. A minCoverage
+of 0 thus has no effect; a minCoverage chosen too large could
+discourage inclusion of "borderline" consensus bases. In practice
+this might manifest as consensus sequences that are truncated at the
+ends.
+
+The value of minCoverage is unclear---it was unclear why it was added,
+why it was deemed necessary. It might be helpful if we could use it
+to completely replace the local coverage calculation. We need to do
+some experiments on extensive datasets to see how, in practice, this
+affects observed truncations in HLA datasets.
+
+
+Known issues
+------------
+
+ - TODO: Pruning not yet implemented
+ - TODO: Explore efficacy of coverage, minCoverage in CCS and LAA contexts.
+ - TODO: Explore bad truncation phenotypes
+ - TODO: Better
+
+ - Local coverage is calculated using the old "tagSpan" approach,
+ rather than the fwd/backward union approach Pat developed later.
+ Not clear how big of a problem this is.
+
+ - The boost graph library is a headache.
+
+ - The core code for the alignment dynamic programming, and the
+ traceback-and-thread operation, is trickier than it needs to be.
+ Each of these methods is implementing a simple state machine, but
+ the code does not reflect this simplicity.
+
+
+---
+David Alexander, 2015
diff --git a/src/poa/PoaAlignmentMatrix.cpp b/src/poa/PoaAlignmentMatrix.cpp
new file mode 100644
index 0000000..437ed07
--- /dev/null
+++ b/src/poa/PoaAlignmentMatrix.cpp
@@ -0,0 +1,128 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <iomanip>
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "PoaAlignmentMatrix.h"
+#include "PoaGraphImpl.h"
+
+using namespace PacBio::Align;
+
+namespace PacBio {
+namespace Poa {
+namespace detail {
+
+void PoaAlignmentMatrixImpl::Print() const
+{
+ const int COL_WIDTH = 6;
+ const int ROW_HEIGHT = 2;
+
+ const std::map<MoveType, char> moveCode = {
+ {InvalidMove, 'Z'}, {StartMove, 'S'}, {EndMove, 'E'}, {MatchMove, '='},
+ {MismatchMove, 'X'}, {DeleteMove, 'D'}, {ExtraMove, 'I'}};
+
+ // Display something like this:
+ //
+ // 0 2 3 4 5 6 7 8 9 1
+ // ^ A C G T A C G T $
+ //
+ // - 0Z 0S 0S 0S -infZ
+ //
+ // A 0S 3= 0S 0S 0S -infZ
+ //
+ // C 0S 0S 6= 2D 0S 0S -infZ
+ //
+ // G 0S 0S 2I 9= 5D 1D 0S -infZ
+ //
+ // T 0S 0S 0S 5I 12= 8D 4D 0S -infZ
+ //
+ // A 0S 3= 0S 1I 8I 15= 11D 7D 3D -infZ
+ //
+ // C 0S 0S 6= 2D 4I 11I 18= 14D 10D -infZ
+ //
+ // G 0S 2I 9= 5D 7I 14I 21= 17D -infZ
+ //
+ std::stringstream header0; // Vertex IDs
+ std::stringstream header1; // Vertex labels
+ std::vector<std::stringstream> outputRows(NumRows());
+
+ header0 << std::setw(COL_WIDTH) << std::right << "";
+ header1 << std::setw(COL_WIDTH) << std::right << "";
+ for (size_t row = 0; row < NumRows(); row++) {
+ char readBase;
+ if (row == 0) {
+ readBase = '-';
+ } else {
+ readBase = readSequence_[row - 1];
+ }
+ outputRows[row] << std::setw(COL_WIDTH) << std::right << readBase;
+ }
+
+ for (const auto& v : graph_->sortedVertices()) {
+ const AlignmentColumn* col = columns_.at(v);
+ const PoaNode& node = graph_->getPoaNode(v);
+
+ header0 << std::setw(COL_WIDTH) << std::right << node.Id;
+ header1 << std::setw(COL_WIDTH) << std::right << node.Base;
+
+ for (size_t j = 0; j < NumRows(); j++) {
+ if (col->HasRow(j)) {
+ float score = col->Score[j];
+ string scoreFmt = score == -FLT_MAX ? "-inf" : std::to_string(int(score));
+ string cellFmt = scoreFmt + moveCode.at(col->ReachingMove[j]);
+ outputRows[j] << std::setw(COL_WIDTH) << std::right << cellFmt;
+ } else {
+ outputRows[j] << std::setw(COL_WIDTH) << std::right << "";
+ }
+ }
+ }
+
+ std::cout << header0.str() << std::endl;
+ std::cout << header1.str() << std::endl;
+ for (size_t row = 0; row < NumRows(); row++) {
+ for (size_t skip = ROW_HEIGHT; skip > 1; skip--) {
+ std::cout << std::endl;
+ }
+ std::cout << outputRows[row].str() << std::endl;
+ }
+}
+}
+}
+} // PacBio::Poa::detail
diff --git a/src/poa/PoaAlignmentMatrix.h b/src/poa/PoaAlignmentMatrix.h
new file mode 100644
index 0000000..9c28b2b
--- /dev/null
+++ b/src/poa/PoaAlignmentMatrix.h
@@ -0,0 +1,121 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+// The POA "alignment matrix" is a set of alignment columns
+// corresponding to each vertex in the graph that the read was aligned
+// against.
+
+#pragma once
+
+#include <pacbio/denovo/PoaGraph.h>
+
+#include <boost/unordered_map.hpp>
+#include <boost/utility.hpp>
+#include <cfloat>
+
+#include "BoostGraph.h"
+#include "VectorL.h"
+
+using boost::noncopyable;
+using boost::unordered_map;
+
+namespace PacBio {
+namespace Poa {
+namespace detail {
+
+enum MoveType
+{
+ InvalidMove, // Invalid move reaching ^ (start)
+ StartMove, // Start move: ^ -> vertex in row 0 of local alignment
+ EndMove, // End move: vertex -> $ in row 0 of local alignment, or
+ // in global alignment, terminal vertex -> $
+ MatchMove,
+ MismatchMove,
+ DeleteMove,
+ ExtraMove
+};
+
+struct AlignmentColumn : noncopyable
+{
+ VD CurrentVertex;
+ VectorL<float> Score;
+ VectorL<MoveType> ReachingMove;
+ VectorL<VD> PreviousVertex;
+
+ AlignmentColumn(VD vertex, int beginRow, int endRow)
+ : CurrentVertex(vertex)
+ , Score(beginRow, endRow, -FLT_MAX)
+ , ReachingMove(beginRow, endRow, InvalidMove)
+ , PreviousVertex(beginRow, endRow, null_vertex)
+ {
+ }
+
+ ~AlignmentColumn() {}
+ size_t BeginRow() const { return Score.BeginRow(); }
+ size_t EndRow() const { return Score.EndRow(); }
+ bool HasRow(size_t i) const { return (BeginRow() <= i) && (i < EndRow()); }
+};
+
+typedef unordered_map<VD, const AlignmentColumn*> AlignmentColumnMap;
+
+class PoaAlignmentMatrixImpl : public PoaAlignmentMatrix
+{
+public:
+ virtual ~PoaAlignmentMatrixImpl()
+ {
+ for (auto& kv : columns_) {
+ delete kv.second;
+ }
+ }
+
+ virtual float Score() const { return score_; }
+ size_t NumRows() const { return readSequence_.length() + 1; }
+ size_t NumCols() const { return columns_.size(); }
+ void Print() const;
+
+public:
+ // TODO: why did I leave these public? why is there no
+ // constructor?
+ const PoaGraphImpl* graph_;
+ AlignmentColumnMap columns_;
+ std::string readSequence_;
+ PacBio::Align::AlignMode mode_;
+ float score_;
+};
+}
+}
+} // PacBio::Poa::detail
diff --git a/src/poa/PoaConsensus.cpp b/src/poa/PoaConsensus.cpp
new file mode 100644
index 0000000..2f6a5b5
--- /dev/null
+++ b/src/poa/PoaConsensus.cpp
@@ -0,0 +1,105 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <string>
+#include <utility>
+#include <vector>
+
+#include <boost/algorithm/string.hpp>
+#include <boost/foreach.hpp>
+
+#include <pacbio/align/AlignConfig.h>
+#include <pacbio/denovo/PoaConsensus.h>
+
+namespace PacBio {
+namespace Poa {
+
+using namespace PacBio::Align;
+
+AlignConfig DefaultPoaConfig(AlignMode mode)
+{
+ AlignParams params(3, -5, -4, -4);
+ AlignConfig config(params, mode);
+ return config;
+}
+
+PoaConsensus::PoaConsensus(const std::string& css, const PoaGraph& g,
+ const std::vector<size_t>& cssPath)
+ : Sequence(css), Graph(g), Path(cssPath)
+{
+}
+
+PoaConsensus::PoaConsensus(const std::string& css, const detail::PoaGraphImpl& gi,
+ const std::vector<size_t>& cssPath)
+ : Sequence(css), Graph(gi), Path(cssPath)
+{
+}
+
+PoaConsensus::~PoaConsensus() {}
+const PoaConsensus* PoaConsensus::FindConsensus(const std::vector<std::string>& reads)
+{
+ return FindConsensus(reads, DefaultPoaConfig(AlignMode::GLOBAL), -INT_MAX);
+}
+
+const PoaConsensus* PoaConsensus::FindConsensus(const std::vector<std::string>& reads,
+ const AlignConfig& config, int minCoverage)
+{
+ PoaGraph pg;
+ for (const std::string& read : reads) {
+ if (read.length() == 0) {
+ throw std::invalid_argument("input sequences must have nonzero length.");
+ }
+ pg.AddRead(read, config);
+ }
+ return pg.FindConsensus(config, minCoverage);
+}
+
+const PoaConsensus* PoaConsensus::FindConsensus(const std::vector<std::string>& reads,
+ AlignMode mode, int minCoverage)
+{
+ return FindConsensus(reads, DefaultPoaConfig(mode), minCoverage);
+}
+
+std::string PoaConsensus::ToGraphViz(int flags) const { return Graph.ToGraphViz(flags, this); }
+
+void PoaConsensus::WriteGraphVizFile(std::string filename, int flags) const
+{
+ Graph.WriteGraphVizFile(filename, flags, this);
+}
+
+} // namespace Poa
+} // namespace PacBio
diff --git a/src/poa/PoaGraph.cpp b/src/poa/PoaGraph.cpp
new file mode 100644
index 0000000..7e7abcc
--- /dev/null
+++ b/src/poa/PoaGraph.cpp
@@ -0,0 +1,103 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+// (Based on the original "Partial Order Aligner" by Lee, Grasso, and Sharlow,
+// and an implementation in C# by Patrick Marks)
+
+#include <pacbio/denovo/PoaGraph.h>
+
+#include "PoaGraphImpl.h"
+
+using namespace PacBio::Align;
+
+namespace PacBio {
+namespace Poa {
+
+// forward declaration
+struct PoaConsensus;
+
+//
+// PIMPL idiom delegation
+//
+void PoaGraph::AddRead(const std::string& sequence, const AlignConfig& config,
+ detail::SdpRangeFinder* rangeFinder, std::vector<Vertex>* readPathOutput)
+{
+ impl->AddRead(sequence, config, rangeFinder, readPathOutput);
+}
+
+void PoaGraph::AddFirstRead(const std::string& sequence, std::vector<Vertex>* readPathOutput)
+{
+ impl->AddFirstRead(sequence, readPathOutput);
+}
+
+PoaAlignmentMatrix* PoaGraph::TryAddRead(const std::string& sequence, const AlignConfig& config,
+ detail::SdpRangeFinder* rangeFinder) const
+{
+ return impl->TryAddRead(sequence, config, rangeFinder);
+}
+
+void PoaGraph::CommitAdd(PoaAlignmentMatrix* mat, std::vector<Vertex>* readPathOutput)
+{
+ impl->CommitAdd(mat, readPathOutput);
+}
+
+size_t PoaGraph::NumReads() const { return impl->NumReads(); }
+
+const PoaConsensus* PoaGraph::FindConsensus(const AlignConfig& config, int minCoverage) const
+{
+ return impl->FindConsensus(config, minCoverage);
+}
+
+string PoaGraph::ToGraphViz(int flags, const PoaConsensus* pc) const
+{
+ return impl->ToGraphViz(flags, pc);
+}
+
+void PoaGraph::WriteGraphVizFile(const string& filename, int flags, const PoaConsensus* pc) const
+{
+ impl->WriteGraphVizFile(filename, flags, pc);
+}
+
+PoaGraph::PoaGraph() { impl = new detail::PoaGraphImpl(); }
+
+PoaGraph::PoaGraph(const PoaGraph& other) { impl = new detail::PoaGraphImpl(*other.impl); }
+
+PoaGraph::PoaGraph(const detail::PoaGraphImpl& o) { impl = new detail::PoaGraphImpl(o); }
+
+PoaGraph::~PoaGraph() { delete impl; }
+
+} // namespace Poa
+} // namespace PacBio
diff --git a/src/poa/PoaGraphImpl.cpp b/src/poa/PoaGraphImpl.cpp
new file mode 100644
index 0000000..9a7d68c
--- /dev/null
+++ b/src/poa/PoaGraphImpl.cpp
@@ -0,0 +1,453 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <set>
+
+#include <boost/foreach.hpp>
+#include <boost/graph/copy.hpp>
+#include <boost/graph/graphviz.hpp>
+#include <boost/graph/topological_sort.hpp>
+
+#include <pacbio/align/AlignConfig.h>
+#include <pacbio/denovo/PoaConsensus.h>
+#include <pacbio/denovo/PoaGraph.h>
+#include <pacbio/denovo/RangeFinder.h>
+
+#include "PoaGraphImpl.h"
+
+using namespace PacBio::Align;
+
+namespace boost {
+
+using namespace PacBio::Poa::detail;
+using namespace PacBio::Poa;
+using boost::format;
+
+class my_label_writer
+{
+public:
+ my_label_writer(VertexInfoMap map, bool color, bool verbose, const PoaConsensus* pc = NULL)
+ : map_(map), cssVtxs_(), color_(color), verbose_(verbose)
+ {
+ if (pc != NULL) {
+ cssVtxs_.insert(pc->Path.begin(), pc->Path.end());
+ }
+ }
+
+ template <class descriptor>
+ void operator()(std::ostream& out, const descriptor& v) const
+ {
+ PoaGraph::Vertex vertexId = map_[v].Id;
+
+ std::string nodeColoringAttribute =
+ (color_ && isInConsensus(vertexId) ? " style=\"filled\", fillcolor=\"lightblue\" ,"
+ : "");
+
+ if (!verbose_) {
+ out << format("[shape=Mrecord,%s label=\"{ %c | %d }\"]") % nodeColoringAttribute %
+ map_[v].Base % map_[v].Reads;
+ } else {
+ out << format(
+ "[shape=Mrecord,%s label=\"{ "
+ "{ %d | %c } | "
+ "{ %d | %d } | "
+ "{ %0.2f | %0.2f } }\"]") %
+ nodeColoringAttribute % vertexId % map_[v].Base % map_[v].Reads %
+ map_[v].SpanningReads % map_[v].Score % map_[v].ReachingScore;
+ }
+ }
+
+private:
+ bool isInConsensus(PoaGraph::Vertex v) const { return cssVtxs_.find(v) != cssVtxs_.end(); }
+ VertexInfoMap map_;
+ std::set<PoaGraph::Vertex> cssVtxs_;
+ bool color_;
+ bool verbose_;
+};
+
+class my_graph_writer
+{
+public:
+ my_graph_writer(bool leftToRight = false) : leftToRight_(leftToRight) {}
+ void operator()(std::ostream& out) const
+ {
+ if (leftToRight_) out << "rankdir=\"LR\";" << std::endl;
+ }
+
+private:
+ bool leftToRight_;
+};
+
+} // namespace boost
+
+namespace PacBio {
+namespace Poa {
+namespace detail {
+
+// ----------------- PoaGraphImpl ---------------------
+
+PoaGraphImpl::PoaGraphImpl()
+ : g_(), vertexInfoMap_(get(vertex_info, g_)), numReads_(0), totalVertices_(0), liveVertices_(0)
+{
+ enterVertex_ = addVertex('^', 0);
+ exitVertex_ = addVertex('$', 0);
+}
+
+PoaGraphImpl::PoaGraphImpl(const PoaGraphImpl& other)
+ : g_(other.g_)
+ , vertexInfoMap_(get(vertex_info, g_))
+ , enterVertex_(other.enterVertex_)
+ , exitVertex_(other.exitVertex_)
+ , numReads_(other.numReads_)
+{
+}
+
+PoaGraphImpl::~PoaGraphImpl() {}
+void PoaGraphImpl::repCheck() const
+{
+#ifndef NDEBUG
+ // assert the representation invariant for the object
+ BOOST_FOREACH (const VD v, vertices(g_)) {
+ if (v == enterVertex_) {
+ assert(in_degree(v, g_) == 0);
+ assert(out_degree(v, g_) > 0 || NumReads() == 0);
+ } else if (v == exitVertex_) {
+ assert(in_degree(v, g_) > 0 || NumReads() == 0);
+ assert(out_degree(v, g_) == 0);
+ } else {
+ assert(in_degree(v, g_) > 0);
+ assert(out_degree(v, g_) > 0);
+ }
+ }
+#endif
+}
+
+static inline vector<const AlignmentColumn*> getPredecessorColumns(const BoostGraph& g, VD v,
+ const AlignmentColumnMap& colMap)
+{
+ vector<const AlignmentColumn*> predecessorColumns;
+ const AlignmentColumn* predCol;
+ for (auto e : inEdges(v, g)) {
+ VD u = source(e, g);
+ predCol = colMap.at(u);
+ assert(predCol != NULL);
+ predecessorColumns.push_back(predCol);
+ }
+ return predecessorColumns;
+}
+
+PoaConsensus* PoaGraphImpl::FindConsensus(const AlignConfig& config, int minCoverage)
+{
+ std::vector<VD> bestPath = consensusPath(config.Mode, minCoverage);
+ std::string consensusSequence = sequenceAlongPath(g_, vertexInfoMap_, bestPath);
+ PoaConsensus* pc = new PoaConsensus(consensusSequence, *this, externalizePath(bestPath));
+ return pc;
+}
+
+const AlignmentColumn* PoaGraphImpl::makeAlignmentColumnForExit(VD v,
+ const AlignmentColumnMap& colMap,
+ const std::string& sequence,
+ const AlignConfig& config) const
+{
+ assert(out_degree(v, g_) == 0);
+
+ // this is kind of unnecessary as we are only actually using one entry in
+ // this column
+ int I = sequence.length();
+ AlignmentColumn* curCol = new AlignmentColumn(v, 0, I + 1);
+
+ float bestScore = -FLT_MAX;
+ VD prevVertex = null_vertex;
+
+ // Under local or semiglobal alignment the vertex $ can be
+ // "reached" in the dynamic programming from any other vertex
+ // in one step via the End move--not just its predecessors in
+ // the graph. In local alignment, it may have been from any
+ // row, not necessarily I.
+ if (config.Mode == AlignMode::SEMIGLOBAL || config.Mode == AlignMode::LOCAL) {
+ BOOST_FOREACH (const VD u, vertices(g_)) {
+ if (u != exitVertex_) {
+ const AlignmentColumn* predCol = colMap.at(u);
+ int prevRow = (config.Mode == AlignMode::LOCAL ? ArgMax(predCol->Score) : I);
+ if (predCol->HasRow(prevRow) && predCol->Score[prevRow] > bestScore) {
+ bestScore = predCol->Score[prevRow];
+ prevVertex = predCol->CurrentVertex;
+ }
+ }
+ }
+ } else {
+ // regular predecessors
+ vector<const AlignmentColumn*> predecessorColumns = getPredecessorColumns(g_, v, colMap);
+ for (const AlignmentColumn* predCol : predecessorColumns) {
+ if (predCol->HasRow(I) && predCol->Score[I] > bestScore) {
+ bestScore = predCol->Score[I];
+ prevVertex = predCol->CurrentVertex;
+ }
+ }
+ }
+ assert(prevVertex != null_vertex);
+ curCol->Score[I] = bestScore;
+ curCol->PreviousVertex[I] = prevVertex;
+ curCol->ReachingMove[I] = EndMove;
+ return curCol;
+}
+
+const AlignmentColumn* PoaGraphImpl::makeAlignmentColumn(VD v, const AlignmentColumnMap& colMap,
+ const std::string& sequence,
+ const AlignConfig& config, int beginRow,
+ int endRow) const
+{
+ AlignmentColumn* curCol;
+ if (beginRow > endRow) {
+ // This happens when there are no anchors in the read. We
+ // want this read to be threaded onto the graph as a singleton
+ // path. We use the START move.
+
+ // This is only going to work in LOCAL aln, assert on that
+
+ curCol = new AlignmentColumn(v, 0, 1);
+ curCol->ReachingMove[0] = StartMove;
+ curCol->PreviousVertex[0] = enterVertex_;
+ curCol->Score[0] = 0; // > -FLT_MAX
+ return curCol;
+ }
+
+ assert(beginRow < endRow || beginRow == 0 || beginRow == static_cast<int>(sequence.length()));
+
+ curCol = new AlignmentColumn(v, beginRow, endRow);
+ const PoaNode& vertexInfo = vertexInfoMap_[v];
+ vector<const AlignmentColumn*> predecessorColumns = getPredecessorColumns(g_, v, colMap);
+
+ // i represents position in array
+ // readPos=i-1 represents position in read
+ for (int i = beginRow; i < endRow; i++) {
+ assert(curCol->HasRow(i));
+
+ float candidateScore, bestScore;
+ VD prevVertex;
+ MoveType reachingMove;
+
+ if (config.Mode == AlignMode::LOCAL) {
+ bestScore = 0;
+ prevVertex = enterVertex_;
+ reachingMove = StartMove;
+ } else {
+ bestScore = -FLT_MAX;
+ prevVertex = null_vertex;
+ reachingMove = InvalidMove;
+ }
+
+ // Special-case the first row, this could probably be factored
+ // more cleanly
+ if (i == 0) {
+ if (predecessorColumns.size() == 0) {
+ // if this vertex doesn't have any in-edges it is ^; has
+ // no reaching move
+ assert(v == enterVertex_);
+ curCol->Score[0] = 0;
+ curCol->ReachingMove[0] = InvalidMove;
+ curCol->PreviousVertex[0] = null_vertex;
+ } else if (config.Mode == AlignMode::SEMIGLOBAL || config.Mode == AlignMode::LOCAL) {
+ // under semiglobal or local alignment, we use the Start move
+ curCol->Score[0] = 0;
+ curCol->ReachingMove[0] = StartMove;
+ curCol->PreviousVertex[0] = enterVertex_;
+ } else {
+ // otherwise it's a deletion
+ for (const AlignmentColumn* prevCol : predecessorColumns) {
+ candidateScore = prevCol->Score[0] + config.Params.Delete;
+ if (candidateScore > bestScore) {
+ bestScore = candidateScore;
+ prevVertex = prevCol->CurrentVertex;
+ reachingMove = DeleteMove;
+ }
+ }
+ assert(reachingMove != InvalidMove);
+ curCol->Score[0] = bestScore;
+ curCol->ReachingMove[0] = reachingMove;
+ curCol->PreviousVertex[0] = prevVertex;
+ }
+ } else {
+ for (const AlignmentColumn* prevCol : predecessorColumns) {
+ // Incorporate (Match or Mismatch)
+ if (prevCol->HasRow(i - 1)) {
+ bool isMatch = sequence[i - 1] == vertexInfo.Base;
+ candidateScore = prevCol->Score[i - 1] +
+ (isMatch ? config.Params.Match : config.Params.Mismatch);
+ if (candidateScore > bestScore) {
+ bestScore = candidateScore;
+ prevVertex = prevCol->CurrentVertex;
+ reachingMove = (isMatch ? MatchMove : MismatchMove);
+ }
+ }
+ // Delete
+ if (prevCol->HasRow(i)) {
+ candidateScore = prevCol->Score[i] + config.Params.Delete;
+ if (candidateScore > bestScore) {
+ bestScore = candidateScore;
+ prevVertex = prevCol->CurrentVertex;
+ reachingMove = DeleteMove;
+ }
+ }
+ }
+ // Extra
+ if (curCol->HasRow(i - 1)) {
+ candidateScore = curCol->Score[i - 1] + config.Params.Insert;
+ if (candidateScore > bestScore) {
+ bestScore = candidateScore;
+ prevVertex = v;
+ reachingMove = ExtraMove;
+ }
+ }
+ assert(reachingMove != InvalidMove);
+ curCol->Score[i] = bestScore;
+ curCol->ReachingMove[i] = reachingMove;
+ curCol->PreviousVertex[i] = prevVertex;
+ }
+ }
+
+ return curCol;
+}
+
+void PoaGraphImpl::AddRead(const std::string& readSeq, const AlignConfig& config,
+ SdpRangeFinder* rangeFinder, std::vector<Vertex>* readPathOutput)
+{
+ if (NumReads() == 0) {
+ AddFirstRead(readSeq, readPathOutput);
+ } else {
+ PoaAlignmentMatrix* mat = TryAddRead(readSeq, config, rangeFinder);
+ CommitAdd(mat, readPathOutput);
+ delete mat;
+ }
+}
+
+void PoaGraphImpl::AddFirstRead(const std::string& readSeq, std::vector<Vertex>* readPathOutput)
+{
+ repCheck();
+ assert(readSeq.length() > 0);
+ assert(numReads_ == 0);
+
+ threadFirstRead(readSeq, readPathOutput);
+ numReads_++;
+ repCheck();
+}
+
+PoaAlignmentMatrix* PoaGraphImpl::TryAddRead(const std::string& readSeq, const AlignConfig& config,
+ SdpRangeFinder* rangeFinder) const
+{
+ repCheck();
+ assert(readSeq.length() > 0);
+ assert(numReads_ > 0);
+
+ // Prepare the range finder, if applicable
+ if (rangeFinder != NULL) {
+ // NB: no minCoverage applicable here; this
+ // "intermediate" consensus may include extra sequence
+ // at either end
+ std::vector<VD> cssPath = consensusPath(config.Mode);
+ std::string cssSeq = sequenceAlongPath(g_, vertexInfoMap_, cssPath);
+ rangeFinder->InitRangeFinder(*this, externalizePath(cssPath), cssSeq, readSeq);
+ }
+
+ // Calculate alignment columns of sequence vs. graph, using sparsity if
+ // we have a range finder.
+ PoaAlignmentMatrixImpl* mat = new PoaAlignmentMatrixImpl();
+ mat->readSequence_ = readSeq;
+ mat->mode_ = config.Mode;
+ mat->graph_ = this;
+
+ vector<VD> sortedVertices(num_vertices(g_));
+ topological_sort(g_, sortedVertices.rbegin());
+ const AlignmentColumn* curCol;
+ for (const auto& v : sortedVertices) {
+ if (v != exitVertex_) {
+ size_t startRow = 0, endRow = readSeq.size() + 1;
+ if (rangeFinder) {
+ // FindAlignableRange returns an alignable sequence range, which is not the same as
+ // the alignable rows (the end is off-by-one, for a normal interval).
+ int startRange, endRange;
+ std::tie(startRange, endRange) = rangeFinder->FindAlignableRange(externalize(v));
+ startRow = startRange;
+ endRow = (endRange == -INT_MAX / 2 ? endRange : endRange + 1);
+ }
+ Vertex vExt = externalize(v); // DEBUGGING
+ curCol = makeAlignmentColumn(v, mat->columns_, readSeq, config, startRow, endRow);
+ } else {
+ curCol = makeAlignmentColumnForExit(v, mat->columns_, readSeq, config);
+ }
+ mat->columns_[v] = curCol;
+ }
+
+ mat->score_ = mat->columns_[exitVertex_]->Score[readSeq.size()];
+ repCheck();
+
+ return mat;
+}
+
+void PoaGraphImpl::CommitAdd(PoaAlignmentMatrix* mat_, std::vector<Vertex>* readPathOutput)
+{
+ repCheck();
+
+ PoaAlignmentMatrixImpl* mat = static_cast<PoaAlignmentMatrixImpl*>(mat_);
+ tracebackAndThread(mat->readSequence_, mat->columns_, mat->mode_, readPathOutput);
+ numReads_++;
+
+ repCheck();
+}
+
+size_t PoaGraphImpl::NumReads() const { return numReads_; }
+
+string PoaGraphImpl::ToGraphViz(int flags, const PoaConsensus* pc) const
+{
+ std::stringstream ss;
+ write_graphviz(ss, g_, my_label_writer(vertexInfoMap_, flags & PoaGraph::COLOR_NODES,
+ flags & PoaGraph::VERBOSE_NODES, pc),
+ default_writer(), // edge writer
+ my_graph_writer(true));
+
+ return ss.str();
+}
+
+void PoaGraphImpl::WriteGraphVizFile(const string& filename, int flags,
+ const PoaConsensus* pc) const
+{
+ std::ofstream outfile(filename.c_str());
+ outfile << ToGraphViz(flags, pc);
+ outfile.close();
+}
+
+} // namespace detail
+} // namespace Poa
+} // namespace PacBio
diff --git a/src/poa/PoaGraphImpl.h b/src/poa/PoaGraphImpl.h
new file mode 100644
index 0000000..00a73d1
--- /dev/null
+++ b/src/poa/PoaGraphImpl.h
@@ -0,0 +1,267 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <cfloat>
+#include <climits>
+#include <vector>
+
+#include <boost/config.hpp>
+#include <boost/format.hpp>
+#include <boost/static_assert.hpp>
+#include <boost/type_traits.hpp>
+
+#include <pacbio/align/AlignConfig.h>
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/denovo/PoaGraph.h>
+
+#include "BoostGraph.h"
+#include "PoaAlignmentMatrix.h"
+
+using std::string;
+using std::vector;
+
+///
+/// Boost graph library typedefs, properties, and graphviz output.
+///
+using namespace boost; // NOLINT
+
+namespace PacBio {
+namespace Poa {
+namespace detail {
+
+// FWD
+class SdpRangeFinder;
+
+struct PoaNode
+{
+ PoaGraph::Vertex Id;
+ char Base;
+ int Reads;
+ // move the below out of here?
+ int SpanningReads;
+ float Score;
+ float ReachingScore;
+
+ void Init(size_t id, char base, int reads)
+ {
+ this->Id = id;
+ this->Base = base;
+ this->Reads = reads;
+ this->SpanningReads = 0;
+ this->Score = 0;
+ this->ReachingScore = 0;
+ }
+
+ PoaNode() { Init(0, 'N', 0); }
+ PoaNode(size_t id, char base) { Init(id, base, 1); }
+ PoaNode(size_t id, char base, int reads) { Init(id, base, reads); }
+};
+
+// External-facing vertex id type
+typedef size_t Vertex;
+
+struct EdgeComparator
+{
+ EdgeComparator(const BoostGraph& g) : g_(g) {}
+ // want lex. comparison... just using pair to get it..
+ bool operator()(ED e1, ED e2) const
+ {
+ std::pair<int, int> vt1, vt2;
+ vt1 = std::make_pair(get(vertex_index, g_, source(e1, g_)),
+ get(vertex_index, g_, target(e1, g_)));
+ vt2 = std::make_pair(get(vertex_index, g_, source(e2, g_)),
+ get(vertex_index, g_, target(e2, g_)));
+ return (vt1 < vt2);
+ }
+
+private:
+ const BoostGraph& g_;
+};
+
+inline std::vector<ED> inEdges(VD v, const BoostGraph& g)
+{
+ // This is a sad workaround the nondeterministic order of iteration
+ // from BGL's in_edges. (see: http://stackoverflow.com/questions/30968690/)
+
+ // Unfortunately, we can't just use the boost::sort range adapter
+ // because it requires an underlying random access iterator, which
+ // we can't get from the std::set container.
+ graph_traits<BoostGraph>::in_edge_iterator begin, end;
+ tie(begin, end) = in_edges(v, g);
+ std::vector<ED> tmp(begin, end);
+ std::sort(tmp.begin(), tmp.end(), EdgeComparator(g));
+ return tmp;
+}
+
+class PoaGraphImpl
+{
+ friend class SdpRangeFinder;
+
+ BoostGraph g_;
+ VertexInfoMap vertexInfoMap_; // NB: this is a reference type and refers to
+ // an "internal" property map
+ index_map_t indexMap_;
+ VD enterVertex_;
+ VD exitVertex_;
+ size_t numReads_;
+ size_t totalVertices_; // includes "ex"-vertices which have since been removed
+ size_t liveVertices_; // vertices that are in the graph. this is needed
+ // for algorithms.
+ std::map<Vertex, VD> vertexLookup_; // external ID -> internal ID
+
+ void repCheck() const;
+
+ VD addVertex(char base, int nReads = 1)
+ {
+ VD vd = add_vertex(g_);
+ Vertex vExt = totalVertices_++;
+ vertexInfoMap_[vd] = PoaNode(vExt, base, nReads);
+ vertexLookup_[vExt] = vd;
+ indexMap_[vd] = liveVertices_++;
+ return vd;
+ }
+
+ //
+ // utility routines
+ //
+ const AlignmentColumn* makeAlignmentColumn(VD v,
+ const AlignmentColumnMap& alignmentColumnForVertex,
+ const std::string& sequence,
+ const PacBio::Align::AlignConfig& config,
+ int beginRow, int endRow) const;
+
+ const AlignmentColumn* makeAlignmentColumnForExit(
+ VD v, const AlignmentColumnMap& alignmentColumnForVertex, const std::string& sequence,
+ const PacBio::Align::AlignConfig& config) const;
+
+public:
+ //
+ // Vertex id translation
+ //
+
+ Vertex externalize(VD vd) const
+ {
+ if (vd == null_vertex) {
+ return PoaGraph::NullVertex;
+ } else {
+ return vertexInfoMap_[vd].Id;
+ }
+ }
+
+ VD internalize(Vertex vertex) const
+ {
+ if (vertex == PoaGraph::NullVertex) {
+ return null_vertex;
+ }
+ return vertexLookup_.at(vertex);
+ }
+
+ std::vector<Vertex> externalizePath(const std::vector<VD>& vds) const
+ {
+ std::vector<Vertex> out(vds.size(), 0);
+ for (size_t i = 0; i < vds.size(); i++) {
+ out[i] = externalize(vds[i]);
+ }
+ return out;
+ }
+
+ std::vector<VD> internalizePath(const std::vector<Vertex>& vertices) const
+ {
+ std::vector<VD> out(vertices.size(), null_vertex);
+ for (size_t i = 0; i < vertices.size(); i++) {
+ out[i] = internalize(vertices[i]);
+ }
+ return out;
+ }
+
+public:
+ //
+ // POA node lookup
+ //
+ const PoaNode& getPoaNode(VD v) const { return vertexInfoMap_[v]; }
+public:
+ //
+ // Graph traversal functions, defined in PoaGraphTraversals
+ //
+
+ std::vector<VD> sortedVertices() const;
+
+ void tagSpan(VD start, VD end);
+
+ std::vector<VD> consensusPath(PacBio::Align::AlignMode mode, int minCoverage = -INT_MAX) const;
+
+ void threadFirstRead(std::string sequence, std::vector<Vertex>* readPathOutput = NULL);
+
+ void tracebackAndThread(std::string sequence,
+ const AlignmentColumnMap& alignmentColumnForVertex,
+ PacBio::Align::AlignMode mode,
+ std::vector<Vertex>* readPathOutput = NULL);
+
+ vector<PacBio::Consensus::ScoredMutation>* findPossibleVariants(
+ const std::vector<Vertex>& bestPath) const;
+
+public:
+ PoaGraphImpl();
+ PoaGraphImpl(const PoaGraphImpl& other);
+ ~PoaGraphImpl();
+
+ void AddRead(const std::string& sequence, const PacBio::Align::AlignConfig& config,
+ SdpRangeFinder* rangeFinder = NULL, std::vector<Vertex>* readPathOutput = NULL);
+
+ void AddFirstRead(const std::string& sequence, std::vector<Vertex>* readPathOutput = NULL);
+
+ PoaAlignmentMatrix* TryAddRead(const std::string& sequence,
+ const PacBio::Align::AlignConfig& config,
+ SdpRangeFinder* rangeFinder = NULL) const;
+
+ void CommitAdd(PoaAlignmentMatrix* mat, std::vector<Vertex>* readPathOutput = NULL);
+
+ PoaConsensus* FindConsensus(const PacBio::Align::AlignConfig& config,
+ int minCoverage = -INT_MAX);
+
+ size_t NumReads() const;
+ string ToGraphViz(int flags, const PoaConsensus* pc) const;
+ void WriteGraphVizFile(const string& filename, int flags, const PoaConsensus* pc) const;
+};
+
+// free functions, we should put these all in traversals
+std::string sequenceAlongPath(const BoostGraph& g, const VertexInfoMap& vertexInfoMap,
+ const std::vector<VD>& path);
+
+} // namespace detail
+} // namespace Poa
+} // namespace PacBio
diff --git a/src/poa/PoaGraphTraversals.cpp b/src/poa/PoaGraphTraversals.cpp
new file mode 100644
index 0000000..a10da98
--- /dev/null
+++ b/src/poa/PoaGraphTraversals.cpp
@@ -0,0 +1,459 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <boost/foreach.hpp>
+#include <boost/graph/topological_sort.hpp>
+#include <boost/unordered_set.hpp>
+
+#include <pacbio/denovo/PoaGraph.h>
+
+#include "PoaGraphImpl.h"
+#include "VectorL.h"
+
+namespace PacBio {
+namespace Poa {
+namespace detail {
+
+using namespace PacBio::Align;
+using namespace PacBio::Consensus;
+
+std::string sequenceAlongPath(const BoostGraph& g, const VertexInfoMap& vertexInfoMap,
+ const std::vector<VD>& path)
+{
+ std::stringstream ss;
+ for (const VD v : path) {
+ ss << vertexInfoMap[v].Base;
+ }
+ return ss.str();
+}
+
+boost::unordered_set<VD> SpanningDFS(const VD start, const VD end, const BoostGraph& g)
+{
+ std::vector<VD> stack;
+ boost::unordered_set<VD> fwd;
+ boost::unordered_set<VD> rev;
+ // find all vertices reachable from start
+ stack.push_back(start);
+ do {
+ VD v = stack.back();
+ stack.pop_back();
+ // mark those we've already visited,
+ // if so, skip
+ if (fwd.find(v) != fwd.end()) continue;
+ fwd.insert(v);
+ BOOST_FOREACH (const ED& e, out_edges(v, g)) {
+ stack.push_back(target(e, g));
+ }
+ } while (!stack.empty());
+ // find all vertices that can reach end
+ // FROM start
+ stack.push_back(end);
+ do {
+ VD v = stack.back();
+ stack.pop_back();
+ // if it's not been visited in the forward pass,
+ // or we've already visited it here, skip
+ if (fwd.find(v) == fwd.end() || rev.find(v) != rev.end()) continue;
+ rev.insert(v);
+ BOOST_FOREACH (const ED& e, in_edges(v, g)) {
+ stack.push_back(source(e, g));
+ }
+ } while (!stack.empty());
+ return rev;
+}
+
+std::vector<VD> PoaGraphImpl::sortedVertices() const
+{
+ vector<VD> sv(num_vertices(g_));
+ topological_sort(g_, sv.rbegin());
+ return sv;
+}
+
+void PoaGraphImpl::tagSpan(VD start, VD end)
+{
+ boost::unordered_set<VD> vertices = SpanningDFS(start, end, g_);
+ for (const VD v : vertices) {
+ vertexInfoMap_[v].SpanningReads++;
+ }
+}
+
+std::vector<VD> PoaGraphImpl::consensusPath(AlignMode mode, int minCoverage) const
+{
+ // Pat's note on the approach here:
+ //
+ // "A node gets a score of NumReads if all reads go through
+ // it, and a score of -NumReads if no reads go through it The
+ // shift of -0.0001 breaks ties in favor of skipping
+ // half-full nodes. In the 2 reads case this will get rid of
+ // insertions which are the more common error."
+ //
+ // The interpretation of minCoverage (which is applicable only
+ // for LOCAL, SEMIGLOBAL modes) is that it represents
+ // application-specific knowledge of the basal coverage level
+ // of reads in the template, such that if a node is contained
+ // in fewer than minCoverage reads, it will be penalized
+ // against inclusion in the consensus.
+ int totalReads = NumReads();
+
+ std::list<VD> path;
+ std::list<VD> sortedVertices(num_vertices(g_));
+ topological_sort(g_, sortedVertices.rbegin());
+ unordered_map<VD, VD> bestPrevVertex;
+
+ // ignore ^ and $
+ // TODO(dalexander): find a cleaner way to do this
+ vertexInfoMap_[sortedVertices.front()].ReachingScore = 0;
+ sortedVertices.pop_back();
+ sortedVertices.pop_front();
+
+ VD bestVertex = null_vertex;
+ float bestReachingScore = -FLT_MAX;
+ for (const VD v : sortedVertices) {
+ PoaNode& vInfo = vertexInfoMap_[v];
+ int containingReads = vInfo.Reads;
+ int spanningReads = vInfo.SpanningReads;
+ float score =
+ (mode != AlignMode::GLOBAL)
+ ? (2 * containingReads - 1 * std::max(spanningReads, minCoverage) - 0.0001f)
+ : (2 * containingReads - 1 * totalReads - 0.0001f);
+ vInfo.Score = score;
+ vInfo.ReachingScore = score;
+ bestPrevVertex[v] = null_vertex;
+ for (const ED& e : inEdges(v, g_)) {
+ VD sourceVertex = source(e, g_);
+ float rsc = score + vertexInfoMap_[sourceVertex].ReachingScore;
+ if (rsc > vInfo.ReachingScore) {
+ vInfo.ReachingScore = rsc;
+ bestPrevVertex[v] = sourceVertex;
+ }
+ if (rsc > bestReachingScore) {
+ bestVertex = v;
+ bestReachingScore = rsc;
+ }
+ // if the score is the same, the order we've encountered vertices
+ // might not be deterministic. Fix this by comparing on
+ // vertex_index
+ else if (rsc == bestReachingScore) {
+ if (get(vertex_index, g_, v) < get(vertex_index, g_, bestVertex)) bestVertex = v;
+ }
+ }
+ }
+ assert(bestVertex != null_vertex);
+
+ // trace back from best-scoring vertex
+ VD v = bestVertex;
+ while (v != null_vertex) {
+ path.push_front(v);
+ v = bestPrevVertex[v];
+ }
+ return std::vector<VD>(path.begin(), path.end());
+}
+
+void PoaGraphImpl::threadFirstRead(std::string sequence, std::vector<Vertex>* outputPath)
+{
+ // first sequence in the alignment
+ VD u = null_vertex, v;
+ VD startSpanVertex = null_vertex, endSpanVertex;
+ int readPos = 0;
+
+ if (outputPath) {
+ outputPath->clear();
+ }
+
+ for (const char base : sequence) {
+ v = addVertex(base);
+ if (outputPath) {
+ outputPath->push_back(externalize(v));
+ }
+ if (readPos == 0) {
+ add_edge(enterVertex_, v, g_);
+ startSpanVertex = v;
+ } else {
+ add_edge(u, v, g_);
+ }
+ u = v;
+ readPos++;
+ }
+ assert(startSpanVertex != null_vertex);
+ assert(u != null_vertex);
+ endSpanVertex = u;
+ add_edge(u, exitVertex_, g_); // terminus -> $
+ tagSpan(startSpanVertex, endSpanVertex);
+}
+
+void PoaGraphImpl::tracebackAndThread(std::string sequence,
+ const AlignmentColumnMap& alignmentColumnForVertex,
+ AlignMode alignMode, std::vector<Vertex>* outputPath)
+{
+ const int I = sequence.length();
+
+ // perform traceback from (I,$), threading the new sequence into
+ // the graph as we go.
+ int i = I;
+ const AlignmentColumn* curCol;
+ VD v = null_vertex, forkVertex = null_vertex;
+ VD u = exitVertex_;
+ VD startSpanVertex;
+ VD endSpanVertex = alignmentColumnForVertex.at(exitVertex_)->PreviousVertex[I];
+
+ if (outputPath) {
+ outputPath->resize(I);
+ std::fill(outputPath->begin(), outputPath->end(), (size_t)-1);
+ }
+
+#define READPOS (i - 1)
+#define VERTEX_ON_PATH(readPos, v) \
+ if (outputPath) { \
+ (*outputPath)[(readPos)] = externalize(v); \
+ }
+
+ while (!(u == enterVertex_ && i == 0)) {
+ // u -> v
+ // u: current vertex
+ // v: vertex last visited in traceback (could be == u)
+ // forkVertex: the vertex that will be the target of a new edge
+
+ Vertex uExt = this->externalize(u); // DEBUGGING
+ Vertex vExt = this->externalize(v); // DEBUGGING
+
+ curCol = alignmentColumnForVertex.at(u);
+ assert(curCol != NULL);
+ PoaNode& curNodeInfo = vertexInfoMap_[u];
+ VD prevVertex = curCol->PreviousVertex[i];
+ MoveType reachingMove = curCol->ReachingMove[i];
+
+ if (reachingMove == StartMove) {
+ assert(v != null_vertex);
+
+ if (forkVertex == null_vertex) {
+ forkVertex = v;
+ }
+ // In local model thread read bases, adjusting i (should stop at 0)
+ while (i > 0) {
+ assert(alignMode == AlignMode::LOCAL);
+ VD newForkVertex = addVertex(sequence[READPOS]);
+ add_edge(newForkVertex, forkVertex, g_);
+ VERTEX_ON_PATH(READPOS, newForkVertex);
+ forkVertex = newForkVertex;
+ i--;
+ }
+ } else if (reachingMove == EndMove) {
+ assert(forkVertex == null_vertex && u == exitVertex_ && v == null_vertex);
+
+ forkVertex = exitVertex_;
+
+ if (alignMode == AlignMode::LOCAL) {
+ // Find the row # we are coming from, walk
+ // back to there, threading read bases onto
+ // graph via forkVertex, adjusting i.
+ const AlignmentColumn* prevCol = alignmentColumnForVertex.at(prevVertex);
+ int prevRow = ArgMax(prevCol->Score);
+
+ while (i > static_cast<int>(prevRow)) {
+ VD newForkVertex = addVertex(sequence[READPOS]);
+ add_edge(newForkVertex, forkVertex, g_);
+ VERTEX_ON_PATH(READPOS, newForkVertex);
+ forkVertex = newForkVertex;
+ i--;
+ }
+ }
+ } else if (reachingMove == MatchMove) {
+ VERTEX_ON_PATH(READPOS, u);
+ // if there is an extant forkVertex, join it
+ if (forkVertex != null_vertex) {
+ add_edge(u, forkVertex, g_);
+ forkVertex = null_vertex;
+ }
+ // add to existing node
+ curNodeInfo.Reads++;
+ i--;
+ } else if (reachingMove == DeleteMove) {
+ if (forkVertex == null_vertex) {
+ forkVertex = v;
+ }
+ } else if (reachingMove == ExtraMove || reachingMove == MismatchMove) {
+ // begin a new arc with this read base
+ VD newForkVertex = addVertex(sequence[READPOS]);
+ if (forkVertex == null_vertex) {
+ forkVertex = v;
+ }
+ add_edge(newForkVertex, forkVertex, g_);
+ VERTEX_ON_PATH(READPOS, newForkVertex);
+ forkVertex = newForkVertex;
+ i--;
+ } else {
+ throw std::runtime_error("unreachable");
+ }
+
+ v = u;
+ u = prevVertex;
+ }
+ startSpanVertex = v;
+
+ // if there is an extant forkVertex, join it to enterVertex
+ if (forkVertex != null_vertex) {
+ add_edge(enterVertex_, forkVertex, g_);
+ startSpanVertex = forkVertex;
+ forkVertex = null_vertex;
+ }
+
+ if (startSpanVertex != exitVertex_) {
+ tagSpan(startSpanVertex, endSpanVertex);
+ }
+
+ // all filled in?
+ assert(outputPath == NULL ||
+ std::find(outputPath->begin(), outputPath->end(), ((size_t)-1)) == outputPath->end());
+
+#undef READPOS
+#undef VERTEX_ON_PATH
+}
+
+static boost::unordered_set<VD> childVertices(VD v, const BoostGraph& g)
+{
+ boost::unordered_set<VD> result;
+ BOOST_FOREACH (const ED& e, out_edges(v, g)) {
+ result.insert(target(e, g));
+ }
+ return result;
+}
+
+static boost::unordered_set<VD> parentVertices(VD v, const BoostGraph& g)
+{
+ boost::unordered_set<VD> result;
+ BOOST_FOREACH (const ED& e, in_edges(v, g)) {
+ result.insert(source(e, g));
+ }
+ return result;
+}
+
+vector<ScoredMutation>* PoaGraphImpl::findPossibleVariants(
+ const std::vector<Vertex>& bestPath) const
+{
+ std::vector<VD> bestPath_ = internalizePath(bestPath);
+
+ // Return value will be deallocated by PoaConsensus destructor.
+ vector<ScoredMutation>* variants = new vector<ScoredMutation>();
+
+ for (int i = 2; i < (int)bestPath_.size() - 2; i++) // NOLINT
+ {
+ VD v = bestPath_[i];
+ boost::unordered_set<VD> children = childVertices(v, g_);
+
+ // Look for a direct edge from the current node to the node
+ // two spaces down---suggesting a deletion with respect to
+ // the consensus sequence.
+ if (children.find(bestPath_[i + 2]) != children.end()) {
+ float score = -vertexInfoMap_[bestPath_[i + 1]].Score;
+ variants->push_back(Mutation(MutationType::DELETION, i + 1, '-').WithScore(score));
+ }
+
+ // Look for a child node that connects immediately back to i + 1.
+ // This indicates we should try inserting the base at i + 1.
+
+ // Parents of (i + 1)
+ boost::unordered_set<VD> lookBack = parentVertices(bestPath_[i + 1], g_);
+
+ // (We could do this in STL using std::set sorted on score, which would
+ // then
+ // provide an intersection mechanism (in <algorithm>) but that actually
+ // ends
+ // up being more code. Sad.)
+ float bestInsertScore = -FLT_MAX;
+ VD bestInsertVertex = null_vertex;
+
+ for (const VD v : children) {
+ boost::unordered_set<VD>::iterator found = lookBack.find(v);
+ if (found != lookBack.end()) {
+ float score = vertexInfoMap_[*found].Score;
+ if (score > bestInsertScore) {
+ bestInsertScore = score;
+ bestInsertVertex = *found;
+ } else if (score == bestInsertScore) {
+ if (get(vertex_index, g_, *found) < get(vertex_index, g_, bestInsertVertex))
+ bestInsertVertex = *found;
+ }
+ }
+ }
+
+ if (bestInsertVertex != null_vertex) {
+ char base = vertexInfoMap_[bestInsertVertex].Base;
+ variants->push_back(
+ Mutation(MutationType::INSERTION, i + 1, base).WithScore(bestInsertScore));
+ }
+
+ // Look for a child node not in the consensus that connects immediately
+ // to i + 2. This indicates we should try mismatching the base i + 1.
+
+ // Parents of (i + 2)
+ lookBack = parentVertices(bestPath_[i + 2], g_);
+
+ float bestMismatchScore = -FLT_MAX;
+ VD bestMismatchVertex = null_vertex;
+
+ for (const VD v : children) {
+ if (v == bestPath_[i + 1]) continue;
+
+ boost::unordered_set<VD>::iterator found = lookBack.find(v);
+ if (found != lookBack.end()) {
+ float score = vertexInfoMap_[*found].Score;
+ if (score > bestMismatchScore) {
+ bestMismatchScore = score;
+ bestMismatchVertex = *found;
+ } else if (score == bestMismatchScore) {
+ if (get(vertex_index, g_, *found) < get(vertex_index, g_, bestMismatchVertex))
+ bestMismatchVertex = *found;
+ }
+ }
+ }
+
+ if (bestMismatchVertex != null_vertex) {
+ // TODO(dalexander): As implemented (compatibility), this returns
+ // the score of the mismatch node. I think it should return the
+ // score
+ // difference, no?
+ char base = vertexInfoMap_[bestMismatchVertex].Base;
+ variants->push_back(
+ Mutation(MutationType::SUBSTITUTION, i + 1, base).WithScore(bestMismatchScore));
+ }
+ }
+ return variants;
+}
+
+} // namespace detail
+} // namespace Poa
+} // namespace PacBio
diff --git a/src/poa/RangeFinder.cpp b/src/poa/RangeFinder.cpp
new file mode 100644
index 0000000..a346458
--- /dev/null
+++ b/src/poa/RangeFinder.cpp
@@ -0,0 +1,251 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <algorithm>
+#include <map>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include <boost/foreach.hpp>
+#include <boost/graph/topological_sort.hpp>
+#include <boost/optional.hpp>
+#include <boost/range/adaptor/reversed.hpp>
+
+#include <pacbio/denovo/RangeFinder.h>
+
+#include "PoaGraphImpl.h"
+
+#define WIDTH 30
+#define DEBUG_RANGE_FINDER 0
+
+#if DEBUG_RANGE_FINDER
+#include <iostream>
+using std::cout;
+using std::endl;
+#endif // DEBUG_RANGE_FINDER
+
+namespace PacBio {
+namespace Poa {
+namespace detail {
+
+using std::min;
+using std::max;
+using boost::optional;
+
+static inline bool compareAnchorsOnCssPos(const SdpAnchor& a1, const SdpAnchor& a2)
+{
+ return a1.first < a2.first;
+}
+
+static const SdpAnchor* binarySearchAnchors(const SdpAnchorVector& anchors, size_t cssPosition)
+{
+ typedef SdpAnchorVector::const_iterator iter_t;
+ iter_t found = std::lower_bound(anchors.begin(), anchors.end(), std::make_pair(cssPosition, -1),
+ compareAnchorsOnCssPos);
+ if (found != anchors.end() && (*found).first == cssPosition) {
+ return &(*found);
+ } else {
+ return NULL;
+ }
+}
+
+typedef std::pair<int, int> Interval;
+
+std::string formatIntervalEndpoint(int i)
+{
+ if (i == INT_MAX / 2) {
+ return "inf";
+ } else if (i == -INT_MAX / 2) {
+ return "-inf";
+ } else {
+ return std::to_string(i);
+ }
+}
+
+std::string formatInterval(const Interval& ival)
+{
+ return (std::string("[") + formatIntervalEndpoint(ival.first) + std::string(", ") +
+ formatIntervalEndpoint(ival.second) + std::string(")"));
+}
+
+// Canonical empty interval....
+const Interval emptyInterval = Interval(INT_MAX / 2, -INT_MAX / 2);
+
+inline Interval RangeUnion(const Interval& range1, const Interval& range2)
+{
+ return Interval(min(range1.first, range2.first), max(range1.second, range2.second));
+}
+
+inline Interval RangeUnion(const std::vector<Interval>& ranges)
+{
+ Interval result = emptyInterval;
+ for (const Interval& r : ranges) {
+ result = RangeUnion(result, r);
+ }
+ return result;
+}
+
+inline Interval next(const Interval& v, int upperBound)
+{
+ if (v == emptyInterval)
+ return emptyInterval;
+ else
+ return Interval(min(v.first + 1, upperBound), min(v.second + 1, upperBound));
+}
+
+inline Interval prev(const Interval& v, int lowerBound = 0)
+{
+ if (v == emptyInterval)
+ return emptyInterval;
+ else
+ return Interval(max(v.first - 1, lowerBound), max(v.second - 1, lowerBound));
+}
+
+SdpRangeFinder::~SdpRangeFinder() {}
+void SdpRangeFinder::InitRangeFinder(const PoaGraphImpl& poaGraph,
+ const std::vector<Vertex>& consensusPath,
+ const std::string& consensusSequence,
+ const std::string& readSequence)
+{
+#if DEBUG_RANGE_FINDER
+ poaGraph.WriteGraphVizFile("debug-graph.dot", PoaGraph::VERBOSE_NODES, NULL);
+ std::map<Vertex, const SdpAnchor*> anchorByVertex;
+#endif
+ // Clear prexisting state first!
+ alignableReadIntervalByVertex_.clear();
+
+ const int readLength = readSequence.size();
+ SdpAnchorVector anchors = FindAnchors(consensusSequence, readSequence);
+#if DEBUG_RANGE_FINDER
+ std::cout << "Consensus: " << consensusSequence << std::endl;
+ std::cout << "Read : " << readSequence << std::endl;
+ std::cout << "RawAnchors length: " << anchors.size() << std::endl;
+#endif
+
+ std::map<VD, optional<Interval>> directRanges;
+ std::map<VD, Interval> fwdMarks, revMarks;
+
+ std::vector<VD> sortedVertices(num_vertices(poaGraph.g_));
+ topological_sort(poaGraph.g_, sortedVertices.rbegin());
+ for (const VD v : sortedVertices) {
+ directRanges[v] = boost::none;
+ }
+
+ // Find the "direct ranges" implied by the anchors between the
+ // css and this read. Possibly null.
+ for (size_t cssPos = 0; cssPos < consensusPath.size(); cssPos++) {
+ Vertex vExt = consensusPath[cssPos];
+ VD v = poaGraph.internalize(vExt);
+ const SdpAnchor* anchor = binarySearchAnchors(anchors, cssPos);
+ if (anchor != NULL) {
+#if DEBUG_RANGE_FINDER
+ anchorByVertex[vExt] = anchor;
+#endif
+ directRanges[v] = Interval(max(int(anchor->second) - WIDTH, 0),
+ min(int(anchor->second) + WIDTH, readLength));
+ } else {
+ directRanges[v] = boost::none;
+ }
+ }
+
+ // Use the direct ranges as a seed and perform a forward recursion,
+ // letting a node with null direct range have a range that is the
+ // union of the "forward stepped" ranges of its predecessors
+ for (const VD v : sortedVertices) {
+ Vertex vExt = poaGraph.externalize(v); // DEBUGGING
+
+ optional<Interval> directRange = directRanges.at(v);
+ if (directRange) {
+ fwdMarks[v] = directRange.get();
+ } else {
+ std::vector<Interval> predRangesStepped;
+ for (const ED& e : inEdges(v, poaGraph.g_)) {
+ VD pred = source(e, poaGraph.g_);
+ Vertex predExt = poaGraph.externalize(pred); // DEBUGGING
+ Interval predRangeStepped = next(fwdMarks.at(pred), readLength);
+ predRangesStepped.push_back(predRangeStepped);
+ }
+ Interval fwdInterval = RangeUnion(predRangesStepped);
+ fwdMarks[v] = fwdInterval;
+ }
+ }
+
+ // Do the same thing, but as a backwards recursion
+ for (const VD v : boost::adaptors::reverse(sortedVertices)) {
+ Vertex vExt = poaGraph.externalize(v); // DEBUGGING
+
+ optional<Interval> directRange = directRanges.at(v);
+ if (directRange) {
+ revMarks[v] = directRange.get();
+ } else {
+ std::vector<Interval> succRangesStepped;
+ BOOST_FOREACH (const ED& e, out_edges(v, poaGraph.g_)) {
+ VD succ = target(e, poaGraph.g_);
+ Vertex succExt = poaGraph.externalize(succ); // DEBUGGING
+ Interval succRangeStepped = prev(revMarks.at(succ), 0);
+ succRangesStepped.push_back(succRangeStepped);
+ }
+ Interval revInterval = RangeUnion(succRangesStepped);
+ revMarks[v] = revInterval;
+ }
+ }
+
+ // take hulls of extents from forward and reverse recursions
+ for (const VD v : sortedVertices) {
+ Vertex vExt = poaGraph.externalize(v);
+ alignableReadIntervalByVertex_[vExt] = RangeUnion(fwdMarks.at(v), revMarks.at(v));
+#if DEBUG_RANGE_FINDER
+ cout << vExt << "\t";
+ if (anchorByVertex.find(vExt) != anchorByVertex.end()) {
+ cout << " @ " << anchorByVertex.at(vExt)->second << "\t";
+ } else {
+ cout << "\t";
+ }
+ cout << "Fwd mark: " << formatInterval(fwdMarks[v]) << "\t"
+ << "Rev mark: " << formatInterval(revMarks[v]) << "\t"
+ << "Range: " << formatInterval(alignableReadIntervalByVertex_[vExt]) << endl;
+#endif
+ }
+}
+
+Interval SdpRangeFinder::FindAlignableRange(Vertex v)
+{
+ return alignableReadIntervalByVertex_.at(v);
+}
+
+} // namespace detail
+} // namespace Poa
+} // namespace PacBio
diff --git a/src/poa/VectorL.h b/src/poa/VectorL.h
new file mode 100644
index 0000000..47b8c8e
--- /dev/null
+++ b/src/poa/VectorL.h
@@ -0,0 +1,113 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <algorithm>
+#include <cassert>
+#include <vector>
+
+namespace PacBio {
+namespace Poa {
+namespace detail {
+
+// This is necessary because of dumb C++ linker rules.
+// see: http://isocpp.org/wiki/faq/templates#template-friends
+// and: http://yosefk.com/c++fqa/templates.html#fqa-35.16 (for hilarious
+// rejoinder)
+template <typename T>
+class VectorL; // fwd
+template <typename T>
+T Max(const VectorL<T>& v);
+template <typename T>
+size_t ArgMax(const VectorL<T>& v);
+
+//
+// Vector class that stores only a subsequence of the rows
+// (SparseVector has a lot of weird functionality built-in, so we can't use it
+// without
+// cleaning it up/refactoring it quite a bit)
+//
+template <typename T>
+class VectorL
+{
+private:
+ std::vector<T> storage_;
+ size_t beginRow_;
+ size_t endRow_;
+
+public:
+ VectorL(int beginRow, int endRow, T defaultVal = T())
+ : storage_(endRow - beginRow, defaultVal), beginRow_(beginRow), endRow_(endRow)
+ {
+ }
+
+ T& operator[](size_t pos)
+ {
+ assert(beginRow_ <= pos && pos < endRow_);
+ return storage_[pos - beginRow_];
+ }
+
+ const T& operator[](size_t pos) const
+ {
+ assert(beginRow_ <= pos && pos < endRow_);
+ return storage_[pos - beginRow_];
+ }
+
+ size_t BeginRow() const { return beginRow_; }
+ size_t EndRow() const { return endRow_; }
+ friend T Max<>(const VectorL<T>& v);
+ friend size_t ArgMax<>(const VectorL<T>& v);
+};
+
+using std::max_element;
+using std::distance;
+
+template <typename T>
+T Max(const VectorL<T>& v)
+{
+ return *max_element(v.storage_.begin(), v.storage_.end());
+}
+
+template <typename T>
+size_t ArgMax(const VectorL<T>& v)
+{
+ return v.beginRow_ +
+ distance(v.storage_.begin(), max_element(v.storage_.begin(), v.storage_.end()));
+}
+
+} // namespace detail
+} // namespace Poa
+} // PacBio
diff --git a/swig/Alignment.i b/swig/Alignment.i
new file mode 100644
index 0000000..5c36d3b
--- /dev/null
+++ b/swig/Alignment.i
@@ -0,0 +1,17 @@
+
+%{
+#include <pacbio/align/AlignConfig.h>
+#include <pacbio/align/PairwiseAlignment.h>
+#include <pacbio/align/AffineAlignment.h>
+#include <pacbio/align/LinearAlignment.h>
+%}
+
+%newobject PacBio::Align::Align;
+%newobject PacBio::Align::AlignAffine;
+%newobject PacBio::Align::AlignAffineIupac;
+%newobject PacBio::Align::AlignLinear;
+
+%include <pacbio/align/AlignConfig.h>
+%include <pacbio/align/PairwiseAlignment.h>
+%include <pacbio/align/AffineAlignment.h>
+%include <pacbio/align/LinearAlignment.h>
diff --git a/swig/CMakeLists.txt b/swig/CMakeLists.txt
new file mode 100644
index 0000000..e9c9319
--- /dev/null
+++ b/swig/CMakeLists.txt
@@ -0,0 +1,61 @@
+
+# output directory
+file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/swig/lib)
+
+include(uny-findpythonpath)
+find_python_inc(PYTHON_INCLUDE_DIRS)
+find_numpy_inc(NUMPY_INCLUDE_DIRS)
+
+include_directories(SYSTEM
+ ${Boost_INCLUDE_DIRS}
+ ${PYTHON_INCLUDE_DIRS}
+ ${NUMPY_INCLUDE_DIRS}
+)
+
+# fPIC is required by a the majority of Linux systems,
+# and the original ConsensusCore used it by default.
+# We could use python -c "print(sysconfig.get_config_var('CCSHARED'))",
+# but it's honestly unnecessary and requires providing PYTHON_EXECUTABLE
+target_compile_options(cc2 PUBLIC -fPIC)
+add_compile_options(-fPIC)
+
+# ConsensusCore2_wrap.cxx
+set(SWIG_COMMAND swig CACHE PATH "swig PATH")
+
+add_custom_command(OUTPUT ConsensusCore2_wrap.cxx
+ COMMAND ${SWIG_COMMAND} -Wextra -c++ -python -builtin -module ConsensusCore2
+ -I${UNY_IncludeDir} -I${CMAKE_BINARY_DIR}/generated
+ -o ${CMAKE_BINARY_DIR}/swig/ConsensusCore2_wrap.cxx -outdir ${CMAKE_BINARY_DIR}/swig
+ ${UNY_SwigDir}/ConsensusCore2.i
+ COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_BINARY_DIR}/swig/ConsensusCore2.py
+ ${CMAKE_BINARY_DIR}/swig/lib/__init__.py
+)
+
+# _ConsensusCore2.so
+add_library(_ConsensusCore2 MODULE
+ ConsensusCore2_wrap.cxx
+)
+
+target_include_directories(_ConsensusCore2
+ PUBLIC ${UNY_IncludeDir}
+ PUBLIC ${CMAKE_BINARY_DIR}/generated
+)
+
+set(CC2_LIBRARIES
+ ${PRE_LINK}
+ cc2
+ ${POST_LINK}
+ CACHE INTERNAL "" FORCE)
+
+target_link_libraries(_ConsensusCore2
+ ${CC2_LIBRARIES}
+)
+
+if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+ target_link_libraries(_ConsensusCore2 "-Wl,-undefined,dynamic_lookup")
+endif()
+
+set_target_properties(_ConsensusCore2 PROPERTIES
+ LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/swig/lib
+ PREFIX ""
+)
diff --git a/swig/ConsensusCore2.i b/swig/ConsensusCore2.i
new file mode 100644
index 0000000..a155a9d
--- /dev/null
+++ b/swig/ConsensusCore2.i
@@ -0,0 +1,96 @@
+%module ConsensusCore2
+
+// for the 309 warning about boost::noncoypable, try to figure out %ignore
+#pragma SWIG nowarn=309
+
+%{
+#define SWIG_FILE_WITH_INIT
+%}
+
+%ignore *::operator[];
+%ignore *::operator=;
+%ignore *::operator<<;
+%ignore *::operator std::tuple<bool&, size_t&, size_t&>;
+%ignore *::operator std::string;
+
+%include <exception.i>
+%include <std_pair.i>
+%include <std_set.i>
+%include <std_string.i>
+%include <std_vector.i>
+%include <stdint.i>
+
+#ifdef SWIGPYTHON
+%include "numpy.i"
+#endif
+
+// generic exception handling
+%exception {
+ try
+ { $action }
+ catch (const std::exception& e)
+ { SWIG_exception(SWIG_RuntimeError, e.what()); }
+}
+
+namespace std
+{
+ // pair types
+ %template(DoublePair) std::pair<double, double>;
+ %template(IntPair) std::pair<int, int>;
+ %template(LengthPair) std::pair<size_t, size_t>;
+
+ %apply const pair<double, double>& {pair<double, double>*};
+ %apply const pair<int, int>& {pair<int, int>*};
+ %apply const pair<size_t, size_t>& {pair<size_t, size_t>*};
+
+ // set types
+ %template(StringSet) std::set<std::string>;
+
+ %apply const set<string>& {set<string>*};
+
+ // vector types
+ %template(DoubleVector) std::vector<double>;
+ %template(IntPairVector) std::vector<std::pair<int, int> >;
+ %template(IntVector) std::vector<int>;
+ %template(StringVector) std::vector<string>;
+ %template(Uint8Vector) std::vector<uint8_t>;
+
+ %apply const vector<double>& {vector<double>*};
+ %apply const vector<pair<int, int> >& {vector<pair<int, int> >*};
+ %apply const vector<int>& {vector<int>*};
+ %apply const vector<string>& {vector<string>*};
+ %apply const vector<uint8_t>& {vector<uint8_t>*};
+}
+
+%define py_tp_str(cls)
+%#ifdef SWIGPYTHON
+%feature("python:slot", "tp_str", functype="reprfunc") cls::as_string();
+%extend cls { std::string as_string() { return std::string(*$self); } }
+%#endif // SWIGPYTHON
+%enddef
+
+// no include dependencies
+%include "State.i"
+%include "Alignment.i"
+%include "Coverage.i"
+%include "Matrix.i"
+%include "ModelConfig.i"
+%include "Mutation.i"
+%include "Polish.i"
+%include "Read.i"
+%include "Version.i"
+
+// after ModelConfig.i and Mutation.i
+// %include "Template.i"
+
+// after Read.i
+%include "Evaluator.i"
+%include "Integrator.i"
+%include "Poa.i"
+
+%init
+%{
+#ifdef SWIGPYTHON
+ import_array();
+#endif // SWIGPYTHON
+%}
diff --git a/swig/Coverage.i b/swig/Coverage.i
new file mode 100644
index 0000000..2f18eaf
--- /dev/null
+++ b/swig/Coverage.i
@@ -0,0 +1,14 @@
+
+%{
+#include <pacbio/consensus/Coverage.h>
+%}
+
+#ifdef SWIGPYTHON
+ %apply (int DIM1, int* IN_ARRAY1)
+ { (int tStartDim, int* tStart),
+ (int tEndDim, int* tEnd) };
+ %apply (int DIM1, int* ARGOUT_ARRAY1)
+ { (int winLen, int* coverage) };
+#endif // SWIGPYTHON
+
+%include <pacbio/consensus/Coverage.h>
diff --git a/swig/Evaluator.i b/swig/Evaluator.i
new file mode 100644
index 0000000..76690dc
--- /dev/null
+++ b/swig/Evaluator.i
@@ -0,0 +1,9 @@
+%{
+#include <pacbio/consensus/Evaluator.h>
+#include <pacbio/consensus/EasyReadScorer.h>
+%}
+
+%newobject PacBio::Consensus::EasyReadScorer::MakeEvaluator;
+
+%include <pacbio/consensus/Evaluator.h>
+%include <pacbio/consensus/EasyReadScorer.h>
diff --git a/swig/Integrator.i b/swig/Integrator.i
new file mode 100644
index 0000000..07cc77d
--- /dev/null
+++ b/swig/Integrator.i
@@ -0,0 +1,17 @@
+
+%{
+#include <pacbio/consensus/AbstractIntegrator.h>
+#include <pacbio/consensus/MonoMolecularIntegrator.h>
+#include <pacbio/consensus/MultiMolecularIntegrator.h>
+%}
+
+%feature("notabstract") PacBio::Consensus::MonoMolecularIntegrator;
+%feature("notabstract") PacBio::Consensus::MultiMolecularIntegrator;
+
+py_tp_str(PacBio::Consensus::AbstractIntegrator);
+py_tp_str(PacBio::Consensus::MonoMolecularIntegrator);
+py_tp_str(PacBio::Consensus::MultiMolecularIntegrator);
+
+%include <pacbio/consensus/AbstractIntegrator.h>
+%include <pacbio/consensus/MonoMolecularIntegrator.h>
+%include <pacbio/consensus/MultiMolecularIntegrator.h>
diff --git a/swig/Matrix.i b/swig/Matrix.i
new file mode 100644
index 0000000..6ff6c94
--- /dev/null
+++ b/swig/Matrix.i
@@ -0,0 +1,12 @@
+%{
+/* Includes the header in the wrapper code */
+#include <pacbio/consensus/AbstractMatrix.h>
+%}
+
+#ifdef SWIGPYTHON
+ // apply this typemap to ToHostMatrix
+ %apply (double** ARGOUTVIEW_ARRAY2, int* DIM1, int* DIM2)
+ { (double** mat, int* rows, int* cols) };
+#endif // SWIGPYTHON
+
+%include <pacbio/consensus/AbstractMatrix.h>
diff --git a/swig/ModelConfig.i b/swig/ModelConfig.i
new file mode 100644
index 0000000..6435e08
--- /dev/null
+++ b/swig/ModelConfig.i
@@ -0,0 +1,12 @@
+
+%{
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/consensus/ModelSelection.h>
+%}
+
+%ignore PacBio::Consensus::TemplatePosition;
+%ignore PacBio::Consensus::MoveType;
+%ignore PacBio::Consensus::ModelConfig;
+
+%include <pacbio/consensus/ModelConfig.h>
+%include <pacbio/consensus/ModelSelection.h>
diff --git a/swig/Mutation.i b/swig/Mutation.i
new file mode 100644
index 0000000..92754da
--- /dev/null
+++ b/swig/Mutation.i
@@ -0,0 +1,9 @@
+
+%{
+#include <pacbio/consensus/Mutation.h>
+%}
+
+py_tp_str(PacBio::Consensus::Mutation);
+py_tp_str(PacBio::Consensus::ScoredMutation);
+
+%include <pacbio/consensus/Mutation.h>
diff --git a/swig/Poa.i b/swig/Poa.i
new file mode 100644
index 0000000..4a79de4
--- /dev/null
+++ b/swig/Poa.i
@@ -0,0 +1,11 @@
+
+%{
+#include <pacbio/denovo/PoaGraph.h>
+#include <pacbio/denovo/PoaConsensus.h>
+%}
+
+%include <pacbio/denovo/PoaGraph.h>
+
+%newobject PacBio::Poa::PoaConsensus::FindConsensus;
+
+%include <pacbio/denovo/PoaConsensus.h>
diff --git a/swig/Polish.i b/swig/Polish.i
new file mode 100644
index 0000000..a9eef96
--- /dev/null
+++ b/swig/Polish.i
@@ -0,0 +1,8 @@
+
+%{
+#include <pacbio/consensus/PolishResult.h>
+#include <pacbio/consensus/Polish.h>
+%}
+
+%include <pacbio/consensus/PolishResult.h>
+%include <pacbio/consensus/Polish.h>
diff --git a/swig/Read.i b/swig/Read.i
new file mode 100644
index 0000000..e39c680
--- /dev/null
+++ b/swig/Read.i
@@ -0,0 +1,15 @@
+
+// TODO(lhepler): remove these, figure out %ignore
+%warnfilter(509) PacBio::Data::Read;
+%warnfilter(509) PacBio::Data::MappedRead;
+
+%{
+#include <pacbio/data/StrandType.h>
+#include <pacbio/data/Read.h>
+%}
+
+%feature("notabstract") PacBio::Data::Read;
+%feature("notabstract") PacBio::Data::MappedRead;
+
+%include <pacbio/data/StrandType.h>
+%include <pacbio/data/Read.h>
diff --git a/swig/State.i b/swig/State.i
new file mode 100644
index 0000000..161788e
--- /dev/null
+++ b/swig/State.i
@@ -0,0 +1,6 @@
+
+%{
+#include <pacbio/data/State.h>
+%}
+
+%include <pacbio/data/State.h>
\ No newline at end of file
diff --git a/swig/Template.i b/swig/Template.i
new file mode 100644
index 0000000..7c588d2
--- /dev/null
+++ b/swig/Template.i
@@ -0,0 +1,11 @@
+
+%{
+#include <pacbio/consensus/Template.h>
+%}
+
+%feature("notabstract") PacBio::Consensus::Template;
+
+%ignore PacBio::Consensus::AbstractTemplate;
+%ignore PacBio::Consensus::VirtualTemplate;
+
+%include <pacbio/consensus/Template.h>
diff --git a/swig/Version.i b/swig/Version.i
new file mode 100644
index 0000000..750733e
--- /dev/null
+++ b/swig/Version.i
@@ -0,0 +1,11 @@
+
+%{
+#include <pacbio/Version.h>
+%}
+
+%pythoncode
+%{
+__version__ = UnanimityVersion()
+%}
+
+%include <pacbio/Version.h>
diff --git a/swig/numpy.i b/swig/numpy.i
new file mode 100644
index 0000000..2ddc11d
--- /dev/null
+++ b/swig/numpy.i
@@ -0,0 +1,3161 @@
+/* -*- C -*- (not really, but good for syntax highlighting) */
+
+/*
+ * Copyright (c) 2005-2015, NumPy Developers.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are
+ * met:
+ *
+ * * Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * * Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ *
+ * * Neither the name of the NumPy Developers nor the names of any
+ * contributors may be used to endorse or promote products derived
+ * from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#ifdef SWIGPYTHON
+
+%{
+#ifndef SWIG_FILE_WITH_INIT
+#define NO_IMPORT_ARRAY
+#endif
+#include "stdio.h"
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+#include <numpy/arrayobject.h>
+%}
+
+/**********************************************************************/
+
+%fragment("NumPy_Backward_Compatibility", "header")
+{
+%#if NPY_API_VERSION < 0x00000007
+%#define NPY_ARRAY_DEFAULT NPY_DEFAULT
+%#define NPY_ARRAY_FARRAY NPY_FARRAY
+%#define NPY_FORTRANORDER NPY_FORTRAN
+%#endif
+}
+
+/**********************************************************************/
+
+/* The following code originally appeared in
+ * enthought/kiva/agg/src/numeric.i written by Eric Jones. It was
+ * translated from C++ to C by John Hunter. Bill Spotz has modified
+ * it to fix some minor bugs, upgrade from Numeric to numpy (all
+ * versions), add some comments and functionality, and convert from
+ * direct code insertion to SWIG fragments.
+ */
+
+%fragment("NumPy_Macros", "header")
+{
+/* Macros to extract array attributes.
+ */
+%#if NPY_API_VERSION < 0x00000007
+%#define is_array(a) ((a) && PyArray_Check((PyArrayObject*)a))
+%#define array_type(a) (int)(PyArray_TYPE((PyArrayObject*)a))
+%#define array_numdims(a) (((PyArrayObject*)a)->nd)
+%#define array_dimensions(a) (((PyArrayObject*)a)->dimensions)
+%#define array_size(a,i) (((PyArrayObject*)a)->dimensions[i])
+%#define array_strides(a) (((PyArrayObject*)a)->strides)
+%#define array_stride(a,i) (((PyArrayObject*)a)->strides[i])
+%#define array_data(a) (((PyArrayObject*)a)->data)
+%#define array_descr(a) (((PyArrayObject*)a)->descr)
+%#define array_flags(a) (((PyArrayObject*)a)->flags)
+%#define array_enableflags(a,f) (((PyArrayObject*)a)->flags) = f
+%#else
+%#define is_array(a) ((a) && PyArray_Check(a))
+%#define array_type(a) PyArray_TYPE((PyArrayObject*)a)
+%#define array_numdims(a) PyArray_NDIM((PyArrayObject*)a)
+%#define array_dimensions(a) PyArray_DIMS((PyArrayObject*)a)
+%#define array_strides(a) PyArray_STRIDES((PyArrayObject*)a)
+%#define array_stride(a,i) PyArray_STRIDE((PyArrayObject*)a,i)
+%#define array_size(a,i) PyArray_DIM((PyArrayObject*)a,i)
+%#define array_data(a) PyArray_DATA((PyArrayObject*)a)
+%#define array_descr(a) PyArray_DESCR((PyArrayObject*)a)
+%#define array_flags(a) PyArray_FLAGS((PyArrayObject*)a)
+%#define array_enableflags(a,f) PyArray_ENABLEFLAGS((PyArrayObject*)a,f)
+%#endif
+%#define array_is_contiguous(a) (PyArray_ISCONTIGUOUS((PyArrayObject*)a))
+%#define array_is_native(a) (PyArray_ISNOTSWAPPED((PyArrayObject*)a))
+%#define array_is_fortran(a) (PyArray_ISFORTRAN((PyArrayObject*)a))
+}
+
+/**********************************************************************/
+
+%fragment("NumPy_Utilities",
+ "header")
+{
+ /* Given a PyObject, return a string describing its type.
+ */
+ const char* pytype_string(PyObject* py_obj)
+ {
+ if (py_obj == NULL ) return "C NULL value";
+ if (py_obj == Py_None ) return "Python None" ;
+ if (PyCallable_Check(py_obj)) return "callable" ;
+ if (PyString_Check( py_obj)) return "string" ;
+ if (PyInt_Check( py_obj)) return "int" ;
+ if (PyFloat_Check( py_obj)) return "float" ;
+ if (PyDict_Check( py_obj)) return "dict" ;
+ if (PyList_Check( py_obj)) return "list" ;
+ if (PyTuple_Check( py_obj)) return "tuple" ;
+%#if PY_MAJOR_VERSION < 3
+ if (PyFile_Check( py_obj)) return "file" ;
+ if (PyModule_Check( py_obj)) return "module" ;
+ if (PyInstance_Check(py_obj)) return "instance" ;
+%#endif
+
+ return "unknown type";
+ }
+
+ /* Given a NumPy typecode, return a string describing the type.
+ */
+ const char* typecode_string(int typecode)
+ {
+ static const char* type_names[25] = {"bool",
+ "byte",
+ "unsigned byte",
+ "short",
+ "unsigned short",
+ "int",
+ "unsigned int",
+ "long",
+ "unsigned long",
+ "long long",
+ "unsigned long long",
+ "float",
+ "double",
+ "long double",
+ "complex float",
+ "complex double",
+ "complex long double",
+ "object",
+ "string",
+ "unicode",
+ "void",
+ "ntypes",
+ "notype",
+ "char",
+ "unknown"};
+ return typecode < 24 ? type_names[typecode] : type_names[24];
+ }
+
+ /* Make sure input has correct numpy type. This now just calls
+ PyArray_EquivTypenums().
+ */
+ int type_match(int actual_type,
+ int desired_type)
+ {
+ return PyArray_EquivTypenums(actual_type, desired_type);
+ }
+
+%#ifdef SWIGPY_USE_CAPSULE
+ void free_cap(PyObject * cap)
+ {
+ void* array = (void*) PyCapsule_GetPointer(cap,SWIGPY_CAPSULE_NAME);
+ if (array != NULL) free(array);
+ }
+%#endif
+
+
+}
+
+/**********************************************************************/
+
+%fragment("NumPy_Object_to_Array",
+ "header",
+ fragment="NumPy_Backward_Compatibility",
+ fragment="NumPy_Macros",
+ fragment="NumPy_Utilities")
+{
+ /* Given a PyObject pointer, cast it to a PyArrayObject pointer if
+ * legal. If not, set the python error string appropriately and
+ * return NULL.
+ */
+ PyArrayObject* obj_to_array_no_conversion(PyObject* input,
+ int typecode)
+ {
+ PyArrayObject* ary = NULL;
+ if (is_array(input) && (typecode == NPY_NOTYPE ||
+ PyArray_EquivTypenums(array_type(input), typecode)))
+ {
+ ary = (PyArrayObject*) input;
+ }
+ else if is_array(input)
+ {
+ const char* desired_type = typecode_string(typecode);
+ const char* actual_type = typecode_string(array_type(input));
+ PyErr_Format(PyExc_TypeError,
+ "Array of type '%s' required. Array of type '%s' given",
+ desired_type, actual_type);
+ ary = NULL;
+ }
+ else
+ {
+ const char* desired_type = typecode_string(typecode);
+ const char* actual_type = pytype_string(input);
+ PyErr_Format(PyExc_TypeError,
+ "Array of type '%s' required. A '%s' was given",
+ desired_type,
+ actual_type);
+ ary = NULL;
+ }
+ return ary;
+ }
+
+ /* Convert the given PyObject to a NumPy array with the given
+ * typecode. On success, return a valid PyArrayObject* with the
+ * correct type. On failure, the python error string will be set and
+ * the routine returns NULL.
+ */
+ PyArrayObject* obj_to_array_allow_conversion(PyObject* input,
+ int typecode,
+ int* is_new_object)
+ {
+ PyArrayObject* ary = NULL;
+ PyObject* py_obj;
+ if (is_array(input) && (typecode == NPY_NOTYPE ||
+ PyArray_EquivTypenums(array_type(input),typecode)))
+ {
+ ary = (PyArrayObject*) input;
+ *is_new_object = 0;
+ }
+ else
+ {
+ py_obj = PyArray_FROMANY(input, typecode, 0, 0, NPY_ARRAY_DEFAULT);
+ /* If NULL, PyArray_FromObject will have set python error value.*/
+ ary = (PyArrayObject*) py_obj;
+ *is_new_object = 1;
+ }
+ return ary;
+ }
+
+ /* Given a PyArrayObject, check to see if it is contiguous. If so,
+ * return the input pointer and flag it as not a new object. If it is
+ * not contiguous, create a new PyArrayObject using the original data,
+ * flag it as a new object and return the pointer.
+ */
+ PyArrayObject* make_contiguous(PyArrayObject* ary,
+ int* is_new_object,
+ int min_dims,
+ int max_dims)
+ {
+ PyArrayObject* result;
+ if (array_is_contiguous(ary))
+ {
+ result = ary;
+ *is_new_object = 0;
+ }
+ else
+ {
+ result = (PyArrayObject*) PyArray_ContiguousFromObject((PyObject*)ary,
+ array_type(ary),
+ min_dims,
+ max_dims);
+ *is_new_object = 1;
+ }
+ return result;
+ }
+
+ /* Given a PyArrayObject, check to see if it is Fortran-contiguous.
+ * If so, return the input pointer, but do not flag it as not a new
+ * object. If it is not Fortran-contiguous, create a new
+ * PyArrayObject using the original data, flag it as a new object
+ * and return the pointer.
+ */
+ PyArrayObject* make_fortran(PyArrayObject* ary,
+ int* is_new_object)
+ {
+ PyArrayObject* result;
+ if (array_is_fortran(ary))
+ {
+ result = ary;
+ *is_new_object = 0;
+ }
+ else
+ {
+ Py_INCREF(array_descr(ary));
+ result = (PyArrayObject*) PyArray_FromArray(ary,
+ array_descr(ary),
+ NPY_FORTRANORDER);
+ *is_new_object = 1;
+ }
+ return result;
+ }
+
+ /* Convert a given PyObject to a contiguous PyArrayObject of the
+ * specified type. If the input object is not a contiguous
+ * PyArrayObject, a new one will be created and the new object flag
+ * will be set.
+ */
+ PyArrayObject* obj_to_array_contiguous_allow_conversion(PyObject* input,
+ int typecode,
+ int* is_new_object)
+ {
+ int is_new1 = 0;
+ int is_new2 = 0;
+ PyArrayObject* ary2;
+ PyArrayObject* ary1 = obj_to_array_allow_conversion(input,
+ typecode,
+ &is_new1);
+ if (ary1)
+ {
+ ary2 = make_contiguous(ary1, &is_new2, 0, 0);
+ if ( is_new1 && is_new2)
+ {
+ Py_DECREF(ary1);
+ }
+ ary1 = ary2;
+ }
+ *is_new_object = is_new1 || is_new2;
+ return ary1;
+ }
+
+ /* Convert a given PyObject to a Fortran-ordered PyArrayObject of the
+ * specified type. If the input object is not a Fortran-ordered
+ * PyArrayObject, a new one will be created and the new object flag
+ * will be set.
+ */
+ PyArrayObject* obj_to_array_fortran_allow_conversion(PyObject* input,
+ int typecode,
+ int* is_new_object)
+ {
+ int is_new1 = 0;
+ int is_new2 = 0;
+ PyArrayObject* ary2;
+ PyArrayObject* ary1 = obj_to_array_allow_conversion(input,
+ typecode,
+ &is_new1);
+ if (ary1)
+ {
+ ary2 = make_fortran(ary1, &is_new2);
+ if (is_new1 && is_new2)
+ {
+ Py_DECREF(ary1);
+ }
+ ary1 = ary2;
+ }
+ *is_new_object = is_new1 || is_new2;
+ return ary1;
+ }
+} /* end fragment */
+
+/**********************************************************************/
+
+%fragment("NumPy_Array_Requirements",
+ "header",
+ fragment="NumPy_Backward_Compatibility",
+ fragment="NumPy_Macros")
+{
+ /* Test whether a python object is contiguous. If array is
+ * contiguous, return 1. Otherwise, set the python error string and
+ * return 0.
+ */
+ int require_contiguous(PyArrayObject* ary)
+ {
+ int contiguous = 1;
+ if (!array_is_contiguous(ary))
+ {
+ PyErr_SetString(PyExc_TypeError,
+ "Array must be contiguous. A non-contiguous array was given");
+ contiguous = 0;
+ }
+ return contiguous;
+ }
+
+ /* Test whether a python object is (C_ or F_) contiguous. If array is
+ * contiguous, return 1. Otherwise, set the python error string and
+ * return 0.
+ */
+ int require_c_or_f_contiguous(PyArrayObject* ary)
+ {
+ int contiguous = 1;
+ if (!(array_is_contiguous(ary) || array_is_fortran(ary)))
+ {
+ PyErr_SetString(PyExc_TypeError,
+ "Array must be contiguous (C_ or F_). A non-contiguous array was given");
+ contiguous = 0;
+ }
+ return contiguous;
+ }
+
+ /* Require that a numpy array is not byte-swapped. If the array is
+ * not byte-swapped, return 1. Otherwise, set the python error string
+ * and return 0.
+ */
+ int require_native(PyArrayObject* ary)
+ {
+ int native = 1;
+ if (!array_is_native(ary))
+ {
+ PyErr_SetString(PyExc_TypeError,
+ "Array must have native byteorder. "
+ "A byte-swapped array was given");
+ native = 0;
+ }
+ return native;
+ }
+
+ /* Require the given PyArrayObject to have a specified number of
+ * dimensions. If the array has the specified number of dimensions,
+ * return 1. Otherwise, set the python error string and return 0.
+ */
+ int require_dimensions(PyArrayObject* ary,
+ int exact_dimensions)
+ {
+ int success = 1;
+ if (array_numdims(ary) != exact_dimensions)
+ {
+ PyErr_Format(PyExc_TypeError,
+ "Array must have %d dimensions. Given array has %d dimensions",
+ exact_dimensions,
+ array_numdims(ary));
+ success = 0;
+ }
+ return success;
+ }
+
+ /* Require the given PyArrayObject to have one of a list of specified
+ * number of dimensions. If the array has one of the specified number
+ * of dimensions, return 1. Otherwise, set the python error string
+ * and return 0.
+ */
+ int require_dimensions_n(PyArrayObject* ary,
+ int* exact_dimensions,
+ int n)
+ {
+ int success = 0;
+ int i;
+ char dims_str[255] = "";
+ char s[255];
+ for (i = 0; i < n && !success; i++)
+ {
+ if (array_numdims(ary) == exact_dimensions[i])
+ {
+ success = 1;
+ }
+ }
+ if (!success)
+ {
+ for (i = 0; i < n-1; i++)
+ {
+ sprintf(s, "%d, ", exact_dimensions[i]);
+ strcat(dims_str,s);
+ }
+ sprintf(s, " or %d", exact_dimensions[n-1]);
+ strcat(dims_str,s);
+ PyErr_Format(PyExc_TypeError,
+ "Array must have %s dimensions. Given array has %d dimensions",
+ dims_str,
+ array_numdims(ary));
+ }
+ return success;
+ }
+
+ /* Require the given PyArrayObject to have a specified shape. If the
+ * array has the specified shape, return 1. Otherwise, set the python
+ * error string and return 0.
+ */
+ int require_size(PyArrayObject* ary,
+ npy_intp* size,
+ int n)
+ {
+ int i;
+ int success = 1;
+ int len;
+ char desired_dims[255] = "[";
+ char s[255];
+ char actual_dims[255] = "[";
+ for(i=0; i < n;i++)
+ {
+ if (size[i] != -1 && size[i] != array_size(ary,i))
+ {
+ success = 0;
+ }
+ }
+ if (!success)
+ {
+ for (i = 0; i < n; i++)
+ {
+ if (size[i] == -1)
+ {
+ sprintf(s, "*,");
+ }
+ else
+ {
+ sprintf(s, "%ld,", (long int)size[i]);
+ }
+ strcat(desired_dims,s);
+ }
+ len = strlen(desired_dims);
+ desired_dims[len-1] = ']';
+ for (i = 0; i < n; i++)
+ {
+ sprintf(s, "%ld,", (long int)array_size(ary,i));
+ strcat(actual_dims,s);
+ }
+ len = strlen(actual_dims);
+ actual_dims[len-1] = ']';
+ PyErr_Format(PyExc_TypeError,
+ "Array must have shape of %s. Given array has shape of %s",
+ desired_dims,
+ actual_dims);
+ }
+ return success;
+ }
+
+ /* Require the given PyArrayObject to to be Fortran ordered. If the
+ * the PyArrayObject is already Fortran ordered, do nothing. Else,
+ * set the Fortran ordering flag and recompute the strides.
+ */
+ int require_fortran(PyArrayObject* ary)
+ {
+ int success = 1;
+ int nd = array_numdims(ary);
+ int i;
+ npy_intp * strides = array_strides(ary);
+ if (array_is_fortran(ary)) return success;
+ /* Set the Fortran ordered flag */
+ array_enableflags(ary,NPY_ARRAY_FARRAY);
+ /* Recompute the strides */
+ strides[0] = strides[nd-1];
+ for (i=1; i < nd; ++i)
+ strides[i] = strides[i-1] * array_size(ary,i-1);
+ return success;
+ }
+}
+
+/* Combine all NumPy fragments into one for convenience */
+%fragment("NumPy_Fragments",
+ "header",
+ fragment="NumPy_Backward_Compatibility",
+ fragment="NumPy_Macros",
+ fragment="NumPy_Utilities",
+ fragment="NumPy_Object_to_Array",
+ fragment="NumPy_Array_Requirements")
+{
+}
+
+/* End John Hunter translation (with modifications by Bill Spotz)
+ */
+
+/* %numpy_typemaps() macro
+ *
+ * This macro defines a family of 75 typemaps that allow C arguments
+ * of the form
+ *
+ * 1. (DATA_TYPE IN_ARRAY1[ANY])
+ * 2. (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
+ * 3. (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
+ *
+ * 4. (DATA_TYPE IN_ARRAY2[ANY][ANY])
+ * 5. (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ * 6. (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
+ * 7. (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ * 8. (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
+ *
+ * 9. (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
+ * 10. (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ * 11. (DATA_TYPE** IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ * 12. (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_ARRAY3)
+ * 13. (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ * 14. (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_FARRAY3)
+ *
+ * 15. (DATA_TYPE IN_ARRAY4[ANY][ANY][ANY][ANY])
+ * 16. (DATA_TYPE* IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ * 17. (DATA_TYPE** IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ * 18. (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, , DIM_TYPE DIM4, DATA_TYPE* IN_ARRAY4)
+ * 19. (DATA_TYPE* IN_FARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ * 20. (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* IN_FARRAY4)
+ *
+ * 21. (DATA_TYPE INPLACE_ARRAY1[ANY])
+ * 22. (DATA_TYPE* INPLACE_ARRAY1, DIM_TYPE DIM1)
+ * 23. (DIM_TYPE DIM1, DATA_TYPE* INPLACE_ARRAY1)
+ *
+ * 24. (DATA_TYPE INPLACE_ARRAY2[ANY][ANY])
+ * 25. (DATA_TYPE* INPLACE_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ * 26. (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_ARRAY2)
+ * 27. (DATA_TYPE* INPLACE_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ * 28. (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_FARRAY2)
+ *
+ * 29. (DATA_TYPE INPLACE_ARRAY3[ANY][ANY][ANY])
+ * 30. (DATA_TYPE* INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ * 31. (DATA_TYPE** INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ * 32. (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_ARRAY3)
+ * 33. (DATA_TYPE* INPLACE_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ * 34. (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_FARRAY3)
+ *
+ * 35. (DATA_TYPE INPLACE_ARRAY4[ANY][ANY][ANY][ANY])
+ * 36. (DATA_TYPE* INPLACE_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ * 37. (DATA_TYPE** INPLACE_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ * 38. (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* INPLACE_ARRAY4)
+ * 39. (DATA_TYPE* INPLACE_FARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ * 40. (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* INPLACE_FARRAY4)
+ *
+ * 41. (DATA_TYPE ARGOUT_ARRAY1[ANY])
+ * 42. (DATA_TYPE* ARGOUT_ARRAY1, DIM_TYPE DIM1)
+ * 43. (DIM_TYPE DIM1, DATA_TYPE* ARGOUT_ARRAY1)
+ *
+ * 44. (DATA_TYPE ARGOUT_ARRAY2[ANY][ANY])
+ *
+ * 45. (DATA_TYPE ARGOUT_ARRAY3[ANY][ANY][ANY])
+ *
+ * 46. (DATA_TYPE ARGOUT_ARRAY4[ANY][ANY][ANY][ANY])
+ *
+ * 47. (DATA_TYPE** ARGOUTVIEW_ARRAY1, DIM_TYPE* DIM1)
+ * 48. (DIM_TYPE* DIM1, DATA_TYPE** ARGOUTVIEW_ARRAY1)
+ *
+ * 49. (DATA_TYPE** ARGOUTVIEW_ARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+ * 50. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_ARRAY2)
+ * 51. (DATA_TYPE** ARGOUTVIEW_FARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+ * 52. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_FARRAY2)
+ *
+ * 53. (DATA_TYPE** ARGOUTVIEW_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+ * 54. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_ARRAY3)
+ * 55. (DATA_TYPE** ARGOUTVIEW_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+ * 56. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_FARRAY3)
+ *
+ * 57. (DATA_TYPE** ARGOUTVIEW_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ * 58. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEW_ARRAY4)
+ * 59. (DATA_TYPE** ARGOUTVIEW_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ * 60. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEW_FARRAY4)
+ *
+ * 61. (DATA_TYPE** ARGOUTVIEWM_ARRAY1, DIM_TYPE* DIM1)
+ * 62. (DIM_TYPE* DIM1, DATA_TYPE** ARGOUTVIEWM_ARRAY1)
+ *
+ * 63. (DATA_TYPE** ARGOUTVIEWM_ARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+ * 64. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEWM_ARRAY2)
+ * 65. (DATA_TYPE** ARGOUTVIEWM_FARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+ * 66. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEWM_FARRAY2)
+ *
+ * 67. (DATA_TYPE** ARGOUTVIEWM_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+ * 68. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEWM_ARRAY3)
+ * 69. (DATA_TYPE** ARGOUTVIEWM_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+ * 70. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEWM_FARRAY3)
+ *
+ * 71. (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ * 72. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+ * 73. (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ * 74. (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+ *
+ * 75. (DATA_TYPE* INPLACE_ARRAY_FLAT, DIM_TYPE DIM_FLAT)
+ *
+ * where "DATA_TYPE" is any type supported by the NumPy module, and
+ * "DIM_TYPE" is any int-like type suitable for specifying dimensions.
+ * The difference between "ARRAY" typemaps and "FARRAY" typemaps is
+ * that the "FARRAY" typemaps expect Fortran ordering of
+ * multidimensional arrays. In python, the dimensions will not need
+ * to be specified (except for the "DATA_TYPE* ARGOUT_ARRAY1"
+ * typemaps). The IN_ARRAYs can be a numpy array or any sequence that
+ * can be converted to a numpy array of the specified type. The
+ * INPLACE_ARRAYs must be numpy arrays of the appropriate type. The
+ * ARGOUT_ARRAYs will be returned as new numpy arrays of the
+ * appropriate type.
+ *
+ * These typemaps can be applied to existing functions using the
+ * %apply directive. For example:
+ *
+ * %apply (double* IN_ARRAY1, int DIM1) {(double* series, int length)};
+ * double prod(double* series, int length);
+ *
+ * %apply (int DIM1, int DIM2, double* INPLACE_ARRAY2)
+ * {(int rows, int cols, double* matrix )};
+ * void floor(int rows, int cols, double* matrix, double f);
+ *
+ * %apply (double IN_ARRAY3[ANY][ANY][ANY])
+ * {(double tensor[2][2][2] )};
+ * %apply (double ARGOUT_ARRAY3[ANY][ANY][ANY])
+ * {(double low[2][2][2] )};
+ * %apply (double ARGOUT_ARRAY3[ANY][ANY][ANY])
+ * {(double upp[2][2][2] )};
+ * void luSplit(double tensor[2][2][2],
+ * double low[2][2][2],
+ * double upp[2][2][2] );
+ *
+ * or directly with
+ *
+ * double prod(double* IN_ARRAY1, int DIM1);
+ *
+ * void floor(int DIM1, int DIM2, double* INPLACE_ARRAY2, double f);
+ *
+ * void luSplit(double IN_ARRAY3[ANY][ANY][ANY],
+ * double ARGOUT_ARRAY3[ANY][ANY][ANY],
+ * double ARGOUT_ARRAY3[ANY][ANY][ANY]);
+ */
+
+%define %numpy_typemaps(DATA_TYPE, DATA_TYPECODE, DIM_TYPE)
+
+/************************/
+/* Input Array Typemaps */
+/************************/
+
+/* Typemap suite for (DATA_TYPE IN_ARRAY1[ANY])
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE IN_ARRAY1[ANY])
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE IN_ARRAY1[ANY])
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[1] = { $1_dim0 };
+ array = obj_to_array_contiguous_allow_conversion($input,
+ DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 1) ||
+ !require_size(array, size, 1)) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+%typemap(freearg)
+ (DATA_TYPE IN_ARRAY1[ANY])
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[1] = { -1 };
+ array = obj_to_array_contiguous_allow_conversion($input,
+ DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 1) ||
+ !require_size(array, size, 1)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+}
+%typemap(freearg)
+ (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[1] = {-1};
+ array = obj_to_array_contiguous_allow_conversion($input,
+ DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 1) ||
+ !require_size(array, size, 1)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DATA_TYPE*) array_data(array);
+}
+%typemap(freearg)
+ (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE IN_ARRAY2[ANY][ANY])
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE IN_ARRAY2[ANY][ANY])
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE IN_ARRAY2[ANY][ANY])
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[2] = { $1_dim0, $1_dim1 };
+ array = obj_to_array_contiguous_allow_conversion($input,
+ DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 2) ||
+ !require_size(array, size, 2)) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+%typemap(freearg)
+ (DATA_TYPE IN_ARRAY2[ANY][ANY])
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[2] = { -1, -1 };
+ array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 2) ||
+ !require_size(array, size, 2)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+}
+%typemap(freearg)
+ (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[2] = { -1, -1 };
+ array = obj_to_array_contiguous_allow_conversion($input,
+ DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 2) ||
+ !require_size(array, size, 2)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DATA_TYPE*) array_data(array);
+}
+%typemap(freearg)
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[2] = { -1, -1 };
+ array = obj_to_array_fortran_allow_conversion($input,
+ DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 2) ||
+ !require_size(array, size, 2) || !require_fortran(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+}
+%typemap(freearg)
+ (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[2] = { -1, -1 };
+ array = obj_to_array_fortran_allow_conversion($input,
+ DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 2) ||
+ !require_size(array, size, 2) || !require_fortran(array)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DATA_TYPE*) array_data(array);
+}
+%typemap(freearg)
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[3] = { $1_dim0, $1_dim1, $1_dim2 };
+ array = obj_to_array_contiguous_allow_conversion($input,
+ DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 3) ||
+ !require_size(array, size, 3)) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+%typemap(freearg)
+ (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[3] = { -1, -1, -1 };
+ array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 3) ||
+ !require_size(array, size, 3)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+ $4 = (DIM_TYPE) array_size(array,2);
+}
+%typemap(freearg)
+ (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE** IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE** IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ /* for now, only concerned with lists */
+ $1 = PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE** IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ (DATA_TYPE** array=NULL, PyArrayObject** object_array=NULL, int* is_new_object_array=NULL)
+{
+ npy_intp size[2] = { -1, -1 };
+ PyArrayObject* temp_array;
+ Py_ssize_t i;
+ int is_new_object;
+
+ /* length of the list */
+ $2 = PyList_Size($input);
+
+ /* the arrays */
+ array = (DATA_TYPE **)malloc($2*sizeof(DATA_TYPE *));
+ object_array = (PyArrayObject **)calloc($2,sizeof(PyArrayObject *));
+ is_new_object_array = (int *)calloc($2,sizeof(int));
+
+ if (array == NULL || object_array == NULL || is_new_object_array == NULL)
+ {
+ SWIG_fail;
+ }
+
+ for (i=0; i<$2; i++)
+ {
+ temp_array = obj_to_array_contiguous_allow_conversion(PySequence_GetItem($input,i), DATA_TYPECODE, &is_new_object);
+
+ /* the new array must be stored so that it can be destroyed in freearg */
+ object_array[i] = temp_array;
+ is_new_object_array[i] = is_new_object;
+
+ if (!temp_array || !require_dimensions(temp_array, 2)) SWIG_fail;
+
+ /* store the size of the first array in the list, then use that for comparison. */
+ if (i == 0)
+ {
+ size[0] = array_size(temp_array,0);
+ size[1] = array_size(temp_array,1);
+ }
+
+ if (!require_size(temp_array, size, 2)) SWIG_fail;
+
+ array[i] = (DATA_TYPE*) array_data(temp_array);
+ }
+
+ $1 = (DATA_TYPE**) array;
+ $3 = (DIM_TYPE) size[0];
+ $4 = (DIM_TYPE) size[1];
+}
+%typemap(freearg)
+ (DATA_TYPE** IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ Py_ssize_t i;
+
+ if (array$argnum!=NULL) free(array$argnum);
+
+ /*freeing the individual arrays if needed */
+ if (object_array$argnum!=NULL)
+ {
+ if (is_new_object_array$argnum!=NULL)
+ {
+ for (i=0; i<$2; i++)
+ {
+ if (object_array$argnum[i] != NULL && is_new_object_array$argnum[i])
+ { Py_DECREF(object_array$argnum[i]); }
+ }
+ free(is_new_object_array$argnum);
+ }
+ free(object_array$argnum);
+ }
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3,
+ * DATA_TYPE* IN_ARRAY3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_ARRAY3)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_ARRAY3)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[3] = { -1, -1, -1 };
+ array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 3) ||
+ !require_size(array, size, 3)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DIM_TYPE) array_size(array,2);
+ $4 = (DATA_TYPE*) array_data(array);
+}
+%typemap(freearg)
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_ARRAY3)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[3] = { -1, -1, -1 };
+ array = obj_to_array_fortran_allow_conversion($input, DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 3) ||
+ !require_size(array, size, 3) | !require_fortran(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+ $4 = (DIM_TYPE) array_size(array,2);
+}
+%typemap(freearg)
+ (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3,
+ * DATA_TYPE* IN_FARRAY3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_FARRAY3)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_FARRAY3)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[3] = { -1, -1, -1 };
+ array = obj_to_array_fortran_allow_conversion($input,
+ DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 3) ||
+ !require_size(array, size, 3) || !require_fortran(array)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DIM_TYPE) array_size(array,2);
+ $4 = (DATA_TYPE*) array_data(array);
+}
+%typemap(freearg)
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_FARRAY3)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE IN_ARRAY4[ANY][ANY][ANY][ANY])
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE IN_ARRAY4[ANY][ANY][ANY][ANY])
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE IN_ARRAY4[ANY][ANY][ANY][ANY])
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[4] = { $1_dim0, $1_dim1, $1_dim2 , $1_dim3};
+ array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 4) ||
+ !require_size(array, size, 4)) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+%typemap(freearg)
+ (DATA_TYPE IN_ARRAY4[ANY][ANY][ANY][ANY])
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE* IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3, DIM_TYPE DIM4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[4] = { -1, -1, -1, -1 };
+ array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 4) ||
+ !require_size(array, size, 4)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+ $4 = (DIM_TYPE) array_size(array,2);
+ $5 = (DIM_TYPE) array_size(array,3);
+}
+%typemap(freearg)
+ (DATA_TYPE* IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE** IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3, DIM_TYPE DIM4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE** IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ /* for now, only concerned with lists */
+ $1 = PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE** IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ (DATA_TYPE** array=NULL, PyArrayObject** object_array=NULL, int* is_new_object_array=NULL)
+{
+ npy_intp size[3] = { -1, -1, -1 };
+ PyArrayObject* temp_array;
+ Py_ssize_t i;
+ int is_new_object;
+
+ /* length of the list */
+ $2 = PyList_Size($input);
+
+ /* the arrays */
+ array = (DATA_TYPE **)malloc($2*sizeof(DATA_TYPE *));
+ object_array = (PyArrayObject **)calloc($2,sizeof(PyArrayObject *));
+ is_new_object_array = (int *)calloc($2,sizeof(int));
+
+ if (array == NULL || object_array == NULL || is_new_object_array == NULL)
+ {
+ SWIG_fail;
+ }
+
+ for (i=0; i<$2; i++)
+ {
+ temp_array = obj_to_array_contiguous_allow_conversion(PySequence_GetItem($input,i), DATA_TYPECODE, &is_new_object);
+
+ /* the new array must be stored so that it can be destroyed in freearg */
+ object_array[i] = temp_array;
+ is_new_object_array[i] = is_new_object;
+
+ if (!temp_array || !require_dimensions(temp_array, 3)) SWIG_fail;
+
+ /* store the size of the first array in the list, then use that for comparison. */
+ if (i == 0)
+ {
+ size[0] = array_size(temp_array,0);
+ size[1] = array_size(temp_array,1);
+ size[2] = array_size(temp_array,2);
+ }
+
+ if (!require_size(temp_array, size, 3)) SWIG_fail;
+
+ array[i] = (DATA_TYPE*) array_data(temp_array);
+ }
+
+ $1 = (DATA_TYPE**) array;
+ $3 = (DIM_TYPE) size[0];
+ $4 = (DIM_TYPE) size[1];
+ $5 = (DIM_TYPE) size[2];
+}
+%typemap(freearg)
+ (DATA_TYPE** IN_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ Py_ssize_t i;
+
+ if (array$argnum!=NULL) free(array$argnum);
+
+ /*freeing the individual arrays if needed */
+ if (object_array$argnum!=NULL)
+ {
+ if (is_new_object_array$argnum!=NULL)
+ {
+ for (i=0; i<$2; i++)
+ {
+ if (object_array$argnum[i] != NULL && is_new_object_array$argnum[i])
+ { Py_DECREF(object_array$argnum[i]); }
+ }
+ free(is_new_object_array$argnum);
+ }
+ free(object_array$argnum);
+ }
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4,
+ * DATA_TYPE* IN_ARRAY4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* IN_ARRAY4)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* IN_ARRAY4)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[4] = { -1, -1, -1 , -1};
+ array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 4) ||
+ !require_size(array, size, 4)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DIM_TYPE) array_size(array,2);
+ $4 = (DIM_TYPE) array_size(array,3);
+ $5 = (DATA_TYPE*) array_data(array);
+}
+%typemap(freearg)
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* IN_ARRAY4)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DATA_TYPE* IN_FARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3, DIM_TYPE DIM4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* IN_FARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* IN_FARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[4] = { -1, -1, -1, -1 };
+ array = obj_to_array_fortran_allow_conversion($input, DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 4) ||
+ !require_size(array, size, 4) | !require_fortran(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+ $4 = (DIM_TYPE) array_size(array,2);
+ $5 = (DIM_TYPE) array_size(array,3);
+}
+%typemap(freearg)
+ (DATA_TYPE* IN_FARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4,
+ * DATA_TYPE* IN_FARRAY4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* IN_FARRAY4)
+{
+ $1 = is_array($input) || PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* IN_FARRAY4)
+ (PyArrayObject* array=NULL, int is_new_object=0)
+{
+ npy_intp size[4] = { -1, -1, -1 , -1 };
+ array = obj_to_array_fortran_allow_conversion($input, DATA_TYPECODE,
+ &is_new_object);
+ if (!array || !require_dimensions(array, 4) ||
+ !require_size(array, size, 4) || !require_fortran(array)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DIM_TYPE) array_size(array,2);
+ $4 = (DIM_TYPE) array_size(array,3);
+ $5 = (DATA_TYPE*) array_data(array);
+}
+%typemap(freearg)
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* IN_FARRAY4)
+{
+ if (is_new_object$argnum && array$argnum)
+ { Py_DECREF(array$argnum); }
+}
+
+/***************************/
+/* In-Place Array Typemaps */
+/***************************/
+
+/* Typemap suite for (DATA_TYPE INPLACE_ARRAY1[ANY])
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE INPLACE_ARRAY1[ANY])
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE INPLACE_ARRAY1[ANY])
+ (PyArrayObject* array=NULL)
+{
+ npy_intp size[1] = { $1_dim0 };
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,1) || !require_size(array, size, 1) ||
+ !require_contiguous(array) || !require_native(array)) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE* INPLACE_ARRAY1, DIM_TYPE DIM1)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* INPLACE_ARRAY1, DIM_TYPE DIM1)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* INPLACE_ARRAY1, DIM_TYPE DIM1)
+ (PyArrayObject* array=NULL, int i=1)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,1) || !require_contiguous(array)
+ || !require_native(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = 1;
+ for (i=0; i < array_numdims(array); ++i) $2 *= array_size(array,i);
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DATA_TYPE* INPLACE_ARRAY1)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DATA_TYPE* INPLACE_ARRAY1)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DATA_TYPE* INPLACE_ARRAY1)
+ (PyArrayObject* array=NULL, int i=0)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,1) || !require_contiguous(array)
+ || !require_native(array)) SWIG_fail;
+ $1 = 1;
+ for (i=0; i < array_numdims(array); ++i) $1 *= array_size(array,i);
+ $2 = (DATA_TYPE*) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE INPLACE_ARRAY2[ANY][ANY])
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE INPLACE_ARRAY2[ANY][ANY])
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE INPLACE_ARRAY2[ANY][ANY])
+ (PyArrayObject* array=NULL)
+{
+ npy_intp size[2] = { $1_dim0, $1_dim1 };
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,2) || !require_size(array, size, 2) ||
+ !require_contiguous(array) || !require_native(array)) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE* INPLACE_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* INPLACE_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* INPLACE_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,2) || !require_contiguous(array)
+ || !require_native(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_ARRAY2)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_ARRAY2)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_ARRAY2)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,2) || !require_contiguous(array) ||
+ !require_native(array)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DATA_TYPE*) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE* INPLACE_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* INPLACE_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* INPLACE_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,2) || !require_contiguous(array)
+ || !require_native(array) || !require_fortran(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_FARRAY2)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_FARRAY2)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_FARRAY2)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,2) || !require_contiguous(array) ||
+ !require_native(array) || !require_fortran(array)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DATA_TYPE*) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE INPLACE_ARRAY3[ANY][ANY][ANY])
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE INPLACE_ARRAY3[ANY][ANY][ANY])
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE INPLACE_ARRAY3[ANY][ANY][ANY])
+ (PyArrayObject* array=NULL)
+{
+ npy_intp size[3] = { $1_dim0, $1_dim1, $1_dim2 };
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,3) || !require_size(array, size, 3) ||
+ !require_contiguous(array) || !require_native(array)) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE* INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,3) || !require_contiguous(array) ||
+ !require_native(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+ $4 = (DIM_TYPE) array_size(array,2);
+}
+
+/* Typemap suite for (DATA_TYPE** INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE** INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ $1 = PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE** INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ (DATA_TYPE** array=NULL, PyArrayObject** object_array=NULL)
+{
+ npy_intp size[2] = { -1, -1 };
+ PyArrayObject* temp_array;
+ Py_ssize_t i;
+
+ /* length of the list */
+ $2 = PyList_Size($input);
+
+ /* the arrays */
+ array = (DATA_TYPE **)malloc($2*sizeof(DATA_TYPE *));
+ object_array = (PyArrayObject **)calloc($2,sizeof(PyArrayObject *));
+
+ if (array == NULL || object_array == NULL)
+ {
+ SWIG_fail;
+ }
+
+ for (i=0; i<$2; i++)
+ {
+ temp_array = obj_to_array_no_conversion(PySequence_GetItem($input,i), DATA_TYPECODE);
+
+ /* the new array must be stored so that it can be destroyed in freearg */
+ object_array[i] = temp_array;
+
+ if ( !temp_array || !require_dimensions(temp_array, 2) ||
+ !require_contiguous(temp_array) ||
+ !require_native(temp_array) ||
+ !PyArray_EquivTypenums(array_type(temp_array), DATA_TYPECODE)
+ ) SWIG_fail;
+
+ /* store the size of the first array in the list, then use that for comparison. */
+ if (i == 0)
+ {
+ size[0] = array_size(temp_array,0);
+ size[1] = array_size(temp_array,1);
+ }
+
+ if (!require_size(temp_array, size, 2)) SWIG_fail;
+
+ array[i] = (DATA_TYPE*) array_data(temp_array);
+ }
+
+ $1 = (DATA_TYPE**) array;
+ $3 = (DIM_TYPE) size[0];
+ $4 = (DIM_TYPE) size[1];
+}
+%typemap(freearg)
+ (DATA_TYPE** INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ if (array$argnum!=NULL) free(array$argnum);
+ if (object_array$argnum!=NULL) free(object_array$argnum);
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3,
+ * DATA_TYPE* INPLACE_ARRAY3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_ARRAY3)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_ARRAY3)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,3) || !require_contiguous(array)
+ || !require_native(array)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DIM_TYPE) array_size(array,2);
+ $4 = (DATA_TYPE*) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE* INPLACE_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* INPLACE_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* INPLACE_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,3) || !require_contiguous(array) ||
+ !require_native(array) || !require_fortran(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+ $4 = (DIM_TYPE) array_size(array,2);
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3,
+ * DATA_TYPE* INPLACE_FARRAY3)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_FARRAY3)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_FARRAY3)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,3) || !require_contiguous(array)
+ || !require_native(array) || !require_fortran(array)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DIM_TYPE) array_size(array,2);
+ $4 = (DATA_TYPE*) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE INPLACE_ARRAY4[ANY][ANY][ANY][ANY])
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE INPLACE_ARRAY4[ANY][ANY][ANY][ANY])
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE INPLACE_ARRAY4[ANY][ANY][ANY][ANY])
+ (PyArrayObject* array=NULL)
+{
+ npy_intp size[4] = { $1_dim0, $1_dim1, $1_dim2 , $1_dim3 };
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,4) || !require_size(array, size, 4) ||
+ !require_contiguous(array) || !require_native(array)) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE* INPLACE_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3, DIM_TYPE DIM4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* INPLACE_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* INPLACE_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,4) || !require_contiguous(array) ||
+ !require_native(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+ $4 = (DIM_TYPE) array_size(array,2);
+ $5 = (DIM_TYPE) array_size(array,3);
+}
+
+/* Typemap suite for (DATA_TYPE** INPLACE_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3, DIM_TYPE DIM4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE** INPLACE_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ $1 = PySequence_Check($input);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE** INPLACE_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ (DATA_TYPE** array=NULL, PyArrayObject** object_array=NULL)
+{
+ npy_intp size[3] = { -1, -1, -1 };
+ PyArrayObject* temp_array;
+ Py_ssize_t i;
+
+ /* length of the list */
+ $2 = PyList_Size($input);
+
+ /* the arrays */
+ array = (DATA_TYPE **)malloc($2*sizeof(DATA_TYPE *));
+ object_array = (PyArrayObject **)calloc($2,sizeof(PyArrayObject *));
+
+ if (array == NULL || object_array == NULL)
+ {
+ SWIG_fail;
+ }
+
+ for (i=0; i<$2; i++)
+ {
+ temp_array = obj_to_array_no_conversion(PySequence_GetItem($input,i), DATA_TYPECODE);
+
+ /* the new array must be stored so that it can be destroyed in freearg */
+ object_array[i] = temp_array;
+
+ if ( !temp_array || !require_dimensions(temp_array, 3) ||
+ !require_contiguous(temp_array) ||
+ !require_native(temp_array) ||
+ !PyArray_EquivTypenums(array_type(temp_array), DATA_TYPECODE)
+ ) SWIG_fail;
+
+ /* store the size of the first array in the list, then use that for comparison. */
+ if (i == 0)
+ {
+ size[0] = array_size(temp_array,0);
+ size[1] = array_size(temp_array,1);
+ size[2] = array_size(temp_array,2);
+ }
+
+ if (!require_size(temp_array, size, 3)) SWIG_fail;
+
+ array[i] = (DATA_TYPE*) array_data(temp_array);
+ }
+
+ $1 = (DATA_TYPE**) array;
+ $3 = (DIM_TYPE) size[0];
+ $4 = (DIM_TYPE) size[1];
+ $5 = (DIM_TYPE) size[2];
+}
+%typemap(freearg)
+ (DATA_TYPE** INPLACE_ARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ if (array$argnum!=NULL) free(array$argnum);
+ if (object_array$argnum!=NULL) free(object_array$argnum);
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4,
+ * DATA_TYPE* INPLACE_ARRAY4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* INPLACE_ARRAY4)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* INPLACE_ARRAY4)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,4) || !require_contiguous(array)
+ || !require_native(array)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DIM_TYPE) array_size(array,2);
+ $4 = (DIM_TYPE) array_size(array,3);
+ $5 = (DATA_TYPE*) array_data(array);
+}
+
+/* Typemap suite for (DATA_TYPE* INPLACE_FARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2,
+ * DIM_TYPE DIM3, DIM_TYPE DIM4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* INPLACE_FARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* INPLACE_FARRAY4, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,4) || !require_contiguous(array) ||
+ !require_native(array) || !require_fortran(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = (DIM_TYPE) array_size(array,0);
+ $3 = (DIM_TYPE) array_size(array,1);
+ $4 = (DIM_TYPE) array_size(array,2);
+ $5 = (DIM_TYPE) array_size(array,3);
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3,
+ * DATA_TYPE* INPLACE_FARRAY4)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* INPLACE_FARRAY4)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DIM_TYPE DIM4, DATA_TYPE* INPLACE_FARRAY4)
+ (PyArrayObject* array=NULL)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_dimensions(array,4) || !require_contiguous(array)
+ || !require_native(array) || !require_fortran(array)) SWIG_fail;
+ $1 = (DIM_TYPE) array_size(array,0);
+ $2 = (DIM_TYPE) array_size(array,1);
+ $3 = (DIM_TYPE) array_size(array,2);
+ $4 = (DIM_TYPE) array_size(array,3);
+ $5 = (DATA_TYPE*) array_data(array);
+}
+
+/*************************/
+/* Argout Array Typemaps */
+/*************************/
+
+/* Typemap suite for (DATA_TYPE ARGOUT_ARRAY1[ANY])
+ */
+%typemap(in,numinputs=0,
+ fragment="NumPy_Backward_Compatibility,NumPy_Macros")
+ (DATA_TYPE ARGOUT_ARRAY1[ANY])
+ (PyObject* array = NULL)
+{
+ npy_intp dims[1] = { $1_dim0 };
+ array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
+ if (!array) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+%typemap(argout)
+ (DATA_TYPE ARGOUT_ARRAY1[ANY])
+{
+ $result = SWIG_Python_AppendOutput($result,(PyObject*)array$argnum);
+}
+
+/* Typemap suite for (DATA_TYPE* ARGOUT_ARRAY1, DIM_TYPE DIM1)
+ */
+%typemap(in,numinputs=1,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* ARGOUT_ARRAY1, DIM_TYPE DIM1)
+ (PyObject* array = NULL)
+{
+ npy_intp dims[1];
+ if (!PyInt_Check($input))
+ {
+ const char* typestring = pytype_string($input);
+ PyErr_Format(PyExc_TypeError,
+ "Int dimension expected. '%s' given.",
+ typestring);
+ SWIG_fail;
+ }
+ $2 = (DIM_TYPE) PyInt_AsLong($input);
+ dims[0] = (npy_intp) $2;
+ array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
+ if (!array) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+}
+%typemap(argout)
+ (DATA_TYPE* ARGOUT_ARRAY1, DIM_TYPE DIM1)
+{
+ $result = SWIG_Python_AppendOutput($result,(PyObject*)array$argnum);
+}
+
+/* Typemap suite for (DIM_TYPE DIM1, DATA_TYPE* ARGOUT_ARRAY1)
+ */
+%typemap(in,numinputs=1,
+ fragment="NumPy_Fragments")
+ (DIM_TYPE DIM1, DATA_TYPE* ARGOUT_ARRAY1)
+ (PyObject* array = NULL)
+{
+ npy_intp dims[1];
+ if (!PyInt_Check($input))
+ {
+ const char* typestring = pytype_string($input);
+ PyErr_Format(PyExc_TypeError,
+ "Int dimension expected. '%s' given.",
+ typestring);
+ SWIG_fail;
+ }
+ $1 = (DIM_TYPE) PyInt_AsLong($input);
+ dims[0] = (npy_intp) $1;
+ array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
+ if (!array) SWIG_fail;
+ $2 = (DATA_TYPE*) array_data(array);
+}
+%typemap(argout)
+ (DIM_TYPE DIM1, DATA_TYPE* ARGOUT_ARRAY1)
+{
+ $result = SWIG_Python_AppendOutput($result,(PyObject*)array$argnum);
+}
+
+/* Typemap suite for (DATA_TYPE ARGOUT_ARRAY2[ANY][ANY])
+ */
+%typemap(in,numinputs=0,
+ fragment="NumPy_Backward_Compatibility,NumPy_Macros")
+ (DATA_TYPE ARGOUT_ARRAY2[ANY][ANY])
+ (PyObject* array = NULL)
+{
+ npy_intp dims[2] = { $1_dim0, $1_dim1 };
+ array = PyArray_SimpleNew(2, dims, DATA_TYPECODE);
+ if (!array) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+%typemap(argout)
+ (DATA_TYPE ARGOUT_ARRAY2[ANY][ANY])
+{
+ $result = SWIG_Python_AppendOutput($result,(PyObject*)array$argnum);
+}
+
+/* Typemap suite for (DATA_TYPE ARGOUT_ARRAY3[ANY][ANY][ANY])
+ */
+%typemap(in,numinputs=0,
+ fragment="NumPy_Backward_Compatibility,NumPy_Macros")
+ (DATA_TYPE ARGOUT_ARRAY3[ANY][ANY][ANY])
+ (PyObject* array = NULL)
+{
+ npy_intp dims[3] = { $1_dim0, $1_dim1, $1_dim2 };
+ array = PyArray_SimpleNew(3, dims, DATA_TYPECODE);
+ if (!array) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+%typemap(argout)
+ (DATA_TYPE ARGOUT_ARRAY3[ANY][ANY][ANY])
+{
+ $result = SWIG_Python_AppendOutput($result,(PyObject*)array$argnum);
+}
+
+/* Typemap suite for (DATA_TYPE ARGOUT_ARRAY4[ANY][ANY][ANY][ANY])
+ */
+%typemap(in,numinputs=0,
+ fragment="NumPy_Backward_Compatibility,NumPy_Macros")
+ (DATA_TYPE ARGOUT_ARRAY4[ANY][ANY][ANY][ANY])
+ (PyObject* array = NULL)
+{
+ npy_intp dims[4] = { $1_dim0, $1_dim1, $1_dim2, $1_dim3 };
+ array = PyArray_SimpleNew(4, dims, DATA_TYPECODE);
+ if (!array) SWIG_fail;
+ $1 = ($1_ltype) array_data(array);
+}
+%typemap(argout)
+ (DATA_TYPE ARGOUT_ARRAY4[ANY][ANY][ANY][ANY])
+{
+ $result = SWIG_Python_AppendOutput($result,(PyObject*)array$argnum);
+}
+
+/*****************************/
+/* Argoutview Array Typemaps */
+/*****************************/
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_ARRAY1, DIM_TYPE* DIM1)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEW_ARRAY1, DIM_TYPE* DIM1 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility")
+ (DATA_TYPE** ARGOUTVIEW_ARRAY1, DIM_TYPE* DIM1)
+{
+ npy_intp dims[1] = { *$2 };
+ PyObject* obj = PyArray_SimpleNewFromData(1, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DATA_TYPE** ARGOUTVIEW_ARRAY1)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DATA_TYPE** ARGOUTVIEW_ARRAY1)
+ (DIM_TYPE dim_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim_temp;
+ $2 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility")
+ (DIM_TYPE* DIM1, DATA_TYPE** ARGOUTVIEW_ARRAY1)
+{
+ npy_intp dims[1] = { *$1 };
+ PyObject* obj = PyArray_SimpleNewFromData(1, dims, DATA_TYPECODE, (void*)(*$2));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_ARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEW_ARRAY2, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility")
+ (DATA_TYPE** ARGOUTVIEW_ARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+{
+ npy_intp dims[2] = { *$2, *$3 };
+ PyObject* obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_ARRAY2)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DATA_TYPE** ARGOUTVIEW_ARRAY2)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_ARRAY2)
+{
+ npy_intp dims[2] = { *$1, *$2 };
+ PyObject* obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$3));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_FARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEW_FARRAY2, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
+ (DATA_TYPE** ARGOUTVIEW_FARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+{
+ npy_intp dims[2] = { *$2, *$3 };
+ PyObject* obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_FARRAY2)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DATA_TYPE** ARGOUTVIEW_FARRAY2)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_FARRAY2)
+{
+ npy_intp dims[2] = { *$1, *$2 };
+ PyObject* obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$3));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEW_ARRAY3, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility")
+ (DATA_TYPE** ARGOUTVIEW_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+{
+ npy_intp dims[3] = { *$2, *$3, *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3,
+ DATA_TYPE** ARGOUTVIEW_ARRAY3)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_ARRAY3)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DATA_TYPE* data_temp = NULL)
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_ARRAY3)
+{
+ npy_intp dims[3] = { *$1, *$2, *$3 };
+ PyObject* obj = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$4));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEW_FARRAY3, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
+ (DATA_TYPE** ARGOUTVIEW_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+{
+ npy_intp dims[3] = { *$2, *$3, *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3,
+ DATA_TYPE** ARGOUTVIEW_FARRAY3)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DATA_TYPE** ARGOUTVIEW_FARRAY3)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_FARRAY3)
+{
+ npy_intp dims[3] = { *$1, *$2, *$3 };
+ PyObject* obj = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$4));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEW_ARRAY4, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+ $5 = &dim4_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility")
+ (DATA_TYPE** ARGOUTVIEW_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+{
+ npy_intp dims[4] = { *$2, *$3, *$4 , *$5 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4,
+ DATA_TYPE** ARGOUTVIEW_ARRAY4)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 , DATA_TYPE** ARGOUTVIEW_ARRAY4)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &dim4_temp;
+ $5 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEW_ARRAY4)
+{
+ npy_intp dims[4] = { *$1, *$2, *$3 , *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$5));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEW_FARRAY4, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+ $5 = &dim4_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
+ (DATA_TYPE** ARGOUTVIEW_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+{
+ npy_intp dims[4] = { *$2, *$3, *$4 , *$5 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4,
+ DATA_TYPE** ARGOUTVIEW_FARRAY4)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 , DATA_TYPE** ARGOUTVIEW_FARRAY4)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &dim4_temp;
+ $5 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEW_FARRAY4)
+{
+ npy_intp dims[4] = { *$1, *$2, *$3 , *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$5));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/*************************************/
+/* Managed Argoutview Array Typemaps */
+/*************************************/
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_ARRAY1, DIM_TYPE* DIM1)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY1, DIM_TYPE* DIM1 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY1, DIM_TYPE* DIM1)
+{
+ npy_intp dims[1] = { *$2 };
+ PyObject* obj = PyArray_SimpleNewFromData(1, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DATA_TYPE** ARGOUTVIEWM_ARRAY1)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DATA_TYPE** ARGOUTVIEWM_ARRAY1)
+ (DIM_TYPE dim_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim_temp;
+ $2 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DIM_TYPE* DIM1, DATA_TYPE** ARGOUTVIEWM_ARRAY1)
+{
+ npy_intp dims[1] = { *$1 };
+ PyObject* obj = PyArray_SimpleNewFromData(1, dims, DATA_TYPECODE, (void*)(*$2));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_ARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY2, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+{
+ npy_intp dims[2] = { *$2, *$3 };
+ PyObject* obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEWM_ARRAY2)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DATA_TYPE** ARGOUTVIEWM_ARRAY2)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEWM_ARRAY2)
+{
+ npy_intp dims[2] = { *$1, *$2 };
+ PyObject* obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$3));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_FARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEWM_FARRAY2, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+ (DATA_TYPE** ARGOUTVIEWM_FARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
+{
+ npy_intp dims[2] = { *$2, *$3 };
+ PyObject* obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEWM_FARRAY2)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DATA_TYPE** ARGOUTVIEWM_FARRAY2)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEWM_FARRAY2)
+{
+ npy_intp dims[2] = { *$1, *$2 };
+ PyObject* obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$3));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY3, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+{
+ npy_intp dims[3] = { *$2, *$3, *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3,
+ DATA_TYPE** ARGOUTVIEWM_ARRAY3)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DATA_TYPE** ARGOUTVIEWM_ARRAY3)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEWM_ARRAY3)
+{
+ npy_intp dims[3] = { *$1, *$2, *$3 };
+ PyObject* obj= PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$4));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEWM_FARRAY3, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+ (DATA_TYPE** ARGOUTVIEWM_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+{
+ npy_intp dims[3] = { *$2, *$3, *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3,
+ DATA_TYPE** ARGOUTVIEWM_FARRAY3)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DATA_TYPE** ARGOUTVIEWM_FARRAY3)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEWM_FARRAY3)
+{
+ npy_intp dims[3] = { *$1, *$2, *$3 };
+ PyObject* obj = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$4));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+ $5 = &dim4_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+{
+ npy_intp dims[4] = { *$2, *$3, *$4 , *$5 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4,
+ DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 , DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &dim4_temp;
+ $5 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+{
+ npy_intp dims[4] = { *$1, *$2, *$3 , *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$5));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+ $5 = &dim4_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+ (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+{
+ npy_intp dims[4] = { *$2, *$3, *$4 , *$5 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4,
+ DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 , DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &dim4_temp;
+ $5 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+{
+ npy_intp dims[4] = { *$1, *$2, *$3 , *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$5));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+ $5 = &dim4_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+{
+ npy_intp dims[4] = { *$2, *$3, *$4 , *$5 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4,
+ DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 , DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &dim4_temp;
+ $5 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+{
+ npy_intp dims[4] = { *$1, *$2, *$3 , *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$5));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+ DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ */
+%typemap(in,numinputs=0)
+ (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 )
+ (DATA_TYPE* data_temp = NULL , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp)
+{
+ $1 = &data_temp;
+ $2 = &dim1_temp;
+ $3 = &dim2_temp;
+ $4 = &dim3_temp;
+ $5 = &dim4_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+ (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+{
+ npy_intp dims[4] = { *$2, *$3, *$4 , *$5 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$1));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4,
+ DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+ */
+%typemap(in,numinputs=0)
+ (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DIM_TYPE* DIM3 , DIM_TYPE* DIM4 , DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+ (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp, DATA_TYPE* data_temp = NULL )
+{
+ $1 = &dim1_temp;
+ $2 = &dim2_temp;
+ $3 = &dim3_temp;
+ $4 = &dim4_temp;
+ $5 = &data_temp;
+}
+%typemap(argout,
+ fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+ (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+{
+ npy_intp dims[4] = { *$1, *$2, *$3 , *$4 };
+ PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$5));
+ PyArrayObject* array = (PyArrayObject*) obj;
+
+ if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+ PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+ PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+ PyArray_BASE(array) = cap;
+%#else
+ PyArray_SetBaseObject(array,cap);
+%#endif
+
+ $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/**************************************/
+/* In-Place Array Typemap - flattened */
+/**************************************/
+
+/* Typemap suite for (DATA_TYPE* INPLACE_ARRAY_FLAT, DIM_TYPE DIM_FLAT)
+ */
+%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
+ fragment="NumPy_Macros")
+ (DATA_TYPE* INPLACE_ARRAY_FLAT, DIM_TYPE DIM_FLAT)
+{
+ $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
+ DATA_TYPECODE);
+}
+%typemap(in,
+ fragment="NumPy_Fragments")
+ (DATA_TYPE* INPLACE_ARRAY_FLAT, DIM_TYPE DIM_FLAT)
+ (PyArrayObject* array=NULL, int i=1)
+{
+ array = obj_to_array_no_conversion($input, DATA_TYPECODE);
+ if (!array || !require_c_or_f_contiguous(array)
+ || !require_native(array)) SWIG_fail;
+ $1 = (DATA_TYPE*) array_data(array);
+ $2 = 1;
+ for (i=0; i < array_numdims(array); ++i) $2 *= array_size(array,i);
+}
+
+%enddef /* %numpy_typemaps() macro */
+/* *************************************************************** */
+
+/* Concrete instances of the %numpy_typemaps() macro: Each invocation
+ * below applies all of the typemaps above to the specified data type.
+ */
+%numpy_typemaps(signed char , NPY_BYTE , int)
+%numpy_typemaps(unsigned char , NPY_UBYTE , int)
+%numpy_typemaps(short , NPY_SHORT , int)
+%numpy_typemaps(unsigned short , NPY_USHORT , int)
+%numpy_typemaps(int , NPY_INT , int)
+%numpy_typemaps(unsigned int , NPY_UINT , int)
+%numpy_typemaps(long , NPY_LONG , int)
+%numpy_typemaps(unsigned long , NPY_ULONG , int)
+%numpy_typemaps(long long , NPY_LONGLONG , int)
+%numpy_typemaps(unsigned long long, NPY_ULONGLONG, int)
+%numpy_typemaps(float , NPY_FLOAT , int)
+%numpy_typemaps(double , NPY_DOUBLE , int)
+
+/* ***************************************************************
+ * The follow macro expansion does not work, because C++ bool is 4
+ * bytes and NPY_BOOL is 1 byte
+ *
+ * %numpy_typemaps(bool, NPY_BOOL, int)
+ */
+
+/* ***************************************************************
+ * On my Mac, I get the following warning for this macro expansion:
+ * 'swig/python detected a memory leak of type 'long double *', no destructor found.'
+ *
+ * %numpy_typemaps(long double, NPY_LONGDOUBLE, int)
+ */
+
+#ifdef __cplusplus
+
+%include <std_complex.i>
+
+%numpy_typemaps(std::complex<float>, NPY_CFLOAT , int)
+%numpy_typemaps(std::complex<double>, NPY_CDOUBLE, int)
+
+#endif
+
+#endif /* SWIGPYTHON */
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
new file mode 100644
index 0000000..605ff2b
--- /dev/null
+++ b/tests/CMakeLists.txt
@@ -0,0 +1,67 @@
+enable_testing()
+
+# pthread
+find_package(Threads)
+
+if (EXTENSIVE_TESTING)
+ add_definitions(-DEXTENSIVE_TESTING=1)
+endif()
+
+# gmock/gtest
+set(GMOCK_RootDir ${UNY_ThirdPartyDir}/gmock-1.7.0)
+set(GMOCK_IncludeDir ${GMOCK_RootDir})
+
+file(GLOB GMOCK_CC "${GMOCK_RootDir}/*.cc")
+file(GLOB_RECURSE GMOCK_H "${GMOCK_RootDir}/*.h")
+
+# Generate paths for test data
+configure_file(
+ ${UNY_TestsDir}/unit/TestData.h.in
+ ${CMAKE_BINARY_DIR}/generated/TestData.h
+)
+
+include_directories(SYSTEM
+ ${GMOCK_IncludeDir}
+ ${UNY_ThirdPartyDir}
+ ${UNY_IncludeDir}
+ ${CMAKE_BINARY_DIR}/generated
+ ${Boost_INCLUDE_DIRS}
+ ${ZLIB_INCLUDE_DIRS}
+ ${HTSLIB_INCLUDE_DIRS}
+ ${UNY_ThirdPartyDir}/seqan/include
+ ${CPPOPTPARSE_IncludeDir}
+ unit/
+ ${PacBioBAM_INCLUDE_DIRS}
+)
+
+file(GLOB UNY_TEST_CPP "unit/*.cpp")
+
+add_executable(test_unanimity EXCLUDE_FROM_ALL
+ ${UNY_TEST_CPP}
+ ${GMOCK_CC}
+ ${GMOCK_H}
+)
+
+target_link_libraries(test_unanimity
+ ${UNY_LIBRARIES}
+ ${CMAKE_THREAD_LIBS_INIT}
+ ${CMAKE_DL_LIBS}
+ ${ZLIB_LIBRARIES}
+)
+
+if(${ROOT_PROJECT_NAME} STREQUAL "UNANIMITY")
+ add_custom_target(check
+ COMMAND ${UNY_RootDir}/tools/check-formatting --all
+ COMMAND test_unanimity --gtest_output=xml:${CMAKE_BINARY_DIR}/uny-unit.xml
+ COMMAND __PBTEST_CCS_EXE=${CMAKE_BINARY_DIR}/ccs ${UNY_RootDir}/scripts/cram --xunit-file=${CMAKE_BINARY_DIR}/uny-cram.xml ${UNY_TestsDir}/cram/*.t
+ COMMAND __PBTEST_CCS_EXE=${CMAKE_BINARY_DIR}/ccs ${UNY_TestsDir}/python/test_tool_contract.py
+ DEPENDS ccs
+ WORKING_DIRECTORY ${UNY_RootDir})
+endif()
+
+# add_test(test test_unanimity)
+
+if(CMAKE_BUILD_TYPE STREQUAL "Debug" AND UNY_inc_coverage)
+ include(uny-codecoverage)
+ SETUP_TARGET_FOR_COVERAGE(coverage test_unanimity coverage)
+endif()
diff --git a/tests/cram/0passes.t b/tests/cram/0passes.t
new file mode 100644
index 0000000..270a9fc
--- /dev/null
+++ b/tests/cram/0passes.t
@@ -0,0 +1,11 @@
+
+Test doing 0-pass ccs on a subread from the lexogen-SIRV dataset
+
+ $ $__PBTEST_CCS_EXE --logLevel=DEBUG --minPasses=0 --minPredictedAccuracy=0.85 $TESTDIR/../data/0passes.bam test.fq
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- main -|- [0-9,a-f,x]+|| -|- Found consensus models for: (P6-C4, S/P1-C1) (re)
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- main -|- [0-9,a-f,x]+|| -|- Using consensus models for: (P6-C4) (re)
+ $ cat test.fq
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/170/ccs np:i:0 rq:f:0.877758
+ AGGAAACTCCCGCTCCACCCAGGACATGTAGAGAAAGATCATGCCCTCACCAGGAGATGGTAGATAAAGATCCGGGAAACGACCCTCCCTAAGGAAACGCTTTGCGACCTTTGTTCACCCACGAAAAGCGGTGACCGTAGTATCTCCTCTCAACGAGGCTGTGACTTCACATCCAACGATGAATTGCTACTGTGTCGGTTAAGACCACACAACGATTTGATATAGGTTGTGCTAGCTTCTACTTTGTCATGCTTCTCCAATCCTGTAAACATCCGCTTAAGATCGCAATATGCGGGATTAAAGCTGCTAGTTTCTATTGACCATAAACGTCGCGCTTTCCGCGTTGACATGGCTGAGACTAGCCATCCCTCCAGCCCGCTTCGTGACCCTTCCTAAAAAGATAGTGAGGTTCTGCCAGTGACAAGTTTCTCCATCTCAGCCTTCTAAGGGCGATCGCGTAGCTGATTTAGTAGACCGTTGTTACTTGCAT [...]
+ +
+ .(-'--)+&..*)+'.*&..+(-*)+,*++*+*'--*++)+,*&..+)+'.+(-+*+,(-++*++'--*++'-'-,'--)+*&..+&..,(-(-'--)*)(-,*)+*'.(-,*)-)*&..**+&---*)(-+**'.+++*+++)+'.+)+)(-*++(-),*+****-)+)++'.(-*++,*(-*-*),**,*+*+)(-)-(-**'.*)+)(-*++(-,*+++++(-*-*+*),+*)*-),**(-,*+)+,*)*-)+'.(-+'.,*+'--)++'.*)*-(-*++)*)(-++,*)'--+*-'--*),*),+*(-,),**-**'.++'--)++)*)*)(-,'.*)+*-**)+,(-),*+***,+*'.++&..+'.+*&..*)*-)++**&..),'.,&---,*+++*+*+(-)-),*'.+*+**)(-*(-,)+'.++)+)+*'.*-),(-'--)+++)*)+++*),*+(-,+*++**'.+*-*)-***-*)+, [...]
diff --git a/tests/cram/100zmws.t b/tests/cram/100zmws.t
new file mode 100644
index 0000000..77a8634
--- /dev/null
+++ b/tests/cram/100zmws.t
@@ -0,0 +1,411 @@
+
+Test ccs on 100 zmws from the lexogen-SIRV dataset
+
+ $ $__PBTEST_CCS_EXE --logLevel=DEBUG --minZScore -100 --maxDropFrac 0.8 $TESTDIR/../data/100zmws.bam test.fq
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- main -|- [0-9,a-f,x]+|| -|- Found consensus models for: (P6-C4, S/P1-C1) (re)
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- main -|- [0-9,a-f,x]+|| -|- Using consensus models for: (P6-C4) (re)
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- Consensus -|- [0-9,a-f,x]+|| -|- Skipping read m150825_055401_42161_c100844482550000001823159012311525_s1_p0/413/9570_12297, ALPHA/BETA MISMATCH (re)
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- Consensus -|- [0-9,a-f,x]+|| -|- Skipping read m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2359/6103_8488, ALPHA/BETA MISMATCH (re)
+ $ grep -c ^@ test.fq
+ 100
+ $ cat test.fq
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/170/ccs np:i:10 rq:f:0.999803
+ AAGCAGTGGTATCAACGCAGAGTACGGGAAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTT [...]
+ +
+ x~~~~~~l~~~~~u~~~~~~~~~~~\~~I~~~n~~m~i~m~~~~pp~~~~~~~%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~qn~~~~~~~~~~n~~~n~~{8~m{xR~V~~q~W~n~~~~Z~~~~k~~|j~[~~h~~~~o~o~~v~I~~~~~k~~t~^~~_~m~~~q~~~~~h~~~j~~~~~nwsR~~~~~~l<~m~~~o~M~~S~~~~~~~~~j~~~~~g~~~~~u~o[~~O~~~~hn~ms~rl~~~~r~_m~H~~~~~W~~~~r~~op~~o~\~~~~~\~~g~e~p~~a~~~~~~~~f~~~~~~~{~g~j~q{a~~]~~~~a~~~~~wy~~\~~~~q~~~~~y~~~o~~~sqc~y~~K~~~~~o~~~~~~~~V~|n~~g~~~y~~~~~~~t~|~~p~o~~~~b~~~~~~z~~~V~~~~{~~~~oYY~~~~u~~a~{~z~~~w~l~~~~~~~~~{~~~~~~x~~~~e~~e~~~~u~~O~~}~~~k~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/230/ccs np:i:12 rq:f:0.999378
+ AAGCAGTGGTATCAACGCAGAGTACGGGGATCCATTTTGGAGGGGTGGGGATTTGTTCAATGAATGAGGCAATAAACCACCGCAACCTCTGTAATTGACGAGAAACTTGTATAAGGTCATCAAAAAGAATAGATGAACATAAAGATTGAATACGGCTGGGTGAGGTTAATTCAGATTTCCCAAATTATGTAGATGAAAAGATGGTAAGTTTATTGATAGGTAAAAAATCAAGAGAGGGTAATAAAGAAGAAAGAATAATCAAAAGATAGAGCATGCAAACATTACATGGTAGTATTGTTATAGGCGGTATATTGGTAAATGACGATCCTTGACTTAGTTTTTTACATCGAACGGTTGCAAATCCTAGCATACTTGATATTAATAGTAGATACTGAAATATATCTGAGTATATCAAGGGAAATCGAGATGTAACAATAAGTCGAGGAAATTAAGGTCAATTTAGTGCTTATCATAGAAATAACTACTTAAG [...]
+ +
+ ]~~~~~~{~~~~~~~~~~~m~~~~~^~~~~~u~~k~~~y~~;~~~|I~~~~r~~~_~~~~~~~~~~~s~~~~~k~~[~~w~~~x~x~~~~~~~~~~~~~~~Yp~~~~~~~~~~~s~~~~~~)~~~~~z~~~r~~~~~x~~~~~~~~~~~~~~~h~~~Y~~~~~|~~~~~~~~~~~[~~'~~o~~~~w~~~~~~~~\~~~~~~T~~y~~W~~~~~~~~~U~~<~~~~~~~~~y~w~]~~~~~~c~~~w~~~~~~~~~z~~~I~~~v~~~}~~~~~~~s~~~~~~~~~~T~~~~~~~~wf~~~~v~{c~~~~~}~n~~~~~~r~c~~~m~~~~~~}~~k=~~~~~~~~~~~v~~A~~~~~a~~~d~~~~~~~~~~~~~~~~~~~~~g~~d~~~~~xQ~~~~~~~~~~~~~~~~~~u~Q~~g~~~~w~~~~~~~~~~~~~~~~~}~j~k~~~~~~n~~~~~n~~~~~f~~~~~~~~~|u~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/301/ccs np:i:12 rq:f:0.999668
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTGAAGTTCAATAACTTCGATGGTTACGTTGTCCTTAGTAACTGGGTTAATGACCTAATGACTGTCTCCCTATACGTCAAAATACTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATCTTCTTTAAGCTAACGATTAGGTTGTCCATTAGGTAACAATCACGGATAATAAGTGGCAGGACTACGTCAAGCAGGTAAACCCGCAAGGGCATAGTGTGCAAGTCCTTACTCAACCGTTTCGTTACGTTTTGCTTGGACACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTT [...]
+ +
+ K~r~~Xhc~}~~|y~~ft~y~~~~|&~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~g~}~~~~~tw~~g~p~~~~j~~~]~b~ee~V~~~N~~~~g~xxza~~c}~_~~~~~{~f~~~}~~~|~P9~~~~~~~~e~~~~~Z~~~qt~~e~v~j~~~~~~~~~~~ww~~R~~xe~~r~~k~~~|n~}~g~v~~~~y~~~u~zd~~~~~~~n~ttf~~m~~~~~~~~~}~~~~~u~k~|~v~~~~pR~~q~vw~zvJnZ~O~H~~oj~~b~~~s~z~~~~~~Vj~~~~r~~]~~W~~gz~~f~~Y~{~~~|kc~o~~~r~~~~~~_O~^~~X~~~tx~|~zG~~~z~{~j~~~~~h~~P~z~~~~~~~~~z~{|~~~yI~~~~K~~P~~I~~~~`~~~~~~|~~~~~~n~~~~~~~~~~~~~~~Vn~s~y~~~~~~\~~~~~~~j~~~~~~~~~g~~l,~~~~~~~}~|~~_~~~~qs~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/322/ccs np:i:16 rq:f:0.99988
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAG [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~o~~r~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~~S~~~~~~~~i~~Y~~~~~~~~~~~~~~~~~~~~~~~~W~~g~~~~~~~v~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~C~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~U~~~~~~~|~~~~~~f~~~~~~~~~~k~~~~O~~~~~~~~~~~~~~~~~~~~~~~~~~~Z~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/335/ccs np:i:18 rq:f:0.999746
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAATCGGTAGTATCTGCAGTCAAGTCGTAGTCGTAGGTATGGCACTTGTCGTGCGTCTAGGACGCGTTGAAGCTATCTTATTGCCCGAAGGAGCCGAAAGTCTGGGACACGTCGTGGGACGTATCGTTAGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAA [...]
+ +
+ ~~~~~~~l~~~~~~~~~~~~~~~~~Q~~~~y~~~~~~~|~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~}~~~~s~~~~~~~~~g~~~~~~~~~m~~}~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~~~~~~~~~~~~~~~~~~kw~~~~~~~~~~~~y~~y~~`~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~j~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~j~~~~~~g~~~~~~~~~~~~~~r~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/413/ccs np:i:12 rq:f:0.999906
+ AAGCAGTGGTATCAACGCAGAGTACGGGGATTGGATTAAAAAAGTTGTAGTAAACCACAACGAAGTTAGGTAGCTGGTAAGGTTATAGATGCGTTCTGTCGTTGTAGTCCCAATGAACATAGTATGGTTTCGCATAGTAACTGACCTAAAAGACCGCCACATAGTGAAAATACTTAAAACGCAAGTTTCATAGGATTAAGTGGTAGAGGCTATAGAAAATGATATCATAACTATAACGAATATAACAGCAAATTAAAATGCACTGGAAGTGGAAAATTTCAGCAAGAGAGTCGAAGTCGTCATAGATTAGCATGGACGAAAGAAAAGTCGCAAAGATCGGAAATCAAGACGCAAAACAAAACGGAGAAGTTCAAATCGAACTCGTAGAACATATCGCTGGAACATATTAAACTCTTGGTATCGCTCAGTTACAAAAGGAGACACGTAGACACGAAAGAAACTGGAACAACAGACATATTTGTGGATAATG [...]
+ +
+ ~~~~~~~b~~~~~~~sxw~~~b~~~T~~~~~~p~~~~D~~~~~~h~~~~t~\~~_~~u~~~~~~tx~~~~~~~~~q~~~~u~~~~~~~~~~~~~~~~~~~~q~~~d~~Y~~~~~~|~X~~~~^x~r~~~~~xy}~~~~]~~~r~m~~R~~~~~o~~X~}~zw~~~uX~~~~~~~~^~~~u~~~~~~~~~~~~v~~~~~~~~r~~~~~a~~~~~~z^~~~~~~~~~~~~~~~~~~o~~~z~~~~~~~~~~|~~~~]~~~~~~~~~x~~~~~p~c~~~o~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~e~~~~~~~~~~~~u~~~~~~b~~~~~~~~~~v~~e~~~~b~~~~~~~|~~~z~~`~~~~zA~~~~O~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~h~~~~~~c~~~~i~~}t~~~q~~~~|~~~~~~~~~~~S~~~Y~~~~~~~~S~~~~~~~~~~_~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/418/ccs np:i:10 rq:f:0.999163
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGTTT [...]
+ +
+ I~~}~~tX~~~~jf~|~k~|~~O~q'~~~~~~~~~~~~~~~~~~~~~~~~~idrv~c{mjY~h~~we}~dF~b~~i~@~x~~T~~~~~~m~~~tT~~~m~K~~I~`x~n~Y~~o~]~~~m~Y~~X~&~[[~~~q~~~l'~~~Z~ifN~dH~~~~~E~~~~~t~{~T~~~X~M~~i~z~~~m~~~d~}~z|k~~~MeH~~l~~Q~~~~~~~~;~wa~V~~@~~j~J~~~qq\~~~n~~~~~d~|~U~~~~~W~~y~T~ym~F~~~}c~j~^~~}~~~~pNV~Y~ob[~kV~~^q@~~~~~]~sX%Mk~~~%~oAmW[~zp~pdf~~:VYsW@}~~~f~~e}~~~k~l~n~n~i~f~L~\~~~~~~{O~~Z~S~~k~~~~~~~}~~~~X~~itbX~QU~wS~~j~j~~f~f|h~ukpii~b`g~~tphY~j~~bTp~~~~t~~k~~p~o~rn~~~s_~^~~ImU~rk~~_~i~~~^~n\h~f~qnoi]rE~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/420/ccs np:i:20 rq:f:0.999865
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCT [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~(~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~r~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~w~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/428/ccs np:i:16 rq:f:0.999632
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTA [...]
+ +
+ i~~d~~~b~~~[~}~~Vizw~~~~~M~~~~e~b~~~~~}F~~t~~v~D~~i~~~~zi~~s~r~~~H~~~~~~~~~~2~~~~~~~~f~r~o~~~~i~~~~~u~~u~~~~~~~~~~~b~~uuuz~~~U~~~~~~k~~~~~~s~~~~~~~~y~~m~~~~|r~~~~~~~~~~~~~x~~w~z~~~~~~~}~~uj~~j~~~z~~~\~~~~~~~~~~~~~X~~c~]~9~~~g~~~~~~~~~~~rj~~~~uv]~~~~~~~~~~~~~~~m~v~~~v~~~~~~~R~V~~akn~~w~~w^~~~~~~~~z~\~~~n~~~~~~~~~}~~~~~~~~b~~~~h~~~~Y~~~~~l~~y~~~~~~~~~~~ym~~~~~~}~~~}~~i}~~~~~p~x~~~~~~~~~~~t~~~~w~~nr~~~k~~~~~~z~~~v~~~~~uW~w~~~~~~~~~w~~{~~hW~^~~c~c~H~W}~~~~x~w~~r~~~~~p~~~j~|~~~~y~~M~~~m~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/429/ccs np:i:10 rq:f:0.999251
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAAT [...]
+ +
+ {~~~~~~o~~~~mk~n~~~yn~~~~b~~~~~z~~~~d^~~~{X~z~~~||z{~~o~z~~k~~~~|~~z~~~k~~~~~rQ~~~~]~~~~~~~~~o~~~~~~~U~l~Q~~~~|~~H~~~~~~]~~o~~~~~~~z~u~~~~~^~~}r~~~[~~~m~~U~~x~~~~~u~~~~~~~~~n~~~~~~~]~~~~~F~~~~l~~~~}~\~~x~X~~~~~~~e~o~~~~~~)~~~~~~g~{~D~~~~eW~~~~~~~~~~~~~~~~}~~~{~~~r~~z~{~m~v~~~~~y~`L~~w~~~_~~~~~~d~~~~~~x~C~~~~~~~J~j~v~~~~{~~~~~~j~~~d~~~~~n~~~~~v~~~j~~l~~~~r~~~\~~~p~~~~~~\~~~~~~N{lcm~o~~~o~~~~~~~~~f~~~~~|~~~c~~~~Z~zLy~~~~~~~~~~~]~w~~~~~~~D~~~~~~~~~m~~~~~~q~~y~~~|~~~~~w~~{~~~~~~~~~~~nuqz~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/456/ccs np:i:17 rq:f:0.999773
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGTTCCATGCGAATGTAAACGATTAGGCG [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~&~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~_~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~\~~~~~y~~~~~~~~~~~S~~~~~~~~~~~~~~~r~~~~~~~~~~~~i~~~~m~~~~~~~~~~~~\~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~y~~~~~~`~~~~~~~~~~~~~~j~~~~~~~~~~~~~~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~h~~~~~~~~~~~~~~~~|~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/578/ccs np:i:10 rq:f:0.999474
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGACAC [...]
+ +
+ _~~~~~~l~~~w~_~flU~~~_~~n9~~~~~ifn~{tM~|~ry~~~~r~H~~~~v~~a~~E~~~~d~[m~~e~~^~~~~~~Z~V~~X~j~nm~~q~~l~B~~V~~[~~`~~~~~z~{R~~~~s~h~~b~^~~~`~~~~[~d~~~~c~|g]zP|yQQ~y~\>~~~Y~~X~~l~~h~Y~~~~~V~~Z~~~G~~~~k~l~k}p~~e~~~B~,}j~k~~j~~J~~Y~[nRj~~N~~~~Z~|Q~~~~U~~-~~~Udizxh~g~~~~~~R~~~jU~|~~~Y~~~Y~~g~~~j}{x~g~~~VY~~~}nUj~~}M~~l~W~~~x~q~~~H~}?~~~qg~~q~~~l~~}Yy~~G~~eSkk~~S~?~{m~~~~I~~~}VU~~jeM~~~~k~|njT~j~~l{ehZ~~n~~T~p@~R~f~~~~zTm~G~~~}~~~~s~~~~~or~~~k~~U\~~j~~~~~f~~n~{~~-~~~~~~{P~~~~u~~~~a~~~~m~~~~~~~|~k [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/603/ccs np:i:12 rq:f:0.999894
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTAACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGAGATG [...]
+ +
+ ~~~~~~~~~~~~~\~~~~k~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~a~~~~i~~~~r~~{~~~~~~~~~~~~~~h~~~~~~~~~j~~~~~~~~~~|~~~d~~~~~~~~~~~~~~~~~~y~~~a~~~~x~~~~~e~~e~~~~~~~~~~~~y~~~g~~z~~~d~~~~}~~~~~~~~~~~~~~~~o~~~z~~~~~~~~y~~~~~~~~~~~r~~~~|~~m~~~u~~~~~~~~~~~~~~~~~~V~~~~~~~~~~~\~~~~~~~~s~x~~~~m~~~~~~~~~~~~~~~~v~~~~~~m~~~~~\~v~~~w~~~~~~~~ve~~~~~~~~~rs~~~~~~~~~~~T~~~~~~~u~~k~~~~i~~~~~~~}~~~~~v~~r~~~~~~~~~~~~{~~~~~~~~~~~`~~~w~~~J~~~~~~z~~m~~~~~~~~x~~{~`~~x~~~~~Q~~~~~~~p~~yb~~z~~Y~~u~c~~~~~~~~~~{~w~~~~~~~~q [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/624/ccs np:i:14 rq:f:0.999806
+ TGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAG [...]
+ +
+ ~^~~~~~~~~~~wh~~~~~b~~~~~~~~~~~~~~~~~~~~~_~~~~~~~~~~~~~~~~~u~~~~~~~~~~g~~~~~~~~s~~~~~~~~p~~~~~~~~~~~~~~~~~~~~p~~~~~x~~~h~~~~~~~~~~~~~U~~~~~~~~~~~~~r~~~~~~~~~t~~~~~~~~~~~~~m~~~~~~o~~~k~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~x~_~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~w~~l~~~~~~~~~~s~~~~~~~b~~~~~z~~~~~~~~~~~~~~~Q~~~~~~v~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~z~~~~~~~~~~~~~x~~~~~~n~~~~t~~~~{~~~~k~~~~~~~~~Z~~~~~~~~~~~m~~n~~r~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/657/ccs np:i:18 rq:f:0.999147
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGTTCCATGCGAATGTAAACGATTAGG [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y{~~h~~~~~~~~T~~~~~~~~~k~~~~~~~~~~~~~~~q~~w~~~~~~~~~~~~~~~~~~~~H~~~~~~~~u~~~~~~~L~~~~~~~~~~~T~~~~~~~~~~~~~~~~~s~~~~k~~~~~T~~~~z~~~~~~~~z~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ux~~~~~~|~~~~v~e~~~~~~~~~~~~~~%~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~u~~~~~x~~k~~~~m~~~~~~~~~~~~~~`~~M~~~~~~~~~~P~~~~y~~~~~~~x~~~~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~v~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/692/ccs np:i:14 rq:f:0.999458
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTATCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ h~~v~o~D~~~~~~~~~~~~~~~~x5~~~~l~g~k~~~~u~~v~~~~}~~~~l~G~~d~~~~~l~~h~~~y~|q~s~~~~~~~~~~~~~~_~~~~|c~~}Y~~~~F~~~~~~~~~{m~~~~~~~~~y~m~d~~~~~~~~~~m~~~q~m~~m~I~~~~~e~~j~ievqf~a~r~~~}~~~~~~~t~m~~~~~~~~~~a~~~~~W~~~~{~~~~~~~~~~~m~xh~~~z~~p~~n~~o~~~~~~~~~~m~~Wk~}~~r~~~~~n~~~J~~~T~{s~~~~n~~:~~~~~m~~v~~~~~j~~~o~~_~f~~z~~~~Q~wpi|~~~~~r~~o~u~~~~~b~~H~~[~~~s~~{~~~~~j~~~~u~i~~~d~~~~}~~~u~}~m~~~x~c~~~g~u~~y~m~p~T~~J~~~~~~~~}~~~~~~~a~~mk~~~~~_~~u~o~\~~~p~~~~~~~P~E~~~~~~~}p~q|~~~s~k~~~~~~~~~~~~~~i~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/705/ccs np:i:18 rq:f:0.999647
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTA [...]
+ +
+ ~~~u~~~o~~~~~~~h~~~~~~~~~F~~~~~~m~~~~~~~~~~~~~~m~~F~~~~~~~~~~~~~~U~~~~~~~~~~C~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~X~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~X~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~~~~~~~~U~~~~~~~~~~~~~~[~~~~a~~~~~~~~m~~~~~~~~~~~~X~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~h~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~|~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/734/ccs np:i:25 rq:f:0.99968
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAATCGGTAGTATCTGCAGTCAAGTCGTAGTCGTAGGTATGGCACTTGTCGTGCGTCTAGGACGCGTTGAAGCTATCTTATTGCCCGAAGGAGCCGAAAGTCTGGGACACGTCGTGGGACGTATCGTTAGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAGTAAGACTGTATCGGAGACGACTTTTTAATAGTAGTAATTCTCGGTACAACTAAACCAGTAATTTCAGACACTG [...]
+ +
+ ~~~~~~~d~~~~~~~~~~~~~~~~~c~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~]~~~~~~~~~~K~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~n~~~~~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/820/ccs np:i:20 rq:f:0.999826
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~[~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/822/ccs np:i:13 rq:f:0.999284
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGACAC [...]
+ +
+ (W]Kc3SR~}~~gE~fjiiDaW~~h2~~~~~~~V~Ejp~x~tb~[~~h~H~~~~~f~~~p0~~Tp{~~X~Xq~~6~~r~W~ZnN~~ITv~nV~:s^~_~]~@at~U~zY~~wWrWX_XW~~|TVP~~~mF~~|h~}n~M~Pp2T~j~j~kfZ}]~@~4~VC~~yP{~e~Flp~U~M~~~~~S~l:~~x9qd~m`~P~|Hw1tD~U~~~?~^~h_o^{ry~~R~~hbF~~=~~~~rj~N~~~|;~b~~Xnw9xa{cn}b~~~~|X~Xijq~{{eQ>~~~mt~:~~~}VmrfC~~jfR~v~~nZWr~~K~~kd@~J at e~[~j~L~kU~~~\M~~~~\~li~tWp[M3w~~j^~~~?~^H~hVu~~8~~~q~]~~~L2~~X~~~~uep~b~k~~x~~~~~~~^~~h~W~d~`~Qw~q~[~~~r|~Dzt~~r[~S~~~~R~~s|~~i~~~F~X~~mZg~~[~~~~~~rH~~~dG~}t~Y~v~~r~MI~em~~~s [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/873/ccs np:i:26 rq:f:0.999769
+ AAGCAGTGGTATCAACGCAGAGTACGGGAATCCGAAATCGAGATGGAGAGAAAGTTTGACTAAACTTTGTTACAGTATTTTTGAAGGCAATCAACCTGGAACTTTGGATTTCATCAAGTAAACACCCATATTTAGCGAAAATGCAAGCTAACTGCGAACTAACAAGGTAACTCTTTTTCGATTTCAAAATATGGTCAGTAGCAATATGTTAAGTGATCCATTTTGGAGGGGTGGGGATTTGTTCAATGAATGAGGCAATAAACCACCGCAACCTCTGTAATTGACGAGAAACTTGTATAAGGTCATCAAAAAGAATAGATGAACATAAAGATTGAATACGGCTGGGTGAGGTTAATTCAGATTTCCCAAATTATGTAGATGAAAAGATGGTAAGTTTATTGATAGGTAAAAAATCAAGAGAGGGTAATAAAGAAGAAAGAATAATCAAAAGATAGAGCATGCAAACATTACATGGTAGTATTGTTATAGG [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~X~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/938/ccs np:i:13 rq:f:0.999697
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACACTTATT [...]
+ +
+ z|w~~~~I~~~~~d~~~~~~~~~~~$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~klVL~~~~~~~~~t~~~~~r~~~h~~]~~~~q~u~~v~z~o~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~b~P~~R~~~~~~}~~~~~~~}~~~~c~~~~~~~{~~`~~~~~~bst`~~~]~U~~~~~|~~~~~~}~{Q~~~oK~r~~~WW~~~~ow~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~G~~~z~~~~~~~~~~~~~~~L~~~~~u~uw~~~~~~~~~{~M~~~~~~~~x~~~j~~`~~~~~e~\D~~~~~~~~~~~~~~~~~k~~zn~Y~~~~~~~yk~~\~~~~~j~~~~~~~~~~~~~u~~e~~~~~~~~~~~~~~~~~~h~~~~~d~~~~~~~~~P~~}~~v~~}~s~~~~~~~~~~~~~~~~~~~}}~J~~~~~~A~~~~~~|~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1034/ccs np:i:23 rq:f:0.999169
+ AAGCAGTGGTATCAACGCAGAGTACGGGATCGTGGCCCAGTCAGTGGATTACGTTGACCATGAGTCTGGCTGTTCTTGGTTCACCATTAGCTGTGGTGACAATAACGGGCATTGTGGCAACGATACGTCGTACTGCAAGTCCCACTGTAACTAAGACAATTCGGATTCGACCGATACTTGGTCTGGTTCGTTAACTTCGCGTACCTTCTGCTTTACCAGCAGGTCGTCAACGACGAGCCACCGTAACGAGTGTGGTTTCGGTTCGCTTGGTTGGGTGCCCAATTTCCAGTACCGAAGAGGTAATTGCAACTTCAATTGCTTAGTTGACGTGACCTTTCGGGTGTCATGGACTACCGACGGTATCTCATACGTGACCTCGTTGTTGACCTCGTTCTTCATCTGCACAGACTACAACGTTAGGACTACGGAACCAGTGTGAAGTTGACGGACGCGCTAGTTTACAGATGCGGTTTATTGGATTGGTTACAAC [...]
+ +
+ ~~~T~~~~~~~~~f~~~y~~~~~~~'~~~~~~~l~h~~~~~~~~~~~~~~~~~~~~~e~~~t~~~z~~~~~~~~~~~~~q~~~g~~~~~~~~~~q~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~q~~~~~~p~~~~~j~~~~p~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~0~~~s~~[~~~~~~~~~~~b~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e{~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~t~~~~~~~~f~~~~~~~~~~~~|~~~~~~~~~~~~~~~i~~~~~~~~~~~~s~~~~~~~~~~~~_~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1091/ccs np:i:12 rq:f:0.999764
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGTT [...]
+ +
+ ~~~~~~~Y~~~~~{~~~~~~~~~~~$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~l~~~~~T~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~l~~~~~~~~~~~\~~^~~~~~~~~~~~~P~~~~~~~~~~~~~~~M~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~?~~~~~~~~~~~~~~~~~~~~~c~~~~~S~~R~~~~~~~~~~m~~~~~^~~~~y~~~~Z~~~~~~~~z~~~~~~~~~~~~~~~~~~Z~~~~S~~~~~~~~~a~~~~d~~~~~~~~~~~~~}~v~~~~n~~~~~~~~~~~~~~~~~~~~}~~~w~~~~~~~~~~~~i~{~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~X~~R~~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~~~~|~~~~~~~Z~~~~~~~~~~~k~~~~~~~i~~~~~~~~~~~~~~~~~{~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1092/ccs np:i:21 rq:f:0.999645
+ AAGCAGTGGTATCAACGCAGAGTACGGGGATCGTGGCCCAGTCAGTGGATTACGTTGACCATGAGTCTGGCTGTTCTTGGTTCACCATTAGCTGTGGTGACAATAACGGGCATTGTGGCAACGATACGTCGTACTGCAAGTCCCACTGTAACTAAGACAATTCGGATTCGACCGATACTTGGTCTGGTTCGTTAACTTCGCGTACCTTCTGCTTTACCAGCAGGTCGTCAACGACGAGCCACCGTAACGAGTGTGGTTTCGGTTCGCTTGGTTGGGTGCCCAATTTCCAGTACCGAAGAGGTAATTGCAACTTCAATTGCTTAGTTGACGTGACCTTTCGGGTGTCATGGACTACCGACGGTATCTCATACGTGACCTCGTTGTTGACCTCGTTCTTCATCTGCACAGACTACAACGTTAGGACTACGGAACCAGTGTGAAGTTGACGGACGCGCTAGTTTACAGATGCGGTTTATTGGATTGGTTACAA [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~U~~~~~~~~~~*~~~~~~~~~~~~c~~~~~~~~p~~Y~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~x~w~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1133/ccs np:i:10 rq:f:0.999505
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTACCCTCTCTTGATTTTTTACCTATCAATAAACTTACCATCTTTTCATCTACATAATTTGGGAAATCTGAATTAACCTCACCCAGCCGTATTCAATCTTTATGTTCATCTATTCTTTTTGATGACCTTATACAAGTTTCTCGTCAATTACAGAGGTTGCGGTGGTTTATTGCCTCATTCATTGAACAAATCCCCACCCCTCCAAAATGGATCACTTAACATATTGCTACTGACCATATTTTGAAATCGAAAAAGAGTTACCTTGTTAGTTCGCAGTTAGCTTGCATTTTCGCTAAATATGGGTGTTTACTTGATGAAATCCAAAGTTCCAGGTTGATTGCCTTCAAAAATACTGTAACAAAGTTTAGTCAAACTTTCTCTCCATCTCGATTTCGGATTGTGATGAATATGAAACGTTAAATTGTGATTTTTTCATTTTC [...]
+ +
+ ~~q~~~~4~h~~~b~~ro~~~~~s~$~~~~~~~~~~~~~~~~~~~~~~~~~~~Q~~~~~jn~~~8~~~~~tf~ky~Zz~~a~~~p~i;~wzhO~~~~~~~~~p~Y{~W~~Z~~_~~~i~~Z~~~j~?~fj~\~~w~p~~~~x~~h~z_8~~~~~y~gtFa~~~~~D~~~~~|~~~v~m~~~~t~~xU~~Rx~~~ww~}~~~~z~u~~~wxq~~o~f~~_~~JW~g_~{~l|~~wm~uY~~~K~~~~E~~~~X~_~~~~M~gj~~~t~q~tm~~~~~xr~~~Z~u~~s~P~~~r_~~`~wA~~~~~~~s~~>~_~sx~~x@~~`oW^~~~x~g~~~~;~~~z{x~`~~~~~K~~~dF~~~dd~~~qzf~~v^~^~~~=~Y~~f~h~y~m~~`~c~~P~~~~is~~d~w~\?~~ww~~~z~~h~~ym~~~~~~l~~~~~qu~H~~~t~~r~r~^~~~u~~~~va~~~~y~\~~S~~~w~6~~~~~~~^~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1199/ccs np:i:20 rq:f:0.999746
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAATCGGTAGTATCTGCAGTCAAGTCGTAGTCGTAGGTATGGCACTTGTCGTGCGTCTAGGACGCGTTGAAGCTATCTTATTGCCCGAAGGAGCCGAAAGTCTGGGACACGTCGTGGGACGTATCGTTAGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAGTAAGACTGTATCGGAGACGACTTTTTAATAGTAGTAATTCTCGGTACAACTAAACCAGTAATTTCAGACACTG [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~u~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M~~~~~~~~~~~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1216/ccs np:i:23 rq:f:0.999443
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAAT [...]
+ +
+ ~~~~~~~~~~~~~[~~~~~~~~~~~>~~~~~~~.~~~~~~~~~~~~x~z~~~~~~~~h~~l~l~~~~~~~~~x~~~~~~~~~C~~~~~~~~~~~~~U~~~~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~t~~~c~~j_~~X~~~~~~~~~~~y~~~~~~~~~v~~m~~~L~~~~~~~~~~~~~~~~|~~~~~~u~~~~~~~~~~~~~~~~~{~~_~~~x~~~~~~t~~~~~~~y~~~~~~~~~~~~~~a~~~l~~~~~~q~~~~~~~~~~~~~~~~n~~~~[~~~~4x~~w~~~~~~~~~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~w~~~~~O~~~~~~~~~~x~~~~~~~~~~\~~~~~~~~~~~~~~n~y~~~~~~~~i~~~~|~~~~n~g~~]~~~~~~~~~~~~~~~~n~~m~~~j~~~~~~~~~~~~~~~~~~~~~I~t~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1226/ccs np:i:11 rq:f:0.998883
+ AACGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCAATCTGGCAGATTAGATACAGCTATAGAGCGAATCACACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACAT [...]
+ +
+ `:-)Td~~~~~D~n~{~~n~x}x$~~~~~~~~~~~~~~~~~~~~~~~~~pF;jq~}zpi~f~~km~il~T~q~rWXFz~t~~~t_~~d`({ngey~d~T~nm`zT~~~\~ua~~gJk~~~~.GB~~ogm_~t~Pg.Xtsd{~~g~U~o^~~~R~uk;F~zl~ppxwXWnU~Z~~~io~[~db~~rM{N~*~^~lG~|o]~~MJ~~Ko~t~J~w~ez~ag^jE~~~|~Y~~s~M~~gSn~{~tm~n~~~~e~v^o|qczr~_~~~~[q~z`~~~ia~~n~~S~L~l~t~m~~~soX~l~i~~~p~>~_~J~Z~~~j~~v~~~[~~X~uG~c|~kJVsrV}~glg6L:glVVzf~NP~~zU~~Rg~~{r}D]h~q\esb~w|j~gVMll~u~~]etCqtU~}~@|H~~I~~~~z^~~`\xgL~wt}~~~p~X~|b~f~~~l~qr~~~~~~i~~_~~H~~~~~[v~~~~~x|~e~s~vm~pO~S~m~`rrns~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1234/ccs np:i:10 rq:f:0.999644
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTGACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATCGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGAGATGGTTCG [...]
+ +
+ {~~~~~~j~~~~~y~~b~~~~~~~~(~~~~~~~~~~~~~~~~~~~~~~~~~~~k~|?~~~~m~~~~p~~~~~~~~~~~~l~~jp~}~~~d~~~~~~m~u~^~~~N~~~~~u~~~~~H~~}~~~A~~~h~~~~~~~~crc~~m~~~~y~|~o~~~~~~~W~~_~~~~~~~~S~~~~~~~^~~t~j~~~e~~~~~~~~~~~~t~~~~~Z~~~~~l~~~~R~~u~~~~~~~~~~~~~~~~~~~~~~N~~~~u~~g~~~~~~i~~o~~m~~~~q~i~~~~~~x~~~~~~~~~p~~~x~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~le~~~~~~~n~~n~~~~?~~~~~~~~~~~~~j~~R~~~~~~~~~~~~~j~~~p~~~~z~k~~~~~q~u~~~~~~~~~S~~~}~~~~~~~~~s~~m~~~~~Z~~S~~~~r~~kn~~~~~V~zJ~~~~~~^~}~~~~~w~~~~~~~~n~z~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1241/ccs np:i:17 rq:f:0.999516
+ AAGCAGTGGTATCAACGCAGAGTACGGGACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTACTAGTCTTCTCTGAGGAACCATGAGATGGATAGTGGGGGACCTGAGTCATACTAGGGTAACTTCTTATATGGTGACATCACTCCTACCGTAGAGGGGGACGGTAGTCTGTGGGAAATCTACCCTAGTGAAGAAAGGTAAGAGAATGTCTGAACATTACCTGTAGACGAAGGTACTCTCAGAACAACTACTCTCACATACGGAAAGGTTTGGGTCCTTGGTCAAAGGACTTTACTGACTCTGCAGACGATGAATATCTGAACCAACACTACTATCAAAGATGTTCGACTAGACCTCTCGTGGTAGGGCCTGGAAGTCAAAAGACTTCTCTATGGGTACTAGGTAGGTAGTTAGAGTACGGTCCCTG [...]
+ +
+ y~~~o~r|~~~~~w~u~_~~~~~~~L~~~k~~~~~~V~~~~~~~~~r~~~~~~}~~~~~~~~zn~~~~~~k~~~~~~~~~~~~~:~~~~~~~~~~~~~~zM~~~~~~~u~x~~|~~~}~~~~~~~~~~~~~p~~~~~~~~~x~q~~~~~~~~U~~~~s~E~~~~~v~~k~~~~~~~~~~y~~~~~~\~~|~~~~~~~~~~~~~~~}~X~~~~~~~~~~,~~~~~~~~~~~~~~~~n~~r~~~~~~]~~~~~~~|~~h~~~~~n~~x~~~~~~~~~f~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~m~q~~~~t~~f~~~z~~~~~~~j~~q~~~x~~~z~~~~~~~||~~~ja~~~~~~~~~~~~~VwK~~~~_~~~k~~h~~~~~~j~~~~~~~~~p~~~~~~~|~~~h~~~~}V~~~~~w@~~~~~~~~~~~~~~X~~~~~~~~~~s~~~~~~~~j~~~~~~~~j~~~4 [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1250/ccs np:i:10 rq:f:0.999746
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGGAGAAGCAAATACTTGGATACCGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCC [...]
+ +
+ x~|h~~|T~r]~L=~dcc~yx}~~}C~~~fd~byh~zAKj~v|~e~Y~|~~_~g@~\~~~vug~F~~c~T~w~~q`~O~~~~~~~~e~i~v\~|ypp~u~*~|yy~j}k~~~z:~~~~ae~cg~x~dh~}f}~h`zxax~~u~Rx~wu~~}E~n}|z{g~h~}~~4~~~~~z~fU~zyT~~R~~_~~~c~dx4~~~~S~~~~c~~~s~~~b~~~~~~~~~J~~~~e~~~~t~Z~E~~~~~E~~~vo~~~~[~~~~~~~~~~p~i~F~:~~~~|~~~c~X~~nill~~X~~v~~q^~~~~i~b~~e~~~~o~~~~o~~~q~~~~~~z~ok~~~~~~SwY~e~~h~~~b~~~~zcz~r~~~~~~~~|q~R~~~~~a~^~~I~~_~~q~p~~~~~~~~~~~~~k~X~~~~~Z~~~r~h~~~r~~r~~q~p^~~m~~[~~~~i~~~to~~~|~[~n~~~~~m~~~f~~~~~~~~~-~~~~~~ja~~~r~~~P~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1334/ccs np:i:19 rq:f:0.999331
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTATAAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTG [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~*~~~~~~~~~~~~~~~~~~~~~~~~~w;1H.~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S~~~~u~~~~~s~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~t~~y~~~~~~~~z~~~~~~~~~m~~~~~~t~~M~~~~~~~~~~~~~~~~~~~~~~~~u~~y~~~v~~~~~~m~~~~~~~~~~v~~~z~~~~~~~~~~~~~~~~~~~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~~]~~~~~~~~m~~~~~~~~~~~~~~}~~~~~~~~~~B~~~~U~~~~p~~~~d~~~~~~~~~~~v~~~~~]~~~~~~~q~~~~~~~~~~~~~} [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1378/ccs np:i:10 rq:f:0.999726
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAATGTTA [...]
+ +
+ ~~~mP~~s~~~~sb~~y~~~~~j~xQ~~~~~~tk~~~re~~a~~~~~U~~q~~~s~~~~~P~~Yv~~y~x~~~~7~~~~[~~~j~~~~jf~~~~~~~d~~~R~~~~o~~i~~~~~~~~~~~v~x~~~~~s~~~~~s~~~~~~~q~z~~t~W~~~~~~~]q~~~~~~~~~j~~~~^~~t~~~~xf~~~ms~~w~~^e~~~~`~~~~~~~`~W~~qq~~R~~~~u~~~GmH~~~~~r~~~~~e~v~b~s~~~~~~~~`~~ms~~tf_~~~d~t~w~~~~t~wv~~~~\~c~tsA~~~~~~~~y~~r~~~~?~q~o~~~~q~~~~~~T~~p`~~~~~W~~~}~~j~y~~y~~x~~\~~~f~~~A~d~~~~d~~~[s~~~u~~j~~~~J~~~t~x~~~R~~~~}~~X~V~~~~s~~~h~~~~~~~~~~~}~_~~~~~~~F~~~~~~~~q{~~~~~~]~~h~~~S~~~~~~~~~~~~Y~~~~~i~~~~~~~~H~n [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1407/ccs np:i:9 rq:f:0.998965
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGGAAACATTAAATCAAAGAAGTTTATCAACCAATTAGTACAGTGGCATGTTAAGTAAAACAGAAAGAACGCCAAGTGGCAACAAATGACGTAATTATTTAAGCAAAAAGCGTAAACGCTTACAAAGGCTATTTAAATATCAGTAAATCGTTGGAAATTGGGTATGTGCTGCCTTCATACGCAAAAATGGATGCGACAGAAACGAGTTGTATGGCCTCCACTACGCTCGCCTGCCGCGGACCCTAAACGACAGTCGTTTGCCCAACTACGGCTACGGCATCGCTCAGAACTTCGGGTCTTGGCCCACCTTTCTGACGCCTAGTCAACGTGCGTCGCCTCAGTCTTGGACAAAAAGAAGAAATATCAATTGCAAAAATAACTATAGGTACTTCTTTGAAGAAACCA [...]
+ +
+ ~~~~~w~h~wc~QU~~~~~zxz{~~J~~~z~~~~~{}h~~~~T~~d~~jW~~[~~s_r~~b~~~l~~~~~B~~~~~[m_~~~~~X~I~R~~~K\~P~~~~J~~~~~lm~~n~xi~o~n~{~~p~~n~j~i~~~hY~~i~X~O~~~~~RV~~lr~q~K~r~~~k~pk~~W~~~~~r~~|~o~l[~~Y~~oL~~~~~qilb~~]~qj~~~V~~c~1ylo~~[w~w~zjue`f~~~~~i~Z~J~~U^2~~vy~h~hl~zL~e~xb~~q{h@~~~~~O~{i~hfz|~wW~~q\ulh~~vz~Y~\~~@~vj~td{^mbh]~~?_~xs^~uG~~~I~~fgl;fao]d\~~{B~~u~b~wkI~jvaNe~~v~bxwl~{~w~}U~}G~~xhs~B~U~~~D~Qv~uxcsvwe~~rerfa~y\~?{{y~~M~peF_vJL~c~~{3~~~~ul~g\~~~rv{d{4~aeA~~~~yv~iyv~vU~wcgh~~D~~}Y~~_~~S~@ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1426/ccs np:i:13 rq:f:0.999505
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATTACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAA [...]
+ +
+ |~~O{~hf~~~~~Z~~~N~|~x~~~5~~iil~~K~~~~~~~~v~~~{~b~~e~~~~~T~~{Q,~r~~~~_}~l~~~~~h~~~^~~~~~~w~~~~~~o~~~~~~~~U~~~~t~~~@~~~~~k~~~~~~~u~~hk~l~~~~t~x~~~X~~s~~~~~~~~n{t~~~~~~~~~~o~~[~~~I~~~{~~~|~~~~\~~~g~~~~~~r~~~~~~~~~,~~~~~~fyB~~~r~~~~~~~V~W~a~AH~~~~~~~Yf~~~o~~~lt~~~t~~~~~~c~~v~~~~q~~~~~~~~W~~~qd~~~~~{~~~~~~~~N}k~~~~B~~w~j~^~~~~~}~~~~~~~~|z~~~~~~~L~~}~~~~~~~|~r~~~w~~~~~b~~~~z~~~~~~R~~~~~~~~~~~~~~z~~~{~:~~~~r~~\~~~~~~o~~~~j~~~~~~~~~u~~y~~vv~~s~~~y~~~~~~~~~~t~~Yz~~~~~~t~~~~}~~[~~~s~~]v~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1446/ccs np:i:13 rq:f:0.999412
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTAC [...]
+ +
+ ~~~~~~~A~~~~y^~~~~xd~~~kzR~~~TL~~~E~~~W~~~t~~g~n~Y~~<~~~~~]~~e~~~P~wb~r~z~u~~~~~~~~j~]~~|Q{P~~~V~~~~J~~~~~tm}~Sq~d~~er~~~~~t~X~~~~~~~ijsB~~~k~xj~~~4~~~~{b~~d~e~~|~~}~d~~zk~~q~{~oI~i~~~]P~~Wl~e~~V~~~~l~~~~~~s~v{\~f~~~|~a~~~~|~^~p~}~j{d~~~~~6~ylg~mb~~~~ur~l~~~~fuJxj]z\~Z~~H~eoiO~~R~~vqf8~~e~v~T{g~~~J~~f~A~~~zk~zn~wy~d~X~|x~~~~~e~~[~~L~l5~~D~~iX~~]~x~xi\~y~|u~U~~~X~ypzx~~~~~~~S~~z~xN~O~M~~~~~~o~~~~\~<~~~~~~~~}{~~~{~~k~~~h~~~~cJ~~v~~~@~~~v~~w~~~~s~S~~~~x~~e~e~~~v~d~~~~~~f~m~~~~g~~q~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1448/ccs np:i:9 rq:f:0.999135
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTGCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGTTTA [...]
+ +
+ X~sY~~{X~~j~~[~k~k~~eg~~u'~~~~~~~~~~~~~~~~~~~~~~~~yf~`y^w~~~~~]~~o~~q~\~Tq~vyc~~~~m~m~~~~h~~~~l~~~~~X~~l~~~~~~i~pY~m~|y|~e~Xj~W~~h~jbjx]wwVa{W~~~P~bn~~u~t&~~~~~~~~[~h~~dH~W~~k~~~~~{~~~e~~~~o~~n~~~DqRA~r?~~~~~h~~`~~i~m~~Z~Xk~A~~~~~Y~~n~s~~|yn~r|&~~~~~C~~QjX~TRlH~~~~p~l~O~~~~}z~~>J~b~j|>~wA~w~~\~~l|xa{k~m~~~~l~~}~|c~~~~~|x~~l~r~~=~~~~~x~}xafrg~{nniw~C~~jl~h~~h~zz^V~~D~d~~~~m\=l}haX`~~B~~~~~r~~}~~S~~~~n~~7~k~~~~~g|i~~~~~~~~l~~~~~_Jq~~~~~~~f~~~~~x~Z~~~uP~j~~~]c~b^~~~~n~~~~^vq~wt~s_~~~~t~~g [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1454/ccs np:i:19 rq:f:0.999761
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGCTATCCTGAGGTGCCAGGTTAGAATAGGCCCTACCACATCTAAGCCTTGAAACGGTCTGTTCCTCGTGTCAAGTTCTTTGTCCGCTTATACCGCCATCTCTCGTTGTGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCA [...]
+ +
+ ~~~[~~~~~~~~~~~~~~~~~~~~~d~~~~~~~sv~~~~~~~6~~~~~~p~~l~~~~~^~~y~~~~~~~~~~~~~~~~~~~~~~~m~~~~~[~~~}~~~~C~~~~~~~~~~l~~s~~~~~~~~~~|~~~~~~~~~~~~~~~~s~~~~X~~~~~~~~q~~~~~~~~~r~~~~~~2~~~~t~f~~~~~~~~~~~~~`~~~~~~~~~~~~~~~~~d~~~~~a~~~~~~L~p~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~s~~~~~~f~~b~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~u~~~~~n~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~}~~~~~|~~~W~~~j~~~~~~~~~~e~~~~~w~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1470/ccs np:i:16 rq:f:0.999804
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGT [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~_~~t~~~~~~~~~~~~D~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~_~~~~~~~~~~~~~~~~3~~~~n~~~~~~~~~~~~~~~~~~~r~~~~~y~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~j~~~~~~~~~~`~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~y~~~~~~~~~]~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1511/ccs np:i:18 rq:f:0.999715
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATAAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTA [...]
+ +
+ ~~~~~~~t~~~~~~~~~~~~~~~~~)~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~z~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~b~~~~~~~~C~~~~~~l~~~~~~~~~~~~~~~~~~~z~tJ~~~~^~~~~~~~~~}~~~k~~~~~~]~~m~~~~~~~~~~~~~|~~~~~~~~~~{~~n~~~~~~~~~~|~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~~~~s~~~~~~~~z~~~~~~~~~^~P~~~~~~~~~~~Xv~~~h~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~z~~~~~~~~~~~~~~~~~~~S~}~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~a~~~~~~~~~~s~~~~~~~~~~v~~~~M~~~~~~~~~g~~~~~~~x~~~~~~~~~D~~~~~~~~~~~~~o~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1512/ccs np:i:19 rq:f:0.999939
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGT [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~~~~~~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1549/ccs np:i:12 rq:f:0.999659
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACACTTAT [...]
+ +
+ u~~y~~~o~~~~~w~~qu~p~~rY~(~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}wO~f|~~~~\~~~~~~~`~~~g~~l~~~x~~~~vt~~~~w]nS~q~b~~~~w~~~~~|q~~c~~cu~z~>~~~`~y~~~x~{O~i~~~~~~c~~^~~~~~~~\~r~w:~~xm~~~e~~x~~~~s~ox~~~~~~~Q~~mr~d~~~~r~~u~~~~o[~QPz~~~f~~xw~~~~~an~~~~w~~~{~|~yu~~~~~~~S~z~C~v~~~~~j~~~?~~~~~G~a~~~p~T~wi~~~z~~~~[~~~~~~q~os~o\~~~~z_~i~~v~~~~~N~~~m~yo~~~v~McxV~~~~~q~~~~~wc\i~~R~~{v~N~~K~~~gg~~~V~~t~~e~~j\q~.~~w~~{~{~Q~~[~j~~~e~{wx~~~~~c~~~~~d~~~~~~~~~~|wv~~f~~q~R~~[~_~l~~~~~~~~~t_wry~R~~t~R]D~~~~~u~m~c~~n [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1608/ccs np:i:19 rq:f:0.999663
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAAAGAAGCGAAACGGCATTCGTTTAACAAAACGTCACATA [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~;~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1630/ccs np:i:12 rq:f:0.999673
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ ~~uv~~~m~~~~by~qb~~~~{~~~7~~~~~~l~~~~~~x~~~~~~~~~~~~~~F~~D~~~~~a~~_~~{~~~y~~~~~~~~~~~~~~~~a~~~~d\~~~V~~~~H~~~~~~~~~~~~~~~u~~~~~~~~k~~~~~~~~~~l~~~j~^~~~~Y~~~~~~~~z~~~~z~~~~i~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~m~~s~~~~~~w~~~~~~~~~~~~~~~Q`~~~~~{~~~~y~~~~~~~~~}~~~~m~~~~~}~~~c~~~z~~~~_~~c~~c~~e~vv~~~~y~~~p~~~j~~m~z~~T~~~~~~~~~~~l~~~~|~r~~~~l~~l~~Y~~\~~~~~~~~~~~~~~x~~~~L~~~u~~~~d~~~~~~~m~~~~~z~~~^~t~~z~d~~~~~zG~~~~~~~~~~~~~~~~l~~~i~~~~~Y~~~~~~p~~~o~~~~~~~P~`~~~~~~~~~~~Y~~~w~~~~~~~~~~~~j~~~@~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1649/ccs np:i:11 rq:f:0.999385
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGCTATCCTGAGGTGCCAGGTTAGAATAGGCCCTACCACATCTAAGCCTTGAAACGGTCTGTTCCTCGTGTCAAGTTCTTTGTCCGCTTATACCGCCATCTCTCGTTGTGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCA [...]
+ +
+ t~lnb~~6~~~~ng~~oT~os~~~xLn~~~N~~~n~~~|~~~U~~~~l~F~~H~~~{dW~~]~~sR~~v~Z~v~~~zr~~~r~~~O~~~y~h~~th~~j~J~~~~~~~q~~c~~d~~x~r~~sk~g~~o~~~~~~~p~~tD~~~~~~J~~~~~t~~\~x\~v~pu~`~`k~a~V~vwvz~i~~~~~tnp~y\~~D~~~~~~|}c~qk~~~{~B~~~`[e~~~~~~h~@~p~k~U~m~~jE~~~e~~h~~~~~k~o~~~~p~l~|~~f~~~~k~~~X~~m~x~~o~~~~j~C~~~~j~~~~~~~~~~i~w~~W~~~X~~r~~~~h~~|pho~~M~fz~~r~~p~k~~~h~~~pc~~l~~~qt~~~~~~~~n~~~Vv~~~~f~`~[~~~~~~t~m~\~~~{~A~~=~~~i~~~~~y^}y|~~~~~~^~uO~~~~~b~~~p5_~~~~q~~{p~~~~n~~~~~k~c}A~~~_~bz~y~~o~~[~~{~~K~~g~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1688/ccs np:i:15 rq:f:0.999468
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTA [...]
+ +
+ r~~~~~gk~~~~~p~~~~~~~~~~~k~~~~~~o~~~~~~t~~p~~e~~~~s~~~~~~~~|~~~m~N~~~j}~~~~~I~~~~~~~~~~~~~~y~~w~~Y,~m~~~~y~~r~~~~~~\~~~~~j~~~i~~w~~~|~~~~~~P~~~~~e~~~~vz~f~~~L~~~~}M~~~~~~~~~~~~x4~~~~~~~~~~i~~b~~~~~~m~q~~~~~~~~~~~~Z~~|~t~a~~~V~~~E~~z~~~~~~~~~~~~c~~~~~~o~~~~~~~~~~g~~~~~~~~~~~u~~~~w~~~}~~~~~~~~~~~~~~~{~~~w~{~~~~m~~i~~~~~~~~~~~~~~~~q~d~~~~~}~~~~~~~~~]~~~~~u~~k~~~}~~~~~p~~~~~]~~~b~~~~~~~~~~~i~~~~e~~i~~u~g~~~~~~J~~~~~~~~~~f~q~~~~~~~~~~~~N~~~~~{~~~~}~~~~~~~~~n~d~~~~~~~~p~_~~~~~~m~X~~l~~~o~]~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1757/ccs np:i:12 rq:f:0.999781
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGACAC [...]
+ +
+ ~~~~~~~q~~~~~~~~~~oi~`~~~R~~~~~~~~~[~O~~~~~~~~~~~k~~~~~~~~~~[~~~~u~~}~~r~~Y~~~~~~k~w~~}~~~~@~~~}~P~y~~m~~U~~X~~~~~~~~9~~~~~~@~~~~b~~k|~~~~l~v~~~~~~~~~~~~~~q~~~~V~~~{~~y~~f~~r~^~~~~~i~~l~~~K~~~~{~o{X~h~~`~~~~~g~~~~]~~~~j~~m~~_~~~~X~~~~{~~T~~~~Z~~W~~~~p~p~~~~m~~~nWh~l~Z~~o~~~*~~~~~~c~~~n~n~~k~~~~~~~~~~~y~~~M~~~~f~~~~~~~~~i~~[~~~~{~~~~~~~~~~6~~~j~~~~~~~~w~Wc~r~~~~e~~~~~u~~~nx~~c~~~~~~|~Q~~~~~~~~~~~~_~~l~Y~s~~~~m~~~[~~~~~~~~~~~~~~~z~~~v~Y~~~~l~~~~}o~~~r{~~_~~~~~~~V~~~~g~~~~~~~~~K~~~~~~~s~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1800/ccs np:i:16 rq:f:0.999483
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACA [...]
+ +
+ ~~~~~~~W~~~~~|~~~qy~~o~~~.~~~z`~?~jm~ug~~~u^~`b~~~f~F~~X~~~~}~}~~r~~z~~~p~~~s{~b~~i~R~~~~}~~~~~~~{~~~~D~~~]~~~~I~~w~~~~~|A~~~~q~S~~y~~n~~~eh~~~~~~~~o~~~~~~n~~~~~~~~k~~~~g~v~~n~~~yc~~{~~~~~J~~~~~z~~~|~a~~w~H~~~{~~~K~c~~~k~~R~~~z~~~~~~-~~~~~~n~~~Z~~~txx~~~~~b~d~~Z~~~S~~fp_~~~a~x~{~\~lv~U<~~~~~zZ~~~@~~Y~~~~~~~~~|~z~~~q~~g~~~W~~}~~~=~~~~~j~~~N~~~~}B\~~~~vy~c~~;~~hY~~~l~~~|~~\~sx~z~~~a~d~~~~~c~~~~~e~~~m~~|~~~~~~N~~~~w~~c~~~~~~~~~~x~`~~~~~~~~vS~~~~v~~~df~m~dA~X~~C~~~k~~z~~~~~E~rrx~~~~~~~y~f~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1860/ccs np:i:28 rq:f:0.999702
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAAAGAAGCGAAACGGCATTCGTTTAACAAAACGTCACAT [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~S~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~b~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1902/ccs np:i:9 rq:f:0.9991
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTAAGTTTATTGATAGGTAAAAAATCAAGAGAGGGTAATAAAGAAGAAAGAATAATCAAAAGATAGAGCATGCAAACATTACATGGTAGTATTGTTATAGGCGGTATATTGGTAAATGACGATCCTTGACTTAGTTTTTTACATCGAACGGTTGCAAATCCTAGCATACTTGATATTAATAGTAGATACTGAAATATATCTGAGTATATCAAGGGAAATCGAGATGTAACAATAAGTCGAGGAAATTAAGGTCAATTTAGTGCTTATCATAGAAATAACTACTTAAGCCCTTAACGAACTAACTCAAATTAACGAGGTAGAGGTTATTCTGAATTGTACGAACGTAGTCGAAGTTTGTTACCAAGGGTAAAGCCAAAACAAAACGATTTGACAAGAGAATCTATTCCATGTAGTAGTGCGTTTGTACGACGTTCTATTCGATGTAAATCATTAGGACGAGGG [...]
+ +
+ ~~l~~~}1~vaVYd~~~k~e~gsdi*~~~zz~~4~~~g~~zs~j~~9~~~~~~~e~~{t~[~~~UoBN~~ee~iX~~ja~\b~z~/~~~yuw~~~~~w~Wj]~~~~u~~~~~g~|~~~~[~}d~^~~W~gE~_~~~M~]~~\~~{5~~u~~`~~~~~~k~~o@~~~~~v~~~~~}~th~]~pqF~~nr~~~r`~~xon~~~s~I~q~~~~~~r~n~~~~e~~~~~~~l~nRnm~~~~~_~T~~d~~~~>wo~}~~m~~~~lm~~~r~~H~J~~X~e~r~p~~~q~~~~~~~~~~~~~~~~`~~~Z~~~~qn~Y~~W~~~~9~~t~~r~Z~~~~P~~p~n~~~~G~~~t~]~Q~wf~~~~^~~~p~~~~_~~~~~q~Xii~tY~~cU~~m~t~D~~Zi~~~n~S~~~~R~~~~lj?~~~~~}~r|~Q~~~~~q~n~~~w~kakeo~~~~P~~~}f~Y}~~~~~~~e~~~~~~~d~~~~~u~~q~~~~~R~| [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1945/ccs np:i:27 rq:f:0.999884
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTGGTTCGTACAGCGGTAAATGACTTGTTGAGTCTTGACGTCGACGACCAAAGCGACCACTTTGACCCAATTGCGAACTACTAAATCCTAAGCAAAGACTATTAGGTAGTAGCCAACTTCGTTAATTCCGTTCAGTACTTTTAAATTCTAACCGACCATCTTTCCGAGTTGCTTCAAACCCTCGTCCTAATGATTTACATCGAATAGAACGTCGTACAAACGCACTACTACATGGAATAGATTCTCTTGTCAAATCGTTTTGTTTTGGCTTTACCCTTGGTAACAAACTTCGACTACGTTCGTACAATTCAGAATAACCTCTACCTCGTTAATTTGAGTTAGTTCGTTAAGGGCTTAAGTAGTTATTTCTATGATAAGCACTAAATTGACCTTAATTTCCTCGACTTATTGTTACATCTCGATTTCCCTTGATAT [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1948/ccs np:i:17 rq:f:0.999487
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ ~~~~~~~k~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~}~p~~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~s~~~d~~~~=~~~~~~~~~j~~~~~p~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~J~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~y~~~b~_~~~~~~~~~~~~~k~~~~~~~~~~~~u~~~~~~~~y~~~~~d~f~~~~~~~~~~~~~~w~~~{~~~~~~~~~~~~~~s~~~~~~~~s~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~]~~~~~}~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~Z~~~~~~~~~k~~t~~~~~_~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~~~~<~~~|~~~~~~~~~F~~~~~~~~~~~j~~~~~~~~~}~~~io~~o~~t~~~~x~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1960/ccs np:i:12 rq:f:0.999478
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTTAGTTGAAATAGTTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACA [...]
+ +
+ j~~~~~~z~{~~k`~~~~Gu~yRS~G~~~~~T~f~~~k~~~~L~x1s~lfpH~y0~@dl~~~~}J~~~~t~~~~b~~~b~~~~F~~~tvt~~~m~ta~~~~~~f~_~~~~a~~d~~~~~zp~~~~~~~a~~~~k~~~~~x~~~~~~v{~~~~~~R~~~~x~~cT~~~~~~q~~'~~~~~T~~~~~~~~*~~~~~~~~~~~~o~~~~K~~~~~~~~~n~~yg~~\~~~~w~~~~~N~~~~~x~~~~~y~~~~~~~~~~~_~~~~~~l~l~~e~~~c~~~~~~~ng~~~~~~~~~~~~~H~~~~u~~o|~~~~~~~~~o~~~~\w[~~~~~~5~~vb~~~~Z.~~~~~~~~q~~~y~q~~D~~~.~~~~~E~~~~`~~~~~~~~~~r~~~s~b~~~j~~|~~~~~~e~~~o~_~~~~_~~~{~kxi~~~~~~~v~~~~~~~~zd~~~~~}a~uu~~~~~~S~~O~~~~~~~~~q~~}~~~y~~~z~~~|~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1991/ccs np:i:16 rq:f:0.999913
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGCCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACACTTATTATG [...]
+ +
+ ~~~~~~~N~~~~~~~~~~~~~~~~~*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~{v~~~~~~~~~~~~~~~\~~~~~~~~~~~~~~~~~~~~~Y~k~e~~~~~~~~~~~~~~~~~~~x~~j~~~]~~~r~~~~~~~~~~~~~~~~~~x~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~]~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1999/ccs np:i:10 rq:f:0.999526
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCCTGAGACTATATCATACAAAATTGACCCAAATAATAAACTCGTTCCAATAGTTGAAGTGTTGATTAACACATTGAGACAAGTTGTCCGTACTTTAATCATCAAAGTTTTGGACTGACCTATAAATGAAATATTCGCGTTGTCTTCAGTTTAAGAAGTGATATTATTTTCGGTTTCAAGCCTATGTGGAGAGATACAGGAAATAGGTAAACTATAACTAATATAAATATACGCAGACGAAGCCTGTTAACTTTACCAAATCCAAATAGCGGGAGAC [...]
+ +
+ r~~~~~~`~~~~~~~~~s~~~~~~~d~~~~m~~~~d~~~~~~~~v~~~~~~~~ji~~~~~~q~e~2~~r~~~Y~~~~~~~~~~~~~~~h~~~~U~~~~~|~~~~~~~\~~~~~~|~~_~~~~~~r~~~P~~~~~G~~~~~~~~v~~~k~~~~~~~~_~~~~~~~y~~~ov~~~y~h~v~~~j~~~~~~~m~~~~~~~a~~~~~~~u~u~~~~~U~~~~~~~~~j~~~~~~~~M~~~~~~~`~~f~~~~~ce~~q~~~~~`~~~~~~b~|\~~~lt~~~}~_~~~~~t~~~~~~j~p~~f~~~~~~~R~~~~~~~Z~q~~~F~~~o~~~~~~j~~~~W~~~~k~~~p~~v~~~U~~~~U~~~~W~~p~~j~~p~~~~n~~@~~~~|~h~~~s~~~~~k~~~f~|G~w~~~n~`~A~~~~~~~U~~~|~~~~~~~~~~~{~~~~~~~s~~~~~~~~~o~~[^~~~~s~~~~~p~~~z~l~~~~~~P~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2012/ccs np:i:11 rq:f:0.999194
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGCTATCCTGAGGTGCCAGGTTAGAATAGGCCCTACCACATCTAAGCCTTGAAACGGTCTGTTCCTCGTGTCAAGTTCTTGTCCGCTTATACCGCCATCTCTCGTTGTGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAA [...]
+ +
+ a~~p~~~q~~~~~k~~~mg~~~~i~C~~~~~~\~]~~~lg~~n{r@~n~`~~I~~~|u^~~[~~uK~~L~d~,~~`dgIi~~i~~P~~~~yG~~zh~~~~S~~~~~~~~~~e~~x~yy~~~~~~~x~a~~~~~~~~\~~~x~z~~~~N~~~~~w~~u~zv~~~~~~w~b~~~~v~~~~~~u~~~~~~|~[~~~~D~~~~~~~~{~~~~~~w~C~~~}~l~~~~~~F~~~x~T~V~~v~~f~~~~d~s~~~~~e~c~~~~tn~e~~~y~~~~Q~~yq~ue~~~~~r~`~u~T~~~~y~~~~~~~~~~u~P~tQ~~xc~~~~up~i~n~~~~~cs~uy~j(~o~P~~oa~~~~e~~h~~~~~~~~~v~y~r~~~w~~~~~b~_~u~~~~~~~~~~a~~~b~X~~_~~~~~~|~~~~~~s~x~~~~n~sb~~~~~x~~}~w~~zd~u~~~~~zo~e~~~~~r~~~O~~~\~~~~v~~g~~i~~~~zn~~x~r~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2091/ccs np:i:24 rq:f:0.999763
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTAAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCT [...]
+ +
+ W~~~~~~~~~~~~~~~~~~~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~j~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2097/ccs np:i:10 rq:f:0.999633
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGACCGAAGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAA [...]
+ +
+ ~~~~~~~u~~~~|m~~~bzp~~~~~@~~~~~~S~~~~~f~~~~~~~~~~~~}~|~~p~W~~z~z~~~~iO~~~~~~~e~~~~~d~~~~~~r~Z~~Z~m~fg~~~~~h~w~}f~~x~}s~~~z~~ssP~~~~~xS~~~~f~~eN~y~~Q~t~~~~x~~~~~z~Vkc~~~~S~~~x~~\~~[~~[~M~~~y~\~vc~~~l~~~~T~_~~~eg~i~~~A~u~~~~~~x~~}~~v~~{~u~~@~~~~~~hd~~~~>~~osnwby~u~xws~~~}~{r~~~~x~i~~w?~~~~~~`~~~}~~~~r~}a\t~{~i~~D~~~^~~~~S~~~~jl~h~v~~U~~~ec~~~~~~z|~^:~~~V~~~\z~~~t~~~~m~~~~W~~~}~q~~~~j~~Up~~{~d`~Y~w}~y~~~~~~~N~~g~i~L~e~fq~q~>~~sd}~~~~~z~w~~c~~~_~~~w~~t~~{v~n~~~~~~wW~~~~~~uX~~~~~~~~~}~~~uw~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2126/ccs np:i:23 rq:f:0.999895
+ AAGCAGTGGTATCAACGCAGAGTACGGGAGACCAGTAGTTGGGTCAGAAATTAGACGTGGTTTAGTCTGGTTACCGTGGAAAGAATAGCTGAACTCAAAGAAGCCGACAAAGATAAACAAAGAAGAAACGGTTAATACGATTGAGGAGAAATATTCAATCCAACGGCAACTATTAACGTTTCAACTAGAATCTACGTTTCATACGCGGATTCCACATCCGTTCTTGCAATTAAAGAAACGATGTAGAAAACGCTTTGGTTGGCGACAACTTGGGCGGCAAAATAATTATGGTAGGTAATTGAAGTAGCGTTAAAACGCAAAAAGAAGGAAGCACGGATCACTGCAAAAAGGACTACTCAATAATGGTTTCTAAAGTCATTATGCTGGTGCTCCCTATGGCGGTGGTCAGTACTGTAACTAAAGATGGATTACGGCACTTGTAGAGCACGTATCAGACCCAGCTTTGAAAGAAGGCTGAGTTCGGTTCGGG [...]
+ +
+ 0~~~~~~~~~~~~~~~w~~~~~~~~e~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~~~~w~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~y~~~m~~~~~~~~~~~~~~~~~~t~~~~~~~~~~p~~~~b~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~c~~~m~~~~~~~~~~m~~~~~y]~~j~~~~~{~~~~~~~~]~~~h~~w~~~~~~~~~~}~~~z~~~~~~~~~~~~~~~~~O~~~~~tj~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~|~~y~~~~~~`~~~~i~~~~~~~~t~~~~~p~~~~~y~~{~~a~~v~~~~~~~~C~~~u~~~~~f~~~~~~d~o~r~~~~~~~~~~~~~~~x~~~p~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~U~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2164/ccs np:i:14 rq:f:0.999337
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTAATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGAGATG [...]
+ +
+ ~~~~~~~~~~}~~_~~~o~~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~u~f~~~~~~~~~~~~~~~~~~~~~~~~~~yq~~~~~~~~y~~~~y~~~~~z~~~~~~~et~~~~~~~~~~~~~~~~~g~~~~~~~d~~~~~~~~~~~~j~~~~~~~~~~~~~~i~x~~;~~~o~~~~~~~~~~~~~z~~~~m~~~~~~~~~~~g~~~~~~~~~~~~~~~>~~~~~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~y~~~~~q~~~~~yt~~~~~~~~~~~~~~~\~~~~~~~f~~~~~~~b~~~~(~~~~~~~~~j~~~~~~~~~}~~~~~~f~~~~~m~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~vy~~~~~~l~~~~~X~~x~~~~~~p~~~~~x~h~~~~~~j~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2225/ccs np:i:12 rq:f:0.999347
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAG [...]
+ +
+ ~~~~~~~|~~~~n~~~~o~~~~~~~%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~|~~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~~x~~~~~s~~o~w~~~~~~~~a~~~~~~~~~~~c~~~~n~q~~~M~~~~Z~esw~~~~~~a~~~~~~~~~~~~~s~~~~~~~~_~~~~~~~~~~~~~~~~~~~~~~~~~R~~P~~~~~~~~~~~~~i~~r~~~~~~~s~~Z~~~M~~~n~~k~J~}~m~~~~?~~~~~~~~~~~~~~~~~~~~~k~~c~~~~~s~~~~~~~u~x~~~~w~~~~~~y~m~~~~~v~e~~~{~~~~u~~tj~x~~~~~~~~~~~~~~o~f~~\~~~~~c~~~e~~~~~~i~n~~{m~~~~~~~~v~~~~wc~~~~~~~~s~~~h~~~~~~~~e~g~~~~~~y~~yc~~~~\~~~~_~~~~~~w~~~~~~~~c~~~~~~H~~~~~~Vb~~U~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2255/ccs np:i:29 rq:f:0.999957
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAAT [...]
+ +
+ ~~~~~~~~~~~~~R~~~~~~~~~~~x~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~_~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2286/ccs np:i:14 rq:f:0.999842
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACG [...]
+ +
+ ~~~~~~~{~~~~~^~~~~~~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~n~~~~~~~]~~~~~~~~~~~y~~~~~~~~~~~i~~~~~o~~p~~~~~~|~~~~~~~~~~k~~o~c~~~~~~~~{~~k~~i~~~v~~~~~~~~1~~~~~~~n~x~p~Q~N~~\~~~~~~~~~~~~~~~~~~~~~~~~w~~\~~~~~~~~g~~O~~~~~~~~~h~~~~~U~~~pp~~~~~~~~F~~t~~o~~tpX~~~~Y~~~~l~~~o~~~~~~~~~~~p~~~p~~S~~~{L~~~~~~~~~Y~~~~e~~~~~~~~~~~~~~sd~Q~~O~~~~~~~~puz~~~~~~~~~~~~~k~~~~~~~s~~~~c~Y~~~~~~~~~~~~~~~s~~~~~~~~~~~w~~~~m~~[~~~~~~~~~}~~~~~~~~~~~~~~zu~~~~r~~~p~~~~~~~j~n~~Q~s~~~~Q~~n~~j~l~~~~~~~~~h~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2295/ccs np:i:8 rq:f:0.998774
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTCTGGCAGATTAGATACAGCTATAGAGCGAATCACCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACAC [...]
+ +
+ q~m\~of[~~kjl4o`ptqpob~Zc$~~~~~~~}|~~~~okn{~~}ot~~~}}tgWhW~[~pns~O~q_~~~[~Bbc~~mFl[s\i~lt~N~mkX}i_L~n~\qro_~tp_~uP~~>r^~p@[p~p~qq^On~o~^~q~~t]~~~rl;~~^~r^?~brG~~rR~tu~~rH~b~B~~~]nn\~s9~~`]dmoU~]~q5~~qa~~pn~[raoa}VokWl~~~pqo(~tt_qO~ts~\~i}ksjzrnt~h~te~`~}]nI~q~v~a~~sm^o^r@~zjaL~~]~tp~c~~rM~shvyts\~~sp~tjor_~K~o~m~qruo~n}tj~qm^~~taJflrnn~kR~~okz8cY~~XZ~r~4\~_}Y~~a~~spB\oZ[~pdrud~rl~~mqZRm~L~~oYlU~~U~~~ln\~~c~~sttS~~mk~s[~pfV~Mq_tR~~Y~YolqQ~lmJ~[\k~I~~s~rE~~~|clpF]o~\t~ua~tnVQ~tp~O~o~~t~r [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2305/ccs np:i:22 rq:f:0.999665
+ AAGCAGTGGTATCAACGCAGAGTACGGGACGGTCGTACTAAAATCAGCTACGCGATCGCCGACTTAGAAGGCTGAGATGGAGAAACTTGTCTACTGGCAGACCTCACTATCTTTTAGGAAGGTCACGAAGCGGCTGGAGTGATGGCTAGTCTCAGCCACTGTCAACGGGAAGCGCGACGTTTATGGTCAATATAAACTAGCAGTTTAATCCGTATGGCGATCTTAGCGGATGTTACAGGATGGAGAAGATGACAAAGTAGAAGCTAGACAACTATATCAAATCGTTGTGTGGTCTTAAACCGACACAGTAGCATTCATCGTTGGATGTGGAAGGTCACAGCCTCGTTGGAGGAGATACTACGGTCCCGCTTTTCGTGGGTGACAAAGGTCGCAAAGGTTTCCTTAGGGAGGTCGTTTCCCGGATCTTTATCTACATCTCCTGGGTGAAGGGGATGATCTTTCTCTACATGTCCTGGGTGGAGGGGAGTTT [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~z~~~~~~~~~~~~~~~~~~~~~~l~~s~~~~~~}~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2319/ccs np:i:21 rq:f:0.999835
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAG [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~O~~~~~~~~~~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~jl~~~~~~~~v~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~l~~~~~~~~~~~~~~_~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~e~~~~~~~~~~~~~~~~~~~~~b~~~~~^~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2333/ccs np:i:11 rq:f:0.999423
+ AAGCAGTGGTATCAACGCAGAGTACGGGGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCCTGAGACTATATCATACAAAATTGAC [...]
+ +
+ ~~~~t~~Z~~~o~t~~~~~~~~~~~O~~~^~h~~~~~w~d~~~~l~}~q~I~T~~~~~y~~t~g~~y~>~~~~~~C~~~~~~~y~~~~e~~~~~{~W}~~~~~~~~~~~w~~~~~~~~~~~~~ar~^~n~}sw|K~~~~~H~~~~~~~~~~~~[~~~~~^~~~f~~~I~~~~g~~x~s~~t~~e~l~~f~~}~~~R~}tvY~~X~xV{~J~~~~~e~~~~N~~~q~~c~z~z~~~~o~~~f~j~~~~~~~~M~~~~~~~~~~~~~~~~~u~~~~f~~|~f~~~~R~u~~t~~~~~~~~~~~~z~~~~~~{~~~~p~~S~~~h~~~~~kn~v|k~~~~s~~~~W~~~~~h~U~~y~~x~~~~~~~~~~~~~~~~~~}~]~~~~~b~~~~~j~~~~~~e~~~~~~~~e~~|~~~n~~~~~~~~~~~}~~~~~~~~~~~~~~~m~~~~~X~~~mp~~n~~~g{~~k~~~~~l~~~~~o~~~q~j`~~~~~v~S [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2334/ccs np:i:21 rq:f:0.999733
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGGAGAAGCAAATACTTGGATACCGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCC [...]
+ +
+ ~~~~~~~~~~~~~m~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~\~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Z~~~~~~~~~~~~~~~~~~}~~~~~~~g~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2359/ccs np:i:15 rq:f:0.999424
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGTAGCATAGCAACTGTTCTGAATGTGATATTCGGTCAGGCCACGTTGACACTTACCAAAGCAAGACAGAAGGAAGTTGACGGGACAATAGGGAAGATTGGCAAAGGGATTTAAACATAGTCCAGTTCGCGTGGTGAATGACAGATTGCTACTGTTACCATTGGCGATACTACGTTGGCGACTTTACTTGCCTCGGTAGCGACAGAACAAGTGTCGTCTACGCAACGAACAACCAGCGTGTTAGCTGCAATGTCCCCTGTAGAAGACCCTCTTCTTTCTCTTCTGAATGATGTAGCTGTGGATAGAGCGTCTCCCACGTTAGGGTCTAGCAACCCTCCGGTGGTGTGTGGTTTCGGTTCGCTTGGTTGGGTGCCCAATTTCCAGTACCGAAGAGGTAATTGCAACTTCAATTGCTTAGTTGACGTGACCTTTCGGGTGTCATGGACTACCGACGGTATCTC [...]
+ +
+ ~~~~~~~c~~~~~~~~~~~~~~~~~n~~~~>~~~~~~~~~~~~~~.~~~xp~~~~~~~~]~34~~~~~~~~~~~y~~~~~~~~~p~I~~~~Q~~~~~~q~k~w~~~~Mn~a~~o~X~~~e~~~~~~~~n~~s~~?~~~a~~R~~W~~~~~p~~~t~~~~~n~~~|~~~s~~~v~Y~n~~~~~~H~~~~p~~~~~~~~~~~n~~~~~~~~~~~~~~~\~~~~~~~~~W~~~~~~~t~~~~~~~~q~~~u~~bw~~~~H~t~~~~~~i~~~~~u~x2p~~~~y~d~~~~~~~x~~~~~~~~~d~~g~~~~~~~~~~e~~~~~j~~s~~~~k~~~~~~~~~~~~Q~~~~~~~~f~~~~~~~~~~x~~y~~u~~`~~~~~~~~T~~~~~~~~~~~~p~~~n~~Xzt~~~~V~~z~~~~~~~~L~~~v~~~~w~j~~~~~~~~~~~~~n~~~W~~~~~~~~~~V~~}|~~~|lY~~i~~~~~r~~~~~~\s`~b~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2409/ccs np:i:12 rq:f:0.999732
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTGTTCC [...]
+ +
+ t~~~~~~}~~~~~~~}~~~~~~~~~(~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~w~~~~z~~~~~~~~~~~~~~~~~~~i~~~~~o~~~~~~~~~~~x~~Y~~~~~~~U~~~~W~~~~~~~~~~`~~~~~~c~~~~~~~~~~~~f~~f~~~~w~~~~~~~m~~~{~S~~~~~~b~~Q~~~~w~~~~~~~~y~~~~~~~~l}Y~~W~~~z~~~~~~_~\~~~~~~~~x~~~p~~~~{~~~~~~~~~~~~W~~y~~i~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~S~~~m~~~~k~~~x~~~~~~~~~~~~~~~~~~q~~e~~~~~~~~~Q~~~~~~|~J~~~o~~~~~~~~~~~~~~x~~~~l~h~`~~~~~~~~~~}~~~z~~~~~~o~~~b~~~~)~~~~~~~~~~z~~~~~~~~~~~z~~~~~I~~~~p~~|~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2417/ccs np:i:12 rq:f:0.999393
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGGAGAAGCAAATACTTGGATACCGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCC [...]
+ +
+ ~~~~w~~~~~f~~[~~~~~N~~~~~b~~~~c~~~~~~ve~~~~~q~~~~~~n~[~~b~~~~~Y~{~~~~^~r~~mo~U~~~~m~~~~~~~~R~~~~~~~~c~~~z~~~o~~~~~~~~~~~~~t~~~~~~~~~~~Y~~~u~~m~~~~~~~~~A~~~~~x~~~~~~~S~~~~~~|~~~f~w~~~~~L~~~n~~~F~~~~q~~~~~~~~~~~~Q~~~y~~~~~H~~~~e~~k~~~~~9~~~~~i~~~~~~~}~~~~~~r~~y~~l~~~w~M~~~~~~~~m~~}~~~~~~~~~~q~~~p~~~~y~y~~n~~~~z~~~~c~~~~~~~b~~|~~r~~~~~r~~~~l~~u~~~|~~~~~~x~~~~~~~~d~~~~H~~~~~~~|~~~~~d~~~_~~~~~~~y~~~~~~x~o~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~x~y~~f~~~~~~~~~~~~~~~~H~~~~~~~~~~~~~~~]~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2436/ccs np:i:14 rq:f:0.999194
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGCCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACACTTATTATG [...]
+ +
+ ~~Mjk~~Z~~S[~~~~~~~u~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~nice~~~pfl~]z6~~~e~|~~~}~~P~~o~j~~~~}~}~~~~p^~w~O~it~p]~~}~yr~~W~sqm~s~\~~~S~q~~~~S~Fw=~|frXa^~~?~~~~~~~~~r~tk~~\TM~~w~~~f~2~q~~St`~~u~~e~~d~~p~~~~T~~g~~~~~~N~o~~fms~~~k~~X~~~v~~~~~~~~~~~~vu~~k~~w~<~~zm~~~~~~~j~F~v~~~Z~}~lom~k~UjSp~\y~~u~wW~~~w~~L~uh~{Y~~~~~{~i~~hwr~~ow~~~S~~F~~~v~~~x~~~f~Wc~~i~~~~~~{~f~K~|~j~~w~~~}~~~~_~~~ShO~~~~~~~~[rrTHR~~k~~~~{~~~m~~~~~~~~~u~~i~~1~~~iq~~~:o{~~~Wv~~~~~~my~_~~~~~~}~~~~~~~~o~J~~f~~X<~~~~~~v~uf~wj~~~W [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2451/ccs np:i:17 rq:f:0.999748
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ j~~~~~~|~~~~~~~~~~~~~~~~~\~~~~~~v~~~~~~~~~~~~~~~~~~~~~]~~a~~~~~z~~w~~~~~~w~f~~~~~~~~~~~~~~t~~t~~X~~~~~~~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~[~~~~~~~~~~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~j~~~~~~~[~~~~~h~~E~~~~~~~~~~~~~~~~~~~~s~~r~~~~~{~~~~~~~~|~~~~~y~q~~~~~~~~~~~~L~~~~~~~~~~~y~~e~~~~~~~~t~r~~~~~~~p~~~~t~~k~~~~|~~~~~~~~~~~~~~~u~~~~~~~~x~~~~~~s~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~[~~~~~~~~~d~~~~~~p~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~b~~~v~~~~~~~e~K~~~~~~~~~~~~~~~~~~~~~g~q~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2472/ccs np:i:11 rq:f:0.999706
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGCAATCTGGCAGATTAGATACAGCTATAGAGCGAATCACCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGG [...]
+ +
+ ~~~~~~~W~~~}lE~~~~~~~~~~~$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\\~~t~~~~p~Z~~~~~~~~~~~~~~~}~~~~~~~~~~~~]~~~~~~~z~~~~~~~~~~~~~~^~~~~~~~~~q~~~~~x~~~q~m~~~~~r~~~~~k~~~~~~Z~~~~~~~~~p~~~~~un~p~~~~~~~~~~~~~Zo~~n~Z~~k~~~o~~~b~~~~~~~b~Z~r~~~~~~]~~~~~r~~~~e~~~~~~~~k~~~~~~~~~~~~p~~~~~}~~~~~~~~b~~~~~~~~~~q~~~~~r~~~~~~~~~~~~~~~~oO~~~t~~~~~~]~~~~~~~~\~~~~~~U~~~~~~~~~~~r~e~~k~~~~~~~~~^~~|~~~~~~~~~~~~~~~~~~~~~~~~~YZ~~~~~O~~l~n~p~~~~u~~~~~v~~~~~~o~~x~~h~m~l~~`~~~~~~~~~~~~j~~R~~~~~M~~~~q~~~q~~o~~~~~~~~~~[~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2614/ccs np:i:12 rq:f:0.999667
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGAGA [...]
+ +
+ ~~~~~~~k~~~~O~~ts~~o~~tjr'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ah{~~hg~k[~l~~~~~~~~~~~~m~~s~~~~~~X~~Yk~~~r~~w~~~_~~~o~~~~r~~n~~o~~~U~~q[~~~~~Y~~oq~~~x~~r~~~}{n~~~~~g~X~~@~~~~~~~~W~~~~~~~~~~~~s~~pU~~~~z~~~Sr~oS~~k~~~~s~~~[~~yqx~~y~~t\~}}p~~~~~u~~o~~~~~n~~~~~~~~~p~~~~~~~f~~Z~uo~~~x~~~~~~d~r~~~~~~~~fp~s~~z~~{~~V~~~~~j~p~q~~h|mI~~~~~t~s~~~~l~c~wv~n~~X~~~~y~^k~~X~~~t=~~~~~~~~~l~r~G~~h~~~~~~~~~~~~~X~~~W~Z~~U~j~~r|~\~m~~~~~~~~sj~~pe~~s~~~t~~Y~~~~~~~~X~~~~~t~g~~~l~~~~~]~~<~[~e~~Y~W~~~d~x~~~~~k~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2616/ccs np:i:12 rq:f:0.999335
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCAC [...]
+ +
+ ~~~~~~~~~~~~p`~~~~~~~~~~~(~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~u~~~~~u~~u~^~~~~~~~~~~~y~~~pz~~~~~~}~~~~~q~~O~~~~~~v~~~~n~~~~~r~~~~[~~~~~~~~~~do~~d~~~X~~~~~~~vV~~~~~~~t~y~~ro~K~~y~~~~~~~~~n~~~~~~~~~~~~~zl~~r~~~~~~~~~~~~~~~~Y~~~~G~~~~tn~~~~m~~~~~~~~q~~~~~^~~~~x~~~~W~~~~q~~~~~~~~~~~~~~~~~~~e~~^~~~~t~~y~~~~~~~~~~~}~~~~~~~~~~~~~~~v~~~~.~~~~~~~~~~~~y~~~~~~~y~~~{~d~~~~o~~`~~a~c~~~~~~~~~~~~~~~c~~~~~~~~~~~f~~~~p~~i~~~x~~~c~n~z}rZ~y~~}~c~~~~~yV~`wn~_~~J~t~va~g~4P~E~~ztm~g`~~k~C~~~~xy~~~~~~~~~s [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2628/ccs np:i:26 rq:f:0.999813
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTACAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTGTT [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~X~~~~~i~~~~~~~~~~~~~~~6~~~~~~~~~~~~~i~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~{~r~~L~~~~~~~~~~~~~~~~~~~~~~~~l~~r~~~^~~|~~~i~|~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~^~~:~~~~~~~~~~~~~~~~~~~~~~~~K~}~~~~~~~b~~~~~~~~~~~~c~~~~~~~~~~~~~~~~|~~~~v~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~{~~~~~~~~~~~~~~o~~~~~~~_~~~~~~}~~~~~~~~~~~~~~~Z~~~~O~~~~l~~~~~~~~~~~c~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2648/ccs np:i:18 rq:f:0.999804
+ AAGCAGTGGTATCAACGCAGAGTACGGGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGGTCTTCTAGCGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGT [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~s~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~~~~~~~~~~z~~~|~~~~~~~l~~~~~~~P~~q~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~M~~~]~~~~y~~~~~~~~~~~~~~~~~~~~z~~y~~~~~~~~~~~~~~~~~~b~~~~u~~~~~~_~~~~z~~~~~~n~~~~~~o~~~~~~~~~~~~~~6~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~Q~~~~~~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~u~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~V~~~~c~~~~~~~i~~b~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2673/ccs np:i:12 rq:f:0.999393
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTA [...]
+ +
+ ~~~~~~~>~~~~~c~~~~~~~~~~~m~~~~~~t~~~~~~Y~~e~~~~y~~^~~q~~i~~W~~~~yj~~~~~~~~~~V~~~~~~~~~~|~~~T~~~~~~~~~~~~~P~~~~~~~~~w~~~~~s~~~[~~W~j~~~~~~~~~~~~~~~~~~~~~~}~~~m~~~~~~~~~{n~~~~~~~~q~~~~~~{~~~o~~~~~~Y~~~~~~~~~~~~~~~~~d~~z~~~b~~~~~~~~~~Q~~~~~~~~c~~~A~~~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~~~u~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~d~~~~~`~~~~8~~~~rZ~~~~o~~~~~~~~~~K~~e~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~p~~h`~~~~~~w~~~~~~~~~uV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~v~~~]~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2729/ccs np:i:10 rq:f:0.999539
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGACAC [...]
+ +
+ w~nr}ZdG~~~~pa~~o~~\~^Ri~?~~~~~|~~~~~~~w~y~~~~~r~O~~~~~Z~q~~Q~~~~M~~p~pw~jP~~m~~~s~j~~k~{~~_~~~gs]zo~EW~~k~o]~~~~~~~~S~~~~plF~~~sM~~~n~~v~b~o~p~~p~~~~~~~rTo~~~uZ~~~\~~m~vt~~s~U~~c~~t~pM~~~d~h~~]~nm~spr~p~~~w~m~~~t[~~~v~~kk~~knn~jG~~~~~~wc~~l~r~~~~~~u{ag}T~ob~~~~~m~o|Y~~n~`~O~~|Dt~\~~~~~sm~o~~~~o~~}~~~A~~~L~~~iH~~~~~q~~~a~~O~~~~_~~o~~x~w~~V~~~N~~l~~n~}`~n~~[~~k~H~~~~~c~~~pp~r[~~~~~vZ~h~v~w~~~~~~~~S~~V~~~s~\~ss~}~R~~~~{d~~~~~trgqo~q~q~~q3~eZ~~~~|a~~]~N~~S~~~~~~u%~~qu~~jo~~~o~~}~p~~~~~~~i [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2771/ccs np:i:11 rq:f:0.998887
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ q~Vd~}~c~~h~~`~~~~|T~~~Ys)~~~~~P~q~H~~~N~U~{~~~~k~U~~A~~~~~t~~~~~z{~~>~x~~~~~~~{~~~~~~e~~~~~Z~~~E~~~~N~~~~~~q~~~~~~~~~~~~~~x~vl~~~~~~~~~~X~~~~~~~v~~M~~~~~~~~~~~~~~~~~~p~~pq~~]~~~~v~i~~Ur~~~G~~Z~~Z~~~~~~~~~~~t~~~~~/~~y}im~~~~~~T~~~~~~~X~vs~~S~~~~~~u~~~~gx~e~~~~~~~~~1~~~w~~~~~~f~~~b~~~~~n~~~~~~l~\~~~n~~~~T~~~v~~~~~~~`i~~~~~~~~~~x~~~~~Y~~_~~~~~~~~~~~~~~~~~~~~~~i~~~a~~~~c~~~~~~~B~~~~|D~~~x~x~~~~r~~~p~t0~~~~zut~^~~~~~~~A~~{k~~~~~E~~~~~~g~~~~~~~~~~~F~Z~~~~~~~~|~{x~i~x~~~|~g~~~~~~~~~~o~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2772/ccs np:i:11 rq:f:0.999401
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAAT [...]
+ +
+ 3~~h~})[~p~~~_~~~~jy~~~o~A~~~~~~~F~~~~~~~y~~f~b}B~~J~~l~~j~v~~j~~f~~~~~~M~~~~~X~~~?~~~~~~k~~~~~~i~~~pr~~~]~~r~m~~~g~~~|~~~~~~o~~~~~~~~.~~~v~~~~~~V~~u~~~~~~~~~~q~xj~~~n~~~l~~a~}~P~~~g~~~p~sw~e~~~u~~~~b~4~~~wX~~~~~~~~~~jx~~~_f~~~~~~~~~i~~~~s~wep~~~~~~~~~^~~n~~~~w~~~~~~m~kG~~~~~~~Rp~~~~V~]s~6~Q4e~i~~b~~~~~~~~W{~~s~~~~~uj~~~~~bw\~~~~~~~\~~~l~p~~~~~o~~~~~~~~iv~~i~~~~~~q~~~YQ~~~~~u~]~~~~~~~~~~x=P~o~<~l~~~~q~~~~r~~~tz~9~~{~~~~r~~v~o~~myq~y~}O~~~o~~:~~~mq{~~~~~~j~~x~~i~y~~~`~{~|~x~~~q~rM~~u~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2774/ccs np:i:22 rq:f:0.999941
+ AAGCAGTGGTATCAACGCAGAGTACGGGAGGAAGGTCACGAAGCGGCTGGAGTGATGGCTAGTCTCAGCCACTGTCAACGGGAAGCGCGACGTTTATGGTCAATATAAACTAGCAGTTTAATCCGTATGGCGATCTTAGCGGATGTTACAGGATGGAGAAGATGACAAAGTAGAAGCTAGACAACTATATCAAATCGTTGTGTGGTCTTAAACCGACACAGTAGCATTCATCGTTGGATGTGGAAGGTCACAGCCTCGTTGGAGGAGATACTACGGTCCCGCTTTTCGTGGGTGACAAAGGTCGCAAAGGTTTCCTTAGGGAGGTCGTTTCCCGGATCTTTATCTACATCTCCTGGGTGAAGGGGATGATCTTTCTCTACATGTCCTGGGTGGAGGGGAGTTTCCTTGTATGGGTGGAACCCAACCCGCCGGTGAGGGTGAGTTACGGTCGGCGGTCATATGTGGGTATGACGGGTATGACGTCATAAAT [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2786/ccs np:i:12 rq:f:0.999144
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCAC [...]
+ +
+ ~~}~~~~`~~~~bW~d~y~x~~~~h%~~~~~~~~~~~~~~~~~~~~~~~~~~~~*~~~~~~~~~~~o~~~vt~~xrzc~~~~~t~N~~~~~~t~~~~q~z~|~~e~~~~i~p~~~H~~c~~}~~~j~~~~p~~{P~o~~~~N~~~~_i~~~~~t~{e~~~W~~~~~~~v8~~~~~u~~~j~~wx~S~~]~~~~~{~~pH~~~~~^~~~~z~~vE~~m~~~~x{~~n~~p~~~~H~h\~L~~~~hd~~d~e~~~~~~~~[~~s~~d~~e~l~~stQ~~~hl~~~v~~~~xW~x~z~Q~~~k~~`~~~~]~~d~s~~s~[~_r~[~~l~i|~~v~qj~o~c~k~w){~~~~~|~]~m~^~o~~~~~X~~}I~m~~u~ncvk~u5~_~~gt~n~~~~~n~~~a~~~~~R~~L~~^~~s~Z~~M~c~s~s|~~~~~~~~~~~~f~m~~q~g~_~~~~zb~~R~r~~>~~~}b~em~~]G~jY~~K~I~~qzd~f [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2802/ccs np:i:27 rq:f:0.999848
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTAC [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~U~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2877/ccs np:i:22 rq:f:0.999657
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGTTCCATGCGAATGTAAACGATTAGGCG [...]
+ +
+ ~~~~~~~~~~~~~h~~~~~~~~~~~(~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~B~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~x~~~~~N~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~U~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~_~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2884/ccs np:i:21 rq:f:0.999944
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTG [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~,~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~J~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Z~~~~~~~~~~~~~~~~~~~~~~~~~~~j~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2899/ccs np:i:11 rq:f:0.999514
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAAT [...]
+ +
+ ~~~a~~`p~~~~dp~~~u~~~w~~|=~~~X~a~~x~}S~~kke~`v~~t}~M~~U~|A~z~v~nF~~~r`~o~lu~~~a~~~~m~~~~~~wu~s~ms\~r~\~r~X~~~~G~~i~~~~~oI~~~~r~M~}~^~f~~\~r~~~~~~p~a~rb~~c_~~~s\~~~r~l~b~u{~yS~~g|k|YS~~~~o@~~]~~~~~~~~N~~~~U~~~sh~~NoH~~~j~~Y~~~ts~~~p~3~~~~~`~~~~~~~~r\]o~aqi|z~e~~~~Q~~}~^~~~q~}~w~^yoa~~w~tkx~~m~~_a~~b~~~~~o~~~i~~~{~l~~rV~vo~~~~~~N~~vq~~~~cT~~}~~pm~b~~~p~`~~T~~~_~~~[~n~~~tp~~~s~~[w~~~~~~~mI~~~~o~~~~~~~~~r~~]~8~~~rR~~iq~|~x~~~~~~~o~t~~~x~~wY~~~~w~\~~b~~~~~la~~o~~~]~u~t~~~~c~~rm~~x[~|~~mto~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2903/ccs np:i:12 rq:f:0.999256
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTGGTTCGTACAGCGGTAAATGACTTGTTGAGTCTTGACGTCGACGACCAAAGCGACCACTTTGACCCAATTGCGAACTACTAAATCCTAAGCAAAGACTATTAGGTAGTAGCCAACTTCGTTAATTCCGTTCAGTACTTTTAAATTCTAACCGACCATCTTTCCGAGTTGCTTCAAACCCTCGTCCTAATGATTTACATCGAATAGAACGTCGTACAAACGCACTACTACATGGAATAGATTCTCTTGTCAAATCGTTTTGTTTTGGCTTTACCCTTGGTAACAAACTTCGACTACGTTCGTACAATTCAGAATAACCTCTACCTCGTTAATTTGAGTTAGTTCGTTAAGGGCTTAAGTAGTTATTTCTATGATAAGCACTAAATTGACCTTAATTTCCTCGACTTATTGTTACATCTCGATTTCCCTTGATA [...]
+ +
+ ~~~~~~~B~~~~~~~~~~~~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~n~~~~~~~~~x~~s~~~~~~}~~z~~~~~~~~~~~~~~u~~~~h~t~~~~~~T~~~v~~~~`~~~~~~~~sk~~~~~~]~~~~~~r~~~`~~M~y~~~~~|~~~~~~~}~~~~O~~~i~~~k~x~{~~l~~~~~V~~~G~~}~T~A~d~o~Z~~~~F~~a~I~~~~~{~~~c~~V~~~~~~f~~~~~~~K~~~~{~~jy~~~~l~~~~~~~_uc~~b~~~f~~~~~~~~t~m~~~}~~~~~~~~~~~`~~~~~_~~~~o~~~g~~[~~~Z~~~~Y~~y~~O~~~Y~~k~~~~i}e~~k~{~~~~~~~~|~~~~v~~~~Nn~~~~r~~~U~~~~~y~~~~~~~~~y~T~~zj~~~~~~i%T~+~~~z~~~~~z~~~~~~W~~R~luB~a~{~L~~p~}~~~~~~~~~~o~~~~~~~~~~v~~g~~~~o~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2944/ccs np:i:16 rq:f:0.999754
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAAT [...]
+ +
+ ~~~cqjoa~~~~~w~~~~~~~~~~~U~~~~~h~~~~~p~~~~m~~~~~~~~H~~_~~~~~~~~~{~~~\~~~~~~u~~~~~~~|~~~~~~s~x~~~~~~~~+~y~_~~~~_~~~~~x~~y~~~~~~~~~~~~~h~~~~`~~~~~~~~I~{~~~~^~~~~~~z~~~~~~~~~~xk~~~~x~~g~~~~~d~~i~n~~w~~~m~~q~W~~~g~~~@~h~~~T~~J~~~~~~~~~~J~~~~~k~~~x~X~d~~~~~~~m~s~~q~~~_~~p~U~~~i~~~~~~~~{~~~~~~~~~o~}~a~~u~~~~~~~~~~~~~~~s~~~~~~[~~y~~~g~~~{~~~~~X~~~~o~~~s~~~~~~~~c~~~J~~~[~u~~~~x~~m~~x~~~~k~~y}~c~~~t~~~~~~~~~~r~~o~+~~~~^~~~~~~~~~~~~~~~t~x~a~~~~~W~~~~~~u~j~~~~~~~W~~Z~~~~~~~vvnk~~~~~a~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2951/ccs np:i:10 rq:f:0.999786
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGACAC [...]
+ +
+ {~~~~~~U~~~~{Y~~~~{wov}~~L~~~|~~~~~~qp~~~|x~~~~x~[~~~~~~~S~uh~~~~W~rw~~z~~\~~x~~~h~c~~y~}~~n~~~~~Z~`~LC~~[~hg~~~~~~~~W~~~x~~n~~~~}~~~v~k~~h~e~~~~~~~~~{}~~~T~n~vW~~~{~~k~~]~~g~Z~~~~~v~}M~~f=~~~~z~z~~~{{~\~~~v~y~~~~}~~~~}~~x~~~~~~~J~~~~x~}V~~~~u~~~~~h~~u~~~vqt~~~~iv~~~~h~~~s\e~~{~~~@~~x~~~{~W~~~ud~~~~}~e~~hU~~x~S~~~~~z~~~W~|E~~~}g~~v~~~|y~~k~~~m~~~}~p~~r~~~~}~~u~j~~~~um~~r~eu;_~~~~~~v~a~rn~fzy~z~~~a~~h~r~w~w~f~~~~^~~~~~~~~~~~~g~~v~b~X~~~[~~b~~~~~t~~~~g~~Y~~~~~~~F~~~~|~}~~S~~~s=~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2986/ccs np:i:13 rq:f:0.99964
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACG [...]
+ +
+ ~~~~~~~y~~~~~~~~~~~~~~~~~%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E,?i~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~r~~~w~r~~N~?~~x~~~~~~~~~~~e~~~~~~~~~~~~/~~~~~~~~~~~~~~~n~~e~~~~~~~~~~~~~~~~~~~x~~~~s~~L~~~~~~~~~~~~~~~~M~~~~`~~~~~q~~~~g~~~~~~~~^~~~~~H~~~~~~~~~=~~~~~~~~~~~~~~~~~~~~~~~~~~qf~~~~~~~~~~~~~~l~~~~x~~~~~~~~~~~~~~~~~~~~<~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~o~~~~~z~~~~~~~~~~~~~~~~~~~~~~|_~~~~~~~~~~~~~~~~~~t~~~~~{~~~~~~~~~~~~~~N~~~~o~~~~~~~y~~~~~~~~~c~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2993/ccs np:i:13 rq:f:0.999271
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCG [...]
+ +
+ {~~igXgg~}{ey~~~~}~~~~~~{'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~F~~~~~~~x~~~~~~n~k~~p~~~~~~s~~~~~~~~~u[~~S~~~~~~~~~j~h~~~~~~~u~~q~~~~~~~~~~~~~~g~~~s~~~~~~~~'~~~~~~~~~x~~~~~C~~k~~~~~iuf~f~~~u~~~~~~~~~~'~z]~~~~K}~~s~~o~e~~v~nw~S~~~z~~~~~o~~~~k~~~~X~~~~~O~~KR(~c~~+~~~~t~~~b~~~m~~~~~~~y~~~r~~R~~x~y~~~w~~z~~~~Xr~h~~~~~~~uo~~~~o~v~~~~M~~~~~l~{~~~W]~}~~~~~f~~~`~~~~r{N}~~~~_~M~~~~~~~~~~r^~~~z~~~~oq~~~~yS~~~yv~~q~J~~~jpin~~~~~p~~~~~~~X~q~~~t~~jp~H~~t~~~~{~~~a~~~~~~TB~~q~~z~<~~q~x~u~~N~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3023/ccs np:i:12 rq:f:0.999683
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAATGTTA [...]
+ +
+ 0~~w~~~^~~~~~k~|grnxgw~l~6~~~~~~~O~~~~^~~~~e~~~o~~n~~~pz~~~~q~~~~~u~~us~~~]~~toN~~~~~K\~~c~~~~~~~Z~|~L~~~~\~~`~~~~~sZ~~t~q~~~~~r~o~~~tq~~~~~~~x`~~~~~~R~~~~{~~v|~~~~~~y~~b~~~~y~~f~~~~~G~~~~~~~k~~yi~~~~V~~~|~~~b~_~~~R~~D~~tS~~i~D~9~~~~~p~~~~~~~~~~~~~P~~l~~~e~~~`~~~pB~~~u~f~{~h~~|~k~~~~~~{~~~~b~~~~~~~~n~~~y~~~i~d~~~~~al~~d~~~]~~~P~~~~~d~~~~~~m~~~~~s~~g~g~~~~~~~t~r~~~~p~~~~~~~~~~~~~~~~p~~~~~}~~~}~~~~g~~~~8~~~~e~~~O~~~~~~K~~~~\~h~w~~~~xR~~~~~~~~~~~|~{~~g~~k~~vr~~~e~m~~~~~wh~~~~~k~q[w~~~~r~g [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3046/ccs np:i:22 rq:f:0.999764
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTACTAGTCTTCTCTGAGGAACCATGAGATGGATAGTGGGGGACCTGAGTCATACTAGGGTAACTTCTTATATGGTGACATCACTCCTACCGTAGAGGGGGGACGGTAGTCTGTGGGAAATCTACCCTAGTGAAGAAAGGTAAGAGA [...]
+ +
+ ~~~~~~~{~~U~~q~L~s~~~~~~~N~~~~~`~~~~~~~x~~~~}~p~~wh{R~~~~~i~~~~~~~~~~~~~~~qz~~~~~~i~~T~~vv~~~~~~T~jmD~O~~~v~~~~I~~~~~T~~r~~~~~~~~~~~~k~~`~~p~~c~~z~~~~~g~~~y~~b~_~~~~~~~~~~~p~~~~~~~~~~~{~~~~~R~~F~~~~~~^~~m~~~~~a~~~~z~y~~~h~~b~~~~~~~~~i~~~~~d~~~n~ut~~~j~~~~~{F~~~~~~~~~~~~~~~~l~~~\~~~~~`~~z~~~j~~~z~~~~~~~~~s~~~~~~~~~~~~~~~d~~u~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~u~~~~~~~~~~~K~~~~~z~~~~w~~~~~~~~i~~~~~~~~~~~~~~~D~~~|~~~~~~~}~~~y~s~~~~D~~~~~~~;~~~~~z~~~c~~;~~~~~~Y~~~~~~s~~~~~~{~~i~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3116/ccs np:i:14 rq:f:0.999312
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAAGCACTAACGTGGTCATCAGACTGGTCTGCGCTATAATCTACGCAATAGAGGCACCAGCGGTCGTTGAAGCC [...]
+ +
+ ~~~~~~~b~~~~~~~~~~~~~~~~~M~~~~~~~~~~~j~~~i~~~~~~~~c~~~~~~~~~~~~~~:~~~~~{~~~f~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~N~~~~~~~~~~~~~~~~~t~~~~~~~~~~~|W~~u~~~~~~~~~~~~~~~~~~~~~a~~~~~~9~~~~~s~~~~X~~~y~c~~t~~~X~~~~~~~~~~~~~~~~~~~~~q~~~~~~~}~w~~~~f~~~~~~~~~~~~~~~~~~~~~~~t~~~~J~~p~~~~~~~~~~~~~R~u~~p~~|~~f~~~~~~~~y~~~~~~~~~~~~~j~~~{~~~~~~~~~~~g~~~~~~~~~~~y~~~~y~~~g~~~e~~~~~~b~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~Z~~~~~~~~~x~U~~~~~~~~~~~~~~~z~~~~u~~~~~~~~~~~~~~~~~~~~~~~u~~~~x~~~Y~~~~~z~~~s~~~~~~~~~_~~\~~n~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3119/ccs np:i:12 rq:f:0.999811
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGACAC [...]
+ +
+ \~Og~{~n~~~~~\~~~~~}}~~{~G~~~~Jw~~~ffm~~~~~~~~~\~T~~~~~~~z~~W~~}~e~~z~~~~~Y~~~~jvy~^~~{~l~~o~~~~~c~w~~M~~v~~y~|~~dr~~e~~~~~~g~~~}~~~~}~~~~C~]~U~~h~~~~~~~}~v~_~w\~~~h~~w~~c~~h~G~~~~~x~Z\~~~Y~WqmZ~t~w~opiY~|~~~k~~~l~~~~~M~~l~~~~g~~N~~~~n~~D~~~mv~N~~r~~XLpoJ~~u~~~~~n~~xoa~Z~y~X~~~~~~T~~~{~~~~{~~~~E~}y~~~T~~~X~~~~2~~~|~l~~~h~fV~~~~c~~v~vE~~~~]~~~[~~_yh~~~[~fg~y~zx~[~~s~~k~~~~R~N]~O~}g~h~~~~~~~~~~fo~~\~~Y~~~t~G~~~{~~N~~~~~~~~_|~~~~~i~~~}~~~d~~X~~~~~~~~~~~~~<~~~w~w~U~~~vt~~~~~~~~~~~~~~~o~~n~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3147/ccs np:i:13 rq:f:0.999238
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGTT [...]
+ +
+ ~~~~w~~[~~~~t~~qp~~~~~~~~&~~~~~~~~~~~~~~~~~~~~~~~~~~~~_\~u~~~~~~~~~c~~~u~k~f~~~~~~k~~~~e~~~~~~n~~~}7~~~w~/~uk~~~~~~j~~}~]~~~m~c~sm~&~m~~~}~~x~}~~f~~~g~~~~~~|~M~~~~~~~y~m~~~y~;~|A~~t~~x~~~l~~~~~~~~~~~}~z-e\~~~~t~~vk~~[~~~~o~u~~J~~~~~k~~~~~~~r~,xv~X~~~~~P~~w~_~~q~c~~~~~~~~7~~~~~~~~~m~j~~~P~~[~~~~p~~~~~~~~~9~bc~K~~|~~{~~~~~v~~Im~z~hB~~~~~~~~z~~~u~}cw~~~f~~~b~s~~Z~Vh|u~~M~\~~q~~~~x~cpR~ryG~~z~zy~~~~zZ~~~~W~~U~|~t~R~Xho~~|~y~z~Vz~~~~~f|~~~jw~{q~~g~g~~e~~{~a~U~~~tf~~P~~_~T~~~|i~a~i`~hvT~k~l~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3151/ccs np:i:21 rq:f:0.999945
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
diff --git a/tests/cram/100zmws_byStrand.t b/tests/cram/100zmws_byStrand.t
new file mode 100644
index 0000000..680d151
--- /dev/null
+++ b/tests/cram/100zmws_byStrand.t
@@ -0,0 +1,813 @@
+
+Test ccs on 100 zmws from the lexogen-SIRV dataset, using --byStrand
+
+ $ $__PBTEST_CCS_EXE --logLevel=DEBUG --minZScore -100 --maxDropFrac 0.8 --byStrand $TESTDIR/../data/100zmws.bam test.fq
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- main -|- [0-9,a-f,x]+|| -|- Found consensus models for: (P6-C4, S/P1-C1) (re)
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- main -|- [0-9,a-f,x]+|| -|- Using consensus models for: (P6-C4) (re)
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- Consensus -|- [0-9,a-f,x]+|| -|- Skipping read m150825_055401_42161_c100844482550000001823159012311525_s1_p0/413/9570_12297, ALPHA/BETA MISMATCH (re)
+ >|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- DEBUG -|- Consensus -|- [0-9,a-f,x]+|| -|- Skipping read m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2359/6103_8488, ALPHA/BETA MISMATCH (re)
+
+ $ grep -c ^+$ test.fq
+ 200
+
+ $ cat test.fq
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/170/ccs/fwd np:i:5 rq:f:0.995204
+ AAGCAGTGGTATCAACGCAGAGTACGGGAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTT [...]
+ +
+ CkZN[ZgGjLYfN>jNZMEX[ZeENAnh<WMDXgHO/<IMNoMB7CX[ZfIM$gjkkkkkkkkkkkkkkkkkkkkkkkkkkkjAArEe[Nh[NXF1b[M at ILX)g-JH+V8ja9L at tBYN[gLnEN[BseTQe:r^GNYISNEAsZ at L/pJSN[?[VFl7_UEhN[ZgZgZ[nN;laKLmUSLBWgY9ooooiL at 0kGlfMAR([o at kONgTNg[b?_[gNZI[OXLXYl78iM;mmc?I;f at DU,=[UKL,/(@W>mmmVK6XVNM8dJW9XmBdDnnNeFBUiLA>lBMYDnnmV=lYc>XXR[XEeZgKl<_\/ApZ.ssYX9ngNQHLKLX'SILdBmmNoZ[nNO*LXa1;?pFlM2hnnfMEYeMEOf;['MYAd[5rg[Bv[n[XEXNYFlZ<g3LbYe+02JC_ENZYZ>nfNd8;ieWB<,klX[BvgKk9dNgNeBL=leNfN`O`J8kR[gYMBdOoX9YM?mmLDXeA%R>9XOoMfK [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/170/ccs/rev np:i:5 rq:f:0.996289
+ AAGCAGTGGTATCAACGCAGAGTACGGGAAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTA [...]
+ +
+ MkMZgNE?rUg[ZVkLNSeNgN[gY:vv[nNVJIZAq[eEX[nZNZeMeMIfY$gZ_gkkkkkkkkkkkkkkkkkkkkkkkkQEkg[gXVZYNgBvgZN[UD0SXRPIe?[[YZ8kMgTB00qeWKKoYI6Y6^P@\gYYBdGkNFl;oYgZgLoONnCni9S at KLY9YNNlY8mmV?[`HYc60:8cmmmlYM.`BdEXNoAp`3SZSZgZ[eELneEXM.jXg[N=lSBuY4mmma at TWNNogGnNoXCmXKQ+llleYBmmNZ[nY9RNnN[99dY[g9ND<^HYNZO4}}|Wg}WfH~rPrXudCa<{Ov3mAzs*zusKGw|dgVLNceAzdX}FccX}W7tdXgeWRcWDzR~`:~~~~sKZgeudcc}QS9OHqAzfuS~X~tSKUFPVuuU~D~fH`XbugugsMqXr3{{_geg}fWN>HccWvQ~_7~ceMddPVdP|N^IbO`CcZ{RvgXeXgg}VMqZGu~eq>GqB~veXf}=k{k [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/230/ccs/fwd np:i:6 rq:f:0.995083
+ AAGCAGTGGTATCAACGCAGAGTACGGGGATCCATTTTGGAGGGGTGGGGATTTGTTCAATGAATGAGGCAATAAACCACCGCAACCTCTGTAATTGACGAGAAACTTGTATAAGGTCATCAAAAAGAATAGATGAACATAAAGATTGAATACGGCTGGGTGAGGTTAATTCAGATTTCCCCAAATTATGTAGATGAAAAGATGGTAAGTTTATTGATAGGTAAAAAATCAAGAGAGGGTAATAAAGAAGAAAGAATAATCAAAAGATAGAGCATGCAAACATTACATGGTAGTATTGTTATAGGCGGTATATTGGTAAATGACCGATCCTTGACTTAGTTTTTTACATCGAACGGTTGCAAATCCTAGCATACTTGATATTAATAGTAGATACTGAAATATATCTGAGTATATCAAGGGAAATCGAGATGTAACAATAAGTCGAGGAAATTAAGGTCAATTTAGTGCTTATCATAGAAATAACTACTTA [...]
+ +
+ ayhM>gtL}sUrODgFTOhhhhqXPHtvxgr>~VGuuuXxSCzzx^6zyj_=wte*tNVt^fVYlhhWvOXvtLvr/[TA~dIBbD~xOxhtFtVwfSPhfQMwuOguhthrG^VvtN>qM(<EU\gHa[hhhtOR\/EMISPWhQVhWvpS?K[Pv>uushhWvdxXvbvOhf=Kut'~~ULdc[`)mf]VhYsZ2tttd>]Fwn3qf<tteSweNj_Vus-tttttq?TtcighLvvtDzs6ttfGtgNvvhWwqH^sN(W^QPcscdhhQhtiO.u[OhguWPXlCsrXg^fcV^.IO]dYtOWvsSrhbxK}t=xmXhO&hgSp=~esg`?BtdQ2vvvvqcLSrGhGtNCsMvf<AqusA~xhhQhtSOoi^_f_\iHl_[^cA\XL^HfK([IO[dWJG`]_]gIf^hIAb8ii'fghI]_]_h^fBdH8bhPj^hI]INj:RS]iNjPihIOUBgiH^h^ITW=H9\XH]FjjRJiJjIIUjP [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/230/ccs/rev np:i:6 rq:f:0.994209
+ AAAGCAGTGGTATCAACGCAGAGTACGGGGATCCATTTTGGAGGGTGGGGATTTGTTCAATGAATGAGGCAATAAACCACCGCAACCTCTGTAATTGACGAGAAACTTGTATAAGTCATCAAAAAGAATAGATGAACATAAAGATTGAATACGGCTGGGTGAGGTTAATTCAGATTTCCCAAATTATGTAGATGAAAAGATGGTAAGTTTATTGATAGGGTAAAAAATCAAGAGAGGGTAATAAAGAAGAAAGAATAATCAAAAGATAGAGCATGCAAACATTACATGGTAGTATTGTTATAGGCGGTATATTGGTAAATGACGATCCTTGACTTAGTTTTTTACATCGAACGGGTTGCAAATCCTAGCATACTTGATATTAATAGTAGATACTGAAATATATCTGAGTATATCAAGGAAATCGAGATGTAACAATAAGTCGAGGAAATTAAGGTCAATTTAGTGCTTATCATAGAAATAACTACTTAAG [...]
+ +
+ 'tQQhs=R at qfqRfVwgOhl'f=Qrh6~~~vSXzp56[UAzX*vs?3b~~tMbjNVZT]MeQ`qgMb>~ibrM>uvM}sWbMc;qUvfgYLT_xVvOwhDE)@TcgUk<e^fds*PQq__%ttn<<PsTj+1OP`s_qh[uuRo-XQasTsh?kRf:~~hPb?rXvcuSphtOo2q\,orAwgEpjRNfrOqMN<s^ZNvf/~gguO<eSkXvLqRn%~QS/VWdhVfhMc7N1Q2DkRUwfAu_OQsPI[SMdlgTtWYCWaQGjM^9V=^UO:UHVlhmCnp_Xg2~WlOcoSc9CjU13=dL-iNngo4_7Q]TltS-tg<pMPUDW;uhBt_;,guvvqjN[NU;P`Z%~[@hQh.xldCsfrOdXdWRPnN]HVTY`n7n+en)VFTh`@KmVh`WrScWOaNhthqXhNH$~Zruhg<nOEaOJVrheu>euCh\AY<~NsvDzgu?uhhdsKW^sPe*bSpsIIpG\@=bvh_STS\aNgNVN [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/301/ccs/fwd np:i:6 rq:f:0.993374
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTGAAGTTCAATAACTTCGATGGTTACGTTGTCCTTAGTAACTGGGTTAATGACCTAATGACTGTCTCCCTATACGTCAAAATACTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATCTTCTTTAAGCTAACGATTAGGTTGTCCATTAGGTAACAATCACGGATAAATAAGTGGCAGGACTACGTCAAGCAGGTAAACCCGCAAGGGCATAGTGTGCAAGTCCTTACTCAACCGTTTCGTTACGTTTTGCTTGGACACTTTCCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCT [...]
+ +
+ 2aHMOF:;yKObCAmR2TaYbYfhY$]dd]`ktz{{{zume`_`cfea_bhhluz{zjdDOP at aKWzYEyLWzZV|DYb]M{U{hZZDzD[3SEl&BcAnLK1FMSpC^`CNG`d>:V[hZe[\@dC|~c;cgTWdZ3ydcc_VeZVaWdQX7||oAPwTDT4QE_YKxZGzYS_R at LU^-W`VBKXIrPGc:cXDZX_.\D\]OpIM[\FsCMXePIXQX3Z;>AvVKqiUxERJJgDU^V|QK~@pZaJrfG{84Y]KwZJ[5N$J7Q*H'F[dU^YeL{VRMsLUZ:U[a.CwZZhK}M5rI6\rZJX|,j<5ccOY_UNYZH|Z[<]G{bFX$;pHzW:[qUHUaRYW)<?CWWTf<aLUgYM}|)daZ[g[fgYPV~ZQBCfU]X1zyn`:gR1r\5v}fZ9}~~xge^RhX}ZM97<D<YfZhVKQXdQU-;QTwK~E{gIu0zz[X|Lp?{tSAQYBcV0]\B%uXZ]6XT1L>meK|[fYD> [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/301/ccs/rev np:i:6 rq:f:0.995666
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTGAAGTTCAATAACTTCGATGGTTACGTTGTCCTTAGTAACTGGGTTAATGACCTAATGACTGTCTCCCTATACGTCCAAAATACTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATCTTCTTTAAGCTAACGATTAGGTTGTCCATTAGGTAACAATCACGGATAATAAGTGGCAGGACTACGTCAAGCAGGTAAACCCGCAAGGGCATAGTGTGCAAGTCCTTACTCAACCGTTTCGTTACGTTTTGCTTGGACACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTT [...]
+ +
+ :F8W[+%*ZTSTZVlZVA`AcYRdD%cZeryzzzzzyukcXKEDGQdkd``e[PMSdie[QX>nZKeZC{SRzVTvQ?aN:f7vd[YE_XQKz5wbDb5zYh=~qXzEe8VM;xOFdJ&VEITLZeC~{]cNJYG],V']gSRdZQH0cZb[ZDr^qPCZ]0rcZE{ZVyZU|[Y}[XKZb8pWCDz[K}dDfffD7SFf[cSyQV}QVdRArY8PSW}YRY\c;WDTX?mzW}Z[hX}ZW]Y}fJ|GiCeL~fXzY4l\=B>@VaIICEwMeLdS=%NF7EYfFvOYQd[KEIHbXEfIz_F`e:[C-QOy=vcDJ8YIUG?+XHcTQJaX}f[cT2y7yR?h]S>B_KXD@{~_DWD\;sd[fZ>rXXaCU\ZfMYeT]Ad[Zf[fB/ki]>2]I at a\5z~lc?mg=5Xa?Lj[jaqV~t\~UTTqS\oSr[NJLa;iO~^~mMv>~{c`~R~J{|dcP~_mdR~xK+~aM]pdLl]NwA5ZOrTNN~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/322/ccs/fwd np:i:8 rq:f:0.998736
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAG [...]
+ +
+ N~qx~v~M~~\~t?~np`~s~rkos&~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql\Zp~k~~u`~nu~mrq~v~u~vQyO~lZ~lu~at~vu~_~o~pi[skinYmuN~~b~m]`~_p}Ou^~~t~q~w~q~Y6~~L}\~u~toS~~c~a~~qP~quk~uR~~~mho~sp~ru~a~u~v~N~~V~~~o^~_eY~o~u~`~,~K~~b~u~Q~~5~~~~omv~q~i\p:~smp~w~~q~C~~G~~|V~~r8~VZ~M~sIqS~~tB~~u_~~~~^~]~q~~u~f~dqg~J?~iN~oP~p]~a~ovt^~~p~Q~~qz[r~su~\sc~utC~~~L~Y~tq~v~P~~t`~L~l^~c~~Q~uPoF~~M~cH~w~t~n<~t~~r~9xd~~vL~~v~`~s~[~~_~^S~~t~J~Z~(~cb_~^~<~kltM~G~~~p~su~~uW~~yy<wm~{C~{l|Y~Rick}kX~wiV~H~aj<~~~tW~kX~|W|zhxljaYc [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/322/ccs/rev np:i:8 rq:f:0.998264
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAG [...]
+ +
+ m~tr~<i^~~n~vg~t_cqp~tp~u&~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}z_~N~r~~v\~kso~uuoZ>J{sa~a~q[~~tipolo_psrp~vrqq~s^oz\c~~\~lpsY~vrs~a~~_~qVooa[~9~[G~Lvt~v~6~~]~O~YrO~tvb~uW~~~u{rt~rk~u~T~\~p~]~.C~~~p^~so_~q~s~P~I~`~~u~a~9~o/~~~SJ~oo~~~w~R~sr~rt~~[~5~~@~~lN}~v`~~b~c~s`tp~~uP~~vo~~~~_~jv~~fA~_ntua~t&~FF~pT~t`~]~qtuY~~i~s~~]~uvjnu~reL~ttF~~tQ~P~a7~sla~qt[~^~p_~b~~s~p\~_~~T~~<{~^rqup~wugI[`~8~~\`~~ujt~K~N~nb~qX~~si]~r~O~~vc~b~N~^|u^~@~~~u~vu~~r5~~q~2~~~VH~~v~M~~u~u~pl~~q^~a~p_;~~~~f~v`~U\~[st]sr~] [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/335/ccs/fwd np:i:9 rq:f:0.998654
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAATCGGTAGTATCTGCAGTCAAGTCGTAGTCGTAGGTATGGCACTTGTCGTGCGTCTAGGACGCGTTGAAGCTATCTTATTGCCCGAAGGAGCCGAAAGTCTGGGACACGTCGTGGGACGTATCGTTAGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAAGTCGAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATA [...]
+ +
+ p~oZ~t|:~u}|p.ulthWnf_wOk-~~~\i~p~N~~pQ~~palrN~~|mr[~vTdE~Xiy`}qMPips|H]~tlg~L~x~kHzbz~[~IzGP|Z~~^~d'jEg~B~q~pYgkkTx{Uzrpj~kgyZqc5Y[gmHj{P~~mzrGqJUC{h~]~\~qsniC~\l~toYmooa~wgrbw`Yt[I~s}Y[~t~oajzp~opuiN~~~x5wKrYi~pyXpcrpt~pzf^~lZDR\T~YZ~rYezchB~fR~sM~|mX~_~eoV~kO~~trkzS~~rXF:nzYahM~~~prh~~ppP~~_~ckSTh0~~~idScloukVU~gRuS3h~loT~bJnl~rZ\~iqDk~~t~p}tp~}jT~h~t\~nUOftf~zN~}MUpOXh~Hz`~~otZJ~~~s~kpP~~iXQR~a\~rltptqv_G~Q~\PznN~c_cLxpp.~~u~qt~tg~qe~j[~Ni~qjX{sX~fL~{~]frG~]n[~k>~y~~v~P~yzk[eaX~uz\ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/335/ccs/rev np:i:9 rq:f:0.997822
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAATCGGTAGTATCTGCAGTCAAGTCGTAGTCGTAGGTATGGCACTTGTCGTGCGTCTAGGACGCGTTGAAGCTATCTTATTGCCCGAAGGAGCCGAAAGTCTGGGACACGTCGTGGGACGTATCGTTAGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAA [...]
+ +
+ W~pcZ=HSego~u^~vsv~_~r~~uF~~~g1~T\SlWCDt~|j}rD~~~u\^ljq~`~[~~ribjR}f1hKM~[uAl=hWftK~s}em~[Zs8~O~oL~~~[Igj\~^VZZdtra~TO~~p<~pi~m{svtL4~j^b]~~\|mQ~N~f~n~]~k~s9F;l~FO~.Ge{TA7bC_]uagr~]u~p?Zk~qp[Wijq~t[ge[~l~fN~_~vi~`~apoowpDf<`M~ibHFVL~__~rvcygtX~~H~h3qbWk~I~{]^~\W~~_~qi?~~}a{pHwqqBQ~~~xkN}~`nY~};~fK~}y@~~~]}~ro[fwt]~fO~~v]~|ua~~~mW~m_[~iMU~~gWFp|mwmg^_~~~cE~x_vj\]~lJ~~^N~mrh~W>+k[SlsB~~~mj_qC~tgr~d~r[~r~IrntbWi~]~`]o[c~\i{[V]pp~on_ii_k~[k~uZ~`=m]blroH~fG~M|C=\C~ouX~l=~~~q_S[~n~[UJs:~|iX~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/413/ccs/fwd np:i:7 rq:f:0.997698
+ AAGCAGTGGTATCAACGCAGAGTACGGGGATTGGATTAAAAAAGTTGTAGTAAACCACAACGAAGTTAGGTAGCTGGTAAGGTTATAGATGCGTTCTGTCGTTGTAGTCCCAATGAACATAGTATGGTTTCGCATAGTAACTGACCTAAAAGACCGCCACATAGTGAAAATACTTAAAACGCAAGTTTCATAGGATTAAGTGGTAGAGGCTATAGAAAATGATATCATAACTATAACGAATATAACAGCAAATTAAAATGCACTGGAAGTGGAAAATTTCAGCAAGAGAGTCGAAGTCGTCATAGATTAGCATGGACGAAAGAAAAGTCGCAAAGATCGGAAATCAAGACGCAAAACAAAACGGAGAAGTTCAAATCGAACTCGTAGAACATATCGCTGGAACATATTAAACTCTTGGTATCGCTCAGTTACAAAAGGAGACACGTAGACACGAAAGAAACTGGAACAACAGACATATTTGTGGATAATG [...]
+ +
+ d~mICi]YrhLNCDQ1Y5jokC`hHHs~|WSz\~if~/~{J3Qmft\sXUY:~u=g^I?mZmZzVZ~n^~}YmFa[~`Gu]~Y~n~opf]n^pj~[~q~^oY~pz at iz9~uZ~chDI*OaknMSoTiU~~_pWT{mq}L~Yn=C9a}L~~~jg>~l){3:1^BiiX4~|hci[i~;y~qDeVQkjO~~CbhVLrT@~M~[wI~{Vk?G|VeLldU9n~~}pi|lsZY}V~]vez)z\oJq]BmT|GeiYN~~cj%tdcbnGeToJpX~p~Ty:r~qO{~HjXJRmmVkUi~^oL~pyCi|]nu\[ci~jd3k~\~CZnD~~pJ~~~p~Xj]Blrioy\Z~O~~w^^~pnVRF>joy];~~_H]rmXF{dA~X*~gfZ at K~]|E?sXOM~^mteHJp[aG~Lm\Y{ohg:~{]~^f~Z~~oy[mG|^ol+~V]G|~oE~TXeFl]q}mib]m]n'~~m?HnW~ZlYz4C`]nqmIm}YQ~~jB[~o~]~tY [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/413/ccs/rev np:i:5 rq:f:0.99754
+ AAGCAGTGGTATCAACGCAGAGTACGGGGATTGGATTAAAAAAGTTGTAGTAAACCACAACGAAGTTAGGTAGCTGGTAAGGTTATAGATGCGTTCTGTCGTTGTAGTCCCAATGAACATAGTATGGTTTCGCATAGTAACTGACCTAAAAGACCGCCACATAGTGAAAATACTTAAAACGCAAGTTTCATAGGATTAAGTGGTAGAGGCTATAGAAAATGATATCATAACTATAACGAATATAACAGCAAATTAAAATGCACTGGAAGTGGAAAATTTCAGCAAGAGAGTCGAAGTCGTCATAGATTAGCATGGACGAAAGAAAAGTCGCAAAGATCGGAAATCAAGACGCAAAACAAAACGGAGAAGTTCAAATCGAAACTCGTAGAACATATCGCTGGAACATATTAAACTCTTGGTATCGCTCAGTTACAAAAGGAGACACGTAGACACGAAAGAAACTGGAACAACAGACATATTTGTGGATAAT [...]
+ +
+ V}TelFO+hD[eeZ|c?ccQ`@a]a+izol=K5ecUt5yzzzkT$<Bbo@`CyyCsmMazc?_w?>ro-idqUdN2NLax9oKgULUNa^@^OPiYRGPcT9jAMERR:ik\Xa>WkPmKTQ3E];fE_dY)CIJWBK2wQbU]@fN(mfT>OQtPOkd_U:\BT>C^^gK[^AZDyyxRJXc~XN}~p{^~L~w^~beZCJ~BgJl;~QPyU^FE~~~hD{mcUU|of~f\[dg{mEO~YrVVul`WmP~~[lT~~~p^q~qpO~n~]m>~4{~SBl~^h\WC~ZcZ]V^q]m~Mon^oq~kGVvJnR]YhYL~~q]>psWU~~~]Yo^oCnlYvom*~O~~VUj~HxAZpF~~dBG~~~pK~{Ec{[Z~jG~gAUZ+~qnhU1KVE`gcon~op]XTK~l~Y|jx^~R~~pokMa-~X{ol2<Tn~^V~aAL~~~M~y^|W`n\C{[qY|o]O~yC;|~ooL~V~@k~p|HzYvf~/~RFeM~~on~o [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/418/ccs/fwd np:i:5 rq:f:0.992468
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGATACTACGAGGACGTCACCCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTATACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTAACGGTGGTAATTTCGCACACTTCGCACGTTTA [...]
+ +
+ RpUIAQ?EkSYT64PJR7AMMNB/0$MZhmmmjaYUTUW`jmmmmmmmldV:55/E4T1>LEBMXG<YOE%SBCNXMUAIBNY.UMZP[WDqWMQ,F[APY5TUFdCIO;X0OQ=m4b^[PY2mS:K1VNmP[T\SY<%YL5]Q71REB[BS^T+mmlXGATLX2N\N+^.jlGo^P\B9\[S:9?TGS>]NX>I?mPDmP8oomSPNpS-VB at kMmM,NMf7kVNM@?FMS:Mm^UN:iMF>TkP^[Ap`MECoS:R,mn\P77;\<qk]TNZ]U]NoCq^[CpE<o]@M9hfP^UP^P[F//NLe.gREW>BkPT[N9OPT.JF_P<fQeL-XW at N[P];i:S^U^[@]BR%d>lYTXUPR7OYBc)hjS^[P[^[^WOZSVHnf:\N<cDS^[*ZJR[@mSGm:Z:\P]UQMj>9DNZNGOAmU[^O7S^NpUO1O>oR7TO^[Hp[PT=m<ok)RL5T\GnC;kEK`N>M>;@HAkPUOE:S:mlC [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/418/ccs/rev np:i:5 rq:f:0.993705
+ AGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGATACTACGAGGACGTCACCACTGAGGGTCTCCGACATGGACACCTAGTCCCGGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTTAACCTACCACCCATAAAACTGCTCTAAACAATTAGTTCGTCGTCGCTTCTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGT [...]
+ +
+ XNU^PU5nY]ESJYLPTZP^O/[T$kkgYORQ?319CMPT]ZST^hkkkkPPUD\PFTM/ZDq^PICRDFfDSY:W&aZYTDGoP^PRZCq]SDGq[\:X/ll%g?@LZT^EmPRoGfDW>TDkP=l4p;+RM]=>FO3)QYT?B7P2M1(W^OEN3ThdPWTNKPBW[UNn?Ta?e=OD\U[^[DrWYQJMhTW08+gSEqR8Thn^UQn8/lVBR)WMKkP=_4Rf[CR:mmOUL`FNQIiPZ3nbTDX74FL\3TESN8aQ`OIhPYBjSATO\H>,6+B7B3(=AO7ON at A)ZQPKDM.CF/$RHNQg*Z%4/RR<PBL/AL(-C921-Ui\RVHVHPDRDQnSL1D1\GfD\Gd?n[P^QPG9d[8m?aS9WFS[DVDCMDN\0h[M94<R.%9=27D9[7VN at VKCNCF/<9=iCHDNDFJ:9 at 6NN4>>NQOQFJQBR]?E<98GdQ\@Cy5ceQDAq6Ff\EoCfwXBU6A1J3mA;AED@, [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/420/ccs/fwd np:i:10 rq:f:0.999173
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAAAGTAATGCCTCTACGTCAGTCGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAG [...]
+ +
+ ~~~\~~~w~~~~pk~~~p~~~~~~~%~~~~~~~~~~~~~~~~~~~~~~~~~~~~j_~~X~~~~_~~~]~~~~~~~~s~{~e-i~~~~~~~]~~m~~~~{~~~q~~~~~~~w~~b~~~~~~~~j~n~~~~~~F~~~tk~~}~m~~~~~Q~~~~w~~~X~~~`~~G~~~n~~~~n~ub~l~~~_~[~~P~~~su~~~:~Xp~~y~h~y~~~~~~_~~E~~~~~n~~~~~d~&~~~~~~~~~~[~~;~~~Y~~~u~{o~~~~~~t~~ic~~~~~~~~h~u~f~~~~~~~gc~~g~~`~~r~lx~u~~~~u~~~~~~~~~~~~s~~~Ts~s~Y~~j4~~~~i~]~[~~~~~[~~j~y~sf~pl~v~~a~~~~~~v~cj~~~~t~l~j~~~S~~~~_~}~w~~~~~c~~vnK~|~O~~~~~r~y~~~g_~S~~~~q|o~~~G~~~~L~~~~c~~~~X~]~~u~~O~~~g~u~~{X~~~~m~xh~~[~~jn{o~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/420/ccs/rev np:i:10 rq:f:0.999056
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGC [...]
+ +
+ d~]s~w~\~s~~~j~~uh~B~_~~~&~~~~~~~~~~~~~~~dY^v~~~~~~~~~~~i^~t`~~qwg~z~z~~~h~~~~w~~~~]~y~~e~pq~~~~~o~t~y~~~~~~~o~~~o~~p~~o~W|~~~~D~~Uv@~~W`~~M~~e~L~~~~~A~~~~\~~~R~~|~~~7~~~~c~~~~~~~~v~r~~~y~~I~~~~v~~~Y~~~~~W~~~L~i~~r~\~~D~~~~r~oq~q~r~t~~q~~~~~t~T~~\~~~[~~~l~~v~m~u~~y~~~W~~ox~j~~z~P~~b}~~~~~~~~~;~~r~~|~~[~[~~uj\iQq~~~~I~|or~m~~~y~~sG~~~x~a~ZO~~~w~q~o~{~~j~n~~m~~h~h~~S~~~~~~~n~u~z~~~~v~f~uef~~B~~~u~f~~s~np~~~~h~L~e~~~b~~~^~E~G~~\~~~~~~~~~qUw~~~D~~~~:~~^~J~~~~~~m~~~~\~x~sjS~~~~g~mz~~z~s~~y~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/428/ccs/fwd np:i:8 rq:f:0.995686
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAA [...]
+ +
+ a}XAQY^6c^c5O at pNCB]Eg[`eB?~jj[F~7~xfceIC~kR~sIqE~Y5~vFT>:ga at oC~Ii?Wn|^l_^boN&geftLI\FC;{C~KMQ}iEebjqjT~oJdK~jJgFSN\hJ~|]9?Lsi]<~rQVNuJ~b]g]PCd}`K`\w^I~`+zRgi:Odc^qcL~\h_X]d9hQ7\RRg|LI[mQ~Sb8zdKQN\?jdc/NHaZ_`WJqbgZ^:nX9~Zb-~~k[meaMp^_~`EXK8R]W~LH>kql^bRIfkjfQJWT?BN~i_H~~bq^b^Y~7}a8T>bg8X^O%PNFaY\U`SZJ:~hqE`Gtm[d<oaP~i>X_MWJ^~aPJCnh]M8po\_]?~iQ~Yjf`daPLV~bG~fZm\`Lo~\RXJ%ChbsgJh_G|cAXSJ?W[c_FLabNDoYLPheK at ks^dqbL~`hGM[RXRO.~^wi^gdgoSYORSH~OZ%pF4_a3d@~GPTE~bgXOtJljM~[Wc\N~Ur=fPCi]_Gkn5v~[^u [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/428/ccs/rev np:i:8 rq:f:0.99215
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAAC [...]
+ +
+ '[:DN8XC~piHbY~b4F;B:XnV^'r~fcAoEs~gXqU%l~ApuP~)nVXRi}_N]Pf_S~DC^](ceh^I\d[Kn-ccekbLcbKgP}En2`VE~[cdXA~dLPCza\`ajYdr:~]:]XO~o\:~n[SVuC~\OoN[M~~^c_Wn\=[E6aO~hcC~g`bG\~is]QOmF~a`UIN~n^aWqIri4F~q<~rL\fGeNoZTWOJTbfJnLJ>~jKs%V.zWI-tp]G~bH~VgVHDw`QJJO,v~jb^pcnRohQ]bmO_IVqb>~~\__^a)jHAMFJ8QbR`gJK_lbW^ip][@XCmmHIA20=`^QmYJevjJWbf_&~Zq`FQfb]3~~JY\C~mH~b<ffp^qbO^8<ydU~dYHhjD at e^hOmN;X^(XR~\`iLV`KXS\O~hXGTbWCCdfZ>DTLe6BKpJLN\`eJWGKk8pVIfA*HeFIZ\EiY4Xu=tXRnC6%d&X}VXaJ~LVQE{Eg[_C~KMN_L^p[WR~g9|m[.{_ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/429/ccs/fwd np:i:5 rq:f:0.993094
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAAACAGCAATAATTGTAGAAGGTAGCAATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGAC [...]
+ +
+ H|_GO;,R}fcL+C`AJV`[P`ePWA|||V|QoO`^a=amKH*y`WgfXbfR}fR{Pe`DwA`aR{fgaW`FzV`OT:HofA\@eyffffWaU4tL[[gff)`0D5~|efGfJ&wwYUM_VFxdG^WzagfaW}R}ff`B,d`ecDN^\H~af`P_9}eOVgfUIG|`fJWA`fa6~]K`Y}aE~|a_a$xx`adJdfadJe2|H;C:pfrUPed6|<t`bR~c3fjgVW|Jb<M/YDXePO|}dAdW|HU`fWfaa?MVe`E{eaJTf^hQ}fMP~W}abbbHAzVacR`agWK~ae6~vTjWbMJ0Zbc`dA^4_7jP]fcFR|fW}^IIznAFyVfbY at zfaa`fOhN:U_3w^@NO||U:vc]O{RmUQ`9~eafTQ'?^OEO8O_N<~f`YOVea`;L``eWcXW{:ljm`=emIDz_NUPeagfae>yDz]\VRSR2__vO?8W|_2jF6@`e:~e at vaWKzW_Aea\aT|TaY}faY}_OK>D [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/429/ccs/rev np:i:5 rq:f:0.992297
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTGACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAAT [...]
+ +
+ IhWbcRV>rdg\cH}NWT^>@W_\_+Vg[MjFtbV]&?imXQO_9bhfF;4Hhh<z at _KH{cdQB^H5SMYGgZDbcY$PcdY>q\WeUbKXc[xhFaRWWMyVd<TbRXUlY'kabcYa8h?:jVyWchG9X*TSeZdhUN>QISO4tUL.?G3}g)QaPgbWQsCQiYdWRUB}yiZNlY9aYHMHGzzZYDdaY[T73h_^]6op_PUUQP]9hhhLqc2kw]Rp>OJW6hjk\7*ZnXPZM`ZcZUdiYicRbQUQndSHiY<>GC)aDgOWHI8/8-^Y6QNA]49ZmQXMolHpaGKJ4gDfIXQK7tSiGTYacJi<TkPU=Shb at kLU@WMlgA^Z1K_FP*KUqP`\ClgbClp`@`Hlbc^DpdTT]PI\.5IWXgGLSwQRNOKVN`LTeIU^9YBdGgggd3\.&RmT``^CVEcEC?ZIsNS\hjb2~og``i:TEYsXjbA`GlaT}RKC`AS_L7]DGz]WFOhZSgY^DYNQwQ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/456/ccs/fwd np:i:8 rq:f:0.999079
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGTTCCATGCGAATGTAAACGATTAGGC [...]
+ +
+ ~~~zplzR~bk^BdsH}c[~~~~sy%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~_[~~h~ybq~{|~@~~~~m_~ay/~~t~~r`Wxx~~~}~h~ZV~XW~lw~pv~a~~\\~m~j~8~~~~UfcV8~N~~]uF?mjPi~e4~~f~4~~l]~lxK~ue]~~m7~;qv~um~_[~v8~~]GI~~~xx{~~2~Zb6~~_~Y~~J~~~R~`|{a~xER|e~dO~zvd~wi~n_~~l~ck}~P~lH~~~]N~lK~r~~~YxSL~~zs~l;~~~wk~E~~~w~D~~N~~~x~L~~~g~~i~~chVdI~~A~tQ~~|~U~~y\~~{~za~ln~~~~zg~MX~d~~;~yd~~O~P~[aje~kh~~~~~~pz~xp~]~~~X~j~~~Y~~V~~e~O~W~O~q~wqU~~v~h~~f~~~~_~jzyX@~~~cE~fm~~~~n~~~~~~m~R~~~~mG~~wo~~|~~F~~n~~~~~~~~i~d~x~~n~~x~[~~~~~r~&n~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/456/ccs/rev np:i:9 rq:f:0.998884
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGTTCCATGCGAATGTAAACGATTAGGCG [...]
+ +
+ FvU~~vWX~ns~~i~~xkhk>ZjG{%~~~~~~~~~~~~~~~~~~~~~~~~~~~{GE~~i~ey|fv`~?~~~~~m~i~V~~uwekZuzE~~{~SK~P]~oS~vrc}~rb~~~[~uB`i-~~~~s~bs]~-~lU`~O~~~m~~R~{x~;~~~~cw~R~~sj~z~\~z~sp~d~~R~~O~~~nC~~~~cvm~;m~rG~~f~2JXR|~p_~l~~~m_bb~{Yze~c~l}k_~kT~~^eKk]~~~zW~~~}R~~Q~~}^~hr~`~~~l~~G~~~~b}<~~~~~:~lV~~qdS8~~~n~~R~lduSuk~~8~}T~~|~]~~iu~obZhf{p@~~rref~~1~x^jm~~Uwsk~D~jT3]~uO~~O~lgn_za@~;~{Te~~xY~k~~Rv~~o`~`~^~_~~Nh~zk~,~hB~{xsg~roZVE~~~eD~t~~~Dni~xDdO~iqH~yvctu~m~/~`vzwK~~~c~~\~sh~U~^~ipSZ~~p]d~~\YfL~|LrlY [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/578/ccs/fwd np:i:5 rq:f:0.989093
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACCGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTTAGGTGCAATCCCCATTCGGGACGGACCACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTGTAGAAAACAATCTAACATAACTATGA [...]
+ +
+ Rw\Qc\cMudc at P2pMGOP[^WbcN6askPb\2PeZ;4YVQMDi[ccLm5ba`^ZN_ at r^8u{ZOEsbMuPEsbFvvcc\_ at u=sl2vM[@Cb[P[cNb2fPI_pB{\Bv^]Z]Zc\Ftts\:ZHv]8OI\_QOpQW\?<BNc]cQ`/V;D&GO):f?]$*+dd].cAEfICcPEf7lkU?@EfI?ffR,MBWIFfIXIRIQT;JPU4O()PV4AY<WR.[MD4_XQI5421KcgXGK<1fSGHEfB6fXHP4:AM=IF8CbBQUIBLHRG;VQIRI at fhV5WUAQeV<CLKeEfXH:,fQXTFQCcNO7llRX1N`cHV=eIXEfI4ONOO<kW:INXRIWR@'UH.dcU;F8bV2c>R at ANIG[5YWPHE*Rc@:1dQJb?QKIR6WEbEBO3?)OKJfXEff%`LLf<kBaRA)AL<WOIRXXRW9WNIRV4;cLf<jV32beFhW at HBDfV4MBGG)PdQXUK1PS_IA]XIXAcIV at KfI9MXQB [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/578/ccs/rev np:i:5 rq:f:0.993311
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGACA [...]
+ +
+ .OIRTGG:YQJVQIW:F(UJY)H>A&]^^UI-T at UBZ9\CTFTuQccBS4rrbZ=TrB\C.S:NZDs)ID}[?]_8{wK]Na;r:T:Hh>POKlPAHD?^1qY.rq:oO:o^\Qb?F8-frrb[M:ajKY6e]Y2wZQb=q at Y?QL4]Y2CUKUKJ8>Mj[6qahMtb4vWIls- at Bitdcb2xZ3vkM=sbc\DsDHCLHO_ at iPa/g'm3[SVtPNP;IX0`&<+>US;VWUa/nV:rbc[2w`C`[PBIIK[<ZQKvcQc[2uZPD;IJ\PX9v|bEacEr``P[NMYB^cZ<NoOOJG'ET[O6si;L1bdg(KRi[Y%uT*cbW?LoMUtM[;VFL9Ld[:|O18ETrbBN%[[Cs[Tp3rpaV3EslKL<jPUtMaNF9>^EsYKMSJRsX at mb%hAAl)eIpVtQZMM\,xxWLbbO[[cR\Rc\UvUuOwbC(UFDtccQcB{c\RQuY3aOTQccQ5sbN?Rkb[N2bZcbCsXVVbR^\b [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/603/ccs/fwd np:i:6 rq:f:0.997493
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTAACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGAGATGG [...]
+ +
+ _~a[Q`jR~hRfD5oE^A%Y__Pf]%~~~~~~~~~~~~~~~~~~~~~~~~lj>~Z7mAUcAxyui?pYH~?jvshst]tjYkq2~occ~Q~ukK~~kgtvlgd~R~pg6~~~ltd~\Q~sQ~~S~pfK~~f>~jPo0b~^fs>veL~~kv`~bLN]MSev^|MRiR~ufP~e^tW~~vtglvfM~clU~ve=~~pUc~ltvgvgL~~vtugsmof[B~svlM~uK~~dF~rveTsL~nfulgvgu\d=~~~iX|se~rR,WRU~h[vdb~:WqcpDRhjL~c[~]frGqfd~j]apa~uR~uT~r2~NrfuP~ktTdIq]5Bd~NXdltgq,LZc~Ojfk^fva>rt~ub~lPlWQ~~]kK~~~~\sk<pT~ksG~uT~gve]fvtdb^`VT~e~[~K~]T~?~~j>~Rw0ppdTb~UqeDuaie~glq1`i2r4~v[~SrUeZ~~d[\cr=sBLE~kgu]L~~Y~L~kqjN~W~wkR~=|{rlqOXsY~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/603/ccs/rev np:i:6 rq:f:0.994991
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTAACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGGTAAGTGCTTCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGAG [...]
+ +
+ \sEHhYO:vhjh`H~_F_j]j\fV`$Z`hq|~vledlw|sidelw~~~~wjelb\N~zK~`]`>~s8C>|jR~Z~eK^KfPe[OT[?yaBE}[~fK@~~\ajfF_G~FjO`H~~~]iH~iX~jO~~R~ha5hi`A~}ahiH~h]_G~D3gf\g\~ah`Q_\5dHq;zZH~g`4~_igE~~gia]haS~aZUuQIH~`<FFaQhQ_Q]?d|fe`Ke\fFRQ~jfFC~|8fhaM~chb\RY~;^Q[ahahja9~vaWUtiG~iaQ~]TwFU~`2{_]jahD~z\Lz\NnjbhhR`Vh-ZadV~_7pPE~PL~Ig_QH~[h]ajhja%\aafJ[iaUgHOGz[Q_^gHO^1~~~f\~\Aga9~~i]<~~~~jhibdJ{[QP~P>w]f`jahjahj`FP~IsNtG~iR~$|yDGZ~R~<vG at Y3SEO`H~fCC^[YOh]W^Y%ri;<m\R[`5yY at dahS~fN>aV5Od.ca=M8VPi]\~R~h\HyR~~fFg\ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/624/ccs/fwd np:i:7 rq:f:0.997543
+ GGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAG [...]
+ +
+ 1~~~g~sY~i\XPwjx~hnAihxn_v<~~py~sW~~M~~u~N~~I~qLq{^~uC~e~]~P~~~qizszi~H~~~~sxPoG~y~{~g~hN{P~g~V~{Cn`~~{~~~{prF~~znTB~~hQ~~~sj~J~vY~s~S~~y\wG~z{~zg~({{FP~}bRvM~b~b[z~g~]~{~@~~ysa~D~~k'~CA~~i~~nfN~zlcocxD{{~siO~~:~Qy<~~_G~vhY~lc~|^gXX~r[~Sd&|~kRdyP`[~lQ[<yYe]~xOS~~XpRnfE~@~gbsR~niqaTe~bt:Yen~]nW~~\E~h~nil'~R7y~~ipd_g]~;jQG~[HC;f[^ih]~~\~gX_Bypw:W~i6~|Q~eWP~~h~mi]EykWrg^nH~yh]`bWcpbb at jwpih~p~[~|p^~~]xmh?~~q]BbcVh_F~U~efdn|G{fVi0U~j]P~0ja[V?yaIom~X{KDmS~~]~]~nS`~h~jr=9{hpW~Z7~l%;~Q|jVb`[U: [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/624/ccs/rev np:i:7 rq:f:0.997786
+ TGGTATCAACGCAGGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCA [...]
+ +
+ =Xdfq}yd~^nHO0x~^~~z+~~~yG~h~~~s~{M~~f~~W~1~K@~~qwtM~se~b~fyF~j~uqmws~c<~~~~vDfsM~`~biR~~C~q}qf[~~utT~~Ttk1Bu~K~~~{~W~jx0~jzyd~Y~j[Iu<%~UZdTh~t[~sZ~`~~{Y~~z~rH~~uKxs~Z~{~l8N~~r{x~L~`gK~~R~~m~~]~ziq~szq~{~]}y\M~~e~~sO~~~f~}]y~{w~C~{qd~rY~qdM~~~`DgwQ~z~cq{~~vGKSxL~~q~{pvT~@~~{~?~~|~k\xs_u{vSbMomc~}sV~[~~y\`~ZI~~jxtz~aM~Ziz^~~cpH~~~nx<~kJ~y~}lvq]yJnd;~yP~qIB~~z~~s~M~^sfNmmb~cZpdilkgpoT~iqe[~o6K~_\A~~~~~r;~~~cqzhnpdM~h~tpsgH{]nfoi\~ioQ~W~]}]V~pt}/~gcnH~]~tU~JmN)j~@iSGfn^mg6~|W~~po~o[ce\Mj~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/657/ccs/fwd np:i:9 rq:f:0.997792
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGTTCCATGCGAATGTAAACGATTAGGC [...]
+ +
+ y~nMmxrI~~i~_i~by^Yx~ysG_&~|{~~~~~~~~~~~~~yjdiuz~~~~~ykb~~7~Ik}~Om~>~~|~_x~`rMzv^~yb~{ah~~xrU`~HUm|RivJvk_~M~~ZJ~{~W|%~~~~N_tiH~G~~ay]&~~L[~LZu[c~F~~~mwULY~~_W~_l;CGVm~``~aP~q1~~~~S~~z~y~~lMnB\K~|Z~d~w?~~yy~Y~iC{\D`hOcNl~y~M`M]~\Wj~u~;ac~j~e4~~~~`~~M~M{m|CnER}s^k~`L~~~~J~I~~qLnS~~Xy~jZ~.~}hKH~fc~l_x_nC~~k}XY~x\~O~~[k~aCkVF~rW~~e`9Rs_s~Mx~*~UMz~W~H~NLoHz`Z~~b~^v`\~wX~E~~{K~g~wmH~lI|{b~a~w~d~]smxI~w]~B~q>~]nhY~]fZ_/s~~F9~~WxkuzJ~nf~y~^z<~}S]xh|t~`~qa~_Yw~`s~Lorsc~?~~~yayl~~y~Y~~`z~a~?N~M [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/657/ccs/rev np:i:9 rq:f:0.997433
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGTTCCATGCGAATGTAAACGATTAGGC [...]
+ +
+ y~`vy_k?~~~}K^~w^tkUWYv~x&~~~~~~~{z~~~|ytmjga]`hy~zx~~o=9~~R~x~w~x7s(w~~okT{QR+~~sSNOh>cQw~N~t3~u;wdi{[ubvv at T~y~d~m1VvD~~~~`yauN~Y~~c_pIu~d\~hj~`v~+Hlzm_~q^z~`m~O~T|MV~~S,~wY~~>~~~fEut~l_qUXM~sw]~~a~0~}b~v_S~b~lvD~xO~x`wauHk9f^T~sW~~R~wMi~t~bB~~~~_~~v~v|_~xMPG~~x\~dO~~~~M~2~uqkfY_~]~~{aj,zu~_~~?~~u`^s`~~d~x[~{qmO~~wS~]w~xh~M]~~~]xi~yZ~bIc;~~wM~N~\pZmWc~wReaQ~ZL^`pIM~G~x~L~^eLtQ~sC~~sY-l:c>~Rvu:Wi`u~,t60~Lu^l~y~|KBz~~za~~sp~oIO~~e~N~x~L~~~yaw~~~N~c\\qFy~ub~b^~bZ~`~~@^s8q~e^g:~jc`si~~J~d [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/692/ccs/fwd np:i:7 rq:f:0.994789
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTATCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCAACACATCACTGAGAAGTTATGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ axePjYg at reRWNNkNeMjcj_Z\=&@fihJgEoOVtih@~aHagcgdfNWt:~+or<uutiM=liNp`]XuOCb;]FnMhZ1idgcQRQGvvhbQIb^:9eW?W,Z]lm`ZgbfKRaU^dNUuhQVQQXFme<b at dTdLiLvv`RxIvU at Z'drn\[QVMQe)LLI9a:`On<a:O[cUdYuUpGYgLRJfELZM0rujUW(m8_K^Mc=ISJ]VX:9PQM)_Q;fcAsTT_b at ea;USmhcGsSwd*Vk;ghQthdhjSwOc at quhB]GIM^]OTpA5x_MidIwj4mHkL`@]]d at tdPrJte9ceWM;iKR(WqWgee0beQd@~haZMDt^-WD:csd at niUuefdi@~VthDdBupd4tY?hElScTR9PKmdNSdAsTcJrOOhfh=tJb9fd.~sl\RKYsOc`PNedb.eMMPsgJsh8~dJkPf)urE?Zb;TMBT&b.,mssrP]aLNb:;cH8Ft9NHE>O``hhdhdfS7xdObPZd [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/692/ccs/rev np:i:7 rq:f:0.995648
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTATCCGCGAGTGTCAACCGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTAC [...]
+ +
+ )\FGI+K&aW_^\OjYD]^HKH`_Z.eQDEBA;Z>H[__UoMPKjLf;ScHuRb$bAS_qgdMvf;tLK at rNFsSvUsdhidhOfOdTd9~~fDL;Qad9ttdd5vwwraNeMeQ<yhMhdYvdTEd<d@~jcRaNefcB at htc>bCgNN]9uvupS6_]9aa4KINHIk8fcgdToLiKJo<]GrgdhcUc5NiFiuiVu7gsVvQcdiicgacJVLNlKf<eeKhJOtd;Hf;kjdhYwaKVg;ucO6tbgjA~eLiN<|/E+nmf3pUJWIDc;~M(phdgM=rtSwFYcMKtqM>iI0a=otbNcUb6qM?bFbNX=QcKd?hTiiNjb5t[,qrBnZgH|gGlLSLDJlIgg=~9oaJNbbaeXoTLAeeh?ttdFKCs^L>X=YX4YPVGc<cL9U]qvgeVuONSgdiNjAplA<~hVu_FX^:Q at U.tttRvjdhidiSu8uuuudh>RCVXb;cg+VSfdSLdjNiWNYJjh at zeb]XLf- [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/705/ccs/fwd np:i:9 rq:f:0.997096
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTA [...]
+ +
+ v~|KTskS~~y~`OvMPLi}h{}{d4~~m^U~B~~~}maX~~<~~w~Z~h0~~cc{@~}P~|~]UE~~~bf{c~~~'~~~PN~~bQ~i~h~h~mL~i~a~g~sJxP~xUxA~~^~J~~~OuB~~\(n~~Nd~7~yL~N~9FryQ|X~{z~xm{cyy_Xz~\gtz~krvbk~^s_~bj*~~O_g~W~zvCzmNz~~~~~~c~~~|bimb~igL}I~uJ~h}2~~{T~`cc~dWyjm]|N~y|~zcIl~~b~~b~~~la~\|y_bz~\N~}[}d~Q|~A~|afO~fOs~~T~Tp]yx}~~~8~zyK~Y~nbif~OY~~~b}aeMV|{~PC{~b}.~~}uee~~g~cu~y~i~M\~~M~~g~c~c~~b~~~|M|hk~bkzJ~~aYd~~~~SqL~~~`~~~~i~~}@z~wnCgU~~d_~a~~~~P~b~~e~~~~~9|~~=~f^\~2~~e~ez]{xz~d~cd~O~~g~y~j`?~~~h{QL~_jMwgO~~;i~e~h [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/705/ccs/rev np:i:9 rq:f:0.997386
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTA [...]
+ +
+ X~HL~<[:vd~wS[Y<Ze~_~N{~i3cgviZ~K~~u;hiE~~`t~gw3~w8v~_g`h~Oh~k~ey.^$ST~QhOb=-_df}b)zgo~RpMk%|vh~cxvwO~y`aT~~_~~vd~~F~~Wffh~mz8~~si\~h~dz}coYx~_~c~~b`vcX~C~~~U~~|~^U|`t6LMkU~~~bk\~~P|}~:~RJY~~p~~^z}9~~l`~a~`hi~_kfOQ~~M~~aFz~~yuU]~~~q~c~{Rf~~GTa~M~~{qOxi~~x~e:dQ~iM~gu[~~b~e]d`~f~~c`X~~g|]]z}|gj~wa}~`L~g~i~l~~}^Jx(SAw{|<cwfWzb~~8~B{aI~~~^Q@~b'~b~kWr\a|c~\-~{rzg`N|vMU~M~S~N~\j~bN~{byWa~ad~LRwbZpJeP[EzsRBk{~mY\Q~~~ia}g~ZOY~~~gxc>L~uqGFLY|RkBdGXT~zQ~|g~L~bg~>~[~sQ~~BM{}~P~]PK|Xhbi~{N~~|~~hf~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/734/ccs/fwd np:i:12 rq:f:0.998898
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAATCGGTAGTATCTGCAGTCAAGTCGTAGTCGTAGGTATGGCACTTGTCGTGCGTCTAGGACGCGTTGAAGCTATCTTATTGCCCGAAGGAGCCGAAAGTCTGGGACACGTCGTGGGACGTATCGTTAGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAGTAAGACTGTATCGGAGACGACTTTTTAATAGTAGTAATTCTCGGTACAACTAAACCAGTAATTTCAGACACTG [...]
+ +
+ ~~|h~~~K~~p~]B~ekU~z~~~b\=~~~~gS~\yO~]a~p9IVW~~z~~k~~_h~<mY~~z~~BdI~G~zy^~z~e~~Rv~~~~~ek~~gF~~~~~o{_~~[~~~j|~~~Y~{~z~V}~~c~~~~L~cXdz~h~j~~~j~~S~ho~bDfT~i~~Hu~@~~~gq~p~~~7~hdb~]~~~N~~_~~f~a~b~~~VvV~~D~~T~~DW~tp~X~y~~M~VX~k~[~~w\~m~~W~~?i~R\~~k~~~TU~~~jx~~V]v~|@~~~o~NocT~Xf~~~~~X~~gz~z\~~u~z0bz~Vd~u~j~~i~TN~~~~~P~W~~~:\/{{n~|~~W~~~~n~~~|~t~MkU~i~~i~k_~bc~|~y~~R~~gRh at h~tq~~w}~vc~~~~~fQ~ojh~~5~~~~~|l~~~~~|b^~~~U~~S~~~~Y~~~i~~~~~_dm`~~gz~c3~~~~d~~~~~~nmb~~~E~d2~~a\gtI~W~~K~\q_k~t~~g~}~^~X~z [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/734/ccs/rev np:i:13 rq:f:0.997555
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAATCGGTAGTATCTGCAGTCAAGTCGTAGTCGTAGGTATGGCACTTGTCGTGCGTCTAGGACGCGTTGAAGCTATCTTATTGCCCGAAGGAGCCGAAAGTCTGGGACACGTCGTGGGACGTATCGTTAGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAGTAAGACTGTATCGGAGACGACTTTTTAATAGTAGTAATTCTCGGTACAACTAAACCAGTAATTTCAGACACTG [...]
+ +
+ ~~Y~~g~:~n~~~x~}fg~V~^~~|(~UUtW~~~gD~~A~~~|~y~k\~b~~cZpi~~j~~dsjqjm~~sj~P~@Y^X~~l~`hq2~qp~EI`e~i~~~t~ih~hqzF~dc~g~~k\~g~~L~it~O~~~~n~RcMH^Pg_nX4~Q~~pZqKpzfr~g>q~Gvk~~F~D5~~S~~5~~Ne~V\~~iq{{)~~~h~xF~Zah:~~~dR~~~~mj~~-~~~tgtC~~lk~|j~~j~~t~~Q~~~s~~bj~~~Nl~Uf~~|c^~~{VpX~_~~~hk~~2ON~~j~qRj~mQ~~z8D2TX}<[=pmyM[+4JhU`tWZ~|~~yd~[i~P~R{f~ygs~ZoPd~A}~~QxZ~~d~~UmtP~~W}~Ni~~~~uz~B~_~cy~wP~~~YHSy|Txi~c?~~~~d}x~~~Ia)hX~~~ktYin~da~~X~~~&Z~~}N~~a~~g~z6~txx~~Z~`:cCs~~M~~~9%wjI~x~zXR~~b~~`t~~Pmbl~O~~~~_E [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/820/ccs/fwd np:i:10 rq:f:0.999584
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ ~~~kc~~U~~~~Y\~fzHv~~~~dmT~~~~~~x~ig~~~S~~gj~~~~~]@eH~^~~G~~~eiS~~v~y~P~G~~C~s~mv~]~~~~~~~k~~x~~P~~jb~~e~-~~~~~~~~~m~~~~wYt~~`}~~~}~~k~]~~~]ue~~~}~w~~~~S~~~~~a~^p~mj~n~~B~f~~pnl~~~v~~z~g~~Y~\~m~~~-~~~~~J~~t~m~]~~`~`~~v{o~|~e~~~~~T~~u~~n~~V~h~e~I~e~~][~K{~y~~zzrf~~~h~~{{~~~v|~[y~~`~~m~~6~~F~^k6~d~~{Ottz~Y~~h~^~Es~ghd~~~}o~s~~~~3~~~~e[~~L~~V~~~V~~c~~`~|N~z~qg~?~~sD~~[~~~y~~ekzG~~Sk{O~~~~~~v_~~Z~~~v^~;~~~~~jb~Wh~~k~|~8~~~y~~R~~I~~k~~~P~~~Z~~fo~n~3~3u`~~kq~~b~~m~lz|~~vZ~~j~~`~~~~~~O~~C~m~y [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/820/ccs/rev np:i:10 rq:f:0.999453
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ ~~n~~q~T~{~z~~~~p~~l~Z~~~4~~~~l~Z~~v~oLg~imi~m~pt~X~q~=~~]~~~~~u~~P~~D{~~h~~~n~~~w~~i~k~~~N~~~~i:~~~n~~x~>~~~~~n~J~~\~~m~~j~x~9qK[V~~~~mlv~~~[~~~I~~~n~gS~~r~qx~~~~~~~~~G~~JqQ~~k~m~jT~Q~T~~~~~z~~jtK~~~e~p~~y~~~~~P~z~~k~m~~o~~~~n~Z~~f~n~Y~~~~v~~m~~G~v~h~~~~O~~e~~D~~k[~~~@{tJc[t~P~~C~~~~Fy~~~~~~~Yq~~o^~~:`P~~~n~~~W~~}iv~~~~x~k~jj~~~6s~I~~M~~d~~yx~hu~nrX~|~m~~X~7zx~}~~bfs~~lOx~~K~~j~_q~nWVyNA}e~|~m~C~j:~~~~~~A~~Z~~~rGrs~~~Y~y~~xp~~u~k~_~~~w~z~~~~~{~I~~~~{~n~~y~~C}~K~x~~~m~vm~`UwY~Ng~~~r~^~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/822/ccs/fwd np:i:7 rq:f:0.989463
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGAGCCTTTCGCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAAATCCCCATGTCGGGACGGACACGCGGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAGACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTA [...]
+ +
+ E\?-Q/6)-KeFJ4i8N9H>[QYKC-fXhOMQOKT.OR;MU@?f?^^DW:Xo`:QGZLV9&TL:JStc4c<CWE$fUZf?c(AA9rsO>MAa at DW-P@_AW at Y7@LZ8rS?aR\Q<DB8;7C[TLN6WWL3Bl`RGtRSe?m7O+1KL[9`SL0QEf0R5U=3`V6/<^C[*JWZ?]0o_T_hDvN(lZJ-'=IQEc9QNRJ)M0P*ePr/PQaMI`HQGD^f1XYON&PFG*P^ph[*XN1rpdQ at _KHb<NM&BbOMOPR-hSS`L+C<=PJTQN<9.c[PLD]+YqgR>PP:3^_PQAVQhI<ABSdR-rkPMCgOE:WNT:G:hJCcXX?/TZRk,\<7NF?IFA2[o_RNSq^3tT$BY:I<KM-_iSDR5WWQO?qSRVCUPO.?_L759RRSQseNgb6YUDYHq=H.^@ARLV9o]N:7QBYBXLM&=BFNL@?ohRFssAR[E(Q;kJN(JRO%bmSR]HR<RET:AN[Q\JVH]3&JM>H [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/822/ccs/rev np:i:6 rq:f:0.985987
+ AGCAGTGGTATCAACGCAGAAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGCAGTCACAGCGCGACCAAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGGCGACCGATTCCAATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAACACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAAATCTAACATAAC [...]
+ +
+ >.<@19)/QLB>3_O?RE+'+-MV?']YSQ]WS,L8<>[LPFCX=bWDW-`fJaP:.AIV.\W;GIZG1H=J\[&3Q9BQ:U at m87]1U/TN2W.D?H?o?b+;HR=SG4YU7(T)7G;@SOI*(;Wh\O&mbLA3L<W0K<8+52f>HQ]:;LL9C4g)FB=-a<Y(Q\AI>B4`7^5mu_PH0V>4PWM-iHN=<H8]R,VQ,H5sMFUc4t'LS=6,7KLA]VBs^:8HkO(j\k`KqT9gZQN'T=9Q^?BO<E<Z>@LMXFMRP;N=M:HOKNJ:+ at YS?QI0TSUL9>.91YX;62V,TcR;/;AN<sU<6:n6 at Sg-UP\3VB3=Pj>?]dJOQTQSdO9B--%<RN92Nmg.c,KM=9OOo,Xj[N[IgYV5)8XQ)ypjWGWKk7zGdYGX^eiUZKHscD]1`FmRP2WgFg8ynZYfV%BMPSFXf2U]Zb4aaBImj;V@`?b8ek at S>jQ;jqoWj9?'vu\G3VMCEa(tGVqDw$ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/873/ccs/fwd np:i:13 rq:f:0.999384
+ AAGCAGTGGTATCAACGCAGAGTACGGGAATCCGAAATCGAGATGGAGAGAAAGTTTGACTAAACTTTGTTACAGTATTTTTGAAGGCAATCAACCTGGAACTTTGGATTTCATCAAGTAAACACCCATATTTAGCGAAAATGCAAGCTAACTGCGAACTAACAAGGTAACTCTTTTTCGATTTCAAAATATGGTCAGTAGCAATATGTTAAGTGATCCATTTTGGAGGGGTGGGGATTTGTTCAATGAATGAGGCAATAAACCACCGCAACCTCTGTAATTGACGAGAAACTTGTATAAGGTCATCAAAAAGAATAGATGAACATAAAGATTGAATACGGCTGGGTGAGGTTAATTCAGATTTCCCAAATTATGTAGATGAAAAGATGGTAAGTTTATTGATAGGTAAAAAATCAAGAGAGGGTAATAAAGAAGAAAGAATAATCAAAAGATAGAGCATGCAAACATTACATGGTAGTATTGTTATAGG [...]
+ +
+ ~~~~~~~e~~~~~m~~~~~~~~~~~k~~~~~|~~N~~~~~~~~~y~~~~~P~~~f~~~~x~d~~~j~~X~~~r~~~jB~~~~~~~w~~~~~~r~V~~}~~~~n~~[~~s~~~p~~2~~~^~~}~^~~~~~e~~~~~~V~~~~~~r~~~~m~a~~~~~~~~(~~w~y~~Z~}~~D~~~~~~~c~~~.~~~~~~y~}in~~~~[b~~~~~~~k~~~~~~u~~B~~cE~~]~~~~E~~~~y~~~~~~~~~~o~~~~h~~o~~d~~}~~x~~~p~x~~|~~~m~~~~~~~~~B~~mz~}~~~~~v~~~~~~I~~~~~m~~~~{~~k~~~~h~~~~~~~~~~~~o~~~R~~~~~g~l~~~|~~~~~N~~d~~s~~~~~~~~~~~~~U~~~~~~X~~l~~S~~~~~~~~~a~sS~~~~~}~m~k~~~Y~~~~~~u~~~~~~q~~~~~~~~~~\~~~~~~~~~~~~~~~o~~~~~~~~~~z~~C~y~~~iY~~~~w~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/873/ccs/rev np:i:13 rq:f:0.99906
+ AAGCAGTGGTATCAACGCAGAGTACGGGAATCCGAAATCGAGATGGAGAGAAAGTTTGACTAAACTTTGTTACAGTATTTTTGAAGGCAATCAACCTGGAACTTTGGATTTCATCAAGTAAACACCCATATTTAGCGAAAATGCAAGCTAACTGCGAACTAACAAGGTAACTCTTTTTCGATTTCAAAATATGGTCAGTAGCAATATGTTAAGTGATCCATTTTGGAGGGGTGGGGATTTGTTCAATGAATGAGGCAATAAACCACCGCAACCTCTGTAATTGACGAGAAACTTGTATAAGGTCATCAAAAAGAATAGATGAACATAAAGATTGAATACGGCTGGGTGAGGTTAATTCAGATTTCCCAAATTATGTAGATGAAAAGATGGTAAGTTTATTGATAGGTAAAAAATCAAGAGAGGGTAATAAAGAAGAAAGAATAATCAAAAGATAGAGCATGCAAACATTACATGGTAGTATTGTTATAGG [...]
+ +
+ K~~~~~~l~~~~~m~~~~~~~~~~~_~~~~~k~~t~~~~~~~~~j~~~~{|~~~q~~~~|jQ~~~i~~~W~~~~~~~8~~~~~r~~~~x~~~~~p~~~~~~~j~~~~~{~~~~~~~~r~(~~~~[~~~~~\~~~r~vu~~~~}~~~~~~~~~~~~~y~~~k~o~~e~~~~~~~^~~~~~~~V~~~Z~~~~~~}~~~~~~~~~t~~~~x~~~~~C~~~~~~E~~~s~~S~~~~=~~~~b~~~w~~~~~~~~~~~g~~~~~|~~~~~o~~~U~l~~~~~ar~~~~~~~~~N~~~~~~]~~x~~~~~~~~Q~~~~~~~~~~~~~~~~~~h~~~~v~~~~~~~~~~~m~~~~~}~}~{~f~~~~~P~~o~~f~~f~~~~~~~~~tc~~~~~~a~~~~~~~~~t~~~~~Y~~S~~~~~~~~~~~~~X~~~~~~K~~{~~vs~~~l~~o~~~b~~~~~v~~~r~~~~~u~~~~j~~~~~{~~~~~~z~~Y~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/938/ccs/fwd np:i:7 rq:f:0.995748
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACACTTATT [...]
+ +
+ \~^\QVa(oIOe[8hTX^h^_Xhg]$~vinv}~~~~~~~~~ync\Z\afq}sX=9$)U`WLf]hP~FrQcMkA}go;eO9OeA[AoLf^NtOo6[hc+weZ3~lpogN?:]<ST~rP{fcP{d]TzziT~gdrrhf]AsGwjT_EaMue?znVbeUmF{FteE_U8SkrbTqj8argpfWbZQmZWl:d7~~N>ZQ~bPVNg1RD9jUV9-`DbOTM+WPG_VF?LvNFW~rithfZeLnqddKlG`~hO{U~pQ`~hoT0Qf_qhQU~fV>c;~X~L~\qYfd^YfliiWOT7~~gnbU`ReN|aNseaTEKpD~rRgoZmUI~hsFsh3baPKU<`9*k\X`SdUAYH_naFdqYk>gg8Uo3o~V~Xf[PWiTKdQ`kQRuwW[F[@rdSfVe\dq>~~\~TFmgG~qhblb\]@2uohsQA~~ZAgpQfb8VfQ]\I~bOaG~QC|3thpUOmMprtsieSMP~'nUCw[S0YUdq[FbZb\WS`~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/938/ccs/rev np:i:6 rq:f:0.995688
+ ACAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAAGGTCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACAC [...]
+ +
+ L-S@`qemCqaZLhM~idir`Nfsrh$~~~~~~~~~~~ytv~~~vrt{~~~~xtw~~POVEwphgXeiO_7kKaYZRh=J=fM3hiegFiJgPGmKqZNO^;~frY~oEoe\~dHenSznc~hh`~gYL~~gD~dcTRO_YB~:q_,Z;VrrS~MF~~QfmH]X|_}i?xxgY~rSMyVIDEdrdg$;H*NfSSFa7XlZieLVMOpX~mlX9hjOW?XNjfOFQ~rhgTY=~hrW~n^lQfpR]uqYeW~q>|b:|C1;dQ~hntseaN~XdK|g`gT-tLkO~b~mQgb~hbiboQj6ttOf\B\D3_~QV~raNiAx&kPLPphX_P~gqEtYNilhhlKJIL~\hhh`~hllSffelf]R{Yc;YG~~Tz7pPI5\e1i~M?O5~~`q]f`~Qkj]d:6XH~ta~O~pQLiHdPOFQprW~thrf<x~~qRnghe9W_LWfOuOOgM~g`~Rvhrrhn^eFnreibPLn@~~_~na2~h~~~m:iN [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1034/ccs/fwd np:i:11 rq:f:0.994946
+ AAGCAGTGGTATCAACGCAGAGTACGGGATCGTGGCCCAGTCAGTGATTACGTTGACCATGAGTCTGGCTGTTCTTGGTTCACCATTAGCTGTGGTGACAATAACGGGCATTGTGGCAACGATACGTCGTACTGCAAGTCCCACTGTAACTAAGACAATTCGGATTCGACCGATACTTGGTCTGGTTCGTTAACTTCGCGTACCTTCTGCTTTACCAGCAGGTCGTCAACGACGAGCCACCGTAACGAGTGTGGTTTCGGTTCGCTTGTTGGTGCTCCAATTTCCAGTACCGAAGAGGTAATTGCAACTTCAATTGCTTAGTTGACGTGACCTTTCGGGTTGTCATGGACTACCGACGGTATCTCATACGTGACCTCGTTGTTGACCTCGTTCTTCATTCTGCACAGACTACAACGTTAGGACTACGGAACCAGTGTGAAGTTGACGGACGCGCTAGTTTATCAGATGCGGTTTATTGGATTGGTTACAA [...]
+ +
+ w~gB}bmSp>NkU7kN=q~m~auZK+mMoGrP~KiA{f[m~fva0&TY}ec\OXT{Aimt at dgg3A%Cot[,AEP[VwNub at Zj]7gmlg|n|D~UbycSn}U}_0Vi|~[u\oR~`^zfhsn~xy~vx~~fc at Ocv{~;v~dnqPpV}RwJoja[\~k~]^~~g~{dx/CSs4NbEy`~yDlO~X{w\d~jj+Z~cHTrzqE~b~e~i63TpeR~~TYZOj`7SzXNUB;NVq~kCzh88*JGjH2KRb_~V|=wSI<MCI0cV;G4;n&GK=0'0HHWE*B<WB^I_K\GY~vx_~~z~h~yg\~_s~PUvr~hh[~rxP~xCSNLt{O~<~ph<~n&GIYLrG8]~e}j@~U~lS~mAS\ukbZj6eu`p5OWObK{Kik]PChX>No~yi~pW/^nhdRb={``:m|dFvmzu~qf~kOtJcQ\$wTyMw~tw4O}F*Qgq=NqyR_jk{ncuL|yp&Kn\R?>c\p.~~}_~XoVdeVzF:[h[_ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1034/ccs/rev np:i:12 rq:f:0.997156
+ AAGCAGTGGTATCAACGCAGAGTACGGGGATCGTGGCCCAGTCAGTGGATTACGTTGACCATGAGTCTGGCTGTTCTTGGTTCACCATTAGCTGTGGTGACAATAACGGGCATTGTGGCAACGATACGTCGTACTGCAAGTCCCACTGTAACTAAGACAATTCGGATTCGACCGATACTTGGTCTGGTTCGTTAACTTCGCGTACCTTCTGCTTTACCAGCAGGTCGTCAACGACGAGCCACCGTAACGAGTGTGGTTTCGGTTCGCTTGGTTGGGTGCCCAATTTCCAGTACCGAAGAGGTAATTGCAACTTCAATTGCTTAGTTGACGTGACCTTTTCGGGTGTCATGGACTACCGACGGTATCTCATACGTGACCTCGTTGTTGACCTCGTTCTTCATCTGCACAGACTACAACGTTAGGACTACGGAACCAGTGTGAAGTTGACGGACGCGCTAGTTTACAGATGCGGTTTATTGGATTGGTTACA [...]
+ +
+ &=(3RZdW~o~{ZP~Vh)RdaetPS'~~]gekst at fJ~~kvo{~sz_~kr~~lj\~w~D~~~R~[RhoS~=uoD~^\uP~K~p[.~~bgc_TVnQ7r3aqVOsZh~}4~~o|mmhs\~mN~k~~~~~~~}n~yu~g[]io~W~~~~~}~~~~xd~~~~t~u~~g~~v~~u~m~o~~~~h~P~[~~Q~m~\~t~r~ksgwd~u~~e~b~j~~mT~~~f~~y{pi~~is~~<~rn~~~~~\~oS~~~h~~gi|~V~i~c~~k at rw~txvc~d~_yB~~~Y\~~h~j~~a~lg~rZ~hJ~ViNe~n~k~Rjk}|Z{ru~;~~W]b~~O~E~~~~K~H~*zzsnG~~_n~~X~b~qfv~B~l~Th~~~~~~x~~~mq~v~N~~{Qb~~`~pBe~~}~N~zG~~~~{of~AY~~~ir~~p~r~q~Y-~~~~rfC}b~O~~nzKlct~~s~ktxa|sUP`Qe~~pM~~~|~~k~~^l~f~~~n~[~~r~\~9]Sc~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1091/ccs/fwd np:i:6 rq:f:0.997974
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGTT [...]
+ +
+ i~mO[n{5~{twLQ~gog]l]gbX_$x~~~~~~~~~~~~~~~~~~~~~~~~~[Pmo\oV~tgn[H~mbWw:pQ~nh|TE[~~g}D~ntgrf]~tgrD~c[la3~nY~o:ze]T~iM~S~dqgtW~pm~;~~k~Rro~o~m4~OC~~g\~]o|Wi~n4~{z|ygog~I~}gn~&~~_]~~g{Bc~tqG~qdfoj~dsuQX~g[~d%~~togb~l@~FTxa~fQ~SWuA~~}ZP8~l<cV~~mQi~?yC~~d^@/{}N^R~ogoM~~~oV~o~9~~~tjmdncO~Q~{sK~sE~~t}6y~f~og~g|>~gW~9~iP~`k~bn|Ynw/`:m`|QL~~~pFz]xc^fwM~gmdm}]U~~r?~h~rotmQmm~Z.~B]un~rfj[Ybqgtos:~xf~gb~~o{\Q~~lX2|x5t<TWqEqkO9t{g|Nbf~c,~insVOm~P~ngtg^~~RrouU\~]dX`~a~~]eI~}]~~b~Nz~gogtgtgn~goTGRnR~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1091/ccs/rev np:i:6 rq:f:0.998009
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGT [...]
+ +
+ J}Y^a_`F~rsdmJ~ld?yaJhh}o%~s{~~~~~~tfYWat~~~|n]RONQcqYWd^ern]}k(fE~}ogo;]\~~\tg}D{on]\~g}RnsD~}mc[~u~gtR~~U~~nsn~]~fE~\~qaU|Xrcb~R~~b~o|;IQD9IXG:ll]C~ZGYj:lS1~~~~~nfA~V~tn>~P~~R~Hh]}]s{FG~bpnha~jvsWU~nD}R7ryw~om~S@~~^~b~oh~on~=xz~~n;~~7SV~\eo_~coJ{~gglC~uZ|H~Mkb.~uodk~:o`~~t~h|\f\m~]~t~]~~6~~~r>~~mtfV[mqD~mf~L~~Y~eX~og^lNpog]~b~o<~~~~xnyj?zosV~n`A`V{I~r~X~U{]d~eod[~r\~R~~gl]f|\yDzmaN{H~~ntpn~sg]}>~Q<`G~p?~gVkqn[dSf~YXpl^kson~g~rQlc]l~QlaU<~~jwe\|&~}~ogY~HxrkmD~mQ~tfy;~~VemaU|oV~WSXxmOH [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1092/ccs/fwd np:i:11 rq:f:0.998396
+ AAGCAGTGGTATCAACGCAGAGTACGGGGATCGTGGCCCAGTCAGTGGATTACGTTGACCATGAGTCTGGCTGTTCTTGGTTCACCATTAGCTGTGGTGACAATAACGGGCATTGTGGCAACGATACGTCGTACTGCAAGTCCCACTGTAACTAAGACAATTCGGATTCGACCGATACTTGGTCTGGTTCGTTAACTTCGCGTACCTTCTGCTTTACCAGCAGGTCGTCAACGACGAGCCACCGTAACGAGTGTGGTTTCGGTTCGCTTGGTTGGGTGCCCAATTTCCAGTACCGAAGAGGTAATTGCAACTTCAATTGCTTAGTTGACGTGACCTTTCGGGTGTCATGGACTACCGACGGTATCTCATACGTGACCTCGTTGTTGACCTCGTTCTTCATCTGCACAGACTACAACGTTAGGACTACGGAACCAGTGTGAAGTTGACGGACGCGCTAGTTTAACAGATGCGGTTTATTGGATTGGTTACA [...]
+ +
+ ~~_|~ms^~xrcd>~hxSo~|~~Nm,{~~v~r~~t~*~~h~~}~]da~c/~\`~f~~e:k^Ni~Y~gyo~~~~~~e,~ct`~]b<~]m~~~{jZ`^~~~{jj~~G~]M~~Osv~~~b~{[~wq~~}{s~}~~~qni_H~xuB~~~kOsua~}~c~~~UR~Y~v_~xV~z~Ra~~~~abj~]~~`~\~l~f~n~a~`G~t~|~~~_~~~h~~he~~HH~~ky~EjMf~~ZMp9d~`ovr2~]0~h|h~a~g~~~~[xC~~d^~i~h|aJ~7~~~A~~z_,~~]~j~~A~w~~tF~mh~~~r~~v~f~~Uh~UcmeS~~~az[~~pS~xQSm~iP`~H~hcf~~~q~ft~H~~QPv=~~mDp~xb{v~sudu|~~~~P~~ft~~~]~~~S~~zw~~r\~Gn~Wqipm^~]K[qoH>ys~L~iS~ms~inl~5~5b}~~L~}l~kz~~xPp~aI[a]v~~~8~~%eilt~~~cl~]~~~m~e~~W~b~3~\v] [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1092/ccs/rev np:i:10 rq:f:0.998561
+ AAGCAGTGGTATCAACGCAGAGTACGGGGATCGTGGCCCCAGTCAGTGGATTACGTGACCATGAGTCTGGCTGTTCTTGGTTCACCATTAGCTGTGGTGACAATAACGGGCATTGTGGCAACGATACGTCGTACTGCAAGTCCCACTGTAACTAAGACAATTCGGATTCGACCGATACTTGGTCTGGTTCGTTAACTTCGCGTACCTTCTGCTTTACCAGCAGGTCGTCAACGACGAGCCACCGTAACGAGTGTGGTTTCGGTTCGCTTGGTTGGGTGCCCAATTTCCAGTACCGAAGAGGTAATTGCAACTTCAATTGCTTAGTTGACGTGACCTTTCGGGTGTCATGGACTACCGACGGTATCTCATACGTGACCTCGTTGTTGACCTCGTTCTTCATCTGCACAGACTACAACGTTAGGACTACGGAACCAGTGTGAAGTTGACGGACGCGCTAGTTTACAGATGCGGTTTATTGGATTGGTTACAA [...]
+ +
+ N~_kweAR~y~}~~~u{u~u~|h~~8~~~~~~bg[~$~~x{uy~~y~c~}T~~~w%Q`X~N-DgT_s~L~Y~cP~~T~[yC~~~r~~v~~~~~nnY~hT~~r~^\~~N~~s~d~u|R~~h~tz}Q~~czza_~~eyvY~z}Q~~~~]d~U~~x~~Q{rF~a~mL~~y~~}~V~c~fz~w~D~~~~i~g~o^y~~~~l~x=bg|~s~y~~~h~N~~~o~~_~~]~d~~~~v~pa~~|~{D~~X~fw}~~O~u^zuM~l~~~c~f~~wqV~GhF~G~~~SG~~~~^~~k~~cr~_~|j~zX@~~s~v~R~~~tg~~~~j~f~d~~xg~bLuk~l~E~Z~~~C~~~[m~~~h~gpL~+ih~~U~{z6~y~~F~tvrg~o~y~|R~rt~v~f~i~hu~~j~~~\~~elqT~}~~w~~h~ozw~~S~~~~~~B~Z~q~~gdvi{~~Rs~xg~E~~~|~crw~g?~~~~~f~zT~_~T~~td~d~~N]7~e~e~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1133/ccs/fwd np:i:5 rq:f:0.993046
+ AAGCAGTGGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTACCCTCTCTTGATTTTTTACCTATCAATAAACTTACCATCTTTTCATCTACATAATTTGGGAAATCTGAATTAACCTCACCCAGCCGTATTCAATCTTTATGTTCATTCTATTCTTTTTGATGACCTTATACAAGTTTCTCGTCAATTACAGAGGTTGCGGTGGTTTATTGGCCTCATTCATTGAACAAATCCCCACCCCTCCAAAATGGATCACTTAACATATTGCTACTGACCATATTTTGAAATCGAAAAAGAGTTACCTTGTTAGTTCGCAGTTAGCTTGCATTTTCGCTAAATATGGGTGTTTACTTGATGAAATCCAAAGTTCCAGGTTGATTGCCTTCAAAAATACTGTAACAAAGTTTAGTCAAACTTTCTCTCCATCTCGATTTCGGATTGTGATGAATATGAAACGTTAAATTGTGATTTTTTCAT [...]
+ +
+ TxGR`]i.wXP^hS8gS]S^]^]g8P$^djpoebcgmrsssssssssssssrkIH/anhRf9RmV]2vvvvmVB\`^e)L[bBosJIjF)[KL3D^a[S^jSj]T[PLq9iDBuqDociSj\.sWk9Q+QAF^=jqHYCt]g`[vR>u?Q6anMMZWhMB%,;e^UqS;uwwq[4g]^G{Us^jY<INZ,`T0RD[PS6fTUHS]]^PxZvGRLujLv;vO5Wt)HBqF<\P`04AL\6YP6e\_,[^iX4imhQ at x@vyyhNwZ7LYRHt?l:Ki^WW]QPGRY)ZGx^_OJvvqF8vuPR\%tn[Q[I\ZuH&A/WPTr^\FuQFRGEZv^\R7s\RH(shT>H<M4hkg_c0vah\%mTX,HZ\DUZ9afN4b7do]@cFzZ=r[v[IVw\3vItS<xxxxi^RbCe6L;7QkYHrlI\iTHxxRCuuSiSi at SZiQLNEGGvtSPuYVtDLE]i]=XTVW\;deQ]9Q8vp[u]gEG'jlZ\eQI? [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1133/ccs/rev np:i:5 rq:f:0.992838
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTACCCTCTCTTGATTTTTTACCTATCAATAAACTTACCATCTTTTCATCTACATAATTTGGGAAATCTGAATTAACCTCACCCAGCCGTATTCAATCTTTATGTTCATCTATTCTTTTTGATGACCTTATACAAGTTTCTCGTCAATTACAGAGGTTGCGGTGGTTTATTGCCTCATTCATTGAACAAATCCCCACCCCTCCAAAATGGGATCACTTAACATATTGCTACTGACCATATTTTGAAATCGAAAAAGAGTTACCTGTTAGTTTCGCAGTTAGCTTGCATTTTCGCTAAATATGGGTGTTTACTTGATGAAATCCAAAGTTTCCAGGTTGATTGCCTTCAAAAATTACTGTAACAAAGTTTAGTCAAACTTTCTCTCCATCTCGATTTTCGGATTGTGATGAATATGAAACGTTAAATTTGTGATTTTTTCA [...]
+ +
+ ]hKS]KT at a?Z?RKiR6=TI,=>\P$D>KSPLKMQVVVX]defffec[QKKX\4j`SR?R9gKU(gggfJ=Ea(;QSJeS;fSJD\D2N<>R+gfOH]TSRD<X*Of=SU9g\:fc87RKMPBbKT5MFEI-sXPQNwS]O>u\Kw\-%bVeYRM`FaIYWaInX+tusUNiLROOa0meD]YTr?:hXCG\S^EBqJqi]g=NEkOmQG at k^DxEwuKLbR8jADeLWY`LU<WtF?s_]@wvgM1ciQS9a=vra\%]/1RX[KMtS5ZCHDITSHCZ]^SiOqH5`'psmMHPE1Y<9`YF]QeS'ce:X.J9Sb<*@GY;?1:NrN:[PxS]i5vvv]S]^(M at IXQ1XKY*CgecY=WPY/AK\\IKo2Wl=+SB5FG9\1mCf5LPN\=s\3vvvo$79RPBDNPB'VB?Gsxg>\]BuuG7okV_VUMri]\\DQh.XYY\Dyh=hOX:F[QRR^hI;GtpVRPwBus)sYQXQh1wwwwu]h [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1199/ccs/fwd np:i:10 rq:f:0.999121
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAATCGGTAGTATCTGCAGTCAAGTCGTAGTCGTAGGTATGGCACTTGTCGTGCGTCTAGGACGCGTTGAAAGCTATCTTATTGCCCGAAGGAGCCGAAAGTCTGGGACACGTCGTGGGACGTATCGTTAGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAGTAAGACTGTATCGGAGACGACTTTTTAATAGTAGTAATTCTCGGTACAACTAAACCAGTAATTTCAGACACT [...]
+ +
+ ~~~O~~~z~~~~R@~zv~~~~~~z~S~~~~/bdh~i~{x~~V<~p~~~~co}~v~s]~`~~~~Hk~e~n~i~v~b~~~~av~c|~~~S~~~V~~{~~]~j~sik~~n6~z~?c~~~~m~~jn~~~~y~^~Co~~~X~~aj]~~~jx~~kwkvd~~$~w|~~~~By~m}~~@~~zz~w~~~E~~i~~~~V~h~~~~w}x~}~~5~~zj~~~~h~~~z]~Jm~y~Q~~~m~~~~W~^~~~~Y~~~s~~~@~~~z{~~ng~~~U~~~~~~hy~p~~~~e~~Z~~r~~uD~~s~~Xw~~m{~{~x~~~{~W~~~z~~~@~~~~~m~~n~~~6xh~o{d~b~~x~~n~~yc~~~zS~~~A~U~y|~~L~~]~~v~~S~~yx~~c~~~~~~l~~~~~~:~~~~y~k~~~y~c~B~~~}~~P~~~~c~x|`~Y~~~oo~~~~~~ek;~~~~l~~~z~R~~Y~r~k~gx~~Lyc~~~F~~d~~~~}~L~~q~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1199/ccs/rev np:i:10 rq:f:0.998808
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAATCGGTAGTATCTGCAGTCAAGTCGTAGTCGTAGGTATGGCACTTGTCGTGCGTCTAGGACGCGTTGAAGCTATCTTATTGCCCGAAGGAGCCGAAAGTCTGGGACACGTCGTGGGACGTATCGTTAGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTTGAAAAAGTAATAGTGCAAATAAGAAAGTAAGACTGTATCGGAGACGACTTTTTAATAGTAGTAATTCTCGGTACAACTAAACCAGTAATTTCAGACACT [...]
+ +
+ v~~aT|p]~z~hy|~lyM~;eyd~a3~~~xlwh~mN~~[~~z~~~~~~(|b~Xm~l~~Y~~ar~m~k~~s~~?~~~~y~~s~~m~_~w~~~]~~~~~~~~c~~~y~~~~ka~vr~~~~w]~_~~~[Y~T^~m~~t~~MRl~w~~~a~~~q~~J~~K~~~~~~~t~~r~~\~~~~~L~~~g~s`~~~~~~H~~}z~~Lu~x~K~~~~{v~U~~S~~P~~~~~~J~~~~u~wv~]]~o~~v~~~t~~iq~~~~1}n(|~tu_~~s`~w~~~~~~]~~~~`~~~~~_q~cs~~~o~3~Q~z8S~~~x~?~~~l~p]a~~~x~m~wl~~~d]U~~lj~v~~U~~~~~~~~~~~~~y~~~~~~i~~S~~q~~~~w~~~yt~~d~~~lqqk~u~7~cX@~~~k~~Y~~~slp~i~~~~~~Z~~~wl~y~l~x~~v~K~yq~~[~~4~~~~~~~~~i~y~~~p~~~~@~Y~~q~o~J~~N~~vqT~c~~~~n~~~~z [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1216/ccs/fwd np:i:11 rq:f:0.99572
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACCGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCA [...]
+ +
+ a~lYaXa\~}P(<&bYWfsS~T~~g<~pt`bnY,~~~~NKmP]eQD:`G`eN~{~v~A~]>_I~li~zlc^iI~~~gsF~zQL~~wQk~Kpybq`r$R[`lfe=~dH~x[qW}YaKueNrIU~~qtOerQ~T~FpK~yd=ZvJk~=3_i;w~r;Bm[c~Qm@]f~Z~f~h~B~~M~cX/~~~h~~Ki~]m~pvDpF~q`~zRC`y~Y~iF~~~p at WU}idB~~2Om8=Y)rBEr$~sccIdL\G^NFpZn;aVo~kj=~~~D~X~mklAxPHusfg^dZmx~i^PB~eaf?MevYFS~~Z~VNw>F]aks~~'~~m~m~c~~U~~m~6~o|~j~~8~~hXZijT~~~0~~^\n~~~B~ziGfW~~~m8k~g$@A]t>hB9~L~ch~Mt~ghj~}F~Hdg~p~~q}2vTx~R~W~UN}=sj*aBdkjd~W~s~~n~3n4~zJ~uj[~j~~~~qfWmm~~p~Q~~~~l0~OO@~l~b~W~UjP]o~qh~~mk [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1216/ccs/rev np:i:12 rq:f:0.997323
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAACACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGC [...]
+ +
+ .eUzt^bFscS~~X|y[H~S^l~~~%sJ[uAZf%~~a\vTPvu~e~_d5xz\~M~LfH~~OPDz~gp~~Jr~F~~i~~b~~[*quuxYe~8}o^~m~U~~g~VQ~e|~T^~:~nxE~ieyiR~PlCe at H]X|~]YT~]1j~~:~gMM~~>~~gl~ZufeViZ~m~ZQl~GjU~}@xjO?~~~DkYfBH[_Il~]eW~Wo~k[6~~+G_Lvpop}okolS|~Z~XN`t~\~~Wqp~M~~q~j~i>Y~j~fVl~j~ko~VE~~~:LJb~~VQ~U^K~~~kocEbi]sdMwwdh>qxrh3XM~~?~~~Y~qosqt~[D~~w~|jT~~v~~_~k~lxZT~kh~~]~`m~kZfCiwh:qRw[>.~Y]^t~~~~qa~~~~jmpPCyD~`~m~~p~i~~ZzXI~Rgf~<~e~|X~~PxL~j~pA~K~}U~~~hpV~eoXhkp~|i[~xDzpZ0~[~~dJmmwYioW~iX~npxK:~Cre}{~U~_~ifQHIql^~BX [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1226/ccs/fwd np:i:5 rq:f:0.986061
+ AACAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTCCAATCTGGCAGATTAGATACAGCTATAGAGCGAATCACCACGTCTCCTAGATAACTGGCAAATCTTCACATTTACGCAAGACCATAGAATAGTCCATAAGCAACATATTGCCGCATCGACCAAATCATGGCTTTGCACCTCCCAACTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCCACTGTTGACCACTCAGCACGCAATCTGCAAGATACGCAGTAATGCTAAACCATACTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGCTA [...]
+ +
+ J>(-2REpTOYP<NQQ at SO@OWE3$jZOTZWWWWZ^ZTQRTTROMKKMRO94C4HQK>7>8OO at 7N)@W9I8IN?:4IUL[HQQ>]2AJ1RNJ4QPQCK'=JFQ:ILK3G;<TUB*;V;CD$*X[ZNK4+B:D,7+QEIDOKB3B/^*=-PPQBT?0./@XIDWC77A052-I;A0 at H3G=U6,UJCE?+?G2YT=C-&;.3MD'/KJH<S;B*MLA<BFFB8;=SRZPO3YOPD%OTW>+9TEPR8ZIjPHCCd3<9K;7LOEDlYRW&LBP9RJEO4fVIYJ7O5WBPCR7SJO:I8QDO<T<N/PIZ4gJYKiNO;GUQTIQ0N[CnhKW8:NM,6%:/2FGC2)7-:@;%>=.N':LM8.S4,2:VQMXK;M;QL?%A at .R@2-M=(%04MKTT7<9(764.;C3B'M+80K>N>ZQ9(=8/D?IFRNGPT6X?+T-CTOBVV;PYQPUT9M?=CJ5ggg\PA?LOQR7:JK2ULPPFRHBE&FP/ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1226/ccs/rev np:i:6 rq:f:0.992886
+ AACGCATGGTATCACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCAATCTGGCAGATTAGATACAGCTATAGAGCGAATCACACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCAATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCCGTGTCAGACTATAGCGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTTGGTAATGCTTGTCTACATTGGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTAC [...]
+ +
+ $1:D9;$9VGQdY3/Y[[RJNF[V$V[]_^][YTLDBELXbkrme`]]^]WC7)*NSeKQ<KlJ^PLW{aDZ;a[cD;>4NMV\XZW at I[>BA]DW;XLHmA_P?8]3jYJ9dZCqR8?LcVcX,OGsaC>YR\Xa?p$&9YU at VaMNJLaWTeUY3yY]51NUIgRRDUNAZIl6acLB[^JyZI``Q*[Wd;i?^Y/nZPH^dE;ma%TYSY`@_G]JR_;EFL(a[LQG`XD`DoYJIVaWUCV`Ek[V^CJPCVRM?<C`<]MDcXDTKBfUK:JhaCZX<N8RKZQ{WZfaZC9[HX>_ZgcY2t[KT&(IdYPIeEe[eKYb$Z'F\VXU at CAqY7M\@LZ6G,MK=X_<MI=dSQEb[BaPUQ;>4.JXRFTXRiM\A_NOL]VRFh_RK?5OR?gab3WLc`;^]YbMAcaHSXF;UZLAbYaA[?b>IiHl\X=P)XYARYN]F^eC_43\KQ_Y;X\Y[d[YGURqFXDDrB$l7ODaNR [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1234/ccs/fwd np:i:5 rq:f:0.995348
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTGACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATCGACGACTCAAAATAAGAAAGGGAGTTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGAGATGGT [...]
+ +
+ Z~HCe`l9^jQjAOnZ5Ee]T`ngO%ct~~~~~~~~~~}skks~~~~~~~g_G2NU0|p`_=mQAQ6~lg]NP;f`m^[@rDCDdG~m`B{b^Hfn_HY~V~GN?y~uZOY~h_~R2x^:[LWEZdY8ey]ah_~\UMByWMdx\nX~XcHl^`VLDw;g^7~iHT~[hm?~z_HW_g8A<LZ<xM\F~rU^K~_Qe_n_D~~nhn(cdam`l=~abF2~fT~~_P~fn_`nW~T]n_Hl_lPV1~|c_W~g^~IYFiJ3h`G~^_~``c2jD~~`X~_R~fHh<j]Kh3i`lX~nX~nJ~nQ~_h_fE~`lI\QkQ]6~p^kH_h`k<]gn_`fH^R[T\<~jhmN~^6~\G~~g`.~~~~ocNbHf`~`U>nj'}]jHf_nh_g_\D;~^~@~]~RJ~H~~`IeAwE~~^_K~`n\.~~__~_`k<]_Ql@~mH~[bHF.~~.ghfO\E~j9=~\_ifD~P/gLh_Q_FlKlg_K~@~~m`eIadQ~< [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1234/ccs/rev np:i:5 rq:f:0.994891
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTGACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATCGACGACTCAAAATAAGAAAGGGAGTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGAGATGGTTCGTA [...]
+ +
+ >uA6_]:=eRlU`K~^NXf_RJhnZ%Xiw~~~~~~~wlefny~~~xmfer_[dZSH0hlO]Q~nN~[~hn`nhnh^R]hN~PH1cWdg^A~{\\bN0\6~'ch`0~~j_k5~gAhd4feP~g_4lXD~~`hnX~\.FBb\@~~^aAfEcHf[_`h^~=~XIbP_`~`nf5~~fi_NTG\~I[N~eI5~~aXX~_nh`h`C~~fne`N[:Y;P~nh_A~S at w~`N~dL\_h[db[h``h_Qh_2UiWJ5|V*~k`_~`L~\J~\.^\]e`f<g}^Q~`Bre[Rc5^X~^R^J@~eN~f_~hN~Gkah_~_R\Jkhm`=~~_g`_nahn`nh_Hk`_n`d1Hix{QZpJT~|;LbgG$u~~jQl`nW~_iMhgN~_i^n`Ol_QjI\Q~G~O~H~nQ~D~|_[iQ~N~xIWV{_h`F~~V>aY\Rl`_eQ=}:EaGf_`O~~`hn`hN~`SQ~\FNl3zK<~I|]RD7gQ~h_X~H~~h_n_mU?oW~`_hm [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1241/ccs/fwd np:i:9 rq:f:0.994309
+ AAGCAGTGGTATCAACGCAGAGTACGGGACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGTACAGCTGATGTGATCCTCTCTACTATCTTCTCTGAGGAACCATGAGATGGATAGTGGGGGACCTGAGTCATACTAGGGTAACTTCTTATATGGTGACATCACTCCTACCGTAGAGGGGGACGGTAGTCTGTGGGAAATCTACCCTAGTGAAGAAAGGTAAGAGAATGTCTGAACATTACCTGTAGACGAAGGTACTCTCAGAACAACTACTCTCACATACGGAAAGGTTTGGGTCCTTGGTCAAAGGACTTTACTGACTCTGCAGACGGATGAATATCTGAACCAACACTTACTATCAAAGATGTTCGACTAGACCTCTCGTGGTAGGGCCTGGAAGTCAAAAGACTTCTCTATGGTACTAGGTAGGTAGTTAAGTACGGTCCCTGGT [...]
+ +
+ Ev_`UWQP~vx>EIjS[;RYshk~r1+V}N~hrWkb2ru}n]kQ{d<nVWnpbAhv_O~yWi7Dy~3mQg=~~x\~prlzVtF~<{jqg_fi~b|hKhIX(lZV\P^QaHg[ScUMI~isog}yDf`&H;wrlmai\X~R~Ow\ymrnZw8turtK`%UG[z|>ze`qanx~~~w|~:~~i\~r.|tY~pd~vY~{nzadywz\rR~~hT~ZhK;l'~~aktWSbxdc~Pknk-~nQ~~gihhDq~@X at bh0hI89\Ty]AdXNRTztft`{qa~?og~~[~knkUn~TiRpS~~lZR[gt~o]egHwb~rl]UeW~nfymdJ~H~~M~Q~p8zziU~Jx3Ne[B]H^~~K8~}jCxZstr[{_^~n~T%gp`eZ~bkyyym\~[\(pRWS*NO]lDRo;z~f\ofJ~j]Vn~jmUY~Md]ZTg/~{[IRsO~SL~P~SfJ3fvjjBZS~uxZv~x&ez~tOlCy_Q<j{~=WyY0j~~j9~|;~~^1~K [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1241/ccs/rev np:i:8 rq:f:0.991317
+ AAGCAGTGGTATCAACGCAGAGTACGGGACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAACAGTATACGCAGGTACAGTGATGTGATCCTCTCTACTAGTCTTCTCTGAGGAACCATGAGATGGATAGTGGGGGACCTGGAGTCATACTAGGGTAACTTCTTATATGGTGACATCACTCTACCGTAGAGGGGGGACGGTAGTCTGTGGGAAATCTACCCTAGTGAAGAAAGGTAAGAGAATGTCTGACATTACCTGTAGACGAAGGTACTCTCAGAACAATACTCTCACAGACGGAAAGGTTTGGGTCCTTGGTCAAAGGACTTTACTGACTCTGCAGACGATGAATATCTGAACAACACTACTATCAAAGATGTTCGACTAGACTCTCGTGGTAGGGCCTGGAAGTCAAAGACTTCTCTATGGGGTACTAGGTAGGTAGTTAGAGTACGGTCCCTGGGGTG [...]
+ +
+ HOD7;XC;dfglZIvCGEsjYfeeZ<~~l&svvsip0~iGFobY`[Wg~s~DdZ~~~M~|>DdIsf]gpf1~~VI|\eQ\SX[`%~~~n~s^w~b[\hAH}Ycmpb)eOS\Hm^dS~{RVevUUyrlB&.E6[Pbmg\lG~9~},mh^M~>h_VEJZ$It~y_MVi(PQih at H@\ci[@Fg^MoJO^ZDXIPcT[w[uxhIeld%J*h|M~iRwJy'XIlxffYVdMKo|[~r~5~~C~~~r~}9~~~z\~te~oA~~`~|N~[DPM~~`fbZ^7TYHz}]~~nh_[ioxNnP~GQ`_Noi}?R{WIR&l`lFkXd]Z-;nJY?epW{D~S5>KT8mFUTwZPIho4zn`Cqj_XcT^e7E8;?L]?HcufVWzgZD0jXbo)A~^oFgscOZcgK~~jIgC3eMf`b]^V_)^=>Qa`?~Pu<pwT~K,~d~W^L(ntUsTU|\gM_vj&7FosdN~vW~cBDpxsEH~teCgJRfVrOG~~d8ooq|\ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1250/ccs/fwd np:i:5 rq:f:0.991787
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGGAGAAGCAAATACTTGGATACCGAATTTAGAGGCCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAGTTTAAGAGCTTTTTGTTCTGCCAGACCGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCC [...]
+ +
+ QnSLVS[4fU<[I6G4NHTN<R]UK.ghg[Ee?M8gQ42<@B at KHh1M@[UA\='d=fiUOJGi$fUP\Q6QHPSQ at P0F`igS\MS<ZFe:4JJNI>IMT/C42KV8RBjj\K7hgSV at DNH2^QiLSUZ<ZO8A>H;IdUOg6NLL9J\R>gK\S\I+X<RLPS*hhhbF>WP=NM[?k[8h[=jjhEb)M%NagJ%aMP\>lk\STLPFgiLVS]US[(ggR>jcIi@@AK(hhhXSMhIYB6XURA&RSQiL]OJ\UJ;VHODc/NLMGOWPVCQDJS:-/B at W'FKH\SZ4g[U]GiUS\?jZEI9QF?K?jAeLUS[@[RCNJFL\LS]U]P+P4d\CeUK2cO[L[>D]SULR@[UQhUST/gg7.J1hG]JCGN8dgSZ<T\SUMIIU;SZ2REf0VL?GR6ii[RF+QS at cS@fKS]K9h[GiUGj\UY&K2F8-TKOFJ1WAXS\HgAHRZRJQKR at KSUQ'hhLG at Y<JjSULSUX9im [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1250/ccs/rev np:i:5 rq:f:0.994948
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGGAGAAGCAAATACTTGGATACCGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTGTTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATTGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGAT [...]
+ +
+ HfJ=ZKB at X>BP&)eP6;ZL]LV]S3iW?+ at cDJQfJ.:OhU]R>\Al]V]4XK;h>jk\HE0SFgV)T?kJj[@Ae>iiifLVT]IE0e\IgNADSXFT(hhhPLVTLIihQK&ebZSB6e<>jHf96KDJDUO@?PFAdY:3=JSK]/AF)UCBJ at R]VM\QOL*dSWgb>M49[K>6fS:gSAgia?l]L.aNObQxxU\FykK at V^T:WZVPSKgTKHtatTFzyZvTb;[3xvieP+\`\_UNxORh^VLz]KQ`KgU7TB\%_*Sov]OLPJAa6[hU]9EuISXYNhS7FeKg`Cn.KFEaT]RWx^i`P{WqGfU_c^QWYFFv_^U[L*OLPRQsvE{i^QxwJV?FUl?f^S`_ONcH>_.lqiUaPj8uT&tSIzo?^Ti`UiOcZi^U`[xGgIix`^TDxw_?^[xUiOc]OcX?\GGvKGjf2f`faYxVe]Dw\hPiKpF\S_RxKufG5YV[Ui^SPR(nZ^^gFN7eUgGSi_ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1334/ccs/fwd np:i:10 rq:f:0.997714
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTGT [...]
+ +
+ N~e_zd~D~~j~JT~`r\zwituUL%~~~~~~~~~~~~~}{|~~~~~~~}|\R^y[puB~v]J~~_tzMw~`~xv_^o*^`NywsxNt~`t~v~cx\~]x~`whk[d~gI~he^~~`~T~[~gxxxwM~x~iP~lao-~b}^uV~~U~_~sxO~xbh~w:~w]Zt]~ZQz|\xL~y~M~?_iKuu~_YlMx:~e~tq]~d~O~~M~t~Q~~B~~~xvjw~zm_smAfX}zw_s}xfB~|L~ywH~pMc~}J~U~_aNQ~~uP~|iH\~hs@~m~nz`Sg[g<uc~J*~ke~tZ~`e~g~savQ~|r~V~}uDattax~A]C~\vR~~rD~*~vW~\~<~~`s~B~~<~_~~m~aY~W~~Mu~R~aQ`~Ya~Mu|w~@~e~~`X~yx|_{q~b~hvys,~~IvM~Xz7~tdu~e~c~~zwSq@~~~\yt[Tsb3k~]Md/poscU~~c\,~tUKT`^L~uL^|i~utI~~~~Vkx<~bK~~^|fJx~t~Go [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1334/ccs/rev np:i:9 rq:f:0.997849
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATAAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTG [...]
+ +
+ _~`ugXp7~yrybr~]LsrGo]d~t%~{~~~~~~~iUIEIYmy~~~~{z|~~yssgDrVZ~x~i_T~}uy~a[e2m]0nI~N~vv~|>|vPfuZ?aq}~}~}T~~g~u~q~~I~~Rjp|~~~~D~tc~h~|zCn~'~@}[~b~~w>~~W~E~peZ~~|V~NDu|yadyk~~~~~~g~b~~~V~~L~~~~m~|sa~V~Y_F~X~>~i~~QoD~c,~~~~[b=W~X~h~`~f~~^|}~g~D~mN~~~G~~j]~~C~[~nWpm~iKGnzSS~_jgg~3|~hyOyh~jeRovF~~c~e~~~7~v~ojdY~{M~ux~B~~d~~Oky}}~ma;{~}d~{~dk~}qg~ny:~b~~c~M~~a~~?~`~~E~~o~xkrqkn~|u~gsg~6~}~c~~i~~~`~H~iS|RS~~m~g~;~H~~N\~z~@~~~Rh~H~~~~~d~~~dS~~~~?~~~j<~n\~Y~~z_y~eY~~j3~gp~e5~~~~j~QV~~h~s~~g~~~VoW [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1378/ccs/fwd np:i:5 rq:f:0.996097
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAATGTT [...]
+ +
+ UtXJ*VbLub\Z9<oQBS\Y\VGZS1rsr`Y^/ISo\`6sV>]ANSS1jbGq@\;IqT\`8qWGWTX=n>W\T\=vlTX9tfa\_FTW;*l`SQb\_3rGX(R\_\EZWFurSEXTKX_LkArA^EXKXLu`EXQ/]E`T\bYFhEZT1V-qqZT`@O==pSV[STWCW at ttZV-rWDiT[TX=srX_ at D^A`Y\:vkTa5sspNTa[Fb'nn`Gyb)ssZTVtWE;.%P_mXWIWp\T\LfBSXAOKOKIMP\X at rDYHp\T*5nRM:b<o@`YbYTr>VFSbYbTAsR4,VlUsT^Y`At5HYbTW,oEgEXb\TLubNuWZ2uB6=pRE`Y0wdYGZa at qYbTYNqBRF>hmTFuubKtDrS\bFx\Y_3HIN>VLM[bY_&o_ZY\T\Y`+kflJPFjFK~>~~~dF~~b4~cf_eTbmRcoT~L~co_mR]/~~~k^h`~dX~dh_dk,~c8^kZG~\M[TelMV~^b8~fcJ~IOWP^4{ocK~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1378/ccs/rev np:i:5 rq:f:0.994102
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTTAAACTAAAACATACAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGGTTCATCCAGTTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAATGT [...]
+ +
+ WuS at D8A1RFATWBc:PU_TLQAFB7i]iFLTW8xpO0GqS at D[XQBAZGDlSYTIuV^E6ZW0=JTHtXUUW[+gKS<t\C,P^LULEm7RWUFWHsLmBt_AAEqT<toXaT<QmFTt?kT\bTIfD[G`TYb[UDX\CRFoRDNXTFuubYVRV>?jSB at PYTbTFuubTMuTKulE^>ErnO+Qb\T\T*@;ssWF8iulYb\]&<mI/@8D)prrW=rSX*\;euvuaDiTaWF+nQU(ZA_T_XaYbT=q^1Fe_>ZGvb\GwVuT\SFR=pV>_Y\T+^W?m9]2qqNuY\`FLsZGQ\YS1pFcGQ\aRBoFUtPX=[\A at rXbYTCwvbSPZG\>IJ>ToTYb;vcN;Vo[/dK:cU`D7p`R)eWTbYTbW:SSSVBKE]9DA_TIXb\T\TZV,h1Zso`;wiTQWSFXbY=C`KGBN1T>5K6]A2svviX`=@+?kSTYT\HwbHgFU*pVTKQ^YUPrQ=?q^S+A>MSbYVu\T) [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1407/ccs/fwd np:i:5 rq:f:0.987519
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGGAAACATTAAATCAAAGAAGTTTATCAACCAATTAGTACAGTGGCATGTTAAGTAAAACAGAAAGAACGCCAAGTGGCAACAAATGACGTAATTATTTAAGCAAAAAGCGTAAACGCTTACAAAGGCCTATTTAAATATCAGTAAATCGTTGGAAATTGGGGTATGTGCTGCCTTCATACGCAAAAATGGATGCGACAGAAACGAGTTGTATGGCCTCCCACTACGCTCGCCTGCCGCGGACCCTAAAACGACAGTCGTTTGCCCAACTACGGCTACCGGCATCGCTCAGAACTTCGGGTCTTGGCCCACCTTTCTGACGCCTAGTCAACGTGCGTCGCCTCAAGTCCTTGGACAAAAAGAAGAAATATCAATTGCAAAAATAACTATAGGTACTTCTTTGAA [...]
+ +
+ QlRNXNPFlV+T8<g<QNYRZQYYN5MbeLRYRNXCL;jXXR4cNMVXO([O3hSJFnYNMlRYFmYNRN5kkhRYL;4bNUMR0M5V.RQLCLk7iiXM*hgQIP<Dj[.VL6L at i8fIiYRYUJW<WFkNT'9Kg:g;V'hhgMPH<`RL at U8Q@j;iRYD[5LhM7OcXRYMNMJNJeC6^hJNRK6MFOaP7IKCkM%K9LiTF.eI=P0^N->j]=LQOGQ:>OQEikYNRMl5J6LX1O$ff??AU<U<LVN(35\I+CWDH70ZhigU-CG<P69BIN,AiU/2A?;TQRDV3H7OT&???5I;4L/;7<BXW==^KEBJ<(OGH$?I59;6$K;F.M?^hQ'ILCG.S?95G8=.$ABOL>EHLJMLCQJhHMgN?mmSNIO3e9eMQ(R-GNGBK;D0=dM<H<9BSIRW<MQAMR;JM9-LRY%:=fFkTI(g\QRKEQM8TTYSXN:]8ZN61gkjeW?K<WDYYG]SFN=jM:hkR>h [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1407/ccs/rev np:i:4 rq:f:0.990503
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGGAAACATTAAATCAAAGAAGTTTATCAACCAATTAGTACAGTGGCATGTTAAGTAAAACAGAAAGAACGCCAAGTGGCAACAAATGACGTAATTATTTAAGCAAAAAGCGTAAACGCTTACAAAGGCTATTTAAATATCAGTAAATCGTTGGAAATTGGGTATGTGCTGCCTTCATACGCAAAAATGGATGCGACAGAAACGAGTTGTATGGCCTCCACTACGCTCGCCTGCCGCGGACCCTAAACGACAGTCGTTTGCCCAACTACGGCTACGGCATCGCTCAGAACTTCGGGTCTTGGCCCACCTTTCTGACGCCTAGTCAACGTGCGTCGCCTCAGTCTTGGACAAAAAGAAGAAATATCAATTTGCAAAAATAACTATAGGTACTTCTTTGAAGAAACC [...]
+ +
+ YmNRUHYCeBTV;9iQNRXI>JCWR3m^KMNYNRYYRFVPYNAQJ7PW8H_dHz[I7%GT5rU_EcOZVZ(YoZVa1S5Tre\`Jq5M:ZrY*1Y:]td\@{sNTqQ at XoaMLTwOzViQu\?Z`DKOaE`ZecAMiP_>I2zj\\Y'/7M>EpZS,bTxVOG|[@yZ at w{dWbFRJRw at uJ7bE1wRE1vz{pV[@8?lz\WY?\_\I|kEyAIbJ]K=LKEWCQW5*=[CYRM/<2W3hi=K1TfXYYNYM at XMFk3MKUSQMNR1kkkkYCkULNRNYRYM7jjQKONMjMCXX0iEYNCiYRYXRNQ=FM4SV%DhNO>iS?mmY?mjRNW:;FBP86bSK=jlMiONWR5bMIQK1_OYW;KN=RYNMlQ*fQ&O>?<J_0i<jlY>J>OWMW8TRNFmYW9WN7eP+<&OLYRM3hAQR1BK4]>PYR'PajS7BW9AihW??NGh-e at 9P1hkkdCKgNBNU>/gB?:IhQ+fWL;jMEia3g [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1426/ccs/fwd np:i:6 rq:f:0.994023
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATTGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTATCGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCA [...]
+ +
+ I~dFW_eQgTVlZL~XcWX`fKah\(~iNJaZk2fj~i at MhXV~TWH_;Rd5lJa at QBm\9G&NEDLlJX(SPH~~nYP6~TTFewU[]~EN_QbTjGSUb[fBhJ2}dNzS~gW4jdTeMI~mlaYen>]F:LdJLm`UWhR~TY3~~NmgMQP(F_coeYOgHndhDc>1W'MQb'eQfROQb>bEYzLk[^B_h\~OZ;~~s[fl\jS%O[`BR<?/HdYA~bcRGdZM[,W.B+)JMCS>cVQ at eZkP^kfHD~jnBlM{>WfWPfMofcWOXVEGicWY@\<T`Av~nbXR~eR~W<c_(QMSZN~c)~fPY+a?ojUb7WsP~ncwdylIu[W[H`saa[VM~co^P~W]Krx\F~rxlXUX{~b-NYawclpC~^oV`v[sDZagnm@~Z^B~5ohcuI~Y,\D~QpZG~JxYCg_pUO\vMl>XVKZH=N~w<~~a;wW[@i at PM=[S~T2<S~~Xf]<GNy_H^~Z~a|2gn0^~Ud~mc` [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1426/ccs/rev np:i:7 rq:f:0.993829
+ AAGCAGTTGGTATCAACGCCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATTACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGATAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCA [...]
+ +
+ 37K*FK%27<N>MY0sZQ*ZR>FFJc\/|w=@+Cn-s;4Wb[ma7~U~ThH~hQ~TQ^S3^bY5/kQTfUkZKP+^mmaPPoU]3MwleL~T~ZcWc\It~[fZM~YDHCMO at qhc.eYQYVBb^`AFSe8l]P?L at JeZd>oG~XFFk~?|bUTK<hf$9A'Uf\mffS7bFR~~V~iWDnroH~cZ^|eKp1idEC~eWnWLH~~nb[lNVk.]TdWacK[3TjTR~~FkeWP*eLcTa8@~fahn[b)GS`e at U;:EQ~PRS~T~h`Q*sEEm~m[BNgbW}\ia4lgc1EngNZfI~kLwPkmmTT:KWx<9z?I~aR at y~dXkGkIzZWlfk2R~lOkd8G5dHNuiUPXmFkG~`L=]mUkj/IQxVd[fojDe0~Nu_LeZTbgcUXZ1f\b@?'dMNcK~`Qb(VWcIqQghH~hnJQLy@\WcXOidZ8wh:nzf_~f[lXh[gm[?uWHGP~mFRUJrM}bV[x%yU]_VlN8~XEyAMI [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1446/ccs/fwd np:i:7 rq:f:0.992319
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGTGTTTAGGTGTGTCGGAGGGCAGAACCAACCGAAAGAAGGAACGATCAACACTTATATAGTGTCCTGTCGGCCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTAC [...]
+ +
+ f{`Xnb`7SNehD8xXXNQNcJf.?6ipo(YHf_]'^YS4f`fTbVJeDq6bkB^hkZG/\KDPWQ%SZL;f:`KjQH?OI7NZYZd at BYREO5Z]F=jkZf5W`RaUGMLbGMlR_gFVmckaKCWLZfHhR]eBIW?~lEM^K/JKW0RP\M<>bSEd-UUBaFIjKpVZSN_QbC^K,eKmfX'@`MJMCVmR7Q_[MMWJU<B`RL=\\\IroH_P at hM[aKYGFUlOdD1DnXVkP)kUPRXSIrfW^3EoDbh^SIQ/1;6J*N?VV=X=OO&OT/[^FO72L;fB`%PN?h_R&DCD$OMOG^H5TAWUGf=LAJ]\_O`9i\>:M+`(Ub0,YUB?idVj_h_R9_L]BIe at bsd-YL5PJ~n]bjVb at X`Qd](jOaJ~bedjnIxRiN5@'hhhskSQeCJhSUSbg1ypfQ~RVeS+vMErYK0cihK~dUJQWfIk9njhoYi]Rb8hZcZnR~knYX_/ObXUceMjSG~iXRUdVV [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1446/ccs/rev np:i:6 rq:f:0.985458
+ AAGGTGGTATCAACGCAGAGTACGGGGCTGTCCGCGAGTGTCAACCGGGTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAAACAGCCTTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTACT [...]
+ +
+ :/)/.-iEFISAqOMLF7(/IOF*Qg]F%>E0[CBC1>F@=B+V+K*a2)iTW[HulCc_RRuDFW9mB]E^_S[AbNH0^.wUK.L;ZnX:urY[2Q]pm_NAQZ.AN2N]@<mYIC[RG-PaY\VNIHB>&VFN?\N\S\b%skZm`BnX at sYQu[\RP]6p`A5GFAvYQD>f=s^FT1KJ.?T.:T;uvi]>_ZaYaN@^X<%Z:la[<W at q\KVFV2e:ROD87BJXRpR/tE<7V<8pMXM^MpE_mRVDC8LKDKO_7hU/HD<B5p]:c\CAJFlp>gNXUMETcQ=pkEpCoEVN>EM?sZC5>m>XHM^N[PMMxa=aZ$nZ7<`W:saI/IJ(Y:A:8:mM;[@t4`m_LfIXHC]WQ_`YM$[TJUW=In$H-2XPN^c_DcOcQHP8uuuq^VLW[R`cYILcIut^8y^P_1>e[R\Ra0lnaKiKB]^VdI_0jgUd at OK4PMTNC=H4hJX6RLXA-W7AL;]WKrbW\@NUZc [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1448/ccs/fwd np:i:5 rq:f:0.990199
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTGCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTTCCCGGTCTACTATCCATCGTTCATGTTCCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCCCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACAATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGTTT [...]
+ +
+ TqXMYXa:m_C\K;eNXLCWYSKYM$hiiiiiihg^UQPTV[ZVYbhheUHIL_;F81bSCQRGjV8LbMY>d,JcWCIeJLbCtWCLXbKlYLC at ocYXb4t\JlCLcJS?oG<Z5j]KIN at lXH_5nZQkMBNM@`XK,H;jcL.I at DP9=XH%SQSW]MXWlKk^4(W>9b[GjaN`JJaYT?pW[JXUj6A[JUf&97_F*al_YMBlWBjX>XWlL9a6Ga5Jhe>K4UhWL=j_SFDVS?3dLaC?iW6F2V>IR(jjjWB^@`EmmbYSBMT3;[<XHC'Q('7A\.XXM\OMcMa8UMMkMllMmW4[MXcMXcMXCtVlM&hjgXWVKDF(5O3.FXbVHE5W\CBnVjSRYTJXRgJ.W6bkW`C;)-]RB;6:PM6eQMSM,YVXbYMllXY5m_8QLcMcM`ALBn]JcMcMa5CXXY`@JA_MmXMYL;TiKCWb:HhKMW9iMjlYMHobJlHIMMllMXJ.KW9DWLXLCLXHJL [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1448/ccs/rev np:i:4 rq:f:0.989633
+ AGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTGCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGGCTCTCTGCAATCTCTCTCAAGATGCCGTAAGCACTTTCAGTAGGACGAATTTACGGTTGGTAATTTCGCACACTTCGCACGTT [...]
+ +
+ +/-:C9?hWHVV,h>J@[J-5 at JG$=63 at FLVZ\b^SMIJR[YYahhKI<?F at GVYcXMb7YbXLDEN?PHEK at V8ZUVCGZ8`XcU>QbXcHcAFKYBncBscXYXcKgJ?jJlAFTGEM$E>X<NG4N>A8?=73,=G<`iX<j=JCaMYM(jjjjj]WK'd>cCS%&0fk?pSXSZIVTSGOaSR7KjVbXLAU,\N&JNK\XGiL<ka2D8jVBjC5>.dhh`XFgE8VVkCJP at Z>H1n^SC_'NI;DFb6*;7TW`LCjLC*llV^KMWK-.gFiCY6cA+Q<TTIPe at AF5-?PRkXRh>TMJhFGFVLCUD6VJFZ<kW2kllk`C`XSPR=TiV7-49M$GSVHHV3)Y5NF;(&9W7hLlkNWLDDB\VWKGKa-TPXYXVjTF>U&MdKcKlR$R at BNOAVTGQ,QWWYVOHUXVlN`cB$QUP\hWcj[F||cmT6i3hk]?8V<yzj1Bo$6Erca{@{{bT4iF\_QrH(YYcVL| [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1454/ccs/fwd np:i:10 rq:f:0.997969
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGCTATCCTGAGGTGCCAGGTTAGAATAGGCCCTACCACATCTAAGCCTTGAAACGGTCTGTTCCTCGTGTCAAGTTCTTTGTCCGCTTATACCGCCATCTCTCGTTGTGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACC [...]
+ +
+ }~bO~exL~t~\]W~cccdbgHVlo<tfxwT~a_J~Pa_~dc*yvbu~Z~B~L-zc`m`F~vL~]e`pxb~G~J~^dr^yc]Orb`B~~ceX4w~uN~~h{*uv{~~b~bKp9~{Y{fb~x{XbeuS~v]u_Tw~qsGpp~O~S|crdE~~vsTW]qV~uV~v~RWnBP\dY\~/~``aV~M~aysxudSgla~~B~~}t`u`yn~ew~vU`x3}`]Km-lzaoR_M~D~f~[~h~w]~f7~vbOldP~wqN~]~L~~a{qgevqvqZbsf|N~be_~yD~_~~dk~yuP~Cx~xxP~uV8^]`f~O]r^~Nh~~sL~maxRX~`~txcactsf~PQb;Sv~bMUg;ES~yrxL~\@w~tcrxnbcA~dsPpc~\oYc~>a~K~R~|pbaww~d\Hr^ia{Hp~W~Wnv~bo~sKcl?s~ed~_r[~d`~a{cOM~x`qYs}gp}/{ruoa_v`C~~hdgT~dg=~~~A~b=LbY<Ql|1~~tygP~~[^ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1454/ccs/rev np:i:9 rq:f:0.997749
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGCTATCCTGAGGTGCCAGGTTAGAATAGGCCCTACCACATCTAAGCCTTGAAACGGTCTGTTCCTCGTGTCAAGTTCTTTGTCCGCTTATACCGCCATCTCTCGTTGTGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACC [...]
+ +
+ @~d.O]cR~s`dgb~gweZhcYckaGz~~hu~m5L~[QV]_u>BWb~S~F{~S~~~tf9~[F~b]a~hV~@~`~blVYsWy]qquM{{au_H~sbP~~^q8~~~ybta`wRTzu;oN`~~togl~K}zcyb_k\P]X~~^P~Azluy4~~~~yas?<gPH3Vr\f~Q~uFFUK&waYP?~/}~bba~we[daje>~~~v`~`ycQsSvguyeR~~dZb:~[jaoz%~NY~roOzQ~QT}c<nuu~awQ~~dwpP~DsuYOOOsS~vRB~~uN]~|x6pnU`asbtEzNqOnG}~|wQ~uSszQ~VxeU~h~bF~pV\~yTspe~Rt~bw~qa^dowtsdZt{bzApYcaHdkT<|tC~r~a~f~Ssi~oi<w^scRtuzrDc\~h~xc~e}dyacH~~eq~G~{@ob`>]Mcxf|pwrRpmdw~qbsOA~~]ow]~bQssygbD~]~fcHrUt~[tpr^IH~_P;~~qKlXdrvyd\~yQ~xds]G~~H~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1470/ccs/fwd np:i:8 rq:f:0.999267
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACG [...]
+ +
+ f~kz~wrP~s[ucf~{hd~xHy~~z%~~~~~~~~~~~~~~~~~~~~~~~~~~VOukp~S]~~_vFf~sdz~|~a~Gu~|~e~~cqc~|~|~~h~wbvb~~~}~K~~e~~O~x~Q~{q~Q~~~|~buxf~T~~x~zu|~|~zP~xD~~{h~~|~uy~z:~~~~~{{f~d~oMt~S~~R~~e~ui~~~S~~~vyr~x~~xt~bc~s8~~~sdd~{b~~Q~c~y(~lvn~H~~~~i/~~yw_~~yOt~|~K~~o~WQ~~dtb~ez|V~~~zP~{~P~~o~y\pyqa~g~~~`~q+~~s~H~~{~|v~|~ClRT{L~~M~zw~{|~ez~||d~u~eB~~~z]p~~a]y~d~ux~f~~S~~~g~v~uzu||zR~sc{9~~u~2wt~qqoyu{~-~meynA~~zqsW~~{ub~~U~y~yl]vtKN~~z~{~e~x>~yrqxcc~B~g{~yO~~e~|~~E~~t{zN~g~~~dR~~@~mc~h~~cdxtxusu~{{|~x{ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1470/ccs/rev np:i:8 rq:f:0.997737
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGGACGAATTTACGGTGGTAATTTCGCCACACTTCGC [...]
+ +
+ n~vx~{pQ~~~~|h~|ze~L~zu~{$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~l~|~~{k~[~~_`]z~c~ny~{~W~y{uf~dpuj~W~t}sb~Iqb~[~~F~u{t{~e~{w~d~s~}~e~z?~Y~~N~z~drxcx0~wQ~~zb~~z_~{)zy,~~~~~nyS~Q~lzL~G~~Q~exG~e~~ug~{VtxN~z~Hv_~wR~fG~~~~df~eR~~f~c~x9~yo~6~~~~{S~~z|y~~eyR~e~H~~uu~H~~z~d~|y{<~~cOt~{t9~~s~|~~dsi~h~~~R~~O~~~^T~~cOxzczcu~|t~]~~u~^]~u\ryc]z|e~c~zB~~~~~f~~e~}~b~cMfj~~?~~~f~@~~O~zycS~~T~V~~|~Yx~~~u~zry~'~~}|~{c~~`~~X~~ysg~~V~wptsc~||h~~{ou{{d{d~|~sczz_u~ze~tQ~~`~Ss~(~tsw;8gU~~rx=~FZp~x~T~~^P=~~z~{S~zzd [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1511/ccs/fwd np:i:9 rq:f:0.997416
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATAAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACCAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAG [...]
+ +
+ o~io|imE~uKklk~d7>=e~ivil$~~xz~~~~~~~~~~~~~~~~~~~~zx|~~~~~zytM~~f[e~sU at zukudfaf?uiwoR~C~lY~viwhcpffviv_~kvnhwgj}vmN~uW~|UkimpLf~J~jYyphLwYwyB|aL~c~r~\qJ~~`~>~~c6ySYP(I;o~~kwg~oNxGm<J~oaYdGvM3~~~tI~s~P~P~s~]~ky0~iWab~G~~E~~~~Zrq~~oHO[P~Dzsur|ngz,~ME|x~M~~g[~~a~d~XK[Q~~q?_CA:pcKrS~e~k{|DrVXojJ~^J~~`tV]~wJ~g~}]kV~oVv5yvd~RbqodeP<`AzbnDpm`9vbnTNxSmKtdlZ~Z~\I~<~_c|`CvC~{:~vS~n_VXsh~`h~ne&s6n~c]~~\~d~l~O~knqgT~~KZT~dn0~mF~X{K~6U@\~D~~~nimXmvp>~{s70~tbi9~u[tQ~~pY]\oI~~_T{l~nl@~~~uQ~^_~qK~bJU] [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1511/ccs/rev np:i:9 rq:f:0.998244
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGT [...]
+ +
+ K~kzwhFO~y~~|_~dgittd{}~s&n{~~tcY_t~~~~~~~~~~~~~~~~~~~~{~+~Odd~}mf~~{~zz~~wsU~wY~d~{`~i~~NbjhT|~~`~xxN2sRj~ntM~pf~~|ujrtvi~Z~e;d_~e~~v~Q~~n~G~[zj~8~~p~e~ix/~b`\ykR~u~six~~z~~u{d~_Vg^MQH8~~~p/~ux`~P~g~@{Uw\p~ssqo7ZwI~~|xPZZ\b|uGTJeazYhc`iX~F~~9v~kT~qIRs~<~Y|\dm`~<}@~~ha~}q|M{n~~h~o~z~UUZpcG|rGcUG~];~W~~e~O~q1gG{}zpe}~{zdnuM~erH~~~g~`~~b~evg~~`]~d~~c~W~~d~cc~E~~K~~Oi~~l~oL~{~q|RP~[~~cQ~~f~jso~g~~~~~R~~U~L~^~<~uj<~X~G~q~E^~P~~~z~kXpds2~}y}>~~~~Z~}]i7~TwPw~~P~}df~^~ei&~||~h~lQ~~d~~FQzz~thr [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1512/ccs/fwd np:i:9 rq:f:0.998832
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGT [...]
+ +
+ ~~~ue~~b~~{~`U~ts`z~|~~~r&~~~~~~~~~~~~~~~~~~~~~~~~~~~~~khuz~~R~y~^~~q~`_qo]~~u7q~Y~fP~~~~7~~Kt~~~F~r~Eh~y~{~b~~~s~crt~~W~X~r~~~e~~a~~~y^~~RyN~~fc~T~~g~X~~u6~~bX~~T~~~v~shqs~~]r(~~~DrZ~~.~~~lU~v~P~<~j~q~N~l~y]~~~b~~D~~~~ue~~~~|~|B~~~~~a~~~~S~xB~~~?~~uo~gc~~~x~xw~~oZ~~~[~~~~T~~~~~~~tK~d~O~oa~~h~~E~ur~i~~w~u~~s~c~~j_su~w~~hVdxh~]~~~`~k~~l~v~Z~~w~~b~~]~r~yb~u_~n~~c~~~~f~[~wz~x~~~~.~Yy~vZ~}~~v|~~d~kx{~W~~]~Z~u~G~~~_~w~q~~x~q~T~~z^~~gM~~Y~~e{8~~~~c~~c~R~~w~x~~s~{tM~g~~sS~~~~Z~~c~~^~~df~y~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1512/ccs/rev np:i:10 rq:f:0.999439
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGT [...]
+ +
+ <pettx~R~vPs~~~~y~~v~t{~~&~rtw~}}~~~~~~~~~~~~~~~~~~~~~~okv~x~~~}wj~~~~~~`~~~g}~b~^~~w~~i~~=x~u{ayb~~~~y~t^~z~V~~K~~y~}~~zv~\~~{~y~~u^~~F~~u~D|c~~~'~vu~^~ctp~~~~~tL~~~~~~~~~~~~{L~t~~~o~z:~~~u~~~~r~~~`~S~s~P~z~~q~V~~M~~~~v~f~~}~x}t~`v~~~j~f~h~~l~~~E~~~O~~`~c~pv~~~~r]~~u~~~~|s~x~~{~y~~~~xw~~<~mZ~tb~~I~u~|~y{~~x~~~|b~vw~~x~~us~~zA~~~b~_~vl~~~`~~~{~v~}v~_~~x~~\~R~~K~~d~~~~l~~~~d~b}t~M~~th~~b~~~i~a~~b~aZ~~\~^~i~G~~w_~q~b~~~zT}P~~z~~\t~~zg~~~~T~~~~]~~c~s~~~~~~ya~~~I~~~qk+zZVmo~wp~~b~~~~s~~~bv [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1549/ccs/fwd np:i:6 rq:f:0.991358
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCCAACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGACAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATAACTTATTTGACTTTGATGTTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATTGTTTTTTACA [...]
+ +
+ Rz[RbIfJaA\SK;TL?OGULZc7P$ZVQSadYY]chnrrssssssssssssssssrZY6u$ACZ\AHB{Wu]Ybd1qQf at mRKvvfRXvRaQ?qF`N;,$M?XTB3WN`a[Sv`UZ`Cce<6D=8P>J0a`ZCgFQ`];ZN6]H_rfRIB:_N?UmZRaNQBgMY=.raJBfJYBtc=YeYLNFR5OaX`_[RAdcVNV2qP[QAJYK_MHC6GM'%@LSW at rI=YM[TTI3BXKY_:X_XC]c_FE|bXvRWt8ydZCtR_LKQ[VwbY.\ZfbZ2rKvXv7C0V;1qYb>]VNV<ZrVNXcALUA^ACsVK^:<uGkWFPaRfZHvZbDh7DsLY=[)2=>VXEZR6l[T^A<?$PZd.YcZOL/n[3\JN%*7EeM;rYB`QAuqU35Q'nSM;BKC]Dd5tgTkKx_RAxeF;_[O]_4YKYbRA_rvb[fR[LUTXRbQAlMVP3rP5oMmN]aRbRbfbeA'IYTt<q^J]0DA4hVgudNPL [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1549/ccs/rev np:i:6 rq:f:0.993149
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACACTTATT [...]
+ +
+ CgRHSSNEcKQd]Yw^SGd<*L0BE%clbVPOX\bltvvumc]ZZ_hruvvtk_[enD><sg]SO\c<uUxfTOJO_TE7q[BwwbGRd]OGTnOzh]SGEq>cNvfPd=NN__T<LYcHwSFDHZb0V\P>vU\gO\SN:uAvv`Zhb<r\:vbO\gXX;sFv[-trOLXPRDrH[R^TcF`;eZ^bXgT\.zs7EROWYFWOwTKO[V`Z5UMOQWOgGxg]@[dSw\OMxdTh]ThTYv9eTPzhRW[OS<h6P$sEeeh]T0q[S3uRMfS7S7`;Q at Q:S]OuTd\Of]g?wjNaLOPZ;SVN:cIWFaEg=mXQ\bT]P5QKJ^cLuhU[QFS[4uM[RXXfTheh\@W:JOFuKAG`Aws9pVdhLSw^<_sTh]9tH6K`S2p[bgbYOYM=dn&34XbTCR7RCOQZ^IK_`PhZBauq[SLSU[OA?EKYFZZ;RAt\G^2q at Kf]h\P:UPTZJ9E=7XfJib at +hm\^OHVBX0]d>d [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1608/ccs/fwd np:i:10 rq:f:0.998309
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAAAGAAGCGAAACGGCATTCGTTTAACAAAACGTCACATA [...]
+ +
+ ~~~V~~~s~~~~~\~~~Eh~~~~ip-~~~~~tnh~~Z~~Q~~~~~~~~J~r~s~X~~n~~~T~p~~~~K~~v~~~~r~-~~~~~]~~~f~~~q|~_~~~~i~R~~h~qd~~~~np~W~~~c~~~~~t~i~qp~~}~~~~~J~~~~`~r~~~^~~H~~n~j~fY~~~~~XwY~~~q~P~~O~~~3~~~Y~~~r~~~~~~~~n~~~~~r]~~~~r~[~~~~~~~~U~]~~~P~~~~~{o^~T~[qvh~l~~~o~~q~{~U~~~~~~~~~~~lq~~b~~~~~{l@~~~~^~q~d~~~^~~~~~~~~o~~~r~~~~Q~~~~~~h~kq~~rr~~[~~~~r~~~~pT~~~~~~o$~~~~Xe~mr~r~t~~~~~g~~~v~~~r~~~~~~n~u~~~q~d~~r~sj~q&[^G~~p~d~_~~^~~~~ikK~~~v~~H~~~~~~l~~~~~~qi~~~i~~D~~~~~W~~D~a~~~o~~~~~~~R~~f~~5~~~ps~s~x}~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1608/ccs/rev np:i:9 rq:f:0.998802
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAAGAAGCGAAACGGCATTCGTTTAACAAAACGTCACATAT [...]
+ +
+ x~os~~uk~V~~~a~~U~~Y~~'M~$~hV~~~~~~~~~~J~~~~~~~~~~Z~~~o~~`~~~~zG~~~~r~~-~~v~~~F~~~~~`~i~-~~j~a~l~o~~~~g~~~r~~~~r~~G~\~~~k~~~~lG~~ll~~~~~r~~{4~{or~~L~~qC~~u~~Zy~~~~~~~~~n~r~~~q~U~~r~~{V~~~k~~p~~ro~Y~yra~~l~~[C~~~t~h~~~~~r~~V~~p~~~j~~~~qnqn~s~~r~s~~~~~p~~~{~~Y~~~~~~~~~k~~k~~p~~~t~~~\~~~`l~~s~~~~c~~~qh~~~qh~~m~~~mW~~~~wnu~jn~~o\~m~8~~g\~~~~s;~~p[~q~m~~~~~p~~~~Yj~~~k~j~~I~o~~~q~~r~~~~ol~C~~~q~m`~y[~st~~~~Y~~~~Y~~h~~~~_hn~~oW~~H~~~~w~u~j~~~o~n~~~|~m*~~~j~~~~~G~~~Q~~~T~~p\~~o~~]~~~~r~r~~~~~` [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1630/ccs/fwd np:i:6 rq:f:0.994006
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCTCTCTACT [...]
+ +
+ d~SDjivY~rmp0:sOOXkjbj[UT5|~~ujNF{U\~j\8~i?bgeuluZ[~Jx6sU2w~[KR0$?B|LBDjXT~9^I~EikW at jvltVdQ~~l_f;~~D=~~Pk*~~dLCQQhRY\~lljGXprAfZjoTi\EgVgrhOWBiq`E}DqkfP*~~yhdTsYU{YDeGliZ~?QlfVGSKSje~Jjb~gIpWvYjTs=raPYX?fM'D_UCsXkXpbUjW~loXrUjhB+rpVgvZ~qWj`~miYmZ~rWHa>OrB~ahtK@{ukB~~kSb?il;WD[~j=~z1bLQ~~JzLuDb=rwi1}jSh>utYliQ>IxWkXS}<`jakkr>rG{Z_WWG~`<~v<\rc<~tN~gWklI{b~l[x;~~e;cQAH@~imoRYuD~}E[gIyYiQ~hiMaX*~jvllj+~~|~h?M~VRVoFsluMxvpC}aJ~i5a6_vUo=~~vJ~qWXbWrFgBo|~yVclrRRJ)`TmY|t_M]PXvlluj\dQb-R=UVYTYv [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1630/ccs/rev np:i:6 rq:f:0.9942
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACCGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTC [...]
+ +
+ PgCSoZb5~h\gT`}C4JE8T3P\T%d[?AUoHyUZ~YV4fZlZvYRQZjJ~DP0XM.OqlhkL~j=}qZa~gF~Ube~gdVjvYhERti2~~PF%EBgdh:~~ju?vbhbtWmZtTD~A?lO]tUtVLVc8XjltTWXZPT<[xtF~;~Xtj3u~~qgb~j=~e^~TsYR~JySsld~YtWW~F_;~bcli at ivYV7~~uYmHc|c~[sVf9 at tYiIuY]oP`rcjBk0VxJTUVB47bQ3unUJjGyk^U~lbVBirXArK~kY@{vsHucXUEhf)~q,~[UmFFpcKtN~eZS~h?Pwf:~W~|'TWnVk`~Tn_JaQNn`r2TUUXfb.Sf<~v>}~?~~mVbkR~FkDKZo1&aK\2~nW[~uj[E~nYVtkgJ~~gt at RlNC//- at K/b[~YVYr1*t~~a\j\~lZvgbPQiAowUG~gLh^@}~[~ZlH~~jF~?it;^h+o:pk|~kuUc[gpRXiu=~liTsZkiIrUS0PN_NeNeVi [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1649/ccs/fwd np:i:6 rq:f:0.99168
+ AAGCAGTGGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAAAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGCTATCCTGAGGTGCCAGGTTAGAATAGGCCCTACCACATCTAAGCCTTGAAACGGTCTGTTCCTCGTGTCAAGTTCTTTGTCCGCTTATACCGCCATCTCTCGTTGTGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTTAGGTGTGTCGGAGGGCAGAAACC [...]
+ +
+ UgF4G\g-jkg\f8'KII3FUGXJZC7K`\G4g\c=v\IVL]c1aJJS9YCSK=ii_4('IaNi\^8_JWh.qKSGFQ9XPf^gWL/jRFX]Eif8DXcI\-qwuZIWL]\IPk\^\H>h7PR=EOLiI3ZH^gZJ[JBD1+SFMYN`1NXXW]3>G*G10<>7=`Nd6ZeHZOiI^H at hOgRYIVPZ6dJSf\0j\VI>>?:)YOHGI_g[7haKF5 at R\\P\gOe at jYV=\>gH:aU$]nXfJ^:ugI`E;MD\jgZIXGHi\g:dP\\Pmg\+s[PmHhYGNigXIe3qbiW<]YISMH^LM]9uRHX%eY57`b6gYK\7cdF^g^gI$\[[iIHgj\K:_^I8hXSA=o^>bGP49GhH^Xk^gOifE0>O]WW3gKfKi\IhGP9ZFd5x^>,c4bm7ZI\I\gI\HhI/[Ni\NEeW02Z+r]PI`MjO7386QZG2Nhe59O9DROi\^g]EkNV%fg]]OifMgMfIPk\Gka4 at XDiU0e [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1649/ccs/rev np:i:5 rq:f:0.992485
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTTCGCCTCTACCAAATACAGCTATCCTGAGGTGCCAGGTTAGAATAGGCCCTACCACATCTAAGCCTTGAAACGGTCTGTTCCTCGATGTCAAGTTCTTTGTCCGCTTATACCGCCATCTCTCGTTGTGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTTAGAAGGTCAACATGGAGTAGGTGTTTAGGTTGTGTCGGAGGGCAGAA [...]
+ +
+ *K8F<GM1RH<ET7OTGB`4MFMfU0DYn\:cCB<^I\FXHOEG\[i at A&si,Vghe^Qi`0 at N7:I\@hNiHh]fGYFGF519Z5dghBHCG5\AhhBI9kk]L]IM4fY-lb(^U[i\eCIBF'Y]g\GXKIfEjcL:uMaHY[7ji\KXWi^[i]JkYW6Yf2WK1I:V'GN:OUh3i\f^fF4\\P(JN/gggbLL\7\e6CeZ62Z,hh_;G4_^AG at C9a$c3JHY8PFXh6DgiI&[ZJKdIRSfOiHLc\eELEZ4ICNi\HJ7Y[INig=uKggIZi][=Q22^YPNa[^g\^\[iIPj?h4Ejj]3h\^\ILi>mC,61D4E\Mi)?OTEQN5YPjI[*[cEP>RILgg\^\^\^IKeI\3RCcGUgDiJ4E-M&Q<ZY\Y[ZHH at hcKKc0XG5kW]eA*Y^dU16b?OqObYMnOs<Esc]La5wcgl&@[\N[m(hgfAvfq<@zoMbr<[9F(Gnq2|(TL`Ob`>fd5~~hjP&t [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1688/ccs/fwd np:i:8 rq:f:0.994343
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTAATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACT [...]
+ +
+ mxPKr3NBoNfbi,qRUnzW~Xdir7jl~sU}@zyLX`]A~kCyuS|6~h-t_UXSZrXIvRs0a.LKhS4RsVic6~~~~q=z\W{I[UQC~JHaTL1pe7~eW^]{fRQFdWsf?~~xlJ;hU`:kkdqG}[pTXNd]7csSnS6_HTqU/wFzyV<ygPb1/TadThWeGyrcT?&cvWsKzJ~dWAxu>coUZ5U8iH<8UnTvWgXc]U=ytSt<XHzzyBvKV$sae>^Sw[UNyRR|VsAq^d`WN1azVvsWreRZ5a]BO||Xz[UXFbRq_haX`2[fcTW[C^Z^dWcTSKfbxLxJ~{sU2QC6qo[nHg7jbzDb^F{_EVAM`kPY4_M-:\gQxaBNnFzWXtEFfrVK||pLITWIxPc:mRRF^cn^oUfVbwDHu]Yk&POBtdVJv|w^SW%zzfnSMaPU85eSudseXexcW@^B2v?cTL2x`NOH~YFOOrDb^Hd;ucIa8LXqGyQsTNURLTVIsgFt_qUz0M [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1688/ccs/rev np:i:7 rq:f:0.996824
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTA [...]
+ +
+ '~R_Ih:J~xopbZ~aUMrzC_fscB~~Y at YyPe~sjaaS~~J~k3~Z~qA~~~c~Q~~T~O~^rAE9X8ioXRW}4~~~~_jZKY]L~juWx_>~|4;_WxK]o;~X>~p]}c~>r~na~P~lXF~~47?`Alb_q]y:~~|_iP~gJTBb~AZC\1ae^km?~Vq[BpdbvQN]U1~~\K\~f~~}F~gE~~|ymhV\Kgof`hY_o~w`k<neJ~XR:~~[5KXeF~`^~jn`~Q~ob~QJB~~pO{x`]VFULl_FUUSmY^T~~~oLh^>~Hpd0J<MlVnq~_v_v`k[}ikoQ~~^M~A~oa~PrTSsq^^jOnPP{_lLg~pM~D~~rd]^]vW~bf_Yp;_`U]Q=n~FoTjSeh]le=W.|x at D]li=~~_nM}r~~ojA~~~b`ba8I?1X=|~X~mgI~~jH`HookwRq?~~_v}`j\^~~y=~~^alj~vo^V~\vm`u}a[E~J]?V~km}LJ~/~{~b`s9y0~lGSc^:~N~o [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1757/ccs/fwd np:i:6 rq:f:0.997228
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACCGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGA [...]
+ +
+ d~g^ohqV~oWW[E{_g[A4A?mo]7MxnZ[^[ZT'\,ngo^]~coYU~D~~YocW}L~Z*~lg^M}YL~]HoQ:mijSboO~P~zL~a~f;~a\IW-~C~]?~p3~Z6nUTOUdDN$slvDE\g.~wo]B~WZVz^gYJs8UDfmLl\ZU[NGem9v@`K9|~`JqiOh\8~oHm9~mYnYU~FCioa6teQHUhQT&J`,cQ4iOm_~=~@PS)}fpfM~oHjZ@[K~Q;c{tcEiL1neh\BjfGWZfFR`Q=b^eJtgVA(HFnFdHfqdYQX*gZSZ\hF~~T9X8J~C~o^eN~cjo\QR~~f6zye_?s~~[XL~^oC~\<~xcgL~p^~Zqg^pf+~~]J~~pgY[~rU~UAnVLZKh@~sU]oV~~mRN~fUshoh^gKxAy]pfIeP~n_t?5~~%YZ~HuG~`1Veo=~~FMAhbX[Yg^gjZM~`~J|.\U~~DzWWfT<rm_gMz\>~~~gpdG<gloIMrj^oM~]ooL~[pWWaa [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1757/ccs/rev np:i:6 rq:f:0.994821
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAAACAGCGTTATTATTTGGAAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAAACTATGAC [...]
+ +
+ f|V^eGO<x_^d^Xz^V]OO]BLL\9ext^dObHbV]CY=b_VxUOd,PHz|dNTXzL|fH|yVY1rKDwEK-d@~uMMTd=xFqtAd:P>(rS^UdEzTv^NzwCwVCxeeUcPbU:yyycFA4isdZAYa2Gi^UcBqBq?Pd\M\LU^UZ at MMzEy]9{hd?cMAw^Nzo8l8vyde_)a^A{|]>yde^F{YZ\@\UcOlVaP at O{fe^XzTD>=WaF{M@\Xzd?zzzeV{]/`>6Z9lY1^G@[?a,aU^UExeVe^EvGR3?X,ZT[$rb\J[>xyeV^WXzI~d]@OxVe_VOFbsU8yxTOGyzsGbUvXcG~];yyo at Oha>jUQTFJD-]p\>~vAQGWzdCg%C_=x\NTEv{e]e at yyb=KwT.gbc?ESNq&g]ZHS]USaaOeeJuaDa%oONzVyU]eUd?~~]Mc8Sc]eU]UcFNp<YLqL[F{kI~dc?J7wcZ-Ld]BtaU<X]U:yxu[.vMX\Vy]bN%tGGbeb at aG [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1800/ccs/fwd np:i:8 rq:f:0.9959
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATAAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAAT [...]
+ +
+ msV\yW]Ir[P?YUtYRH^.uD`wZ)olZAcBs_OM`2lib87bN5\y[FY3jUCrhYTYvHiPEn{MTOTGuXRMKX9_L^WYanZh\fVUYgyYEi\|U'\C`=ee^i5rQS^|]zV]Dh^VsCT2GvD]_CxHjV;t]e^CTXTHcVwWzW8{}{]a|^W-d:StFZD{W5{|oXQxXY|z[aV$ptV\SkXNGBILauZL;ahlKq]m4b2[\^Cw_Mq{lMRtV][v%@3/Wle6gawOqLxDZGz]zUhBqVcT2dRI;lnO8 at TX]EyUJV;3HC9[9UpI_V_]0UJk1]bHcKZQX`_VhV^KUVlCjeW^lKC^XY]QU.sdWW_9sQE0g<3DB&RVPYEV[V\k>jPS=xlV&>=tLfTGQ at VY]SL??M4RdOWL>wVgNjDtX[LkWXF)CUKa7kgdyE}[.Q^VaXb`X]zT^9tNgXYY]wN+x}}wWWHvUWuZvFDZ<kwCZZX=BZDTGlZV+aSSO_rWKqW^UdZ3NW [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1800/ccs/rev np:i:8 rq:f:0.994058
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGTTGGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAAATATACGCAATGATATCCAACCCTACCGAAACAGCATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAGACGGTCCACCCTCAACGCTATGAACGTTAGTTGA [...]
+ +
+ QcMK>Kd/a\HWFFgLOI<MQLQ;E/LUWWBR&Q*,?Z.IilU`;K3NKVOAf5od6hNPRErNQmHoCNQQUJqPWGQHJob,R+Yjd^TIUQVP9prVTcVo?T7j/_tqB5mUAtlPXU=&_?sLTBZSVEk8hpV1ORSVSPWNU:dQTTOTUioCLqVPW^sVoDBOSWSVrqWC2mT?YkrXVJppV[S1VSoTp6sd>]-orfQKlW8e at ns`@V]'_]_RNNjUpPU,lbWbY:[T=,Q\aQ?RZOXV?AQ0SUH9SX8WB7R?IPa>IC`E]J[J=TJ5R?QoV^=IlVV0rX2\QaR`JtrWGoPVHoDlT1lW?5lnDnRo0omPCjRRrT7mrVZ1ECqVpRREY.NW-ooB;=ns^@R]qPU[5pTCY>RVOCUPVVrWpFxrVTP?RVpBW`EYOrPQo1uufXFrrVKtW_SX^TMHE]GsDoWbR\C>Hlqqd at WQn.&0C@&JYBkX)jd`NIjNWQqVeU<h?@BqVW^sUT [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1860/ccs/fwd np:i:14 rq:f:0.997719
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAAAGAAGCGAAACGGCATTCGTTTAACAAAACGTCACAT [...]
+ +
+ ~~~~~~~~~~~~xw~~~~~~~~~~~=~~~~~~~~~~~~s~L~~~~s~~~\~~~~~|~~q~~~~~f~~{~a~~~~~~~b~q~~~{~Y~~`g~~~~~~^~~c~z~p~~~f~u~~~~~~~~~~dl~l~~~}~^~~~~~~~s~~~s~~~v~~y~~~W~~d~~~~~~~~~~~~u~edz~~Q~r~~D~~~2~~~~~~~~~q~j~~c~P~b~~~f<~~~x~~J~p~~q~Z~~Mi~~fh~~~~Q~~~~A~~p~J~b|~~~~~R~~~s~~~~~~~~x~~:}zoB~~_~~dZnX~~~q~~~_~~~M~~~~~~~~~~l(~~~~~[~~j~~`~~~~~~~~~~z~~~~~~~~~uc~~~~~~~z~~~g~^~~y~~~~w~~~~~~~~~~~~y~W~~~~\~e~~~G~c~~~}~i~r9xY[n~~h~~W~~}~~~~~~)~~ny~~J~w~~~~l~~~~~lrI~~~=~w@~~at~~~~r~]~~pv~q~~qy~o~~d~[Xg?Fnx~d~v~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1860/ccs/rev np:i:14 rq:f:0.997517
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGGACTATGGGACTAGTCGTCTTCGGTCTTACAAATGTTGCAATGCCCTGTGAGCTACTTATGAAACATGAATGGTCGGTCTTGTGGTCGCTTTTGTCGAAATCACCGAAGTGCGTATAATTGATGAACGAGTCGAAGTCGAAGTTGTTCAACAAGAGAGTTAGGTAGTGCCGCTTGAAAAAGTAATAGTGCAAATAAGAAAAAGAAGCGAAACGGCATTCGTTTAACAAAACGTCACAT [...]
+ +
+ 0v{~~~~[~~~~~~~~~~~~~}~~~&~~~~~~~~~~~f~~9~~~~~~~~~~~~j~[~~~~~~~~B~~~~~~~~~~~~~~K~~~~~~~z~C~~~~~~~~~~~~~x~~~~y~~x~~}~~P~~~w~~~~B]~~~g~~~~~~~W~d~~e~~~e~~sp~~o~~t~~y~~~m~c~E~~~_~~wi~~~~~~Y~~~~~~z~~~~~d~~dL~~q~t~H~~~~v~~~~~~~~~~~~]~d~t~~w~~z~~~n~~~~~~~~~~Z~~~a~~2~~~~~~M~~{~~o~~W~~~~~~~~~~~w~~i~~~Zvq~~~n~m~~~~~~o~~}x^~~~~~~~W~O~~~S~~~|~`~B~~~~~[~~~a~~_n~~~~~~~y~~V~I~nC~~~~t~\~~}~~~r~N~~~~~~~~R~~hw~c~~~~~~~~f~~~wz~~`~~~S~f~~p~Y~gX~~~~b~~~~~hbA~~~~~~~bM~~~~v~~~sk~~~~I~~~l~~aa~~~~~L~~~~h~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1902/ccs/fwd np:i:5 rq:f:0.991167
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTAAGTTTATTGATAGGTAAAAAAATCAAGAGAGGGTAATAAAGAAGAAAGAATAATCAAAAGATAGAGCATGCAAACATTACATGGTAGTATTGTTATAGGCGGTATATTGGTAAATGACGATCCTTGACTTAGTTTTTTTACATCGAACGGTTGCAAATCCTAGCATACTTGATATTAATAGTAGATACTGAAATATATCTGAGTATATCAAGGGAAATCGAGATGTAACAATAAGTCGAGGAAATTAAGGTCAATTTAGTGCTTATCATAGAAATAACTACTTAAGCCCTTAAACGAACTAACTCAAATTAACGAGGTAGAGGTTATTCTGAATTGTACGAACGTAGTCGAAGTTTGTTACCAAGGGTAAAGCCAAAACAAAACGATTTTGACAAGAGAATCTATTCCATGTAGTAGTGCGTTTGTACGACGTTCTATTCGATGTAAATCATTAGGACG [...]
+ +
+ RkPR[PW5M<+5A&WQPRUJT:SD:(bjjVNkO5kkZIjOENJCmV)gXRai\VRAfP[KL<mmTCU8BdiO;e9:edO9f(9W?O6XWXNA=SI[PRZQ)P<lgRP,aKR[WCmW[PTN-SKIf,TUB]:3cUVO[Ji1iUDkhN9YP:YU4gKlP[RKl[P$iiaQW;<H[URPBX>>LI]894fgVElQLORWS:%FPL:VZ3VMgQPPVBOW?EQWP<liW[QOT9=MEN=?,A>N+e5bO9iiVP5HP[RKWNkRLkTKkPU<MEClGkjKl*P2cWRMj?mbLOWPRImY?OEUUK8gZP<aIWY;8iKMN/ggKl<khRP at V:P>RLVK'afHj<ULKDBZO[P[Cm3d[HlRWP at eJh:U[RM(HOLO[OP'I9cN9kX:9iZAfIf5nfV?SKIEj2kjaJ=jaNLID-jl[PWRJGM>G*Z:LV[GgEj[WPVWOT?HUOQL2\SJ=>INEQPKjOCC at WRKLVPW:ljRPEIm[ClEKO [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1902/ccs/rev np:i:4 rq:f:0.990087
+ AAGCAGTGTATCAACGCAGAGTACGGGGTAAGTTATTGATAGGTAAAAAATCAAGAGAGGGTAATAAAGAAGAAAGAATAATCAAAGATAGAGCATGCAAACATTACATGGTAGTATTGTTATAGGCGGTATATTGGTAAATGGACGATCCTTGACTTAGTTTTTTACATCGAACGGTTGCAATCCTAGCATACTTGATATTAATAGTAGATACTGAAATATATCTGAGTATATCAAGGGAAATCGAGATGTAACAATAAGTCGAGGAAATTAAGGTCAATTTAGTGCTTATCATAGAAATAACTACTTAAGCCCTTAACGAACTAACTCAAATTAACGAGGTAGAGGTTATTCTGAATTGTACGAACGTAGTCGAAGTTTGTTACCAAGGGTAAAGCCAAAACAAAACGATTTGACAAGAGAATCTATTCCATGTAGTAGTGCGTTTGTACGACGTTCTATTCGATGTAAATCATTAGGACGAGGGTTT [...]
+ +
+ 4K9JUNA&G3 at 92[K4:S9GN at A9&JZ`EIlP+\K?hRTFR1SQ%kkdONTQDi@>@,+Q_R2:++WF71XL9jW<FeNIlVO+k[/LWQ7CPN>VP:6hjOVNkWPW[EjE:RTVKiM;XP[U5VN3a+^c^&nL|c8UrQ'LJW\agM~UbYaXAkVA.^peb]]TIdYXM[WKt1sYX-v5KlfaD0NO_JE_W\>D7WCyOa\g_D\P`XPZ;zyO`aUKTcB/AR`fafYTg4wwJ{|gV+DAPKW`?xXQf5 at yYNXY^'Z%oc.jBsKv:WT|OzzaGQZYWzbdY`P`\D}|a>yTN`XOZ/yX,e]JtT|XEOeYe/xWRX1gQGlSzXY[&nNHEF;_?u/>oU[\?pWyXP`Y\?nXVT7BSSAMeEAubK6[`Ly??&VO&Gjz\J|Az|vY/vtbXCHJh]\aYSzF_Z,adUUWJXJ}`QHM138GEOZYW=`tX\IU,YU\FsUdaFvXYMPWd>{pPYaK{aNzaYVX4Y5,T[ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1945/ccs/fwd np:i:13 rq:f:0.998296
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTGGTTCGTACAGCGGTAAATGACTTGTTGAGTCTTGACGTCGACGACCAAAGCGACCACTTTGACCCAATTGCGAACTACTAAATCCTAAGCAAAGACTATTAGGTAGTAGCCAACTTCGTTAATTCCGTTCAGTACTTTTAAATTCTAACCGACCATCTTTCCGAGTTGCTTCAAACCCTCGTCCTAATGATTTACATCGAATAGAACGTCGTACAAACGCACTACTACATGGAATAGATTCTCTGTCAAATCGTTTTGTTTTGGCTTTACCCTTGGTAACAAACTTCGACTACGTTCGTACAATTCAGAATAACCTCTACCTCGTTAATTTGAGTTAGTTCGTTAAGGGCTTAAGTAGTTATTTCTATGATAAGCACTAAATTGACCTTAATTTCCTCGACTTATTGTTACATTCTCGATTTCCCTTGATAT [...]
+ +
+ ~~~~~~~d~~~~~~~~`}v~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~{sl~Q~q~~~nr~~~~~~~r~~~~|~~~~Z~~~~f~_~~~ylfw~~~~~_~h~~~~~~f~t~>~~~~\~~~~~~Znx`~~~~~~Z~~~h~~~~s~e~~~~m~~[~~O~~~~~~~n~~~~|~~q~~k~W~@~~~~~~~~e~W~~q2~~~~r~~~g~~~S~{O~i~~i~~~so~~~e~~S~~Q~~~w~~R~qIikn~q~~~~~~~~N~~~~a~~~~~~~d~j~~Ip~~~t~~~~~~~~~v~~~~~~~F~a%{X~|~~~~~L~~~~[~~~\~~\~~\Y~~~~s~~\~BJ~~~~~~~]R}O~}~~k_~y~^~~~~~o|~~w~b~~~~~>~~xv~~c~g~~y~~~~~~Q~~~q~z~S~~~z~u~~~~~'~~Q~~~~~~~~~s~n~~u~h~~~~~dd~~~Q~f~~~~~~~~~~~~~~qa~~~b$o~~~~~q~~[~~~~~lz~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1945/ccs/rev np:i:14 rq:f:0.999025
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTGGTTCGTACAGCGGTAAATGACTTGTTGAGTCTTGACGTCGACGACCAAAGCGACCACTTTGACCCAATTGCGAACTACTAAATCCTAAGCAAAGACTATTAGGTAGTAGCCAACTTCGTTAATTCCGTTCAGTACTTTTAAATTCTAACCGACCATCTTTCCGAGTTGCTTCAAACCCTCGTCCTAATGATTTACATCGAATAGAACGTCGTACAAACGCACTACTACATGGAATAGATTCTCTTGTCAAATCGTTTTGTTTTGGCTTTACCCTTGGTAACAAACTTCGACTACGTTCGTACAATTCAGAATAACCTCTACCTCGTTAATTTGAGTTAGTTCGTTAAGGGCTTAAGTAGTTATTTCTATGATAAGCACTAAATTGACCTTAATTTCCTCGACTTATTGTTACATCTCGATTTCCCTTGATAT [...]
+ +
+ 4~{~~~~z~~~~~~~~~~~~~~~~~$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~x~y~~s~~~~~pS~~J~~~s~~h~~{~u~~Mwd~h{~~~~~q_~~W~1~~~~~ob~~ps~~~~a~~~~v~`~~L~~s~~~a~~~p~~~~Z~n~~~~~|br~ke~~~~~~e/pl~~r~~et~s~~~j~~~~~k~z~~9~~~f~~f~~~s~QnW~~~~~~`~~n~~~~~~~~}~cb~n8~~~~hme~rfe~~~b~~~~~~~ln~Z~~{~~i~~~_~~g~~~~d~~q~~~~s~~h~`~~~~~q~~~~y~~~~t~~~~hK~~~zW~~~b~~a~~~q~~d~}~~~~~y~~~z~~~~c_~~~V~qsT~a~~~~~~~t~s~~a~~~~~i~~~~s~~~i~~~~~~~~~~~~~~~~~a~~u~~~~~e~~~~~d~~~~~x~~~~~~~~~~x~~~~~~7~~~~~T~~V~~~~~~~~~l~~~~~u~~~~~~~f~~\~~j~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1948/ccs/fwd np:i:9 rq:f:0.998158
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTAACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCT [...]
+ +
+ c~zJVQmW~~X~QI~h~ghxozrAfM~~~lh~e~fS~}~B~~e}mxFz~gX~@~[~~=~~ySiL~~^~hwL~gh~R~h~fyximq~i~m~U~~~~kf~~g=~}a].x~~wl|l}}_c~~~vVh~\V{~R~X~~ekPt~mh~b~~~c~h~zT}7zaaq~cSQM{FZ~clwW~Q~{mcg~{hcO~i~h~~g~Mqj~~~I~~~V~<~qX~g}i|~YUX~d|ig~}~eUppcsQ~~{x~h~~>\_~ZkX~f~yhd~h~~d~Tg~X`x|OE~~kb~~|~i~Wh~oZ~~i~}X~{F~X{gkQ~~}B~~c~[~~j~{^gl~T~ie~ffin}z~~~2~~i~[I~lG~~G~~~F~x]~~m}mP~i~Xe~Z~~U8~}e\e{m}w<~j~:~pc~{2~~z^~y}~l^W~~~~|x4~~~s[iw~ceh~hu|pMg|~R~wR~~C~~q~s}?~oUHheNe~c~R~)~~~PMxtmw~P=u`t`~~s^pGb~]9Xvq`yuN~n`wLf [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1948/ccs/rev np:i:8 rq:f:0.995017
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTA [...]
+ +
+ Y~I^~`_5x<sito~o[FfIa]`~n+ihc^[y:~sPmXt(QQs<S<q>^\g~^~6~d/o~~}vC~fG~i[ZxR99WrR~\MLaoWcF7t[Bo~~b^+~~oH~{ct0|~~~~[W]B,Ii}Kz;i~wkX8ZQ>~v_v_`reX{L~~}K~XkY~d3ujkJZCTZazpS~ZfMN_Ig_ht\~\hUMf at cEoqqq]CBaI)Ntqs-o4~~o~u~bYZ\yT;)g`L}^Ohdv\OVC}Ks`oG~s[~8naE/~$tdn`J~puF at kxQNv9~rVPYkR>Q=G`M/X<ic5Ul^|9DZTNYk~q\]~|\]qj/~NsknPkOdi~KfgErTI[?UL[NVL~u_\o@~h4~~_r~aa~xU~__MoOxJhKI~X~~}BZ]puc~obv~tbE~uul9N~g,B\I7f<k^~_]FkY<~xx~xnWaf]RagN-iNnkEE|h=kjPvo>wC]&ggRbFhfih\Wj>~{i|ifFgr at YNS]_GoWqTBWjUHP87;0PJHgCSSMB] [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1960/ccs/fwd np:i:6 rq:f:0.994341
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTTAGTTGAAATAGTTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCATATAAGTCGAAGCATTTCAAATGGTTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACA [...]
+ +
+ I{[Xa`mKhJKRE'y\`\N]cJM&HClnpYuLhb`hcQ~~hfOo]1`BEGdM~R at pZIABe\`KLcQh_BQC^ZI_GeIm9WI&ML5J+F;Z^IERR6SRacK{8lDnqQF at bGBUy^fJ[GmbOi]~^QMCS}Q~kQ_[)gQk]QbCA}_P^O_E~~g_jQ[7Zp`mhV^^^Y.QJVLQ'DFHz[\KE at s~~`m^6N]i^c?}~^m%u_Z\fmdM}=g\lQ~i,~~i'Z~aj[P)gfcWRP~sEHQDpYZaeA^_[GcGf`Y~hmP~9]kA~gk=~DdYMY`HH|F\MEj`jGK~`e+}I~[La9QfceIfZ_G~M~Q_j6T>diX~\b<}fFHyZ;hD:|djejCh_R\^CjHZK-xaE$|{eO|%|]^gf7s^Ymh`h^_MWGJ^FN8jgNI_W;^jGfd]R]l^^~5j~xhG~d]F~_i6dj^Rf`fN~^~`m^mfH:t~~\D9H~F3}_h^`fJ}_/kZJG~]`^kQb`G~]_H~:]J~`gafXU [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1960/ccs/rev np:i:6 rq:f:0.993141
+ AAGCAGTGGTATCAACGCAAGAGTACGGGGTTGGTTGTATTTATCCCGCTACGTGGTGGGTAATGAACATGGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCACCTCAACGCTATGAACGTTAGTT [...]
+ +
+ 8YWMC]RO|RkfGTa_WF(?A.R'OZ&fkZSf,}$AB^l5~ufV'4<@%4`IC/4HO(3M%8>JNf~hjX%s_`gQSce}Y:bjv:~~ReJ~r]vZ]e`cHrBL[]oq[~O~:s~p]3l^:~wV`a?JqOSy`~f1thSz;hi\OipViDBwrRJ~gxfpZ/~~nh0rZS,nR]CtRb4oS*s~]^@te\~~q`e;~~frQv\NbJ\O~~i[+~kMHThPQrNHW/7X?7WmrM:M>H]u7dc^fqGy~xkxMxbhgXcq_V\X9mNKepB=sSZqEmWWFkLpVbRLG at lje`e\Vk`^~@WL~wZ{;QkWLd>sg]`fboCYUL7IE at yHP\NO)_cXR)uRpE4Fqa^TWPTc2[hNL`Jcp7v~h.kz\OeGsgq at I{vdPm at uaNe<X`[MV>}rsCSdaMJhebN5E at D2m;x~|k0r`JQ at -0TV4QMeOcI{NmMVimkS:~~~~je:lObzhxYei%p@{ekW~jhg>AkaT~iN'zTfQ~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1991/ccs/fwd np:i:8 rq:f:0.997902
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTCGCCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACACTTATTAT [...]
+ +
+ ~~}gyz~2~~_~t<~{{t1{~z~`w&~~~~~~~~~~~~~~~~~~~~~~~~~85lTI~lbtv~c~i~u}t~R~h~c~e9~~wce~IBYN~k~C`d9P~}~H~mdg|O~~~z~)~rpY~}wO~xpF~~eT~|f^~G5jQ~6~~~|lpS~|Y~~gh~}~T~R~fA~jN$~~~xL~my~~~~Oq~~~~t~E|~K~~lf{Q~||\B~Co~|~Wd~eq[~t~~n~pzdy~`~vUHC~~x}|^wW~~u~T~rd~|f~e~~~c~{u~msgt~Xxb~~~sv-~f~y~_~O`{z~~~NpsSw=~~~~|oO{}a~ze~u}~~T~[~~eylc~~g~e^h~~T~t~ztosJK~~udx>~|t~u}~~~~~<~~~{~K~~h~~~~~r~Gb~~}u|X~~~~~~w~~~FPt_|~A~~R~n~s|X~v}dXe|~~B~pQ~~Y~~~\{rfyz~~~~~}_~z~|g~}x~j~|~~|uft~v~~|~zv~\~~M~~~@~~~~~ox~Kp~~x~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1991/ccs/rev np:i:8 rq:f:0.999132
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGCCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACACTTATTAT [...]
+ +
+ _~ov~uz=~i~~^n~uqF|_~q|~u'~~~~~~~~~~~~~~~~~~~~~~~~~~~yt_a~~vhhv~Q~^q:Ym~o~w~Q~uL~~lul~w~vo~[~}e_cG~G~b~~~~_n~k~tlc~~^~]tJ~_~1~g^`~u\~~\E|;~P~t(q~lO~u^~~t_~uk`~E~qJ~~p^~~]G~huu~tku~th\h~~i`s<j~~t^G~r^~d~~~~v}Orksh\~uu~[~~u_t~i~q~N~~u~u_~uo~~}l_~~Z~u[~c~kbo~w~~~vu[~~_n~u~iqJ~FwY~i~ktvm~ngvj~w~R~~tvsglvt\~mb~~w~|[~R~~tu~uxjU~Z~a~ic~~uw~t^sInP]_to~[zk~vuv~u~k~iLtiD~~[~~l~vK~~P~~^~vU~~v~ktl~uk~~^~v~F~~I~m~TrY~ksuka]h~d~k_~uJ~~~}njt`p_x]t~u\~uuu[~uJvR~u~it~w~j~Rrw~u^~V~~p~q`0~~~~~~u~lb~~6~~g [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1999/ccs/fwd np:i:5 rq:f:0.991195
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCCTGAGACTATATCATACAAAATTGACCCAAATAATTAACTCGTTCCAATAGTTGAAGTGTTGATTAACACATTGAGACAAGTTGTCCGTACTTTAATCATCAAAGTTTTGGACTGACCTATAAATGAAATATTCGCGTTGTCTTCAGTTTAAGAAGTGATATTATTTTCGGTTTCAAGCCTATGTGGAGAGATACAGGAAATAGGTAAACTATAACTAATATAAATATACGCAGACGAAGCCTGTTAACTTTACCAAATCCAAATAGCGGGAGACA [...]
+ +
+ W~e]henC~hbp\H~\_MZcRcnOE=~~~pCucWd6hVbkK~7TIdMhheZEHEG_mFcpeU`4Y3zRA~fW6xcd]lMX~[YY_H8>J]>ch>~sZ=VIXPm\EkZFjwcmcaR`JI`WfV_nFdTt-cu_[c/c_^epUn__`~OI~\ep]KjeA~`P~PLc;NW;,%VdOX0>3eJk9ZLbR\gYIBI6BbheL~~~[>ne`~Md?X_n)rmWcheh[Z=UHNYVMJC(B`cWddR9~\@~~oX~'$$zBn]e[g>oKmhLcBPQ/vPlMVB`VU~7|ZQ\fM~O;AH\+LL_~ELL~emIUCzXCw_\eV[F~nM1w_sA~f\i]^-`[\_2~bUc3~f_'Ta2]]a5}HQXVu]Mc6b~Sd_0xaUcglgYnR=VYq\QwF~jF2/MM~nQUcnCud;cSRl:XO1f0z[OfQ~_8nmYUeiFk]pK~nK^LycoeSMCL[idhZMRsd<~lLHzJ~]R~lXL~>~oOJm:97jbcE6i`GR]CL [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/1999/ccs/rev np:i:5 rq:f:0.994586
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCCTGAGACTATATCATACAAAATTGACCCAAATAATAAACTCGTTCCAATAGTTGAAGTGTTGATTAACACATTGAGACAAGTTGTCCGTACTTTAATCATCAAAGTTTTGGACTGACCTATAAATGAAATATTCGCGTTGTCTCAGTTTAAGAAGTGATATTATTTCGGTTTCAAGCCTATGTGGAGAGATACAGGAAATAGGTAAACTATAACTAATATAAATATACGCAGACGAAGCCTGTTAACTTTACCAAATCCAAATAGCGGGAGACACT [...]
+ +
+ <aOGW[]-lfnQd`~MXFEP^Ygj_:~|_aF^Z`X8ycj_U~KrM[Zgi`FahEAaNZ>GA;;>S%m)]adCyoQa:[a~]pcFcVl=no]m&|h8MhQ~X~`Z~S5cXIdEfJBj6uKne\RL~NrDz`g`U8xuQ[h]rT5MagAfJEdM[tg>~f?|hnQS|Wg^M~dcHiOyX~]gL~2i`hlLDc\pe[OR1XgwdnLRM at Hne]nJI~~bT:VneaLeohephp_0[byX~]pEsWD{~e`}bC{~Lfe]KgC~a~hp[$DFNvJY@'CGdBEH_^peoG~XiYc\0YDLcAbR~[;md0qh\gddf&`G~yX5pSnN}SKg]pU~hhRE~qR[J~~feImdZ`\@J[ca&apX8[F=uY:GQ;YUQl5nd1jJ7EFAZzeb~WP|c:_EaCg8,ODdKi5kO~2~shp:\:2xsQGmhZaZZGb\TQDnuhphjcG[nFkMZL~EO}\/6qIg]@~~oQ}Q|lRQ~GZyfk\e*~rhSjepec [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2012/ccs/fwd np:i:6 rq:f:0.993131
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCACCGGGTTTTACAAAGGAGAACTTCCAAACATCAAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACAACAAGCCCGTCGCCTCTACCAAATACAGCTATCCTGAGGTGCCAGGTTAGAATAGGCCCTACCACATCTAAGCCTTGAAACGGTCTGTTCCTCGTGTCAAGTTCTTGTCCGCTTATACCGCCATCTCTCGTTGTGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTTAGGTGTGTCGGAGGGCAGAAACCA [...]
+ +
+ RqXQ[V^Kp\B\Q at jPUODVDU\EP2qq`QKqX\2oWQWDW\@Z8-CnCpl6op]F?/6OGo[W=nPRp?V1OTNBWO2BP^X\E\Cpp[^W9oh:DmlMD1BXpj[X[X[QKp[X[P>n][X^X^Kp^Q[QX]I7I?gp[Fp at pX[^'m[Y^[DZPNnQNqQ[XNqKp^X^TPEdQXNKQHn^[OE\XNEOQnF/chf[Q\Q\Q[XOEPX^Y2mmZXQ1e[X^X\7lNpXV&+`9<\X:jUXY$DCq^QZ[Ds<pp^[Q[V;\[^EoXOCJm^V at X.JoRp[W9lSWKp<ss\F4a[Q[^Q^ApXDsQp=?[kQHs^QZ?:l4P?NX^X\:9X<Oh8)j?Z2nU9=mZ^Y2oV6pXWLSQ]QXQp@\Kp\B:MlX[U=m6k=nTQ^Q^Q[X^2tgZ?n=qm?T<OLE\Q[Q^TFVMm@[Z\PJ[XDs^[X^Kp]@YQp[W=nGr^QMf8-XKp[VDYKp^X)onZUGl]X\@\Q1e[CqnQR-7[XCn9 [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2012/ccs/rev np:i:5 rq:f:0.99375
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGCTATCCTGAGGTGCCAGGTTAGAATAGGCCCTACCACATCTAAGCCTTTGAAACGGTCTGTTCCTCGTGTCAAGTTCTTTGTCCGCTTATACCGCCATCTCTCGTTGTGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAA [...]
+ +
+ /YKA\QNEhUXLWKgWO?CLPO3ER$oooWXLW&VGRMT6CHLOBVKnKo>sT2nokSWEn]/OL?0TP(nOJn=nTA*>Z:XO.[Y.fSHLC/v|aC~~bj>~r^rjZjZjb;aXAMKX~gjZdZPB@&_jcZgjch0||hK~YsXjgE~~~~eH~aG~JH~`QXRh>>'VQYjK~cZcX~HkcjchaE_7`QDc)|||hRdbcKhZbCVY:f3~~]Fa=~P>B<-0uY}A_BnJsaH~YJ~~[TcZP~_bPgB~H~iIKE4RLdhaSigZc)zaDR~i<zEEeZYj%eK~9axgiR~P_Pdcg\~ZS~$wXY2~VH6^R][WJwS~PbZfYOJZ~ZJx^$NPUK?_SWEzgNhS~ZS~jfce`NbZF~YfHjRh^W{ZZXF}J~X~jcfbPbjYR at bWTD^:~~AqcjY<eLhbdZjZGhYfiPe<E<?|Ph[fM~g^^F~gDH}I`^X\~cdI;|hZggHffZ0xoe5cWVeW`bM~jD~~chDQ}~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2091/ccs/fwd np:i:12 rq:f:0.999043
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTAAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGC [...]
+ +
+ ~~~~~~~x~~~~~i~~~~~~~~~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~w~~~~~}~~{~~~|~~\~~G~~~~~~~~~~~~~~~~p~~~~~~~~~~_~~~t~~q~m~}~~~~~~~~~~~`~~{~V~y~~~T~~}~k~~uS~~{X~~?~~~/~a~{~~~~~/~~~d~j~~]~~~~}~~~w~~~~~u~m~o~~~~~~a~~h~~~~~G~~~~Y~~L~~~~~~~~~~P~~K~~~Q~~|~~~L~~~~~al~~~M~~wn]~u~n~~~~~~~~~~~w[~~C~~y~~~~~L~p~~y~u~~z~j~~~~|~~~~~~~~~~~c~~~l~~~~~~~~n~mtn~g~~n~m~~~~h~~w~~g~~S~~~~~yj~~~~~~`~i~~av~~~~~~~~f~~~u~q~~c~X~~~c~~~~~j~d~~~su~M~~~~~~O~~~T~~~~L~~~~S~~~~m~iis~~~W~~}z~9~~~K~~~~~~~f~~]~~p~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2091/ccs/rev np:i:12 rq:f:0.999321
+ AGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTAAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTA [...]
+ +
+ gq~~~~c~~~~~~~~~~~v~u~~~(~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~U~~g~~~~yt~~~~~~ks~~g~~n~~~~~~~r~wW~~r~wxZ~~~~v~~r~~~]~~[~z~~~~~~~~n~~~~~~bx~x~G~~u~y~~~~~N~~o~T~~Y}~~~~~~Y~~~~~~~y~_~~~\~r~~{x~~P~~~j[~~~~~~~n~V~w~d~~~im~=~~T~~~~s~q~~w~n~m~k~~~~~~`~o~~m~~~\~~~y~~o~]~~u~l~~~|~~~~~~~~~~~~O~~t~n~~~~~~B~~m~~o~~S~~~~~~^~~y~~~~~~~~f~_~`~u~u~)~~~~~~~tQ~~~~~~~u~~~yi~X~~s~~YfL~~O~~o~~~~~~T~~~~~~{~>~~~M~~]~~~y~l~~~~~s~~l~{~x~p~~~v~~~\~s~o~~_~~~~~~j~~~c~~|~M~~~~a~~h~l~~n_~~~~~~~D~~~~~Z~~~q<~~]~~r~~~~_~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2097/ccs/fwd np:i:5 rq:f:0.99522
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGACCGAAGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAA [...]
+ +
+ _zVZgT^J~_RdYEsSTBNQ_TNPY*}~}r_b=\GWtVIPQeZgVZUYTPXHcAegH~<r`IeVXxWw;*utSZWzgH~ZXxg>~~gfULFY3ZN<aHvVMwVZWgJsGkDKYoKwVJwReVgT5S/owweY@?nSQY8yMD5xCTP9WHtPUeDeZfVZVZQ><fM[S9z~vKwgJ~U-\l6z<tlXaZDd at 8pwuFvK`T7a,MYUDUe<wUOEvJwPeYEkAeVTsKB~gVZCZ_0EXa`RWEAn~gY4nSP3NAATfVd at V=TvgVeEBiUSZVgVZVY2z^OTXf9yvdBYVKpJ~c/RK_Vb6XU1vvUDxxVg-zzcZfGW1dJ~[At_]VKwgKxUU?IVR at rwZ0F>Y)COST?eVKQ4_XEv2uuPIeGxygU<uU:YX=VX at 9r9iYgWZVWxgWxe1vvCeFvHYFvVIQRb5zsUQ:bOcYPUV<YW2oQrKbbUMWoJz_9VMExgZVWxD1jaeVd;@9ovpUXxgZfFvZ^HO= [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2097/ccs/rev np:i:5 rq:f:0.991395
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGACGAAGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATA [...]
+ +
+ ;bIKCIQJXdaPB at eVY@K>ZYVNU5_^km]Y)PUsU=aaTVRGVVx[bLHlZcaH]5XWP[CTsGrM=~oWFHtf=xVUxPD|qMfXYKn;Zd=U;D08`TFTX<mKnF.RXA]FHuKPC<VQ?1xx^PJO3rc_VLze at 8rUZf7|JaYZQShUgWUCO&LG~VuV9uetAfL1jNJV]Dl)gT[8\7_U1xyTE{ggV<pR`VW at 2bCnZg(8F0hePUYxVKXGwfJ[dEQQWP0cYeNIbC?bZSL*gI?`?V at D_>^X at UStfFWUEbOVKAN2TX=(nudVfa:nueZVWCsGY:R*BaDcSVX3eeY/~bX`2kecS%CuWfJ[U3sy?/7eKSZZgZRI/)Ia\V5vpJTVYxgKwKUfYxLWw?~{aTa?vuMXAoV/,IbETDGx at Q>5S>RImO4fH8iP:tC_%o>K/G]=H)UX>3aMO_VeEUZbOOYQ_3[<RI`oItPa?VH`DVZFER+LjqGP[S=wxqRVfeVaRrReMG [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2126/ccs/fwd np:i:11 rq:f:0.998158
+ AAGCAGTGGTATCAACGCAGAGTACGGGAGACCAGTAGTTGGGTCAGAAATTAGACGTGGTTTAGTCTGGTTACCGTGGAAAGAATAGCTGAACTCAAAGAAGCCGACAAAGATAAACAAAGAAGAAACGGTTAATACGATTGAGGAGAAATATTCAATCCAACGGCAACTATTAACGTTCAACTAGAATCTACGTTTCATACGCGGATTCCACATCCGTTCTTGCAATTAAAGAAACGATGTAGAAAACGCTTTGGTTGGCGACAACTTGGGCGGCAAAATAATTATGGTAGGTAATTGAAGTAGCGTTAAAACGCAAAAAGAAGGAAGCACGGATCACTGCAAAAAGGACTACTCAATAATGGTTTCTAAAGTCATTATGCTGGTGCTCCCTATGGCGGTGGTCAGTACTGTAACTAAAGATGGATTACGGCACTTGTAGAGCACGTATCAGACCCAGCTTTGAAAGAAGGCTGAGTTCGGTTCGGGT [...]
+ +
+ ~~t_~p|K~bytoc~lbnrr~s~sX<~~~nm?~vy~~vTz9z{np~xa~~^~~f~rrp^~I~~~nA\}N~k~~I~u~_~J~~tj~~~dnja}~n~_a~~xj~hJ~s~Zk~~ft}^~~[U~~tN~uE~~pQ~F~V~t~gl5W~m|W~~_S~~RnYuXb~sD~oWWZ~Ul~ftif~h~Td$zdX~dwhn^uzdp~dl=~~Z~]cgnj\~|gq(~|[~vG~_U~ic~qkk~d~4~mPQPwZXlw]`TS2g~~bWcV~~I~e~Z~cYrVu~lX~;~~^H~hC~~~yb~E~}tF{ruKzcx~a~Zq~dqteV=V~8j~~ikUK~~~yirwY~V~iSyjX~|{j|U^ThS~~~~X~~cfRghZg~qB}rF~J~~kuN~~]uA~_~jTjS at J{{kYvDl~wttU~lW~hE~ZRvne~j_Yt5~Xx>~~mvfM~~Y~xR:FQGAd~lx~Yx\j~mny}dCop~9u~~`hX~~Yg~~it~J~fho~df~gE~b~iB~~N [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2126/ccs/rev np:i:12 rq:f:0.99809
+ AGCAGTGGTATCAACGCAGAGTACGGGAGACCAGTAGTTGGGTCAGAAATTAGACGTGGTTTAGTCTGGTTACCGTGGAAAGAATAGCTGAACTCAAAGAAGCCGACAAAGATAAACAAAGAAGAAACGGTTAATACGATTGAGGAGAAATATTCAATCCAACGGCAACTATTAACGTTTCAACTAGAATCTACGTTTCATACGCGGATTCCACATCCGTTCTTGCAATTAAAGAAACGATGTAGAAAACGCTTTGGTTGGCGACAACTTGGGCGGCAAAATAATTATGGTAGGTAATTGAAGTAGCGTTAAAACGCAAAAAGAAGGAAGCACGGATCACTGCAAAAAGGACTACTCAATAATGGTTTCTAAAGTCATTATGCTGGTGCTCCCTATGGCGGTGGTCAGTACTGTAACTAAAGATGGATTACGGCACTTGTAGAGCACGTATCAGACCCAGCTTTGAAAGAAGGCTGAGTTCGGTTCGGGT [...]
+ +
+ ohU^hfD~~~~]\~n6p~[K]v~uA}\vWx\~~`t\cd~A~~~p~]V~~S{Wjlfl~[~_~~llSVgO~K~kN~_~B~O~~lg~~{XgxXS~f~uW~~pm~kC~n]qG~~\y~G~~sD~~YU~WJ~~q=~`i`~unbp~t~^cT~dkC~~~Zp~Lk~~M~g~H*~r_qr~~l~^~voY~~s6~IIge[~zIv~CZ_~~rX~~qXaQ~~o~J~nti]`~a^}_Z~nun~vvP~ra<lwTUy~jWnV,~~yqV7(oyB~|~Tz8a^UF~jRpC~~hA~:L~~~~[~v~x~W~~WQ~~B~d~V`Uo~sm]hX~8|~~Z\@1Nre\kR~Ny`xm`ojGwV~b}a~E]Ep~~|L~gO~\h~dR~~[~~T~X~~p~3~~onIhf~~~pstL~~kx~M~~gzdER:A9e>~tFVn`jn~lx/~ekL~{SU~:Ytn~~RL~@{RjsL;Wlr\uprjppnVq_W?~~oad@{uaAuc[S~W~q~[WkE`FP}PuC4~~P [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2164/ccs/fwd np:i:7 rq:f:0.995633
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATTCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGA [...]
+ +
+ p~y]httc~jM~\8zdfZ|xix~Nh$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~``ZRw\@~~~yM~yZ~G~~zp~~h~mlx~X~j]Y~F~~yZ~~xVuj_YF~e~%lq@~~~rRc~~f~}I~~a~~lY~~sY~~mQb_~{niI~ra~cred~m|t{Oqn~Y~Xk^T~|j1qYul?~~htih^bNzaiJn(a7ys\gH~nnE\pa/|~|s|iyWzozH~h$c'T76~~u`6gn_gWwS~ycuodGc^PM<~~~mU~r`z at B7q_[~o=zbK~UPmfx)~~lN~S\~]hy]Y_b~jse]W~_S~\T~{]~hrcp.~jtR`VrmT]~~QxbjpNyqWTY~m]Wm[M[\0pTWpZhn?~nR~~snD~~~rDrXcsg~n]NlXN~Y<O:ZLDTx\ad&tWW~\~W~]U~Kh}VM~OZ1uoSb<~`IeNymgT~dl|djk)CZ~f1|j\hG9~~<+3/d{T~t]<`/bWm0~xIxO~gTi\~W~|nV~C~t]ms [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2164/ccs/rev np:i:7 rq:f:0.996833
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTAATACATTGACCTAACTCACTACTACGCCTTGGTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTACTCCTACCGCTATTATGGTTGAGAACCTGTTAAATGAGATGG [...]
+ +
+ X~\xjquU~PP9sH~\V6L>gp~~|&~~~~~~}tz~~~~~~~~~~~~~~~~~~rrkuqv3~~}tJ~YVg8~cydefJ[Ly`{f~~xZ~T~}mH~dGO2;Lj_~W~wtGqf~t~P~~i~~Y~~`~jtH~~vV~~xI0A}~{jZ~p9~~l}5~\;adLj^i+SRk)@;Azs~yjgU~~;}a:_r:~x_v~~{L~xQrK~r~[s{u1~}Kcx||WZUKZ~ui\V~~H~~uZ~~|vl_Zzyv{bW=kZev<~~aK8maU~~s9~ab~[a~{K~z]mvp7{~qr~j>~j{~oh{N~pPsjk~pf~[S~WU~c~{j[~i}Hswghm4~~jig0'Y`kwiLzZ]qdJ[Kx=~~qcZ~V:~~S~~Np;~~~oJoqLw~T~o|=~cv~{irhzR~wwi`kY~R~[~A~g~X~bkm~_iF~~roNw\hdi~~p\~vWubpS~~Z}Mu~r|rxM~~|~pxhN~NlR~lmKbOE+SOy^{dYj4~_~oGB~F~~yi=[ExS~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2225/ccs/fwd np:i:6 rq:f:0.995244
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTTCGCAATGAAAAGAATATCCTTATAGACACGAAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCT [...]
+ +
+ e~Uctj]J~xtsRN~UjTslshXZc%~~~~~~~~~~~~~~~~~~~~~~{y~~~~~plvFh_V~xgB~xevG[aH]slycJ~OtPXtslvdTjJUwlvTq^XAL9X`QbMX_^J^:_[lh\lX~Rj:^O_gJQZ`hI~~Wv:~JfYSAynL_?bhI<rfZB|[@|~zWTUleEjg[WK~bgXUK~l;~~cGGfGkN~X~bl?rX~R~jEL`kE^t8~r_uahblggfad1m]R[6ViQagB~z=~~U3Zf@>~M4^'a;7NOPZFV*dc_Z at wkhlL~X~hlb[gZLW`&e\YI~n<b]FcGO~:kdD\]~S at _Cee[h[`SZ]aKWFpU\5~~^;~Lp]Y{XQ6}RV]}LllM~P{^^~[P}Q{|F~|F{QeE_ at JuPChbh7jHIF5>u}Z;YfYoQ}e`g\>>jDR at fJ~8~t^K|F~O}`S`2zCu~l[h_4^e\Cz~PT7~~~hR~l_:Hx9WPDfb<v_4P~G~ka4~~~uX~T)eI/nfVQa[l [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2225/ccs/rev np:i:6 rq:f:0.996238
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTGTAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGGAAGGTTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATTCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAG [...]
+ +
+ TwdmzetS~]wo<e~T_<sUvTXif$LZjx~~~~~wqoqvvrrw}~~~~~{gXM>53,NE<^th~sTZ~sjFvmetmyftk<~Nlgh~qSFgN^eKjNpQ~ftmc_kc`^j;~lE~]ahmxk]f~.~mKvctmsd]w;{{`~TqH]j_$~~iZ~2u'OQ[~yle~_@~vkSZkqufUkh[H~KDi]Z~sB~abkT~jXTwc~NHQ~U~U~thldq.~s8~~~~cyetrhwLlY~G at qETqwOsQ~s;~~T:xvjPyqZ~P~iN>f~rNFdb`a|lx]\~_xuZuewR\ieJ~l8~p_~[FefS~b~BPK<kga~TzGaxh]Gf0<uldrBMD~~~F~b~c;tfCToFc6PNrm[~Pyy]~c=m5v[7~~U~y*oltj+~Ro_bnSoE~xgA~fKsSvVvE~tTu;Eq~ktW~_rNq~N>~d~PznocT~E~UVTobffR=@_elyB~y~Q.pkKvY~_jsmea]~^PNvcp^c4yi\ydt%X~wF~[ktO [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2255/ccs/fwd np:i:14 rq:f:0.999159
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGCAAT [...]
+ +
+ ~~u_~|~p~~~~U/~Xr~~u~i~~~B~~~~~~~C~~~uWrZ~~~Vqo~f~~c~uj~\Q~~pSK~~L~~{t\~R~~~v~]~vyU~~lrl~K~~~q~~g~~c~~~~~k~`:~e~~tL~~~~oB~~n~r~~d~sX^~p~~Gp~~`~~~=~~o{ly~~z~i{m~~~~~m~k~s~l~~i~~~L~~~z~Xyu~va~~~sWJ~~`~~tR~~~jq{~{~~u}~~~~YC~}_V~~T~~mvJ~^~~~~Ixwp_utbki_}fQov~iW~oo0|C~~~XY~jF~x[sndbRq~emoZ~e_`9s~~qaW~~Y~t~~~~~wuH~uh~}v~~NBt~~~bn~Q~{~l~~~\~esSo|jcz~m2ig~qCg_bTbyLU~~~~~|0~~~iB|J~WaR~~~~w~oi}~~}~z1~~}G~Y~mzmX~~{~S~\e]h~Y~{C~~iir~~e~]}~`jrtb~~K~~~y~~m~~kp~~mM~~syB~~Z~nm~t~~~~~j~]~~o~tX~k~~~~~~n [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2255/ccs/rev np:i:15 rq:f:0.998329
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCCAACTAAGGTTCGTCTTGAAGCAAT [...]
+ +
+ U~z~ae~f~~~~~D~w~~~{~~~~{T~~~m~v~:~~~~~xo~a~~~~~d~~r~~~o~`~`r~;~v~{~~~~P~~~~~O~~{L~yldd~o~~~zc_]~~~wub~~~~\}~l~bzA~~zt~r~~~{uA~Z~w~{~8~~|~j~S~~YE~~_~~~~~|vyu|V~~~~~t{~gv&~ef~y~R~~~X~~kf~xY~~xu~_~~~~~iO~~~z~~w~~~~d}~~`~r~~~O~~>~d~xs~Z~~b]]~~k~~}~~~~~U~~~~~X~~qb~~~t~~h~wO~~~~~hvhg~~~mP~~~jG~~nyxe~~k~~e~y~~~{~~s@~~c~~~~~~p~~~~e~~~q~~j`~~ny~u~~xuln~lg~~~~~e~~~c~~V~y~p~~~_{v~~T~i~d~~~~~~^~~~~Se~hwQ~5~c~{K~~~a~~z~~L~g~~b~z~~vb~g~~WW~~~~d~af~~~t~~~~~~~ws~}~~~~^~~~~~)~ki~~~n~n~i~~~~u~~~r~~wY~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2286/ccs/fwd np:i:7 rq:f:0.994484
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAAATTTACGGTGGTAATTTCGCACACTTCG [...]
+ +
+ e~b]k^bS~gZeY9jW^Ll`X^MUY$W_kyyrmlnpaWSV`igiowuqqu}~~~|kgZcSd`/V@\^lP~i@(9IC>QMYdLkS~fHeK~bkVkfN~lYX7z`YWd@~~A~k]dG=H~KJ~N|fFWU:|^7L9~xSj]d[[Ca[BlV5bmDP~mbfmba^$~~~~~\]]E~O~MT).,_j6rb^dWZcX`L~jPZKDj[UILYtXGXC.~~oALLn_D~V)}PI}]CfJUo<~~~l\2{g_\M~ec]X~WRD~f4eVG~i3U(S^Za;|iy^6\[d?~}KjbmeaNAlN~`A<iX7]LVK0y~\fb]f]b3 at G@j1~WJiaM~]bdH``E_:|G{\2lq~fWejeZAEdY~[bfbfm8xfj;mOwXLWa]bN~a2u2ey_PfJjeZfWZf_kL~~]fX.oebflN~~P<=~c1jXb]f]hb\FaJEaFbYMZW~bjOJ3`hVwIYkH@~z^g^eg=h(CY)RRL~~lZ-}dRy`7yBrvPH[SYgHUo]` [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2286/ccs/rev np:i:7 rq:f:0.996434
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACG [...]
+ +
+ :RH at PCW;qnhncG~[_deZi\nhc%~tc_gmnmnniefmu{mQ at 8;IbxsiYST\LcRdfdne]Yf?}gd_nai@~gep^QO~i`PO}Ga`aYO~SbhR~nh^Y;~eP~fNWbhU~_N|U~YeNfQ~JWt>zdL~`:Z\XPNJ~MQy~bHf]^;E_n\+Wx~~jbDJdJ~C`,~CfO&O_KfQ_fiXT~fVa_XpaRW]M~_N~c at gs~h`T~VDdM?VWiMW~dX~>~~Q:KBjfI4D~kJbYs\f%uoWad;~ua<Pq_c]=jfsIV~JWP~~nh]dm^YW~C~mhU~g;wcOQ=~~am_dncYG~cW~9~~U~\O~[NWc^Y`5Kx,^K5U[QZ\\HG7UUhTsaGB[egR~oiR~VQgXR?7F]~jR~'~[[TgefXekQO`_]H]{_ndX~n_l8CvvZhQlYK~`j_ncY^bXlncncT^XbX~PclQc^YY~JXia?kvXM]nhNqhd_X~Bqq_L>mZ<x^Tg>zj_^Nfchb4fD^ahK] [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2295/ccs/fwd np:i:4 rq:f:0.992925
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTCTGGCAGATTAGATACAGCTATAGAGCGAATCACCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGTGGTTTGCACTGTTGACCACCAGCAACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGC [...]
+ +
+ S_GKVGB?[TFSL,ZRKRFJ[KR/B$PV_ddddb\WTSRNKJMRVXMIKPTLHNWU3M:T=fKCJZEcGJ\VU9X6O>YTEIEJSKLaGS\E\@@FLNQ2\IeFISD>cSV at mR6d_FSKfP.;NeJfFO7B at N;\EdFUYLMfV\I=4bU at dKQ1RAI4deJEXHFZTQ5ZFd>RSS;DU?lR/_F9=DJUEc;bP4EKJE`VKNfTR;V;R8CA*CU\UFJQ%_HI=I9dRK\EdBSAQREOVS[BFO=L7MH1F<ZKfS\FdVJD<IAF'^ZD8J4OUFGSJfFdVJ>cQADPRKKf\K>bKPEJH`>SJeOfVKSKfKVSVWGS<PVKC4=ISKM]G5bZNQZ7,2RBf^F9UGR%:L7V at _FFi\KR,D<H<NeVRJQ>XJAOUGJ<VKU:PUI:<9_P:VXTAMHf\CffK\SBf\F at TJ;cP<CTAH>D:eeEI:BSJ4aRF(SKQ=UDcVJWG8g[WQ:>O4<H\KSQQ>eRKL7QRJc1hR [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2295/ccs/rev np:i:4 rq:f:0.976003
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTCTGGCAGATTAGATACAGCTATAGGAGCGAATCACCACGTCTCCTTAGATAACTGGCAAATTCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTTGCACTCAACTTTGCCTGAATCGTGTCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGACGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTA [...]
+ +
+ <XD.GB at 3FB@1A*5/DBF=4)MHB$K at KTND<:COTOE?@GOJB>AJNC>D:3E:<O>TBKIJ%SD5JPJBH-3&KPK'JI2 at 2=8:AK&MA>3M<-:YCU6 at 7BBXB;;VB<XX5PB4UA4ABUEWKBH.AVIK9]KPKH-<;KIN(YN>XH-/TAJ1DTH*MIBKPA3I)G&TOPBJ:>VB%SSIHA4 at 8,AUB$SSG9]OF=P%AG9FJ<G<)?AKPKF:&UKKBH4SBIG6[GBJ+9JB9AKEWBIK5WKBH.IDWCK9\NGJBFKI;YOF68\J4UBDU+TCH0VBHK?BE2SJIBXH:JH4A-TDW9O;GB6 at C8@5IA4>VWIJ')NG?A<M9*PKB:I<F:N=2AKBN39PGG8YK9\GHBKBG?-U;.FBBXIKPKBH?+GHO3XNF;P<XW:YKPKB4UJ>VWD8A1UUHKPI@=AJ2L-IBP6P?1T(=:G9N:GBN1,NF&WMIKB-POLGDDA3AHJ2 at HBBXBD+6LBEW;P;=J [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2305/ccs/fwd np:i:11 rq:f:0.999136
+ AAGCAGTGGTATCAACGCAGAGTACGGGACGGTCGTACTAAAATCAGCTACGCGATCGCCGACTTAGAAGGCTGAGATGGAGAAACTTGTCTACTGGCAGACCTCACTATCTTTTAGGAAGGTCACGAAGCGGCTGGAGTGATGGCTAGTCTCAGCCACTGTCAACGGGAAGCGCGACGTTTATGGTCAATATAAACTAGCAGTTTAATCCGTATGGCGATCTTAGCGGATGTTACAGGATGGAGAAGATGACAAAGTAGAAGCTAGACAACTATATCAAATCGTTGTGTGGTCTTAAACCGACACAGTAGCATTCATCGTTGGATGTGGAAGGTCACAGCCTCGTTGGAGGAGATACTACGGTCCCGCTTTTCGTGGGTGACAAAGGTCGCAAAGGTTTCCTTAGGGAGGTCGTTTCCCGGATCTTTATCTACATCTCCTGGGTGAAGGGGATGATCTTTCTCTACATGTCCTGGGTGGAGGGGAGTTT [...]
+ +
+ ~~]f~~~h~}~~[0|`~dg~{~~~gl~~~_e~~M~~xe~N~~~~Vd~e~cQ~a~c~g~Q~~wQ~~~~T~x~b~~s~u~|~w~T~wR~~~~^~~f~~~fy~sM~~bzX~r~]\~~~u[~a~i~~c~`la~~ch~_~|~w~~~~~x~d~]~~d~Tx~6~z\j|~Bd~ba~~_~~f~`~~U~~~~~~a~~Rk~~~~c~~c~~~P~~z~~q~~R~~~~~~~d~~~P~~~~d~~~~ip~qa~|~v~|~~~_~~~~~bVX~~~~~~U~xb~~~T`@eQ~Y~~~SG~~kd~w~~~ffnn~`~~3~~M~~wZo\o~~ToA|~~O[~J~~~Y~hd~~v~P~s~~[bZu~J~~`i{~n~pe~t~g~dE~vd~~~A~~~bZ~~~O~~o~~~~~_K~~s~~U~dP~~j~@~~G~~~`i~~~|~~Q~\~~F~~~~~~ev~~~~O~nb~~f~N~~a~~~~o~c~~~x~~p~am~y9~U~be~~~~*w~_~~~r~~b~~~~~w~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2305/ccs/rev np:i:11 rq:f:0.998752
+ AAGCAGTGGTATCAACGCAGAGTACGGGACGGTCGTACTAAAATCAGCTACGCGATCGCCGACTTAGAAGGCTGAGATGGAGAAACTTGTCTACTGGCAGACCTCACTATCTTTTAGGAAGGTCACGAAGCGGCTGGAGTGATGGCTAGTCTCAGCCACTGTCAACGGGAAGCGCGACGTTTATGGTCAATATAAACTAGCAGTTTAATCCGTATGGCGATCTTAGCGGATGTTACAGGATGGAGAAGATGACAAAGTAGAAGCTAGACAACTATATCAAATCGTTGTGTGGTCTTAAACCGACACAGTAGCATTCATCGTTGGATGTGGAAGGTCACAGCCTCGTTGGAGGAGATACTACGGTCCCGCTTTTCGTGGGTGACAAAGGTCGCAAAGGTTTCCTTAGGGAGGTCGTTTCCCGGATCTTTATCTACATCTCCTGGGTGAAGGGGATGATCTTTCTCTACATGTCCTGGGTGGAGGGGAGTTT [...]
+ +
+ n~^~~QX<|o~`{~~~_y~_~M~~~A~~|tEsm~_n~~n<~~~juxVu~~z_~^~~x\s~M~~^~yWw~L~~Y]~^~~@~~[3~~~k~N[~m~~~L~xr(ss~~o~~m~m~N~~~~L~~~L~s~~~^n~R~8~~1-dq[3J~~L~~n}_~~o~~Mv~~~|Gk~~~x>~~W~LfQz<~~_V~{^~M~~e|~e~Zc~~~~~]~~NV~~~~mt~ZJ~W<~~R~~~Z~~G~G~~lMZ~~~~5~~~J~~]{~B~[\~`x~~^~~`~~^~~~_~x~~~Y~l~j~t~~m~OJwNaU<Fu~~M~f~~v~N~b~~~\o~_~~Kz\~~~_MQ+~~YYm-kv~O~p~~~~_j~Vu^Y~K~~L~~N~m~~it~-soa~s[oP~~~~Gl5~~}_~~e~~N~~b[~c~~MzP~~v~N~~A~~~@~n~_H~~Q~rG~~m~N~~~o~~~~~i~~r~~6~~~]y~0~~~~oR~~~Y~~~i~~~~~~_~d~l5~z?>Eu;~~~~]^~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2319/ccs/fwd np:i:11 rq:f:0.9989
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTA [...]
+ +
+ ~~~~~~~a~~a~~f~|ge~{~}~u~%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}z_~zys~~}u~~~~~~}~d~}~~@~q~vb~~S~||~vd~gxz~~~~z_ty~y{|~~f~~}~~~~~f~c~d~cy~;~}~~V~~f~t~g~O~J~~u~Q~~fa~]~O~}F~~~{~~~Dq~~~~t~}~y~f~~,~~~~h~~zu~b~q~e~c~h~~~vdvG~~>~~~~{v|~~~~{~v~}~~uzx\{HUzxK~~~Z~~~h~rc~a~~T~~~~gU~~}s~~~~u~f~~a~|Z~~~{<~~J~~`~|M~~h~r~c~|R~~i~`~~Xsrfj'zya~~q~~}U~~~a~N~gY~~~`~~~g~<~mb~h~~v~`G~I~}W~~V~~~w~ze~~~~}{%~ld~~~>~~{~~~x~M~~h~I0|~hzd~x~B~~jz~l~g~~~|e~[~~~~~t~u{|W~~e~H~~~~U~b|~]~\}YO~~f~~~1~~~~~F~~~oK~ch~~g~~~~{~~r [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2319/ccs/rev np:i:10 rq:f:0.998414
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAG [...]
+ +
+ O~VSb~~a~t~u}|~~~Q~x{~C_z&~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}y~~\b~~{G~~{~y{_~fxy~~e~W~hz~~o~|tg}~~~~U~}~~~~~~~~}g~~w~~~~a~z~W~c~~f~~w|~~~~c~~g~h~~~]~$~|MvR~={a~~fV~~V~~~{~wS~~~~}wb~uo~oc~~D~~~}g~}~g|S~~~d~\~q~u{J~~[~~>~~~~K~~~wE~~rc~~~xmx~~~{U~~T~~~K~~gh~~U~^~}~~|~~}W~~fw~~x~a~{{~t~}~~~~~{~|W~~S~~x~~h~j~~hwr~vS~{~uw~~~)q~~~~y~i~B~~~Z~{~~u~}Qe~~{B~S~^h~y~{t~|c~f~~G~~K~~~~~{x~~wy~~c~e~~RO~~g~~~o~b~g~t}O~~g~g~o~J~~~`~|~v~\vyc~G~~~~~}z~~d4~~fy/~~~sjh~}~U~~|sf~~w~xfR~T~~~,~~~~x~QT~~X~~}Ku}_~} [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2333/ccs/fwd np:i:5 rq:f:0.992602
+ AAGCAGTGGTATCAACGCAGAGTACGGGGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAAGAGCTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCCTGAGACTATATCATACAAAATT [...]
+ +
+ c~YLTIh?~krh]PxOZdYV[Xmsf4~wh6u?k~\ZrJ~RlYeWL~[~Fc;c9y~~qXUfqGkGsPTj+^ZakaZj)o`dXmgZI~~dPB~~mh_V^&J~M|eYYiYTmMZTZWK{EF~bVaXC9?WHsPlZkN[UYIefX/~p`pbDipkp[jCsWL|j7{u_H~ZE'ksn::ii at hE_g>IFTBAr`IPEdWVf)K'.@;no%W?E3Yf7~~~oZCoWm[FwUW0bGYlafY]krY[_YsI~BuwwQYlZk9~iP\XciNhj`~f]~WnG~g`lL~\Zm6~xfZ'tW]oYR~T|UrZkIhUcB;.2SNFX<ZM^LEdm4_]]I|~l^aX:sTSLYqgTG~nV]6~ZGXlQm1ycQmHE}~YnUVmXECdPqfZmb~G~Fs~lfY4t^SYh.dZsUj[7vfYSMMqaEjs=iVqgSzZI^N~e]erT~V~ZlP~\~ogQRXPDAMZsW<`pZ8+^Z5|DO\CDUE{~lZlX[b`G]FeNhVk6;_IZYe [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2333/ccs/rev np:i:6 rq:f:0.994191
+ AAGCAGTGGTATTCAACGCAGAGTACGGGGAATTTAGAGGCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATTGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCCTGAGACTATATCATACAAAATTG [...]
+ +
+ 4VXVOZR=KC<%RVBkPZ>c^M^XeV9vr^Iq)X_cJ`Ln-XcN?rChLU/[50?d\MENMNZAJZD\HLPSaXV>`Y_^?T`LwwkVDslLOLEVSRw[uVa`aGKdU>]RXMdcNiLTJRRHTL7T at DA-HE3UGQQ=K9`defWegaOd^P9V<VvkEww_?sa[<[RTcKthRiMY^V[_26:NF>b^:KIPFfkgXAH]WqYIDR*^WF6:R)\UVH)xaJbA]*=:DBLbMG4aYM>rEvo\SOYNC5acVf`UUUrXXvWIt^QOuSdd;r`D<BvuU`VtBakGbBfUe_PbP^jfVXvkV`fVk`f`LmV?sdV;u]KU83TlCJ@^fkeLwe`e=vud^O8dEoUEs_Svv_U`fk``EWSfV_?SV+X(_LLOJNvvk`kYv]XYvbEURFgVXviA]dMiW_)UtJPVGoUeVeJyXv]PWvNwd9RV`UJdV`f`5vvdVffUNhD`,YWkB~oRM;5bViaXJPT8<TUDivtNx` [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2334/ccs/fwd np:i:10 rq:f:0.999086
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGGAGAAGCAAATACTTGGATACCGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCC [...]
+ +
+ |~~S~~~W~zktb-~e~v~r~o|WvH~~~~h~~zV~~gb~~~|fi~i~i~~P~J]~P~~fn~o~c~W~if~d~~aX~2~~~~~{chk~j~~x~y~m~~~w7~~~~xN|i~~ax1~~~~io~dh~E~l~~{~{~uv~zpa~zN~`ov~~Rj~V~k|~zv~~~~~~~+~~~~~~~~swA~H~~m~|F~~~k~~~0~~~?1~~~~l~~~~~|~o~~j~~rq~wQ~~~p7~jW~A~o}I~~~~p|~~~rQ~}~ew~h~<w~~~s[i~~w\~J~u~y~{~~_~~gn~Rwm~el~}^~~SF~~~oO~p~~Vo`guZ~Pk~V~k~}~~~~~~~~hR~~~vwU~~~~H~~i~^|V~~~g|~i~n~|~E~~z~^a~N~~~~~_~o~eY~~9~~~|~L~~~Tcf~hn{W~V~?~~~|~;~~~~{}~~}y~~m~}~~gt~~g~hm~~~~J~ykUg~a~\iK~_~~~m~k~j~}bZvqj{{p~U~~~yj~~~~~~z~~~Y~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2334/ccs/rev np:i:11 rq:f:0.999183
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGGAGAAGCAAATACTTGGATACCGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCCC [...]
+ +
+ V~vn~biR~m`~~a~~~o~y~c~~~C~~~oO~~|_~hoJ~~~}~d~[~~x}m~~~~N~~|i~;~j~~~~M~|~~mT~I~~~yR|~~x~N~~{~~y~~x`~\~~~z~]w]~~U~^~~dypX~~_~k~~z~~yC~o~~~iX~~y~ky~z~~~|{~~mf~m~~yy~~|3~~~~~ykz~~~~m~~y~~V~~~R~uf5~~~~R~~h~_~~~i~~~L~~c~x~~d~X~~~y?~~f~w~skL~~|~a9~~~tj~yz~~xt~u~w~~~@D~y~U~L~~~~|oz~T~~~mygSu~~z~~d~yh_~~~~K~~{n_~~~~~~~|hl~~~p~|~nquk~~o~~~|~~p`tbd~~b~~s6~~X~F[j~M~~x~h~X~ao~9~~~c~i~h~~j~}W~~zXf~vbjn~~~~g`l~P~D~~~mg[~~~z~k~|~|~~f~t{~~m~~f~~a~~~~w~zo~(~lzlYS~q~{~z~^~yi~~}~}~~}~|>~~~~~~jo~|~~{yo^~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2359/ccs/fwd np:i:8 rq:f:0.995075
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGGTAGCATAGCAACTGTTCTGAATGTGATATTCGGGTCAGGCCACGTTGACACTTACCAAAGCAAAGACAGAAGGAAGTTGACGGGACAATAGGGAAGATTGGCAAAGGGGATTTAAACATAGTCCAGTTCGCGTGGTGAATGACAGATTGCTACTGTTACCATTGGCGATACTAACGTTGGCGACTTTACTTGCCTCGGTAGCGACAGAACAAGTGTCGTCTACGCAACGAACAACCAGCCGTGTTAGCTGCAATGTCCCCTGTAGAAGACCCTCTTCTTTCTCTTCTGAATGATGTAGCTGTGGATAGAGCGTCTCCCACGTTAGGGTCTAGCAACCCTCCGGTGGTGTGTGGTTTCGGTTCGCTTGGTTGGGTGCCCAATTTCCAGTACCGAAGAGGTAATTGCAACTTCAATTGCTTAGTTGACGTGACCTTTCGGGTGTCATGGACTACCGACGG [...]
+ +
+ s~fpVr|d~fEWN^~ZuYftQt}7nM~~xN2q~g_nMz~vlZ~\~t8~mhs2~bpRsi~ig~,1~~~r~b~I~sdT5~lflgmT{iYj4~~vq%~tugr}pE~M~C~qj~J6A;XmW\:~|g4p~i~\N^r9~Z@|~${~nzKwd:~Y*asvanL~}q6~SpnDHa~}X_~uZ~lxFaA~0TwQl}w(y~Rf:V~_~G]f~bUy'porn~a~``[qR~~Rg0htQ~~tg~z6rpavqNaY~\@wv~[{+gReiemIZI~q_1~Za{X~wt(`_~Kn~;IG'Ys]~x1b0~~~xHizIX~wvE~z[gD~K;wvffEQB\|]H~e_EO;V`op~db;~d~~ti_[w{:p0~~~rb_~jJ~~~u~ganG~O~qg[~Q~~*~~nOT{R{5~~nL~W~\xeU~>~J~C~~cRG~r=j:sR>~_qk|Z~s8~rmO~ySvGN8oO~tp~lE~j~JS>}Qr.~^yfcqb{_w.~^IU~~|K],R~Kxbp~R9~HP[b~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2359/ccs/rev np:i:7 rq:f:0.994717
+ AAGCAGTGGGTATCAACGCAGAGTACGGGGTGTAGCATAGCAACTGTTTCTGAATGTGATATTTCGGTCAGGCCACGTTGACACTTACCAAAGCAAGACAGAAGGAAGTTGACGGGACAATAGGGAAGATTGGCAAAGGGATTTAAACATAGTCCAGTTCGCGTGGTGAATGACAGATTGCTACTGTTACCATTGGCGATACTACGTTGGCGACTTTACTTGCCTCGGTAGCGACAGAACAAGTGTCGTCTACGCAACGAACAACCAGCGTGTTAGCTGCAATGTCCCCTGTAGAAGACCCTCTTCTTTCTCTTCTGAATGATGTAGCTGTGGATAGAGCGTCTCCCACGTTAGGGTCTAGCAACCCTCGGTGGTGTGTGGTTTCGGTTCGCTTGGTTGGGTTGCCCAATTTCCAGTACCGAAGAGGTAATTGCAACTTCAATTGCTTAGTTGACGTGACCTTTCGGGTGTCATGGACTACCGACGGTAT [...]
+ +
+ @~elwfF%~mp[VS?~jhlufpfIbQBt}roOCU`jojDclM~lrR,~phe,_~_eWMpsu,~7-Dk2RsA~Y~xjiQ~gog\j_vs2~6sf5QRm0PS[XMY?~V~^^e&YT*zr9O?t0X3~`R~QsBsK~lVr~?|x\*~?9{vNruua3Eon;^~UeUdHBx?Ea~Z9n=pPW:~_UrwkG_2~sY~VP~X~kRrGslKsfJ=~C~OIX;U~~s=M~K8cX<R~BAQlhulsc<oS\vc\clgdW`-qi:>d~kP8~;Q~\~whkQqg=~[dR-8ibzohjJ~~~re at SPN~6pR~~sk>~kM~~lskP~krT8SDfu[PpZ&f]fXQ~r.ofpglhsk\B~~tUe@~t>~~Xj\uhlf~4~<-$@pI+UJaT-1P~@~u[RsQ~SOTOxS~=fA~c,TRNz~b~=~v\~uRHqI~^6hUQGa\`~RxTTe~ma~Wd{:tdlP{oIJ~bXSfserZ~@~qU@~eZR0NQ`?iOb\oBx_sRBpO7+ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2409/ccs/fwd np:i:6 rq:f:0.996988
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTGTTCCG [...]
+ +
+ f~lOnVw[~yry^=|`VdihMmsXY$~~`A7Jh~zsrx~~~~{vvux~~~~~~~rl[vV6~yeyqeZs`Z[tNZ~;~`R}ynwLR^>kwVvPuRxdnrel[uf`~q\~rnb\YRx]rWxoUYmyewVwqP~~<~T~ikdu.~~_~\~ynU~oO_~m?~x{^Mal[dsja_P|ly`aP~xA~|~`]qbyL~^~WsKnHj7xqOwlyR~w5~~~cNqmx[xqnySzk]YwexXSW5~\-~~[P~~ec|[P~FzcnaBqxm@~~k9tunvU~i~rysiiKCbj'~bP~~<~kK~bG~N~x`nc~Vg~O~xlWaWuNe]ULT~`m&~v1/~_~ia~`x>~pae~S~yP|K~pR~Z6^K~r?~~dpryetbP~dsZS[Ab7~~ZDmoiUNjar[qMNjQCr~QF3~ctA~~lU};~[~vEk]{G~}^KSS5Yrb=~~bZ&www~MtkMVOg[IUcshU~qdHyKzxl+~~~c;tBA~ZQ~serlOwrl`gW~Nxh [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2409/ccs/rev np:i:6 rq:f:0.993475
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGGTGCCACAAGTTTTCTCTTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTGTT [...]
+ +
+ .IJ]VTZBr__onf~>al``a:=Wj%~~~~~~~{yz}~~|~~~xsty~~~~~~~dbYS^VoAgh[g_pVwernV~bt>e~YLCkep[Li]SKudYg`PS`^jh?~wQsnfg.`gi]b9oj_m=oh]`[wI~q=~W~ezkBH~~W~'k>LY[~_lh~b8~~kdch+tznsyhV]~ekkn7rCD~~~g;~k[Z~Q~7kRuT~=xDkhWf1{a6gy~wKqemq]vdZG~]\xrnpb:H-~~F~~t6xmk`~\0~7~leni~reN~~dX~qypG~MrxrwOuoylNR~U8~^M~cW{jBxc~nde`~xQ~g~X7tnerlOFsSQ~Ub4~~~KfA~a+~j[[zEjN~[~[Z~C~rOujS~G~~H~~[~uDhBg$ji[vMB[r4~qRL~~c_YyU~NqvbvbV~~nzZ{(~=~vcM{LsKyiYHP~O~q[lyb[s\dE~~gx+~~~~SLYpOuH~xm[mze?~znS~X~n8/y~~cW~d\~z\~rnqFgryVqeS~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2417/ccs/fwd np:i:6 rq:f:0.996579
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGGAGAAGCAAATACTTGGATACCGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGAGTCCAACAAGTTTGTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGATCC [...]
+ +
+ `{d\6biRqbYU\:|bVaDW\PmXTDty~hAgVb^~d;-fqhX`M~6u?elBQ7>d at ukYRWEsOqS_hEqGndCNj:r^\^Mf\XaXN~n%FENgJhTiAv~a<U\S at ssm_P~~qngKsKBlEhFQI^VG_S9r_HX>eJ?jJWRX_Pg_'~`UdkLAeLkUQK<ovss_CIegl9f@~jWmj+ly[M[jN-qspI>}cPYL~~ofq_lMvG_,coqfl&~uPGGup at ybYed4pt]_O[vepfO~keZdfXtMPbA)/cM~dZEx4]rlKfndU@~Q7ngdlE~o`~Z5|_QA~l[nQ~H\`Jt~eg8wcXk0~U~eoge-]dAV\RhWIdj-kdEd:~lU~iOG~~neoeHycW\aUVW5~dgpI~t at foR~P~d`~fR~teoZ\Ze[Z~JT^OmM~Cy6~~mcOU~~mPmV~bq_~pN{Pef]N~mO~Z?~RkgMmfmdR~[H^mItO~b)BgHwdS?LAOWnOaXc4|~i;BRP^yf]edES2~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2417/ccs/rev np:i:6 rq:f:0.996522
+ AAGCAGTGGTATCAACGCAGGAGTACGGGGTGGAGAAGCAAATACTTGGATACCGAATTTAGAGGCCATAGGTTATGGAAAAAGTCAGTGGATTAGATAGTAAAAGTCGAAATCTTTATATTCGGTTCGATGTACTACGTTATTCGCGACTGTTCTGTCATGATAGTTTTTTATATAGTCCTAATAAAAGGAGTTTTTAAAGTAAATGACATTTCAGTAGTAAAAGTTTAAGAGCTTTTTGTTCTGCCAGACGTTCTGATAGTTGAGGAAAACGTGTGGTCAGCTAATAACTTGTGGTATGGAGTAAACGAACATCCAACAGTATGTACAATCGTATGAGAAAGGACAAATCTGAAGACGATATTAGAGGGGAGTCCAACAAGTTTGTTGATGATTCACGTAAGGAAATCGAAATGTAAGATTATTCGTCAATGGAGGTATAAGACAACACACCAAGTAATTATACGCGACGAGTTTTCATGTTGACGAT [...]
+ +
+ @dLFIDMBcI.MBAx[ZFb*eVUfd\;~~oCDycZCcX[+xu9a[EzK}bPb@^EC|;t_KV]*SM~da\:zFx^K<t;z~~Y at d\bDMJzK6xb[a9afq;~~s_kfdE~~ZeO~~oqnN~bR~`~feol_lifqofOPzmO~eeePmfqe<~dVaiMl\eoqod6~scf{iSmegNDO~pI~i@~ulAvj_&ophpNq~YqT~~oOmfi&i~dnSqnepC~~~a2y[K~cobf'XnuaY.~cXcL~k9kfdUucCcnqpe?fMUSv0~~sed[`kNPqfoegqZo[^~g]rbnP~PnWHvQ]qE~~fd>udTRNy_~fmPnVXd[Vc9~XeepgKaoeQ~nA~VeR~~qbSIK~doe^RZlO~kfk%~~mn_eNtL~e_~N5|jP1^]O`ajV~Omfbk_~U~@~~qfdB~wYdZ]~OmV~o`~feqf_~SS~lRm[l[]~RQcN~eieiB~K~d^`~_~nXmfefeofend5~~~ekf_`~eofdnq [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2436/ccs/fwd np:i:7 rq:f:0.988106
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTCGCCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAACATGGCTTTGCACTCCAACTTTGCCTGAATCGTGGTCAGACTATAGCGGGACGTTCGACCATACTACTCCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTGGCTACACATATGCTGTTGGGAATGTTTTTTACACTTATTATG [...]
+ +
+ b~4Ykbg4[N.?ADSPiaKh^Qlo^$kURRUZZX]fi`XSQIHO]h_F9777:8=_iQOjMhGf,~KdYlT~\TQRS5p\KPCLXjbLo>SJQ[5.FGT:[BPLSAx^>DF at wkFeQIQmFM1RoX0tg_YZ_?i<B0R0$>(Hra0~q]Z^bjKqEd3KE[F>ICfPwfJRS%LPE\SXGeokWJD?AnkKJHeU]U)\NQm`ZY^\%QU5MUO,Nv]chQWO}b[Jw^bZL^jRSqSILDun at mNIgC~d?7FSnTVGcLM)SG~^X8MD}ABPU<@FEJJ~,6FMEAA+IP?WlIP>TjSDYYdStDD;^[W:CW_:<Uga5~K'JJMGefde5re7M%3JTHgbidekakC`XWRZIerT`sZMnQtUMK:Z9U1te^ZPeF:/`\a%(*cqL~~TwLWX^G|c\>bbRg7<UqFaO$t^K>K`QX:M;ROI'>7W[QNzK\gPz\~xljLoc`j^eufSs%wFFw&i'dxwxfVWRT?dZS{XaZ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2436/ccs/rev np:i:7 rq:f:0.985893
+ AAGCAAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGCCACGTCTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCTAAGACCATAGAATAGTCCTAAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCTCTGAATCGTGTCAGACGTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAATTGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCCGAGCACAACGCTTCTTGGGCTACACATATGCTGCTTGGGAATGTTTTT [...]
+ +
+ RX<.5 at B:6SVNDfZle^h].J_jlT%gUYZTWWVWZ`c[VSQRU\hrsrrrrqSPLU~UbRL'IS at +E=hQT-3C4RLIpR<7fFfFnaV_U~T~lhM_/>_C_6mH1i=?_GIWIH7M,BMHJ3~OF:Mv`D1-\FUO5L+H.a at 5H758fH/jiEQhesU~Gh]CgjFK35iMDqdb3A3^PiZ)D,AYUJO[AqD'`[Kpe_gLtV1LQ[\_WPULR\7 at 6G=T+WH)vL?KkMF]ZBcYHfRcKRsnLjeJo)`QQ[VoU^V]a;>Q?RJl_VBMU_IJ6UR[/E*6FLRYQNeP6~~_ULZ&[V5~I6RFEUO>cGq`6_EadV;YFA?dZ at ogKOdIL4FtSP`UNe[HRccH>K<Z7Y.\VKJ at Y`?TCDS8TR[-jQI;28nZAPjVMnW:2+JNb^7~lPaNrPNF|odfY_esl;aSFbc0nolIHVV\%&DOZfhQLocDcS_>=S'LEB9LNNN`/g?X^iW/;ABZR;[TY2YSF? [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2451/ccs/fwd np:i:8 rq:f:0.994616
+ AGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTAC [...]
+ +
+ AUkzWwO~`B]{o~dDb~ktlkxjFu~~i[~L~hD~KNKvegd{fujuRS~_~H~z7~~~~WK}z>}~Dj~Ub~3~=iTlemiPnP]~t?~iQR16kseVatXl3hbvY>NGVEQP~ii~Ts~`~koWwQ~Tp~lPfprnP~~qR~P~bt`=~~w~dZ}[U|s_~skdhXQuZiTUmb~]\|R~Zon:gXbk[]Z?|tr]~HyS+T_elMj^[^N8uaIZQingc%l`WqQi`fO|lZs?l@`]~PtSXYuCklR~seo~OmDC%rrVGmjP^\cnK~qCphep[J{eQz.b]bO~c[IgxR|HISCWZ]rS~mbDM}akxT~-gIVPy[^aVI~}I~kTk~n@~gTn\nTz]z^~[R~B~~yTb9Qr]~fbln^f5Yrl_`^~jO(~>S]k2P~]Z^E]?jKPSolS~sb[]t[dhA~VKArkq~_My~M~bV>~~dI~lp~WfPE~$~~~~r~dS<\LBaoYQpC~sqQpYbqediP~nT~n\hsp~\ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2451/ccs/rev np:i:9 rq:f:0.998753
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTACT [...]
+ +
+ Yrohtt[R~jesW_~WtEFiT_vmQ9~sYAZkJ|eF~tpV~pfac_~sreG~R|9ouIi~~pfIxuT~nfI~c8lGs\~fote[sxs\j~P~mFz\Ef|fH~v_Z3~~~ymlBiZe^~nKkM]zqQjGGVT~yiqf`~peW.p~mM~\~uij/~~~zp>vcNGe6YRZ__~^~^ofZ~]m]c~^{R~nR_XfRiv~?~~rU~B~Y=~eoRntcncttoa`~u~kwkrmI=Y[rpO~rf[b~^bB~_y^fBlRo~_~on~ra~~uL~~o`~\^~`~fQyoF~~gqvS~~G~__dpM~~tH~~^~I~g?oVdc;~dYa`~oxptqtrt~F~~rYeV~~J~hPV~tV~sX~t]rpT~\ur_~a~~qI~nPIV~q`hXdoHy~iiKS~~a`~qlq~rC~v~vqv6~~~~rcm~^miuf~]pK~nl=~~_~sD~~`ycp@~{cPj~emldoBz3wy}em]jnnqe_Ql`~skWY9e;@koswur~V~serg~qi~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2472/ccs/fwd np:i:5 rq:f:0.996916
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGCAATCTGGCAGATTAGATACAGCTATAGAGCGAATCACCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCCAGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTAAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTAGTCGCGAGCACAACGCTTCTTG [...]
+ +
+ ^~c[8ak+}OOP-2z[L]gcgcoc^%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~B@~]I~o_oP`1Mbga~gcgkRR^c^^2YK^R`_bF~nYNJjf\co^j.g^}8agoW~^oR~^>~~T]_~EKZ1x_~g]L\F~aP:gcTN]4~lQal8fkF~_]C}ZgV~~c>M3EenKVA=mKldo]QnR~^V~~a4%Km=~W~^3~pb=nna4~m\KkKm%e[acGlQneL[8~~f_bM~_a80kOkOLngY;ZQ`~_cga~g^_0^\~^gKchceH`Q`7~mgcP~g_~HT{N~obF~\Qng_ca~gbF~boeJK~S~`~B}`LXJb`U]mR^dE~~`;`j2[aG~bO~c[oaBn6i~IHbIkd^~IM=c9Jlgc]P]aIFpQFa]F~aQneHa_gcn&}nnaHl=~p=tRGSC\~:E~~aMZV~~cgia8~G1PV>\CjJqj:~V~ocO~oc_mKWfd&`Tbg^?~jV;ao\JF`Qb^g^In^aHXe2Z~S [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2472/ccs/rev np:i:6 rq:f:0.995796
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGCAATCTGGCAGATTAGATACAGCTATAGAGCGAATCACCACGTCTCCTTAGATAACTGGCAAATCTTCACAATTACGCAAGACCATAGAATAGTCCTAAGCAACATTTGCCGCATCGACCAAATCATGGCTTTGCACTCCAACTTTGCCTGAATCGTGTCAGGACTATAGCGGGACGTTCGACCATACTACTCATTCGATTACGCATTCACCTGACGAGAATAGCCATTCTTCCTGAACATACGTTAGAAGTAGTTGGTTAATGCTTGTCTACATTTGAGTGCGAAGCCACTAGGTTTGCACTGTTGACCACCAGCACGCAATCGCAAGATACGCAGTTAATGCTAAACCATACTTATTTGACTTTGATGTTCTATCACTGGGTTAATGCCTGCTGCTACCTGACTTTTTAGTCGCGAGCACAACGCTTCT [...]
+ +
+ ;i_bo^QNoeSN`4}Y\Km_n[Pob$~~~vaOFFSg|~~ujcadlw~~~~~~shdmD=~aL~fce?wKm_oX~mHmgoco_^`lNl_o^bJXqOJi+he]^QbbO~Tkj\Pd_~]KM~bA~jM_Qd^oca~X~ocMc]w1jS~ogd^^~hl_gS~gL~]`8~aoD~{^S~^cogc]UR~F~~PbnQI~cKz\UHmcgRl%~I?~~^S~U^N~Qc_g_cco(mmKeoeT[cE~~oc_F~b_oS~nQncgi]QboX~c_oOpgaHaoW~KmS~Q]oa at NZL~fX]S~oW~a4cR~Q\M~bl;k^HIno_VrGbcF'tLx5~^~QZ^4~[QaQnco5jh]o\7Da^_~HQ~ocgjMyB~_C^Tag^F~]mB~mS~o_coc_ca~gc_cS~_lgoc_cn_3na~g_bP3~~Q}=;>UJzoC~dFR`@~~^eQ]W~cgofKjKeC~kF~`~fHQ{Q]cg\4_KNi`^mI%kv~ji1Pb]L[j.Jmca~c_bE~JF [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2614/ccs/fwd np:i:6 rq:f:0.993983
+ AAGCAGTGGTATCCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATTCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGAG [...]
+ +
+ byWQRQMHwNRb+^T_=DOjWhV4BM$gkf]YalrssssssssssssssssssssON5iLUNN_`QW at oT4^=_[dQR`S\X`Wc=vcQVtYvcV?uoQ;Rc>QWuYvZP/rwOBgTviWwiEb`BwcP5mP=KpuQbSJ__ at OS`QJvvWcBgJJM_JSPc8a2uQ%V_QBlPQK6DGciQWMLSuRSBhJN3qpbSCrVi%?N]K'qrbhbOMVcWa3]cVTMvgItvQHv?bQWcVxb>dWOMNLgRCvvtVFpiTvCQJrQVsW5rOFsOBRPcLvpSVtMFXhPc?IOS\T7ObUvN1bcUv^4mOAPb8sWRXQfLRN*sqOIOF\A^OOfDtD\AFB9YP=vwt]RbB;q`.lqiV%e\Yjjj]iQf2sVi at xdG]L`RiP_ZPdiQW5uQqE`2qe1r>ndCGs>^ItsOVTvWcQCupDSuQWdiQVTMHxeYvXcVQKvrQ_\>bEzciEyUPNf0sX+73pVRU9j at _dVCt5^ZLURV [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2614/ccs/rev np:i:6 rq:f:0.993526
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAACGCAAATGCCACCAATACATATGTGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTATTTCCTCTTTCTTTCTATTACTAACTTTGTAACTCTCGCTAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGGATCGTAATCTGCTCTACTTTTGTTATTACAACAAGAACTTCGACTAAAGAACGGACTATCTTGTCTAATAATAATGGCACTAAGTGCATACTTTCTCGACTACATTGACGACTCAAAATAAGAAAGGGAGTTTTTATACATTGACCTAACTCACTACTACGCCTTGGTTACCTTTGAACCTTTCGTTGTCAAAGTTCGTACGATGGTAAGTGCTTTCTACTCCTACCGCTATTTGGTTGAGAACCTGTTAAATGA [...]
+ +
+ NLSWbQUDx\XhXMwXQW;9SO[IC%mssssssmc\]bjqssssssrjb^_^\^fd\ZZXStQP49=kJ2DI7GsOa`dXaU_XQTPhFvOCUsKyhP:RR(PTKIBTq?oST6gRbMJWsc.PLHPp=bPP2`oU0[TQYb0kFP7NoWLt^<_TaTRBfVQV>PpH^O?dNUWvTYTB_oZcWRiXTvXPGf`C<spYNTpQcTUjT4r8*beWe>QPhIyb=;Ip]NvjD5e_<@OiEvfXeLAhSYMW<vwhQYvcXvNVUeVTtPRuU6]GNcXiLwtQTuX?[%UidhXDkNPBL:aeMYh at qL?`WdVTRW;P:T`=K@@brVfXO`S<cVKFN?bWQeWiV-uuufEo=2^I:yqL<;m^STbRbWbHP=6)D=BsViU9VUcV>aUPDuET4`EKdEvM]qQVh:]@trVQYvO]CG`QM3CU=hcV?be2GgKmNOQV-pWRhcWiCaT_EqBQgMLpZ/X'51aOA`8ehLBqIvtTP[ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2616/ccs/fwd np:i:6 rq:f:0.994841
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACG [...]
+ +
+ f~Zer_rN~rnhIGJH^dq]E^r\d%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ldrrr^dbPO^rM~ZN^n6YR~YJj\rP~[drU~_kIDpP~l^mR~Y^YdD~r?xmdl^NGNCOxPiTmOpL~^R~?~~Izdq_pInIQ~cH~~b?~q_q\\r_7~~~~yd^OsP~qQ`}4~g8~rerYcoZpSkrrf^^fd\X[Ta<8g[B~~~nMN~^O~hQtb~e'edQ~O~~~kN6~{ZMBxr_ea~IpF~~frrF~~OpM~K_O*~~f_*f`rT~~lq`oT[hRmU~p]7kZ7p~nYU~~fs^OjYkGVDZ}Rg}YnZb~_]nb^`d^F|Sue:~~~~`a\ROc^pLnJVaSgfLc]cLbHxRVc.YUEvN7V-_[UeOXNeeff[fT^Hlw[gYOd_Ue`H:iUQ=vd7wILEX[fV[TsXWLAdZfZKpUOcV[UN4sUYNZHyiEeVd:Hl:V->O?saOAB[e6x[4s2xj[UA6WOYUvJUI_A? [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2616/ccs/rev np:i:6 rq:f:0.993526
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAATGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCA [...]
+ +
+ e~P^qNZQ~XpnH:~Z__n`l_Ul`%~~}rsw|~~~zupf_^gw~~~~|vmbagq~~`^pqZo^pkGJmTwYHcr`o-~Q[rerR~];\ExepHWoU~mZYLnNYaYFwv%}pr_r^YN~eb~:fWX[h<~`]~:~x_~HVKYaY<?q]=vg]:pN[\oNZ9;{~~no^aFeJlNC-d7X\QxJZDh_rrq<~qr`eO~^aIQRs_U~_>p]pr_L~e>~rN~a~^A}]Q~*~~~^WHO|~f_L~rf_P~_hI~~^\k:mlTXM~e_d4yesL)~bqR~~rs`Uperb~N~\qN~YG~~nr<~='`\p^pO~^a~HkkL~dO~^er_fr\fP~K~^5|~~plfl^t^qN~^T_bgrN~\qP{=~pbgb]b<dkL~W~~blp`qpXYp_rer<~w`n_a~W]Wa9~xerN~rS~_PTPUa.L9]9GG:A at MMQ[0UNYUYLCs,?@S7q:'C?I^:oNR)+Z(_cLTLS%JlfYx2_UT[WeW`REtU[UO [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2628/ccs/fwd np:i:12 rq:f:0.995752
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTACAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTAACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTGTT [...]
+ +
+ ~~~=|~~n~~v~XV~^~]t~q~~vY'~~~~~~~zstz~~~~~~~~~~~~~~~keIQ~~k~~jI~~Ic\N~k&~~~bj~\~^D~~~~N~~`~~~~f~b~Z~~_~v~_p`z~~~~XhEHl[w^j_~>|~:~Wx_Z~~_~D~qda~J~~g~uuyyG~fM_~~4~d[LlR~g[~AnZt.Hhl:W=~bH~~gQV_K~?}p~~~j~Yau~qP~Ys]~~2y~~l]]|{X~h~p<|i~xxMw`~f*~`:5~~c[PO~yL:PKvO~CZw~aY~~nU~_^0.VliDu&~Q)l8wQgXJ~},~i`~ab~Zm]4vc~dd~2|]qgT{W=YaaRZcG~D~~n'~As~Y~2c4~~>g~G~~A~hommy4b~\}}Ce^Va{t^~\\~^~XmaHlIt~NG~~msSnl~U~b~f~I~~N\Bah~0p`|`~RLK~o`~L~(}~~Kv~_c~~i~|5]'x~~E~~~qN~~H~\iMId_Ph|f~~Y>~~~lZl~J|}?ybWZ~^yrz{~v~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2628/ccs/rev np:i:14 rq:f:0.996595
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGGAATGTTTTTAAGCCACCTCAGCTAGT [...]
+ +
+ =k`~|]f7sb~^ic~~c~~a~f~~~%~~~~~xfkx~~~~~~~~~~~~wkjs~rns:nbO]u^;`|\s]~~aS~~^aq7~T~~~~z`y~aw~Ak3s~~~~~c~~]~~~H~~H~~N|Z~~~{TKSfa~a~~q`ty?~~U~4~I{~g2~~yZLtR^~~~p~~b'~~~f~~}~~f~zU]m4v~^n~~?~~~lp~f^s~~~X[=~b~3oYj=Cb5hM.ZgxjG~)9y3Y>wp~Ma{t~`}9}d~~Mz~S&oYFHBx~V~X~~Y|v~^VGzqUw~Z~~z~i~~r{N~lu~^otd5~|0[Ec~uA~w~XsVBmdd~s[s;~eE.vuFs~~v~~K?}~~[~WwKM~uWPr at nQokoxl~F~~:~}.PF~h+xCv\NdZbHQ`t~e~m}Ia~~`}|ZzY~L~G~~Hk_R~~~~~~`~`~wRO~]c4}hbbXpaVeMr~9~~lPFy~~~X~~~d*HYId?~f~E~~_r~~~'~~~~uT)~~~~g~^s~~~~~~~U~v~Eb [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2648/ccs/fwd np:i:9 rq:f:0.998685
+ AAGCAGTGGTATCAACGCAGAGTACGGGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGGTCTTCTAGCGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCT [...]
+ +
+ ~~x{utnb~~t~ue~snr~w~[UqyF~~zvv~w~cw$~~~~~~~~~~~yx~~~~~~~~~~~~~~~~~~~~{{a~~dm~x~tufv~N~N~~|tm~:~~~~gr~xZF~~LiLw~u`j~qv~~]~bp~~S~~y`~|~X~~l@~n~K~7~~~~_t]GH~Y~~uo^E~~bn~u[~st~J~~~stbvE~~^b~v~P~wwu{YL~w9~~@~~~tK~~~ngtl}E~ivV~~`~S~~P~XsK~P~mZjispluugQ~v~dlwo~}^~~P~x__~b~t3~~~~O~~G~uj2~|w{Y~~dg~eKq~~~a~:~~w`~T~qP~~[x~/~~~dO~o`~~vc^m_~~u~|`~~f~E~~sI~t{pxq~rU~~[`sQ~zs~whf9{vIs~Jg%~;B9db~{a~~u]^jwe~t]~T~~~O~Op^~W~~C~~zoc~c~O~_~~KO~oRoE~~O~xuu_~uIUD,m~~KA~~|~n~r<gsW~CkqX;~~xe`S~~~I~q|u|c~~fp~w_ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2648/ccs/rev np:i:9 rq:f:0.998161
+ AAGCAGTGGTATCAACGCAGAGTACGGGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGGTCTTCTAGCGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGT [...]
+ +
+ J~}unyoN~~~Luh~w|xsb~ysmrH~_<}a~tW{s%~~~~wx~~~~zd[at~~~~~~~~~~~~~~~~{tW~~uT~u~~ys|~p~J~~Iho~1~~~~xu~w~X~~u^zrovas~qz`~P~mG~uZ~{pb~`~c~~~c~~op~@~~~~yekw_~F~~cxuU~~g0~`Q~{h~C~}kzH~r,mU3_~{~`~xIgElX~wc~~H~~~~X~~~~y}m})~fn'~~J~F~~P~k\\~c~Oc~r^HgH`tK~q-h_nt5~mN~~ds]`j~]~bO~~~~G~~c~v~Npw{`@~~wo~v@~~~sZn.~~~uuC~~N~~~rtD~~~b~~d~~w|x~^~op~uY~~w~X~~u_~xJ~v_~zJ~~~euU~uY~qlL8~~tepu~S~zue^~vb~~|~w|v`~slzV~~~^~}Z8~c~~W~~utR~d~S~a~laB~cq~Y~~`~u~rd~w~~{?~~~hB~oosqveN~l-~uu`\-~vqr{c~u~Y~~`pH^~~rZ~tL~bc [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2673/ccs/fwd np:i:6 rq:f:0.996071
+ AAGCAGTGGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCA [...]
+ +
+ \~lhtkm(~_^\jR3rOSNNXc]ZEfH~~o;c~6~~vkxb>~~Gy~S~J~]7}b.]RMjb&aTR~L%5S~~htkhktw8~~~~hiEf`~S~hZ4~hQxir1qH~^Rs2~Ua~WkR<sN~~pOQ:{o:GxkKZP~OmUbuQuJ~~khkO~ka~jT~N|ZVL~zRrjT~swR*hvO~Qrkv?~Z=PWhAjZd?~oCtsgKojfRvj]jfQEJfguRi5w~AwXi9~~~9^xkS~h%uijVafI~ZHzSa'uqpVkpOn[u^ScHYFU[~xiT~uh,bkgJzUzodn?s0cZwkcE_rf\s`vtjTxw^K~f~^hjQ~i9~~uLB7/1DPWlO0rfOQ%~~FEJH at U`Jm>H[XH[ZD;n=&~\KuASC|zM`ZSCR~fltgaXQ~m`]djWfrtjAyZRg\xai5dp':~~]rskK~~BHaN]qf80~a~wiuTq]mcStTT~gdO~H~vtxY~Z[Z\ni^hY~G~wY~WkUhU~g~kvSQucfW~\K~~e> [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2673/ccs/rev np:i:6 rq:f:0.997742
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTAAATGTCGGGAAATTGGGTTTGCGCCGCCTTCAGGGGCAGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTA [...]
+ +
+ Cr6ipPKD}ZQfeQ~jQXYQoKEukF~~~kU~Q~~]U]j<~~?~~RwI~nH~~fTfE|eX~b~kxD~y~kwQSgxt=~}}~khvSR~Jl\kB~vZ~htw_Orue<@~rZyo]glsIr~xltY~mj+yn-f;oW~ONhRX[~~hhQd~R^~iN~ArYR5~~irca~t/Jfg^g~j]eGR~~hkh~J~qSP~~\~~e/p8sltT\gjRvlygZjiM~~Y~xhI~~~g~ahg~kR~QvgbY~\<~PS:~~~jgGibvLtTdh[qjE~^i<~~gvSOiP~X~^h^W~\Rt[fltkskdsf1shUw]vZ~b~xlhf~Q?~~WehkvTc~eL]Qqqjf:uutcM:m_T~Rs^q\g]jV~eG~[;~if'tuisxg_[~g`qlt;W~sjxkbVhtwRY~tikO~eES~^dG~~]qxh=~~wlik]tR]G~U~jc]f]u[SdYPX~Oib~X~GsGT~j]uP~drSC~Y~sF~]qikf~>~dHbjYReF~uJ~~i@~i]w [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2729/ccs/fwd np:i:5 rq:f:0.993119
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACCTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTGGTAGAGGTCGTTTCTTTTGTAGAAACAATCTAACATAACTATGACAC [...]
+ +
+ PsRRC@[&j]\\N,oSUP\YZB\.J*<fC3WFZTaZTOuZZ?MSW\UHp<vqSXWCRSo\?wtYTUu[Ko>LpD2qm_\XFEp=sZ at iNnYFpUN><4-=TR;h\CZYFr\]USRaY9ts[D=A8kW[TLuaTLrRBZGvHQ0W^7 at S[UJ/RW1Bq?mT?uvQ0l at EqTGusLm1t?/[EKp=9os`8e[\Q/E:.M?7>DDZWVHmFw\^;*lXaZTtEGRZ<5;nF/etfXPUT at hQFPLn\T\SW<O4TX+H7Cq\ZaTKq=TPY_BSYTBssZ4M=E8lX[XP?8mJqGSYGtTR_SW,qqV)sjXa8vviTaNnNULuT at kXkX6r_OuVAU>_ZLttS6rr_YT at uaLsNIN;EKMo4ts[T\LttZADXXMrFZXOB0k7WT\ZTTPr\PsU+oTLuLqEa=rW<SP_6rpSX=>W`QFR=WFR=pTtGtY<)h29UXSAHkD<X*sYS6Xi_RY\X(eM9JbD<^OuNSFMmT^DYXFSY= [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2729/ccs/rev np:i:5 rq:f:0.994779
+ AAGCAGTGGTATCAACGCAGAGTTACGGGGCATACTGCAAGACTTGTAGGCCATGAATTACCCGCTTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACCAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGAC [...]
+ +
+ Hp:AU:*Bp\`FBMtW;RG'IB,[aY1uuqR[RaYASZMa>_ZPvU]aFJ'l]FR.p>aZ0W_UZ+sa\DfMLGG;fG/CLaGkHvsMuMXS:WRTJV4`Uu/<1sl1C78oEZQYTFS8rgX\UL/pe3@%l>SCqZU_;jFvaU]ZaXGRZUX<EGsTtB9lZfMuaFdCLtrHvBs`QVaFsT4jteHM.VS0lRaZUZUaMuUUB,2ka]ZOQ:A=KmGErGPZTtE5stt]MnD2lTGXGtGXaYSOLH0FKZT>t`U]XBNSI*MWLF(H-YPIX]\<t^GRZUUu2f]ZUIrMGFSM6kVTEuuQ*%TokOGC\XE5rX-ssZPJs[AoOQUZWM*ppT9nY.QY<n=5c@^YA^V6J4DW^Y_6Yn[@CU;/oZaUZUDZQsC[>XUB[`C[`EnQ+eSsLs at q=X\JO=YoZU`FRFYaUX<C at Ss>rKpER:rXBoC_QY:uSB4'[Z9vvbN]`<)]V^ZSrGSSSqB]]Pp=Z`MWkL [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2771/ccs/fwd np:i:6 rq:f:0.990652
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGTGTTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAAACAGCCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCCAGGTACAGCTGATGTGATCCT [...]
+ +
+ Gu6,Lag@~b?2R6eV_ZRcgdnJR*`_rYQ&x^S0QX at 6[7iFDILmEv6a2'MgJ1VBsgOY:KBMX6~?qW~WYFY;al\L5N8Z_cdZ5dRA*LbZb)lrigVHJWQSNbXRG1*WVb^U`TS~o^g]bmN\eC~qXKSSdLeo:~scjcJw]LY45h]gdUlM]AF9__=~]]ZX~Q~cP[JZ`?:Q*[Y+ZU`^A_Z^FRKAOXHVP%we',N0<J0C^Xc1QEd_QL|8~\J~dBg_amFa?~VYJ*M~/~yod[QcmL$h`RaMikaj`M.R~gL~~]][?khGY;K5J/rnLJkkS|D~cGJOnW1fWIY0qgnd\F[hEZ<lfboW;g],qaN~~oN~oT}]gdgL~OjeSvF~iJ:ld[T9cFV at LED1ddM>MP'XROM9f5L6P7;TAQ1R3..-]@0HK]WYejZodnB~~nR~gPgJ%csVfUgBuyjLie]ejTc6y/jLL_\^^bEg?-9(LHEhi:.E76PV\MKeIOl3kB [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2771/ccs/rev np:i:5 rq:f:0.993412
+ AAGCAGTGGTATCAACGCAGGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCCACTTCGATCTGTAAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCT [...]
+ +
+ KZA<P=@CqUIXXKtXSYV0WE?B/3$?XqKIX4H:kOV9H?cV^kR~Gy?~~<\~~yWN~vT~zPMsS*kJ~M~o|smads^]xlH~~s at b5~yj<~qh[D~~~~abHbzjJ`lOrmV~VYOCVC:SV[p_N\fGd5~yzU~PbKgm2~~~j]g~nUsnl~o|fV~D~XKYc{B~lbk?j:`C(9sGa*mnP~z=~}qyX^V^Zx_Szoblv1{ccN_LuschfG%ngazM{[~Aw:Jnb1ttOZ[PV|RWk^J~D~rm`QqbZ`2vzxEeCSL=ZYU~o3~zladL~uZzj~XdNuue7nfS~0ne[M^YUOtns)Kp\SmZugk^r]~pLm`?~~E~~N~~s\~Zf~gyQz]~b~|V~D~|yI~zox@~yblxn\P~~nzPIzmh^~di|sxW~`[`vc$s~~qkq?EI)LzrYrfo%v^0<;~Ve~qC~sLkdX9~tnZ~VTU_UQ0~9~~~~n|gpZT`ngotO~r{ozQl\f|sfqd3p]~mi\ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2772/ccs/fwd np:i:6 rq:f:0.993765
+ AGCAGTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCCTGGATGCAATTGTGCTCGCCATTTCAACTTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAAGC [...]
+ +
+ .JYcL?>gfedL0rW_S2C_]d7K4||yX]Mf4r]_Q@]aUSdEz?69p83\ELcf at e:TJ7yaFadeHR\Cw}OX`5rbS+aVRXN^6YHViXPL~|\YI?[C.DID8<N^V2^aZS\F{Ph^C_i>kWQ[`-ixj`ZG~S~j`0~KA|~aib\cXi_;_[ah[hafE`F~O,WJZ;nra>bb].]YXy[MVaK~gZ~JX+s`rBEZXfQhgZaVIB;R~f2@`z_QW\XWxB_<JN<\'89Q]BcBeTEd1M[0LnhN>jX|cVJ?SH0x|fC^R8,AfGdQ)^=BQ+Z_BHCQNnY7jU`f9N_i[BxaK~aS_UI0|}YhIDQ<HYIhYQ`J~QV4OEd`jh`:~ha[Y~ajR~j`@~s]NVUIrtM,GYhQ`eF_.o7YhahQeX^KK&WES<nOdjhjR~[ifE~`gEP|2gsiR~b_]WVfY|Jh_5`E\E^JGdXOG}Y-ea[f5V9OU~`TLHInJh_HfF}Zf5zQ~Z~E^NZXy83aWY [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2772/ccs/rev np:i:5 rq:f:0.992486
+ AAGCAGTTGGTATCAACGCAGAGTACGGGGCGATGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGCTCGCCACAGCGGTGGCATATGTCCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGTGTGTTATAGTTTACGCTAGTCCAATCTGTATCGTGGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAATTGTGCTCGCCATTTCAACTAGTGCAGTTGCTAAAGTGCCAACTAAGGTTCGTCTTGAA [...]
+ +
+ @^T2:U8L6X+XXcRyeZd[WEKZZe._<ChZcR*L0;fdIRD;VCcDS-wj8L[ANZLH]glUb_0oef`eD+vyhPeEsWg5}qnUIhUj]f[gZ/vQI8J`zbO~`M~PyBQEm`KJ[ThlWUM[l_tTm^h7~}\=`~KuPVG~~>~u]T`HJKi^WM>*[GR.<b[Cm`U~S_2~yoJXT[5H<A[,[bZKKfN\9e+xtjP4BKETBV_\]7I]MtdNEm}]YUZfJpB~jfnW{pNXjMgphZgcZOY``Y~VnYzM~ribQtL9v^LgS`lHPy]Zb0[&EXNNt:I=FR8]YKmQilgpQl'BEh]K~jNvUI:zdQO^MG6nbsqj``3yjMYgLk^krLUsI`iIcJO8BI@,'DeXnQ?wrfO+UQND]IvQ~XeZ[TYndWT6cPmKZ$?>oGET at XM`PNr]bQM~Ft_K^]eS<MR>mBeUZ2MOUnT%LaXH~^BQXMY=bUPlQZi at sRNcIB~THZRLsKlClTaoW:~[:~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2774/ccs/fwd np:i:11 rq:f:0.998209
+ AAGCAGTGGTATCAACGCAGAGTACGGGAGGAAGGTCACGAAGCGGCTGGAGTGATGGCTAGTCTCAGCCACTGTCAACGGGAAGCGCGACGTTTATGGTCAATATAAACTAGCAGTTTAATCCGTATGGCGATCTTAGCGGATGTTACAGGATGGAGAAGATGACAAAGTAGAAGCTAGACAACTATATCAAATCGTTGTGTGGTCTTAAACCGACACAGTAGCATTCATCGTTGGATGTGGAAGGTCACAGCCTCGTTGGAGGAGATACTACGGTCCCGCTTTTCGTGGGTGACAAAGGTCGCAAAGGTTTCCTTAGGGAGGTCGTTTCCCGGATCTTTATCTACATCTCCTGGGTGAAGGGGATGATCTTTCTCTACATGTCCTGGGTGGAGGGGAGTTTCCTTGTATGGGTGGAACCCAACCCGCCGGTGAGGGTGAGTTACGGTCGGCGGTCATATGTGGGTATGACGGGTATGACGTCATAAAT [...]
+ +
+ ~~~~~~~i~~~~~g~_Zi~~~~~z~q~~~~~t~n~~}~~~d~~~l~~~~~|~~~~~r~~~~~~X~m{~a~~~~~~~m~~b~~f~~~~~~S|~R~~~~m~~yh~~~~^~~~~x~~~~b~~Y~~V~~{~~N~~~~~jz~~~~^~~~~x~~~WO~m~p~u~_~_x|ss~e~~~~r~X~~~~~~~t|~~~j~~~~c~~~o~v~i~i~W~~Fl~C~jJ~~~\~~~~~4~~~~~t~~~|r~i~~~~~w~r~f~~~~_~~\~~v~~~y~~&~~~o~~{~~~t~~Q~~~qT~~~v|~j~~~~msc~~e~~_~tQ~~x~Z~~o~c~~S~~~b~}t~X~~4~~%~~~~d~~~~s~~s~~~~^~~^~~~~m~]~~~~~~q~~f~~~~X~~[~~}~Q~~f~~~w~m>~~~~~Q~a-~~~~~~~S~~~c~o~\~~j~<~~~^~h~~~~f~~~~\~~~~ss~~~g~~k~~_~~~~~~]~~b~~~~~K~~~~~|m~~~q[~V~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2774/ccs/rev np:i:11 rq:f:0.998888
+ AAGCAGTGGTATCAACGCAGAGTACGGGAGGAAGGTCACGAAGCGGCTGGAGTGATGGCTAGTCTCAGCCACTGTCAACGGGAAGCGCGACGTTTATGGTCAATATAAACTAGCAGTTTAATCCGTATGGCGATCTTAGCGGATGTTACAGGATGGAGAAGATGACAAAGTAGAAGCTAGACAACTATATCAAATCGTTGTGTGGTCTTAAACCGACACAGTAGCATTCATCGTTGGATGTGGAAGGTCACAGCCTCGTTGGAGGAGATACTACGGTCCCGCTTTTCGTGGGTGACAAAGGTCGCAAAGGTTTCCTTAGGGAGGTCGTTTCCCGGATCTTTATCTACATCTCCTGGGTGAAGGGGATGATCTTTCTCTACATGTCCTGGGTGGAGGGGAGTTTCCTTGTATGGGTGGAACCCAACCCGCCGGTGAGGGTGAGTTACGGTCGGCGGTCATATGTGGGTATGACGGGTATGACGTCATAAAT [...]
+ +
+ j~~~~~|s~~~~~B~~~o~g}~~~~P~~~z~g~o~~~~qdV~~~A~~u_~~~~f~~[~{~~zf~y~~~Y~~~~|}~x~~X~~T~~~h~i~~yS~~s~u~u~x~~~~]~~~~~~~~~]~~~~~~~w]~|g~~y~~~G~uw~R~~P~@~~~~4~~jc~~~\~~~y~~~?~~w~~~w~~~y~~~~E~~~~~~~ki~~~~}x~~Ot>f~~~y~?~~s~~~p~~~~~~~~~E~~~~~~E~C~~~~~h~i~r~~~~~~c}~~~~}~c~~d~~;|g~~~~rv~}[~~~{R~~~~~~H~~~~~~W~~a~~}v~p~~g~o~~o~|~~U~~~`~~~}X~~b~~t~~~~H~~~R~~~~~~~w~~~P~~~~~~H~~~~~~~~~u~~~~~~~~~~~~~~~Y~~~s~~G~~~t~R~~n~c~~~~~`~~~T~w~V~~~~8~~w_~p~}~~,~~~~~~s~~~y~k~s~~s~~~~~~|~~X~~h~|}~~A~~&~~~~~~~~~~n~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2786/ccs/fwd np:i:6 rq:f:0.990738
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACCACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGAATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCA [...]
+ +
+ VvSPn]aL~pnnQJ\+b>iOkgmk>$pwxxxxxxxxxxxxxxxxxvrntwvnkd'ljrxxxxxxvS=lknMJleALKE`[QeoRj.LDPqecVfnQkCxNaBhkRo_Ob>qTVep:~nTjdDTKf>feAb<lmR,n_?nc_v1~eYS<BdpfpeOvL;mkP0dicqn`oP*jXRUF>e^zV|R?NY/uwSxmReTMnkY1e;QNd;vQlfS^xNEsPKqxmXQZof4wmE~^tQC[=E_;vy[DNNrrLOJwWdQSyelHtt?nXKys=RB~dO]7rpxdKwajMxl[fd,XTflIm6~om>oZ)vhHNMPb>ofSqQn7rOLoUxxJwO^qMbm?dm>d?~ZqR5unxhVYPJC\CkGr=dpepmD{lS&XiofnfReMwU2s at mmb[ZQlomphOhbmOyrQPN.rmMVj7wwOlE~i=TC\DNE[cLIE[QkNYPoQUrJjlPOO_D{dQhO?qmQnfpi2iQNdX`AhsXJ+RTAvm8t4ePQfPe [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2786/ccs/rev np:i:6 rq:f:0.984912
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTCTTACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTAAGTTCGTCGTCGCCTTCTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGGACATATACAGATTTCTCAATGGTATTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTC [...]
+ +
+ \mL[aJJ5NHAN2.[ZK\cJ^KbdK(b[UOUVQNNS_edaWMHIR]_^ZE;<$7DHIR[[VVRNM*)4J][WGP=x^[H=CVAV`RZJ_>PM[^NiLSZW4$Na\^Jf>K@],d80paZ[?]MWITkOp[PZKLiKJi>jiLeDIA>E at 8D_PFmm[3ydIDEEHG)[NT^QX<FV4ZUUDU=[F,TIP`WPLa88KaIXFCb\]0=+8C%[UZ7GKXUGCfICa\JaA\V'SS9V1SLYYD&WBDR,DJ\L]F]3dcT;S.PSJdIQKE8'L4'&A^CHJ]_N`HaH5?AQ<V0JN[TDX\]B0TQHF1N)4GE=.@=-66N>%PR7KJ*LSG at Q.)7.3Ob[LDC>ECZ:[H5^98E.cZG/J1ED/B*42:IM&F?F;$594BG<VZ7VIV3g^L]KF]@$IKO,W9K:]Y0VCLQ\LBIOV`WTVSGJHM//DPBCDAY;`>WLSC?C%C.93-]MP:)=6'LI37G8,BF4\7GE=55F0FD.R2 [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2802/ccs/fwd np:i:14 rq:f:0.998759
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTAC [...]
+ +
+ ~~~~~~~~~~l~~~~~n~~~~~~k~K~~~r~~~~]~~r~~~~~~t~~b~8~{_~~~m,n~~~~~~o~v~~C~z~v~~o~~~~~~~{~~~~~~~~~_~~~~7~~~~~~~~~s~~~~~~~~~~~~~~{~~r~~~~~p~~~~~~~~~~~~;~~~~~q~~r~~|~~~~{~~~~~~~~s~r~a~~y~~y~g~~u~~~~~B~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~}?~e~`~~~Z~~~~u~n~~v~~j~a~~~~~~~~~l~~~~~~~~~~b~~~V~~~~~{~~;~~~v~Q~~~Z~~~~k~~r~~~~i~~~~~~~~~~~~~~~+~~~~r~~~O~~m~~~L~~~~m~~~X~~~~~~Q~~~j~l~~~~~~~~y~c~~a~~W~~~~~~~~~~X~~~~~~>~~~~~m~~~~~~y~~~\~~~~~~~~~<~~~~~~V~~~a~~_}~~~P~%|~~ac~~~g~s?hqn~~~ys~~~~~j~~~~}~X~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2802/ccs/rev np:i:13 rq:f:0.999331
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTGTGAGGCGCAAGGTACATGCTCTTACCCCACTCTCAGCACGTAGGGAGCGGAGTGTGGAAGACCAACAAGCCCGTCGCCTCTACCAAATACAGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTAC [...]
+ +
+ ~~~~~|~Y~~~~~~~~s~~~~~~~|7~~~~x~Y~|~~~q~ub]~~~~~~J~~h~~~~~~~~\~~y~~~~~~~~~~~~~~z~P~~~P~~~~~p~~~]~~~~?~~~~~~~~~~a~~|~~~~~~~~}~t~~~~~~~~~~d~~~r~~~l~~g~~~~~~~~~~~~~~~~~~^~~~~~~Q~~~~~~_~~~~~~~~~~~~~v~~~~~~~~~~j~~~z~~(~~~e~5~~t~~~c~~~g~~~~~~~~k~~~{o~}~~~~~~~~~~~~~~~~~~s~~~T~~Gpq~~Z~~W~~~~~~~~~~~~~~~~~~~~~Y~s~~~~~~~~~~~~~~~~~~~Q~d~~~~~~~L~~p~~~~~~~~~~~~~~~~~o~~V~w~~~~~~~~l~~~~~~~~~~~~x~~~~~~wS~h~~~~~~~mR~~~~~~~~~~~~~~~~~~~Lm~~~~~K~~~~p~t~~~~v~~~~~~~~[~~~~~~~}~~~~~~~o~u~~~x~~~~~~~~~~~~~~~~~~~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2877/ccs/fwd np:i:11 rq:f:0.998386
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTGCGTAACTATCTTAAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGTTCCATGCGAATGTAAACGATTAGGCGC [...]
+ +
+ ~~x~~~~U~~m~s_~~~p~~~k~~`%~~~~~~~~~~~~~~~~~~~~~~~~~k_qr~q~q~s~~;r%~~~~blf~~yG~uAXK~j~~~~~~~~^~~j~~r~~~v|R~5~~~p~~~~~S~~~~Is~rQo7q~~~~9~~~~~~`~~t~W~~~psnmU~~vt~~~n~s~~~~e~qo~~O~~~mL~~~~~{~se~r~s~~m~r~~=~~~u~q~o{~^]R~~t~n~x~~~qr~~M~~w~~~w~q~~E~~~~u~~|~w~~~s~~X~~s~~~M~~~~N~Q~~f<tC|~B~~~~q%~~~b~~f~r~{u~[~{j~qw~~~~;~~~C~nt~~u~~f~~Xg~w~~~~p~~\~~~x~~[Q~+dve~ln~~~K~~~r~~O~P~~~b~e~~~`~pe~~}~r~r~|~k~~wk~~~~`~~q~xh~w~~~~qH~~~~Y~~z~~~~Q~~~~~~~~Z~~~~~n~~~~~~~~~W~~~~~~E~~~~u~~~~~~T~~~~b~~~~~~~~g~VO~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2877/ccs/rev np:i:11 rq:f:0.999268
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCGTAACTATCTTAAAAACTTCTAAACTGCTGCTTAGTAGGCAATAATCGACTAAATCCATAATTTTTGCGACCAAACGCAAACTTCAAGAATTTTAGACTTTGAAGACCGCATCGGCAAACCCCATTTTAGATACCACTTTAATTTCCAGTTAATCTACGACGCAAGTCACTTCTTTGTCGTTAAGTTTTATTTAACTGTCGCAAACAACAAAATGGTTTTCTAAATTTACTAAAACCAGGACGCACCTAACTTTCTAAACAAGCACAAGTTTAGCTTCTTCGTAAACGTCACCGCGAACTTTGACGCAAGAATTTTCCATGACCATTTCTGGTTGGTTAGCCGAATTTGGCAGTTCATGTTTTTCCACATAGCCATTGACTCCCACGAATAGGTCTCTTTCTTCTTGTTCCATGCGAATGTAAACGATTAGGC [...]
+ +
+ M~~~~~~[~~~~~*~rt~~{~w~~~'~~~~~~~~~~~~~~~~~~~~~~~~~~~~xsUjq>~~~~~~^~C~~~~~)~~rk~~{bf>]B>i~~~j~i~s~~|~~~~~~~~h~~oq~~~~~D~~~~h}K~b~b~~~sZ6~~~u~~V~~~~I~~~~~~~Q~~q~~~~O~nt~~~\~K_~~Z~~~~G~~~_Tp\ka~~hp~~w~T~~e~~~h~~~~~W~x~~~~xv~Z~~~~{~~J~~rb~~N~n~~V~~~~]~~r~vmSx~VLbp~~w~wX~~~sj~)~~~nch~~I~~~~xQ~~~u~~]~~c~g~X~~h~sd~~\~T~~a{~~v~~u~~S~~~u~p~~N~~~]S~~{~~~~s~r~}[~~c~~~~|}}~~ul~P~~~a~~~a~O~~J~~`r[~`~`~>~~~u~q{~K~x:~~~~K~~~H~8~~~~r~~s~v~~x~~q~e~~va~~~~~t~~~^~~no~G~~~r~cW~qK~L~~Uq]h~~~~~X~~pU~s~~;~l [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2884/ccs/fwd np:i:11 rq:f:0.999473
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTGT [...]
+ +
+ ~~g~~~~f~~_~~~~`~~~~~x~y~%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M~~~|~~{w~~c~z~d~z~~Z_g~Y~~H~~~~aw~L~~~~f~}~~~`~~~~w~~~x~v~t~~~~H~u~~~~u~v~~~vg~~R~_t{~~~b~~g~v~z~c~~~^~wY~~~~~~~`~~v~sq~z~s~q~~Y~~~mz~~~W~j~~~a~I~z~~~~~~3~sN~~~~~~~~~~~~~p~~~~~~~~~~U~~D~~~j~~~~~~k~z~~e~@~~~\~~~q~~~~t~l~s~~~~~~~~n~se~~Q~~u~~a~0~~~q~t~~q~~~x~~~xz~~~Z~~{d~~~c~@~~l~t~l~~b`~u~~f~v~~~~uQ~C~~]~~~~~~L~~W~e~v~~M~L~~rb~~~ty~~~h~~~~~T~~~vb~~~\~~~~~q~?~~Z~t~\~~~~v~~v~~a~~~uB~~~~c~~\~]~~~~w~~~~~xg~a~~~L~~~~R~c^~~L~~~~~~~~~~~r [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2884/ccs/rev np:i:10 rq:f:0.999298
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGT [...]
+ +
+ a~{~~u~V~~~w~~~l~H~`~~x~~&~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Uu[_~~~vj~~~~~~~rd~~0~x~|~|T~~~~~c~~~~~y~~~~~C~~{~~]Z~~c~~~{X~x~~~o~~~~~pu~~~~U~~~~b~v~|~h~~~~e~Y~R~~~~~~?~~~~~~~~~~~~~v~~q~~N~qT~~|~{~~~z~~~~~f~~~N~~~~~~R~l0~~~~~~~~~~~~~z~~~~p~w~y~V~~B~~eH~~a_~~qp-~Ylwy~~Rt~~iq~k~m`~\~|x~Z~wqr^w~d:~~n~sv~~A~k~~w~e~~W~x~~z~~~u~~]~~i~yp9~~~@~{~~j~|~j~~~~~k~~c~t~~V~}w~_~~S~~I~~e~T~x~~~~nj`~&~~~~`~~r~r~m~h~~~~U=~~o~r~Y~b~~~~~i~`~[pnTx\~~~~~~~~T~S~~~~)~~~sp~~~~Q~~~~q~~t~~~V~j~~~>~~~~~~sq~~X~w~~r~~~~g [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2899/ccs/fwd np:i:5 rq:f:0.991516
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAAATGGTAAAACTTGTCACCCCCATTTACATTGCGAACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACA [...]
+ +
+ YwY+]ZGNu]I\@8aOZMVTKZ]KQ/YaX-rKtYSW_-ZIGDDr[S`\PW^;l]KtJL[FrRZE(n^^ZPZ?a2CJGKGovS[Jvv]][^<DPA\LZ`\LXDYJZ2vcFK at qUIvuT\Z=/`[?X=q/ZCR?UJpZ%SUS`^\WQIFY2sCKVUH,_^X=4KLXH[LV'L;IKJ4\S;PQdY-rlOJK*]_/MMGWWZZX5g\S`CuvqMG\M-R%d[HGKt^6Z]YPQdL\7D'EFdY_GvqGOaQv[Q@$;MUE&:RM-EKqJS7V^X\=t_^LuNW[X0NBPuSZE<WH^S6cX$.ZU at gO]]]@oZ\KHTZMW<N$0:0>l\Oa[]6tsSQtRH\E3wx\Za\SvWWR[LqUR`8vhR6rlT<q at aLJFEb`[^]X5>YKQXXSQ/.e;2X0=^WWR_[V\<FPAc/smP6:saL at _IY>_YU]LZ^LuQv[^>\KS:viQQ=DMrZCuVVRZF8r_EoGP9cSXP\K]ZBVH:M\^[PuKIWG<@ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2899/ccs/rev np:i:6 rq:f:0.99341
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATTGAACATGGATGCGAACGACATTTCGAAATATACGCAATGAATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTGAGACAATG [...]
+ +
+ BhRXXM:<`J^]EQw[RH^R]>^_L/^WEIU6\OCK>*c\EHBW'ENHEGO/]M-U=,PKMaC[IAY=J91LPc[S^[_;ttYN=]h]Z_GHS[E_DA&Y_G]9q>tFvw`\)YNA;c[ZNQ;q_Pt'B@[ZN?]=UW]O at D\G^[_KR;dD7MG<Grp\SIV[RC`AKZS[S[O7_YHF2$$DnpW^A4]IOFGZRMR_8wp[\3luqHB\^?eGww\?>Y5wwVEBs+I[^/ZX`\F:qs[TGQtRER]E[=FWSY]@Md^_;w^E`BtXKFvPt=LO;M2]X>\Y5P`[RuS^Ewk>nS^G^Qv`\.^YSN\JqUNG\FEy`QvRK9uuD at uWX^?BfE=S\5;m,JSM>L*X^8.5Y(ta]@\Oj[^OLu^Q6[RGZS_[PG_R_<tW\S_[^Ta[^`RIV]X1F(Yp\9mY>NnT`[^`Sa^P[CvCoM`[`]E=uq_[[]0pP?tR^[PGJbBKt`ZAcDPDY[]RBuZRAs\=6PZMGZQv`S [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2903/ccs/fwd np:i:6 rq:f:0.993546
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTGGTTCGTACAGCGGTAAATGACTTGTTGAGTCTTGACGTCGACGACCAAAGCGACCACTTTGACCCAATTGCGAACTACTAAATCCTAAGCAAAGACTATTAGGTAGTAGCCAACTTCGTTAATTCCGTTCAGTACTTTTAAAATTCTAAACCGACCATCTTTCCGAGTTGCTTCAAACCCTCGTCCTAATGATTTTACATCGAATAGAACGTCGTAACAAACGCACTACTACATGGAATAGATTCTCTTGTCAAATCGTTTTGTTTTGGCTTTACCCTTGGTAACAAACTTCGACTACGTTCGTACAATTCAGAATAACCTCTACCTCGTTAATTTGAGTTAGTTCGTTAAGGGCTTAAGTAGTTTATTTCTATGATAAGCACTAAATTGACCCTTAATTTCCTCGACTTATTGTTACATCTCGATTTCCCT [...]
+ +
+ a~lTShT2xea`TU`RQ at ejRWnRU$|}}}}}}}}}}}}}}}}}}}}}{qjkmSL>nVy:zRjogSUiUZ~oN~~ng_I]tfL{iSkiVK}khSSlDT`Sif>IMp~kUkd+^>AQz~kg2~rStNxSUi3xTnSUp=ccjG~oG|kUMq{RPBMXYtNY~qhll?iEiDnS7{Rg\{UvYpE~OBb=WUU>G/WHF&d`IG['^)D1,O;J$U6>>FZ\0h)MSYa]0IWQ>sN,MenTjT1uPPXJQ\&p{dbS9iP>Dznfj7zVioViR&CR?]`@kSM?lhVoe at MiV}5yS>PWOyUlV]xTnV>||WUk:~~}kM~~zF{U@}xa,kg_~IonBcB>v{TO{UfPTob*cYwQ>Z=SVg^|VhkE~iQVF}oVk*)poQeM{U`.}lc;hM}gl\fTT[zD_>WwS6qUlkgf[6LVQ>{}TTOjiF>F]RReVn=||McSQ/mg\yTw6||D~kSkhV\}T\~fEaLC_PSQ?ihP~n;~t[ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2903/ccs/rev np:i:6 rq:f:0.991972
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTGGTTCGTACAGCGGTAAATGACTTGTTGAGTCTTGACGTCGACGACCAAAGCGACCACTTTGACCCAATTGCGAACTACTAAATCCTAAGCAAAGGACTATTAGGTAGTAGCCAACTTCGTTAATTCCGTTCAGTACTTTTAAATTCTAACCGACCATCTTTTCCGAGTTGCTTCAAACCCTCGTCCTAATGATTTACATCGAATAGAACGTCGTACAAACGCACTACTACATGGAATAGATTCTCTTGTCAAATCGTTTTGTTTTGGCTTTACCCTTGGTAACAAACTTCGACTACGTTCGTACAATTCAGAATAACCTCTACCTCGTTAATTTGAGTTAGTTCGTTAAGGGCTTAAGTAGTTATTTTCTATGATAAGCACTAAATTGACCTTAATTTCCTCGACTTATTGTTACATCTCGATTTCCCTT [...]
+ +
+ 1[UloCP1PcU:Q\yQTkmVVTSjj%||{whSKOXZY_b`XPKMVdqrja[UOQiqneI>cU}lDRTjoUP?haCu^gVo`9GCOvQOShl/_VojTTiAWjWnIpG~qAjSgIlnkB~{RTI`v\tR`Oh+YZjNPi`Agg`XpgM}Uj8sp'V^Y\TF_nD~dkWhkRZ~`~R8sgQ+]L]7zV~QClOPOQmk:uV_BtvE^PdHo0`WoZ~k^k$wlRD^BOUQrVlW~SC~pK{macA_W~_[MQUWNSg`RcEPNTd5BNVpaOI`N^bJIp_D7Q(H at O_VD__J?xTm]cMXJsa\INlM4^:r]I`M7bojM at kraBu`0n_RIim9]0g^Ur`1YeN+7N(IKIc`;+R]N[^`VpLsadNQd_TpRq^_XEB\5OL.kUpFrnNdNMq^NLraNM[Rf7jcI9iUnO]`D8.J-`Sc^HaHHE[MdN]Xa\;3d'9;KPn)h=Q7noMn3TLLZKhaLqGHi`^DZa^aO`DYkHqqK^ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2944/ccs/fwd np:i:8 rq:f:0.995773
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATAATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCCACCTCAACGCTATGAACGTTAGTTGAGACA [...]
+ +
+ dpZCn[[Z~qH[@.tOWBaj_mZZLAm~~d~K~viX_E~~^p2~ZCb]QkrJ~tN~svn`}R\_Z~an1Pa@|Tj%I4Td~VmEgguswm at mDQg\jL[bt,vTNn7m~[W*ZYQ~aTtYT_{`FvV~mvpXO{L~ttlPYG_sUS\Z$s\eiijm9~~vNj=EMWcenj`B_gKFwwleXubAuumhWDpuPfSXjRfdgGU`=f.[f5,gjR+|@kumRqlIwvuOWuPWLV'qs~i at nY/Lg;A9LbBNheiJEJjP4_hjGpDWjQuW[DeG^AVCfSMuPadLjdYLKtfg8ugKmMjijJugVTe;SUk;WlfYXI=8hKvdlGwvMHqNdic,rjfW(hg<^QjNeYveNf at ltM0qrk@s6WKZS9~^PWDF3JaiNeeTM='bdcjNkeSJQUd`KeI0>/e\fj6uvdYvgmK1ifmk`=Qu,VShNmgL*tvsVNWZu^QqekQgi%~ZX6VUBGj:aLjEDe+QKeLmje^wcfYU8U [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2944/ccs/rev np:i:8 rq:f:0.996531
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTTGGTGTATTTATCCGCTACGTGGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGGTAAACTTGTCACCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAAT [...]
+ +
+ MmBD(39+h^dwrVz]OhrFFHxpo3xn\OVBYB?`wH}lwQ`tWqoboRZ*F8>=K(tYf~]zwF~xtO_Fd~pEwqwU~~sZV~~cWonWUY^JUCoQas9~U~M~~a\7wQJ~kIaSIa~yQkNiMYPRZv?yt:C4rcfcq{xWM~DtXpRIv~yp_QYRHzQ`xUrTt3HTwxWE~UJ~~L]UDkB=B?gQIKPfH~vYg<R_W``Rf:}M~~d'u=?-~~pb{U`m{E~~~~yK|_lOpByOVPbl[B^DYJLQ_yI[8xh;p&~qrF~at@[>\OOnbAqkZU[mEf8dItdKu_]ts_~uvPYlTa}Y~vUuwX?}9Ow=S7~~oS~lesSN~~qvtaa~DslSchCYvD~zX;ydo<~_xXjQS~q>YeSujF]>OGFQoL~kh1KmqLqjlaUnFbXAJ(T~sI~~Se~VrYqlB^_GrEw_`/Mndvn>kdz~m`=X-_v>cXB^Yqm?Xgbf~kQI,E&KQj`P6m`QAmTuTkmMws [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2951/ccs/fwd np:i:5 rq:f:0.99569
+ AAGCAGTGGTATCAAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGACA [...]
+ +
+ ^~b^g^e;}KfkG${]^c]Q`RanfI=w~v]QkR^ncWEeTU\K~blQQtD~khncX~]~9C~kaX;NMM~]C|H;k~iK]f>~7rcO~_~bCnNKSkCl0gD:fe1?6<~gk^Qbnc@~~h9\cU~~h_S~n_OpK_f/G>bfcn]R^haFJ]cd-H,=?<~~hN~PB~]A~wS~F~~hlQR~H?~~Z:gPl_T~\O]aFHN/~bhZiLgQl^HxbVc]~QS~nc_Uji3~~~eJ~F5zcc_T~fHfZ5\chchc[FY~g^b2R~^c\Lkc^]EH~{;]mgE~w=K]bE~?~l`cO~^_PFaF~\54xcHj,~ye^lG~^l@~];~~~a>~lK~ckJBL`D~~^J~~kLX@`lT~lQl8l]Ty7~yg[;T~~hcNb35yQcL]cLjB_VK`FIJq:\~PD~|B~2YJID~M[hcmJ~~\Kfncn_hc\JM]E~J~?tg^F~~9xfhbKP~n_bK~]@t~kKjQa.~~~]GqXHU1z]gj%}]nhnbR^h [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2951/ccs/rev np:i:5 rq:f:0.994585
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGAC [...]
+ +
+ ,A?V\TZ4hZ_FW1aXMPK8>61[W(ssQ@]F^SSS:HiT_ at NtT\aEl$iNWESF_+qf`@wnTS=pF1cXLu\>wL0^UaKuGurKu*XTKuTXTH8rQc)+ok7pRKs_FS`TIS6qtr`V;8br`XGvZ at EbARaKuEhJS4WaX_>VTW>^HtUuX9wwfFraFuX<sc5D2pr[\aEYV,pq-%l]\XF_>_W>VTaGqC\=qHwa\XUuT\T at sXCu\UXLhF%jn_aOuX>wvaWCO^XaXTXO.L^P<J;n_U\XErSTW>YHI78<ZXaX\a'^]XZTXTFY9rYQ36kSa\XQ:siTAjWQUDuusVETtX[8`A+qrf=Jt\LpTFSX\TFuuX0vRDCXPpO at Y\a\QsQ>bCuu^W[8sE+J23*0Z\aUXTKs?q>DQARNuaNu_*nMGuUuHsSq;PaT[2s\ST_FS\VFQW>^XMV8T6o_W6qoEdUaTaEYYWQ=pX8uvhT\_>9ossXTtFW[CoRC+;nVE^ESaX [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2986/ccs/fwd np:i:6 rq:f:0.99674
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGT [...]
+ +
+ e~ur~t}O~z~{rX~ntr~tzope]$n~~~~~~~~~~~~~~~~~~~~~~~~~~~srt~}gr`=rqh[~~sq|]{U~fr~u~H~]Xd\~tepNsP~jqsA~{Rr}F~}^~t\go`X~]KvO~|jhHL~W4~7~zB~l~glr~lZ~r5~~qE~fi~jpyo*~~~~zsrD~Y~nVc~Q~k3jmaNVm~{J~k`h[T~mc;ml~o>~pA~~~}\b~kl~i`~i~F%~op`u9~~~fI=~~lS&~{oim~kc+~~\|h,~xqdL~p[q5~~iWS~s}\~~tzryIqfJuO~_N\~Q4~~h}R~~k[qq|ob, at bQkM~~l~vl~]stZ^w[G^~\sH,~~~\Wr|zqqtsHeBk{t~h9~}~T~l~Qmc]nBf~=J~X~~q|~ri{TzSr~th:~jdg^6~}u{:P~~sSO~~c~qe\~s~tK2z{Xut}s~qF~nb]m\s{3~lC{qL~~qjrgaZ~fruY~4~aTpM~|M~~m~J~~tupTpfmI~U\mVquN [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2986/ccs/rev np:i:7 rq:f:0.997959
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGC [...]
+ +
+ PvF\eOLKdhfQ]F~^^_g]N\hg^$~~~~~~~~{qhdir{~~~~~|sjeebiq}~~~qirr\qitsigmG~qig]etG~sgA\kV~sgGNsSpintWrkBkJ~trVY:~^Eya[\esC~fb~D~\[0ZGxL;~)~1+~gr`jdqeMqhJ~~iD~ohlhfng'~~~~ligSsF~\gF{<ov?hZdZSgsqLN}Yqie^vjq^fP~hV~h,~~vnja~TV~sW~<|eO~ha~C~~~mj@~jPQ^~ndiR~fe1~th]p>~kSqX~eM^)~~hcb~dYW~~qYertg]>~L~]qV~@8~~stW~~W]eaditb~iQ~I~zN~c=yhg]hfXcfD~O~h2~~{bYPfiitgGb~ihjg\qY~tsYy>~qhshhRQ~rZ~H~~gspjp[XnZgqRpL~rR[hc~rgckV~~LoW~mK~h]hsh]eRNw[gohYg[gb~Ro]Uihtb~hisiN~kinbGqV~shRJt;~~rhB{+T~]a~Jvxhie[grh;~fRi [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2993/ccs/fwd np:i:7 rq:f:0.993571
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTATATCCTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCAACCGCGTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACAC [...]
+ +
+ \zXQ7BJBV7JL>EhSGHkaWarWU$fgdegjmrqlcZSU\iywqkc\\^TMIHKMOSaRdGRb:4opiXbWNzk]`Z[U@~W]t`U>~W\j9}amV>qQ~n]mK~ik`DCzT/}j]tUJFi\8p7~ghK at JPGJkA~oR~HhL\aqK`}H5om^S~g^rTNXT$kYh[XXLb~Q~s]^~8ciO{TEdB(;=V=~kmDJa~UO^WYeZ7pD?@oZ\K%;GaN~VFfM{BU`/6`2gegB[M}x\WBuf]+K|\NDciWXE:k]H&&+cKCT2nZO:\PT4PXY/EHXagSuGmN at BfgB~_,d at tpIWb]ZOlT`/EaD~hTb^Nj5HFVHdDKCna~\3~~z`QMda[SU9VfT`mGle7fo at .`JC8JO*E?_SmX.c4iQIYjHfoim at 5>ZVIdWGfFDneIR at 5fi_BH~kIm-WUFl/b3YKrjFl0fDW[W~_)iJCZSD|^A=IA]K4iLpWM~aD:TtOkjUF<Q^E`YQyIhrLaN\NVH [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/2993/ccs/rev np:i:6 rq:f:0.99642
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTATACTACGAGGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTTCGCACACTT [...]
+ +
+ +JG816=<sfR:[]k]ZV`=PMI[G$cvoc_VXallnkf`^bhnssnjiks}~~~~~~{WZdikxgwfdZy0}pgjebjzW~ffpPdQy5f`W~f}hvbC~vV{V~rrcR4}VE~dOLjzX~fS~P|MqVzW~OKxBt{Y~g}VXWQ[R~jH~sfA~@PrvcNb&~~~~~a]JzHglaCp(~?<~f`Apc[JQIfjGRZ;}amS\T~b;~^>l~wXJb~J.pjJq9~_?~`c~>~~rYJT~gY:a~m]bY|Zh.\[\Sj0aP3V)d9_[;~~pYXdZXK at TS]^ZmXdIiMtmsO~Z2i~nCR~~`A[`A^@KfIMS@~nO~\\~`Hib[WKZNuKo^7tktcd9P4`t`?)~JYh]mtP~WrS~\~pIUWa\YuqRx9~~]mtbshifSJoHqL~~bQJO~k[eZ?~iFYO~lArVT^A]+W6L~fakaib^WI~FPbHa\lQsHISZ)/?LI]YmK~r`H`~MTtd0(rTM~kM~/n~UIZKoHd`3{ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3023/ccs/fwd np:i:6 rq:f:0.996632
+ AAGCAGTGGTATCAACGCAGAGTACGGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACCTTGTCACCCCCCATTTACATTGCGACAGACACAGTTATGGAGTGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGAACAATGT [...]
+ +
+ 4c=C\PfHz_QcO3nPB<BT:Uc;R*vvdVdOApvefEwXRc9SWfBoZHzcMUWuTaO>fNPWTWWwS at NTeHxuUW?uted]4SXQ/nVWffedEwGf<wwfeDmO/Y[RRR=;]\P]ECQX9T=WFvMcWUeeaXTOdXHwVeU9U?YpeUfeUWVvWcJ\]`q_G~~o]Lc]FliokW5~}[pLEg6W]K9D^Yj0phRHlo=:i6VREA~n<n~p&_`~Jj-Q%H?:PhjVz~ZWe^~`]`q]q[iX at Yp`Nz\W9ko=XM~DoM~-pEj:k]L~9NaLn`q\NyYV@~~^~IkXU;~onFbXYFLB_danEAH_j=~<d5~k[+~\ke_C~~ZpnpM~^\[O9f]GWErx]L~~qN~N~]jcGzq`qp_lZ^[]`Xf_qIgqX_p]q`oHoq`kIn]a~;~~~[@~y]-}\Y[lgHjUZQJxDfZc\oYGAsp`iJ[\jPNSGCF^lBu_Dop[M~X\JdGgMMmLX5bb[Zf<[R*JENki]^ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3023/ccs/rev np:i:6 rq:f:0.993395
+ AGCAGTGGTATCAACGCAGAGTACGGGGTGTATTTATCCGCTACGTGGTGGATGAACATGGATGCGAACGACATTTCGAAATATACGCAATGATATCCAACCCTACCGAAACAGCAATAATTGTAGAAGGTAGCATATCATGCCGAGAGTTTACTACGTTGTAGCGAGTTTAGTTGAAATAGTTTGTGATGTGTAAACTAAAACATACCAAATGGTAAAACTTGTCACCCCATTTACATTGCGACAGGACACAGTTATGGAGTGGGATGGAAGTGTGTTCGACTGTCAAGACCCTTCTATAATAGTCGAACCAGTACGGTAAGTGGGCAACATGCCCATATAAGTCGAAGCATTTCAAATGGTTCATCCAGTAGACGACGATGTCCTAGACAGTCATGTCTCTTCCCCCATTTGAAGTCATGTAGTGGTTGTCTACTTTTTCATTGAAGACGTCCACCTCAACGCTATGAACGTTAGTTGAGACAATGTT [...]
+ +
+ 'LAdS:7iJ_eS@`MFMDDNCSQD9nyxeR]c.p[^N:fTVHKUR^GlP>Y^c<DtSYeH{feSU?SrCTcWd,iV at 90rtcbM8+QUSZbUfef^6_S[1xqWd9wSHwrUMSW?sdAWLvUeeTIr at med?=`A\PWfdA.[UfUfT4\\dU7bVABaS_XUR;dT<kYdUNvT at Yi\MT3ttUUTaXUdTOIxvWd1vvpUMcc-KAunJ2=6)Y_[VFiA`Cb%uvaG<oucUYBWSU at cUM-jeUMUeS$pbbHzfO;,plfeHzTtLDJGGBZRQIVbTN at RuVc?|^@pWbfeTXefTOVS/sDXeU_AAEvSHoSd/XlVGuS_dUBz{`dacAv at bWUUwTAc?ZoVNvvQGnEsVdM.H`TOc at dWT`RUdO at cHzefUcAdKeVaXS7?KUDj&rvuMK-VSJDIOeWdH%6]TN4q59=_VHGR1uwwcULEuTQvVcWUaFtYHy_<FtUU<C7VTSpU at TuMSWwU`@cWTweT3r [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3046/ccs/fwd np:i:11 rq:f:0.997092
+ AAGCAGTGGTAATCAACGCAGAGTACGGGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATACGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATGCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTACTAGTCTTCTCTGAGGAACCATGAGATGGATAGTGGGGGACCTGAGTCATACTAGGGTAACTTCTTATATGGTGACATCACTCCTACCGTAGAGGGGGGACGGTAGTCTGTGGGAAATCTACCCTAGTGAAGAAAGGTAAG [...]
+ +
+ ~~Sbs]^R{C,cl]Jh/QHvexUoeW=~~~fFEG=BcZ,iAk;WjUgKiD`J97p~~W~@vaNmRi`otczarF{EOrLYWmn)VuM=wMgN]KxBX{]~=TEd8~cPSvh~FCgef^`/^X<M6}~T~`dsdoe<~~7~t+uR?hhO~W~dcD~~gN~m?~B~~ecwlfh~E~FPzxXfs~gqhpHu^TO_1~~@akJ~{n?}nQk`Rfg>}PwfOp8d~gFys=QZ~zRmvUk7bWd~W;`KdMhA^mqt?l?p^~P5gtwmpe_~ad{`MPgQW~~Z/~ps~t-;~{;_eGD|~s8keY_a\XJxS~~~~R~c_9H7ETLb8~^GYsP^JS~pd[dx_N~bSm>r~hr~dn`BlPs_gd~R~F~P~LRK\S~tR~~pzTa0y}~~~@~pg~Une~`oTc~?~|mZfNW~dN~~kem5~qT`gxi\_]TS~s~M}SX]g~5~~~~~eeS~ljeo5bSyE~eApYa\d~>~iix[b8b~hW~rI~gA~_ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3046/ccs/rev np:i:11 rq:f:0.994641
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTTAGAAAGGTCACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCTACTAGTCTTCTCTGAGGAACCATGAGATGGATAGTGGGGGACCTGAGTCATACTAGGGTAACTTCTTATATGGTGACATCACTCCTACCGTAGAGGGGGGACGTAGTCTGTGGGAAAATCTACCCTAGTGAAGAAAGGTAAGAG [...]
+ +
+ F~Ulufb9~|`f]Vz?\Mi\HNikP.`^q~u>_~lvi[~Z~o~^EpFse.=S6~r_lvD~e<~bT]Ljjf[~kqGFYb8dWS]^Q;qr=KpW~~FN+\URB(];8IRL(Bel(FM:[[FsoXP|m?Rz_SwYs`=&M*'lhm`=~gL~T}WFDwva:~\Ex;sugVZgJN~hlKPIkukxbAHAcR|Wf~]AbL)ghIq~~@~~>~TUQiD~mHgK~WcdgD~_EbY]QApgjYI~~nVWJeZaBuU7^jfL~h~Y\M/lf\boNVza`hxn~h~6qukMX`6~~I~~_\]p<~~bIxYUdzi~Xt9~~qvjjhooeuOgVe=kbO]Kgh`jmoSVJgzU~aSWf^S_fAEOgarScMpW\R~b~Y~s\MiQ^wU~QmL]w8;a~~tS~^CTDOfLxj[siH~~~^~Vm~fg~]w?L1~XW=lgni\ehC~kq>SA_iKp$sus|ijJ?CheYe`a=8Od(mqTM[oVA}~vj\_]D~\GGNT~}Itad` [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3116/ccs/fwd np:i:7 rq:f:0.995734
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAAGCACTAACGTGGTCATCAGACTGGTCTGCGCTATAATCTACGCAATAGAGGCACCAGCGGTCGTTGAAAGCC [...]
+ +
+ f~hMnftC~Xpt^Z~_i`/e[eTB_3~~vw~dilMBnQ~fYC~qS~ivrs at kqc\O~n`~ErieuJ~~\dqR~n9:xzteP~SzibZMoFh~VeiW~e`~ee~V~Fb8~~dn=R}[]hdhuQ~b[b[AXlgO`~Z~sR*~l>lBbolir\uiriegW<oimIf>~jN~]h&r~~MsAeO~]8~QnLgA~oK~b]=n~jOhueqmnk[;__VMV~udF~pircgK at mA_k_i.~<^ZtiLoJYIfofZRbP~r`S~G~mee$\Cppp6N\GO`~iub/~>LhD~QAd^CjsW~cZp@@fteM~iU~uU{KMI~{bWAbeO~KCqdpe1xrb]]dkir\gD~tje`~euZ~sQ:go]eqh=~\ULheu\hq'vNlrOsiurq8VuXPvQPLrI~mEqH{brs^siq96B1~lLcqqSdV~RaFdtJlLhuX~uerq:lKVbuV~k^ndMT]dffHQlaYBcib+~qPJoX~_gFb at eP9UEcg8yi(~ibA| [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3116/ccs/rev np:i:7 rq:f:0.993861
+ AAGCAGTGGTATCAACGCAGAGTACGGGGGGCGACAATTGTGGACCGTATGGACTCCATTATGCTGGACTCCTCGGGTCAACCGCTCTAAAGCGAAGTTGTTGGACAAACAGTTATGCGTAACTGTAAAGCAAGGTGCCCAAAGTAGACTGAGCGACAGTCGAAACCAGCCCCAATGAACAAGACGCCATTGCAAAACGTCTATACGCTACGGTCAAAGACGCTTCCACACCACATGCTCTCATGTAGCCTACCTTACGAAGAAATCGCACAAGTCGGTCGCCCAGCGGTGGCATATGTCTTGCCTAACGTTTCTAGACCGATCAGCCTCACGAGTAGCCTGCTTGTGGTGTTTATAGTTTACGCTAGTCCAATCTGTATCGTGCCGCTTGGTATGGCTATTGTCGGCCTGGATGCAAGCACTAACGTGGTCATCAGACTGGTCTGCGCTATAATCTACGCAATAGAGGCACCAGCGGTCGTTTGAAGCC [...]
+ +
+ C~]h]`0 at wkVZdS~e_Wuduer]i4~wowp`_\gGy:~S\GytX~foqGDw\eqG~l1{OEVip3~rho6~rfE^I\hR~Y~dRYRY?~|ehP`~_Vxe_~Pxoh7~~_ccO~q.Zgb\d~hW2kJ~~Lge~Q~VKN~~@~hNF^boeoHV\<Isiteaed=~vU~[b6~~`UWS]Q~gBr_UN`CvbJ~Jd9~~|hN^c at R=dhdhsuhQupQK~~dte_i^~Vztg\Y~uit\baAfrivpOmULW~]sV~LwnRcJnNI~~rieeXba~bZSDgXbdGyb\WcDnaG~aflnYcnRV~PM|[S~ie>~{gEn9lU~fVriueW~\gefeucFpM6j\ch:eJC&=ANKpvSVk^F~~\eMbfl`WY~c~qjoOn\ph_SfY~eiV~PsGq`3yNmVO~drh?mF~[U~rGbhQ~eh\dkP~hcF?~TcmriZJjaDQ~qhZSSTiilZNnUcoWfdRP~VretD~dmM~sLdQqrgK,~kdb~KMn [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3119/ccs/fwd np:i:6 rq:f:0.99553
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCATTCGGGGACGGACACGCGAGAGCGTTAGTCGGCGCGTGCGCGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAACTAACTGGCAAAAGCCTAAGTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTATGACAC [...]
+ +
+ [~FD^E_ at zfMOX4yE[F_YP]d6VA~~~ZNMd\d. at 5k]ODE}]he7w2nx]h]F~V~dD~{Z\Z~gO~\X~f6~y\L^bK|>x`Mx*JN/XW\]c8'>NZ3p_Ls^KS7e[%X`Y=y~~f\]>~~f\Q~h]O~\]I(]El,\d/cZP]\\F[MKgAr;=icP3kCMrNCbcNq.[`SVFMh'F;bafEfOWMFLLQPXNA at 3o\RY~A~edFW~^hX0yOOyPEGB`b%=RMIp[$p[Y]FEB%ETK]YGd]NF[\A~P]h[BfIOI>c5W4B)]LZcN8SScEK<EbOuOZ[*eGeh\]9[eC7at^g<~~fEeFfDfCaEAr~{^JfeCdUE\ULEGz|[6~a3D[X~hO~U>UHeZFj6eVJW^Fyzg];|[/_Ld[X]=tGuZJX\^X~:Go:JmaP~NlKw4_HWOYc7}}VZbZc`R;dVgF`E}_~N~WMJ{b/~bBajT~neQ^qO%~~~PjKOB~~Y:Lql`nU~fpYN~eoDndm`[] [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3119/ccs/rev np:i:6 rq:f:0.992635
+ AAGCAGTGGTATCAACGCAGAGTACGGGGCAATACTGCAAGACTTGTAGGCCCATGAATTACCCGCTTAGGCAATGGGTAGACCTTTCCTTGCCGCGTGGAACAAACCGCCATGAGTGTTTTACGTTTACGGTCGGCGACCGGAGTCACAGCGCGACCAACGGGGCCAGGCAAAGGCCCATAGGCTTTTCCATCGGCACGCGACCGATTCCATCAAGTGTTAGGTGCAATCCCCATTCGGGACGGACACGCGAAGAGCGTTAGTCGGCGCGTGCGCGGGACTATTTAGCGAAGGTCGCCGATCGTTTGCCCGTAAAAACTAACTGGCAAAAGCCTAAGTTGCTGTTTCGGGTGCAATGGTATAACTTCCCACATTTAGCCGGAATAGCGCCAACAGCGTTATTATTTGGAACCAAGCAGTGGGCGATGTCAGCGACAATTCCACTTTGGTAGAGGTCGTTCTTTTGTAGAAAACAATCTAACATAACTAT [...]
+ +
+ %a+DcWa<]=df]I~]XYTENJegP(cy|]&OPJZPYGW~\h_JgHegFr<YcXf\Un>h03v{DX,t[Lz]VadCyeQb-4Nl9v^MdAtUO{[QIQKfZ~\;liDbTN~gPZa<[ZGt~~h^\J~qZBM~g^M~^\b;Q8wIXbYh^hYGX\BeL|?X]<~~~P~eJdZ9Yo:z6~z^ehM~^<zbX=_'JN;Z\hZVTYR8UCcRYKaceGW|[>,>LV=id[\C^b?uatfFh]D~maHMnO\fSVXG9,DQCO[UcgKf]L}]JHDdF\XY5}~g^bd=UV_W^[UyM~gZG=kW5K\F7Vm[>~mVf,]btaZgF|(N7yB,t^pC:gNTvI$SYZg[4}p\,]LMV.Vxb,=2=`RaARzD~hJVA7YZfW:x.ZVf&aC/TI\MiZX[^ZM`=8\T2{H*ySwJv3yVVMOd8~~ZRJCCI/bF[EeIDkMlO}f\;bbJ}Lf\hMe;\[A}U/MAQHMMY3ziZ]Ipf^gX}EegV~]OeJ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3147/ccs/fwd np:i:7 rq:f:0.995375
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCCTAGTCCCGGACTCACCGAACCTACACCGTTCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCGGTCTACTATCCATCGTTCATGTTCGGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTGTGGGCTAGGGCACCGCGTTTTGAAGTAATAGATGTAACCTACCACCCATAAACTGCTCTAAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGTGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGAGAATTTACGGTGGTAATTTCGCACACTTCGCACGTTTA [...]
+ +
+ Ar:GV<i>pQ]f9Kh7FJZY^]kIG%hllllllllllkfabgllllllllllk60r`Zb[Hm^G\^Kh^MY_L^>rKKjV^M]UJj=y\ZJWRNp[GK%nmn_Wf&^RKhBCXDF;\WPm.^U at 2R6_HNh.yJWF5X`\e]YeHCl]KHe^]j\[PJ0mfVUYK\[jHgT;MO/m7Zc9T\<Z6h?{^lK][PHYSZ]cG*;6IcOSG8OS\9kX1ZZbIB^<PZ>cPe]I5kkYJNmb]E'WU at mmKo]2kkK^<xWKW:oom\LmYg,LIWY\X[kEc>xkH7G\7^hV`4n[Jo\HdFV4V7.CABmlMo]Y`J\lK\lFw;r_lJ6iln]Jj\VKNLd?kIGi]k_6b][=r^j^J`EJXKlJ0S7dhYeYKWfQP45WTGAe[HMHDkk\j7 at co\Z.aZMmKiB_5Y96>hbLlJkFF95VZWX]FYk7[RFKINPgJ^ZR^MoB2NSEmlZHKml;ukAlHnnG[7[D at 97E8X5H9]Arqb [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3147/ccs/rev np:i:6 rq:f:0.993731
+ AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTATACTACGAGGACGTCACCACTGAGGTCTCCGACATGGACACCTAGTCCCGGACTCACCGAACCTACACCGTTCCCTTCAGTGTGTTCTTTCGGAGTAGTGAAAAAACGTTGGTCTTCCCGGTCTACTATCCATCGTTCATGTTCGCTTTTACAAGTTACCTTCAACAATTTTACAAAGCAATGCTTGTGGGCTAGGCACCGCGTTTTGAAGTAAATAGATGTAACCTACCACCCATAAACTGCTCTAACAATTTAAGTTCGTCGTCGCCTTCTTTTTATATCACTAACGATGTACCTACCTTAGAGCGTTACCAAAGTACATATACAGATTTCTCAATGTATTTGACCTGGCTCTCTGCAATCTCTCTCAAGATGCGTAAGCACTTTCAGTAGGACGAATTTACGGTGGTAATTTCGCACACTTCGCACGT [...]
+ +
+ EjH[>GM/a\Y_\`o[K[hFHGMi\$ha]SUX`hiaYTU[cdeikibZTQQ[WQTJX/9NZ\Kj[F`8gm]>T>LIn\V]Jo>tK[^HeKo\l^/qj\T9jFL9_,eD<{l\`\lKlJLmLm[k\lNnL at f+kF?k[iEMI48AUV7Pl\>jbHIMKLJ:lmnnm\L?k-^XX?Z7iZ.c[\Kj]^l`Npl^YDOm\jKGAlZ5R2dfkh]^k;E\lKmMmYLd[[k-ZjdP\QnmK\_oI6[0F<]8jl]^k+tK\CcIGH2]:IH_mKZA^m^jIW\J^:lJm^lMoXDpo\;Qjm\^J\[S[Ll[9?+jbPcI>kXF\[;_VL4\'b?,_ccb_VKVPFLMS`UD'ECB_HcSFFN6\]1I2?EId`>P6aJ9EJQZ2O2J>K?5(IIRUSVbS?R^:dYDdAeN*kSUSQ>F at TRPRPPP@K=>UbDdUDADTUa2R`S>C6>Z/NX9odTC3a2_DU at 5N@5]R at a-_]SCRN>\QIcP?@[SD4 [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3151/ccs/fwd np:i:10 rq:f:0.998931
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCT [...]
+ +
+ ~~n~~~~x~~~~vO~~cvr~~v~u~_~~~~z~y~vf~~~x~~~w~{~~~~q~q~k~~X~~~rv@~~x~~~r~~~~u~c~vX~~\~~~~~~j~~r~~w~~~<~~~~A~~~~x~y~x~y~~~~zb~~f~~~~v~~~x~x~:~~k~~~v~G~~t~2~~~~~^~{z~~a~~~~s~y~~~{q~~~~~~r~z~w~~~~~~~~U~~~x~f~~c~~`w~~v\~~~~~a~~~~~~~~~v~~u~~x~~`~~~~~a~v~~~f~}t~R~~~~Jp~A~+~~~w~~~~~~yz~~h~~f~~L~~N~C~~~G~~~c~~c~f~~~~u~~@~i~~~~~~q~~~~~~_~~~~|a~~d~~D~~~g~~'~~~~~~x~b~`v~U~~~x~~w]w~s~~~|~O~~~~~y~~~x~~~~~~e~~~~~~G~~~~~tx~~~~~~~c~W~~~S~~f~~I~~~~{~X~~~d~~~u~~~f~-~~~~e{~~1~~~~z~p~~nz~|~~~~~~~~u~q~~~~t~ [...]
+ @m150825_055401_42161_c100844482550000001823159012311525_s1_p0/3151/ccs/rev np:i:11 rq:f:0.999437
+ AAGCAGTGGTATCAACGCAGAGTACGGGGTGAGGCTTGTCCGCGAGTGTCAACCGGGTTTTACAAAGGAGAACTTCCAACATCAGTGTATGGGATGTTTCAAACACCCCCAGAGACGGAGACAATAGTGTGGTCACGTACATTTAGGAAGATAAAAATAACAACAACAGAAGGTACAAGAGTTGGTTACTCTCAGTCCCATTCCCAACACATCACTGAGAAGTATAGAGCCTAGTGGTCATTAGAAGGTCAACATGGAGTAGGTGTTTAGGTGTGTCGGAGGGCAGAAACCAACGAAAGAAAGGAAACGATCAACACTTATATAGTGTCCTGTCGGGCCCAAATCCTAAGAGACCTTAGGTTTACCACATTAGTACTAAACAGCCTGTTGTATACCGTGAGCCCCCACTTCGATCTGTAAATTGGTAATCCCTTGTAAAACCTCATCTCCAAAAACAGTATACGCAGGTACAGCTGATGTGATCCTCTCT [...]
+ +
+ x~vy~~uc~~~~~y~~~c~~~~~~~J~~oe~~s~~Z~v~S~~|~~~~~I~c~e~[~~9~~~~~x~~a~~~~~|v~t~r~~~~y~|{|~~~T~~~~~M~~~>~~~~J~~~~~~~~z~h~~|~~~~~~~~~s^~~~~~~J~~~;~~~c~g~~~[P~~~~~E~NT~~?~~~~x~f~~~~s~~~y>~Q~g~~|~~a~~~~\~~~t~g~~L~L~~~~~~~{~~~~~~~~r~|~~y~~~~~s~~~~K~~~~~d~_~g~~~~f~o~p~d~~~X~~~d~~~~~r~Q~~N~v|~{N~~w~~~~~P~~~y~~t~Q~~~~~~bt~~~~q~~r~p~~~~~v~~~t~E~~T~~;~r_w~~p~~~~~v~q~~d~[~~oO~~~~}~~~En~~k~~~~~y~~~q~ws~~~i~~u~~~K~~~~~~a~~~~~ypx~u~~5~w~km~oa~~d~~~I~~~t~F~~~~~c~N~~~~~~y~kjo~~~~i~~~~\y~~n~~t~~~So~~~~~d [...]
diff --git a/tests/cram/43385286.t b/tests/cram/43385286.t
new file mode 100644
index 0000000..4b07488
--- /dev/null
+++ b/tests/cram/43385286.t
@@ -0,0 +1,8 @@
+Test a tiny collection of a few ZMWs, write to FASTQ for inspection
+
+ $ $__PBTEST_CCS_EXE --minReadScore=0 --minSnr=0 --minZScore=nan $TESTDIR/../data/43385286.bam 43385286.fq
+ $ cat 43385286.fq
+ @m54016_160202_014733/43385286/ccs np:i:7 rq:f:0.993967
+ GGCCGGAGCTTCCTGAGTGGAGAGCCGAGCCAGGCAGACGTGCAGCCACTGGGCCCCAGCAGCCTGGCGGTGCACACTATTCTGCCCCAGGAGAGCCCCGCCCTGCCCACGTCGCTGCCATCCTCGCTGGTCCCACCCGTGACCGCAGCCCAGTT
+ +
+ =`_|OyeYlMdLzhgW_]@tXVb.MU[]6>?KTg`jjlV4+0KLhXrTf^3^BK^[fhjWaj_}LJuiVajgb^IO^T8+\hY^@pqm_YvWSf%9clWg<hY;LEg^W>-8`RXG?UbeWOlIN_fR,OU7_?HF_qiljj[ghERPC]a`V/b
diff --git a/tests/cram/nozfilter.t b/tests/cram/nozfilter.t
new file mode 100644
index 0000000..a85fa88
--- /dev/null
+++ b/tests/cram/nozfilter.t
@@ -0,0 +1,8 @@
+Test to ensure the Z filtering can be disabled, the NaN parsing appears a bit finicky on some platforms
+
+ $ $__PBTEST_CCS_EXE --zmws=111715 --minZScore=NaN $TESTDIR/../data/tiny.bam nofilter.fq
+ $ cat nofilter.fq
+ @m150404_101626_42267_c100807920800000001823174110291514_s1_p0/111715/ccs np:i:24 rq:f:0.99999
+ GCGTCGGATCGCCAACAACATGCCGGAACAGTACGACGAAAAGCCGCAGGTACAGCAGGTAGCGCAGATCATCAACGGTGTGTTCAGCCAGTTACTGGCAACTTTCCCGGCGAGCCTGGCTAACCGTGACCAGAACGAAGTGAACGAAATCCGTCGCCAGTGGGTTCTGGCTTTTCGGGAAAACGGGATCACCACGATGGAACAGGTTAACGCAGGAATGCGCGTAGCCCGTCGGCAGAATCGACCATTTCTGCCATCACCCGGGCAGTTTGTTGCATGGTGCCGGGAAGAAGCATCCGTTACCGCCGGACTGCCAAACGTCAGCGAGCTGGTTGATATGGTTTACGAGTATTGCCGGAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCA [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~u~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~}~~~~6~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~z~~~~~u~~~~~~~~~~~~~~~u~~~~~~~~~~~~~~~~~~~~m~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~ [...]
diff --git a/tests/cram/tiny.t b/tests/cram/tiny.t
new file mode 100644
index 0000000..a997a8d
--- /dev/null
+++ b/tests/cram/tiny.t
@@ -0,0 +1,28 @@
+Test a tiny collection of a few ZMWs, write to FASTQ for inspection
+
+ $ $__PBTEST_CCS_EXE $TESTDIR/../data/tiny.bam tiny.fq
+ $ cat tiny.fq
+ @m150404_101626_42267_c100807920800000001823174110291514_s1_p0/109097/ccs np:i:22 rq:f:0.99949
+ CATGTACCGGATGTGTTCTGCCATGCGCTCCTGAAACTCAACATCGTCATCAAACGCACGGGTAATGGATTTTTTGCTGGCCCCGTGGCGTTGCAAATGATCGATGCATAGCGATTCAAACAGGTGCTGGGGCAGGCCTTTTTCCATGTCGTCTGCCAGTTCTGCCTCTTTCTCTTCACGGGCGAGCTGCTGGTAGTGACGCGCCCAGCTCTGAGCCTCAAGACGATCCTGAATGTAATAAGCGTTCATGGCTGAACTCCTGAAATAGCTGTGAAAATATCGCCCGCGAAATGCCGGGCTGATTAGGAAAACAGGAAAGGGGGTTAGTGAATGCTTTTGCTTGATCTCAGTTTCAGTATTAATATCCATTTTTTATAAGCGTCGACGGCTTCACGAAACATCTTTTCATCGCCAATAAAAGTGGCGATAGTGAATTTAGTCTGGATAGCCATAAGTGTTTGATCCATTCTTTGGGACTCCTGGCTGATTA [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~U~~~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~6~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150404_101626_42267_c100807920800000001823174110291514_s1_p0/109700/ccs np:i:18 rq:f:0.999452
+ GCGTGCTTGTGGTGGGTAACCGTCGTATTCCCGGCGCGTTTATTCAGCAACTGAAAAATGGCCGGTGGCATGTCATGCAGCGTGTGGCTGGGAAAAACCGTTACCCCATTGATGTGGTGAAAATCCCGATGGCGGTGCCGCTGACCACGGCGTTTAAACAAAATATTGAGCGGATACGGCGTGAACGTCTTCCGAAAGAGCTGGGCTATGCGCTGCAGCATCAACTGAGGATGGTAATAAAGCGATGAAACATACTGAACTCCGTGCAGCCGTACTGGATGCACTGGAGAAGCATGACACCGGGGCGACGTTTTTTGATGGTCGCCCCGCTGTTTTTGATGAGGCGGATTTTCCGGCAGTTGCCGTTTATCTCACCGGCGCTGAATACACGGGCGAAGAGCTGGACAGCGATACCTGGCAGGCGGAGCTGCATATCGAAGTTTTCCTGCCTGCTCAGGTGCCGGATTCAGAGCTGGATGCGTGGATGGAG [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~{~~~~:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~2~~~~~~~~~~m~~~~~~~~~~~~~~~d~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~u~~~~~~~~%~~~~~~~~~~~~~a~~~~~~~3~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150404_101626_42267_c100807920800000001823174110291514_s1_p0/110513/ccs np:i:25 rq:f:0.999989
+ AAAACTGTACGATAAACGGTACGCTGAGGGCGGAAAAAATCGTCGGGGACATTGTAAAGGCGGCGAGCGCGGCTTTTCCGCGCCAGCGTGAAAGCAGTGTGGACTGGCCGTCAGGTACCCGTACTGTCACCGTGACCGATGACCATCCTTTTGATCGCCAGATAGTGGTGCTTCCGCTGACGTTTCGCGGAAGTAAGCGTACTGTCAGCGGCAGGACAACGTATTCGATGTGTTATCTGAAAGTACTGATGAACGGTGCGGTGATTTATGATGGCGCGGCGAACGAGGCGGTACAGGTGTTCTCCCGTATTGTTGACATGCCAGCGGGTCGGGGAAACGTGATCCTGACGTTCACGCTTACGTCCACACGGCATTCGGCAGATATTCCGCCGTATACGTTTGCCAGCGATGTGCAGGTTATGGTGATTAAGAAACAGGCGCTGGGCATCAGCGTGGTCTGAGTGTGTTACAGAGGTTCGTCCGGGAACGG [...]
+ +
+ J~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~R~~~~~~~~~~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~6~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~u~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150404_101626_42267_c100807920800000001823174110291514_s1_p0/111500/ccs np:i:26 rq:f:0.999802
+ TATCCAGACTAAATTCACTATCGCCACTTTTATTGGCGATGAAAAGATGTTTCGTGAAGCCGTCGACGCTTATAAAAAATGGATATTAATACTGAAACTGAGATCAAGCAAAAGCATTCACTAACCCCCTTTCCTGTTTTCCTAATCAGCCCGGCATTTCGCGGGCGATATTTTCACAGCTATTTCAGGAGTTCAGCCATGAACGCTTATTACATTCAGGATCGTCTTGAGGCTCAGAGCTGGGCGCGTCACTACCAGCAGCTCGCCCGTGAAGAGAAAGAGGCAGAACTGGCAGACGACATGGAAAAAGGCCTGCCCAGCACCTGTTTGAATCGCTATGCATCGATCATTTGCAACGCCACGGGGCCAGCAAAAAATCCATTACCCGTGCGTTTGATGACGATGTTGAGTTTCAGGAGCGCATGGCAGAACACATCCGGTACATGGTTGAAACCATTGCTCACCACCAGGTTGATATTGATTCAGAGGT [...]
+ +
+ ~of~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~~~~w~~~~~~~~]~~~~~~v~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~9~~~~~~~~~~<~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~_~~~~~~~~-~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [...]
+ @m150404_101626_42267_c100807920800000001823174110291514_s1_p0/111715/ccs np:i:24 rq:f:0.999951
+ GCGTCGGATCGCCAACAACATGCCGGAACAGTACGACGAAAAGCCGCAGGTACAGCAGGTAGCGCAGATCATCAACGGTGTGTTCAGCCAGTTACTGGCAACTTTCCCGGCGAGCCTGGCTAACCGTGACCAGAACGAAGTGAACGAAATCCGTCGCCAGTGGGTTCTGGCTTTTCGGGAAAACGGGATCACCACGATGGAACAGGTTAACGCAGGAATGCGCGTAGCCCGTCGGCAGAATCGACCATTTCTGCCATCACCCGGGCAGTTTGTTGCATGGTGCCGGGAAGAAGCATCCGTTACCGCCGGACTGCCAAACGTCAGCGAGCTGGTTGATATGGTTTACGAGTATTGCCGGAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCA [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~u~~~~/~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~z~~~~~u~~~~~~~~~~~~~~~u~~~~~~~~~~~~~~~~~~~~m~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~~ [...]
+ @m150404_101626_42267_c100807920800000001823174110291514_s1_p0/112044/ccs np:i:30 rq:f:0.999999
+ ATATCATTTTACGTTTCTCGTTCAGCTTTTTTATACTAAGTTGGCATTATAAAAAAGCATTGCTTATCAATTTGTTGCAACGAACAGGTCACTATCAGTCAAAATAAAATCATTATTTGATTTCAATTTTGTCCCACTCCCTGCCTCTGTCATCACGATACTGTGATGCCATGGTGTCCGACTTATGCCCGAGAAGATGTTGAGCAAACTTATCGCTTATCTGCTTCTCATAGAGTCTTGCAGACAAACTGCGCAACTCGTGAAAGGTAGGCGGATCCCCTTCGAAGGAAAGACCTGATGCTTTTCGTGCGCGCATAAAATACCTTGATACTGTGCCGGATGAAAGCGGTTCGCGACGAGTAGATGCAATTATGGTTTCTCCGCCAAGAATCTCTTTGCATTTATCAAGTGTTTCCTTCATTGATATTCCGAGAGCATCAATATGCAATGCTGTTGGGATGGCAATTTTTACGCCTGTTTTGCTTTGCTC [...]
+ +
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~B~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~J~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~~H~~~~~~~~~~~~~~~~~~~~~~~~ [...]
diff --git a/tests/data/0passes.bam b/tests/data/0passes.bam
new file mode 100644
index 0000000..476dc7b
Binary files /dev/null and b/tests/data/0passes.bam differ
diff --git a/tests/data/100zmws.bam b/tests/data/100zmws.bam
new file mode 100644
index 0000000..7e9aed9
Binary files /dev/null and b/tests/data/100zmws.bam differ
diff --git a/tests/data/43385286.bam b/tests/data/43385286.bam
new file mode 100644
index 0000000..e5a8677
Binary files /dev/null and b/tests/data/43385286.bam differ
diff --git a/tests/data/Malformed.json b/tests/data/Malformed.json
new file mode 100644
index 0000000..e69de29
diff --git a/tests/data/chimera_extensive.fasta b/tests/data/chimera_extensive.fasta
new file mode 100644
index 0000000..ff33fc9
--- /dev/null
+++ b/tests/data/chimera_extensive.fasta
@@ -0,0 +1,503 @@
+>Barcode0_Cluster1_Phase0_NumReads476
+TGGCCAAGACTCAGGGAGACATTGAGACAGAGCGCTTGGCACAGGAGCAGAGGGGTCAGGGCGAAGTCCC
+AGGGCCCCAGGCGTGGCTCTCAGGGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTT
+GGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTATGTAGGGTCCTTCTTCCTGGATAC
+TCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGC
+GGTCGCGGTTCTAAAGTCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTC
+ATGGCGCCCCGAACCCTCGTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGT
+GCGGGGTCGGGAGGGAAACGGCCTCTGTGGGGAGAAGCAAGGGGCCCGCCCGGCGGGGGCGCAGGACCCG
+GGAAGCCGCGCCTGGAGGAGGGTCGGGCGGGTCTCAGCCACTCCTCGCCCCCAGGCTCCCACTCCATGAG
+GTATTTCTACACCTCCATGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGAC
+GACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAG
+AGCAGGAGGGGCCGGAGTATTGGGACCGGAACACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGT
+GGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCCGGGGCGCAG
+GTCACGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCGCCCCGAA
+GCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTA
+GGCCAAAAATCCCCCCGGGTTGGTCGGGGCGGGGCGGGGCTCGGGGGACCGGGCTGACCTCGGGGTCCGG
+GCCAGGTTCTCACACCATCCAGAGGATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGG
+TACCACCAGTACGCCTACGACGGCAAGGATTACATCGCCCTGAAAGAGGACCTGCGCTCTTGGACCGCGG
+CGGACATGGCAGCTCAGACCACCAAGCACAAGTGGGAGGCGGCCCATGTGGCGGAGCAGTGGAGAGCCTA
+CCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACG
+GGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTGTAGATCTCCCGGGCTGGCCTCCCACAAGGAGGG
+GAGACAATTGGGACCAACACTAGAATATCGCCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGGTT
+TCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAATC
+TCTGAAGGAATGACGGGAAGACGATCCCTCGAATACTGATGAGTGGTTCCCTTTGACACACACAGGCAGC
+AGCCTTGGGCCCGTGACTTTTCCTCTCAGGCCTTGTTCTCTGCTTCACACTCAATGTGTGTGGGGGTCTG
+AGTCCAGCACTTCTGAGTCCCTCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCCTCTTCAGGG
+ACTAGAATTTTCCACGGAATAGGAGATTATCCCAGGTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGC
+TCCCTTCCCCATCCCAGGTGTCCTGTCCATTCTCAAGATAGCCACATGTGTGCTGGAGGAGTGTCCCATG
+ACAGATGCAAAATGCCTGAATGATCTGACTCTTCCTGACAGACGCCCCCAAAACGCATATGACTCACCAC
+GCTGTCTCTGACCATGAAGCCACCCTGAGGTGCTGGGCCCTGAGCTTCTACCCTGCGGAGATCACACTGA
+CCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGG
+AACCTTCCAGAAGTGGGTGGCTGTGGTGGTGCCTTCTGGACAGGAGCAGAGATACACCTGCCATGTGCAG
+CATGAGGGTTTGCCCAAGCCCCTCACCCTGAGATGGGGTAAGGAGGGAGACGGGGGTGTCATGTCTTTTA
+GGGAAAGCAGGAGCCTCTCTGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTTTTCCCAGAGCC
+GTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCTTTGGAGCTGTGATCACT
+GGAGCTGTGGTCGCTGCTGTGATGTGGAGGAGGAAGAGCTCAGGTGGGGAAGGGGTGAAGGGTGGGTCTG
+AGATTTCTTGTCTCACTGAGGGTTCCAAGACCCAGGTAGAAGTGTGCCCTGCCTCGTTACTGGGAAGCAC
+CACCCACAATTATGGGCCTACCCAGCCTGGGCCCTGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGT
+TAAAATGAAGGACAGATTTATCACCTTGATTACAGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCA
+CAGGGGAAGGTCCCTGAGGACCTTCAGGAGGGCGGTTGGTCCAGGACCCACACCTGCTTTCTTCATGTTT
+CCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGAGGTCCAAGACTTGGAGGTTC
+CTCTAGGACCTTAAGGCCCTGACTCCTTTCTGGTATCTCACAGGACATTTTCTTCCCACAGATAGAAAAG
+GAGGGAGCTACTCTCAGGCTGCAAGTAAGTATGAAGGAGGCTGATGCCTGAGGTCCTTGGGATATTGTGT
+TTGGGAGCCCATGGGGGAGCTCACCCACCCCACAATTCCTCCTCTAGCCACATCTTCTGTGGGATCTGAC
+CAGGTTCTGTTTTTGTTCTACCCCAGGCAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGT
+AAAGGTGAGAGCCTGGAGGGCCTGATGTGTGTTGGGTGTTGGGCGGAACAGTGGACACAGCTGTGCTATG
+GGGTTTCTTTCCATTGGATGTATTGAGCATGCGATGGGCTGTTTAAAGTGTGACCCCTCACTGTGACAGA
+TACGAATTTGTTCATGAATATTTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTGGGACTGAGAGGCAAG
+AGTTGTTCCTGCCCTTCCCTTTGTGACTTGAAGAACCCTGACTTTGTTTCTGCAAAGGCACCTGCATGTG
+TCTGTGTTCGTGTAGGCATAATGTGAGGAGGTGGGGAGACCACCCCACCCCCATGTCCACCATGACCCTC
+TTCCCACGCTGACCTGTGCTCCCTCCCCAA
+>Barcode0_Cluster0_Phase3_NumReads344
+TCAGGCACACAGTGTGACAAAGATGCTTGGTGTAGGAGAAGAGGGATCAGGACGAAGTCCCAGGTCCCGG
+GCGGGGCTCTCAGGGTCTCAGGCTCCAAGGGCCGTGTCTGCACTGGGGAGGCGCCGCGTTGAGGATTCTC
+CACTCCCCTGAGTTTCACTTCTTCTTCCAACCTGCGTCGGGTCCTTCTTCCTGAATACTCATGACGCGTC
+CCCAATTCCCACTCCCATTGGGTGTCGGGTTCTAGAGAAGCCAATCAGCGTCTCCGCAGTCCCGGTTCTA
+AAGTCCCCAGTCACCCACCCGGACTCGGATTCTCCCCAGACGCCGAGATGCGGGTCATGGCGCCCCGAAC
+CCTCATCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCTGGGCCTGTGAGTGCGAGGTTGGGAGG
+GAAACGGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGGAGCCGCGCAGG
+GAGGAGGGTCGGGCGGGTCTCAGCCCCTCCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTACACCG
+CCGTGTCCCGGCCCGGCCGCGGAGAGCCCCGCTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGT
+GCAGTTCGACAGCGACGCCGCGAGTCCAAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCG
+GAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGGAACC
+TGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCCCTCC
+CCATCCCCCACGGACGGCCCGGGTCGCCCCGAGTCTCCCGGTCTGAGATCCACCCCGAGGCTGCGGAACC
+CGCCCAGACCCTCGACCGGAGAGAGCCCCAGTCACCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAT
+CCCCGCGGGTTGGTCGGGGCTGGGGCGGGGCTCGGGGGACGGGGCTGACCACGGGGGCGGGGCCAGGGTC
+TCACACCCTCCAGAGGATGTATGGCTGCGACCTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATAACCAG
+TTCGCCTACGACGGCAAGGATTACATCGCCCTGAATGAGGACCTGCGCTCCTGGACCGCCGCGGACAAGG
+CGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCGGAGAGCCTACCTGGAGGG
+CACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGAAGACGCTGCAGCGCGCGGGTACCAGG
+GGCAGTGGGGAGCCTTCCCCATCTCCTGTAGATCTCCCGGGATGGCCTCCCACGAGGAGGGGAGGAAAAT
+GGGATCAGCGCTGGAATATCGCCCTCCCTTGAATGGAGAATGGGATGAGTTTTCCTGAGTTTCTTCTGAG
+GGCCCCCTCTGCTCTCTAGGACAATTAAGGGATGAAGTCCTTGAGGAAATGGAGGGGAAGACAGTCCCTG
+GAATACTGATCAGGGGTCCCCTTTGACCACTTTGACCACTGCAGCAGCTGTGGTCAGGCTGCTGACCTTT
+CTCTCAGGCCTTGTTCTCTGCCTCACGCTCAATGTGTTTAAAGGTTTGATTCCAACTTTTCTGAGTCCTT
+CGGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCTCCCTCAGAGACTAGAACTTTCCAATGAATAG
+GAGATTATCCCAGGTGCCTGTGTCCAGGCTGGCGTCTGGGTTCTGTGCCCCCTTCCCCACCCCAGGTGTC
+CTGTCCATTCTCAGGATGGTCACATGGGCACTGTTGGAGTGTCGCAAGAGAGATACAAAGTGTCTGAATT
+TTCTGACTCTTCCCGTCAGAACACCCAAAGACACACGTGACCCACCATCCCGTCTCTGACCATGAGGCCA
+CCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGCGAGGA
+CCAAACTCAGGACACCGAGCTTGTGGAGACCAGGCCAGCAGGAGATGGAACCTTCCAGAAGTGGGCAGCT
+GTGGTGGTGCCTTCTGGAGAAGAGCAGAGATACACGTGCCATGTGCAGCACGAGGGGCTGCCAGAGCCCC
+TCACCCTGAGATGGGGTAAGGAGGGGGATGAGGGGTCATGTGTCTTCTCAGGGAAAGCAGAAGTCCTGGA
+GCCCTTCAGCCGGGTCAGGGCTGAGGCTTGGGGGTCAGGGCCCCTCACCTTCCCCTCCTTTCCCAGGGCC
+ATCTTCCCAGCCCACCATCCCCATCGTGGGCATCGTTGCTGGCCTGGCTGTCCTGGCTGTCCTAGCTGTC
+CTAGGAGCTGTGATGGCTGTTGTGATGTGTAGGAGGAAGAGCTCAGGTAGGGAAGGGGTGAGGAGTGGGG
+TCTGGGTTTTCTTGTCCCACTGGGAGTTTCAAGCCCCAGGTAGAAGTGTGCCCCACCTCGTTACTGGAAG
+CACCATCCACACATGGGCCATCCCAGCCTGGGACCCTGTGTGCTAGCACTTACTCTGTTGTGAAGCACAT
+GACAATGAAGGACAGATGTATCACCTTGATGATTATGGTGTTGGGGTCCTTGATTCCAGCATTCATGAGT
+CAGGGGAAGGTCCCTGCTAAGGACAGACCTTAGGAGGGCAGTTGCTCCAGAACCCACAGCTGCTTTCCCC
+GTGTTTCCTGATCCTGCCCTGGGTCTGCAGTCATAGTTCTGGAAACTTCTCTTGGGTCCAAGACTAGGAG
+GTTCCCCTAAGATCGCATGGCCCTGCCTCCTCCCTGTCCCCTCACAGGGCATTTTCTTCCCACAGGTGGA
+AAAGGAGGGAGCTGCTCTCAGGCTGCGTGTAAGTGATGGCGGTGGGCGTGTGGAGGAGCTCACCCACCCC
+ATAATTCCTCTTGTCCCACATCTCCTGCGGGCTCTGACCAGGTCTTTTTTTTTGTTCTACCCCAGCCAGC
+AACAGTGCCCAGGGCTCTGATGAGTCTCTCATCGCTTGTAAAGGTGAGATTCTGGGGAGCTGAAGTGGTC
+GGGGGTGGGGCAGAGGGAAAAGGCCTAGGTAATGGGGATCCTTTGATTGGGACGTTTCGAATGTGTGGTG
+AGCTGTTCAGAGTGTCATCACTTACCATGACTGACCTGAATTTGTTCATGACTATTGTGTTCTGTAGCCT
+GAGACAGCTGCCTGTGTGGGACTGAGATGCAGGATTTCTTCACACCTTTCCTTTGTGACTTCAAGAGCCT
+CTGGCATCTCTTTCTGCAAAGGCATCTGAATGTGTCTGCGTTCCTGTTAGCATAATGTGAGGAGGTGGAG
+AGACAGCCCACCCCCGTGTCCACCGTGACCCCTGTCCCACACTGACCTGTGTTCCCTCCCCC
+>Barcode0_Cluster2_Phase3_NumReads285
+TCAGGCACACAGTGTGACAAAGATGCTTGGTGTAGGAGAAGAGGAATCAGGACGAAGTCCCAGGTCCCGG
+GCGGGGCTCTCAGGGTCTCAGGCTCCAAGGGCCGTGTCTGCACTGGGGAGGCGCCGCGTTGAGGATTCTC
+CACTCCCCTGAGTTTCACTTCTTCTCCCAACCTGCGTCGGGTCCTTCTTCCTGAATACTCATGACGCGTC
+CCCAATTCCCACTCCCATTGGGTGTCGGATTCTAGAGAAGCCAATCAGCGTCTCCGCAGTCCCGGTTCTG
+AAGTCCCCAGTCACCCACCCGGACTCAGATTCTCCCCAGACGCCGAGATGCGGGTCATGGCGCCCCGAAC
+CCTCATCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCTGGGCCGGTGAGTGCGGGGTTGGGAGG
+GAATCGGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGGAGCCGCGCAGG
+GAGGAGGGTCGGGCGGGTCTCAGCCCCTCCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTACACCG
+CTGTGTCCCGGCCCGGCCGCGGGGAGCCCCACTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGT
+GCGGTTCGACAGCGACGCCGCGAGTCCGAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCG
+GAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGGAACC
+TGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCCCTCC
+TCATCCCCCACGGACGGCCCGGGTCGCCCCAAGTCTCCCGGTCTGAGATCCACCCCGAGGCTGCGGAACC
+CGCCCAGACCCTCGACCGGAGAGAGCCCCAGTCACCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAT
+CCCCGCGGGTTGGTCGGGGCGGGGCGGGGCTCGGGGGACGGGGCTGACCGCGGGGGCGGGGCCAGGGTCT
+CACATCATCCAGAGGATGTACGGCTGCGACGTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGT
+ACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGATCTGCGCTCCTGGACCGCCGCGGACACGGC
+GGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCTGAGAGCCTACCTGGAGGGC
+CTGTGCGTGGAGTGGCTCCGCAGATACCTGAAGAATGGGAAGGAGACGCTGCAGCGCGCGGGTACCAGGG
+GCAGTGGGGAGCCTTCCCCATCTCCTGTAGATCTCCCGGGATGGCCTCCCACGAGGAGGGGAGGAAAATG
+GGATCAGCGCTAGAATATCGCCCTCCCTTGAATGGAGAATGGGATGAGTTTTCCTGAGTTTCCTCTGAGG
+GCCCCCTCTGCTCTCTAGGACAATTAAGGGATGAAGTCCTTGAGGAAATGGAGGGGAAGACAGTCCCTAG
+AATACTGATCAGGGGTCCCCTTTGACCACTTTGACCACTGCAGCAGCTGTGGTCAGGCTGCTGACCTTTC
+TCTCAGGCCTTGTTCTCTGCCTCACGCTCAATGTGTTTGAAGGTTTGATTCCAGCTTTTCTGAGTCCTTC
+GGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCTCCCTCAGAGACTAGAACTTTCCAATGAATAGG
+AGATTATCCCAGGTGCCTGTGTCCAGGCTGGCGTCTGGGTTCTGTGCCCCCTTCCCCACCCCAGGTGTCC
+TGTCCGTTCTCAGGATGGTCACATGGGCGCTGTTGGAGTGTCGCAAGAGAGATACAAAGTGTCTGAATTT
+TCTGACTCTTCCCGTCAGAACACCCAAAGACACACGTGACCCACCATCCCGTCTCTGACCATGAGGCCAC
+CCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGTGGGATGGGGAGGAC
+CAAACTCAGGACACTGAGCTTGTGGAGACCAGGCCAGCAGGAGATGGAACCTTCCAGAAGTGGGCAGCTG
+TGGTGGTGCCTTCTGGAGAAGAGCAGAGATACACGTGCCATGTGCAGCACGAGGGGCTGCCGGAGCCCCT
+CACCCTGAGATGGGGTAAGGAGGGGGATGAGGGGTCATATCTGTTCTCAGGGAAAGCAGGAGCCCTTCTG
+GAGCCCTTCAGCAGGGTCAGGGCCCCTCACCTTCCCCTCCTTTCCCAGAGCCGTCTTCCCAGCCCACCAT
+CCCCATCGTGGGCATCGTTGCTGGCCTGGCTGTCCTGGCTGTCCTAGCTGTCCTAGGAGCTGTGGTGGCT
+GTTGTGATGTGTAGGAGGAAGAGCTCAGGTAGGGAAGGGGTGAGGAGTGGGGTCTGGGTTTTCTTGTTCC
+ACTGGGAGTTTCAAGCCCCAGGTAGAAGTGTGCCCCACCTCGTTACTGGAAGCACCATCCACACATGGGC
+CATCCCAGCCTGGGACCCTGTGTGCCAGCACTTACTCTGTTGTGAAGCACATGACAATGAAGGACAGATG
+TATCACCTTGATGATTATGGTGTTGGGGTCCTTGATTCCAGCATTCATGAGTCAGGGGAAGGTCCCTGCT
+AAGGACAGACCTTAGGAGGGCAGTTGCTCCAGAACCCACAGCTGCTTTCCCCGTGTTTCCTGATCCTGCC
+CTGGGTCTGCAGTCATAGTTCTGGAAACTTCTCTTGGGTCCAAGACTAGGAGGTTCCCCTAAGATCGCAT
+GGCCCTGACTCCTCCCTGTCCCCTCACAGGGCATTTTCTTCCCACAGGTGGAAAAGGAGGGAGCTGCTCT
+CAGGCTGCGTGTAAGTGATGGCGGTGGGCGTGTGGAGGAGCTCACCCACCCCATAATTCCTCTTGTCCCA
+CATCTCCTGCGGGCTCTGACCAGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCTCT
+GATGAGTCTCTCATCGCTTGTAAAGGTGAGATTCTGGGGAGCTGAAGTGGTCGGGGGTGGGGCAGAGGGA
+AAAGGCCTAGGTAATGGGGATCCTTTGATTGGGACGTTTCGAATGTGTGGTGAGCTGTTCAGAGTGTGAT
+CACTTACCATGACTGACCTGAATTTGTTCATGACTATTGTGTTCTGTAGCCTGAGACAGCTGCCTGTGTG
+GGACTGAGATGCAGGATTTCTTCACACCTCTCCTTTGTGACTTCAAGAGCCTCTGGCATCTCTTTCTGCA
+AAGGCATCTGAATGTGTCTGCGTTCCTGTTAGCATAATGTGAGGAGGTGGACAGACAGCCCACCCCCGTG
+TCCACCGTGACCCCTGTCCCACACTGACCTGTGTTCCCTCCCC
+>Barcode0_Cluster3_Phase1_NumReads185
+CCGCAAGCTTCTGGGGAGGAAACACAGGTCAGCATGGGAACAGGGGTCACAGTGGACACAAGGGTGGGCT
+GTCTCTCCACCTCCTCACATTATGCTAACAGGGACGCAGACACATTCAGGTGCCTTTGCAGAAAGAGATG
+CCAGAGGCTCTTGAAGTCACAAAGGGGAGGCGTGAAGAAATCCTGCATCTCAGTCCCTCACAAGACAGCT
+GTCTCAGGCTACAGAAAACAACAGTCATGAACAAATTCTGGTTAGTCATGGTAAGTGATGACACTCTGAA
+CAGCCCACGACACACGCGAAACATCCCAATCAAAGAATCTCCATTACCCAGGCCTTTCCCCACTGCCCCA
+CCCACCCCCAGACCCGCCACCCCACCCACTCTAGACCCCAAGAATCTCACCTTTTCAAGCTGTGAGAGAC
+ACATCAGAGCCCTGGGCACTGTCGCTGGCTGGAGTAGAACAAAAACAGGACCTGGTCAGAGCCCGCAGGA
+GACGTGGGACAGGAGGAATTATGGGGTGGGTGAGCTCCTCCACACTCCCACCCCCACCACTTACACGCAG
+CCTGAGAGTAGCTCCCTCCTTTTCCACCTGTGGGAAGAAAATGTCCTGTGAGGGGACTGGGAGGAAGCAG
+GACCATGAGATCTTAGAGGAACCTCCTCGTCTTGGAACCAAAAGGAATTTCCAGAAGTATGACTACAGAC
+CCAGGGCAGGATCAGGAAACACGAGGAAAGCAAGTGTGGGTCCTGGACCAACTGCCCTCCTAAGGTCTGT
+CCTTAGCAGGGACCTTCCCCTGACTCATGAATGCTGGAATCAGGACCCCAACACCACAACCATCAAGGCG
+ATACATCTGTCCTTCATTGTCACATGTGCTGCACAAAAGAGTAAGTGCTGGCACACAGGGTCCCAGGCTG
+CGTTAGCCCCTGTGTGGATGCTGCTTCCCAGTAATGAGGCAGGGAACACTTCTACCTGGGGCTTGAAACC
+CCCAGTGGGACAAGAAAACCCAGACCCCACCCCTCACCCCTTCCCTACCTGAGCTCTTCCTCCTACACAT
+CACAGTAGCGACCACAGCTCCGATGACCACAACTGCTAGGACAGCCAGGCCAGCAACAATGCCCACGATG
+GGGATGGTGGACTGGGAAGATGGCTCTGGGAAAGGAGGGGAAGATGAGGGGCCCTGACCCTGCTGAAGGG
+CTCCAGAAGGGCTCCTGCTTTCCCTGAGAACAGATATGACCCCTCATCCCCCTCCTTACCCCATCTCAGG
+GTGAGGGGCTTCGGCAGCCCCTCATGCTGTACATGGCATGTGTATCTCTGCTCTTCTCCAGAAGGCACCA
+CCACAGCTGCCCACTTCTGGAAGGTTCTATCTCCTGCTGGTCTGGTCTCCACAAGCTCGGTGTCCTGAGT
+TTGGTCCTCGCCATCCCGCTGCCAGGTCAGTGTGATCTCCGCAGGGTAGAAGCCCAGGGCCCAGCACCTC
+AGGGTGGCCTCATGGTCAGAGATGGGGTGGTGGGTCACATGTGTCTTTGGGGGGTCTGATGGGAAGAGTC
+AGAAAATTCAGGCGCTTTGCATCTCTCATGGGACACCCTAGGACCACCCATGTGACCAGCCTGAGAATGG
+ACAGGACACCTGGGGTGGGGAAGGGGCACAGAACCCAGACACCAGCCTGGACGCAGGCACCTGGGATAAT
+CTCCTATTCATTGGAAAGTTCGAGTCTCTGAGCGGGGAACAGGGACTTCTGCTCCTGATCTGAGTGGAGG
+TAAAGTGACTCAGAAGTGCTGGAATCAGAGCCCCAAACACACTGAGTGTGAGGCAGAGAACAAGGCCTGA
+GAGGAAAAGTCACGGTTCCCAAGGCTGCTGCAGGGGTCAAAGGGGACCCCTGATCACTATCCTAGGGACT
+GTCTTCCCCTCCATTTCCTCAGAGACGTCATCCCTTAATTGTCCTAGAGAGAAGAGGGGGCCCTCAGAGG
+AAACTCAGGAAAACTCATGCCATTCTCCATTCAAGGGAGGGCGACATTCTAGCGCTGATCCCATTTTCCT
+CCTCTTCTCGTGGGAGGCCATCCCCGGCGACCTATAGGAGATGGGGAAGGCTCCCCACTGCCCCTGGTAC
+CCGCGCGCTGCAGCGTCTCCTTCCCGTTCTCCAGGTATCTGCGGAGCCACTCCACGCACAGGCCCTCCAG
+GTAGGCTCTCAGCTGCTCCGCCTCACGGGCCGCCTCCCACTTGCGCTGGGTGATCTGAGCCGCCGTGTCC
+GCCGCGGTCCAGGAGCTCAGGTCCTCGTTCAGGGCGATGTAATCCTTGCCGTCGTAGGCGTACTGGTCAT
+GCCCGCGGAGGAGGCGCCCGTCCGGCCCCACGTCGCAGCCGTACATCCTCTGGAGGGTGTGAGACCCTGG
+CCCAGGCCCCGCGGTCAGCCCCGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCC
+TCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTTTGGGCGGGTCCCGCG
+GCCTCAGGGGGGCGGATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGTACGTGGGGGATGGGGAGTC
+GTGACCTGCGCCCCAGGCCGGGGTCACTCACCGGCCTCGCTCTGGTTGTAGTAGCCGCGCAGGTTCCGCA
+GGCTCTCTCGGTAAGTCTGTGTGTTGGTCTTGCAGATCTGTGTGTTCCGGTCCCAATACTCCGGCCCCTC
+CTGCTCTATCCACGGCGCCCGCGGCTCCTCTCTCGGACTCGCGGCGTCGCTGTCGAACCTCACGAACTGC
+GTGTCGTCCACGTAGCCCACTGAGATGAAGCGGGGCTCCCCGCGGCCGGGCCGGGACATGGCGGTGTAGA
+AATACCTCATGGAGTGGGAGCCTGGGGGCGAGGAGGGGCTGAGACCCGCCCGACCCTCCTCCCGGCGCGG
+CTCCCCGGGTCCTGCGCCCCCGCCTGCGGTCCCCTCGCTCCTCCCCACAGAGGCCATTTCCCTGCCGACC
+CCGCACTCACCGGCCCAGGTCTCGGTCAGGGCCAGGGCTCCCGAGAGCAGCAGGAGGACGGTTCGGGGCG
+CCGTGACCCGCATCTCGGCGTCTGAGGAGATTTTGAGTCCGGGTGGGTGCGTGGGGACTTTAGAACTGGG
+ACCCCGGCGACACTGATTGGCTTCTCTAGACACCCGACACCCAATGGGAGTGGGAAATGGGGACGCGTCA
+CGAGTATCCTGGAAGAAGGACCCGACATAGGTTGGGAGAAGAAGTGAAACTCGTGGGAGTGGGGAATCCC
+CAACGCTGCGCCTCCCCAATGCAGACAAGGCTCTCGGAGCCTGAGACCCTGAGAGCCCCGTCCGGGACCT
+GGGACTTCGTCCTGATCCCTCTTCTCCTACACCAGCCTCTTTGTCACACTGTCTGCC
+>Barcode0_Cluster5_Phase0_NumReads158
+GGCAGACAGTGTGACAAAGAGGCTTGGTGTAGGAGAAGAGGGATCAGGACGAAGTCCCAGGTCCCGGACG
+GGGCTCTCAGGGTCTCAGGCTCCGAGGGCCGCGTCTGCAATGGGGAGGCGCAGCGTTGGGGATTCCCCAC
+TCCCCTGAGTTTCACTTCTTCTCCCAACTTGTGTCGGGTCCTTCTTCCAGGATACTCGTGACGCATCCCC
+ACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCAGCGTCGCCGGGGTCCCAGTTCTAAA
+GTCCCCACGCACCCACCCGGACTCAGAGTCTCCTCAGACGCCAAGATGCTGGTCATGGCGCCCCGAACCG
+TCCTCCTGCTGCTCTCGGCGGCCCTGGCCCTGACCGAGACCTGGGCCGGTGAGTGCGGGTCGGGAGGGAA
+ATGGCCTCTGCCGGGAGGAGCGAGGGGACCGCAGGCGGGGGCGCAGGACCTGAGGAGCCGCGCCGGGAGG
+AGGGTCGGGCGGGTTTCAGCCCCTCCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTACACCGCCGT
+GTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCTCAGTGGGCTACGTGGACGACACGCAGTTCGTGAGG
+TTCGACAGCGACGCCGCGAGTCCGAGAGAGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAAT
+ATTGGGACCGGAACACACAGATCTGCAAGACCAACACACAGACTGACCGAGAGAGCCTGCGGAACCTGCG
+CGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACTCCCCATCCC
+CCACGGACGGCCCGGGTCGCCCCGAGTCTCCGGGTCCGAGATCCGCCTCCCTGAGGCCGCGGGACCCGCC
+CAGACCCTCGACCGGCGAGAGCCCCAGGCGCGTTTACCCGGTTTCATTTTCAGTTGAGGCCAAAATCCCC
+GCGGGTTGGGCGGGGCGGGGCGGGGCTCGGGGGGACTGGGCTGACCGCGGGGGCGGGGCCAGGGTCTCAC
+ACCCTCCAGTGGATGTATGGCTGCGACGTGGGGCCGGACGGGCGCCTCCTCCGCGGGTATAACCAGTTCG
+CCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGAGCTCCTGGACCGCGGCGGACACCGCGGC
+TCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCGGAGAGCCTACCTGGAGGGCACG
+TGCGTGGAGTGGCTCCGCAGACACCTGGAGAACGGGAAGGAGACGCTGCAGCGCGCGGGTACCAGGGGCA
+GTGGGGAGCCTTCCCCATCTCCTATAGGTCGCCGGGGATGGCCTCCCACGAGAAGAAGAGGAAAATGGGA
+TCAGCGCTAGAATGTCGCCCTCCCTTGAATGGAGAATGGCATGAGTTTTCCTGAGTTTCCTCTGAGGGCC
+CCCTCTTCTCTCTAGGACAATTAAGGGATGACGTCTCTGAGGAAATGGAGGGGAAGACAGTCCCTAGAAT
+ACTGATCAGGGGTCCCCTTTGACCCCTGCAGCAGCCTTGGGAACCATGACTTTTCTTCTCAGGCCTTGTT
+CTCTGCCTCACACTCAGTGTGTTTGGGGCTCTGATTCCAGCACTTCTGAGTCACTTTACCTCCACTCAGA
+TCAGGAGCAGAAGTCTCTGTTCCCCGCTCAGAGACTCGAACTTTCCAATGAATAGATTATCCCAGGTGCC
+TGCGTCCAGGCTGGTGTCTGGGTTCTGTGTCCCTTCCCCACCCCAGGTGTCCTGTCCATTCTCAGGCTGG
+TCACATGGGTGGTCCTAGGGTGTCCCATGAGAGATGCAAAGCGCCTGAATTTTCTGACTCTTCCCATCAG
+ACCCCCCAAAGACACATGTGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCT
+GGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGCGAGGACCAAACTCAGGACACCGAG
+CTTGTGGAGACCAGACCAGCAGGAGACAGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGAG
+AAGAGCAGAGATACACATGCCATGTACAGCATGAGGGGCTGCCGAAGCCCCTCACCCTGAGATGGGGTAA
+GGAGGGGGATGAGGGGTCATATCTCTTCTCAGGGAAAGCAGGAGCCCTTCAGCAGGGTCAGGGCCCCTCA
+TCTTCCCCTCCTTTCCCAGAGCCATCTTCCCAGTCCACCGTCCCCATCGTGGGCATTGTTGCTGGCCTGG
+CTGTCCTAGCAGTTGTGGTCATCGGAGCTGTGGTCGCTGCTGTGATGTGTAGGAGGAAGAGTTCAGGTAG
+GGAAGGGGTGAGGGGTGGGGTCTGGGTTTTCTTGTCCCACTGGGGGTTTCAAGCCCCAGGTAGAAGTGTT
+CCCTGCATCATTACTGGGAAGCAGCATGCACACAGGGGCTAACGCAGCCTGGGACCCTGTGTGCCAGCAC
+TTACTCTTTTGTGCAGCACATGTGACAATGAAGGACGGATGTATCACCTTGATGGTTGTGGTGTTGGGGT
+CCTGATTCCAGCATTCATGAGTCAGGGGAAGGTCCCTGCTAAGGACAGACCTTAGGAGGGCAGTTGGTCC
+AGGACCCACACTTGCTTTCCTCGTGTTTCCTGATCCTGCCCTGGGTCTGTAGTCATACTTCTGGAAATTC
+CTTTTGGGTCCAAGACTAGGAGGTTCCTCTAAGATCTCATGGCCCTGCTTCCTCCCAGTCCCCTCACAGG
+ACATTTTCTTCCCACAGGTGGAAAAGGAGGGAGCTACTCTCAGGCTGCGTGTAAGTGGTGGGGGTGGGAG
+TGTGGAGGAGCTCACCCACCCCATAATTCCTCCTGTCCCACGTCTCCTGTGGGCTCTGACCAGGTCCTGT
+TTTTGTTCTACTCCAGCCAGCGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGAAAAGGTGAGA
+TTCTTGGGGTCTAGAGTGGGCGGGGGGGCGGGGAGGGGGCAGAGGGGAAAGGCCTGGGTAATGGAGATTC
+TTTGATTGGGATGTTTCGCGTGTGTGATGGGCTGTTCAGAGTGTCATCACTTACCATGACTAACCAGAAT
+TTGTTCATGACTGTTGTTTTCTGTAGCCTGAGACAGCTGTCTTGTGAGGGACTGAGATGCAGGATTTCTT
+CACGCCTCCCCTTTGTGACTTCAAGAGCCTCTGGCATCTCTTTCTGCAAAGGCACCTGAATGTGTCTGCG
+TCCCTGTTAGCATAATGTGAGGAGGTGGAGAGACAGCCCACCCTTGTGTCCACTGTGACCCCTGTTCCCA
+TGCTGACCTGTGTTTCCTCCCCAGAAGCTTGCGG
+>Barcode0_Cluster4_Phase1_NumReads129
+TTGGGCCAAGACTCAGGGAGACATTGAGACAGAGCGCTTGGCACAGAAGCAGAGGGGTCAGGGCGAAGTC
+CCAGGGCCCCAGGCGTGGCTCTCAGGGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCC
+TTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTATGTAGGGTCCTTCTTCCTGGAT
+ACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTC
+GCGGTCGCTGTTCTAAAGTCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCG
+TCATGGCGCCCCGAACCCTCGTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCAGGTGA
+GTGCGGGGTCGGGAGGGAAACGGCCTCTGCGGGGAGAAGCAAGGGGCCCGCCTGGCGGGGGCGCAAGACC
+CGGGAAGCCGCGCCGGGAGGAGGGTCGGGCGGGTCTCAGCCACTCCTCGTCCCCAGGCTCCCACTCCATG
+AGGTATTTCTCCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGG
+ACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGAT
+AGAGCAGGAGGGGCCGGAGTATTGGGACGAGGAGACAGGGAAAGTGAAGGCCCACTCACAGACTGACCGA
+GAGAACCTGCGGATCGCGCTCCGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCCGGGGCGC
+AGGTCACGACCCCTCATCCCCCACGGACGGGCCGGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCG
+AAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTAACCCGGTTTCATTTTCAGTT
+TAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCCGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCG
+GGGCCAGGTTCTCACACCCTCCAGATGATGTTTGGCTGCGACGTGGGGTCGGACGGGCGCTTCCTCCGCG
+GGTACCACCAGTACGCCTACGACGGCAAGGATTACATCGCCCTGAAAGAGGACCTGCGCTCTTGGACCGC
+GGCGGACATGGCGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGTGGCGGAGCAGTTGAGAGCC
+TACCTGGAGGGCACGTGCGTGGACGGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCA
+CGGGTACCAGGGGCCACGGGGCGCCTACCTGATCGCCTGTAGGTCTCCCGGGCTGGCCTCCCACAAGGAG
+GGGAGACAATTGGGACCAACACTAGAATATCGCCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGG
+TTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAA
+TCTCTGACGGAATGACGGAAAGACGATCCCTCGAATACTGATGACTGGTTCCCTTTGACACCGGCAGCAG
+CCTTGGGACCGTGACTTTTCCTCTCAGGCCTTGTTCTCTGCTTCACACTCAATGTGTGTGGGGGTCTGAG
+TCCAGCACTTCTGAGTCCCTCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCCTCCTCAGGGAA
+TAGAAGATTATCCCAGGTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGT
+GTCCTGTCCATTCTCAAGATGGCCACATGCATGCTGGTGGAGTGTCCCATGACAGATGCAAAATGCCTGA
+ATTTTCTGACTCTTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGG
+CCACTCTGAGATGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGA
+GGACCAGACCCAGGACACGGAGCTTGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCA
+GCTGTGGTGGTACCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGC
+CCCTCACCCTGAGATGGGGTAAGGAGGGAGATGGGGGTGTCATGTCTCTTAGGGAAAGCAGGAGCCTCTC
+TGGAGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTTTTCCCAGAGCCATCTTCCCAGCCCACC
+GTCCACATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTG
+CTGTGATGTGGAGGAGGAACAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCTGAGATTTCTTGTCTCA
+CTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATTACTGGGAAGCACCATCCACAATCATGG
+GCCGACCCAGCCTGGGCCCTGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGTGACAATGAAGGACAG
+ATTTATCACCTTGATTATGGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCACAGGGGAAGGTCCCT
+GACGACAGATCTCAGGAGGGCGATTGGTCCAGGGCCCACATCTGCTTTCTTCATGTTTCCTGATCCTGCC
+CTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTT
+AAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTCCCACAGATAGAAAAGGAGGGAGCTACT
+CTCAGGCTGCAAGTAAGTATGAAGGAGGCTGATGCCTGAGGTCCTTGGGATATTGTGTTTGGGAGCCCAT
+GGGGGAGCTCAACCACCCCACAATTCCTCCTCTAGCCACATCTTCTGTGGGATCTGACCAGGTTCTGTTT
+TTGTTCTACCCCAGGCAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGTAAAGGTGAGAGC
+TTGGAGGGCCTGATGTGTGTTGGGTGTTGGGCGGAACAGTGGACACAGCTGTGCTATGGGGTTTCTTTGC
+ATTGGATGTATTGAGCATGCGATGGGCTGTTTAAAGTGTGACCCCTCACTGTGACAGATATGAAGTTGTT
+CATGAATTTTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTGGGACTGAGAGGCAAGAGTTGTTCCTGCC
+CTTCCCTTTGTGACTTGAAGAACCCTGACTTTGTTTCTGCAAAGGCACCTGCATGTGTCTGTGTTCATGT
+AGGCATAATGTGAGGAGGTGGGGAGACCACCCCACCCCCATGTCCACCATGACCCTCTTCCCACGCTGAC
+CTGTGCTCCCTCCCCAA
+>Barcode0_Cluster2_Phase2_NumReads57
+TCAGGCACACAGTGTGACAAAGATGCTTGGTGTAGGAGAAGAGGAATCAGGACGAAGTCCCAGGTCCCGG
+GCGGGGCTCTCAGGGTCTCAGGCTCCAAGGGCCGTGTCTGCACTGGGGAGGCGCCGCGTTGAGGATTCTC
+CACTCCCCTGAGTTTCACTTCTTCTCCCAACCTGCGTCGGGTCCTTCTTCCTGAATACTCATGACGCGTC
+CCCAATTCCCACTCCCATTGGGTGTCGGATTCTAGAGAAGCCAATCAGCGTCTCCGCAGTCCCGGTTCTG
+AAGTCCCCAGTCACCCACCCGGACTCAGATTCTCCCCAGACGCCGAGATGCGGGTCATGGCGCCCCGAAC
+CCTCATCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCTGGGCCGGTGAGTGCGGGGTTGGGAGG
+GAATCGGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGGAGCCGCGCAGG
+GAGGAGGGTCGGGCGGGTCTCAGCCCCTCCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTACACCG
+CTGTGTCCCGGCCCGGCCGCGGGGAGCCCCACTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGT
+GCGGTTCGACAGCGACGCCGCGAGTCCGAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCG
+GAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGGAACC
+TGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCCCTCC
+TCATCCCCCACGGACGGCCCGGGTCGCCCCAAGTCTCCCGGTCTGAGATCCACCCCGAGGCTGCGGAACC
+CGCCCAGACCCTCGACCGGAGAGAGCCCCAGTCACCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAT
+CCCCGCGGGTTGGTCGGGGCGGGGCGGGGCTCGGGGGACGGGGCTGACCGCGGGGGCGGGGCCAGGGTCT
+CACATCATCCAGAGGATGTACGGCTGCGACGTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGT
+ACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGATCTGCGCTCCTGGACCGCCGCGGACACGGC
+GGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCTGAGAGCCTACCTGGAGGGC
+CTGTGCGTGGAGTGGCTCCGCAGATACCTGAAGAATGGGAAGGAGACGCTGCAGCGCGCGGGTACCAGGG
+GCAGTGGGGAGCCTTCCCCATCTCCTGTAGATCTCCCGGGATGGCCTCCCACGAGGAGGGGAGGAAAATG
+GGATCAGCGCTAGAATATCGCCCTCCCTTGAATGGAGAATGGGATGAGTTTTCCTGAGTTTCCTCTGAGG
+GCCCCCTCTGCTCTCTAGGACAATTAAGGGATGAAGTCCTTGAGGAAATGGAGGGGAAGACAGTCCCTAG
+AATACTGATCAGGGGTCCCCTTTGACCACTTTGACCACTGCAGCAGCTGTGGTCAGGCTGCTGACCTTTC
+TCTCAGGCCTTGTTCTCTGCCTCACGCTCAATGTGTTTGAAGGTTTGATTCCAGCTTTTCTGAGTCCTTC
+GGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCTCCCTCAGAGACTAGAACTTTCCAATGAATAGG
+AGATTATCCCAGGTGCCTGTGTCCAGGCTGGCGTCTGGGTTCTGTGCCCCCTTCCCCACCCCAGGTGTCC
+TGTCCGTTCTCAGGATGGTCACATGGGCGCTGTTGGAGTGTCGCAAGAGAGATACAAAGTGTCTGAATTT
+TCTGACTCTTCCCGTCAGAACACCCAAAGACACACGTGACCCACCATCCCGTCTCTGACCATGAGGCCAC
+CCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGTGGGATGGGGAGGAC
+CAAACTCAGGACACTGAGCTTGTGGAGACCAGGCCAGCAGGAGATGGAACCTTCCAGAAGTGGGCAGCTG
+TGGTGGTGCCTTCTGGAGAAGAGCAGAGATACACGTGCCATGTGCAGCACGAGGGGCTGCCGGAGCCCCT
+CACCCTGAGATGGGGTAAGGAGGGGGATGAGGGGTCATATCTGTTCTCAGGGAAAGCAGGAGCCCTTCTG
+GAGCCCTTCAGCAGGGTCAGGGCCCCTCACCTTCCCCTCCTTTCCCAGAGCCGTCTTCCCAGCCCACCAT
+CCCCATCGTGGGCATCGTTGCTGGCCTGGCTGTCCTGGCTGTCCTAGCTGTCCTAGGAGCTGTGGTGGCT
+GTTGTGATGTGTAGGAGGAAGAGCTCAGGTAGGGAAGGGGTGAGGAGTGGGGTCTGGGTTTTCTTGTTCC
+ACTGGGAGTTTCAAGCCCCAGGTAGAAGTGTGCCCCACCTCGTTACTGGAAGCACCATCCACACATGGGC
+CATCCCAGCCTGGGACCCTGTGTGCCAGCACTTACTCTGTTGTGAAGCACATGACAATGAAGGACAGATG
+TATCACCTTGATGATTATGGTGTTGGGGTCCTTGATTCCAGCATTCATGAGTCAGGGGAAGGTCCCTGCT
+AAGGACAGACCTTAGGAGGGCAGTTGCTCCAGAACCCACAGCTGCTTTCCCCGTGTTTCCTGATCCTGCC
+CTGGGTCTGCAGTCATAGTTCTGGAAACTTCTCTTGGGTCCAAGACTAGGAGGTTCCCCTAAGATCGCAT
+GGCCCTGACTCCTCCCTGTCCCCTCACAGGGCATTTTCTTCCCACAGGTGGAAAAGGAGGGAGCTGCTCT
+CAGGCTGCGTGTAAGTGATGGCGGTGGGCGTGTGGAGGAGCTCACCCACCCCATAATTCCTCTTGTCCCA
+CATCTCCTGCGGGCTCTGACCAGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCTCT
+GATGAGTCTCTCATCGCTTGTAAAGGTGAGATTCTGGGGAGCTGAAGTGGTCGGGGGTGGGGCAGAGGGA
+AAAGGCCTAGGTAATGGGGATCCTTTGATTGGGACGTTTCGAATGTGTGGTGAGCTGTTCAGAGTGTCAT
+CACTTACCATGACTGACCTGAATTTGTTCATGACTATTGTGTTCTGTAGCCTGAGACAGCTGCCTGTGTG
+GGACTGAGATGCAGGATTTCTTCACACCTTTCCTTTGTGACTTCAAGAGCCTCTGGCATCTCTTTCTGCA
+AAGGCATCTGAATGTGTCTGCGTTCCTGTTAGCATAATGTGAGGAGGTGGAGAGACAGCCCACCCCCGTG
+TCCACCGTGACCCCTGTCCCCACACTGACCTGTGTTCCCTCCCC
+>Barcode0_Cluster0_Phase2_NumReads52
+TCAGGCACACAGTGTGACAAAGATGCTTGGTGTAGGAGAAGAGGGATCAGGACGAAGTCCCAGGTCCCGG
+GCGGGGCTCTCAGGGTCTCAGGCTCCAAGGGCCGTGTCTGCACTGGGGAGGCGCCGCGTTGAGGATTCTC
+CACTCCCCTGAGTTTCACTTCTTCTTCCAACCTGCGTCGGGTCCTTCTTCCTGAATACTCATGACGCGTC
+CCCAATTCCCACTCCCATTGGGTGTCGGGTTCTAGAGAAGCCAATCAGCGTCTCCGCAGTCCCGGTTCTA
+AAGTCCCCAGTCACCCACCCGGACTCGGATTCTCCCCAGACGCCGAGATGCGGGTCATGGCGCCCCGAAC
+CCTCATCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCTGGGCCTGTGAGTGCGAGGTTGGGAGG
+GAAACGGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGGAGCCGCGCAGG
+GAGGAGGGTCGGGCGGGTCTCAGCCCCTCCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTACACCG
+CCGTGTCCCGGCCCGGCCGCGGAGAGCCCCGCTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGT
+GCAGTTCGACAGCGACGCCGCGAGTCCAAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCG
+GAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGGAACC
+TGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCCCTCC
+CCATCCCCCACGGACGGCCCGGGTCGCCCCGAGTCTCCCGGTCTGAGATCCACCCCGAGGCTGCGGAACC
+CGCCCAGACCCTCGACCGGAGAGAGCCCCAGTCACCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAT
+CCCCGCGGGTTGGTCGGGGCTGGGGCGGGGCTCGGGGGACGGGGCTGACCACGGGGGCGGGGCCAGGGTC
+TCACACCCTCCAGAGGATGTATGGCTGCGACCTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATAACCAG
+TTCGCCTACGACGGCAAGGATTACATCGCCCTGAATGAGGACCTGCGCTCCTGGACCGCCGCGGACAAGG
+CGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCGGAGAGCCTACCTGGAGGG
+CACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGAAGACGCTGCAGCGCGCGGGTACCAGG
+GGCAGTGGGGAGCCTTCCCCATCTCCTGTAGATCTCCCGGGATGGCCTCCCACGAGGAGGGGAGGAAAAT
+GGGATCAGCGCTGGAATATCGCCCTCCCTTGAATGGAGAATGGGATGAGTTTTCCTGAGTTTCTTCTGAG
+GGCCCCCTCTGCTCTCTAGGACAATTAAGGGATGAAGTCCTTGAGGAAATGGAGGGGAAGACAGTCCCTG
+GAATACTGATCAGGGGTCCCCTTTGACCACTTTGACCACTGCAGCAGCTGTGGTCAGGCTGCTGACCTTT
+CTCTCAGGCCTTGTTCTCTGCCTCACGCTCAATGTGTTTAAAGGTTTGATTCCAACTTTTCTGAGTCCTT
+CGGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCTCCCTCAGAGACTAGAACTTTCCAATGAATAG
+GAGATTATCCCAGGTGCCTGTGTCCAGGCTGGCGTCTGGGTTCTGTGCCCCCTTCCCCACCCCAGGTGTC
+CTGTCCATTCTCAGGATGGTCACATGGGCACTGTTGGAGTGTCGCAAGAGAGATACAAAGTGTCTGAATT
+TTCTGACTCTTCCCGTCAGAACACCCAAAGACACACGTGACCCACCATCCCGTCTCTGACCATGAGGCCA
+CCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGCGAGGA
+CCAAACTCAGGACACCGAGCTTGTGGAGACCAGGCCAGCAGGAGATGGAACCTTCCAGAAGTGGGCAGCT
+GTGGTGGTGCCTTCTGGAGAAGAGCAGAGATACACGTGCCATGTGCAGCACGAGGGGCTGCCAGAGCCCC
+TCACCCTGAGATGGGGTAAGGAGGGGGATGAGGGGTCATGTGTCTTCTCAGGGAAAGCAGAAGTCCTGGA
+GCCCTTCAGCCGGGTCAGGGCTGAGGCTTGGGGGTCAGGGCCCCTCACCTTCCCCTCCTTTCCCAGGGCC
+ATCTTCCCAGCCCACCATCCCCATCGTGGGCATCGTTGCTGGCCTGGCTGTCCTGGCTGTCCTAGCTGTC
+CTAGGAGCTGTGATGGCTGTTGTGATGTGTAGGAGGAAGAGCTCAGGTAGGGAAGGGGTGAGGAGTGGGG
+TCTGGGTTTTCTTGTCCCACTGGGAGTTTCAAGCCCCAGGTAGAAGTGTGCCCCACCTCGTTACTGGAAG
+CACCATCCACACATGGGCCATCCCAGCCTGGGACCCTGTGTGCTAGCACTTACTCTGTTGTGAAGCACAT
+GACAATGAAGGACAGATGTATCACCTTGATGATTATGGTGTTGGGGTCCTTGATTCCAGCATTCATGAGT
+CAGGGGAAGGTCCCTGCTAAGGACAGACCTTAGGAGGGCAGTTGCTCCAGAACCCACAGCTGCTTTCCCC
+GTGTTTCCTGATCCTGCCCTGGGTCTGCAGTCATAGTTCTGGAAACTTCTCTTGGGTCCAAGACTAGGAG
+GTTCCCCTAAGATCGCATGGCCCTGACTCCTCCCTGTCCCCTCACAGGGCATTTTCTTCCCACAGGTGGA
+AAAGGAGGGAGCTGCTCTCAGGCTGCGTGTAAGTGATGGCGGTGGGCGTGTGGAGGAGCTCACCCACCCC
+ATAATTCCTCTTGTCCCACATCTCCTGCGGGCTCTGACCAGGTCTTTTTTTTTGTTCTACCCCAGCCAGC
+AACAGTGCCCAGGGCTCTGATGAGTCTCTCATCGCTTGTAAAGGTGAGATTCTGGGGAGCTGAAGTGGTC
+GGGGGTGGGGCAGAGGGAAAAGGCCTAGGTAATGGGGATCCTTTGATTGGGACGTTTCGAATGTGTGGTG
+AGCTGTTCAGAGTGTGATCACTTACCATGACTGACCTGAATTTGTTCATGACTATTGTGTTCTGTAGCCT
+GAGACAGCTGCCTGTGTGGGACTGAGATGCAGGATTTCTTCACACCTCTCCTTTGTGACTTCAAGAGCCT
+CTGGCATCTCTTTCTGCAAAGGCATCTGAATGTGTCTGCGTTCCTGTTAGCATAATGTGAGGAGGTGGAC
+AGACAGCCCACCCCCGTGTCCACCGTGACCCCTGTCCCACACTGACCTGTGTTCCCTCCCCC
+>Barcode0_Cluster3_Phase0_NumReads45
+CCGCAAGCTTCTGGGGAGGAAACACAGGTCAGCATGGGAACAGGGGTCACAGTGGACACAAGGGTGGGCT
+GTCTCTCCACCTCCTCACATTATGCTAACAGGGACGCAGACACATTCAGGTGCCTTTGCAGAAAGAGATG
+CCAGAGGCTCTTGAAGTCACAAAGGGGAGGCGTGAAGAAATCCTGCATCTCAGTCCCTCACAAGACAGCT
+GTCTCAGGCTACAGAAAACAACAGTCATGAACAAATTCTGGTTAGTCATGGTAAGTGATGACACTCTGAA
+CAGCCCACGACACACGCGAAACATCCCAATCAAAGAATCTCCATTACCCAGGCCTTTCCCCACTGCCCCA
+CCCACCCCCAGACCCGCCACCCCACCCACTCTAGACCCCAAGAATCTCACCTTTTCAAGCTGTGAGAGAC
+ACATCAGAGCCCTGGGCACTGTCGCTGGCTGGAGTAGAACAAAAACAGGACCTGGTCAGAGCCCGCAGGA
+GACGTGGGACAGGAGGAATTATGGGGTGGGTGAGCTCCTCCACACTCCCACCCCCACCACTTACACGCAG
+CCTGAGAGTAGCTCCCTCCTTTTCCACCTGTGGGAAGAAAATGTCCTGTGAGGGGACTGGGAGGAAGCAG
+GACCATGAGATCTTAGAGGAACCTCCTCGTCTTGGAACCAAAAGGAATTTCCAGAAGTATGACTACAGAC
+CCAGGGCAGGATCAGGAAACACGAGGAAAGCAAGTGTGGGTCCTGGACCAACTGCCCTCCTAAGGTCTGT
+CCTTAGCAGGGACCTTCCCCTGACTCATGAATGCTGGAATCAGGACCCCAACACCACAACCATCAAGGCG
+ATACATCTGTCCTTCATTGTCACATGTGCTGCACAAAAGAGTAAGTGCTGGCACACAGGGTCCCAGGCTG
+CGTTAGCCCCTGTGTGGATGCTGCTTCCCAGTAATGAGGCAGGGAACACTTCTACCTGGGGCTTGAAACC
+CCCAGTGGGACAAGAAAACCCAGACCCCACCCCTCACCCCTTCCCTACCTGAGCTCTTCCTCCTACACAT
+CACAGTAGCGACCACAGCTCCGATGACCACAACTGCTAGGACAGCCAGGCCAGCAACAATGCCCACGATG
+GGGATGGTGGACTGGGAAGATGGCTCTGGGAAAGGAGGGGAAGATGAGGGGCCCTGACCCTGCTGAAGGG
+CTCCAGAAGGGCTCCTGCTTTCCCTGAGAACAGATATGACCCCTCATCCCCCTCCTTACCCCATCTCAGG
+GTGAGGGGCTTCGGCAGCCCCTCATGCTGTACATGGCATGTGTATCTCTGCTCTTCTCCAGAAGGCACCA
+CCACAGCTGCCCACTTCTGGAAGGTTCTATCTCCTGCTGGTCTGGTCTCCACAAGCTCGGTGTCCTGAGT
+TTGGTCCTCGCCATCCCGCTGCCAGGTCAGTGTGATCTCCGCAGGGTAGAAGCCCAGGGCCCAGCACCTC
+AGGGTGGCCTCATGGTCAGAGATGGGGTGGTGGGTCACATGTGTCTTTGGGGGGTCTGATGGGAAGAGTC
+AGAAAATTCAGGCGCTTTGCATCTCTCATGGGACACCCTAGGACCACCCATGTGACCAGCCTGAGAATGG
+ACAGGACACCTGGGGTGGGGAAGGGGCACAGAACCCAGACACCAGCCTGGACGCAGGCACCTGGGATAAT
+CTCCTATTCATTGGAAAGTTCGAGTCTCTGAGCGGGGAACAGGGACTTCTGCTCCTGATCTGAGTGGAGG
+TAAAGTGACTCAGAAGTGCTGGAATCAGAGCCCCAAACACACTGAGTGTGAGGCAGAGAACAAGGCCTGA
+GAGGAAAAGTCACGGTTCCCAAGGCTGCTGCAGGGGTCAAAGGGGACCCCTGATCACTATCCTAGGGACT
+GTCTTCCCCTCCATTTCCTCAGAGACGTCATCCCTTAATTGTCCTAGAGAGAAGAGGGGGCCCTCAGAGG
+AAACTCAGGAAAACTCATGCCATTCTCCATTCAAGGGAGGGCGACATTCTAGCGCTGATCCCATTTTCCT
+CCTCTTCTCGTGGGAGGCCATCCCCGGCGACCTATAGGAGATGGGGAAGGCTCCCCACTGCCCCTGGTAC
+CCGCGCGCTGCAGCGTCTCCTTCCCGTTCTCCAGGTATCTGCGGAGCCACTCCACGCACAGGCCCTCCAG
+GTAGGCTCTCAGCTGCTCCGCCTCACGGGCCGCCTCCCACTTGCGCTGGGTGATCTGAGCCGCCGTGTCC
+GCCGCGGTCCAGGAGCTCAGGTCCTCGTTCAGGGCGATGTAATCCTTGCCGTCGTAGGCGTACTGGTCAT
+GCCCGCGGAGGAGGCGCCCGTCCGGCCCCACGTCGCAGCCGTACATCCTCTGGAGGGTGTGAGACCCTGG
+CCCAGGCCCCGCGGTCAGCCCGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCT
+CAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTTTGGGCGGGTCCCGCGG
+CCTCAGGGAGGCGGATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGTACGTGGGGGATGGGGAGTCG
+TGACCTGCGCCCCAGGCCGGGGTCACTCACCGGCCTCGCTCTGGTTGTAGTAGCCGCGCAGGTTCCGCAG
+GCTCTCTCGGTAAGTCTGTGTGTTGGTCTTGCAGATCTGTGTGTTCCGGTCCCAATATTCCGGCCCCTCC
+TGCTCTATCCACGGCGCCCGCGGCTCCTCTCTCGGACTCGCGGCGTCGCTGTCGAACCTCACGAACTGCG
+TGTCGTCCACGTAGCCCACTGAGATGAAGCGGGGCTCCCCGCGGCCGGGCCGGGACACGGCGGTGTAGAA
+ATACCTCATGGAGTGGGAGCCTGGGGGCGAGGAGGGGCTGAAACCCGCCCGACCCTCCTCCCGGCGCGGC
+TCCTCAGGTCCTGCGCCCCCGCCTGCGGTCCCCTCGCTCCTCCCGGCAGAGGCCATTTCCCTCCCGACCC
+GCACTCACCGGCCCAGGTCTCGGTCAGGGCCAGGGCCGCCGAGAGCAGCAGGAGGACGGTTCGGGGCGCC
+ATGACCAGCATCTTGGCGTCTGAGGAGACTCTGAGTCCGGGTGGGTGCGTGGGGACTTTAGAACTGGGAC
+CCCGGCGACGCTGATTGGCTTCTCTAGATATCCGACACCCAATGGGAGTGGGAAGTGGGGATGCGTCACG
+AGTATCCTGGAAGAAGGACCCGACACAAGTTGGGAGAAGAAGTGAAACTCAGGGGAGTGGGGAATCCCCA
+ACGCTGCGCCTCCCCATTGCAGACGCGGCCCTCGGAGCCTGAGACCCTGAGAGCCCCGTCCGGGACCTGG
+GACTTCGTCCTGATCCCTCTTCTCCTACACCAAGCCTCTTTGTCACACTGTCTGCC
+>Barcode0_Cluster4_Phase0_NumReads40
+TTGGGCCAAGACTCAGGGAGACATTGAGACAGAGCGCTTGGCACAGGAGCAGAGGGGTCAGGGCGAAGTC
+CCAGGGCCCCAGGCGTGGCTCTCAGGGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCC
+TTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTATGTAGGGTCCTTCTTCCTGGAT
+ACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTC
+GCGGTCGCGGTTCTAAAGTCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCG
+TCATGGCGCCCCGAACCCTCGTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGA
+GTGCGGGGTCGGGAGGGAAACGGCCTCTGTGGGGAGAAGCAAGGGGCCCGCCCGGCGGGGGCGCAGGACC
+CGGGAAGCCGCGCCTGGAGGAGGGTCGGGCGGGTCTCAGCCACTCCTCGCCCCCAGGCTCCCACTCCATG
+AGGTATTTCTACACCTCCATGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGG
+ACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGAT
+AGAGCAGGAGGGGCCGGAGTATTGGGACCGGAACACACGGAATGTGAAGGCCCAGTCACAGACTGACCGA
+GTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCCGGGGCGC
+AGGTCACGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCGCCCCG
+AAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTT
+TAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCGGGGCGGGGCTCGGGGGACCGGGCTGACCTCGGGGTCC
+GGGCCAGGTTCTCACACCATCCAGAGGATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCG
+GGTACCACCAGTACGCCTACGACGGCAAGGATTACATCGCCCTGAAAGAGGACCTGCGCTCTTGGACCGC
+GGCGGACATGGCAGCTCAGACCACCAAGCACAAGTGGGAGGCGGCCCATGTGGCGGAGCAGTGGAGAGCC
+TACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCA
+CGGGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTGTAGATCTCCCGGGCTGGCCTCCCACAAGGAG
+GGGAGACAATTGGGACCAACACTAGAATATCGCCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGG
+TTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAA
+TCTCTGACGGAATGACGGAAAGACGATCCCTCGAATACTGATGACTGGTTCCCTTTGACACCGGCAGCAG
+CCTTGGGACCGTGACTTTTCCTCTCAGGCCTTGTTCTCTGCTTCACACTCAATGTGTGTGGGGGTCTGAG
+TCCAGCACTTCTGAGTCCCTCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCCTCCTCAGGGAA
+TAGAAGATTATCCCAGGTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGT
+GTCCTGTCCATTCTCAAGATGGCCACATGCATGCTGGTGGAGTGTCCCATGACAGATGCAAAATGCCTGA
+ATTTTCTGACTCTTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGG
+CCACTCTGAGATGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGA
+GGACCAGACCCAGGACACGGAGCTTGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCA
+GCTGTGGTGGTACCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGC
+CCCTCACCCTGAGATGGGGTAAGGAGGGAGATGGGGGTGTCATGTCTCTTAGGGAAAGCAGGAGCCTCTC
+TGGAGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTTTTCCCAGAGCCATCTTCCCAGCCCACC
+GTCCACATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTG
+CTGTGATGTGGAGGAGGAACAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCTGAGATTTCTTGTCTCA
+CTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATTACTGGGAAGCACCATCCACAATCATGG
+GCCGACCCAGCCTGGGCCCTGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGTGACAATGAAGGACAG
+ATTTATCACCTTGATTATGGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCACAGGGGAAGGTCCCT
+GACGACAGATCTCAGGAGGGCGATTGGTCCAGGGCCCACATCTGCTTTCTTCATGTTTCCTGATCCTGCC
+CTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTT
+AAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTCCCACAGATAGAAAAGGAGGGAGCTACT
+CTCAGGCTGCAAGTAAGTATGAAGGAGGCTGATGCCTGAGGTCCTTGGGATATTGTGTTTGGGAGCCCAT
+GGGGGAGCTCAACCACCCCACAATTCCTCCTCTAGCCACATCTTCTGTGGGATCTGACCAGGTTCTGTTT
+TTGTTCTACCCCAGGCAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGTAAAGGTGAGAGC
+TTGGAGGGCCTGATGTGTGTTGGGTGTTGGGCGGAACAGTGGACACAGCTGTGCTATGGGGTTTCTTTGC
+ATTGGATGTATTGAGCATGCGATGGGCTGTTTAAAGTGTGACCCCTCACTGTGACAGATATGAAGTTGTT
+CATGAATTTTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTGGGACTGAGAGGCAAGAGTTGTTCCTGCC
+CTTCCCTTTGTGACTTGAAGAACCCTGACTTTGTTTCTGCAAAGGCACCTGCATGTGTCTGTGTTCATGT
+AGGCATAATGTGAGGAGGTGGGGAGACCACCCCACCCCCATGTCCACCATGACCCTCTTCCCACGCTGAC
+CTGTGCTCCCTCCCCAA
diff --git a/tests/data/chimera_minimal.fasta b/tests/data/chimera_minimal.fasta
new file mode 100644
index 0000000..f2eb86c
--- /dev/null
+++ b/tests/data/chimera_minimal.fasta
@@ -0,0 +1,220 @@
+>Barcode0--0_Cluster1_Phase1_NumReads297
+GCAGGTGCCTTTGCAGAAACAAAGTCAGGGTTCTTCAAGTCACAAAGGGAAGGGCAGGAA
+CAACTCTTGCCTCTCAGTCCCACACAAGGCAGCTGTCTCACACTATAGAAAAAAATATTC
+ATGAACAAATTCGTATCTGTCACAGTGAGGGGTCACACTTTAAACAGCCCATCGCATGCT
+CAATACATCCAATGGAAAGAAACCCCATAGCACAGCTGTGTCCACTGTTCCGCCCAACAC
+CCAACACACATCAGGCCCTCCAGGCTCTCACCTTTACAAGCTGTGAGAGACACATCAGAG
+CCCTGGGCACTGTCACTGCCTGGGGTAGAACAAAAACAGAACCTGGTCAGATCCCACAGA
+AGATGTGGCTAGAGGAGGAATTGTGGGGTGGGTGAGCTCCCCCATGGGCTCCCAAACACA
+ATATCCCAAGGACCTCAGGCATCAGCCTCCTTCATACTTACTTGCAGCCTGAGAGTAGCT
+CCCTCCTTTTCTATCTGTGGGAAGAAAATGTCCTGTGAGATACCAGAAAGGAGTCAGGGC
+CTTAAGGTCCTAGAGGAACCTCCAAGTCTTGGACCTCAGAGAAGTTTCCAGAAATGTGTG
+ACTGCAGACCCAGGGCGGGATCAGGAAACATGAAGAAAGCAGGTGTGGGTCCTGGACCAA
+CCGCCCTCCTGAAGGTCCTCAGGGACCTTCCCCTGTGACTTGTGACTGCTGGGATCAGGT
+CCCATCACCGCTGTAATCAAGGTGATAAATCTGTCCTTCATTTTAACAGGTGCTTTACAA
+AAGAGTAAGTGCTGGCACACAGGGCCCAGGCTGGGTAGGCCCATAATTGTGGGTGGTGCT
+TCCCAGTAACGAGGCAGGGCACACTTCTACCTGGGTCTTGGAACCCTCAGTGAGACAAGA
+AATCTCAGACCCACCCTTCACCCCTTCCCCACCTGAGCTCTTCCTCCTCCACATCACAGC
+AGCGACCACAGCTCCAGTGATCACAGCTCCAAAGAGAACCAGGCCAGCAATGATGCCCAC
+GATGGGGATGGTGGGCTGGGAAGACGGCTCTGGGAAAAGAGGGGAAGGTGAGGGGCCCTG
+ACCCTGCTAAAGGTCAGAGAGGCTCCTGCTTTCCCTAAAAGACATGACACCCCCGTCTCC
+CTCCTTACCCCATCTCAGGGTGAGGGGCTTGGGCAAACCCTCATGCTGCACATGGCAGGT
+GTATCTCTGCTCCTGTCCAGAAGGCACCACCACAGCCGCCCACTTCTGGAAGGTTCCATC
+CCCTGCAGGCCTGGTCTCCACGAGCTCCGTGTCCTGGGTCTGGTCCTCCCCATCCCGCTG
+CCAGGTCAGTGTGATCTCCGCAGGGTAGAAGCTCAGGGCCCAGCACCTCAGGGTGGCTTC
+ATGGTCAGAGACAGCGTGGTGAGTCATATGCGTTTTGGGGGCGTCTGTCAGGAAGAGTCA
+GATCATTCAGGCATTTTGCATCTGTCATGGGACACTCCTCCAGCACACATGTGGCTATCT
+TGAGAATGGACAGGACACCTGGGATGGGGAAGGGAGCACAGAACCCAGACACCAGCCTGG
+ACACAGGCACCTGGGATAATCTCCTATTCCGTGGAAAATTCTAGTCCCTGAAGAGGGAAC
+AGCGACTTCTGGTCCTGACCTGAGTGGAGGCTGAAGGACTCAGAAGTGCTGGACTCAGAC
+CCCCACACACATTGAGTGTGAAGCAGAGAACAAGGCCTGAGAGGAAAAGTCACGGGCCCA
+AGGCTGCTGCCTGTGTGTGTCAAAGGGAACCACTCATCAGTATTCGAGGGATCGTCTTCC
+CGTCATTCCTTCAGAGATTTTATCCCTTAATTGTGTCAGAGAGCAGGGCGGAACCTCAGA
+GTCACTCTCTGGTACAGGATCTGGAAACCCAGGAGGATTCCTCTCCCTCAGGACCAGAGG
+GAGGGCGATATTCTAGTGTTGGTCCCAATTGTCTCCCCTCCTTGTGGGAGGCCAGCCCGG
+GAGATCTACAGGCGATCAGGGAGGCGCCCCGTGGCCCCTGGTACCCGTGCGCTGCAGCGT
+CTCCTTCCCGTTCTCCAGGTATCTGCGGAGCCACTCCACGCACGTGCCCTCCAGGTAGGC
+TCTCAACTGCTCCGCCACATGGGCCGCCTCCCACTTGTGCTTGGTGGTCTGAGCTGCCAT
+GTCCGCCGCGGTCCAAGAGCGCAGGTCCTCTTTCAGGGCGATGTAATCCTTGCCGTCGTA
+GGCGTACTGGTGGTACCCGCGGAGGAAGCGCCAGTCCGACCCCACGTCGCAGCCATACAT
+CCTCTGGACGGTGTGAGAACCTGGCCCGGACCCCGCGGTCAGCCCGGTCCCCCGAGCCCC
+GCCCCGCCCCGACCAACCTGGGGGGATTTTTGGCCTAAACTGAAAATGAAACCGGGTAAA
+GGCGCCTGGGCCTCTCCCGGGGCAAGGGTCTCGGGGTCCCGCGGCTTCGGGGCGGATCTC
+GGACCCGGAGACTGTGGGCGACCTGGCCCGTCCGTGGGGGATGAGAGGTCGTGACCTGCG
+CCCCGGGCCGGGGTCACTCACCGGCCTCGCTCTGGTTGTAGTAGCCGCGCAGGGTCCCCA
+GGTCCACTCGGTGAGTCTGTGAGTGGGCCTTCACTTTCCGTGTCTCCCCGTCCCAATACT
+CCGGACCCTCCTGCTCTATCCACGGCGCCCGCGGCTCCATCCTCTGGCTCGCGGCGTCGC
+TGTCGAACCGCACGAACTGCGTGTCGTCCACGTAGCCCACTGCGATGAAGCGGGGCTCCC
+CGCGGCCGGGCCGGGACACGGATGTGAAGAAATACCTCATGGAGTGAGAGCCTGGGGACG
+AGGAGTGGCTGAGACCCGCCCGACCCTCCTCCCGGCGCGGCTTCCCGGGTCCTGCGCCCC
+CGCCAGGCGGGCCCGTTGCTTCTCCCCACAGAGGCCGTTTCCCTCCCGACCCCGCACTCA
+CCCGCCCAGGTCTGGGTCAGGGCCAGAGCCCCCGAGAGTAGCAGGACGAGGGTTCGGGGC
+GCCATGACGGCCATCCTCGGCGTCTGGGGAGAATCTGAGTCCCGGTGGGTGCGTGCGGAC
+TTTAGAACCGCGACCGCGACGACACTGATTGGCTTCTCTGGAAACCCGACACCCAATGGG
+AGTGAGAACTGGGTCCGCGTCGTGAGTATCCA
+>Barcode0--0_Cluster3_Phase1_NumReads294
+GCAGGTGCCTTTGCAGAAACAAAGTCAGGGTTCTTCAAGTCACAAAGGGAAGGGCAGGAA
+CAACTCTTGCCTCTCAGTCCCACACAAGGCAGCTGTCTCACACTATAGAAAAAAATATTC
+ATGAACAAATTCATATCCATCACAGTGAGGGGTCACACCTTAAACAGCCCATCGCATGCT
+CAATACATCCAATGCAAAGAAACCCCATAGCACAGCTGTGTCCACTGTTCCGCCCAACAC
+CCAACACACATTAGGTCCTCCAAGCTCTCACCTTTACAAGCTGTGAGGGACACATCAGAG
+CCCTGGGCACTGTCACTGCCTGGGGTAGAACAAAAACAGAACCTGGTCAGATCCCACAGA
+AGATGTGGCTAGAGGAGGAATTGTGAGGTGGGTGGGCTCCCCCATGGGCTCCCAAACACA
+ATATCCCAAGGACCTCAGGCATCAGCCTCCTTCATACTTACTTGCAGCCTGAGTGTAACT
+CCCTCCTTTTCTATCTGTGAGAAGAAAATGTCCTGTGAGATACCAGAAAGGAGCCAGGGC
+CTTAAGGTCCTAGAGGAACCTCCTAGTCTTGGACCCCAGAGAAGTTTCCAGAAATGTGTG
+ACTGCAGACCCAGGGCGGGATCAGGAAACATGAAGAAAGCAGGTGTGGGTCCTGGACCAA
+TAGCCCTCCTGAGGTCTGTCCTCAGGGACCTTCCCCTGTGACTTGTGACTGCTGGGATCA
+GGTCCCATCACCGCCGTAATCAAGGTGATAAATCTGTCCTTCATTTTAACAGGTGCTTTA
+CAAAAGAGTAAGTGCTGGCACACAGGGCCCAGACTGGGTAGGCCCATGATTGTGGACGGT
+GCTTCCCAGTAATGAGACAGGGCACATTTCTAGCTGGGGCTTGGAACCCTCAGTGAGACA
+AGAAATCTCAGACCCCACCCTTCACCCCTTCTCCACCTGAGCTCTTCCTCCTCCACATCA
+CGGCAGCGACCACAGCTCCAGTGATCACAGCTCCAAGGAGAACCAGGCCAGCAATGATGC
+CCACGATGGGGATGGTGGGCTGGGAAGACAGCTCTGGGAAAAGAGGGGAAGGTGAGGGGC
+CCTGACCCTGCTAAAGGTCTCCAGAGAGGCTCCTGCTTTCCCTAAGAGACATGACACCCC
+CATCTCCCTCCTTACCCCATCTCAGGGTGAGGGGCTTGGGCAGACCCTCATGCTGCACAT
+GGCAGGTGTATCTCTGCTCCTCTCCAGAAGGCACCACCACAGCCGCCCACTTCTGGAAGG
+TTCCATCCCCTGCAGGCCTGGTCTCCACGAGCTCCGTGTCCTGGGTCTGGTCCTCCCCAT
+CCCGCTGCCAGGTCAGTGTGATCTCCGCAGGGTAGAAGCCCAGGGCCCAGCACCTCAGGG
+TGGCCTCATGGTCAGAGATGGGGTGGTGGGTCATATGTGTCTTGGGGGGGTCTGACGGGA
+AGAGTCAGAAAATTCAGGCATTTTGCATCTGTCATGGGACACTCCACCAGCACGCATGTG
+GCCATCTTGAGAATGGACAGGACACCCGGGATGGGGAAGAGAGCACAGAACCCAGACACC
+AGCCTGGACACAGGCACCTGGGATAATCTTCTATTCCCTGAGAAGGGAACAGCGACTTCT
+GGTCCTGACCTGAGTGGAGGCTGAGGGACTCAGAAGTGCTGGACTCAGACCCCCACACAC
+ATTGAGTGTGAAGCAGAGAACAAGGCCTGAGAGGAAAAGTCACGGGCCCAAGGCTGCTGC
+CGGTGTCAAAGGGAACCACTCATCAGTATTCGAGGGATCGTCTTCCCGTCACTCCTTCAG
+AGATTTTATCCCTTAATTGTGTCAGAGAGCAGGGCGGAACCTCAGAGTCACTCTCTGGTA
+CAGGATCTGGAACCCAGGAGGATTCCTCTCCCTCAGGACCAGAGGGAGGGTGATATTCTA
+GTGTTGGTCCCAATTGTCTCCCCTCCTTGTGGGAGGCCAGCCCGGGAGATCTACAGGCGA
+TCAGGGAGGCGCCCCGTGGCCCCTGGTACCCGTGCGCTGCAGCGTCTCCTTCCCGTTCTC
+CAGGTATCTGCGGAGCCACTCCACGCACGTGCCATCCAGGTAGGCTCTCAACTGCTCCGC
+CTCATGGGCCGCCTCCCACTTGCGCTTGGTGATCTGAGCCGCCATGTCCGCCGCGGTCCA
+AGAGCGCAGGTCCTCGTTCAGGGCGATGTAATCCTTGCCGTCGTAGGCGTCCTGCCGGTA
+CCCGCGGAGGAAGCGCCCGTCCGACCCCACGTCGCAGCCATACATTATCTGGATGGTGTG
+AGAACCTGGCCCCGACCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCAGCCCCGACCA
+ACCCGGGGGGATTTTTGGCCTAAACTGAAAATGAAACCGGGTAAAGGCGCCTGGGCCTCT
+CCCGGGGCAAGGGTCTCGGGGTCCCGCGGCTTCGGGGTGGATCTCGGACCCGGAGACTGT
+GGGCGACCTGGCCCGTCCGTGGGGGATGAGGGGTCCTGACCTGCGCCCCCGGCCGGGGTC
+ACTCACCGGCCTCGCTCTGGTTGTAGTAGCCGCGCAGGGTCCCCAGGTCCACTCGGTCAG
+TCTGTGACTGGGCCTTCACATTCCGTGTCTCCTGGTCCCAATACTCCGGCCCCTCCTGCT
+CTATCCACGGCGCCCGCGGCTCCATCCTCTGGCTCGCGGCGTCGCTGTCGAACCGCACGA
+ACTGCGTGTCGTCCACGTAGCCCACGGCGATGAAGCGGGGCTCCCCGCGGCCGGGCCGGG
+ACACGGATGTGAAGAAATACCTCATGGAGTGGGAGCCTGGGGGCGAGCAGTGGCTGAGAC
+CTGCCCGACCCTCGTCCCGGCGCGGCTCCCCCGGTCCTGCGCCCCCGCCAGGAGGGCCCC
+TTGCTTCTCCCCGCAGAGGCGGTTTCCCTCCCGACCCCGCACTCACCCGCCCAGGTCTGG
+GTCAGGGCCAGGGCCCCCGAGAGTAGCAGGAGGAGGGTTCGGGGCGCCATGACGGCCATC
+CTCGGCGTCTGGGGAGAATCTGAGTCCCGGTGGGTGCGTGCGGGCTTTAGAACAGCGACC
+GCGACGACACTGATTGGCTTCTCTGGAAACCCGACACCCAATGGGAGTGAGAACTGGGTC
+CGCGTCGTGAGTATCCA
+>Barcode0--0_Cluster0_Phase2_NumReads92
+CTGGGGAGGAAACACAGGTCAGCATGGGAACAGGGGTCACAGTGGACACGGGGGTGGGCT
+GTCTCTCCACCTCCTCACATTATGCTAACAGGGACGCAGACACATTCAGGTGCCTTTGCA
+GAAAGAGATGCCAGAGGCTCTTGAAGTCACAAAGGGGAGGAGTGAAGAAATCCTGCATCT
+CAGTCCCTCACAAGACAGCTGTCTCAGGCTACAGAAAACAACAGTCATGAACAAATTCTG
+GTTAGTCATGGTAAGTGATGACACTCTAAACAGCCCACCACACACGCGAAACATCCCAAT
+CAAAGAATCTCCATTACCCAGGCCTTTCCCCTCTGCCCCCTCCCCACCCCACCCCCCCCG
+CCCACTCTAGACCCCAAGAATCTCACCTTTTCAAGCTGTGAGAGACACATCAGAGCCCTG
+GGCACTGTCGCTGGCTGGAGTAGAACAAAAACAGGACCTGGTCAGAGCCCGCAGGAGACG
+TGGGACAGGAGGAATTATGGGGTGGGTGAGCTCCTCCACACTCCCACCCCCACCACTTAC
+ACGCAGCCTGAGAGTAGCTCCCTCCTTTTCCACCTGTGGGAAGAAAATGTCCTGTGAGGG
+GACTGGGAGGAAGCAGGGCCATGAGATCTTAGAGGAACCTCCTCGTCTTGGACCCAAAAG
+GAATTTCCAGAAGTATGACTACAGACCCAAGGCAGGATCAGGAAACACGAGGAAAGCAAG
+TGTGGGTCCTGGACCAACTGCCCTCCTAAGGTCTGTCCTTAGCAGGGACCTTCCCCTGAC
+TCATGAATGCTGAAATCAGGACCCCAACACCACAACCATCAAGGTGATACATCCGTCCTT
+CATTGTCACATGTGCTGCACAAAAGAGTAAGTGCTGGCACACAGGGTCCCAGGCTGCATT
+AGCCCCTGTGTGGATGCTGCTTCCCAGTAATGAGGCAGGGAACACTTCTACCTGGGGCTT
+GAAACCCCCAGTGGGACAAGAAAACCCAGACCCCACCCCTCACCCCTTCCCTACCTGAGC
+TCTTCCTCCTACACATCACAGTAGCGACCACAGCTCCGATGACCACAACTGCTAGGACAG
+CCAGGCCAGCAACAATGCCCACGATGGGGATGGTGGACTGGGAAGATGGCTCTGGGAAAG
+GAGGGGAAGACGAGGGGCCCTGACCCTGCTGAAGGGCTCCAGAAGGGCTCCTGCTTTCCC
+TGAGAAGAGATATGACCCCTCATCCCCCTCCTTACCCCATCTCAGGGTGAGGGGCTTCGG
+CAGCCCCTCATGCTGTACATGGCATGTGTATCTCTGCTCTTCTCCAGAAGGCACCACCAC
+AGCTGCCCACTTCTGGAAGGTTCTATCTCCTGCTGGTCTGGTCTCCACAAGCTCAGTGTC
+CTGAGTTTGGTCCTCGCCATCCCGCTGCCAGGTCAGTGTGATCTCCGCAGGGTAGAAGCC
+CAGGGCCCAGCACCTCAGGGTGGCCTCATGGTCAGAGATGGGGTGGTGGGTCACGTGTGT
+CTTTGGGGGGTCTGATGGGAAGAGTCAGAAAATTCAGGCGCTTTGCATCTCTCATAGGAC
+ACCCTAGGACCACCCATGTGACCAGCCTGAGAATGGACAGGACACCTGGGGTGGGGAAGG
+GGCACAGAACCCAGACACCAGCCTGGACGCAGGCACCTGGGATAATCTCCTATTCATTGG
+AAAGTTCGAGTCTCTGAGCGGGGAACAGGGACTTCTGCTCCTGATCTGAGTGGAGGTAAA
+GTGACTCAGAAGTGCTGGAATCAGAGCCCCAAACACACTGAGTGTGAGGCAGAGAACAAG
+GCCTGAGAGGAAAAGTCACGGTTCCCAAGGCTGCTGCAGGGGTCAAAGAGGACCCCTGAT
+CAGTATTCTAGGGACTGTCTTCCCCTCCATTTCCTCAGAGACGTCATCCCTTAATTGTCC
+TAGAGAGAAGAGGGGGCCCTCAGAGGAAACTCAGGAAAACTCATGCCATTCTCCATTCAA
+GGGAGGGCGACATTCTAGCGCTGATCCCATTTTCCTCCTCTTCTCGTGGGAGGCCATCCC
+CGGCGACCTATAGGAGATGGGGAAGGCTCCCCACTGCCCCTGGTACCCGCGCGCTGCAGC
+GTCTCCTTCCCGTTCTCCAGGTATCTGCGGAGCCACTCCACGCACAGGCCCTCCAGGTAG
+GCTCTCAGCTGCTCCGCCACACGGGCCGCCTCCCACTTGCGCTGGGTGATCTGAGCCGCG
+GTGTCCGCCGCGGTCCAGGAGCTCAGGTCCTCGTTCAGGGCGATGTAATCCTTGCCGTCG
+TAGGCTAACTGGTTATGCCCGCGGAGGAGGCGCCCGTCCGGCCCCAGGTCGCAGCCATAC
+ATCGTCTGCCAAGTGTGAGACCCTGGCCCCGGCCCCGCGGTCAGCCCCGTCCCCCGAGCC
+CCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAA
+ACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCG
+GATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGTACGTGGGGGATGGGGAGTCGTGA
+CCTGCGCCCCGGGCCGGGGTCACTCACCGGCCTCGCTCTGGTTGTAGTAGCCGCGCAGGT
+TCCGCAGGCTCTCTCGGTCAGTCTGTGCCTGGGCCTTGTAGATCTGTGTGTTCCGGTCCC
+AATACTCCGGCCCCTCCTGCTCTATCCACGGCGCCCGCGGCTCCTCTCTCGGACTCGCGG
+CGTCGCTGTCGAACCTCACGAACTGCGTGTCGTCCACGTAGCCCACTGCGATGAAGCGGG
+GCTCCCCGCGGCCGGGCCGGGACATGGCGGTGTAGAAATACCTCATGGAGTGGGAGCCTG
+GGGGCGAGGAGGGGCTGAGACCCGCCAGACCCTCCTCCCGGCGCGGCTCCCCGGGTCCTG
+CGCCCCCGCCTGCGGTCCCCTCGCTCCTCCCCACAGAGGCCATTTCCCTCCCGACCCGCA
+CTCACCGGCCCAGGTCTCGGTCAGGGCCAGGGCCCCCCAGAGCAGCAGGAGGAGGGTTCG
+GGGTGCCGTGACCCGCATCTCGGTGTCTGAGGAGACTCTGAGTCCGGGTGGGTGCGTGGG
+GACTTTAGAACTGGGACCCCGGCGACACTGATTGGCTTCTCTAGACACCCGACACCCAAT
+GGGAGTGGGAAATGGGGACGCGTCACGAGTATCCTGGAAGAAGGACCCGACATAGGTTGG
+GAGAAGAAGTGAAACTCGTGGGAGTGGGGAATCCCCAACGCTGCGCCTCCCCAATGCAGA
+CGCGGCCCTCGGAGCCTGAGACCCTGAGAGCCCCGTCCGGGACATGGGACTTCGTCCTGA
+TCCCTCTTCTCCTACACCAGCCTCTTTGTCACACTGTCTGCC
+>Barcode0--0_Cluster1_Phase3_NumReads56
+GCAGGTGCCTTTGCAGAAACAAAGTCAGGGTTCTTCAAGTCACAAAGGGAAGGGCAGGAA
+CAACTCTTGCCTCTCAGTCCCACACAAGGCAGCTGTCTCACACTATAGAAAAAAATATTC
+ATGAACAAATTCGTATCTGTCACAGTGAGGGGTCACACTTTAAACAGCCCATCGCATGCT
+CAATACATCCAATGGAAAGAAACCCCATAGCACAGCTGTGTCCACTGTTCCGCCCAACAC
+CCAACACACATCAGGCCCTCCAGGCTCTCACCTTTACAAGCTGTGAGAGACACATCAGAG
+CCCTGGGCACTGTCACTGCCTGGGGTAGAACAAAAACAGAACCTGGTCAGATCCCACAGA
+AGATGTGGCTAGAGGAGGAATTGTGGGGTGGGTGAGCTCCCCCATGGGCTCCCAAACACA
+ATATCCCAAGGACCTCAGGCATCAGCCTCCTTCATACTTACTTGCAGCCTGAGAGTAGCT
+CCCTCCTTTTCTATCTGTGGGAAGAAAATGTCCTGTGAGATACCAGAAAGGAGTCAGGGC
+CTTAAGGTCCTAGAGGAACCTCCAAGTCTTGGACCTCAGAGAAGTTTCCAGAAATGTGTG
+ACTGCAGACCCAGGGCGGGATCAGGAAACATGAAGAAAGCAGGTGTGGGTCCTGGACCAA
+CCGCCCTCCTGAAGGTCCTCAGGGACCTTCCCCTGTGACTTGTGACTGCTGGGATCAGGT
+CCCATCACCGCTGTAATCAAGGTGATAAATCTGTCCTTCATTTTAACAGGTGCTTTACAA
+AAGAGTAAGTGCTGGCACACAGGGCCCAGGCTGGGTAGGCCCATAATTGTGGGTGGTGCT
+TCCCAGTAACGAGGCAGGGCACACTTCTACCTGGGTCTTGGAACCCTCAGTGAGACAAGA
+AATCTCAGACCCACCCTTCACCCCTTCCCCACCTGAGCTCTTCCTCCTCCACATCACAGC
+AGCGACCACAGCTCCAGTGATCACAGCTCCAAAGAGAACCAGGCCAGCAATGATGCCCAC
+GATGGGGATGGTGGGCTGGGAAGACGGCTCTGGGAAAAGAGGGGAAGGTGAGGGGCCCTG
+ACCCTGCTAAAGGTCAGAGAGGCTCCTGCTTTCCCTAAAAGACATGACACCCCCGTCTCC
+CTCCTTACCCCATCTCAGGGTGAGGGGCTTGGGCAAACCCTCATGCTGCACATGGCAGGT
+GTATCTCTGCTCCTGTCCAGAAGGCACCACCACAGCCGCCCACTTCTGGAAGGTTCCATC
+CCCTGCAGGCCTGGTCTCCACGAGCTCCGTGTCCTGGGTCTGGTCCTCCCCATCCCGCTG
+CCAGGTCAGTGTGATCTCCGCAGGGTAGAAGCTCAGGGCCCAGCACCTCAGGGTGGCTTC
+ATGGTCAGAGACAGCGTGGTGAGTCATATGCGTTTTGGGGGCGTCTGTCAGGAAGAGTCA
+GATCATTCAGGCATTTTGCATCTGTCATGGGACACTCCTCCAGCACACATGTGGCTATCT
+TGAGAATGGACAGGACACCTGGGATGGGGAAGGGAGCACAGAACCCAGACACCAGCCTGG
+ACACAGGCACCTGGGATAATCTCCTATTCCGTGGAAAATTCTAGTCCCTGAAGAGGGAAC
+AGCGACTTCTGGTCCTGACCTGAGTGGAGGCTGAAGGACTCAGAAGTGCTGGACTCAGAC
+CCCCACACACATTGAGTGTGAAGCAGAGAACAAGGCCTGAGAGGAAAAGTCACGGGCCCA
+AGGCTGCTGCCTGTGTGTGTCAAAGGGAACCACTCATCAGTATTCGAGGGATCGTCTTCC
+CGTCATTCCTTCAGAGATTTTATCCCTTAATTGTGTCAGAGAGCAGGGCGGAACCTCAGA
+GTCACTCTCTGGTACAGGATCTGGAACCCAGGAGGATTCCTCTCCCTCAGGACCAGAGGG
+AGGGCGATATTCTAGTGTTGGTCCCAATTGTCTCCCCTCCTTGTGGGAGGCCAGCCCGGG
+AGATCTACAGGCGATCAGGGAGGCGCCCCGTGGCCCCTGGTACCCGTGCGCTGCAGCGTC
+TCCTTCCCGTTCTCCAGGTATCTGCGGAGCCACTCCACGCACGTGCCATCCAGGTAGGCT
+CTCAACTGCTCCGCCTCATGGGCCGCCTCCCACTTGCGCTTGGTGATCTGAGCCGCCATG
+TCCGCCGCGGTCCAAGAGCGCAGGTCCTCGTTCAGGGCGATGTAATCCTTGCCGTCGTAG
+GCGTCCTGCCGGTACCCGCGGAGGAAGCGCCCGTCCGACCCCACGTCGCAGCCATACATT
+ATCTGGATGGTGTGAGAACCTGGCCCCGACCCCGCGGTCAGCCCAGTCCCCCGAGCCCCG
+CCCAGCCCCGACCAACCCGGGGGGATTTTTGGCCTAAACTGAAAATGAAACCGGGTAAAG
+GCGCCTGGGCCTCTCCCGGGGCAAGGGTCTCGGGGTCCCGCGGCTTCGGGGTGGATCTCG
+GACCCGGAGACTGTGGGCGACCTGGCCCGTCCGTGGGGGATGAGGGGTCCTGACCTGCGC
+CCCCGGCCGGGGTCACTCACCGGCCTCGCTCTGGTTGTAGTAGCCGCGCAGGGTCCCCAG
+GTCCACTCGGTCAGTCTGTGACTGGGCCTTCACATTCCGTGTCTCCTGGTCCCAATACTC
+CGGCCCCTCCTGCTCTATCCACGGCGCCCGCGGCTCCATCCTCTGGCTCGCGGCGTCGCT
+GTCGAACCGCACGAACTGCGTGTCGTCCACGTAGCCCACGGCGATGAAGCGGGGCTCCCC
+GCGGCCGGGCCGGGACACGGATGTGAAGAAATACCTCATGGAGTGGGAGCCTGGGGGCGA
+GCAGTGGCTGAGACCTGCCCGACCCTCGTCCCGGCGCGGCTCCCCCGGTCCTGCGCCCCC
+GCCAGGAGGGCCCCTTGCTTCTCCCCGCAGAGGCGGTTTCCCTCCCGACCCCGCACTCAC
+CCGCCCAGGTCTGGGTCAGGGCCAGGGCCCCCGAGAGTAGCAGGAGGAGGGTTCGGGGCG
+CCATGACGGCCATCCTCGGCGTCTGGGGAGAATCTGAGTCCCGGTGGGTGCGTGCGGGCT
+TTAGAACAGCGACCGCGACGACACTGATTGGCTTCTCTGGAAACCCGACACCCAATGGGA
+GTGAGAACTGGGTCCGCGTCGTGAGTATCCA
\ No newline at end of file
diff --git a/tests/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.fasta b/tests/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.fasta
new file mode 100644
index 0000000..df0296f
--- /dev/null
+++ b/tests/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.fasta
@@ -0,0 +1,109 @@
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/0_480
+GACGAAAAAAACGCCTCGAGTGAAAAGCGTTAATTGGTATGGCGGTAAAAACCCGCACTC
+AGGCGGCCTTGATAGTCCATATCATCTGAAATCAAAATATTCCTGATGTATCGATAATCG
+GTAATTCTTATTCCTTCGCTACCATCCCATTGGAGGCCATCCTTCCTGACCATTCCCATC
+ATTCATCGACACTCACACACAACAACCATATGCATTTAAGTCGCTTGAAATTGCCTATAA
+GCAGAGCATGTTGCGCCAGCATGATTTAATACAGCATTTAAACAGAGCCGTGTTTATTCG
+AGTCGGTATTTCAGAGTCTGACCAGAAATTATCTAATCCTGGTGAAGTTTTTCCTCTGTC
+ATTACGGTCATGGTCGATTTCAATTCTATGATGCTTTCCAGTCGAAACAATGATGTATTT
+TTTGTGTTTGACATTGTTCATATCCTCAACAGATAAAAAATCGCGCCCTCACACTGGAGA
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/525_1145
+CCAGTGTGAGGGCGATTATTTTATCTGTGAGGATATGAACAGATGTCAAACATCAAAAAA
+TACATCATTGATTACCGACTAGAAAAGCATCAATAAGAAATTGAAAATCGAACCATGACG
+TAATGACAACCGAGCGAAAAACTTCAGCCAGATTCAATAATTTCTGGTCAGGACTCTGAA
+TACCGACTCAATAAACAACGGCTCTGTATTCAAATGCTGTATTAATCATGCTGGCGCAAC
+ATGCTCTGCCTTATAGCAATTTTCCAAGCGACTTAAATGCATATGTGTTTGTGGAGTTCG
+ACCTGGAATGATGGAAATGTCAGGAAGGATGGTCAATGGAATGGTAATAGCGAAGAATAA
+GAATTACGATATCGATACATCAGGAATATTTGATTCAGATGATATGACTATCAAGGCCGC
+CTGAGTGCGGTTTTACCGCATTACCAATAACGCCTTCACTCGAGCGTTTTTCGTTATGTA
+ATAAAATAAGGAGCACACGCATGCAATATGCAATTGCAGGTGGCCCTGTTGCTGGCTGCC
+CTTCCGAATCTTTACTTGAACGAATCCACCCGTAAATTACGTGACGGATGGAAACCGCCT
+TATCGACATACTTAATCAGC
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/1192_1809
+GCTGATTAAGTATGTCGATAAGGCGTTTCATCCGTCCAACGTAATTTAAACGGGTGATTC
+GTTTCAGTAAAGATTCGGAAAGGGCAGCCAGCAACCAAGCCACCCTGCAATGGCATATTG
+CATGGTGTGCTCCTTATTTATACATAACCGAAAAACGCCTCGAGTGACAGCGTTATTGGT
+ATCGCGGTAAACCGCACTCAGGCGGCTTGATAGTCATATCATCTGATCAAATATTCCTGA
+TGTATCGATATCGGTAATTCTTATTCCTTCGCTACCATCCATTGGAGGCCATCCTTCCTG
+ACCATTTCCATCCATTCCAGTCGAACTCACACACCAACACCATAATGCATTTAAGTCGCT
+TGAAATTGCCTATAAGGCCAAGCATGTTGCGCAGCTGATAATACAGCATTTAATACAGAG
+CCGTGTTTATGAGTCGGGTATTCCAGAGTCTGAACCAGAAATTATTAATCTGGTGAAGTT
+TTTCCTCTGTCATTACGTCATGGTCGATTTCCCAATTTCTATTGATGCTTTCCAGTCCGT
+AATCAATGATGTATTTTTTGATGTTTTGACATCCTGTTCATATCCTCACAGATAAAAAAT
+CGCCCTCACACTGGAGA
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/1855_2488
+CTCCCAGTGTGAGGGCGATTTTTTATCTGTGAGGATAATGAACAGATGTCAAACATCAAA
+AAATACATCATTGATTAACCGACTGGAAAGCATCAATAGAAATTGAAAATCGACCATGAC
+GTAATGACAGAGGAAAAACTTCAGCCAAGATTAATAATTTCTGGTCACGACTTGAATACG
+CGACTCAATAAACACGGCTCTGTATTAAAATGCCTGTATTATCATGCTGGCGCAACCATG
+CTCTGCTTATACAATTTCAAGCCGACTTAAATGCATTACTGGTGTTGTGTGTGGAGTTCG
+ACCTGGAATGATAGGAATGGTCAGGAAGGATGGCCTCCAAATGGATGGTAGCGAAGGAAT
+AAGAATTACCGAATATCCGATACATCAGGAATATTTGATTCAGATGATATGACTATCAAA
+GGCCGCCTGAGTGCGGTTTTAAACGCATACCATTCCCATAACGCTTCACTCGAGTCGTTT
+TTTCGTTATGTATAAATAAGGAGCACACCATGCAATATGCCATTGCAGCGGTGGCCTGTT
+GCTGGCTGCCCTTCCGAATCTTTACTTGAACCGAATCACCCGTAAAATTTACGTGACGGA
+TGGAAACGCCTTATCGACATTACTCTAATCAGC
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/2530_3148
+GCCTGATTAAAGTATGCGACTAAGCGTTTTCATCCGTCACGTAATTTACGGTGATTCGTC
+TCAGTAAAAGATTCGGAAGGGCAGCCAGCAACAGCCACCCTGCAATGGCATATTGCAATG
+TGTGCTCCTTATTTATACATAACGAAAAAACGCCTCGAGTGAAGCGTTATTGTATGCGGT
+AAAACCGCACTCAAGGCGGCCTTGATAGTCATCACTCATCTGAATCAAATATTCCTGAAT
+GTATCGATATCGTAATCTCCTTAATTCCTTCGCTACCATCCATCTGGAGGCATCCCTTCC
+CTGAACCCATTTCCATCATTCCAAATCGAACTCACACACAACACCATATGCATTTAAGGT
+CGCTATAATTGCATAAGCAGAGCATGTTGCGCCAGCATGATTTAACTACAGCATTTAATA
+CAGAGCCGTGTTTATTGAGTCGGTATTCAGAGTCTGACCAGAAATTAATTAATCTGGTGA
+AGTTTTTCCTCTGTCATTACGTCATGGTCCGATTTCAATTTCTATTGATGCTTTCCAGTC
+GTAATCAAATGAGTGTATTTTTTGATTTTGACATCTGTTCATATCCTCACAGATAAAAAA
+TCGCCCTCACACTGGAAG
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/3195_3818
+CTCCAGTGTGAGGGCGATTTTTTATCTGTGAGGATATGAACAGATGTCAAACTCAAAAAA
+TACATCATTCGATTACAGACTGGAAAGCATCATTAGAAAATTGAAATCGACCATGACGTA
+ATGACCACAGAGGAAAAACTTCACCAGATAATAATTTCTGGTCAGACTCCTGAATACCGA
+CTCAATAAACACGGCTCCCTGTATTAAATGCTGTATTAATCATGCTGGGCGCAACATGCT
+CTGCTTATAGCAATTCAACGGCGACTTAAATGCATATGGTGTTGTGTGTGAGTTCGACTG
+GAATATGGAAATGGTCACGGAAGGATGGCCTCCCAATGGAATGGTAGCGAAGGAATAAGA
+ATTACCGATATCGATACATCGGAATATTTGATTCAGATGATATGACTATCAAGGCCGCCT
+GAGTGCGGTTTTACCGCATACCAAATAACGCTTCACTCCCGAGGCGTTTTTCGTTATGTA
+AAAATACAGGAGCACACCCATGCAATATGGCCAATTGCAGGGTGGCCTGTTGCTGGCTGC
+CCTTCCGAATCTTTACTTGAACGAAATCACCCCGTAAATTACGTGACGGATGGAAACGCC
+TTAATCGACATACTTAATCAGCC
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/3864_4486
+GCTGATTAAGTATGTCCGATAAGGCGGTTTCCCATCCGTCACGTAATTTACGGGTGATTC
+GTTCAATTTAAAGATTCGGAAAGGGCAGCCAGCAACAGCCACCCTGCAATGGCATAATTG
+CATGGTTGCTCCGTATTTATACATAACGAAAAACGCCTCGAGTGAAGCGTTATTGGTATG
+CGGTAAAACCCACTCAGGCGGCCTTGATAGTCATATCATTCTGAATCCAAAATATTCCTG
+ATGTATCGATATCGGTAATTCTTCATTCCTTCGCTACCATCCCATCTGGAGCCATCCTGT
+CCTGACCCATTTCCATCATTCCAGTCGAACTCAACACACAACACCCTATGCTTTCAAGCG
+CTTTGAAATTGCTATAAGCAGAGCATGTTGCGCCAGCATGATTAATACAGCATTTAATAC
+AGAGCCGTGTTTATTGAGTCGGTATTCAGAGTCTGACCAGAAATTATTAAAATCTGGTGA
+AGTTTTTCCTCATGTCATTACGTCCATGGTGATTTCCAATTTCTATTGATGCTTTCCAGT
+CGTAAATCAATGATGTATTTTTTTGATGTTTTGACATCTGTTCCATATCCTCACAGATAC
+AAAAATCGCCCCTCACACTGAG
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/4532_5139
+CTCCAGTGTGAGCGGCGATTTTTTATTCTGTGAGGATATGAACAGAATGTCATACATCAA
+AAAATACATCATTGATTACACTGAAAGCATCAATAGAAATTGAAATCGACCATGACGTAA
+TGACAGAGAAAAACACTTCACCAATTAATAATTTCCCTGGTCAGACCTGAATACCGACTC
+AATAAACACGGCTCTGTATTAAAATGCTGTATTCATCATGCTGGCGCAACATGCTCTGCT
+TAATAGCAATTTCAAGCGACTTAAATGCCATTGGTGTTGTGTGTGAGTTCGACTGGAATG
+ATGGAAATGGTCAGGAAGGAATGGCCTCCAATGGATGGTACGAAGGAATAAGATTACCGA
+TATCGATACAATCAGGAGTATTTGATTCAGATGATATGACTATCAAGGCCGCCTGAGTGC
+GGTTTACCGCTAAACAATAACGCTTCACTCGAGGCGTTTTTCGTTATGTATAAATAAGGA
+GCCCACATGCAATATGCCATTTGCGGTGGCCTGTGCTGGCTGCCCTTCGAATCTTTACTT
+TTGAACGAATCACCCGTAAATTAACGTGACGGATGGAAAACGCCTTATCCGACCATACTT
+AATCAGC
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/5189_5805
+GCCTGATTAAGTATGTCGATAAGGCGTTTCCATCCGTCACGTAATTTACGGGTGATTCGT
+TCAAGTAAAAAGATTCGGAAGGGGCAAGCCAGCAACAGGCCACCCTGCAATGGCATATTG
+CATGGTGTGCTCCTTATTTATACATAACGAAAAACCCTCGAGTGAACGTTAATTGGTATG
+CGGTAAAAACCGCACTCAGGCGGCCTTGATAGTCTATCATCTGAATCAAATATTCCTGAT
+GTATCGATATCGGTAATTCTTATTCCCTATCGCTACATCCATTGAGGCCATCCTTCTGAC
+CATTTCCAATCATTCCCAGTCGAACTCACACACAACACCATATGCATTTTTAAGTCGCTT
+GAAATTGCTATAAGCAGAGCATGTTGCGCCAGCATGATTAATAACAGCATTTAATACAGA
+GCCGTGTTTATTGAGTCGGTATTCAGAGTCTGACCAGAAATTATTTAATTCTGGTGAAGT
+TTTTCCTCTGTCATTACTCATGGTCCGATTTCAATTTCTAATTTGAATGCTTTCCAGTCG
+TAATCAATGATGTATTTTTGATGTTTGACATCTGTTCATATCCTCACAAGATAAAAAATC
+CGCCCTCACACTGGAG
+>m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6251/5851_5993
+CCTCCCCAGTGTGAGGCGATTTTTTATCTGTTGAGTGAACAGATGTCCAAACATCAAAAA
+TACAATCCATTGTTACGACTGAAAAGCATCAAATAGAAATTGAAAATCGACCATGACGTA
+ATGACAGAGGAAAAACTTCACC
diff --git a/tests/data/mapping.xml b/tests/data/mapping.xml
new file mode 100644
index 0000000..e0e5fa4
--- /dev/null
+++ b/tests/data/mapping.xml
@@ -0,0 +1,142 @@
+<?xml version="1.0" encoding="utf-8"?>
+<MappingTable>
+ <DefaultSequencingChemistry>XL-C2</DefaultSequencingChemistry>
+ <Mapping>
+ <SequencingChemistry>C2</SequencingChemistry>
+ <BindingKit>001672551</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>1.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>C2</SequencingChemistry>
+ <BindingKit>001672551</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>2.0</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>C2</SequencingChemistry>
+ <BindingKit>001672551</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>2.1</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>C2</SequencingChemistry>
+ <BindingKit>001672551</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>2.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>XL-C2</SequencingChemistry>
+ <BindingKit>100150800</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>1.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>XL-C2</SequencingChemistry>
+ <BindingKit>100150800</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>2.0</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>XL-C2</SequencingChemistry>
+ <BindingKit>100150800</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>2.1</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>XL-C2</SequencingChemistry>
+ <BindingKit>100150800</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>2.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>XL-XL</SequencingChemistry>
+ <BindingKit>100150800</BindingKit>
+ <SequencingKit>100180800</SequencingKit>
+ <SoftwareVersion>1.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>XL-XL</SequencingChemistry>
+ <BindingKit>100150800</BindingKit>
+ <SequencingKit>100180800</SequencingKit>
+ <SoftwareVersion>2.0</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>XL-XL</SequencingChemistry>
+ <BindingKit>100150800</BindingKit>
+ <SequencingKit>100180800</SequencingKit>
+ <SoftwareVersion>2.1</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>XL-XL</SequencingChemistry>
+ <BindingKit>100150800</BindingKit>
+ <SequencingKit>100180800</SequencingKit>
+ <SoftwareVersion>2.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P4-C2</SequencingChemistry>
+ <BindingKit>100236500</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>1.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P4-C2</SequencingChemistry>
+ <BindingKit>100236500</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>2.0</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P4-C2</SequencingChemistry>
+ <BindingKit>100236500</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>2.1</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P4-C2</SequencingChemistry>
+ <BindingKit>100236500</BindingKit>
+ <SequencingKit>001558034</SequencingKit>
+ <SoftwareVersion>2.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P4-XL</SequencingChemistry>
+ <BindingKit>100236500</BindingKit>
+ <SequencingKit>100180800</SequencingKit>
+ <SoftwareVersion>2.0</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P4-XL</SequencingChemistry>
+ <BindingKit>100236500</BindingKit>
+ <SequencingKit>100180800</SequencingKit>
+ <SoftwareVersion>2.1</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P4-XL</SequencingChemistry>
+ <BindingKit>100236500</BindingKit>
+ <SequencingKit>100180800</SequencingKit>
+ <SoftwareVersion>2.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P5-C3</SequencingChemistry>
+ <BindingKit>100256000</BindingKit>
+ <SequencingKit>100254800</SequencingKit>
+ <SoftwareVersion>2.1</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P5-C3</SequencingChemistry>
+ <BindingKit>100256000</BindingKit>
+ <SequencingKit>100254800</SequencingKit>
+ <SoftwareVersion>2.3</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P6-C4</SequencingChemistry>
+ <BindingKit>100356300</BindingKit>
+ <SequencingKit>100356200</SequencingKit>
+ <SoftwareVersion>2.1</SoftwareVersion>
+ </Mapping>
+ <Mapping>
+ <SequencingChemistry>P6-C4</SequencingChemistry>
+ <BindingKit>100356300</BindingKit>
+ <SequencingKit>100356200</SequencingKit>
+ <SoftwareVersion>2.3</SoftwareVersion>
+ </Mapping>
+</MappingTable>
diff --git a/tests/data/params/SP1C1Beta.json b/tests/data/params/SP1C1Beta.json
new file mode 100644
index 0000000..198e278
--- /dev/null
+++ b/tests/data/params/SP1C1Beta.json
@@ -0,0 +1,208 @@
+{
+ "ConsensusModelVersion": "3.0.0",
+ "ChemistryName": "S/P1-C1/beta",
+ "ModelForm": "Marginal",
+ "EmissionParameters": [
+ [
+ [
+ 0.979840156,
+ 0.012582917,
+ 0.005185205,
+ 0.002391722
+ ],
+ [
+ 0.015528755,
+ 0.984439781,
+ 7.91000E-07,
+ 3.07000E-05
+ ],
+ [
+ 0.002667013,
+ 0.002095727,
+ 0.961571053,
+ 0.033666207
+ ],
+ [
+ 0.000506358,
+ 0.001057035,
+ 0.116124340,
+ 0.882312267
+ ],
+ [
+ 0.980417570,
+ 0.011537479,
+ 0.005804964,
+ 0.002239987
+ ],
+ [
+ 0.026122324,
+ 0.972937583,
+ 0.000367796,
+ 0.000572296
+ ],
+ [
+ 0.002544283,
+ 0.002239375,
+ 0.962042375,
+ 0.033173967
+ ],
+ [
+ 0.000509814,
+ 0.001489097,
+ 0.094228328,
+ 0.903772761
+ ]
+ ],
+ [
+ [
+ 1,
+ 0,
+ 0,
+ 0
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ 0
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ 0
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ],
+ [
+ 1,
+ 0,
+ 0,
+ 0
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ 0
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ 0
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ],
+ [
+ [
+ 0.000000000,
+ 0.210676350,
+ 0.615161689,
+ 0.174161960
+ ],
+ [
+ 0.357451562,
+ 0.000000000,
+ 0.473482915,
+ 0.169065523
+ ],
+ [
+ 0.577147745,
+ 0.169785817,
+ 0.000000000,
+ 0.253066438
+ ],
+ [
+ 0.446834358,
+ 0.144605809,
+ 0.408559833,
+ 0.000000000
+ ],
+ [
+ 0.000000000,
+ 0.254503401,
+ 0.574809968,
+ 0.170686631
+ ],
+ [
+ 0.399446202,
+ 0.000000000,
+ 0.510664061,
+ 0.089889737
+ ],
+ [
+ 0.505214805,
+ 0.188597323,
+ 0.000000000,
+ 0.306187872
+ ],
+ [
+ 0.361855644,
+ 0.132870306,
+ 0.505274050,
+ 0.000000000
+ ]
+ ]
+ ],
+ "TransitionParameters": [
+ [
+ 0.857630366,
+ 0.072058988,
+ 0.036435296,
+ 0.033875351
+ ],
+ [
+ 0.846000625,
+ 0.032981179,
+ 0.076759732,
+ 0.044258463
+ ],
+ [
+ 0.881462348,
+ 0.042444137,
+ 0.039293952,
+ 0.036799562
+ ],
+ [
+ 0.879087800,
+ 0.022178294,
+ 0.057073518,
+ 0.041660389
+ ],
+ [
+ 0.888913751,
+ 0.021169653,
+ 0.034937054,
+ 0.054979542
+ ],
+ [
+ 0.835822697,
+ 0.036126801,
+ 0.091992041,
+ 0.036058461
+ ],
+ [
+ 0.886427657,
+ 0.022596867,
+ 0.039619893,
+ 0.051355584
+ ],
+ [
+ 0.821252207,
+ 0.072798639,
+ 0.068161389,
+ 0.037787765
+ ]
+ ],
+ "CounterWeight": 1.0
+}
diff --git a/tests/data/params/SP1C1v1.json b/tests/data/params/SP1C1v1.json
new file mode 100644
index 0000000..77779d7
--- /dev/null
+++ b/tests/data/params/SP1C1v1.json
@@ -0,0 +1,1012 @@
+{
+ "ConsensusModelVersion": "3.0.0",
+ "ChemistryName": "S/P1-C1.1",
+ "ModelForm": "PwSnrA",
+ "SnrRanges": [
+ 4.0,
+ 10.65
+ ],
+ "EmissionParameters": [
+ [
+ [
+ 0.0516695237,
+ 0.000856759021,
+ 0.000805765869,
+ 6.40098033e-05,
+ 0.0735681929,
+ 0.000490647727,
+ 0.00171763848,
+ 1.66588276e-05,
+ 0.864949369,
+ 0.00298262543,
+ 0.0027926093,
+ 6.28389773e-05
+ ],
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diff --git a/tests/data/params/SP1C1v2.json b/tests/data/params/SP1C1v2.json
new file mode 100644
index 0000000..09ac375
--- /dev/null
+++ b/tests/data/params/SP1C1v2.json
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diff --git a/tests/data/test.fastq b/tests/data/test.fastq
new file mode 100644
index 0000000..7456d78
--- /dev/null
+++ b/tests/data/test.fastq
@@ -0,0 +1,40 @@
+ at Barcode0_Cluster2_Phase2_NumReads57
+TCAGGCACACAGTGTGACAAAGATGCTTGGTGTAGGAGAAGAGGAATCAGGACGAAGTCCCAGGTCCCGGGCGGGGCTCTCAGGGTCTCAGGCTCCAAGGGCCGTGTCTGCACTGGGGAGGCGCCGCGTTGAGGATTCTCCACTCCCCTGAGTTTCACTTCTTCTCCCAACCTGCGTCGGGTCCTTCTTCCTGAATACTCATGACGCGTCCCCAATTCCCACTCCCATTGGGTGTCGGATTCTAGAGAAGCCAATCAGCGTCTCCGCAGTCCCGGTTCTGAAGTCCCCAGTCACCCACCCGGACTCAGATTCTCCCCAGACGCCGAGATGCGGGTCATGGCGCCCCGAACCCTCATCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCTGGGCCGGTGAGTGCGGGGTTGGGAGGGAATCGGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGGAGCCGCGCAGGGA [...]
++
+qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqGqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqiqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq]qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqdqqqqqqqqqqqqqqqq [...]
+ at Barcode0_Cluster0_Phase2_NumReads52
+TCAGGCACACAGTGTGACAAAGATGCTTGGTGTAGGAGAAGAGGGATCAGGACGAAGTCCCAGGTCCCGGGCGGGGCTCTCAGGGTCTCAGGCTCCAAGGGCCGTGTCTGCACTGGGGAGGCGCCGCGTTGAGGATTCTCCACTCCCCTGAGTTTCACTTCTTCTTCCAACCTGCGTCGGGTCCTTCTTCCTGAATACTCATGACGCGTCCCCAATTCCCACTCCCATTGGGTGTCGGGTTCTAGAGAAGCCAATCAGCGTCTCCGCAGTCCCGGTTCTAAAGTCCCCAGTCACCCACCCGGACTCGGATTCTCCCCAGACGCCGAGATGCGGGTCATGGCGCCCCGAACCCTCATCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCTGGGCCTGTGAGTGCGAGGTTGGGAGGGAAACGGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGGAGCCGCGCAGGGA [...]
++
+qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqcqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqfqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqaqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqfqqqqqqiqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqaqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqLqqqLqqqqqqqqqqqZqqqqqqqqqqqqqqqqqqqqqqqqqqqqq [...]
+ at Barcode0_Cluster3_Phase0_NumReads45
+CCGCAAGCTTCTGGGGAGGAAACACAGGTCAGCATGGGAACAGGGGTCACAGTGGACACAAGGGTGGGCTGTCTCTCCACCTCCTCACATTATGCTAACAGGGACGCAGACACATTCAGGTGCCTTTGCAGAAAGAGATGCCAGAGGCTCTTGAAGTCACAAAGGGGAGGCGTGAAGAAATCCTGCATCTCAGTCCCTCACAAGACAGCTGTCTCAGGCTACAGAAAACAACAGTCATGAACAAATTCTGGTTAGTCATGGTAAGTGATGACACTCTGAACAGCCCACGACACACGCGAAACATCCCAATCAAAGAATCTCCATTACCCAGGCCTTTCCCCACTGCCCCACCCACCCCCAGACCCGCCACCCCACCCACTCTAGACCCCAAGAATCTCACCTTTTCAAGCTGTGAGAGACACATCAGAGCCCTGGGCACTGTCGCTGGCTGGAGTAGAACAAAAACAGGACCTGGTCAGAGCCCGCAGGAGA [...]
++
+q=C>.>CB?D=C5ACB at 7A6B=@C8?9ED=C=9<D=DA0AB at +AD:3C>B<5=+@?9 at 08C,AGC4D=1=?C:BAB2??8D@/C@?@??A?>>BB><ACD<<>DCD:AC@<D:BC?<<ADB@)93BE>C>D8DC9?4;D<?FDDD(74587=:9CC>:@C8<B0CAB=.?A==89BBB>D=>?DB<BC<C06DB)DDD0C5AD;C9>?B=@B=>:A;C:>=?DD4DDCB6A>3<=;D:%;:21;92:B:9D:D at AB)@B3C98?2:/;?C>6B;3AA9(D5@>8DF75CA-=>;BD?D9CB<C99>D>E;;6C?9:=9EE+F at +=>>C9=<@:E8F?)=<B:663)@74@&;49+3BCEA@>1CC83 at B(@??:$==BC at 9;C at D9F>A=B6<A at AC3(*>7><:C>ECB36??<6AA::13<;D=BAB5E:D<@@>=C?1=C<A=<EDB:I<EDDB>D8. at CFDG@9EE3B:4=B9=55D9A=>?DBHFFD [...]
+ at Barcode0_Cluster4_Phase0_NumReads40
+TTGGGCCAAGACTCAGGGAGACATTGAGACAGAGCGCTTGGCACAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAGGGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTATGTAGGGTCCTTCTTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCGGTTCTAAAGTCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCGTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACGGCCTCTGTGGGGAGAAGCAAGGGGCCCGCCCGGCGGGGGCGCAGGACCCG [...]
++
+q'255/955254*14+4452145350;8902(121275;896:94':8587.8#289:981::6#79;9':;87;8%::;;4:772/7/:375:/=::874:(9-::-#4;2996:4305929969)9:<;481@=<:4=6<+<<;<0;/7;82<:;7=47=556=<*<==7<29=;36+;:+86A>BB16=2:;>;B=?<=B8;;'@9:4<A;?7@==:@:B?,BB=:, at A>?9<<:A at B5:1B>A7A9.:8/4459::=B<BA4FBB@@1:;4=?A?6?.-997==:38=B95<<::7>6';@@<97BB=>?4=;=5>=B;BA;BA*ABCB5@>A4?0;4B??:B9B5 at 05?28/0%8>89AA5BB@<822B at 39>=>B:1<+@?>82>B at 6A6<@8<B,BB@/A@@A(A>:.84=(88;>=,7 at 60>'BB9-9;6;>A>B3BB:9;73 at A>?;<?A.;C(??;2C>0(>C9A;+B::??@8A,516A?4 [...]
+ at Barcode0_Cluster1_Phase0_NumReads476
+TGGCCAAGACTCAGGGAGACATTGAGACAGAGCGCTTGGCACAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAGGGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTATGTAGGGTCCTTCTTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCGGTTCTAAAGTCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCGTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACGGCCTCTGTGGGGAGAAGCAAGGGGCCCGCCCGGCGGGGGCGCAGGACCCGGG [...]
++
+qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq [...]
+ at Barcode0_Cluster0_Phase3_NumReads344
+TCAGGCACACAGTGTGACAAAGATGCTTGGTGTAGGAGAAGAGGGATCAGGACGAAGTCCCAGGTCCCGGGCGGGGCTCTCAGGGTCTCAGGCTCCAAGGGCCGTGTCTGCACTGGGGAGGCGCCGCGTTGAGGATTCTCCACTCCCCTGAGTTTCACTTCTTCTTCCAACCTGCGTCGGGTCCTTCTTCCTGAATACTCATGACGCGTCCCCAATTCCCACTCCCATTGGGTGTCGGGTTCTAGAGAAGCCAATCAGCGTCTCCGCAGTCCCGGTTCTAAAGTCCCCAGTCACCCACCCGGACTCGGATTCTCCCCAGACGCCGAGATGCGGGTCATGGCGCCCCGAACCCTCATCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCTGGGCCTGTGAGTGCGAGGTTGGGAGGGAAACGGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGGAGCCGCGCAGGGA [...]
++
+qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq [...]
+ at Barcode0_Cluster2_Phase3_NumReads285
+TCAGGCACACAGTGTGACAAAGATGCTTGGTGTAGGAGAAGAGGAATCAGGACGAAGTCCCAGGTCCCGGGCGGGGCTCTCAGGGTCTCAGGCTCCAAGGGCCGTGTCTGCACTGGGGAGGCGCCGCGTTGAGGATTCTCCACTCCCCTGAGTTTCACTTCTTCTCCCAACCTGCGTCGGGTCCTTCTTCCTGAATACTCATGACGCGTCCCCAATTCCCACTCCCATTGGGTGTCGGATTCTAGAGAAGCCAATCAGCGTCTCCGCAGTCCCGGTTCTGAAGTCCCCAGTCACCCACCCGGACTCAGATTCTCCCCAGACGCCGAGATGCGGGTCATGGCGCCCCGAACCCTCATCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCTGGGCCGGTGAGTGCGGGGTTGGGAGGGAATCGGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGGAGCCGCGCAGGGA [...]
++
+qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq [...]
+ at Barcode0_Cluster3_Phase1_NumReads185
+CCGCAAGCTTCTGGGGAGGAAACACAGGTCAGCATGGGAACAGGGGTCACAGTGGACACAAGGGTGGGCTGTCTCTCCACCTCCTCACATTATGCTAACAGGGACGCAGACACATTCAGGTGCCTTTGCAGAAAGAGATGCCAGAGGCTCTTGAAGTCACAAAGGGGAGGCGTGAAGAAATCCTGCATCTCAGTCCCTCACAAGACAGCTGTCTCAGGCTACAGAAAACAACAGTCATGAACAAATTCTGGTTAGTCATGGTAAGTGATGACACTCTGAACAGCCCACGACACACGCGAAACATCCCAATCAAAGAATCTCCATTACCCAGGCCTTTCCCCACTGCCCCACCCACCCCCAGACCCGCCACCCCACCCACTCTAGACCCCAAGAATCTCACCTTTTCAAGCTGTGAGAGACACATCAGAGCCCTGGGCACTGTCGCTGGCTGGAGTAGAACAAAAACAGGACCTGGTCAGAGCCCGCAGGAGA [...]
++
+qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq [...]
+ at Barcode0_Cluster5_Phase0_NumReads158
+GGCAGACAGTGTGACAAAGAGGCTTGGTGTAGGAGAAGAGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTCCGAGGGCCGCGTCTGCAATGGGGAGGCGCAGCGTTGGGGATTCCCCACTCCCCTGAGTTTCACTTCTTCTCCCAACTTGTGTCGGGTCCTTCTTCCAGGATACTCGTGACGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCAGCGTCGCCGGGGTCCCAGTTCTAAAGTCCCCACGCACCCACCCGGACTCAGAGTCTCCTCAGACGCCAAGATGCTGGTCATGGCGCCCCGAACCGTCCTCCTGCTGCTCTCGGCGGCCCTGGCCCTGACCGAGACCTGGGCCGGTGAGTGCGGGTCGGGAGGGAAATGGCCTCTGCCGGGAGGAGCGAGGGGACCGCAGGCGGGGGCGCAGGACCTGAGGAGCCGCGCCGGGAGGAG [...]
++
+qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq [...]
+ at Barcode0_Cluster4_Phase1_NumReads129
+TTGGGCCAAGACTCAGGGAGACATTGAGACAGAGCGCTTGGCACAGAAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAGGGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTATGTAGGGTCCTTCTTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGTCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCGTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCAGGTGAGTGCGGGGTCGGGAGGGAAACGGCCTCTGCGGGGAGAAGCAAGGGGCCCGCCTGGCGGGGGCGCAAGACCCG [...]
++
+qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq [...]
diff --git a/tests/data/tiny.bam b/tests/data/tiny.bam
new file mode 100644
index 0000000..f733b30
Binary files /dev/null and b/tests/data/tiny.bam differ
diff --git a/tests/python/test_tool_contract.py b/tests/python/test_tool_contract.py
new file mode 100755
index 0000000..de47ca1
--- /dev/null
+++ b/tests/python/test_tool_contract.py
@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+
+"""
+Test for tool contract interface support, using a SubreadSet with filters
+applied as input.
+"""
+
+import logging
+import tempfile
+import unittest
+import os.path as op
+import os
+
+import pbcommand.testkit
+from pbcore.io import ConsensusReadSet, SubreadSet
+
+import pbtestdata
+
+logging.basicConfig(level=logging.INFO)
+CCS_DIR = op.dirname(op.dirname(op.dirname(__file__)))
+CHUNK_INDEX = 1
+
+class TestCCSApp(pbcommand.testkit.PbTestApp):
+ # FIXME eventually the 'ccs' binary should handle TCI directly
+ DRIVER_BASE = op.join(CCS_DIR, "scripts", "task_pbccs_ccs")
+ REQUIRES_PBCORE = True
+ INPUT_FILES = [tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name]
+ TASK_OPTIONS = {
+ "pbccs.task_options.min_snr": 3,
+ "pbccs.task_options.min_read_score": 0.75,
+ "pbccs.task_options.min_length": 10,
+ "pbccs.task_options.min_passes": 3,
+ "pbccs.task_options.min_zscore": -5,
+ "pbccs.task_options.max_drop_frac": 0.33,
+ "pbccs.task_options.no_polish": True,
+ }
+
+ def setUp(self):
+ BAM_IN = pbtestdata.get_file("subreads-bam")
+ ds = SubreadSet(BAM_IN, strict=True)
+ chunks = ds.split(zmws=True, chunks=2, targetSize=2)
+ assert len(chunks) == 2
+ self.zmw_range = chunks[CHUNK_INDEX].zmwRanges[0][1:3]
+ logging.info("zmwRanges[CHUNK_INDEX] = {r}".format(
+ r=str(chunks[CHUNK_INDEX].zmwRanges)))
+ logging.info("SubreadSet = {f}".format(f=self.INPUT_FILES[0]))
+ chunks[CHUNK_INDEX].write(self.INPUT_FILES[0])
+ #tf = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
+ #print tf
+ #chunks[int(not CHUNK_INDEX)].write(tf)
+
+ def run_after(self, rtc, output_dir):
+ with ConsensusReadSet(rtc.task.output_files[0]) as ds_out:
+ zmws = set(ds_out.resourceReaders()[0].holeNumber)
+ logging.info("ZMWs = {z}".format(z=zmws))
+ for z in zmws:
+ self.assertTrue(self.zmw_range[0] < z < self.zmw_range[1])
+
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/ChimeraTest.cpp b/tests/unit/ChimeraTest.cpp
new file mode 100644
index 0000000..ba3af92
--- /dev/null
+++ b/tests/unit/ChimeraTest.cpp
@@ -0,0 +1,97 @@
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <seqan/seq_io.h>
+
+#include "pacbio/chimera/ChimeraLabel.h"
+#include "pacbio/chimera/ChimeraLabeler.h"
+
+#include "TestData.h"
+
+using namespace PacBio::Chimera;
+
+const std::string FILENAME1 = tests::DataDir + "/chimera_minimal.fasta";
+const std::string FILENAME2 = tests::DataDir + "/chimera_extensive.fasta";
+
+TEST(ChimeraLabeler, MinimalEndToEnd)
+{
+ using namespace seqan;
+
+ SeqFileIn inputHandle(FILENAME1.c_str());
+
+ // Parse the records
+ StringSet<CharString> ids;
+ StringSet<Dna5String> seqs;
+ readRecords(ids, seqs, inputHandle);
+
+ // Declare the vectors we'll use to actually perform the Chimera-labeling
+ std::vector<std::string> idList;
+ std::vector<Dna5String> seqList;
+
+ for (size_t i = 0; i < length(ids); ++i) {
+ idList.push_back(toCString(static_cast<CharString>(ids[i])));
+ seqList.push_back(static_cast<Dna5String>(seqs[i]));
+ }
+
+ // Label the Records
+ ChimeraLabeler chimeraLabeler;
+ const auto& labels = chimeraLabeler.LabelChimeras(idList, seqList);
+
+ // Expect 4 labels
+ EXPECT_EQ(labels.size(), 4);
+
+ // Expect the first 2 (non-Chimeric) sequences to have no score
+ EXPECT_EQ(labels[0].score, -1.0);
+ EXPECT_EQ(labels[1].score, -1.0);
+
+ // Expect the next (homologous) sequence to have a low, non-zero score
+ EXPECT_LT(labels[2].score, 1.0);
+ EXPECT_GT(labels[2].score, 0.0);
+
+ // Expect the last (Chimeric) sequence to have a high score
+ EXPECT_GT(labels[3].score, 1.0);
+}
+
+#if EXTENSIVE_TESTING
+TEST(ChimeraLabeler, ExtensiveEndToEnd)
+{
+ using namespace seqan;
+
+ SeqFileIn inputHandle(FILENAME2.c_str());
+
+ // Parse the records
+ StringSet<CharString> ids;
+ StringSet<Dna5String> seqs;
+ readRecords(ids, seqs, inputHandle);
+
+ // Declare the vectors we'll use to actually perform the Chimera-labeling
+ std::vector<std::string> idList;
+ std::vector<Dna5String> seqList;
+
+ for (size_t i = 0; i < length(ids); ++i) {
+ idList.push_back(toCString(static_cast<CharString>(ids[i])));
+ seqList.push_back(static_cast<Dna5String>(seqs[i]));
+ }
+
+ // Label the Records
+ ChimeraLabeler chimeraLabeler;
+ const auto& labels = chimeraLabeler.LabelChimeras(idList, seqList);
+
+ // Expect 10 labels
+ EXPECT_EQ(labels.size(), 10);
+
+ // Expect the first 6 (non-Chimeric) sequences to have low scores
+ EXPECT_LT(labels[0].score, 1.0);
+ EXPECT_LT(labels[1].score, 1.0);
+ EXPECT_LT(labels[2].score, 1.0);
+ EXPECT_LT(labels[3].score, 1.0);
+ EXPECT_LT(labels[4].score, 1.0);
+ EXPECT_LT(labels[5].score, 1.0);
+
+ // Expect the last 4 (Chimeric) sequences to have high scores
+ EXPECT_GT(labels[6].score, 1.0);
+ EXPECT_GT(labels[7].score, 1.0);
+ EXPECT_GT(labels[8].score, 1.0);
+ EXPECT_GT(labels[9].score, 1.0);
+}
+#endif
\ No newline at end of file
diff --git a/tests/unit/Mutations.cpp b/tests/unit/Mutations.cpp
new file mode 100644
index 0000000..1e57b8a
--- /dev/null
+++ b/tests/unit/Mutations.cpp
@@ -0,0 +1,67 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include "Mutations.h"
+
+std::vector<PacBio::Consensus::Mutation> Mutations(const std::string& tpl, const size_t start,
+ const size_t end)
+{
+ using namespace PacBio::Consensus;
+
+ constexpr auto bases = "ACGT";
+
+ std::vector<Mutation> result;
+
+ for (size_t i = start; i < end; ++i) {
+ for (size_t j = 0; j < 4; ++j)
+ result.push_back(Mutation(MutationType::INSERTION, i, bases[j]));
+
+ result.push_back(Mutation(MutationType::DELETION, i));
+
+ for (size_t j = 0; j < 4; ++j)
+ if (bases[j] != tpl[i])
+ result.push_back(Mutation(MutationType::SUBSTITUTION, i, bases[j]));
+ }
+
+ for (size_t j = 0; j < 4; ++j)
+ result.push_back(Mutation(MutationType::INSERTION, tpl.length(), bases[j]));
+
+ return result;
+}
+
+std::vector<PacBio::Consensus::Mutation> Mutations(const std::string& tpl)
+{
+ return Mutations(tpl, 0, tpl.length());
+}
diff --git a/tests/unit/Mutations.h b/tests/unit/Mutations.h
new file mode 100644
index 0000000..550242c
--- /dev/null
+++ b/tests/unit/Mutations.h
@@ -0,0 +1,46 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include <pacbio/consensus/Mutation.h>
+
+std::vector<PacBio::Consensus::Mutation> Mutations(const std::string& tpl, const size_t start,
+ const size_t end);
+
+std::vector<PacBio::Consensus::Mutation> Mutations(const std::string& tpl);
diff --git a/tests/unit/RandomDNA.cpp b/tests/unit/RandomDNA.cpp
new file mode 100644
index 0000000..ca0963f
--- /dev/null
+++ b/tests/unit/RandomDNA.cpp
@@ -0,0 +1,60 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include "RandomDNA.h"
+
+using namespace std;
+
+string RandomDNA(const size_t n, mt19937* const gen)
+{
+ constexpr auto bases = "ACGT";
+ string result(n, 'A');
+ uniform_int_distribution<size_t> rand(0, 3);
+
+ for (size_t i = 0; i < n; ++i)
+ result[i] = bases[rand(*gen)];
+
+ return result;
+}
+
+std::vector<uint8_t> RandomPW(const size_t n, mt19937* const gen)
+{
+ std::vector<uint8_t> result(n);
+ uniform_int_distribution<size_t> rand(1, 4);
+ for (size_t i = 0; i < n; ++i)
+ result[i] = rand(*gen);
+
+ return result;
+}
diff --git a/tests/unit/RandomDNA.h b/tests/unit/RandomDNA.h
new file mode 100644
index 0000000..b9d7185
--- /dev/null
+++ b/tests/unit/RandomDNA.h
@@ -0,0 +1,42 @@
+// Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#pragma once
+
+#include <random>
+#include <string>
+#include <vector>
+std::string RandomDNA(const size_t n, std::mt19937* const gen);
+std::vector<uint8_t> RandomPW(const size_t n, std::mt19937* const gen);
\ No newline at end of file
diff --git a/tests/unit/TestAlignment.cpp b/tests/unit/TestAlignment.cpp
new file mode 100644
index 0000000..dfd2d8c
--- /dev/null
+++ b/tests/unit/TestAlignment.cpp
@@ -0,0 +1,370 @@
+// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Authors: David Alexander, Lance Hepler
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <pacbio/align/AffineAlignment.h>
+#include <pacbio/align/LinearAlignment.h>
+#include <pacbio/align/PairwiseAlignment.h>
+
+using namespace PacBio::Align; // NOLINT
+using ::testing::ElementsAreArray;
+
+TEST(PairwiseAlignmentTests, RepresentationTests)
+{
+ PairwiseAlignment a("GATC", "GA-C");
+ EXPECT_EQ("GATC", a.Target());
+ EXPECT_EQ("GA-C", a.Query());
+ EXPECT_EQ(4, a.Length());
+ EXPECT_EQ(3, a.Matches());
+ EXPECT_EQ(1, a.Deletions());
+ EXPECT_EQ(0, a.Mismatches());
+ EXPECT_EQ(0, a.Insertions());
+ EXPECT_FLOAT_EQ(0.75, a.Accuracy());
+ EXPECT_EQ("MMDM", a.Transcript());
+
+ PairwiseAlignment a2("GATTA-CA", "CA-TAACA");
+ EXPECT_EQ("RMDMMIMM", a2.Transcript());
+ EXPECT_FLOAT_EQ(5. / 8, a2.Accuracy());
+ EXPECT_EQ(1, a2.Mismatches());
+ EXPECT_EQ(1, a2.Deletions());
+ EXPECT_EQ(1, a2.Insertions());
+ EXPECT_EQ(5, a2.Matches());
+}
+
+TEST(PairwiseAlignmentTests, GlobalAlignmentTests)
+{
+ PairwiseAlignment* a = Align("GATT", "GATT");
+ EXPECT_FLOAT_EQ(1.0, a->Accuracy());
+ EXPECT_EQ("GATT", a->Target());
+ EXPECT_EQ("GATT", a->Query());
+ EXPECT_EQ("MMMM", a->Transcript());
+ delete a;
+
+ a = Align("GATT", "GAT");
+ EXPECT_FLOAT_EQ(0.75, a->Accuracy());
+ EXPECT_EQ("GATT", a->Target());
+ EXPECT_EQ("GA-T", a->Query());
+ EXPECT_EQ("MMDM", a->Transcript());
+ delete a;
+
+ a = Align("GATTACA", "TT");
+ EXPECT_EQ("GATTACA", a->Target());
+ EXPECT_EQ("--TT---", a->Query());
+ EXPECT_FLOAT_EQ(2. / 7, a->Accuracy());
+ delete a;
+}
+
+TEST(PairwiseAlignmentTests, TargetPositionsInQueryTest)
+{
+ // MMM -> 0123
+ {
+ int expected[] = {0, 1, 2, 3};
+ ASSERT_THAT(TargetToQueryPositions("MMM"), ElementsAreArray(expected));
+ }
+
+ // DMM -> 0012, MDM -> 0112, MMD -> 0122,
+ {
+ int expected1[] = {0, 0, 1, 2};
+ int expected2[] = {0, 1, 1, 2};
+ int expected3[] = {0, 1, 2, 2};
+ ASSERT_THAT(TargetToQueryPositions("DMM"), ElementsAreArray(expected1));
+ ASSERT_THAT(TargetToQueryPositions("MDM"), ElementsAreArray(expected2));
+ ASSERT_THAT(TargetToQueryPositions("MMD"), ElementsAreArray(expected3));
+ }
+
+ // IMM -> 123, MIM -> 023, MMI -> 013,
+ {
+ int expected1[] = {1, 2, 3};
+ int expected2[] = {0, 2, 3};
+ int expected3[] = {0, 1, 3};
+ ASSERT_THAT(TargetToQueryPositions("IMM"), ElementsAreArray(expected1));
+ ASSERT_THAT(TargetToQueryPositions("MIM"), ElementsAreArray(expected2));
+ ASSERT_THAT(TargetToQueryPositions("MMI"), ElementsAreArray(expected3));
+ }
+
+ // MRM, MDIM -> 0123
+ // MIDM -> 0223
+ {
+ int expected1[] = {0, 1, 2, 3};
+ int expected2[] = {0, 2, 2, 3};
+ ASSERT_THAT(TargetToQueryPositions("MRM"), ElementsAreArray(expected1));
+ ASSERT_THAT(TargetToQueryPositions("MDIM"), ElementsAreArray(expected1));
+ ASSERT_THAT(TargetToQueryPositions("MIDM"), ElementsAreArray(expected2));
+ }
+}
+
+// ------------------ AffineAlignment tests ---------------------
+
+TEST(AffineAlignmentTests, BasicTests)
+{
+ PairwiseAlignment* a = AlignAffine("ATT", "ATT");
+ EXPECT_EQ("ATT", a->Target());
+ EXPECT_EQ("ATT", a->Query());
+ delete a;
+
+ a = AlignAffine("AT", "ATT");
+ EXPECT_EQ("A-T", a->Target());
+ EXPECT_EQ("ATT", a->Query());
+ delete a;
+
+ a = AlignAffine("GA", "GAT");
+ EXPECT_EQ("GA-", a->Target());
+ EXPECT_EQ("GAT", a->Query());
+ delete a;
+
+ a = AlignAffine("GAT", "GA");
+ EXPECT_EQ("GAT", a->Target());
+ EXPECT_EQ("GA-", a->Query());
+ delete a;
+
+ a = AlignAffine("GA", "TGA");
+ EXPECT_EQ("-GA", a->Target());
+ EXPECT_EQ("TGA", a->Query());
+ delete a;
+
+ a = AlignAffine("TGA", "GA");
+ EXPECT_EQ("TGA", a->Target());
+ EXPECT_EQ("-GA", a->Query());
+ delete a;
+
+ a = AlignAffine("GATTACA", "GATTTACA");
+ EXPECT_EQ("GA-TTACA", a->Target());
+ EXPECT_EQ("GATTTACA", a->Query());
+ delete a;
+}
+
+TEST(AffineAlignmentTests, LargeGapTest)
+{
+ // Test a real-world large insertion, found in an E. Coli
+ // experiment
+ const char* target =
+ "AACGATTTTATGATGGCATGTGACATGTATTTCCGTTGGGGGCATTTTAATAAGTGAGGA"
+ "AGTGATAGGAAGTGACCAGATAATACATATATGTTCTGTACTCTCTTGCGCATTTTGATT"
+ "GTTGACTGAGTAACCAGACAGTTGATGTGCACGATTTCCCCTCGCCCTAACAGACGTGGG"
+ "CGGGGGCACCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTT"
+ "CTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGC"
+ "TCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGACCCCCGGTCGGGGCT"
+ "TCTCATCCCCCCGGTGTGTGCAATACACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCT"
+ "TCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCG"
+ "CTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGC"
+ "TTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTC"
+ "TTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCC"
+ "GCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGG"
+ "CTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCT"
+ "CTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA"
+ "CTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTG"
+ "CTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAAA"
+ "TCGCGCGTTTATTCAAACTTCAATCAATGTGTGGTTTTAATAAGCGAAAT";
+
+ const char* query =
+ "AACGATTTTATGATGGCATGTGACATGTATTTCCGTTGGGGGCATTTTAATAAGTGAGGA"
+ "AGTGATAGGAAGTGACCAGATAATACATATATGTTCTGTACTCTCTTGCGCATTTTGATT"
+ "GTTGACTGAGTAACCAGACAGTTGATGTGCACGATTTCCCCTCGCCCTAACAGACGTGGG"
+ "CGGGGGCACCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTT"
+ "CTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGC"
+ "TCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGACCCCCGGTCGGGGCT"
+ "TCTCATCCCCCCGGTGTGTGCAATACACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCT"
+ "TCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCG"
+ "CTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGC"
+ "TTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTC"
+ "TTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCC"
+ "GCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGG"
+ "CTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCT"
+ "CTTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCC"
+ "CGCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGG"
+ "GCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGC"
+ "TCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC"
+ "ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTT"
+ "GCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAA"
+ "ATCGCGCGTTTATTCAAACTTCAATCAATGTGTGGTTTTAATAAGCGAAAT";
+
+ const char* expectedAlignedTarget =
+ "AACGATTTTATGATGGCATGTGACATGTATTTCCGTTGGGGGCATTTTAATAAGTGAGGA"
+ "AGTGATAGGAAGTGACCAGATAATACATATATGTTCTGTACTCTCTTGCGCATTTTGATT"
+ "GTTGACTGAGTAACCAGACAGTTGATGTGCACGATTTCCCCTCGCCCTAACAGACGTGGG"
+ "CGGGGGCACCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTT"
+ "CTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGC"
+ "TCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGACCCCCGGTCGGGGCT"
+ "TCTCATCCCCCCGGTGTGTGCAATAC----------------------------------"
+ "------------------------------------------------------------"
+ "------------------------------------------------------------"
+ "---------------------------ACGAAAAAAAAGCCCGTACTTTCGTACGAGCTC"
+ "TTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCC"
+ "GCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGG"
+ "CTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCT"
+ "CTTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCC"
+ "CGCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGG"
+ "GCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGC"
+ "TCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC"
+ "ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTT"
+ "GCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAA"
+ "ATCGCGCGTTTATTCAAACTTCAATCAATGTGTGGTTTTAATAAGCGAAAT";
+
+ PairwiseAlignment* a = AlignAffine(target, query);
+ ASSERT_EQ(expectedAlignedTarget, a->Target());
+ delete a;
+}
+
+// ------------------ IUPAC-aware alignment tests ---------------------
+
+TEST(IupacAlignmentTests, BasicTest)
+{
+ PairwiseAlignment* a;
+ a = AlignAffineIupac("GATTTT", "GMTTT");
+ ASSERT_EQ("GATTTT", a->Target());
+ ASSERT_EQ("GM-TTT", a->Query());
+ delete a;
+
+ a = AlignAffineIupac("TTTTAG", "TTTMG");
+ ASSERT_EQ("TTTTAG", a->Target());
+ ASSERT_EQ("-TTTMG", a->Query());
+ delete a;
+}
+
+// ---------------- Linear-space alignment tests -----------------------
+
+TEST(LinearAlignmentTests, BasicTest)
+{
+ AlignParams params(2, -1, -2, -2);
+ AlignConfig config(params, AlignMode::GLOBAL);
+
+ int score, peerScore;
+ PairwiseAlignment *a, *peerAlignment;
+
+ a = AlignLinear("GATTACA", "GATTACA", &score);
+ EXPECT_EQ("GATTACA", a->Target());
+ EXPECT_EQ("GATTACA", a->Query());
+ EXPECT_EQ("MMMMMMM", a->Transcript());
+ EXPECT_EQ(14, score);
+ delete a;
+
+ a = AlignLinear("CGAC", "GAAAACGAC", &score);
+ EXPECT_EQ("-----CGAC", a->Target());
+ EXPECT_EQ("GAAAACGAC", a->Query());
+ EXPECT_EQ("IIIIIMMMM", a->Transcript());
+ delete a;
+
+ a = AlignLinear(
+ "CATCAGGTAAGAAAGTACGATGCTACAGCTTGTGACTGGTGCGGCACTTTTGGCTGAGTTTCCTGTCCACCTCATGTATTCTGCCCTAAC"
+ "GTCGGTCTTCACGCCATTACTAGACCGACAAAATGGAACCGGGGCCTTAAACCCCGTTCGAGGCGTAGCAAGGAGATAGGGTTATGAACT"
+ "CTCCCAGTCAATATACCAACACATCGTGGGACGGATTGCAGAGCGAATCTATCCGCGCTCGCATAATTTAGTGTTGATC",
+ "CATCAGGTAAGAAAAGTACGATGCTACAGCTGTGACTGGTGCGGCACTTTTTGGCCTGAGTTTCCTGTCCACTCATGTATTCTGGCCCTA"
+ "ACTTAGGTCGGTCTTCACGCCATTTACTAGCACGAAAACGACAAAATTGGAAGCCGGGGCCTAAACACCCGTTCGAGGCGGTAGCAAGGA"
+ "GATTAGGGTTATGAACTCTCCCAGTCAATGATACAAACAATCGTGGGACGGAATTGCAGAGCGAATCTATCCGCGCTCAAGCATAATTTA"
+ "GTGTTGATC",
+ &score);
+ delete a;
+
+ a = AlignLinear(
+ "CATCAGGTAAGAAAGTACGATGCTACAGCTTGTGACTGGTGCGGCACTTTTGGCTGAGTTTCCTGTCCACCTCATGTATTCTGCCCTAAC"
+ "GTCGGTCTTCACGCCATTACTAGACCGACAAAATGGAAGCCGGGGCCTTAAACCCCGTTCGAGGCGTAGCAAGGAGATAGGGTTATGAAC"
+ "TCTCCCAGTCAATATACCAACACATCGTGGGACGGATTGCAGAGCGAATCTATCCGCGCTCGCATAATTTAGTGTTGATC",
+ "CCCCGGGAATCTCTAGAATGCATCAGGTAAGAAAGTAACGATGCTTACACTTGTGACTGGTTGCGGCACTTTTGGTGAGTTTCCTGTCCA"
+ "CTCAATGTATTCTGCCTAACGTCGTGTCTTCACGCCATTTACTAGACCGAGAAGGAAATTGGAAGGCCCGGGGGCCTTAAACGCCCGTTC"
+ "GAGCGTAGCTAAGGAGATAGGGTTATGAACTCTCCCAGTCATATAGCCAACACATCGTGGAACGGAATTGCAGAGCGAATCTATCCGCTG"
+ "CTCGCATAAATTTAGTGTTGATCCATAAAGCTTGCTGAGGACTAGTAGCTT",
+ &score);
+ delete a;
+
+ a = AlignLinear("TATGC", "AGTACGCA", &score);
+ EXPECT_EQ("--TATGC-", a->Target());
+ EXPECT_EQ("AGTACGCA", a->Query());
+ EXPECT_EQ("IIMMRMMI", a->Transcript());
+ EXPECT_EQ(1, score);
+ delete a;
+
+ a = AlignLinear("AGTACGCA", "TATGC", &score);
+ EXPECT_EQ("AGTACGCA", a->Target());
+ EXPECT_EQ("--TATGC-", a->Query());
+ EXPECT_EQ("DDMMRMMD", a->Transcript());
+ EXPECT_EQ(1, score);
+ delete a;
+
+ a = AlignLinear("GATT", "GATT");
+ EXPECT_FLOAT_EQ(1.0, a->Accuracy());
+ EXPECT_EQ("GATT", a->Target());
+ EXPECT_EQ("GATT", a->Query());
+ EXPECT_EQ("MMMM", a->Transcript());
+ delete a;
+
+ a = AlignLinear("GATT", "GAT");
+ EXPECT_FLOAT_EQ(0.75, a->Accuracy());
+ EXPECT_EQ("GATT", a->Target());
+ EXPECT_EQ("GA-T", a->Query());
+ EXPECT_EQ("MMDM", a->Transcript());
+ delete a;
+
+ a = AlignLinear("GATTACA", "TT");
+ EXPECT_EQ("GATTACA", a->Target());
+ EXPECT_EQ("--TT---", a->Query());
+ EXPECT_FLOAT_EQ(2. / 7, a->Accuracy());
+ delete a;
+
+ const char* ref =
+ "GTATTTTAAATAAAAACATTAAGTTATGACGAAGAAGAACGGAAACGCCTTAAACCGGAAAATTTTCATAAATAGCGAAAACCCGCGAGG"
+ "TCGCCGCCC";
+ const char* read =
+ "GTATTTTAAATAAAAAAACATTATAGTTTAATGAACGAGAATGAACGGTAATACGCCTTTAAAGCCTGAAATATTTTTCCATAAATGTAA"
+ "TTTCTGTATATAATCTCCGCGAGTGTCTGCCGCCC";
+
+ a = AlignLinear(ref, read, &score);
+ peerAlignment = Align(ref, read, &peerScore, config);
+ EXPECT_EQ(score, peerScore);
+
+ delete a;
+ delete peerAlignment;
+}
+
+#if 0
+TEST(LinearAlignmentTests, SemiglobalTests)
+{
+ AlignParams params(2, -1, -2, -2);
+ int score, peerScore;
+ PairwiseAlignment *a, *peerAlignment;
+
+ a = AlignLinear("AGTCGATACACCCC", "GATTACA");
+ EXPECT_EQ("AGTCGA-TACACCCC", a->Target());
+ EXPECT_EQ("----GATTACA----", a->Query());
+
+ // we got:
+ // -AGTCGATACACCCC
+ // GA-T---TACA----
+
+}
+#endif
diff --git a/tests/unit/TestChemistry.cpp b/tests/unit/TestChemistry.cpp
new file mode 100644
index 0000000..14122a8
--- /dev/null
+++ b/tests/unit/TestChemistry.cpp
@@ -0,0 +1,50 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <iostream>
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <pacbio/data/ChemistryMapping.h>
+#include <pacbio/data/ChemistryTriple.h>
+
+TEST(ChemistryTest, LoadTest)
+{
+ // TODO(lhepler) add tests here for loading chemistry
+ EXPECT_EQ(true, true);
+}
diff --git a/tests/unit/TestConsensus.cpp b/tests/unit/TestConsensus.cpp
new file mode 100644
index 0000000..17a8ca8
--- /dev/null
+++ b/tests/unit/TestConsensus.cpp
@@ -0,0 +1,96 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+#include <vector>
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <pbbam/Accuracy.h>
+#include <pbbam/LocalContextFlags.h>
+
+#include <pacbio/ccs/Consensus.h>
+#include <pacbio/data/ReadId.h>
+#include <pacbio/data/SubreadResultCounter.h>
+
+#include <OptionParser.h>
+
+using namespace PacBio::CCS;
+typedef ReadType<ReadId> Subread;
+
+TEST(ConsensusTest, TestReadFilter)
+{
+ std::vector<Subread> data;
+ std::string seq =
+ "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA";
+ auto movieName = std::make_shared<std::string>("fakeName");
+ LocalContextFlags flags = LocalContextFlags::ADAPTER_BEFORE | LocalContextFlags::ADAPTER_AFTER;
+ for (int i = 0; i < 10; i++) {
+ data.emplace_back(Subread{ReadId(movieName, 1, Interval(0, seq.size())), seq,
+ std::vector<uint8_t>(seq.size(), 0),
+ std::vector<uint8_t>(seq.size(), 0), flags, .99});
+ }
+
+ auto parser = optparse::OptionParser();
+ ConsensusSettings::AddOptions(&parser);
+ const auto options = parser.parse_args({});
+ ConsensusSettings settings(options);
+ settings.MinLength = 10;
+ settings.MinReadScore = 0.0;
+
+ // Nothing filtered
+ SubreadResultCounter counter{};
+ auto result = FilterReads(data, settings, &counter);
+ EXPECT_EQ(0, counter.FilteredBySize);
+ // reset
+ counter.Success = 0;
+
+ // All removed
+ settings.MinLength = 1000;
+ auto result2 = FilterReads(data, settings, &counter);
+ EXPECT_EQ(10, counter.FilteredBySize);
+ EXPECT_EQ(0, counter.Success);
+ counter.FilteredBySize = 0;
+ counter.Success = 0;
+
+ // Just one
+ auto longSeq = seq + seq + seq;
+ settings.MinLength = 10;
+ data.emplace_back(Subread{ReadId(movieName, 2, Interval(0, longSeq.size())), longSeq,
+ std::vector<uint8_t>(longSeq.size(), 0),
+ std::vector<uint8_t>(longSeq.size(), 0), flags, .99});
+ auto result3 = FilterReads(data, settings, &counter);
+ EXPECT_EQ(1, counter.FilteredBySize);
+}
diff --git a/tests/unit/TestCoverage.cpp b/tests/unit/TestCoverage.cpp
new file mode 100644
index 0000000..371e52f
--- /dev/null
+++ b/tests/unit/TestCoverage.cpp
@@ -0,0 +1,94 @@
+// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Authors: David Alexander, Lance Hepler
+
+#include <tuple>
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <pacbio/consensus/Coverage.h>
+
+using namespace PacBio::Consensus; // NOLINT
+using ::testing::ElementsAre;
+using ::testing::ElementsAreArray;
+
+#define t(a, b) (std::make_pair((a), (b)))
+
+TEST(CoverageTests, CoverageInWindowTest)
+{
+ int coverage[10];
+ int tStart[] = {1, 2, 3, 8, 10, 15};
+ int tEnd[] = {3, 4, 5, 10, 10, 200};
+
+ CoverageInWindow(6, tStart, 6, tEnd, 0, 10, coverage);
+ int expectedCoverage1[] = {0, 1, 2, 2, 1, 0, 0, 0, 1, 1};
+ ASSERT_THAT(coverage, ElementsAreArray(expectedCoverage1, 10));
+
+ CoverageInWindow(6, tStart, 6, tEnd, 10, 10, coverage);
+ int expectedCoverage2[] = {0, 0, 0, 0, 0, 1, 1, 1, 1, 1};
+ ASSERT_THAT(coverage, ElementsAreArray(expectedCoverage2, 10));
+}
+
+TEST(CoverageTests, CoveredIntervalsTest)
+{
+ // CHECK:
+ // CoveredIntervals(0, [1,2,3,8,900,2000], [3,4,5,10,1010,20000], 0, 10000) -> ((0, 10000),)
+ // CoveredIntervals(1, [1,2,3,8,900,2000], [3,4,5,10,1010,20000], 0, 10000) -> ((1, 5), (8, 10),
+ // (900, 1010), (2000, 10000)) // NOLINT
+ // CoveredIntervals(2, [1,2,3,8,900,2000], [3,4,5,10,1010,20000], 0, 10000) -> ((2, 4),)
+ // CoveredIntervals(3, [1,2,3,8,900,2000], [3,4,5,10,1010,20000], 0, 10000) -> ()
+
+ int tStart[] = {1, 2, 3, 8, 900, 2000};
+ int tEnd[] = {3, 4, 5, 10, 1010, 20000};
+ ASSERT_THAT(CoveredIntervals(0, 6, tStart, 6, tEnd, 0, 10000), ElementsAre(t(0, 10000)));
+ ASSERT_THAT(CoveredIntervals(1, 6, tStart, 6, tEnd, 0, 10000),
+ ElementsAre(t(1, 5), t(8, 10), t(900, 1010), t(2000, 10000))); // NOLINT
+ ASSERT_THAT(CoveredIntervals(2, 6, tStart, 6, tEnd, 0, 10000), ElementsAre(t(2, 4)));
+ ASSERT_THAT(CoveredIntervals(3, 6, tStart, 6, tEnd, 0, 10000), ElementsAre());
+
+ ASSERT_THAT(CoveredIntervals(0, 6, tStart, 6, tEnd, 100, 9900), ElementsAre(t(100, 10000)));
+ ASSERT_THAT(CoveredIntervals(1, 6, tStart, 6, tEnd, 100, 9900),
+ ElementsAre(t(900, 1010), t(2000, 10000))); // NOLINT
+}
+
+TEST(CoverageTests, CoveredIntervalsTest2)
+{
+ // Regression test
+ int tStart[] = {48853};
+ int tEnd[] = {50687};
+ ASSERT_THAT(CoveredIntervals(1, 1, tStart, 1, tEnd, 50000, 500), ElementsAre(t(50000, 50500)));
+}
diff --git a/tests/unit/TestData.h.in b/tests/unit/TestData.h.in
new file mode 100644
index 0000000..42d6a48
--- /dev/null
+++ b/tests/unit/TestData.h.in
@@ -0,0 +1,47 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#pragma once
+
+#include <string>
+
+namespace tests {
+
+const std::string DataDir("@UNY_TestsDir@/data");
+const std::string ccsExe("@CMAKE_BINARY_DIR@/ccs");
+
+} // namespace tests
diff --git a/tests/unit/TestIntegrator.cpp b/tests/unit/TestIntegrator.cpp
new file mode 100644
index 0000000..6ac09b7
--- /dev/null
+++ b/tests/unit/TestIntegrator.cpp
@@ -0,0 +1,375 @@
+// Copyright (c) 2011-2014, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <algorithm>
+#include <chrono>
+#include <iostream>
+#include <limits>
+#include <random>
+#include <set>
+#include <string>
+#include <tuple>
+#include <vector>
+
+#include <pacbio/consensus/MonoMolecularIntegrator.h>
+#include <pacbio/consensus/MultiMolecularIntegrator.h>
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/data/Sequence.h>
+
+#include "Mutations.h"
+#include "RandomDNA.h"
+
+using std::string;
+using std::vector;
+using std::cerr;
+using std::cout;
+using std::endl;
+
+using namespace PacBio::Consensus; // NOLINT
+using namespace PacBio::Data; // NOLINT
+
+using ::testing::UnorderedElementsAreArray;
+
+namespace {
+
+#if EXTENSIVE_TESTING
+constexpr int numSamples = 333;
+#else
+constexpr int numSamples = 3;
+#endif
+
+const double prec = 0.001; // alpha/beta mismatch tolerance
+const SNR snr(10, 7, 5, 11);
+const string P6C4 = "P6-C4";
+const string SP1C1 = "S/P1-C1.1";
+const string SP1C1v2 = "S/P1-C1.2";
+
+const string longTpl =
+ "GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCAT"
+ "AACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCC"
+ "TCTGTCGTTTCCTTTCTCTGTTTTTGTCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATT"
+ "TTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGG"
+ "TAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAA"
+ "AGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTATTGAGTACGAA"
+ "CGCCATCGACTTACGCGTGCGCAGGCCGACGCACAGGAACTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGA"
+ "AACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGT"
+ "CGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATG"
+ "AACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGC"
+ "TGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGAT"
+ "GCTAATTACTATCTCCCGAAAGAATC";
+const string longRead =
+ "GGGCGGCGACCTCGCGGGTTTTCGCTATTTCTGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCAT"
+ "AACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCC"
+ "TCTGTCGTTTCCTTTCTCTGTTTTTGTCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATT"
+ "TTCGGTGGAGTATCCGTACCATTCAGAACTGGCAGGACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTA"
+ "ATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAATAG"
+ "CTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTATTGAGTACGAACG"
+ "CCATCGACTTACGCGTGCGCAGGCCGACGCACAGGAACTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAA"
+ "CCGCATTCCCCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTG"
+ "TCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCAT"
+ "GAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGG"
+ "CTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAACGGATGCT"
+ "AATTACTATCTCCCGAAAGAATC";
+const IntegratorConfig cfg(std::numeric_limits<double>::quiet_NaN());
+
+Read MkRead(const string& seq, const SNR& snr, const string& mdl, const vector<uint8_t>& pw)
+{
+ vector<uint8_t> ipd(0, seq.length());
+ return Read("NA", seq, ipd, pw, snr, mdl);
+}
+
+#if EXTENSIVE_TESTING
+TEST(IntegratorTest, TestLongTemplate)
+{
+ // TODO: Write a test for a longer molecule
+ const string mdl = P6C4;
+ vector<uint8_t> pw(longTpl.length(), 1);
+ MonoMolecularIntegrator ai(longTpl, cfg, snr, mdl);
+ EXPECT_EQ(State::VALID,
+ ai.AddRead(MappedRead(MkRead(longRead, snr, mdl, pw), StrandType::FORWARD, 0,
+ longTpl.length(), true, true)));
+ EXPECT_NEAR(-148.92614949338801011, ai.LL(), prec);
+}
+
+void TestTiming(const string& mdl)
+{
+ const vector<uint8_t> pws(longTpl.length(), 2);
+ const size_t nsamp = 5000;
+ MonoMolecularIntegrator ai(longTpl, cfg, snr, mdl);
+ const auto stime = std::chrono::high_resolution_clock::now();
+ for (size_t i = 0; i < nsamp; ++i)
+ EXPECT_EQ(State::VALID,
+ ai.AddRead(MappedRead(MkRead(longRead, snr, mdl, pws), StrandType::FORWARD, 0,
+ longTpl.length(), true, true)));
+ const auto etime = std::chrono::high_resolution_clock::now();
+ const auto duration =
+ std::chrono::duration_cast<std::chrono::microseconds>(etime - stime).count();
+ // std::cout << "avg duration: " << duration / nsamp << "us" << std::endl;
+ EXPECT_LT(duration / nsamp, 1500);
+}
+
+// disable this test under debug builds (which are not fast enough to pass these timings)
+#ifndef NDEBUG
+TEST(IntegratorTest, DISABLED_TestLongTemplateTimingP6C4)
+#else
+TEST(IntegratorTest, TestLongTemplateTimingP6C4)
+#endif
+{
+ TestTiming(P6C4);
+}
+
+// disable this test under debug builds (which are not fast enough to pass these timings)
+#ifndef NDEBUG
+TEST(IntegratorTest, DISABLED_TestLongTemplateTimingSP1C1)
+#else
+TEST(IntegratorTest, TestLongTemplateTimingSP1C1)
+#endif
+{
+ TestTiming(SP1C1);
+}
+
+// disable this test under debug builds (which are not fast enough to pass these timings)
+#ifndef NDEBUG
+TEST(IntegratorTest, DISABLED_TestLongTemplateTimingSP1C1v2)
+#else
+TEST(IntegratorTest, TestLongTemplateTimingSP1C1v2)
+#endif
+{
+ TestTiming(SP1C1v2);
+}
+#endif
+
+std::tuple<string, StrandType> Mutate(const string& tpl, const size_t nmut, std::mt19937* const gen)
+{
+ string result;
+
+ if (nmut == 0)
+ result = tpl;
+ else {
+ vector<Mutation> muts;
+ std::uniform_int_distribution<size_t> rand(0, tpl.length() - 1);
+ std::set<size_t> sites;
+
+ while (sites.size() < nmut)
+ sites.insert(rand(*gen));
+
+ for (const size_t site : sites) {
+ vector<Mutation> possible = Mutations(tpl, site, site + 1);
+ std::uniform_int_distribution<size_t> rand2(0, possible.size() - 1);
+ muts.push_back(possible[rand2(*gen)]);
+ }
+
+ result = ApplyMutations(tpl, &muts);
+ }
+
+ std::bernoulli_distribution coin(0.5);
+
+ if (coin(*gen)) return std::make_tuple(result, StrandType::FORWARD);
+
+ return std::make_tuple(ReverseComplement(result), StrandType::REVERSE);
+}
+
+template <typename F, typename G>
+void MutationEquivalence(const size_t nsamp, const size_t nmut, const F& makeIntegrator,
+ const G& addRead, const string& mdl)
+{
+ std::random_device rd;
+ std::mt19937 gen(rd());
+ // increase the floor by 3 because we do not support templates or reads with lt 2 bases,
+ // and we explore edit-1 space around the template to generate reads
+ std::uniform_int_distribution<size_t> rand(3 + nmut, 30);
+
+ // count how bad we do
+ size_t ntests = 0;
+ size_t nerror = 0;
+
+ for (size_t i = 0; i < nsamp; ++i) {
+ const string tpl = RandomDNA(rand(gen), &gen);
+ vector<Mutation> mutations = Mutations(tpl);
+ for (const auto& mut : mutations) {
+ string read;
+ StrandType strand;
+ vector<Mutation> muts{mut};
+ const string app = ApplyMutations(tpl, &muts); // template with mutation applied
+ std::tie(read, strand) = Mutate(app, nmut, &gen);
+ vector<uint8_t> pws = RandomPW(read.length(), &gen);
+ try {
+ auto ai1 = makeIntegrator(tpl);
+ const auto arr1 = addRead(ai1, MappedRead(MkRead(read, snr, mdl, pws), strand, 0,
+ tpl.length(), true, true));
+ EXPECT_EQ(State::VALID, arr1);
+ if (arr1 != State::VALID) {
+ std::cerr << std::endl << "!! alpha/beta mismatch:" << std::endl;
+ std::cerr << " " << tpl.length() << ", " << tpl << std::endl;
+ std::cerr << " " << read.length() << ", " << read << std::endl;
+ }
+ auto ai2 = makeIntegrator(app);
+ const auto arr2 = addRead(ai2, MappedRead(MkRead(read, snr, mdl, pws), strand, 0,
+ app.length(), true, true));
+ EXPECT_EQ(State::VALID, arr2);
+ if (arr2 != State::VALID) {
+ std::cerr << std::endl << "!! alpha/beta mismatch:" << std::endl;
+ std::cerr << " " << app.length() << ", " << app << std::endl;
+ std::cerr << " " << read.length() << ", " << read << std::endl;
+ }
+ const double exp = ai2.LL();
+ const double obs0 = ai1.LL();
+ const double obs1 = ai1.LL(mut);
+ EXPECT_EQ(string(ai1), tpl);
+ ai1.ApplyMutations(&muts);
+ const double obs2 = ai1.LL();
+ // Nigel says the following is not necessarily true
+ // if (nmut == 0) EXPECT_LT(obs0, exp);
+ // EXPECT_NEAR(obs1, exp, prec);
+ // EXPECT_NEAR(obs2, exp, prec);
+ EXPECT_EQ(string(ai1), app);
+ EXPECT_EQ(string(ai2), app);
+ const double diff1 = std::abs(1.0 - obs1 / exp);
+ const double diff2 = std::abs(1.0 - obs2 / exp);
+ if (diff1 >= prec || diff2 >= prec) {
+ std::cerr << std::endl
+ << "!! intolerable difference: exp: " << exp << ", obs1: " << obs1
+ << ", obs2: " << obs2 << std::endl;
+ std::cerr << " " << mut << std::endl;
+ std::cerr << " " << tpl.length() << ", " << tpl << std::endl;
+ std::cerr << " " << app.length() << ", " << app << std::endl;
+ std::cerr << " " << ai1.TemplateLength() << ", " << string(ai1) << std::endl;
+ std::stringstream result;
+ std::copy(pws.begin(), pws.end(), std::ostream_iterator<int>(result, " "));
+ std::cerr << " " << read.length() << ", " << read << " - " << result.str()
+ << std::endl;
+
+ ++nerror;
+ }
+ } catch (const std::exception& e) {
+ std::cerr << std::endl
+ << "!! caught unexpected exception: " << e.what() << std::endl;
+ std::cerr << " " << mut << std::endl;
+ std::cerr << " " << tpl.length() << ", " << tpl << std::endl;
+ std::cerr << " " << app.length() << ", " << app << std::endl;
+ std::cerr << " " << read.length() << ", " << read << std::endl;
+ ++nerror;
+ }
+ ++ntests;
+ }
+ }
+
+ EXPECT_EQ(nerror, 0);
+ // EXPECT_LT(nerror, ntests / 1000);
+}
+
+void MonoEquivalence(const string& mdl)
+{
+ auto makeMono = [mdl](const string& tpl) {
+ return MonoMolecularIntegrator(tpl, cfg, snr, mdl);
+ };
+ auto monoRead = [](MonoMolecularIntegrator& ai, const MappedRead& mr) {
+ return ai.AddRead(mr);
+ };
+ MutationEquivalence(numSamples, 2, makeMono, monoRead, mdl);
+ MutationEquivalence(numSamples, 1, makeMono, monoRead, mdl);
+ MutationEquivalence(numSamples, 0, makeMono, monoRead, mdl);
+}
+
+TEST(IntegratorTest, TestMonoMutationEquivalenceP6C4) { MonoEquivalence(P6C4); }
+TEST(IntegratorTest, TestMonoMutationEquivalenceSP1C1) { MonoEquivalence(SP1C1); }
+TEST(IntegratorTest, TestMonoMutationEquivalenceSP1C1v2) { MonoEquivalence(SP1C1v2); }
+void MultiEquivalence(const string& mdl)
+{
+ auto makeMulti = [](const string& tpl) { return MultiMolecularIntegrator(tpl, cfg); };
+ auto multiRead = [](MultiMolecularIntegrator& ai, const MappedRead& mr) {
+ return ai.AddRead(mr);
+ };
+ MutationEquivalence(numSamples, 2, makeMulti, multiRead, mdl);
+ MutationEquivalence(numSamples, 1, makeMulti, multiRead, mdl);
+ MutationEquivalence(numSamples, 0, makeMulti, multiRead, mdl);
+}
+
+TEST(IntegratorTest, TestMultiMutationEquivalenceP6C4) { MultiEquivalence(P6C4); }
+TEST(IntegratorTest, TestMultiMutationEquivalenceSP1C1) { MultiEquivalence(SP1C1); }
+TEST(IntegratorTest, TestMultiMutationEquivalenceSP1C1v2) { MultiEquivalence(SP1C1v2); }
+// TODO(lhepler): test multi/mono equivalence
+// TODO(lhepler): test multiple mutation testing mono and multi
+
+TEST(IntegratorTest, TestP6C4NoCovAgainstCSharpModel)
+{
+ const string tpl = "ACGTCGT";
+ const vector<uint8_t> pw(tpl.length(), 1);
+ auto mdl = P6C4;
+ MultiMolecularIntegrator ai(tpl, cfg);
+
+ EXPECT_EQ(State::VALID,
+ ai.AddRead(MappedRead(MkRead("ACGTACGT", snr, mdl, pw), StrandType::FORWARD, 0,
+ tpl.length(), true, true)));
+ auto score = [&ai](Mutation&& mut) { return ai.LL(mut) - ai.LL(); };
+ EXPECT_NEAR(-4.74517984808494, ai.LL(), prec);
+ EXPECT_NEAR(4.00250386364592, score(Mutation(MutationType::INSERTION, 4, 'A')), prec);
+ EXPECT_NEAR(-5.19526526492876, score(Mutation(MutationType::SUBSTITUTION, 2, 'C')), prec);
+ EXPECT_NEAR(-4.33430539094949, score(Mutation(MutationType::DELETION, 4)), prec);
+ EXPECT_NEAR(-9.70299447206563, score(Mutation(MutationType::DELETION, 6)), prec);
+ EXPECT_NEAR(-10.5597017942167, score(Mutation(MutationType::DELETION, 0)), prec);
+ EXPECT_NEAR(-0.166992912601578, score(Mutation(MutationType::SUBSTITUTION, 4, 'A')), prec);
+ EXPECT_NEAR(-1.60697112438296, score(Mutation(MutationType::INSERTION, 4, 'G')), prec);
+}
+
+TEST(IntegratorTest, TestFailAddRead)
+{
+ const string tpl = "A";
+ const vector<uint8_t> pw(tpl.length(), 1);
+ auto mdl = P6C4;
+ MultiMolecularIntegrator ai(tpl, cfg);
+
+ EXPECT_EQ(State::TEMPLATE_TOO_SMALL,
+ ai.AddRead(MappedRead(MkRead(tpl, snr, mdl, pw), StrandType::FORWARD, 0, tpl.length(),
+ true, true)));
+}
+
+TEST(IntegratorTest, TestSuccessAddRead)
+{
+ const string tpl = "AA";
+ const vector<uint8_t> pw(tpl.length(), 1);
+ const auto mdl = P6C4;
+ MultiMolecularIntegrator ai(tpl, cfg);
+
+ EXPECT_EQ(State::VALID, ai.AddRead(MappedRead(MkRead(tpl, snr, mdl, pw), StrandType::FORWARD, 0,
+ tpl.length(), true, true)));
+}
+
+} // namespace anonymous
diff --git a/tests/unit/TestInterval.cpp b/tests/unit/TestInterval.cpp
new file mode 100644
index 0000000..20a2e4a
--- /dev/null
+++ b/tests/unit/TestInterval.cpp
@@ -0,0 +1,249 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <iostream>
+#include <stdexcept>
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <pacbio/data/Interval.h>
+#include <pacbio/data/IntervalTree.h>
+
+using namespace PacBio::Data;
+
+TEST(IntervalTest, Merging)
+{
+ IntervalTree tree;
+
+ tree.Insert(Interval(1, 3));
+ tree.Insert(Interval(3, 5));
+
+ EXPECT_EQ(tree.size(), 1);
+
+ for (const auto& i : tree) {
+ EXPECT_EQ(i.Right(), 5);
+ EXPECT_EQ(i.Left(), 1);
+ }
+}
+
+TEST(IntervalTest, Merging2)
+{
+ IntervalTree tree;
+
+ tree.Insert(Interval(1, 3));
+ tree.Insert(Interval(5, 7));
+ tree.Insert(Interval(9, 11));
+
+ EXPECT_EQ(tree.size(), 3);
+
+ tree.Insert(Interval(3, 9));
+
+ EXPECT_EQ(tree.size(), 1);
+
+ for (const auto& i : tree) {
+ EXPECT_EQ(i.Right(), 11);
+ EXPECT_EQ(i.Left(), 1);
+ }
+}
+
+TEST(IntervalTest, Merging3)
+{
+ IntervalTree tree;
+
+ tree.Insert(Interval(1, 3));
+ tree.Insert(Interval(5, 6));
+ tree.Insert(Interval(4, 6));
+
+ EXPECT_EQ(tree.size(), 2);
+}
+
+TEST(IntervalTest, Iteration)
+{
+ Interval interval(0, 11);
+ size_t i = interval.Left();
+
+ for (const auto j : interval) {
+ EXPECT_EQ(j, i++);
+ }
+}
+
+TEST(IntervalTest, Gaps)
+{
+ IntervalTree tree;
+
+ tree.Insert(Interval(1, 3));
+ tree.Insert(Interval(5, 7));
+ tree.Insert(Interval(9, 11));
+
+ IntervalTree gaps = tree.Gaps();
+
+ EXPECT_EQ(gaps.size(), 2);
+
+ size_t l = 3;
+ size_t r = 5;
+
+ for (const auto& i : gaps) {
+ EXPECT_EQ(i.Left(), l);
+ EXPECT_EQ(i.Right(), r);
+
+ l += 4;
+ r += 4;
+ }
+}
+
+TEST(IntervalTest, Gaps2)
+{
+ IntervalTree tree;
+
+ tree.Insert(Interval(3, 9));
+
+ IntervalTree gaps = tree.Gaps(Interval(5, 11));
+
+ EXPECT_EQ(gaps.size(), 1);
+
+ for (auto& i : gaps) {
+ EXPECT_EQ(i.Left(), 9);
+ EXPECT_EQ(i.Right(), 11);
+ }
+
+ gaps = tree.Gaps(Interval(1, 11));
+
+ EXPECT_EQ(gaps.size(), 2);
+
+ size_t l = 1;
+ size_t r = 3;
+
+ for (const auto& i : gaps) {
+ EXPECT_EQ(i.Left(), l);
+ EXPECT_EQ(i.Right(), r);
+
+ l += 8;
+ r += 8;
+ }
+
+ gaps = tree.Gaps(Interval(11, 15));
+
+ EXPECT_EQ(gaps.size(), 1);
+
+ for (const auto& i : gaps) {
+ EXPECT_EQ(i.Left(), 11);
+ EXPECT_EQ(i.Right(), 15);
+ }
+}
+
+TEST(IntervalTest, Gaps3)
+{
+ IntervalTree tree;
+
+ tree.Insert(Interval(3, 5));
+ tree.Insert(Interval(7, 9));
+
+ IntervalTree gaps = tree.Gaps(Interval(4, 9));
+
+ EXPECT_EQ(gaps.size(), 1);
+
+ for (const auto& i : gaps) {
+ EXPECT_EQ(i.Left(), 5);
+ EXPECT_EQ(i.Right(), 7);
+ }
+}
+
+TEST(IntervalTest, ZMW25300)
+{
+ IntervalTree tree;
+
+ tree.Insert(Interval(252, 295));
+ tree.Insert(Interval(293, 338));
+
+ for (const auto& i : tree) {
+ EXPECT_EQ(i.Left(), 252);
+ EXPECT_EQ(i.Right(), 338);
+ }
+}
+
+TEST(IntervalTest, FromString)
+{
+ Interval a = Interval::FromString("1");
+
+ EXPECT_EQ(a.Left(), 1);
+ EXPECT_EQ(a.Right(), 2);
+
+ IntervalTree tree = IntervalTree::FromString("1,3-4");
+
+ size_t l = 1, r = 2;
+
+ for (const auto& i : tree) {
+ EXPECT_EQ(i.Left(), l);
+ EXPECT_EQ(i.Right(), r);
+ l = 3;
+ r = 5;
+ }
+
+ EXPECT_THROW({ IntervalTree tree = IntervalTree::FromString("A,15-22"); },
+ std::invalid_argument);
+
+ EXPECT_THROW({ IntervalTree tree = IntervalTree::FromString("15-2"); }, std::invalid_argument);
+
+ tree = IntervalTree::FromString("2-2");
+
+ for (const auto& i : tree) {
+ EXPECT_EQ(i.Left(), 2);
+ EXPECT_EQ(i.Right(), 3);
+ }
+}
+
+TEST(IntervalTest, Contains)
+{
+ Interval a = Interval::FromString("2");
+
+ EXPECT_FALSE(a.Contains(1));
+ EXPECT_TRUE(a.Contains(2));
+ EXPECT_FALSE(a.Contains(3));
+
+ IntervalTree tree = IntervalTree::FromString("5,8-10");
+
+ EXPECT_FALSE(tree.Contains(4));
+ EXPECT_TRUE(tree.Contains(5));
+ EXPECT_FALSE(tree.Contains(6));
+
+ EXPECT_FALSE(tree.Contains(7));
+ EXPECT_TRUE(tree.Contains(8));
+ EXPECT_TRUE(tree.Contains(9));
+ EXPECT_TRUE(tree.Contains(10));
+ EXPECT_FALSE(tree.Contains(11));
+}
diff --git a/tests/unit/TestLoadModels.cpp b/tests/unit/TestLoadModels.cpp
new file mode 100644
index 0000000..0a57f44
--- /dev/null
+++ b/tests/unit/TestLoadModels.cpp
@@ -0,0 +1,235 @@
+// Copyright (c) 2016, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <algorithm>
+#include <chrono>
+#include <iterator>
+#include <set>
+#include <string>
+#include <vector>
+
+#include <sys/stat.h>
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <pacbio/consensus/ModelSelection.h>
+#include <pacbio/consensus/MonoMolecularIntegrator.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/data/State.h>
+
+#include "TestData.h"
+
+using namespace std;
+using namespace PacBio::Consensus; // NOLINT
+using namespace PacBio::Data; // NOLINT
+
+namespace {
+const SNR snr(10, 7, 5, 11);
+const string SP1C1 = "S/P1-C1.1";
+const string SP1C1v2 = "S/P1-C1.2";
+
+const string longTpl =
+ "GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCAT"
+ "AACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCC"
+ "TCTGTCGTTTCCTTTCTCTGTTTTTGTCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATT"
+ "TTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGG"
+ "TAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAA"
+ "AGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTATTGAGTACGAA"
+ "CGCCATCGACTTACGCGTGCGCAGGCCGACGCACAGGAACTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGA"
+ "AACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGT"
+ "CGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATG"
+ "AACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGC"
+ "TGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGAT"
+ "GCTAATTACTATCTCCCGAAAGAATC";
+
+const string longRead =
+ "GGGCGGCGACCTCGCGGGTTTTCGCTATTTCTGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCAT"
+ "AACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCC"
+ "TCTGTCGTTTCCTTTCTCTGTTTTTGTCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATT"
+ "TTCGGTGGAGTATCCGTACCATTCAGAACTGGCAGGACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTA"
+ "ATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAATAG"
+ "CTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTATTGAGTACGAACG"
+ "CCATCGACTTACGCGTGCGCAGGCCGACGCACAGGAACTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAA"
+ "CCGCATTCCCCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTG"
+ "TCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCAT"
+ "GAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGG"
+ "CTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAACGGATGCT"
+ "AATTACTATCTCCCGAAAGAATC";
+
+const std::vector<uint8_t> longPws(837, 2);
+const IntegratorConfig cfg(-100.0); // disable zscore filtering
+
+Read MkRead(const string& seq, const SNR& snr, const string& mdl, const vector<uint8_t>& pw)
+{
+ vector<uint8_t> ipd(0, seq.length());
+ return Read("NA", seq, ipd, pw, snr, mdl);
+}
+}
+
+TEST(LoadModelsTest, SupportedChemistries)
+{
+ const std::set<std::string> chem = {"P6-C4", "S/P1-C1/beta", "S/P1-C1.1", "S/P1-C1.2"};
+ const std::set<std::string> supp = SupportedChemistries();
+ std::set<std::string> diff;
+ std::set_difference(chem.begin(), chem.end(), supp.begin(), supp.end(),
+ std::inserter(diff, diff.begin()));
+ EXPECT_TRUE(diff.size() == 0);
+}
+
+TEST(LoadModelsTest, Malformed)
+{
+ std::string malformed = tests::DataDir + "/Malformed.json";
+ struct stat st;
+ ASSERT_TRUE(stat(malformed.c_str(), &st) == 0 && S_ISREG(st.st_mode));
+ ASSERT_FALSE(LoadModels(malformed));
+}
+
+// disable this test because we cannot load S/P1-C1.2 more than once
+// TEST(LoadModelsTest, DISABLED_SingleFile)
+// {
+// std::string sp1c1v2 = tests::DataDir + "/params/SP1C1v2.json";
+// ASSERT_TRUE(LoadModelFromFile(sp1c1v2));
+// std::set<std::string> chems = SupportedChemistries();
+// ASSERT_TRUE(chems.find("S/P1-C1.2::PwSnr") != chems.end());
+// }
+
+TEST(LoadModelsTest, Directory)
+{
+ ASSERT_TRUE(LoadModels(tests::DataDir + "/params"));
+ std::set<std::string> chems = SupportedModels();
+ ASSERT_TRUE(chems.find("S/P1-C1/beta::Marginal::FromFile") != chems.end());
+ ASSERT_TRUE(chems.find("S/P1-C1.1::PwSnrA::FromFile") != chems.end());
+ ASSERT_TRUE(chems.find("S/P1-C1.2::PwSnr::FromFile") != chems.end());
+
+// test identity between S/P1-C1/beta and S/P1-C1/beta::Marginal (loaded)
+// disabled until S_P1C1Beta is fixed
+#if 0
+ {
+ MonoMolecularIntegrator ai1(longTpl, cfg, snr, "S/P1-C1/beta::Compiled");
+ EXPECT_EQ(State::VALID,
+ ai1.AddRead(MappedRead(MkRead(longRead, snr, "S/P1-C1/beta::Compiled", longPws),
+ StrandType::FORWARD, 0, longTpl.length(), true, true)));
+
+ MonoMolecularIntegrator ai2(longTpl, cfg, snr, "S/P1-C1/beta::Marginal");
+ EXPECT_EQ(State::VALID,
+ ai2.AddRead(MappedRead(MkRead(longRead, snr, "S/P1-C1/beta::Marginal", longPws),
+ StrandType::FORWARD, 0, longTpl.length(), true, true)));
+
+ EXPECT_NEAR(ai1.LL(), ai2.LL(), 1.0e-5);
+ }
+#endif
+
+ // test identity between S/P1-C1.1 and S/P1-C1.1::PwSnrA (loaded)
+ {
+ MonoMolecularIntegrator ai1(longTpl, cfg, snr, "S/P1-C1.1::PwSnrA::Compiled");
+ EXPECT_EQ(State::VALID, ai1.AddRead(MappedRead(
+ MkRead(longRead, snr, "S/P1-C1.1::PwSnrA::Compiled", longPws),
+ StrandType::FORWARD, 0, longTpl.length(), true, true)));
+
+ MonoMolecularIntegrator ai2(longTpl, cfg, snr, "S/P1-C1.1::PwSnrA::FromFile");
+ EXPECT_EQ(State::VALID, ai2.AddRead(MappedRead(
+ MkRead(longRead, snr, "S/P1-C1.1::PwSnrA::FromFile", longPws),
+ StrandType::FORWARD, 0, longTpl.length(), true, true)));
+
+ EXPECT_NEAR(ai1.LL(), ai2.LL(), 1.0e-5);
+ }
+
+ // test identity between S/P1-C1.2 and S/P1-C1.2::PwSnr
+ {
+ MonoMolecularIntegrator ai1(longTpl, cfg, snr, "S/P1-C1.2::PwSnr::Compiled");
+ EXPECT_EQ(State::VALID, ai1.AddRead(MappedRead(
+ MkRead(longRead, snr, "S/P1-C1.2::PwSnr::Compiled", longPws),
+ StrandType::FORWARD, 0, longTpl.length(), true, true)));
+
+ MonoMolecularIntegrator ai2(longTpl, cfg, snr, "S/P1-C1.2::PwSnr::FromFile");
+ EXPECT_EQ(State::VALID, ai2.AddRead(MappedRead(
+ MkRead(longRead, snr, "S/P1-C1.2::PwSnr::FromFile", longPws),
+ StrandType::FORWARD, 0, longTpl.length(), true, true)));
+
+ EXPECT_NEAR(ai1.LL(), ai2.LL(), 1.0e-5);
+ }
+}
+
+#if EXTENSIVE_TESTING
+#ifndef NDEBUG
+TEST(LoadModelsTest, DISABLED_ModelTiming)
+#else
+TEST(LoadModelsTest, ModelTiming)
+#endif
+{
+ // load required models just in case they haven't been already
+ LoadModels(tests::DataDir + "/params");
+
+ const size_t nsamp = 100;
+ const std::vector<std::string> mdls = {"S/P1-C1/beta::Marginal::FromFile",
+ "S/P1-C1.1::PwSnrA::FromFile",
+ "S/P1-C1.2::PwSnr::FromFile"};
+ for (const auto mdl : mdls) {
+ MonoMolecularIntegrator ai(longTpl, cfg, snr, mdl);
+ const auto stime = std::chrono::high_resolution_clock::now();
+ for (size_t i = 0; i < nsamp; ++i)
+ EXPECT_EQ(State::VALID,
+ ai.AddRead(MappedRead(MkRead(longRead, snr, mdl, longPws),
+ StrandType::FORWARD, 0, longTpl.length(), true, true)));
+ const auto etime = std::chrono::high_resolution_clock::now();
+ const auto duration =
+ std::chrono::duration_cast<std::chrono::microseconds>(etime - stime).count();
+ // std::cout << "avg duration: " << duration / nsamp << "us" << std::endl;
+ EXPECT_LT(duration / nsamp, 1500);
+ }
+}
+#endif
+
+TEST(LoadModelsTest, ModelOverride)
+{
+ MonoMolecularIntegrator ai1(longTpl, cfg, snr, "S/P1-C1.2");
+ EXPECT_EQ(State::VALID,
+ ai1.AddRead(MappedRead(MkRead(longRead, snr, "S/P1-C1.2", longPws),
+ StrandType::FORWARD, 0, longTpl.length(), true, true)));
+
+ ASSERT_TRUE(OverrideModel("S/P1-C1.2"));
+
+ MonoMolecularIntegrator ai2(longTpl, cfg, snr, "S/P1-C1.1");
+ EXPECT_EQ(State::VALID,
+ ai2.AddRead(MappedRead(MkRead(longRead, snr, "S/P1-C1.1", longPws),
+ StrandType::FORWARD, 0, longTpl.length(), true, true)));
+
+ EXPECT_NEAR(ai1.LL(), ai2.LL(), 1.0e-5);
+
+ ASSERT_TRUE(UnOverrideModel());
+}
diff --git a/tests/unit/TestMutationEnumerator.cpp b/tests/unit/TestMutationEnumerator.cpp
new file mode 100644
index 0000000..b2fdb8c
--- /dev/null
+++ b/tests/unit/TestMutationEnumerator.cpp
@@ -0,0 +1,124 @@
+// Copyright (c) 2011-2014, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <algorithm>
+#include <iostream>
+#include <set>
+#include <string>
+#include <vector>
+
+#include <pacbio/consensus/MonoMolecularIntegrator.h>
+#include <pacbio/consensus/MultiMolecularIntegrator.h>
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/data/Read.h>
+
+using std::string;
+using std::vector;
+using std::cout;
+using std::endl;
+
+using namespace PacBio::Data;
+
+namespace PacBio {
+namespace Consensus {
+
+vector<Mutation> Mutations(const AbstractIntegrator& ai, const size_t start, const size_t end);
+
+vector<Mutation> Mutations(const AbstractIntegrator& ai);
+
+vector<Mutation> NearbyMutations(vector<Mutation>* applied, vector<Mutation>* centers,
+ const AbstractIntegrator& ai, const size_t neighborhood);
+}
+}
+
+using namespace PacBio::Consensus; // NOLINT
+
+using ::testing::UnorderedElementsAreArray;
+
+TEST(MutationEnumerationTest, TestAllMutationsMono)
+{
+ string tpl = "GAATC";
+ MonoMolecularIntegrator ai(tpl, IntegratorConfig(), SNR(4, 4, 4, 4), "P6-C4");
+ vector<Mutation> result = Mutations(ai);
+ // 3 insertions, 3 substitutions, and 1 deletion per base
+ // and +4 for terminal insertions (1 beginning, 3 end)
+ // and -1 for the homopolymer AA deletion
+ EXPECT_EQ(7 * tpl.length() + 4 - 1, result.size());
+}
+
+TEST(MutationEnumerationTest, TestAllMutationsMulti)
+{
+ string tpl = "GAATC";
+ MultiMolecularIntegrator ai(tpl, IntegratorConfig());
+ vector<Mutation> result = Mutations(ai);
+ EXPECT_EQ(7 * tpl.length() + 4 - 1, result.size());
+}
+
+TEST(MutationEnumerationTest, TestNearbyMutations)
+{
+ string tpl = "GAATT";
+ MonoMolecularIntegrator ai(tpl, IntegratorConfig(), SNR(4, 4, 4, 4), "P6-C4");
+
+ vector<Mutation> centers = {Mutation(MutationType::SUBSTITUTION, 2, 'T')};
+ vector<Mutation> result = NearbyMutations(¢ers, ¢ers, ai, 1);
+ // 7 for each of ATT,
+ // and +3 for terminal insertions (end)
+ // and -1 for hompolymer TT deletion
+ EXPECT_EQ(7 * 3 + 3 - 1, result.size());
+
+ centers.back() = Mutation(MutationType::SUBSTITUTION, 1, 'T');
+
+ result = NearbyMutations(¢ers, ¢ers, ai, 1);
+ // 7 for each of ATT,
+ // and +4 for terminal insertions (1 beg, 3 end)
+ // and -1 for hompolymer TT deletion
+ EXPECT_EQ(7 * 3 + 4 - 1, result.size());
+
+ result = NearbyMutations(¢ers, ¢ers, ai, 2);
+ // 8 mutations for each of GAAT, except -2 for the homopolymer AA indels,
+ // and +3 for terminal insertions (not T, because it's not the first)
+ EXPECT_EQ(7 * 4 + 4 - 1, result.size());
+
+ centers.push_back(Mutation(MutationType::SUBSTITUTION, 3, 'G'));
+ result = NearbyMutations(¢ers, ¢ers, ai, 2);
+ vector<Mutation> expected = Mutations(ai);
+ EXPECT_EQ(expected.size(), result.size());
+ EXPECT_THAT(result, UnorderedElementsAreArray(expected));
+}
diff --git a/tests/unit/TestPoaConsensus.cpp b/tests/unit/TestPoaConsensus.cpp
new file mode 100644
index 0000000..a2fb219
--- /dev/null
+++ b/tests/unit/TestPoaConsensus.cpp
@@ -0,0 +1,603 @@
+// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <algorithm>
+#include <boost/algorithm/string.hpp>
+#include <boost/assign.hpp>
+#include <boost/assign/std/vector.hpp>
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include <pacbio/align/AlignConfig.h>
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/denovo/PoaConsensus.h>
+
+using std::string;
+using std::vector;
+using std::cout;
+using std::endl;
+using boost::erase_all_copy;
+
+using namespace boost::assign; // NOLINT
+using namespace PacBio::Consensus; // NOLINT
+using namespace PacBio::Poa; // NOLINT
+using namespace PacBio::Align; // NOLINT
+
+#define MAKE_ALL_PLOTS false
+
+static void plotConsensus(const PoaConsensus* pc, string description,
+ bool REALLY_MAKE_THIS_ONE = false)
+{
+ if (MAKE_ALL_PLOTS || REALLY_MAKE_THIS_ONE) {
+ string dotFname = description + ".dot";
+ string pngFname = description + ".png";
+ string cmd = string("dot -Tpng ") + dotFname + " > " + pngFname;
+ pc->Graph.WriteGraphVizFile(description + ".dot",
+ (PoaGraph::COLOR_NODES | PoaGraph::VERBOSE_NODES), pc);
+ // cout << cmd << endl;
+ int ret = system(cmd.c_str());
+ }
+}
+
+// TEST(PoaGraph, NoReadsTest)
+// {
+// // Test that it works with no reads
+// vector<const SequenceFeatures*> reads;
+// const PoaConsensus* pc = PoaConsensus::findConsensus(reads,
+// PoaConfig::GLOBAL_ALIGNMENT);
+// string dot = pc->getGraph()->toGraphViz();
+// cout << dot << endl;
+// }
+
+TEST(PoaGraph, SmallBasicTest1)
+{
+ // Test that it works with a single sequence
+ vector<string> reads;
+ reads += "GGG";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 1 }\"];"
+ "3[shape=Mrecord, label=\"{ G | 1 }\"];"
+ "4[shape=Mrecord, label=\"{ G | 1 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "}";
+ plotConsensus(pc, "small-basic-1");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GGG", pc->Sequence);
+ delete pc;
+}
+
+TEST(PoaGraph, SmallBasicTest2)
+{
+ // Test that it works with two identical sequences
+ vector<string> reads;
+ reads += "GGG", "GGG";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "3[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "4[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "}";
+ plotConsensus(pc, "small-basic-2");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GGG", pc->Sequence);
+
+ delete pc;
+}
+
+TEST(PoaGraph, SmallExtraTests)
+{
+ // Extra at beginning
+ {
+ vector<string> reads;
+ reads += "GGG", "TGGG";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "3[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "4[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "5[shape=Mrecord, label=\"{ T | 1 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "5->2 ;"
+ "0->5 ;"
+ "}";
+ plotConsensus(pc, "extra-at-beginning");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GGG", pc->Sequence);
+ delete pc;
+ }
+
+ // Extra in middle
+ {
+ vector<string> reads;
+ reads += "GGG", "GTGG";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ // this would be easier if we could use the C++0x raw
+ // strings feature (in g++ 4.5+)
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "3[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "4[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "5[shape=Mrecord, label=\"{ T | 1 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "5->3 ;"
+ "2->5 ;"
+ "}";
+ plotConsensus(pc, "extra-in-middle");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GGG", pc->Sequence);
+ delete pc;
+ }
+
+ // Extra at end
+ {
+ vector<string> reads;
+ reads += "GGG", "GGGT";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "3[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "4[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "5[shape=Mrecord, label=\"{ T | 1 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "5->1 ;"
+ "4->5 ;"
+ "}";
+ plotConsensus(pc, "extra-at-end");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GGG", pc->Sequence);
+ delete pc;
+ }
+}
+
+TEST(PoaGraph, SmallMismatchTests)
+{
+ // Mismatch at beginning
+ {
+ vector<string> reads;
+ reads += "GGG", "TGG";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 1 }\"];"
+ "3[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "4[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "5[shape=Mrecord, label=\"{ T | 1 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "5->3 ;"
+ "0->5 ;"
+ "}";
+ plotConsensus(pc, "mismatch-at-beginning");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GG", pc->Sequence);
+ delete pc;
+ }
+
+ // Mismatch in middle
+ {
+ vector<string> reads;
+ reads += "GGG", "GTG", "GTG";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 3 }\"];"
+ "3[shape=Mrecord, label=\"{ G | 1 }\"];"
+ "4[shape=Mrecord, label=\"{ G | 3 }\"];"
+ "5[shape=Mrecord, label=\"{ T | 2 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "5->4 ;"
+ "2->5 ;"
+ "}";
+ plotConsensus(pc, "mismatch-in-middle");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GTG", pc->Sequence);
+ delete pc;
+ }
+
+ // Mismatch at end
+ {
+ vector<string> reads;
+ reads += "GGG", "GGT";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "3[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "4[shape=Mrecord, label=\"{ G | 1 }\"];"
+ "5[shape=Mrecord, label=\"{ T | 1 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "5->1 ;"
+ "3->5 ;"
+ "}";
+ plotConsensus(pc, "mismatch-at-end");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GG", pc->Sequence);
+ delete pc;
+ }
+}
+
+TEST(PoaGraph, SmallDeletionTests)
+{
+ // Deletion at beginning
+ {
+ vector<string> reads;
+ reads += "GAT", "AT";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 1 }\"];"
+ "3[shape=Mrecord, label=\"{ A | 2 }\"];"
+ "4[shape=Mrecord, label=\"{ T | 2 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "0->3 ;"
+ "}";
+ plotConsensus(pc, "deletion-at-beginning");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("AT", pc->Sequence);
+ delete pc;
+ }
+
+ // Deletion in middle
+ {
+ vector<string> reads;
+ reads += "GAT", "GT";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "3[shape=Mrecord, label=\"{ A | 1 }\"];"
+ "4[shape=Mrecord, label=\"{ T | 2 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "2->4 ;"
+ "}";
+ plotConsensus(pc, "deletion-in-middle");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ delete pc;
+ }
+
+ // Deletion at end
+ {
+ vector<string> reads;
+ reads += "GAT", "GA";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz();
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "3[shape=Mrecord, label=\"{ A | 2 }\"];"
+ "4[shape=Mrecord, label=\"{ T | 1 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "3->1 ;"
+ "}";
+ plotConsensus(pc, "deletion-at-end");
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GA", pc->Sequence);
+ delete pc;
+ }
+}
+
+TEST(PoaConsensus, TestSimple)
+{
+ vector<string> reads;
+ reads += "TTTACAGGATAGTCCAGT", "ACAGGATACCCCGTCCAGT", "ACAGGATAGTCCAGT",
+ "TTTACAGGATAGTCCAGTCCCC", "TTTACAGGATTAGTCCAGT", "TTTACAGGATTAGGTCCCAGT",
+ "TTTACAGGATAGTCCAGT";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ plotConsensus(pc, "simple");
+ EXPECT_EQ("TTTACAGGATAGTCCAGT", pc->Sequence);
+ delete pc;
+}
+
+TEST(PoaConsensus, TestOverhangSecond)
+{
+ vector<string> reads;
+ reads += "TTTACAGGATAGTCCAGT", "TTTACAGGATAGTCCAGTAAA", "TTTACAGGATAGTCCAGTAAA";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ EXPECT_EQ("TTTACAGGATAGTCCAGTAAA", pc->Sequence);
+ delete pc;
+}
+
+TEST(PoaConsensus, SmallSemiglobalTest)
+{
+ vector<string> reads;
+ reads += "GGTGG", "GGTGG", "T";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::SEMIGLOBAL);
+ plotConsensus(pc, "small-semiglobal");
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ ^ | 0 }\"];"
+ "1[shape=Mrecord, label=\"{ $ | 0 }\"];"
+ "2[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "3[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "4[shape=Mrecord, label=\"{ T | 3 }\"];"
+ "5[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "6[shape=Mrecord, label=\"{ G | 2 }\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->5 ;"
+ "5->6 ;"
+ "6->1 ;"
+ "4->1 ;"
+ "0->4 ;"
+ "}";
+ string dot = pc->Graph.ToGraphViz();
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ EXPECT_EQ("GGTGG", pc->Sequence);
+ delete pc;
+}
+
+TEST(PoaConsensus, SmallTilingTest)
+{
+ vector<string> reads;
+ reads += "GGGGAAAA", "AAAATTTT", "TTTTCCCC", "CCCCAGGA";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::SEMIGLOBAL);
+ plotConsensus(pc, "small-tiling");
+ EXPECT_EQ("GGGGAAAATTTTCCCCAGGA", pc->Sequence);
+ delete pc;
+}
+
+TEST(PoaConsensus, TestVerboseGraphVizOutput)
+{
+ vector<string> reads;
+ reads += "GGG", "TGGG";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ string dot = pc->Graph.ToGraphViz(PoaGraph::COLOR_NODES | PoaGraph::VERBOSE_NODES, pc);
+
+ string expectedDot =
+ "digraph G {"
+ "rankdir=\"LR\";"
+ "0[shape=Mrecord, label=\"{ { 0 | ^ } | { 0 | 0 } | { 0.00 | 0.00 } "
+ "}\"];"
+ "1[shape=Mrecord, label=\"{ { 1 | $ } | { 0 | 0 } | { 0.00 | 0.00 } "
+ "}\"];"
+ "2[shape=Mrecord, style=\"filled\", fillcolor=\"lightblue\" ,"
+ " label=\"{ { 2 | G } | { 2 | 2 } | { 2.00 | 2.00 } }\"];"
+ "3[shape=Mrecord, style=\"filled\", fillcolor=\"lightblue\" ,"
+ " label=\"{ { 3 | G } | { 2 | 2 } | { 2.00 | 4.00 } }\"];"
+ "4[shape=Mrecord, style=\"filled\", fillcolor=\"lightblue\" ,"
+ " label=\"{ { 4 | G } | { 2 | 2 } | { 2.00 | 6.00 } }\"];"
+ "5[shape=Mrecord, label=\"{ { 5 | T } | { 1 | 1 } | { -0.00 | -0.00 } "
+ "}\"];"
+ "0->2 ;"
+ "2->3 ;"
+ "3->4 ;"
+ "4->1 ;"
+ "5->2 ;"
+ "0->5 ;}";
+
+ EXPECT_EQ(expectedDot, erase_all_copy(dot, "\n"));
+ delete pc;
+}
+
+TEST(PoaConsensus, TestLocalStaggered)
+{
+ // Adapted from Pat's C# test
+ vector<string> reads;
+ reads += "TTTACAGGATAGTGCCGCCAATCTTCCAGT", "GATACCCCGTGCCGCCAATCTTCCAGTATATACAGCACGAGTAGC",
+ "ATAGTGCCGCCAATCTTCCAGTATATACAGCACGGAGTAGCATCACGTACGTACGTCTACACGTAATT",
+ "ACGTCTACACGTAATTTTGGAGAGCCCTCTCTCACG", "ACACGTAATTTTGGAGAGCCCTCTCTTCACG",
+ "AGGATAGTGCCGCCAATCTTCCAGTAATATACAGCACGGAGTAGCATCACGTACG",
+ "ATAGTGCCGCCAATCTTCCAGTATATACAGCACGGAGTAGCATCACGTACGTACGTCTACACGT";
+
+ // 4 is a magic number here. the .NET code had an entrenched
+ // assumption that sequences in POA were subreads from a ZMW, so
+ // the minCoverage was (numReads - 3), under assumption that basal
+ // coverage for CCS is (numReads-2) (beginning, end read).
+ // Application has to provide a sensible minCoverage.
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::LOCAL, 4);
+ plotConsensus(pc, "local-staggered", true);
+ EXPECT_EQ("ATAGTGCCGCCAATCTTCCAGTATATACAGCACGGAGTAGCATCACGTACGTACGTCTACACGTAATT", pc->Sequence);
+ delete pc;
+}
+
+TEST(PoaConsensus, TestLongInsert)
+{
+ // Adapted from Pat's C# test
+ vector<string> reads;
+ reads +=
+ "TTTACAGGATAGTGCCGCCAATCTTCCAGTGATACCCCGTGCCGCCAATCTTCCAGTATATACAGCACGA"
+ "GGTAGC",
+ "TTTACAGGATAGTGCCGGCCAATCTTCCAGTGATACCCCGTGCCGCCAATCTTCCAGTATATACAGCACG"
+ "AGTAGC",
+ "TTGTACAGGATAGTGCCGCCAATCTTCCAGTGATGGGGGGGGGGGGGGGGGGGGGGGGGGGACCCCGTGC"
+ "CGCCAATCTTCCAGTATATACAGCACGAGTAGC";
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+ EXPECT_EQ(
+ "TTTACAGGATAGTGCCGCCAATCTTCCAGTGATACCCCGTGCCGCCAATCTTCCAGTATATACAGCACGA"
+ "GTAGC",
+ pc->Sequence);
+ delete pc;
+}
+
+#if 0
+TEST(PoaConsensus, TestMutations)
+{
+ using ::testing::ElementsAreArray;
+
+ vector<string> reads;
+ reads += "TGATTACAT",
+ "TGATTACAT",
+ "TGATTCAT", // Deletion @ 5
+ "TGATTATAT", // Substitution @ 6
+ "TGATTGACAT"; // Insertion @ 5
+
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, GLOBAL);
+
+ const vector<ScoredMutation>* scoredMutations = pc->Mutations();
+ vector<string> variantDescriptions;
+ foreach (const ScoredMutation& scoredMutation, *scoredMutations)
+ {
+ variantDescriptions.push_back(scoredMutation.ToString());
+ }
+ sort(variantDescriptions.begin(), variantDescriptions.end());
+ const char* expectedDescriptions[] = { "Deletion @5:6 -3.00",
+ "Insertion (G) @5 -3.00",
+ "Substitution (T) @6:7 -3.00" };
+ ASSERT_THAT(variantDescriptions, ElementsAreArray(expectedDescriptions));
+ delete pc;
+}
+#endif
+
+TEST(PoaConsensus, NondeterminismRegressionTest)
+{
+ //
+ // This is a regression test for a real-world case of
+ // nondeterminism found in the POA on a quiver job on Staph.
+ //
+ vector<string> reads;
+ reads +=
+ "TATCAATCAACGAAATTCGCCAATTCCGTCATGAATGTCAATATCTAACTACACTTTAGAATACATTCTT"
+ "TGACATGCCTGGCCTATTGATATTTCAATAAAATCAGACTATAAAGACAACTTACAAATGATCCTATAAA"
+ "TTAAAGATCGAGAATCTAAAGAGTGAAATTAAAGCTAATTACTGCTTTAAAAATTTTACGTGCACACAAA"
+ "AATGAATTTATCCTCATTATATCGAAAATACCATGAAGTATAGTAAGCTAACTTGAATATGATCATTAAT"
+ "CGGCTATATGATTATTTTGATAATGCAATGAGCATCAATCTGAATTTATGACCTATCATTCGCGTTGCAT"
+ "TTATTGAAGTGAAAATTCATGTACGCTTTTTTATTTTATTAATATAATCCTTGATATTGGTTATATACCA"
+ "CGCTGTCACATAATTTTCAATAAATTTTTCTACTAAATGAAGTGTCTGTTATCTATCAC";
+ reads +=
+ "TATCAACAACGAAAATGCGCAGTTACGTCATGATTTATGTCAAATAATCTAAACGACACTTTCAGAAATA"
+ "AATACATTCGAGAAGATGAATGCCTGGCGCAAAGTGATTATTTCAATAAAATATTTGTACCTTGAAAGAC"
+ "AATTTACAAATGAATGCTATAAAATTTAAATGGATCCGGAGAATCTTTAAAGTACGTGAAATTAAAGGCT"
+ "AAGATTACTGCGAAAAATTTTCGTGCACAAGAAATGAATGTTCCAGATTAGTATCGGAAAATAAGCCATG"
+ "AAGAAGCTAGCATTAACTTGAATATGATCGATTTAATCGGCAGTATTGGTAATTATCTTGATAAGCAATT"
+ "GAGCATCAACTGAAATTGAATGACTCTACATGCCTCGCTGAGTATGCGATTTATTGAAAGTGAAATTCAG"
+ "TAAAGTTTATTGTTATGAATAAATGCGTACTTGGATGAATATCCCGACGGTAGTTCAAGTGTAAATGGAG"
+ "TGAGGGGGTTCTTTCTTATAGAATAGTTTTATACTACTGATAAGGTGTAACCTGAGTGAGTCGTGATTTT"
+ "AGAGTTACTTGCGAAC";
+
+ std::set<string> answers;
+ for (int run = 0; run < 100; run++) {
+ const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, AlignMode::GLOBAL);
+#if 0
+ char fname[100];
+ sprintf(fname, "/tmp/gr%03d.dot", run);
+ pc->WriteGraphVizFile(fname, (PoaGraph::VERBOSE_NODES | PoaGraph::COLOR_NODES));
+#endif
+ answers.insert(pc->Sequence);
+ delete pc;
+ }
+ ASSERT_EQ(1, answers.size());
+}
diff --git a/tests/unit/TestPolish.cpp b/tests/unit/TestPolish.cpp
new file mode 100644
index 0000000..bd5e441
--- /dev/null
+++ b/tests/unit/TestPolish.cpp
@@ -0,0 +1,90 @@
+// Copyright (c) 2011-2014, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <string>
+#include <tuple>
+
+#include <pacbio/consensus/MonoMolecularIntegrator.h>
+#include <pacbio/consensus/MultiMolecularIntegrator.h>
+#include <pacbio/consensus/Polish.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/data/Sequence.h>
+
+using namespace PacBio::Consensus; // NOLINT
+using namespace PacBio::Data; // NOLINT
+
+namespace {
+
+Read MkRead(const std::string& seq, const SNR& snr, const std::string& mdl)
+{
+ std::vector<uint8_t> cov(0, seq.length());
+ return Read("NA", seq, cov, cov, snr, mdl);
+}
+
+const SNR snr(10, 7, 5, 11);
+
+TEST(PolishTest, MonoBasic)
+{
+ MonoMolecularIntegrator ai("GCGTCGT", IntegratorConfig(), snr, "P6-C4");
+
+ ai.AddRead(MappedRead(MkRead("ACGTACGT", snr, "P6-C4"), StrandType::FORWARD, 0, 7, true, true));
+ ai.AddRead(MappedRead(MkRead("ACGACGT", snr, "P6-C4"), StrandType::FORWARD, 0, 7, true, true));
+ ai.AddRead(MappedRead(MkRead("ACGACGT", snr, "P6-C4"), StrandType::FORWARD, 0, 7, true, true));
+
+ Polish(&ai, PolishConfig());
+
+ EXPECT_EQ("ACGACGT", std::string(ai));
+}
+
+TEST(PolishTest, MultiBasic)
+{
+ MultiMolecularIntegrator ai("GCGTCGT", IntegratorConfig());
+
+ ai.AddRead(MappedRead(MkRead("ACGTACGT", snr, "P6-C4"), StrandType::FORWARD, 0, 7, true, true));
+ ai.AddRead(MappedRead(MkRead(ReverseComplement("ACGACGT"), snr, "P6-C4"), StrandType::REVERSE,
+ 0, 7, true, true));
+ ai.AddRead(MappedRead(MkRead("ACGACGT", snr, "P6-C4"), StrandType::FORWARD, 0, 7, true, true));
+
+ const auto result = Polish(&ai, PolishConfig());
+
+ EXPECT_TRUE(result.hasConverged);
+ EXPECT_EQ("ACGACGT", std::string(ai));
+}
+}
diff --git a/tests/unit/TestSequence.cpp b/tests/unit/TestSequence.cpp
new file mode 100644
index 0000000..5ff3782
--- /dev/null
+++ b/tests/unit/TestSequence.cpp
@@ -0,0 +1,52 @@
+// Copyright (c) 2011-2014, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <string>
+
+#include <pacbio/data/Sequence.h>
+
+using std::string;
+
+using namespace PacBio::Data; // NOLINT
+
+namespace {
+
+TEST(SequenceTest, ReverseComplement) { EXPECT_EQ("TACGAT", ReverseComplement("ATCGTA")); }
+}
diff --git a/tests/unit/TestSparseAlign.cpp b/tests/unit/TestSparseAlign.cpp
new file mode 100644
index 0000000..c63da31
--- /dev/null
+++ b/tests/unit/TestSparseAlign.cpp
@@ -0,0 +1,163 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <pacbio/ccs/SparseAlignment.h>
+
+TEST(SparseAlignTest, ExactAlign)
+{
+ using namespace std;
+
+ const size_t K = 5;
+ string s1 = "ACGTACACACAGTACAGTACAAGTTTCACGGACATTTGGTTCCCACTTGTACAGTGCACACGGGTTACACGT";
+ auto chain = PacBio::CCS::SparseAlign<K>(s1, s1);
+ auto fst = chain[0];
+ auto lst = chain[chain.size() - 1];
+
+ EXPECT_EQ(s1.size() - K + 1, chain.size());
+ EXPECT_EQ(0, fst.first);
+ EXPECT_EQ(0, fst.second);
+ EXPECT_EQ(s1.size() - K, lst.first);
+ EXPECT_EQ(s1.size() - K, lst.second);
+}
+
+TEST(SparseAlignTest, ExactPartial)
+{
+ using namespace std;
+
+ const size_t K = 5;
+ string s1 = "ACGTACACACAGTACAGTACAAGTTTCACGGACATTTGGTTCCCACTTGTACAGTGCACACGGGTTACACGT";
+ string s2 = "TTTGGTTCCCACTTGTACAGTGCACACGGGTTACACGT";
+ auto chain = PacBio::CCS::SparseAlign<K>(s1, s2);
+ auto fst = chain[0];
+ auto lst = chain[chain.size() - 1];
+
+ EXPECT_EQ(s2.size() - K + 1, chain.size());
+ EXPECT_EQ(34, fst.first);
+ EXPECT_EQ(0, fst.second);
+ EXPECT_EQ(s1.size() - K, lst.first);
+ EXPECT_EQ(s2.size() - K, lst.second);
+}
+
+TEST(SparseAlignTest, InsertAlign)
+{
+ using namespace std;
+
+ const size_t K = 5;
+ string s1 = "ACGTACACACAGTACAGTACAAGTTTCACGGACATTTGGTTCCCACTTGTACAGTGCACACGGGTTACACGT";
+ string s2 =
+ "ACGTACACACAGTACAGTACAAGTTTCACGGACATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTGGTTCCCACTTGTAC"
+ "AGTGCACACGGGTTACACGT";
+ auto chain = PacBio::CCS::SparseAlign<K>(s1, s2);
+ auto fst = chain[0];
+ auto lst = chain[chain.size() - 1];
+
+ EXPECT_EQ(0, fst.first);
+ EXPECT_EQ(0, fst.second);
+ EXPECT_EQ(s1.size() - K, lst.first);
+ EXPECT_EQ(s2.size() - K, lst.second);
+}
+
+TEST(SparseAlignTest, NoAlign)
+{
+ using namespace std;
+
+ const size_t K = 5;
+ string s1 = "ACGTACACACAGTACAGTACAAGTTTCACGGACATTTGGTTCCCACTTGTACAGTGCACACGGGTTACACGT";
+ string s2 = "AAAATCCCCCCCCCCAGGGGG";
+ auto chain = PacBio::CCS::SparseAlign<K>(s1, s2);
+
+ EXPECT_EQ(0, chain.size());
+}
+
+TEST(SparseAlignTest, SimpleAlign)
+{
+ using namespace std;
+
+ const size_t K = 5;
+ string s1 = "ACGTACACACAGTACAGTACAAGTTTCACGGACATTTGGTTCCCACTTGTACAGTGCACACGGGTTACACGT";
+ string s2 = "ACGTACACCAGTAAGTACAAGTTTCACGCGAATTTGGTTCCCACTTGTCAAGTGCACACGGGTTACACGT";
+ auto chain = PacBio::CCS::SparseAlign<K>(s1, s2);
+ auto fst = chain[0];
+ auto lst = chain[chain.size() - 1];
+
+ EXPECT_EQ(0, fst.first);
+ EXPECT_EQ(0, fst.second);
+ EXPECT_EQ(s1.size() - K, lst.first);
+ EXPECT_EQ(s2.size() - K, lst.second);
+}
+
+TEST(SparseAlignTest, LongAlign)
+{
+ using namespace std;
+
+ const size_t K = 5;
+ string s1 =
+ "AGAGAACATCGCTATCCGCAGATAAAGCAAATCCTTCCAGACCAACAACCAATCGTAGCAAAAACATTCAGCGAACAGCAACACGCAGTT"
+ "AGACCAACGAAAACTATGGGACAGCTAGATAGACACACAACATACAAAAAATATAACTCGCCCCATAGATCACAATAGAGCTGGATGCAG"
+ "AAAGACTAGAAGAAGTGGGTGTATACGCAGCATTAAACAGCAGAGAGATAGTTCCTAACAAACAGACATATGGGTAATAAGACACAATCA"
+ "ACAAAGCAAACATAAGAGCGAATATTGCAGGATAACTAATTAGAAGCTAATAAATACGAAACTACAGAGCAGTAAGACCAGATTAAATGA"
+ "GAAATCGACGAACCGAGACTGGACTCATGGAAGTGGAAGAACAGATAAGAAAGACAAGAACATGAAAAAATCAGATATAAGATATATACT"
+ "CCAGATGGACAGAACAATAACATAATGCACATACTAATACACACAGAGAGCGAATCAAGACGACTGAAATATATAACAAATATATACACA"
+ "TTGTACACACAACAACAGGATATTCTGAGTACCAAAGCTCAACAGTATTGCAGGATAAAATACACAGAAGAGACACATATATACGGATAT"
+ "ACAGGGAACCAGAAATACACGCGAATGACTGTTCTGGAAGCCATTTATAGACAGTAAGAATATGGCACCCAATACATACACGCACGTATA"
+ "CTGACACACAAAGACAGATTACATCATACACACAATGACACATTTGGGCGAGAGATTACAACCACGTATGAATACAACAAGAGAAACCGA"
+ "CGCAAACAACATAGATCAGATATTTAGCTGAAAAATGTACCAGAACTTTAGAAGAAAGGAAAATACACTACAAGCATAGGTGAGAAGCAC"
+ "AACCATTCGATTATGCAACAGAATCTACAGATACTATAT";
+ string s2 =
+ "AGAGAACAATCGCTATCCGCAAGATAAAGCAAATCCTTCCAGACCAACAACCAATCAGTAGCAAAAACATTCAGCGAACAGCAAACACGC"
+ "AGTTAGACCAGACGAAAACTATGGGACTAAGCTAGATAGACACACAACATACAAAAAATATAAGACAGTCGAGCCAGCCATAAGAGAGAG"
+ "AGTGTGAGAGTATATCACAATAGAGCTGGATGCAGAAAGACTAAGAAGAAGTGGGTGTATACGCAGCATTAAAAGCAGAGAGATGTTCCT"
+ "AACAAACAGACATATGGGTAATAAGACAATCAACAAAGCAAACATAAGAGCGAAATATTGCAGGAGTTAACTAATTAGAAGCTAAATAAA"
+ "TACGAAACTACAGAGCAGTAAGACCAGATTAAATTCATGGAAGTGGAAGAACAGATAAGAAAGACAAAGAACATGAAAAAATCAGATATA"
+ "AGATATAGATACTCCAGATGGACAGAACAATAACAAGTAATGCACATACTAATACACACAGAGAGCGAATCAAGACGACTGAAATATATA"
+ "ACAAATATATACACATTGTACACACAACAACAGGATATTCTGAGTACCAAAGCTCAACAGTATTGCAGGATAAAATACACAGAAGAGACA"
+ "CATATATACGGATATACAGGGAACCAGAAATACACGCGAATGACTGTTCTGGAAGCCATTTATAGACAGTAAGAATATGGCACCCAATAC"
+ "ATACACGCACGTATACTGACACACAAAGACAGATTACATCATACACACAATGACACATTTGGGCGAGAGATTACAACCACGTATGAATAC"
+ "AACAAGAGAAACCGACGCAAACAACATAGATCAGATATTTAGCTGAAAAATGTACCAGAACTTTAGAAGAAAGGAAAATACACGTACAAG"
+ "CATAGGTGAGAAGCACAACCATTCGATTATGCAACAGAATCTACAGATACTATAT";
+ auto chain = PacBio::CCS::SparseAlign<K>(s1, s2);
+ auto fst = chain[0];
+ auto lst = chain[chain.size() - 1];
+
+ EXPECT_EQ(0, fst.first);
+ EXPECT_EQ(0, fst.second);
+ EXPECT_GT(lst.first, 900);
+ EXPECT_GT(lst.second, 900);
+}
diff --git a/tests/unit/TestSparsePoa.cpp b/tests/unit/TestSparsePoa.cpp
new file mode 100644
index 0000000..975edbf
--- /dev/null
+++ b/tests/unit/TestSparsePoa.cpp
@@ -0,0 +1,299 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <iostream>
+#include <random>
+
+#include <boost/assign.hpp>
+#include <boost/assign/std/vector.hpp>
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <pacbio/denovo/PoaConsensus.h>
+#include <pacbio/denovo/SparsePoa.h>
+
+#include "TestData.h"
+#include "TestUtility.h"
+
+using std::vector;
+using std::string;
+
+using namespace boost::assign;
+
+using namespace PacBio::Poa;
+using ::testing::Ge;
+
+TEST(SparsePoaTest, TestLocalStaggered)
+{
+ // Adapted from Pat's C# test
+ vector<std::string> reads;
+
+ // Don't let clang-format break the whitespace here!!
+ // clang-format off
+
+ // 0123456789012345678901234567890
+ reads += "TTTACAGGATAGTGCCGCCAATCTTCCAGT",
+ // 0123456789012345678901234567890123456789012345
+ "GATACCCCGTGCCGCCAATCTTCCAGTATATACAGCACGAGTAGC",
+ // 012345678901234567890123456789012345678901234567890123456789012345678
+ "ATAGTGCCGCCAATCTTCCAGTATATACAGCACGGAGTAGCATCACGTACGTACGTCTACACGTAATT",
+ // 0123456789012345678901234567890123456
+ "ACGTCTACACGTAATTTTGGAGAGCCCTCTCTCACG",
+ // 01234567890123456789012345678901
+ "ACACGTAATTTTGGAGAGCCCTCTCTTCACG",
+ // 01234567890123456789012345678901234567890123456789012345
+ "AGGATAGTGCCGCCAATCTTCCAGTAATATACAGCACGGAGTAGCATCACGTACG",
+ // 01234567890123456789012345678901234567890123456789012345678901234
+ "ATAGTGCCGCCAATCTTCCAGTATATACAGCACGGAGTAGCATCACGTACGTACGTCTACACGT";
+ // -----------------------------------------------------------------------------------
+ // 012345678901234567890123456789012345678901234567890123456789012345678
+ // "ATAGTGCCGCCAATCTTCCAGTATATACAGCACGGAGTAGCATCACGTACGTACGTCTACACGTAATT",
+
+ // clang-format on
+
+ SparsePoa sp;
+ for (auto& read : reads) {
+ SparsePoa::ReadKey id = sp.OrientAndAddRead(read);
+ EXPECT_THAT(id, Ge(0));
+ }
+
+ vector<PoaAlignmentSummary> summaries;
+ string consensusSeq = sp.FindConsensus(4, &summaries)->Sequence;
+
+ EXPECT_EQ("ATAGTGCCGCCAATCTTCCAGTATATACAGCACGGAGTAGCATCACGTACGTACGTCTACACGTAATT", consensusSeq);
+
+ EXPECT_FALSE(summaries[0].ReverseComplementedRead);
+ EXPECT_EQ(Interval(8, 30), summaries[0].ExtentOnRead);
+ EXPECT_EQ(Interval(0, 22), summaries[0].ExtentOnConsensus);
+
+ EXPECT_FALSE(summaries[1].ReverseComplementedRead);
+ EXPECT_EQ(Interval(8, 45), summaries[1].ExtentOnRead);
+ EXPECT_EQ(Interval(3, 41), summaries[1].ExtentOnConsensus);
+
+ EXPECT_FALSE(summaries[2].ReverseComplementedRead);
+ EXPECT_EQ(Interval(0, 68), summaries[2].ExtentOnRead);
+ EXPECT_EQ(Interval(0, 68), summaries[2].ExtentOnConsensus);
+
+ EXPECT_FALSE(summaries[3].ReverseComplementedRead);
+ EXPECT_EQ(Interval(0, 16), summaries[3].ExtentOnRead);
+ EXPECT_EQ(Interval(52, 68), summaries[3].ExtentOnConsensus);
+
+ EXPECT_FALSE(summaries[4].ReverseComplementedRead);
+ EXPECT_EQ(Interval(0, 10), summaries[4].ExtentOnRead);
+ EXPECT_EQ(Interval(58, 68), summaries[4].ExtentOnConsensus);
+
+ EXPECT_FALSE(summaries[5].ReverseComplementedRead);
+ EXPECT_EQ(Interval(3, 55), summaries[5].ExtentOnRead);
+ EXPECT_EQ(Interval(0, 51), summaries[5].ExtentOnConsensus);
+
+ EXPECT_FALSE(summaries[6].ReverseComplementedRead);
+ EXPECT_EQ(Interval(0, 64), summaries[6].ExtentOnRead);
+ EXPECT_EQ(Interval(0, 64), summaries[6].ExtentOnConsensus);
+}
+
+TEST(SparsePoaTest, TestOrientation)
+{
+ vector<std::string> reads = {"AAAGATTACAGGG", "CCCTGTAATCTTT", "AAAGATTACAGGG"};
+ SparsePoa sp;
+ for (auto& read : reads) {
+ SparsePoa::ReadKey id = sp.OrientAndAddRead(read);
+ EXPECT_THAT(id, Ge(0));
+ }
+
+ vector<PoaAlignmentSummary> summaries;
+ string consensusSeq = sp.FindConsensus(2, &summaries)->Sequence;
+
+ EXPECT_EQ("AAAGATTACAGGG", consensusSeq);
+
+ EXPECT_FALSE(summaries[0].ReverseComplementedRead);
+ EXPECT_TRUE(summaries[1].ReverseComplementedRead);
+ EXPECT_FALSE(summaries[2].ReverseComplementedRead);
+}
+
+TEST(SparsePoaTest, TestZmw6251)
+{
+ using std::cout;
+ using std::endl;
+
+ std::string fastaFname =
+ tests::DataDir + "/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.fasta";
+ vector<string> ids, seqs;
+ LoadFastaSequences(fastaFname, ids, seqs);
+
+ SparsePoa sp;
+ for (const auto& seq : seqs) {
+ SparsePoa::ReadKey id = sp.OrientAndAddRead(seq);
+ EXPECT_THAT(id, Ge(0));
+ }
+
+ vector<PoaAlignmentSummary> summaries;
+ auto pc = sp.FindConsensus(8, &summaries);
+ ASSERT_EQ(10, pc->Graph.NumReads());
+
+ string consensusSeq = pc->Sequence;
+ // pc->WriteGraphVizFile("/tmp/zmw6251.dot");
+
+ // What it looks like:
+ //
+ // r0: >>>>>>>>>>>
+ // r1: <<<<<<<<<<<<<<<
+ // r2: >>>>>>>>>>>>>>>
+ // ..
+ // r8: >>>>>>>>>>>>>>>
+ // r9: <<<<<
+ for (int i = 0; i <= 9; i++) {
+ if (i % 2 == 0)
+ EXPECT_FALSE(summaries[0].ReverseComplementedRead);
+ else
+ EXPECT_TRUE(summaries[1].ReverseComplementedRead);
+ }
+
+ // css ~ 600 bases; check that things hit roughly as expected
+ EXPECT_TRUE(summaries[0].ExtentOnConsensus.Covers(Interval(300, 595)));
+ for (int i = 1; i <= 8; i++)
+ EXPECT_TRUE(summaries[1].ExtentOnConsensus.Covers(Interval(5, 595)));
+ EXPECT_TRUE(summaries[0].ExtentOnConsensus.Covers(Interval(300, 595)));
+}
+
+std::string rc(const std::string& a)
+{
+ const size_t len = a.length();
+ std::string b;
+
+ b.reserve(len);
+
+ for (size_t i = 0; i < len; ++i) {
+ char c = a[len - 1 - i];
+ switch (c) {
+ case 'A':
+ c = 'T';
+ break;
+ case 'C':
+ c = 'G';
+ break;
+ case 'G':
+ c = 'C';
+ break;
+ case 'T':
+ c = 'A';
+ break;
+ }
+ b.push_back(c);
+ }
+
+ return b;
+}
+
+#if EXTENSIVE_TESTING
+constexpr size_t numIterations = 100;
+#else
+constexpr size_t numIterations = 10;
+#endif
+
+TEST(SparsePoaTest, SingleReadNTimes)
+{
+ std::mt19937 gen(42);
+ std::uniform_int_distribution<size_t> d(2000, 20000);
+ std::uniform_int_distribution<size_t> b(0, 3);
+
+ const std::string bases = "ACGT";
+
+ for (size_t i = 0; i < numIterations; ++i) {
+ size_t len = 0;
+ std::string seq;
+
+ while (len < 300)
+ len = d(gen);
+
+ seq.reserve(len);
+
+ for (size_t j = 0; j < len; ++j)
+ seq.push_back(bases[b(gen)]);
+
+ SparsePoa sp;
+ SparsePoa::ReadKey id = sp.OrientAndAddRead(seq);
+
+ vector<PoaAlignmentSummary> summaries;
+ std::string poa = sp.FindConsensus(1, &summaries)->Sequence;
+
+ EXPECT_EQ(seq, poa);
+ EXPECT_EQ(Interval(0, len), summaries[id].ExtentOnRead);
+ EXPECT_EQ(Interval(0, len), summaries[id].ExtentOnConsensus);
+ EXPECT_FALSE(summaries[id].ReverseComplementedRead);
+ }
+}
+
+TEST(SparsePoaTest, SingleAndHalfNTimes)
+{
+ std::mt19937 gen(42);
+ std::uniform_int_distribution<size_t> d(1000, 5000);
+ std::uniform_int_distribution<size_t> b(0, 3);
+
+ const std::string bases = "ACGT";
+
+ for (size_t i = 0; i < numIterations; ++i) {
+ size_t len = 0;
+ std::string seq1, seq2;
+
+ while (len < 300)
+ len = d(gen);
+
+ seq1.reserve(len);
+ seq2.reserve(len / 3);
+
+ for (size_t j = 0; j < len; ++j)
+ seq1.push_back(bases[b(gen)]);
+
+ seq2 = rc(seq1).substr(0, len / 3);
+
+ SparsePoa sp;
+ SparsePoa::ReadKey id1 = sp.OrientAndAddRead(seq1);
+ SparsePoa::ReadKey id2 = sp.OrientAndAddRead(seq2);
+
+ vector<PoaAlignmentSummary> summaries;
+ std::string poa = sp.FindConsensus(1, &summaries)->Sequence;
+
+ EXPECT_EQ(seq1, poa);
+ EXPECT_EQ(Interval(0, len), summaries[id1].ExtentOnRead);
+ EXPECT_EQ(Interval(0, len), summaries[id1].ExtentOnConsensus);
+ EXPECT_FALSE(summaries[id1].ReverseComplementedRead);
+ EXPECT_EQ(Interval(0, len / 3), summaries[id2].ExtentOnRead);
+ EXPECT_EQ(Interval(len - len / 3, len), summaries[id2].ExtentOnConsensus);
+ EXPECT_TRUE(summaries[id2].ReverseComplementedRead);
+ }
+}
diff --git a/tests/unit/TestSparseVector.cpp b/tests/unit/TestSparseVector.cpp
new file mode 100644
index 0000000..cfae8f8
--- /dev/null
+++ b/tests/unit/TestSparseVector.cpp
@@ -0,0 +1,101 @@
+// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <gtest/gtest.h>
+
+#include <limits>
+
+#include "../src/matrix/SparseVector.h"
+
+using namespace PacBio::Consensus; // NOLINT
+
+TEST(SparseVectorTest, BasicTest)
+{
+ SparseVector sv(100, 10, 20);
+ EXPECT_LE(10, sv.AllocatedEntries());
+
+ for (int i = 0; i < 100; i++) {
+ EXPECT_EQ(0, sv(i));
+ }
+
+ for (int i = 10; i < 20; i++) {
+ sv.Set(i, i);
+ }
+ for (int i = 0; i < 100; i++) {
+ if (i >= 10 && i < 20)
+ EXPECT_EQ(i, sv(i));
+ else
+ EXPECT_EQ(0, sv(i)); // NOLINT
+ }
+
+ sv.Set(50, 50);
+ EXPECT_LE(40, sv.AllocatedEntries());
+ for (int i = 0; i < 100; i++) {
+ if (i >= 10 && i < 20)
+ EXPECT_EQ(i, sv(i));
+ else if (i == 50)
+ EXPECT_EQ(i, sv(i));
+ else
+ EXPECT_EQ(0, sv(i)); // NOLINT
+ }
+}
+
+TEST(SparseVectorTest, BasicTest2)
+{
+ SparseVector sv(100, 50, 60);
+
+ sv.Set(5, 5);
+ for (int i = 0; i < 100; i++) {
+ if (i == 5)
+ EXPECT_EQ(i, sv(i));
+ else
+ EXPECT_EQ(0, sv(i)); // NOLINT
+ }
+}
+
+TEST(SparseVector, CopyTest)
+{
+ SparseVector sv(10, 3, 7);
+ sv.Set(4, 5);
+
+ SparseVector svCopy(sv);
+ ASSERT_EQ(5, svCopy(4));
+
+ for (int i = 0; i < 10; i++) {
+ ASSERT_EQ(sv(i), svCopy(i));
+ }
+}
diff --git a/tests/unit/TestTemplate.cpp b/tests/unit/TestTemplate.cpp
new file mode 100644
index 0000000..38f8fe7
--- /dev/null
+++ b/tests/unit/TestTemplate.cpp
@@ -0,0 +1,338 @@
+// Copyright (c) 2011-2014, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <iostream>
+#include <random>
+#include <string>
+#include <tuple>
+#include <utility>
+#include <vector>
+
+#include <pacbio/consensus/ModelConfig.h>
+#include <pacbio/consensus/Mutation.h>
+#include <pacbio/consensus/Template.h>
+#include <pacbio/data/Read.h>
+#include <pacbio/exception/StateError.h>
+
+#include "../src/ModelFactory.h"
+#include "Mutations.h"
+#include "RandomDNA.h"
+
+using namespace std;
+using namespace PacBio::Consensus; // NOLINT
+using namespace PacBio::Exception; // NOLINT
+
+using ::testing::UnorderedElementsAreArray;
+
+namespace PacBio {
+namespace Consensus {
+
+bool operator==(const TemplatePosition& lhs, const TemplatePosition& rhs)
+{
+ return lhs.Base == rhs.Base && lhs.Match == rhs.Match && lhs.Branch == rhs.Branch &&
+ lhs.Stick == rhs.Stick && lhs.Deletion == rhs.Deletion;
+}
+
+bool operator!=(const TemplatePosition& lhs, const TemplatePosition& rhs) { return !(lhs == rhs); }
+bool operator==(const AbstractTemplate& lhs, const AbstractTemplate& rhs)
+{
+ if (lhs.Length() != rhs.Length()) return false;
+
+ const size_t len = lhs.Length();
+
+ // do not test the last base, can vary
+ for (size_t i = 0; i + 1 < len; ++i)
+ if (lhs[i] != rhs[i]) return false;
+
+ // check the last base
+ if (len > 0 && lhs[len - 1].Base != rhs[len - 1].Base) return false;
+
+ return true;
+}
+
+bool operator!=(const AbstractTemplate& lhs, const AbstractTemplate& rhs) { return !(lhs == rhs); }
+#if 0
+ostream& operator<<(ostream& os, const AbstractTemplate& tpl)
+{
+ os << "Template:" << endl;
+ for (size_t i = 0; i < tpl.Length(); ++i)
+ os << " " << tpl[i] << endl;
+ return os;
+}
+#endif
+
+} // namespace Consensus
+} // namespace PacBio
+
+namespace {
+
+const string mdl = "P6-C4";
+const SNR snr(10, 7, 5, 11);
+
+string ApplyMutations(const string& tpl, vector<Mutation>&& muts)
+{
+ return ApplyMutations(tpl, &muts);
+}
+
+TEST(TemplateTest, ApplyMutations)
+{
+ constexpr auto INS = MutationType::INSERTION;
+ constexpr auto DEL = MutationType::DELETION;
+ constexpr auto SUB = MutationType::SUBSTITUTION;
+
+ // insertion
+ EXPECT_EQ("ACGT", ApplyMutations("CGT", {Mutation(INS, 0, 'A')}));
+ EXPECT_EQ("ACGT", ApplyMutations("AGT", {Mutation(INS, 1, 'C')}));
+ EXPECT_EQ("ACGT", ApplyMutations("ACT", {Mutation(INS, 2, 'G')}));
+ EXPECT_EQ("ACGT", ApplyMutations("ACG", {Mutation(INS, 3, 'T')}));
+
+ // substitution
+ EXPECT_EQ("ACGT", ApplyMutations("XCGT", {Mutation(SUB, 0, 'A')}));
+ EXPECT_EQ("ACGT", ApplyMutations("AXGT", {Mutation(SUB, 1, 'C')}));
+ EXPECT_EQ("ACGT", ApplyMutations("ACXT", {Mutation(SUB, 2, 'G')}));
+ EXPECT_EQ("ACGT", ApplyMutations("ACGX", {Mutation(SUB, 3, 'T')}));
+
+ // deletion
+ EXPECT_EQ("ACGT", ApplyMutations("XACGT", {Mutation(DEL, 0)}));
+ EXPECT_EQ("ACGT", ApplyMutations("AXCGT", {Mutation(DEL, 1)}));
+ EXPECT_EQ("ACGT", ApplyMutations("ACXGT", {Mutation(DEL, 2)}));
+ EXPECT_EQ("ACGT", ApplyMutations("ACGXT", {Mutation(DEL, 3)}));
+ EXPECT_EQ("ACGT", ApplyMutations("ACGTX", {Mutation(DEL, 4)}));
+}
+
+string ToString(const AbstractTemplate& tpl)
+{
+ string result;
+ result.reserve(tpl.Length());
+ for (size_t i = 0; i < tpl.Length(); ++i)
+ result.push_back(tpl[i].Base);
+ return result;
+}
+
+void TemplateEquivalence(const size_t nsamp, const size_t nvirt, const size_t len = 100)
+{
+ std::random_device rd;
+ mt19937 gen(rd());
+ uniform_int_distribution<size_t> randIdx(0, len - 1);
+ bernoulli_distribution randPin(0.5);
+ bernoulli_distribution randSpanning(0.33);
+
+ for (size_t i = 0; i < nsamp; ++i) {
+ const string tpl = RandomDNA(len, &gen);
+ Template master(tpl, ModelFactory::Create(mdl, snr));
+ EXPECT_EQ(tpl, ToString(master));
+ vector<tuple<size_t, size_t, bool, bool>> coords;
+ vector<VirtualTemplate> vtpls;
+ vector<Template> rtpls;
+ for (size_t j = 0; j < nvirt; ++j) {
+ int start = 0;
+ int end = len;
+ // roughly 33% of the time having a spanning read
+ if (randSpanning(gen)) {
+ do {
+ start = randIdx(gen);
+ end = randIdx(gen);
+ } while (std::abs(start - end) < 2);
+ if (end < start) swap(start, end);
+ ++end; // increment b by one (end-exclusive)
+ }
+ const bool pinStart = (start == 0) ? randPin(gen) : false;
+ const bool pinEnd = (end == static_cast<int>(len)) ? randPin(gen) : false;
+ ASSERT_LT(start, end);
+ coords.emplace_back(make_tuple(start, end, pinStart, pinEnd));
+ vtpls.emplace_back(VirtualTemplate(master, start, end, pinStart, pinEnd));
+ const string vtpl = tpl.substr(start, end - start);
+ rtpls.emplace_back(
+ Template(vtpl, ModelFactory::Create(mdl, snr), start, end, pinStart, pinEnd));
+ EXPECT_EQ(vtpl, ToString(vtpls.back()));
+ EXPECT_EQ(end - start, vtpls.back().Length());
+ }
+ vector<Mutation> mutations = Mutations(tpl);
+ for (const auto& mut : mutations) {
+ vector<Mutation> muts{mut};
+ const string app = ApplyMutations(tpl, &muts);
+ master.Mutate(mut);
+ EXPECT_EQ(app, ToString(master));
+ {
+ Template mutated(app, ModelFactory::Create(mdl, snr));
+ EXPECT_EQ(mutated, master);
+ }
+ for (size_t j = 0; j < nvirt; ++j) {
+ size_t start, end;
+ bool pinStart, pinEnd;
+ tie(start, end, pinStart, pinEnd) = coords[j];
+ const string vtpl = tpl.substr(start, end - start);
+ vector<Mutation> vmuts;
+ if ((pinStart || start < mut.End()) && (pinEnd || mut.Start() < end))
+ vmuts.emplace_back(Mutation(mut.Type, mut.Start() - start, mut.Base));
+ const string vapp = ApplyMutations(vtpl, &vmuts);
+ vtpls[j].Mutate(mut);
+ rtpls[j].Mutate(mut);
+ EXPECT_EQ(vapp, ToString(rtpls[j]));
+ EXPECT_EQ(vapp, ToString(vtpls[j]));
+ if (vapp != ToString(vtpls[j])) {
+ const size_t c =
+ start + ((pinStart || mut.End() < start) ? mut.LengthDiff() : 0);
+ const size_t d = end + ((pinEnd || mut.Start() < end) ? mut.LengthDiff() : 0);
+ cerr << "mut: " << mut << endl;
+ if (!vmuts.empty()) cerr << "vmut: " << vmuts.back() << endl;
+ cerr << "off: " << mut.LengthDiff() << endl;
+ cerr << "tpl: " << tpl << endl;
+ cerr << "s,e: " << start << "," << end << endl;
+ cerr << "ps,e: " << pinStart << "," << pinEnd << endl;
+ cerr << "ms,e: " << mut.Start() << "," << mut.End() << endl;
+ cerr << "app: " << app << endl;
+ cerr << "c,d: " << c << "," << d << endl;
+ cerr << "vtpl: " << vtpl << endl;
+ cerr << "vapp: " << vapp << endl;
+ // cerr << "sub: " << app.substr(a + ((mut.Start() <= a) ? mut.LengthDiff() :
+ // 0), vapp.length()) << endl;
+ cerr << "vchl: " << ToString(vtpls[j]) << endl;
+ cerr << "rchl: " << ToString(rtpls[j]) << endl;
+ cerr << "vxxx: " << ToString(master).substr(c, d - c) << endl;
+ }
+ const int off = vmuts.empty() ? 0 : vmuts.back().LengthDiff();
+ EXPECT_EQ(end - start + off, vtpls[j].Length());
+ EXPECT_EQ(end - start + off, rtpls[j].Length());
+ {
+ Template child(vapp, ModelFactory::Create(mdl, snr));
+ EXPECT_EQ(child, vtpls[j]);
+ EXPECT_EQ(child, rtpls[j]);
+ }
+ vtpls[j].Reset();
+ rtpls[j].Reset();
+ }
+ master.Reset();
+ }
+ }
+}
+
+TEST(TemplateTest, TestVirtualTemplateEquivalence)
+{
+#if EXTENSIVE_TESTING
+ const int numSamples = 1000;
+#else
+ const int numSamples = 10;
+#endif
+ TemplateEquivalence(numSamples, 20, 10);
+ TemplateEquivalence(numSamples / 2, 20, 30);
+}
+
+TEST(TemplateTest, TestPinning)
+{
+ constexpr size_t len = 5;
+ const string tpl(len, 'C');
+ const string A(1, 'A');
+
+ // pinStart and pinEnd
+ {
+ Template master(tpl, ModelFactory::Create(mdl, snr), 0, len, true, true);
+ EXPECT_EQ(len, master.Length());
+ EXPECT_EQ(tpl, ToString(master));
+ master.ApplyMutation(Mutation(MutationType::INSERTION, len, 'A'));
+ EXPECT_EQ(len + 1, master.Length());
+ EXPECT_EQ(tpl + A, ToString(master));
+ master.ApplyMutation(Mutation(MutationType::INSERTION, 0, 'A'));
+ EXPECT_EQ(len + 2, master.Length());
+ EXPECT_EQ(A + tpl + A, ToString(master));
+ }
+ // no pinStart but pinEnd
+ {
+ Template master(tpl, ModelFactory::Create(mdl, snr), 0, len, false, true);
+ EXPECT_EQ(len, master.Length());
+ EXPECT_EQ(tpl, ToString(master));
+ master.ApplyMutation(Mutation(MutationType::INSERTION, 0, 'A'));
+ EXPECT_EQ(len, master.Length());
+ EXPECT_EQ(tpl, ToString(master));
+ // the coords are now 1..6, so a new terminal mutation is at len+1
+ master.ApplyMutation(Mutation(MutationType::INSERTION, len + 1, 'A'));
+ EXPECT_EQ(len + 1, master.Length());
+ EXPECT_EQ(tpl + A, ToString(master));
+ }
+ // pinStart but no pinEnd
+ {
+ Template master(tpl, ModelFactory::Create(mdl, snr), 0, len, true, false);
+ EXPECT_EQ(len, master.Length());
+ EXPECT_EQ(tpl, ToString(master));
+ master.ApplyMutation(Mutation(MutationType::INSERTION, len, 'A'));
+ EXPECT_EQ(len, master.Length());
+ EXPECT_EQ(tpl, ToString(master));
+ master.ApplyMutation(Mutation(MutationType::INSERTION, 0, 'A'));
+ EXPECT_EQ(len + 1, master.Length());
+ EXPECT_EQ(A + tpl, ToString(master));
+ }
+ // no pinStart or pinEnd
+ {
+ Template master(tpl, ModelFactory::Create(mdl, snr), 0, len, false, false);
+ EXPECT_EQ(len, master.Length());
+ EXPECT_EQ(tpl, ToString(master));
+ master.ApplyMutation(Mutation(MutationType::INSERTION, len, 'A'));
+ EXPECT_EQ(len, master.Length());
+ EXPECT_EQ(tpl, ToString(master));
+ master.ApplyMutation(Mutation(MutationType::INSERTION, 0, 'A'));
+ EXPECT_EQ(len, master.Length());
+ EXPECT_EQ(tpl, ToString(master));
+ }
+}
+
+TEST(TemplateTest, NullTemplate)
+{
+ const string tpl = "ACGT";
+ const size_t len = tpl.length();
+ const Mutation mut(MutationType::DELETION, 0, '-');
+
+ ASSERT_THROW(Template("A", ModelFactory::Create(mdl, snr), 0, 1, true, true), TemplateTooSmall);
+
+ ASSERT_NO_THROW(Template("AA", ModelFactory::Create(mdl, snr), 0, 2, true, true));
+}
+
+TEST(TemplateTest, P6SiteNormalParameters)
+{
+ const string tpl = "ACGATACATACGATCGA";
+ const SNR snr(10, 7, 5, 11);
+ auto mdl = "P6-C4";
+ Template tester(tpl, ModelFactory::Create(mdl, snr));
+ auto results = tester.NormalParameters();
+
+ EXPECT_EQ(-9.3915588824261888, results.first);
+ EXPECT_EQ(26.883352639390957, results.second);
+}
+
+} // namespace anonymous
diff --git a/tests/unit/TestUtility.cpp b/tests/unit/TestUtility.cpp
new file mode 100644
index 0000000..81ce6b0
--- /dev/null
+++ b/tests/unit/TestUtility.cpp
@@ -0,0 +1,74 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander, Lance Hepler
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <seqan/seq_io.h>
+
+#include <pacbio/io/Utility.h>
+
+#include "TestUtility.h"
+
+bool LoadFastaSequences(std::string fastaFname, std::vector<std::string>& ids,
+ std::vector<std::string>& seqs)
+{
+ seqan::StringSet<seqan::CharString> sIds;
+ seqan::StringSet<seqan::CharString> sSeqs;
+
+ seqan::SeqFileIn seqFileIn(fastaFname.c_str());
+ readRecords(sIds, sSeqs, seqFileIn);
+
+ for (auto& sId : sIds) {
+ ids.push_back(toCString(sId));
+ }
+ for (auto& sSeq : sSeqs) {
+ seqs.push_back(toCString(sSeq));
+ }
+
+ return true;
+}
+
+TEST(UtilityTest, TestFileExtension)
+{
+ using PacBio::IO::FileExtension;
+
+ EXPECT_EQ("bar", FileExtension("/path/to/foo.bar"));
+ EXPECT_EQ("bar", FileExtension("/foo.bar"));
+ EXPECT_EQ("bar", FileExtension("foo.bar"));
+ EXPECT_EQ("", FileExtension("foo"));
+}
diff --git a/tests/unit/TestUtility.h b/tests/unit/TestUtility.h
new file mode 100644
index 0000000..aebe6e7
--- /dev/null
+++ b/tests/unit/TestUtility.h
@@ -0,0 +1,44 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: David Alexander
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+bool LoadFastaSequences(std::string fastaFname, std::vector<std::string>& ids,
+ std::vector<std::string>& sequences);
diff --git a/tests/unit/TestWhitelist.cpp b/tests/unit/TestWhitelist.cpp
new file mode 100644
index 0000000..0cc5d05
--- /dev/null
+++ b/tests/unit/TestWhitelist.cpp
@@ -0,0 +1,80 @@
+// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
+//
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted (subject to the limitations in the
+// disclaimer below) provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following
+// disclaimer in the documentation and/or other materials provided
+// with the distribution.
+//
+// * Neither the name of Pacific Biosciences nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+
+// Author: Lance Hepler
+
+#include <iostream>
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include <pacbio/ccs/Whitelist.h>
+
+using namespace PacBio::CCS;
+
+TEST(WhitelistTest, AllTest)
+{
+ Whitelist wl1("all"), wl2("*:*");
+ EXPECT_TRUE(wl1.Contains("movieName", 34) && wl2.Contains("movieName", 42));
+}
+
+TEST(WhitelistTest, CrazyTests)
+{
+ EXPECT_THROW(Whitelist("1-3;movieName:*"), std::invalid_argument);
+ EXPECT_THROW(Whitelist("movieName:*;1-3"), std::invalid_argument);
+ EXPECT_THROW(Whitelist("all;1-3"), std::invalid_argument);
+ EXPECT_THROW(Whitelist("1-3;all"), std::invalid_argument);
+ EXPECT_THROW(Whitelist("movieName:1-3;movieName:4-5"), std::invalid_argument);
+}
+
+TEST(WhitelistTest, SingleRange)
+{
+ Whitelist wls[] = {Whitelist("1-3"), Whitelist("*:1-3")};
+
+ for (const auto& wl : wls) {
+ EXPECT_TRUE(wl.Contains("", 1) && wl.Contains("", 2) && wl.Contains("", 3));
+ EXPECT_FALSE(wl.Contains("", 0) || wl.Contains("", 4));
+ }
+}
+
+TEST(WhitelistTest, TwoMovieRanges)
+{
+ Whitelist wl("movie1:*;movie2:1-3");
+
+ EXPECT_TRUE(wl.Contains("movie1", 42));
+ EXPECT_TRUE(wl.Contains("movie2", 3));
+ EXPECT_FALSE(wl.Contains("movie2", 4));
+ EXPECT_FALSE(wl.Contains("movie3", 1));
+}
diff --git a/third-party/cpp-optparse-fix-warnings.patch b/third-party/cpp-optparse-fix-warnings.patch
new file mode 100644
index 0000000..653dc55
--- /dev/null
+++ b/third-party/cpp-optparse-fix-warnings.patch
@@ -0,0 +1,19 @@
+--- a/OptionParser.h
++++ b/OptionParser.h
+@@ -222,7 +222,7 @@
+ class OptionGroup : public OptionParser {
+ public:
+ OptionGroup(const OptionParser& p, const std::string& t, const std::string& d = "") :
+- _parser(p), _title(t), _group_description(d) {}
++ _title(t), _group_description(d) {}
+ virtual ~OptionGroup() {}
+
+ OptionGroup& title(const std::string& t) { _title = t; return *this; }
+@@ -231,7 +231,6 @@
+ const std::string& group_description() const { return _group_description; }
+
+ private:
+- const OptionParser& _parser;
+ std::string _title;
+ std::string _group_description;
+ };
diff --git a/third-party/cpp-optparse/Makefile b/third-party/cpp-optparse/Makefile
new file mode 100644
index 0000000..595e520
--- /dev/null
+++ b/third-party/cpp-optparse/Makefile
@@ -0,0 +1,21 @@
+ifdef ICC
+CXX = icpc
+WARN_FLAGS = -O3 -ipo -g -Wall -wd981 -wd383 -wd2259 -Werror # -Weffc++
+else
+CXX = g++
+WARN_FLAGS = -O3 -g -Wall -Wextra -Wabi -Wctor-dtor-privacy -Wnon-virtual-dtor -Wreorder -Wstrict-null-sentinel -Woverloaded-virtual -Wshadow -Wcast-align -Wpointer-arith -Wwrite-strings -Wundef -Wredundant-decls -Werror # -Weffc++
+endif
+
+BIN = test
+OBJECTS = OptionParser.o test.o
+
+$(BIN): $(OBJECTS)
+ $(CXX) -o $@ $(OBJECTS) $(WARN_FLAGS) $(LINKFLAGS)
+
+%.o: %.cpp OptionParser.h
+ $(CXX) $(WARN_FLAGS) $(CXXFLAGS) -c $< -o $@
+
+.PHONY: clean
+
+clean:
+ rm -f *.o $(BIN)
diff --git a/third-party/cpp-optparse/OptionParser.cpp b/third-party/cpp-optparse/OptionParser.cpp
new file mode 100644
index 0000000..359b7a9
--- /dev/null
+++ b/third-party/cpp-optparse/OptionParser.cpp
@@ -0,0 +1,577 @@
+/**
+ * Copyright (C) 2010 Johannes Weißl <jargon at molb.org>
+ * License: your favourite BSD-style license
+ *
+ * See OptionParser.h for help.
+ */
+
+#include "OptionParser.h"
+
+#include <cstdlib>
+#include <algorithm>
+#include <complex>
+#include <ciso646>
+
+#if defined(ENABLE_NLS) && ENABLE_NLS
+# include <libintl.h>
+# define _(s) gettext(s)
+#else
+# define _(s) ((const char *) (s))
+#endif
+
+using namespace std;
+
+namespace optparse {
+
+////////// auxiliary (string) functions { //////////
+class str_wrap {
+public:
+ str_wrap(const string& l, const string& r) : lwrap(l), rwrap(r) {}
+ str_wrap(const string& w) : lwrap(w), rwrap(w) {}
+ string operator() (const string& s) { return lwrap + s + rwrap; }
+ const string lwrap, rwrap;
+};
+template<typename InputIterator, typename UnaryOperator>
+static string str_join_trans(const string& sep, InputIterator begin, InputIterator end, UnaryOperator op) {
+ string buf;
+ for (InputIterator it = begin; it != end; ++it) {
+ if (it != begin)
+ buf += sep;
+ buf += op(*it);
+ }
+ return buf;
+}
+template<class InputIterator>
+static string str_join(const string& sep, InputIterator begin, InputIterator end) {
+ return str_join_trans(sep, begin, end, str_wrap(""));
+}
+static string& str_replace(string& s, const string& patt, const string& repl) {
+ size_t pos = 0, n = patt.length();
+ while (true) {
+ pos = s.find(patt, pos);
+ if (pos == string::npos)
+ break;
+ s.replace(pos, n, repl);
+ pos += repl.size();
+ }
+ return s;
+}
+static string str_replace(const string& s, const string& patt, const string& repl) {
+ string tmp = s;
+ str_replace(tmp, patt, repl);
+ return tmp;
+}
+static string str_format(const string& s, size_t pre, size_t len, bool indent_first = true) {
+ stringstream ss;
+ string p;
+ if (indent_first)
+ p = string(pre, ' ');
+
+ size_t pos = 0, linestart = 0;
+ size_t line = 0;
+ while (true) {
+ bool wrap = false;
+
+ size_t new_pos = s.find_first_of(" \n\t", pos);
+ if (new_pos == string::npos)
+ break;
+ if (s[new_pos] == '\n') {
+ pos = new_pos + 1;
+ wrap = true;
+ }
+ if (line == 1)
+ p = string(pre, ' ');
+ if (wrap || new_pos + pre > linestart + len) {
+ ss << p << s.substr(linestart, pos - linestart - 1) << endl;
+ linestart = pos;
+ line++;
+ }
+ pos = new_pos + 1;
+ }
+ ss << p << s.substr(linestart) << endl;
+ return ss.str();
+}
+static string str_inc(const string& s) {
+ stringstream ss;
+ string v = (s != "") ? s : "0";
+ long i;
+ istringstream(v) >> i;
+ ss << i+1;
+ return ss.str();
+}
+static unsigned int cols() {
+ unsigned int n = 80;
+#ifndef _WIN32
+ const char *s = getenv("COLUMNS");
+ if (s)
+ istringstream(s) >> n;
+#endif
+ return n;
+}
+static string basename(const string& s) {
+ string b = s;
+ size_t i = b.find_last_not_of('/');
+ if (i == string::npos) {
+ if (b[0] == '/')
+ b.erase(1);
+ return b;
+ }
+ b.erase(i+1, b.length()-i-1);
+ i = b.find_last_of("/");
+ if (i != string::npos)
+ b.erase(0, i+1);
+ return b;
+}
+////////// } auxiliary (string) functions //////////
+
+
+////////// class OptionParser { //////////
+OptionParser::OptionParser() :
+ _usage(_("%prog [options]")),
+ _add_help_option(true),
+ _add_version_option(true),
+ _interspersed_args(true) {}
+
+Option& OptionParser::add_option(const string& opt) {
+ const string tmp[1] = { opt };
+ return add_option(vector<string>(&tmp[0], &tmp[1]));
+}
+Option& OptionParser::add_option(const string& opt1, const string& opt2) {
+ const string tmp[2] = { opt1, opt2 };
+ return add_option(vector<string>(&tmp[0], &tmp[2]));
+}
+Option& OptionParser::add_option(const string& opt1, const string& opt2, const string& opt3) {
+ const string tmp[3] = { opt1, opt2, opt3 };
+ return add_option(vector<string>(&tmp[0], &tmp[3]));
+}
+Option& OptionParser::add_option(const vector<string>& v) {
+ _opts.resize(_opts.size()+1);
+ Option& option = _opts.back();
+ string dest_fallback;
+ for (vector<string>::const_iterator it = v.begin(); it != v.end(); ++it) {
+ if (it->substr(0,2) == "--") {
+ const string s = it->substr(2);
+ if (option.dest() == "")
+ option.dest(str_replace(s, "-", "_"));
+ option._long_opts.insert(s);
+ _optmap_l[s] = &option;
+ } else {
+ const string s = it->substr(1,1);
+ if (dest_fallback == "")
+ dest_fallback = s;
+ option._short_opts.insert(s);
+ _optmap_s[s] = &option;
+ }
+ }
+ if (option.dest() == "")
+ option.dest(dest_fallback);
+ return option;
+}
+
+OptionParser& OptionParser::add_option_group(const OptionGroup& group) {
+ _groups.push_back(group);
+ OptionGroup& currentGroup = _groups.back();
+
+ for (list<Option>::const_iterator oit = currentGroup._opts.begin(); oit != currentGroup._opts.end(); ++oit) {
+ const Option& option = *oit;
+ for (set<string>::const_iterator it = option._short_opts.begin(); it != option._short_opts.end(); ++it)
+ _optmap_s[*it] = &option;
+ for (set<string>::const_iterator it = option._long_opts.begin(); it != option._long_opts.end(); ++it)
+ _optmap_l[*it] = &option;
+ }
+
+ return *this;
+}
+
+const Option& OptionParser::lookup_short_opt(const string& opt) const {
+ optMap::const_iterator it = _optmap_s.find(opt);
+ if (it == _optmap_s.end())
+ error(_("no such option") + string(": -") + opt);
+ return *it->second;
+}
+
+void OptionParser::handle_short_opt(const string& opt, const string& arg) {
+
+ _remaining.pop_front();
+ string value;
+
+ const Option& option = lookup_short_opt(opt);
+ if (option._nargs == 1) {
+ value = arg.substr(2);
+ if (value == "") {
+ if (_remaining.empty())
+ error("-" + opt + " " + _("option requires an argument"));
+ value = _remaining.front();
+ _remaining.pop_front();
+ }
+ } else {
+ if (arg.length() > 2)
+ _remaining.push_front(string("-") + arg.substr(2));
+ }
+
+ process_opt(option, string("-") + opt, value);
+}
+
+const Option& OptionParser::lookup_long_opt(const string& opt) const {
+
+ list<string> matching;
+ for (optMap::const_iterator it = _optmap_l.begin(); it != _optmap_l.end(); ++it) {
+ if (it->first.compare(0, opt.length(), opt) == 0)
+ matching.push_back(it->first);
+ }
+ if (matching.size() > 1) {
+ string x = str_join(", ", matching.begin(), matching.end());
+ error(_("ambiguous option") + string(": --") + opt + " (" + x + "?)");
+ }
+ if (matching.size() == 0)
+ error(_("no such option") + string(": --") + opt);
+
+ return *_optmap_l.find(matching.front())->second;
+}
+
+void OptionParser::handle_long_opt(const string& optstr) {
+
+ _remaining.pop_front();
+ string opt, value;
+
+ size_t delim = optstr.find("=");
+ if (delim != string::npos) {
+ opt = optstr.substr(0, delim);
+ value = optstr.substr(delim+1);
+ } else
+ opt = optstr;
+
+ const Option& option = lookup_long_opt(opt);
+ if (option._nargs == 1 and delim == string::npos) {
+ if (not _remaining.empty()) {
+ value = _remaining.front();
+ _remaining.pop_front();
+ }
+ }
+
+ if (option._nargs == 1 and value == "")
+ error("--" + opt + " " + _("option requires an argument"));
+
+ process_opt(option, string("--") + opt, value);
+}
+
+Values& OptionParser::parse_args(const int argc, char const* const* const argv) {
+ if (prog() == "")
+ prog(basename(argv[0]));
+ return parse_args(&argv[1], &argv[argc]);
+}
+Values& OptionParser::parse_args(const vector<string>& v) {
+
+ _remaining.assign(v.begin(), v.end());
+
+ if (add_version_option() and version() != "") {
+ add_option("--version") .action("version") .help(_("Show program's version number and exit."));
+ _opts.splice(_opts.begin(), _opts, --(_opts.end()));
+ }
+ if (add_help_option()) {
+ add_option("-h", "--help") .action("help") .help(_("Show this help message and exit."));
+ _opts.splice(_opts.begin(), _opts, --(_opts.end()));
+ }
+
+ while (not _remaining.empty()) {
+ const string arg = _remaining.front();
+
+ if (arg == "--") {
+ _remaining.pop_front();
+ break;
+ }
+
+ if (arg.substr(0,2) == "--") {
+ handle_long_opt(arg.substr(2));
+ } else if (arg.substr(0,1) == "-" and arg.length() > 1) {
+ handle_short_opt(arg.substr(1,1), arg);
+ } else {
+ _remaining.pop_front();
+ _leftover.push_back(arg);
+ if (not interspersed_args())
+ break;
+ }
+ }
+ while (not _remaining.empty()) {
+ const string arg = _remaining.front();
+ _remaining.pop_front();
+ _leftover.push_back(arg);
+ }
+
+ for (strMap::const_iterator it = _defaults.begin(); it != _defaults.end(); ++it) {
+ if (not _values.is_set(it->first))
+ _values[it->first] = it->second;
+ }
+
+ for (list<Option>::const_iterator it = _opts.begin(); it != _opts.end(); ++it) {
+ if (not _values.is_set(it->dest()))
+ _values[it->dest()] = it->get_default();
+ }
+
+ for (list<OptionGroup>::iterator group_it = _groups.begin(); group_it != _groups.end(); ++group_it) {
+ for (strMap::const_iterator it = group_it->_defaults.begin(); it != group_it->_defaults.end(); ++it) {
+ if (not _values.is_set(it->first))
+ _values[it->first] = it->second;
+ }
+
+ for (list<Option>::const_iterator it = group_it->_opts.begin(); it != group_it->_opts.end(); ++it) {
+ if (it->get_default() != "" and not _values.is_set(it->dest()))
+ _values[it->dest()] = it->get_default();
+ }
+ }
+
+ return _values;
+}
+
+void OptionParser::process_opt(const Option& o, const string& opt, const string& value) {
+ if (o.action() == "store") {
+ string err = o.check_type(opt, value);
+ if (err != "")
+ error(err);
+ _values[o.dest()] = value;
+ _values.is_set_by_user(o.dest(), true);
+ }
+ else if (o.action() == "store_const") {
+ _values[o.dest()] = o.get_const();
+ _values.is_set_by_user(o.dest(), true);
+ }
+ else if (o.action() == "store_true") {
+ _values[o.dest()] = "1";
+ _values.is_set_by_user(o.dest(), true);
+ }
+ else if (o.action() == "store_false") {
+ _values[o.dest()] = "0";
+ _values.is_set_by_user(o.dest(), true);
+ }
+ else if (o.action() == "append") {
+ string err = o.check_type(opt, value);
+ if (err != "")
+ error(err);
+ _values[o.dest()] = value;
+ _values.all(o.dest()).push_back(value);
+ _values.is_set_by_user(o.dest(), true);
+ }
+ else if (o.action() == "append_const") {
+ _values[o.dest()] = o.get_const();
+ _values.all(o.dest()).push_back(o.get_const());
+ _values.is_set_by_user(o.dest(), true);
+ }
+ else if (o.action() == "count") {
+ _values[o.dest()] = str_inc(_values[o.dest()]);
+ _values.is_set_by_user(o.dest(), true);
+ }
+ else if (o.action() == "help") {
+ print_help();
+ std::exit(0);
+ }
+ else if (o.action() == "version") {
+ print_version();
+ std::exit(0);
+ }
+ else if (o.action() == "callback" && o.callback()) {
+ (*o.callback())(o, opt, value, *this);
+ }
+}
+
+string OptionParser::format_option_help(unsigned int indent /* = 2 */) const {
+ stringstream ss;
+
+ if (_opts.empty())
+ return ss.str();
+
+ for (list<Option>::const_iterator it = _opts.begin(); it != _opts.end(); ++it) {
+ if (it->help() != SUPPRESS_HELP)
+ ss << it->format_help(indent);
+ }
+
+ return ss.str();
+}
+
+string OptionParser::format_help() const {
+ stringstream ss;
+
+ if (usage() != SUPPRESS_USAGE)
+ ss << get_usage() << endl;
+
+ if (description() != "")
+ ss << str_format(description(), 0, cols()) << endl;
+
+ ss << _("Options") << ":" << endl;
+ ss << format_option_help();
+
+ for (list<OptionGroup>::const_iterator it = _groups.begin(); it != _groups.end(); ++it) {
+ const OptionGroup& group = *it;
+ ss << endl << " " << group.title() << ":" << endl;
+ if (group.group_description() != "")
+ ss << str_format(group.group_description(), 4, cols()) << endl;
+ ss << group.format_option_help(4);
+ }
+
+ if (epilog() != "")
+ ss << endl << str_format(epilog(), 0, cols());
+
+ return ss.str();
+}
+void OptionParser::print_help() const {
+ cout << format_help();
+}
+
+void OptionParser::set_usage(const string& u) {
+ string lower = u;
+ transform(lower.begin(), lower.end(), lower.begin(), ::tolower);
+ if (lower.compare(0, 7, "usage: ") == 0)
+ _usage = u.substr(7);
+ else
+ _usage = u;
+}
+string OptionParser::format_usage(const string& u) const {
+ stringstream ss;
+ ss << _("Usage") << ": " << u << endl;
+ return ss.str();
+}
+string OptionParser::get_usage() const {
+ if (usage() == SUPPRESS_USAGE)
+ return string("");
+ return format_usage(str_replace(usage(), "%prog", prog()));
+}
+void OptionParser::print_usage(ostream& out) const {
+ string u = get_usage();
+ if (u != "")
+ out << u << endl;
+}
+void OptionParser::print_usage() const {
+ print_usage(cout);
+}
+
+string OptionParser::get_version() const {
+ return str_replace(_version, "%prog", prog());
+}
+void OptionParser::print_version(ostream& out) const {
+ out << get_version() << endl;
+}
+void OptionParser::print_version() const {
+ print_version(cout);
+}
+
+void OptionParser::exit() const {
+ std::exit(2);
+}
+void OptionParser::error(const string& msg) const {
+ print_usage(cerr);
+ cerr << prog() << ": " << _("error") << ": " << msg << endl;
+ exit();
+}
+////////// } class OptionParser //////////
+
+////////// class Values { //////////
+void Values::is_set_by_user(const string& d, bool yes) {
+ if (yes)
+ _userSet.insert(d);
+ else
+ _userSet.erase(d);
+}
+////////// } class Values //////////
+
+////////// class Option { //////////
+string Option::check_type(const string& opt, const string& val) const {
+ istringstream ss(val);
+ stringstream err;
+
+ if (type() == "int" || type() == "long") {
+ long t;
+ if (not (ss >> t))
+ err << _("option") << " " << opt << ": " << _("invalid integer value") << ": '" << val << "'";
+ }
+ else if (type() == "float" || type() == "double") {
+ double t;
+ if (not (ss >> t) && ss.str() != "NaN" && ss.str() != "nan" )
+ err << _("option") << " " << opt << ": " << _("invalid floating-point value") << ": '" << val << "'";
+ }
+ else if (type() == "choice") {
+ if (find(choices().begin(), choices().end(), val) == choices().end()) {
+ list<string> tmp = choices();
+ transform(tmp.begin(), tmp.end(), tmp.begin(), str_wrap("'"));
+ err << _("option") << " " << opt << ": " << _("invalid choice") << ": '" << val << "'"
+ << " (" << _("choose from") << " " << str_join(", ", tmp.begin(), tmp.end()) << ")";
+ }
+ }
+ else if (type() == "complex") {
+ complex<double> t;
+ if (not (ss >> t))
+ err << _("option") << " " << opt << ": " << _("invalid complex value") << ": '" << val << "'";
+ }
+
+ return err.str();
+}
+
+string Option::format_option_help(unsigned int indent /* = 2 */) const {
+
+ string mvar_short, mvar_long;
+ if (nargs() == 1) {
+ string mvar = metavar();
+ if (mvar == "") {
+ mvar = type();
+ transform(mvar.begin(), mvar.end(), mvar.begin(), ::toupper);
+ }
+ mvar_short = " " + mvar;
+ mvar_long = "=" + mvar;
+ }
+
+ stringstream ss;
+ ss << string(indent, ' ');
+
+ if (not _short_opts.empty()) {
+ ss << str_join_trans(", ", _short_opts.begin(), _short_opts.end(), str_wrap("-", mvar_short));
+ if (not _long_opts.empty())
+ ss << ", ";
+ }
+ if (not _long_opts.empty())
+ ss << str_join_trans(", ", _long_opts.begin(), _long_opts.end(), str_wrap("--", mvar_long));
+
+ return ss.str();
+}
+
+string Option::format_help(unsigned int indent /* = 2 */) const {
+ stringstream ss;
+ string h = format_option_help(indent);
+ unsigned int width = cols();
+ unsigned int opt_width = min(width*3/10, 36u);
+ bool indent_first = false;
+ ss << h;
+ // if the option list is too long, start a new paragraph
+ if (h.length() >= (opt_width-1)) {
+ ss << endl;
+ indent_first = true;
+ } else {
+ ss << string(opt_width - h.length(), ' ');
+ if (help() == "")
+ ss << endl;
+ }
+ if (help() != "") {
+ string help_str = (get_default() != "") ? str_replace(help(), "%default", get_default()) : help();
+ ss << str_format(help_str, opt_width, width, indent_first);
+ }
+ return ss.str();
+}
+
+Option& Option::action(const string& a) {
+ _action = a;
+ if (a == "store_true")
+ {
+ _default = "0";
+ nargs(0);
+ }
+ else if (a == "store_false")
+ {
+ _default = "1";
+ nargs(0);
+ }
+ else if (a == "store_const" || a == "append_const" || a == "count" || a == "help" || a == "version")
+ {
+ nargs(0);
+ }
+ return *this;
+}
+////////// } class Option //////////
+
+}
diff --git a/third-party/cpp-optparse/OptionParser.h b/third-party/cpp-optparse/OptionParser.h
new file mode 100644
index 0000000..5e316a1
--- /dev/null
+++ b/third-party/cpp-optparse/OptionParser.h
@@ -0,0 +1,367 @@
+/**
+ * Copyright (C) 2010 Johannes Weißl <jargon at molb.org>
+ * License: your favourite BSD-style license
+ *
+ * git clone http://github.com/weisslj/cpp-optparse.git
+ *
+ * This is yet another option parser for C++. It is modelled after the
+ * excellent Python optparse API. Although incomplete, anyone familiar to
+ * optparse should feel at home:
+ * http://docs.python.org/library/optparse.html
+ *
+ * Design decisions:
+ * - elegant and easy usage more important than speed / flexibility
+ * - shortness more important than feature completeness
+ * * no unicode
+ * * no checking for user programming errors
+ *
+ * Why not use getopt/getopt_long?
+ * - not C++ / not completely POSIX
+ * - too cumbersome to use, would need lot of additional code
+ *
+ * Why not use Boost.Program_options?
+ * - boost not installed on all target platforms (esp. cluster, HPC, ...)
+ * - too big to include just for option handling:
+ * 322 *.h (44750 lines) + 7 *.cpp (2078 lines)
+ *
+ * Why not use tclap/Opag/Options/CmdLine/Anyoption/Argument_helper/...?
+ * - no reason, writing one is faster than code inspection :-)
+ * - similarity to Python desired for faster learning curve
+ *
+ * Future work:
+ * - nargs > 1?
+ * - comments?
+ *
+ * Python only features:
+ * - conflict handlers
+ * - adding new actions
+ *
+ *
+ * Example:
+ *
+ * using optparse::OptionParser;
+ *
+ * OptionParser parser = OptionParser() .description("just an example");
+ *
+ * parser.add_option("-f", "--file") .dest("filename")
+ * .help("write report to FILE") .metavar("FILE");
+ * parser.add_option("-q", "--quiet")
+ * .action("store_false") .dest("verbose") .set_default("1")
+ * .help("don't print status messages to stdout");
+ *
+ * optparse::Values options = parser.parse_args(argc, argv);
+ * vector<string> args = parser.args();
+ *
+ * if (options.get("verbose"))
+ * cout << options["filename"] << endl;
+ *
+ */
+
+#ifndef OPTIONPARSER_H_
+#define OPTIONPARSER_H_
+
+#include <algorithm>
+#include <cctype>
+#include <iostream>
+#include <limits>
+#include <list>
+#include <map>
+#include <set>
+#include <sstream>
+#include <stdexcept>
+#include <string>
+#include <type_traits>
+#include <vector>
+
+namespace optparse {
+
+class OptionParser;
+class OptionGroup;
+class Option;
+class Values;
+class Value;
+class Callback;
+
+typedef std::map<std::string,std::string> strMap;
+typedef std::map<std::string,std::list<std::string> > lstMap;
+typedef std::map<std::string,Option const*> optMap;
+
+const char* const SUPPRESS_HELP = "SUPPRESS" "HELP";
+const char* const SUPPRESS_USAGE = "SUPPRESS" "USAGE";
+
+//Exception classes for error conditions
+class InvalidValueCast : public std::runtime_error {
+ public:
+ InvalidValueCast() : std::runtime_error("invalid cast of Value") {}
+};
+
+class InvalidOption : public std::runtime_error {
+ public:
+ InvalidOption() : std::runtime_error("invalid Option") {}
+};
+
+
+
+namespace {
+
+template <typename T>
+T integralConvert(bool valid, const std::string& s)
+{
+ T t;
+ if (valid && (std::istringstream(s) >> t))
+ return t;
+ else
+ throw InvalidValueCast();
+}
+
+template <typename T>
+T floatingPointConvert(bool valid, const std::string& s)
+{
+ T t;
+ if (valid && (std::istringstream(s) >> t))
+ return t;
+ else if (valid) {
+ std::string lc(s);
+ std::transform(lc.begin(), lc.end(), lc.begin(), ::tolower);
+ if (lc == "inf")
+ return std::numeric_limits<T>::infinity();
+ else if (lc == "nan")
+ return std::numeric_limits<T>::quiet_NaN();
+ }
+ throw InvalidValueCast();
+}
+
+} // anon namespace
+
+
+
+//! Class for automatic conversion from string -> anytype
+class Value {
+ public:
+ Value() : str(), valid(false) {}
+ Value(const std::string& v) : str(v), valid(true) {}
+
+ operator const char*() { return str.c_str(); }
+ operator bool() { return integralConvert<bool>(valid, str); }
+ operator bool() const { return integralConvert<bool>(valid, str); }
+ operator short() { return integralConvert<short>(valid, str); }
+ operator short() const { return integralConvert<short>(valid, str); }
+ operator unsigned short() { return integralConvert<unsigned short>(valid, str); }
+ operator unsigned short() const { return integralConvert<unsigned short>(valid, str); }
+ operator int() { return integralConvert<int>(valid, str); }
+ operator int() const { return integralConvert<int>(valid, str); }
+ operator unsigned int() { return integralConvert<unsigned int>(valid, str); }
+ operator unsigned int() const { return integralConvert<unsigned int>(valid, str); }
+ operator long() { return integralConvert<long>(valid, str); }
+ operator long() const { return integralConvert<long>(valid, str); }
+ operator unsigned long() { return integralConvert<unsigned long>(valid, str); }
+ operator unsigned long() const { return integralConvert<unsigned long>(valid, str); }
+ operator float() { return floatingPointConvert<float>(valid, str); }
+ operator float() const { return floatingPointConvert<float>(valid, str); }
+ operator double() { return floatingPointConvert<double>(valid, str); }
+ operator double() const { return floatingPointConvert<double>(valid, str); }
+ operator long double() { return floatingPointConvert<long double>(valid, str); }
+ operator long double() const { return floatingPointConvert<long double>(valid, str); }
+
+private:
+ const std::string str;
+ bool valid;
+};
+
+class Values {
+ public:
+ Values() : _map() {}
+ const std::string& operator[] (const std::string& d) const {
+ strMap::const_iterator it = _map.find(d);
+ if (it != _map.end()) return it->second;
+ throw InvalidOption();
+ }
+ std::string& operator[] (const std::string& d) { return _map[d]; }
+ bool is_set(const std::string& d) const { return _map.find(d) != _map.end(); }
+ bool is_set_by_user(const std::string& d) const { return _userSet.find(d) != _userSet.end(); }
+ void is_set_by_user(const std::string& d, bool yes);
+ Value get(const std::string& d) const { return Value((*this)[d]); }
+
+ typedef std::list<std::string>::iterator iterator;
+ typedef std::list<std::string>::const_iterator const_iterator;
+ std::list<std::string>& all(const std::string& d) { return _appendMap[d]; }
+ const std::list<std::string>& all(const std::string& d) const { return _appendMap.find(d)->second; }
+
+ private:
+ strMap _map;
+ lstMap _appendMap;
+ std::set<std::string> _userSet;
+};
+
+class OptionParser {
+ public:
+ OptionParser();
+ virtual ~OptionParser() {}
+
+ OptionParser& usage(const std::string& u) { set_usage(u); return *this; }
+ OptionParser& version(const std::string& v) { _version = v; return *this; }
+ OptionParser& description(const std::string& d) { _description = d; return *this; }
+ OptionParser& add_help_option(bool h) { _add_help_option = h; return *this; }
+ OptionParser& add_version_option(bool v) { _add_version_option = v; return *this; }
+ OptionParser& prog(const std::string& p) { _prog = p; return *this; }
+ OptionParser& epilog(const std::string& e) { _epilog = e; return *this; }
+ OptionParser& set_defaults(const std::string& dest, const std::string& val) {
+ _defaults[dest] = val; return *this;
+ }
+ OptionParser& enable_interspersed_args() { _interspersed_args = true; return *this; }
+ OptionParser& disable_interspersed_args() { _interspersed_args = false; return *this; }
+ OptionParser& add_option_group(const OptionGroup& group);
+
+ const std::string& usage() const { return _usage; }
+ const std::string& version() const { return _version; }
+ const std::string& description() const { return _description; }
+ bool add_help_option() const { return _add_help_option; }
+ bool add_version_option() const { return _add_version_option; }
+ const std::string& prog() const { return _prog; }
+ const std::string& epilog() const { return _epilog; }
+ bool interspersed_args() const { return _interspersed_args; }
+
+ Option& add_option(const std::string& opt);
+ Option& add_option(const std::string& opt1, const std::string& opt2);
+ Option& add_option(const std::string& opt1, const std::string& opt2, const std::string& opt3);
+ Option& add_option(const std::vector<std::string>& opt);
+
+ Values& parse_args(int argc, char const* const* argv);
+ Values& parse_args(const std::vector<std::string>& args);
+ template<typename InputIterator>
+ Values& parse_args(InputIterator begin, InputIterator end) {
+ return parse_args(std::vector<std::string>(begin, end));
+ }
+
+ const std::list<std::string>& args() const { return _leftover; }
+ std::vector<std::string> args() {
+ return std::vector<std::string>(_leftover.begin(), _leftover.end());
+ }
+
+ std::string format_help() const;
+ std::string format_option_help(unsigned int indent = 2) const;
+ void print_help() const;
+
+ void set_usage(const std::string& u);
+ std::string get_usage() const;
+ void print_usage(std::ostream& out) const;
+ void print_usage() const;
+
+ std::string get_version() const;
+ void print_version(std::ostream& out) const;
+ void print_version() const;
+
+ void error(const std::string& msg) const;
+ void exit() const;
+
+ private:
+ const Option& lookup_short_opt(const std::string& opt) const;
+ const Option& lookup_long_opt(const std::string& opt) const;
+
+ void handle_short_opt(const std::string& opt, const std::string& arg);
+ void handle_long_opt(const std::string& optstr);
+
+ void process_opt(const Option& option, const std::string& opt, const std::string& value);
+
+ std::string format_usage(const std::string& u) const;
+
+ std::string _usage;
+ std::string _version;
+ std::string _description;
+ bool _add_help_option;
+ bool _add_version_option;
+ std::string _prog;
+ std::string _epilog;
+ bool _interspersed_args;
+
+ Values _values;
+
+ std::list<Option> _opts;
+ optMap _optmap_s;
+ optMap _optmap_l;
+ strMap _defaults;
+ std::list<OptionGroup> _groups;
+
+ std::list<std::string> _remaining;
+ std::list<std::string> _leftover;
+};
+
+class OptionGroup : public OptionParser {
+ public:
+ OptionGroup(const OptionParser&, const std::string& t, const std::string& d = "") :
+ _title(t), _group_description(d) {}
+ virtual ~OptionGroup() {}
+
+ OptionGroup& title(const std::string& t) { _title = t; return *this; }
+ OptionGroup& group_description(const std::string& d) { _group_description = d; return *this; }
+ const std::string& title() const { return _title; }
+ const std::string& group_description() const { return _group_description; }
+
+ private:
+ std::string _title;
+ std::string _group_description;
+};
+
+class Option {
+ public:
+ Option() : _action("store"), _type("string"), _nargs(1), _callback(0) {}
+ virtual ~Option() {}
+
+ Option& action(const std::string& a);
+ Option& type(const std::string& t) { _type = t; return *this; }
+ Option& dest(const std::string& d) { _dest = d; return *this; }
+ Option& set_default(const std::string& d) { _default = d; return *this; }
+ template<typename T>
+ Option& set_default(T t) { std::ostringstream ss; ss << t; _default = ss.str(); return *this; }
+ Option& nargs(size_t n) { _nargs = n; return *this; }
+ Option& set_const(const std::string& c) { _const = c; return *this; }
+ template<typename InputIterator>
+ Option& choices(InputIterator begin, InputIterator end) {
+ _choices.assign(begin, end); type("choice"); return *this;
+ }
+ Option& help(const std::string& h) { _help = h; return *this; }
+ Option& metavar(const std::string& m) { _metavar = m; return *this; }
+ Option& callback(Callback& c) { _callback = &c; return *this; }
+
+ const std::string& action() const { return _action; }
+ const std::string& type() const { return _type; }
+ const std::string& dest() const { return _dest; }
+ const std::string& get_default() const { return _default; }
+ size_t nargs() const { return _nargs; }
+ const std::string& get_const() const { return _const; }
+ const std::list<std::string>& choices() const { return _choices; }
+ const std::string& help() const { return _help; }
+ const std::string& metavar() const { return _metavar; }
+ Callback* callback() const { return _callback; }
+
+ private:
+ std::string check_type(const std::string& opt, const std::string& val) const;
+ std::string format_option_help(unsigned int indent = 2) const;
+ std::string format_help(unsigned int indent = 2) const;
+
+ std::set<std::string> _short_opts;
+ std::set<std::string> _long_opts;
+
+ std::string _action;
+ std::string _type;
+ std::string _dest;
+ std::string _default;
+ size_t _nargs;
+ std::string _const;
+ std::list<std::string> _choices;
+ std::string _help;
+ std::string _metavar;
+ Callback* _callback;
+
+ friend class OptionParser;
+};
+
+class Callback {
+public:
+ virtual void operator() (const Option& option, const std::string& opt, const std::string& val, const OptionParser& parser) = 0;
+ virtual ~Callback() {}
+};
+
+}
+
+#endif
diff --git a/third-party/cpp-optparse/README b/third-party/cpp-optparse/README
new file mode 100644
index 0000000..ec97c83
--- /dev/null
+++ b/third-party/cpp-optparse/README
@@ -0,0 +1,51 @@
+cpp-optparse
+
+This is yet another option parser for C++. It is modelled after the
+excellent Python optparse API. Although incomplete, anyone familiar to
+optparse should feel at home:
+http://docs.python.org/library/optparse.html
+
+Copyright (C) 2010 Johannes Weißl <jargon at molb.org>
+License: your favourite BSD-style license
+
+Design decisions:
+- elegant and easy usage more important than speed / flexibility
+- shortness more important than feature completeness
+ * no unicode
+ * no checking for user programming errors
+
+Why not use getopt/getopt_long?
+- not C++ / not completely POSIX
+- too cumbersome to use, would need lot of additional code
+
+Why not use Boost.Program_options?
+- boost not installed on all target platforms (esp. cluster, HPC, ...)
+- too big to include just for option handling:
+ 322 *.h (44750 lines) + 7 *.cpp (2078 lines)
+
+Why not use tclap/Opag/Options/CmdLine/Anyoption/Argument_helper/...?
+- no reason, writing one is faster than code inspection :-)
+- similarity to Python desired for faster learning curve
+
+Future work:
+- nargs > 1?
+- comments?
+
+
+Example:
+
+using optparse::OptionParser;
+
+OptionParser parser = OptionParser() .description("just an example");
+
+parser.add_option("-f", "--file") .dest("filename")
+ .help("write report to FILE") .metavar("FILE");
+parser.add_option("-q", "--quiet")
+ .action("store_false") .dest("verbose") .set_default("1")
+ .help("don't print status messages to stdout");
+
+optparse::Values options = parser.parse_args(argc, argv);
+vector<string> args = parser.args();
+
+if (options.get("verbose"))
+ cout << options["filename"] << endl;
diff --git a/third-party/cpp-optparse/test.cpp b/third-party/cpp-optparse/test.cpp
new file mode 100644
index 0000000..b0a85cc
--- /dev/null
+++ b/third-party/cpp-optparse/test.cpp
@@ -0,0 +1,153 @@
+#include "OptionParser.h"
+
+#include <iostream>
+#include <sstream>
+#include <string>
+#include <complex>
+#include <algorithm>
+
+using namespace std;
+
+using namespace optparse;
+
+class Output {
+public:
+ Output(const string& d) : delim(d), first(true) {}
+ void operator() (const string& s) {
+ if (first)
+ first = false;
+ else
+ cout << delim;
+ cout << s;
+ }
+ ~Output() { cout << endl; }
+ const string& delim;
+ bool first;
+};
+
+class MyCallback : public optparse::Callback {
+public:
+ MyCallback() : counter(0) {}
+ void operator() (const Option& option, const string& opt, const string& val, const OptionParser& parser) {
+ counter++;
+ cout << "--- MyCallback --- " << counter << ". time called" << endl;
+ cout << "--- MyCallback --- option.action(): " << option.action() << endl;
+ cout << "--- MyCallback --- opt: " << opt << endl;
+ cout << "--- MyCallback --- val: " << val << endl;
+ cout << "--- MyCallback --- parser.usage(): " << parser.usage() << endl;
+ cout << endl;
+ }
+ int counter;
+};
+
+int main(int argc, char *argv[])
+{
+#ifndef DISABLE_USAGE
+ const string usage = "usage: %prog [OPTION]... DIR [FILE]...";
+#else
+ const string usage = SUPPRESS_USAGE;
+#endif
+ const string version = "%prog 1.0\nCopyright (C) 2010 Johannes Weißl\n"
+ "License GPLv3+: GNU GPL version 3 or later "
+ "<http://gnu.org/licenses/gpl.html>.\n"
+ "This is free software: you are free to change and redistribute it.\n"
+ "There is NO WARRANTY, to the extent permitted by law.";
+ const string desc = "Lorem ipsum dolor sit amet, consectetur adipisicing"
+ " elit, sed do eiusmod tempor incididunt ut labore et dolore magna"
+ " aliqua.\nUt enim ad minim veniam, quis nostrud exercitation ullamco"
+ " laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor"
+ " in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla"
+ " pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa"
+ " qui officia deserunt mollit anim id est laborum.";
+ const string epilog = "Sed ut perspiciatis unde omnis iste natus error sit"
+ " voluptatem accusantium doloremque laudantium, totam rem aperiam, eaque"
+ " ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae"
+ " dicta sunt explicabo. Nemo enim ipsam voluptatem quia voluptas sit"
+ " aspernatur aut odit aut fugit, sed quia consequuntur magni dolores eos"
+ " qui ratione voluptatem sequi nesciunt. Neque porro quisquam est, qui"
+ " dolorem ipsum quia dolor sit amet, consectetur, adipisci velit, sed quia"
+ " non numquam eius modi tempora incidunt ut labore et dolore magnam"
+ " aliquam quaerat voluptatem.";
+
+ OptionParser parser = OptionParser()
+ .usage(usage)
+ .version(version)
+ .description(desc)
+ .epilog(epilog)
+#ifdef DISABLE_INTERSPERSED_ARGS
+ .disable_interspersed_args()
+#endif
+ ;
+
+ parser.set_defaults("verbosity", "50");
+ parser.set_defaults("no_clear", "0");
+
+ // test all actions
+ parser.add_option("--clear") .action("store_false") .dest("no_clear") .help("clear (default)");
+ parser.add_option("--no-clear") .action("store_true") .help("not clear");
+ parser.add_option("--string")
+ .help("This is a really long text... very long indeed! It must be wrapped on normal terminals.");
+ parser.add_option("-x", "--clause", "--sentence") .metavar("SENTENCE") .set_default("I'm a sentence")
+ .help("This is a really long text... very long indeed! It must be wrapped on normal terminals. "
+ "Also it should appear not on the same line as the option.");
+ parser.add_option("-k") .action("count") .help("how many times?");
+ parser.add_option("-v", "--verbose") .action("store_const") .set_const("100") .dest("verbosity") .help("be verbose!");
+ parser.add_option("-s", "--silent") .action("store_const") .set_const("0") .dest("verbosity") .help("be silent!");
+ parser.add_option("-n", "--number") .type("int") .set_default("1") .metavar("NUM") .help("number of files (default: %default)");
+ parser.add_option("-H") .action("help") .help("alternative help");
+ parser.add_option("-V") .action("version") .help("alternative version");
+ parser.add_option("-i", "--int") .action("store") .type("int") .set_default(3) .help("default: %default");
+ parser.add_option("-f", "--float") .action("store") .type("float") .set_default(5.3) .help("default: %default");
+ parser.add_option("-c", "--complex") .action("store") .type("complex");
+ char const* const choices[] = { "foo", "bar", "baz" };
+ parser.add_option("-C", "--choices") .choices(&choices[0], &choices[3]);
+ parser.add_option("-m", "--more") .action("append");
+ parser.add_option("--more-milk") .action("append_const") .set_const("milk");
+ parser.add_option("--hidden") .help(SUPPRESS_HELP);
+
+ MyCallback mc;
+ parser.add_option("-K", "--callback") .action("callback") .callback(mc) .help("callback test");
+
+ OptionGroup group = OptionGroup(parser, "Dangerous Options",
+ "Caution: use these options at your own risk. "
+ "It is believed that some of them bite.");
+ group.add_option("-g") .action("store_true") .help("Group option.") .set_default("0");
+ parser.add_option_group(group);
+
+ Values& options = parser.parse_args(argc, argv);
+ vector<string> args = parser.args();
+
+ cout << "clear: " << (options.get("no_clear") ? "false" : "true") << endl;
+ cout << "string: " << options["string"] << endl;
+ cout << "clause: " << options["clause"] << endl;
+ cout << "k: " << options["k"] << endl;
+ cout << "verbosity: " << options["verbosity"] << endl;
+ cout << "number: " << (int) options.get("number") << endl;
+ cout << "int: " << (int) options.get("int") << endl;
+ cout << "float: " << (float) options.get("float") << endl;
+ complex<double> c = 0;
+ if (options.is_set("complex")) {
+ stringstream ss;
+ ss << options["complex"];
+ ss >> c;
+ }
+ cout << "complex: " << c << endl;
+ cout << "choices: " << (const char*) options.get("choices") << endl;
+ cout << "more: ";
+ for_each(options.all("more").begin(), options.all("more").end(), Output(", "));
+ cout << "more_milk: ";
+ {
+ Output out(", ");
+ for (Values::iterator it = options.all("more_milk").begin(); it != options.all("more_milk").end(); ++it)
+ out(*it);
+ }
+ cout << "hidden: " << options["hidden"] << endl;
+ cout << "group: " << (options.get("g") ? "true" : "false") << endl;
+
+ cout << endl << "leftover arguments: " << endl;
+ for (vector<string>::const_iterator it = args.begin(); it != args.end(); ++it) {
+ cout << "arg: " << *it << endl;
+ }
+
+ return 0;
+}
diff --git a/third-party/gmock-1.7.0/gmock-gtest-all.cc b/third-party/gmock-1.7.0/gmock-gtest-all.cc
new file mode 100644
index 0000000..1a63a8c
--- /dev/null
+++ b/third-party/gmock-1.7.0/gmock-gtest-all.cc
@@ -0,0 +1,11443 @@
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: mheule at google.com (Markus Heule)
+//
+// Google C++ Testing Framework (Google Test)
+//
+// Sometimes it's desirable to build Google Test by compiling a single file.
+// This file serves this purpose.
+
+// This line ensures that gtest.h can be compiled on its own, even
+// when it's fused.
+#include "gtest/gtest.h"
+
+// The following lines pull in the real gtest *.cc files.
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+//
+// The Google C++ Testing Framework (Google Test)
+
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+//
+// Utilities for testing Google Test itself and code that uses Google Test
+// (e.g. frameworks built on top of Google Test).
+
+#ifndef GTEST_INCLUDE_GTEST_GTEST_SPI_H_
+#define GTEST_INCLUDE_GTEST_GTEST_SPI_H_
+
+
+namespace testing {
+
+// This helper class can be used to mock out Google Test failure reporting
+// so that we can test Google Test or code that builds on Google Test.
+//
+// An object of this class appends a TestPartResult object to the
+// TestPartResultArray object given in the constructor whenever a Google Test
+// failure is reported. It can either intercept only failures that are
+// generated in the same thread that created this object or it can intercept
+// all generated failures. The scope of this mock object can be controlled with
+// the second argument to the two arguments constructor.
+class GTEST_API_ ScopedFakeTestPartResultReporter
+ : public TestPartResultReporterInterface {
+ public:
+ // The two possible mocking modes of this object.
+ enum InterceptMode {
+ INTERCEPT_ONLY_CURRENT_THREAD, // Intercepts only thread local failures.
+ INTERCEPT_ALL_THREADS // Intercepts all failures.
+ };
+
+ // The c'tor sets this object as the test part result reporter used
+ // by Google Test. The 'result' parameter specifies where to report the
+ // results. This reporter will only catch failures generated in the current
+ // thread. DEPRECATED
+ explicit ScopedFakeTestPartResultReporter(TestPartResultArray* result);
+
+ // Same as above, but you can choose the interception scope of this object.
+ ScopedFakeTestPartResultReporter(InterceptMode intercept_mode,
+ TestPartResultArray* result);
+
+ // The d'tor restores the previous test part result reporter.
+ virtual ~ScopedFakeTestPartResultReporter();
+
+ // Appends the TestPartResult object to the TestPartResultArray
+ // received in the constructor.
+ //
+ // This method is from the TestPartResultReporterInterface
+ // interface.
+ virtual void ReportTestPartResult(const TestPartResult& result);
+ private:
+ void Init();
+
+ const InterceptMode intercept_mode_;
+ TestPartResultReporterInterface* old_reporter_;
+ TestPartResultArray* const result_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ScopedFakeTestPartResultReporter);
+};
+
+namespace internal {
+
+// A helper class for implementing EXPECT_FATAL_FAILURE() and
+// EXPECT_NONFATAL_FAILURE(). Its destructor verifies that the given
+// TestPartResultArray contains exactly one failure that has the given
+// type and contains the given substring. If that's not the case, a
+// non-fatal failure will be generated.
+class GTEST_API_ SingleFailureChecker {
+ public:
+ // The constructor remembers the arguments.
+ SingleFailureChecker(const TestPartResultArray* results,
+ TestPartResult::Type type,
+ const string& substr);
+ ~SingleFailureChecker();
+ private:
+ const TestPartResultArray* const results_;
+ const TestPartResult::Type type_;
+ const string substr_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(SingleFailureChecker);
+};
+
+} // namespace internal
+
+} // namespace testing
+
+// A set of macros for testing Google Test assertions or code that's expected
+// to generate Google Test fatal failures. It verifies that the given
+// statement will cause exactly one fatal Google Test failure with 'substr'
+// being part of the failure message.
+//
+// There are two different versions of this macro. EXPECT_FATAL_FAILURE only
+// affects and considers failures generated in the current thread and
+// EXPECT_FATAL_FAILURE_ON_ALL_THREADS does the same but for all threads.
+//
+// The verification of the assertion is done correctly even when the statement
+// throws an exception or aborts the current function.
+//
+// Known restrictions:
+// - 'statement' cannot reference local non-static variables or
+// non-static members of the current object.
+// - 'statement' cannot return a value.
+// - You cannot stream a failure message to this macro.
+//
+// Note that even though the implementations of the following two
+// macros are much alike, we cannot refactor them to use a common
+// helper macro, due to some peculiarity in how the preprocessor
+// works. The AcceptsMacroThatExpandsToUnprotectedComma test in
+// gtest_unittest.cc will fail to compile if we do that.
+#define EXPECT_FATAL_FAILURE(statement, substr) \
+ do { \
+ class GTestExpectFatalFailureHelper {\
+ public:\
+ static void Execute() { statement; }\
+ };\
+ ::testing::TestPartResultArray gtest_failures;\
+ ::testing::internal::SingleFailureChecker gtest_checker(\
+ >est_failures, ::testing::TestPartResult::kFatalFailure, (substr));\
+ {\
+ ::testing::ScopedFakeTestPartResultReporter gtest_reporter(\
+ ::testing::ScopedFakeTestPartResultReporter:: \
+ INTERCEPT_ONLY_CURRENT_THREAD, >est_failures);\
+ GTestExpectFatalFailureHelper::Execute();\
+ }\
+ } while (::testing::internal::AlwaysFalse())
+
+#define EXPECT_FATAL_FAILURE_ON_ALL_THREADS(statement, substr) \
+ do { \
+ class GTestExpectFatalFailureHelper {\
+ public:\
+ static void Execute() { statement; }\
+ };\
+ ::testing::TestPartResultArray gtest_failures;\
+ ::testing::internal::SingleFailureChecker gtest_checker(\
+ >est_failures, ::testing::TestPartResult::kFatalFailure, (substr));\
+ {\
+ ::testing::ScopedFakeTestPartResultReporter gtest_reporter(\
+ ::testing::ScopedFakeTestPartResultReporter:: \
+ INTERCEPT_ALL_THREADS, >est_failures);\
+ GTestExpectFatalFailureHelper::Execute();\
+ }\
+ } while (::testing::internal::AlwaysFalse())
+
+// A macro for testing Google Test assertions or code that's expected to
+// generate Google Test non-fatal failures. It asserts that the given
+// statement will cause exactly one non-fatal Google Test failure with 'substr'
+// being part of the failure message.
+//
+// There are two different versions of this macro. EXPECT_NONFATAL_FAILURE only
+// affects and considers failures generated in the current thread and
+// EXPECT_NONFATAL_FAILURE_ON_ALL_THREADS does the same but for all threads.
+//
+// 'statement' is allowed to reference local variables and members of
+// the current object.
+//
+// The verification of the assertion is done correctly even when the statement
+// throws an exception or aborts the current function.
+//
+// Known restrictions:
+// - You cannot stream a failure message to this macro.
+//
+// Note that even though the implementations of the following two
+// macros are much alike, we cannot refactor them to use a common
+// helper macro, due to some peculiarity in how the preprocessor
+// works. If we do that, the code won't compile when the user gives
+// EXPECT_NONFATAL_FAILURE() a statement that contains a macro that
+// expands to code containing an unprotected comma. The
+// AcceptsMacroThatExpandsToUnprotectedComma test in gtest_unittest.cc
+// catches that.
+//
+// For the same reason, we have to write
+// if (::testing::internal::AlwaysTrue()) { statement; }
+// instead of
+// GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement)
+// to avoid an MSVC warning on unreachable code.
+#define EXPECT_NONFATAL_FAILURE(statement, substr) \
+ do {\
+ ::testing::TestPartResultArray gtest_failures;\
+ ::testing::internal::SingleFailureChecker gtest_checker(\
+ >est_failures, ::testing::TestPartResult::kNonFatalFailure, \
+ (substr));\
+ {\
+ ::testing::ScopedFakeTestPartResultReporter gtest_reporter(\
+ ::testing::ScopedFakeTestPartResultReporter:: \
+ INTERCEPT_ONLY_CURRENT_THREAD, >est_failures);\
+ if (::testing::internal::AlwaysTrue()) { statement; }\
+ }\
+ } while (::testing::internal::AlwaysFalse())
+
+#define EXPECT_NONFATAL_FAILURE_ON_ALL_THREADS(statement, substr) \
+ do {\
+ ::testing::TestPartResultArray gtest_failures;\
+ ::testing::internal::SingleFailureChecker gtest_checker(\
+ >est_failures, ::testing::TestPartResult::kNonFatalFailure, \
+ (substr));\
+ {\
+ ::testing::ScopedFakeTestPartResultReporter gtest_reporter(\
+ ::testing::ScopedFakeTestPartResultReporter::INTERCEPT_ALL_THREADS, \
+ >est_failures);\
+ if (::testing::internal::AlwaysTrue()) { statement; }\
+ }\
+ } while (::testing::internal::AlwaysFalse())
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_SPI_H_
+
+#include <ctype.h>
+#include <math.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <time.h>
+#include <wchar.h>
+#include <wctype.h>
+
+#include <algorithm>
+#include <iomanip>
+#include <limits>
+#include <ostream> // NOLINT
+#include <sstream>
+#include <vector>
+
+#if GTEST_OS_LINUX
+
+// TODO(kenton at google.com): Use autoconf to detect availability of
+// gettimeofday().
+# define GTEST_HAS_GETTIMEOFDAY_ 1
+
+# include <fcntl.h> // NOLINT
+# include <limits.h> // NOLINT
+# include <sched.h> // NOLINT
+// Declares vsnprintf(). This header is not available on Windows.
+# include <strings.h> // NOLINT
+# include <sys/mman.h> // NOLINT
+# include <sys/time.h> // NOLINT
+# include <unistd.h> // NOLINT
+# include <string>
+
+#elif GTEST_OS_SYMBIAN
+# define GTEST_HAS_GETTIMEOFDAY_ 1
+# include <sys/time.h> // NOLINT
+
+#elif GTEST_OS_ZOS
+# define GTEST_HAS_GETTIMEOFDAY_ 1
+# include <sys/time.h> // NOLINT
+
+// On z/OS we additionally need strings.h for strcasecmp.
+# include <strings.h> // NOLINT
+
+#elif GTEST_OS_WINDOWS_MOBILE // We are on Windows CE.
+
+# include <windows.h> // NOLINT
+
+#elif GTEST_OS_WINDOWS // We are on Windows proper.
+
+# include <io.h> // NOLINT
+# include <sys/timeb.h> // NOLINT
+# include <sys/types.h> // NOLINT
+# include <sys/stat.h> // NOLINT
+
+# if GTEST_OS_WINDOWS_MINGW
+// MinGW has gettimeofday() but not _ftime64().
+// TODO(kenton at google.com): Use autoconf to detect availability of
+// gettimeofday().
+// TODO(kenton at google.com): There are other ways to get the time on
+// Windows, like GetTickCount() or GetSystemTimeAsFileTime(). MinGW
+// supports these. consider using them instead.
+# define GTEST_HAS_GETTIMEOFDAY_ 1
+# include <sys/time.h> // NOLINT
+# endif // GTEST_OS_WINDOWS_MINGW
+
+// cpplint thinks that the header is already included, so we want to
+// silence it.
+# include <windows.h> // NOLINT
+
+#else
+
+// Assume other platforms have gettimeofday().
+// TODO(kenton at google.com): Use autoconf to detect availability of
+// gettimeofday().
+# define GTEST_HAS_GETTIMEOFDAY_ 1
+
+// cpplint thinks that the header is already included, so we want to
+// silence it.
+# include <sys/time.h> // NOLINT
+# include <unistd.h> // NOLINT
+
+#endif // GTEST_OS_LINUX
+
+#if GTEST_HAS_EXCEPTIONS
+# include <stdexcept>
+#endif
+
+#if GTEST_CAN_STREAM_RESULTS_
+# include <arpa/inet.h> // NOLINT
+# include <netdb.h> // NOLINT
+#endif
+
+// Indicates that this translation unit is part of Google Test's
+// implementation. It must come before gtest-internal-inl.h is
+// included, or there will be a compiler error. This trick is to
+// prevent a user from accidentally including gtest-internal-inl.h in
+// his code.
+#define GTEST_IMPLEMENTATION_ 1
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+// Utility functions and classes used by the Google C++ testing framework.
+//
+// Author: wan at google.com (Zhanyong Wan)
+//
+// This file contains purely Google Test's internal implementation. Please
+// DO NOT #INCLUDE IT IN A USER PROGRAM.
+
+#ifndef GTEST_SRC_GTEST_INTERNAL_INL_H_
+#define GTEST_SRC_GTEST_INTERNAL_INL_H_
+
+// GTEST_IMPLEMENTATION_ is defined to 1 iff the current translation unit is
+// part of Google Test's implementation; otherwise it's undefined.
+#if !GTEST_IMPLEMENTATION_
+// A user is trying to include this from his code - just say no.
+# error "gtest-internal-inl.h is part of Google Test's internal implementation."
+# error "It must not be included except by Google Test itself."
+#endif // GTEST_IMPLEMENTATION_
+
+#ifndef _WIN32_WCE
+# include <errno.h>
+#endif // !_WIN32_WCE
+#include <stddef.h>
+#include <stdlib.h> // For strtoll/_strtoul64/malloc/free.
+#include <string.h> // For memmove.
+
+#include <algorithm>
+#include <string>
+#include <vector>
+
+
+#if GTEST_CAN_STREAM_RESULTS_
+# include <arpa/inet.h> // NOLINT
+# include <netdb.h> // NOLINT
+#endif
+
+#if GTEST_OS_WINDOWS
+# include <windows.h> // NOLINT
+#endif // GTEST_OS_WINDOWS
+
+
+namespace testing {
+
+// Declares the flags.
+//
+// We don't want the users to modify this flag in the code, but want
+// Google Test's own unit tests to be able to access it. Therefore we
+// declare it here as opposed to in gtest.h.
+GTEST_DECLARE_bool_(death_test_use_fork);
+
+namespace internal {
+
+// The value of GetTestTypeId() as seen from within the Google Test
+// library. This is solely for testing GetTestTypeId().
+GTEST_API_ extern const TypeId kTestTypeIdInGoogleTest;
+
+// Names of the flags (needed for parsing Google Test flags).
+const char kAlsoRunDisabledTestsFlag[] = "also_run_disabled_tests";
+const char kBreakOnFailureFlag[] = "break_on_failure";
+const char kCatchExceptionsFlag[] = "catch_exceptions";
+const char kColorFlag[] = "color";
+const char kFilterFlag[] = "filter";
+const char kListTestsFlag[] = "list_tests";
+const char kOutputFlag[] = "output";
+const char kPrintTimeFlag[] = "print_time";
+const char kRandomSeedFlag[] = "random_seed";
+const char kRepeatFlag[] = "repeat";
+const char kShuffleFlag[] = "shuffle";
+const char kStackTraceDepthFlag[] = "stack_trace_depth";
+const char kStreamResultToFlag[] = "stream_result_to";
+const char kThrowOnFailureFlag[] = "throw_on_failure";
+
+// A valid random seed must be in [1, kMaxRandomSeed].
+const int kMaxRandomSeed = 99999;
+
+// g_help_flag is true iff the --help flag or an equivalent form is
+// specified on the command line.
+GTEST_API_ extern bool g_help_flag;
+
+// Returns the current time in milliseconds.
+GTEST_API_ TimeInMillis GetTimeInMillis();
+
+// Returns true iff Google Test should use colors in the output.
+GTEST_API_ bool ShouldUseColor(bool stdout_is_tty);
+
+// Formats the given time in milliseconds as seconds.
+GTEST_API_ std::string FormatTimeInMillisAsSeconds(TimeInMillis ms);
+
+// Converts the given time in milliseconds to a date string in the ISO 8601
+// format, without the timezone information. N.B.: due to the use the
+// non-reentrant localtime() function, this function is not thread safe. Do
+// not use it in any code that can be called from multiple threads.
+GTEST_API_ std::string FormatEpochTimeInMillisAsIso8601(TimeInMillis ms);
+
+// Parses a string for an Int32 flag, in the form of "--flag=value".
+//
+// On success, stores the value of the flag in *value, and returns
+// true. On failure, returns false without changing *value.
+GTEST_API_ bool ParseInt32Flag(
+ const char* str, const char* flag, Int32* value);
+
+// Returns a random seed in range [1, kMaxRandomSeed] based on the
+// given --gtest_random_seed flag value.
+inline int GetRandomSeedFromFlag(Int32 random_seed_flag) {
+ const unsigned int raw_seed = (random_seed_flag == 0) ?
+ static_cast<unsigned int>(GetTimeInMillis()) :
+ static_cast<unsigned int>(random_seed_flag);
+
+ // Normalizes the actual seed to range [1, kMaxRandomSeed] such that
+ // it's easy to type.
+ const int normalized_seed =
+ static_cast<int>((raw_seed - 1U) %
+ static_cast<unsigned int>(kMaxRandomSeed)) + 1;
+ return normalized_seed;
+}
+
+// Returns the first valid random seed after 'seed'. The behavior is
+// undefined if 'seed' is invalid. The seed after kMaxRandomSeed is
+// considered to be 1.
+inline int GetNextRandomSeed(int seed) {
+ GTEST_CHECK_(1 <= seed && seed <= kMaxRandomSeed)
+ << "Invalid random seed " << seed << " - must be in [1, "
+ << kMaxRandomSeed << "].";
+ const int next_seed = seed + 1;
+ return (next_seed > kMaxRandomSeed) ? 1 : next_seed;
+}
+
+// This class saves the values of all Google Test flags in its c'tor, and
+// restores them in its d'tor.
+class GTestFlagSaver {
+ public:
+ // The c'tor.
+ GTestFlagSaver() {
+ also_run_disabled_tests_ = GTEST_FLAG(also_run_disabled_tests);
+ break_on_failure_ = GTEST_FLAG(break_on_failure);
+ catch_exceptions_ = GTEST_FLAG(catch_exceptions);
+ color_ = GTEST_FLAG(color);
+ death_test_style_ = GTEST_FLAG(death_test_style);
+ death_test_use_fork_ = GTEST_FLAG(death_test_use_fork);
+ filter_ = GTEST_FLAG(filter);
+ internal_run_death_test_ = GTEST_FLAG(internal_run_death_test);
+ list_tests_ = GTEST_FLAG(list_tests);
+ output_ = GTEST_FLAG(output);
+ print_time_ = GTEST_FLAG(print_time);
+ random_seed_ = GTEST_FLAG(random_seed);
+ repeat_ = GTEST_FLAG(repeat);
+ shuffle_ = GTEST_FLAG(shuffle);
+ stack_trace_depth_ = GTEST_FLAG(stack_trace_depth);
+ stream_result_to_ = GTEST_FLAG(stream_result_to);
+ throw_on_failure_ = GTEST_FLAG(throw_on_failure);
+ }
+
+ // The d'tor is not virtual. DO NOT INHERIT FROM THIS CLASS.
+ ~GTestFlagSaver() {
+ GTEST_FLAG(also_run_disabled_tests) = also_run_disabled_tests_;
+ GTEST_FLAG(break_on_failure) = break_on_failure_;
+ GTEST_FLAG(catch_exceptions) = catch_exceptions_;
+ GTEST_FLAG(color) = color_;
+ GTEST_FLAG(death_test_style) = death_test_style_;
+ GTEST_FLAG(death_test_use_fork) = death_test_use_fork_;
+ GTEST_FLAG(filter) = filter_;
+ GTEST_FLAG(internal_run_death_test) = internal_run_death_test_;
+ GTEST_FLAG(list_tests) = list_tests_;
+ GTEST_FLAG(output) = output_;
+ GTEST_FLAG(print_time) = print_time_;
+ GTEST_FLAG(random_seed) = random_seed_;
+ GTEST_FLAG(repeat) = repeat_;
+ GTEST_FLAG(shuffle) = shuffle_;
+ GTEST_FLAG(stack_trace_depth) = stack_trace_depth_;
+ GTEST_FLAG(stream_result_to) = stream_result_to_;
+ GTEST_FLAG(throw_on_failure) = throw_on_failure_;
+ }
+
+ private:
+ // Fields for saving the original values of flags.
+ bool also_run_disabled_tests_;
+ bool break_on_failure_;
+ bool catch_exceptions_;
+ std::string color_;
+ std::string death_test_style_;
+ bool death_test_use_fork_;
+ std::string filter_;
+ std::string internal_run_death_test_;
+ bool list_tests_;
+ std::string output_;
+ bool print_time_;
+ internal::Int32 random_seed_;
+ internal::Int32 repeat_;
+ bool shuffle_;
+ internal::Int32 stack_trace_depth_;
+ std::string stream_result_to_;
+ bool throw_on_failure_;
+} GTEST_ATTRIBUTE_UNUSED_;
+
+// Converts a Unicode code point to a narrow string in UTF-8 encoding.
+// code_point parameter is of type UInt32 because wchar_t may not be
+// wide enough to contain a code point.
+// If the code_point is not a valid Unicode code point
+// (i.e. outside of Unicode range U+0 to U+10FFFF) it will be converted
+// to "(Invalid Unicode 0xXXXXXXXX)".
+GTEST_API_ std::string CodePointToUtf8(UInt32 code_point);
+
+// Converts a wide string to a narrow string in UTF-8 encoding.
+// The wide string is assumed to have the following encoding:
+// UTF-16 if sizeof(wchar_t) == 2 (on Windows, Cygwin, Symbian OS)
+// UTF-32 if sizeof(wchar_t) == 4 (on Linux)
+// Parameter str points to a null-terminated wide string.
+// Parameter num_chars may additionally limit the number
+// of wchar_t characters processed. -1 is used when the entire string
+// should be processed.
+// If the string contains code points that are not valid Unicode code points
+// (i.e. outside of Unicode range U+0 to U+10FFFF) they will be output
+// as '(Invalid Unicode 0xXXXXXXXX)'. If the string is in UTF16 encoding
+// and contains invalid UTF-16 surrogate pairs, values in those pairs
+// will be encoded as individual Unicode characters from Basic Normal Plane.
+GTEST_API_ std::string WideStringToUtf8(const wchar_t* str, int num_chars);
+
+// Reads the GTEST_SHARD_STATUS_FILE environment variable, and creates the file
+// if the variable is present. If a file already exists at this location, this
+// function will write over it. If the variable is present, but the file cannot
+// be created, prints an error and exits.
+void WriteToShardStatusFileIfNeeded();
+
+// Checks whether sharding is enabled by examining the relevant
+// environment variable values. If the variables are present,
+// but inconsistent (e.g., shard_index >= total_shards), prints
+// an error and exits. If in_subprocess_for_death_test, sharding is
+// disabled because it must only be applied to the original test
+// process. Otherwise, we could filter out death tests we intended to execute.
+GTEST_API_ bool ShouldShard(const char* total_shards_str,
+ const char* shard_index_str,
+ bool in_subprocess_for_death_test);
+
+// Parses the environment variable var as an Int32. If it is unset,
+// returns default_val. If it is not an Int32, prints an error and
+// and aborts.
+GTEST_API_ Int32 Int32FromEnvOrDie(const char* env_var, Int32 default_val);
+
+// Given the total number of shards, the shard index, and the test id,
+// returns true iff the test should be run on this shard. The test id is
+// some arbitrary but unique non-negative integer assigned to each test
+// method. Assumes that 0 <= shard_index < total_shards.
+GTEST_API_ bool ShouldRunTestOnShard(
+ int total_shards, int shard_index, int test_id);
+
+// STL container utilities.
+
+// Returns the number of elements in the given container that satisfy
+// the given predicate.
+template <class Container, typename Predicate>
+inline int CountIf(const Container& c, Predicate predicate) {
+ // Implemented as an explicit loop since std::count_if() in libCstd on
+ // Solaris has a non-standard signature.
+ int count = 0;
+ for (typename Container::const_iterator it = c.begin(); it != c.end(); ++it) {
+ if (predicate(*it))
+ ++count;
+ }
+ return count;
+}
+
+// Applies a function/functor to each element in the container.
+template <class Container, typename Functor>
+void ForEach(const Container& c, Functor functor) {
+ std::for_each(c.begin(), c.end(), functor);
+}
+
+// Returns the i-th element of the vector, or default_value if i is not
+// in range [0, v.size()).
+template <typename E>
+inline E GetElementOr(const std::vector<E>& v, int i, E default_value) {
+ return (i < 0 || i >= static_cast<int>(v.size())) ? default_value : v[i];
+}
+
+// Performs an in-place shuffle of a range of the vector's elements.
+// 'begin' and 'end' are element indices as an STL-style range;
+// i.e. [begin, end) are shuffled, where 'end' == size() means to
+// shuffle to the end of the vector.
+template <typename E>
+void ShuffleRange(internal::Random* random, int begin, int end,
+ std::vector<E>* v) {
+ const int size = static_cast<int>(v->size());
+ GTEST_CHECK_(0 <= begin && begin <= size)
+ << "Invalid shuffle range start " << begin << ": must be in range [0, "
+ << size << "].";
+ GTEST_CHECK_(begin <= end && end <= size)
+ << "Invalid shuffle range finish " << end << ": must be in range ["
+ << begin << ", " << size << "].";
+
+ // Fisher-Yates shuffle, from
+ // http://en.wikipedia.org/wiki/Fisher-Yates_shuffle
+ for (int range_width = end - begin; range_width >= 2; range_width--) {
+ const int last_in_range = begin + range_width - 1;
+ const int selected = begin + random->Generate(range_width);
+ std::swap((*v)[selected], (*v)[last_in_range]);
+ }
+}
+
+// Performs an in-place shuffle of the vector's elements.
+template <typename E>
+inline void Shuffle(internal::Random* random, std::vector<E>* v) {
+ ShuffleRange(random, 0, static_cast<int>(v->size()), v);
+}
+
+// A function for deleting an object. Handy for being used as a
+// functor.
+template <typename T>
+static void Delete(T* x) {
+ delete x;
+}
+
+// A predicate that checks the key of a TestProperty against a known key.
+//
+// TestPropertyKeyIs is copyable.
+class TestPropertyKeyIs {
+ public:
+ // Constructor.
+ //
+ // TestPropertyKeyIs has NO default constructor.
+ explicit TestPropertyKeyIs(const std::string& key) : key_(key) {}
+
+ // Returns true iff the test name of test property matches on key_.
+ bool operator()(const TestProperty& test_property) const {
+ return test_property.key() == key_;
+ }
+
+ private:
+ std::string key_;
+};
+
+// Class UnitTestOptions.
+//
+// This class contains functions for processing options the user
+// specifies when running the tests. It has only static members.
+//
+// In most cases, the user can specify an option using either an
+// environment variable or a command line flag. E.g. you can set the
+// test filter using either GTEST_FILTER or --gtest_filter. If both
+// the variable and the flag are present, the latter overrides the
+// former.
+class GTEST_API_ UnitTestOptions {
+ public:
+ // Functions for processing the gtest_output flag.
+
+ // Returns the output format, or "" for normal printed output.
+ static std::string GetOutputFormat();
+
+ // Returns the absolute path of the requested output file, or the
+ // default (test_detail.xml in the original working directory) if
+ // none was explicitly specified.
+ static std::string GetAbsolutePathToOutputFile();
+
+ // Functions for processing the gtest_filter flag.
+
+ // Returns true iff the wildcard pattern matches the string. The
+ // first ':' or '\0' character in pattern marks the end of it.
+ //
+ // This recursive algorithm isn't very efficient, but is clear and
+ // works well enough for matching test names, which are short.
+ static bool PatternMatchesString(const char *pattern, const char *str);
+
+ // Returns true iff the user-specified filter matches the test case
+ // name and the test name.
+ static bool FilterMatchesTest(const std::string &test_case_name,
+ const std::string &test_name);
+
+#if GTEST_OS_WINDOWS
+ // Function for supporting the gtest_catch_exception flag.
+
+ // Returns EXCEPTION_EXECUTE_HANDLER if Google Test should handle the
+ // given SEH exception, or EXCEPTION_CONTINUE_SEARCH otherwise.
+ // This function is useful as an __except condition.
+ static int GTestShouldProcessSEH(DWORD exception_code);
+#endif // GTEST_OS_WINDOWS
+
+ // Returns true if "name" matches the ':' separated list of glob-style
+ // filters in "filter".
+ static bool MatchesFilter(const std::string& name, const char* filter);
+};
+
+// Returns the current application's name, removing directory path if that
+// is present. Used by UnitTestOptions::GetOutputFile.
+GTEST_API_ FilePath GetCurrentExecutableName();
+
+// The role interface for getting the OS stack trace as a string.
+class OsStackTraceGetterInterface {
+ public:
+ OsStackTraceGetterInterface() {}
+ virtual ~OsStackTraceGetterInterface() {}
+
+ // Returns the current OS stack trace as an std::string. Parameters:
+ //
+ // max_depth - the maximum number of stack frames to be included
+ // in the trace.
+ // skip_count - the number of top frames to be skipped; doesn't count
+ // against max_depth.
+ virtual string CurrentStackTrace(int max_depth, int skip_count) = 0;
+
+ // UponLeavingGTest() should be called immediately before Google Test calls
+ // user code. It saves some information about the current stack that
+ // CurrentStackTrace() will use to find and hide Google Test stack frames.
+ virtual void UponLeavingGTest() = 0;
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(OsStackTraceGetterInterface);
+};
+
+// A working implementation of the OsStackTraceGetterInterface interface.
+class OsStackTraceGetter : public OsStackTraceGetterInterface {
+ public:
+ OsStackTraceGetter() : caller_frame_(NULL) {}
+
+ virtual string CurrentStackTrace(int max_depth, int skip_count)
+ GTEST_LOCK_EXCLUDED_(mutex_);
+
+ virtual void UponLeavingGTest() GTEST_LOCK_EXCLUDED_(mutex_);
+
+ // This string is inserted in place of stack frames that are part of
+ // Google Test's implementation.
+ static const char* const kElidedFramesMarker;
+
+ private:
+ Mutex mutex_; // protects all internal state
+
+ // We save the stack frame below the frame that calls user code.
+ // We do this because the address of the frame immediately below
+ // the user code changes between the call to UponLeavingGTest()
+ // and any calls to CurrentStackTrace() from within the user code.
+ void* caller_frame_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(OsStackTraceGetter);
+};
+
+// Information about a Google Test trace point.
+struct TraceInfo {
+ const char* file;
+ int line;
+ std::string message;
+};
+
+// This is the default global test part result reporter used in UnitTestImpl.
+// This class should only be used by UnitTestImpl.
+class DefaultGlobalTestPartResultReporter
+ : public TestPartResultReporterInterface {
+ public:
+ explicit DefaultGlobalTestPartResultReporter(UnitTestImpl* unit_test);
+ // Implements the TestPartResultReporterInterface. Reports the test part
+ // result in the current test.
+ virtual void ReportTestPartResult(const TestPartResult& result);
+
+ private:
+ UnitTestImpl* const unit_test_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(DefaultGlobalTestPartResultReporter);
+};
+
+// This is the default per thread test part result reporter used in
+// UnitTestImpl. This class should only be used by UnitTestImpl.
+class DefaultPerThreadTestPartResultReporter
+ : public TestPartResultReporterInterface {
+ public:
+ explicit DefaultPerThreadTestPartResultReporter(UnitTestImpl* unit_test);
+ // Implements the TestPartResultReporterInterface. The implementation just
+ // delegates to the current global test part result reporter of *unit_test_.
+ virtual void ReportTestPartResult(const TestPartResult& result);
+
+ private:
+ UnitTestImpl* const unit_test_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(DefaultPerThreadTestPartResultReporter);
+};
+
+// The private implementation of the UnitTest class. We don't protect
+// the methods under a mutex, as this class is not accessible by a
+// user and the UnitTest class that delegates work to this class does
+// proper locking.
+class GTEST_API_ UnitTestImpl {
+ public:
+ explicit UnitTestImpl(UnitTest* parent);
+ virtual ~UnitTestImpl();
+
+ // There are two different ways to register your own TestPartResultReporter.
+ // You can register your own repoter to listen either only for test results
+ // from the current thread or for results from all threads.
+ // By default, each per-thread test result repoter just passes a new
+ // TestPartResult to the global test result reporter, which registers the
+ // test part result for the currently running test.
+
+ // Returns the global test part result reporter.
+ TestPartResultReporterInterface* GetGlobalTestPartResultReporter();
+
+ // Sets the global test part result reporter.
+ void SetGlobalTestPartResultReporter(
+ TestPartResultReporterInterface* reporter);
+
+ // Returns the test part result reporter for the current thread.
+ TestPartResultReporterInterface* GetTestPartResultReporterForCurrentThread();
+
+ // Sets the test part result reporter for the current thread.
+ void SetTestPartResultReporterForCurrentThread(
+ TestPartResultReporterInterface* reporter);
+
+ // Gets the number of successful test cases.
+ int successful_test_case_count() const;
+
+ // Gets the number of failed test cases.
+ int failed_test_case_count() const;
+
+ // Gets the number of all test cases.
+ int total_test_case_count() const;
+
+ // Gets the number of all test cases that contain at least one test
+ // that should run.
+ int test_case_to_run_count() const;
+
+ // Gets the number of successful tests.
+ int successful_test_count() const;
+
+ // Gets the number of failed tests.
+ int failed_test_count() const;
+
+ // Gets the number of disabled tests that will be reported in the XML report.
+ int reportable_disabled_test_count() const;
+
+ // Gets the number of disabled tests.
+ int disabled_test_count() const;
+
+ // Gets the number of tests to be printed in the XML report.
+ int reportable_test_count() const;
+
+ // Gets the number of all tests.
+ int total_test_count() const;
+
+ // Gets the number of tests that should run.
+ int test_to_run_count() const;
+
+ // Gets the time of the test program start, in ms from the start of the
+ // UNIX epoch.
+ TimeInMillis start_timestamp() const { return start_timestamp_; }
+
+ // Gets the elapsed time, in milliseconds.
+ TimeInMillis elapsed_time() const { return elapsed_time_; }
+
+ // Returns true iff the unit test passed (i.e. all test cases passed).
+ bool Passed() const { return !Failed(); }
+
+ // Returns true iff the unit test failed (i.e. some test case failed
+ // or something outside of all tests failed).
+ bool Failed() const {
+ return failed_test_case_count() > 0 || ad_hoc_test_result()->Failed();
+ }
+
+ // Gets the i-th test case among all the test cases. i can range from 0 to
+ // total_test_case_count() - 1. If i is not in that range, returns NULL.
+ const TestCase* GetTestCase(int i) const {
+ const int index = GetElementOr(test_case_indices_, i, -1);
+ return index < 0 ? NULL : test_cases_[i];
+ }
+
+ // Gets the i-th test case among all the test cases. i can range from 0 to
+ // total_test_case_count() - 1. If i is not in that range, returns NULL.
+ TestCase* GetMutableTestCase(int i) {
+ const int index = GetElementOr(test_case_indices_, i, -1);
+ return index < 0 ? NULL : test_cases_[index];
+ }
+
+ // Provides access to the event listener list.
+ TestEventListeners* listeners() { return &listeners_; }
+
+ // Returns the TestResult for the test that's currently running, or
+ // the TestResult for the ad hoc test if no test is running.
+ TestResult* current_test_result();
+
+ // Returns the TestResult for the ad hoc test.
+ const TestResult* ad_hoc_test_result() const { return &ad_hoc_test_result_; }
+
+ // Sets the OS stack trace getter.
+ //
+ // Does nothing if the input and the current OS stack trace getter
+ // are the same; otherwise, deletes the old getter and makes the
+ // input the current getter.
+ void set_os_stack_trace_getter(OsStackTraceGetterInterface* getter);
+
+ // Returns the current OS stack trace getter if it is not NULL;
+ // otherwise, creates an OsStackTraceGetter, makes it the current
+ // getter, and returns it.
+ OsStackTraceGetterInterface* os_stack_trace_getter();
+
+ // Returns the current OS stack trace as an std::string.
+ //
+ // The maximum number of stack frames to be included is specified by
+ // the gtest_stack_trace_depth flag. The skip_count parameter
+ // specifies the number of top frames to be skipped, which doesn't
+ // count against the number of frames to be included.
+ //
+ // For example, if Foo() calls Bar(), which in turn calls
+ // CurrentOsStackTraceExceptTop(1), Foo() will be included in the
+ // trace but Bar() and CurrentOsStackTraceExceptTop() won't.
+ std::string CurrentOsStackTraceExceptTop(int skip_count) GTEST_NO_INLINE_;
+
+ // Finds and returns a TestCase with the given name. If one doesn't
+ // exist, creates one and returns it.
+ //
+ // Arguments:
+ //
+ // test_case_name: name of the test case
+ // type_param: the name of the test's type parameter, or NULL if
+ // this is not a typed or a type-parameterized test.
+ // set_up_tc: pointer to the function that sets up the test case
+ // tear_down_tc: pointer to the function that tears down the test case
+ TestCase* GetTestCase(const char* test_case_name,
+ const char* type_param,
+ Test::SetUpTestCaseFunc set_up_tc,
+ Test::TearDownTestCaseFunc tear_down_tc);
+
+ // Adds a TestInfo to the unit test.
+ //
+ // Arguments:
+ //
+ // set_up_tc: pointer to the function that sets up the test case
+ // tear_down_tc: pointer to the function that tears down the test case
+ // test_info: the TestInfo object
+ void AddTestInfo(Test::SetUpTestCaseFunc set_up_tc,
+ Test::TearDownTestCaseFunc tear_down_tc,
+ TestInfo* test_info) {
+ // In order to support thread-safe death tests, we need to
+ // remember the original working directory when the test program
+ // was first invoked. We cannot do this in RUN_ALL_TESTS(), as
+ // the user may have changed the current directory before calling
+ // RUN_ALL_TESTS(). Therefore we capture the current directory in
+ // AddTestInfo(), which is called to register a TEST or TEST_F
+ // before main() is reached.
+ if (original_working_dir_.IsEmpty()) {
+ original_working_dir_.Set(FilePath::GetCurrentDir());
+ GTEST_CHECK_(!original_working_dir_.IsEmpty())
+ << "Failed to get the current working directory.";
+ }
+
+ GetTestCase(test_info->test_case_name(),
+ test_info->type_param(),
+ set_up_tc,
+ tear_down_tc)->AddTestInfo(test_info);
+ }
+
+#if GTEST_HAS_PARAM_TEST
+ // Returns ParameterizedTestCaseRegistry object used to keep track of
+ // value-parameterized tests and instantiate and register them.
+ internal::ParameterizedTestCaseRegistry& parameterized_test_registry() {
+ return parameterized_test_registry_;
+ }
+#endif // GTEST_HAS_PARAM_TEST
+
+ // Sets the TestCase object for the test that's currently running.
+ void set_current_test_case(TestCase* a_current_test_case) {
+ current_test_case_ = a_current_test_case;
+ }
+
+ // Sets the TestInfo object for the test that's currently running. If
+ // current_test_info is NULL, the assertion results will be stored in
+ // ad_hoc_test_result_.
+ void set_current_test_info(TestInfo* a_current_test_info) {
+ current_test_info_ = a_current_test_info;
+ }
+
+ // Registers all parameterized tests defined using TEST_P and
+ // INSTANTIATE_TEST_CASE_P, creating regular tests for each test/parameter
+ // combination. This method can be called more then once; it has guards
+ // protecting from registering the tests more then once. If
+ // value-parameterized tests are disabled, RegisterParameterizedTests is
+ // present but does nothing.
+ void RegisterParameterizedTests();
+
+ // Runs all tests in this UnitTest object, prints the result, and
+ // returns true if all tests are successful. If any exception is
+ // thrown during a test, this test is considered to be failed, but
+ // the rest of the tests will still be run.
+ bool RunAllTests();
+
+ // Clears the results of all tests, except the ad hoc tests.
+ void ClearNonAdHocTestResult() {
+ ForEach(test_cases_, TestCase::ClearTestCaseResult);
+ }
+
+ // Clears the results of ad-hoc test assertions.
+ void ClearAdHocTestResult() {
+ ad_hoc_test_result_.Clear();
+ }
+
+ // Adds a TestProperty to the current TestResult object when invoked in a
+ // context of a test or a test case, or to the global property set. If the
+ // result already contains a property with the same key, the value will be
+ // updated.
+ void RecordProperty(const TestProperty& test_property);
+
+ enum ReactionToSharding {
+ HONOR_SHARDING_PROTOCOL,
+ IGNORE_SHARDING_PROTOCOL
+ };
+
+ // Matches the full name of each test against the user-specified
+ // filter to decide whether the test should run, then records the
+ // result in each TestCase and TestInfo object.
+ // If shard_tests == HONOR_SHARDING_PROTOCOL, further filters tests
+ // based on sharding variables in the environment.
+ // Returns the number of tests that should run.
+ int FilterTests(ReactionToSharding shard_tests);
+
+ // Prints the names of the tests matching the user-specified filter flag.
+ void ListTestsMatchingFilter();
+
+ const TestCase* current_test_case() const { return current_test_case_; }
+ TestInfo* current_test_info() { return current_test_info_; }
+ const TestInfo* current_test_info() const { return current_test_info_; }
+
+ // Returns the vector of environments that need to be set-up/torn-down
+ // before/after the tests are run.
+ std::vector<Environment*>& environments() { return environments_; }
+
+ // Getters for the per-thread Google Test trace stack.
+ std::vector<TraceInfo>& gtest_trace_stack() {
+ return *(gtest_trace_stack_.pointer());
+ }
+ const std::vector<TraceInfo>& gtest_trace_stack() const {
+ return gtest_trace_stack_.get();
+ }
+
+#if GTEST_HAS_DEATH_TEST
+ void InitDeathTestSubprocessControlInfo() {
+ internal_run_death_test_flag_.reset(ParseInternalRunDeathTestFlag());
+ }
+ // Returns a pointer to the parsed --gtest_internal_run_death_test
+ // flag, or NULL if that flag was not specified.
+ // This information is useful only in a death test child process.
+ // Must not be called before a call to InitGoogleTest.
+ const InternalRunDeathTestFlag* internal_run_death_test_flag() const {
+ return internal_run_death_test_flag_.get();
+ }
+
+ // Returns a pointer to the current death test factory.
+ internal::DeathTestFactory* death_test_factory() {
+ return death_test_factory_.get();
+ }
+
+ void SuppressTestEventsIfInSubprocess();
+
+ friend class ReplaceDeathTestFactory;
+#endif // GTEST_HAS_DEATH_TEST
+
+ // Initializes the event listener performing XML output as specified by
+ // UnitTestOptions. Must not be called before InitGoogleTest.
+ void ConfigureXmlOutput();
+
+#if GTEST_CAN_STREAM_RESULTS_
+ // Initializes the event listener for streaming test results to a socket.
+ // Must not be called before InitGoogleTest.
+ void ConfigureStreamingOutput();
+#endif
+
+ // Performs initialization dependent upon flag values obtained in
+ // ParseGoogleTestFlagsOnly. Is called from InitGoogleTest after the call to
+ // ParseGoogleTestFlagsOnly. In case a user neglects to call InitGoogleTest
+ // this function is also called from RunAllTests. Since this function can be
+ // called more than once, it has to be idempotent.
+ void PostFlagParsingInit();
+
+ // Gets the random seed used at the start of the current test iteration.
+ int random_seed() const { return random_seed_; }
+
+ // Gets the random number generator.
+ internal::Random* random() { return &random_; }
+
+ // Shuffles all test cases, and the tests within each test case,
+ // making sure that death tests are still run first.
+ void ShuffleTests();
+
+ // Restores the test cases and tests to their order before the first shuffle.
+ void UnshuffleTests();
+
+ // Returns the value of GTEST_FLAG(catch_exceptions) at the moment
+ // UnitTest::Run() starts.
+ bool catch_exceptions() const { return catch_exceptions_; }
+
+ private:
+ friend class ::testing::UnitTest;
+
+ // Used by UnitTest::Run() to capture the state of
+ // GTEST_FLAG(catch_exceptions) at the moment it starts.
+ void set_catch_exceptions(bool value) { catch_exceptions_ = value; }
+
+ // The UnitTest object that owns this implementation object.
+ UnitTest* const parent_;
+
+ // The working directory when the first TEST() or TEST_F() was
+ // executed.
+ internal::FilePath original_working_dir_;
+
+ // The default test part result reporters.
+ DefaultGlobalTestPartResultReporter default_global_test_part_result_reporter_;
+ DefaultPerThreadTestPartResultReporter
+ default_per_thread_test_part_result_reporter_;
+
+ // Points to (but doesn't own) the global test part result reporter.
+ TestPartResultReporterInterface* global_test_part_result_repoter_;
+
+ // Protects read and write access to global_test_part_result_reporter_.
+ internal::Mutex global_test_part_result_reporter_mutex_;
+
+ // Points to (but doesn't own) the per-thread test part result reporter.
+ internal::ThreadLocal<TestPartResultReporterInterface*>
+ per_thread_test_part_result_reporter_;
+
+ // The vector of environments that need to be set-up/torn-down
+ // before/after the tests are run.
+ std::vector<Environment*> environments_;
+
+ // The vector of TestCases in their original order. It owns the
+ // elements in the vector.
+ std::vector<TestCase*> test_cases_;
+
+ // Provides a level of indirection for the test case list to allow
+ // easy shuffling and restoring the test case order. The i-th
+ // element of this vector is the index of the i-th test case in the
+ // shuffled order.
+ std::vector<int> test_case_indices_;
+
+#if GTEST_HAS_PARAM_TEST
+ // ParameterizedTestRegistry object used to register value-parameterized
+ // tests.
+ internal::ParameterizedTestCaseRegistry parameterized_test_registry_;
+
+ // Indicates whether RegisterParameterizedTests() has been called already.
+ bool parameterized_tests_registered_;
+#endif // GTEST_HAS_PARAM_TEST
+
+ // Index of the last death test case registered. Initially -1.
+ int last_death_test_case_;
+
+ // This points to the TestCase for the currently running test. It
+ // changes as Google Test goes through one test case after another.
+ // When no test is running, this is set to NULL and Google Test
+ // stores assertion results in ad_hoc_test_result_. Initially NULL.
+ TestCase* current_test_case_;
+
+ // This points to the TestInfo for the currently running test. It
+ // changes as Google Test goes through one test after another. When
+ // no test is running, this is set to NULL and Google Test stores
+ // assertion results in ad_hoc_test_result_. Initially NULL.
+ TestInfo* current_test_info_;
+
+ // Normally, a user only writes assertions inside a TEST or TEST_F,
+ // or inside a function called by a TEST or TEST_F. Since Google
+ // Test keeps track of which test is current running, it can
+ // associate such an assertion with the test it belongs to.
+ //
+ // If an assertion is encountered when no TEST or TEST_F is running,
+ // Google Test attributes the assertion result to an imaginary "ad hoc"
+ // test, and records the result in ad_hoc_test_result_.
+ TestResult ad_hoc_test_result_;
+
+ // The list of event listeners that can be used to track events inside
+ // Google Test.
+ TestEventListeners listeners_;
+
+ // The OS stack trace getter. Will be deleted when the UnitTest
+ // object is destructed. By default, an OsStackTraceGetter is used,
+ // but the user can set this field to use a custom getter if that is
+ // desired.
+ OsStackTraceGetterInterface* os_stack_trace_getter_;
+
+ // True iff PostFlagParsingInit() has been called.
+ bool post_flag_parse_init_performed_;
+
+ // The random number seed used at the beginning of the test run.
+ int random_seed_;
+
+ // Our random number generator.
+ internal::Random random_;
+
+ // The time of the test program start, in ms from the start of the
+ // UNIX epoch.
+ TimeInMillis start_timestamp_;
+
+ // How long the test took to run, in milliseconds.
+ TimeInMillis elapsed_time_;
+
+#if GTEST_HAS_DEATH_TEST
+ // The decomposed components of the gtest_internal_run_death_test flag,
+ // parsed when RUN_ALL_TESTS is called.
+ internal::scoped_ptr<InternalRunDeathTestFlag> internal_run_death_test_flag_;
+ internal::scoped_ptr<internal::DeathTestFactory> death_test_factory_;
+#endif // GTEST_HAS_DEATH_TEST
+
+ // A per-thread stack of traces created by the SCOPED_TRACE() macro.
+ internal::ThreadLocal<std::vector<TraceInfo> > gtest_trace_stack_;
+
+ // The value of GTEST_FLAG(catch_exceptions) at the moment RunAllTests()
+ // starts.
+ bool catch_exceptions_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(UnitTestImpl);
+}; // class UnitTestImpl
+
+// Convenience function for accessing the global UnitTest
+// implementation object.
+inline UnitTestImpl* GetUnitTestImpl() {
+ return UnitTest::GetInstance()->impl();
+}
+
+#if GTEST_USES_SIMPLE_RE
+
+// Internal helper functions for implementing the simple regular
+// expression matcher.
+GTEST_API_ bool IsInSet(char ch, const char* str);
+GTEST_API_ bool IsAsciiDigit(char ch);
+GTEST_API_ bool IsAsciiPunct(char ch);
+GTEST_API_ bool IsRepeat(char ch);
+GTEST_API_ bool IsAsciiWhiteSpace(char ch);
+GTEST_API_ bool IsAsciiWordChar(char ch);
+GTEST_API_ bool IsValidEscape(char ch);
+GTEST_API_ bool AtomMatchesChar(bool escaped, char pattern, char ch);
+GTEST_API_ bool ValidateRegex(const char* regex);
+GTEST_API_ bool MatchRegexAtHead(const char* regex, const char* str);
+GTEST_API_ bool MatchRepetitionAndRegexAtHead(
+ bool escaped, char ch, char repeat, const char* regex, const char* str);
+GTEST_API_ bool MatchRegexAnywhere(const char* regex, const char* str);
+
+#endif // GTEST_USES_SIMPLE_RE
+
+// Parses the command line for Google Test flags, without initializing
+// other parts of Google Test.
+GTEST_API_ void ParseGoogleTestFlagsOnly(int* argc, char** argv);
+GTEST_API_ void ParseGoogleTestFlagsOnly(int* argc, wchar_t** argv);
+
+#if GTEST_HAS_DEATH_TEST
+
+// Returns the message describing the last system error, regardless of the
+// platform.
+GTEST_API_ std::string GetLastErrnoDescription();
+
+# if GTEST_OS_WINDOWS
+// Provides leak-safe Windows kernel handle ownership.
+class AutoHandle {
+ public:
+ AutoHandle() : handle_(INVALID_HANDLE_VALUE) {}
+ explicit AutoHandle(HANDLE handle) : handle_(handle) {}
+
+ ~AutoHandle() { Reset(); }
+
+ HANDLE Get() const { return handle_; }
+ void Reset() { Reset(INVALID_HANDLE_VALUE); }
+ void Reset(HANDLE handle) {
+ if (handle != handle_) {
+ if (handle_ != INVALID_HANDLE_VALUE)
+ ::CloseHandle(handle_);
+ handle_ = handle;
+ }
+ }
+
+ private:
+ HANDLE handle_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(AutoHandle);
+};
+# endif // GTEST_OS_WINDOWS
+
+// Attempts to parse a string into a positive integer pointed to by the
+// number parameter. Returns true if that is possible.
+// GTEST_HAS_DEATH_TEST implies that we have ::std::string, so we can use
+// it here.
+template <typename Integer>
+bool ParseNaturalNumber(const ::std::string& str, Integer* number) {
+ // Fail fast if the given string does not begin with a digit;
+ // this bypasses strtoXXX's "optional leading whitespace and plus
+ // or minus sign" semantics, which are undesirable here.
+ if (str.empty() || !IsDigit(str[0])) {
+ return false;
+ }
+ errno = 0;
+
+ char* end;
+ // BiggestConvertible is the largest integer type that system-provided
+ // string-to-number conversion routines can return.
+
+# if GTEST_OS_WINDOWS && !defined(__GNUC__)
+
+ // MSVC and C++ Builder define __int64 instead of the standard long long.
+ typedef unsigned __int64 BiggestConvertible;
+ const BiggestConvertible parsed = _strtoui64(str.c_str(), &end, 10);
+
+# else
+
+ typedef unsigned long long BiggestConvertible; // NOLINT
+ const BiggestConvertible parsed = strtoull(str.c_str(), &end, 10);
+
+# endif // GTEST_OS_WINDOWS && !defined(__GNUC__)
+
+ const bool parse_success = *end == '\0' && errno == 0;
+
+ // TODO(vladl at google.com): Convert this to compile time assertion when it is
+ // available.
+ GTEST_CHECK_(sizeof(Integer) <= sizeof(parsed));
+
+ const Integer result = static_cast<Integer>(parsed);
+ if (parse_success && static_cast<BiggestConvertible>(result) == parsed) {
+ *number = result;
+ return true;
+ }
+ return false;
+}
+#endif // GTEST_HAS_DEATH_TEST
+
+// TestResult contains some private methods that should be hidden from
+// Google Test user but are required for testing. This class allow our tests
+// to access them.
+//
+// This class is supplied only for the purpose of testing Google Test's own
+// constructs. Do not use it in user tests, either directly or indirectly.
+class TestResultAccessor {
+ public:
+ static void RecordProperty(TestResult* test_result,
+ const std::string& xml_element,
+ const TestProperty& property) {
+ test_result->RecordProperty(xml_element, property);
+ }
+
+ static void ClearTestPartResults(TestResult* test_result) {
+ test_result->ClearTestPartResults();
+ }
+
+ static const std::vector<testing::TestPartResult>& test_part_results(
+ const TestResult& test_result) {
+ return test_result.test_part_results();
+ }
+};
+
+#if GTEST_CAN_STREAM_RESULTS_
+
+// Streams test results to the given port on the given host machine.
+class StreamingListener : public EmptyTestEventListener {
+ public:
+ // Abstract base class for writing strings to a socket.
+ class AbstractSocketWriter {
+ public:
+ virtual ~AbstractSocketWriter() {}
+
+ // Sends a string to the socket.
+ virtual void Send(const string& message) = 0;
+
+ // Closes the socket.
+ virtual void CloseConnection() {}
+
+ // Sends a string and a newline to the socket.
+ void SendLn(const string& message) {
+ Send(message + "\n");
+ }
+ };
+
+ // Concrete class for actually writing strings to a socket.
+ class SocketWriter : public AbstractSocketWriter {
+ public:
+ SocketWriter(const string& host, const string& port)
+ : sockfd_(-1), host_name_(host), port_num_(port) {
+ MakeConnection();
+ }
+
+ virtual ~SocketWriter() {
+ if (sockfd_ != -1)
+ CloseConnection();
+ }
+
+ // Sends a string to the socket.
+ virtual void Send(const string& message) {
+ GTEST_CHECK_(sockfd_ != -1)
+ << "Send() can be called only when there is a connection.";
+
+ const int len = static_cast<int>(message.length());
+ if (write(sockfd_, message.c_str(), len) != len) {
+ GTEST_LOG_(WARNING)
+ << "stream_result_to: failed to stream to "
+ << host_name_ << ":" << port_num_;
+ }
+ }
+
+ private:
+ // Creates a client socket and connects to the server.
+ void MakeConnection();
+
+ // Closes the socket.
+ void CloseConnection() {
+ GTEST_CHECK_(sockfd_ != -1)
+ << "CloseConnection() can be called only when there is a connection.";
+
+ close(sockfd_);
+ sockfd_ = -1;
+ }
+
+ int sockfd_; // socket file descriptor
+ const string host_name_;
+ const string port_num_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(SocketWriter);
+ }; // class SocketWriter
+
+ // Escapes '=', '&', '%', and '\n' characters in str as "%xx".
+ static string UrlEncode(const char* str);
+
+ StreamingListener(const string& host, const string& port)
+ : socket_writer_(new SocketWriter(host, port)) { Start(); }
+
+ explicit StreamingListener(AbstractSocketWriter* socket_writer)
+ : socket_writer_(socket_writer) { Start(); }
+
+ void OnTestProgramStart(const UnitTest& /* unit_test */) {
+ SendLn("event=TestProgramStart");
+ }
+
+ void OnTestProgramEnd(const UnitTest& unit_test) {
+ // Note that Google Test current only report elapsed time for each
+ // test iteration, not for the entire test program.
+ SendLn("event=TestProgramEnd&passed=" + FormatBool(unit_test.Passed()));
+
+ // Notify the streaming server to stop.
+ socket_writer_->CloseConnection();
+ }
+
+ void OnTestIterationStart(const UnitTest& /* unit_test */, int iteration) {
+ SendLn("event=TestIterationStart&iteration=" +
+ StreamableToString(iteration));
+ }
+
+ void OnTestIterationEnd(const UnitTest& unit_test, int /* iteration */) {
+ SendLn("event=TestIterationEnd&passed=" +
+ FormatBool(unit_test.Passed()) + "&elapsed_time=" +
+ StreamableToString(unit_test.elapsed_time()) + "ms");
+ }
+
+ void OnTestCaseStart(const TestCase& test_case) {
+ SendLn(std::string("event=TestCaseStart&name=") + test_case.name());
+ }
+
+ void OnTestCaseEnd(const TestCase& test_case) {
+ SendLn("event=TestCaseEnd&passed=" + FormatBool(test_case.Passed())
+ + "&elapsed_time=" + StreamableToString(test_case.elapsed_time())
+ + "ms");
+ }
+
+ void OnTestStart(const TestInfo& test_info) {
+ SendLn(std::string("event=TestStart&name=") + test_info.name());
+ }
+
+ void OnTestEnd(const TestInfo& test_info) {
+ SendLn("event=TestEnd&passed=" +
+ FormatBool((test_info.result())->Passed()) +
+ "&elapsed_time=" +
+ StreamableToString((test_info.result())->elapsed_time()) + "ms");
+ }
+
+ void OnTestPartResult(const TestPartResult& test_part_result) {
+ const char* file_name = test_part_result.file_name();
+ if (file_name == NULL)
+ file_name = "";
+ SendLn("event=TestPartResult&file=" + UrlEncode(file_name) +
+ "&line=" + StreamableToString(test_part_result.line_number()) +
+ "&message=" + UrlEncode(test_part_result.message()));
+ }
+
+ private:
+ // Sends the given message and a newline to the socket.
+ void SendLn(const string& message) { socket_writer_->SendLn(message); }
+
+ // Called at the start of streaming to notify the receiver what
+ // protocol we are using.
+ void Start() { SendLn("gtest_streaming_protocol_version=1.0"); }
+
+ string FormatBool(bool value) { return value ? "1" : "0"; }
+
+ const scoped_ptr<AbstractSocketWriter> socket_writer_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(StreamingListener);
+}; // class StreamingListener
+
+#endif // GTEST_CAN_STREAM_RESULTS_
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_SRC_GTEST_INTERNAL_INL_H_
+#undef GTEST_IMPLEMENTATION_
+
+#if GTEST_OS_WINDOWS
+# define vsnprintf _vsnprintf
+#endif // GTEST_OS_WINDOWS
+
+namespace testing {
+
+using internal::CountIf;
+using internal::ForEach;
+using internal::GetElementOr;
+using internal::Shuffle;
+
+// Constants.
+
+// A test whose test case name or test name matches this filter is
+// disabled and not run.
+static const char kDisableTestFilter[] = "DISABLED_*:*/DISABLED_*";
+
+// A test case whose name matches this filter is considered a death
+// test case and will be run before test cases whose name doesn't
+// match this filter.
+static const char kDeathTestCaseFilter[] = "*DeathTest:*DeathTest/*";
+
+// A test filter that matches everything.
+static const char kUniversalFilter[] = "*";
+
+// The default output file for XML output.
+static const char kDefaultOutputFile[] = "test_detail.xml";
+
+// The environment variable name for the test shard index.
+static const char kTestShardIndex[] = "GTEST_SHARD_INDEX";
+// The environment variable name for the total number of test shards.
+static const char kTestTotalShards[] = "GTEST_TOTAL_SHARDS";
+// The environment variable name for the test shard status file.
+static const char kTestShardStatusFile[] = "GTEST_SHARD_STATUS_FILE";
+
+namespace internal {
+
+// The text used in failure messages to indicate the start of the
+// stack trace.
+const char kStackTraceMarker[] = "\nStack trace:\n";
+
+// g_help_flag is true iff the --help flag or an equivalent form is
+// specified on the command line.
+bool g_help_flag = false;
+
+} // namespace internal
+
+static const char* GetDefaultFilter() {
+ return kUniversalFilter;
+}
+
+GTEST_DEFINE_bool_(
+ also_run_disabled_tests,
+ internal::BoolFromGTestEnv("also_run_disabled_tests", false),
+ "Run disabled tests too, in addition to the tests normally being run.");
+
+GTEST_DEFINE_bool_(
+ break_on_failure,
+ internal::BoolFromGTestEnv("break_on_failure", false),
+ "True iff a failed assertion should be a debugger break-point.");
+
+GTEST_DEFINE_bool_(
+ catch_exceptions,
+ internal::BoolFromGTestEnv("catch_exceptions", true),
+ "True iff " GTEST_NAME_
+ " should catch exceptions and treat them as test failures.");
+
+GTEST_DEFINE_string_(
+ color,
+ internal::StringFromGTestEnv("color", "auto"),
+ "Whether to use colors in the output. Valid values: yes, no, "
+ "and auto. 'auto' means to use colors if the output is "
+ "being sent to a terminal and the TERM environment variable "
+ "is set to a terminal type that supports colors.");
+
+GTEST_DEFINE_string_(
+ filter,
+ internal::StringFromGTestEnv("filter", GetDefaultFilter()),
+ "A colon-separated list of glob (not regex) patterns "
+ "for filtering the tests to run, optionally followed by a "
+ "'-' and a : separated list of negative patterns (tests to "
+ "exclude). A test is run if it matches one of the positive "
+ "patterns and does not match any of the negative patterns.");
+
+GTEST_DEFINE_bool_(list_tests, false,
+ "List all tests without running them.");
+
+GTEST_DEFINE_string_(
+ output,
+ internal::StringFromGTestEnv("output", ""),
+ "A format (currently must be \"xml\"), optionally followed "
+ "by a colon and an output file name or directory. A directory "
+ "is indicated by a trailing pathname separator. "
+ "Examples: \"xml:filename.xml\", \"xml::directoryname/\". "
+ "If a directory is specified, output files will be created "
+ "within that directory, with file-names based on the test "
+ "executable's name and, if necessary, made unique by adding "
+ "digits.");
+
+GTEST_DEFINE_bool_(
+ print_time,
+ internal::BoolFromGTestEnv("print_time", true),
+ "True iff " GTEST_NAME_
+ " should display elapsed time in text output.");
+
+GTEST_DEFINE_int32_(
+ random_seed,
+ internal::Int32FromGTestEnv("random_seed", 0),
+ "Random number seed to use when shuffling test orders. Must be in range "
+ "[1, 99999], or 0 to use a seed based on the current time.");
+
+GTEST_DEFINE_int32_(
+ repeat,
+ internal::Int32FromGTestEnv("repeat", 1),
+ "How many times to repeat each test. Specify a negative number "
+ "for repeating forever. Useful for shaking out flaky tests.");
+
+GTEST_DEFINE_bool_(
+ show_internal_stack_frames, false,
+ "True iff " GTEST_NAME_ " should include internal stack frames when "
+ "printing test failure stack traces.");
+
+GTEST_DEFINE_bool_(
+ shuffle,
+ internal::BoolFromGTestEnv("shuffle", false),
+ "True iff " GTEST_NAME_
+ " should randomize tests' order on every run.");
+
+GTEST_DEFINE_int32_(
+ stack_trace_depth,
+ internal::Int32FromGTestEnv("stack_trace_depth", kMaxStackTraceDepth),
+ "The maximum number of stack frames to print when an "
+ "assertion fails. The valid range is 0 through 100, inclusive.");
+
+GTEST_DEFINE_string_(
+ stream_result_to,
+ internal::StringFromGTestEnv("stream_result_to", ""),
+ "This flag specifies the host name and the port number on which to stream "
+ "test results. Example: \"localhost:555\". The flag is effective only on "
+ "Linux.");
+
+GTEST_DEFINE_bool_(
+ throw_on_failure,
+ internal::BoolFromGTestEnv("throw_on_failure", false),
+ "When this flag is specified, a failed assertion will throw an exception "
+ "if exceptions are enabled or exit the program with a non-zero code "
+ "otherwise.");
+
+namespace internal {
+
+// Generates a random number from [0, range), using a Linear
+// Congruential Generator (LCG). Crashes if 'range' is 0 or greater
+// than kMaxRange.
+UInt32 Random::Generate(UInt32 range) {
+ // These constants are the same as are used in glibc's rand(3).
+ state_ = (1103515245U*state_ + 12345U) % kMaxRange;
+
+ GTEST_CHECK_(range > 0)
+ << "Cannot generate a number in the range [0, 0).";
+ GTEST_CHECK_(range <= kMaxRange)
+ << "Generation of a number in [0, " << range << ") was requested, "
+ << "but this can only generate numbers in [0, " << kMaxRange << ").";
+
+ // Converting via modulus introduces a bit of downward bias, but
+ // it's simple, and a linear congruential generator isn't too good
+ // to begin with.
+ return state_ % range;
+}
+
+// GTestIsInitialized() returns true iff the user has initialized
+// Google Test. Useful for catching the user mistake of not initializing
+// Google Test before calling RUN_ALL_TESTS().
+//
+// A user must call testing::InitGoogleTest() to initialize Google
+// Test. g_init_gtest_count is set to the number of times
+// InitGoogleTest() has been called. We don't protect this variable
+// under a mutex as it is only accessed in the main thread.
+GTEST_API_ int g_init_gtest_count = 0;
+static bool GTestIsInitialized() { return g_init_gtest_count != 0; }
+
+// Iterates over a vector of TestCases, keeping a running sum of the
+// results of calling a given int-returning method on each.
+// Returns the sum.
+static int SumOverTestCaseList(const std::vector<TestCase*>& case_list,
+ int (TestCase::*method)() const) {
+ int sum = 0;
+ for (size_t i = 0; i < case_list.size(); i++) {
+ sum += (case_list[i]->*method)();
+ }
+ return sum;
+}
+
+// Returns true iff the test case passed.
+static bool TestCasePassed(const TestCase* test_case) {
+ return test_case->should_run() && test_case->Passed();
+}
+
+// Returns true iff the test case failed.
+static bool TestCaseFailed(const TestCase* test_case) {
+ return test_case->should_run() && test_case->Failed();
+}
+
+// Returns true iff test_case contains at least one test that should
+// run.
+static bool ShouldRunTestCase(const TestCase* test_case) {
+ return test_case->should_run();
+}
+
+// AssertHelper constructor.
+AssertHelper::AssertHelper(TestPartResult::Type type,
+ const char* file,
+ int line,
+ const char* message)
+ : data_(new AssertHelperData(type, file, line, message)) {
+}
+
+AssertHelper::~AssertHelper() {
+ delete data_;
+}
+
+// Message assignment, for assertion streaming support.
+void AssertHelper::operator=(const Message& message) const {
+ UnitTest::GetInstance()->
+ AddTestPartResult(data_->type, data_->file, data_->line,
+ AppendUserMessage(data_->message, message),
+ UnitTest::GetInstance()->impl()
+ ->CurrentOsStackTraceExceptTop(1)
+ // Skips the stack frame for this function itself.
+ ); // NOLINT
+}
+
+// Mutex for linked pointers.
+GTEST_API_ GTEST_DEFINE_STATIC_MUTEX_(g_linked_ptr_mutex);
+
+// Application pathname gotten in InitGoogleTest.
+std::string g_executable_path;
+
+// Returns the current application's name, removing directory path if that
+// is present.
+FilePath GetCurrentExecutableName() {
+ FilePath result;
+
+#if GTEST_OS_WINDOWS
+ result.Set(FilePath(g_executable_path).RemoveExtension("exe"));
+#else
+ result.Set(FilePath(g_executable_path));
+#endif // GTEST_OS_WINDOWS
+
+ return result.RemoveDirectoryName();
+}
+
+// Functions for processing the gtest_output flag.
+
+// Returns the output format, or "" for normal printed output.
+std::string UnitTestOptions::GetOutputFormat() {
+ const char* const gtest_output_flag = GTEST_FLAG(output).c_str();
+ if (gtest_output_flag == NULL) return std::string("");
+
+ const char* const colon = strchr(gtest_output_flag, ':');
+ return (colon == NULL) ?
+ std::string(gtest_output_flag) :
+ std::string(gtest_output_flag, colon - gtest_output_flag);
+}
+
+// Returns the name of the requested output file, or the default if none
+// was explicitly specified.
+std::string UnitTestOptions::GetAbsolutePathToOutputFile() {
+ const char* const gtest_output_flag = GTEST_FLAG(output).c_str();
+ if (gtest_output_flag == NULL)
+ return "";
+
+ const char* const colon = strchr(gtest_output_flag, ':');
+ if (colon == NULL)
+ return internal::FilePath::ConcatPaths(
+ internal::FilePath(
+ UnitTest::GetInstance()->original_working_dir()),
+ internal::FilePath(kDefaultOutputFile)).string();
+
+ internal::FilePath output_name(colon + 1);
+ if (!output_name.IsAbsolutePath())
+ // TODO(wan at google.com): on Windows \some\path is not an absolute
+ // path (as its meaning depends on the current drive), yet the
+ // following logic for turning it into an absolute path is wrong.
+ // Fix it.
+ output_name = internal::FilePath::ConcatPaths(
+ internal::FilePath(UnitTest::GetInstance()->original_working_dir()),
+ internal::FilePath(colon + 1));
+
+ if (!output_name.IsDirectory())
+ return output_name.string();
+
+ internal::FilePath result(internal::FilePath::GenerateUniqueFileName(
+ output_name, internal::GetCurrentExecutableName(),
+ GetOutputFormat().c_str()));
+ return result.string();
+}
+
+// Returns true iff the wildcard pattern matches the string. The
+// first ':' or '\0' character in pattern marks the end of it.
+//
+// This recursive algorithm isn't very efficient, but is clear and
+// works well enough for matching test names, which are short.
+bool UnitTestOptions::PatternMatchesString(const char *pattern,
+ const char *str) {
+ switch (*pattern) {
+ case '\0':
+ case ':': // Either ':' or '\0' marks the end of the pattern.
+ return *str == '\0';
+ case '?': // Matches any single character.
+ return *str != '\0' && PatternMatchesString(pattern + 1, str + 1);
+ case '*': // Matches any string (possibly empty) of characters.
+ return (*str != '\0' && PatternMatchesString(pattern, str + 1)) ||
+ PatternMatchesString(pattern + 1, str);
+ default: // Non-special character. Matches itself.
+ return *pattern == *str &&
+ PatternMatchesString(pattern + 1, str + 1);
+ }
+}
+
+bool UnitTestOptions::MatchesFilter(
+ const std::string& name, const char* filter) {
+ const char *cur_pattern = filter;
+ for (;;) {
+ if (PatternMatchesString(cur_pattern, name.c_str())) {
+ return true;
+ }
+
+ // Finds the next pattern in the filter.
+ cur_pattern = strchr(cur_pattern, ':');
+
+ // Returns if no more pattern can be found.
+ if (cur_pattern == NULL) {
+ return false;
+ }
+
+ // Skips the pattern separater (the ':' character).
+ cur_pattern++;
+ }
+}
+
+// Returns true iff the user-specified filter matches the test case
+// name and the test name.
+bool UnitTestOptions::FilterMatchesTest(const std::string &test_case_name,
+ const std::string &test_name) {
+ const std::string& full_name = test_case_name + "." + test_name.c_str();
+
+ // Split --gtest_filter at '-', if there is one, to separate into
+ // positive filter and negative filter portions
+ const char* const p = GTEST_FLAG(filter).c_str();
+ const char* const dash = strchr(p, '-');
+ std::string positive;
+ std::string negative;
+ if (dash == NULL) {
+ positive = GTEST_FLAG(filter).c_str(); // Whole string is a positive filter
+ negative = "";
+ } else {
+ positive = std::string(p, dash); // Everything up to the dash
+ negative = std::string(dash + 1); // Everything after the dash
+ if (positive.empty()) {
+ // Treat '-test1' as the same as '*-test1'
+ positive = kUniversalFilter;
+ }
+ }
+
+ // A filter is a colon-separated list of patterns. It matches a
+ // test if any pattern in it matches the test.
+ return (MatchesFilter(full_name, positive.c_str()) &&
+ !MatchesFilter(full_name, negative.c_str()));
+}
+
+#if GTEST_HAS_SEH
+// Returns EXCEPTION_EXECUTE_HANDLER if Google Test should handle the
+// given SEH exception, or EXCEPTION_CONTINUE_SEARCH otherwise.
+// This function is useful as an __except condition.
+int UnitTestOptions::GTestShouldProcessSEH(DWORD exception_code) {
+ // Google Test should handle a SEH exception if:
+ // 1. the user wants it to, AND
+ // 2. this is not a breakpoint exception, AND
+ // 3. this is not a C++ exception (VC++ implements them via SEH,
+ // apparently).
+ //
+ // SEH exception code for C++ exceptions.
+ // (see http://support.microsoft.com/kb/185294 for more information).
+ const DWORD kCxxExceptionCode = 0xe06d7363;
+
+ bool should_handle = true;
+
+ if (!GTEST_FLAG(catch_exceptions))
+ should_handle = false;
+ else if (exception_code == EXCEPTION_BREAKPOINT)
+ should_handle = false;
+ else if (exception_code == kCxxExceptionCode)
+ should_handle = false;
+
+ return should_handle ? EXCEPTION_EXECUTE_HANDLER : EXCEPTION_CONTINUE_SEARCH;
+}
+#endif // GTEST_HAS_SEH
+
+} // namespace internal
+
+// The c'tor sets this object as the test part result reporter used by
+// Google Test. The 'result' parameter specifies where to report the
+// results. Intercepts only failures from the current thread.
+ScopedFakeTestPartResultReporter::ScopedFakeTestPartResultReporter(
+ TestPartResultArray* result)
+ : intercept_mode_(INTERCEPT_ONLY_CURRENT_THREAD),
+ result_(result) {
+ Init();
+}
+
+// The c'tor sets this object as the test part result reporter used by
+// Google Test. The 'result' parameter specifies where to report the
+// results.
+ScopedFakeTestPartResultReporter::ScopedFakeTestPartResultReporter(
+ InterceptMode intercept_mode, TestPartResultArray* result)
+ : intercept_mode_(intercept_mode),
+ result_(result) {
+ Init();
+}
+
+void ScopedFakeTestPartResultReporter::Init() {
+ internal::UnitTestImpl* const impl = internal::GetUnitTestImpl();
+ if (intercept_mode_ == INTERCEPT_ALL_THREADS) {
+ old_reporter_ = impl->GetGlobalTestPartResultReporter();
+ impl->SetGlobalTestPartResultReporter(this);
+ } else {
+ old_reporter_ = impl->GetTestPartResultReporterForCurrentThread();
+ impl->SetTestPartResultReporterForCurrentThread(this);
+ }
+}
+
+// The d'tor restores the test part result reporter used by Google Test
+// before.
+ScopedFakeTestPartResultReporter::~ScopedFakeTestPartResultReporter() {
+ internal::UnitTestImpl* const impl = internal::GetUnitTestImpl();
+ if (intercept_mode_ == INTERCEPT_ALL_THREADS) {
+ impl->SetGlobalTestPartResultReporter(old_reporter_);
+ } else {
+ impl->SetTestPartResultReporterForCurrentThread(old_reporter_);
+ }
+}
+
+// Increments the test part result count and remembers the result.
+// This method is from the TestPartResultReporterInterface interface.
+void ScopedFakeTestPartResultReporter::ReportTestPartResult(
+ const TestPartResult& result) {
+ result_->Append(result);
+}
+
+namespace internal {
+
+// Returns the type ID of ::testing::Test. We should always call this
+// instead of GetTypeId< ::testing::Test>() to get the type ID of
+// testing::Test. This is to work around a suspected linker bug when
+// using Google Test as a framework on Mac OS X. The bug causes
+// GetTypeId< ::testing::Test>() to return different values depending
+// on whether the call is from the Google Test framework itself or
+// from user test code. GetTestTypeId() is guaranteed to always
+// return the same value, as it always calls GetTypeId<>() from the
+// gtest.cc, which is within the Google Test framework.
+TypeId GetTestTypeId() {
+ return GetTypeId<Test>();
+}
+
+// The value of GetTestTypeId() as seen from within the Google Test
+// library. This is solely for testing GetTestTypeId().
+extern const TypeId kTestTypeIdInGoogleTest = GetTestTypeId();
+
+// This predicate-formatter checks that 'results' contains a test part
+// failure of the given type and that the failure message contains the
+// given substring.
+AssertionResult HasOneFailure(const char* /* results_expr */,
+ const char* /* type_expr */,
+ const char* /* substr_expr */,
+ const TestPartResultArray& results,
+ TestPartResult::Type type,
+ const string& substr) {
+ const std::string expected(type == TestPartResult::kFatalFailure ?
+ "1 fatal failure" :
+ "1 non-fatal failure");
+ Message msg;
+ if (results.size() != 1) {
+ msg << "Expected: " << expected << "\n"
+ << " Actual: " << results.size() << " failures";
+ for (int i = 0; i < results.size(); i++) {
+ msg << "\n" << results.GetTestPartResult(i);
+ }
+ return AssertionFailure() << msg;
+ }
+
+ const TestPartResult& r = results.GetTestPartResult(0);
+ if (r.type() != type) {
+ return AssertionFailure() << "Expected: " << expected << "\n"
+ << " Actual:\n"
+ << r;
+ }
+
+ if (strstr(r.message(), substr.c_str()) == NULL) {
+ return AssertionFailure() << "Expected: " << expected << " containing \""
+ << substr << "\"\n"
+ << " Actual:\n"
+ << r;
+ }
+
+ return AssertionSuccess();
+}
+
+// The constructor of SingleFailureChecker remembers where to look up
+// test part results, what type of failure we expect, and what
+// substring the failure message should contain.
+SingleFailureChecker:: SingleFailureChecker(
+ const TestPartResultArray* results,
+ TestPartResult::Type type,
+ const string& substr)
+ : results_(results),
+ type_(type),
+ substr_(substr) {}
+
+// The destructor of SingleFailureChecker verifies that the given
+// TestPartResultArray contains exactly one failure that has the given
+// type and contains the given substring. If that's not the case, a
+// non-fatal failure will be generated.
+SingleFailureChecker::~SingleFailureChecker() {
+ EXPECT_PRED_FORMAT3(HasOneFailure, *results_, type_, substr_);
+}
+
+DefaultGlobalTestPartResultReporter::DefaultGlobalTestPartResultReporter(
+ UnitTestImpl* unit_test) : unit_test_(unit_test) {}
+
+void DefaultGlobalTestPartResultReporter::ReportTestPartResult(
+ const TestPartResult& result) {
+ unit_test_->current_test_result()->AddTestPartResult(result);
+ unit_test_->listeners()->repeater()->OnTestPartResult(result);
+}
+
+DefaultPerThreadTestPartResultReporter::DefaultPerThreadTestPartResultReporter(
+ UnitTestImpl* unit_test) : unit_test_(unit_test) {}
+
+void DefaultPerThreadTestPartResultReporter::ReportTestPartResult(
+ const TestPartResult& result) {
+ unit_test_->GetGlobalTestPartResultReporter()->ReportTestPartResult(result);
+}
+
+// Returns the global test part result reporter.
+TestPartResultReporterInterface*
+UnitTestImpl::GetGlobalTestPartResultReporter() {
+ internal::MutexLock lock(&global_test_part_result_reporter_mutex_);
+ return global_test_part_result_repoter_;
+}
+
+// Sets the global test part result reporter.
+void UnitTestImpl::SetGlobalTestPartResultReporter(
+ TestPartResultReporterInterface* reporter) {
+ internal::MutexLock lock(&global_test_part_result_reporter_mutex_);
+ global_test_part_result_repoter_ = reporter;
+}
+
+// Returns the test part result reporter for the current thread.
+TestPartResultReporterInterface*
+UnitTestImpl::GetTestPartResultReporterForCurrentThread() {
+ return per_thread_test_part_result_reporter_.get();
+}
+
+// Sets the test part result reporter for the current thread.
+void UnitTestImpl::SetTestPartResultReporterForCurrentThread(
+ TestPartResultReporterInterface* reporter) {
+ per_thread_test_part_result_reporter_.set(reporter);
+}
+
+// Gets the number of successful test cases.
+int UnitTestImpl::successful_test_case_count() const {
+ return CountIf(test_cases_, TestCasePassed);
+}
+
+// Gets the number of failed test cases.
+int UnitTestImpl::failed_test_case_count() const {
+ return CountIf(test_cases_, TestCaseFailed);
+}
+
+// Gets the number of all test cases.
+int UnitTestImpl::total_test_case_count() const {
+ return static_cast<int>(test_cases_.size());
+}
+
+// Gets the number of all test cases that contain at least one test
+// that should run.
+int UnitTestImpl::test_case_to_run_count() const {
+ return CountIf(test_cases_, ShouldRunTestCase);
+}
+
+// Gets the number of successful tests.
+int UnitTestImpl::successful_test_count() const {
+ return SumOverTestCaseList(test_cases_, &TestCase::successful_test_count);
+}
+
+// Gets the number of failed tests.
+int UnitTestImpl::failed_test_count() const {
+ return SumOverTestCaseList(test_cases_, &TestCase::failed_test_count);
+}
+
+// Gets the number of disabled tests that will be reported in the XML report.
+int UnitTestImpl::reportable_disabled_test_count() const {
+ return SumOverTestCaseList(test_cases_,
+ &TestCase::reportable_disabled_test_count);
+}
+
+// Gets the number of disabled tests.
+int UnitTestImpl::disabled_test_count() const {
+ return SumOverTestCaseList(test_cases_, &TestCase::disabled_test_count);
+}
+
+// Gets the number of tests to be printed in the XML report.
+int UnitTestImpl::reportable_test_count() const {
+ return SumOverTestCaseList(test_cases_, &TestCase::reportable_test_count);
+}
+
+// Gets the number of all tests.
+int UnitTestImpl::total_test_count() const {
+ return SumOverTestCaseList(test_cases_, &TestCase::total_test_count);
+}
+
+// Gets the number of tests that should run.
+int UnitTestImpl::test_to_run_count() const {
+ return SumOverTestCaseList(test_cases_, &TestCase::test_to_run_count);
+}
+
+// Returns the current OS stack trace as an std::string.
+//
+// The maximum number of stack frames to be included is specified by
+// the gtest_stack_trace_depth flag. The skip_count parameter
+// specifies the number of top frames to be skipped, which doesn't
+// count against the number of frames to be included.
+//
+// For example, if Foo() calls Bar(), which in turn calls
+// CurrentOsStackTraceExceptTop(1), Foo() will be included in the
+// trace but Bar() and CurrentOsStackTraceExceptTop() won't.
+std::string UnitTestImpl::CurrentOsStackTraceExceptTop(int skip_count) {
+ (void)skip_count;
+ return "";
+}
+
+// Returns the current time in milliseconds.
+TimeInMillis GetTimeInMillis() {
+#if GTEST_OS_WINDOWS_MOBILE || defined(__BORLANDC__)
+ // Difference between 1970-01-01 and 1601-01-01 in milliseconds.
+ // http://analogous.blogspot.com/2005/04/epoch.html
+ const TimeInMillis kJavaEpochToWinFileTimeDelta =
+ static_cast<TimeInMillis>(116444736UL) * 100000UL;
+ const DWORD kTenthMicrosInMilliSecond = 10000;
+
+ SYSTEMTIME now_systime;
+ FILETIME now_filetime;
+ ULARGE_INTEGER now_int64;
+ // TODO(kenton at google.com): Shouldn't this just use
+ // GetSystemTimeAsFileTime()?
+ GetSystemTime(&now_systime);
+ if (SystemTimeToFileTime(&now_systime, &now_filetime)) {
+ now_int64.LowPart = now_filetime.dwLowDateTime;
+ now_int64.HighPart = now_filetime.dwHighDateTime;
+ now_int64.QuadPart = (now_int64.QuadPart / kTenthMicrosInMilliSecond) -
+ kJavaEpochToWinFileTimeDelta;
+ return now_int64.QuadPart;
+ }
+ return 0;
+#elif GTEST_OS_WINDOWS && !GTEST_HAS_GETTIMEOFDAY_
+ __timeb64 now;
+
+# ifdef _MSC_VER
+
+ // MSVC 8 deprecates _ftime64(), so we want to suppress warning 4996
+ // (deprecated function) there.
+ // TODO(kenton at google.com): Use GetTickCount()? Or use
+ // SystemTimeToFileTime()
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4996) // Temporarily disables warning 4996.
+ _ftime64(&now);
+# pragma warning(pop) // Restores the warning state.
+# else
+
+ _ftime64(&now);
+
+# endif // _MSC_VER
+
+ return static_cast<TimeInMillis>(now.time) * 1000 + now.millitm;
+#elif GTEST_HAS_GETTIMEOFDAY_
+ struct timeval now;
+ gettimeofday(&now, NULL);
+ return static_cast<TimeInMillis>(now.tv_sec) * 1000 + now.tv_usec / 1000;
+#else
+# error "Don't know how to get the current time on your system."
+#endif
+}
+
+// Utilities
+
+// class String.
+
+#if GTEST_OS_WINDOWS_MOBILE
+// Creates a UTF-16 wide string from the given ANSI string, allocating
+// memory using new. The caller is responsible for deleting the return
+// value using delete[]. Returns the wide string, or NULL if the
+// input is NULL.
+LPCWSTR String::AnsiToUtf16(const char* ansi) {
+ if (!ansi) return NULL;
+ const int length = strlen(ansi);
+ const int unicode_length =
+ MultiByteToWideChar(CP_ACP, 0, ansi, length,
+ NULL, 0);
+ WCHAR* unicode = new WCHAR[unicode_length + 1];
+ MultiByteToWideChar(CP_ACP, 0, ansi, length,
+ unicode, unicode_length);
+ unicode[unicode_length] = 0;
+ return unicode;
+}
+
+// Creates an ANSI string from the given wide string, allocating
+// memory using new. The caller is responsible for deleting the return
+// value using delete[]. Returns the ANSI string, or NULL if the
+// input is NULL.
+const char* String::Utf16ToAnsi(LPCWSTR utf16_str) {
+ if (!utf16_str) return NULL;
+ const int ansi_length =
+ WideCharToMultiByte(CP_ACP, 0, utf16_str, -1,
+ NULL, 0, NULL, NULL);
+ char* ansi = new char[ansi_length + 1];
+ WideCharToMultiByte(CP_ACP, 0, utf16_str, -1,
+ ansi, ansi_length, NULL, NULL);
+ ansi[ansi_length] = 0;
+ return ansi;
+}
+
+#endif // GTEST_OS_WINDOWS_MOBILE
+
+// Compares two C strings. Returns true iff they have the same content.
+//
+// Unlike strcmp(), this function can handle NULL argument(s). A NULL
+// C string is considered different to any non-NULL C string,
+// including the empty string.
+bool String::CStringEquals(const char * lhs, const char * rhs) {
+ if ( lhs == NULL ) return rhs == NULL;
+
+ if ( rhs == NULL ) return false;
+
+ return strcmp(lhs, rhs) == 0;
+}
+
+#if GTEST_HAS_STD_WSTRING || GTEST_HAS_GLOBAL_WSTRING
+
+// Converts an array of wide chars to a narrow string using the UTF-8
+// encoding, and streams the result to the given Message object.
+static void StreamWideCharsToMessage(const wchar_t* wstr, size_t length,
+ Message* msg) {
+ for (size_t i = 0; i != length; ) { // NOLINT
+ if (wstr[i] != L'\0') {
+ *msg << WideStringToUtf8(wstr + i, static_cast<int>(length - i));
+ while (i != length && wstr[i] != L'\0')
+ i++;
+ } else {
+ *msg << '\0';
+ i++;
+ }
+ }
+}
+
+#endif // GTEST_HAS_STD_WSTRING || GTEST_HAS_GLOBAL_WSTRING
+
+} // namespace internal
+
+// Constructs an empty Message.
+// We allocate the stringstream separately because otherwise each use of
+// ASSERT/EXPECT in a procedure adds over 200 bytes to the procedure's
+// stack frame leading to huge stack frames in some cases; gcc does not reuse
+// the stack space.
+Message::Message() : ss_(new ::std::stringstream) {
+ // By default, we want there to be enough precision when printing
+ // a double to a Message.
+ *ss_ << std::setprecision(std::numeric_limits<double>::digits10 + 2);
+}
+
+// These two overloads allow streaming a wide C string to a Message
+// using the UTF-8 encoding.
+Message& Message::operator <<(const wchar_t* wide_c_str) {
+ return *this << internal::String::ShowWideCString(wide_c_str);
+}
+Message& Message::operator <<(wchar_t* wide_c_str) {
+ return *this << internal::String::ShowWideCString(wide_c_str);
+}
+
+#if GTEST_HAS_STD_WSTRING
+// Converts the given wide string to a narrow string using the UTF-8
+// encoding, and streams the result to this Message object.
+Message& Message::operator <<(const ::std::wstring& wstr) {
+ internal::StreamWideCharsToMessage(wstr.c_str(), wstr.length(), this);
+ return *this;
+}
+#endif // GTEST_HAS_STD_WSTRING
+
+#if GTEST_HAS_GLOBAL_WSTRING
+// Converts the given wide string to a narrow string using the UTF-8
+// encoding, and streams the result to this Message object.
+Message& Message::operator <<(const ::wstring& wstr) {
+ internal::StreamWideCharsToMessage(wstr.c_str(), wstr.length(), this);
+ return *this;
+}
+#endif // GTEST_HAS_GLOBAL_WSTRING
+
+// Gets the text streamed to this object so far as an std::string.
+// Each '\0' character in the buffer is replaced with "\\0".
+std::string Message::GetString() const {
+ return internal::StringStreamToString(ss_.get());
+}
+
+// AssertionResult constructors.
+// Used in EXPECT_TRUE/FALSE(assertion_result).
+AssertionResult::AssertionResult(const AssertionResult& other)
+ : success_(other.success_),
+ message_(other.message_.get() != NULL ?
+ new ::std::string(*other.message_) :
+ static_cast< ::std::string*>(NULL)) {
+}
+
+// Returns the assertion's negation. Used with EXPECT/ASSERT_FALSE.
+AssertionResult AssertionResult::operator!() const {
+ AssertionResult negation(!success_);
+ if (message_.get() != NULL)
+ negation << *message_;
+ return negation;
+}
+
+// Makes a successful assertion result.
+AssertionResult AssertionSuccess() {
+ return AssertionResult(true);
+}
+
+// Makes a failed assertion result.
+AssertionResult AssertionFailure() {
+ return AssertionResult(false);
+}
+
+// Makes a failed assertion result with the given failure message.
+// Deprecated; use AssertionFailure() << message.
+AssertionResult AssertionFailure(const Message& message) {
+ return AssertionFailure() << message;
+}
+
+namespace internal {
+
+// Constructs and returns the message for an equality assertion
+// (e.g. ASSERT_EQ, EXPECT_STREQ, etc) failure.
+//
+// The first four parameters are the expressions used in the assertion
+// and their values, as strings. For example, for ASSERT_EQ(foo, bar)
+// where foo is 5 and bar is 6, we have:
+//
+// expected_expression: "foo"
+// actual_expression: "bar"
+// expected_value: "5"
+// actual_value: "6"
+//
+// The ignoring_case parameter is true iff the assertion is a
+// *_STRCASEEQ*. When it's true, the string " (ignoring case)" will
+// be inserted into the message.
+AssertionResult EqFailure(const char* expected_expression,
+ const char* actual_expression,
+ const std::string& expected_value,
+ const std::string& actual_value,
+ bool ignoring_case) {
+ Message msg;
+ msg << "Value of: " << actual_expression;
+ if (actual_value != actual_expression) {
+ msg << "\n Actual: " << actual_value;
+ }
+
+ msg << "\nExpected: " << expected_expression;
+ if (ignoring_case) {
+ msg << " (ignoring case)";
+ }
+ if (expected_value != expected_expression) {
+ msg << "\nWhich is: " << expected_value;
+ }
+
+ return AssertionFailure() << msg;
+}
+
+// Constructs a failure message for Boolean assertions such as EXPECT_TRUE.
+std::string GetBoolAssertionFailureMessage(
+ const AssertionResult& assertion_result,
+ const char* expression_text,
+ const char* actual_predicate_value,
+ const char* expected_predicate_value) {
+ const char* actual_message = assertion_result.message();
+ Message msg;
+ msg << "Value of: " << expression_text
+ << "\n Actual: " << actual_predicate_value;
+ if (actual_message[0] != '\0')
+ msg << " (" << actual_message << ")";
+ msg << "\nExpected: " << expected_predicate_value;
+ return msg.GetString();
+}
+
+// Helper function for implementing ASSERT_NEAR.
+AssertionResult DoubleNearPredFormat(const char* expr1,
+ const char* expr2,
+ const char* abs_error_expr,
+ double val1,
+ double val2,
+ double abs_error) {
+ const double diff = fabs(val1 - val2);
+ if (diff <= abs_error) return AssertionSuccess();
+
+ // TODO(wan): do not print the value of an expression if it's
+ // already a literal.
+ return AssertionFailure()
+ << "The difference between " << expr1 << " and " << expr2
+ << " is " << diff << ", which exceeds " << abs_error_expr << ", where\n"
+ << expr1 << " evaluates to " << val1 << ",\n"
+ << expr2 << " evaluates to " << val2 << ", and\n"
+ << abs_error_expr << " evaluates to " << abs_error << ".";
+}
+
+
+// Helper template for implementing FloatLE() and DoubleLE().
+template <typename RawType>
+AssertionResult FloatingPointLE(const char* expr1,
+ const char* expr2,
+ RawType val1,
+ RawType val2) {
+ // Returns success if val1 is less than val2,
+ if (val1 < val2) {
+ return AssertionSuccess();
+ }
+
+ // or if val1 is almost equal to val2.
+ const FloatingPoint<RawType> lhs(val1), rhs(val2);
+ if (lhs.AlmostEquals(rhs)) {
+ return AssertionSuccess();
+ }
+
+ // Note that the above two checks will both fail if either val1 or
+ // val2 is NaN, as the IEEE floating-point standard requires that
+ // any predicate involving a NaN must return false.
+
+ ::std::stringstream val1_ss;
+ val1_ss << std::setprecision(std::numeric_limits<RawType>::digits10 + 2)
+ << val1;
+
+ ::std::stringstream val2_ss;
+ val2_ss << std::setprecision(std::numeric_limits<RawType>::digits10 + 2)
+ << val2;
+
+ return AssertionFailure()
+ << "Expected: (" << expr1 << ") <= (" << expr2 << ")\n"
+ << " Actual: " << StringStreamToString(&val1_ss) << " vs "
+ << StringStreamToString(&val2_ss);
+}
+
+} // namespace internal
+
+// Asserts that val1 is less than, or almost equal to, val2. Fails
+// otherwise. In particular, it fails if either val1 or val2 is NaN.
+AssertionResult FloatLE(const char* expr1, const char* expr2,
+ float val1, float val2) {
+ return internal::FloatingPointLE<float>(expr1, expr2, val1, val2);
+}
+
+// Asserts that val1 is less than, or almost equal to, val2. Fails
+// otherwise. In particular, it fails if either val1 or val2 is NaN.
+AssertionResult DoubleLE(const char* expr1, const char* expr2,
+ double val1, double val2) {
+ return internal::FloatingPointLE<double>(expr1, expr2, val1, val2);
+}
+
+namespace internal {
+
+// The helper function for {ASSERT|EXPECT}_EQ with int or enum
+// arguments.
+AssertionResult CmpHelperEQ(const char* expected_expression,
+ const char* actual_expression,
+ BiggestInt expected,
+ BiggestInt actual) {
+ if (expected == actual) {
+ return AssertionSuccess();
+ }
+
+ return EqFailure(expected_expression,
+ actual_expression,
+ FormatForComparisonFailureMessage(expected, actual),
+ FormatForComparisonFailureMessage(actual, expected),
+ false);
+}
+
+// A macro for implementing the helper functions needed to implement
+// ASSERT_?? and EXPECT_?? with integer or enum arguments. It is here
+// just to avoid copy-and-paste of similar code.
+#define GTEST_IMPL_CMP_HELPER_(op_name, op)\
+AssertionResult CmpHelper##op_name(const char* expr1, const char* expr2, \
+ BiggestInt val1, BiggestInt val2) {\
+ if (val1 op val2) {\
+ return AssertionSuccess();\
+ } else {\
+ return AssertionFailure() \
+ << "Expected: (" << expr1 << ") " #op " (" << expr2\
+ << "), actual: " << FormatForComparisonFailureMessage(val1, val2)\
+ << " vs " << FormatForComparisonFailureMessage(val2, val1);\
+ }\
+}
+
+// Implements the helper function for {ASSERT|EXPECT}_NE with int or
+// enum arguments.
+GTEST_IMPL_CMP_HELPER_(NE, !=)
+// Implements the helper function for {ASSERT|EXPECT}_LE with int or
+// enum arguments.
+GTEST_IMPL_CMP_HELPER_(LE, <=)
+// Implements the helper function for {ASSERT|EXPECT}_LT with int or
+// enum arguments.
+GTEST_IMPL_CMP_HELPER_(LT, < )
+// Implements the helper function for {ASSERT|EXPECT}_GE with int or
+// enum arguments.
+GTEST_IMPL_CMP_HELPER_(GE, >=)
+// Implements the helper function for {ASSERT|EXPECT}_GT with int or
+// enum arguments.
+GTEST_IMPL_CMP_HELPER_(GT, > )
+
+#undef GTEST_IMPL_CMP_HELPER_
+
+// The helper function for {ASSERT|EXPECT}_STREQ.
+AssertionResult CmpHelperSTREQ(const char* expected_expression,
+ const char* actual_expression,
+ const char* expected,
+ const char* actual) {
+ if (String::CStringEquals(expected, actual)) {
+ return AssertionSuccess();
+ }
+
+ return EqFailure(expected_expression,
+ actual_expression,
+ PrintToString(expected),
+ PrintToString(actual),
+ false);
+}
+
+// The helper function for {ASSERT|EXPECT}_STRCASEEQ.
+AssertionResult CmpHelperSTRCASEEQ(const char* expected_expression,
+ const char* actual_expression,
+ const char* expected,
+ const char* actual) {
+ if (String::CaseInsensitiveCStringEquals(expected, actual)) {
+ return AssertionSuccess();
+ }
+
+ return EqFailure(expected_expression,
+ actual_expression,
+ PrintToString(expected),
+ PrintToString(actual),
+ true);
+}
+
+// The helper function for {ASSERT|EXPECT}_STRNE.
+AssertionResult CmpHelperSTRNE(const char* s1_expression,
+ const char* s2_expression,
+ const char* s1,
+ const char* s2) {
+ if (!String::CStringEquals(s1, s2)) {
+ return AssertionSuccess();
+ } else {
+ return AssertionFailure() << "Expected: (" << s1_expression << ") != ("
+ << s2_expression << "), actual: \""
+ << s1 << "\" vs \"" << s2 << "\"";
+ }
+}
+
+// The helper function for {ASSERT|EXPECT}_STRCASENE.
+AssertionResult CmpHelperSTRCASENE(const char* s1_expression,
+ const char* s2_expression,
+ const char* s1,
+ const char* s2) {
+ if (!String::CaseInsensitiveCStringEquals(s1, s2)) {
+ return AssertionSuccess();
+ } else {
+ return AssertionFailure()
+ << "Expected: (" << s1_expression << ") != ("
+ << s2_expression << ") (ignoring case), actual: \""
+ << s1 << "\" vs \"" << s2 << "\"";
+ }
+}
+
+} // namespace internal
+
+namespace {
+
+// Helper functions for implementing IsSubString() and IsNotSubstring().
+
+// This group of overloaded functions return true iff needle is a
+// substring of haystack. NULL is considered a substring of itself
+// only.
+
+bool IsSubstringPred(const char* needle, const char* haystack) {
+ if (needle == NULL || haystack == NULL)
+ return needle == haystack;
+
+ return strstr(haystack, needle) != NULL;
+}
+
+bool IsSubstringPred(const wchar_t* needle, const wchar_t* haystack) {
+ if (needle == NULL || haystack == NULL)
+ return needle == haystack;
+
+ return wcsstr(haystack, needle) != NULL;
+}
+
+// StringType here can be either ::std::string or ::std::wstring.
+template <typename StringType>
+bool IsSubstringPred(const StringType& needle,
+ const StringType& haystack) {
+ return haystack.find(needle) != StringType::npos;
+}
+
+// This function implements either IsSubstring() or IsNotSubstring(),
+// depending on the value of the expected_to_be_substring parameter.
+// StringType here can be const char*, const wchar_t*, ::std::string,
+// or ::std::wstring.
+template <typename StringType>
+AssertionResult IsSubstringImpl(
+ bool expected_to_be_substring,
+ const char* needle_expr, const char* haystack_expr,
+ const StringType& needle, const StringType& haystack) {
+ if (IsSubstringPred(needle, haystack) == expected_to_be_substring)
+ return AssertionSuccess();
+
+ const bool is_wide_string = sizeof(needle[0]) > 1;
+ const char* const begin_string_quote = is_wide_string ? "L\"" : "\"";
+ return AssertionFailure()
+ << "Value of: " << needle_expr << "\n"
+ << " Actual: " << begin_string_quote << needle << "\"\n"
+ << "Expected: " << (expected_to_be_substring ? "" : "not ")
+ << "a substring of " << haystack_expr << "\n"
+ << "Which is: " << begin_string_quote << haystack << "\"";
+}
+
+} // namespace
+
+// IsSubstring() and IsNotSubstring() check whether needle is a
+// substring of haystack (NULL is considered a substring of itself
+// only), and return an appropriate error message when they fail.
+
+AssertionResult IsSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const char* needle, const char* haystack) {
+ return IsSubstringImpl(true, needle_expr, haystack_expr, needle, haystack);
+}
+
+AssertionResult IsSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const wchar_t* needle, const wchar_t* haystack) {
+ return IsSubstringImpl(true, needle_expr, haystack_expr, needle, haystack);
+}
+
+AssertionResult IsNotSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const char* needle, const char* haystack) {
+ return IsSubstringImpl(false, needle_expr, haystack_expr, needle, haystack);
+}
+
+AssertionResult IsNotSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const wchar_t* needle, const wchar_t* haystack) {
+ return IsSubstringImpl(false, needle_expr, haystack_expr, needle, haystack);
+}
+
+AssertionResult IsSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const ::std::string& needle, const ::std::string& haystack) {
+ return IsSubstringImpl(true, needle_expr, haystack_expr, needle, haystack);
+}
+
+AssertionResult IsNotSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const ::std::string& needle, const ::std::string& haystack) {
+ return IsSubstringImpl(false, needle_expr, haystack_expr, needle, haystack);
+}
+
+#if GTEST_HAS_STD_WSTRING
+AssertionResult IsSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const ::std::wstring& needle, const ::std::wstring& haystack) {
+ return IsSubstringImpl(true, needle_expr, haystack_expr, needle, haystack);
+}
+
+AssertionResult IsNotSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const ::std::wstring& needle, const ::std::wstring& haystack) {
+ return IsSubstringImpl(false, needle_expr, haystack_expr, needle, haystack);
+}
+#endif // GTEST_HAS_STD_WSTRING
+
+namespace internal {
+
+#if GTEST_OS_WINDOWS
+
+namespace {
+
+// Helper function for IsHRESULT{SuccessFailure} predicates
+AssertionResult HRESULTFailureHelper(const char* expr,
+ const char* expected,
+ long hr) { // NOLINT
+# if GTEST_OS_WINDOWS_MOBILE
+
+ // Windows CE doesn't support FormatMessage.
+ const char error_text[] = "";
+
+# else
+
+ // Looks up the human-readable system message for the HRESULT code
+ // and since we're not passing any params to FormatMessage, we don't
+ // want inserts expanded.
+ const DWORD kFlags = FORMAT_MESSAGE_FROM_SYSTEM |
+ FORMAT_MESSAGE_IGNORE_INSERTS;
+ const DWORD kBufSize = 4096;
+ // Gets the system's human readable message string for this HRESULT.
+ char error_text[kBufSize] = { '\0' };
+ DWORD message_length = ::FormatMessageA(kFlags,
+ 0, // no source, we're asking system
+ hr, // the error
+ 0, // no line width restrictions
+ error_text, // output buffer
+ kBufSize, // buf size
+ NULL); // no arguments for inserts
+ // Trims tailing white space (FormatMessage leaves a trailing CR-LF)
+ for (; message_length && IsSpace(error_text[message_length - 1]);
+ --message_length) {
+ error_text[message_length - 1] = '\0';
+ }
+
+# endif // GTEST_OS_WINDOWS_MOBILE
+
+ const std::string error_hex("0x" + String::FormatHexInt(hr));
+ return ::testing::AssertionFailure()
+ << "Expected: " << expr << " " << expected << ".\n"
+ << " Actual: " << error_hex << " " << error_text << "\n";
+}
+
+} // namespace
+
+AssertionResult IsHRESULTSuccess(const char* expr, long hr) { // NOLINT
+ if (SUCCEEDED(hr)) {
+ return AssertionSuccess();
+ }
+ return HRESULTFailureHelper(expr, "succeeds", hr);
+}
+
+AssertionResult IsHRESULTFailure(const char* expr, long hr) { // NOLINT
+ if (FAILED(hr)) {
+ return AssertionSuccess();
+ }
+ return HRESULTFailureHelper(expr, "fails", hr);
+}
+
+#endif // GTEST_OS_WINDOWS
+
+// Utility functions for encoding Unicode text (wide strings) in
+// UTF-8.
+
+// A Unicode code-point can have upto 21 bits, and is encoded in UTF-8
+// like this:
+//
+// Code-point length Encoding
+// 0 - 7 bits 0xxxxxxx
+// 8 - 11 bits 110xxxxx 10xxxxxx
+// 12 - 16 bits 1110xxxx 10xxxxxx 10xxxxxx
+// 17 - 21 bits 11110xxx 10xxxxxx 10xxxxxx 10xxxxxx
+
+// The maximum code-point a one-byte UTF-8 sequence can represent.
+const UInt32 kMaxCodePoint1 = (static_cast<UInt32>(1) << 7) - 1;
+
+// The maximum code-point a two-byte UTF-8 sequence can represent.
+const UInt32 kMaxCodePoint2 = (static_cast<UInt32>(1) << (5 + 6)) - 1;
+
+// The maximum code-point a three-byte UTF-8 sequence can represent.
+const UInt32 kMaxCodePoint3 = (static_cast<UInt32>(1) << (4 + 2*6)) - 1;
+
+// The maximum code-point a four-byte UTF-8 sequence can represent.
+const UInt32 kMaxCodePoint4 = (static_cast<UInt32>(1) << (3 + 3*6)) - 1;
+
+// Chops off the n lowest bits from a bit pattern. Returns the n
+// lowest bits. As a side effect, the original bit pattern will be
+// shifted to the right by n bits.
+inline UInt32 ChopLowBits(UInt32* bits, int n) {
+ const UInt32 low_bits = *bits & ((static_cast<UInt32>(1) << n) - 1);
+ *bits >>= n;
+ return low_bits;
+}
+
+// Converts a Unicode code point to a narrow string in UTF-8 encoding.
+// code_point parameter is of type UInt32 because wchar_t may not be
+// wide enough to contain a code point.
+// If the code_point is not a valid Unicode code point
+// (i.e. outside of Unicode range U+0 to U+10FFFF) it will be converted
+// to "(Invalid Unicode 0xXXXXXXXX)".
+std::string CodePointToUtf8(UInt32 code_point) {
+ if (code_point > kMaxCodePoint4) {
+ return "(Invalid Unicode 0x" + String::FormatHexInt(code_point) + ")";
+ }
+
+ char str[5]; // Big enough for the largest valid code point.
+ if (code_point <= kMaxCodePoint1) {
+ str[1] = '\0';
+ str[0] = static_cast<char>(code_point); // 0xxxxxxx
+ } else if (code_point <= kMaxCodePoint2) {
+ str[2] = '\0';
+ str[1] = static_cast<char>(0x80 | ChopLowBits(&code_point, 6)); // 10xxxxxx
+ str[0] = static_cast<char>(0xC0 | code_point); // 110xxxxx
+ } else if (code_point <= kMaxCodePoint3) {
+ str[3] = '\0';
+ str[2] = static_cast<char>(0x80 | ChopLowBits(&code_point, 6)); // 10xxxxxx
+ str[1] = static_cast<char>(0x80 | ChopLowBits(&code_point, 6)); // 10xxxxxx
+ str[0] = static_cast<char>(0xE0 | code_point); // 1110xxxx
+ } else { // code_point <= kMaxCodePoint4
+ str[4] = '\0';
+ str[3] = static_cast<char>(0x80 | ChopLowBits(&code_point, 6)); // 10xxxxxx
+ str[2] = static_cast<char>(0x80 | ChopLowBits(&code_point, 6)); // 10xxxxxx
+ str[1] = static_cast<char>(0x80 | ChopLowBits(&code_point, 6)); // 10xxxxxx
+ str[0] = static_cast<char>(0xF0 | code_point); // 11110xxx
+ }
+ return str;
+}
+
+// The following two functions only make sense if the the system
+// uses UTF-16 for wide string encoding. All supported systems
+// with 16 bit wchar_t (Windows, Cygwin, Symbian OS) do use UTF-16.
+
+// Determines if the arguments constitute UTF-16 surrogate pair
+// and thus should be combined into a single Unicode code point
+// using CreateCodePointFromUtf16SurrogatePair.
+inline bool IsUtf16SurrogatePair(wchar_t first, wchar_t second) {
+ return sizeof(wchar_t) == 2 &&
+ (first & 0xFC00) == 0xD800 && (second & 0xFC00) == 0xDC00;
+}
+
+// Creates a Unicode code point from UTF16 surrogate pair.
+inline UInt32 CreateCodePointFromUtf16SurrogatePair(wchar_t first,
+ wchar_t second) {
+ const UInt32 mask = (1 << 10) - 1;
+ return (sizeof(wchar_t) == 2) ?
+ (((first & mask) << 10) | (second & mask)) + 0x10000 :
+ // This function should not be called when the condition is
+ // false, but we provide a sensible default in case it is.
+ static_cast<UInt32>(first);
+}
+
+// Converts a wide string to a narrow string in UTF-8 encoding.
+// The wide string is assumed to have the following encoding:
+// UTF-16 if sizeof(wchar_t) == 2 (on Windows, Cygwin, Symbian OS)
+// UTF-32 if sizeof(wchar_t) == 4 (on Linux)
+// Parameter str points to a null-terminated wide string.
+// Parameter num_chars may additionally limit the number
+// of wchar_t characters processed. -1 is used when the entire string
+// should be processed.
+// If the string contains code points that are not valid Unicode code points
+// (i.e. outside of Unicode range U+0 to U+10FFFF) they will be output
+// as '(Invalid Unicode 0xXXXXXXXX)'. If the string is in UTF16 encoding
+// and contains invalid UTF-16 surrogate pairs, values in those pairs
+// will be encoded as individual Unicode characters from Basic Normal Plane.
+std::string WideStringToUtf8(const wchar_t* str, int num_chars) {
+ if (num_chars == -1)
+ num_chars = static_cast<int>(wcslen(str));
+
+ ::std::stringstream stream;
+ for (int i = 0; i < num_chars; ++i) {
+ UInt32 unicode_code_point;
+
+ if (str[i] == L'\0') {
+ break;
+ } else if (i + 1 < num_chars && IsUtf16SurrogatePair(str[i], str[i + 1])) {
+ unicode_code_point = CreateCodePointFromUtf16SurrogatePair(str[i],
+ str[i + 1]);
+ i++;
+ } else {
+ unicode_code_point = static_cast<UInt32>(str[i]);
+ }
+
+ stream << CodePointToUtf8(unicode_code_point);
+ }
+ return StringStreamToString(&stream);
+}
+
+// Converts a wide C string to an std::string using the UTF-8 encoding.
+// NULL will be converted to "(null)".
+std::string String::ShowWideCString(const wchar_t * wide_c_str) {
+ if (wide_c_str == NULL) return "(null)";
+
+ return internal::WideStringToUtf8(wide_c_str, -1);
+}
+
+// Compares two wide C strings. Returns true iff they have the same
+// content.
+//
+// Unlike wcscmp(), this function can handle NULL argument(s). A NULL
+// C string is considered different to any non-NULL C string,
+// including the empty string.
+bool String::WideCStringEquals(const wchar_t * lhs, const wchar_t * rhs) {
+ if (lhs == NULL) return rhs == NULL;
+
+ if (rhs == NULL) return false;
+
+ return wcscmp(lhs, rhs) == 0;
+}
+
+// Helper function for *_STREQ on wide strings.
+AssertionResult CmpHelperSTREQ(const char* expected_expression,
+ const char* actual_expression,
+ const wchar_t* expected,
+ const wchar_t* actual) {
+ if (String::WideCStringEquals(expected, actual)) {
+ return AssertionSuccess();
+ }
+
+ return EqFailure(expected_expression,
+ actual_expression,
+ PrintToString(expected),
+ PrintToString(actual),
+ false);
+}
+
+// Helper function for *_STRNE on wide strings.
+AssertionResult CmpHelperSTRNE(const char* s1_expression,
+ const char* s2_expression,
+ const wchar_t* s1,
+ const wchar_t* s2) {
+ if (!String::WideCStringEquals(s1, s2)) {
+ return AssertionSuccess();
+ }
+
+ return AssertionFailure() << "Expected: (" << s1_expression << ") != ("
+ << s2_expression << "), actual: "
+ << PrintToString(s1)
+ << " vs " << PrintToString(s2);
+}
+
+// Compares two C strings, ignoring case. Returns true iff they have
+// the same content.
+//
+// Unlike strcasecmp(), this function can handle NULL argument(s). A
+// NULL C string is considered different to any non-NULL C string,
+// including the empty string.
+bool String::CaseInsensitiveCStringEquals(const char * lhs, const char * rhs) {
+ if (lhs == NULL)
+ return rhs == NULL;
+ if (rhs == NULL)
+ return false;
+ return posix::StrCaseCmp(lhs, rhs) == 0;
+}
+
+ // Compares two wide C strings, ignoring case. Returns true iff they
+ // have the same content.
+ //
+ // Unlike wcscasecmp(), this function can handle NULL argument(s).
+ // A NULL C string is considered different to any non-NULL wide C string,
+ // including the empty string.
+ // NB: The implementations on different platforms slightly differ.
+ // On windows, this method uses _wcsicmp which compares according to LC_CTYPE
+ // environment variable. On GNU platform this method uses wcscasecmp
+ // which compares according to LC_CTYPE category of the current locale.
+ // On MacOS X, it uses towlower, which also uses LC_CTYPE category of the
+ // current locale.
+bool String::CaseInsensitiveWideCStringEquals(const wchar_t* lhs,
+ const wchar_t* rhs) {
+ if (lhs == NULL) return rhs == NULL;
+
+ if (rhs == NULL) return false;
+
+#if GTEST_OS_WINDOWS
+ return _wcsicmp(lhs, rhs) == 0;
+#elif GTEST_OS_LINUX && !GTEST_OS_LINUX_ANDROID
+ return wcscasecmp(lhs, rhs) == 0;
+#else
+ // Android, Mac OS X and Cygwin don't define wcscasecmp.
+ // Other unknown OSes may not define it either.
+ wint_t left, right;
+ do {
+ left = towlower(*lhs++);
+ right = towlower(*rhs++);
+ } while (left && left == right);
+ return left == right;
+#endif // OS selector
+}
+
+// Returns true iff str ends with the given suffix, ignoring case.
+// Any string is considered to end with an empty suffix.
+bool String::EndsWithCaseInsensitive(
+ const std::string& str, const std::string& suffix) {
+ const size_t str_len = str.length();
+ const size_t suffix_len = suffix.length();
+ return (str_len >= suffix_len) &&
+ CaseInsensitiveCStringEquals(str.c_str() + str_len - suffix_len,
+ suffix.c_str());
+}
+
+// Formats an int value as "%02d".
+std::string String::FormatIntWidth2(int value) {
+ std::stringstream ss;
+ ss << std::setfill('0') << std::setw(2) << value;
+ return ss.str();
+}
+
+// Formats an int value as "%X".
+std::string String::FormatHexInt(int value) {
+ std::stringstream ss;
+ ss << std::hex << std::uppercase << value;
+ return ss.str();
+}
+
+// Formats a byte as "%02X".
+std::string String::FormatByte(unsigned char value) {
+ std::stringstream ss;
+ ss << std::setfill('0') << std::setw(2) << std::hex << std::uppercase
+ << static_cast<unsigned int>(value);
+ return ss.str();
+}
+
+// Converts the buffer in a stringstream to an std::string, converting NUL
+// bytes to "\\0" along the way.
+std::string StringStreamToString(::std::stringstream* ss) {
+ const ::std::string& str = ss->str();
+ const char* const start = str.c_str();
+ const char* const end = start + str.length();
+
+ std::string result;
+ result.reserve(2 * (end - start));
+ for (const char* ch = start; ch != end; ++ch) {
+ if (*ch == '\0') {
+ result += "\\0"; // Replaces NUL with "\\0";
+ } else {
+ result += *ch;
+ }
+ }
+
+ return result;
+}
+
+// Appends the user-supplied message to the Google-Test-generated message.
+std::string AppendUserMessage(const std::string& gtest_msg,
+ const Message& user_msg) {
+ // Appends the user message if it's non-empty.
+ const std::string user_msg_string = user_msg.GetString();
+ if (user_msg_string.empty()) {
+ return gtest_msg;
+ }
+
+ return gtest_msg + "\n" + user_msg_string;
+}
+
+} // namespace internal
+
+// class TestResult
+
+// Creates an empty TestResult.
+TestResult::TestResult()
+ : death_test_count_(0),
+ elapsed_time_(0) {
+}
+
+// D'tor.
+TestResult::~TestResult() {
+}
+
+// Returns the i-th test part result among all the results. i can
+// range from 0 to total_part_count() - 1. If i is not in that range,
+// aborts the program.
+const TestPartResult& TestResult::GetTestPartResult(int i) const {
+ if (i < 0 || i >= total_part_count())
+ internal::posix::Abort();
+ return test_part_results_.at(i);
+}
+
+// Returns the i-th test property. i can range from 0 to
+// test_property_count() - 1. If i is not in that range, aborts the
+// program.
+const TestProperty& TestResult::GetTestProperty(int i) const {
+ if (i < 0 || i >= test_property_count())
+ internal::posix::Abort();
+ return test_properties_.at(i);
+}
+
+// Clears the test part results.
+void TestResult::ClearTestPartResults() {
+ test_part_results_.clear();
+}
+
+// Adds a test part result to the list.
+void TestResult::AddTestPartResult(const TestPartResult& test_part_result) {
+ test_part_results_.push_back(test_part_result);
+}
+
+// Adds a test property to the list. If a property with the same key as the
+// supplied property is already represented, the value of this test_property
+// replaces the old value for that key.
+void TestResult::RecordProperty(const std::string& xml_element,
+ const TestProperty& test_property) {
+ if (!ValidateTestProperty(xml_element, test_property)) {
+ return;
+ }
+ internal::MutexLock lock(&test_properites_mutex_);
+ const std::vector<TestProperty>::iterator property_with_matching_key =
+ std::find_if(test_properties_.begin(), test_properties_.end(),
+ internal::TestPropertyKeyIs(test_property.key()));
+ if (property_with_matching_key == test_properties_.end()) {
+ test_properties_.push_back(test_property);
+ return;
+ }
+ property_with_matching_key->SetValue(test_property.value());
+}
+
+// The list of reserved attributes used in the <testsuites> element of XML
+// output.
+static const char* const kReservedTestSuitesAttributes[] = {
+ "disabled",
+ "errors",
+ "failures",
+ "name",
+ "random_seed",
+ "tests",
+ "time",
+ "timestamp"
+};
+
+// The list of reserved attributes used in the <testsuite> element of XML
+// output.
+static const char* const kReservedTestSuiteAttributes[] = {
+ "disabled",
+ "errors",
+ "failures",
+ "name",
+ "tests",
+ "time"
+};
+
+// The list of reserved attributes used in the <testcase> element of XML output.
+static const char* const kReservedTestCaseAttributes[] = {
+ "classname",
+ "name",
+ "status",
+ "time",
+ "type_param",
+ "value_param"
+};
+
+template <int kSize>
+std::vector<std::string> ArrayAsVector(const char* const (&array)[kSize]) {
+ return std::vector<std::string>(array, array + kSize);
+}
+
+static std::vector<std::string> GetReservedAttributesForElement(
+ const std::string& xml_element) {
+ if (xml_element == "testsuites") {
+ return ArrayAsVector(kReservedTestSuitesAttributes);
+ } else if (xml_element == "testsuite") {
+ return ArrayAsVector(kReservedTestSuiteAttributes);
+ } else if (xml_element == "testcase") {
+ return ArrayAsVector(kReservedTestCaseAttributes);
+ } else {
+ GTEST_CHECK_(false) << "Unrecognized xml_element provided: " << xml_element;
+ }
+ // This code is unreachable but some compilers may not realizes that.
+ return std::vector<std::string>();
+}
+
+static std::string FormatWordList(const std::vector<std::string>& words) {
+ Message word_list;
+ for (size_t i = 0; i < words.size(); ++i) {
+ if (i > 0 && words.size() > 2) {
+ word_list << ", ";
+ }
+ if (i == words.size() - 1) {
+ word_list << "and ";
+ }
+ word_list << "'" << words[i] << "'";
+ }
+ return word_list.GetString();
+}
+
+bool ValidateTestPropertyName(const std::string& property_name,
+ const std::vector<std::string>& reserved_names) {
+ if (std::find(reserved_names.begin(), reserved_names.end(), property_name) !=
+ reserved_names.end()) {
+ ADD_FAILURE() << "Reserved key used in RecordProperty(): " << property_name
+ << " (" << FormatWordList(reserved_names)
+ << " are reserved by " << GTEST_NAME_ << ")";
+ return false;
+ }
+ return true;
+}
+
+// Adds a failure if the key is a reserved attribute of the element named
+// xml_element. Returns true if the property is valid.
+bool TestResult::ValidateTestProperty(const std::string& xml_element,
+ const TestProperty& test_property) {
+ return ValidateTestPropertyName(test_property.key(),
+ GetReservedAttributesForElement(xml_element));
+}
+
+// Clears the object.
+void TestResult::Clear() {
+ test_part_results_.clear();
+ test_properties_.clear();
+ death_test_count_ = 0;
+ elapsed_time_ = 0;
+}
+
+// Returns true iff the test failed.
+bool TestResult::Failed() const {
+ for (int i = 0; i < total_part_count(); ++i) {
+ if (GetTestPartResult(i).failed())
+ return true;
+ }
+ return false;
+}
+
+// Returns true iff the test part fatally failed.
+static bool TestPartFatallyFailed(const TestPartResult& result) {
+ return result.fatally_failed();
+}
+
+// Returns true iff the test fatally failed.
+bool TestResult::HasFatalFailure() const {
+ return CountIf(test_part_results_, TestPartFatallyFailed) > 0;
+}
+
+// Returns true iff the test part non-fatally failed.
+static bool TestPartNonfatallyFailed(const TestPartResult& result) {
+ return result.nonfatally_failed();
+}
+
+// Returns true iff the test has a non-fatal failure.
+bool TestResult::HasNonfatalFailure() const {
+ return CountIf(test_part_results_, TestPartNonfatallyFailed) > 0;
+}
+
+// Gets the number of all test parts. This is the sum of the number
+// of successful test parts and the number of failed test parts.
+int TestResult::total_part_count() const {
+ return static_cast<int>(test_part_results_.size());
+}
+
+// Returns the number of the test properties.
+int TestResult::test_property_count() const {
+ return static_cast<int>(test_properties_.size());
+}
+
+// class Test
+
+// Creates a Test object.
+
+// The c'tor saves the values of all Google Test flags.
+Test::Test()
+ : gtest_flag_saver_(new internal::GTestFlagSaver) {
+}
+
+// The d'tor restores the values of all Google Test flags.
+Test::~Test() {
+ delete gtest_flag_saver_;
+}
+
+// Sets up the test fixture.
+//
+// A sub-class may override this.
+void Test::SetUp() {
+}
+
+// Tears down the test fixture.
+//
+// A sub-class may override this.
+void Test::TearDown() {
+}
+
+// Allows user supplied key value pairs to be recorded for later output.
+void Test::RecordProperty(const std::string& key, const std::string& value) {
+ UnitTest::GetInstance()->RecordProperty(key, value);
+}
+
+// Allows user supplied key value pairs to be recorded for later output.
+void Test::RecordProperty(const std::string& key, int value) {
+ Message value_message;
+ value_message << value;
+ RecordProperty(key, value_message.GetString().c_str());
+}
+
+namespace internal {
+
+void ReportFailureInUnknownLocation(TestPartResult::Type result_type,
+ const std::string& message) {
+ // This function is a friend of UnitTest and as such has access to
+ // AddTestPartResult.
+ UnitTest::GetInstance()->AddTestPartResult(
+ result_type,
+ NULL, // No info about the source file where the exception occurred.
+ -1, // We have no info on which line caused the exception.
+ message,
+ ""); // No stack trace, either.
+}
+
+} // namespace internal
+
+// Google Test requires all tests in the same test case to use the same test
+// fixture class. This function checks if the current test has the
+// same fixture class as the first test in the current test case. If
+// yes, it returns true; otherwise it generates a Google Test failure and
+// returns false.
+bool Test::HasSameFixtureClass() {
+ internal::UnitTestImpl* const impl = internal::GetUnitTestImpl();
+ const TestCase* const test_case = impl->current_test_case();
+
+ // Info about the first test in the current test case.
+ const TestInfo* const first_test_info = test_case->test_info_list()[0];
+ const internal::TypeId first_fixture_id = first_test_info->fixture_class_id_;
+ const char* const first_test_name = first_test_info->name();
+
+ // Info about the current test.
+ const TestInfo* const this_test_info = impl->current_test_info();
+ const internal::TypeId this_fixture_id = this_test_info->fixture_class_id_;
+ const char* const this_test_name = this_test_info->name();
+
+ if (this_fixture_id != first_fixture_id) {
+ // Is the first test defined using TEST?
+ const bool first_is_TEST = first_fixture_id == internal::GetTestTypeId();
+ // Is this test defined using TEST?
+ const bool this_is_TEST = this_fixture_id == internal::GetTestTypeId();
+
+ if (first_is_TEST || this_is_TEST) {
+ // The user mixed TEST and TEST_F in this test case - we'll tell
+ // him/her how to fix it.
+
+ // Gets the name of the TEST and the name of the TEST_F. Note
+ // that first_is_TEST and this_is_TEST cannot both be true, as
+ // the fixture IDs are different for the two tests.
+ const char* const TEST_name =
+ first_is_TEST ? first_test_name : this_test_name;
+ const char* const TEST_F_name =
+ first_is_TEST ? this_test_name : first_test_name;
+
+ ADD_FAILURE()
+ << "All tests in the same test case must use the same test fixture\n"
+ << "class, so mixing TEST_F and TEST in the same test case is\n"
+ << "illegal. In test case " << this_test_info->test_case_name()
+ << ",\n"
+ << "test " << TEST_F_name << " is defined using TEST_F but\n"
+ << "test " << TEST_name << " is defined using TEST. You probably\n"
+ << "want to change the TEST to TEST_F or move it to another test\n"
+ << "case.";
+ } else {
+ // The user defined two fixture classes with the same name in
+ // two namespaces - we'll tell him/her how to fix it.
+ ADD_FAILURE()
+ << "All tests in the same test case must use the same test fixture\n"
+ << "class. However, in test case "
+ << this_test_info->test_case_name() << ",\n"
+ << "you defined test " << first_test_name
+ << " and test " << this_test_name << "\n"
+ << "using two different test fixture classes. This can happen if\n"
+ << "the two classes are from different namespaces or translation\n"
+ << "units and have the same name. You should probably rename one\n"
+ << "of the classes to put the tests into different test cases.";
+ }
+ return false;
+ }
+
+ return true;
+}
+
+#if GTEST_HAS_SEH
+
+// Adds an "exception thrown" fatal failure to the current test. This
+// function returns its result via an output parameter pointer because VC++
+// prohibits creation of objects with destructors on stack in functions
+// using __try (see error C2712).
+static std::string* FormatSehExceptionMessage(DWORD exception_code,
+ const char* location) {
+ Message message;
+ message << "SEH exception with code 0x" << std::setbase(16) <<
+ exception_code << std::setbase(10) << " thrown in " << location << ".";
+
+ return new std::string(message.GetString());
+}
+
+#endif // GTEST_HAS_SEH
+
+namespace internal {
+
+#if GTEST_HAS_EXCEPTIONS
+
+// Adds an "exception thrown" fatal failure to the current test.
+static std::string FormatCxxExceptionMessage(const char* description,
+ const char* location) {
+ Message message;
+ if (description != NULL) {
+ message << "C++ exception with description \"" << description << "\"";
+ } else {
+ message << "Unknown C++ exception";
+ }
+ message << " thrown in " << location << ".";
+
+ return message.GetString();
+}
+
+static std::string PrintTestPartResultToString(
+ const TestPartResult& test_part_result);
+
+GoogleTestFailureException::GoogleTestFailureException(
+ const TestPartResult& failure)
+ : ::std::runtime_error(PrintTestPartResultToString(failure).c_str()) {}
+
+#endif // GTEST_HAS_EXCEPTIONS
+
+// We put these helper functions in the internal namespace as IBM's xlC
+// compiler rejects the code if they were declared static.
+
+// Runs the given method and handles SEH exceptions it throws, when
+// SEH is supported; returns the 0-value for type Result in case of an
+// SEH exception. (Microsoft compilers cannot handle SEH and C++
+// exceptions in the same function. Therefore, we provide a separate
+// wrapper function for handling SEH exceptions.)
+template <class T, typename Result>
+Result HandleSehExceptionsInMethodIfSupported(
+ T* object, Result (T::*method)(), const char* location) {
+#if GTEST_HAS_SEH
+ __try {
+ return (object->*method)();
+ } __except (internal::UnitTestOptions::GTestShouldProcessSEH( // NOLINT
+ GetExceptionCode())) {
+ // We create the exception message on the heap because VC++ prohibits
+ // creation of objects with destructors on stack in functions using __try
+ // (see error C2712).
+ std::string* exception_message = FormatSehExceptionMessage(
+ GetExceptionCode(), location);
+ internal::ReportFailureInUnknownLocation(TestPartResult::kFatalFailure,
+ *exception_message);
+ delete exception_message;
+ return static_cast<Result>(0);
+ }
+#else
+ (void)location;
+ return (object->*method)();
+#endif // GTEST_HAS_SEH
+}
+
+// Runs the given method and catches and reports C++ and/or SEH-style
+// exceptions, if they are supported; returns the 0-value for type
+// Result in case of an SEH exception.
+template <class T, typename Result>
+Result HandleExceptionsInMethodIfSupported(
+ T* object, Result (T::*method)(), const char* location) {
+ // NOTE: The user code can affect the way in which Google Test handles
+ // exceptions by setting GTEST_FLAG(catch_exceptions), but only before
+ // RUN_ALL_TESTS() starts. It is technically possible to check the flag
+ // after the exception is caught and either report or re-throw the
+ // exception based on the flag's value:
+ //
+ // try {
+ // // Perform the test method.
+ // } catch (...) {
+ // if (GTEST_FLAG(catch_exceptions))
+ // // Report the exception as failure.
+ // else
+ // throw; // Re-throws the original exception.
+ // }
+ //
+ // However, the purpose of this flag is to allow the program to drop into
+ // the debugger when the exception is thrown. On most platforms, once the
+ // control enters the catch block, the exception origin information is
+ // lost and the debugger will stop the program at the point of the
+ // re-throw in this function -- instead of at the point of the original
+ // throw statement in the code under test. For this reason, we perform
+ // the check early, sacrificing the ability to affect Google Test's
+ // exception handling in the method where the exception is thrown.
+ if (internal::GetUnitTestImpl()->catch_exceptions()) {
+#if GTEST_HAS_EXCEPTIONS
+ try {
+ return HandleSehExceptionsInMethodIfSupported(object, method, location);
+ } catch (const internal::GoogleTestFailureException&) { // NOLINT
+ // This exception type can only be thrown by a failed Google
+ // Test assertion with the intention of letting another testing
+ // framework catch it. Therefore we just re-throw it.
+ throw;
+ } catch (const std::exception& e) { // NOLINT
+ internal::ReportFailureInUnknownLocation(
+ TestPartResult::kFatalFailure,
+ FormatCxxExceptionMessage(e.what(), location));
+ } catch (...) { // NOLINT
+ internal::ReportFailureInUnknownLocation(
+ TestPartResult::kFatalFailure,
+ FormatCxxExceptionMessage(NULL, location));
+ }
+ return static_cast<Result>(0);
+#else
+ return HandleSehExceptionsInMethodIfSupported(object, method, location);
+#endif // GTEST_HAS_EXCEPTIONS
+ } else {
+ return (object->*method)();
+ }
+}
+
+} // namespace internal
+
+// Runs the test and updates the test result.
+void Test::Run() {
+ if (!HasSameFixtureClass()) return;
+
+ internal::UnitTestImpl* const impl = internal::GetUnitTestImpl();
+ impl->os_stack_trace_getter()->UponLeavingGTest();
+ internal::HandleExceptionsInMethodIfSupported(this, &Test::SetUp, "SetUp()");
+ // We will run the test only if SetUp() was successful.
+ if (!HasFatalFailure()) {
+ impl->os_stack_trace_getter()->UponLeavingGTest();
+ internal::HandleExceptionsInMethodIfSupported(
+ this, &Test::TestBody, "the test body");
+ }
+
+ // However, we want to clean up as much as possible. Hence we will
+ // always call TearDown(), even if SetUp() or the test body has
+ // failed.
+ impl->os_stack_trace_getter()->UponLeavingGTest();
+ internal::HandleExceptionsInMethodIfSupported(
+ this, &Test::TearDown, "TearDown()");
+}
+
+// Returns true iff the current test has a fatal failure.
+bool Test::HasFatalFailure() {
+ return internal::GetUnitTestImpl()->current_test_result()->HasFatalFailure();
+}
+
+// Returns true iff the current test has a non-fatal failure.
+bool Test::HasNonfatalFailure() {
+ return internal::GetUnitTestImpl()->current_test_result()->
+ HasNonfatalFailure();
+}
+
+// class TestInfo
+
+// Constructs a TestInfo object. It assumes ownership of the test factory
+// object.
+TestInfo::TestInfo(const std::string& a_test_case_name,
+ const std::string& a_name,
+ const char* a_type_param,
+ const char* a_value_param,
+ internal::TypeId fixture_class_id,
+ internal::TestFactoryBase* factory)
+ : test_case_name_(a_test_case_name),
+ name_(a_name),
+ type_param_(a_type_param ? new std::string(a_type_param) : NULL),
+ value_param_(a_value_param ? new std::string(a_value_param) : NULL),
+ fixture_class_id_(fixture_class_id),
+ should_run_(false),
+ is_disabled_(false),
+ matches_filter_(false),
+ factory_(factory),
+ result_() {}
+
+// Destructs a TestInfo object.
+TestInfo::~TestInfo() { delete factory_; }
+
+namespace internal {
+
+// Creates a new TestInfo object and registers it with Google Test;
+// returns the created object.
+//
+// Arguments:
+//
+// test_case_name: name of the test case
+// name: name of the test
+// type_param: the name of the test's type parameter, or NULL if
+// this is not a typed or a type-parameterized test.
+// value_param: text representation of the test's value parameter,
+// or NULL if this is not a value-parameterized test.
+// fixture_class_id: ID of the test fixture class
+// set_up_tc: pointer to the function that sets up the test case
+// tear_down_tc: pointer to the function that tears down the test case
+// factory: pointer to the factory that creates a test object.
+// The newly created TestInfo instance will assume
+// ownership of the factory object.
+TestInfo* MakeAndRegisterTestInfo(
+ const char* test_case_name,
+ const char* name,
+ const char* type_param,
+ const char* value_param,
+ TypeId fixture_class_id,
+ SetUpTestCaseFunc set_up_tc,
+ TearDownTestCaseFunc tear_down_tc,
+ TestFactoryBase* factory) {
+ TestInfo* const test_info =
+ new TestInfo(test_case_name, name, type_param, value_param,
+ fixture_class_id, factory);
+ GetUnitTestImpl()->AddTestInfo(set_up_tc, tear_down_tc, test_info);
+ return test_info;
+}
+
+#if GTEST_HAS_PARAM_TEST
+void ReportInvalidTestCaseType(const char* test_case_name,
+ const char* file, int line) {
+ Message errors;
+ errors
+ << "Attempted redefinition of test case " << test_case_name << ".\n"
+ << "All tests in the same test case must use the same test fixture\n"
+ << "class. However, in test case " << test_case_name << ", you tried\n"
+ << "to define a test using a fixture class different from the one\n"
+ << "used earlier. This can happen if the two fixture classes are\n"
+ << "from different namespaces and have the same name. You should\n"
+ << "probably rename one of the classes to put the tests into different\n"
+ << "test cases.";
+
+ fprintf(stderr, "%s %s", FormatFileLocation(file, line).c_str(),
+ errors.GetString().c_str());
+}
+#endif // GTEST_HAS_PARAM_TEST
+
+} // namespace internal
+
+namespace {
+
+// A predicate that checks the test name of a TestInfo against a known
+// value.
+//
+// This is used for implementation of the TestCase class only. We put
+// it in the anonymous namespace to prevent polluting the outer
+// namespace.
+//
+// TestNameIs is copyable.
+class TestNameIs {
+ public:
+ // Constructor.
+ //
+ // TestNameIs has NO default constructor.
+ explicit TestNameIs(const char* name)
+ : name_(name) {}
+
+ // Returns true iff the test name of test_info matches name_.
+ bool operator()(const TestInfo * test_info) const {
+ return test_info && test_info->name() == name_;
+ }
+
+ private:
+ std::string name_;
+};
+
+} // namespace
+
+namespace internal {
+
+// This method expands all parameterized tests registered with macros TEST_P
+// and INSTANTIATE_TEST_CASE_P into regular tests and registers those.
+// This will be done just once during the program runtime.
+void UnitTestImpl::RegisterParameterizedTests() {
+#if GTEST_HAS_PARAM_TEST
+ if (!parameterized_tests_registered_) {
+ parameterized_test_registry_.RegisterTests();
+ parameterized_tests_registered_ = true;
+ }
+#endif
+}
+
+} // namespace internal
+
+// Creates the test object, runs it, records its result, and then
+// deletes it.
+void TestInfo::Run() {
+ if (!should_run_) return;
+
+ // Tells UnitTest where to store test result.
+ internal::UnitTestImpl* const impl = internal::GetUnitTestImpl();
+ impl->set_current_test_info(this);
+
+ TestEventListener* repeater = UnitTest::GetInstance()->listeners().repeater();
+
+ // Notifies the unit test event listeners that a test is about to start.
+ repeater->OnTestStart(*this);
+
+ const TimeInMillis start = internal::GetTimeInMillis();
+
+ impl->os_stack_trace_getter()->UponLeavingGTest();
+
+ // Creates the test object.
+ Test* const test = internal::HandleExceptionsInMethodIfSupported(
+ factory_, &internal::TestFactoryBase::CreateTest,
+ "the test fixture's constructor");
+
+ // Runs the test only if the test object was created and its
+ // constructor didn't generate a fatal failure.
+ if ((test != NULL) && !Test::HasFatalFailure()) {
+ // This doesn't throw as all user code that can throw are wrapped into
+ // exception handling code.
+ test->Run();
+ }
+
+ // Deletes the test object.
+ impl->os_stack_trace_getter()->UponLeavingGTest();
+ internal::HandleExceptionsInMethodIfSupported(
+ test, &Test::DeleteSelf_, "the test fixture's destructor");
+
+ result_.set_elapsed_time(internal::GetTimeInMillis() - start);
+
+ // Notifies the unit test event listener that a test has just finished.
+ repeater->OnTestEnd(*this);
+
+ // Tells UnitTest to stop associating assertion results to this
+ // test.
+ impl->set_current_test_info(NULL);
+}
+
+// class TestCase
+
+// Gets the number of successful tests in this test case.
+int TestCase::successful_test_count() const {
+ return CountIf(test_info_list_, TestPassed);
+}
+
+// Gets the number of failed tests in this test case.
+int TestCase::failed_test_count() const {
+ return CountIf(test_info_list_, TestFailed);
+}
+
+// Gets the number of disabled tests that will be reported in the XML report.
+int TestCase::reportable_disabled_test_count() const {
+ return CountIf(test_info_list_, TestReportableDisabled);
+}
+
+// Gets the number of disabled tests in this test case.
+int TestCase::disabled_test_count() const {
+ return CountIf(test_info_list_, TestDisabled);
+}
+
+// Gets the number of tests to be printed in the XML report.
+int TestCase::reportable_test_count() const {
+ return CountIf(test_info_list_, TestReportable);
+}
+
+// Get the number of tests in this test case that should run.
+int TestCase::test_to_run_count() const {
+ return CountIf(test_info_list_, ShouldRunTest);
+}
+
+// Gets the number of all tests.
+int TestCase::total_test_count() const {
+ return static_cast<int>(test_info_list_.size());
+}
+
+// Creates a TestCase with the given name.
+//
+// Arguments:
+//
+// name: name of the test case
+// a_type_param: the name of the test case's type parameter, or NULL if
+// this is not a typed or a type-parameterized test case.
+// set_up_tc: pointer to the function that sets up the test case
+// tear_down_tc: pointer to the function that tears down the test case
+TestCase::TestCase(const char* a_name, const char* a_type_param,
+ Test::SetUpTestCaseFunc set_up_tc,
+ Test::TearDownTestCaseFunc tear_down_tc)
+ : name_(a_name),
+ type_param_(a_type_param ? new std::string(a_type_param) : NULL),
+ set_up_tc_(set_up_tc),
+ tear_down_tc_(tear_down_tc),
+ should_run_(false),
+ elapsed_time_(0) {
+}
+
+// Destructor of TestCase.
+TestCase::~TestCase() {
+ // Deletes every Test in the collection.
+ ForEach(test_info_list_, internal::Delete<TestInfo>);
+}
+
+// Returns the i-th test among all the tests. i can range from 0 to
+// total_test_count() - 1. If i is not in that range, returns NULL.
+const TestInfo* TestCase::GetTestInfo(int i) const {
+ const int index = GetElementOr(test_indices_, i, -1);
+ return index < 0 ? NULL : test_info_list_[index];
+}
+
+// Returns the i-th test among all the tests. i can range from 0 to
+// total_test_count() - 1. If i is not in that range, returns NULL.
+TestInfo* TestCase::GetMutableTestInfo(int i) {
+ const int index = GetElementOr(test_indices_, i, -1);
+ return index < 0 ? NULL : test_info_list_[index];
+}
+
+// Adds a test to this test case. Will delete the test upon
+// destruction of the TestCase object.
+void TestCase::AddTestInfo(TestInfo * test_info) {
+ test_info_list_.push_back(test_info);
+ test_indices_.push_back(static_cast<int>(test_indices_.size()));
+}
+
+// Runs every test in this TestCase.
+void TestCase::Run() {
+ if (!should_run_) return;
+
+ internal::UnitTestImpl* const impl = internal::GetUnitTestImpl();
+ impl->set_current_test_case(this);
+
+ TestEventListener* repeater = UnitTest::GetInstance()->listeners().repeater();
+
+ repeater->OnTestCaseStart(*this);
+ impl->os_stack_trace_getter()->UponLeavingGTest();
+ internal::HandleExceptionsInMethodIfSupported(
+ this, &TestCase::RunSetUpTestCase, "SetUpTestCase()");
+
+ const internal::TimeInMillis start = internal::GetTimeInMillis();
+ for (int i = 0; i < total_test_count(); i++) {
+ GetMutableTestInfo(i)->Run();
+ }
+ elapsed_time_ = internal::GetTimeInMillis() - start;
+
+ impl->os_stack_trace_getter()->UponLeavingGTest();
+ internal::HandleExceptionsInMethodIfSupported(
+ this, &TestCase::RunTearDownTestCase, "TearDownTestCase()");
+
+ repeater->OnTestCaseEnd(*this);
+ impl->set_current_test_case(NULL);
+}
+
+// Clears the results of all tests in this test case.
+void TestCase::ClearResult() {
+ ad_hoc_test_result_.Clear();
+ ForEach(test_info_list_, TestInfo::ClearTestResult);
+}
+
+// Shuffles the tests in this test case.
+void TestCase::ShuffleTests(internal::Random* random) {
+ Shuffle(random, &test_indices_);
+}
+
+// Restores the test order to before the first shuffle.
+void TestCase::UnshuffleTests() {
+ for (size_t i = 0; i < test_indices_.size(); i++) {
+ test_indices_[i] = static_cast<int>(i);
+ }
+}
+
+// Formats a countable noun. Depending on its quantity, either the
+// singular form or the plural form is used. e.g.
+//
+// FormatCountableNoun(1, "formula", "formuli") returns "1 formula".
+// FormatCountableNoun(5, "book", "books") returns "5 books".
+static std::string FormatCountableNoun(int count,
+ const char * singular_form,
+ const char * plural_form) {
+ return internal::StreamableToString(count) + " " +
+ (count == 1 ? singular_form : plural_form);
+}
+
+// Formats the count of tests.
+static std::string FormatTestCount(int test_count) {
+ return FormatCountableNoun(test_count, "test", "tests");
+}
+
+// Formats the count of test cases.
+static std::string FormatTestCaseCount(int test_case_count) {
+ return FormatCountableNoun(test_case_count, "test case", "test cases");
+}
+
+// Converts a TestPartResult::Type enum to human-friendly string
+// representation. Both kNonFatalFailure and kFatalFailure are translated
+// to "Failure", as the user usually doesn't care about the difference
+// between the two when viewing the test result.
+static const char * TestPartResultTypeToString(TestPartResult::Type type) {
+ switch (type) {
+ case TestPartResult::kSuccess:
+ return "Success";
+
+ case TestPartResult::kNonFatalFailure:
+ case TestPartResult::kFatalFailure:
+#ifdef _MSC_VER
+ return "error: ";
+#else
+ return "Failure\n";
+#endif
+ default:
+ return "Unknown result type";
+ }
+}
+
+namespace internal {
+
+// Prints a TestPartResult to an std::string.
+static std::string PrintTestPartResultToString(
+ const TestPartResult& test_part_result) {
+ return (Message()
+ << internal::FormatFileLocation(test_part_result.file_name(),
+ test_part_result.line_number())
+ << " " << TestPartResultTypeToString(test_part_result.type())
+ << test_part_result.message()).GetString();
+}
+
+// Prints a TestPartResult.
+static void PrintTestPartResult(const TestPartResult& test_part_result) {
+ const std::string& result =
+ PrintTestPartResultToString(test_part_result);
+ printf("%s\n", result.c_str());
+ fflush(stdout);
+ // If the test program runs in Visual Studio or a debugger, the
+ // following statements add the test part result message to the Output
+ // window such that the user can double-click on it to jump to the
+ // corresponding source code location; otherwise they do nothing.
+#if GTEST_OS_WINDOWS && !GTEST_OS_WINDOWS_MOBILE
+ // We don't call OutputDebugString*() on Windows Mobile, as printing
+ // to stdout is done by OutputDebugString() there already - we don't
+ // want the same message printed twice.
+ ::OutputDebugStringA(result.c_str());
+ ::OutputDebugStringA("\n");
+#endif
+}
+
+// class PrettyUnitTestResultPrinter
+
+enum GTestColor {
+ COLOR_DEFAULT,
+ COLOR_RED,
+ COLOR_GREEN,
+ COLOR_YELLOW
+};
+
+#if GTEST_OS_WINDOWS && !GTEST_OS_WINDOWS_MOBILE
+
+// Returns the character attribute for the given color.
+WORD GetColorAttribute(GTestColor color) {
+ switch (color) {
+ case COLOR_RED: return FOREGROUND_RED;
+ case COLOR_GREEN: return FOREGROUND_GREEN;
+ case COLOR_YELLOW: return FOREGROUND_RED | FOREGROUND_GREEN;
+ default: return 0;
+ }
+}
+
+#else
+
+// Returns the ANSI color code for the given color. COLOR_DEFAULT is
+// an invalid input.
+const char* GetAnsiColorCode(GTestColor color) {
+ switch (color) {
+ case COLOR_RED: return "1";
+ case COLOR_GREEN: return "2";
+ case COLOR_YELLOW: return "3";
+ default: return NULL;
+ };
+}
+
+#endif // GTEST_OS_WINDOWS && !GTEST_OS_WINDOWS_MOBILE
+
+// Returns true iff Google Test should use colors in the output.
+bool ShouldUseColor(bool stdout_is_tty) {
+ const char* const gtest_color = GTEST_FLAG(color).c_str();
+
+ if (String::CaseInsensitiveCStringEquals(gtest_color, "auto")) {
+#if GTEST_OS_WINDOWS
+ // On Windows the TERM variable is usually not set, but the
+ // console there does support colors.
+ return stdout_is_tty;
+#else
+ // On non-Windows platforms, we rely on the TERM variable.
+ const char* const term = posix::GetEnv("TERM");
+ const bool term_supports_color =
+ String::CStringEquals(term, "xterm") ||
+ String::CStringEquals(term, "xterm-color") ||
+ String::CStringEquals(term, "xterm-256color") ||
+ String::CStringEquals(term, "screen") ||
+ String::CStringEquals(term, "screen-256color") ||
+ String::CStringEquals(term, "linux") ||
+ String::CStringEquals(term, "cygwin");
+ return stdout_is_tty && term_supports_color;
+#endif // GTEST_OS_WINDOWS
+ }
+
+ return String::CaseInsensitiveCStringEquals(gtest_color, "yes") ||
+ String::CaseInsensitiveCStringEquals(gtest_color, "true") ||
+ String::CaseInsensitiveCStringEquals(gtest_color, "t") ||
+ String::CStringEquals(gtest_color, "1");
+ // We take "yes", "true", "t", and "1" as meaning "yes". If the
+ // value is neither one of these nor "auto", we treat it as "no" to
+ // be conservative.
+}
+
+// Helpers for printing colored strings to stdout. Note that on Windows, we
+// cannot simply emit special characters and have the terminal change colors.
+// This routine must actually emit the characters rather than return a string
+// that would be colored when printed, as can be done on Linux.
+void ColoredPrintf(GTestColor color, const char* fmt, ...) {
+ va_list args;
+ va_start(args, fmt);
+
+#if GTEST_OS_WINDOWS_MOBILE || GTEST_OS_SYMBIAN || GTEST_OS_ZOS || GTEST_OS_IOS
+ const bool use_color = false;
+#else
+ static const bool in_color_mode =
+ ShouldUseColor(posix::IsATTY(posix::FileNo(stdout)) != 0);
+ const bool use_color = in_color_mode && (color != COLOR_DEFAULT);
+#endif // GTEST_OS_WINDOWS_MOBILE || GTEST_OS_SYMBIAN || GTEST_OS_ZOS
+ // The '!= 0' comparison is necessary to satisfy MSVC 7.1.
+
+ if (!use_color) {
+ vprintf(fmt, args);
+ va_end(args);
+ return;
+ }
+
+#if GTEST_OS_WINDOWS && !GTEST_OS_WINDOWS_MOBILE
+ const HANDLE stdout_handle = GetStdHandle(STD_OUTPUT_HANDLE);
+
+ // Gets the current text color.
+ CONSOLE_SCREEN_BUFFER_INFO buffer_info;
+ GetConsoleScreenBufferInfo(stdout_handle, &buffer_info);
+ const WORD old_color_attrs = buffer_info.wAttributes;
+
+ // We need to flush the stream buffers into the console before each
+ // SetConsoleTextAttribute call lest it affect the text that is already
+ // printed but has not yet reached the console.
+ fflush(stdout);
+ SetConsoleTextAttribute(stdout_handle,
+ GetColorAttribute(color) | FOREGROUND_INTENSITY);
+ vprintf(fmt, args);
+
+ fflush(stdout);
+ // Restores the text color.
+ SetConsoleTextAttribute(stdout_handle, old_color_attrs);
+#else
+ printf("\033[0;3%sm", GetAnsiColorCode(color));
+ vprintf(fmt, args);
+ printf("\033[m"); // Resets the terminal to default.
+#endif // GTEST_OS_WINDOWS && !GTEST_OS_WINDOWS_MOBILE
+ va_end(args);
+}
+
+// Text printed in Google Test's text output and --gunit_list_tests
+// output to label the type parameter and value parameter for a test.
+static const char kTypeParamLabel[] = "TypeParam";
+static const char kValueParamLabel[] = "GetParam()";
+
+void PrintFullTestCommentIfPresent(const TestInfo& test_info) {
+ const char* const type_param = test_info.type_param();
+ const char* const value_param = test_info.value_param();
+
+ if (type_param != NULL || value_param != NULL) {
+ printf(", where ");
+ if (type_param != NULL) {
+ printf("%s = %s", kTypeParamLabel, type_param);
+ if (value_param != NULL)
+ printf(" and ");
+ }
+ if (value_param != NULL) {
+ printf("%s = %s", kValueParamLabel, value_param);
+ }
+ }
+}
+
+// This class implements the TestEventListener interface.
+//
+// Class PrettyUnitTestResultPrinter is copyable.
+class PrettyUnitTestResultPrinter : public TestEventListener {
+ public:
+ PrettyUnitTestResultPrinter() {}
+ static void PrintTestName(const char * test_case, const char * test) {
+ printf("%s.%s", test_case, test);
+ }
+
+ // The following methods override what's in the TestEventListener class.
+ virtual void OnTestProgramStart(const UnitTest& /*unit_test*/) {}
+ virtual void OnTestIterationStart(const UnitTest& unit_test, int iteration);
+ virtual void OnEnvironmentsSetUpStart(const UnitTest& unit_test);
+ virtual void OnEnvironmentsSetUpEnd(const UnitTest& /*unit_test*/) {}
+ virtual void OnTestCaseStart(const TestCase& test_case);
+ virtual void OnTestStart(const TestInfo& test_info);
+ virtual void OnTestPartResult(const TestPartResult& result);
+ virtual void OnTestEnd(const TestInfo& test_info);
+ virtual void OnTestCaseEnd(const TestCase& test_case);
+ virtual void OnEnvironmentsTearDownStart(const UnitTest& unit_test);
+ virtual void OnEnvironmentsTearDownEnd(const UnitTest& /*unit_test*/) {}
+ virtual void OnTestIterationEnd(const UnitTest& unit_test, int iteration);
+ virtual void OnTestProgramEnd(const UnitTest& /*unit_test*/) {}
+
+ private:
+ static void PrintFailedTests(const UnitTest& unit_test);
+};
+
+ // Fired before each iteration of tests starts.
+void PrettyUnitTestResultPrinter::OnTestIterationStart(
+ const UnitTest& unit_test, int iteration) {
+ if (GTEST_FLAG(repeat) != 1)
+ printf("\nRepeating all tests (iteration %d) . . .\n\n", iteration + 1);
+
+ const char* const filter = GTEST_FLAG(filter).c_str();
+
+ // Prints the filter if it's not *. This reminds the user that some
+ // tests may be skipped.
+ if (!String::CStringEquals(filter, kUniversalFilter)) {
+ ColoredPrintf(COLOR_YELLOW,
+ "Note: %s filter = %s\n", GTEST_NAME_, filter);
+ }
+
+ if (internal::ShouldShard(kTestTotalShards, kTestShardIndex, false)) {
+ const Int32 shard_index = Int32FromEnvOrDie(kTestShardIndex, -1);
+ ColoredPrintf(COLOR_YELLOW,
+ "Note: This is test shard %d of %s.\n",
+ static_cast<int>(shard_index) + 1,
+ internal::posix::GetEnv(kTestTotalShards));
+ }
+
+ if (GTEST_FLAG(shuffle)) {
+ ColoredPrintf(COLOR_YELLOW,
+ "Note: Randomizing tests' orders with a seed of %d .\n",
+ unit_test.random_seed());
+ }
+
+ ColoredPrintf(COLOR_GREEN, "[==========] ");
+ printf("Running %s from %s.\n",
+ FormatTestCount(unit_test.test_to_run_count()).c_str(),
+ FormatTestCaseCount(unit_test.test_case_to_run_count()).c_str());
+ fflush(stdout);
+}
+
+void PrettyUnitTestResultPrinter::OnEnvironmentsSetUpStart(
+ const UnitTest& /*unit_test*/) {
+ ColoredPrintf(COLOR_GREEN, "[----------] ");
+ printf("Global test environment set-up.\n");
+ fflush(stdout);
+}
+
+void PrettyUnitTestResultPrinter::OnTestCaseStart(const TestCase& test_case) {
+ const std::string counts =
+ FormatCountableNoun(test_case.test_to_run_count(), "test", "tests");
+ ColoredPrintf(COLOR_GREEN, "[----------] ");
+ printf("%s from %s", counts.c_str(), test_case.name());
+ if (test_case.type_param() == NULL) {
+ printf("\n");
+ } else {
+ printf(", where %s = %s\n", kTypeParamLabel, test_case.type_param());
+ }
+ fflush(stdout);
+}
+
+void PrettyUnitTestResultPrinter::OnTestStart(const TestInfo& test_info) {
+ ColoredPrintf(COLOR_GREEN, "[ RUN ] ");
+ PrintTestName(test_info.test_case_name(), test_info.name());
+ printf("\n");
+ fflush(stdout);
+}
+
+// Called after an assertion failure.
+void PrettyUnitTestResultPrinter::OnTestPartResult(
+ const TestPartResult& result) {
+ // If the test part succeeded, we don't need to do anything.
+ if (result.type() == TestPartResult::kSuccess)
+ return;
+
+ // Print failure message from the assertion (e.g. expected this and got that).
+ PrintTestPartResult(result);
+ fflush(stdout);
+}
+
+void PrettyUnitTestResultPrinter::OnTestEnd(const TestInfo& test_info) {
+ if (test_info.result()->Passed()) {
+ ColoredPrintf(COLOR_GREEN, "[ OK ] ");
+ } else {
+ ColoredPrintf(COLOR_RED, "[ FAILED ] ");
+ }
+ PrintTestName(test_info.test_case_name(), test_info.name());
+ if (test_info.result()->Failed())
+ PrintFullTestCommentIfPresent(test_info);
+
+ if (GTEST_FLAG(print_time)) {
+ printf(" (%s ms)\n", internal::StreamableToString(
+ test_info.result()->elapsed_time()).c_str());
+ } else {
+ printf("\n");
+ }
+ fflush(stdout);
+}
+
+void PrettyUnitTestResultPrinter::OnTestCaseEnd(const TestCase& test_case) {
+ if (!GTEST_FLAG(print_time)) return;
+
+ const std::string counts =
+ FormatCountableNoun(test_case.test_to_run_count(), "test", "tests");
+ ColoredPrintf(COLOR_GREEN, "[----------] ");
+ printf("%s from %s (%s ms total)\n\n",
+ counts.c_str(), test_case.name(),
+ internal::StreamableToString(test_case.elapsed_time()).c_str());
+ fflush(stdout);
+}
+
+void PrettyUnitTestResultPrinter::OnEnvironmentsTearDownStart(
+ const UnitTest& /*unit_test*/) {
+ ColoredPrintf(COLOR_GREEN, "[----------] ");
+ printf("Global test environment tear-down\n");
+ fflush(stdout);
+}
+
+// Internal helper for printing the list of failed tests.
+void PrettyUnitTestResultPrinter::PrintFailedTests(const UnitTest& unit_test) {
+ const int failed_test_count = unit_test.failed_test_count();
+ if (failed_test_count == 0) {
+ return;
+ }
+
+ for (int i = 0; i < unit_test.total_test_case_count(); ++i) {
+ const TestCase& test_case = *unit_test.GetTestCase(i);
+ if (!test_case.should_run() || (test_case.failed_test_count() == 0)) {
+ continue;
+ }
+ for (int j = 0; j < test_case.total_test_count(); ++j) {
+ const TestInfo& test_info = *test_case.GetTestInfo(j);
+ if (!test_info.should_run() || test_info.result()->Passed()) {
+ continue;
+ }
+ ColoredPrintf(COLOR_RED, "[ FAILED ] ");
+ printf("%s.%s", test_case.name(), test_info.name());
+ PrintFullTestCommentIfPresent(test_info);
+ printf("\n");
+ }
+ }
+}
+
+void PrettyUnitTestResultPrinter::OnTestIterationEnd(const UnitTest& unit_test,
+ int /*iteration*/) {
+ ColoredPrintf(COLOR_GREEN, "[==========] ");
+ printf("%s from %s ran.",
+ FormatTestCount(unit_test.test_to_run_count()).c_str(),
+ FormatTestCaseCount(unit_test.test_case_to_run_count()).c_str());
+ if (GTEST_FLAG(print_time)) {
+ printf(" (%s ms total)",
+ internal::StreamableToString(unit_test.elapsed_time()).c_str());
+ }
+ printf("\n");
+ ColoredPrintf(COLOR_GREEN, "[ PASSED ] ");
+ printf("%s.\n", FormatTestCount(unit_test.successful_test_count()).c_str());
+
+ int num_failures = unit_test.failed_test_count();
+ if (!unit_test.Passed()) {
+ const int failed_test_count = unit_test.failed_test_count();
+ ColoredPrintf(COLOR_RED, "[ FAILED ] ");
+ printf("%s, listed below:\n", FormatTestCount(failed_test_count).c_str());
+ PrintFailedTests(unit_test);
+ printf("\n%2d FAILED %s\n", num_failures,
+ num_failures == 1 ? "TEST" : "TESTS");
+ }
+
+ int num_disabled = unit_test.reportable_disabled_test_count();
+ if (num_disabled && !GTEST_FLAG(also_run_disabled_tests)) {
+ if (!num_failures) {
+ printf("\n"); // Add a spacer if no FAILURE banner is displayed.
+ }
+ ColoredPrintf(COLOR_YELLOW,
+ " YOU HAVE %d DISABLED %s\n\n",
+ num_disabled,
+ num_disabled == 1 ? "TEST" : "TESTS");
+ }
+ // Ensure that Google Test output is printed before, e.g., heapchecker output.
+ fflush(stdout);
+}
+
+// End PrettyUnitTestResultPrinter
+
+// class TestEventRepeater
+//
+// This class forwards events to other event listeners.
+class TestEventRepeater : public TestEventListener {
+ public:
+ TestEventRepeater() : forwarding_enabled_(true) {}
+ virtual ~TestEventRepeater();
+ void Append(TestEventListener *listener);
+ TestEventListener* Release(TestEventListener* listener);
+
+ // Controls whether events will be forwarded to listeners_. Set to false
+ // in death test child processes.
+ bool forwarding_enabled() const { return forwarding_enabled_; }
+ void set_forwarding_enabled(bool enable) { forwarding_enabled_ = enable; }
+
+ virtual void OnTestProgramStart(const UnitTest& unit_test);
+ virtual void OnTestIterationStart(const UnitTest& unit_test, int iteration);
+ virtual void OnEnvironmentsSetUpStart(const UnitTest& unit_test);
+ virtual void OnEnvironmentsSetUpEnd(const UnitTest& unit_test);
+ virtual void OnTestCaseStart(const TestCase& test_case);
+ virtual void OnTestStart(const TestInfo& test_info);
+ virtual void OnTestPartResult(const TestPartResult& result);
+ virtual void OnTestEnd(const TestInfo& test_info);
+ virtual void OnTestCaseEnd(const TestCase& test_case);
+ virtual void OnEnvironmentsTearDownStart(const UnitTest& unit_test);
+ virtual void OnEnvironmentsTearDownEnd(const UnitTest& unit_test);
+ virtual void OnTestIterationEnd(const UnitTest& unit_test, int iteration);
+ virtual void OnTestProgramEnd(const UnitTest& unit_test);
+
+ private:
+ // Controls whether events will be forwarded to listeners_. Set to false
+ // in death test child processes.
+ bool forwarding_enabled_;
+ // The list of listeners that receive events.
+ std::vector<TestEventListener*> listeners_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(TestEventRepeater);
+};
+
+TestEventRepeater::~TestEventRepeater() {
+ ForEach(listeners_, Delete<TestEventListener>);
+}
+
+void TestEventRepeater::Append(TestEventListener *listener) {
+ listeners_.push_back(listener);
+}
+
+// TODO(vladl at google.com): Factor the search functionality into Vector::Find.
+TestEventListener* TestEventRepeater::Release(TestEventListener *listener) {
+ for (size_t i = 0; i < listeners_.size(); ++i) {
+ if (listeners_[i] == listener) {
+ listeners_.erase(listeners_.begin() + i);
+ return listener;
+ }
+ }
+
+ return NULL;
+}
+
+// Since most methods are very similar, use macros to reduce boilerplate.
+// This defines a member that forwards the call to all listeners.
+#define GTEST_REPEATER_METHOD_(Name, Type) \
+void TestEventRepeater::Name(const Type& parameter) { \
+ if (forwarding_enabled_) { \
+ for (size_t i = 0; i < listeners_.size(); i++) { \
+ listeners_[i]->Name(parameter); \
+ } \
+ } \
+}
+// This defines a member that forwards the call to all listeners in reverse
+// order.
+#define GTEST_REVERSE_REPEATER_METHOD_(Name, Type) \
+void TestEventRepeater::Name(const Type& parameter) { \
+ if (forwarding_enabled_) { \
+ for (int i = static_cast<int>(listeners_.size()) - 1; i >= 0; i--) { \
+ listeners_[i]->Name(parameter); \
+ } \
+ } \
+}
+
+GTEST_REPEATER_METHOD_(OnTestProgramStart, UnitTest)
+GTEST_REPEATER_METHOD_(OnEnvironmentsSetUpStart, UnitTest)
+GTEST_REPEATER_METHOD_(OnTestCaseStart, TestCase)
+GTEST_REPEATER_METHOD_(OnTestStart, TestInfo)
+GTEST_REPEATER_METHOD_(OnTestPartResult, TestPartResult)
+GTEST_REPEATER_METHOD_(OnEnvironmentsTearDownStart, UnitTest)
+GTEST_REVERSE_REPEATER_METHOD_(OnEnvironmentsSetUpEnd, UnitTest)
+GTEST_REVERSE_REPEATER_METHOD_(OnEnvironmentsTearDownEnd, UnitTest)
+GTEST_REVERSE_REPEATER_METHOD_(OnTestEnd, TestInfo)
+GTEST_REVERSE_REPEATER_METHOD_(OnTestCaseEnd, TestCase)
+GTEST_REVERSE_REPEATER_METHOD_(OnTestProgramEnd, UnitTest)
+
+#undef GTEST_REPEATER_METHOD_
+#undef GTEST_REVERSE_REPEATER_METHOD_
+
+void TestEventRepeater::OnTestIterationStart(const UnitTest& unit_test,
+ int iteration) {
+ if (forwarding_enabled_) {
+ for (size_t i = 0; i < listeners_.size(); i++) {
+ listeners_[i]->OnTestIterationStart(unit_test, iteration);
+ }
+ }
+}
+
+void TestEventRepeater::OnTestIterationEnd(const UnitTest& unit_test,
+ int iteration) {
+ if (forwarding_enabled_) {
+ for (int i = static_cast<int>(listeners_.size()) - 1; i >= 0; i--) {
+ listeners_[i]->OnTestIterationEnd(unit_test, iteration);
+ }
+ }
+}
+
+// End TestEventRepeater
+
+// This class generates an XML output file.
+class XmlUnitTestResultPrinter : public EmptyTestEventListener {
+ public:
+ explicit XmlUnitTestResultPrinter(const char* output_file);
+
+ virtual void OnTestIterationEnd(const UnitTest& unit_test, int iteration);
+
+ private:
+ // Is c a whitespace character that is normalized to a space character
+ // when it appears in an XML attribute value?
+ static bool IsNormalizableWhitespace(char c) {
+ return c == 0x9 || c == 0xA || c == 0xD;
+ }
+
+ // May c appear in a well-formed XML document?
+ static bool IsValidXmlCharacter(char c) {
+ return IsNormalizableWhitespace(c) || c >= 0x20;
+ }
+
+ // Returns an XML-escaped copy of the input string str. If
+ // is_attribute is true, the text is meant to appear as an attribute
+ // value, and normalizable whitespace is preserved by replacing it
+ // with character references.
+ static std::string EscapeXml(const std::string& str, bool is_attribute);
+
+ // Returns the given string with all characters invalid in XML removed.
+ static std::string RemoveInvalidXmlCharacters(const std::string& str);
+
+ // Convenience wrapper around EscapeXml when str is an attribute value.
+ static std::string EscapeXmlAttribute(const std::string& str) {
+ return EscapeXml(str, true);
+ }
+
+ // Convenience wrapper around EscapeXml when str is not an attribute value.
+ static std::string EscapeXmlText(const char* str) {
+ return EscapeXml(str, false);
+ }
+
+ // Verifies that the given attribute belongs to the given element and
+ // streams the attribute as XML.
+ static void OutputXmlAttribute(std::ostream* stream,
+ const std::string& element_name,
+ const std::string& name,
+ const std::string& value);
+
+ // Streams an XML CDATA section, escaping invalid CDATA sequences as needed.
+ static void OutputXmlCDataSection(::std::ostream* stream, const char* data);
+
+ // Streams an XML representation of a TestInfo object.
+ static void OutputXmlTestInfo(::std::ostream* stream,
+ const char* test_case_name,
+ const TestInfo& test_info);
+
+ // Prints an XML representation of a TestCase object
+ static void PrintXmlTestCase(::std::ostream* stream,
+ const TestCase& test_case);
+
+ // Prints an XML summary of unit_test to output stream out.
+ static void PrintXmlUnitTest(::std::ostream* stream,
+ const UnitTest& unit_test);
+
+ // Produces a string representing the test properties in a result as space
+ // delimited XML attributes based on the property key="value" pairs.
+ // When the std::string is not empty, it includes a space at the beginning,
+ // to delimit this attribute from prior attributes.
+ static std::string TestPropertiesAsXmlAttributes(const TestResult& result);
+
+ // The output file.
+ const std::string output_file_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(XmlUnitTestResultPrinter);
+};
+
+// Creates a new XmlUnitTestResultPrinter.
+XmlUnitTestResultPrinter::XmlUnitTestResultPrinter(const char* output_file)
+ : output_file_(output_file) {
+ if (output_file_.c_str() == NULL || output_file_.empty()) {
+ fprintf(stderr, "XML output file may not be null\n");
+ fflush(stderr);
+ exit(EXIT_FAILURE);
+ }
+}
+
+// Called after the unit test ends.
+void XmlUnitTestResultPrinter::OnTestIterationEnd(const UnitTest& unit_test,
+ int /*iteration*/) {
+ FILE* xmlout = NULL;
+ FilePath output_file(output_file_);
+ FilePath output_dir(output_file.RemoveFileName());
+
+ if (output_dir.CreateDirectoriesRecursively()) {
+ xmlout = posix::FOpen(output_file_.c_str(), "w");
+ }
+ if (xmlout == NULL) {
+ // TODO(wan): report the reason of the failure.
+ //
+ // We don't do it for now as:
+ //
+ // 1. There is no urgent need for it.
+ // 2. It's a bit involved to make the errno variable thread-safe on
+ // all three operating systems (Linux, Windows, and Mac OS).
+ // 3. To interpret the meaning of errno in a thread-safe way,
+ // we need the strerror_r() function, which is not available on
+ // Windows.
+ fprintf(stderr,
+ "Unable to open file \"%s\"\n",
+ output_file_.c_str());
+ fflush(stderr);
+ exit(EXIT_FAILURE);
+ }
+ std::stringstream stream;
+ PrintXmlUnitTest(&stream, unit_test);
+ fprintf(xmlout, "%s", StringStreamToString(&stream).c_str());
+ fclose(xmlout);
+}
+
+// Returns an XML-escaped copy of the input string str. If is_attribute
+// is true, the text is meant to appear as an attribute value, and
+// normalizable whitespace is preserved by replacing it with character
+// references.
+//
+// Invalid XML characters in str, if any, are stripped from the output.
+// It is expected that most, if not all, of the text processed by this
+// module will consist of ordinary English text.
+// If this module is ever modified to produce version 1.1 XML output,
+// most invalid characters can be retained using character references.
+// TODO(wan): It might be nice to have a minimally invasive, human-readable
+// escaping scheme for invalid characters, rather than dropping them.
+std::string XmlUnitTestResultPrinter::EscapeXml(
+ const std::string& str, bool is_attribute) {
+ Message m;
+
+ for (size_t i = 0; i < str.size(); ++i) {
+ const char ch = str[i];
+ switch (ch) {
+ case '<':
+ m << "<";
+ break;
+ case '>':
+ m << ">";
+ break;
+ case '&':
+ m << "&";
+ break;
+ case '\'':
+ if (is_attribute)
+ m << "'";
+ else
+ m << '\'';
+ break;
+ case '"':
+ if (is_attribute)
+ m << """;
+ else
+ m << '"';
+ break;
+ default:
+ if (IsValidXmlCharacter(ch)) {
+ if (is_attribute && IsNormalizableWhitespace(ch))
+ m << "&#x" << String::FormatByte(static_cast<unsigned char>(ch))
+ << ";";
+ else
+ m << ch;
+ }
+ break;
+ }
+ }
+
+ return m.GetString();
+}
+
+// Returns the given string with all characters invalid in XML removed.
+// Currently invalid characters are dropped from the string. An
+// alternative is to replace them with certain characters such as . or ?.
+std::string XmlUnitTestResultPrinter::RemoveInvalidXmlCharacters(
+ const std::string& str) {
+ std::string output;
+ output.reserve(str.size());
+ for (std::string::const_iterator it = str.begin(); it != str.end(); ++it)
+ if (IsValidXmlCharacter(*it))
+ output.push_back(*it);
+
+ return output;
+}
+
+// The following routines generate an XML representation of a UnitTest
+// object.
+//
+// This is how Google Test concepts map to the DTD:
+//
+// <testsuites name="AllTests"> <-- corresponds to a UnitTest object
+// <testsuite name="testcase-name"> <-- corresponds to a TestCase object
+// <testcase name="test-name"> <-- corresponds to a TestInfo object
+// <failure message="...">...</failure>
+// <failure message="...">...</failure>
+// <failure message="...">...</failure>
+// <-- individual assertion failures
+// </testcase>
+// </testsuite>
+// </testsuites>
+
+// Formats the given time in milliseconds as seconds.
+std::string FormatTimeInMillisAsSeconds(TimeInMillis ms) {
+ ::std::stringstream ss;
+ ss << ms/1000.0;
+ return ss.str();
+}
+
+// Converts the given epoch time in milliseconds to a date string in the ISO
+// 8601 format, without the timezone information.
+std::string FormatEpochTimeInMillisAsIso8601(TimeInMillis ms) {
+ // Using non-reentrant version as localtime_r is not portable.
+ time_t seconds = static_cast<time_t>(ms / 1000);
+#ifdef _MSC_VER
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4996) // Temporarily disables warning 4996
+ // (function or variable may be unsafe).
+ const struct tm* const time_struct = localtime(&seconds); // NOLINT
+# pragma warning(pop) // Restores the warning state again.
+#else
+ const struct tm* const time_struct = localtime(&seconds); // NOLINT
+#endif
+ if (time_struct == NULL)
+ return ""; // Invalid ms value
+
+ // YYYY-MM-DDThh:mm:ss
+ return StreamableToString(time_struct->tm_year + 1900) + "-" +
+ String::FormatIntWidth2(time_struct->tm_mon + 1) + "-" +
+ String::FormatIntWidth2(time_struct->tm_mday) + "T" +
+ String::FormatIntWidth2(time_struct->tm_hour) + ":" +
+ String::FormatIntWidth2(time_struct->tm_min) + ":" +
+ String::FormatIntWidth2(time_struct->tm_sec);
+}
+
+// Streams an XML CDATA section, escaping invalid CDATA sequences as needed.
+void XmlUnitTestResultPrinter::OutputXmlCDataSection(::std::ostream* stream,
+ const char* data) {
+ const char* segment = data;
+ *stream << "<![CDATA[";
+ for (;;) {
+ const char* const next_segment = strstr(segment, "]]>");
+ if (next_segment != NULL) {
+ stream->write(
+ segment, static_cast<std::streamsize>(next_segment - segment));
+ *stream << "]]>]]><![CDATA[";
+ segment = next_segment + strlen("]]>");
+ } else {
+ *stream << segment;
+ break;
+ }
+ }
+ *stream << "]]>";
+}
+
+void XmlUnitTestResultPrinter::OutputXmlAttribute(
+ std::ostream* stream,
+ const std::string& element_name,
+ const std::string& name,
+ const std::string& value) {
+ const std::vector<std::string>& allowed_names =
+ GetReservedAttributesForElement(element_name);
+
+ GTEST_CHECK_(std::find(allowed_names.begin(), allowed_names.end(), name) !=
+ allowed_names.end())
+ << "Attribute " << name << " is not allowed for element <" << element_name
+ << ">.";
+
+ *stream << " " << name << "=\"" << EscapeXmlAttribute(value) << "\"";
+}
+
+// Prints an XML representation of a TestInfo object.
+// TODO(wan): There is also value in printing properties with the plain printer.
+void XmlUnitTestResultPrinter::OutputXmlTestInfo(::std::ostream* stream,
+ const char* test_case_name,
+ const TestInfo& test_info) {
+ const TestResult& result = *test_info.result();
+ const std::string kTestcase = "testcase";
+
+ *stream << " <testcase";
+ OutputXmlAttribute(stream, kTestcase, "name", test_info.name());
+
+ if (test_info.value_param() != NULL) {
+ OutputXmlAttribute(stream, kTestcase, "value_param",
+ test_info.value_param());
+ }
+ if (test_info.type_param() != NULL) {
+ OutputXmlAttribute(stream, kTestcase, "type_param", test_info.type_param());
+ }
+
+ OutputXmlAttribute(stream, kTestcase, "status",
+ test_info.should_run() ? "run" : "notrun");
+ OutputXmlAttribute(stream, kTestcase, "time",
+ FormatTimeInMillisAsSeconds(result.elapsed_time()));
+ OutputXmlAttribute(stream, kTestcase, "classname", test_case_name);
+ *stream << TestPropertiesAsXmlAttributes(result);
+
+ int failures = 0;
+ for (int i = 0; i < result.total_part_count(); ++i) {
+ const TestPartResult& part = result.GetTestPartResult(i);
+ if (part.failed()) {
+ if (++failures == 1) {
+ *stream << ">\n";
+ }
+ const string location = internal::FormatCompilerIndependentFileLocation(
+ part.file_name(), part.line_number());
+ const string summary = location + "\n" + part.summary();
+ *stream << " <failure message=\""
+ << EscapeXmlAttribute(summary.c_str())
+ << "\" type=\"\">";
+ const string detail = location + "\n" + part.message();
+ OutputXmlCDataSection(stream, RemoveInvalidXmlCharacters(detail).c_str());
+ *stream << "</failure>\n";
+ }
+ }
+
+ if (failures == 0)
+ *stream << " />\n";
+ else
+ *stream << " </testcase>\n";
+}
+
+// Prints an XML representation of a TestCase object
+void XmlUnitTestResultPrinter::PrintXmlTestCase(std::ostream* stream,
+ const TestCase& test_case) {
+ const std::string kTestsuite = "testsuite";
+ *stream << " <" << kTestsuite;
+ OutputXmlAttribute(stream, kTestsuite, "name", test_case.name());
+ OutputXmlAttribute(stream, kTestsuite, "tests",
+ StreamableToString(test_case.reportable_test_count()));
+ OutputXmlAttribute(stream, kTestsuite, "failures",
+ StreamableToString(test_case.failed_test_count()));
+ OutputXmlAttribute(
+ stream, kTestsuite, "disabled",
+ StreamableToString(test_case.reportable_disabled_test_count()));
+ OutputXmlAttribute(stream, kTestsuite, "errors", "0");
+ OutputXmlAttribute(stream, kTestsuite, "time",
+ FormatTimeInMillisAsSeconds(test_case.elapsed_time()));
+ *stream << TestPropertiesAsXmlAttributes(test_case.ad_hoc_test_result())
+ << ">\n";
+
+ for (int i = 0; i < test_case.total_test_count(); ++i) {
+ if (test_case.GetTestInfo(i)->is_reportable())
+ OutputXmlTestInfo(stream, test_case.name(), *test_case.GetTestInfo(i));
+ }
+ *stream << " </" << kTestsuite << ">\n";
+}
+
+// Prints an XML summary of unit_test to output stream out.
+void XmlUnitTestResultPrinter::PrintXmlUnitTest(std::ostream* stream,
+ const UnitTest& unit_test) {
+ const std::string kTestsuites = "testsuites";
+
+ *stream << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
+ *stream << "<" << kTestsuites;
+
+ OutputXmlAttribute(stream, kTestsuites, "tests",
+ StreamableToString(unit_test.reportable_test_count()));
+ OutputXmlAttribute(stream, kTestsuites, "failures",
+ StreamableToString(unit_test.failed_test_count()));
+ OutputXmlAttribute(
+ stream, kTestsuites, "disabled",
+ StreamableToString(unit_test.reportable_disabled_test_count()));
+ OutputXmlAttribute(stream, kTestsuites, "errors", "0");
+ OutputXmlAttribute(
+ stream, kTestsuites, "timestamp",
+ FormatEpochTimeInMillisAsIso8601(unit_test.start_timestamp()));
+ OutputXmlAttribute(stream, kTestsuites, "time",
+ FormatTimeInMillisAsSeconds(unit_test.elapsed_time()));
+
+ if (GTEST_FLAG(shuffle)) {
+ OutputXmlAttribute(stream, kTestsuites, "random_seed",
+ StreamableToString(unit_test.random_seed()));
+ }
+
+ *stream << TestPropertiesAsXmlAttributes(unit_test.ad_hoc_test_result());
+
+ OutputXmlAttribute(stream, kTestsuites, "name", "AllTests");
+ *stream << ">\n";
+
+ for (int i = 0; i < unit_test.total_test_case_count(); ++i) {
+ if (unit_test.GetTestCase(i)->reportable_test_count() > 0)
+ PrintXmlTestCase(stream, *unit_test.GetTestCase(i));
+ }
+ *stream << "</" << kTestsuites << ">\n";
+}
+
+// Produces a string representing the test properties in a result as space
+// delimited XML attributes based on the property key="value" pairs.
+std::string XmlUnitTestResultPrinter::TestPropertiesAsXmlAttributes(
+ const TestResult& result) {
+ Message attributes;
+ for (int i = 0; i < result.test_property_count(); ++i) {
+ const TestProperty& property = result.GetTestProperty(i);
+ attributes << " " << property.key() << "="
+ << "\"" << EscapeXmlAttribute(property.value()) << "\"";
+ }
+ return attributes.GetString();
+}
+
+// End XmlUnitTestResultPrinter
+
+#if GTEST_CAN_STREAM_RESULTS_
+
+// Checks if str contains '=', '&', '%' or '\n' characters. If yes,
+// replaces them by "%xx" where xx is their hexadecimal value. For
+// example, replaces "=" with "%3D". This algorithm is O(strlen(str))
+// in both time and space -- important as the input str may contain an
+// arbitrarily long test failure message and stack trace.
+string StreamingListener::UrlEncode(const char* str) {
+ string result;
+ result.reserve(strlen(str) + 1);
+ for (char ch = *str; ch != '\0'; ch = *++str) {
+ switch (ch) {
+ case '%':
+ case '=':
+ case '&':
+ case '\n':
+ result.append("%" + String::FormatByte(static_cast<unsigned char>(ch)));
+ break;
+ default:
+ result.push_back(ch);
+ break;
+ }
+ }
+ return result;
+}
+
+void StreamingListener::SocketWriter::MakeConnection() {
+ GTEST_CHECK_(sockfd_ == -1)
+ << "MakeConnection() can't be called when there is already a connection.";
+
+ addrinfo hints;
+ memset(&hints, 0, sizeof(hints));
+ hints.ai_family = AF_UNSPEC; // To allow both IPv4 and IPv6 addresses.
+ hints.ai_socktype = SOCK_STREAM;
+ addrinfo* servinfo = NULL;
+
+ // Use the getaddrinfo() to get a linked list of IP addresses for
+ // the given host name.
+ const int error_num = getaddrinfo(
+ host_name_.c_str(), port_num_.c_str(), &hints, &servinfo);
+ if (error_num != 0) {
+ GTEST_LOG_(WARNING) << "stream_result_to: getaddrinfo() failed: "
+ << gai_strerror(error_num);
+ }
+
+ // Loop through all the results and connect to the first we can.
+ for (addrinfo* cur_addr = servinfo; sockfd_ == -1 && cur_addr != NULL;
+ cur_addr = cur_addr->ai_next) {
+ sockfd_ = socket(
+ cur_addr->ai_family, cur_addr->ai_socktype, cur_addr->ai_protocol);
+ if (sockfd_ != -1) {
+ // Connect the client socket to the server socket.
+ if (connect(sockfd_, cur_addr->ai_addr, cur_addr->ai_addrlen) == -1) {
+ close(sockfd_);
+ sockfd_ = -1;
+ }
+ }
+ }
+
+ freeaddrinfo(servinfo); // all done with this structure
+
+ if (sockfd_ == -1) {
+ GTEST_LOG_(WARNING) << "stream_result_to: failed to connect to "
+ << host_name_ << ":" << port_num_;
+ }
+}
+
+// End of class Streaming Listener
+#endif // GTEST_CAN_STREAM_RESULTS__
+
+// Class ScopedTrace
+
+// Pushes the given source file location and message onto a per-thread
+// trace stack maintained by Google Test.
+ScopedTrace::ScopedTrace(const char* file, int line, const Message& message)
+ GTEST_LOCK_EXCLUDED_(&UnitTest::mutex_) {
+ TraceInfo trace;
+ trace.file = file;
+ trace.line = line;
+ trace.message = message.GetString();
+
+ UnitTest::GetInstance()->PushGTestTrace(trace);
+}
+
+// Pops the info pushed by the c'tor.
+ScopedTrace::~ScopedTrace()
+ GTEST_LOCK_EXCLUDED_(&UnitTest::mutex_) {
+ UnitTest::GetInstance()->PopGTestTrace();
+}
+
+
+// class OsStackTraceGetter
+
+// Returns the current OS stack trace as an std::string. Parameters:
+//
+// max_depth - the maximum number of stack frames to be included
+// in the trace.
+// skip_count - the number of top frames to be skipped; doesn't count
+// against max_depth.
+//
+string OsStackTraceGetter::CurrentStackTrace(int /* max_depth */,
+ int /* skip_count */)
+ GTEST_LOCK_EXCLUDED_(mutex_) {
+ return "";
+}
+
+void OsStackTraceGetter::UponLeavingGTest()
+ GTEST_LOCK_EXCLUDED_(mutex_) {
+}
+
+const char* const
+OsStackTraceGetter::kElidedFramesMarker =
+ "... " GTEST_NAME_ " internal frames ...";
+
+// A helper class that creates the premature-exit file in its
+// constructor and deletes the file in its destructor.
+class ScopedPrematureExitFile {
+ public:
+ explicit ScopedPrematureExitFile(const char* premature_exit_filepath)
+ : premature_exit_filepath_(premature_exit_filepath) {
+ // If a path to the premature-exit file is specified...
+ if (premature_exit_filepath != NULL && *premature_exit_filepath != '\0') {
+ // create the file with a single "0" character in it. I/O
+ // errors are ignored as there's nothing better we can do and we
+ // don't want to fail the test because of this.
+ FILE* pfile = posix::FOpen(premature_exit_filepath, "w");
+ fwrite("0", 1, 1, pfile);
+ fclose(pfile);
+ }
+ }
+
+ ~ScopedPrematureExitFile() {
+ if (premature_exit_filepath_ != NULL && *premature_exit_filepath_ != '\0') {
+ remove(premature_exit_filepath_);
+ }
+ }
+
+ private:
+ const char* const premature_exit_filepath_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ScopedPrematureExitFile);
+};
+
+} // namespace internal
+
+// class TestEventListeners
+
+TestEventListeners::TestEventListeners()
+ : repeater_(new internal::TestEventRepeater()),
+ default_result_printer_(NULL),
+ default_xml_generator_(NULL) {
+}
+
+TestEventListeners::~TestEventListeners() { delete repeater_; }
+
+// Returns the standard listener responsible for the default console
+// output. Can be removed from the listeners list to shut down default
+// console output. Note that removing this object from the listener list
+// with Release transfers its ownership to the user.
+void TestEventListeners::Append(TestEventListener* listener) {
+ repeater_->Append(listener);
+}
+
+// Removes the given event listener from the list and returns it. It then
+// becomes the caller's responsibility to delete the listener. Returns
+// NULL if the listener is not found in the list.
+TestEventListener* TestEventListeners::Release(TestEventListener* listener) {
+ if (listener == default_result_printer_)
+ default_result_printer_ = NULL;
+ else if (listener == default_xml_generator_)
+ default_xml_generator_ = NULL;
+ return repeater_->Release(listener);
+}
+
+// Returns repeater that broadcasts the TestEventListener events to all
+// subscribers.
+TestEventListener* TestEventListeners::repeater() { return repeater_; }
+
+// Sets the default_result_printer attribute to the provided listener.
+// The listener is also added to the listener list and previous
+// default_result_printer is removed from it and deleted. The listener can
+// also be NULL in which case it will not be added to the list. Does
+// nothing if the previous and the current listener objects are the same.
+void TestEventListeners::SetDefaultResultPrinter(TestEventListener* listener) {
+ if (default_result_printer_ != listener) {
+ // It is an error to pass this method a listener that is already in the
+ // list.
+ delete Release(default_result_printer_);
+ default_result_printer_ = listener;
+ if (listener != NULL)
+ Append(listener);
+ }
+}
+
+// Sets the default_xml_generator attribute to the provided listener. The
+// listener is also added to the listener list and previous
+// default_xml_generator is removed from it and deleted. The listener can
+// also be NULL in which case it will not be added to the list. Does
+// nothing if the previous and the current listener objects are the same.
+void TestEventListeners::SetDefaultXmlGenerator(TestEventListener* listener) {
+ if (default_xml_generator_ != listener) {
+ // It is an error to pass this method a listener that is already in the
+ // list.
+ delete Release(default_xml_generator_);
+ default_xml_generator_ = listener;
+ if (listener != NULL)
+ Append(listener);
+ }
+}
+
+// Controls whether events will be forwarded by the repeater to the
+// listeners in the list.
+bool TestEventListeners::EventForwardingEnabled() const {
+ return repeater_->forwarding_enabled();
+}
+
+void TestEventListeners::SuppressEventForwarding() {
+ repeater_->set_forwarding_enabled(false);
+}
+
+// class UnitTest
+
+// Gets the singleton UnitTest object. The first time this method is
+// called, a UnitTest object is constructed and returned. Consecutive
+// calls will return the same object.
+//
+// We don't protect this under mutex_ as a user is not supposed to
+// call this before main() starts, from which point on the return
+// value will never change.
+UnitTest* UnitTest::GetInstance() {
+ // When compiled with MSVC 7.1 in optimized mode, destroying the
+ // UnitTest object upon exiting the program messes up the exit code,
+ // causing successful tests to appear failed. We have to use a
+ // different implementation in this case to bypass the compiler bug.
+ // This implementation makes the compiler happy, at the cost of
+ // leaking the UnitTest object.
+
+ // CodeGear C++Builder insists on a public destructor for the
+ // default implementation. Use this implementation to keep good OO
+ // design with private destructor.
+
+#if (_MSC_VER == 1310 && !defined(_DEBUG)) || defined(__BORLANDC__)
+ static UnitTest* const instance = new UnitTest;
+ return instance;
+#else
+ static UnitTest instance;
+ return &instance;
+#endif // (_MSC_VER == 1310 && !defined(_DEBUG)) || defined(__BORLANDC__)
+}
+
+// Gets the number of successful test cases.
+int UnitTest::successful_test_case_count() const {
+ return impl()->successful_test_case_count();
+}
+
+// Gets the number of failed test cases.
+int UnitTest::failed_test_case_count() const {
+ return impl()->failed_test_case_count();
+}
+
+// Gets the number of all test cases.
+int UnitTest::total_test_case_count() const {
+ return impl()->total_test_case_count();
+}
+
+// Gets the number of all test cases that contain at least one test
+// that should run.
+int UnitTest::test_case_to_run_count() const {
+ return impl()->test_case_to_run_count();
+}
+
+// Gets the number of successful tests.
+int UnitTest::successful_test_count() const {
+ return impl()->successful_test_count();
+}
+
+// Gets the number of failed tests.
+int UnitTest::failed_test_count() const { return impl()->failed_test_count(); }
+
+// Gets the number of disabled tests that will be reported in the XML report.
+int UnitTest::reportable_disabled_test_count() const {
+ return impl()->reportable_disabled_test_count();
+}
+
+// Gets the number of disabled tests.
+int UnitTest::disabled_test_count() const {
+ return impl()->disabled_test_count();
+}
+
+// Gets the number of tests to be printed in the XML report.
+int UnitTest::reportable_test_count() const {
+ return impl()->reportable_test_count();
+}
+
+// Gets the number of all tests.
+int UnitTest::total_test_count() const { return impl()->total_test_count(); }
+
+// Gets the number of tests that should run.
+int UnitTest::test_to_run_count() const { return impl()->test_to_run_count(); }
+
+// Gets the time of the test program start, in ms from the start of the
+// UNIX epoch.
+internal::TimeInMillis UnitTest::start_timestamp() const {
+ return impl()->start_timestamp();
+}
+
+// Gets the elapsed time, in milliseconds.
+internal::TimeInMillis UnitTest::elapsed_time() const {
+ return impl()->elapsed_time();
+}
+
+// Returns true iff the unit test passed (i.e. all test cases passed).
+bool UnitTest::Passed() const { return impl()->Passed(); }
+
+// Returns true iff the unit test failed (i.e. some test case failed
+// or something outside of all tests failed).
+bool UnitTest::Failed() const { return impl()->Failed(); }
+
+// Gets the i-th test case among all the test cases. i can range from 0 to
+// total_test_case_count() - 1. If i is not in that range, returns NULL.
+const TestCase* UnitTest::GetTestCase(int i) const {
+ return impl()->GetTestCase(i);
+}
+
+// Returns the TestResult containing information on test failures and
+// properties logged outside of individual test cases.
+const TestResult& UnitTest::ad_hoc_test_result() const {
+ return *impl()->ad_hoc_test_result();
+}
+
+// Gets the i-th test case among all the test cases. i can range from 0 to
+// total_test_case_count() - 1. If i is not in that range, returns NULL.
+TestCase* UnitTest::GetMutableTestCase(int i) {
+ return impl()->GetMutableTestCase(i);
+}
+
+// Returns the list of event listeners that can be used to track events
+// inside Google Test.
+TestEventListeners& UnitTest::listeners() {
+ return *impl()->listeners();
+}
+
+// Registers and returns a global test environment. When a test
+// program is run, all global test environments will be set-up in the
+// order they were registered. After all tests in the program have
+// finished, all global test environments will be torn-down in the
+// *reverse* order they were registered.
+//
+// The UnitTest object takes ownership of the given environment.
+//
+// We don't protect this under mutex_, as we only support calling it
+// from the main thread.
+Environment* UnitTest::AddEnvironment(Environment* env) {
+ if (env == NULL) {
+ return NULL;
+ }
+
+ impl_->environments().push_back(env);
+ return env;
+}
+
+// Adds a TestPartResult to the current TestResult object. All Google Test
+// assertion macros (e.g. ASSERT_TRUE, EXPECT_EQ, etc) eventually call
+// this to report their results. The user code should use the
+// assertion macros instead of calling this directly.
+void UnitTest::AddTestPartResult(
+ TestPartResult::Type result_type,
+ const char* file_name,
+ int line_number,
+ const std::string& message,
+ const std::string& os_stack_trace) GTEST_LOCK_EXCLUDED_(mutex_) {
+ Message msg;
+ msg << message;
+
+ internal::MutexLock lock(&mutex_);
+ if (impl_->gtest_trace_stack().size() > 0) {
+ msg << "\n" << GTEST_NAME_ << " trace:";
+
+ for (int i = static_cast<int>(impl_->gtest_trace_stack().size());
+ i > 0; --i) {
+ const internal::TraceInfo& trace = impl_->gtest_trace_stack()[i - 1];
+ msg << "\n" << internal::FormatFileLocation(trace.file, trace.line)
+ << " " << trace.message;
+ }
+ }
+
+ if (os_stack_trace.c_str() != NULL && !os_stack_trace.empty()) {
+ msg << internal::kStackTraceMarker << os_stack_trace;
+ }
+
+ const TestPartResult result =
+ TestPartResult(result_type, file_name, line_number,
+ msg.GetString().c_str());
+ impl_->GetTestPartResultReporterForCurrentThread()->
+ ReportTestPartResult(result);
+
+ if (result_type != TestPartResult::kSuccess) {
+ // gtest_break_on_failure takes precedence over
+ // gtest_throw_on_failure. This allows a user to set the latter
+ // in the code (perhaps in order to use Google Test assertions
+ // with another testing framework) and specify the former on the
+ // command line for debugging.
+ if (GTEST_FLAG(break_on_failure)) {
+#if GTEST_OS_WINDOWS
+ // Using DebugBreak on Windows allows gtest to still break into a debugger
+ // when a failure happens and both the --gtest_break_on_failure and
+ // the --gtest_catch_exceptions flags are specified.
+ DebugBreak();
+#else
+ // Dereference NULL through a volatile pointer to prevent the compiler
+ // from removing. We use this rather than abort() or __builtin_trap() for
+ // portability: Symbian doesn't implement abort() well, and some debuggers
+ // don't correctly trap abort().
+ *static_cast<volatile int*>(NULL) = 1;
+#endif // GTEST_OS_WINDOWS
+ } else if (GTEST_FLAG(throw_on_failure)) {
+#if GTEST_HAS_EXCEPTIONS
+ throw internal::GoogleTestFailureException(result);
+#else
+ // We cannot call abort() as it generates a pop-up in debug mode
+ // that cannot be suppressed in VC 7.1 or below.
+ exit(1);
+#endif
+ }
+ }
+}
+
+// Adds a TestProperty to the current TestResult object when invoked from
+// inside a test, to current TestCase's ad_hoc_test_result_ when invoked
+// from SetUpTestCase or TearDownTestCase, or to the global property set
+// when invoked elsewhere. If the result already contains a property with
+// the same key, the value will be updated.
+void UnitTest::RecordProperty(const std::string& key,
+ const std::string& value) {
+ impl_->RecordProperty(TestProperty(key, value));
+}
+
+// Runs all tests in this UnitTest object and prints the result.
+// Returns 0 if successful, or 1 otherwise.
+//
+// We don't protect this under mutex_, as we only support calling it
+// from the main thread.
+int UnitTest::Run() {
+ const bool in_death_test_child_process =
+ internal::GTEST_FLAG(internal_run_death_test).length() > 0;
+
+ // Google Test implements this protocol for catching that a test
+ // program exits before returning control to Google Test:
+ //
+ // 1. Upon start, Google Test creates a file whose absolute path
+ // is specified by the environment variable
+ // TEST_PREMATURE_EXIT_FILE.
+ // 2. When Google Test has finished its work, it deletes the file.
+ //
+ // This allows a test runner to set TEST_PREMATURE_EXIT_FILE before
+ // running a Google-Test-based test program and check the existence
+ // of the file at the end of the test execution to see if it has
+ // exited prematurely.
+
+ // If we are in the child process of a death test, don't
+ // create/delete the premature exit file, as doing so is unnecessary
+ // and will confuse the parent process. Otherwise, create/delete
+ // the file upon entering/leaving this function. If the program
+ // somehow exits before this function has a chance to return, the
+ // premature-exit file will be left undeleted, causing a test runner
+ // that understands the premature-exit-file protocol to report the
+ // test as having failed.
+ const internal::ScopedPrematureExitFile premature_exit_file(
+ in_death_test_child_process ?
+ NULL : internal::posix::GetEnv("TEST_PREMATURE_EXIT_FILE"));
+
+ // Captures the value of GTEST_FLAG(catch_exceptions). This value will be
+ // used for the duration of the program.
+ impl()->set_catch_exceptions(GTEST_FLAG(catch_exceptions));
+
+#if GTEST_HAS_SEH
+ // Either the user wants Google Test to catch exceptions thrown by the
+ // tests or this is executing in the context of death test child
+ // process. In either case the user does not want to see pop-up dialogs
+ // about crashes - they are expected.
+ if (impl()->catch_exceptions() || in_death_test_child_process) {
+# if !GTEST_OS_WINDOWS_MOBILE
+ // SetErrorMode doesn't exist on CE.
+ SetErrorMode(SEM_FAILCRITICALERRORS | SEM_NOALIGNMENTFAULTEXCEPT |
+ SEM_NOGPFAULTERRORBOX | SEM_NOOPENFILEERRORBOX);
+# endif // !GTEST_OS_WINDOWS_MOBILE
+
+# if (defined(_MSC_VER) || GTEST_OS_WINDOWS_MINGW) && !GTEST_OS_WINDOWS_MOBILE
+ // Death test children can be terminated with _abort(). On Windows,
+ // _abort() can show a dialog with a warning message. This forces the
+ // abort message to go to stderr instead.
+ _set_error_mode(_OUT_TO_STDERR);
+# endif
+
+# if _MSC_VER >= 1400 && !GTEST_OS_WINDOWS_MOBILE
+ // In the debug version, Visual Studio pops up a separate dialog
+ // offering a choice to debug the aborted program. We need to suppress
+ // this dialog or it will pop up for every EXPECT/ASSERT_DEATH statement
+ // executed. Google Test will notify the user of any unexpected
+ // failure via stderr.
+ //
+ // VC++ doesn't define _set_abort_behavior() prior to the version 8.0.
+ // Users of prior VC versions shall suffer the agony and pain of
+ // clicking through the countless debug dialogs.
+ // TODO(vladl at google.com): find a way to suppress the abort dialog() in the
+ // debug mode when compiled with VC 7.1 or lower.
+ if (!GTEST_FLAG(break_on_failure))
+ _set_abort_behavior(
+ 0x0, // Clear the following flags:
+ _WRITE_ABORT_MSG | _CALL_REPORTFAULT); // pop-up window, core dump.
+# endif
+ }
+#endif // GTEST_HAS_SEH
+
+ return internal::HandleExceptionsInMethodIfSupported(
+ impl(),
+ &internal::UnitTestImpl::RunAllTests,
+ "auxiliary test code (environments or event listeners)") ? 0 : 1;
+}
+
+// Returns the working directory when the first TEST() or TEST_F() was
+// executed.
+const char* UnitTest::original_working_dir() const {
+ return impl_->original_working_dir_.c_str();
+}
+
+// Returns the TestCase object for the test that's currently running,
+// or NULL if no test is running.
+const TestCase* UnitTest::current_test_case() const
+ GTEST_LOCK_EXCLUDED_(mutex_) {
+ internal::MutexLock lock(&mutex_);
+ return impl_->current_test_case();
+}
+
+// Returns the TestInfo object for the test that's currently running,
+// or NULL if no test is running.
+const TestInfo* UnitTest::current_test_info() const
+ GTEST_LOCK_EXCLUDED_(mutex_) {
+ internal::MutexLock lock(&mutex_);
+ return impl_->current_test_info();
+}
+
+// Returns the random seed used at the start of the current test run.
+int UnitTest::random_seed() const { return impl_->random_seed(); }
+
+#if GTEST_HAS_PARAM_TEST
+// Returns ParameterizedTestCaseRegistry object used to keep track of
+// value-parameterized tests and instantiate and register them.
+internal::ParameterizedTestCaseRegistry&
+ UnitTest::parameterized_test_registry()
+ GTEST_LOCK_EXCLUDED_(mutex_) {
+ return impl_->parameterized_test_registry();
+}
+#endif // GTEST_HAS_PARAM_TEST
+
+// Creates an empty UnitTest.
+UnitTest::UnitTest() {
+ impl_ = new internal::UnitTestImpl(this);
+}
+
+// Destructor of UnitTest.
+UnitTest::~UnitTest() {
+ delete impl_;
+}
+
+// Pushes a trace defined by SCOPED_TRACE() on to the per-thread
+// Google Test trace stack.
+void UnitTest::PushGTestTrace(const internal::TraceInfo& trace)
+ GTEST_LOCK_EXCLUDED_(mutex_) {
+ internal::MutexLock lock(&mutex_);
+ impl_->gtest_trace_stack().push_back(trace);
+}
+
+// Pops a trace from the per-thread Google Test trace stack.
+void UnitTest::PopGTestTrace()
+ GTEST_LOCK_EXCLUDED_(mutex_) {
+ internal::MutexLock lock(&mutex_);
+ impl_->gtest_trace_stack().pop_back();
+}
+
+namespace internal {
+
+UnitTestImpl::UnitTestImpl(UnitTest* parent)
+ : parent_(parent),
+#ifdef _MSC_VER
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4355) // Temporarily disables warning 4355
+ // (using this in initializer).
+ default_global_test_part_result_reporter_(this),
+ default_per_thread_test_part_result_reporter_(this),
+# pragma warning(pop) // Restores the warning state again.
+#else
+ default_global_test_part_result_reporter_(this),
+ default_per_thread_test_part_result_reporter_(this),
+#endif // _MSC_VER
+ global_test_part_result_repoter_(
+ &default_global_test_part_result_reporter_),
+ per_thread_test_part_result_reporter_(
+ &default_per_thread_test_part_result_reporter_),
+#if GTEST_HAS_PARAM_TEST
+ parameterized_test_registry_(),
+ parameterized_tests_registered_(false),
+#endif // GTEST_HAS_PARAM_TEST
+ last_death_test_case_(-1),
+ current_test_case_(NULL),
+ current_test_info_(NULL),
+ ad_hoc_test_result_(),
+ os_stack_trace_getter_(NULL),
+ post_flag_parse_init_performed_(false),
+ random_seed_(0), // Will be overridden by the flag before first use.
+ random_(0), // Will be reseeded before first use.
+ start_timestamp_(0),
+ elapsed_time_(0),
+#if GTEST_HAS_DEATH_TEST
+ death_test_factory_(new DefaultDeathTestFactory),
+#endif
+ // Will be overridden by the flag before first use.
+ catch_exceptions_(false) {
+ listeners()->SetDefaultResultPrinter(new PrettyUnitTestResultPrinter);
+}
+
+UnitTestImpl::~UnitTestImpl() {
+ // Deletes every TestCase.
+ ForEach(test_cases_, internal::Delete<TestCase>);
+
+ // Deletes every Environment.
+ ForEach(environments_, internal::Delete<Environment>);
+
+ delete os_stack_trace_getter_;
+}
+
+// Adds a TestProperty to the current TestResult object when invoked in a
+// context of a test, to current test case's ad_hoc_test_result when invoke
+// from SetUpTestCase/TearDownTestCase, or to the global property set
+// otherwise. If the result already contains a property with the same key,
+// the value will be updated.
+void UnitTestImpl::RecordProperty(const TestProperty& test_property) {
+ std::string xml_element;
+ TestResult* test_result; // TestResult appropriate for property recording.
+
+ if (current_test_info_ != NULL) {
+ xml_element = "testcase";
+ test_result = &(current_test_info_->result_);
+ } else if (current_test_case_ != NULL) {
+ xml_element = "testsuite";
+ test_result = &(current_test_case_->ad_hoc_test_result_);
+ } else {
+ xml_element = "testsuites";
+ test_result = &ad_hoc_test_result_;
+ }
+ test_result->RecordProperty(xml_element, test_property);
+}
+
+#if GTEST_HAS_DEATH_TEST
+// Disables event forwarding if the control is currently in a death test
+// subprocess. Must not be called before InitGoogleTest.
+void UnitTestImpl::SuppressTestEventsIfInSubprocess() {
+ if (internal_run_death_test_flag_.get() != NULL)
+ listeners()->SuppressEventForwarding();
+}
+#endif // GTEST_HAS_DEATH_TEST
+
+// Initializes event listeners performing XML output as specified by
+// UnitTestOptions. Must not be called before InitGoogleTest.
+void UnitTestImpl::ConfigureXmlOutput() {
+ const std::string& output_format = UnitTestOptions::GetOutputFormat();
+ if (output_format == "xml") {
+ listeners()->SetDefaultXmlGenerator(new XmlUnitTestResultPrinter(
+ UnitTestOptions::GetAbsolutePathToOutputFile().c_str()));
+ } else if (output_format != "") {
+ printf("WARNING: unrecognized output format \"%s\" ignored.\n",
+ output_format.c_str());
+ fflush(stdout);
+ }
+}
+
+#if GTEST_CAN_STREAM_RESULTS_
+// Initializes event listeners for streaming test results in string form.
+// Must not be called before InitGoogleTest.
+void UnitTestImpl::ConfigureStreamingOutput() {
+ const std::string& target = GTEST_FLAG(stream_result_to);
+ if (!target.empty()) {
+ const size_t pos = target.find(':');
+ if (pos != std::string::npos) {
+ listeners()->Append(new StreamingListener(target.substr(0, pos),
+ target.substr(pos+1)));
+ } else {
+ printf("WARNING: unrecognized streaming target \"%s\" ignored.\n",
+ target.c_str());
+ fflush(stdout);
+ }
+ }
+}
+#endif // GTEST_CAN_STREAM_RESULTS_
+
+// Performs initialization dependent upon flag values obtained in
+// ParseGoogleTestFlagsOnly. Is called from InitGoogleTest after the call to
+// ParseGoogleTestFlagsOnly. In case a user neglects to call InitGoogleTest
+// this function is also called from RunAllTests. Since this function can be
+// called more than once, it has to be idempotent.
+void UnitTestImpl::PostFlagParsingInit() {
+ // Ensures that this function does not execute more than once.
+ if (!post_flag_parse_init_performed_) {
+ post_flag_parse_init_performed_ = true;
+
+#if GTEST_HAS_DEATH_TEST
+ InitDeathTestSubprocessControlInfo();
+ SuppressTestEventsIfInSubprocess();
+#endif // GTEST_HAS_DEATH_TEST
+
+ // Registers parameterized tests. This makes parameterized tests
+ // available to the UnitTest reflection API without running
+ // RUN_ALL_TESTS.
+ RegisterParameterizedTests();
+
+ // Configures listeners for XML output. This makes it possible for users
+ // to shut down the default XML output before invoking RUN_ALL_TESTS.
+ ConfigureXmlOutput();
+
+#if GTEST_CAN_STREAM_RESULTS_
+ // Configures listeners for streaming test results to the specified server.
+ ConfigureStreamingOutput();
+#endif // GTEST_CAN_STREAM_RESULTS_
+ }
+}
+
+// A predicate that checks the name of a TestCase against a known
+// value.
+//
+// This is used for implementation of the UnitTest class only. We put
+// it in the anonymous namespace to prevent polluting the outer
+// namespace.
+//
+// TestCaseNameIs is copyable.
+class TestCaseNameIs {
+ public:
+ // Constructor.
+ explicit TestCaseNameIs(const std::string& name)
+ : name_(name) {}
+
+ // Returns true iff the name of test_case matches name_.
+ bool operator()(const TestCase* test_case) const {
+ return test_case != NULL && strcmp(test_case->name(), name_.c_str()) == 0;
+ }
+
+ private:
+ std::string name_;
+};
+
+// Finds and returns a TestCase with the given name. If one doesn't
+// exist, creates one and returns it. It's the CALLER'S
+// RESPONSIBILITY to ensure that this function is only called WHEN THE
+// TESTS ARE NOT SHUFFLED.
+//
+// Arguments:
+//
+// test_case_name: name of the test case
+// type_param: the name of the test case's type parameter, or NULL if
+// this is not a typed or a type-parameterized test case.
+// set_up_tc: pointer to the function that sets up the test case
+// tear_down_tc: pointer to the function that tears down the test case
+TestCase* UnitTestImpl::GetTestCase(const char* test_case_name,
+ const char* type_param,
+ Test::SetUpTestCaseFunc set_up_tc,
+ Test::TearDownTestCaseFunc tear_down_tc) {
+ // Can we find a TestCase with the given name?
+ const std::vector<TestCase*>::const_iterator test_case =
+ std::find_if(test_cases_.begin(), test_cases_.end(),
+ TestCaseNameIs(test_case_name));
+
+ if (test_case != test_cases_.end())
+ return *test_case;
+
+ // No. Let's create one.
+ TestCase* const new_test_case =
+ new TestCase(test_case_name, type_param, set_up_tc, tear_down_tc);
+
+ // Is this a death test case?
+ if (internal::UnitTestOptions::MatchesFilter(test_case_name,
+ kDeathTestCaseFilter)) {
+ // Yes. Inserts the test case after the last death test case
+ // defined so far. This only works when the test cases haven't
+ // been shuffled. Otherwise we may end up running a death test
+ // after a non-death test.
+ ++last_death_test_case_;
+ test_cases_.insert(test_cases_.begin() + last_death_test_case_,
+ new_test_case);
+ } else {
+ // No. Appends to the end of the list.
+ test_cases_.push_back(new_test_case);
+ }
+
+ test_case_indices_.push_back(static_cast<int>(test_case_indices_.size()));
+ return new_test_case;
+}
+
+// Helpers for setting up / tearing down the given environment. They
+// are for use in the ForEach() function.
+static void SetUpEnvironment(Environment* env) { env->SetUp(); }
+static void TearDownEnvironment(Environment* env) { env->TearDown(); }
+
+// Runs all tests in this UnitTest object, prints the result, and
+// returns true if all tests are successful. If any exception is
+// thrown during a test, the test is considered to be failed, but the
+// rest of the tests will still be run.
+//
+// When parameterized tests are enabled, it expands and registers
+// parameterized tests first in RegisterParameterizedTests().
+// All other functions called from RunAllTests() may safely assume that
+// parameterized tests are ready to be counted and run.
+bool UnitTestImpl::RunAllTests() {
+ // Makes sure InitGoogleTest() was called.
+ if (!GTestIsInitialized()) {
+ printf("%s",
+ "\nThis test program did NOT call ::testing::InitGoogleTest "
+ "before calling RUN_ALL_TESTS(). Please fix it.\n");
+ return false;
+ }
+
+ // Do not run any test if the --help flag was specified.
+ if (g_help_flag)
+ return true;
+
+ // Repeats the call to the post-flag parsing initialization in case the
+ // user didn't call InitGoogleTest.
+ PostFlagParsingInit();
+
+ // Even if sharding is not on, test runners may want to use the
+ // GTEST_SHARD_STATUS_FILE to query whether the test supports the sharding
+ // protocol.
+ internal::WriteToShardStatusFileIfNeeded();
+
+ // True iff we are in a subprocess for running a thread-safe-style
+ // death test.
+ bool in_subprocess_for_death_test = false;
+
+#if GTEST_HAS_DEATH_TEST
+ in_subprocess_for_death_test = (internal_run_death_test_flag_.get() != NULL);
+#endif // GTEST_HAS_DEATH_TEST
+
+ const bool should_shard = ShouldShard(kTestTotalShards, kTestShardIndex,
+ in_subprocess_for_death_test);
+
+ // Compares the full test names with the filter to decide which
+ // tests to run.
+ const bool has_tests_to_run = FilterTests(should_shard
+ ? HONOR_SHARDING_PROTOCOL
+ : IGNORE_SHARDING_PROTOCOL) > 0;
+
+ // Lists the tests and exits if the --gtest_list_tests flag was specified.
+ if (GTEST_FLAG(list_tests)) {
+ // This must be called *after* FilterTests() has been called.
+ ListTestsMatchingFilter();
+ return true;
+ }
+
+ random_seed_ = GTEST_FLAG(shuffle) ?
+ GetRandomSeedFromFlag(GTEST_FLAG(random_seed)) : 0;
+
+ // True iff at least one test has failed.
+ bool failed = false;
+
+ TestEventListener* repeater = listeners()->repeater();
+
+ start_timestamp_ = GetTimeInMillis();
+ repeater->OnTestProgramStart(*parent_);
+
+ // How many times to repeat the tests? We don't want to repeat them
+ // when we are inside the subprocess of a death test.
+ const int repeat = in_subprocess_for_death_test ? 1 : GTEST_FLAG(repeat);
+ // Repeats forever if the repeat count is negative.
+ const bool forever = repeat < 0;
+ for (int i = 0; forever || i != repeat; i++) {
+ // We want to preserve failures generated by ad-hoc test
+ // assertions executed before RUN_ALL_TESTS().
+ ClearNonAdHocTestResult();
+
+ const TimeInMillis start = GetTimeInMillis();
+
+ // Shuffles test cases and tests if requested.
+ if (has_tests_to_run && GTEST_FLAG(shuffle)) {
+ random()->Reseed(random_seed_);
+ // This should be done before calling OnTestIterationStart(),
+ // such that a test event listener can see the actual test order
+ // in the event.
+ ShuffleTests();
+ }
+
+ // Tells the unit test event listeners that the tests are about to start.
+ repeater->OnTestIterationStart(*parent_, i);
+
+ // Runs each test case if there is at least one test to run.
+ if (has_tests_to_run) {
+ // Sets up all environments beforehand.
+ repeater->OnEnvironmentsSetUpStart(*parent_);
+ ForEach(environments_, SetUpEnvironment);
+ repeater->OnEnvironmentsSetUpEnd(*parent_);
+
+ // Runs the tests only if there was no fatal failure during global
+ // set-up.
+ if (!Test::HasFatalFailure()) {
+ for (int test_index = 0; test_index < total_test_case_count();
+ test_index++) {
+ GetMutableTestCase(test_index)->Run();
+ }
+ }
+
+ // Tears down all environments in reverse order afterwards.
+ repeater->OnEnvironmentsTearDownStart(*parent_);
+ std::for_each(environments_.rbegin(), environments_.rend(),
+ TearDownEnvironment);
+ repeater->OnEnvironmentsTearDownEnd(*parent_);
+ }
+
+ elapsed_time_ = GetTimeInMillis() - start;
+
+ // Tells the unit test event listener that the tests have just finished.
+ repeater->OnTestIterationEnd(*parent_, i);
+
+ // Gets the result and clears it.
+ if (!Passed()) {
+ failed = true;
+ }
+
+ // Restores the original test order after the iteration. This
+ // allows the user to quickly repro a failure that happens in the
+ // N-th iteration without repeating the first (N - 1) iterations.
+ // This is not enclosed in "if (GTEST_FLAG(shuffle)) { ... }", in
+ // case the user somehow changes the value of the flag somewhere
+ // (it's always safe to unshuffle the tests).
+ UnshuffleTests();
+
+ if (GTEST_FLAG(shuffle)) {
+ // Picks a new random seed for each iteration.
+ random_seed_ = GetNextRandomSeed(random_seed_);
+ }
+ }
+
+ repeater->OnTestProgramEnd(*parent_);
+
+ return !failed;
+}
+
+// Reads the GTEST_SHARD_STATUS_FILE environment variable, and creates the file
+// if the variable is present. If a file already exists at this location, this
+// function will write over it. If the variable is present, but the file cannot
+// be created, prints an error and exits.
+void WriteToShardStatusFileIfNeeded() {
+ const char* const test_shard_file = posix::GetEnv(kTestShardStatusFile);
+ if (test_shard_file != NULL) {
+ FILE* const file = posix::FOpen(test_shard_file, "w");
+ if (file == NULL) {
+ ColoredPrintf(COLOR_RED,
+ "Could not write to the test shard status file \"%s\" "
+ "specified by the %s environment variable.\n",
+ test_shard_file, kTestShardStatusFile);
+ fflush(stdout);
+ exit(EXIT_FAILURE);
+ }
+ fclose(file);
+ }
+}
+
+// Checks whether sharding is enabled by examining the relevant
+// environment variable values. If the variables are present,
+// but inconsistent (i.e., shard_index >= total_shards), prints
+// an error and exits. If in_subprocess_for_death_test, sharding is
+// disabled because it must only be applied to the original test
+// process. Otherwise, we could filter out death tests we intended to execute.
+bool ShouldShard(const char* total_shards_env,
+ const char* shard_index_env,
+ bool in_subprocess_for_death_test) {
+ if (in_subprocess_for_death_test) {
+ return false;
+ }
+
+ const Int32 total_shards = Int32FromEnvOrDie(total_shards_env, -1);
+ const Int32 shard_index = Int32FromEnvOrDie(shard_index_env, -1);
+
+ if (total_shards == -1 && shard_index == -1) {
+ return false;
+ } else if (total_shards == -1 && shard_index != -1) {
+ const Message msg = Message()
+ << "Invalid environment variables: you have "
+ << kTestShardIndex << " = " << shard_index
+ << ", but have left " << kTestTotalShards << " unset.\n";
+ ColoredPrintf(COLOR_RED, msg.GetString().c_str());
+ fflush(stdout);
+ exit(EXIT_FAILURE);
+ } else if (total_shards != -1 && shard_index == -1) {
+ const Message msg = Message()
+ << "Invalid environment variables: you have "
+ << kTestTotalShards << " = " << total_shards
+ << ", but have left " << kTestShardIndex << " unset.\n";
+ ColoredPrintf(COLOR_RED, msg.GetString().c_str());
+ fflush(stdout);
+ exit(EXIT_FAILURE);
+ } else if (shard_index < 0 || shard_index >= total_shards) {
+ const Message msg = Message()
+ << "Invalid environment variables: we require 0 <= "
+ << kTestShardIndex << " < " << kTestTotalShards
+ << ", but you have " << kTestShardIndex << "=" << shard_index
+ << ", " << kTestTotalShards << "=" << total_shards << ".\n";
+ ColoredPrintf(COLOR_RED, msg.GetString().c_str());
+ fflush(stdout);
+ exit(EXIT_FAILURE);
+ }
+
+ return total_shards > 1;
+}
+
+// Parses the environment variable var as an Int32. If it is unset,
+// returns default_val. If it is not an Int32, prints an error
+// and aborts.
+Int32 Int32FromEnvOrDie(const char* var, Int32 default_val) {
+ const char* str_val = posix::GetEnv(var);
+ if (str_val == NULL) {
+ return default_val;
+ }
+
+ Int32 result;
+ if (!ParseInt32(Message() << "The value of environment variable " << var,
+ str_val, &result)) {
+ exit(EXIT_FAILURE);
+ }
+ return result;
+}
+
+// Given the total number of shards, the shard index, and the test id,
+// returns true iff the test should be run on this shard. The test id is
+// some arbitrary but unique non-negative integer assigned to each test
+// method. Assumes that 0 <= shard_index < total_shards.
+bool ShouldRunTestOnShard(int total_shards, int shard_index, int test_id) {
+ return (test_id % total_shards) == shard_index;
+}
+
+// Compares the name of each test with the user-specified filter to
+// decide whether the test should be run, then records the result in
+// each TestCase and TestInfo object.
+// If shard_tests == true, further filters tests based on sharding
+// variables in the environment - see
+// http://code.google.com/p/googletest/wiki/GoogleTestAdvancedGuide.
+// Returns the number of tests that should run.
+int UnitTestImpl::FilterTests(ReactionToSharding shard_tests) {
+ const Int32 total_shards = shard_tests == HONOR_SHARDING_PROTOCOL ?
+ Int32FromEnvOrDie(kTestTotalShards, -1) : -1;
+ const Int32 shard_index = shard_tests == HONOR_SHARDING_PROTOCOL ?
+ Int32FromEnvOrDie(kTestShardIndex, -1) : -1;
+
+ // num_runnable_tests are the number of tests that will
+ // run across all shards (i.e., match filter and are not disabled).
+ // num_selected_tests are the number of tests to be run on
+ // this shard.
+ int num_runnable_tests = 0;
+ int num_selected_tests = 0;
+ for (size_t i = 0; i < test_cases_.size(); i++) {
+ TestCase* const test_case = test_cases_[i];
+ const std::string &test_case_name = test_case->name();
+ test_case->set_should_run(false);
+
+ for (size_t j = 0; j < test_case->test_info_list().size(); j++) {
+ TestInfo* const test_info = test_case->test_info_list()[j];
+ const std::string test_name(test_info->name());
+ // A test is disabled if test case name or test name matches
+ // kDisableTestFilter.
+ const bool is_disabled =
+ internal::UnitTestOptions::MatchesFilter(test_case_name,
+ kDisableTestFilter) ||
+ internal::UnitTestOptions::MatchesFilter(test_name,
+ kDisableTestFilter);
+ test_info->is_disabled_ = is_disabled;
+
+ const bool matches_filter =
+ internal::UnitTestOptions::FilterMatchesTest(test_case_name,
+ test_name);
+ test_info->matches_filter_ = matches_filter;
+
+ const bool is_runnable =
+ (GTEST_FLAG(also_run_disabled_tests) || !is_disabled) &&
+ matches_filter;
+
+ const bool is_selected = is_runnable &&
+ (shard_tests == IGNORE_SHARDING_PROTOCOL ||
+ ShouldRunTestOnShard(total_shards, shard_index,
+ num_runnable_tests));
+
+ num_runnable_tests += is_runnable;
+ num_selected_tests += is_selected;
+
+ test_info->should_run_ = is_selected;
+ test_case->set_should_run(test_case->should_run() || is_selected);
+ }
+ }
+ return num_selected_tests;
+}
+
+// Prints the given C-string on a single line by replacing all '\n'
+// characters with string "\\n". If the output takes more than
+// max_length characters, only prints the first max_length characters
+// and "...".
+static void PrintOnOneLine(const char* str, int max_length) {
+ if (str != NULL) {
+ for (int i = 0; *str != '\0'; ++str) {
+ if (i >= max_length) {
+ printf("...");
+ break;
+ }
+ if (*str == '\n') {
+ printf("\\n");
+ i += 2;
+ } else {
+ printf("%c", *str);
+ ++i;
+ }
+ }
+ }
+}
+
+// Prints the names of the tests matching the user-specified filter flag.
+void UnitTestImpl::ListTestsMatchingFilter() {
+ // Print at most this many characters for each type/value parameter.
+ const int kMaxParamLength = 250;
+
+ for (size_t i = 0; i < test_cases_.size(); i++) {
+ const TestCase* const test_case = test_cases_[i];
+ bool printed_test_case_name = false;
+
+ for (size_t j = 0; j < test_case->test_info_list().size(); j++) {
+ const TestInfo* const test_info =
+ test_case->test_info_list()[j];
+ if (test_info->matches_filter_) {
+ if (!printed_test_case_name) {
+ printed_test_case_name = true;
+ printf("%s.", test_case->name());
+ if (test_case->type_param() != NULL) {
+ printf(" # %s = ", kTypeParamLabel);
+ // We print the type parameter on a single line to make
+ // the output easy to parse by a program.
+ PrintOnOneLine(test_case->type_param(), kMaxParamLength);
+ }
+ printf("\n");
+ }
+ printf(" %s", test_info->name());
+ if (test_info->value_param() != NULL) {
+ printf(" # %s = ", kValueParamLabel);
+ // We print the value parameter on a single line to make the
+ // output easy to parse by a program.
+ PrintOnOneLine(test_info->value_param(), kMaxParamLength);
+ }
+ printf("\n");
+ }
+ }
+ }
+ fflush(stdout);
+}
+
+// Sets the OS stack trace getter.
+//
+// Does nothing if the input and the current OS stack trace getter are
+// the same; otherwise, deletes the old getter and makes the input the
+// current getter.
+void UnitTestImpl::set_os_stack_trace_getter(
+ OsStackTraceGetterInterface* getter) {
+ if (os_stack_trace_getter_ != getter) {
+ delete os_stack_trace_getter_;
+ os_stack_trace_getter_ = getter;
+ }
+}
+
+// Returns the current OS stack trace getter if it is not NULL;
+// otherwise, creates an OsStackTraceGetter, makes it the current
+// getter, and returns it.
+OsStackTraceGetterInterface* UnitTestImpl::os_stack_trace_getter() {
+ if (os_stack_trace_getter_ == NULL) {
+ os_stack_trace_getter_ = new OsStackTraceGetter;
+ }
+
+ return os_stack_trace_getter_;
+}
+
+// Returns the TestResult for the test that's currently running, or
+// the TestResult for the ad hoc test if no test is running.
+TestResult* UnitTestImpl::current_test_result() {
+ return current_test_info_ ?
+ &(current_test_info_->result_) : &ad_hoc_test_result_;
+}
+
+// Shuffles all test cases, and the tests within each test case,
+// making sure that death tests are still run first.
+void UnitTestImpl::ShuffleTests() {
+ // Shuffles the death test cases.
+ ShuffleRange(random(), 0, last_death_test_case_ + 1, &test_case_indices_);
+
+ // Shuffles the non-death test cases.
+ ShuffleRange(random(), last_death_test_case_ + 1,
+ static_cast<int>(test_cases_.size()), &test_case_indices_);
+
+ // Shuffles the tests inside each test case.
+ for (size_t i = 0; i < test_cases_.size(); i++) {
+ test_cases_[i]->ShuffleTests(random());
+ }
+}
+
+// Restores the test cases and tests to their order before the first shuffle.
+void UnitTestImpl::UnshuffleTests() {
+ for (size_t i = 0; i < test_cases_.size(); i++) {
+ // Unshuffles the tests in each test case.
+ test_cases_[i]->UnshuffleTests();
+ // Resets the index of each test case.
+ test_case_indices_[i] = static_cast<int>(i);
+ }
+}
+
+// Returns the current OS stack trace as an std::string.
+//
+// The maximum number of stack frames to be included is specified by
+// the gtest_stack_trace_depth flag. The skip_count parameter
+// specifies the number of top frames to be skipped, which doesn't
+// count against the number of frames to be included.
+//
+// For example, if Foo() calls Bar(), which in turn calls
+// GetCurrentOsStackTraceExceptTop(..., 1), Foo() will be included in
+// the trace but Bar() and GetCurrentOsStackTraceExceptTop() won't.
+std::string GetCurrentOsStackTraceExceptTop(UnitTest* /*unit_test*/,
+ int skip_count) {
+ // We pass skip_count + 1 to skip this wrapper function in addition
+ // to what the user really wants to skip.
+ return GetUnitTestImpl()->CurrentOsStackTraceExceptTop(skip_count + 1);
+}
+
+// Used by the GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_ macro to
+// suppress unreachable code warnings.
+namespace {
+class ClassUniqueToAlwaysTrue {};
+}
+
+bool IsTrue(bool condition) { return condition; }
+
+bool AlwaysTrue() {
+#if GTEST_HAS_EXCEPTIONS
+ // This condition is always false so AlwaysTrue() never actually throws,
+ // but it makes the compiler think that it may throw.
+ if (IsTrue(false))
+ throw ClassUniqueToAlwaysTrue();
+#endif // GTEST_HAS_EXCEPTIONS
+ return true;
+}
+
+// If *pstr starts with the given prefix, modifies *pstr to be right
+// past the prefix and returns true; otherwise leaves *pstr unchanged
+// and returns false. None of pstr, *pstr, and prefix can be NULL.
+bool SkipPrefix(const char* prefix, const char** pstr) {
+ const size_t prefix_len = strlen(prefix);
+ if (strncmp(*pstr, prefix, prefix_len) == 0) {
+ *pstr += prefix_len;
+ return true;
+ }
+ return false;
+}
+
+// Parses a string as a command line flag. The string should have
+// the format "--flag=value". When def_optional is true, the "=value"
+// part can be omitted.
+//
+// Returns the value of the flag, or NULL if the parsing failed.
+const char* ParseFlagValue(const char* str,
+ const char* flag,
+ bool def_optional) {
+ // str and flag must not be NULL.
+ if (str == NULL || flag == NULL) return NULL;
+
+ // The flag must start with "--" followed by GTEST_FLAG_PREFIX_.
+ const std::string flag_str = std::string("--") + GTEST_FLAG_PREFIX_ + flag;
+ const size_t flag_len = flag_str.length();
+ if (strncmp(str, flag_str.c_str(), flag_len) != 0) return NULL;
+
+ // Skips the flag name.
+ const char* flag_end = str + flag_len;
+
+ // When def_optional is true, it's OK to not have a "=value" part.
+ if (def_optional && (flag_end[0] == '\0')) {
+ return flag_end;
+ }
+
+ // If def_optional is true and there are more characters after the
+ // flag name, or if def_optional is false, there must be a '=' after
+ // the flag name.
+ if (flag_end[0] != '=') return NULL;
+
+ // Returns the string after "=".
+ return flag_end + 1;
+}
+
+// Parses a string for a bool flag, in the form of either
+// "--flag=value" or "--flag".
+//
+// In the former case, the value is taken as true as long as it does
+// not start with '0', 'f', or 'F'.
+//
+// In the latter case, the value is taken as true.
+//
+// On success, stores the value of the flag in *value, and returns
+// true. On failure, returns false without changing *value.
+bool ParseBoolFlag(const char* str, const char* flag, bool* value) {
+ // Gets the value of the flag as a string.
+ const char* const value_str = ParseFlagValue(str, flag, true);
+
+ // Aborts if the parsing failed.
+ if (value_str == NULL) return false;
+
+ // Converts the string value to a bool.
+ *value = !(*value_str == '0' || *value_str == 'f' || *value_str == 'F');
+ return true;
+}
+
+// Parses a string for an Int32 flag, in the form of
+// "--flag=value".
+//
+// On success, stores the value of the flag in *value, and returns
+// true. On failure, returns false without changing *value.
+bool ParseInt32Flag(const char* str, const char* flag, Int32* value) {
+ // Gets the value of the flag as a string.
+ const char* const value_str = ParseFlagValue(str, flag, false);
+
+ // Aborts if the parsing failed.
+ if (value_str == NULL) return false;
+
+ // Sets *value to the value of the flag.
+ return ParseInt32(Message() << "The value of flag --" << flag,
+ value_str, value);
+}
+
+// Parses a string for a string flag, in the form of
+// "--flag=value".
+//
+// On success, stores the value of the flag in *value, and returns
+// true. On failure, returns false without changing *value.
+bool ParseStringFlag(const char* str, const char* flag, std::string* value) {
+ // Gets the value of the flag as a string.
+ const char* const value_str = ParseFlagValue(str, flag, false);
+
+ // Aborts if the parsing failed.
+ if (value_str == NULL) return false;
+
+ // Sets *value to the value of the flag.
+ *value = value_str;
+ return true;
+}
+
+// Determines whether a string has a prefix that Google Test uses for its
+// flags, i.e., starts with GTEST_FLAG_PREFIX_ or GTEST_FLAG_PREFIX_DASH_.
+// If Google Test detects that a command line flag has its prefix but is not
+// recognized, it will print its help message. Flags starting with
+// GTEST_INTERNAL_PREFIX_ followed by "internal_" are considered Google Test
+// internal flags and do not trigger the help message.
+static bool HasGoogleTestFlagPrefix(const char* str) {
+ return (SkipPrefix("--", &str) ||
+ SkipPrefix("-", &str) ||
+ SkipPrefix("/", &str)) &&
+ !SkipPrefix(GTEST_FLAG_PREFIX_ "internal_", &str) &&
+ (SkipPrefix(GTEST_FLAG_PREFIX_, &str) ||
+ SkipPrefix(GTEST_FLAG_PREFIX_DASH_, &str));
+}
+
+// Prints a string containing code-encoded text. The following escape
+// sequences can be used in the string to control the text color:
+//
+// @@ prints a single '@' character.
+// @R changes the color to red.
+// @G changes the color to green.
+// @Y changes the color to yellow.
+// @D changes to the default terminal text color.
+//
+// TODO(wan at google.com): Write tests for this once we add stdout
+// capturing to Google Test.
+static void PrintColorEncoded(const char* str) {
+ GTestColor color = COLOR_DEFAULT; // The current color.
+
+ // Conceptually, we split the string into segments divided by escape
+ // sequences. Then we print one segment at a time. At the end of
+ // each iteration, the str pointer advances to the beginning of the
+ // next segment.
+ for (;;) {
+ const char* p = strchr(str, '@');
+ if (p == NULL) {
+ ColoredPrintf(color, "%s", str);
+ return;
+ }
+
+ ColoredPrintf(color, "%s", std::string(str, p).c_str());
+
+ const char ch = p[1];
+ str = p + 2;
+ if (ch == '@') {
+ ColoredPrintf(color, "@");
+ } else if (ch == 'D') {
+ color = COLOR_DEFAULT;
+ } else if (ch == 'R') {
+ color = COLOR_RED;
+ } else if (ch == 'G') {
+ color = COLOR_GREEN;
+ } else if (ch == 'Y') {
+ color = COLOR_YELLOW;
+ } else {
+ --str;
+ }
+ }
+}
+
+static const char kColorEncodedHelpMessage[] =
+"This program contains tests written using " GTEST_NAME_ ". You can use the\n"
+"following command line flags to control its behavior:\n"
+"\n"
+"Test Selection:\n"
+" @G--" GTEST_FLAG_PREFIX_ "list_tests at D\n"
+" List the names of all tests instead of running them. The name of\n"
+" TEST(Foo, Bar) is \"Foo.Bar\".\n"
+" @G--" GTEST_FLAG_PREFIX_ "filter=@YPOSTIVE_PATTERNS"
+ "[@G- at YNEGATIVE_PATTERNS]@D\n"
+" Run only the tests whose name matches one of the positive patterns but\n"
+" none of the negative patterns. '?' matches any single character; '*'\n"
+" matches any substring; ':' separates two patterns.\n"
+" @G--" GTEST_FLAG_PREFIX_ "also_run_disabled_tests at D\n"
+" Run all disabled tests too.\n"
+"\n"
+"Test Execution:\n"
+" @G--" GTEST_FLAG_PREFIX_ "repeat=@Y[COUNT]@D\n"
+" Run the tests repeatedly; use a negative count to repeat forever.\n"
+" @G--" GTEST_FLAG_PREFIX_ "shuffle at D\n"
+" Randomize tests' orders on every iteration.\n"
+" @G--" GTEST_FLAG_PREFIX_ "random_seed=@Y[NUMBER]@D\n"
+" Random number seed to use for shuffling test orders (between 1 and\n"
+" 99999, or 0 to use a seed based on the current time).\n"
+"\n"
+"Test Output:\n"
+" @G--" GTEST_FLAG_PREFIX_ "color=@Y(@Gyes at Y|@Gno at Y|@Gauto at Y)@D\n"
+" Enable/disable colored output. The default is @Gauto at D.\n"
+" - at G-" GTEST_FLAG_PREFIX_ "print_time=0 at D\n"
+" Don't print the elapsed time of each test.\n"
+" @G--" GTEST_FLAG_PREFIX_ "output=xml at Y[@G:@YDIRECTORY_PATH at G"
+ GTEST_PATH_SEP_ "@Y|@G:@YFILE_PATH]@D\n"
+" Generate an XML report in the given directory or with the given file\n"
+" name. @YFILE_PATH at D defaults to @Gtest_details.xml at D.\n"
+#if GTEST_CAN_STREAM_RESULTS_
+" @G--" GTEST_FLAG_PREFIX_ "stream_result_to=@YHOST at G:@YPORT at D\n"
+" Stream test results to the given server.\n"
+#endif // GTEST_CAN_STREAM_RESULTS_
+"\n"
+"Assertion Behavior:\n"
+#if GTEST_HAS_DEATH_TEST && !GTEST_OS_WINDOWS
+" @G--" GTEST_FLAG_PREFIX_ "death_test_style=@Y(@Gfast at Y|@Gthreadsafe at Y)@D\n"
+" Set the default death test style.\n"
+#endif // GTEST_HAS_DEATH_TEST && !GTEST_OS_WINDOWS
+" @G--" GTEST_FLAG_PREFIX_ "break_on_failure at D\n"
+" Turn assertion failures into debugger break-points.\n"
+" @G--" GTEST_FLAG_PREFIX_ "throw_on_failure at D\n"
+" Turn assertion failures into C++ exceptions.\n"
+" @G--" GTEST_FLAG_PREFIX_ "catch_exceptions=0 at D\n"
+" Do not report exceptions as test failures. Instead, allow them\n"
+" to crash the program or throw a pop-up (on Windows).\n"
+"\n"
+"Except for @G--" GTEST_FLAG_PREFIX_ "list_tests at D, you can alternatively set "
+ "the corresponding\n"
+"environment variable of a flag (all letters in upper-case). For example, to\n"
+"disable colored text output, you can either specify @G--" GTEST_FLAG_PREFIX_
+ "color=no at D or set\n"
+"the @G" GTEST_FLAG_PREFIX_UPPER_ "COLOR at D environment variable to @Gno at D.\n"
+"\n"
+"For more information, please read the " GTEST_NAME_ " documentation at\n"
+"@G" GTEST_PROJECT_URL_ "@D. If you find a bug in " GTEST_NAME_ "\n"
+"(not one in your own code or tests), please report it to\n"
+"@G<" GTEST_DEV_EMAIL_ ">@D.\n";
+
+// Parses the command line for Google Test flags, without initializing
+// other parts of Google Test. The type parameter CharType can be
+// instantiated to either char or wchar_t.
+template <typename CharType>
+void ParseGoogleTestFlagsOnlyImpl(int* argc, CharType** argv) {
+ for (int i = 1; i < *argc; i++) {
+ const std::string arg_string = StreamableToString(argv[i]);
+ const char* const arg = arg_string.c_str();
+
+ using internal::ParseBoolFlag;
+ using internal::ParseInt32Flag;
+ using internal::ParseStringFlag;
+
+ // Do we see a Google Test flag?
+ if (ParseBoolFlag(arg, kAlsoRunDisabledTestsFlag,
+ >EST_FLAG(also_run_disabled_tests)) ||
+ ParseBoolFlag(arg, kBreakOnFailureFlag,
+ >EST_FLAG(break_on_failure)) ||
+ ParseBoolFlag(arg, kCatchExceptionsFlag,
+ >EST_FLAG(catch_exceptions)) ||
+ ParseStringFlag(arg, kColorFlag, >EST_FLAG(color)) ||
+ ParseStringFlag(arg, kDeathTestStyleFlag,
+ >EST_FLAG(death_test_style)) ||
+ ParseBoolFlag(arg, kDeathTestUseFork,
+ >EST_FLAG(death_test_use_fork)) ||
+ ParseStringFlag(arg, kFilterFlag, >EST_FLAG(filter)) ||
+ ParseStringFlag(arg, kInternalRunDeathTestFlag,
+ >EST_FLAG(internal_run_death_test)) ||
+ ParseBoolFlag(arg, kListTestsFlag, >EST_FLAG(list_tests)) ||
+ ParseStringFlag(arg, kOutputFlag, >EST_FLAG(output)) ||
+ ParseBoolFlag(arg, kPrintTimeFlag, >EST_FLAG(print_time)) ||
+ ParseInt32Flag(arg, kRandomSeedFlag, >EST_FLAG(random_seed)) ||
+ ParseInt32Flag(arg, kRepeatFlag, >EST_FLAG(repeat)) ||
+ ParseBoolFlag(arg, kShuffleFlag, >EST_FLAG(shuffle)) ||
+ ParseInt32Flag(arg, kStackTraceDepthFlag,
+ >EST_FLAG(stack_trace_depth)) ||
+ ParseStringFlag(arg, kStreamResultToFlag,
+ >EST_FLAG(stream_result_to)) ||
+ ParseBoolFlag(arg, kThrowOnFailureFlag,
+ >EST_FLAG(throw_on_failure))
+ ) {
+ // Yes. Shift the remainder of the argv list left by one. Note
+ // that argv has (*argc + 1) elements, the last one always being
+ // NULL. The following loop moves the trailing NULL element as
+ // well.
+ for (int j = i; j != *argc; j++) {
+ argv[j] = argv[j + 1];
+ }
+
+ // Decrements the argument count.
+ (*argc)--;
+
+ // We also need to decrement the iterator as we just removed
+ // an element.
+ i--;
+ } else if (arg_string == "--help" || arg_string == "-h" ||
+ arg_string == "-?" || arg_string == "/?" ||
+ HasGoogleTestFlagPrefix(arg)) {
+ // Both help flag and unrecognized Google Test flags (excluding
+ // internal ones) trigger help display.
+ g_help_flag = true;
+ }
+ }
+
+ if (g_help_flag) {
+ // We print the help here instead of in RUN_ALL_TESTS(), as the
+ // latter may not be called at all if the user is using Google
+ // Test with another testing framework.
+ PrintColorEncoded(kColorEncodedHelpMessage);
+ }
+}
+
+// Parses the command line for Google Test flags, without initializing
+// other parts of Google Test.
+void ParseGoogleTestFlagsOnly(int* argc, char** argv) {
+ ParseGoogleTestFlagsOnlyImpl(argc, argv);
+}
+void ParseGoogleTestFlagsOnly(int* argc, wchar_t** argv) {
+ ParseGoogleTestFlagsOnlyImpl(argc, argv);
+}
+
+// The internal implementation of InitGoogleTest().
+//
+// The type parameter CharType can be instantiated to either char or
+// wchar_t.
+template <typename CharType>
+void InitGoogleTestImpl(int* argc, CharType** argv) {
+ g_init_gtest_count++;
+
+ // We don't want to run the initialization code twice.
+ if (g_init_gtest_count != 1) return;
+
+ if (*argc <= 0) return;
+
+ internal::g_executable_path = internal::StreamableToString(argv[0]);
+
+#if GTEST_HAS_DEATH_TEST
+
+ g_argvs.clear();
+ for (int i = 0; i != *argc; i++) {
+ g_argvs.push_back(StreamableToString(argv[i]));
+ }
+
+#endif // GTEST_HAS_DEATH_TEST
+
+ ParseGoogleTestFlagsOnly(argc, argv);
+ GetUnitTestImpl()->PostFlagParsingInit();
+}
+
+} // namespace internal
+
+// Initializes Google Test. This must be called before calling
+// RUN_ALL_TESTS(). In particular, it parses a command line for the
+// flags that Google Test recognizes. Whenever a Google Test flag is
+// seen, it is removed from argv, and *argc is decremented.
+//
+// No value is returned. Instead, the Google Test flag variables are
+// updated.
+//
+// Calling the function for the second time has no user-visible effect.
+void InitGoogleTest(int* argc, char** argv) {
+ internal::InitGoogleTestImpl(argc, argv);
+}
+
+// This overloaded version can be used in Windows programs compiled in
+// UNICODE mode.
+void InitGoogleTest(int* argc, wchar_t** argv) {
+ internal::InitGoogleTestImpl(argc, argv);
+}
+
+} // namespace testing
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan), vladl at google.com (Vlad Losev)
+//
+// This file implements death tests.
+
+
+#if GTEST_HAS_DEATH_TEST
+
+# if GTEST_OS_MAC
+# include <crt_externs.h>
+# endif // GTEST_OS_MAC
+
+# include <errno.h>
+# include <fcntl.h>
+# include <limits.h>
+
+# if GTEST_OS_LINUX
+# include <signal.h>
+# endif // GTEST_OS_LINUX
+
+# include <stdarg.h>
+
+# if GTEST_OS_WINDOWS
+# include <windows.h>
+# else
+# include <sys/mman.h>
+# include <sys/wait.h>
+# endif // GTEST_OS_WINDOWS
+
+# if GTEST_OS_QNX
+# include <spawn.h>
+# endif // GTEST_OS_QNX
+
+#endif // GTEST_HAS_DEATH_TEST
+
+
+// Indicates that this translation unit is part of Google Test's
+// implementation. It must come before gtest-internal-inl.h is
+// included, or there will be a compiler error. This trick is to
+// prevent a user from accidentally including gtest-internal-inl.h in
+// his code.
+#define GTEST_IMPLEMENTATION_ 1
+#undef GTEST_IMPLEMENTATION_
+
+namespace testing {
+
+// Constants.
+
+// The default death test style.
+static const char kDefaultDeathTestStyle[] = "fast";
+
+GTEST_DEFINE_string_(
+ death_test_style,
+ internal::StringFromGTestEnv("death_test_style", kDefaultDeathTestStyle),
+ "Indicates how to run a death test in a forked child process: "
+ "\"threadsafe\" (child process re-executes the test binary "
+ "from the beginning, running only the specific death test) or "
+ "\"fast\" (child process runs the death test immediately "
+ "after forking).");
+
+GTEST_DEFINE_bool_(
+ death_test_use_fork,
+ internal::BoolFromGTestEnv("death_test_use_fork", false),
+ "Instructs to use fork()/_exit() instead of clone() in death tests. "
+ "Ignored and always uses fork() on POSIX systems where clone() is not "
+ "implemented. Useful when running under valgrind or similar tools if "
+ "those do not support clone(). Valgrind 3.3.1 will just fail if "
+ "it sees an unsupported combination of clone() flags. "
+ "It is not recommended to use this flag w/o valgrind though it will "
+ "work in 99% of the cases. Once valgrind is fixed, this flag will "
+ "most likely be removed.");
+
+namespace internal {
+GTEST_DEFINE_string_(
+ internal_run_death_test, "",
+ "Indicates the file, line number, temporal index of "
+ "the single death test to run, and a file descriptor to "
+ "which a success code may be sent, all separated by "
+ "the '|' characters. This flag is specified if and only if the current "
+ "process is a sub-process launched for running a thread-safe "
+ "death test. FOR INTERNAL USE ONLY.");
+} // namespace internal
+
+#if GTEST_HAS_DEATH_TEST
+
+namespace internal {
+
+// Valid only for fast death tests. Indicates the code is running in the
+// child process of a fast style death test.
+static bool g_in_fast_death_test_child = false;
+
+// Returns a Boolean value indicating whether the caller is currently
+// executing in the context of the death test child process. Tools such as
+// Valgrind heap checkers may need this to modify their behavior in death
+// tests. IMPORTANT: This is an internal utility. Using it may break the
+// implementation of death tests. User code MUST NOT use it.
+bool InDeathTestChild() {
+# if GTEST_OS_WINDOWS
+
+ // On Windows, death tests are thread-safe regardless of the value of the
+ // death_test_style flag.
+ return !GTEST_FLAG(internal_run_death_test).empty();
+
+# else
+
+ if (GTEST_FLAG(death_test_style) == "threadsafe")
+ return !GTEST_FLAG(internal_run_death_test).empty();
+ else
+ return g_in_fast_death_test_child;
+#endif
+}
+
+} // namespace internal
+
+// ExitedWithCode constructor.
+ExitedWithCode::ExitedWithCode(int exit_code) : exit_code_(exit_code) {
+}
+
+// ExitedWithCode function-call operator.
+bool ExitedWithCode::operator()(int exit_status) const {
+# if GTEST_OS_WINDOWS
+
+ return exit_status == exit_code_;
+
+# else
+
+ return WIFEXITED(exit_status) && WEXITSTATUS(exit_status) == exit_code_;
+
+# endif // GTEST_OS_WINDOWS
+}
+
+# if !GTEST_OS_WINDOWS
+// KilledBySignal constructor.
+KilledBySignal::KilledBySignal(int signum) : signum_(signum) {
+}
+
+// KilledBySignal function-call operator.
+bool KilledBySignal::operator()(int exit_status) const {
+ return WIFSIGNALED(exit_status) && WTERMSIG(exit_status) == signum_;
+}
+# endif // !GTEST_OS_WINDOWS
+
+namespace internal {
+
+// Utilities needed for death tests.
+
+// Generates a textual description of a given exit code, in the format
+// specified by wait(2).
+static std::string ExitSummary(int exit_code) {
+ Message m;
+
+# if GTEST_OS_WINDOWS
+
+ m << "Exited with exit status " << exit_code;
+
+# else
+
+ if (WIFEXITED(exit_code)) {
+ m << "Exited with exit status " << WEXITSTATUS(exit_code);
+ } else if (WIFSIGNALED(exit_code)) {
+ m << "Terminated by signal " << WTERMSIG(exit_code);
+ }
+# ifdef WCOREDUMP
+ if (WCOREDUMP(exit_code)) {
+ m << " (core dumped)";
+ }
+# endif
+# endif // GTEST_OS_WINDOWS
+
+ return m.GetString();
+}
+
+// Returns true if exit_status describes a process that was terminated
+// by a signal, or exited normally with a nonzero exit code.
+bool ExitedUnsuccessfully(int exit_status) {
+ return !ExitedWithCode(0)(exit_status);
+}
+
+# if !GTEST_OS_WINDOWS
+// Generates a textual failure message when a death test finds more than
+// one thread running, or cannot determine the number of threads, prior
+// to executing the given statement. It is the responsibility of the
+// caller not to pass a thread_count of 1.
+static std::string DeathTestThreadWarning(size_t thread_count) {
+ Message msg;
+ msg << "Death tests use fork(), which is unsafe particularly"
+ << " in a threaded context. For this test, " << GTEST_NAME_ << " ";
+ if (thread_count == 0)
+ msg << "couldn't detect the number of threads.";
+ else
+ msg << "detected " << thread_count << " threads.";
+ return msg.GetString();
+}
+# endif // !GTEST_OS_WINDOWS
+
+// Flag characters for reporting a death test that did not die.
+static const char kDeathTestLived = 'L';
+static const char kDeathTestReturned = 'R';
+static const char kDeathTestThrew = 'T';
+static const char kDeathTestInternalError = 'I';
+
+// An enumeration describing all of the possible ways that a death test can
+// conclude. DIED means that the process died while executing the test
+// code; LIVED means that process lived beyond the end of the test code;
+// RETURNED means that the test statement attempted to execute a return
+// statement, which is not allowed; THREW means that the test statement
+// returned control by throwing an exception. IN_PROGRESS means the test
+// has not yet concluded.
+// TODO(vladl at google.com): Unify names and possibly values for
+// AbortReason, DeathTestOutcome, and flag characters above.
+enum DeathTestOutcome { IN_PROGRESS, DIED, LIVED, RETURNED, THREW };
+
+// Routine for aborting the program which is safe to call from an
+// exec-style death test child process, in which case the error
+// message is propagated back to the parent process. Otherwise, the
+// message is simply printed to stderr. In either case, the program
+// then exits with status 1.
+void DeathTestAbort(const std::string& message) {
+ // On a POSIX system, this function may be called from a threadsafe-style
+ // death test child process, which operates on a very small stack. Use
+ // the heap for any additional non-minuscule memory requirements.
+ const InternalRunDeathTestFlag* const flag =
+ GetUnitTestImpl()->internal_run_death_test_flag();
+ if (flag != NULL) {
+ FILE* parent = posix::FDOpen(flag->write_fd(), "w");
+ fputc(kDeathTestInternalError, parent);
+ fprintf(parent, "%s", message.c_str());
+ fflush(parent);
+ _exit(1);
+ } else {
+ fprintf(stderr, "%s", message.c_str());
+ fflush(stderr);
+ posix::Abort();
+ }
+}
+
+// A replacement for CHECK that calls DeathTestAbort if the assertion
+// fails.
+# define GTEST_DEATH_TEST_CHECK_(expression) \
+ do { \
+ if (!::testing::internal::IsTrue(expression)) { \
+ DeathTestAbort( \
+ ::std::string("CHECK failed: File ") + __FILE__ + ", line " \
+ + ::testing::internal::StreamableToString(__LINE__) + ": " \
+ + #expression); \
+ } \
+ } while (::testing::internal::AlwaysFalse())
+
+// This macro is similar to GTEST_DEATH_TEST_CHECK_, but it is meant for
+// evaluating any system call that fulfills two conditions: it must return
+// -1 on failure, and set errno to EINTR when it is interrupted and
+// should be tried again. The macro expands to a loop that repeatedly
+// evaluates the expression as long as it evaluates to -1 and sets
+// errno to EINTR. If the expression evaluates to -1 but errno is
+// something other than EINTR, DeathTestAbort is called.
+# define GTEST_DEATH_TEST_CHECK_SYSCALL_(expression) \
+ do { \
+ int gtest_retval; \
+ do { \
+ gtest_retval = (expression); \
+ } while (gtest_retval == -1 && errno == EINTR); \
+ if (gtest_retval == -1) { \
+ DeathTestAbort( \
+ ::std::string("CHECK failed: File ") + __FILE__ + ", line " \
+ + ::testing::internal::StreamableToString(__LINE__) + ": " \
+ + #expression + " != -1"); \
+ } \
+ } while (::testing::internal::AlwaysFalse())
+
+// Returns the message describing the last system error in errno.
+std::string GetLastErrnoDescription() {
+ return errno == 0 ? "" : posix::StrError(errno);
+}
+
+// This is called from a death test parent process to read a failure
+// message from the death test child process and log it with the FATAL
+// severity. On Windows, the message is read from a pipe handle. On other
+// platforms, it is read from a file descriptor.
+static void FailFromInternalError(int fd) {
+ Message error;
+ char buffer[256];
+ int num_read;
+
+ do {
+ while ((num_read = posix::Read(fd, buffer, 255)) > 0) {
+ buffer[num_read] = '\0';
+ error << buffer;
+ }
+ } while (num_read == -1 && errno == EINTR);
+
+ if (num_read == 0) {
+ GTEST_LOG_(FATAL) << error.GetString();
+ } else {
+ const int last_error = errno;
+ GTEST_LOG_(FATAL) << "Error while reading death test internal: "
+ << GetLastErrnoDescription() << " [" << last_error << "]";
+ }
+}
+
+// Death test constructor. Increments the running death test count
+// for the current test.
+DeathTest::DeathTest() {
+ TestInfo* const info = GetUnitTestImpl()->current_test_info();
+ if (info == NULL) {
+ DeathTestAbort("Cannot run a death test outside of a TEST or "
+ "TEST_F construct");
+ }
+}
+
+// Creates and returns a death test by dispatching to the current
+// death test factory.
+bool DeathTest::Create(const char* statement, const RE* regex,
+ const char* file, int line, DeathTest** test) {
+ return GetUnitTestImpl()->death_test_factory()->Create(
+ statement, regex, file, line, test);
+}
+
+const char* DeathTest::LastMessage() {
+ return last_death_test_message_.c_str();
+}
+
+void DeathTest::set_last_death_test_message(const std::string& message) {
+ last_death_test_message_ = message;
+}
+
+std::string DeathTest::last_death_test_message_;
+
+// Provides cross platform implementation for some death functionality.
+class DeathTestImpl : public DeathTest {
+ protected:
+ DeathTestImpl(const char* a_statement, const RE* a_regex)
+ : statement_(a_statement),
+ regex_(a_regex),
+ spawned_(false),
+ status_(-1),
+ outcome_(IN_PROGRESS),
+ read_fd_(-1),
+ write_fd_(-1) {}
+
+ // read_fd_ is expected to be closed and cleared by a derived class.
+ ~DeathTestImpl() { GTEST_DEATH_TEST_CHECK_(read_fd_ == -1); }
+
+ void Abort(AbortReason reason);
+ virtual bool Passed(bool status_ok);
+
+ const char* statement() const { return statement_; }
+ const RE* regex() const { return regex_; }
+ bool spawned() const { return spawned_; }
+ void set_spawned(bool is_spawned) { spawned_ = is_spawned; }
+ int status() const { return status_; }
+ void set_status(int a_status) { status_ = a_status; }
+ DeathTestOutcome outcome() const { return outcome_; }
+ void set_outcome(DeathTestOutcome an_outcome) { outcome_ = an_outcome; }
+ int read_fd() const { return read_fd_; }
+ void set_read_fd(int fd) { read_fd_ = fd; }
+ int write_fd() const { return write_fd_; }
+ void set_write_fd(int fd) { write_fd_ = fd; }
+
+ // Called in the parent process only. Reads the result code of the death
+ // test child process via a pipe, interprets it to set the outcome_
+ // member, and closes read_fd_. Outputs diagnostics and terminates in
+ // case of unexpected codes.
+ void ReadAndInterpretStatusByte();
+
+ private:
+ // The textual content of the code this object is testing. This class
+ // doesn't own this string and should not attempt to delete it.
+ const char* const statement_;
+ // The regular expression which test output must match. DeathTestImpl
+ // doesn't own this object and should not attempt to delete it.
+ const RE* const regex_;
+ // True if the death test child process has been successfully spawned.
+ bool spawned_;
+ // The exit status of the child process.
+ int status_;
+ // How the death test concluded.
+ DeathTestOutcome outcome_;
+ // Descriptor to the read end of the pipe to the child process. It is
+ // always -1 in the child process. The child keeps its write end of the
+ // pipe in write_fd_.
+ int read_fd_;
+ // Descriptor to the child's write end of the pipe to the parent process.
+ // It is always -1 in the parent process. The parent keeps its end of the
+ // pipe in read_fd_.
+ int write_fd_;
+};
+
+// Called in the parent process only. Reads the result code of the death
+// test child process via a pipe, interprets it to set the outcome_
+// member, and closes read_fd_. Outputs diagnostics and terminates in
+// case of unexpected codes.
+void DeathTestImpl::ReadAndInterpretStatusByte() {
+ char flag;
+ int bytes_read;
+
+ // The read() here blocks until data is available (signifying the
+ // failure of the death test) or until the pipe is closed (signifying
+ // its success), so it's okay to call this in the parent before
+ // the child process has exited.
+ do {
+ bytes_read = posix::Read(read_fd(), &flag, 1);
+ } while (bytes_read == -1 && errno == EINTR);
+
+ if (bytes_read == 0) {
+ set_outcome(DIED);
+ } else if (bytes_read == 1) {
+ switch (flag) {
+ case kDeathTestReturned:
+ set_outcome(RETURNED);
+ break;
+ case kDeathTestThrew:
+ set_outcome(THREW);
+ break;
+ case kDeathTestLived:
+ set_outcome(LIVED);
+ break;
+ case kDeathTestInternalError:
+ FailFromInternalError(read_fd()); // Does not return.
+ break;
+ default:
+ GTEST_LOG_(FATAL) << "Death test child process reported "
+ << "unexpected status byte ("
+ << static_cast<unsigned int>(flag) << ")";
+ }
+ } else {
+ GTEST_LOG_(FATAL) << "Read from death test child process failed: "
+ << GetLastErrnoDescription();
+ }
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(posix::Close(read_fd()));
+ set_read_fd(-1);
+}
+
+// Signals that the death test code which should have exited, didn't.
+// Should be called only in a death test child process.
+// Writes a status byte to the child's status file descriptor, then
+// calls _exit(1).
+void DeathTestImpl::Abort(AbortReason reason) {
+ // The parent process considers the death test to be a failure if
+ // it finds any data in our pipe. So, here we write a single flag byte
+ // to the pipe, then exit.
+ const char status_ch =
+ reason == TEST_DID_NOT_DIE ? kDeathTestLived :
+ reason == TEST_THREW_EXCEPTION ? kDeathTestThrew : kDeathTestReturned;
+
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(posix::Write(write_fd(), &status_ch, 1));
+ // We are leaking the descriptor here because on some platforms (i.e.,
+ // when built as Windows DLL), destructors of global objects will still
+ // run after calling _exit(). On such systems, write_fd_ will be
+ // indirectly closed from the destructor of UnitTestImpl, causing double
+ // close if it is also closed here. On debug configurations, double close
+ // may assert. As there are no in-process buffers to flush here, we are
+ // relying on the OS to close the descriptor after the process terminates
+ // when the destructors are not run.
+ _exit(1); // Exits w/o any normal exit hooks (we were supposed to crash)
+}
+
+// Returns an indented copy of stderr output for a death test.
+// This makes distinguishing death test output lines from regular log lines
+// much easier.
+static ::std::string FormatDeathTestOutput(const ::std::string& output) {
+ ::std::string ret;
+ for (size_t at = 0; ; ) {
+ const size_t line_end = output.find('\n', at);
+ ret += "[ DEATH ] ";
+ if (line_end == ::std::string::npos) {
+ ret += output.substr(at);
+ break;
+ }
+ ret += output.substr(at, line_end + 1 - at);
+ at = line_end + 1;
+ }
+ return ret;
+}
+
+// Assesses the success or failure of a death test, using both private
+// members which have previously been set, and one argument:
+//
+// Private data members:
+// outcome: An enumeration describing how the death test
+// concluded: DIED, LIVED, THREW, or RETURNED. The death test
+// fails in the latter three cases.
+// status: The exit status of the child process. On *nix, it is in the
+// in the format specified by wait(2). On Windows, this is the
+// value supplied to the ExitProcess() API or a numeric code
+// of the exception that terminated the program.
+// regex: A regular expression object to be applied to
+// the test's captured standard error output; the death test
+// fails if it does not match.
+//
+// Argument:
+// status_ok: true if exit_status is acceptable in the context of
+// this particular death test, which fails if it is false
+//
+// Returns true iff all of the above conditions are met. Otherwise, the
+// first failing condition, in the order given above, is the one that is
+// reported. Also sets the last death test message string.
+bool DeathTestImpl::Passed(bool status_ok) {
+ if (!spawned())
+ return false;
+
+ const std::string error_message = GetCapturedStderr();
+
+ bool success = false;
+ Message buffer;
+
+ buffer << "Death test: " << statement() << "\n";
+ switch (outcome()) {
+ case LIVED:
+ buffer << " Result: failed to die.\n"
+ << " Error msg:\n" << FormatDeathTestOutput(error_message);
+ break;
+ case THREW:
+ buffer << " Result: threw an exception.\n"
+ << " Error msg:\n" << FormatDeathTestOutput(error_message);
+ break;
+ case RETURNED:
+ buffer << " Result: illegal return in test statement.\n"
+ << " Error msg:\n" << FormatDeathTestOutput(error_message);
+ break;
+ case DIED:
+ if (status_ok) {
+ const bool matched = RE::PartialMatch(error_message.c_str(), *regex());
+ if (matched) {
+ success = true;
+ } else {
+ buffer << " Result: died but not with expected error.\n"
+ << " Expected: " << regex()->pattern() << "\n"
+ << "Actual msg:\n" << FormatDeathTestOutput(error_message);
+ }
+ } else {
+ buffer << " Result: died but not with expected exit code:\n"
+ << " " << ExitSummary(status()) << "\n"
+ << "Actual msg:\n" << FormatDeathTestOutput(error_message);
+ }
+ break;
+ case IN_PROGRESS:
+ default:
+ GTEST_LOG_(FATAL)
+ << "DeathTest::Passed somehow called before conclusion of test";
+ }
+
+ DeathTest::set_last_death_test_message(buffer.GetString());
+ return success;
+}
+
+# if GTEST_OS_WINDOWS
+// WindowsDeathTest implements death tests on Windows. Due to the
+// specifics of starting new processes on Windows, death tests there are
+// always threadsafe, and Google Test considers the
+// --gtest_death_test_style=fast setting to be equivalent to
+// --gtest_death_test_style=threadsafe there.
+//
+// A few implementation notes: Like the Linux version, the Windows
+// implementation uses pipes for child-to-parent communication. But due to
+// the specifics of pipes on Windows, some extra steps are required:
+//
+// 1. The parent creates a communication pipe and stores handles to both
+// ends of it.
+// 2. The parent starts the child and provides it with the information
+// necessary to acquire the handle to the write end of the pipe.
+// 3. The child acquires the write end of the pipe and signals the parent
+// using a Windows event.
+// 4. Now the parent can release the write end of the pipe on its side. If
+// this is done before step 3, the object's reference count goes down to
+// 0 and it is destroyed, preventing the child from acquiring it. The
+// parent now has to release it, or read operations on the read end of
+// the pipe will not return when the child terminates.
+// 5. The parent reads child's output through the pipe (outcome code and
+// any possible error messages) from the pipe, and its stderr and then
+// determines whether to fail the test.
+//
+// Note: to distinguish Win32 API calls from the local method and function
+// calls, the former are explicitly resolved in the global namespace.
+//
+class WindowsDeathTest : public DeathTestImpl {
+ public:
+ WindowsDeathTest(const char* a_statement,
+ const RE* a_regex,
+ const char* file,
+ int line)
+ : DeathTestImpl(a_statement, a_regex), file_(file), line_(line) {}
+
+ // All of these virtual functions are inherited from DeathTest.
+ virtual int Wait();
+ virtual TestRole AssumeRole();
+
+ private:
+ // The name of the file in which the death test is located.
+ const char* const file_;
+ // The line number on which the death test is located.
+ const int line_;
+ // Handle to the write end of the pipe to the child process.
+ AutoHandle write_handle_;
+ // Child process handle.
+ AutoHandle child_handle_;
+ // Event the child process uses to signal the parent that it has
+ // acquired the handle to the write end of the pipe. After seeing this
+ // event the parent can release its own handles to make sure its
+ // ReadFile() calls return when the child terminates.
+ AutoHandle event_handle_;
+};
+
+// Waits for the child in a death test to exit, returning its exit
+// status, or 0 if no child process exists. As a side effect, sets the
+// outcome data member.
+int WindowsDeathTest::Wait() {
+ if (!spawned())
+ return 0;
+
+ // Wait until the child either signals that it has acquired the write end
+ // of the pipe or it dies.
+ const HANDLE wait_handles[2] = { child_handle_.Get(), event_handle_.Get() };
+ switch (::WaitForMultipleObjects(2,
+ wait_handles,
+ FALSE, // Waits for any of the handles.
+ INFINITE)) {
+ case WAIT_OBJECT_0:
+ case WAIT_OBJECT_0 + 1:
+ break;
+ default:
+ GTEST_DEATH_TEST_CHECK_(false); // Should not get here.
+ }
+
+ // The child has acquired the write end of the pipe or exited.
+ // We release the handle on our side and continue.
+ write_handle_.Reset();
+ event_handle_.Reset();
+
+ ReadAndInterpretStatusByte();
+
+ // Waits for the child process to exit if it haven't already. This
+ // returns immediately if the child has already exited, regardless of
+ // whether previous calls to WaitForMultipleObjects synchronized on this
+ // handle or not.
+ GTEST_DEATH_TEST_CHECK_(
+ WAIT_OBJECT_0 == ::WaitForSingleObject(child_handle_.Get(),
+ INFINITE));
+ DWORD status_code;
+ GTEST_DEATH_TEST_CHECK_(
+ ::GetExitCodeProcess(child_handle_.Get(), &status_code) != FALSE);
+ child_handle_.Reset();
+ set_status(static_cast<int>(status_code));
+ return status();
+}
+
+// The AssumeRole process for a Windows death test. It creates a child
+// process with the same executable as the current process to run the
+// death test. The child process is given the --gtest_filter and
+// --gtest_internal_run_death_test flags such that it knows to run the
+// current death test only.
+DeathTest::TestRole WindowsDeathTest::AssumeRole() {
+ const UnitTestImpl* const impl = GetUnitTestImpl();
+ const InternalRunDeathTestFlag* const flag =
+ impl->internal_run_death_test_flag();
+ const TestInfo* const info = impl->current_test_info();
+ const int death_test_index = info->result()->death_test_count();
+
+ if (flag != NULL) {
+ // ParseInternalRunDeathTestFlag() has performed all the necessary
+ // processing.
+ set_write_fd(flag->write_fd());
+ return EXECUTE_TEST;
+ }
+
+ // WindowsDeathTest uses an anonymous pipe to communicate results of
+ // a death test.
+ SECURITY_ATTRIBUTES handles_are_inheritable = {
+ sizeof(SECURITY_ATTRIBUTES), NULL, TRUE };
+ HANDLE read_handle, write_handle;
+ GTEST_DEATH_TEST_CHECK_(
+ ::CreatePipe(&read_handle, &write_handle, &handles_are_inheritable,
+ 0) // Default buffer size.
+ != FALSE);
+ set_read_fd(::_open_osfhandle(reinterpret_cast<intptr_t>(read_handle),
+ O_RDONLY));
+ write_handle_.Reset(write_handle);
+ event_handle_.Reset(::CreateEvent(
+ &handles_are_inheritable,
+ TRUE, // The event will automatically reset to non-signaled state.
+ FALSE, // The initial state is non-signalled.
+ NULL)); // The even is unnamed.
+ GTEST_DEATH_TEST_CHECK_(event_handle_.Get() != NULL);
+ const std::string filter_flag =
+ std::string("--") + GTEST_FLAG_PREFIX_ + kFilterFlag + "=" +
+ info->test_case_name() + "." + info->name();
+ const std::string internal_flag =
+ std::string("--") + GTEST_FLAG_PREFIX_ + kInternalRunDeathTestFlag +
+ "=" + file_ + "|" + StreamableToString(line_) + "|" +
+ StreamableToString(death_test_index) + "|" +
+ StreamableToString(static_cast<unsigned int>(::GetCurrentProcessId())) +
+ // size_t has the same width as pointers on both 32-bit and 64-bit
+ // Windows platforms.
+ // See http://msdn.microsoft.com/en-us/library/tcxf1dw6.aspx.
+ "|" + StreamableToString(reinterpret_cast<size_t>(write_handle)) +
+ "|" + StreamableToString(reinterpret_cast<size_t>(event_handle_.Get()));
+
+ char executable_path[_MAX_PATH + 1]; // NOLINT
+ GTEST_DEATH_TEST_CHECK_(
+ _MAX_PATH + 1 != ::GetModuleFileNameA(NULL,
+ executable_path,
+ _MAX_PATH));
+
+ std::string command_line =
+ std::string(::GetCommandLineA()) + " " + filter_flag + " \"" +
+ internal_flag + "\"";
+
+ DeathTest::set_last_death_test_message("");
+
+ CaptureStderr();
+ // Flush the log buffers since the log streams are shared with the child.
+ FlushInfoLog();
+
+ // The child process will share the standard handles with the parent.
+ STARTUPINFOA startup_info;
+ memset(&startup_info, 0, sizeof(STARTUPINFO));
+ startup_info.dwFlags = STARTF_USESTDHANDLES;
+ startup_info.hStdInput = ::GetStdHandle(STD_INPUT_HANDLE);
+ startup_info.hStdOutput = ::GetStdHandle(STD_OUTPUT_HANDLE);
+ startup_info.hStdError = ::GetStdHandle(STD_ERROR_HANDLE);
+
+ PROCESS_INFORMATION process_info;
+ GTEST_DEATH_TEST_CHECK_(::CreateProcessA(
+ executable_path,
+ const_cast<char*>(command_line.c_str()),
+ NULL, // Retuned process handle is not inheritable.
+ NULL, // Retuned thread handle is not inheritable.
+ TRUE, // Child inherits all inheritable handles (for write_handle_).
+ 0x0, // Default creation flags.
+ NULL, // Inherit the parent's environment.
+ UnitTest::GetInstance()->original_working_dir(),
+ &startup_info,
+ &process_info) != FALSE);
+ child_handle_.Reset(process_info.hProcess);
+ ::CloseHandle(process_info.hThread);
+ set_spawned(true);
+ return OVERSEE_TEST;
+}
+# else // We are not on Windows.
+
+// ForkingDeathTest provides implementations for most of the abstract
+// methods of the DeathTest interface. Only the AssumeRole method is
+// left undefined.
+class ForkingDeathTest : public DeathTestImpl {
+ public:
+ ForkingDeathTest(const char* statement, const RE* regex);
+
+ // All of these virtual functions are inherited from DeathTest.
+ virtual int Wait();
+
+ protected:
+ void set_child_pid(pid_t child_pid) { child_pid_ = child_pid; }
+
+ private:
+ // PID of child process during death test; 0 in the child process itself.
+ pid_t child_pid_;
+};
+
+// Constructs a ForkingDeathTest.
+ForkingDeathTest::ForkingDeathTest(const char* a_statement, const RE* a_regex)
+ : DeathTestImpl(a_statement, a_regex),
+ child_pid_(-1) {}
+
+// Waits for the child in a death test to exit, returning its exit
+// status, or 0 if no child process exists. As a side effect, sets the
+// outcome data member.
+int ForkingDeathTest::Wait() {
+ if (!spawned())
+ return 0;
+
+ ReadAndInterpretStatusByte();
+
+ int status_value;
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(waitpid(child_pid_, &status_value, 0));
+ set_status(status_value);
+ return status_value;
+}
+
+// A concrete death test class that forks, then immediately runs the test
+// in the child process.
+class NoExecDeathTest : public ForkingDeathTest {
+ public:
+ NoExecDeathTest(const char* a_statement, const RE* a_regex) :
+ ForkingDeathTest(a_statement, a_regex) { }
+ virtual TestRole AssumeRole();
+};
+
+// The AssumeRole process for a fork-and-run death test. It implements a
+// straightforward fork, with a simple pipe to transmit the status byte.
+DeathTest::TestRole NoExecDeathTest::AssumeRole() {
+ const size_t thread_count = GetThreadCount();
+ if (thread_count != 1) {
+ GTEST_LOG_(WARNING) << DeathTestThreadWarning(thread_count);
+ }
+
+ int pipe_fd[2];
+ GTEST_DEATH_TEST_CHECK_(pipe(pipe_fd) != -1);
+
+ DeathTest::set_last_death_test_message("");
+ CaptureStderr();
+ // When we fork the process below, the log file buffers are copied, but the
+ // file descriptors are shared. We flush all log files here so that closing
+ // the file descriptors in the child process doesn't throw off the
+ // synchronization between descriptors and buffers in the parent process.
+ // This is as close to the fork as possible to avoid a race condition in case
+ // there are multiple threads running before the death test, and another
+ // thread writes to the log file.
+ FlushInfoLog();
+
+ const pid_t child_pid = fork();
+ GTEST_DEATH_TEST_CHECK_(child_pid != -1);
+ set_child_pid(child_pid);
+ if (child_pid == 0) {
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(close(pipe_fd[0]));
+ set_write_fd(pipe_fd[1]);
+ // Redirects all logging to stderr in the child process to prevent
+ // concurrent writes to the log files. We capture stderr in the parent
+ // process and append the child process' output to a log.
+ LogToStderr();
+ // Event forwarding to the listeners of event listener API mush be shut
+ // down in death test subprocesses.
+ GetUnitTestImpl()->listeners()->SuppressEventForwarding();
+ g_in_fast_death_test_child = true;
+ return EXECUTE_TEST;
+ } else {
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(close(pipe_fd[1]));
+ set_read_fd(pipe_fd[0]);
+ set_spawned(true);
+ return OVERSEE_TEST;
+ }
+}
+
+// A concrete death test class that forks and re-executes the main
+// program from the beginning, with command-line flags set that cause
+// only this specific death test to be run.
+class ExecDeathTest : public ForkingDeathTest {
+ public:
+ ExecDeathTest(const char* a_statement, const RE* a_regex,
+ const char* file, int line) :
+ ForkingDeathTest(a_statement, a_regex), file_(file), line_(line) { }
+ virtual TestRole AssumeRole();
+ private:
+ static ::std::vector<testing::internal::string>
+ GetArgvsForDeathTestChildProcess() {
+ ::std::vector<testing::internal::string> args = GetInjectableArgvs();
+ return args;
+ }
+ // The name of the file in which the death test is located.
+ const char* const file_;
+ // The line number on which the death test is located.
+ const int line_;
+};
+
+// Utility class for accumulating command-line arguments.
+class Arguments {
+ public:
+ Arguments() {
+ args_.push_back(NULL);
+ }
+
+ ~Arguments() {
+ for (std::vector<char*>::iterator i = args_.begin(); i != args_.end();
+ ++i) {
+ free(*i);
+ }
+ }
+ void AddArgument(const char* argument) {
+ args_.insert(args_.end() - 1, posix::StrDup(argument));
+ }
+
+ template <typename Str>
+ void AddArguments(const ::std::vector<Str>& arguments) {
+ for (typename ::std::vector<Str>::const_iterator i = arguments.begin();
+ i != arguments.end();
+ ++i) {
+ args_.insert(args_.end() - 1, posix::StrDup(i->c_str()));
+ }
+ }
+ char* const* Argv() {
+ return &args_[0];
+ }
+
+ private:
+ std::vector<char*> args_;
+};
+
+// A struct that encompasses the arguments to the child process of a
+// threadsafe-style death test process.
+struct ExecDeathTestArgs {
+ char* const* argv; // Command-line arguments for the child's call to exec
+ int close_fd; // File descriptor to close; the read end of a pipe
+};
+
+# if GTEST_OS_MAC
+inline char** GetEnviron() {
+ // When Google Test is built as a framework on MacOS X, the environ variable
+ // is unavailable. Apple's documentation (man environ) recommends using
+ // _NSGetEnviron() instead.
+ return *_NSGetEnviron();
+}
+# else
+// Some POSIX platforms expect you to declare environ. extern "C" makes
+// it reside in the global namespace.
+extern "C" char** environ;
+inline char** GetEnviron() { return environ; }
+# endif // GTEST_OS_MAC
+
+# if !GTEST_OS_QNX
+// The main function for a threadsafe-style death test child process.
+// This function is called in a clone()-ed process and thus must avoid
+// any potentially unsafe operations like malloc or libc functions.
+static int ExecDeathTestChildMain(void* child_arg) {
+ ExecDeathTestArgs* const args = static_cast<ExecDeathTestArgs*>(child_arg);
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(close(args->close_fd));
+
+ // We need to execute the test program in the same environment where
+ // it was originally invoked. Therefore we change to the original
+ // working directory first.
+ const char* const original_dir =
+ UnitTest::GetInstance()->original_working_dir();
+ // We can safely call chdir() as it's a direct system call.
+ if (chdir(original_dir) != 0) {
+ DeathTestAbort(std::string("chdir(\"") + original_dir + "\") failed: " +
+ GetLastErrnoDescription());
+ return EXIT_FAILURE;
+ }
+
+ // We can safely call execve() as it's a direct system call. We
+ // cannot use execvp() as it's a libc function and thus potentially
+ // unsafe. Since execve() doesn't search the PATH, the user must
+ // invoke the test program via a valid path that contains at least
+ // one path separator.
+ execve(args->argv[0], args->argv, GetEnviron());
+ DeathTestAbort(std::string("execve(") + args->argv[0] + ", ...) in " +
+ original_dir + " failed: " +
+ GetLastErrnoDescription());
+ return EXIT_FAILURE;
+}
+# endif // !GTEST_OS_QNX
+
+// Two utility routines that together determine the direction the stack
+// grows.
+// This could be accomplished more elegantly by a single recursive
+// function, but we want to guard against the unlikely possibility of
+// a smart compiler optimizing the recursion away.
+//
+// GTEST_NO_INLINE_ is required to prevent GCC 4.6 from inlining
+// StackLowerThanAddress into StackGrowsDown, which then doesn't give
+// correct answer.
+void StackLowerThanAddress(const void* ptr, bool* result) GTEST_NO_INLINE_;
+void StackLowerThanAddress(const void* ptr, bool* result) {
+ int dummy;
+ *result = (&dummy < ptr);
+}
+
+bool StackGrowsDown() {
+ int dummy;
+ bool result;
+ StackLowerThanAddress(&dummy, &result);
+ return result;
+}
+
+// Spawns a child process with the same executable as the current process in
+// a thread-safe manner and instructs it to run the death test. The
+// implementation uses fork(2) + exec. On systems where clone(2) is
+// available, it is used instead, being slightly more thread-safe. On QNX,
+// fork supports only single-threaded environments, so this function uses
+// spawn(2) there instead. The function dies with an error message if
+// anything goes wrong.
+static pid_t ExecDeathTestSpawnChild(char* const* argv, int close_fd) {
+ ExecDeathTestArgs args = { argv, close_fd };
+ pid_t child_pid = -1;
+
+# if GTEST_OS_QNX
+ // Obtains the current directory and sets it to be closed in the child
+ // process.
+ const int cwd_fd = open(".", O_RDONLY);
+ GTEST_DEATH_TEST_CHECK_(cwd_fd != -1);
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(fcntl(cwd_fd, F_SETFD, FD_CLOEXEC));
+ // We need to execute the test program in the same environment where
+ // it was originally invoked. Therefore we change to the original
+ // working directory first.
+ const char* const original_dir =
+ UnitTest::GetInstance()->original_working_dir();
+ // We can safely call chdir() as it's a direct system call.
+ if (chdir(original_dir) != 0) {
+ DeathTestAbort(std::string("chdir(\"") + original_dir + "\") failed: " +
+ GetLastErrnoDescription());
+ return EXIT_FAILURE;
+ }
+
+ int fd_flags;
+ // Set close_fd to be closed after spawn.
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(fd_flags = fcntl(close_fd, F_GETFD));
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(fcntl(close_fd, F_SETFD,
+ fd_flags | FD_CLOEXEC));
+ struct inheritance inherit = {0};
+ // spawn is a system call.
+ child_pid = spawn(args.argv[0], 0, NULL, &inherit, args.argv, GetEnviron());
+ // Restores the current working directory.
+ GTEST_DEATH_TEST_CHECK_(fchdir(cwd_fd) != -1);
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(close(cwd_fd));
+
+# else // GTEST_OS_QNX
+# if GTEST_OS_LINUX
+ // When a SIGPROF signal is received while fork() or clone() are executing,
+ // the process may hang. To avoid this, we ignore SIGPROF here and re-enable
+ // it after the call to fork()/clone() is complete.
+ struct sigaction saved_sigprof_action;
+ struct sigaction ignore_sigprof_action;
+ memset(&ignore_sigprof_action, 0, sizeof(ignore_sigprof_action));
+ sigemptyset(&ignore_sigprof_action.sa_mask);
+ ignore_sigprof_action.sa_handler = SIG_IGN;
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(sigaction(
+ SIGPROF, &ignore_sigprof_action, &saved_sigprof_action));
+# endif // GTEST_OS_LINUX
+
+# if GTEST_HAS_CLONE
+ const bool use_fork = GTEST_FLAG(death_test_use_fork);
+
+ if (!use_fork) {
+ static const bool stack_grows_down = StackGrowsDown();
+ const size_t stack_size = getpagesize();
+ // MMAP_ANONYMOUS is not defined on Mac, so we use MAP_ANON instead.
+ void* const stack = mmap(NULL, stack_size, PROT_READ | PROT_WRITE,
+ MAP_ANON | MAP_PRIVATE, -1, 0);
+ GTEST_DEATH_TEST_CHECK_(stack != MAP_FAILED);
+
+ // Maximum stack alignment in bytes: For a downward-growing stack, this
+ // amount is subtracted from size of the stack space to get an address
+ // that is within the stack space and is aligned on all systems we care
+ // about. As far as I know there is no ABI with stack alignment greater
+ // than 64. We assume stack and stack_size already have alignment of
+ // kMaxStackAlignment.
+ const size_t kMaxStackAlignment = 64;
+ void* const stack_top =
+ static_cast<char*>(stack) +
+ (stack_grows_down ? stack_size - kMaxStackAlignment : 0);
+ GTEST_DEATH_TEST_CHECK_(stack_size > kMaxStackAlignment &&
+ reinterpret_cast<intptr_t>(stack_top) % kMaxStackAlignment == 0);
+
+ child_pid = clone(&ExecDeathTestChildMain, stack_top, SIGCHLD, &args);
+
+ GTEST_DEATH_TEST_CHECK_(munmap(stack, stack_size) != -1);
+ }
+# else
+ const bool use_fork = true;
+# endif // GTEST_HAS_CLONE
+
+ if (use_fork && (child_pid = fork()) == 0) {
+ ExecDeathTestChildMain(&args);
+ _exit(0);
+ }
+# endif // GTEST_OS_QNX
+# if GTEST_OS_LINUX
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(
+ sigaction(SIGPROF, &saved_sigprof_action, NULL));
+# endif // GTEST_OS_LINUX
+
+ GTEST_DEATH_TEST_CHECK_(child_pid != -1);
+ return child_pid;
+}
+
+// The AssumeRole process for a fork-and-exec death test. It re-executes the
+// main program from the beginning, setting the --gtest_filter
+// and --gtest_internal_run_death_test flags to cause only the current
+// death test to be re-run.
+DeathTest::TestRole ExecDeathTest::AssumeRole() {
+ const UnitTestImpl* const impl = GetUnitTestImpl();
+ const InternalRunDeathTestFlag* const flag =
+ impl->internal_run_death_test_flag();
+ const TestInfo* const info = impl->current_test_info();
+ const int death_test_index = info->result()->death_test_count();
+
+ if (flag != NULL) {
+ set_write_fd(flag->write_fd());
+ return EXECUTE_TEST;
+ }
+
+ int pipe_fd[2];
+ GTEST_DEATH_TEST_CHECK_(pipe(pipe_fd) != -1);
+ // Clear the close-on-exec flag on the write end of the pipe, lest
+ // it be closed when the child process does an exec:
+ GTEST_DEATH_TEST_CHECK_(fcntl(pipe_fd[1], F_SETFD, 0) != -1);
+
+ const std::string filter_flag =
+ std::string("--") + GTEST_FLAG_PREFIX_ + kFilterFlag + "="
+ + info->test_case_name() + "." + info->name();
+ const std::string internal_flag =
+ std::string("--") + GTEST_FLAG_PREFIX_ + kInternalRunDeathTestFlag + "="
+ + file_ + "|" + StreamableToString(line_) + "|"
+ + StreamableToString(death_test_index) + "|"
+ + StreamableToString(pipe_fd[1]);
+ Arguments args;
+ args.AddArguments(GetArgvsForDeathTestChildProcess());
+ args.AddArgument(filter_flag.c_str());
+ args.AddArgument(internal_flag.c_str());
+
+ DeathTest::set_last_death_test_message("");
+
+ CaptureStderr();
+ // See the comment in NoExecDeathTest::AssumeRole for why the next line
+ // is necessary.
+ FlushInfoLog();
+
+ const pid_t child_pid = ExecDeathTestSpawnChild(args.Argv(), pipe_fd[0]);
+ GTEST_DEATH_TEST_CHECK_SYSCALL_(close(pipe_fd[1]));
+ set_child_pid(child_pid);
+ set_read_fd(pipe_fd[0]);
+ set_spawned(true);
+ return OVERSEE_TEST;
+}
+
+# endif // !GTEST_OS_WINDOWS
+
+// Creates a concrete DeathTest-derived class that depends on the
+// --gtest_death_test_style flag, and sets the pointer pointed to
+// by the "test" argument to its address. If the test should be
+// skipped, sets that pointer to NULL. Returns true, unless the
+// flag is set to an invalid value.
+bool DefaultDeathTestFactory::Create(const char* statement, const RE* regex,
+ const char* file, int line,
+ DeathTest** test) {
+ UnitTestImpl* const impl = GetUnitTestImpl();
+ const InternalRunDeathTestFlag* const flag =
+ impl->internal_run_death_test_flag();
+ const int death_test_index = impl->current_test_info()
+ ->increment_death_test_count();
+
+ if (flag != NULL) {
+ if (death_test_index > flag->index()) {
+ DeathTest::set_last_death_test_message(
+ "Death test count (" + StreamableToString(death_test_index)
+ + ") somehow exceeded expected maximum ("
+ + StreamableToString(flag->index()) + ")");
+ return false;
+ }
+
+ if (!(flag->file() == file && flag->line() == line &&
+ flag->index() == death_test_index)) {
+ *test = NULL;
+ return true;
+ }
+ }
+
+# if GTEST_OS_WINDOWS
+
+ if (GTEST_FLAG(death_test_style) == "threadsafe" ||
+ GTEST_FLAG(death_test_style) == "fast") {
+ *test = new WindowsDeathTest(statement, regex, file, line);
+ }
+
+# else
+
+ if (GTEST_FLAG(death_test_style) == "threadsafe") {
+ *test = new ExecDeathTest(statement, regex, file, line);
+ } else if (GTEST_FLAG(death_test_style) == "fast") {
+ *test = new NoExecDeathTest(statement, regex);
+ }
+
+# endif // GTEST_OS_WINDOWS
+
+ else { // NOLINT - this is more readable than unbalanced brackets inside #if.
+ DeathTest::set_last_death_test_message(
+ "Unknown death test style \"" + GTEST_FLAG(death_test_style)
+ + "\" encountered");
+ return false;
+ }
+
+ return true;
+}
+
+// Splits a given string on a given delimiter, populating a given
+// vector with the fields. GTEST_HAS_DEATH_TEST implies that we have
+// ::std::string, so we can use it here.
+static void SplitString(const ::std::string& str, char delimiter,
+ ::std::vector< ::std::string>* dest) {
+ ::std::vector< ::std::string> parsed;
+ ::std::string::size_type pos = 0;
+ while (::testing::internal::AlwaysTrue()) {
+ const ::std::string::size_type colon = str.find(delimiter, pos);
+ if (colon == ::std::string::npos) {
+ parsed.push_back(str.substr(pos));
+ break;
+ } else {
+ parsed.push_back(str.substr(pos, colon - pos));
+ pos = colon + 1;
+ }
+ }
+ dest->swap(parsed);
+}
+
+# if GTEST_OS_WINDOWS
+// Recreates the pipe and event handles from the provided parameters,
+// signals the event, and returns a file descriptor wrapped around the pipe
+// handle. This function is called in the child process only.
+int GetStatusFileDescriptor(unsigned int parent_process_id,
+ size_t write_handle_as_size_t,
+ size_t event_handle_as_size_t) {
+ AutoHandle parent_process_handle(::OpenProcess(PROCESS_DUP_HANDLE,
+ FALSE, // Non-inheritable.
+ parent_process_id));
+ if (parent_process_handle.Get() == INVALID_HANDLE_VALUE) {
+ DeathTestAbort("Unable to open parent process " +
+ StreamableToString(parent_process_id));
+ }
+
+ // TODO(vladl at google.com): Replace the following check with a
+ // compile-time assertion when available.
+ GTEST_CHECK_(sizeof(HANDLE) <= sizeof(size_t));
+
+ const HANDLE write_handle =
+ reinterpret_cast<HANDLE>(write_handle_as_size_t);
+ HANDLE dup_write_handle;
+
+ // The newly initialized handle is accessible only in in the parent
+ // process. To obtain one accessible within the child, we need to use
+ // DuplicateHandle.
+ if (!::DuplicateHandle(parent_process_handle.Get(), write_handle,
+ ::GetCurrentProcess(), &dup_write_handle,
+ 0x0, // Requested privileges ignored since
+ // DUPLICATE_SAME_ACCESS is used.
+ FALSE, // Request non-inheritable handler.
+ DUPLICATE_SAME_ACCESS)) {
+ DeathTestAbort("Unable to duplicate the pipe handle " +
+ StreamableToString(write_handle_as_size_t) +
+ " from the parent process " +
+ StreamableToString(parent_process_id));
+ }
+
+ const HANDLE event_handle = reinterpret_cast<HANDLE>(event_handle_as_size_t);
+ HANDLE dup_event_handle;
+
+ if (!::DuplicateHandle(parent_process_handle.Get(), event_handle,
+ ::GetCurrentProcess(), &dup_event_handle,
+ 0x0,
+ FALSE,
+ DUPLICATE_SAME_ACCESS)) {
+ DeathTestAbort("Unable to duplicate the event handle " +
+ StreamableToString(event_handle_as_size_t) +
+ " from the parent process " +
+ StreamableToString(parent_process_id));
+ }
+
+ const int write_fd =
+ ::_open_osfhandle(reinterpret_cast<intptr_t>(dup_write_handle), O_APPEND);
+ if (write_fd == -1) {
+ DeathTestAbort("Unable to convert pipe handle " +
+ StreamableToString(write_handle_as_size_t) +
+ " to a file descriptor");
+ }
+
+ // Signals the parent that the write end of the pipe has been acquired
+ // so the parent can release its own write end.
+ ::SetEvent(dup_event_handle);
+
+ return write_fd;
+}
+# endif // GTEST_OS_WINDOWS
+
+// Returns a newly created InternalRunDeathTestFlag object with fields
+// initialized from the GTEST_FLAG(internal_run_death_test) flag if
+// the flag is specified; otherwise returns NULL.
+InternalRunDeathTestFlag* ParseInternalRunDeathTestFlag() {
+ if (GTEST_FLAG(internal_run_death_test) == "") return NULL;
+
+ // GTEST_HAS_DEATH_TEST implies that we have ::std::string, so we
+ // can use it here.
+ int line = -1;
+ int index = -1;
+ ::std::vector< ::std::string> fields;
+ SplitString(GTEST_FLAG(internal_run_death_test).c_str(), '|', &fields);
+ int write_fd = -1;
+
+# if GTEST_OS_WINDOWS
+
+ unsigned int parent_process_id = 0;
+ size_t write_handle_as_size_t = 0;
+ size_t event_handle_as_size_t = 0;
+
+ if (fields.size() != 6
+ || !ParseNaturalNumber(fields[1], &line)
+ || !ParseNaturalNumber(fields[2], &index)
+ || !ParseNaturalNumber(fields[3], &parent_process_id)
+ || !ParseNaturalNumber(fields[4], &write_handle_as_size_t)
+ || !ParseNaturalNumber(fields[5], &event_handle_as_size_t)) {
+ DeathTestAbort("Bad --gtest_internal_run_death_test flag: " +
+ GTEST_FLAG(internal_run_death_test));
+ }
+ write_fd = GetStatusFileDescriptor(parent_process_id,
+ write_handle_as_size_t,
+ event_handle_as_size_t);
+# else
+
+ if (fields.size() != 4
+ || !ParseNaturalNumber(fields[1], &line)
+ || !ParseNaturalNumber(fields[2], &index)
+ || !ParseNaturalNumber(fields[3], &write_fd)) {
+ DeathTestAbort("Bad --gtest_internal_run_death_test flag: "
+ + GTEST_FLAG(internal_run_death_test));
+ }
+
+# endif // GTEST_OS_WINDOWS
+
+ return new InternalRunDeathTestFlag(fields[0], line, index, write_fd);
+}
+
+} // namespace internal
+
+#endif // GTEST_HAS_DEATH_TEST
+
+} // namespace testing
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Authors: keith.ray at gmail.com (Keith Ray)
+
+
+#include <stdlib.h>
+
+#if GTEST_OS_WINDOWS_MOBILE
+# include <windows.h>
+#elif GTEST_OS_WINDOWS
+# include <direct.h>
+# include <io.h>
+#elif GTEST_OS_SYMBIAN
+// Symbian OpenC has PATH_MAX in sys/syslimits.h
+# include <sys/syslimits.h>
+#else
+# include <limits.h>
+# include <climits> // Some Linux distributions define PATH_MAX here.
+#endif // GTEST_OS_WINDOWS_MOBILE
+
+#if GTEST_OS_WINDOWS
+# define GTEST_PATH_MAX_ _MAX_PATH
+#elif defined(PATH_MAX)
+# define GTEST_PATH_MAX_ PATH_MAX
+#elif defined(_XOPEN_PATH_MAX)
+# define GTEST_PATH_MAX_ _XOPEN_PATH_MAX
+#else
+# define GTEST_PATH_MAX_ _POSIX_PATH_MAX
+#endif // GTEST_OS_WINDOWS
+
+
+namespace testing {
+namespace internal {
+
+#if GTEST_OS_WINDOWS
+// On Windows, '\\' is the standard path separator, but many tools and the
+// Windows API also accept '/' as an alternate path separator. Unless otherwise
+// noted, a file path can contain either kind of path separators, or a mixture
+// of them.
+const char kPathSeparator = '\\';
+const char kAlternatePathSeparator = '/';
+const char kPathSeparatorString[] = "\\";
+const char kAlternatePathSeparatorString[] = "/";
+# if GTEST_OS_WINDOWS_MOBILE
+// Windows CE doesn't have a current directory. You should not use
+// the current directory in tests on Windows CE, but this at least
+// provides a reasonable fallback.
+const char kCurrentDirectoryString[] = "\\";
+// Windows CE doesn't define INVALID_FILE_ATTRIBUTES
+const DWORD kInvalidFileAttributes = 0xffffffff;
+# else
+const char kCurrentDirectoryString[] = ".\\";
+# endif // GTEST_OS_WINDOWS_MOBILE
+#else
+const char kPathSeparator = '/';
+const char kPathSeparatorString[] = "/";
+const char kCurrentDirectoryString[] = "./";
+#endif // GTEST_OS_WINDOWS
+
+// Returns whether the given character is a valid path separator.
+static bool IsPathSeparator(char c) {
+#if GTEST_HAS_ALT_PATH_SEP_
+ return (c == kPathSeparator) || (c == kAlternatePathSeparator);
+#else
+ return c == kPathSeparator;
+#endif
+}
+
+// Returns the current working directory, or "" if unsuccessful.
+FilePath FilePath::GetCurrentDir() {
+#if GTEST_OS_WINDOWS_MOBILE
+ // Windows CE doesn't have a current directory, so we just return
+ // something reasonable.
+ return FilePath(kCurrentDirectoryString);
+#elif GTEST_OS_WINDOWS
+ char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
+ return FilePath(_getcwd(cwd, sizeof(cwd)) == NULL ? "" : cwd);
+#else
+ char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
+ return FilePath(getcwd(cwd, sizeof(cwd)) == NULL ? "" : cwd);
+#endif // GTEST_OS_WINDOWS_MOBILE
+}
+
+// Returns a copy of the FilePath with the case-insensitive extension removed.
+// Example: FilePath("dir/file.exe").RemoveExtension("EXE") returns
+// FilePath("dir/file"). If a case-insensitive extension is not
+// found, returns a copy of the original FilePath.
+FilePath FilePath::RemoveExtension(const char* extension) const {
+ const std::string dot_extension = std::string(".") + extension;
+ if (String::EndsWithCaseInsensitive(pathname_, dot_extension)) {
+ return FilePath(pathname_.substr(
+ 0, pathname_.length() - dot_extension.length()));
+ }
+ return *this;
+}
+
+// Returns a pointer to the last occurence of a valid path separator in
+// the FilePath. On Windows, for example, both '/' and '\' are valid path
+// separators. Returns NULL if no path separator was found.
+const char* FilePath::FindLastPathSeparator() const {
+ const char* const last_sep = strrchr(c_str(), kPathSeparator);
+#if GTEST_HAS_ALT_PATH_SEP_
+ const char* const last_alt_sep = strrchr(c_str(), kAlternatePathSeparator);
+ // Comparing two pointers of which only one is NULL is undefined.
+ if (last_alt_sep != NULL &&
+ (last_sep == NULL || last_alt_sep > last_sep)) {
+ return last_alt_sep;
+ }
+#endif
+ return last_sep;
+}
+
+// Returns a copy of the FilePath with the directory part removed.
+// Example: FilePath("path/to/file").RemoveDirectoryName() returns
+// FilePath("file"). If there is no directory part ("just_a_file"), it returns
+// the FilePath unmodified. If there is no file part ("just_a_dir/") it
+// returns an empty FilePath ("").
+// On Windows platform, '\' is the path separator, otherwise it is '/'.
+FilePath FilePath::RemoveDirectoryName() const {
+ const char* const last_sep = FindLastPathSeparator();
+ return last_sep ? FilePath(last_sep + 1) : *this;
+}
+
+// RemoveFileName returns the directory path with the filename removed.
+// Example: FilePath("path/to/file").RemoveFileName() returns "path/to/".
+// If the FilePath is "a_file" or "/a_file", RemoveFileName returns
+// FilePath("./") or, on Windows, FilePath(".\\"). If the filepath does
+// not have a file, like "just/a/dir/", it returns the FilePath unmodified.
+// On Windows platform, '\' is the path separator, otherwise it is '/'.
+FilePath FilePath::RemoveFileName() const {
+ const char* const last_sep = FindLastPathSeparator();
+ std::string dir;
+ if (last_sep) {
+ dir = std::string(c_str(), last_sep + 1 - c_str());
+ } else {
+ dir = kCurrentDirectoryString;
+ }
+ return FilePath(dir);
+}
+
+// Helper functions for naming files in a directory for xml output.
+
+// Given directory = "dir", base_name = "test", number = 0,
+// extension = "xml", returns "dir/test.xml". If number is greater
+// than zero (e.g., 12), returns "dir/test_12.xml".
+// On Windows platform, uses \ as the separator rather than /.
+FilePath FilePath::MakeFileName(const FilePath& directory,
+ const FilePath& base_name,
+ int number,
+ const char* extension) {
+ std::string file;
+ if (number == 0) {
+ file = base_name.string() + "." + extension;
+ } else {
+ file = base_name.string() + "_" + StreamableToString(number)
+ + "." + extension;
+ }
+ return ConcatPaths(directory, FilePath(file));
+}
+
+// Given directory = "dir", relative_path = "test.xml", returns "dir/test.xml".
+// On Windows, uses \ as the separator rather than /.
+FilePath FilePath::ConcatPaths(const FilePath& directory,
+ const FilePath& relative_path) {
+ if (directory.IsEmpty())
+ return relative_path;
+ const FilePath dir(directory.RemoveTrailingPathSeparator());
+ return FilePath(dir.string() + kPathSeparator + relative_path.string());
+}
+
+// Returns true if pathname describes something findable in the file-system,
+// either a file, directory, or whatever.
+bool FilePath::FileOrDirectoryExists() const {
+#if GTEST_OS_WINDOWS_MOBILE
+ LPCWSTR unicode = String::AnsiToUtf16(pathname_.c_str());
+ const DWORD attributes = GetFileAttributes(unicode);
+ delete [] unicode;
+ return attributes != kInvalidFileAttributes;
+#else
+ posix::StatStruct file_stat;
+ return posix::Stat(pathname_.c_str(), &file_stat) == 0;
+#endif // GTEST_OS_WINDOWS_MOBILE
+}
+
+// Returns true if pathname describes a directory in the file-system
+// that exists.
+bool FilePath::DirectoryExists() const {
+ bool result = false;
+#if GTEST_OS_WINDOWS
+ // Don't strip off trailing separator if path is a root directory on
+ // Windows (like "C:\\").
+ const FilePath& path(IsRootDirectory() ? *this :
+ RemoveTrailingPathSeparator());
+#else
+ const FilePath& path(*this);
+#endif
+
+#if GTEST_OS_WINDOWS_MOBILE
+ LPCWSTR unicode = String::AnsiToUtf16(path.c_str());
+ const DWORD attributes = GetFileAttributes(unicode);
+ delete [] unicode;
+ if ((attributes != kInvalidFileAttributes) &&
+ (attributes & FILE_ATTRIBUTE_DIRECTORY)) {
+ result = true;
+ }
+#else
+ posix::StatStruct file_stat;
+ result = posix::Stat(path.c_str(), &file_stat) == 0 &&
+ posix::IsDir(file_stat);
+#endif // GTEST_OS_WINDOWS_MOBILE
+
+ return result;
+}
+
+// Returns true if pathname describes a root directory. (Windows has one
+// root directory per disk drive.)
+bool FilePath::IsRootDirectory() const {
+#if GTEST_OS_WINDOWS
+ // TODO(wan at google.com): on Windows a network share like
+ // \\server\share can be a root directory, although it cannot be the
+ // current directory. Handle this properly.
+ return pathname_.length() == 3 && IsAbsolutePath();
+#else
+ return pathname_.length() == 1 && IsPathSeparator(pathname_.c_str()[0]);
+#endif
+}
+
+// Returns true if pathname describes an absolute path.
+bool FilePath::IsAbsolutePath() const {
+ const char* const name = pathname_.c_str();
+#if GTEST_OS_WINDOWS
+ return pathname_.length() >= 3 &&
+ ((name[0] >= 'a' && name[0] <= 'z') ||
+ (name[0] >= 'A' && name[0] <= 'Z')) &&
+ name[1] == ':' &&
+ IsPathSeparator(name[2]);
+#else
+ return IsPathSeparator(name[0]);
+#endif
+}
+
+// Returns a pathname for a file that does not currently exist. The pathname
+// will be directory/base_name.extension or
+// directory/base_name_<number>.extension if directory/base_name.extension
+// already exists. The number will be incremented until a pathname is found
+// that does not already exist.
+// Examples: 'dir/foo_test.xml' or 'dir/foo_test_1.xml'.
+// There could be a race condition if two or more processes are calling this
+// function at the same time -- they could both pick the same filename.
+FilePath FilePath::GenerateUniqueFileName(const FilePath& directory,
+ const FilePath& base_name,
+ const char* extension) {
+ FilePath full_pathname;
+ int number = 0;
+ do {
+ full_pathname.Set(MakeFileName(directory, base_name, number++, extension));
+ } while (full_pathname.FileOrDirectoryExists());
+ return full_pathname;
+}
+
+// Returns true if FilePath ends with a path separator, which indicates that
+// it is intended to represent a directory. Returns false otherwise.
+// This does NOT check that a directory (or file) actually exists.
+bool FilePath::IsDirectory() const {
+ return !pathname_.empty() &&
+ IsPathSeparator(pathname_.c_str()[pathname_.length() - 1]);
+}
+
+// Create directories so that path exists. Returns true if successful or if
+// the directories already exist; returns false if unable to create directories
+// for any reason.
+bool FilePath::CreateDirectoriesRecursively() const {
+ if (!this->IsDirectory()) {
+ return false;
+ }
+
+ if (pathname_.length() == 0 || this->DirectoryExists()) {
+ return true;
+ }
+
+ const FilePath parent(this->RemoveTrailingPathSeparator().RemoveFileName());
+ return parent.CreateDirectoriesRecursively() && this->CreateFolder();
+}
+
+// Create the directory so that path exists. Returns true if successful or
+// if the directory already exists; returns false if unable to create the
+// directory for any reason, including if the parent directory does not
+// exist. Not named "CreateDirectory" because that's a macro on Windows.
+bool FilePath::CreateFolder() const {
+#if GTEST_OS_WINDOWS_MOBILE
+ FilePath removed_sep(this->RemoveTrailingPathSeparator());
+ LPCWSTR unicode = String::AnsiToUtf16(removed_sep.c_str());
+ int result = CreateDirectory(unicode, NULL) ? 0 : -1;
+ delete [] unicode;
+#elif GTEST_OS_WINDOWS
+ int result = _mkdir(pathname_.c_str());
+#else
+ int result = mkdir(pathname_.c_str(), 0777);
+#endif // GTEST_OS_WINDOWS_MOBILE
+
+ if (result == -1) {
+ return this->DirectoryExists(); // An error is OK if the directory exists.
+ }
+ return true; // No error.
+}
+
+// If input name has a trailing separator character, remove it and return the
+// name, otherwise return the name string unmodified.
+// On Windows platform, uses \ as the separator, other platforms use /.
+FilePath FilePath::RemoveTrailingPathSeparator() const {
+ return IsDirectory()
+ ? FilePath(pathname_.substr(0, pathname_.length() - 1))
+ : *this;
+}
+
+// Removes any redundant separators that might be in the pathname.
+// For example, "bar///foo" becomes "bar/foo". Does not eliminate other
+// redundancies that might be in a pathname involving "." or "..".
+// TODO(wan at google.com): handle Windows network shares (e.g. \\server\share).
+void FilePath::Normalize() {
+ if (pathname_.c_str() == NULL) {
+ pathname_ = "";
+ return;
+ }
+ const char* src = pathname_.c_str();
+ char* const dest = new char[pathname_.length() + 1];
+ char* dest_ptr = dest;
+ memset(dest_ptr, 0, pathname_.length() + 1);
+
+ while (*src != '\0') {
+ *dest_ptr = *src;
+ if (!IsPathSeparator(*src)) {
+ src++;
+ } else {
+#if GTEST_HAS_ALT_PATH_SEP_
+ if (*dest_ptr == kAlternatePathSeparator) {
+ *dest_ptr = kPathSeparator;
+ }
+#endif
+ while (IsPathSeparator(*src))
+ src++;
+ }
+ dest_ptr++;
+ }
+ *dest_ptr = '\0';
+ pathname_ = dest;
+ delete[] dest;
+}
+
+} // namespace internal
+} // namespace testing
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+
+#include <limits.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+
+#if GTEST_OS_WINDOWS_MOBILE
+# include <windows.h> // For TerminateProcess()
+#elif GTEST_OS_WINDOWS
+# include <io.h>
+# include <sys/stat.h>
+#else
+# include <unistd.h>
+#endif // GTEST_OS_WINDOWS_MOBILE
+
+#if GTEST_OS_MAC
+# include <mach/mach_init.h>
+# include <mach/task.h>
+# include <mach/vm_map.h>
+#endif // GTEST_OS_MAC
+
+#if GTEST_OS_QNX
+# include <devctl.h>
+# include <sys/procfs.h>
+#endif // GTEST_OS_QNX
+
+
+// Indicates that this translation unit is part of Google Test's
+// implementation. It must come before gtest-internal-inl.h is
+// included, or there will be a compiler error. This trick is to
+// prevent a user from accidentally including gtest-internal-inl.h in
+// his code.
+#define GTEST_IMPLEMENTATION_ 1
+#undef GTEST_IMPLEMENTATION_
+
+namespace testing {
+namespace internal {
+
+#if defined(_MSC_VER) || defined(__BORLANDC__)
+// MSVC and C++Builder do not provide a definition of STDERR_FILENO.
+const int kStdOutFileno = 1;
+const int kStdErrFileno = 2;
+#else
+const int kStdOutFileno = STDOUT_FILENO;
+const int kStdErrFileno = STDERR_FILENO;
+#endif // _MSC_VER
+
+#if GTEST_OS_MAC
+
+// Returns the number of threads running in the process, or 0 to indicate that
+// we cannot detect it.
+size_t GetThreadCount() {
+ const task_t task = mach_task_self();
+ mach_msg_type_number_t thread_count;
+ thread_act_array_t thread_list;
+ const kern_return_t status = task_threads(task, &thread_list, &thread_count);
+ if (status == KERN_SUCCESS) {
+ // task_threads allocates resources in thread_list and we need to free them
+ // to avoid leaks.
+ vm_deallocate(task,
+ reinterpret_cast<vm_address_t>(thread_list),
+ sizeof(thread_t) * thread_count);
+ return static_cast<size_t>(thread_count);
+ } else {
+ return 0;
+ }
+}
+
+#elif GTEST_OS_QNX
+
+// Returns the number of threads running in the process, or 0 to indicate that
+// we cannot detect it.
+size_t GetThreadCount() {
+ const int fd = open("/proc/self/as", O_RDONLY);
+ if (fd < 0) {
+ return 0;
+ }
+ procfs_info process_info;
+ const int status =
+ devctl(fd, DCMD_PROC_INFO, &process_info, sizeof(process_info), NULL);
+ close(fd);
+ if (status == EOK) {
+ return static_cast<size_t>(process_info.num_threads);
+ } else {
+ return 0;
+ }
+}
+
+#else
+
+size_t GetThreadCount() {
+ // There's no portable way to detect the number of threads, so we just
+ // return 0 to indicate that we cannot detect it.
+ return 0;
+}
+
+#endif // GTEST_OS_MAC
+
+#if GTEST_USES_POSIX_RE
+
+// Implements RE. Currently only needed for death tests.
+
+RE::~RE() {
+ if (is_valid_) {
+ // regfree'ing an invalid regex might crash because the content
+ // of the regex is undefined. Since the regex's are essentially
+ // the same, one cannot be valid (or invalid) without the other
+ // being so too.
+ regfree(&partial_regex_);
+ regfree(&full_regex_);
+ }
+ free(const_cast<char*>(pattern_));
+}
+
+// Returns true iff regular expression re matches the entire str.
+bool RE::FullMatch(const char* str, const RE& re) {
+ if (!re.is_valid_) return false;
+
+ regmatch_t match;
+ return regexec(&re.full_regex_, str, 1, &match, 0) == 0;
+}
+
+// Returns true iff regular expression re matches a substring of str
+// (including str itself).
+bool RE::PartialMatch(const char* str, const RE& re) {
+ if (!re.is_valid_) return false;
+
+ regmatch_t match;
+ return regexec(&re.partial_regex_, str, 1, &match, 0) == 0;
+}
+
+// Initializes an RE from its string representation.
+void RE::Init(const char* regex) {
+ pattern_ = posix::StrDup(regex);
+
+ // Reserves enough bytes to hold the regular expression used for a
+ // full match.
+ const size_t full_regex_len = strlen(regex) + 10;
+ char* const full_pattern = new char[full_regex_len];
+
+ snprintf(full_pattern, full_regex_len, "^(%s)$", regex);
+ is_valid_ = regcomp(&full_regex_, full_pattern, REG_EXTENDED) == 0;
+ // We want to call regcomp(&partial_regex_, ...) even if the
+ // previous expression returns false. Otherwise partial_regex_ may
+ // not be properly initialized can may cause trouble when it's
+ // freed.
+ //
+ // Some implementation of POSIX regex (e.g. on at least some
+ // versions of Cygwin) doesn't accept the empty string as a valid
+ // regex. We change it to an equivalent form "()" to be safe.
+ if (is_valid_) {
+ const char* const partial_regex = (*regex == '\0') ? "()" : regex;
+ is_valid_ = regcomp(&partial_regex_, partial_regex, REG_EXTENDED) == 0;
+ }
+ EXPECT_TRUE(is_valid_)
+ << "Regular expression \"" << regex
+ << "\" is not a valid POSIX Extended regular expression.";
+
+ delete[] full_pattern;
+}
+
+#elif GTEST_USES_SIMPLE_RE
+
+// Returns true iff ch appears anywhere in str (excluding the
+// terminating '\0' character).
+bool IsInSet(char ch, const char* str) {
+ return ch != '\0' && strchr(str, ch) != NULL;
+}
+
+// Returns true iff ch belongs to the given classification. Unlike
+// similar functions in <ctype.h>, these aren't affected by the
+// current locale.
+bool IsAsciiDigit(char ch) { return '0' <= ch && ch <= '9'; }
+bool IsAsciiPunct(char ch) {
+ return IsInSet(ch, "^-!\"#$%&'()*+,./:;<=>?@[\\]_`{|}~");
+}
+bool IsRepeat(char ch) { return IsInSet(ch, "?*+"); }
+bool IsAsciiWhiteSpace(char ch) { return IsInSet(ch, " \f\n\r\t\v"); }
+bool IsAsciiWordChar(char ch) {
+ return ('a' <= ch && ch <= 'z') || ('A' <= ch && ch <= 'Z') ||
+ ('0' <= ch && ch <= '9') || ch == '_';
+}
+
+// Returns true iff "\\c" is a supported escape sequence.
+bool IsValidEscape(char c) {
+ return (IsAsciiPunct(c) || IsInSet(c, "dDfnrsStvwW"));
+}
+
+// Returns true iff the given atom (specified by escaped and pattern)
+// matches ch. The result is undefined if the atom is invalid.
+bool AtomMatchesChar(bool escaped, char pattern_char, char ch) {
+ if (escaped) { // "\\p" where p is pattern_char.
+ switch (pattern_char) {
+ case 'd': return IsAsciiDigit(ch);
+ case 'D': return !IsAsciiDigit(ch);
+ case 'f': return ch == '\f';
+ case 'n': return ch == '\n';
+ case 'r': return ch == '\r';
+ case 's': return IsAsciiWhiteSpace(ch);
+ case 'S': return !IsAsciiWhiteSpace(ch);
+ case 't': return ch == '\t';
+ case 'v': return ch == '\v';
+ case 'w': return IsAsciiWordChar(ch);
+ case 'W': return !IsAsciiWordChar(ch);
+ }
+ return IsAsciiPunct(pattern_char) && pattern_char == ch;
+ }
+
+ return (pattern_char == '.' && ch != '\n') || pattern_char == ch;
+}
+
+// Helper function used by ValidateRegex() to format error messages.
+std::string FormatRegexSyntaxError(const char* regex, int index) {
+ return (Message() << "Syntax error at index " << index
+ << " in simple regular expression \"" << regex << "\": ").GetString();
+}
+
+// Generates non-fatal failures and returns false if regex is invalid;
+// otherwise returns true.
+bool ValidateRegex(const char* regex) {
+ if (regex == NULL) {
+ // TODO(wan at google.com): fix the source file location in the
+ // assertion failures to match where the regex is used in user
+ // code.
+ ADD_FAILURE() << "NULL is not a valid simple regular expression.";
+ return false;
+ }
+
+ bool is_valid = true;
+
+ // True iff ?, *, or + can follow the previous atom.
+ bool prev_repeatable = false;
+ for (int i = 0; regex[i]; i++) {
+ if (regex[i] == '\\') { // An escape sequence
+ i++;
+ if (regex[i] == '\0') {
+ ADD_FAILURE() << FormatRegexSyntaxError(regex, i - 1)
+ << "'\\' cannot appear at the end.";
+ return false;
+ }
+
+ if (!IsValidEscape(regex[i])) {
+ ADD_FAILURE() << FormatRegexSyntaxError(regex, i - 1)
+ << "invalid escape sequence \"\\" << regex[i] << "\".";
+ is_valid = false;
+ }
+ prev_repeatable = true;
+ } else { // Not an escape sequence.
+ const char ch = regex[i];
+
+ if (ch == '^' && i > 0) {
+ ADD_FAILURE() << FormatRegexSyntaxError(regex, i)
+ << "'^' can only appear at the beginning.";
+ is_valid = false;
+ } else if (ch == '$' && regex[i + 1] != '\0') {
+ ADD_FAILURE() << FormatRegexSyntaxError(regex, i)
+ << "'$' can only appear at the end.";
+ is_valid = false;
+ } else if (IsInSet(ch, "()[]{}|")) {
+ ADD_FAILURE() << FormatRegexSyntaxError(regex, i)
+ << "'" << ch << "' is unsupported.";
+ is_valid = false;
+ } else if (IsRepeat(ch) && !prev_repeatable) {
+ ADD_FAILURE() << FormatRegexSyntaxError(regex, i)
+ << "'" << ch << "' can only follow a repeatable token.";
+ is_valid = false;
+ }
+
+ prev_repeatable = !IsInSet(ch, "^$?*+");
+ }
+ }
+
+ return is_valid;
+}
+
+// Matches a repeated regex atom followed by a valid simple regular
+// expression. The regex atom is defined as c if escaped is false,
+// or \c otherwise. repeat is the repetition meta character (?, *,
+// or +). The behavior is undefined if str contains too many
+// characters to be indexable by size_t, in which case the test will
+// probably time out anyway. We are fine with this limitation as
+// std::string has it too.
+bool MatchRepetitionAndRegexAtHead(
+ bool escaped, char c, char repeat, const char* regex,
+ const char* str) {
+ const size_t min_count = (repeat == '+') ? 1 : 0;
+ const size_t max_count = (repeat == '?') ? 1 :
+ static_cast<size_t>(-1) - 1;
+ // We cannot call numeric_limits::max() as it conflicts with the
+ // max() macro on Windows.
+
+ for (size_t i = 0; i <= max_count; ++i) {
+ // We know that the atom matches each of the first i characters in str.
+ if (i >= min_count && MatchRegexAtHead(regex, str + i)) {
+ // We have enough matches at the head, and the tail matches too.
+ // Since we only care about *whether* the pattern matches str
+ // (as opposed to *how* it matches), there is no need to find a
+ // greedy match.
+ return true;
+ }
+ if (str[i] == '\0' || !AtomMatchesChar(escaped, c, str[i]))
+ return false;
+ }
+ return false;
+}
+
+// Returns true iff regex matches a prefix of str. regex must be a
+// valid simple regular expression and not start with "^", or the
+// result is undefined.
+bool MatchRegexAtHead(const char* regex, const char* str) {
+ if (*regex == '\0') // An empty regex matches a prefix of anything.
+ return true;
+
+ // "$" only matches the end of a string. Note that regex being
+ // valid guarantees that there's nothing after "$" in it.
+ if (*regex == '$')
+ return *str == '\0';
+
+ // Is the first thing in regex an escape sequence?
+ const bool escaped = *regex == '\\';
+ if (escaped)
+ ++regex;
+ if (IsRepeat(regex[1])) {
+ // MatchRepetitionAndRegexAtHead() calls MatchRegexAtHead(), so
+ // here's an indirect recursion. It terminates as the regex gets
+ // shorter in each recursion.
+ return MatchRepetitionAndRegexAtHead(
+ escaped, regex[0], regex[1], regex + 2, str);
+ } else {
+ // regex isn't empty, isn't "$", and doesn't start with a
+ // repetition. We match the first atom of regex with the first
+ // character of str and recurse.
+ return (*str != '\0') && AtomMatchesChar(escaped, *regex, *str) &&
+ MatchRegexAtHead(regex + 1, str + 1);
+ }
+}
+
+// Returns true iff regex matches any substring of str. regex must be
+// a valid simple regular expression, or the result is undefined.
+//
+// The algorithm is recursive, but the recursion depth doesn't exceed
+// the regex length, so we won't need to worry about running out of
+// stack space normally. In rare cases the time complexity can be
+// exponential with respect to the regex length + the string length,
+// but usually it's must faster (often close to linear).
+bool MatchRegexAnywhere(const char* regex, const char* str) {
+ if (regex == NULL || str == NULL)
+ return false;
+
+ if (*regex == '^')
+ return MatchRegexAtHead(regex + 1, str);
+
+ // A successful match can be anywhere in str.
+ do {
+ if (MatchRegexAtHead(regex, str))
+ return true;
+ } while (*str++ != '\0');
+ return false;
+}
+
+// Implements the RE class.
+
+RE::~RE() {
+ free(const_cast<char*>(pattern_));
+ free(const_cast<char*>(full_pattern_));
+}
+
+// Returns true iff regular expression re matches the entire str.
+bool RE::FullMatch(const char* str, const RE& re) {
+ return re.is_valid_ && MatchRegexAnywhere(re.full_pattern_, str);
+}
+
+// Returns true iff regular expression re matches a substring of str
+// (including str itself).
+bool RE::PartialMatch(const char* str, const RE& re) {
+ return re.is_valid_ && MatchRegexAnywhere(re.pattern_, str);
+}
+
+// Initializes an RE from its string representation.
+void RE::Init(const char* regex) {
+ pattern_ = full_pattern_ = NULL;
+ if (regex != NULL) {
+ pattern_ = posix::StrDup(regex);
+ }
+
+ is_valid_ = ValidateRegex(regex);
+ if (!is_valid_) {
+ // No need to calculate the full pattern when the regex is invalid.
+ return;
+ }
+
+ const size_t len = strlen(regex);
+ // Reserves enough bytes to hold the regular expression used for a
+ // full match: we need space to prepend a '^', append a '$', and
+ // terminate the string with '\0'.
+ char* buffer = static_cast<char*>(malloc(len + 3));
+ full_pattern_ = buffer;
+
+ if (*regex != '^')
+ *buffer++ = '^'; // Makes sure full_pattern_ starts with '^'.
+
+ // We don't use snprintf or strncpy, as they trigger a warning when
+ // compiled with VC++ 8.0.
+ memcpy(buffer, regex, len);
+ buffer += len;
+
+ if (len == 0 || regex[len - 1] != '$')
+ *buffer++ = '$'; // Makes sure full_pattern_ ends with '$'.
+
+ *buffer = '\0';
+}
+
+#endif // GTEST_USES_POSIX_RE
+
+const char kUnknownFile[] = "unknown file";
+
+// Formats a source file path and a line number as they would appear
+// in an error message from the compiler used to compile this code.
+GTEST_API_ ::std::string FormatFileLocation(const char* file, int line) {
+ const std::string file_name(file == NULL ? kUnknownFile : file);
+
+ if (line < 0) {
+ return file_name + ":";
+ }
+#ifdef _MSC_VER
+ return file_name + "(" + StreamableToString(line) + "):";
+#else
+ return file_name + ":" + StreamableToString(line) + ":";
+#endif // _MSC_VER
+}
+
+// Formats a file location for compiler-independent XML output.
+// Although this function is not platform dependent, we put it next to
+// FormatFileLocation in order to contrast the two functions.
+// Note that FormatCompilerIndependentFileLocation() does NOT append colon
+// to the file location it produces, unlike FormatFileLocation().
+GTEST_API_ ::std::string FormatCompilerIndependentFileLocation(
+ const char* file, int line) {
+ const std::string file_name(file == NULL ? kUnknownFile : file);
+
+ if (line < 0)
+ return file_name;
+ else
+ return file_name + ":" + StreamableToString(line);
+}
+
+
+GTestLog::GTestLog(GTestLogSeverity severity, const char* file, int line)
+ : severity_(severity) {
+ const char* const marker =
+ severity == GTEST_INFO ? "[ INFO ]" :
+ severity == GTEST_WARNING ? "[WARNING]" :
+ severity == GTEST_ERROR ? "[ ERROR ]" : "[ FATAL ]";
+ GetStream() << ::std::endl << marker << " "
+ << FormatFileLocation(file, line).c_str() << ": ";
+}
+
+// Flushes the buffers and, if severity is GTEST_FATAL, aborts the program.
+GTestLog::~GTestLog() {
+ GetStream() << ::std::endl;
+ if (severity_ == GTEST_FATAL) {
+ fflush(stderr);
+ posix::Abort();
+ }
+}
+// Disable Microsoft deprecation warnings for POSIX functions called from
+// this class (creat, dup, dup2, and close)
+#ifdef _MSC_VER
+# pragma warning(push)
+# pragma warning(disable: 4996)
+#endif // _MSC_VER
+
+#if GTEST_HAS_STREAM_REDIRECTION
+
+// Object that captures an output stream (stdout/stderr).
+class CapturedStream {
+ public:
+ // The ctor redirects the stream to a temporary file.
+ explicit CapturedStream(int fd) : fd_(fd), uncaptured_fd_(dup(fd)) {
+# if GTEST_OS_WINDOWS
+ char temp_dir_path[MAX_PATH + 1] = { '\0' }; // NOLINT
+ char temp_file_path[MAX_PATH + 1] = { '\0' }; // NOLINT
+
+ ::GetTempPathA(sizeof(temp_dir_path), temp_dir_path);
+ const UINT success = ::GetTempFileNameA(temp_dir_path,
+ "gtest_redir",
+ 0, // Generate unique file name.
+ temp_file_path);
+ GTEST_CHECK_(success != 0)
+ << "Unable to create a temporary file in " << temp_dir_path;
+ const int captured_fd = creat(temp_file_path, _S_IREAD | _S_IWRITE);
+ GTEST_CHECK_(captured_fd != -1) << "Unable to open temporary file "
+ << temp_file_path;
+ filename_ = temp_file_path;
+# else
+ // There's no guarantee that a test has write access to the current
+ // directory, so we create the temporary file in the /tmp directory
+ // instead. We use /tmp on most systems, and /sdcard on Android.
+ // That's because Android doesn't have /tmp.
+# if GTEST_OS_LINUX_ANDROID
+ // Note: Android applications are expected to call the framework's
+ // Context.getExternalStorageDirectory() method through JNI to get
+ // the location of the world-writable SD Card directory. However,
+ // this requires a Context handle, which cannot be retrieved
+ // globally from native code. Doing so also precludes running the
+ // code as part of a regular standalone executable, which doesn't
+ // run in a Dalvik process (e.g. when running it through 'adb shell').
+ //
+ // The location /sdcard is directly accessible from native code
+ // and is the only location (unofficially) supported by the Android
+ // team. It's generally a symlink to the real SD Card mount point
+ // which can be /mnt/sdcard, /mnt/sdcard0, /system/media/sdcard, or
+ // other OEM-customized locations. Never rely on these, and always
+ // use /sdcard.
+ char name_template[] = "/sdcard/gtest_captured_stream.XXXXXX";
+# else
+ char name_template[] = "/tmp/captured_stream.XXXXXX";
+# endif // GTEST_OS_LINUX_ANDROID
+ const int captured_fd = mkstemp(name_template);
+ filename_ = name_template;
+# endif // GTEST_OS_WINDOWS
+ fflush(NULL);
+ dup2(captured_fd, fd_);
+ close(captured_fd);
+ }
+
+ ~CapturedStream() {
+ remove(filename_.c_str());
+ }
+
+ std::string GetCapturedString() {
+ if (uncaptured_fd_ != -1) {
+ // Restores the original stream.
+ fflush(NULL);
+ dup2(uncaptured_fd_, fd_);
+ close(uncaptured_fd_);
+ uncaptured_fd_ = -1;
+ }
+
+ FILE* const file = posix::FOpen(filename_.c_str(), "r");
+ const std::string content = ReadEntireFile(file);
+ posix::FClose(file);
+ return content;
+ }
+
+ private:
+ // Reads the entire content of a file as an std::string.
+ static std::string ReadEntireFile(FILE* file);
+
+ // Returns the size (in bytes) of a file.
+ static size_t GetFileSize(FILE* file);
+
+ const int fd_; // A stream to capture.
+ int uncaptured_fd_;
+ // Name of the temporary file holding the stderr output.
+ ::std::string filename_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(CapturedStream);
+};
+
+// Returns the size (in bytes) of a file.
+size_t CapturedStream::GetFileSize(FILE* file) {
+ fseek(file, 0, SEEK_END);
+ return static_cast<size_t>(ftell(file));
+}
+
+// Reads the entire content of a file as a string.
+std::string CapturedStream::ReadEntireFile(FILE* file) {
+ const size_t file_size = GetFileSize(file);
+ char* const buffer = new char[file_size];
+
+ size_t bytes_last_read = 0; // # of bytes read in the last fread()
+ size_t bytes_read = 0; // # of bytes read so far
+
+ fseek(file, 0, SEEK_SET);
+
+ // Keeps reading the file until we cannot read further or the
+ // pre-determined file size is reached.
+ do {
+ bytes_last_read = fread(buffer+bytes_read, 1, file_size-bytes_read, file);
+ bytes_read += bytes_last_read;
+ } while (bytes_last_read > 0 && bytes_read < file_size);
+
+ const std::string content(buffer, bytes_read);
+ delete[] buffer;
+
+ return content;
+}
+
+# ifdef _MSC_VER
+# pragma warning(pop)
+# endif // _MSC_VER
+
+static CapturedStream* g_captured_stderr = NULL;
+static CapturedStream* g_captured_stdout = NULL;
+
+// Starts capturing an output stream (stdout/stderr).
+void CaptureStream(int fd, const char* stream_name, CapturedStream** stream) {
+ if (*stream != NULL) {
+ GTEST_LOG_(FATAL) << "Only one " << stream_name
+ << " capturer can exist at a time.";
+ }
+ *stream = new CapturedStream(fd);
+}
+
+// Stops capturing the output stream and returns the captured string.
+std::string GetCapturedStream(CapturedStream** captured_stream) {
+ const std::string content = (*captured_stream)->GetCapturedString();
+
+ delete *captured_stream;
+ *captured_stream = NULL;
+
+ return content;
+}
+
+// Starts capturing stdout.
+void CaptureStdout() {
+ CaptureStream(kStdOutFileno, "stdout", &g_captured_stdout);
+}
+
+// Starts capturing stderr.
+void CaptureStderr() {
+ CaptureStream(kStdErrFileno, "stderr", &g_captured_stderr);
+}
+
+// Stops capturing stdout and returns the captured string.
+std::string GetCapturedStdout() {
+ return GetCapturedStream(&g_captured_stdout);
+}
+
+// Stops capturing stderr and returns the captured string.
+std::string GetCapturedStderr() {
+ return GetCapturedStream(&g_captured_stderr);
+}
+
+#endif // GTEST_HAS_STREAM_REDIRECTION
+
+#if GTEST_HAS_DEATH_TEST
+
+// A copy of all command line arguments. Set by InitGoogleTest().
+::std::vector<testing::internal::string> g_argvs;
+
+static const ::std::vector<testing::internal::string>* g_injected_test_argvs =
+ NULL; // Owned.
+
+void SetInjectableArgvs(const ::std::vector<testing::internal::string>* argvs) {
+ if (g_injected_test_argvs != argvs)
+ delete g_injected_test_argvs;
+ g_injected_test_argvs = argvs;
+}
+
+const ::std::vector<testing::internal::string>& GetInjectableArgvs() {
+ if (g_injected_test_argvs != NULL) {
+ return *g_injected_test_argvs;
+ }
+ return g_argvs;
+}
+#endif // GTEST_HAS_DEATH_TEST
+
+#if GTEST_OS_WINDOWS_MOBILE
+namespace posix {
+void Abort() {
+ DebugBreak();
+ TerminateProcess(GetCurrentProcess(), 1);
+}
+} // namespace posix
+#endif // GTEST_OS_WINDOWS_MOBILE
+
+// Returns the name of the environment variable corresponding to the
+// given flag. For example, FlagToEnvVar("foo") will return
+// "GTEST_FOO" in the open-source version.
+static std::string FlagToEnvVar(const char* flag) {
+ const std::string full_flag =
+ (Message() << GTEST_FLAG_PREFIX_ << flag).GetString();
+
+ Message env_var;
+ for (size_t i = 0; i != full_flag.length(); i++) {
+ env_var << ToUpper(full_flag.c_str()[i]);
+ }
+
+ return env_var.GetString();
+}
+
+// Parses 'str' for a 32-bit signed integer. If successful, writes
+// the result to *value and returns true; otherwise leaves *value
+// unchanged and returns false.
+bool ParseInt32(const Message& src_text, const char* str, Int32* value) {
+ // Parses the environment variable as a decimal integer.
+ char* end = NULL;
+ const long long_value = strtol(str, &end, 10); // NOLINT
+
+ // Has strtol() consumed all characters in the string?
+ if (*end != '\0') {
+ // No - an invalid character was encountered.
+ Message msg;
+ msg << "WARNING: " << src_text
+ << " is expected to be a 32-bit integer, but actually"
+ << " has value \"" << str << "\".\n";
+ printf("%s", msg.GetString().c_str());
+ fflush(stdout);
+ return false;
+ }
+
+ // Is the parsed value in the range of an Int32?
+ const Int32 result = static_cast<Int32>(long_value);
+ if (long_value == LONG_MAX || long_value == LONG_MIN ||
+ // The parsed value overflows as a long. (strtol() returns
+ // LONG_MAX or LONG_MIN when the input overflows.)
+ result != long_value
+ // The parsed value overflows as an Int32.
+ ) {
+ Message msg;
+ msg << "WARNING: " << src_text
+ << " is expected to be a 32-bit integer, but actually"
+ << " has value " << str << ", which overflows.\n";
+ printf("%s", msg.GetString().c_str());
+ fflush(stdout);
+ return false;
+ }
+
+ *value = result;
+ return true;
+}
+
+// Reads and returns the Boolean environment variable corresponding to
+// the given flag; if it's not set, returns default_value.
+//
+// The value is considered true iff it's not "0".
+bool BoolFromGTestEnv(const char* flag, bool default_value) {
+ const std::string env_var = FlagToEnvVar(flag);
+ const char* const string_value = posix::GetEnv(env_var.c_str());
+ return string_value == NULL ?
+ default_value : strcmp(string_value, "0") != 0;
+}
+
+// Reads and returns a 32-bit integer stored in the environment
+// variable corresponding to the given flag; if it isn't set or
+// doesn't represent a valid 32-bit integer, returns default_value.
+Int32 Int32FromGTestEnv(const char* flag, Int32 default_value) {
+ const std::string env_var = FlagToEnvVar(flag);
+ const char* const string_value = posix::GetEnv(env_var.c_str());
+ if (string_value == NULL) {
+ // The environment variable is not set.
+ return default_value;
+ }
+
+ Int32 result = default_value;
+ if (!ParseInt32(Message() << "Environment variable " << env_var,
+ string_value, &result)) {
+ printf("The default value %s is used.\n",
+ (Message() << default_value).GetString().c_str());
+ fflush(stdout);
+ return default_value;
+ }
+
+ return result;
+}
+
+// Reads and returns the string environment variable corresponding to
+// the given flag; if it's not set, returns default_value.
+const char* StringFromGTestEnv(const char* flag, const char* default_value) {
+ const std::string env_var = FlagToEnvVar(flag);
+ const char* const value = posix::GetEnv(env_var.c_str());
+ return value == NULL ? default_value : value;
+}
+
+} // namespace internal
+} // namespace testing
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Test - The Google C++ Testing Framework
+//
+// This file implements a universal value printer that can print a
+// value of any type T:
+//
+// void ::testing::internal::UniversalPrinter<T>::Print(value, ostream_ptr);
+//
+// It uses the << operator when possible, and prints the bytes in the
+// object otherwise. A user can override its behavior for a class
+// type Foo by defining either operator<<(::std::ostream&, const Foo&)
+// or void PrintTo(const Foo&, ::std::ostream*) in the namespace that
+// defines Foo.
+
+#include <ctype.h>
+#include <stdio.h>
+#include <ostream> // NOLINT
+#include <string>
+
+namespace testing {
+
+namespace {
+
+using ::std::ostream;
+
+// Prints a segment of bytes in the given object.
+void PrintByteSegmentInObjectTo(const unsigned char* obj_bytes, size_t start,
+ size_t count, ostream* os) {
+ char text[5] = "";
+ for (size_t i = 0; i != count; i++) {
+ const size_t j = start + i;
+ if (i != 0) {
+ // Organizes the bytes into groups of 2 for easy parsing by
+ // human.
+ if ((j % 2) == 0)
+ *os << ' ';
+ else
+ *os << '-';
+ }
+ GTEST_SNPRINTF_(text, sizeof(text), "%02X", obj_bytes[j]);
+ *os << text;
+ }
+}
+
+// Prints the bytes in the given value to the given ostream.
+void PrintBytesInObjectToImpl(const unsigned char* obj_bytes, size_t count,
+ ostream* os) {
+ // Tells the user how big the object is.
+ *os << count << "-byte object <";
+
+ const size_t kThreshold = 132;
+ const size_t kChunkSize = 64;
+ // If the object size is bigger than kThreshold, we'll have to omit
+ // some details by printing only the first and the last kChunkSize
+ // bytes.
+ // TODO(wan): let the user control the threshold using a flag.
+ if (count < kThreshold) {
+ PrintByteSegmentInObjectTo(obj_bytes, 0, count, os);
+ } else {
+ PrintByteSegmentInObjectTo(obj_bytes, 0, kChunkSize, os);
+ *os << " ... ";
+ // Rounds up to 2-byte boundary.
+ const size_t resume_pos = (count - kChunkSize + 1)/2*2;
+ PrintByteSegmentInObjectTo(obj_bytes, resume_pos, count - resume_pos, os);
+ }
+ *os << ">";
+}
+
+} // namespace
+
+namespace internal2 {
+
+// Delegates to PrintBytesInObjectToImpl() to print the bytes in the
+// given object. The delegation simplifies the implementation, which
+// uses the << operator and thus is easier done outside of the
+// ::testing::internal namespace, which contains a << operator that
+// sometimes conflicts with the one in STL.
+void PrintBytesInObjectTo(const unsigned char* obj_bytes, size_t count,
+ ostream* os) {
+ PrintBytesInObjectToImpl(obj_bytes, count, os);
+}
+
+} // namespace internal2
+
+namespace internal {
+
+// Depending on the value of a char (or wchar_t), we print it in one
+// of three formats:
+// - as is if it's a printable ASCII (e.g. 'a', '2', ' '),
+// - as a hexidecimal escape sequence (e.g. '\x7F'), or
+// - as a special escape sequence (e.g. '\r', '\n').
+enum CharFormat {
+ kAsIs,
+ kHexEscape,
+ kSpecialEscape
+};
+
+// Returns true if c is a printable ASCII character. We test the
+// value of c directly instead of calling isprint(), which is buggy on
+// Windows Mobile.
+inline bool IsPrintableAscii(wchar_t c) {
+ return 0x20 <= c && c <= 0x7E;
+}
+
+// Prints a wide or narrow char c as a character literal without the
+// quotes, escaping it when necessary; returns how c was formatted.
+// The template argument UnsignedChar is the unsigned version of Char,
+// which is the type of c.
+template <typename UnsignedChar, typename Char>
+static CharFormat PrintAsCharLiteralTo(Char c, ostream* os) {
+ switch (static_cast<wchar_t>(c)) {
+ case L'\0':
+ *os << "\\0";
+ break;
+ case L'\'':
+ *os << "\\'";
+ break;
+ case L'\\':
+ *os << "\\\\";
+ break;
+ case L'\a':
+ *os << "\\a";
+ break;
+ case L'\b':
+ *os << "\\b";
+ break;
+ case L'\f':
+ *os << "\\f";
+ break;
+ case L'\n':
+ *os << "\\n";
+ break;
+ case L'\r':
+ *os << "\\r";
+ break;
+ case L'\t':
+ *os << "\\t";
+ break;
+ case L'\v':
+ *os << "\\v";
+ break;
+ default:
+ if (IsPrintableAscii(c)) {
+ *os << static_cast<char>(c);
+ return kAsIs;
+ } else {
+ *os << "\\x" + String::FormatHexInt(static_cast<UnsignedChar>(c));
+ return kHexEscape;
+ }
+ }
+ return kSpecialEscape;
+}
+
+// Prints a wchar_t c as if it's part of a string literal, escaping it when
+// necessary; returns how c was formatted.
+static CharFormat PrintAsStringLiteralTo(wchar_t c, ostream* os) {
+ switch (c) {
+ case L'\'':
+ *os << "'";
+ return kAsIs;
+ case L'"':
+ *os << "\\\"";
+ return kSpecialEscape;
+ default:
+ return PrintAsCharLiteralTo<wchar_t>(c, os);
+ }
+}
+
+// Prints a char c as if it's part of a string literal, escaping it when
+// necessary; returns how c was formatted.
+static CharFormat PrintAsStringLiteralTo(char c, ostream* os) {
+ return PrintAsStringLiteralTo(
+ static_cast<wchar_t>(static_cast<unsigned char>(c)), os);
+}
+
+// Prints a wide or narrow character c and its code. '\0' is printed
+// as "'\\0'", other unprintable characters are also properly escaped
+// using the standard C++ escape sequence. The template argument
+// UnsignedChar is the unsigned version of Char, which is the type of c.
+template <typename UnsignedChar, typename Char>
+void PrintCharAndCodeTo(Char c, ostream* os) {
+ // First, print c as a literal in the most readable form we can find.
+ *os << ((sizeof(c) > 1) ? "L'" : "'");
+ const CharFormat format = PrintAsCharLiteralTo<UnsignedChar>(c, os);
+ *os << "'";
+
+ // To aid user debugging, we also print c's code in decimal, unless
+ // it's 0 (in which case c was printed as '\\0', making the code
+ // obvious).
+ if (c == 0)
+ return;
+ *os << " (" << static_cast<int>(c);
+
+ // For more convenience, we print c's code again in hexidecimal,
+ // unless c was already printed in the form '\x##' or the code is in
+ // [1, 9].
+ if (format == kHexEscape || (1 <= c && c <= 9)) {
+ // Do nothing.
+ } else {
+ *os << ", 0x" << String::FormatHexInt(static_cast<UnsignedChar>(c));
+ }
+ *os << ")";
+}
+
+void PrintTo(unsigned char c, ::std::ostream* os) {
+ PrintCharAndCodeTo<unsigned char>(c, os);
+}
+void PrintTo(signed char c, ::std::ostream* os) {
+ PrintCharAndCodeTo<unsigned char>(c, os);
+}
+
+// Prints a wchar_t as a symbol if it is printable or as its internal
+// code otherwise and also as its code. L'\0' is printed as "L'\\0'".
+void PrintTo(wchar_t wc, ostream* os) {
+ PrintCharAndCodeTo<wchar_t>(wc, os);
+}
+
+// Prints the given array of characters to the ostream. CharType must be either
+// char or wchar_t.
+// The array starts at begin, the length is len, it may include '\0' characters
+// and may not be NUL-terminated.
+template <typename CharType>
+static void PrintCharsAsStringTo(
+ const CharType* begin, size_t len, ostream* os) {
+ const char* const kQuoteBegin = sizeof(CharType) == 1 ? "\"" : "L\"";
+ *os << kQuoteBegin;
+ bool is_previous_hex = false;
+ for (size_t index = 0; index < len; ++index) {
+ const CharType cur = begin[index];
+ if (is_previous_hex && IsXDigit(cur)) {
+ // Previous character is of '\x..' form and this character can be
+ // interpreted as another hexadecimal digit in its number. Break string to
+ // disambiguate.
+ *os << "\" " << kQuoteBegin;
+ }
+ is_previous_hex = PrintAsStringLiteralTo(cur, os) == kHexEscape;
+ }
+ *os << "\"";
+}
+
+// Prints a (const) char/wchar_t array of 'len' elements, starting at address
+// 'begin'. CharType must be either char or wchar_t.
+template <typename CharType>
+static void UniversalPrintCharArray(
+ const CharType* begin, size_t len, ostream* os) {
+ // The code
+ // const char kFoo[] = "foo";
+ // generates an array of 4, not 3, elements, with the last one being '\0'.
+ //
+ // Therefore when printing a char array, we don't print the last element if
+ // it's '\0', such that the output matches the string literal as it's
+ // written in the source code.
+ if (len > 0 && begin[len - 1] == '\0') {
+ PrintCharsAsStringTo(begin, len - 1, os);
+ return;
+ }
+
+ // If, however, the last element in the array is not '\0', e.g.
+ // const char kFoo[] = { 'f', 'o', 'o' };
+ // we must print the entire array. We also print a message to indicate
+ // that the array is not NUL-terminated.
+ PrintCharsAsStringTo(begin, len, os);
+ *os << " (no terminating NUL)";
+}
+
+// Prints a (const) char array of 'len' elements, starting at address 'begin'.
+void UniversalPrintArray(const char* begin, size_t len, ostream* os) {
+ UniversalPrintCharArray(begin, len, os);
+}
+
+// Prints a (const) wchar_t array of 'len' elements, starting at address
+// 'begin'.
+void UniversalPrintArray(const wchar_t* begin, size_t len, ostream* os) {
+ UniversalPrintCharArray(begin, len, os);
+}
+
+// Prints the given C string to the ostream.
+void PrintTo(const char* s, ostream* os) {
+ if (s == NULL) {
+ *os << "NULL";
+ } else {
+ *os << ImplicitCast_<const void*>(s) << " pointing to ";
+ PrintCharsAsStringTo(s, strlen(s), os);
+ }
+}
+
+// MSVC compiler can be configured to define whar_t as a typedef
+// of unsigned short. Defining an overload for const wchar_t* in that case
+// would cause pointers to unsigned shorts be printed as wide strings,
+// possibly accessing more memory than intended and causing invalid
+// memory accesses. MSVC defines _NATIVE_WCHAR_T_DEFINED symbol when
+// wchar_t is implemented as a native type.
+#if !defined(_MSC_VER) || defined(_NATIVE_WCHAR_T_DEFINED)
+// Prints the given wide C string to the ostream.
+void PrintTo(const wchar_t* s, ostream* os) {
+ if (s == NULL) {
+ *os << "NULL";
+ } else {
+ *os << ImplicitCast_<const void*>(s) << " pointing to ";
+ PrintCharsAsStringTo(s, wcslen(s), os);
+ }
+}
+#endif // wchar_t is native
+
+// Prints a ::string object.
+#if GTEST_HAS_GLOBAL_STRING
+void PrintStringTo(const ::string& s, ostream* os) {
+ PrintCharsAsStringTo(s.data(), s.size(), os);
+}
+#endif // GTEST_HAS_GLOBAL_STRING
+
+void PrintStringTo(const ::std::string& s, ostream* os) {
+ PrintCharsAsStringTo(s.data(), s.size(), os);
+}
+
+// Prints a ::wstring object.
+#if GTEST_HAS_GLOBAL_WSTRING
+void PrintWideStringTo(const ::wstring& s, ostream* os) {
+ PrintCharsAsStringTo(s.data(), s.size(), os);
+}
+#endif // GTEST_HAS_GLOBAL_WSTRING
+
+#if GTEST_HAS_STD_WSTRING
+void PrintWideStringTo(const ::std::wstring& s, ostream* os) {
+ PrintCharsAsStringTo(s.data(), s.size(), os);
+}
+#endif // GTEST_HAS_STD_WSTRING
+
+} // namespace internal
+
+} // namespace testing
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: mheule at google.com (Markus Heule)
+//
+// The Google C++ Testing Framework (Google Test)
+
+
+// Indicates that this translation unit is part of Google Test's
+// implementation. It must come before gtest-internal-inl.h is
+// included, or there will be a compiler error. This trick is to
+// prevent a user from accidentally including gtest-internal-inl.h in
+// his code.
+#define GTEST_IMPLEMENTATION_ 1
+#undef GTEST_IMPLEMENTATION_
+
+namespace testing {
+
+using internal::GetUnitTestImpl;
+
+// Gets the summary of the failure message by omitting the stack trace
+// in it.
+std::string TestPartResult::ExtractSummary(const char* message) {
+ const char* const stack_trace = strstr(message, internal::kStackTraceMarker);
+ return stack_trace == NULL ? message :
+ std::string(message, stack_trace);
+}
+
+// Prints a TestPartResult object.
+std::ostream& operator<<(std::ostream& os, const TestPartResult& result) {
+ return os
+ << result.file_name() << ":" << result.line_number() << ": "
+ << (result.type() == TestPartResult::kSuccess ? "Success" :
+ result.type() == TestPartResult::kFatalFailure ? "Fatal failure" :
+ "Non-fatal failure") << ":\n"
+ << result.message() << std::endl;
+}
+
+// Appends a TestPartResult to the array.
+void TestPartResultArray::Append(const TestPartResult& result) {
+ array_.push_back(result);
+}
+
+// Returns the TestPartResult at the given index (0-based).
+const TestPartResult& TestPartResultArray::GetTestPartResult(int index) const {
+ if (index < 0 || index >= size()) {
+ printf("\nInvalid index (%d) into TestPartResultArray.\n", index);
+ internal::posix::Abort();
+ }
+
+ return array_[index];
+}
+
+// Returns the number of TestPartResult objects in the array.
+int TestPartResultArray::size() const {
+ return static_cast<int>(array_.size());
+}
+
+namespace internal {
+
+HasNewFatalFailureHelper::HasNewFatalFailureHelper()
+ : has_new_fatal_failure_(false),
+ original_reporter_(GetUnitTestImpl()->
+ GetTestPartResultReporterForCurrentThread()) {
+ GetUnitTestImpl()->SetTestPartResultReporterForCurrentThread(this);
+}
+
+HasNewFatalFailureHelper::~HasNewFatalFailureHelper() {
+ GetUnitTestImpl()->SetTestPartResultReporterForCurrentThread(
+ original_reporter_);
+}
+
+void HasNewFatalFailureHelper::ReportTestPartResult(
+ const TestPartResult& result) {
+ if (result.fatally_failed())
+ has_new_fatal_failure_ = true;
+ original_reporter_->ReportTestPartResult(result);
+}
+
+} // namespace internal
+
+} // namespace testing
+// Copyright 2008 Google Inc.
+// All Rights Reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+
+namespace testing {
+namespace internal {
+
+#if GTEST_HAS_TYPED_TEST_P
+
+// Skips to the first non-space char in str. Returns an empty string if str
+// contains only whitespace characters.
+static const char* SkipSpaces(const char* str) {
+ while (IsSpace(*str))
+ str++;
+ return str;
+}
+
+// Verifies that registered_tests match the test names in
+// defined_test_names_; returns registered_tests if successful, or
+// aborts the program otherwise.
+const char* TypedTestCasePState::VerifyRegisteredTestNames(
+ const char* file, int line, const char* registered_tests) {
+ typedef ::std::set<const char*>::const_iterator DefinedTestIter;
+ registered_ = true;
+
+ // Skip initial whitespace in registered_tests since some
+ // preprocessors prefix stringizied literals with whitespace.
+ registered_tests = SkipSpaces(registered_tests);
+
+ Message errors;
+ ::std::set<std::string> tests;
+ for (const char* names = registered_tests; names != NULL;
+ names = SkipComma(names)) {
+ const std::string name = GetPrefixUntilComma(names);
+ if (tests.count(name) != 0) {
+ errors << "Test " << name << " is listed more than once.\n";
+ continue;
+ }
+
+ bool found = false;
+ for (DefinedTestIter it = defined_test_names_.begin();
+ it != defined_test_names_.end();
+ ++it) {
+ if (name == *it) {
+ found = true;
+ break;
+ }
+ }
+
+ if (found) {
+ tests.insert(name);
+ } else {
+ errors << "No test named " << name
+ << " can be found in this test case.\n";
+ }
+ }
+
+ for (DefinedTestIter it = defined_test_names_.begin();
+ it != defined_test_names_.end();
+ ++it) {
+ if (tests.count(*it) == 0) {
+ errors << "You forgot to list test " << *it << ".\n";
+ }
+ }
+
+ const std::string& errors_str = errors.GetString();
+ if (errors_str != "") {
+ fprintf(stderr, "%s %s", FormatFileLocation(file, line).c_str(),
+ errors_str.c_str());
+ fflush(stderr);
+ posix::Abort();
+ }
+
+ return registered_tests;
+}
+
+#endif // GTEST_HAS_TYPED_TEST_P
+
+} // namespace internal
+} // namespace testing
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+//
+// Google C++ Mocking Framework (Google Mock)
+//
+// This file #includes all Google Mock implementation .cc files. The
+// purpose is to allow a user to build Google Mock by compiling this
+// file alone.
+
+// This line ensures that gmock.h can be compiled on its own, even
+// when it's fused.
+#include "gmock/gmock.h"
+
+// The following lines pull in the real gmock *.cc files.
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements cardinalities.
+
+
+#include <limits.h>
+#include <ostream> // NOLINT
+#include <sstream>
+#include <string>
+
+namespace testing {
+
+namespace {
+
+// Implements the Between(m, n) cardinality.
+class BetweenCardinalityImpl : public CardinalityInterface {
+ public:
+ BetweenCardinalityImpl(int min, int max)
+ : min_(min >= 0 ? min : 0),
+ max_(max >= min_ ? max : min_) {
+ std::stringstream ss;
+ if (min < 0) {
+ ss << "The invocation lower bound must be >= 0, "
+ << "but is actually " << min << ".";
+ internal::Expect(false, __FILE__, __LINE__, ss.str());
+ } else if (max < 0) {
+ ss << "The invocation upper bound must be >= 0, "
+ << "but is actually " << max << ".";
+ internal::Expect(false, __FILE__, __LINE__, ss.str());
+ } else if (min > max) {
+ ss << "The invocation upper bound (" << max
+ << ") must be >= the invocation lower bound (" << min
+ << ").";
+ internal::Expect(false, __FILE__, __LINE__, ss.str());
+ }
+ }
+
+ // Conservative estimate on the lower/upper bound of the number of
+ // calls allowed.
+ virtual int ConservativeLowerBound() const { return min_; }
+ virtual int ConservativeUpperBound() const { return max_; }
+
+ virtual bool IsSatisfiedByCallCount(int call_count) const {
+ return min_ <= call_count && call_count <= max_;
+ }
+
+ virtual bool IsSaturatedByCallCount(int call_count) const {
+ return call_count >= max_;
+ }
+
+ virtual void DescribeTo(::std::ostream* os) const;
+
+ private:
+ const int min_;
+ const int max_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(BetweenCardinalityImpl);
+};
+
+// Formats "n times" in a human-friendly way.
+inline internal::string FormatTimes(int n) {
+ if (n == 1) {
+ return "once";
+ } else if (n == 2) {
+ return "twice";
+ } else {
+ std::stringstream ss;
+ ss << n << " times";
+ return ss.str();
+ }
+}
+
+// Describes the Between(m, n) cardinality in human-friendly text.
+void BetweenCardinalityImpl::DescribeTo(::std::ostream* os) const {
+ if (min_ == 0) {
+ if (max_ == 0) {
+ *os << "never called";
+ } else if (max_ == INT_MAX) {
+ *os << "called any number of times";
+ } else {
+ *os << "called at most " << FormatTimes(max_);
+ }
+ } else if (min_ == max_) {
+ *os << "called " << FormatTimes(min_);
+ } else if (max_ == INT_MAX) {
+ *os << "called at least " << FormatTimes(min_);
+ } else {
+ // 0 < min_ < max_ < INT_MAX
+ *os << "called between " << min_ << " and " << max_ << " times";
+ }
+}
+
+} // Unnamed namespace
+
+// Describes the given call count to an ostream.
+void Cardinality::DescribeActualCallCountTo(int actual_call_count,
+ ::std::ostream* os) {
+ if (actual_call_count > 0) {
+ *os << "called " << FormatTimes(actual_call_count);
+ } else {
+ *os << "never called";
+ }
+}
+
+// Creates a cardinality that allows at least n calls.
+GTEST_API_ Cardinality AtLeast(int n) { return Between(n, INT_MAX); }
+
+// Creates a cardinality that allows at most n calls.
+GTEST_API_ Cardinality AtMost(int n) { return Between(0, n); }
+
+// Creates a cardinality that allows any number of calls.
+GTEST_API_ Cardinality AnyNumber() { return AtLeast(0); }
+
+// Creates a cardinality that allows between min and max calls.
+GTEST_API_ Cardinality Between(int min, int max) {
+ return Cardinality(new BetweenCardinalityImpl(min, max));
+}
+
+// Creates a cardinality that allows exactly n calls.
+GTEST_API_ Cardinality Exactly(int n) { return Between(n, n); }
+
+} // namespace testing
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file defines some utilities useful for implementing Google
+// Mock. They are subject to change without notice, so please DO NOT
+// USE THEM IN USER CODE.
+
+
+#include <ctype.h>
+#include <ostream> // NOLINT
+#include <string>
+
+namespace testing {
+namespace internal {
+
+// Converts an identifier name to a space-separated list of lower-case
+// words. Each maximum substring of the form [A-Za-z][a-z]*|\d+ is
+// treated as one word. For example, both "FooBar123" and
+// "foo_bar_123" are converted to "foo bar 123".
+GTEST_API_ string ConvertIdentifierNameToWords(const char* id_name) {
+ string result;
+ char prev_char = '\0';
+ for (const char* p = id_name; *p != '\0'; prev_char = *(p++)) {
+ // We don't care about the current locale as the input is
+ // guaranteed to be a valid C++ identifier name.
+ const bool starts_new_word = IsUpper(*p) ||
+ (!IsAlpha(prev_char) && IsLower(*p)) ||
+ (!IsDigit(prev_char) && IsDigit(*p));
+
+ if (IsAlNum(*p)) {
+ if (starts_new_word && result != "")
+ result += ' ';
+ result += ToLower(*p);
+ }
+ }
+ return result;
+}
+
+// This class reports Google Mock failures as Google Test failures. A
+// user can define another class in a similar fashion if he intends to
+// use Google Mock with a testing framework other than Google Test.
+class GoogleTestFailureReporter : public FailureReporterInterface {
+ public:
+ virtual void ReportFailure(FailureType type, const char* file, int line,
+ const string& message) {
+ AssertHelper(type == kFatal ?
+ TestPartResult::kFatalFailure :
+ TestPartResult::kNonFatalFailure,
+ file,
+ line,
+ message.c_str()) = Message();
+ if (type == kFatal) {
+ posix::Abort();
+ }
+ }
+};
+
+// Returns the global failure reporter. Will create a
+// GoogleTestFailureReporter and return it the first time called.
+GTEST_API_ FailureReporterInterface* GetFailureReporter() {
+ // Points to the global failure reporter used by Google Mock. gcc
+ // guarantees that the following use of failure_reporter is
+ // thread-safe. We may need to add additional synchronization to
+ // protect failure_reporter if we port Google Mock to other
+ // compilers.
+ static FailureReporterInterface* const failure_reporter =
+ new GoogleTestFailureReporter();
+ return failure_reporter;
+}
+
+// Protects global resources (stdout in particular) used by Log().
+static GTEST_DEFINE_STATIC_MUTEX_(g_log_mutex);
+
+// Returns true iff a log with the given severity is visible according
+// to the --gmock_verbose flag.
+GTEST_API_ bool LogIsVisible(LogSeverity severity) {
+ if (GMOCK_FLAG(verbose) == kInfoVerbosity) {
+ // Always show the log if --gmock_verbose=info.
+ return true;
+ } else if (GMOCK_FLAG(verbose) == kErrorVerbosity) {
+ // Always hide it if --gmock_verbose=error.
+ return false;
+ } else {
+ // If --gmock_verbose is neither "info" nor "error", we treat it
+ // as "warning" (its default value).
+ return severity == kWarning;
+ }
+}
+
+// Prints the given message to stdout iff 'severity' >= the level
+// specified by the --gmock_verbose flag. If stack_frames_to_skip >=
+// 0, also prints the stack trace excluding the top
+// stack_frames_to_skip frames. In opt mode, any positive
+// stack_frames_to_skip is treated as 0, since we don't know which
+// function calls will be inlined by the compiler and need to be
+// conservative.
+GTEST_API_ void Log(LogSeverity severity,
+ const string& message,
+ int stack_frames_to_skip) {
+ if (!LogIsVisible(severity))
+ return;
+
+ // Ensures that logs from different threads don't interleave.
+ MutexLock l(&g_log_mutex);
+
+ // "using ::std::cout;" doesn't work with Symbian's STLport, where cout is a
+ // macro.
+
+ if (severity == kWarning) {
+ // Prints a GMOCK WARNING marker to make the warnings easily searchable.
+ std::cout << "\nGMOCK WARNING:";
+ }
+ // Pre-pends a new-line to message if it doesn't start with one.
+ if (message.empty() || message[0] != '\n') {
+ std::cout << "\n";
+ }
+ std::cout << message;
+ if (stack_frames_to_skip >= 0) {
+#ifdef NDEBUG
+ // In opt mode, we have to be conservative and skip no stack frame.
+ const int actual_to_skip = 0;
+#else
+ // In dbg mode, we can do what the caller tell us to do (plus one
+ // for skipping this function's stack frame).
+ const int actual_to_skip = stack_frames_to_skip + 1;
+#endif // NDEBUG
+
+ // Appends a new-line to message if it doesn't end with one.
+ if (!message.empty() && *message.rbegin() != '\n') {
+ std::cout << "\n";
+ }
+ std::cout << "Stack trace:\n"
+ << ::testing::internal::GetCurrentOsStackTraceExceptTop(
+ ::testing::UnitTest::GetInstance(), actual_to_skip);
+ }
+ std::cout << ::std::flush;
+}
+
+} // namespace internal
+} // namespace testing
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements Matcher<const string&>, Matcher<string>, and
+// utilities for defining matchers.
+
+
+#include <string.h>
+#include <sstream>
+#include <string>
+
+namespace testing {
+
+// Constructs a matcher that matches a const string& whose value is
+// equal to s.
+Matcher<const internal::string&>::Matcher(const internal::string& s) {
+ *this = Eq(s);
+}
+
+// Constructs a matcher that matches a const string& whose value is
+// equal to s.
+Matcher<const internal::string&>::Matcher(const char* s) {
+ *this = Eq(internal::string(s));
+}
+
+// Constructs a matcher that matches a string whose value is equal to s.
+Matcher<internal::string>::Matcher(const internal::string& s) { *this = Eq(s); }
+
+// Constructs a matcher that matches a string whose value is equal to s.
+Matcher<internal::string>::Matcher(const char* s) {
+ *this = Eq(internal::string(s));
+}
+
+#if GTEST_HAS_STRING_PIECE_
+// Constructs a matcher that matches a const StringPiece& whose value is
+// equal to s.
+Matcher<const StringPiece&>::Matcher(const internal::string& s) {
+ *this = Eq(s);
+}
+
+// Constructs a matcher that matches a const StringPiece& whose value is
+// equal to s.
+Matcher<const StringPiece&>::Matcher(const char* s) {
+ *this = Eq(internal::string(s));
+}
+
+// Constructs a matcher that matches a const StringPiece& whose value is
+// equal to s.
+Matcher<const StringPiece&>::Matcher(StringPiece s) {
+ *this = Eq(s.ToString());
+}
+
+// Constructs a matcher that matches a StringPiece whose value is equal to s.
+Matcher<StringPiece>::Matcher(const internal::string& s) {
+ *this = Eq(s);
+}
+
+// Constructs a matcher that matches a StringPiece whose value is equal to s.
+Matcher<StringPiece>::Matcher(const char* s) {
+ *this = Eq(internal::string(s));
+}
+
+// Constructs a matcher that matches a StringPiece whose value is equal to s.
+Matcher<StringPiece>::Matcher(StringPiece s) {
+ *this = Eq(s.ToString());
+}
+#endif // GTEST_HAS_STRING_PIECE_
+
+namespace internal {
+
+// Joins a vector of strings as if they are fields of a tuple; returns
+// the joined string.
+GTEST_API_ string JoinAsTuple(const Strings& fields) {
+ switch (fields.size()) {
+ case 0:
+ return "";
+ case 1:
+ return fields[0];
+ default:
+ string result = "(" + fields[0];
+ for (size_t i = 1; i < fields.size(); i++) {
+ result += ", ";
+ result += fields[i];
+ }
+ result += ")";
+ return result;
+ }
+}
+
+// Returns the description for a matcher defined using the MATCHER*()
+// macro where the user-supplied description string is "", if
+// 'negation' is false; otherwise returns the description of the
+// negation of the matcher. 'param_values' contains a list of strings
+// that are the print-out of the matcher's parameters.
+GTEST_API_ string FormatMatcherDescription(bool negation,
+ const char* matcher_name,
+ const Strings& param_values) {
+ string result = ConvertIdentifierNameToWords(matcher_name);
+ if (param_values.size() >= 1)
+ result += " " + JoinAsTuple(param_values);
+ return negation ? "not (" + result + ")" : result;
+}
+
+// FindMaxBipartiteMatching and its helper class.
+//
+// Uses the well-known Ford-Fulkerson max flow method to find a maximum
+// bipartite matching. Flow is considered to be from left to right.
+// There is an implicit source node that is connected to all of the left
+// nodes, and an implicit sink node that is connected to all of the
+// right nodes. All edges have unit capacity.
+//
+// Neither the flow graph nor the residual flow graph are represented
+// explicitly. Instead, they are implied by the information in 'graph' and
+// a vector<int> called 'left_' whose elements are initialized to the
+// value kUnused. This represents the initial state of the algorithm,
+// where the flow graph is empty, and the residual flow graph has the
+// following edges:
+// - An edge from source to each left_ node
+// - An edge from each right_ node to sink
+// - An edge from each left_ node to each right_ node, if the
+// corresponding edge exists in 'graph'.
+//
+// When the TryAugment() method adds a flow, it sets left_[l] = r for some
+// nodes l and r. This induces the following changes:
+// - The edges (source, l), (l, r), and (r, sink) are added to the
+// flow graph.
+// - The same three edges are removed from the residual flow graph.
+// - The reverse edges (l, source), (r, l), and (sink, r) are added
+// to the residual flow graph, which is a directional graph
+// representing unused flow capacity.
+//
+// When the method augments a flow (moving left_[l] from some r1 to some
+// other r2), this can be thought of as "undoing" the above steps with
+// respect to r1 and "redoing" them with respect to r2.
+//
+// It bears repeating that the flow graph and residual flow graph are
+// never represented explicitly, but can be derived by looking at the
+// information in 'graph' and in left_.
+//
+// As an optimization, there is a second vector<int> called right_ which
+// does not provide any new information. Instead, it enables more
+// efficient queries about edges entering or leaving the right-side nodes
+// of the flow or residual flow graphs. The following invariants are
+// maintained:
+//
+// left[l] == kUnused or right[left[l]] == l
+// right[r] == kUnused or left[right[r]] == r
+//
+// . [ source ] .
+// . ||| .
+// . ||| .
+// . ||\--> left[0]=1 ---\ right[0]=-1 ----\ .
+// . || | | .
+// . |\---> left[1]=-1 \--> right[1]=0 ---\| .
+// . | || .
+// . \----> left[2]=2 ------> right[2]=2 --\|| .
+// . ||| .
+// . elements matchers vvv .
+// . [ sink ] .
+//
+// See Also:
+// [1] Cormen, et al (2001). "Section 26.2: The Ford–Fulkerson method".
+// "Introduction to Algorithms (Second ed.)", pp. 651–664.
+// [2] "Ford–Fulkerson algorithm", Wikipedia,
+// 'http://en.wikipedia.org/wiki/Ford%E2%80%93Fulkerson_algorithm'
+class MaxBipartiteMatchState {
+ public:
+ explicit MaxBipartiteMatchState(const MatchMatrix& graph)
+ : graph_(&graph),
+ left_(graph_->LhsSize(), kUnused),
+ right_(graph_->RhsSize(), kUnused) {
+ }
+
+ // Returns the edges of a maximal match, each in the form {left, right}.
+ ElementMatcherPairs Compute() {
+ // 'seen' is used for path finding { 0: unseen, 1: seen }.
+ ::std::vector<char> seen;
+ // Searches the residual flow graph for a path from each left node to
+ // the sink in the residual flow graph, and if one is found, add flow
+ // to the graph. It's okay to search through the left nodes once. The
+ // edge from the implicit source node to each previously-visited left
+ // node will have flow if that left node has any path to the sink
+ // whatsoever. Subsequent augmentations can only add flow to the
+ // network, and cannot take away that previous flow unit from the source.
+ // Since the source-to-left edge can only carry one flow unit (or,
+ // each element can be matched to only one matcher), there is no need
+ // to visit the left nodes more than once looking for augmented paths.
+ // The flow is known to be possible or impossible by looking at the
+ // node once.
+ for (size_t ilhs = 0; ilhs < graph_->LhsSize(); ++ilhs) {
+ // Reset the path-marking vector and try to find a path from
+ // source to sink starting at the left_[ilhs] node.
+ GTEST_CHECK_(left_[ilhs] == kUnused)
+ << "ilhs: " << ilhs << ", left_[ilhs]: " << left_[ilhs];
+ // 'seen' initialized to 'graph_->RhsSize()' copies of 0.
+ seen.assign(graph_->RhsSize(), 0);
+ TryAugment(ilhs, &seen);
+ }
+ ElementMatcherPairs result;
+ for (size_t ilhs = 0; ilhs < left_.size(); ++ilhs) {
+ size_t irhs = left_[ilhs];
+ if (irhs == kUnused) continue;
+ result.push_back(ElementMatcherPair(ilhs, irhs));
+ }
+ return result;
+ }
+
+ private:
+ static const size_t kUnused = static_cast<size_t>(-1);
+
+ // Perform a depth-first search from left node ilhs to the sink. If a
+ // path is found, flow is added to the network by linking the left and
+ // right vector elements corresponding each segment of the path.
+ // Returns true if a path to sink was found, which means that a unit of
+ // flow was added to the network. The 'seen' vector elements correspond
+ // to right nodes and are marked to eliminate cycles from the search.
+ //
+ // Left nodes will only be explored at most once because they
+ // are accessible from at most one right node in the residual flow
+ // graph.
+ //
+ // Note that left_[ilhs] is the only element of left_ that TryAugment will
+ // potentially transition from kUnused to another value. Any other
+ // left_ element holding kUnused before TryAugment will be holding it
+ // when TryAugment returns.
+ //
+ bool TryAugment(size_t ilhs, ::std::vector<char>* seen) {
+ for (size_t irhs = 0; irhs < graph_->RhsSize(); ++irhs) {
+ if ((*seen)[irhs])
+ continue;
+ if (!graph_->HasEdge(ilhs, irhs))
+ continue;
+ // There's an available edge from ilhs to irhs.
+ (*seen)[irhs] = 1;
+ // Next a search is performed to determine whether
+ // this edge is a dead end or leads to the sink.
+ //
+ // right_[irhs] == kUnused means that there is residual flow from
+ // right node irhs to the sink, so we can use that to finish this
+ // flow path and return success.
+ //
+ // Otherwise there is residual flow to some ilhs. We push flow
+ // along that path and call ourselves recursively to see if this
+ // ultimately leads to sink.
+ if (right_[irhs] == kUnused || TryAugment(right_[irhs], seen)) {
+ // Add flow from left_[ilhs] to right_[irhs].
+ left_[ilhs] = irhs;
+ right_[irhs] = ilhs;
+ return true;
+ }
+ }
+ return false;
+ }
+
+ const MatchMatrix* graph_; // not owned
+ // Each element of the left_ vector represents a left hand side node
+ // (i.e. an element) and each element of right_ is a right hand side
+ // node (i.e. a matcher). The values in the left_ vector indicate
+ // outflow from that node to a node on the the right_ side. The values
+ // in the right_ indicate inflow, and specify which left_ node is
+ // feeding that right_ node, if any. For example, left_[3] == 1 means
+ // there's a flow from element #3 to matcher #1. Such a flow would also
+ // be redundantly represented in the right_ vector as right_[1] == 3.
+ // Elements of left_ and right_ are either kUnused or mutually
+ // referent. Mutually referent means that left_[right_[i]] = i and
+ // right_[left_[i]] = i.
+ ::std::vector<size_t> left_;
+ ::std::vector<size_t> right_;
+
+ GTEST_DISALLOW_ASSIGN_(MaxBipartiteMatchState);
+};
+
+const size_t MaxBipartiteMatchState::kUnused;
+
+GTEST_API_ ElementMatcherPairs
+FindMaxBipartiteMatching(const MatchMatrix& g) {
+ return MaxBipartiteMatchState(g).Compute();
+}
+
+static void LogElementMatcherPairVec(const ElementMatcherPairs& pairs,
+ ::std::ostream* stream) {
+ typedef ElementMatcherPairs::const_iterator Iter;
+ ::std::ostream& os = *stream;
+ os << "{";
+ const char *sep = "";
+ for (Iter it = pairs.begin(); it != pairs.end(); ++it) {
+ os << sep << "\n ("
+ << "element #" << it->first << ", "
+ << "matcher #" << it->second << ")";
+ sep = ",";
+ }
+ os << "\n}";
+}
+
+// Tries to find a pairing, and explains the result.
+GTEST_API_ bool FindPairing(const MatchMatrix& matrix,
+ MatchResultListener* listener) {
+ ElementMatcherPairs matches = FindMaxBipartiteMatching(matrix);
+
+ size_t max_flow = matches.size();
+ bool result = (max_flow == matrix.RhsSize());
+
+ if (!result) {
+ if (listener->IsInterested()) {
+ *listener << "where no permutation of the elements can "
+ "satisfy all matchers, and the closest match is "
+ << max_flow << " of " << matrix.RhsSize()
+ << " matchers with the pairings:\n";
+ LogElementMatcherPairVec(matches, listener->stream());
+ }
+ return false;
+ }
+
+ if (matches.size() > 1) {
+ if (listener->IsInterested()) {
+ const char *sep = "where:\n";
+ for (size_t mi = 0; mi < matches.size(); ++mi) {
+ *listener << sep << " - element #" << matches[mi].first
+ << " is matched by matcher #" << matches[mi].second;
+ sep = ",\n";
+ }
+ }
+ }
+ return true;
+}
+
+bool MatchMatrix::NextGraph() {
+ for (size_t ilhs = 0; ilhs < LhsSize(); ++ilhs) {
+ for (size_t irhs = 0; irhs < RhsSize(); ++irhs) {
+ char& b = matched_[SpaceIndex(ilhs, irhs)];
+ if (!b) {
+ b = 1;
+ return true;
+ }
+ b = 0;
+ }
+ }
+ return false;
+}
+
+void MatchMatrix::Randomize() {
+ for (size_t ilhs = 0; ilhs < LhsSize(); ++ilhs) {
+ for (size_t irhs = 0; irhs < RhsSize(); ++irhs) {
+ char& b = matched_[SpaceIndex(ilhs, irhs)];
+ b = static_cast<char>(rand() & 1); // NOLINT
+ }
+ }
+}
+
+string MatchMatrix::DebugString() const {
+ ::std::stringstream ss;
+ const char *sep = "";
+ for (size_t i = 0; i < LhsSize(); ++i) {
+ ss << sep;
+ for (size_t j = 0; j < RhsSize(); ++j) {
+ ss << HasEdge(i, j);
+ }
+ sep = ";";
+ }
+ return ss.str();
+}
+
+void UnorderedElementsAreMatcherImplBase::DescribeToImpl(
+ ::std::ostream* os) const {
+ if (matcher_describers_.empty()) {
+ *os << "is empty";
+ return;
+ }
+ if (matcher_describers_.size() == 1) {
+ *os << "has " << Elements(1) << " and that element ";
+ matcher_describers_[0]->DescribeTo(os);
+ return;
+ }
+ *os << "has " << Elements(matcher_describers_.size())
+ << " and there exists some permutation of elements such that:\n";
+ const char* sep = "";
+ for (size_t i = 0; i != matcher_describers_.size(); ++i) {
+ *os << sep << " - element #" << i << " ";
+ matcher_describers_[i]->DescribeTo(os);
+ sep = ", and\n";
+ }
+}
+
+void UnorderedElementsAreMatcherImplBase::DescribeNegationToImpl(
+ ::std::ostream* os) const {
+ if (matcher_describers_.empty()) {
+ *os << "isn't empty";
+ return;
+ }
+ if (matcher_describers_.size() == 1) {
+ *os << "doesn't have " << Elements(1)
+ << ", or has " << Elements(1) << " that ";
+ matcher_describers_[0]->DescribeNegationTo(os);
+ return;
+ }
+ *os << "doesn't have " << Elements(matcher_describers_.size())
+ << ", or there exists no permutation of elements such that:\n";
+ const char* sep = "";
+ for (size_t i = 0; i != matcher_describers_.size(); ++i) {
+ *os << sep << " - element #" << i << " ";
+ matcher_describers_[i]->DescribeTo(os);
+ sep = ", and\n";
+ }
+}
+
+// Checks that all matchers match at least one element, and that all
+// elements match at least one matcher. This enables faster matching
+// and better error reporting.
+// Returns false, writing an explanation to 'listener', if and only
+// if the success criteria are not met.
+bool UnorderedElementsAreMatcherImplBase::
+VerifyAllElementsAndMatchersAreMatched(
+ const ::std::vector<string>& element_printouts,
+ const MatchMatrix& matrix,
+ MatchResultListener* listener) const {
+ bool result = true;
+ ::std::vector<char> element_matched(matrix.LhsSize(), 0);
+ ::std::vector<char> matcher_matched(matrix.RhsSize(), 0);
+
+ for (size_t ilhs = 0; ilhs < matrix.LhsSize(); ilhs++) {
+ for (size_t irhs = 0; irhs < matrix.RhsSize(); irhs++) {
+ char matched = matrix.HasEdge(ilhs, irhs);
+ element_matched[ilhs] |= matched;
+ matcher_matched[irhs] |= matched;
+ }
+ }
+
+ {
+ const char* sep =
+ "where the following matchers don't match any elements:\n";
+ for (size_t mi = 0; mi < matcher_matched.size(); ++mi) {
+ if (matcher_matched[mi])
+ continue;
+ result = false;
+ if (listener->IsInterested()) {
+ *listener << sep << "matcher #" << mi << ": ";
+ matcher_describers_[mi]->DescribeTo(listener->stream());
+ sep = ",\n";
+ }
+ }
+ }
+
+ {
+ const char* sep =
+ "where the following elements don't match any matchers:\n";
+ const char* outer_sep = "";
+ if (!result) {
+ outer_sep = "\nand ";
+ }
+ for (size_t ei = 0; ei < element_matched.size(); ++ei) {
+ if (element_matched[ei])
+ continue;
+ result = false;
+ if (listener->IsInterested()) {
+ *listener << outer_sep << sep << "element #" << ei << ": "
+ << element_printouts[ei];
+ sep = ",\n";
+ outer_sep = "";
+ }
+ }
+ }
+ return result;
+}
+
+} // namespace internal
+} // namespace testing
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements the spec builder syntax (ON_CALL and
+// EXPECT_CALL).
+
+
+#include <stdlib.h>
+#include <iostream> // NOLINT
+#include <map>
+#include <set>
+#include <string>
+
+#if GTEST_OS_CYGWIN || GTEST_OS_LINUX || GTEST_OS_MAC
+# include <unistd.h> // NOLINT
+#endif
+
+namespace testing {
+namespace internal {
+
+// Protects the mock object registry (in class Mock), all function
+// mockers, and all expectations.
+GTEST_API_ GTEST_DEFINE_STATIC_MUTEX_(g_gmock_mutex);
+
+// Logs a message including file and line number information.
+GTEST_API_ void LogWithLocation(testing::internal::LogSeverity severity,
+ const char* file, int line,
+ const string& message) {
+ ::std::ostringstream s;
+ s << file << ":" << line << ": " << message << ::std::endl;
+ Log(severity, s.str(), 0);
+}
+
+// Constructs an ExpectationBase object.
+ExpectationBase::ExpectationBase(const char* a_file,
+ int a_line,
+ const string& a_source_text)
+ : file_(a_file),
+ line_(a_line),
+ source_text_(a_source_text),
+ cardinality_specified_(false),
+ cardinality_(Exactly(1)),
+ call_count_(0),
+ retired_(false),
+ extra_matcher_specified_(false),
+ repeated_action_specified_(false),
+ retires_on_saturation_(false),
+ last_clause_(kNone),
+ action_count_checked_(false) {}
+
+// Destructs an ExpectationBase object.
+ExpectationBase::~ExpectationBase() {}
+
+// Explicitly specifies the cardinality of this expectation. Used by
+// the subclasses to implement the .Times() clause.
+void ExpectationBase::SpecifyCardinality(const Cardinality& a_cardinality) {
+ cardinality_specified_ = true;
+ cardinality_ = a_cardinality;
+}
+
+// Retires all pre-requisites of this expectation.
+void ExpectationBase::RetireAllPreRequisites()
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ if (is_retired()) {
+ // We can take this short-cut as we never retire an expectation
+ // until we have retired all its pre-requisites.
+ return;
+ }
+
+ for (ExpectationSet::const_iterator it = immediate_prerequisites_.begin();
+ it != immediate_prerequisites_.end(); ++it) {
+ ExpectationBase* const prerequisite = it->expectation_base().get();
+ if (!prerequisite->is_retired()) {
+ prerequisite->RetireAllPreRequisites();
+ prerequisite->Retire();
+ }
+ }
+}
+
+// Returns true iff all pre-requisites of this expectation have been
+// satisfied.
+bool ExpectationBase::AllPrerequisitesAreSatisfied() const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ for (ExpectationSet::const_iterator it = immediate_prerequisites_.begin();
+ it != immediate_prerequisites_.end(); ++it) {
+ if (!(it->expectation_base()->IsSatisfied()) ||
+ !(it->expectation_base()->AllPrerequisitesAreSatisfied()))
+ return false;
+ }
+ return true;
+}
+
+// Adds unsatisfied pre-requisites of this expectation to 'result'.
+void ExpectationBase::FindUnsatisfiedPrerequisites(ExpectationSet* result) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ for (ExpectationSet::const_iterator it = immediate_prerequisites_.begin();
+ it != immediate_prerequisites_.end(); ++it) {
+ if (it->expectation_base()->IsSatisfied()) {
+ // If *it is satisfied and has a call count of 0, some of its
+ // pre-requisites may not be satisfied yet.
+ if (it->expectation_base()->call_count_ == 0) {
+ it->expectation_base()->FindUnsatisfiedPrerequisites(result);
+ }
+ } else {
+ // Now that we know *it is unsatisfied, we are not so interested
+ // in whether its pre-requisites are satisfied. Therefore we
+ // don't recursively call FindUnsatisfiedPrerequisites() here.
+ *result += *it;
+ }
+ }
+}
+
+// Describes how many times a function call matching this
+// expectation has occurred.
+void ExpectationBase::DescribeCallCountTo(::std::ostream* os) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+
+ // Describes how many times the function is expected to be called.
+ *os << " Expected: to be ";
+ cardinality().DescribeTo(os);
+ *os << "\n Actual: ";
+ Cardinality::DescribeActualCallCountTo(call_count(), os);
+
+ // Describes the state of the expectation (e.g. is it satisfied?
+ // is it active?).
+ *os << " - " << (IsOverSaturated() ? "over-saturated" :
+ IsSaturated() ? "saturated" :
+ IsSatisfied() ? "satisfied" : "unsatisfied")
+ << " and "
+ << (is_retired() ? "retired" : "active");
+}
+
+// Checks the action count (i.e. the number of WillOnce() and
+// WillRepeatedly() clauses) against the cardinality if this hasn't
+// been done before. Prints a warning if there are too many or too
+// few actions.
+void ExpectationBase::CheckActionCountIfNotDone() const
+ GTEST_LOCK_EXCLUDED_(mutex_) {
+ bool should_check = false;
+ {
+ MutexLock l(&mutex_);
+ if (!action_count_checked_) {
+ action_count_checked_ = true;
+ should_check = true;
+ }
+ }
+
+ if (should_check) {
+ if (!cardinality_specified_) {
+ // The cardinality was inferred - no need to check the action
+ // count against it.
+ return;
+ }
+
+ // The cardinality was explicitly specified.
+ const int action_count = static_cast<int>(untyped_actions_.size());
+ const int upper_bound = cardinality().ConservativeUpperBound();
+ const int lower_bound = cardinality().ConservativeLowerBound();
+ bool too_many; // True if there are too many actions, or false
+ // if there are too few.
+ if (action_count > upper_bound ||
+ (action_count == upper_bound && repeated_action_specified_)) {
+ too_many = true;
+ } else if (0 < action_count && action_count < lower_bound &&
+ !repeated_action_specified_) {
+ too_many = false;
+ } else {
+ return;
+ }
+
+ ::std::stringstream ss;
+ DescribeLocationTo(&ss);
+ ss << "Too " << (too_many ? "many" : "few")
+ << " actions specified in " << source_text() << "...\n"
+ << "Expected to be ";
+ cardinality().DescribeTo(&ss);
+ ss << ", but has " << (too_many ? "" : "only ")
+ << action_count << " WillOnce()"
+ << (action_count == 1 ? "" : "s");
+ if (repeated_action_specified_) {
+ ss << " and a WillRepeatedly()";
+ }
+ ss << ".";
+ Log(kWarning, ss.str(), -1); // -1 means "don't print stack trace".
+ }
+}
+
+// Implements the .Times() clause.
+void ExpectationBase::UntypedTimes(const Cardinality& a_cardinality) {
+ if (last_clause_ == kTimes) {
+ ExpectSpecProperty(false,
+ ".Times() cannot appear "
+ "more than once in an EXPECT_CALL().");
+ } else {
+ ExpectSpecProperty(last_clause_ < kTimes,
+ ".Times() cannot appear after "
+ ".InSequence(), .WillOnce(), .WillRepeatedly(), "
+ "or .RetiresOnSaturation().");
+ }
+ last_clause_ = kTimes;
+
+ SpecifyCardinality(a_cardinality);
+}
+
+// Points to the implicit sequence introduced by a living InSequence
+// object (if any) in the current thread or NULL.
+GTEST_API_ ThreadLocal<Sequence*> g_gmock_implicit_sequence;
+
+// Reports an uninteresting call (whose description is in msg) in the
+// manner specified by 'reaction'.
+void ReportUninterestingCall(CallReaction reaction, const string& msg) {
+ switch (reaction) {
+ case kAllow:
+ Log(kInfo, msg, 3);
+ break;
+ case kWarn:
+ Log(kWarning, msg, 3);
+ break;
+ default: // FAIL
+ Expect(false, NULL, -1, msg);
+ }
+}
+
+UntypedFunctionMockerBase::UntypedFunctionMockerBase()
+ : mock_obj_(NULL), name_("") {}
+
+UntypedFunctionMockerBase::~UntypedFunctionMockerBase() {}
+
+// Sets the mock object this mock method belongs to, and registers
+// this information in the global mock registry. Will be called
+// whenever an EXPECT_CALL() or ON_CALL() is executed on this mock
+// method.
+void UntypedFunctionMockerBase::RegisterOwner(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ {
+ MutexLock l(&g_gmock_mutex);
+ mock_obj_ = mock_obj;
+ }
+ Mock::Register(mock_obj, this);
+}
+
+// Sets the mock object this mock method belongs to, and sets the name
+// of the mock function. Will be called upon each invocation of this
+// mock function.
+void UntypedFunctionMockerBase::SetOwnerAndName(const void* mock_obj,
+ const char* name)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ // We protect name_ under g_gmock_mutex in case this mock function
+ // is called from two threads concurrently.
+ MutexLock l(&g_gmock_mutex);
+ mock_obj_ = mock_obj;
+ name_ = name;
+}
+
+// Returns the name of the function being mocked. Must be called
+// after RegisterOwner() or SetOwnerAndName() has been called.
+const void* UntypedFunctionMockerBase::MockObject() const
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ const void* mock_obj;
+ {
+ // We protect mock_obj_ under g_gmock_mutex in case this mock
+ // function is called from two threads concurrently.
+ MutexLock l(&g_gmock_mutex);
+ Assert(mock_obj_ != NULL, __FILE__, __LINE__,
+ "MockObject() must not be called before RegisterOwner() or "
+ "SetOwnerAndName() has been called.");
+ mock_obj = mock_obj_;
+ }
+ return mock_obj;
+}
+
+// Returns the name of this mock method. Must be called after
+// SetOwnerAndName() has been called.
+const char* UntypedFunctionMockerBase::Name() const
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ const char* name;
+ {
+ // We protect name_ under g_gmock_mutex in case this mock
+ // function is called from two threads concurrently.
+ MutexLock l(&g_gmock_mutex);
+ Assert(name_ != NULL, __FILE__, __LINE__,
+ "Name() must not be called before SetOwnerAndName() has "
+ "been called.");
+ name = name_;
+ }
+ return name;
+}
+
+// Calculates the result of invoking this mock function with the given
+// arguments, prints it, and returns it. The caller is responsible
+// for deleting the result.
+const UntypedActionResultHolderBase*
+UntypedFunctionMockerBase::UntypedInvokeWith(const void* const untyped_args)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ if (untyped_expectations_.size() == 0) {
+ // No expectation is set on this mock method - we have an
+ // uninteresting call.
+
+ // We must get Google Mock's reaction on uninteresting calls
+ // made on this mock object BEFORE performing the action,
+ // because the action may DELETE the mock object and make the
+ // following expression meaningless.
+ const CallReaction reaction =
+ Mock::GetReactionOnUninterestingCalls(MockObject());
+
+ // True iff we need to print this call's arguments and return
+ // value. This definition must be kept in sync with
+ // the behavior of ReportUninterestingCall().
+ const bool need_to_report_uninteresting_call =
+ // If the user allows this uninteresting call, we print it
+ // only when he wants informational messages.
+ reaction == kAllow ? LogIsVisible(kInfo) :
+ // If the user wants this to be a warning, we print it only
+ // when he wants to see warnings.
+ reaction == kWarn ? LogIsVisible(kWarning) :
+ // Otherwise, the user wants this to be an error, and we
+ // should always print detailed information in the error.
+ true;
+
+ if (!need_to_report_uninteresting_call) {
+ // Perform the action without printing the call information.
+ return this->UntypedPerformDefaultAction(untyped_args, "");
+ }
+
+ // Warns about the uninteresting call.
+ ::std::stringstream ss;
+ this->UntypedDescribeUninterestingCall(untyped_args, &ss);
+
+ // Calculates the function result.
+ const UntypedActionResultHolderBase* const result =
+ this->UntypedPerformDefaultAction(untyped_args, ss.str());
+
+ // Prints the function result.
+ if (result != NULL)
+ result->PrintAsActionResult(&ss);
+
+ ReportUninterestingCall(reaction, ss.str());
+ return result;
+ }
+
+ bool is_excessive = false;
+ ::std::stringstream ss;
+ ::std::stringstream why;
+ ::std::stringstream loc;
+ const void* untyped_action = NULL;
+
+ // The UntypedFindMatchingExpectation() function acquires and
+ // releases g_gmock_mutex.
+ const ExpectationBase* const untyped_expectation =
+ this->UntypedFindMatchingExpectation(
+ untyped_args, &untyped_action, &is_excessive,
+ &ss, &why);
+ const bool found = untyped_expectation != NULL;
+
+ // True iff we need to print the call's arguments and return value.
+ // This definition must be kept in sync with the uses of Expect()
+ // and Log() in this function.
+ const bool need_to_report_call =
+ !found || is_excessive || LogIsVisible(kInfo);
+ if (!need_to_report_call) {
+ // Perform the action without printing the call information.
+ return
+ untyped_action == NULL ?
+ this->UntypedPerformDefaultAction(untyped_args, "") :
+ this->UntypedPerformAction(untyped_action, untyped_args);
+ }
+
+ ss << " Function call: " << Name();
+ this->UntypedPrintArgs(untyped_args, &ss);
+
+ // In case the action deletes a piece of the expectation, we
+ // generate the message beforehand.
+ if (found && !is_excessive) {
+ untyped_expectation->DescribeLocationTo(&loc);
+ }
+
+ const UntypedActionResultHolderBase* const result =
+ untyped_action == NULL ?
+ this->UntypedPerformDefaultAction(untyped_args, ss.str()) :
+ this->UntypedPerformAction(untyped_action, untyped_args);
+ if (result != NULL)
+ result->PrintAsActionResult(&ss);
+ ss << "\n" << why.str();
+
+ if (!found) {
+ // No expectation matches this call - reports a failure.
+ Expect(false, NULL, -1, ss.str());
+ } else if (is_excessive) {
+ // We had an upper-bound violation and the failure message is in ss.
+ Expect(false, untyped_expectation->file(),
+ untyped_expectation->line(), ss.str());
+ } else {
+ // We had an expected call and the matching expectation is
+ // described in ss.
+ Log(kInfo, loc.str() + ss.str(), 2);
+ }
+
+ return result;
+}
+
+// Returns an Expectation object that references and co-owns exp,
+// which must be an expectation on this mock function.
+Expectation UntypedFunctionMockerBase::GetHandleOf(ExpectationBase* exp) {
+ for (UntypedExpectations::const_iterator it =
+ untyped_expectations_.begin();
+ it != untyped_expectations_.end(); ++it) {
+ if (it->get() == exp) {
+ return Expectation(*it);
+ }
+ }
+
+ Assert(false, __FILE__, __LINE__, "Cannot find expectation.");
+ return Expectation();
+ // The above statement is just to make the code compile, and will
+ // never be executed.
+}
+
+// Verifies that all expectations on this mock function have been
+// satisfied. Reports one or more Google Test non-fatal failures
+// and returns false if not.
+bool UntypedFunctionMockerBase::VerifyAndClearExpectationsLocked()
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ bool expectations_met = true;
+ for (UntypedExpectations::const_iterator it =
+ untyped_expectations_.begin();
+ it != untyped_expectations_.end(); ++it) {
+ ExpectationBase* const untyped_expectation = it->get();
+ if (untyped_expectation->IsOverSaturated()) {
+ // There was an upper-bound violation. Since the error was
+ // already reported when it occurred, there is no need to do
+ // anything here.
+ expectations_met = false;
+ } else if (!untyped_expectation->IsSatisfied()) {
+ expectations_met = false;
+ ::std::stringstream ss;
+ ss << "Actual function call count doesn't match "
+ << untyped_expectation->source_text() << "...\n";
+ // No need to show the source file location of the expectation
+ // in the description, as the Expect() call that follows already
+ // takes care of it.
+ untyped_expectation->MaybeDescribeExtraMatcherTo(&ss);
+ untyped_expectation->DescribeCallCountTo(&ss);
+ Expect(false, untyped_expectation->file(),
+ untyped_expectation->line(), ss.str());
+ }
+ }
+
+ // Deleting our expectations may trigger other mock objects to be deleted, for
+ // example if an action contains a reference counted smart pointer to that
+ // mock object, and that is the last reference. So if we delete our
+ // expectations within the context of the global mutex we may deadlock when
+ // this method is called again. Instead, make a copy of the set of
+ // expectations to delete, clear our set within the mutex, and then clear the
+ // copied set outside of it.
+ UntypedExpectations expectations_to_delete;
+ untyped_expectations_.swap(expectations_to_delete);
+
+ g_gmock_mutex.Unlock();
+ expectations_to_delete.clear();
+ g_gmock_mutex.Lock();
+
+ return expectations_met;
+}
+
+} // namespace internal
+
+// Class Mock.
+
+namespace {
+
+typedef std::set<internal::UntypedFunctionMockerBase*> FunctionMockers;
+
+// The current state of a mock object. Such information is needed for
+// detecting leaked mock objects and explicitly verifying a mock's
+// expectations.
+struct MockObjectState {
+ MockObjectState()
+ : first_used_file(NULL), first_used_line(-1), leakable(false) {}
+
+ // Where in the source file an ON_CALL or EXPECT_CALL is first
+ // invoked on this mock object.
+ const char* first_used_file;
+ int first_used_line;
+ ::std::string first_used_test_case;
+ ::std::string first_used_test;
+ bool leakable; // true iff it's OK to leak the object.
+ FunctionMockers function_mockers; // All registered methods of the object.
+};
+
+// A global registry holding the state of all mock objects that are
+// alive. A mock object is added to this registry the first time
+// Mock::AllowLeak(), ON_CALL(), or EXPECT_CALL() is called on it. It
+// is removed from the registry in the mock object's destructor.
+class MockObjectRegistry {
+ public:
+ // Maps a mock object (identified by its address) to its state.
+ typedef std::map<const void*, MockObjectState> StateMap;
+
+ // This destructor will be called when a program exits, after all
+ // tests in it have been run. By then, there should be no mock
+ // object alive. Therefore we report any living object as test
+ // failure, unless the user explicitly asked us to ignore it.
+ ~MockObjectRegistry() {
+ // "using ::std::cout;" doesn't work with Symbian's STLport, where cout is
+ // a macro.
+
+ if (!GMOCK_FLAG(catch_leaked_mocks))
+ return;
+
+ int leaked_count = 0;
+ for (StateMap::const_iterator it = states_.begin(); it != states_.end();
+ ++it) {
+ if (it->second.leakable) // The user said it's fine to leak this object.
+ continue;
+
+ // TODO(wan at google.com): Print the type of the leaked object.
+ // This can help the user identify the leaked object.
+ std::cout << "\n";
+ const MockObjectState& state = it->second;
+ std::cout << internal::FormatFileLocation(state.first_used_file,
+ state.first_used_line);
+ std::cout << " ERROR: this mock object";
+ if (state.first_used_test != "") {
+ std::cout << " (used in test " << state.first_used_test_case << "."
+ << state.first_used_test << ")";
+ }
+ std::cout << " should be deleted but never is. Its address is @"
+ << it->first << ".";
+ leaked_count++;
+ }
+ if (leaked_count > 0) {
+ std::cout << "\nERROR: " << leaked_count
+ << " leaked mock " << (leaked_count == 1 ? "object" : "objects")
+ << " found at program exit.\n";
+ std::cout.flush();
+ ::std::cerr.flush();
+ // RUN_ALL_TESTS() has already returned when this destructor is
+ // called. Therefore we cannot use the normal Google Test
+ // failure reporting mechanism.
+ _exit(1); // We cannot call exit() as it is not reentrant and
+ // may already have been called.
+ }
+ }
+
+ StateMap& states() { return states_; }
+
+ private:
+ StateMap states_;
+};
+
+// Protected by g_gmock_mutex.
+MockObjectRegistry g_mock_object_registry;
+
+// Maps a mock object to the reaction Google Mock should have when an
+// uninteresting method is called. Protected by g_gmock_mutex.
+std::map<const void*, internal::CallReaction> g_uninteresting_call_reaction;
+
+// Sets the reaction Google Mock should have when an uninteresting
+// method of the given mock object is called.
+void SetReactionOnUninterestingCalls(const void* mock_obj,
+ internal::CallReaction reaction)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ internal::MutexLock l(&internal::g_gmock_mutex);
+ g_uninteresting_call_reaction[mock_obj] = reaction;
+}
+
+} // namespace
+
+// Tells Google Mock to allow uninteresting calls on the given mock
+// object.
+void Mock::AllowUninterestingCalls(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ SetReactionOnUninterestingCalls(mock_obj, internal::kAllow);
+}
+
+// Tells Google Mock to warn the user about uninteresting calls on the
+// given mock object.
+void Mock::WarnUninterestingCalls(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ SetReactionOnUninterestingCalls(mock_obj, internal::kWarn);
+}
+
+// Tells Google Mock to fail uninteresting calls on the given mock
+// object.
+void Mock::FailUninterestingCalls(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ SetReactionOnUninterestingCalls(mock_obj, internal::kFail);
+}
+
+// Tells Google Mock the given mock object is being destroyed and its
+// entry in the call-reaction table should be removed.
+void Mock::UnregisterCallReaction(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ internal::MutexLock l(&internal::g_gmock_mutex);
+ g_uninteresting_call_reaction.erase(mock_obj);
+}
+
+// Returns the reaction Google Mock will have on uninteresting calls
+// made on the given mock object.
+internal::CallReaction Mock::GetReactionOnUninterestingCalls(
+ const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ internal::MutexLock l(&internal::g_gmock_mutex);
+ return (g_uninteresting_call_reaction.count(mock_obj) == 0) ?
+ internal::kDefault : g_uninteresting_call_reaction[mock_obj];
+}
+
+// Tells Google Mock to ignore mock_obj when checking for leaked mock
+// objects.
+void Mock::AllowLeak(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ internal::MutexLock l(&internal::g_gmock_mutex);
+ g_mock_object_registry.states()[mock_obj].leakable = true;
+}
+
+// Verifies and clears all expectations on the given mock object. If
+// the expectations aren't satisfied, generates one or more Google
+// Test non-fatal failures and returns false.
+bool Mock::VerifyAndClearExpectations(void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ internal::MutexLock l(&internal::g_gmock_mutex);
+ return VerifyAndClearExpectationsLocked(mock_obj);
+}
+
+// Verifies all expectations on the given mock object and clears its
+// default actions and expectations. Returns true iff the
+// verification was successful.
+bool Mock::VerifyAndClear(void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ internal::MutexLock l(&internal::g_gmock_mutex);
+ ClearDefaultActionsLocked(mock_obj);
+ return VerifyAndClearExpectationsLocked(mock_obj);
+}
+
+// Verifies and clears all expectations on the given mock object. If
+// the expectations aren't satisfied, generates one or more Google
+// Test non-fatal failures and returns false.
+bool Mock::VerifyAndClearExpectationsLocked(void* mock_obj)
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(internal::g_gmock_mutex) {
+ internal::g_gmock_mutex.AssertHeld();
+ if (g_mock_object_registry.states().count(mock_obj) == 0) {
+ // No EXPECT_CALL() was set on the given mock object.
+ return true;
+ }
+
+ // Verifies and clears the expectations on each mock method in the
+ // given mock object.
+ bool expectations_met = true;
+ FunctionMockers& mockers =
+ g_mock_object_registry.states()[mock_obj].function_mockers;
+ for (FunctionMockers::const_iterator it = mockers.begin();
+ it != mockers.end(); ++it) {
+ if (!(*it)->VerifyAndClearExpectationsLocked()) {
+ expectations_met = false;
+ }
+ }
+
+ // We don't clear the content of mockers, as they may still be
+ // needed by ClearDefaultActionsLocked().
+ return expectations_met;
+}
+
+// Registers a mock object and a mock method it owns.
+void Mock::Register(const void* mock_obj,
+ internal::UntypedFunctionMockerBase* mocker)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ internal::MutexLock l(&internal::g_gmock_mutex);
+ g_mock_object_registry.states()[mock_obj].function_mockers.insert(mocker);
+}
+
+// Tells Google Mock where in the source code mock_obj is used in an
+// ON_CALL or EXPECT_CALL. In case mock_obj is leaked, this
+// information helps the user identify which object it is.
+void Mock::RegisterUseByOnCallOrExpectCall(const void* mock_obj,
+ const char* file, int line)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex) {
+ internal::MutexLock l(&internal::g_gmock_mutex);
+ MockObjectState& state = g_mock_object_registry.states()[mock_obj];
+ if (state.first_used_file == NULL) {
+ state.first_used_file = file;
+ state.first_used_line = line;
+ const TestInfo* const test_info =
+ UnitTest::GetInstance()->current_test_info();
+ if (test_info != NULL) {
+ // TODO(wan at google.com): record the test case name when the
+ // ON_CALL or EXPECT_CALL is invoked from SetUpTestCase() or
+ // TearDownTestCase().
+ state.first_used_test_case = test_info->test_case_name();
+ state.first_used_test = test_info->name();
+ }
+ }
+}
+
+// Unregisters a mock method; removes the owning mock object from the
+// registry when the last mock method associated with it has been
+// unregistered. This is called only in the destructor of
+// FunctionMockerBase.
+void Mock::UnregisterLocked(internal::UntypedFunctionMockerBase* mocker)
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(internal::g_gmock_mutex) {
+ internal::g_gmock_mutex.AssertHeld();
+ for (MockObjectRegistry::StateMap::iterator it =
+ g_mock_object_registry.states().begin();
+ it != g_mock_object_registry.states().end(); ++it) {
+ FunctionMockers& mockers = it->second.function_mockers;
+ if (mockers.erase(mocker) > 0) {
+ // mocker was in mockers and has been just removed.
+ if (mockers.empty()) {
+ g_mock_object_registry.states().erase(it);
+ }
+ return;
+ }
+ }
+}
+
+// Clears all ON_CALL()s set on the given mock object.
+void Mock::ClearDefaultActionsLocked(void* mock_obj)
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(internal::g_gmock_mutex) {
+ internal::g_gmock_mutex.AssertHeld();
+
+ if (g_mock_object_registry.states().count(mock_obj) == 0) {
+ // No ON_CALL() was set on the given mock object.
+ return;
+ }
+
+ // Clears the default actions for each mock method in the given mock
+ // object.
+ FunctionMockers& mockers =
+ g_mock_object_registry.states()[mock_obj].function_mockers;
+ for (FunctionMockers::const_iterator it = mockers.begin();
+ it != mockers.end(); ++it) {
+ (*it)->ClearDefaultActionsLocked();
+ }
+
+ // We don't clear the content of mockers, as they may still be
+ // needed by VerifyAndClearExpectationsLocked().
+}
+
+Expectation::Expectation() {}
+
+Expectation::Expectation(
+ const internal::linked_ptr<internal::ExpectationBase>& an_expectation_base)
+ : expectation_base_(an_expectation_base) {}
+
+Expectation::~Expectation() {}
+
+// Adds an expectation to a sequence.
+void Sequence::AddExpectation(const Expectation& expectation) const {
+ if (*last_expectation_ != expectation) {
+ if (last_expectation_->expectation_base() != NULL) {
+ expectation.expectation_base()->immediate_prerequisites_
+ += *last_expectation_;
+ }
+ *last_expectation_ = expectation;
+ }
+}
+
+// Creates the implicit sequence if there isn't one.
+InSequence::InSequence() {
+ if (internal::g_gmock_implicit_sequence.get() == NULL) {
+ internal::g_gmock_implicit_sequence.set(new Sequence);
+ sequence_created_ = true;
+ } else {
+ sequence_created_ = false;
+ }
+}
+
+// Deletes the implicit sequence if it was created by the constructor
+// of this object.
+InSequence::~InSequence() {
+ if (sequence_created_) {
+ delete internal::g_gmock_implicit_sequence.get();
+ internal::g_gmock_implicit_sequence.set(NULL);
+ }
+}
+
+} // namespace testing
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+
+namespace testing {
+
+// TODO(wan at google.com): support using environment variables to
+// control the flag values, like what Google Test does.
+
+GMOCK_DEFINE_bool_(catch_leaked_mocks, true,
+ "true iff Google Mock should report leaked mock objects "
+ "as failures.");
+
+GMOCK_DEFINE_string_(verbose, internal::kWarningVerbosity,
+ "Controls how verbose Google Mock's output is."
+ " Valid values:\n"
+ " info - prints all messages.\n"
+ " warning - prints warnings and errors.\n"
+ " error - prints errors only.");
+
+namespace internal {
+
+// Parses a string as a command line flag. The string should have the
+// format "--gmock_flag=value". When def_optional is true, the
+// "=value" part can be omitted.
+//
+// Returns the value of the flag, or NULL if the parsing failed.
+static const char* ParseGoogleMockFlagValue(const char* str,
+ const char* flag,
+ bool def_optional) {
+ // str and flag must not be NULL.
+ if (str == NULL || flag == NULL) return NULL;
+
+ // The flag must start with "--gmock_".
+ const std::string flag_str = std::string("--gmock_") + flag;
+ const size_t flag_len = flag_str.length();
+ if (strncmp(str, flag_str.c_str(), flag_len) != 0) return NULL;
+
+ // Skips the flag name.
+ const char* flag_end = str + flag_len;
+
+ // When def_optional is true, it's OK to not have a "=value" part.
+ if (def_optional && (flag_end[0] == '\0')) {
+ return flag_end;
+ }
+
+ // If def_optional is true and there are more characters after the
+ // flag name, or if def_optional is false, there must be a '=' after
+ // the flag name.
+ if (flag_end[0] != '=') return NULL;
+
+ // Returns the string after "=".
+ return flag_end + 1;
+}
+
+// Parses a string for a Google Mock bool flag, in the form of
+// "--gmock_flag=value".
+//
+// On success, stores the value of the flag in *value, and returns
+// true. On failure, returns false without changing *value.
+static bool ParseGoogleMockBoolFlag(const char* str, const char* flag,
+ bool* value) {
+ // Gets the value of the flag as a string.
+ const char* const value_str = ParseGoogleMockFlagValue(str, flag, true);
+
+ // Aborts if the parsing failed.
+ if (value_str == NULL) return false;
+
+ // Converts the string value to a bool.
+ *value = !(*value_str == '0' || *value_str == 'f' || *value_str == 'F');
+ return true;
+}
+
+// Parses a string for a Google Mock string flag, in the form of
+// "--gmock_flag=value".
+//
+// On success, stores the value of the flag in *value, and returns
+// true. On failure, returns false without changing *value.
+static bool ParseGoogleMockStringFlag(const char* str, const char* flag,
+ std::string* value) {
+ // Gets the value of the flag as a string.
+ const char* const value_str = ParseGoogleMockFlagValue(str, flag, false);
+
+ // Aborts if the parsing failed.
+ if (value_str == NULL) return false;
+
+ // Sets *value to the value of the flag.
+ *value = value_str;
+ return true;
+}
+
+// The internal implementation of InitGoogleMock().
+//
+// The type parameter CharType can be instantiated to either char or
+// wchar_t.
+template <typename CharType>
+void InitGoogleMockImpl(int* argc, CharType** argv) {
+ // Makes sure Google Test is initialized. InitGoogleTest() is
+ // idempotent, so it's fine if the user has already called it.
+ InitGoogleTest(argc, argv);
+ if (*argc <= 0) return;
+
+ for (int i = 1; i != *argc; i++) {
+ const std::string arg_string = StreamableToString(argv[i]);
+ const char* const arg = arg_string.c_str();
+
+ // Do we see a Google Mock flag?
+ if (ParseGoogleMockBoolFlag(arg, "catch_leaked_mocks",
+ &GMOCK_FLAG(catch_leaked_mocks)) ||
+ ParseGoogleMockStringFlag(arg, "verbose", &GMOCK_FLAG(verbose))) {
+ // Yes. Shift the remainder of the argv list left by one. Note
+ // that argv has (*argc + 1) elements, the last one always being
+ // NULL. The following loop moves the trailing NULL element as
+ // well.
+ for (int j = i; j != *argc; j++) {
+ argv[j] = argv[j + 1];
+ }
+
+ // Decrements the argument count.
+ (*argc)--;
+
+ // We also need to decrement the iterator as we just removed
+ // an element.
+ i--;
+ }
+ }
+}
+
+} // namespace internal
+
+// Initializes Google Mock. This must be called before running the
+// tests. In particular, it parses a command line for the flags that
+// Google Mock recognizes. Whenever a Google Mock flag is seen, it is
+// removed from argv, and *argc is decremented.
+//
+// No value is returned. Instead, the Google Mock flag variables are
+// updated.
+//
+// Since Google Test is needed for Google Mock to work, this function
+// also initializes Google Test and parses its flags, if that hasn't
+// been done.
+GTEST_API_ void InitGoogleMock(int* argc, char** argv) {
+ internal::InitGoogleMockImpl(argc, argv);
+}
+
+// This overloaded version can be used in Windows programs compiled in
+// UNICODE mode.
+GTEST_API_ void InitGoogleMock(int* argc, wchar_t** argv) {
+ internal::InitGoogleMockImpl(argc, argv);
+}
+
+} // namespace testing
diff --git a/third-party/gmock-1.7.0/gmock/gmock.h b/third-party/gmock-1.7.0/gmock/gmock.h
new file mode 100644
index 0000000..e8dd7fc
--- /dev/null
+++ b/third-party/gmock-1.7.0/gmock/gmock.h
@@ -0,0 +1,14198 @@
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This is the main header file a user should include.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_H_
+
+// This file implements the following syntax:
+//
+// ON_CALL(mock_object.Method(...))
+// .With(...) ?
+// .WillByDefault(...);
+//
+// where With() is optional and WillByDefault() must appear exactly
+// once.
+//
+// EXPECT_CALL(mock_object.Method(...))
+// .With(...) ?
+// .Times(...) ?
+// .InSequence(...) *
+// .WillOnce(...) *
+// .WillRepeatedly(...) ?
+// .RetiresOnSaturation() ? ;
+//
+// where all clauses are optional and WillOnce() can be repeated.
+
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements some commonly used actions.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_ACTIONS_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_ACTIONS_H_
+
+#ifndef _WIN32_WCE
+# include <errno.h>
+#endif
+
+#include <algorithm>
+#include <string>
+
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file defines some utilities useful for implementing Google
+// Mock. They are subject to change without notice, so please DO NOT
+// USE THEM IN USER CODE.
+
+#ifndef GMOCK_INCLUDE_GMOCK_INTERNAL_GMOCK_INTERNAL_UTILS_H_
+#define GMOCK_INCLUDE_GMOCK_INTERNAL_GMOCK_INTERNAL_UTILS_H_
+
+#include <stdio.h>
+#include <ostream> // NOLINT
+#include <string>
+
+// This file was GENERATED by command:
+// pump.py gmock-generated-internal-utils.h.pump
+// DO NOT EDIT BY HAND!!!
+
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file contains template meta-programming utility classes needed
+// for implementing Google Mock.
+
+#ifndef GMOCK_INCLUDE_GMOCK_INTERNAL_GMOCK_GENERATED_INTERNAL_UTILS_H_
+#define GMOCK_INCLUDE_GMOCK_INTERNAL_GMOCK_GENERATED_INTERNAL_UTILS_H_
+
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: vadimb at google.com (Vadim Berman)
+//
+// Low-level types and utilities for porting Google Mock to various
+// platforms. They are subject to change without notice. DO NOT USE
+// THEM IN USER CODE.
+
+#ifndef GMOCK_INCLUDE_GMOCK_INTERNAL_GMOCK_PORT_H_
+#define GMOCK_INCLUDE_GMOCK_INTERNAL_GMOCK_PORT_H_
+
+#include <assert.h>
+#include <stdlib.h>
+#include <iostream>
+
+// Most of the types needed for porting Google Mock are also required
+// for Google Test and are defined in gtest-port.h.
+#include "gtest/gtest.h"
+
+// To avoid conditional compilation everywhere, we make it
+// gmock-port.h's responsibility to #include the header implementing
+// tr1/tuple. gmock-port.h does this via gtest-port.h, which is
+// guaranteed to pull in the tuple header.
+
+// For MS Visual C++, check the compiler version. At least VS 2003 is
+// required to compile Google Mock.
+#if defined(_MSC_VER) && _MSC_VER < 1310
+# error "At least Visual C++ 2003 (7.1) is required to compile Google Mock."
+#endif
+
+// Macro for referencing flags. This is public as we want the user to
+// use this syntax to reference Google Mock flags.
+#define GMOCK_FLAG(name) FLAGS_gmock_##name
+
+// Macros for declaring flags.
+#define GMOCK_DECLARE_bool_(name) extern GTEST_API_ bool GMOCK_FLAG(name)
+#define GMOCK_DECLARE_int32_(name) \
+ extern GTEST_API_ ::testing::internal::Int32 GMOCK_FLAG(name)
+#define GMOCK_DECLARE_string_(name) \
+ extern GTEST_API_ ::std::string GMOCK_FLAG(name)
+
+// Macros for defining flags.
+#define GMOCK_DEFINE_bool_(name, default_val, doc) \
+ GTEST_API_ bool GMOCK_FLAG(name) = (default_val)
+#define GMOCK_DEFINE_int32_(name, default_val, doc) \
+ GTEST_API_ ::testing::internal::Int32 GMOCK_FLAG(name) = (default_val)
+#define GMOCK_DEFINE_string_(name, default_val, doc) \
+ GTEST_API_ ::std::string GMOCK_FLAG(name) = (default_val)
+
+#endif // GMOCK_INCLUDE_GMOCK_INTERNAL_GMOCK_PORT_H_
+
+namespace testing {
+
+template <typename T>
+class Matcher;
+
+namespace internal {
+
+// An IgnoredValue object can be implicitly constructed from ANY value.
+// This is used in implementing the IgnoreResult(a) action.
+class IgnoredValue {
+ public:
+ // This constructor template allows any value to be implicitly
+ // converted to IgnoredValue. The object has no data member and
+ // doesn't try to remember anything about the argument. We
+ // deliberately omit the 'explicit' keyword in order to allow the
+ // conversion to be implicit.
+ template <typename T>
+ IgnoredValue(const T& /* ignored */) {} // NOLINT(runtime/explicit)
+};
+
+// MatcherTuple<T>::type is a tuple type where each field is a Matcher
+// for the corresponding field in tuple type T.
+template <typename Tuple>
+struct MatcherTuple;
+
+template <>
+struct MatcherTuple< ::std::tr1::tuple<> > {
+ typedef ::std::tr1::tuple< > type;
+};
+
+template <typename A1>
+struct MatcherTuple< ::std::tr1::tuple<A1> > {
+ typedef ::std::tr1::tuple<Matcher<A1> > type;
+};
+
+template <typename A1, typename A2>
+struct MatcherTuple< ::std::tr1::tuple<A1, A2> > {
+ typedef ::std::tr1::tuple<Matcher<A1>, Matcher<A2> > type;
+};
+
+template <typename A1, typename A2, typename A3>
+struct MatcherTuple< ::std::tr1::tuple<A1, A2, A3> > {
+ typedef ::std::tr1::tuple<Matcher<A1>, Matcher<A2>, Matcher<A3> > type;
+};
+
+template <typename A1, typename A2, typename A3, typename A4>
+struct MatcherTuple< ::std::tr1::tuple<A1, A2, A3, A4> > {
+ typedef ::std::tr1::tuple<Matcher<A1>, Matcher<A2>, Matcher<A3>,
+ Matcher<A4> > type;
+};
+
+template <typename A1, typename A2, typename A3, typename A4, typename A5>
+struct MatcherTuple< ::std::tr1::tuple<A1, A2, A3, A4, A5> > {
+ typedef ::std::tr1::tuple<Matcher<A1>, Matcher<A2>, Matcher<A3>, Matcher<A4>,
+ Matcher<A5> > type;
+};
+
+template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6>
+struct MatcherTuple< ::std::tr1::tuple<A1, A2, A3, A4, A5, A6> > {
+ typedef ::std::tr1::tuple<Matcher<A1>, Matcher<A2>, Matcher<A3>, Matcher<A4>,
+ Matcher<A5>, Matcher<A6> > type;
+};
+
+template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7>
+struct MatcherTuple< ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7> > {
+ typedef ::std::tr1::tuple<Matcher<A1>, Matcher<A2>, Matcher<A3>, Matcher<A4>,
+ Matcher<A5>, Matcher<A6>, Matcher<A7> > type;
+};
+
+template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8>
+struct MatcherTuple< ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8> > {
+ typedef ::std::tr1::tuple<Matcher<A1>, Matcher<A2>, Matcher<A3>, Matcher<A4>,
+ Matcher<A5>, Matcher<A6>, Matcher<A7>, Matcher<A8> > type;
+};
+
+template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8, typename A9>
+struct MatcherTuple< ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8, A9> > {
+ typedef ::std::tr1::tuple<Matcher<A1>, Matcher<A2>, Matcher<A3>, Matcher<A4>,
+ Matcher<A5>, Matcher<A6>, Matcher<A7>, Matcher<A8>, Matcher<A9> > type;
+};
+
+template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8, typename A9, typename A10>
+struct MatcherTuple< ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8, A9,
+ A10> > {
+ typedef ::std::tr1::tuple<Matcher<A1>, Matcher<A2>, Matcher<A3>, Matcher<A4>,
+ Matcher<A5>, Matcher<A6>, Matcher<A7>, Matcher<A8>, Matcher<A9>,
+ Matcher<A10> > type;
+};
+
+// Template struct Function<F>, where F must be a function type, contains
+// the following typedefs:
+//
+// Result: the function's return type.
+// ArgumentN: the type of the N-th argument, where N starts with 1.
+// ArgumentTuple: the tuple type consisting of all parameters of F.
+// ArgumentMatcherTuple: the tuple type consisting of Matchers for all
+// parameters of F.
+// MakeResultVoid: the function type obtained by substituting void
+// for the return type of F.
+// MakeResultIgnoredValue:
+// the function type obtained by substituting Something
+// for the return type of F.
+template <typename F>
+struct Function;
+
+template <typename R>
+struct Function<R()> {
+ typedef R Result;
+ typedef ::std::tr1::tuple<> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid();
+ typedef IgnoredValue MakeResultIgnoredValue();
+};
+
+template <typename R, typename A1>
+struct Function<R(A1)>
+ : Function<R()> {
+ typedef A1 Argument1;
+ typedef ::std::tr1::tuple<A1> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1);
+ typedef IgnoredValue MakeResultIgnoredValue(A1);
+};
+
+template <typename R, typename A1, typename A2>
+struct Function<R(A1, A2)>
+ : Function<R(A1)> {
+ typedef A2 Argument2;
+ typedef ::std::tr1::tuple<A1, A2> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1, A2);
+ typedef IgnoredValue MakeResultIgnoredValue(A1, A2);
+};
+
+template <typename R, typename A1, typename A2, typename A3>
+struct Function<R(A1, A2, A3)>
+ : Function<R(A1, A2)> {
+ typedef A3 Argument3;
+ typedef ::std::tr1::tuple<A1, A2, A3> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1, A2, A3);
+ typedef IgnoredValue MakeResultIgnoredValue(A1, A2, A3);
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4>
+struct Function<R(A1, A2, A3, A4)>
+ : Function<R(A1, A2, A3)> {
+ typedef A4 Argument4;
+ typedef ::std::tr1::tuple<A1, A2, A3, A4> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1, A2, A3, A4);
+ typedef IgnoredValue MakeResultIgnoredValue(A1, A2, A3, A4);
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5>
+struct Function<R(A1, A2, A3, A4, A5)>
+ : Function<R(A1, A2, A3, A4)> {
+ typedef A5 Argument5;
+ typedef ::std::tr1::tuple<A1, A2, A3, A4, A5> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1, A2, A3, A4, A5);
+ typedef IgnoredValue MakeResultIgnoredValue(A1, A2, A3, A4, A5);
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6>
+struct Function<R(A1, A2, A3, A4, A5, A6)>
+ : Function<R(A1, A2, A3, A4, A5)> {
+ typedef A6 Argument6;
+ typedef ::std::tr1::tuple<A1, A2, A3, A4, A5, A6> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1, A2, A3, A4, A5, A6);
+ typedef IgnoredValue MakeResultIgnoredValue(A1, A2, A3, A4, A5, A6);
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7>
+struct Function<R(A1, A2, A3, A4, A5, A6, A7)>
+ : Function<R(A1, A2, A3, A4, A5, A6)> {
+ typedef A7 Argument7;
+ typedef ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1, A2, A3, A4, A5, A6, A7);
+ typedef IgnoredValue MakeResultIgnoredValue(A1, A2, A3, A4, A5, A6, A7);
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8>
+struct Function<R(A1, A2, A3, A4, A5, A6, A7, A8)>
+ : Function<R(A1, A2, A3, A4, A5, A6, A7)> {
+ typedef A8 Argument8;
+ typedef ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1, A2, A3, A4, A5, A6, A7, A8);
+ typedef IgnoredValue MakeResultIgnoredValue(A1, A2, A3, A4, A5, A6, A7, A8);
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8, typename A9>
+struct Function<R(A1, A2, A3, A4, A5, A6, A7, A8, A9)>
+ : Function<R(A1, A2, A3, A4, A5, A6, A7, A8)> {
+ typedef A9 Argument9;
+ typedef ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8, A9> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1, A2, A3, A4, A5, A6, A7, A8, A9);
+ typedef IgnoredValue MakeResultIgnoredValue(A1, A2, A3, A4, A5, A6, A7, A8,
+ A9);
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8, typename A9,
+ typename A10>
+struct Function<R(A1, A2, A3, A4, A5, A6, A7, A8, A9, A10)>
+ : Function<R(A1, A2, A3, A4, A5, A6, A7, A8, A9)> {
+ typedef A10 Argument10;
+ typedef ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8, A9,
+ A10> ArgumentTuple;
+ typedef typename MatcherTuple<ArgumentTuple>::type ArgumentMatcherTuple;
+ typedef void MakeResultVoid(A1, A2, A3, A4, A5, A6, A7, A8, A9, A10);
+ typedef IgnoredValue MakeResultIgnoredValue(A1, A2, A3, A4, A5, A6, A7, A8,
+ A9, A10);
+};
+
+} // namespace internal
+
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_INTERNAL_GMOCK_GENERATED_INTERNAL_UTILS_H_
+
+namespace testing {
+namespace internal {
+
+// Converts an identifier name to a space-separated list of lower-case
+// words. Each maximum substring of the form [A-Za-z][a-z]*|\d+ is
+// treated as one word. For example, both "FooBar123" and
+// "foo_bar_123" are converted to "foo bar 123".
+GTEST_API_ string ConvertIdentifierNameToWords(const char* id_name);
+
+// PointeeOf<Pointer>::type is the type of a value pointed to by a
+// Pointer, which can be either a smart pointer or a raw pointer. The
+// following default implementation is for the case where Pointer is a
+// smart pointer.
+template <typename Pointer>
+struct PointeeOf {
+ // Smart pointer classes define type element_type as the type of
+ // their pointees.
+ typedef typename Pointer::element_type type;
+};
+// This specialization is for the raw pointer case.
+template <typename T>
+struct PointeeOf<T*> { typedef T type; }; // NOLINT
+
+// GetRawPointer(p) returns the raw pointer underlying p when p is a
+// smart pointer, or returns p itself when p is already a raw pointer.
+// The following default implementation is for the smart pointer case.
+template <typename Pointer>
+inline const typename Pointer::element_type* GetRawPointer(const Pointer& p) {
+ return p.get();
+}
+// This overloaded version is for the raw pointer case.
+template <typename Element>
+inline Element* GetRawPointer(Element* p) { return p; }
+
+// This comparator allows linked_ptr to be stored in sets.
+template <typename T>
+struct LinkedPtrLessThan {
+ bool operator()(const ::testing::internal::linked_ptr<T>& lhs,
+ const ::testing::internal::linked_ptr<T>& rhs) const {
+ return lhs.get() < rhs.get();
+ }
+};
+
+// Symbian compilation can be done with wchar_t being either a native
+// type or a typedef. Using Google Mock with OpenC without wchar_t
+// should require the definition of _STLP_NO_WCHAR_T.
+//
+// MSVC treats wchar_t as a native type usually, but treats it as the
+// same as unsigned short when the compiler option /Zc:wchar_t- is
+// specified. It defines _NATIVE_WCHAR_T_DEFINED symbol when wchar_t
+// is a native type.
+#if (GTEST_OS_SYMBIAN && defined(_STLP_NO_WCHAR_T)) || \
+ (defined(_MSC_VER) && !defined(_NATIVE_WCHAR_T_DEFINED))
+// wchar_t is a typedef.
+#else
+# define GMOCK_WCHAR_T_IS_NATIVE_ 1
+#endif
+
+// signed wchar_t and unsigned wchar_t are NOT in the C++ standard.
+// Using them is a bad practice and not portable. So DON'T use them.
+//
+// Still, Google Mock is designed to work even if the user uses signed
+// wchar_t or unsigned wchar_t (obviously, assuming the compiler
+// supports them).
+//
+// To gcc,
+// wchar_t == signed wchar_t != unsigned wchar_t == unsigned int
+#ifdef __GNUC__
+// signed/unsigned wchar_t are valid types.
+# define GMOCK_HAS_SIGNED_WCHAR_T_ 1
+#endif
+
+// In what follows, we use the term "kind" to indicate whether a type
+// is bool, an integer type (excluding bool), a floating-point type,
+// or none of them. This categorization is useful for determining
+// when a matcher argument type can be safely converted to another
+// type in the implementation of SafeMatcherCast.
+enum TypeKind {
+ kBool, kInteger, kFloatingPoint, kOther
+};
+
+// KindOf<T>::value is the kind of type T.
+template <typename T> struct KindOf {
+ enum { value = kOther }; // The default kind.
+};
+
+// This macro declares that the kind of 'type' is 'kind'.
+#define GMOCK_DECLARE_KIND_(type, kind) \
+ template <> struct KindOf<type> { enum { value = kind }; }
+
+GMOCK_DECLARE_KIND_(bool, kBool);
+
+// All standard integer types.
+GMOCK_DECLARE_KIND_(char, kInteger);
+GMOCK_DECLARE_KIND_(signed char, kInteger);
+GMOCK_DECLARE_KIND_(unsigned char, kInteger);
+GMOCK_DECLARE_KIND_(short, kInteger); // NOLINT
+GMOCK_DECLARE_KIND_(unsigned short, kInteger); // NOLINT
+GMOCK_DECLARE_KIND_(int, kInteger);
+GMOCK_DECLARE_KIND_(unsigned int, kInteger);
+GMOCK_DECLARE_KIND_(long, kInteger); // NOLINT
+GMOCK_DECLARE_KIND_(unsigned long, kInteger); // NOLINT
+
+#if GMOCK_WCHAR_T_IS_NATIVE_
+GMOCK_DECLARE_KIND_(wchar_t, kInteger);
+#endif
+
+// Non-standard integer types.
+GMOCK_DECLARE_KIND_(Int64, kInteger);
+GMOCK_DECLARE_KIND_(UInt64, kInteger);
+
+// All standard floating-point types.
+GMOCK_DECLARE_KIND_(float, kFloatingPoint);
+GMOCK_DECLARE_KIND_(double, kFloatingPoint);
+GMOCK_DECLARE_KIND_(long double, kFloatingPoint);
+
+#undef GMOCK_DECLARE_KIND_
+
+// Evaluates to the kind of 'type'.
+#define GMOCK_KIND_OF_(type) \
+ static_cast< ::testing::internal::TypeKind>( \
+ ::testing::internal::KindOf<type>::value)
+
+// Evaluates to true iff integer type T is signed.
+#define GMOCK_IS_SIGNED_(T) (static_cast<T>(-1) < 0)
+
+// LosslessArithmeticConvertibleImpl<kFromKind, From, kToKind, To>::value
+// is true iff arithmetic type From can be losslessly converted to
+// arithmetic type To.
+//
+// It's the user's responsibility to ensure that both From and To are
+// raw (i.e. has no CV modifier, is not a pointer, and is not a
+// reference) built-in arithmetic types, kFromKind is the kind of
+// From, and kToKind is the kind of To; the value is
+// implementation-defined when the above pre-condition is violated.
+template <TypeKind kFromKind, typename From, TypeKind kToKind, typename To>
+struct LosslessArithmeticConvertibleImpl : public false_type {};
+
+// Converting bool to bool is lossless.
+template <>
+struct LosslessArithmeticConvertibleImpl<kBool, bool, kBool, bool>
+ : public true_type {}; // NOLINT
+
+// Converting bool to any integer type is lossless.
+template <typename To>
+struct LosslessArithmeticConvertibleImpl<kBool, bool, kInteger, To>
+ : public true_type {}; // NOLINT
+
+// Converting bool to any floating-point type is lossless.
+template <typename To>
+struct LosslessArithmeticConvertibleImpl<kBool, bool, kFloatingPoint, To>
+ : public true_type {}; // NOLINT
+
+// Converting an integer to bool is lossy.
+template <typename From>
+struct LosslessArithmeticConvertibleImpl<kInteger, From, kBool, bool>
+ : public false_type {}; // NOLINT
+
+// Converting an integer to another non-bool integer is lossless iff
+// the target type's range encloses the source type's range.
+template <typename From, typename To>
+struct LosslessArithmeticConvertibleImpl<kInteger, From, kInteger, To>
+ : public bool_constant<
+ // When converting from a smaller size to a larger size, we are
+ // fine as long as we are not converting from signed to unsigned.
+ ((sizeof(From) < sizeof(To)) &&
+ (!GMOCK_IS_SIGNED_(From) || GMOCK_IS_SIGNED_(To))) ||
+ // When converting between the same size, the signedness must match.
+ ((sizeof(From) == sizeof(To)) &&
+ (GMOCK_IS_SIGNED_(From) == GMOCK_IS_SIGNED_(To)))> {}; // NOLINT
+
+#undef GMOCK_IS_SIGNED_
+
+// Converting an integer to a floating-point type may be lossy, since
+// the format of a floating-point number is implementation-defined.
+template <typename From, typename To>
+struct LosslessArithmeticConvertibleImpl<kInteger, From, kFloatingPoint, To>
+ : public false_type {}; // NOLINT
+
+// Converting a floating-point to bool is lossy.
+template <typename From>
+struct LosslessArithmeticConvertibleImpl<kFloatingPoint, From, kBool, bool>
+ : public false_type {}; // NOLINT
+
+// Converting a floating-point to an integer is lossy.
+template <typename From, typename To>
+struct LosslessArithmeticConvertibleImpl<kFloatingPoint, From, kInteger, To>
+ : public false_type {}; // NOLINT
+
+// Converting a floating-point to another floating-point is lossless
+// iff the target type is at least as big as the source type.
+template <typename From, typename To>
+struct LosslessArithmeticConvertibleImpl<
+ kFloatingPoint, From, kFloatingPoint, To>
+ : public bool_constant<sizeof(From) <= sizeof(To)> {}; // NOLINT
+
+// LosslessArithmeticConvertible<From, To>::value is true iff arithmetic
+// type From can be losslessly converted to arithmetic type To.
+//
+// It's the user's responsibility to ensure that both From and To are
+// raw (i.e. has no CV modifier, is not a pointer, and is not a
+// reference) built-in arithmetic types; the value is
+// implementation-defined when the above pre-condition is violated.
+template <typename From, typename To>
+struct LosslessArithmeticConvertible
+ : public LosslessArithmeticConvertibleImpl<
+ GMOCK_KIND_OF_(From), From, GMOCK_KIND_OF_(To), To> {}; // NOLINT
+
+// This interface knows how to report a Google Mock failure (either
+// non-fatal or fatal).
+class FailureReporterInterface {
+ public:
+ // The type of a failure (either non-fatal or fatal).
+ enum FailureType {
+ kNonfatal, kFatal
+ };
+
+ virtual ~FailureReporterInterface() {}
+
+ // Reports a failure that occurred at the given source file location.
+ virtual void ReportFailure(FailureType type, const char* file, int line,
+ const string& message) = 0;
+};
+
+// Returns the failure reporter used by Google Mock.
+GTEST_API_ FailureReporterInterface* GetFailureReporter();
+
+// Asserts that condition is true; aborts the process with the given
+// message if condition is false. We cannot use LOG(FATAL) or CHECK()
+// as Google Mock might be used to mock the log sink itself. We
+// inline this function to prevent it from showing up in the stack
+// trace.
+inline void Assert(bool condition, const char* file, int line,
+ const string& msg) {
+ if (!condition) {
+ GetFailureReporter()->ReportFailure(FailureReporterInterface::kFatal,
+ file, line, msg);
+ }
+}
+inline void Assert(bool condition, const char* file, int line) {
+ Assert(condition, file, line, "Assertion failed.");
+}
+
+// Verifies that condition is true; generates a non-fatal failure if
+// condition is false.
+inline void Expect(bool condition, const char* file, int line,
+ const string& msg) {
+ if (!condition) {
+ GetFailureReporter()->ReportFailure(FailureReporterInterface::kNonfatal,
+ file, line, msg);
+ }
+}
+inline void Expect(bool condition, const char* file, int line) {
+ Expect(condition, file, line, "Expectation failed.");
+}
+
+// Severity level of a log.
+enum LogSeverity {
+ kInfo = 0,
+ kWarning = 1
+};
+
+// Valid values for the --gmock_verbose flag.
+
+// All logs (informational and warnings) are printed.
+const char kInfoVerbosity[] = "info";
+// Only warnings are printed.
+const char kWarningVerbosity[] = "warning";
+// No logs are printed.
+const char kErrorVerbosity[] = "error";
+
+// Returns true iff a log with the given severity is visible according
+// to the --gmock_verbose flag.
+GTEST_API_ bool LogIsVisible(LogSeverity severity);
+
+// Prints the given message to stdout iff 'severity' >= the level
+// specified by the --gmock_verbose flag. If stack_frames_to_skip >=
+// 0, also prints the stack trace excluding the top
+// stack_frames_to_skip frames. In opt mode, any positive
+// stack_frames_to_skip is treated as 0, since we don't know which
+// function calls will be inlined by the compiler and need to be
+// conservative.
+GTEST_API_ void Log(LogSeverity severity,
+ const string& message,
+ int stack_frames_to_skip);
+
+// TODO(wan at google.com): group all type utilities together.
+
+// Type traits.
+
+// is_reference<T>::value is non-zero iff T is a reference type.
+template <typename T> struct is_reference : public false_type {};
+template <typename T> struct is_reference<T&> : public true_type {};
+
+// type_equals<T1, T2>::value is non-zero iff T1 and T2 are the same type.
+template <typename T1, typename T2> struct type_equals : public false_type {};
+template <typename T> struct type_equals<T, T> : public true_type {};
+
+// remove_reference<T>::type removes the reference from type T, if any.
+template <typename T> struct remove_reference { typedef T type; }; // NOLINT
+template <typename T> struct remove_reference<T&> { typedef T type; }; // NOLINT
+
+// DecayArray<T>::type turns an array type U[N] to const U* and preserves
+// other types. Useful for saving a copy of a function argument.
+template <typename T> struct DecayArray { typedef T type; }; // NOLINT
+template <typename T, size_t N> struct DecayArray<T[N]> {
+ typedef const T* type;
+};
+// Sometimes people use arrays whose size is not available at the use site
+// (e.g. extern const char kNamePrefix[]). This specialization covers that
+// case.
+template <typename T> struct DecayArray<T[]> {
+ typedef const T* type;
+};
+
+// Invalid<T>() returns an invalid value of type T. This is useful
+// when a value of type T is needed for compilation, but the statement
+// will not really be executed (or we don't care if the statement
+// crashes).
+template <typename T>
+inline T Invalid() {
+ return const_cast<typename remove_reference<T>::type&>(
+ *static_cast<volatile typename remove_reference<T>::type*>(NULL));
+}
+template <>
+inline void Invalid<void>() {}
+
+// Given a raw type (i.e. having no top-level reference or const
+// modifier) RawContainer that's either an STL-style container or a
+// native array, class StlContainerView<RawContainer> has the
+// following members:
+//
+// - type is a type that provides an STL-style container view to
+// (i.e. implements the STL container concept for) RawContainer;
+// - const_reference is a type that provides a reference to a const
+// RawContainer;
+// - ConstReference(raw_container) returns a const reference to an STL-style
+// container view to raw_container, which is a RawContainer.
+// - Copy(raw_container) returns an STL-style container view of a
+// copy of raw_container, which is a RawContainer.
+//
+// This generic version is used when RawContainer itself is already an
+// STL-style container.
+template <class RawContainer>
+class StlContainerView {
+ public:
+ typedef RawContainer type;
+ typedef const type& const_reference;
+
+ static const_reference ConstReference(const RawContainer& container) {
+ // Ensures that RawContainer is not a const type.
+ testing::StaticAssertTypeEq<RawContainer,
+ GTEST_REMOVE_CONST_(RawContainer)>();
+ return container;
+ }
+ static type Copy(const RawContainer& container) { return container; }
+};
+
+// This specialization is used when RawContainer is a native array type.
+template <typename Element, size_t N>
+class StlContainerView<Element[N]> {
+ public:
+ typedef GTEST_REMOVE_CONST_(Element) RawElement;
+ typedef internal::NativeArray<RawElement> type;
+ // NativeArray<T> can represent a native array either by value or by
+ // reference (selected by a constructor argument), so 'const type'
+ // can be used to reference a const native array. We cannot
+ // 'typedef const type& const_reference' here, as that would mean
+ // ConstReference() has to return a reference to a local variable.
+ typedef const type const_reference;
+
+ static const_reference ConstReference(const Element (&array)[N]) {
+ // Ensures that Element is not a const type.
+ testing::StaticAssertTypeEq<Element, RawElement>();
+#if GTEST_OS_SYMBIAN
+ // The Nokia Symbian compiler confuses itself in template instantiation
+ // for this call without the cast to Element*:
+ // function call '[testing::internal::NativeArray<char *>].NativeArray(
+ // {lval} const char *[4], long, testing::internal::RelationToSource)'
+ // does not match
+ // 'testing::internal::NativeArray<char *>::NativeArray(
+ // char *const *, unsigned int, testing::internal::RelationToSource)'
+ // (instantiating: 'testing::internal::ContainsMatcherImpl
+ // <const char * (&)[4]>::Matches(const char * (&)[4]) const')
+ // (instantiating: 'testing::internal::StlContainerView<char *[4]>::
+ // ConstReference(const char * (&)[4])')
+ // (and though the N parameter type is mismatched in the above explicit
+ // conversion of it doesn't help - only the conversion of the array).
+ return type(const_cast<Element*>(&array[0]), N, kReference);
+#else
+ return type(array, N, kReference);
+#endif // GTEST_OS_SYMBIAN
+ }
+ static type Copy(const Element (&array)[N]) {
+#if GTEST_OS_SYMBIAN
+ return type(const_cast<Element*>(&array[0]), N, kCopy);
+#else
+ return type(array, N, kCopy);
+#endif // GTEST_OS_SYMBIAN
+ }
+};
+
+// This specialization is used when RawContainer is a native array
+// represented as a (pointer, size) tuple.
+template <typename ElementPointer, typename Size>
+class StlContainerView< ::std::tr1::tuple<ElementPointer, Size> > {
+ public:
+ typedef GTEST_REMOVE_CONST_(
+ typename internal::PointeeOf<ElementPointer>::type) RawElement;
+ typedef internal::NativeArray<RawElement> type;
+ typedef const type const_reference;
+
+ static const_reference ConstReference(
+ const ::std::tr1::tuple<ElementPointer, Size>& array) {
+ using ::std::tr1::get;
+ return type(get<0>(array), get<1>(array), kReference);
+ }
+ static type Copy(const ::std::tr1::tuple<ElementPointer, Size>& array) {
+ using ::std::tr1::get;
+ return type(get<0>(array), get<1>(array), kCopy);
+ }
+};
+
+// The following specialization prevents the user from instantiating
+// StlContainer with a reference type.
+template <typename T> class StlContainerView<T&>;
+
+// A type transform to remove constness from the first part of a pair.
+// Pairs like that are used as the value_type of associative containers,
+// and this transform produces a similar but assignable pair.
+template <typename T>
+struct RemoveConstFromKey {
+ typedef T type;
+};
+
+// Partially specialized to remove constness from std::pair<const K, V>.
+template <typename K, typename V>
+struct RemoveConstFromKey<std::pair<const K, V> > {
+ typedef std::pair<K, V> type;
+};
+
+// Mapping from booleans to types. Similar to boost::bool_<kValue> and
+// std::integral_constant<bool, kValue>.
+template <bool kValue>
+struct BooleanConstant {};
+
+} // namespace internal
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_INTERNAL_GMOCK_INTERNAL_UTILS_H_
+
+namespace testing {
+
+// To implement an action Foo, define:
+// 1. a class FooAction that implements the ActionInterface interface, and
+// 2. a factory function that creates an Action object from a
+// const FooAction*.
+//
+// The two-level delegation design follows that of Matcher, providing
+// consistency for extension developers. It also eases ownership
+// management as Action objects can now be copied like plain values.
+
+namespace internal {
+
+template <typename F1, typename F2>
+class ActionAdaptor;
+
+// BuiltInDefaultValue<T>::Get() returns the "built-in" default
+// value for type T, which is NULL when T is a pointer type, 0 when T
+// is a numeric type, false when T is bool, or "" when T is string or
+// std::string. For any other type T, this value is undefined and the
+// function will abort the process.
+template <typename T>
+class BuiltInDefaultValue {
+ public:
+ // This function returns true iff type T has a built-in default value.
+ static bool Exists() { return false; }
+ static T Get() {
+ Assert(false, __FILE__, __LINE__,
+ "Default action undefined for the function return type.");
+ return internal::Invalid<T>();
+ // The above statement will never be reached, but is required in
+ // order for this function to compile.
+ }
+};
+
+// This partial specialization says that we use the same built-in
+// default value for T and const T.
+template <typename T>
+class BuiltInDefaultValue<const T> {
+ public:
+ static bool Exists() { return BuiltInDefaultValue<T>::Exists(); }
+ static T Get() { return BuiltInDefaultValue<T>::Get(); }
+};
+
+// This partial specialization defines the default values for pointer
+// types.
+template <typename T>
+class BuiltInDefaultValue<T*> {
+ public:
+ static bool Exists() { return true; }
+ static T* Get() { return NULL; }
+};
+
+// The following specializations define the default values for
+// specific types we care about.
+#define GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(type, value) \
+ template <> \
+ class BuiltInDefaultValue<type> { \
+ public: \
+ static bool Exists() { return true; } \
+ static type Get() { return value; } \
+ }
+
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(void, ); // NOLINT
+#if GTEST_HAS_GLOBAL_STRING
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(::string, "");
+#endif // GTEST_HAS_GLOBAL_STRING
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(::std::string, "");
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(bool, false);
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(unsigned char, '\0');
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(signed char, '\0');
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(char, '\0');
+
+// There's no need for a default action for signed wchar_t, as that
+// type is the same as wchar_t for gcc, and invalid for MSVC.
+//
+// There's also no need for a default action for unsigned wchar_t, as
+// that type is the same as unsigned int for gcc, and invalid for
+// MSVC.
+#if GMOCK_WCHAR_T_IS_NATIVE_
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(wchar_t, 0U); // NOLINT
+#endif
+
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(unsigned short, 0U); // NOLINT
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(signed short, 0); // NOLINT
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(unsigned int, 0U);
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(signed int, 0);
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(unsigned long, 0UL); // NOLINT
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(signed long, 0L); // NOLINT
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(UInt64, 0);
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(Int64, 0);
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(float, 0);
+GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_(double, 0);
+
+#undef GMOCK_DEFINE_DEFAULT_ACTION_FOR_RETURN_TYPE_
+
+} // namespace internal
+
+// When an unexpected function call is encountered, Google Mock will
+// let it return a default value if the user has specified one for its
+// return type, or if the return type has a built-in default value;
+// otherwise Google Mock won't know what value to return and will have
+// to abort the process.
+//
+// The DefaultValue<T> class allows a user to specify the
+// default value for a type T that is both copyable and publicly
+// destructible (i.e. anything that can be used as a function return
+// type). The usage is:
+//
+// // Sets the default value for type T to be foo.
+// DefaultValue<T>::Set(foo);
+template <typename T>
+class DefaultValue {
+ public:
+ // Sets the default value for type T; requires T to be
+ // copy-constructable and have a public destructor.
+ static void Set(T x) {
+ delete value_;
+ value_ = new T(x);
+ }
+
+ // Unsets the default value for type T.
+ static void Clear() {
+ delete value_;
+ value_ = NULL;
+ }
+
+ // Returns true iff the user has set the default value for type T.
+ static bool IsSet() { return value_ != NULL; }
+
+ // Returns true if T has a default return value set by the user or there
+ // exists a built-in default value.
+ static bool Exists() {
+ return IsSet() || internal::BuiltInDefaultValue<T>::Exists();
+ }
+
+ // Returns the default value for type T if the user has set one;
+ // otherwise returns the built-in default value if there is one;
+ // otherwise aborts the process.
+ static T Get() {
+ return value_ == NULL ?
+ internal::BuiltInDefaultValue<T>::Get() : *value_;
+ }
+
+ private:
+ static const T* value_;
+};
+
+// This partial specialization allows a user to set default values for
+// reference types.
+template <typename T>
+class DefaultValue<T&> {
+ public:
+ // Sets the default value for type T&.
+ static void Set(T& x) { // NOLINT
+ address_ = &x;
+ }
+
+ // Unsets the default value for type T&.
+ static void Clear() {
+ address_ = NULL;
+ }
+
+ // Returns true iff the user has set the default value for type T&.
+ static bool IsSet() { return address_ != NULL; }
+
+ // Returns true if T has a default return value set by the user or there
+ // exists a built-in default value.
+ static bool Exists() {
+ return IsSet() || internal::BuiltInDefaultValue<T&>::Exists();
+ }
+
+ // Returns the default value for type T& if the user has set one;
+ // otherwise returns the built-in default value if there is one;
+ // otherwise aborts the process.
+ static T& Get() {
+ return address_ == NULL ?
+ internal::BuiltInDefaultValue<T&>::Get() : *address_;
+ }
+
+ private:
+ static T* address_;
+};
+
+// This specialization allows DefaultValue<void>::Get() to
+// compile.
+template <>
+class DefaultValue<void> {
+ public:
+ static bool Exists() { return true; }
+ static void Get() {}
+};
+
+// Points to the user-set default value for type T.
+template <typename T>
+const T* DefaultValue<T>::value_ = NULL;
+
+// Points to the user-set default value for type T&.
+template <typename T>
+T* DefaultValue<T&>::address_ = NULL;
+
+// Implement this interface to define an action for function type F.
+template <typename F>
+class ActionInterface {
+ public:
+ typedef typename internal::Function<F>::Result Result;
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ ActionInterface() {}
+ virtual ~ActionInterface() {}
+
+ // Performs the action. This method is not const, as in general an
+ // action can have side effects and be stateful. For example, a
+ // get-the-next-element-from-the-collection action will need to
+ // remember the current element.
+ virtual Result Perform(const ArgumentTuple& args) = 0;
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ActionInterface);
+};
+
+// An Action<F> is a copyable and IMMUTABLE (except by assignment)
+// object that represents an action to be taken when a mock function
+// of type F is called. The implementation of Action<T> is just a
+// linked_ptr to const ActionInterface<T>, so copying is fairly cheap.
+// Don't inherit from Action!
+//
+// You can view an object implementing ActionInterface<F> as a
+// concrete action (including its current state), and an Action<F>
+// object as a handle to it.
+template <typename F>
+class Action {
+ public:
+ typedef typename internal::Function<F>::Result Result;
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ // Constructs a null Action. Needed for storing Action objects in
+ // STL containers.
+ Action() : impl_(NULL) {}
+
+ // Constructs an Action from its implementation. A NULL impl is
+ // used to represent the "do-default" action.
+ explicit Action(ActionInterface<F>* impl) : impl_(impl) {}
+
+ // Copy constructor.
+ Action(const Action& action) : impl_(action.impl_) {}
+
+ // This constructor allows us to turn an Action<Func> object into an
+ // Action<F>, as long as F's arguments can be implicitly converted
+ // to Func's and Func's return type can be implicitly converted to
+ // F's.
+ template <typename Func>
+ explicit Action(const Action<Func>& action);
+
+ // Returns true iff this is the DoDefault() action.
+ bool IsDoDefault() const { return impl_.get() == NULL; }
+
+ // Performs the action. Note that this method is const even though
+ // the corresponding method in ActionInterface is not. The reason
+ // is that a const Action<F> means that it cannot be re-bound to
+ // another concrete action, not that the concrete action it binds to
+ // cannot change state. (Think of the difference between a const
+ // pointer and a pointer to const.)
+ Result Perform(const ArgumentTuple& args) const {
+ internal::Assert(
+ !IsDoDefault(), __FILE__, __LINE__,
+ "You are using DoDefault() inside a composite action like "
+ "DoAll() or WithArgs(). This is not supported for technical "
+ "reasons. Please instead spell out the default action, or "
+ "assign the default action to an Action variable and use "
+ "the variable in various places.");
+ return impl_->Perform(args);
+ }
+
+ private:
+ template <typename F1, typename F2>
+ friend class internal::ActionAdaptor;
+
+ internal::linked_ptr<ActionInterface<F> > impl_;
+};
+
+// The PolymorphicAction class template makes it easy to implement a
+// polymorphic action (i.e. an action that can be used in mock
+// functions of than one type, e.g. Return()).
+//
+// To define a polymorphic action, a user first provides a COPYABLE
+// implementation class that has a Perform() method template:
+//
+// class FooAction {
+// public:
+// template <typename Result, typename ArgumentTuple>
+// Result Perform(const ArgumentTuple& args) const {
+// // Processes the arguments and returns a result, using
+// // tr1::get<N>(args) to get the N-th (0-based) argument in the tuple.
+// }
+// ...
+// };
+//
+// Then the user creates the polymorphic action using
+// MakePolymorphicAction(object) where object has type FooAction. See
+// the definition of Return(void) and SetArgumentPointee<N>(value) for
+// complete examples.
+template <typename Impl>
+class PolymorphicAction {
+ public:
+ explicit PolymorphicAction(const Impl& impl) : impl_(impl) {}
+
+ template <typename F>
+ operator Action<F>() const {
+ return Action<F>(new MonomorphicImpl<F>(impl_));
+ }
+
+ private:
+ template <typename F>
+ class MonomorphicImpl : public ActionInterface<F> {
+ public:
+ typedef typename internal::Function<F>::Result Result;
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ explicit MonomorphicImpl(const Impl& impl) : impl_(impl) {}
+
+ virtual Result Perform(const ArgumentTuple& args) {
+ return impl_.template Perform<Result>(args);
+ }
+
+ private:
+ Impl impl_;
+
+ GTEST_DISALLOW_ASSIGN_(MonomorphicImpl);
+ };
+
+ Impl impl_;
+
+ GTEST_DISALLOW_ASSIGN_(PolymorphicAction);
+};
+
+// Creates an Action from its implementation and returns it. The
+// created Action object owns the implementation.
+template <typename F>
+Action<F> MakeAction(ActionInterface<F>* impl) {
+ return Action<F>(impl);
+}
+
+// Creates a polymorphic action from its implementation. This is
+// easier to use than the PolymorphicAction<Impl> constructor as it
+// doesn't require you to explicitly write the template argument, e.g.
+//
+// MakePolymorphicAction(foo);
+// vs
+// PolymorphicAction<TypeOfFoo>(foo);
+template <typename Impl>
+inline PolymorphicAction<Impl> MakePolymorphicAction(const Impl& impl) {
+ return PolymorphicAction<Impl>(impl);
+}
+
+namespace internal {
+
+// Allows an Action<F2> object to pose as an Action<F1>, as long as F2
+// and F1 are compatible.
+template <typename F1, typename F2>
+class ActionAdaptor : public ActionInterface<F1> {
+ public:
+ typedef typename internal::Function<F1>::Result Result;
+ typedef typename internal::Function<F1>::ArgumentTuple ArgumentTuple;
+
+ explicit ActionAdaptor(const Action<F2>& from) : impl_(from.impl_) {}
+
+ virtual Result Perform(const ArgumentTuple& args) {
+ return impl_->Perform(args);
+ }
+
+ private:
+ const internal::linked_ptr<ActionInterface<F2> > impl_;
+
+ GTEST_DISALLOW_ASSIGN_(ActionAdaptor);
+};
+
+// Implements the polymorphic Return(x) action, which can be used in
+// any function that returns the type of x, regardless of the argument
+// types.
+//
+// Note: The value passed into Return must be converted into
+// Function<F>::Result when this action is cast to Action<F> rather than
+// when that action is performed. This is important in scenarios like
+//
+// MOCK_METHOD1(Method, T(U));
+// ...
+// {
+// Foo foo;
+// X x(&foo);
+// EXPECT_CALL(mock, Method(_)).WillOnce(Return(x));
+// }
+//
+// In the example above the variable x holds reference to foo which leaves
+// scope and gets destroyed. If copying X just copies a reference to foo,
+// that copy will be left with a hanging reference. If conversion to T
+// makes a copy of foo, the above code is safe. To support that scenario, we
+// need to make sure that the type conversion happens inside the EXPECT_CALL
+// statement, and conversion of the result of Return to Action<T(U)> is a
+// good place for that.
+//
+template <typename R>
+class ReturnAction {
+ public:
+ // Constructs a ReturnAction object from the value to be returned.
+ // 'value' is passed by value instead of by const reference in order
+ // to allow Return("string literal") to compile.
+ explicit ReturnAction(R value) : value_(value) {}
+
+ // This template type conversion operator allows Return(x) to be
+ // used in ANY function that returns x's type.
+ template <typename F>
+ operator Action<F>() const {
+ // Assert statement belongs here because this is the best place to verify
+ // conditions on F. It produces the clearest error messages
+ // in most compilers.
+ // Impl really belongs in this scope as a local class but can't
+ // because MSVC produces duplicate symbols in different translation units
+ // in this case. Until MS fixes that bug we put Impl into the class scope
+ // and put the typedef both here (for use in assert statement) and
+ // in the Impl class. But both definitions must be the same.
+ typedef typename Function<F>::Result Result;
+ GTEST_COMPILE_ASSERT_(
+ !internal::is_reference<Result>::value,
+ use_ReturnRef_instead_of_Return_to_return_a_reference);
+ return Action<F>(new Impl<F>(value_));
+ }
+
+ private:
+ // Implements the Return(x) action for a particular function type F.
+ template <typename F>
+ class Impl : public ActionInterface<F> {
+ public:
+ typedef typename Function<F>::Result Result;
+ typedef typename Function<F>::ArgumentTuple ArgumentTuple;
+
+ // The implicit cast is necessary when Result has more than one
+ // single-argument constructor (e.g. Result is std::vector<int>) and R
+ // has a type conversion operator template. In that case, value_(value)
+ // won't compile as the compiler doesn't known which constructor of
+ // Result to call. ImplicitCast_ forces the compiler to convert R to
+ // Result without considering explicit constructors, thus resolving the
+ // ambiguity. value_ is then initialized using its copy constructor.
+ explicit Impl(R value)
+ : value_(::testing::internal::ImplicitCast_<Result>(value)) {}
+
+ virtual Result Perform(const ArgumentTuple&) { return value_; }
+
+ private:
+ GTEST_COMPILE_ASSERT_(!internal::is_reference<Result>::value,
+ Result_cannot_be_a_reference_type);
+ Result value_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ R value_;
+
+ GTEST_DISALLOW_ASSIGN_(ReturnAction);
+};
+
+// Implements the ReturnNull() action.
+class ReturnNullAction {
+ public:
+ // Allows ReturnNull() to be used in any pointer-returning function.
+ template <typename Result, typename ArgumentTuple>
+ static Result Perform(const ArgumentTuple&) {
+ GTEST_COMPILE_ASSERT_(internal::is_pointer<Result>::value,
+ ReturnNull_can_be_used_to_return_a_pointer_only);
+ return NULL;
+ }
+};
+
+// Implements the Return() action.
+class ReturnVoidAction {
+ public:
+ // Allows Return() to be used in any void-returning function.
+ template <typename Result, typename ArgumentTuple>
+ static void Perform(const ArgumentTuple&) {
+ CompileAssertTypesEqual<void, Result>();
+ }
+};
+
+// Implements the polymorphic ReturnRef(x) action, which can be used
+// in any function that returns a reference to the type of x,
+// regardless of the argument types.
+template <typename T>
+class ReturnRefAction {
+ public:
+ // Constructs a ReturnRefAction object from the reference to be returned.
+ explicit ReturnRefAction(T& ref) : ref_(ref) {} // NOLINT
+
+ // This template type conversion operator allows ReturnRef(x) to be
+ // used in ANY function that returns a reference to x's type.
+ template <typename F>
+ operator Action<F>() const {
+ typedef typename Function<F>::Result Result;
+ // Asserts that the function return type is a reference. This
+ // catches the user error of using ReturnRef(x) when Return(x)
+ // should be used, and generates some helpful error message.
+ GTEST_COMPILE_ASSERT_(internal::is_reference<Result>::value,
+ use_Return_instead_of_ReturnRef_to_return_a_value);
+ return Action<F>(new Impl<F>(ref_));
+ }
+
+ private:
+ // Implements the ReturnRef(x) action for a particular function type F.
+ template <typename F>
+ class Impl : public ActionInterface<F> {
+ public:
+ typedef typename Function<F>::Result Result;
+ typedef typename Function<F>::ArgumentTuple ArgumentTuple;
+
+ explicit Impl(T& ref) : ref_(ref) {} // NOLINT
+
+ virtual Result Perform(const ArgumentTuple&) {
+ return ref_;
+ }
+
+ private:
+ T& ref_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ T& ref_;
+
+ GTEST_DISALLOW_ASSIGN_(ReturnRefAction);
+};
+
+// Implements the polymorphic ReturnRefOfCopy(x) action, which can be
+// used in any function that returns a reference to the type of x,
+// regardless of the argument types.
+template <typename T>
+class ReturnRefOfCopyAction {
+ public:
+ // Constructs a ReturnRefOfCopyAction object from the reference to
+ // be returned.
+ explicit ReturnRefOfCopyAction(const T& value) : value_(value) {} // NOLINT
+
+ // This template type conversion operator allows ReturnRefOfCopy(x) to be
+ // used in ANY function that returns a reference to x's type.
+ template <typename F>
+ operator Action<F>() const {
+ typedef typename Function<F>::Result Result;
+ // Asserts that the function return type is a reference. This
+ // catches the user error of using ReturnRefOfCopy(x) when Return(x)
+ // should be used, and generates some helpful error message.
+ GTEST_COMPILE_ASSERT_(
+ internal::is_reference<Result>::value,
+ use_Return_instead_of_ReturnRefOfCopy_to_return_a_value);
+ return Action<F>(new Impl<F>(value_));
+ }
+
+ private:
+ // Implements the ReturnRefOfCopy(x) action for a particular function type F.
+ template <typename F>
+ class Impl : public ActionInterface<F> {
+ public:
+ typedef typename Function<F>::Result Result;
+ typedef typename Function<F>::ArgumentTuple ArgumentTuple;
+
+ explicit Impl(const T& value) : value_(value) {} // NOLINT
+
+ virtual Result Perform(const ArgumentTuple&) {
+ return value_;
+ }
+
+ private:
+ T value_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ const T value_;
+
+ GTEST_DISALLOW_ASSIGN_(ReturnRefOfCopyAction);
+};
+
+// Implements the polymorphic DoDefault() action.
+class DoDefaultAction {
+ public:
+ // This template type conversion operator allows DoDefault() to be
+ // used in any function.
+ template <typename F>
+ operator Action<F>() const { return Action<F>(NULL); }
+};
+
+// Implements the Assign action to set a given pointer referent to a
+// particular value.
+template <typename T1, typename T2>
+class AssignAction {
+ public:
+ AssignAction(T1* ptr, T2 value) : ptr_(ptr), value_(value) {}
+
+ template <typename Result, typename ArgumentTuple>
+ void Perform(const ArgumentTuple& /* args */) const {
+ *ptr_ = value_;
+ }
+
+ private:
+ T1* const ptr_;
+ const T2 value_;
+
+ GTEST_DISALLOW_ASSIGN_(AssignAction);
+};
+
+#if !GTEST_OS_WINDOWS_MOBILE
+
+// Implements the SetErrnoAndReturn action to simulate return from
+// various system calls and libc functions.
+template <typename T>
+class SetErrnoAndReturnAction {
+ public:
+ SetErrnoAndReturnAction(int errno_value, T result)
+ : errno_(errno_value),
+ result_(result) {}
+ template <typename Result, typename ArgumentTuple>
+ Result Perform(const ArgumentTuple& /* args */) const {
+ errno = errno_;
+ return result_;
+ }
+
+ private:
+ const int errno_;
+ const T result_;
+
+ GTEST_DISALLOW_ASSIGN_(SetErrnoAndReturnAction);
+};
+
+#endif // !GTEST_OS_WINDOWS_MOBILE
+
+// Implements the SetArgumentPointee<N>(x) action for any function
+// whose N-th argument (0-based) is a pointer to x's type. The
+// template parameter kIsProto is true iff type A is ProtocolMessage,
+// proto2::Message, or a sub-class of those.
+template <size_t N, typename A, bool kIsProto>
+class SetArgumentPointeeAction {
+ public:
+ // Constructs an action that sets the variable pointed to by the
+ // N-th function argument to 'value'.
+ explicit SetArgumentPointeeAction(const A& value) : value_(value) {}
+
+ template <typename Result, typename ArgumentTuple>
+ void Perform(const ArgumentTuple& args) const {
+ CompileAssertTypesEqual<void, Result>();
+ *::std::tr1::get<N>(args) = value_;
+ }
+
+ private:
+ const A value_;
+
+ GTEST_DISALLOW_ASSIGN_(SetArgumentPointeeAction);
+};
+
+template <size_t N, typename Proto>
+class SetArgumentPointeeAction<N, Proto, true> {
+ public:
+ // Constructs an action that sets the variable pointed to by the
+ // N-th function argument to 'proto'. Both ProtocolMessage and
+ // proto2::Message have the CopyFrom() method, so the same
+ // implementation works for both.
+ explicit SetArgumentPointeeAction(const Proto& proto) : proto_(new Proto) {
+ proto_->CopyFrom(proto);
+ }
+
+ template <typename Result, typename ArgumentTuple>
+ void Perform(const ArgumentTuple& args) const {
+ CompileAssertTypesEqual<void, Result>();
+ ::std::tr1::get<N>(args)->CopyFrom(*proto_);
+ }
+
+ private:
+ const internal::linked_ptr<Proto> proto_;
+
+ GTEST_DISALLOW_ASSIGN_(SetArgumentPointeeAction);
+};
+
+// Implements the InvokeWithoutArgs(f) action. The template argument
+// FunctionImpl is the implementation type of f, which can be either a
+// function pointer or a functor. InvokeWithoutArgs(f) can be used as an
+// Action<F> as long as f's type is compatible with F (i.e. f can be
+// assigned to a tr1::function<F>).
+template <typename FunctionImpl>
+class InvokeWithoutArgsAction {
+ public:
+ // The c'tor makes a copy of function_impl (either a function
+ // pointer or a functor).
+ explicit InvokeWithoutArgsAction(FunctionImpl function_impl)
+ : function_impl_(function_impl) {}
+
+ // Allows InvokeWithoutArgs(f) to be used as any action whose type is
+ // compatible with f.
+ template <typename Result, typename ArgumentTuple>
+ Result Perform(const ArgumentTuple&) { return function_impl_(); }
+
+ private:
+ FunctionImpl function_impl_;
+
+ GTEST_DISALLOW_ASSIGN_(InvokeWithoutArgsAction);
+};
+
+// Implements the InvokeWithoutArgs(object_ptr, &Class::Method) action.
+template <class Class, typename MethodPtr>
+class InvokeMethodWithoutArgsAction {
+ public:
+ InvokeMethodWithoutArgsAction(Class* obj_ptr, MethodPtr method_ptr)
+ : obj_ptr_(obj_ptr), method_ptr_(method_ptr) {}
+
+ template <typename Result, typename ArgumentTuple>
+ Result Perform(const ArgumentTuple&) const {
+ return (obj_ptr_->*method_ptr_)();
+ }
+
+ private:
+ Class* const obj_ptr_;
+ const MethodPtr method_ptr_;
+
+ GTEST_DISALLOW_ASSIGN_(InvokeMethodWithoutArgsAction);
+};
+
+// Implements the IgnoreResult(action) action.
+template <typename A>
+class IgnoreResultAction {
+ public:
+ explicit IgnoreResultAction(const A& action) : action_(action) {}
+
+ template <typename F>
+ operator Action<F>() const {
+ // Assert statement belongs here because this is the best place to verify
+ // conditions on F. It produces the clearest error messages
+ // in most compilers.
+ // Impl really belongs in this scope as a local class but can't
+ // because MSVC produces duplicate symbols in different translation units
+ // in this case. Until MS fixes that bug we put Impl into the class scope
+ // and put the typedef both here (for use in assert statement) and
+ // in the Impl class. But both definitions must be the same.
+ typedef typename internal::Function<F>::Result Result;
+
+ // Asserts at compile time that F returns void.
+ CompileAssertTypesEqual<void, Result>();
+
+ return Action<F>(new Impl<F>(action_));
+ }
+
+ private:
+ template <typename F>
+ class Impl : public ActionInterface<F> {
+ public:
+ typedef typename internal::Function<F>::Result Result;
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ explicit Impl(const A& action) : action_(action) {}
+
+ virtual void Perform(const ArgumentTuple& args) {
+ // Performs the action and ignores its result.
+ action_.Perform(args);
+ }
+
+ private:
+ // Type OriginalFunction is the same as F except that its return
+ // type is IgnoredValue.
+ typedef typename internal::Function<F>::MakeResultIgnoredValue
+ OriginalFunction;
+
+ const Action<OriginalFunction> action_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ const A action_;
+
+ GTEST_DISALLOW_ASSIGN_(IgnoreResultAction);
+};
+
+// A ReferenceWrapper<T> object represents a reference to type T,
+// which can be either const or not. It can be explicitly converted
+// from, and implicitly converted to, a T&. Unlike a reference,
+// ReferenceWrapper<T> can be copied and can survive template type
+// inference. This is used to support by-reference arguments in the
+// InvokeArgument<N>(...) action. The idea was from "reference
+// wrappers" in tr1, which we don't have in our source tree yet.
+template <typename T>
+class ReferenceWrapper {
+ public:
+ // Constructs a ReferenceWrapper<T> object from a T&.
+ explicit ReferenceWrapper(T& l_value) : pointer_(&l_value) {} // NOLINT
+
+ // Allows a ReferenceWrapper<T> object to be implicitly converted to
+ // a T&.
+ operator T&() const { return *pointer_; }
+ private:
+ T* pointer_;
+};
+
+// Allows the expression ByRef(x) to be printed as a reference to x.
+template <typename T>
+void PrintTo(const ReferenceWrapper<T>& ref, ::std::ostream* os) {
+ T& value = ref;
+ UniversalPrinter<T&>::Print(value, os);
+}
+
+// Does two actions sequentially. Used for implementing the DoAll(a1,
+// a2, ...) action.
+template <typename Action1, typename Action2>
+class DoBothAction {
+ public:
+ DoBothAction(Action1 action1, Action2 action2)
+ : action1_(action1), action2_(action2) {}
+
+ // This template type conversion operator allows DoAll(a1, ..., a_n)
+ // to be used in ANY function of compatible type.
+ template <typename F>
+ operator Action<F>() const {
+ return Action<F>(new Impl<F>(action1_, action2_));
+ }
+
+ private:
+ // Implements the DoAll(...) action for a particular function type F.
+ template <typename F>
+ class Impl : public ActionInterface<F> {
+ public:
+ typedef typename Function<F>::Result Result;
+ typedef typename Function<F>::ArgumentTuple ArgumentTuple;
+ typedef typename Function<F>::MakeResultVoid VoidResult;
+
+ Impl(const Action<VoidResult>& action1, const Action<F>& action2)
+ : action1_(action1), action2_(action2) {}
+
+ virtual Result Perform(const ArgumentTuple& args) {
+ action1_.Perform(args);
+ return action2_.Perform(args);
+ }
+
+ private:
+ const Action<VoidResult> action1_;
+ const Action<F> action2_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ Action1 action1_;
+ Action2 action2_;
+
+ GTEST_DISALLOW_ASSIGN_(DoBothAction);
+};
+
+} // namespace internal
+
+// An Unused object can be implicitly constructed from ANY value.
+// This is handy when defining actions that ignore some or all of the
+// mock function arguments. For example, given
+//
+// MOCK_METHOD3(Foo, double(const string& label, double x, double y));
+// MOCK_METHOD3(Bar, double(int index, double x, double y));
+//
+// instead of
+//
+// double DistanceToOriginWithLabel(const string& label, double x, double y) {
+// return sqrt(x*x + y*y);
+// }
+// double DistanceToOriginWithIndex(int index, double x, double y) {
+// return sqrt(x*x + y*y);
+// }
+// ...
+// EXEPCT_CALL(mock, Foo("abc", _, _))
+// .WillOnce(Invoke(DistanceToOriginWithLabel));
+// EXEPCT_CALL(mock, Bar(5, _, _))
+// .WillOnce(Invoke(DistanceToOriginWithIndex));
+//
+// you could write
+//
+// // We can declare any uninteresting argument as Unused.
+// double DistanceToOrigin(Unused, double x, double y) {
+// return sqrt(x*x + y*y);
+// }
+// ...
+// EXEPCT_CALL(mock, Foo("abc", _, _)).WillOnce(Invoke(DistanceToOrigin));
+// EXEPCT_CALL(mock, Bar(5, _, _)).WillOnce(Invoke(DistanceToOrigin));
+typedef internal::IgnoredValue Unused;
+
+// This constructor allows us to turn an Action<From> object into an
+// Action<To>, as long as To's arguments can be implicitly converted
+// to From's and From's return type cann be implicitly converted to
+// To's.
+template <typename To>
+template <typename From>
+Action<To>::Action(const Action<From>& from)
+ : impl_(new internal::ActionAdaptor<To, From>(from)) {}
+
+// Creates an action that returns 'value'. 'value' is passed by value
+// instead of const reference - otherwise Return("string literal")
+// will trigger a compiler error about using array as initializer.
+template <typename R>
+internal::ReturnAction<R> Return(R value) {
+ return internal::ReturnAction<R>(value);
+}
+
+// Creates an action that returns NULL.
+inline PolymorphicAction<internal::ReturnNullAction> ReturnNull() {
+ return MakePolymorphicAction(internal::ReturnNullAction());
+}
+
+// Creates an action that returns from a void function.
+inline PolymorphicAction<internal::ReturnVoidAction> Return() {
+ return MakePolymorphicAction(internal::ReturnVoidAction());
+}
+
+// Creates an action that returns the reference to a variable.
+template <typename R>
+inline internal::ReturnRefAction<R> ReturnRef(R& x) { // NOLINT
+ return internal::ReturnRefAction<R>(x);
+}
+
+// Creates an action that returns the reference to a copy of the
+// argument. The copy is created when the action is constructed and
+// lives as long as the action.
+template <typename R>
+inline internal::ReturnRefOfCopyAction<R> ReturnRefOfCopy(const R& x) {
+ return internal::ReturnRefOfCopyAction<R>(x);
+}
+
+// Creates an action that does the default action for the give mock function.
+inline internal::DoDefaultAction DoDefault() {
+ return internal::DoDefaultAction();
+}
+
+// Creates an action that sets the variable pointed by the N-th
+// (0-based) function argument to 'value'.
+template <size_t N, typename T>
+PolymorphicAction<
+ internal::SetArgumentPointeeAction<
+ N, T, internal::IsAProtocolMessage<T>::value> >
+SetArgPointee(const T& x) {
+ return MakePolymorphicAction(internal::SetArgumentPointeeAction<
+ N, T, internal::IsAProtocolMessage<T>::value>(x));
+}
+
+#if !((GTEST_GCC_VER_ && GTEST_GCC_VER_ < 40000) || GTEST_OS_SYMBIAN)
+// This overload allows SetArgPointee() to accept a string literal.
+// GCC prior to the version 4.0 and Symbian C++ compiler cannot distinguish
+// this overload from the templated version and emit a compile error.
+template <size_t N>
+PolymorphicAction<
+ internal::SetArgumentPointeeAction<N, const char*, false> >
+SetArgPointee(const char* p) {
+ return MakePolymorphicAction(internal::SetArgumentPointeeAction<
+ N, const char*, false>(p));
+}
+
+template <size_t N>
+PolymorphicAction<
+ internal::SetArgumentPointeeAction<N, const wchar_t*, false> >
+SetArgPointee(const wchar_t* p) {
+ return MakePolymorphicAction(internal::SetArgumentPointeeAction<
+ N, const wchar_t*, false>(p));
+}
+#endif
+
+// The following version is DEPRECATED.
+template <size_t N, typename T>
+PolymorphicAction<
+ internal::SetArgumentPointeeAction<
+ N, T, internal::IsAProtocolMessage<T>::value> >
+SetArgumentPointee(const T& x) {
+ return MakePolymorphicAction(internal::SetArgumentPointeeAction<
+ N, T, internal::IsAProtocolMessage<T>::value>(x));
+}
+
+// Creates an action that sets a pointer referent to a given value.
+template <typename T1, typename T2>
+PolymorphicAction<internal::AssignAction<T1, T2> > Assign(T1* ptr, T2 val) {
+ return MakePolymorphicAction(internal::AssignAction<T1, T2>(ptr, val));
+}
+
+#if !GTEST_OS_WINDOWS_MOBILE
+
+// Creates an action that sets errno and returns the appropriate error.
+template <typename T>
+PolymorphicAction<internal::SetErrnoAndReturnAction<T> >
+SetErrnoAndReturn(int errval, T result) {
+ return MakePolymorphicAction(
+ internal::SetErrnoAndReturnAction<T>(errval, result));
+}
+
+#endif // !GTEST_OS_WINDOWS_MOBILE
+
+// Various overloads for InvokeWithoutArgs().
+
+// Creates an action that invokes 'function_impl' with no argument.
+template <typename FunctionImpl>
+PolymorphicAction<internal::InvokeWithoutArgsAction<FunctionImpl> >
+InvokeWithoutArgs(FunctionImpl function_impl) {
+ return MakePolymorphicAction(
+ internal::InvokeWithoutArgsAction<FunctionImpl>(function_impl));
+}
+
+// Creates an action that invokes the given method on the given object
+// with no argument.
+template <class Class, typename MethodPtr>
+PolymorphicAction<internal::InvokeMethodWithoutArgsAction<Class, MethodPtr> >
+InvokeWithoutArgs(Class* obj_ptr, MethodPtr method_ptr) {
+ return MakePolymorphicAction(
+ internal::InvokeMethodWithoutArgsAction<Class, MethodPtr>(
+ obj_ptr, method_ptr));
+}
+
+// Creates an action that performs an_action and throws away its
+// result. In other words, it changes the return type of an_action to
+// void. an_action MUST NOT return void, or the code won't compile.
+template <typename A>
+inline internal::IgnoreResultAction<A> IgnoreResult(const A& an_action) {
+ return internal::IgnoreResultAction<A>(an_action);
+}
+
+// Creates a reference wrapper for the given L-value. If necessary,
+// you can explicitly specify the type of the reference. For example,
+// suppose 'derived' is an object of type Derived, ByRef(derived)
+// would wrap a Derived&. If you want to wrap a const Base& instead,
+// where Base is a base class of Derived, just write:
+//
+// ByRef<const Base>(derived)
+template <typename T>
+inline internal::ReferenceWrapper<T> ByRef(T& l_value) { // NOLINT
+ return internal::ReferenceWrapper<T>(l_value);
+}
+
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_ACTIONS_H_
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements some commonly used cardinalities. More
+// cardinalities can be defined by the user implementing the
+// CardinalityInterface interface if necessary.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_CARDINALITIES_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_CARDINALITIES_H_
+
+#include <limits.h>
+#include <ostream> // NOLINT
+
+namespace testing {
+
+// To implement a cardinality Foo, define:
+// 1. a class FooCardinality that implements the
+// CardinalityInterface interface, and
+// 2. a factory function that creates a Cardinality object from a
+// const FooCardinality*.
+//
+// The two-level delegation design follows that of Matcher, providing
+// consistency for extension developers. It also eases ownership
+// management as Cardinality objects can now be copied like plain values.
+
+// The implementation of a cardinality.
+class CardinalityInterface {
+ public:
+ virtual ~CardinalityInterface() {}
+
+ // Conservative estimate on the lower/upper bound of the number of
+ // calls allowed.
+ virtual int ConservativeLowerBound() const { return 0; }
+ virtual int ConservativeUpperBound() const { return INT_MAX; }
+
+ // Returns true iff call_count calls will satisfy this cardinality.
+ virtual bool IsSatisfiedByCallCount(int call_count) const = 0;
+
+ // Returns true iff call_count calls will saturate this cardinality.
+ virtual bool IsSaturatedByCallCount(int call_count) const = 0;
+
+ // Describes self to an ostream.
+ virtual void DescribeTo(::std::ostream* os) const = 0;
+};
+
+// A Cardinality is a copyable and IMMUTABLE (except by assignment)
+// object that specifies how many times a mock function is expected to
+// be called. The implementation of Cardinality is just a linked_ptr
+// to const CardinalityInterface, so copying is fairly cheap.
+// Don't inherit from Cardinality!
+class GTEST_API_ Cardinality {
+ public:
+ // Constructs a null cardinality. Needed for storing Cardinality
+ // objects in STL containers.
+ Cardinality() {}
+
+ // Constructs a Cardinality from its implementation.
+ explicit Cardinality(const CardinalityInterface* impl) : impl_(impl) {}
+
+ // Conservative estimate on the lower/upper bound of the number of
+ // calls allowed.
+ int ConservativeLowerBound() const { return impl_->ConservativeLowerBound(); }
+ int ConservativeUpperBound() const { return impl_->ConservativeUpperBound(); }
+
+ // Returns true iff call_count calls will satisfy this cardinality.
+ bool IsSatisfiedByCallCount(int call_count) const {
+ return impl_->IsSatisfiedByCallCount(call_count);
+ }
+
+ // Returns true iff call_count calls will saturate this cardinality.
+ bool IsSaturatedByCallCount(int call_count) const {
+ return impl_->IsSaturatedByCallCount(call_count);
+ }
+
+ // Returns true iff call_count calls will over-saturate this
+ // cardinality, i.e. exceed the maximum number of allowed calls.
+ bool IsOverSaturatedByCallCount(int call_count) const {
+ return impl_->IsSaturatedByCallCount(call_count) &&
+ !impl_->IsSatisfiedByCallCount(call_count);
+ }
+
+ // Describes self to an ostream
+ void DescribeTo(::std::ostream* os) const { impl_->DescribeTo(os); }
+
+ // Describes the given actual call count to an ostream.
+ static void DescribeActualCallCountTo(int actual_call_count,
+ ::std::ostream* os);
+
+ private:
+ internal::linked_ptr<const CardinalityInterface> impl_;
+};
+
+// Creates a cardinality that allows at least n calls.
+GTEST_API_ Cardinality AtLeast(int n);
+
+// Creates a cardinality that allows at most n calls.
+GTEST_API_ Cardinality AtMost(int n);
+
+// Creates a cardinality that allows any number of calls.
+GTEST_API_ Cardinality AnyNumber();
+
+// Creates a cardinality that allows between min and max calls.
+GTEST_API_ Cardinality Between(int min, int max);
+
+// Creates a cardinality that allows exactly n calls.
+GTEST_API_ Cardinality Exactly(int n);
+
+// Creates a cardinality from its implementation.
+inline Cardinality MakeCardinality(const CardinalityInterface* c) {
+ return Cardinality(c);
+}
+
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_CARDINALITIES_H_
+// This file was GENERATED by a script. DO NOT EDIT BY HAND!!!
+
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements some commonly used variadic actions.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_ACTIONS_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_ACTIONS_H_
+
+
+namespace testing {
+namespace internal {
+
+// InvokeHelper<F> knows how to unpack an N-tuple and invoke an N-ary
+// function or method with the unpacked values, where F is a function
+// type that takes N arguments.
+template <typename Result, typename ArgumentTuple>
+class InvokeHelper;
+
+template <typename R>
+class InvokeHelper<R, ::std::tr1::tuple<> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<>&) {
+ return function();
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<>&) {
+ return (obj_ptr->*method_ptr)();
+ }
+};
+
+template <typename R, typename A1>
+class InvokeHelper<R, ::std::tr1::tuple<A1> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args));
+ }
+};
+
+template <typename R, typename A1, typename A2>
+class InvokeHelper<R, ::std::tr1::tuple<A1, A2> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1, A2>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args), get<1>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1, A2>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args), get<1>(args));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3>
+class InvokeHelper<R, ::std::tr1::tuple<A1, A2, A3> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1, A2,
+ A3>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args), get<1>(args), get<2>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1, A2, A3>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args), get<1>(args), get<2>(args));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4>
+class InvokeHelper<R, ::std::tr1::tuple<A1, A2, A3, A4> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1, A2, A3,
+ A4>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args), get<1>(args), get<2>(args), get<3>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1, A2, A3, A4>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args), get<1>(args), get<2>(args),
+ get<3>(args));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5>
+class InvokeHelper<R, ::std::tr1::tuple<A1, A2, A3, A4, A5> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1, A2, A3, A4,
+ A5>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args), get<1>(args), get<2>(args), get<3>(args),
+ get<4>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1, A2, A3, A4, A5>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args), get<1>(args), get<2>(args),
+ get<3>(args), get<4>(args));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6>
+class InvokeHelper<R, ::std::tr1::tuple<A1, A2, A3, A4, A5, A6> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1, A2, A3, A4,
+ A5, A6>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args), get<1>(args), get<2>(args), get<3>(args),
+ get<4>(args), get<5>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1, A2, A3, A4, A5, A6>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args), get<1>(args), get<2>(args),
+ get<3>(args), get<4>(args), get<5>(args));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7>
+class InvokeHelper<R, ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1, A2, A3, A4,
+ A5, A6, A7>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args), get<1>(args), get<2>(args), get<3>(args),
+ get<4>(args), get<5>(args), get<6>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1, A2, A3, A4, A5, A6,
+ A7>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args), get<1>(args), get<2>(args),
+ get<3>(args), get<4>(args), get<5>(args), get<6>(args));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8>
+class InvokeHelper<R, ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1, A2, A3, A4,
+ A5, A6, A7, A8>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args), get<1>(args), get<2>(args), get<3>(args),
+ get<4>(args), get<5>(args), get<6>(args), get<7>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7,
+ A8>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args), get<1>(args), get<2>(args),
+ get<3>(args), get<4>(args), get<5>(args), get<6>(args), get<7>(args));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8, typename A9>
+class InvokeHelper<R, ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8, A9> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1, A2, A3, A4,
+ A5, A6, A7, A8, A9>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args), get<1>(args), get<2>(args), get<3>(args),
+ get<4>(args), get<5>(args), get<6>(args), get<7>(args), get<8>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8,
+ A9>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args), get<1>(args), get<2>(args),
+ get<3>(args), get<4>(args), get<5>(args), get<6>(args), get<7>(args),
+ get<8>(args));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8, typename A9,
+ typename A10>
+class InvokeHelper<R, ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8, A9,
+ A10> > {
+ public:
+ template <typename Function>
+ static R Invoke(Function function, const ::std::tr1::tuple<A1, A2, A3, A4,
+ A5, A6, A7, A8, A9, A10>& args) {
+ using ::std::tr1::get;
+ return function(get<0>(args), get<1>(args), get<2>(args), get<3>(args),
+ get<4>(args), get<5>(args), get<6>(args), get<7>(args), get<8>(args),
+ get<9>(args));
+ }
+
+ template <class Class, typename MethodPtr>
+ static R InvokeMethod(Class* obj_ptr,
+ MethodPtr method_ptr,
+ const ::std::tr1::tuple<A1, A2, A3, A4, A5, A6, A7, A8,
+ A9, A10>& args) {
+ using ::std::tr1::get;
+ return (obj_ptr->*method_ptr)(get<0>(args), get<1>(args), get<2>(args),
+ get<3>(args), get<4>(args), get<5>(args), get<6>(args), get<7>(args),
+ get<8>(args), get<9>(args));
+ }
+};
+
+// CallableHelper has static methods for invoking "callables",
+// i.e. function pointers and functors. It uses overloading to
+// provide a uniform interface for invoking different kinds of
+// callables. In particular, you can use:
+//
+// CallableHelper<R>::Call(callable, a1, a2, ..., an)
+//
+// to invoke an n-ary callable, where R is its return type. If an
+// argument, say a2, needs to be passed by reference, you should write
+// ByRef(a2) instead of a2 in the above expression.
+template <typename R>
+class CallableHelper {
+ public:
+ // Calls a nullary callable.
+ template <typename Function>
+ static R Call(Function function) { return function(); }
+
+ // Calls a unary callable.
+
+ // We deliberately pass a1 by value instead of const reference here
+ // in case it is a C-string literal. If we had declared the
+ // parameter as 'const A1& a1' and write Call(function, "Hi"), the
+ // compiler would've thought A1 is 'char[3]', which causes trouble
+ // when you need to copy a value of type A1. By declaring the
+ // parameter as 'A1 a1', the compiler will correctly infer that A1
+ // is 'const char*' when it sees Call(function, "Hi").
+ //
+ // Since this function is defined inline, the compiler can get rid
+ // of the copying of the arguments. Therefore the performance won't
+ // be hurt.
+ template <typename Function, typename A1>
+ static R Call(Function function, A1 a1) { return function(a1); }
+
+ // Calls a binary callable.
+ template <typename Function, typename A1, typename A2>
+ static R Call(Function function, A1 a1, A2 a2) {
+ return function(a1, a2);
+ }
+
+ // Calls a ternary callable.
+ template <typename Function, typename A1, typename A2, typename A3>
+ static R Call(Function function, A1 a1, A2 a2, A3 a3) {
+ return function(a1, a2, a3);
+ }
+
+ // Calls a 4-ary callable.
+ template <typename Function, typename A1, typename A2, typename A3,
+ typename A4>
+ static R Call(Function function, A1 a1, A2 a2, A3 a3, A4 a4) {
+ return function(a1, a2, a3, a4);
+ }
+
+ // Calls a 5-ary callable.
+ template <typename Function, typename A1, typename A2, typename A3,
+ typename A4, typename A5>
+ static R Call(Function function, A1 a1, A2 a2, A3 a3, A4 a4, A5 a5) {
+ return function(a1, a2, a3, a4, a5);
+ }
+
+ // Calls a 6-ary callable.
+ template <typename Function, typename A1, typename A2, typename A3,
+ typename A4, typename A5, typename A6>
+ static R Call(Function function, A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6) {
+ return function(a1, a2, a3, a4, a5, a6);
+ }
+
+ // Calls a 7-ary callable.
+ template <typename Function, typename A1, typename A2, typename A3,
+ typename A4, typename A5, typename A6, typename A7>
+ static R Call(Function function, A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6,
+ A7 a7) {
+ return function(a1, a2, a3, a4, a5, a6, a7);
+ }
+
+ // Calls a 8-ary callable.
+ template <typename Function, typename A1, typename A2, typename A3,
+ typename A4, typename A5, typename A6, typename A7, typename A8>
+ static R Call(Function function, A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6,
+ A7 a7, A8 a8) {
+ return function(a1, a2, a3, a4, a5, a6, a7, a8);
+ }
+
+ // Calls a 9-ary callable.
+ template <typename Function, typename A1, typename A2, typename A3,
+ typename A4, typename A5, typename A6, typename A7, typename A8,
+ typename A9>
+ static R Call(Function function, A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6,
+ A7 a7, A8 a8, A9 a9) {
+ return function(a1, a2, a3, a4, a5, a6, a7, a8, a9);
+ }
+
+ // Calls a 10-ary callable.
+ template <typename Function, typename A1, typename A2, typename A3,
+ typename A4, typename A5, typename A6, typename A7, typename A8,
+ typename A9, typename A10>
+ static R Call(Function function, A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6,
+ A7 a7, A8 a8, A9 a9, A10 a10) {
+ return function(a1, a2, a3, a4, a5, a6, a7, a8, a9, a10);
+ }
+}; // class CallableHelper
+
+// An INTERNAL macro for extracting the type of a tuple field. It's
+// subject to change without notice - DO NOT USE IN USER CODE!
+#define GMOCK_FIELD_(Tuple, N) \
+ typename ::std::tr1::tuple_element<N, Tuple>::type
+
+// SelectArgs<Result, ArgumentTuple, k1, k2, ..., k_n>::type is the
+// type of an n-ary function whose i-th (1-based) argument type is the
+// k{i}-th (0-based) field of ArgumentTuple, which must be a tuple
+// type, and whose return type is Result. For example,
+// SelectArgs<int, ::std::tr1::tuple<bool, char, double, long>, 0, 3>::type
+// is int(bool, long).
+//
+// SelectArgs<Result, ArgumentTuple, k1, k2, ..., k_n>::Select(args)
+// returns the selected fields (k1, k2, ..., k_n) of args as a tuple.
+// For example,
+// SelectArgs<int, ::std::tr1::tuple<bool, char, double>, 2, 0>::Select(
+// ::std::tr1::make_tuple(true, 'a', 2.5))
+// returns ::std::tr1::tuple (2.5, true).
+//
+// The numbers in list k1, k2, ..., k_n must be >= 0, where n can be
+// in the range [0, 10]. Duplicates are allowed and they don't have
+// to be in an ascending or descending order.
+
+template <typename Result, typename ArgumentTuple, int k1, int k2, int k3,
+ int k4, int k5, int k6, int k7, int k8, int k9, int k10>
+class SelectArgs {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1),
+ GMOCK_FIELD_(ArgumentTuple, k2), GMOCK_FIELD_(ArgumentTuple, k3),
+ GMOCK_FIELD_(ArgumentTuple, k4), GMOCK_FIELD_(ArgumentTuple, k5),
+ GMOCK_FIELD_(ArgumentTuple, k6), GMOCK_FIELD_(ArgumentTuple, k7),
+ GMOCK_FIELD_(ArgumentTuple, k8), GMOCK_FIELD_(ArgumentTuple, k9),
+ GMOCK_FIELD_(ArgumentTuple, k10));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args), get<k2>(args), get<k3>(args),
+ get<k4>(args), get<k5>(args), get<k6>(args), get<k7>(args),
+ get<k8>(args), get<k9>(args), get<k10>(args));
+ }
+};
+
+template <typename Result, typename ArgumentTuple>
+class SelectArgs<Result, ArgumentTuple,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef Result type();
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& /* args */) {
+ using ::std::tr1::get;
+ return SelectedArgs();
+ }
+};
+
+template <typename Result, typename ArgumentTuple, int k1>
+class SelectArgs<Result, ArgumentTuple,
+ k1, -1, -1, -1, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args));
+ }
+};
+
+template <typename Result, typename ArgumentTuple, int k1, int k2>
+class SelectArgs<Result, ArgumentTuple,
+ k1, k2, -1, -1, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1),
+ GMOCK_FIELD_(ArgumentTuple, k2));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args), get<k2>(args));
+ }
+};
+
+template <typename Result, typename ArgumentTuple, int k1, int k2, int k3>
+class SelectArgs<Result, ArgumentTuple,
+ k1, k2, k3, -1, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1),
+ GMOCK_FIELD_(ArgumentTuple, k2), GMOCK_FIELD_(ArgumentTuple, k3));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args), get<k2>(args), get<k3>(args));
+ }
+};
+
+template <typename Result, typename ArgumentTuple, int k1, int k2, int k3,
+ int k4>
+class SelectArgs<Result, ArgumentTuple,
+ k1, k2, k3, k4, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1),
+ GMOCK_FIELD_(ArgumentTuple, k2), GMOCK_FIELD_(ArgumentTuple, k3),
+ GMOCK_FIELD_(ArgumentTuple, k4));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args), get<k2>(args), get<k3>(args),
+ get<k4>(args));
+ }
+};
+
+template <typename Result, typename ArgumentTuple, int k1, int k2, int k3,
+ int k4, int k5>
+class SelectArgs<Result, ArgumentTuple,
+ k1, k2, k3, k4, k5, -1, -1, -1, -1, -1> {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1),
+ GMOCK_FIELD_(ArgumentTuple, k2), GMOCK_FIELD_(ArgumentTuple, k3),
+ GMOCK_FIELD_(ArgumentTuple, k4), GMOCK_FIELD_(ArgumentTuple, k5));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args), get<k2>(args), get<k3>(args),
+ get<k4>(args), get<k5>(args));
+ }
+};
+
+template <typename Result, typename ArgumentTuple, int k1, int k2, int k3,
+ int k4, int k5, int k6>
+class SelectArgs<Result, ArgumentTuple,
+ k1, k2, k3, k4, k5, k6, -1, -1, -1, -1> {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1),
+ GMOCK_FIELD_(ArgumentTuple, k2), GMOCK_FIELD_(ArgumentTuple, k3),
+ GMOCK_FIELD_(ArgumentTuple, k4), GMOCK_FIELD_(ArgumentTuple, k5),
+ GMOCK_FIELD_(ArgumentTuple, k6));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args), get<k2>(args), get<k3>(args),
+ get<k4>(args), get<k5>(args), get<k6>(args));
+ }
+};
+
+template <typename Result, typename ArgumentTuple, int k1, int k2, int k3,
+ int k4, int k5, int k6, int k7>
+class SelectArgs<Result, ArgumentTuple,
+ k1, k2, k3, k4, k5, k6, k7, -1, -1, -1> {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1),
+ GMOCK_FIELD_(ArgumentTuple, k2), GMOCK_FIELD_(ArgumentTuple, k3),
+ GMOCK_FIELD_(ArgumentTuple, k4), GMOCK_FIELD_(ArgumentTuple, k5),
+ GMOCK_FIELD_(ArgumentTuple, k6), GMOCK_FIELD_(ArgumentTuple, k7));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args), get<k2>(args), get<k3>(args),
+ get<k4>(args), get<k5>(args), get<k6>(args), get<k7>(args));
+ }
+};
+
+template <typename Result, typename ArgumentTuple, int k1, int k2, int k3,
+ int k4, int k5, int k6, int k7, int k8>
+class SelectArgs<Result, ArgumentTuple,
+ k1, k2, k3, k4, k5, k6, k7, k8, -1, -1> {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1),
+ GMOCK_FIELD_(ArgumentTuple, k2), GMOCK_FIELD_(ArgumentTuple, k3),
+ GMOCK_FIELD_(ArgumentTuple, k4), GMOCK_FIELD_(ArgumentTuple, k5),
+ GMOCK_FIELD_(ArgumentTuple, k6), GMOCK_FIELD_(ArgumentTuple, k7),
+ GMOCK_FIELD_(ArgumentTuple, k8));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args), get<k2>(args), get<k3>(args),
+ get<k4>(args), get<k5>(args), get<k6>(args), get<k7>(args),
+ get<k8>(args));
+ }
+};
+
+template <typename Result, typename ArgumentTuple, int k1, int k2, int k3,
+ int k4, int k5, int k6, int k7, int k8, int k9>
+class SelectArgs<Result, ArgumentTuple,
+ k1, k2, k3, k4, k5, k6, k7, k8, k9, -1> {
+ public:
+ typedef Result type(GMOCK_FIELD_(ArgumentTuple, k1),
+ GMOCK_FIELD_(ArgumentTuple, k2), GMOCK_FIELD_(ArgumentTuple, k3),
+ GMOCK_FIELD_(ArgumentTuple, k4), GMOCK_FIELD_(ArgumentTuple, k5),
+ GMOCK_FIELD_(ArgumentTuple, k6), GMOCK_FIELD_(ArgumentTuple, k7),
+ GMOCK_FIELD_(ArgumentTuple, k8), GMOCK_FIELD_(ArgumentTuple, k9));
+ typedef typename Function<type>::ArgumentTuple SelectedArgs;
+ static SelectedArgs Select(const ArgumentTuple& args) {
+ using ::std::tr1::get;
+ return SelectedArgs(get<k1>(args), get<k2>(args), get<k3>(args),
+ get<k4>(args), get<k5>(args), get<k6>(args), get<k7>(args),
+ get<k8>(args), get<k9>(args));
+ }
+};
+
+#undef GMOCK_FIELD_
+
+// Implements the WithArgs action.
+template <typename InnerAction, int k1 = -1, int k2 = -1, int k3 = -1,
+ int k4 = -1, int k5 = -1, int k6 = -1, int k7 = -1, int k8 = -1,
+ int k9 = -1, int k10 = -1>
+class WithArgsAction {
+ public:
+ explicit WithArgsAction(const InnerAction& action) : action_(action) {}
+
+ template <typename F>
+ operator Action<F>() const { return MakeAction(new Impl<F>(action_)); }
+
+ private:
+ template <typename F>
+ class Impl : public ActionInterface<F> {
+ public:
+ typedef typename Function<F>::Result Result;
+ typedef typename Function<F>::ArgumentTuple ArgumentTuple;
+
+ explicit Impl(const InnerAction& action) : action_(action) {}
+
+ virtual Result Perform(const ArgumentTuple& args) {
+ return action_.Perform(SelectArgs<Result, ArgumentTuple, k1, k2, k3, k4,
+ k5, k6, k7, k8, k9, k10>::Select(args));
+ }
+
+ private:
+ typedef typename SelectArgs<Result, ArgumentTuple,
+ k1, k2, k3, k4, k5, k6, k7, k8, k9, k10>::type InnerFunctionType;
+
+ Action<InnerFunctionType> action_;
+ };
+
+ const InnerAction action_;
+
+ GTEST_DISALLOW_ASSIGN_(WithArgsAction);
+};
+
+// A macro from the ACTION* family (defined later in this file)
+// defines an action that can be used in a mock function. Typically,
+// these actions only care about a subset of the arguments of the mock
+// function. For example, if such an action only uses the second
+// argument, it can be used in any mock function that takes >= 2
+// arguments where the type of the second argument is compatible.
+//
+// Therefore, the action implementation must be prepared to take more
+// arguments than it needs. The ExcessiveArg type is used to
+// represent those excessive arguments. In order to keep the compiler
+// error messages tractable, we define it in the testing namespace
+// instead of testing::internal. However, this is an INTERNAL TYPE
+// and subject to change without notice, so a user MUST NOT USE THIS
+// TYPE DIRECTLY.
+struct ExcessiveArg {};
+
+// A helper class needed for implementing the ACTION* macros.
+template <typename Result, class Impl>
+class ActionHelper {
+ public:
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<>(args, ExcessiveArg(),
+ ExcessiveArg(), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg(), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg());
+ }
+
+ template <typename A0>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0>(args, get<0>(args),
+ ExcessiveArg(), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg(), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg());
+ }
+
+ template <typename A0, typename A1>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0, A1>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0, A1>(args, get<0>(args),
+ get<1>(args), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg(), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg());
+ }
+
+ template <typename A0, typename A1, typename A2>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0, A1, A2>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0, A1, A2>(args, get<0>(args),
+ get<1>(args), get<2>(args), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg(), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg());
+ }
+
+ template <typename A0, typename A1, typename A2, typename A3>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0, A1, A2,
+ A3>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0, A1, A2, A3>(args, get<0>(args),
+ get<1>(args), get<2>(args), get<3>(args), ExcessiveArg(),
+ ExcessiveArg(), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg());
+ }
+
+ template <typename A0, typename A1, typename A2, typename A3, typename A4>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0, A1, A2, A3,
+ A4>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0, A1, A2, A3, A4>(args,
+ get<0>(args), get<1>(args), get<2>(args), get<3>(args), get<4>(args),
+ ExcessiveArg(), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg());
+ }
+
+ template <typename A0, typename A1, typename A2, typename A3, typename A4,
+ typename A5>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0, A1, A2, A3, A4,
+ A5>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0, A1, A2, A3, A4, A5>(args,
+ get<0>(args), get<1>(args), get<2>(args), get<3>(args), get<4>(args),
+ get<5>(args), ExcessiveArg(), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg());
+ }
+
+ template <typename A0, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0, A1, A2, A3, A4,
+ A5, A6>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0, A1, A2, A3, A4, A5, A6>(args,
+ get<0>(args), get<1>(args), get<2>(args), get<3>(args), get<4>(args),
+ get<5>(args), get<6>(args), ExcessiveArg(), ExcessiveArg(),
+ ExcessiveArg());
+ }
+
+ template <typename A0, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0, A1, A2, A3, A4,
+ A5, A6, A7>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0, A1, A2, A3, A4, A5, A6,
+ A7>(args, get<0>(args), get<1>(args), get<2>(args), get<3>(args),
+ get<4>(args), get<5>(args), get<6>(args), get<7>(args), ExcessiveArg(),
+ ExcessiveArg());
+ }
+
+ template <typename A0, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0, A1, A2, A3, A4,
+ A5, A6, A7, A8>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0, A1, A2, A3, A4, A5, A6, A7,
+ A8>(args, get<0>(args), get<1>(args), get<2>(args), get<3>(args),
+ get<4>(args), get<5>(args), get<6>(args), get<7>(args), get<8>(args),
+ ExcessiveArg());
+ }
+
+ template <typename A0, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8, typename A9>
+ static Result Perform(Impl* impl, const ::std::tr1::tuple<A0, A1, A2, A3, A4,
+ A5, A6, A7, A8, A9>& args) {
+ using ::std::tr1::get;
+ return impl->template gmock_PerformImpl<A0, A1, A2, A3, A4, A5, A6, A7, A8,
+ A9>(args, get<0>(args), get<1>(args), get<2>(args), get<3>(args),
+ get<4>(args), get<5>(args), get<6>(args), get<7>(args), get<8>(args),
+ get<9>(args));
+ }
+};
+
+} // namespace internal
+
+// Various overloads for Invoke().
+
+// WithArgs<N1, N2, ..., Nk>(an_action) creates an action that passes
+// the selected arguments of the mock function to an_action and
+// performs it. It serves as an adaptor between actions with
+// different argument lists. C++ doesn't support default arguments for
+// function templates, so we have to overload it.
+template <int k1, typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1>(action);
+}
+
+template <int k1, int k2, typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1, k2>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1, k2>(action);
+}
+
+template <int k1, int k2, int k3, typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1, k2, k3>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1, k2, k3>(action);
+}
+
+template <int k1, int k2, int k3, int k4, typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1, k2, k3, k4>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1, k2, k3, k4>(action);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5>(action);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6>(action);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, int k7,
+ typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6, k7>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6,
+ k7>(action);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, int k7, int k8,
+ typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6, k7, k8>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6, k7,
+ k8>(action);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, int k7, int k8,
+ int k9, typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6, k7, k8, k9>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6, k7, k8,
+ k9>(action);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, int k7, int k8,
+ int k9, int k10, typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6, k7, k8,
+ k9, k10>
+WithArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k1, k2, k3, k4, k5, k6, k7, k8,
+ k9, k10>(action);
+}
+
+// Creates an action that does actions a1, a2, ..., sequentially in
+// each invocation.
+template <typename Action1, typename Action2>
+inline internal::DoBothAction<Action1, Action2>
+DoAll(Action1 a1, Action2 a2) {
+ return internal::DoBothAction<Action1, Action2>(a1, a2);
+}
+
+template <typename Action1, typename Action2, typename Action3>
+inline internal::DoBothAction<Action1, internal::DoBothAction<Action2,
+ Action3> >
+DoAll(Action1 a1, Action2 a2, Action3 a3) {
+ return DoAll(a1, DoAll(a2, a3));
+}
+
+template <typename Action1, typename Action2, typename Action3,
+ typename Action4>
+inline internal::DoBothAction<Action1, internal::DoBothAction<Action2,
+ internal::DoBothAction<Action3, Action4> > >
+DoAll(Action1 a1, Action2 a2, Action3 a3, Action4 a4) {
+ return DoAll(a1, DoAll(a2, a3, a4));
+}
+
+template <typename Action1, typename Action2, typename Action3,
+ typename Action4, typename Action5>
+inline internal::DoBothAction<Action1, internal::DoBothAction<Action2,
+ internal::DoBothAction<Action3, internal::DoBothAction<Action4,
+ Action5> > > >
+DoAll(Action1 a1, Action2 a2, Action3 a3, Action4 a4, Action5 a5) {
+ return DoAll(a1, DoAll(a2, a3, a4, a5));
+}
+
+template <typename Action1, typename Action2, typename Action3,
+ typename Action4, typename Action5, typename Action6>
+inline internal::DoBothAction<Action1, internal::DoBothAction<Action2,
+ internal::DoBothAction<Action3, internal::DoBothAction<Action4,
+ internal::DoBothAction<Action5, Action6> > > > >
+DoAll(Action1 a1, Action2 a2, Action3 a3, Action4 a4, Action5 a5, Action6 a6) {
+ return DoAll(a1, DoAll(a2, a3, a4, a5, a6));
+}
+
+template <typename Action1, typename Action2, typename Action3,
+ typename Action4, typename Action5, typename Action6, typename Action7>
+inline internal::DoBothAction<Action1, internal::DoBothAction<Action2,
+ internal::DoBothAction<Action3, internal::DoBothAction<Action4,
+ internal::DoBothAction<Action5, internal::DoBothAction<Action6,
+ Action7> > > > > >
+DoAll(Action1 a1, Action2 a2, Action3 a3, Action4 a4, Action5 a5, Action6 a6,
+ Action7 a7) {
+ return DoAll(a1, DoAll(a2, a3, a4, a5, a6, a7));
+}
+
+template <typename Action1, typename Action2, typename Action3,
+ typename Action4, typename Action5, typename Action6, typename Action7,
+ typename Action8>
+inline internal::DoBothAction<Action1, internal::DoBothAction<Action2,
+ internal::DoBothAction<Action3, internal::DoBothAction<Action4,
+ internal::DoBothAction<Action5, internal::DoBothAction<Action6,
+ internal::DoBothAction<Action7, Action8> > > > > > >
+DoAll(Action1 a1, Action2 a2, Action3 a3, Action4 a4, Action5 a5, Action6 a6,
+ Action7 a7, Action8 a8) {
+ return DoAll(a1, DoAll(a2, a3, a4, a5, a6, a7, a8));
+}
+
+template <typename Action1, typename Action2, typename Action3,
+ typename Action4, typename Action5, typename Action6, typename Action7,
+ typename Action8, typename Action9>
+inline internal::DoBothAction<Action1, internal::DoBothAction<Action2,
+ internal::DoBothAction<Action3, internal::DoBothAction<Action4,
+ internal::DoBothAction<Action5, internal::DoBothAction<Action6,
+ internal::DoBothAction<Action7, internal::DoBothAction<Action8,
+ Action9> > > > > > > >
+DoAll(Action1 a1, Action2 a2, Action3 a3, Action4 a4, Action5 a5, Action6 a6,
+ Action7 a7, Action8 a8, Action9 a9) {
+ return DoAll(a1, DoAll(a2, a3, a4, a5, a6, a7, a8, a9));
+}
+
+template <typename Action1, typename Action2, typename Action3,
+ typename Action4, typename Action5, typename Action6, typename Action7,
+ typename Action8, typename Action9, typename Action10>
+inline internal::DoBothAction<Action1, internal::DoBothAction<Action2,
+ internal::DoBothAction<Action3, internal::DoBothAction<Action4,
+ internal::DoBothAction<Action5, internal::DoBothAction<Action6,
+ internal::DoBothAction<Action7, internal::DoBothAction<Action8,
+ internal::DoBothAction<Action9, Action10> > > > > > > > >
+DoAll(Action1 a1, Action2 a2, Action3 a3, Action4 a4, Action5 a5, Action6 a6,
+ Action7 a7, Action8 a8, Action9 a9, Action10 a10) {
+ return DoAll(a1, DoAll(a2, a3, a4, a5, a6, a7, a8, a9, a10));
+}
+
+} // namespace testing
+
+// The ACTION* family of macros can be used in a namespace scope to
+// define custom actions easily. The syntax:
+//
+// ACTION(name) { statements; }
+//
+// will define an action with the given name that executes the
+// statements. The value returned by the statements will be used as
+// the return value of the action. Inside the statements, you can
+// refer to the K-th (0-based) argument of the mock function by
+// 'argK', and refer to its type by 'argK_type'. For example:
+//
+// ACTION(IncrementArg1) {
+// arg1_type temp = arg1;
+// return ++(*temp);
+// }
+//
+// allows you to write
+//
+// ...WillOnce(IncrementArg1());
+//
+// You can also refer to the entire argument tuple and its type by
+// 'args' and 'args_type', and refer to the mock function type and its
+// return type by 'function_type' and 'return_type'.
+//
+// Note that you don't need to specify the types of the mock function
+// arguments. However rest assured that your code is still type-safe:
+// you'll get a compiler error if *arg1 doesn't support the ++
+// operator, or if the type of ++(*arg1) isn't compatible with the
+// mock function's return type, for example.
+//
+// Sometimes you'll want to parameterize the action. For that you can use
+// another macro:
+//
+// ACTION_P(name, param_name) { statements; }
+//
+// For example:
+//
+// ACTION_P(Add, n) { return arg0 + n; }
+//
+// will allow you to write:
+//
+// ...WillOnce(Add(5));
+//
+// Note that you don't need to provide the type of the parameter
+// either. If you need to reference the type of a parameter named
+// 'foo', you can write 'foo_type'. For example, in the body of
+// ACTION_P(Add, n) above, you can write 'n_type' to refer to the type
+// of 'n'.
+//
+// We also provide ACTION_P2, ACTION_P3, ..., up to ACTION_P10 to support
+// multi-parameter actions.
+//
+// For the purpose of typing, you can view
+//
+// ACTION_Pk(Foo, p1, ..., pk) { ... }
+//
+// as shorthand for
+//
+// template <typename p1_type, ..., typename pk_type>
+// FooActionPk<p1_type, ..., pk_type> Foo(p1_type p1, ..., pk_type pk) { ... }
+//
+// In particular, you can provide the template type arguments
+// explicitly when invoking Foo(), as in Foo<long, bool>(5, false);
+// although usually you can rely on the compiler to infer the types
+// for you automatically. You can assign the result of expression
+// Foo(p1, ..., pk) to a variable of type FooActionPk<p1_type, ...,
+// pk_type>. This can be useful when composing actions.
+//
+// You can also overload actions with different numbers of parameters:
+//
+// ACTION_P(Plus, a) { ... }
+// ACTION_P2(Plus, a, b) { ... }
+//
+// While it's tempting to always use the ACTION* macros when defining
+// a new action, you should also consider implementing ActionInterface
+// or using MakePolymorphicAction() instead, especially if you need to
+// use the action a lot. While these approaches require more work,
+// they give you more control on the types of the mock function
+// arguments and the action parameters, which in general leads to
+// better compiler error messages that pay off in the long run. They
+// also allow overloading actions based on parameter types (as opposed
+// to just based on the number of parameters).
+//
+// CAVEAT:
+//
+// ACTION*() can only be used in a namespace scope. The reason is
+// that C++ doesn't yet allow function-local types to be used to
+// instantiate templates. The up-coming C++0x standard will fix this.
+// Once that's done, we'll consider supporting using ACTION*() inside
+// a function.
+//
+// MORE INFORMATION:
+//
+// To learn more about using these macros, please search for 'ACTION'
+// on http://code.google.com/p/googlemock/wiki/CookBook.
+
+// An internal macro needed for implementing ACTION*().
+#define GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_\
+ const args_type& args GTEST_ATTRIBUTE_UNUSED_, \
+ arg0_type arg0 GTEST_ATTRIBUTE_UNUSED_, \
+ arg1_type arg1 GTEST_ATTRIBUTE_UNUSED_, \
+ arg2_type arg2 GTEST_ATTRIBUTE_UNUSED_, \
+ arg3_type arg3 GTEST_ATTRIBUTE_UNUSED_, \
+ arg4_type arg4 GTEST_ATTRIBUTE_UNUSED_, \
+ arg5_type arg5 GTEST_ATTRIBUTE_UNUSED_, \
+ arg6_type arg6 GTEST_ATTRIBUTE_UNUSED_, \
+ arg7_type arg7 GTEST_ATTRIBUTE_UNUSED_, \
+ arg8_type arg8 GTEST_ATTRIBUTE_UNUSED_, \
+ arg9_type arg9 GTEST_ATTRIBUTE_UNUSED_
+
+// Sometimes you want to give an action explicit template parameters
+// that cannot be inferred from its value parameters. ACTION() and
+// ACTION_P*() don't support that. ACTION_TEMPLATE() remedies that
+// and can be viewed as an extension to ACTION() and ACTION_P*().
+//
+// The syntax:
+//
+// ACTION_TEMPLATE(ActionName,
+// HAS_m_TEMPLATE_PARAMS(kind1, name1, ..., kind_m, name_m),
+// AND_n_VALUE_PARAMS(p1, ..., p_n)) { statements; }
+//
+// defines an action template that takes m explicit template
+// parameters and n value parameters. name_i is the name of the i-th
+// template parameter, and kind_i specifies whether it's a typename,
+// an integral constant, or a template. p_i is the name of the i-th
+// value parameter.
+//
+// Example:
+//
+// // DuplicateArg<k, T>(output) converts the k-th argument of the mock
+// // function to type T and copies it to *output.
+// ACTION_TEMPLATE(DuplicateArg,
+// HAS_2_TEMPLATE_PARAMS(int, k, typename, T),
+// AND_1_VALUE_PARAMS(output)) {
+// *output = T(std::tr1::get<k>(args));
+// }
+// ...
+// int n;
+// EXPECT_CALL(mock, Foo(_, _))
+// .WillOnce(DuplicateArg<1, unsigned char>(&n));
+//
+// To create an instance of an action template, write:
+//
+// ActionName<t1, ..., t_m>(v1, ..., v_n)
+//
+// where the ts are the template arguments and the vs are the value
+// arguments. The value argument types are inferred by the compiler.
+// If you want to explicitly specify the value argument types, you can
+// provide additional template arguments:
+//
+// ActionName<t1, ..., t_m, u1, ..., u_k>(v1, ..., v_n)
+//
+// where u_i is the desired type of v_i.
+//
+// ACTION_TEMPLATE and ACTION/ACTION_P* can be overloaded on the
+// number of value parameters, but not on the number of template
+// parameters. Without the restriction, the meaning of the following
+// is unclear:
+//
+// OverloadedAction<int, bool>(x);
+//
+// Are we using a single-template-parameter action where 'bool' refers
+// to the type of x, or are we using a two-template-parameter action
+// where the compiler is asked to infer the type of x?
+//
+// Implementation notes:
+//
+// GMOCK_INTERNAL_*_HAS_m_TEMPLATE_PARAMS and
+// GMOCK_INTERNAL_*_AND_n_VALUE_PARAMS are internal macros for
+// implementing ACTION_TEMPLATE. The main trick we use is to create
+// new macro invocations when expanding a macro. For example, we have
+//
+// #define ACTION_TEMPLATE(name, template_params, value_params)
+// ... GMOCK_INTERNAL_DECL_##template_params ...
+//
+// which causes ACTION_TEMPLATE(..., HAS_1_TEMPLATE_PARAMS(typename, T), ...)
+// to expand to
+//
+// ... GMOCK_INTERNAL_DECL_HAS_1_TEMPLATE_PARAMS(typename, T) ...
+//
+// Since GMOCK_INTERNAL_DECL_HAS_1_TEMPLATE_PARAMS is a macro, the
+// preprocessor will continue to expand it to
+//
+// ... typename T ...
+//
+// This technique conforms to the C++ standard and is portable. It
+// allows us to implement action templates using O(N) code, where N is
+// the maximum number of template/value parameters supported. Without
+// using it, we'd have to devote O(N^2) amount of code to implement all
+// combinations of m and n.
+
+// Declares the template parameters.
+#define GMOCK_INTERNAL_DECL_HAS_1_TEMPLATE_PARAMS(kind0, name0) kind0 name0
+#define GMOCK_INTERNAL_DECL_HAS_2_TEMPLATE_PARAMS(kind0, name0, kind1, \
+ name1) kind0 name0, kind1 name1
+#define GMOCK_INTERNAL_DECL_HAS_3_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2) kind0 name0, kind1 name1, kind2 name2
+#define GMOCK_INTERNAL_DECL_HAS_4_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3) kind0 name0, kind1 name1, kind2 name2, \
+ kind3 name3
+#define GMOCK_INTERNAL_DECL_HAS_5_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4) kind0 name0, kind1 name1, \
+ kind2 name2, kind3 name3, kind4 name4
+#define GMOCK_INTERNAL_DECL_HAS_6_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4, kind5, name5) kind0 name0, \
+ kind1 name1, kind2 name2, kind3 name3, kind4 name4, kind5 name5
+#define GMOCK_INTERNAL_DECL_HAS_7_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4, kind5, name5, kind6, \
+ name6) kind0 name0, kind1 name1, kind2 name2, kind3 name3, kind4 name4, \
+ kind5 name5, kind6 name6
+#define GMOCK_INTERNAL_DECL_HAS_8_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4, kind5, name5, kind6, name6, \
+ kind7, name7) kind0 name0, kind1 name1, kind2 name2, kind3 name3, \
+ kind4 name4, kind5 name5, kind6 name6, kind7 name7
+#define GMOCK_INTERNAL_DECL_HAS_9_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4, kind5, name5, kind6, name6, \
+ kind7, name7, kind8, name8) kind0 name0, kind1 name1, kind2 name2, \
+ kind3 name3, kind4 name4, kind5 name5, kind6 name6, kind7 name7, \
+ kind8 name8
+#define GMOCK_INTERNAL_DECL_HAS_10_TEMPLATE_PARAMS(kind0, name0, kind1, \
+ name1, kind2, name2, kind3, name3, kind4, name4, kind5, name5, kind6, \
+ name6, kind7, name7, kind8, name8, kind9, name9) kind0 name0, \
+ kind1 name1, kind2 name2, kind3 name3, kind4 name4, kind5 name5, \
+ kind6 name6, kind7 name7, kind8 name8, kind9 name9
+
+// Lists the template parameters.
+#define GMOCK_INTERNAL_LIST_HAS_1_TEMPLATE_PARAMS(kind0, name0) name0
+#define GMOCK_INTERNAL_LIST_HAS_2_TEMPLATE_PARAMS(kind0, name0, kind1, \
+ name1) name0, name1
+#define GMOCK_INTERNAL_LIST_HAS_3_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2) name0, name1, name2
+#define GMOCK_INTERNAL_LIST_HAS_4_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3) name0, name1, name2, name3
+#define GMOCK_INTERNAL_LIST_HAS_5_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4) name0, name1, name2, name3, \
+ name4
+#define GMOCK_INTERNAL_LIST_HAS_6_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4, kind5, name5) name0, name1, \
+ name2, name3, name4, name5
+#define GMOCK_INTERNAL_LIST_HAS_7_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4, kind5, name5, kind6, \
+ name6) name0, name1, name2, name3, name4, name5, name6
+#define GMOCK_INTERNAL_LIST_HAS_8_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4, kind5, name5, kind6, name6, \
+ kind7, name7) name0, name1, name2, name3, name4, name5, name6, name7
+#define GMOCK_INTERNAL_LIST_HAS_9_TEMPLATE_PARAMS(kind0, name0, kind1, name1, \
+ kind2, name2, kind3, name3, kind4, name4, kind5, name5, kind6, name6, \
+ kind7, name7, kind8, name8) name0, name1, name2, name3, name4, name5, \
+ name6, name7, name8
+#define GMOCK_INTERNAL_LIST_HAS_10_TEMPLATE_PARAMS(kind0, name0, kind1, \
+ name1, kind2, name2, kind3, name3, kind4, name4, kind5, name5, kind6, \
+ name6, kind7, name7, kind8, name8, kind9, name9) name0, name1, name2, \
+ name3, name4, name5, name6, name7, name8, name9
+
+// Declares the types of value parameters.
+#define GMOCK_INTERNAL_DECL_TYPE_AND_0_VALUE_PARAMS()
+#define GMOCK_INTERNAL_DECL_TYPE_AND_1_VALUE_PARAMS(p0) , typename p0##_type
+#define GMOCK_INTERNAL_DECL_TYPE_AND_2_VALUE_PARAMS(p0, p1) , \
+ typename p0##_type, typename p1##_type
+#define GMOCK_INTERNAL_DECL_TYPE_AND_3_VALUE_PARAMS(p0, p1, p2) , \
+ typename p0##_type, typename p1##_type, typename p2##_type
+#define GMOCK_INTERNAL_DECL_TYPE_AND_4_VALUE_PARAMS(p0, p1, p2, p3) , \
+ typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type
+#define GMOCK_INTERNAL_DECL_TYPE_AND_5_VALUE_PARAMS(p0, p1, p2, p3, p4) , \
+ typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type
+#define GMOCK_INTERNAL_DECL_TYPE_AND_6_VALUE_PARAMS(p0, p1, p2, p3, p4, p5) , \
+ typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type
+#define GMOCK_INTERNAL_DECL_TYPE_AND_7_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6) , typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type
+#define GMOCK_INTERNAL_DECL_TYPE_AND_8_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6, p7) , typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type
+#define GMOCK_INTERNAL_DECL_TYPE_AND_9_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6, p7, p8) , typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type
+#define GMOCK_INTERNAL_DECL_TYPE_AND_10_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6, p7, p8, p9) , typename p0##_type, typename p1##_type, \
+ typename p2##_type, typename p3##_type, typename p4##_type, \
+ typename p5##_type, typename p6##_type, typename p7##_type, \
+ typename p8##_type, typename p9##_type
+
+// Initializes the value parameters.
+#define GMOCK_INTERNAL_INIT_AND_0_VALUE_PARAMS()\
+ ()
+#define GMOCK_INTERNAL_INIT_AND_1_VALUE_PARAMS(p0)\
+ (p0##_type gmock_p0) : p0(gmock_p0)
+#define GMOCK_INTERNAL_INIT_AND_2_VALUE_PARAMS(p0, p1)\
+ (p0##_type gmock_p0, p1##_type gmock_p1) : p0(gmock_p0), p1(gmock_p1)
+#define GMOCK_INTERNAL_INIT_AND_3_VALUE_PARAMS(p0, p1, p2)\
+ (p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2)
+#define GMOCK_INTERNAL_INIT_AND_4_VALUE_PARAMS(p0, p1, p2, p3)\
+ (p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3)
+#define GMOCK_INTERNAL_INIT_AND_5_VALUE_PARAMS(p0, p1, p2, p3, p4)\
+ (p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4) : p0(gmock_p0), p1(gmock_p1), \
+ p2(gmock_p2), p3(gmock_p3), p4(gmock_p4)
+#define GMOCK_INTERNAL_INIT_AND_6_VALUE_PARAMS(p0, p1, p2, p3, p4, p5)\
+ (p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5)
+#define GMOCK_INTERNAL_INIT_AND_7_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6)\
+ (p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6)
+#define GMOCK_INTERNAL_INIT_AND_8_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, p7)\
+ (p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6, p7##_type gmock_p7) : p0(gmock_p0), p1(gmock_p1), \
+ p2(gmock_p2), p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), \
+ p7(gmock_p7)
+#define GMOCK_INTERNAL_INIT_AND_9_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8)\
+ (p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6, p7##_type gmock_p7, \
+ p8##_type gmock_p8) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), p7(gmock_p7), \
+ p8(gmock_p8)
+#define GMOCK_INTERNAL_INIT_AND_10_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8, p9)\
+ (p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6, p7##_type gmock_p7, p8##_type gmock_p8, \
+ p9##_type gmock_p9) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), p7(gmock_p7), \
+ p8(gmock_p8), p9(gmock_p9)
+
+// Declares the fields for storing the value parameters.
+#define GMOCK_INTERNAL_DEFN_AND_0_VALUE_PARAMS()
+#define GMOCK_INTERNAL_DEFN_AND_1_VALUE_PARAMS(p0) p0##_type p0;
+#define GMOCK_INTERNAL_DEFN_AND_2_VALUE_PARAMS(p0, p1) p0##_type p0; \
+ p1##_type p1;
+#define GMOCK_INTERNAL_DEFN_AND_3_VALUE_PARAMS(p0, p1, p2) p0##_type p0; \
+ p1##_type p1; p2##_type p2;
+#define GMOCK_INTERNAL_DEFN_AND_4_VALUE_PARAMS(p0, p1, p2, p3) p0##_type p0; \
+ p1##_type p1; p2##_type p2; p3##_type p3;
+#define GMOCK_INTERNAL_DEFN_AND_5_VALUE_PARAMS(p0, p1, p2, p3, \
+ p4) p0##_type p0; p1##_type p1; p2##_type p2; p3##_type p3; p4##_type p4;
+#define GMOCK_INTERNAL_DEFN_AND_6_VALUE_PARAMS(p0, p1, p2, p3, p4, \
+ p5) p0##_type p0; p1##_type p1; p2##_type p2; p3##_type p3; p4##_type p4; \
+ p5##_type p5;
+#define GMOCK_INTERNAL_DEFN_AND_7_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6) p0##_type p0; p1##_type p1; p2##_type p2; p3##_type p3; p4##_type p4; \
+ p5##_type p5; p6##_type p6;
+#define GMOCK_INTERNAL_DEFN_AND_8_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7) p0##_type p0; p1##_type p1; p2##_type p2; p3##_type p3; p4##_type p4; \
+ p5##_type p5; p6##_type p6; p7##_type p7;
+#define GMOCK_INTERNAL_DEFN_AND_9_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8) p0##_type p0; p1##_type p1; p2##_type p2; p3##_type p3; \
+ p4##_type p4; p5##_type p5; p6##_type p6; p7##_type p7; p8##_type p8;
+#define GMOCK_INTERNAL_DEFN_AND_10_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8, p9) p0##_type p0; p1##_type p1; p2##_type p2; p3##_type p3; \
+ p4##_type p4; p5##_type p5; p6##_type p6; p7##_type p7; p8##_type p8; \
+ p9##_type p9;
+
+// Lists the value parameters.
+#define GMOCK_INTERNAL_LIST_AND_0_VALUE_PARAMS()
+#define GMOCK_INTERNAL_LIST_AND_1_VALUE_PARAMS(p0) p0
+#define GMOCK_INTERNAL_LIST_AND_2_VALUE_PARAMS(p0, p1) p0, p1
+#define GMOCK_INTERNAL_LIST_AND_3_VALUE_PARAMS(p0, p1, p2) p0, p1, p2
+#define GMOCK_INTERNAL_LIST_AND_4_VALUE_PARAMS(p0, p1, p2, p3) p0, p1, p2, p3
+#define GMOCK_INTERNAL_LIST_AND_5_VALUE_PARAMS(p0, p1, p2, p3, p4) p0, p1, \
+ p2, p3, p4
+#define GMOCK_INTERNAL_LIST_AND_6_VALUE_PARAMS(p0, p1, p2, p3, p4, p5) p0, \
+ p1, p2, p3, p4, p5
+#define GMOCK_INTERNAL_LIST_AND_7_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6) p0, p1, p2, p3, p4, p5, p6
+#define GMOCK_INTERNAL_LIST_AND_8_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7) p0, p1, p2, p3, p4, p5, p6, p7
+#define GMOCK_INTERNAL_LIST_AND_9_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8) p0, p1, p2, p3, p4, p5, p6, p7, p8
+#define GMOCK_INTERNAL_LIST_AND_10_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8, p9) p0, p1, p2, p3, p4, p5, p6, p7, p8, p9
+
+// Lists the value parameter types.
+#define GMOCK_INTERNAL_LIST_TYPE_AND_0_VALUE_PARAMS()
+#define GMOCK_INTERNAL_LIST_TYPE_AND_1_VALUE_PARAMS(p0) , p0##_type
+#define GMOCK_INTERNAL_LIST_TYPE_AND_2_VALUE_PARAMS(p0, p1) , p0##_type, \
+ p1##_type
+#define GMOCK_INTERNAL_LIST_TYPE_AND_3_VALUE_PARAMS(p0, p1, p2) , p0##_type, \
+ p1##_type, p2##_type
+#define GMOCK_INTERNAL_LIST_TYPE_AND_4_VALUE_PARAMS(p0, p1, p2, p3) , \
+ p0##_type, p1##_type, p2##_type, p3##_type
+#define GMOCK_INTERNAL_LIST_TYPE_AND_5_VALUE_PARAMS(p0, p1, p2, p3, p4) , \
+ p0##_type, p1##_type, p2##_type, p3##_type, p4##_type
+#define GMOCK_INTERNAL_LIST_TYPE_AND_6_VALUE_PARAMS(p0, p1, p2, p3, p4, p5) , \
+ p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, p5##_type
+#define GMOCK_INTERNAL_LIST_TYPE_AND_7_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6) , p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, p5##_type, \
+ p6##_type
+#define GMOCK_INTERNAL_LIST_TYPE_AND_8_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6, p7) , p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type, p7##_type
+#define GMOCK_INTERNAL_LIST_TYPE_AND_9_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6, p7, p8) , p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type, p7##_type, p8##_type
+#define GMOCK_INTERNAL_LIST_TYPE_AND_10_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6, p7, p8, p9) , p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type, p7##_type, p8##_type, p9##_type
+
+// Declares the value parameters.
+#define GMOCK_INTERNAL_DECL_AND_0_VALUE_PARAMS()
+#define GMOCK_INTERNAL_DECL_AND_1_VALUE_PARAMS(p0) p0##_type p0
+#define GMOCK_INTERNAL_DECL_AND_2_VALUE_PARAMS(p0, p1) p0##_type p0, \
+ p1##_type p1
+#define GMOCK_INTERNAL_DECL_AND_3_VALUE_PARAMS(p0, p1, p2) p0##_type p0, \
+ p1##_type p1, p2##_type p2
+#define GMOCK_INTERNAL_DECL_AND_4_VALUE_PARAMS(p0, p1, p2, p3) p0##_type p0, \
+ p1##_type p1, p2##_type p2, p3##_type p3
+#define GMOCK_INTERNAL_DECL_AND_5_VALUE_PARAMS(p0, p1, p2, p3, \
+ p4) p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, p4##_type p4
+#define GMOCK_INTERNAL_DECL_AND_6_VALUE_PARAMS(p0, p1, p2, p3, p4, \
+ p5) p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, p4##_type p4, \
+ p5##_type p5
+#define GMOCK_INTERNAL_DECL_AND_7_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, \
+ p6) p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, p4##_type p4, \
+ p5##_type p5, p6##_type p6
+#define GMOCK_INTERNAL_DECL_AND_8_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7) p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, p4##_type p4, \
+ p5##_type p5, p6##_type p6, p7##_type p7
+#define GMOCK_INTERNAL_DECL_AND_9_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8) p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, \
+ p4##_type p4, p5##_type p5, p6##_type p6, p7##_type p7, p8##_type p8
+#define GMOCK_INTERNAL_DECL_AND_10_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8, p9) p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, \
+ p4##_type p4, p5##_type p5, p6##_type p6, p7##_type p7, p8##_type p8, \
+ p9##_type p9
+
+// The suffix of the class template implementing the action template.
+#define GMOCK_INTERNAL_COUNT_AND_0_VALUE_PARAMS()
+#define GMOCK_INTERNAL_COUNT_AND_1_VALUE_PARAMS(p0) P
+#define GMOCK_INTERNAL_COUNT_AND_2_VALUE_PARAMS(p0, p1) P2
+#define GMOCK_INTERNAL_COUNT_AND_3_VALUE_PARAMS(p0, p1, p2) P3
+#define GMOCK_INTERNAL_COUNT_AND_4_VALUE_PARAMS(p0, p1, p2, p3) P4
+#define GMOCK_INTERNAL_COUNT_AND_5_VALUE_PARAMS(p0, p1, p2, p3, p4) P5
+#define GMOCK_INTERNAL_COUNT_AND_6_VALUE_PARAMS(p0, p1, p2, p3, p4, p5) P6
+#define GMOCK_INTERNAL_COUNT_AND_7_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6) P7
+#define GMOCK_INTERNAL_COUNT_AND_8_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7) P8
+#define GMOCK_INTERNAL_COUNT_AND_9_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8) P9
+#define GMOCK_INTERNAL_COUNT_AND_10_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, \
+ p7, p8, p9) P10
+
+// The name of the class template implementing the action template.
+#define GMOCK_ACTION_CLASS_(name, value_params)\
+ GTEST_CONCAT_TOKEN_(name##Action, GMOCK_INTERNAL_COUNT_##value_params)
+
+#define ACTION_TEMPLATE(name, template_params, value_params)\
+ template <GMOCK_INTERNAL_DECL_##template_params\
+ GMOCK_INTERNAL_DECL_TYPE_##value_params>\
+ class GMOCK_ACTION_CLASS_(name, value_params) {\
+ public:\
+ GMOCK_ACTION_CLASS_(name, value_params)\
+ GMOCK_INTERNAL_INIT_##value_params {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ explicit gmock_Impl GMOCK_INTERNAL_INIT_##value_params {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ GMOCK_INTERNAL_DEFN_##value_params\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(\
+ new gmock_Impl<F>(GMOCK_INTERNAL_LIST_##value_params));\
+ }\
+ GMOCK_INTERNAL_DEFN_##value_params\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(GMOCK_ACTION_CLASS_(name, value_params));\
+ };\
+ template <GMOCK_INTERNAL_DECL_##template_params\
+ GMOCK_INTERNAL_DECL_TYPE_##value_params>\
+ inline GMOCK_ACTION_CLASS_(name, value_params)<\
+ GMOCK_INTERNAL_LIST_##template_params\
+ GMOCK_INTERNAL_LIST_TYPE_##value_params> name(\
+ GMOCK_INTERNAL_DECL_##value_params) {\
+ return GMOCK_ACTION_CLASS_(name, value_params)<\
+ GMOCK_INTERNAL_LIST_##template_params\
+ GMOCK_INTERNAL_LIST_TYPE_##value_params>(\
+ GMOCK_INTERNAL_LIST_##value_params);\
+ }\
+ template <GMOCK_INTERNAL_DECL_##template_params\
+ GMOCK_INTERNAL_DECL_TYPE_##value_params>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ GMOCK_ACTION_CLASS_(name, value_params)<\
+ GMOCK_INTERNAL_LIST_##template_params\
+ GMOCK_INTERNAL_LIST_TYPE_##value_params>::gmock_Impl<F>::\
+ gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION(name)\
+ class name##Action {\
+ public:\
+ name##Action() {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl() {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>());\
+ }\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##Action);\
+ };\
+ inline name##Action name() {\
+ return name##Action();\
+ }\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##Action::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P(name, p0)\
+ template <typename p0##_type>\
+ class name##ActionP {\
+ public:\
+ name##ActionP(p0##_type gmock_p0) : p0(gmock_p0) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ explicit gmock_Impl(p0##_type gmock_p0) : p0(gmock_p0) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0));\
+ }\
+ p0##_type p0;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP);\
+ };\
+ template <typename p0##_type>\
+ inline name##ActionP<p0##_type> name(p0##_type p0) {\
+ return name##ActionP<p0##_type>(p0);\
+ }\
+ template <typename p0##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP<p0##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P2(name, p0, p1)\
+ template <typename p0##_type, typename p1##_type>\
+ class name##ActionP2 {\
+ public:\
+ name##ActionP2(p0##_type gmock_p0, p1##_type gmock_p1) : p0(gmock_p0), \
+ p1(gmock_p1) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1) : p0(gmock_p0), \
+ p1(gmock_p1) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ p1##_type p1;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0, p1));\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP2);\
+ };\
+ template <typename p0##_type, typename p1##_type>\
+ inline name##ActionP2<p0##_type, p1##_type> name(p0##_type p0, \
+ p1##_type p1) {\
+ return name##ActionP2<p0##_type, p1##_type>(p0, p1);\
+ }\
+ template <typename p0##_type, typename p1##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP2<p0##_type, p1##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P3(name, p0, p1, p2)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type>\
+ class name##ActionP3 {\
+ public:\
+ name##ActionP3(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0, p1, p2));\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP3);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type>\
+ inline name##ActionP3<p0##_type, p1##_type, p2##_type> name(p0##_type p0, \
+ p1##_type p1, p2##_type p2) {\
+ return name##ActionP3<p0##_type, p1##_type, p2##_type>(p0, p1, p2);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP3<p0##_type, p1##_type, \
+ p2##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P4(name, p0, p1, p2, p3)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type>\
+ class name##ActionP4 {\
+ public:\
+ name##ActionP4(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3) : p0(gmock_p0), p1(gmock_p1), \
+ p2(gmock_p2), p3(gmock_p3) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0, p1, p2, p3));\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP4);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type>\
+ inline name##ActionP4<p0##_type, p1##_type, p2##_type, \
+ p3##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, \
+ p3##_type p3) {\
+ return name##ActionP4<p0##_type, p1##_type, p2##_type, p3##_type>(p0, p1, \
+ p2, p3);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP4<p0##_type, p1##_type, p2##_type, \
+ p3##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P5(name, p0, p1, p2, p3, p4)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type>\
+ class name##ActionP5 {\
+ public:\
+ name##ActionP5(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, \
+ p4##_type gmock_p4) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4) : p0(gmock_p0), \
+ p1(gmock_p1), p2(gmock_p2), p3(gmock_p3), p4(gmock_p4) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0, p1, p2, p3, p4));\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP5);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type>\
+ inline name##ActionP5<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, \
+ p4##_type p4) {\
+ return name##ActionP5<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type>(p0, p1, p2, p3, p4);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP5<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P6(name, p0, p1, p2, p3, p4, p5)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type>\
+ class name##ActionP6 {\
+ public:\
+ name##ActionP6(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0, p1, p2, p3, p4, p5));\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP6);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type>\
+ inline name##ActionP6<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, \
+ p3##_type p3, p4##_type p4, p5##_type p5) {\
+ return name##ActionP6<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type>(p0, p1, p2, p3, p4, p5);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP6<p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P7(name, p0, p1, p2, p3, p4, p5, p6)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type>\
+ class name##ActionP7 {\
+ public:\
+ name##ActionP7(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5, p6##_type gmock_p6) : p0(gmock_p0), p1(gmock_p1), \
+ p2(gmock_p2), p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), \
+ p6(gmock_p6) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0, p1, p2, p3, p4, p5, \
+ p6));\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP7);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type>\
+ inline name##ActionP7<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type> name(p0##_type p0, p1##_type p1, \
+ p2##_type p2, p3##_type p3, p4##_type p4, p5##_type p5, \
+ p6##_type p6) {\
+ return name##ActionP7<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type>(p0, p1, p2, p3, p4, p5, p6);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP7<p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P8(name, p0, p1, p2, p3, p4, p5, p6, p7)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type>\
+ class name##ActionP8 {\
+ public:\
+ name##ActionP8(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5, p6##_type gmock_p6, \
+ p7##_type gmock_p7) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), \
+ p7(gmock_p7) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6, p7##_type gmock_p7) : p0(gmock_p0), \
+ p1(gmock_p1), p2(gmock_p2), p3(gmock_p3), p4(gmock_p4), \
+ p5(gmock_p5), p6(gmock_p6), p7(gmock_p7) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0, p1, p2, p3, p4, p5, \
+ p6, p7));\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP8);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type>\
+ inline name##ActionP8<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type> name(p0##_type p0, \
+ p1##_type p1, p2##_type p2, p3##_type p3, p4##_type p4, p5##_type p5, \
+ p6##_type p6, p7##_type p7) {\
+ return name##ActionP8<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type>(p0, p1, p2, p3, p4, p5, \
+ p6, p7);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP8<p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type, \
+ p7##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P9(name, p0, p1, p2, p3, p4, p5, p6, p7, p8)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type>\
+ class name##ActionP9 {\
+ public:\
+ name##ActionP9(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5, p6##_type gmock_p6, p7##_type gmock_p7, \
+ p8##_type gmock_p8) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), p7(gmock_p7), \
+ p8(gmock_p8) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6, p7##_type gmock_p7, \
+ p8##_type gmock_p8) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), \
+ p7(gmock_p7), p8(gmock_p8) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ p8##_type p8;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0, p1, p2, p3, p4, p5, \
+ p6, p7, p8));\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ p8##_type p8;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP9);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type>\
+ inline name##ActionP9<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, \
+ p8##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, \
+ p4##_type p4, p5##_type p5, p6##_type p6, p7##_type p7, \
+ p8##_type p8) {\
+ return name##ActionP9<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, p8##_type>(p0, p1, p2, \
+ p3, p4, p5, p6, p7, p8);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP9<p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type, p7##_type, \
+ p8##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+#define ACTION_P10(name, p0, p1, p2, p3, p4, p5, p6, p7, p8, p9)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type, \
+ typename p9##_type>\
+ class name##ActionP10 {\
+ public:\
+ name##ActionP10(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5, p6##_type gmock_p6, p7##_type gmock_p7, \
+ p8##_type gmock_p8, p9##_type gmock_p9) : p0(gmock_p0), p1(gmock_p1), \
+ p2(gmock_p2), p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), \
+ p7(gmock_p7), p8(gmock_p8), p9(gmock_p9) {}\
+ template <typename F>\
+ class gmock_Impl : public ::testing::ActionInterface<F> {\
+ public:\
+ typedef F function_type;\
+ typedef typename ::testing::internal::Function<F>::Result return_type;\
+ typedef typename ::testing::internal::Function<F>::ArgumentTuple\
+ args_type;\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6, p7##_type gmock_p7, p8##_type gmock_p8, \
+ p9##_type gmock_p9) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), \
+ p7(gmock_p7), p8(gmock_p8), p9(gmock_p9) {}\
+ virtual return_type Perform(const args_type& args) {\
+ return ::testing::internal::ActionHelper<return_type, gmock_Impl>::\
+ Perform(this, args);\
+ }\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ return_type gmock_PerformImpl(const args_type& args, arg0_type arg0, \
+ arg1_type arg1, arg2_type arg2, arg3_type arg3, arg4_type arg4, \
+ arg5_type arg5, arg6_type arg6, arg7_type arg7, arg8_type arg8, \
+ arg9_type arg9) const;\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ p8##_type p8;\
+ p9##_type p9;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename F> operator ::testing::Action<F>() const {\
+ return ::testing::Action<F>(new gmock_Impl<F>(p0, p1, p2, p3, p4, p5, \
+ p6, p7, p8, p9));\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ p8##_type p8;\
+ p9##_type p9;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##ActionP10);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type, \
+ typename p9##_type>\
+ inline name##ActionP10<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, p8##_type, \
+ p9##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, \
+ p4##_type p4, p5##_type p5, p6##_type p6, p7##_type p7, p8##_type p8, \
+ p9##_type p9) {\
+ return name##ActionP10<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, p8##_type, p9##_type>(p0, \
+ p1, p2, p3, p4, p5, p6, p7, p8, p9);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type, \
+ typename p9##_type>\
+ template <typename F>\
+ template <typename arg0_type, typename arg1_type, typename arg2_type, \
+ typename arg3_type, typename arg4_type, typename arg5_type, \
+ typename arg6_type, typename arg7_type, typename arg8_type, \
+ typename arg9_type>\
+ typename ::testing::internal::Function<F>::Result\
+ name##ActionP10<p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type, p7##_type, p8##_type, \
+ p9##_type>::gmock_Impl<F>::gmock_PerformImpl(\
+ GMOCK_ACTION_ARG_TYPES_AND_NAMES_UNUSED_) const
+
+namespace testing {
+
+// The ACTION*() macros trigger warning C4100 (unreferenced formal
+// parameter) in MSVC with -W4. Unfortunately they cannot be fixed in
+// the macro definition, as the warnings are generated when the macro
+// is expanded and macro expansion cannot contain #pragma. Therefore
+// we suppress them here.
+#ifdef _MSC_VER
+# pragma warning(push)
+# pragma warning(disable:4100)
+#endif
+
+// Various overloads for InvokeArgument<N>().
+//
+// The InvokeArgument<N>(a1, a2, ..., a_k) action invokes the N-th
+// (0-based) argument, which must be a k-ary callable, of the mock
+// function, with arguments a1, a2, ..., a_k.
+//
+// Notes:
+//
+// 1. The arguments are passed by value by default. If you need to
+// pass an argument by reference, wrap it inside ByRef(). For
+// example,
+//
+// InvokeArgument<1>(5, string("Hello"), ByRef(foo))
+//
+// passes 5 and string("Hello") by value, and passes foo by
+// reference.
+//
+// 2. If the callable takes an argument by reference but ByRef() is
+// not used, it will receive the reference to a copy of the value,
+// instead of the original value. For example, when the 0-th
+// argument of the mock function takes a const string&, the action
+//
+// InvokeArgument<0>(string("Hello"))
+//
+// makes a copy of the temporary string("Hello") object and passes a
+// reference of the copy, instead of the original temporary object,
+// to the callable. This makes it easy for a user to define an
+// InvokeArgument action from temporary values and have it performed
+// later.
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_0_VALUE_PARAMS()) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args));
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_1_VALUE_PARAMS(p0)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0);
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_2_VALUE_PARAMS(p0, p1)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0, p1);
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_3_VALUE_PARAMS(p0, p1, p2)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0, p1, p2);
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_4_VALUE_PARAMS(p0, p1, p2, p3)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0, p1, p2, p3);
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_5_VALUE_PARAMS(p0, p1, p2, p3, p4)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0, p1, p2, p3, p4);
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_6_VALUE_PARAMS(p0, p1, p2, p3, p4, p5)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0, p1, p2, p3, p4, p5);
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_7_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0, p1, p2, p3, p4, p5, p6);
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_8_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, p7)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0, p1, p2, p3, p4, p5, p6, p7);
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_9_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, p7, p8)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0, p1, p2, p3, p4, p5, p6, p7, p8);
+}
+
+ACTION_TEMPLATE(InvokeArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_10_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, p7, p8, p9)) {
+ return internal::CallableHelper<return_type>::Call(
+ ::std::tr1::get<k>(args), p0, p1, p2, p3, p4, p5, p6, p7, p8, p9);
+}
+
+// Various overloads for ReturnNew<T>().
+//
+// The ReturnNew<T>(a1, a2, ..., a_k) action returns a pointer to a new
+// instance of type T, constructed on the heap with constructor arguments
+// a1, a2, ..., and a_k. The caller assumes ownership of the returned value.
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_0_VALUE_PARAMS()) {
+ return new T();
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_1_VALUE_PARAMS(p0)) {
+ return new T(p0);
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_2_VALUE_PARAMS(p0, p1)) {
+ return new T(p0, p1);
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_3_VALUE_PARAMS(p0, p1, p2)) {
+ return new T(p0, p1, p2);
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_4_VALUE_PARAMS(p0, p1, p2, p3)) {
+ return new T(p0, p1, p2, p3);
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_5_VALUE_PARAMS(p0, p1, p2, p3, p4)) {
+ return new T(p0, p1, p2, p3, p4);
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_6_VALUE_PARAMS(p0, p1, p2, p3, p4, p5)) {
+ return new T(p0, p1, p2, p3, p4, p5);
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_7_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6)) {
+ return new T(p0, p1, p2, p3, p4, p5, p6);
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_8_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, p7)) {
+ return new T(p0, p1, p2, p3, p4, p5, p6, p7);
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_9_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, p7, p8)) {
+ return new T(p0, p1, p2, p3, p4, p5, p6, p7, p8);
+}
+
+ACTION_TEMPLATE(ReturnNew,
+ HAS_1_TEMPLATE_PARAMS(typename, T),
+ AND_10_VALUE_PARAMS(p0, p1, p2, p3, p4, p5, p6, p7, p8, p9)) {
+ return new T(p0, p1, p2, p3, p4, p5, p6, p7, p8, p9);
+}
+
+#ifdef _MSC_VER
+# pragma warning(pop)
+#endif
+
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_ACTIONS_H_
+// This file was GENERATED by command:
+// pump.py gmock-generated-function-mockers.h.pump
+// DO NOT EDIT BY HAND!!!
+
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements function mockers of various arities.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_FUNCTION_MOCKERS_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_FUNCTION_MOCKERS_H_
+
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements the ON_CALL() and EXPECT_CALL() macros.
+//
+// A user can use the ON_CALL() macro to specify the default action of
+// a mock method. The syntax is:
+//
+// ON_CALL(mock_object, Method(argument-matchers))
+// .With(multi-argument-matcher)
+// .WillByDefault(action);
+//
+// where the .With() clause is optional.
+//
+// A user can use the EXPECT_CALL() macro to specify an expectation on
+// a mock method. The syntax is:
+//
+// EXPECT_CALL(mock_object, Method(argument-matchers))
+// .With(multi-argument-matchers)
+// .Times(cardinality)
+// .InSequence(sequences)
+// .After(expectations)
+// .WillOnce(action)
+// .WillRepeatedly(action)
+// .RetiresOnSaturation();
+//
+// where all clauses are optional, and .InSequence()/.After()/
+// .WillOnce() can appear any number of times.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_SPEC_BUILDERS_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_SPEC_BUILDERS_H_
+
+#include <map>
+#include <set>
+#include <sstream>
+#include <string>
+#include <vector>
+
+#if GTEST_HAS_EXCEPTIONS
+# include <stdexcept> // NOLINT
+#endif
+
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements some commonly used argument matchers. More
+// matchers can be defined by the user implementing the
+// MatcherInterface<T> interface if necessary.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_MATCHERS_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_MATCHERS_H_
+
+#include <math.h>
+#include <algorithm>
+#include <iterator>
+#include <limits>
+#include <ostream> // NOLINT
+#include <sstream>
+#include <string>
+#include <utility>
+#include <vector>
+
+
+#if GTEST_LANG_CXX11
+#include <initializer_list> // NOLINT -- must be after gtest.h
+#endif
+
+namespace testing {
+
+// To implement a matcher Foo for type T, define:
+// 1. a class FooMatcherImpl that implements the
+// MatcherInterface<T> interface, and
+// 2. a factory function that creates a Matcher<T> object from a
+// FooMatcherImpl*.
+//
+// The two-level delegation design makes it possible to allow a user
+// to write "v" instead of "Eq(v)" where a Matcher is expected, which
+// is impossible if we pass matchers by pointers. It also eases
+// ownership management as Matcher objects can now be copied like
+// plain values.
+
+// MatchResultListener is an abstract class. Its << operator can be
+// used by a matcher to explain why a value matches or doesn't match.
+//
+// TODO(wan at google.com): add method
+// bool InterestedInWhy(bool result) const;
+// to indicate whether the listener is interested in why the match
+// result is 'result'.
+class MatchResultListener {
+ public:
+ // Creates a listener object with the given underlying ostream. The
+ // listener does not own the ostream, and does not dereference it
+ // in the constructor or destructor.
+ explicit MatchResultListener(::std::ostream* os) : stream_(os) {}
+ virtual ~MatchResultListener() = 0; // Makes this class abstract.
+
+ // Streams x to the underlying ostream; does nothing if the ostream
+ // is NULL.
+ template <typename T>
+ MatchResultListener& operator<<(const T& x) {
+ if (stream_ != NULL)
+ *stream_ << x;
+ return *this;
+ }
+
+ // Returns the underlying ostream.
+ ::std::ostream* stream() { return stream_; }
+
+ // Returns true iff the listener is interested in an explanation of
+ // the match result. A matcher's MatchAndExplain() method can use
+ // this information to avoid generating the explanation when no one
+ // intends to hear it.
+ bool IsInterested() const { return stream_ != NULL; }
+
+ private:
+ ::std::ostream* const stream_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MatchResultListener);
+};
+
+inline MatchResultListener::~MatchResultListener() {
+}
+
+// An instance of a subclass of this knows how to describe itself as a
+// matcher.
+class MatcherDescriberInterface {
+ public:
+ virtual ~MatcherDescriberInterface() {}
+
+ // Describes this matcher to an ostream. The function should print
+ // a verb phrase that describes the property a value matching this
+ // matcher should have. The subject of the verb phrase is the value
+ // being matched. For example, the DescribeTo() method of the Gt(7)
+ // matcher prints "is greater than 7".
+ virtual void DescribeTo(::std::ostream* os) const = 0;
+
+ // Describes the negation of this matcher to an ostream. For
+ // example, if the description of this matcher is "is greater than
+ // 7", the negated description could be "is not greater than 7".
+ // You are not required to override this when implementing
+ // MatcherInterface, but it is highly advised so that your matcher
+ // can produce good error messages.
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "not (";
+ DescribeTo(os);
+ *os << ")";
+ }
+};
+
+// The implementation of a matcher.
+template <typename T>
+class MatcherInterface : public MatcherDescriberInterface {
+ public:
+ // Returns true iff the matcher matches x; also explains the match
+ // result to 'listener' if necessary (see the next paragraph), in
+ // the form of a non-restrictive relative clause ("which ...",
+ // "whose ...", etc) that describes x. For example, the
+ // MatchAndExplain() method of the Pointee(...) matcher should
+ // generate an explanation like "which points to ...".
+ //
+ // Implementations of MatchAndExplain() should add an explanation of
+ // the match result *if and only if* they can provide additional
+ // information that's not already present (or not obvious) in the
+ // print-out of x and the matcher's description. Whether the match
+ // succeeds is not a factor in deciding whether an explanation is
+ // needed, as sometimes the caller needs to print a failure message
+ // when the match succeeds (e.g. when the matcher is used inside
+ // Not()).
+ //
+ // For example, a "has at least 10 elements" matcher should explain
+ // what the actual element count is, regardless of the match result,
+ // as it is useful information to the reader; on the other hand, an
+ // "is empty" matcher probably only needs to explain what the actual
+ // size is when the match fails, as it's redundant to say that the
+ // size is 0 when the value is already known to be empty.
+ //
+ // You should override this method when defining a new matcher.
+ //
+ // It's the responsibility of the caller (Google Mock) to guarantee
+ // that 'listener' is not NULL. This helps to simplify a matcher's
+ // implementation when it doesn't care about the performance, as it
+ // can talk to 'listener' without checking its validity first.
+ // However, in order to implement dummy listeners efficiently,
+ // listener->stream() may be NULL.
+ virtual bool MatchAndExplain(T x, MatchResultListener* listener) const = 0;
+
+ // Inherits these methods from MatcherDescriberInterface:
+ // virtual void DescribeTo(::std::ostream* os) const = 0;
+ // virtual void DescribeNegationTo(::std::ostream* os) const;
+};
+
+// A match result listener that stores the explanation in a string.
+class StringMatchResultListener : public MatchResultListener {
+ public:
+ StringMatchResultListener() : MatchResultListener(&ss_) {}
+
+ // Returns the explanation accumulated so far.
+ internal::string str() const { return ss_.str(); }
+
+ // Clears the explanation accumulated so far.
+ void Clear() { ss_.str(""); }
+
+ private:
+ ::std::stringstream ss_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(StringMatchResultListener);
+};
+
+namespace internal {
+
+// A match result listener that ignores the explanation.
+class DummyMatchResultListener : public MatchResultListener {
+ public:
+ DummyMatchResultListener() : MatchResultListener(NULL) {}
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(DummyMatchResultListener);
+};
+
+// A match result listener that forwards the explanation to a given
+// ostream. The difference between this and MatchResultListener is
+// that the former is concrete.
+class StreamMatchResultListener : public MatchResultListener {
+ public:
+ explicit StreamMatchResultListener(::std::ostream* os)
+ : MatchResultListener(os) {}
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(StreamMatchResultListener);
+};
+
+// An internal class for implementing Matcher<T>, which will derive
+// from it. We put functionalities common to all Matcher<T>
+// specializations here to avoid code duplication.
+template <typename T>
+class MatcherBase {
+ public:
+ // Returns true iff the matcher matches x; also explains the match
+ // result to 'listener'.
+ bool MatchAndExplain(T x, MatchResultListener* listener) const {
+ return impl_->MatchAndExplain(x, listener);
+ }
+
+ // Returns true iff this matcher matches x.
+ bool Matches(T x) const {
+ DummyMatchResultListener dummy;
+ return MatchAndExplain(x, &dummy);
+ }
+
+ // Describes this matcher to an ostream.
+ void DescribeTo(::std::ostream* os) const { impl_->DescribeTo(os); }
+
+ // Describes the negation of this matcher to an ostream.
+ void DescribeNegationTo(::std::ostream* os) const {
+ impl_->DescribeNegationTo(os);
+ }
+
+ // Explains why x matches, or doesn't match, the matcher.
+ void ExplainMatchResultTo(T x, ::std::ostream* os) const {
+ StreamMatchResultListener listener(os);
+ MatchAndExplain(x, &listener);
+ }
+
+ // Returns the describer for this matcher object; retains ownership
+ // of the describer, which is only guaranteed to be alive when
+ // this matcher object is alive.
+ const MatcherDescriberInterface* GetDescriber() const {
+ return impl_.get();
+ }
+
+ protected:
+ MatcherBase() {}
+
+ // Constructs a matcher from its implementation.
+ explicit MatcherBase(const MatcherInterface<T>* impl)
+ : impl_(impl) {}
+
+ virtual ~MatcherBase() {}
+
+ private:
+ // shared_ptr (util/gtl/shared_ptr.h) and linked_ptr have similar
+ // interfaces. The former dynamically allocates a chunk of memory
+ // to hold the reference count, while the latter tracks all
+ // references using a circular linked list without allocating
+ // memory. It has been observed that linked_ptr performs better in
+ // typical scenarios. However, shared_ptr can out-perform
+ // linked_ptr when there are many more uses of the copy constructor
+ // than the default constructor.
+ //
+ // If performance becomes a problem, we should see if using
+ // shared_ptr helps.
+ ::testing::internal::linked_ptr<const MatcherInterface<T> > impl_;
+};
+
+} // namespace internal
+
+// A Matcher<T> is a copyable and IMMUTABLE (except by assignment)
+// object that can check whether a value of type T matches. The
+// implementation of Matcher<T> is just a linked_ptr to const
+// MatcherInterface<T>, so copying is fairly cheap. Don't inherit
+// from Matcher!
+template <typename T>
+class Matcher : public internal::MatcherBase<T> {
+ public:
+ // Constructs a null matcher. Needed for storing Matcher objects in STL
+ // containers. A default-constructed matcher is not yet initialized. You
+ // cannot use it until a valid value has been assigned to it.
+ Matcher() {}
+
+ // Constructs a matcher from its implementation.
+ explicit Matcher(const MatcherInterface<T>* impl)
+ : internal::MatcherBase<T>(impl) {}
+
+ // Implicit constructor here allows people to write
+ // EXPECT_CALL(foo, Bar(5)) instead of EXPECT_CALL(foo, Bar(Eq(5))) sometimes
+ Matcher(T value); // NOLINT
+};
+
+// The following two specializations allow the user to write str
+// instead of Eq(str) and "foo" instead of Eq("foo") when a string
+// matcher is expected.
+template <>
+class GTEST_API_ Matcher<const internal::string&>
+ : public internal::MatcherBase<const internal::string&> {
+ public:
+ Matcher() {}
+
+ explicit Matcher(const MatcherInterface<const internal::string&>* impl)
+ : internal::MatcherBase<const internal::string&>(impl) {}
+
+ // Allows the user to write str instead of Eq(str) sometimes, where
+ // str is a string object.
+ Matcher(const internal::string& s); // NOLINT
+
+ // Allows the user to write "foo" instead of Eq("foo") sometimes.
+ Matcher(const char* s); // NOLINT
+};
+
+template <>
+class GTEST_API_ Matcher<internal::string>
+ : public internal::MatcherBase<internal::string> {
+ public:
+ Matcher() {}
+
+ explicit Matcher(const MatcherInterface<internal::string>* impl)
+ : internal::MatcherBase<internal::string>(impl) {}
+
+ // Allows the user to write str instead of Eq(str) sometimes, where
+ // str is a string object.
+ Matcher(const internal::string& s); // NOLINT
+
+ // Allows the user to write "foo" instead of Eq("foo") sometimes.
+ Matcher(const char* s); // NOLINT
+};
+
+#if GTEST_HAS_STRING_PIECE_
+// The following two specializations allow the user to write str
+// instead of Eq(str) and "foo" instead of Eq("foo") when a StringPiece
+// matcher is expected.
+template <>
+class GTEST_API_ Matcher<const StringPiece&>
+ : public internal::MatcherBase<const StringPiece&> {
+ public:
+ Matcher() {}
+
+ explicit Matcher(const MatcherInterface<const StringPiece&>* impl)
+ : internal::MatcherBase<const StringPiece&>(impl) {}
+
+ // Allows the user to write str instead of Eq(str) sometimes, where
+ // str is a string object.
+ Matcher(const internal::string& s); // NOLINT
+
+ // Allows the user to write "foo" instead of Eq("foo") sometimes.
+ Matcher(const char* s); // NOLINT
+
+ // Allows the user to pass StringPieces directly.
+ Matcher(StringPiece s); // NOLINT
+};
+
+template <>
+class GTEST_API_ Matcher<StringPiece>
+ : public internal::MatcherBase<StringPiece> {
+ public:
+ Matcher() {}
+
+ explicit Matcher(const MatcherInterface<StringPiece>* impl)
+ : internal::MatcherBase<StringPiece>(impl) {}
+
+ // Allows the user to write str instead of Eq(str) sometimes, where
+ // str is a string object.
+ Matcher(const internal::string& s); // NOLINT
+
+ // Allows the user to write "foo" instead of Eq("foo") sometimes.
+ Matcher(const char* s); // NOLINT
+
+ // Allows the user to pass StringPieces directly.
+ Matcher(StringPiece s); // NOLINT
+};
+#endif // GTEST_HAS_STRING_PIECE_
+
+// The PolymorphicMatcher class template makes it easy to implement a
+// polymorphic matcher (i.e. a matcher that can match values of more
+// than one type, e.g. Eq(n) and NotNull()).
+//
+// To define a polymorphic matcher, a user should provide an Impl
+// class that has a DescribeTo() method and a DescribeNegationTo()
+// method, and define a member function (or member function template)
+//
+// bool MatchAndExplain(const Value& value,
+// MatchResultListener* listener) const;
+//
+// See the definition of NotNull() for a complete example.
+template <class Impl>
+class PolymorphicMatcher {
+ public:
+ explicit PolymorphicMatcher(const Impl& an_impl) : impl_(an_impl) {}
+
+ // Returns a mutable reference to the underlying matcher
+ // implementation object.
+ Impl& mutable_impl() { return impl_; }
+
+ // Returns an immutable reference to the underlying matcher
+ // implementation object.
+ const Impl& impl() const { return impl_; }
+
+ template <typename T>
+ operator Matcher<T>() const {
+ return Matcher<T>(new MonomorphicImpl<T>(impl_));
+ }
+
+ private:
+ template <typename T>
+ class MonomorphicImpl : public MatcherInterface<T> {
+ public:
+ explicit MonomorphicImpl(const Impl& impl) : impl_(impl) {}
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ impl_.DescribeTo(os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ impl_.DescribeNegationTo(os);
+ }
+
+ virtual bool MatchAndExplain(T x, MatchResultListener* listener) const {
+ return impl_.MatchAndExplain(x, listener);
+ }
+
+ private:
+ const Impl impl_;
+
+ GTEST_DISALLOW_ASSIGN_(MonomorphicImpl);
+ };
+
+ Impl impl_;
+
+ GTEST_DISALLOW_ASSIGN_(PolymorphicMatcher);
+};
+
+// Creates a matcher from its implementation. This is easier to use
+// than the Matcher<T> constructor as it doesn't require you to
+// explicitly write the template argument, e.g.
+//
+// MakeMatcher(foo);
+// vs
+// Matcher<const string&>(foo);
+template <typename T>
+inline Matcher<T> MakeMatcher(const MatcherInterface<T>* impl) {
+ return Matcher<T>(impl);
+}
+
+// Creates a polymorphic matcher from its implementation. This is
+// easier to use than the PolymorphicMatcher<Impl> constructor as it
+// doesn't require you to explicitly write the template argument, e.g.
+//
+// MakePolymorphicMatcher(foo);
+// vs
+// PolymorphicMatcher<TypeOfFoo>(foo);
+template <class Impl>
+inline PolymorphicMatcher<Impl> MakePolymorphicMatcher(const Impl& impl) {
+ return PolymorphicMatcher<Impl>(impl);
+}
+
+// Anything inside the 'internal' namespace IS INTERNAL IMPLEMENTATION
+// and MUST NOT BE USED IN USER CODE!!!
+namespace internal {
+
+// The MatcherCastImpl class template is a helper for implementing
+// MatcherCast(). We need this helper in order to partially
+// specialize the implementation of MatcherCast() (C++ allows
+// class/struct templates to be partially specialized, but not
+// function templates.).
+
+// This general version is used when MatcherCast()'s argument is a
+// polymorphic matcher (i.e. something that can be converted to a
+// Matcher but is not one yet; for example, Eq(value)) or a value (for
+// example, "hello").
+template <typename T, typename M>
+class MatcherCastImpl {
+ public:
+ static Matcher<T> Cast(M polymorphic_matcher_or_value) {
+ // M can be a polymorhic matcher, in which case we want to use
+ // its conversion operator to create Matcher<T>. Or it can be a value
+ // that should be passed to the Matcher<T>'s constructor.
+ //
+ // We can't call Matcher<T>(polymorphic_matcher_or_value) when M is a
+ // polymorphic matcher because it'll be ambiguous if T has an implicit
+ // constructor from M (this usually happens when T has an implicit
+ // constructor from any type).
+ //
+ // It won't work to unconditionally implict_cast
+ // polymorphic_matcher_or_value to Matcher<T> because it won't trigger
+ // a user-defined conversion from M to T if one exists (assuming M is
+ // a value).
+ return CastImpl(
+ polymorphic_matcher_or_value,
+ BooleanConstant<
+ internal::ImplicitlyConvertible<M, Matcher<T> >::value>());
+ }
+
+ private:
+ static Matcher<T> CastImpl(M value, BooleanConstant<false>) {
+ // M can't be implicitly converted to Matcher<T>, so M isn't a polymorphic
+ // matcher. It must be a value then. Use direct initialization to create
+ // a matcher.
+ return Matcher<T>(ImplicitCast_<T>(value));
+ }
+
+ static Matcher<T> CastImpl(M polymorphic_matcher_or_value,
+ BooleanConstant<true>) {
+ // M is implicitly convertible to Matcher<T>, which means that either
+ // M is a polymorhpic matcher or Matcher<T> has an implicit constructor
+ // from M. In both cases using the implicit conversion will produce a
+ // matcher.
+ //
+ // Even if T has an implicit constructor from M, it won't be called because
+ // creating Matcher<T> would require a chain of two user-defined conversions
+ // (first to create T from M and then to create Matcher<T> from T).
+ return polymorphic_matcher_or_value;
+ }
+};
+
+// This more specialized version is used when MatcherCast()'s argument
+// is already a Matcher. This only compiles when type T can be
+// statically converted to type U.
+template <typename T, typename U>
+class MatcherCastImpl<T, Matcher<U> > {
+ public:
+ static Matcher<T> Cast(const Matcher<U>& source_matcher) {
+ return Matcher<T>(new Impl(source_matcher));
+ }
+
+ private:
+ class Impl : public MatcherInterface<T> {
+ public:
+ explicit Impl(const Matcher<U>& source_matcher)
+ : source_matcher_(source_matcher) {}
+
+ // We delegate the matching logic to the source matcher.
+ virtual bool MatchAndExplain(T x, MatchResultListener* listener) const {
+ return source_matcher_.MatchAndExplain(static_cast<U>(x), listener);
+ }
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ source_matcher_.DescribeTo(os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ source_matcher_.DescribeNegationTo(os);
+ }
+
+ private:
+ const Matcher<U> source_matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+};
+
+// This even more specialized version is used for efficiently casting
+// a matcher to its own type.
+template <typename T>
+class MatcherCastImpl<T, Matcher<T> > {
+ public:
+ static Matcher<T> Cast(const Matcher<T>& matcher) { return matcher; }
+};
+
+} // namespace internal
+
+// In order to be safe and clear, casting between different matcher
+// types is done explicitly via MatcherCast<T>(m), which takes a
+// matcher m and returns a Matcher<T>. It compiles only when T can be
+// statically converted to the argument type of m.
+template <typename T, typename M>
+inline Matcher<T> MatcherCast(M matcher) {
+ return internal::MatcherCastImpl<T, M>::Cast(matcher);
+}
+
+// Implements SafeMatcherCast().
+//
+// We use an intermediate class to do the actual safe casting as Nokia's
+// Symbian compiler cannot decide between
+// template <T, M> ... (M) and
+// template <T, U> ... (const Matcher<U>&)
+// for function templates but can for member function templates.
+template <typename T>
+class SafeMatcherCastImpl {
+ public:
+ // This overload handles polymorphic matchers and values only since
+ // monomorphic matchers are handled by the next one.
+ template <typename M>
+ static inline Matcher<T> Cast(M polymorphic_matcher_or_value) {
+ return internal::MatcherCastImpl<T, M>::Cast(polymorphic_matcher_or_value);
+ }
+
+ // This overload handles monomorphic matchers.
+ //
+ // In general, if type T can be implicitly converted to type U, we can
+ // safely convert a Matcher<U> to a Matcher<T> (i.e. Matcher is
+ // contravariant): just keep a copy of the original Matcher<U>, convert the
+ // argument from type T to U, and then pass it to the underlying Matcher<U>.
+ // The only exception is when U is a reference and T is not, as the
+ // underlying Matcher<U> may be interested in the argument's address, which
+ // is not preserved in the conversion from T to U.
+ template <typename U>
+ static inline Matcher<T> Cast(const Matcher<U>& matcher) {
+ // Enforce that T can be implicitly converted to U.
+ GTEST_COMPILE_ASSERT_((internal::ImplicitlyConvertible<T, U>::value),
+ T_must_be_implicitly_convertible_to_U);
+ // Enforce that we are not converting a non-reference type T to a reference
+ // type U.
+ GTEST_COMPILE_ASSERT_(
+ internal::is_reference<T>::value || !internal::is_reference<U>::value,
+ cannot_convert_non_referentce_arg_to_reference);
+ // In case both T and U are arithmetic types, enforce that the
+ // conversion is not lossy.
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(T) RawT;
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(U) RawU;
+ const bool kTIsOther = GMOCK_KIND_OF_(RawT) == internal::kOther;
+ const bool kUIsOther = GMOCK_KIND_OF_(RawU) == internal::kOther;
+ GTEST_COMPILE_ASSERT_(
+ kTIsOther || kUIsOther ||
+ (internal::LosslessArithmeticConvertible<RawT, RawU>::value),
+ conversion_of_arithmetic_types_must_be_lossless);
+ return MatcherCast<T>(matcher);
+ }
+};
+
+template <typename T, typename M>
+inline Matcher<T> SafeMatcherCast(const M& polymorphic_matcher) {
+ return SafeMatcherCastImpl<T>::Cast(polymorphic_matcher);
+}
+
+// A<T>() returns a matcher that matches any value of type T.
+template <typename T>
+Matcher<T> A();
+
+// Anything inside the 'internal' namespace IS INTERNAL IMPLEMENTATION
+// and MUST NOT BE USED IN USER CODE!!!
+namespace internal {
+
+// If the explanation is not empty, prints it to the ostream.
+inline void PrintIfNotEmpty(const internal::string& explanation,
+ ::std::ostream* os) {
+ if (explanation != "" && os != NULL) {
+ *os << ", " << explanation;
+ }
+}
+
+// Returns true if the given type name is easy to read by a human.
+// This is used to decide whether printing the type of a value might
+// be helpful.
+inline bool IsReadableTypeName(const string& type_name) {
+ // We consider a type name readable if it's short or doesn't contain
+ // a template or function type.
+ return (type_name.length() <= 20 ||
+ type_name.find_first_of("<(") == string::npos);
+}
+
+// Matches the value against the given matcher, prints the value and explains
+// the match result to the listener. Returns the match result.
+// 'listener' must not be NULL.
+// Value cannot be passed by const reference, because some matchers take a
+// non-const argument.
+template <typename Value, typename T>
+bool MatchPrintAndExplain(Value& value, const Matcher<T>& matcher,
+ MatchResultListener* listener) {
+ if (!listener->IsInterested()) {
+ // If the listener is not interested, we do not need to construct the
+ // inner explanation.
+ return matcher.Matches(value);
+ }
+
+ StringMatchResultListener inner_listener;
+ const bool match = matcher.MatchAndExplain(value, &inner_listener);
+
+ UniversalPrint(value, listener->stream());
+#if GTEST_HAS_RTTI
+ const string& type_name = GetTypeName<Value>();
+ if (IsReadableTypeName(type_name))
+ *listener->stream() << " (of type " << type_name << ")";
+#endif
+ PrintIfNotEmpty(inner_listener.str(), listener->stream());
+
+ return match;
+}
+
+// An internal helper class for doing compile-time loop on a tuple's
+// fields.
+template <size_t N>
+class TuplePrefix {
+ public:
+ // TuplePrefix<N>::Matches(matcher_tuple, value_tuple) returns true
+ // iff the first N fields of matcher_tuple matches the first N
+ // fields of value_tuple, respectively.
+ template <typename MatcherTuple, typename ValueTuple>
+ static bool Matches(const MatcherTuple& matcher_tuple,
+ const ValueTuple& value_tuple) {
+ using ::std::tr1::get;
+ return TuplePrefix<N - 1>::Matches(matcher_tuple, value_tuple)
+ && get<N - 1>(matcher_tuple).Matches(get<N - 1>(value_tuple));
+ }
+
+ // TuplePrefix<N>::ExplainMatchFailuresTo(matchers, values, os)
+ // describes failures in matching the first N fields of matchers
+ // against the first N fields of values. If there is no failure,
+ // nothing will be streamed to os.
+ template <typename MatcherTuple, typename ValueTuple>
+ static void ExplainMatchFailuresTo(const MatcherTuple& matchers,
+ const ValueTuple& values,
+ ::std::ostream* os) {
+ using ::std::tr1::tuple_element;
+ using ::std::tr1::get;
+
+ // First, describes failures in the first N - 1 fields.
+ TuplePrefix<N - 1>::ExplainMatchFailuresTo(matchers, values, os);
+
+ // Then describes the failure (if any) in the (N - 1)-th (0-based)
+ // field.
+ typename tuple_element<N - 1, MatcherTuple>::type matcher =
+ get<N - 1>(matchers);
+ typedef typename tuple_element<N - 1, ValueTuple>::type Value;
+ Value value = get<N - 1>(values);
+ StringMatchResultListener listener;
+ if (!matcher.MatchAndExplain(value, &listener)) {
+ // TODO(wan): include in the message the name of the parameter
+ // as used in MOCK_METHOD*() when possible.
+ *os << " Expected arg #" << N - 1 << ": ";
+ get<N - 1>(matchers).DescribeTo(os);
+ *os << "\n Actual: ";
+ // We remove the reference in type Value to prevent the
+ // universal printer from printing the address of value, which
+ // isn't interesting to the user most of the time. The
+ // matcher's MatchAndExplain() method handles the case when
+ // the address is interesting.
+ internal::UniversalPrint(value, os);
+ PrintIfNotEmpty(listener.str(), os);
+ *os << "\n";
+ }
+ }
+};
+
+// The base case.
+template <>
+class TuplePrefix<0> {
+ public:
+ template <typename MatcherTuple, typename ValueTuple>
+ static bool Matches(const MatcherTuple& /* matcher_tuple */,
+ const ValueTuple& /* value_tuple */) {
+ return true;
+ }
+
+ template <typename MatcherTuple, typename ValueTuple>
+ static void ExplainMatchFailuresTo(const MatcherTuple& /* matchers */,
+ const ValueTuple& /* values */,
+ ::std::ostream* /* os */) {}
+};
+
+// TupleMatches(matcher_tuple, value_tuple) returns true iff all
+// matchers in matcher_tuple match the corresponding fields in
+// value_tuple. It is a compiler error if matcher_tuple and
+// value_tuple have different number of fields or incompatible field
+// types.
+template <typename MatcherTuple, typename ValueTuple>
+bool TupleMatches(const MatcherTuple& matcher_tuple,
+ const ValueTuple& value_tuple) {
+ using ::std::tr1::tuple_size;
+ // Makes sure that matcher_tuple and value_tuple have the same
+ // number of fields.
+ GTEST_COMPILE_ASSERT_(tuple_size<MatcherTuple>::value ==
+ tuple_size<ValueTuple>::value,
+ matcher_and_value_have_different_numbers_of_fields);
+ return TuplePrefix<tuple_size<ValueTuple>::value>::
+ Matches(matcher_tuple, value_tuple);
+}
+
+// Describes failures in matching matchers against values. If there
+// is no failure, nothing will be streamed to os.
+template <typename MatcherTuple, typename ValueTuple>
+void ExplainMatchFailureTupleTo(const MatcherTuple& matchers,
+ const ValueTuple& values,
+ ::std::ostream* os) {
+ using ::std::tr1::tuple_size;
+ TuplePrefix<tuple_size<MatcherTuple>::value>::ExplainMatchFailuresTo(
+ matchers, values, os);
+}
+
+// TransformTupleValues and its helper.
+//
+// TransformTupleValuesHelper hides the internal machinery that
+// TransformTupleValues uses to implement a tuple traversal.
+template <typename Tuple, typename Func, typename OutIter>
+class TransformTupleValuesHelper {
+ private:
+ typedef typename ::std::tr1::tuple_size<Tuple> TupleSize;
+
+ public:
+ // For each member of tuple 't', taken in order, evaluates '*out++ = f(t)'.
+ // Returns the final value of 'out' in case the caller needs it.
+ static OutIter Run(Func f, const Tuple& t, OutIter out) {
+ return IterateOverTuple<Tuple, TupleSize::value>()(f, t, out);
+ }
+
+ private:
+ template <typename Tup, size_t kRemainingSize>
+ struct IterateOverTuple {
+ OutIter operator() (Func f, const Tup& t, OutIter out) const {
+ *out++ = f(::std::tr1::get<TupleSize::value - kRemainingSize>(t));
+ return IterateOverTuple<Tup, kRemainingSize - 1>()(f, t, out);
+ }
+ };
+ template <typename Tup>
+ struct IterateOverTuple<Tup, 0> {
+ OutIter operator() (Func /* f */, const Tup& /* t */, OutIter out) const {
+ return out;
+ }
+ };
+};
+
+// Successively invokes 'f(element)' on each element of the tuple 't',
+// appending each result to the 'out' iterator. Returns the final value
+// of 'out'.
+template <typename Tuple, typename Func, typename OutIter>
+OutIter TransformTupleValues(Func f, const Tuple& t, OutIter out) {
+ return TransformTupleValuesHelper<Tuple, Func, OutIter>::Run(f, t, out);
+}
+
+// Implements A<T>().
+template <typename T>
+class AnyMatcherImpl : public MatcherInterface<T> {
+ public:
+ virtual bool MatchAndExplain(
+ T /* x */, MatchResultListener* /* listener */) const { return true; }
+ virtual void DescribeTo(::std::ostream* os) const { *os << "is anything"; }
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ // This is mostly for completeness' safe, as it's not very useful
+ // to write Not(A<bool>()). However we cannot completely rule out
+ // such a possibility, and it doesn't hurt to be prepared.
+ *os << "never matches";
+ }
+};
+
+// Implements _, a matcher that matches any value of any
+// type. This is a polymorphic matcher, so we need a template type
+// conversion operator to make it appearing as a Matcher<T> for any
+// type T.
+class AnythingMatcher {
+ public:
+ template <typename T>
+ operator Matcher<T>() const { return A<T>(); }
+};
+
+// Implements a matcher that compares a given value with a
+// pre-supplied value using one of the ==, <=, <, etc, operators. The
+// two values being compared don't have to have the same type.
+//
+// The matcher defined here is polymorphic (for example, Eq(5) can be
+// used to match an int, a short, a double, etc). Therefore we use
+// a template type conversion operator in the implementation.
+//
+// We define this as a macro in order to eliminate duplicated source
+// code.
+//
+// The following template definition assumes that the Rhs parameter is
+// a "bare" type (i.e. neither 'const T' nor 'T&').
+#define GMOCK_IMPLEMENT_COMPARISON_MATCHER_( \
+ name, op, relation, negated_relation) \
+ template <typename Rhs> class name##Matcher { \
+ public: \
+ explicit name##Matcher(const Rhs& rhs) : rhs_(rhs) {} \
+ template <typename Lhs> \
+ operator Matcher<Lhs>() const { \
+ return MakeMatcher(new Impl<Lhs>(rhs_)); \
+ } \
+ private: \
+ template <typename Lhs> \
+ class Impl : public MatcherInterface<Lhs> { \
+ public: \
+ explicit Impl(const Rhs& rhs) : rhs_(rhs) {} \
+ virtual bool MatchAndExplain(\
+ Lhs lhs, MatchResultListener* /* listener */) const { \
+ return lhs op rhs_; \
+ } \
+ virtual void DescribeTo(::std::ostream* os) const { \
+ *os << relation " "; \
+ UniversalPrint(rhs_, os); \
+ } \
+ virtual void DescribeNegationTo(::std::ostream* os) const { \
+ *os << negated_relation " "; \
+ UniversalPrint(rhs_, os); \
+ } \
+ private: \
+ Rhs rhs_; \
+ GTEST_DISALLOW_ASSIGN_(Impl); \
+ }; \
+ Rhs rhs_; \
+ GTEST_DISALLOW_ASSIGN_(name##Matcher); \
+ }
+
+// Implements Eq(v), Ge(v), Gt(v), Le(v), Lt(v), and Ne(v)
+// respectively.
+GMOCK_IMPLEMENT_COMPARISON_MATCHER_(Eq, ==, "is equal to", "isn't equal to");
+GMOCK_IMPLEMENT_COMPARISON_MATCHER_(Ge, >=, "is >=", "isn't >=");
+GMOCK_IMPLEMENT_COMPARISON_MATCHER_(Gt, >, "is >", "isn't >");
+GMOCK_IMPLEMENT_COMPARISON_MATCHER_(Le, <=, "is <=", "isn't <=");
+GMOCK_IMPLEMENT_COMPARISON_MATCHER_(Lt, <, "is <", "isn't <");
+GMOCK_IMPLEMENT_COMPARISON_MATCHER_(Ne, !=, "isn't equal to", "is equal to");
+
+#undef GMOCK_IMPLEMENT_COMPARISON_MATCHER_
+
+// Implements the polymorphic IsNull() matcher, which matches any raw or smart
+// pointer that is NULL.
+class IsNullMatcher {
+ public:
+ template <typename Pointer>
+ bool MatchAndExplain(const Pointer& p,
+ MatchResultListener* /* listener */) const {
+ return GetRawPointer(p) == NULL;
+ }
+
+ void DescribeTo(::std::ostream* os) const { *os << "is NULL"; }
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "isn't NULL";
+ }
+};
+
+// Implements the polymorphic NotNull() matcher, which matches any raw or smart
+// pointer that is not NULL.
+class NotNullMatcher {
+ public:
+ template <typename Pointer>
+ bool MatchAndExplain(const Pointer& p,
+ MatchResultListener* /* listener */) const {
+ return GetRawPointer(p) != NULL;
+ }
+
+ void DescribeTo(::std::ostream* os) const { *os << "isn't NULL"; }
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "is NULL";
+ }
+};
+
+// Ref(variable) matches any argument that is a reference to
+// 'variable'. This matcher is polymorphic as it can match any
+// super type of the type of 'variable'.
+//
+// The RefMatcher template class implements Ref(variable). It can
+// only be instantiated with a reference type. This prevents a user
+// from mistakenly using Ref(x) to match a non-reference function
+// argument. For example, the following will righteously cause a
+// compiler error:
+//
+// int n;
+// Matcher<int> m1 = Ref(n); // This won't compile.
+// Matcher<int&> m2 = Ref(n); // This will compile.
+template <typename T>
+class RefMatcher;
+
+template <typename T>
+class RefMatcher<T&> {
+ // Google Mock is a generic framework and thus needs to support
+ // mocking any function types, including those that take non-const
+ // reference arguments. Therefore the template parameter T (and
+ // Super below) can be instantiated to either a const type or a
+ // non-const type.
+ public:
+ // RefMatcher() takes a T& instead of const T&, as we want the
+ // compiler to catch using Ref(const_value) as a matcher for a
+ // non-const reference.
+ explicit RefMatcher(T& x) : object_(x) {} // NOLINT
+
+ template <typename Super>
+ operator Matcher<Super&>() const {
+ // By passing object_ (type T&) to Impl(), which expects a Super&,
+ // we make sure that Super is a super type of T. In particular,
+ // this catches using Ref(const_value) as a matcher for a
+ // non-const reference, as you cannot implicitly convert a const
+ // reference to a non-const reference.
+ return MakeMatcher(new Impl<Super>(object_));
+ }
+
+ private:
+ template <typename Super>
+ class Impl : public MatcherInterface<Super&> {
+ public:
+ explicit Impl(Super& x) : object_(x) {} // NOLINT
+
+ // MatchAndExplain() takes a Super& (as opposed to const Super&)
+ // in order to match the interface MatcherInterface<Super&>.
+ virtual bool MatchAndExplain(
+ Super& x, MatchResultListener* listener) const {
+ *listener << "which is located @" << static_cast<const void*>(&x);
+ return &x == &object_;
+ }
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "references the variable ";
+ UniversalPrinter<Super&>::Print(object_, os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "does not reference the variable ";
+ UniversalPrinter<Super&>::Print(object_, os);
+ }
+
+ private:
+ const Super& object_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ T& object_;
+
+ GTEST_DISALLOW_ASSIGN_(RefMatcher);
+};
+
+// Polymorphic helper functions for narrow and wide string matchers.
+inline bool CaseInsensitiveCStringEquals(const char* lhs, const char* rhs) {
+ return String::CaseInsensitiveCStringEquals(lhs, rhs);
+}
+
+inline bool CaseInsensitiveCStringEquals(const wchar_t* lhs,
+ const wchar_t* rhs) {
+ return String::CaseInsensitiveWideCStringEquals(lhs, rhs);
+}
+
+// String comparison for narrow or wide strings that can have embedded NUL
+// characters.
+template <typename StringType>
+bool CaseInsensitiveStringEquals(const StringType& s1,
+ const StringType& s2) {
+ // Are the heads equal?
+ if (!CaseInsensitiveCStringEquals(s1.c_str(), s2.c_str())) {
+ return false;
+ }
+
+ // Skip the equal heads.
+ const typename StringType::value_type nul = 0;
+ const size_t i1 = s1.find(nul), i2 = s2.find(nul);
+
+ // Are we at the end of either s1 or s2?
+ if (i1 == StringType::npos || i2 == StringType::npos) {
+ return i1 == i2;
+ }
+
+ // Are the tails equal?
+ return CaseInsensitiveStringEquals(s1.substr(i1 + 1), s2.substr(i2 + 1));
+}
+
+// String matchers.
+
+// Implements equality-based string matchers like StrEq, StrCaseNe, and etc.
+template <typename StringType>
+class StrEqualityMatcher {
+ public:
+ StrEqualityMatcher(const StringType& str, bool expect_eq,
+ bool case_sensitive)
+ : string_(str), expect_eq_(expect_eq), case_sensitive_(case_sensitive) {}
+
+ // Accepts pointer types, particularly:
+ // const char*
+ // char*
+ // const wchar_t*
+ // wchar_t*
+ template <typename CharType>
+ bool MatchAndExplain(CharType* s, MatchResultListener* listener) const {
+ if (s == NULL) {
+ return !expect_eq_;
+ }
+ return MatchAndExplain(StringType(s), listener);
+ }
+
+ // Matches anything that can convert to StringType.
+ //
+ // This is a template, not just a plain function with const StringType&,
+ // because StringPiece has some interfering non-explicit constructors.
+ template <typename MatcheeStringType>
+ bool MatchAndExplain(const MatcheeStringType& s,
+ MatchResultListener* /* listener */) const {
+ const StringType& s2(s);
+ const bool eq = case_sensitive_ ? s2 == string_ :
+ CaseInsensitiveStringEquals(s2, string_);
+ return expect_eq_ == eq;
+ }
+
+ void DescribeTo(::std::ostream* os) const {
+ DescribeToHelper(expect_eq_, os);
+ }
+
+ void DescribeNegationTo(::std::ostream* os) const {
+ DescribeToHelper(!expect_eq_, os);
+ }
+
+ private:
+ void DescribeToHelper(bool expect_eq, ::std::ostream* os) const {
+ *os << (expect_eq ? "is " : "isn't ");
+ *os << "equal to ";
+ if (!case_sensitive_) {
+ *os << "(ignoring case) ";
+ }
+ UniversalPrint(string_, os);
+ }
+
+ const StringType string_;
+ const bool expect_eq_;
+ const bool case_sensitive_;
+
+ GTEST_DISALLOW_ASSIGN_(StrEqualityMatcher);
+};
+
+// Implements the polymorphic HasSubstr(substring) matcher, which
+// can be used as a Matcher<T> as long as T can be converted to a
+// string.
+template <typename StringType>
+class HasSubstrMatcher {
+ public:
+ explicit HasSubstrMatcher(const StringType& substring)
+ : substring_(substring) {}
+
+ // Accepts pointer types, particularly:
+ // const char*
+ // char*
+ // const wchar_t*
+ // wchar_t*
+ template <typename CharType>
+ bool MatchAndExplain(CharType* s, MatchResultListener* listener) const {
+ return s != NULL && MatchAndExplain(StringType(s), listener);
+ }
+
+ // Matches anything that can convert to StringType.
+ //
+ // This is a template, not just a plain function with const StringType&,
+ // because StringPiece has some interfering non-explicit constructors.
+ template <typename MatcheeStringType>
+ bool MatchAndExplain(const MatcheeStringType& s,
+ MatchResultListener* /* listener */) const {
+ const StringType& s2(s);
+ return s2.find(substring_) != StringType::npos;
+ }
+
+ // Describes what this matcher matches.
+ void DescribeTo(::std::ostream* os) const {
+ *os << "has substring ";
+ UniversalPrint(substring_, os);
+ }
+
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "has no substring ";
+ UniversalPrint(substring_, os);
+ }
+
+ private:
+ const StringType substring_;
+
+ GTEST_DISALLOW_ASSIGN_(HasSubstrMatcher);
+};
+
+// Implements the polymorphic StartsWith(substring) matcher, which
+// can be used as a Matcher<T> as long as T can be converted to a
+// string.
+template <typename StringType>
+class StartsWithMatcher {
+ public:
+ explicit StartsWithMatcher(const StringType& prefix) : prefix_(prefix) {
+ }
+
+ // Accepts pointer types, particularly:
+ // const char*
+ // char*
+ // const wchar_t*
+ // wchar_t*
+ template <typename CharType>
+ bool MatchAndExplain(CharType* s, MatchResultListener* listener) const {
+ return s != NULL && MatchAndExplain(StringType(s), listener);
+ }
+
+ // Matches anything that can convert to StringType.
+ //
+ // This is a template, not just a plain function with const StringType&,
+ // because StringPiece has some interfering non-explicit constructors.
+ template <typename MatcheeStringType>
+ bool MatchAndExplain(const MatcheeStringType& s,
+ MatchResultListener* /* listener */) const {
+ const StringType& s2(s);
+ return s2.length() >= prefix_.length() &&
+ s2.substr(0, prefix_.length()) == prefix_;
+ }
+
+ void DescribeTo(::std::ostream* os) const {
+ *os << "starts with ";
+ UniversalPrint(prefix_, os);
+ }
+
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "doesn't start with ";
+ UniversalPrint(prefix_, os);
+ }
+
+ private:
+ const StringType prefix_;
+
+ GTEST_DISALLOW_ASSIGN_(StartsWithMatcher);
+};
+
+// Implements the polymorphic EndsWith(substring) matcher, which
+// can be used as a Matcher<T> as long as T can be converted to a
+// string.
+template <typename StringType>
+class EndsWithMatcher {
+ public:
+ explicit EndsWithMatcher(const StringType& suffix) : suffix_(suffix) {}
+
+ // Accepts pointer types, particularly:
+ // const char*
+ // char*
+ // const wchar_t*
+ // wchar_t*
+ template <typename CharType>
+ bool MatchAndExplain(CharType* s, MatchResultListener* listener) const {
+ return s != NULL && MatchAndExplain(StringType(s), listener);
+ }
+
+ // Matches anything that can convert to StringType.
+ //
+ // This is a template, not just a plain function with const StringType&,
+ // because StringPiece has some interfering non-explicit constructors.
+ template <typename MatcheeStringType>
+ bool MatchAndExplain(const MatcheeStringType& s,
+ MatchResultListener* /* listener */) const {
+ const StringType& s2(s);
+ return s2.length() >= suffix_.length() &&
+ s2.substr(s2.length() - suffix_.length()) == suffix_;
+ }
+
+ void DescribeTo(::std::ostream* os) const {
+ *os << "ends with ";
+ UniversalPrint(suffix_, os);
+ }
+
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "doesn't end with ";
+ UniversalPrint(suffix_, os);
+ }
+
+ private:
+ const StringType suffix_;
+
+ GTEST_DISALLOW_ASSIGN_(EndsWithMatcher);
+};
+
+// Implements polymorphic matchers MatchesRegex(regex) and
+// ContainsRegex(regex), which can be used as a Matcher<T> as long as
+// T can be converted to a string.
+class MatchesRegexMatcher {
+ public:
+ MatchesRegexMatcher(const RE* regex, bool full_match)
+ : regex_(regex), full_match_(full_match) {}
+
+ // Accepts pointer types, particularly:
+ // const char*
+ // char*
+ // const wchar_t*
+ // wchar_t*
+ template <typename CharType>
+ bool MatchAndExplain(CharType* s, MatchResultListener* listener) const {
+ return s != NULL && MatchAndExplain(internal::string(s), listener);
+ }
+
+ // Matches anything that can convert to internal::string.
+ //
+ // This is a template, not just a plain function with const internal::string&,
+ // because StringPiece has some interfering non-explicit constructors.
+ template <class MatcheeStringType>
+ bool MatchAndExplain(const MatcheeStringType& s,
+ MatchResultListener* /* listener */) const {
+ const internal::string& s2(s);
+ return full_match_ ? RE::FullMatch(s2, *regex_) :
+ RE::PartialMatch(s2, *regex_);
+ }
+
+ void DescribeTo(::std::ostream* os) const {
+ *os << (full_match_ ? "matches" : "contains")
+ << " regular expression ";
+ UniversalPrinter<internal::string>::Print(regex_->pattern(), os);
+ }
+
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "doesn't " << (full_match_ ? "match" : "contain")
+ << " regular expression ";
+ UniversalPrinter<internal::string>::Print(regex_->pattern(), os);
+ }
+
+ private:
+ const internal::linked_ptr<const RE> regex_;
+ const bool full_match_;
+
+ GTEST_DISALLOW_ASSIGN_(MatchesRegexMatcher);
+};
+
+// Implements a matcher that compares the two fields of a 2-tuple
+// using one of the ==, <=, <, etc, operators. The two fields being
+// compared don't have to have the same type.
+//
+// The matcher defined here is polymorphic (for example, Eq() can be
+// used to match a tuple<int, short>, a tuple<const long&, double>,
+// etc). Therefore we use a template type conversion operator in the
+// implementation.
+//
+// We define this as a macro in order to eliminate duplicated source
+// code.
+#define GMOCK_IMPLEMENT_COMPARISON2_MATCHER_(name, op, relation) \
+ class name##2Matcher { \
+ public: \
+ template <typename T1, typename T2> \
+ operator Matcher< ::std::tr1::tuple<T1, T2> >() const { \
+ return MakeMatcher(new Impl< ::std::tr1::tuple<T1, T2> >); \
+ } \
+ template <typename T1, typename T2> \
+ operator Matcher<const ::std::tr1::tuple<T1, T2>&>() const { \
+ return MakeMatcher(new Impl<const ::std::tr1::tuple<T1, T2>&>); \
+ } \
+ private: \
+ template <typename Tuple> \
+ class Impl : public MatcherInterface<Tuple> { \
+ public: \
+ virtual bool MatchAndExplain( \
+ Tuple args, \
+ MatchResultListener* /* listener */) const { \
+ return ::std::tr1::get<0>(args) op ::std::tr1::get<1>(args); \
+ } \
+ virtual void DescribeTo(::std::ostream* os) const { \
+ *os << "are " relation; \
+ } \
+ virtual void DescribeNegationTo(::std::ostream* os) const { \
+ *os << "aren't " relation; \
+ } \
+ }; \
+ }
+
+// Implements Eq(), Ge(), Gt(), Le(), Lt(), and Ne() respectively.
+GMOCK_IMPLEMENT_COMPARISON2_MATCHER_(Eq, ==, "an equal pair");
+GMOCK_IMPLEMENT_COMPARISON2_MATCHER_(
+ Ge, >=, "a pair where the first >= the second");
+GMOCK_IMPLEMENT_COMPARISON2_MATCHER_(
+ Gt, >, "a pair where the first > the second");
+GMOCK_IMPLEMENT_COMPARISON2_MATCHER_(
+ Le, <=, "a pair where the first <= the second");
+GMOCK_IMPLEMENT_COMPARISON2_MATCHER_(
+ Lt, <, "a pair where the first < the second");
+GMOCK_IMPLEMENT_COMPARISON2_MATCHER_(Ne, !=, "an unequal pair");
+
+#undef GMOCK_IMPLEMENT_COMPARISON2_MATCHER_
+
+// Implements the Not(...) matcher for a particular argument type T.
+// We do not nest it inside the NotMatcher class template, as that
+// will prevent different instantiations of NotMatcher from sharing
+// the same NotMatcherImpl<T> class.
+template <typename T>
+class NotMatcherImpl : public MatcherInterface<T> {
+ public:
+ explicit NotMatcherImpl(const Matcher<T>& matcher)
+ : matcher_(matcher) {}
+
+ virtual bool MatchAndExplain(T x, MatchResultListener* listener) const {
+ return !matcher_.MatchAndExplain(x, listener);
+ }
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ matcher_.DescribeNegationTo(os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ matcher_.DescribeTo(os);
+ }
+
+ private:
+ const Matcher<T> matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(NotMatcherImpl);
+};
+
+// Implements the Not(m) matcher, which matches a value that doesn't
+// match matcher m.
+template <typename InnerMatcher>
+class NotMatcher {
+ public:
+ explicit NotMatcher(InnerMatcher matcher) : matcher_(matcher) {}
+
+ // This template type conversion operator allows Not(m) to be used
+ // to match any type m can match.
+ template <typename T>
+ operator Matcher<T>() const {
+ return Matcher<T>(new NotMatcherImpl<T>(SafeMatcherCast<T>(matcher_)));
+ }
+
+ private:
+ InnerMatcher matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(NotMatcher);
+};
+
+// Implements the AllOf(m1, m2) matcher for a particular argument type
+// T. We do not nest it inside the BothOfMatcher class template, as
+// that will prevent different instantiations of BothOfMatcher from
+// sharing the same BothOfMatcherImpl<T> class.
+template <typename T>
+class BothOfMatcherImpl : public MatcherInterface<T> {
+ public:
+ BothOfMatcherImpl(const Matcher<T>& matcher1, const Matcher<T>& matcher2)
+ : matcher1_(matcher1), matcher2_(matcher2) {}
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "(";
+ matcher1_.DescribeTo(os);
+ *os << ") and (";
+ matcher2_.DescribeTo(os);
+ *os << ")";
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "(";
+ matcher1_.DescribeNegationTo(os);
+ *os << ") or (";
+ matcher2_.DescribeNegationTo(os);
+ *os << ")";
+ }
+
+ virtual bool MatchAndExplain(T x, MatchResultListener* listener) const {
+ // If either matcher1_ or matcher2_ doesn't match x, we only need
+ // to explain why one of them fails.
+ StringMatchResultListener listener1;
+ if (!matcher1_.MatchAndExplain(x, &listener1)) {
+ *listener << listener1.str();
+ return false;
+ }
+
+ StringMatchResultListener listener2;
+ if (!matcher2_.MatchAndExplain(x, &listener2)) {
+ *listener << listener2.str();
+ return false;
+ }
+
+ // Otherwise we need to explain why *both* of them match.
+ const internal::string s1 = listener1.str();
+ const internal::string s2 = listener2.str();
+
+ if (s1 == "") {
+ *listener << s2;
+ } else {
+ *listener << s1;
+ if (s2 != "") {
+ *listener << ", and " << s2;
+ }
+ }
+ return true;
+ }
+
+ private:
+ const Matcher<T> matcher1_;
+ const Matcher<T> matcher2_;
+
+ GTEST_DISALLOW_ASSIGN_(BothOfMatcherImpl);
+};
+
+#if GTEST_LANG_CXX11
+// MatcherList provides mechanisms for storing a variable number of matchers in
+// a list structure (ListType) and creating a combining matcher from such a
+// list.
+// The template is defined recursively using the following template paramters:
+// * kSize is the length of the MatcherList.
+// * Head is the type of the first matcher of the list.
+// * Tail denotes the types of the remaining matchers of the list.
+template <int kSize, typename Head, typename... Tail>
+struct MatcherList {
+ typedef MatcherList<kSize - 1, Tail...> MatcherListTail;
+ typedef ::std::pair<Head, typename MatcherListTail::ListType> ListType;
+
+ // BuildList stores variadic type values in a nested pair structure.
+ // Example:
+ // MatcherList<3, int, string, float>::BuildList(5, "foo", 2.0) will return
+ // the corresponding result of type pair<int, pair<string, float>>.
+ static ListType BuildList(const Head& matcher, const Tail&... tail) {
+ return ListType(matcher, MatcherListTail::BuildList(tail...));
+ }
+
+ // CreateMatcher<T> creates a Matcher<T> from a given list of matchers (built
+ // by BuildList()). CombiningMatcher<T> is used to combine the matchers of the
+ // list. CombiningMatcher<T> must implement MatcherInterface<T> and have a
+ // constructor taking two Matcher<T>s as input.
+ template <typename T, template <typename /* T */> class CombiningMatcher>
+ static Matcher<T> CreateMatcher(const ListType& matchers) {
+ return Matcher<T>(new CombiningMatcher<T>(
+ SafeMatcherCast<T>(matchers.first),
+ MatcherListTail::template CreateMatcher<T, CombiningMatcher>(
+ matchers.second)));
+ }
+};
+
+// The following defines the base case for the recursive definition of
+// MatcherList.
+template <typename Matcher1, typename Matcher2>
+struct MatcherList<2, Matcher1, Matcher2> {
+ typedef ::std::pair<Matcher1, Matcher2> ListType;
+
+ static ListType BuildList(const Matcher1& matcher1,
+ const Matcher2& matcher2) {
+ return ::std::pair<Matcher1, Matcher2>(matcher1, matcher2);
+ }
+
+ template <typename T, template <typename /* T */> class CombiningMatcher>
+ static Matcher<T> CreateMatcher(const ListType& matchers) {
+ return Matcher<T>(new CombiningMatcher<T>(
+ SafeMatcherCast<T>(matchers.first),
+ SafeMatcherCast<T>(matchers.second)));
+ }
+};
+
+// VariadicMatcher is used for the variadic implementation of
+// AllOf(m_1, m_2, ...) and AnyOf(m_1, m_2, ...).
+// CombiningMatcher<T> is used to recursively combine the provided matchers
+// (of type Args...).
+template <template <typename T> class CombiningMatcher, typename... Args>
+class VariadicMatcher {
+ public:
+ VariadicMatcher(const Args&... matchers) // NOLINT
+ : matchers_(MatcherListType::BuildList(matchers...)) {}
+
+ // This template type conversion operator allows an
+ // VariadicMatcher<Matcher1, Matcher2...> object to match any type that
+ // all of the provided matchers (Matcher1, Matcher2, ...) can match.
+ template <typename T>
+ operator Matcher<T>() const {
+ return MatcherListType::template CreateMatcher<T, CombiningMatcher>(
+ matchers_);
+ }
+
+ private:
+ typedef MatcherList<sizeof...(Args), Args...> MatcherListType;
+
+ const typename MatcherListType::ListType matchers_;
+
+ GTEST_DISALLOW_ASSIGN_(VariadicMatcher);
+};
+
+template <typename... Args>
+using AllOfMatcher = VariadicMatcher<BothOfMatcherImpl, Args...>;
+
+#endif // GTEST_LANG_CXX11
+
+// Used for implementing the AllOf(m_1, ..., m_n) matcher, which
+// matches a value that matches all of the matchers m_1, ..., and m_n.
+template <typename Matcher1, typename Matcher2>
+class BothOfMatcher {
+ public:
+ BothOfMatcher(Matcher1 matcher1, Matcher2 matcher2)
+ : matcher1_(matcher1), matcher2_(matcher2) {}
+
+ // This template type conversion operator allows a
+ // BothOfMatcher<Matcher1, Matcher2> object to match any type that
+ // both Matcher1 and Matcher2 can match.
+ template <typename T>
+ operator Matcher<T>() const {
+ return Matcher<T>(new BothOfMatcherImpl<T>(SafeMatcherCast<T>(matcher1_),
+ SafeMatcherCast<T>(matcher2_)));
+ }
+
+ private:
+ Matcher1 matcher1_;
+ Matcher2 matcher2_;
+
+ GTEST_DISALLOW_ASSIGN_(BothOfMatcher);
+};
+
+// Implements the AnyOf(m1, m2) matcher for a particular argument type
+// T. We do not nest it inside the AnyOfMatcher class template, as
+// that will prevent different instantiations of AnyOfMatcher from
+// sharing the same EitherOfMatcherImpl<T> class.
+template <typename T>
+class EitherOfMatcherImpl : public MatcherInterface<T> {
+ public:
+ EitherOfMatcherImpl(const Matcher<T>& matcher1, const Matcher<T>& matcher2)
+ : matcher1_(matcher1), matcher2_(matcher2) {}
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "(";
+ matcher1_.DescribeTo(os);
+ *os << ") or (";
+ matcher2_.DescribeTo(os);
+ *os << ")";
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "(";
+ matcher1_.DescribeNegationTo(os);
+ *os << ") and (";
+ matcher2_.DescribeNegationTo(os);
+ *os << ")";
+ }
+
+ virtual bool MatchAndExplain(T x, MatchResultListener* listener) const {
+ // If either matcher1_ or matcher2_ matches x, we just need to
+ // explain why *one* of them matches.
+ StringMatchResultListener listener1;
+ if (matcher1_.MatchAndExplain(x, &listener1)) {
+ *listener << listener1.str();
+ return true;
+ }
+
+ StringMatchResultListener listener2;
+ if (matcher2_.MatchAndExplain(x, &listener2)) {
+ *listener << listener2.str();
+ return true;
+ }
+
+ // Otherwise we need to explain why *both* of them fail.
+ const internal::string s1 = listener1.str();
+ const internal::string s2 = listener2.str();
+
+ if (s1 == "") {
+ *listener << s2;
+ } else {
+ *listener << s1;
+ if (s2 != "") {
+ *listener << ", and " << s2;
+ }
+ }
+ return false;
+ }
+
+ private:
+ const Matcher<T> matcher1_;
+ const Matcher<T> matcher2_;
+
+ GTEST_DISALLOW_ASSIGN_(EitherOfMatcherImpl);
+};
+
+#if GTEST_LANG_CXX11
+// AnyOfMatcher is used for the variadic implementation of AnyOf(m_1, m_2, ...).
+template <typename... Args>
+using AnyOfMatcher = VariadicMatcher<EitherOfMatcherImpl, Args...>;
+
+#endif // GTEST_LANG_CXX11
+
+// Used for implementing the AnyOf(m_1, ..., m_n) matcher, which
+// matches a value that matches at least one of the matchers m_1, ...,
+// and m_n.
+template <typename Matcher1, typename Matcher2>
+class EitherOfMatcher {
+ public:
+ EitherOfMatcher(Matcher1 matcher1, Matcher2 matcher2)
+ : matcher1_(matcher1), matcher2_(matcher2) {}
+
+ // This template type conversion operator allows a
+ // EitherOfMatcher<Matcher1, Matcher2> object to match any type that
+ // both Matcher1 and Matcher2 can match.
+ template <typename T>
+ operator Matcher<T>() const {
+ return Matcher<T>(new EitherOfMatcherImpl<T>(
+ SafeMatcherCast<T>(matcher1_), SafeMatcherCast<T>(matcher2_)));
+ }
+
+ private:
+ Matcher1 matcher1_;
+ Matcher2 matcher2_;
+
+ GTEST_DISALLOW_ASSIGN_(EitherOfMatcher);
+};
+
+// Used for implementing Truly(pred), which turns a predicate into a
+// matcher.
+template <typename Predicate>
+class TrulyMatcher {
+ public:
+ explicit TrulyMatcher(Predicate pred) : predicate_(pred) {}
+
+ // This method template allows Truly(pred) to be used as a matcher
+ // for type T where T is the argument type of predicate 'pred'. The
+ // argument is passed by reference as the predicate may be
+ // interested in the address of the argument.
+ template <typename T>
+ bool MatchAndExplain(T& x, // NOLINT
+ MatchResultListener* /* listener */) const {
+ // Without the if-statement, MSVC sometimes warns about converting
+ // a value to bool (warning 4800).
+ //
+ // We cannot write 'return !!predicate_(x);' as that doesn't work
+ // when predicate_(x) returns a class convertible to bool but
+ // having no operator!().
+ if (predicate_(x))
+ return true;
+ return false;
+ }
+
+ void DescribeTo(::std::ostream* os) const {
+ *os << "satisfies the given predicate";
+ }
+
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "doesn't satisfy the given predicate";
+ }
+
+ private:
+ Predicate predicate_;
+
+ GTEST_DISALLOW_ASSIGN_(TrulyMatcher);
+};
+
+// Used for implementing Matches(matcher), which turns a matcher into
+// a predicate.
+template <typename M>
+class MatcherAsPredicate {
+ public:
+ explicit MatcherAsPredicate(M matcher) : matcher_(matcher) {}
+
+ // This template operator() allows Matches(m) to be used as a
+ // predicate on type T where m is a matcher on type T.
+ //
+ // The argument x is passed by reference instead of by value, as
+ // some matcher may be interested in its address (e.g. as in
+ // Matches(Ref(n))(x)).
+ template <typename T>
+ bool operator()(const T& x) const {
+ // We let matcher_ commit to a particular type here instead of
+ // when the MatcherAsPredicate object was constructed. This
+ // allows us to write Matches(m) where m is a polymorphic matcher
+ // (e.g. Eq(5)).
+ //
+ // If we write Matcher<T>(matcher_).Matches(x) here, it won't
+ // compile when matcher_ has type Matcher<const T&>; if we write
+ // Matcher<const T&>(matcher_).Matches(x) here, it won't compile
+ // when matcher_ has type Matcher<T>; if we just write
+ // matcher_.Matches(x), it won't compile when matcher_ is
+ // polymorphic, e.g. Eq(5).
+ //
+ // MatcherCast<const T&>() is necessary for making the code work
+ // in all of the above situations.
+ return MatcherCast<const T&>(matcher_).Matches(x);
+ }
+
+ private:
+ M matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(MatcherAsPredicate);
+};
+
+// For implementing ASSERT_THAT() and EXPECT_THAT(). The template
+// argument M must be a type that can be converted to a matcher.
+template <typename M>
+class PredicateFormatterFromMatcher {
+ public:
+ explicit PredicateFormatterFromMatcher(const M& m) : matcher_(m) {}
+
+ // This template () operator allows a PredicateFormatterFromMatcher
+ // object to act as a predicate-formatter suitable for using with
+ // Google Test's EXPECT_PRED_FORMAT1() macro.
+ template <typename T>
+ AssertionResult operator()(const char* value_text, const T& x) const {
+ // We convert matcher_ to a Matcher<const T&> *now* instead of
+ // when the PredicateFormatterFromMatcher object was constructed,
+ // as matcher_ may be polymorphic (e.g. NotNull()) and we won't
+ // know which type to instantiate it to until we actually see the
+ // type of x here.
+ //
+ // We write SafeMatcherCast<const T&>(matcher_) instead of
+ // Matcher<const T&>(matcher_), as the latter won't compile when
+ // matcher_ has type Matcher<T> (e.g. An<int>()).
+ // We don't write MatcherCast<const T&> either, as that allows
+ // potentially unsafe downcasting of the matcher argument.
+ const Matcher<const T&> matcher = SafeMatcherCast<const T&>(matcher_);
+ StringMatchResultListener listener;
+ if (MatchPrintAndExplain(x, matcher, &listener))
+ return AssertionSuccess();
+
+ ::std::stringstream ss;
+ ss << "Value of: " << value_text << "\n"
+ << "Expected: ";
+ matcher.DescribeTo(&ss);
+ ss << "\n Actual: " << listener.str();
+ return AssertionFailure() << ss.str();
+ }
+
+ private:
+ const M matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(PredicateFormatterFromMatcher);
+};
+
+// A helper function for converting a matcher to a predicate-formatter
+// without the user needing to explicitly write the type. This is
+// used for implementing ASSERT_THAT() and EXPECT_THAT().
+template <typename M>
+inline PredicateFormatterFromMatcher<M>
+MakePredicateFormatterFromMatcher(const M& matcher) {
+ return PredicateFormatterFromMatcher<M>(matcher);
+}
+
+// Implements the polymorphic floating point equality matcher, which matches
+// two float values using ULP-based approximation or, optionally, a
+// user-specified epsilon. The template is meant to be instantiated with
+// FloatType being either float or double.
+template <typename FloatType>
+class FloatingEqMatcher {
+ public:
+ // Constructor for FloatingEqMatcher.
+ // The matcher's input will be compared with rhs. The matcher treats two
+ // NANs as equal if nan_eq_nan is true. Otherwise, under IEEE standards,
+ // equality comparisons between NANs will always return false. We specify a
+ // negative max_abs_error_ term to indicate that ULP-based approximation will
+ // be used for comparison.
+ FloatingEqMatcher(FloatType rhs, bool nan_eq_nan) :
+ rhs_(rhs), nan_eq_nan_(nan_eq_nan), max_abs_error_(-1) {
+ }
+
+ // Constructor that supports a user-specified max_abs_error that will be used
+ // for comparison instead of ULP-based approximation. The max absolute
+ // should be non-negative.
+ FloatingEqMatcher(FloatType rhs, bool nan_eq_nan, FloatType max_abs_error) :
+ rhs_(rhs), nan_eq_nan_(nan_eq_nan), max_abs_error_(max_abs_error) {
+ GTEST_CHECK_(max_abs_error >= 0)
+ << ", where max_abs_error is" << max_abs_error;
+ }
+
+ // Implements floating point equality matcher as a Matcher<T>.
+ template <typename T>
+ class Impl : public MatcherInterface<T> {
+ public:
+ Impl(FloatType rhs, bool nan_eq_nan, FloatType max_abs_error) :
+ rhs_(rhs), nan_eq_nan_(nan_eq_nan), max_abs_error_(max_abs_error) {}
+
+ virtual bool MatchAndExplain(T value,
+ MatchResultListener* /* listener */) const {
+ const FloatingPoint<FloatType> lhs(value), rhs(rhs_);
+
+ // Compares NaNs first, if nan_eq_nan_ is true.
+ if (lhs.is_nan() || rhs.is_nan()) {
+ if (lhs.is_nan() && rhs.is_nan()) {
+ return nan_eq_nan_;
+ }
+ // One is nan; the other is not nan.
+ return false;
+ }
+ if (HasMaxAbsError()) {
+ // We perform an equality check so that inf will match inf, regardless
+ // of error bounds. If the result of value - rhs_ would result in
+ // overflow or if either value is inf, the default result is infinity,
+ // which should only match if max_abs_error_ is also infinity.
+ return value == rhs_ || fabs(value - rhs_) <= max_abs_error_;
+ } else {
+ return lhs.AlmostEquals(rhs);
+ }
+ }
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ // os->precision() returns the previously set precision, which we
+ // store to restore the ostream to its original configuration
+ // after outputting.
+ const ::std::streamsize old_precision = os->precision(
+ ::std::numeric_limits<FloatType>::digits10 + 2);
+ if (FloatingPoint<FloatType>(rhs_).is_nan()) {
+ if (nan_eq_nan_) {
+ *os << "is NaN";
+ } else {
+ *os << "never matches";
+ }
+ } else {
+ *os << "is approximately " << rhs_;
+ if (HasMaxAbsError()) {
+ *os << " (absolute error <= " << max_abs_error_ << ")";
+ }
+ }
+ os->precision(old_precision);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ // As before, get original precision.
+ const ::std::streamsize old_precision = os->precision(
+ ::std::numeric_limits<FloatType>::digits10 + 2);
+ if (FloatingPoint<FloatType>(rhs_).is_nan()) {
+ if (nan_eq_nan_) {
+ *os << "isn't NaN";
+ } else {
+ *os << "is anything";
+ }
+ } else {
+ *os << "isn't approximately " << rhs_;
+ if (HasMaxAbsError()) {
+ *os << " (absolute error > " << max_abs_error_ << ")";
+ }
+ }
+ // Restore original precision.
+ os->precision(old_precision);
+ }
+
+ private:
+ bool HasMaxAbsError() const {
+ return max_abs_error_ >= 0;
+ }
+
+ const FloatType rhs_;
+ const bool nan_eq_nan_;
+ // max_abs_error will be used for value comparison when >= 0.
+ const FloatType max_abs_error_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ // The following 3 type conversion operators allow FloatEq(rhs) and
+ // NanSensitiveFloatEq(rhs) to be used as a Matcher<float>, a
+ // Matcher<const float&>, or a Matcher<float&>, but nothing else.
+ // (While Google's C++ coding style doesn't allow arguments passed
+ // by non-const reference, we may see them in code not conforming to
+ // the style. Therefore Google Mock needs to support them.)
+ operator Matcher<FloatType>() const {
+ return MakeMatcher(new Impl<FloatType>(rhs_, nan_eq_nan_, max_abs_error_));
+ }
+
+ operator Matcher<const FloatType&>() const {
+ return MakeMatcher(
+ new Impl<const FloatType&>(rhs_, nan_eq_nan_, max_abs_error_));
+ }
+
+ operator Matcher<FloatType&>() const {
+ return MakeMatcher(new Impl<FloatType&>(rhs_, nan_eq_nan_, max_abs_error_));
+ }
+
+ private:
+ const FloatType rhs_;
+ const bool nan_eq_nan_;
+ // max_abs_error will be used for value comparison when >= 0.
+ const FloatType max_abs_error_;
+
+ GTEST_DISALLOW_ASSIGN_(FloatingEqMatcher);
+};
+
+// Implements the Pointee(m) matcher for matching a pointer whose
+// pointee matches matcher m. The pointer can be either raw or smart.
+template <typename InnerMatcher>
+class PointeeMatcher {
+ public:
+ explicit PointeeMatcher(const InnerMatcher& matcher) : matcher_(matcher) {}
+
+ // This type conversion operator template allows Pointee(m) to be
+ // used as a matcher for any pointer type whose pointee type is
+ // compatible with the inner matcher, where type Pointer can be
+ // either a raw pointer or a smart pointer.
+ //
+ // The reason we do this instead of relying on
+ // MakePolymorphicMatcher() is that the latter is not flexible
+ // enough for implementing the DescribeTo() method of Pointee().
+ template <typename Pointer>
+ operator Matcher<Pointer>() const {
+ return MakeMatcher(new Impl<Pointer>(matcher_));
+ }
+
+ private:
+ // The monomorphic implementation that works for a particular pointer type.
+ template <typename Pointer>
+ class Impl : public MatcherInterface<Pointer> {
+ public:
+ typedef typename PointeeOf<GTEST_REMOVE_CONST_( // NOLINT
+ GTEST_REMOVE_REFERENCE_(Pointer))>::type Pointee;
+
+ explicit Impl(const InnerMatcher& matcher)
+ : matcher_(MatcherCast<const Pointee&>(matcher)) {}
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "points to a value that ";
+ matcher_.DescribeTo(os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "does not point to a value that ";
+ matcher_.DescribeTo(os);
+ }
+
+ virtual bool MatchAndExplain(Pointer pointer,
+ MatchResultListener* listener) const {
+ if (GetRawPointer(pointer) == NULL)
+ return false;
+
+ *listener << "which points to ";
+ return MatchPrintAndExplain(*pointer, matcher_, listener);
+ }
+
+ private:
+ const Matcher<const Pointee&> matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ const InnerMatcher matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(PointeeMatcher);
+};
+
+// Implements the Field() matcher for matching a field (i.e. member
+// variable) of an object.
+template <typename Class, typename FieldType>
+class FieldMatcher {
+ public:
+ FieldMatcher(FieldType Class::*field,
+ const Matcher<const FieldType&>& matcher)
+ : field_(field), matcher_(matcher) {}
+
+ void DescribeTo(::std::ostream* os) const {
+ *os << "is an object whose given field ";
+ matcher_.DescribeTo(os);
+ }
+
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "is an object whose given field ";
+ matcher_.DescribeNegationTo(os);
+ }
+
+ template <typename T>
+ bool MatchAndExplain(const T& value, MatchResultListener* listener) const {
+ return MatchAndExplainImpl(
+ typename ::testing::internal::
+ is_pointer<GTEST_REMOVE_CONST_(T)>::type(),
+ value, listener);
+ }
+
+ private:
+ // The first argument of MatchAndExplainImpl() is needed to help
+ // Symbian's C++ compiler choose which overload to use. Its type is
+ // true_type iff the Field() matcher is used to match a pointer.
+ bool MatchAndExplainImpl(false_type /* is_not_pointer */, const Class& obj,
+ MatchResultListener* listener) const {
+ *listener << "whose given field is ";
+ return MatchPrintAndExplain(obj.*field_, matcher_, listener);
+ }
+
+ bool MatchAndExplainImpl(true_type /* is_pointer */, const Class* p,
+ MatchResultListener* listener) const {
+ if (p == NULL)
+ return false;
+
+ *listener << "which points to an object ";
+ // Since *p has a field, it must be a class/struct/union type and
+ // thus cannot be a pointer. Therefore we pass false_type() as
+ // the first argument.
+ return MatchAndExplainImpl(false_type(), *p, listener);
+ }
+
+ const FieldType Class::*field_;
+ const Matcher<const FieldType&> matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(FieldMatcher);
+};
+
+// Implements the Property() matcher for matching a property
+// (i.e. return value of a getter method) of an object.
+template <typename Class, typename PropertyType>
+class PropertyMatcher {
+ public:
+ // The property may have a reference type, so 'const PropertyType&'
+ // may cause double references and fail to compile. That's why we
+ // need GTEST_REFERENCE_TO_CONST, which works regardless of
+ // PropertyType being a reference or not.
+ typedef GTEST_REFERENCE_TO_CONST_(PropertyType) RefToConstProperty;
+
+ PropertyMatcher(PropertyType (Class::*property)() const,
+ const Matcher<RefToConstProperty>& matcher)
+ : property_(property), matcher_(matcher) {}
+
+ void DescribeTo(::std::ostream* os) const {
+ *os << "is an object whose given property ";
+ matcher_.DescribeTo(os);
+ }
+
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "is an object whose given property ";
+ matcher_.DescribeNegationTo(os);
+ }
+
+ template <typename T>
+ bool MatchAndExplain(const T&value, MatchResultListener* listener) const {
+ return MatchAndExplainImpl(
+ typename ::testing::internal::
+ is_pointer<GTEST_REMOVE_CONST_(T)>::type(),
+ value, listener);
+ }
+
+ private:
+ // The first argument of MatchAndExplainImpl() is needed to help
+ // Symbian's C++ compiler choose which overload to use. Its type is
+ // true_type iff the Property() matcher is used to match a pointer.
+ bool MatchAndExplainImpl(false_type /* is_not_pointer */, const Class& obj,
+ MatchResultListener* listener) const {
+ *listener << "whose given property is ";
+ // Cannot pass the return value (for example, int) to MatchPrintAndExplain,
+ // which takes a non-const reference as argument.
+ RefToConstProperty result = (obj.*property_)();
+ return MatchPrintAndExplain(result, matcher_, listener);
+ }
+
+ bool MatchAndExplainImpl(true_type /* is_pointer */, const Class* p,
+ MatchResultListener* listener) const {
+ if (p == NULL)
+ return false;
+
+ *listener << "which points to an object ";
+ // Since *p has a property method, it must be a class/struct/union
+ // type and thus cannot be a pointer. Therefore we pass
+ // false_type() as the first argument.
+ return MatchAndExplainImpl(false_type(), *p, listener);
+ }
+
+ PropertyType (Class::*property_)() const;
+ const Matcher<RefToConstProperty> matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(PropertyMatcher);
+};
+
+// Type traits specifying various features of different functors for ResultOf.
+// The default template specifies features for functor objects.
+// Functor classes have to typedef argument_type and result_type
+// to be compatible with ResultOf.
+template <typename Functor>
+struct CallableTraits {
+ typedef typename Functor::result_type ResultType;
+ typedef Functor StorageType;
+
+ static void CheckIsValid(Functor /* functor */) {}
+ template <typename T>
+ static ResultType Invoke(Functor f, T arg) { return f(arg); }
+};
+
+// Specialization for function pointers.
+template <typename ArgType, typename ResType>
+struct CallableTraits<ResType(*)(ArgType)> {
+ typedef ResType ResultType;
+ typedef ResType(*StorageType)(ArgType);
+
+ static void CheckIsValid(ResType(*f)(ArgType)) {
+ GTEST_CHECK_(f != NULL)
+ << "NULL function pointer is passed into ResultOf().";
+ }
+ template <typename T>
+ static ResType Invoke(ResType(*f)(ArgType), T arg) {
+ return (*f)(arg);
+ }
+};
+
+// Implements the ResultOf() matcher for matching a return value of a
+// unary function of an object.
+template <typename Callable>
+class ResultOfMatcher {
+ public:
+ typedef typename CallableTraits<Callable>::ResultType ResultType;
+
+ ResultOfMatcher(Callable callable, const Matcher<ResultType>& matcher)
+ : callable_(callable), matcher_(matcher) {
+ CallableTraits<Callable>::CheckIsValid(callable_);
+ }
+
+ template <typename T>
+ operator Matcher<T>() const {
+ return Matcher<T>(new Impl<T>(callable_, matcher_));
+ }
+
+ private:
+ typedef typename CallableTraits<Callable>::StorageType CallableStorageType;
+
+ template <typename T>
+ class Impl : public MatcherInterface<T> {
+ public:
+ Impl(CallableStorageType callable, const Matcher<ResultType>& matcher)
+ : callable_(callable), matcher_(matcher) {}
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "is mapped by the given callable to a value that ";
+ matcher_.DescribeTo(os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "is mapped by the given callable to a value that ";
+ matcher_.DescribeNegationTo(os);
+ }
+
+ virtual bool MatchAndExplain(T obj, MatchResultListener* listener) const {
+ *listener << "which is mapped by the given callable to ";
+ // Cannot pass the return value (for example, int) to
+ // MatchPrintAndExplain, which takes a non-const reference as argument.
+ ResultType result =
+ CallableTraits<Callable>::template Invoke<T>(callable_, obj);
+ return MatchPrintAndExplain(result, matcher_, listener);
+ }
+
+ private:
+ // Functors often define operator() as non-const method even though
+ // they are actualy stateless. But we need to use them even when
+ // 'this' is a const pointer. It's the user's responsibility not to
+ // use stateful callables with ResultOf(), which does't guarantee
+ // how many times the callable will be invoked.
+ mutable CallableStorageType callable_;
+ const Matcher<ResultType> matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ }; // class Impl
+
+ const CallableStorageType callable_;
+ const Matcher<ResultType> matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(ResultOfMatcher);
+};
+
+// Implements a matcher that checks the size of an STL-style container.
+template <typename SizeMatcher>
+class SizeIsMatcher {
+ public:
+ explicit SizeIsMatcher(const SizeMatcher& size_matcher)
+ : size_matcher_(size_matcher) {
+ }
+
+ template <typename Container>
+ operator Matcher<Container>() const {
+ return MakeMatcher(new Impl<Container>(size_matcher_));
+ }
+
+ template <typename Container>
+ class Impl : public MatcherInterface<Container> {
+ public:
+ typedef internal::StlContainerView<
+ GTEST_REMOVE_REFERENCE_AND_CONST_(Container)> ContainerView;
+ typedef typename ContainerView::type::size_type SizeType;
+ explicit Impl(const SizeMatcher& size_matcher)
+ : size_matcher_(MatcherCast<SizeType>(size_matcher)) {}
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "size ";
+ size_matcher_.DescribeTo(os);
+ }
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "size ";
+ size_matcher_.DescribeNegationTo(os);
+ }
+
+ virtual bool MatchAndExplain(Container container,
+ MatchResultListener* listener) const {
+ SizeType size = container.size();
+ StringMatchResultListener size_listener;
+ const bool result = size_matcher_.MatchAndExplain(size, &size_listener);
+ *listener
+ << "whose size " << size << (result ? " matches" : " doesn't match");
+ PrintIfNotEmpty(size_listener.str(), listener->stream());
+ return result;
+ }
+
+ private:
+ const Matcher<SizeType> size_matcher_;
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ private:
+ const SizeMatcher size_matcher_;
+ GTEST_DISALLOW_ASSIGN_(SizeIsMatcher);
+};
+
+// Implements an equality matcher for any STL-style container whose elements
+// support ==. This matcher is like Eq(), but its failure explanations provide
+// more detailed information that is useful when the container is used as a set.
+// The failure message reports elements that are in one of the operands but not
+// the other. The failure messages do not report duplicate or out-of-order
+// elements in the containers (which don't properly matter to sets, but can
+// occur if the containers are vectors or lists, for example).
+//
+// Uses the container's const_iterator, value_type, operator ==,
+// begin(), and end().
+template <typename Container>
+class ContainerEqMatcher {
+ public:
+ typedef internal::StlContainerView<Container> View;
+ typedef typename View::type StlContainer;
+ typedef typename View::const_reference StlContainerReference;
+
+ // We make a copy of rhs in case the elements in it are modified
+ // after this matcher is created.
+ explicit ContainerEqMatcher(const Container& rhs) : rhs_(View::Copy(rhs)) {
+ // Makes sure the user doesn't instantiate this class template
+ // with a const or reference type.
+ (void)testing::StaticAssertTypeEq<Container,
+ GTEST_REMOVE_REFERENCE_AND_CONST_(Container)>();
+ }
+
+ void DescribeTo(::std::ostream* os) const {
+ *os << "equals ";
+ UniversalPrint(rhs_, os);
+ }
+ void DescribeNegationTo(::std::ostream* os) const {
+ *os << "does not equal ";
+ UniversalPrint(rhs_, os);
+ }
+
+ template <typename LhsContainer>
+ bool MatchAndExplain(const LhsContainer& lhs,
+ MatchResultListener* listener) const {
+ // GTEST_REMOVE_CONST_() is needed to work around an MSVC 8.0 bug
+ // that causes LhsContainer to be a const type sometimes.
+ typedef internal::StlContainerView<GTEST_REMOVE_CONST_(LhsContainer)>
+ LhsView;
+ typedef typename LhsView::type LhsStlContainer;
+ StlContainerReference lhs_stl_container = LhsView::ConstReference(lhs);
+ if (lhs_stl_container == rhs_)
+ return true;
+
+ ::std::ostream* const os = listener->stream();
+ if (os != NULL) {
+ // Something is different. Check for extra values first.
+ bool printed_header = false;
+ for (typename LhsStlContainer::const_iterator it =
+ lhs_stl_container.begin();
+ it != lhs_stl_container.end(); ++it) {
+ if (internal::ArrayAwareFind(rhs_.begin(), rhs_.end(), *it) ==
+ rhs_.end()) {
+ if (printed_header) {
+ *os << ", ";
+ } else {
+ *os << "which has these unexpected elements: ";
+ printed_header = true;
+ }
+ UniversalPrint(*it, os);
+ }
+ }
+
+ // Now check for missing values.
+ bool printed_header2 = false;
+ for (typename StlContainer::const_iterator it = rhs_.begin();
+ it != rhs_.end(); ++it) {
+ if (internal::ArrayAwareFind(
+ lhs_stl_container.begin(), lhs_stl_container.end(), *it) ==
+ lhs_stl_container.end()) {
+ if (printed_header2) {
+ *os << ", ";
+ } else {
+ *os << (printed_header ? ",\nand" : "which")
+ << " doesn't have these expected elements: ";
+ printed_header2 = true;
+ }
+ UniversalPrint(*it, os);
+ }
+ }
+ }
+
+ return false;
+ }
+
+ private:
+ const StlContainer rhs_;
+
+ GTEST_DISALLOW_ASSIGN_(ContainerEqMatcher);
+};
+
+// A comparator functor that uses the < operator to compare two values.
+struct LessComparator {
+ template <typename T, typename U>
+ bool operator()(const T& lhs, const U& rhs) const { return lhs < rhs; }
+};
+
+// Implements WhenSortedBy(comparator, container_matcher).
+template <typename Comparator, typename ContainerMatcher>
+class WhenSortedByMatcher {
+ public:
+ WhenSortedByMatcher(const Comparator& comparator,
+ const ContainerMatcher& matcher)
+ : comparator_(comparator), matcher_(matcher) {}
+
+ template <typename LhsContainer>
+ operator Matcher<LhsContainer>() const {
+ return MakeMatcher(new Impl<LhsContainer>(comparator_, matcher_));
+ }
+
+ template <typename LhsContainer>
+ class Impl : public MatcherInterface<LhsContainer> {
+ public:
+ typedef internal::StlContainerView<
+ GTEST_REMOVE_REFERENCE_AND_CONST_(LhsContainer)> LhsView;
+ typedef typename LhsView::type LhsStlContainer;
+ typedef typename LhsView::const_reference LhsStlContainerReference;
+ // Transforms std::pair<const Key, Value> into std::pair<Key, Value>
+ // so that we can match associative containers.
+ typedef typename RemoveConstFromKey<
+ typename LhsStlContainer::value_type>::type LhsValue;
+
+ Impl(const Comparator& comparator, const ContainerMatcher& matcher)
+ : comparator_(comparator), matcher_(matcher) {}
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "(when sorted) ";
+ matcher_.DescribeTo(os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "(when sorted) ";
+ matcher_.DescribeNegationTo(os);
+ }
+
+ virtual bool MatchAndExplain(LhsContainer lhs,
+ MatchResultListener* listener) const {
+ LhsStlContainerReference lhs_stl_container = LhsView::ConstReference(lhs);
+ ::std::vector<LhsValue> sorted_container(lhs_stl_container.begin(),
+ lhs_stl_container.end());
+ ::std::sort(
+ sorted_container.begin(), sorted_container.end(), comparator_);
+
+ if (!listener->IsInterested()) {
+ // If the listener is not interested, we do not need to
+ // construct the inner explanation.
+ return matcher_.Matches(sorted_container);
+ }
+
+ *listener << "which is ";
+ UniversalPrint(sorted_container, listener->stream());
+ *listener << " when sorted";
+
+ StringMatchResultListener inner_listener;
+ const bool match = matcher_.MatchAndExplain(sorted_container,
+ &inner_listener);
+ PrintIfNotEmpty(inner_listener.str(), listener->stream());
+ return match;
+ }
+
+ private:
+ const Comparator comparator_;
+ const Matcher<const ::std::vector<LhsValue>&> matcher_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(Impl);
+ };
+
+ private:
+ const Comparator comparator_;
+ const ContainerMatcher matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(WhenSortedByMatcher);
+};
+
+// Implements Pointwise(tuple_matcher, rhs_container). tuple_matcher
+// must be able to be safely cast to Matcher<tuple<const T1&, const
+// T2&> >, where T1 and T2 are the types of elements in the LHS
+// container and the RHS container respectively.
+template <typename TupleMatcher, typename RhsContainer>
+class PointwiseMatcher {
+ public:
+ typedef internal::StlContainerView<RhsContainer> RhsView;
+ typedef typename RhsView::type RhsStlContainer;
+ typedef typename RhsStlContainer::value_type RhsValue;
+
+ // Like ContainerEq, we make a copy of rhs in case the elements in
+ // it are modified after this matcher is created.
+ PointwiseMatcher(const TupleMatcher& tuple_matcher, const RhsContainer& rhs)
+ : tuple_matcher_(tuple_matcher), rhs_(RhsView::Copy(rhs)) {
+ // Makes sure the user doesn't instantiate this class template
+ // with a const or reference type.
+ (void)testing::StaticAssertTypeEq<RhsContainer,
+ GTEST_REMOVE_REFERENCE_AND_CONST_(RhsContainer)>();
+ }
+
+ template <typename LhsContainer>
+ operator Matcher<LhsContainer>() const {
+ return MakeMatcher(new Impl<LhsContainer>(tuple_matcher_, rhs_));
+ }
+
+ template <typename LhsContainer>
+ class Impl : public MatcherInterface<LhsContainer> {
+ public:
+ typedef internal::StlContainerView<
+ GTEST_REMOVE_REFERENCE_AND_CONST_(LhsContainer)> LhsView;
+ typedef typename LhsView::type LhsStlContainer;
+ typedef typename LhsView::const_reference LhsStlContainerReference;
+ typedef typename LhsStlContainer::value_type LhsValue;
+ // We pass the LHS value and the RHS value to the inner matcher by
+ // reference, as they may be expensive to copy. We must use tuple
+ // instead of pair here, as a pair cannot hold references (C++ 98,
+ // 20.2.2 [lib.pairs]).
+ typedef ::std::tr1::tuple<const LhsValue&, const RhsValue&> InnerMatcherArg;
+
+ Impl(const TupleMatcher& tuple_matcher, const RhsStlContainer& rhs)
+ // mono_tuple_matcher_ holds a monomorphic version of the tuple matcher.
+ : mono_tuple_matcher_(SafeMatcherCast<InnerMatcherArg>(tuple_matcher)),
+ rhs_(rhs) {}
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "contains " << rhs_.size()
+ << " values, where each value and its corresponding value in ";
+ UniversalPrinter<RhsStlContainer>::Print(rhs_, os);
+ *os << " ";
+ mono_tuple_matcher_.DescribeTo(os);
+ }
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "doesn't contain exactly " << rhs_.size()
+ << " values, or contains a value x at some index i"
+ << " where x and the i-th value of ";
+ UniversalPrint(rhs_, os);
+ *os << " ";
+ mono_tuple_matcher_.DescribeNegationTo(os);
+ }
+
+ virtual bool MatchAndExplain(LhsContainer lhs,
+ MatchResultListener* listener) const {
+ LhsStlContainerReference lhs_stl_container = LhsView::ConstReference(lhs);
+ const size_t actual_size = lhs_stl_container.size();
+ if (actual_size != rhs_.size()) {
+ *listener << "which contains " << actual_size << " values";
+ return false;
+ }
+
+ typename LhsStlContainer::const_iterator left = lhs_stl_container.begin();
+ typename RhsStlContainer::const_iterator right = rhs_.begin();
+ for (size_t i = 0; i != actual_size; ++i, ++left, ++right) {
+ const InnerMatcherArg value_pair(*left, *right);
+
+ if (listener->IsInterested()) {
+ StringMatchResultListener inner_listener;
+ if (!mono_tuple_matcher_.MatchAndExplain(
+ value_pair, &inner_listener)) {
+ *listener << "where the value pair (";
+ UniversalPrint(*left, listener->stream());
+ *listener << ", ";
+ UniversalPrint(*right, listener->stream());
+ *listener << ") at index #" << i << " don't match";
+ PrintIfNotEmpty(inner_listener.str(), listener->stream());
+ return false;
+ }
+ } else {
+ if (!mono_tuple_matcher_.Matches(value_pair))
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ private:
+ const Matcher<InnerMatcherArg> mono_tuple_matcher_;
+ const RhsStlContainer rhs_;
+
+ GTEST_DISALLOW_ASSIGN_(Impl);
+ };
+
+ private:
+ const TupleMatcher tuple_matcher_;
+ const RhsStlContainer rhs_;
+
+ GTEST_DISALLOW_ASSIGN_(PointwiseMatcher);
+};
+
+// Holds the logic common to ContainsMatcherImpl and EachMatcherImpl.
+template <typename Container>
+class QuantifierMatcherImpl : public MatcherInterface<Container> {
+ public:
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(Container) RawContainer;
+ typedef StlContainerView<RawContainer> View;
+ typedef typename View::type StlContainer;
+ typedef typename View::const_reference StlContainerReference;
+ typedef typename StlContainer::value_type Element;
+
+ template <typename InnerMatcher>
+ explicit QuantifierMatcherImpl(InnerMatcher inner_matcher)
+ : inner_matcher_(
+ testing::SafeMatcherCast<const Element&>(inner_matcher)) {}
+
+ // Checks whether:
+ // * All elements in the container match, if all_elements_should_match.
+ // * Any element in the container matches, if !all_elements_should_match.
+ bool MatchAndExplainImpl(bool all_elements_should_match,
+ Container container,
+ MatchResultListener* listener) const {
+ StlContainerReference stl_container = View::ConstReference(container);
+ size_t i = 0;
+ for (typename StlContainer::const_iterator it = stl_container.begin();
+ it != stl_container.end(); ++it, ++i) {
+ StringMatchResultListener inner_listener;
+ const bool matches = inner_matcher_.MatchAndExplain(*it, &inner_listener);
+
+ if (matches != all_elements_should_match) {
+ *listener << "whose element #" << i
+ << (matches ? " matches" : " doesn't match");
+ PrintIfNotEmpty(inner_listener.str(), listener->stream());
+ return !all_elements_should_match;
+ }
+ }
+ return all_elements_should_match;
+ }
+
+ protected:
+ const Matcher<const Element&> inner_matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(QuantifierMatcherImpl);
+};
+
+// Implements Contains(element_matcher) for the given argument type Container.
+// Symmetric to EachMatcherImpl.
+template <typename Container>
+class ContainsMatcherImpl : public QuantifierMatcherImpl<Container> {
+ public:
+ template <typename InnerMatcher>
+ explicit ContainsMatcherImpl(InnerMatcher inner_matcher)
+ : QuantifierMatcherImpl<Container>(inner_matcher) {}
+
+ // Describes what this matcher does.
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "contains at least one element that ";
+ this->inner_matcher_.DescribeTo(os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "doesn't contain any element that ";
+ this->inner_matcher_.DescribeTo(os);
+ }
+
+ virtual bool MatchAndExplain(Container container,
+ MatchResultListener* listener) const {
+ return this->MatchAndExplainImpl(false, container, listener);
+ }
+
+ private:
+ GTEST_DISALLOW_ASSIGN_(ContainsMatcherImpl);
+};
+
+// Implements Each(element_matcher) for the given argument type Container.
+// Symmetric to ContainsMatcherImpl.
+template <typename Container>
+class EachMatcherImpl : public QuantifierMatcherImpl<Container> {
+ public:
+ template <typename InnerMatcher>
+ explicit EachMatcherImpl(InnerMatcher inner_matcher)
+ : QuantifierMatcherImpl<Container>(inner_matcher) {}
+
+ // Describes what this matcher does.
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "only contains elements that ";
+ this->inner_matcher_.DescribeTo(os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "contains some element that ";
+ this->inner_matcher_.DescribeNegationTo(os);
+ }
+
+ virtual bool MatchAndExplain(Container container,
+ MatchResultListener* listener) const {
+ return this->MatchAndExplainImpl(true, container, listener);
+ }
+
+ private:
+ GTEST_DISALLOW_ASSIGN_(EachMatcherImpl);
+};
+
+// Implements polymorphic Contains(element_matcher).
+template <typename M>
+class ContainsMatcher {
+ public:
+ explicit ContainsMatcher(M m) : inner_matcher_(m) {}
+
+ template <typename Container>
+ operator Matcher<Container>() const {
+ return MakeMatcher(new ContainsMatcherImpl<Container>(inner_matcher_));
+ }
+
+ private:
+ const M inner_matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(ContainsMatcher);
+};
+
+// Implements polymorphic Each(element_matcher).
+template <typename M>
+class EachMatcher {
+ public:
+ explicit EachMatcher(M m) : inner_matcher_(m) {}
+
+ template <typename Container>
+ operator Matcher<Container>() const {
+ return MakeMatcher(new EachMatcherImpl<Container>(inner_matcher_));
+ }
+
+ private:
+ const M inner_matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(EachMatcher);
+};
+
+// Implements Key(inner_matcher) for the given argument pair type.
+// Key(inner_matcher) matches an std::pair whose 'first' field matches
+// inner_matcher. For example, Contains(Key(Ge(5))) can be used to match an
+// std::map that contains at least one element whose key is >= 5.
+template <typename PairType>
+class KeyMatcherImpl : public MatcherInterface<PairType> {
+ public:
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(PairType) RawPairType;
+ typedef typename RawPairType::first_type KeyType;
+
+ template <typename InnerMatcher>
+ explicit KeyMatcherImpl(InnerMatcher inner_matcher)
+ : inner_matcher_(
+ testing::SafeMatcherCast<const KeyType&>(inner_matcher)) {
+ }
+
+ // Returns true iff 'key_value.first' (the key) matches the inner matcher.
+ virtual bool MatchAndExplain(PairType key_value,
+ MatchResultListener* listener) const {
+ StringMatchResultListener inner_listener;
+ const bool match = inner_matcher_.MatchAndExplain(key_value.first,
+ &inner_listener);
+ const internal::string explanation = inner_listener.str();
+ if (explanation != "") {
+ *listener << "whose first field is a value " << explanation;
+ }
+ return match;
+ }
+
+ // Describes what this matcher does.
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "has a key that ";
+ inner_matcher_.DescribeTo(os);
+ }
+
+ // Describes what the negation of this matcher does.
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "doesn't have a key that ";
+ inner_matcher_.DescribeTo(os);
+ }
+
+ private:
+ const Matcher<const KeyType&> inner_matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(KeyMatcherImpl);
+};
+
+// Implements polymorphic Key(matcher_for_key).
+template <typename M>
+class KeyMatcher {
+ public:
+ explicit KeyMatcher(M m) : matcher_for_key_(m) {}
+
+ template <typename PairType>
+ operator Matcher<PairType>() const {
+ return MakeMatcher(new KeyMatcherImpl<PairType>(matcher_for_key_));
+ }
+
+ private:
+ const M matcher_for_key_;
+
+ GTEST_DISALLOW_ASSIGN_(KeyMatcher);
+};
+
+// Implements Pair(first_matcher, second_matcher) for the given argument pair
+// type with its two matchers. See Pair() function below.
+template <typename PairType>
+class PairMatcherImpl : public MatcherInterface<PairType> {
+ public:
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(PairType) RawPairType;
+ typedef typename RawPairType::first_type FirstType;
+ typedef typename RawPairType::second_type SecondType;
+
+ template <typename FirstMatcher, typename SecondMatcher>
+ PairMatcherImpl(FirstMatcher first_matcher, SecondMatcher second_matcher)
+ : first_matcher_(
+ testing::SafeMatcherCast<const FirstType&>(first_matcher)),
+ second_matcher_(
+ testing::SafeMatcherCast<const SecondType&>(second_matcher)) {
+ }
+
+ // Describes what this matcher does.
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "has a first field that ";
+ first_matcher_.DescribeTo(os);
+ *os << ", and has a second field that ";
+ second_matcher_.DescribeTo(os);
+ }
+
+ // Describes what the negation of this matcher does.
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "has a first field that ";
+ first_matcher_.DescribeNegationTo(os);
+ *os << ", or has a second field that ";
+ second_matcher_.DescribeNegationTo(os);
+ }
+
+ // Returns true iff 'a_pair.first' matches first_matcher and 'a_pair.second'
+ // matches second_matcher.
+ virtual bool MatchAndExplain(PairType a_pair,
+ MatchResultListener* listener) const {
+ if (!listener->IsInterested()) {
+ // If the listener is not interested, we don't need to construct the
+ // explanation.
+ return first_matcher_.Matches(a_pair.first) &&
+ second_matcher_.Matches(a_pair.second);
+ }
+ StringMatchResultListener first_inner_listener;
+ if (!first_matcher_.MatchAndExplain(a_pair.first,
+ &first_inner_listener)) {
+ *listener << "whose first field does not match";
+ PrintIfNotEmpty(first_inner_listener.str(), listener->stream());
+ return false;
+ }
+ StringMatchResultListener second_inner_listener;
+ if (!second_matcher_.MatchAndExplain(a_pair.second,
+ &second_inner_listener)) {
+ *listener << "whose second field does not match";
+ PrintIfNotEmpty(second_inner_listener.str(), listener->stream());
+ return false;
+ }
+ ExplainSuccess(first_inner_listener.str(), second_inner_listener.str(),
+ listener);
+ return true;
+ }
+
+ private:
+ void ExplainSuccess(const internal::string& first_explanation,
+ const internal::string& second_explanation,
+ MatchResultListener* listener) const {
+ *listener << "whose both fields match";
+ if (first_explanation != "") {
+ *listener << ", where the first field is a value " << first_explanation;
+ }
+ if (second_explanation != "") {
+ *listener << ", ";
+ if (first_explanation != "") {
+ *listener << "and ";
+ } else {
+ *listener << "where ";
+ }
+ *listener << "the second field is a value " << second_explanation;
+ }
+ }
+
+ const Matcher<const FirstType&> first_matcher_;
+ const Matcher<const SecondType&> second_matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(PairMatcherImpl);
+};
+
+// Implements polymorphic Pair(first_matcher, second_matcher).
+template <typename FirstMatcher, typename SecondMatcher>
+class PairMatcher {
+ public:
+ PairMatcher(FirstMatcher first_matcher, SecondMatcher second_matcher)
+ : first_matcher_(first_matcher), second_matcher_(second_matcher) {}
+
+ template <typename PairType>
+ operator Matcher<PairType> () const {
+ return MakeMatcher(
+ new PairMatcherImpl<PairType>(
+ first_matcher_, second_matcher_));
+ }
+
+ private:
+ const FirstMatcher first_matcher_;
+ const SecondMatcher second_matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(PairMatcher);
+};
+
+// Implements ElementsAre() and ElementsAreArray().
+template <typename Container>
+class ElementsAreMatcherImpl : public MatcherInterface<Container> {
+ public:
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(Container) RawContainer;
+ typedef internal::StlContainerView<RawContainer> View;
+ typedef typename View::type StlContainer;
+ typedef typename View::const_reference StlContainerReference;
+ typedef typename StlContainer::value_type Element;
+
+ // Constructs the matcher from a sequence of element values or
+ // element matchers.
+ template <typename InputIter>
+ ElementsAreMatcherImpl(InputIter first, InputIter last) {
+ while (first != last) {
+ matchers_.push_back(MatcherCast<const Element&>(*first++));
+ }
+ }
+
+ // Describes what this matcher does.
+ virtual void DescribeTo(::std::ostream* os) const {
+ if (count() == 0) {
+ *os << "is empty";
+ } else if (count() == 1) {
+ *os << "has 1 element that ";
+ matchers_[0].DescribeTo(os);
+ } else {
+ *os << "has " << Elements(count()) << " where\n";
+ for (size_t i = 0; i != count(); ++i) {
+ *os << "element #" << i << " ";
+ matchers_[i].DescribeTo(os);
+ if (i + 1 < count()) {
+ *os << ",\n";
+ }
+ }
+ }
+ }
+
+ // Describes what the negation of this matcher does.
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ if (count() == 0) {
+ *os << "isn't empty";
+ return;
+ }
+
+ *os << "doesn't have " << Elements(count()) << ", or\n";
+ for (size_t i = 0; i != count(); ++i) {
+ *os << "element #" << i << " ";
+ matchers_[i].DescribeNegationTo(os);
+ if (i + 1 < count()) {
+ *os << ", or\n";
+ }
+ }
+ }
+
+ virtual bool MatchAndExplain(Container container,
+ MatchResultListener* listener) const {
+ // To work with stream-like "containers", we must only walk
+ // through the elements in one pass.
+
+ const bool listener_interested = listener->IsInterested();
+
+ // explanations[i] is the explanation of the element at index i.
+ ::std::vector<internal::string> explanations(count());
+ StlContainerReference stl_container = View::ConstReference(container);
+ typename StlContainer::const_iterator it = stl_container.begin();
+ size_t exam_pos = 0;
+ bool mismatch_found = false; // Have we found a mismatched element yet?
+
+ // Go through the elements and matchers in pairs, until we reach
+ // the end of either the elements or the matchers, or until we find a
+ // mismatch.
+ for (; it != stl_container.end() && exam_pos != count(); ++it, ++exam_pos) {
+ bool match; // Does the current element match the current matcher?
+ if (listener_interested) {
+ StringMatchResultListener s;
+ match = matchers_[exam_pos].MatchAndExplain(*it, &s);
+ explanations[exam_pos] = s.str();
+ } else {
+ match = matchers_[exam_pos].Matches(*it);
+ }
+
+ if (!match) {
+ mismatch_found = true;
+ break;
+ }
+ }
+ // If mismatch_found is true, 'exam_pos' is the index of the mismatch.
+
+ // Find how many elements the actual container has. We avoid
+ // calling size() s.t. this code works for stream-like "containers"
+ // that don't define size().
+ size_t actual_count = exam_pos;
+ for (; it != stl_container.end(); ++it) {
+ ++actual_count;
+ }
+
+ if (actual_count != count()) {
+ // The element count doesn't match. If the container is empty,
+ // there's no need to explain anything as Google Mock already
+ // prints the empty container. Otherwise we just need to show
+ // how many elements there actually are.
+ if (listener_interested && (actual_count != 0)) {
+ *listener << "which has " << Elements(actual_count);
+ }
+ return false;
+ }
+
+ if (mismatch_found) {
+ // The element count matches, but the exam_pos-th element doesn't match.
+ if (listener_interested) {
+ *listener << "whose element #" << exam_pos << " doesn't match";
+ PrintIfNotEmpty(explanations[exam_pos], listener->stream());
+ }
+ return false;
+ }
+
+ // Every element matches its expectation. We need to explain why
+ // (the obvious ones can be skipped).
+ if (listener_interested) {
+ bool reason_printed = false;
+ for (size_t i = 0; i != count(); ++i) {
+ const internal::string& s = explanations[i];
+ if (!s.empty()) {
+ if (reason_printed) {
+ *listener << ",\nand ";
+ }
+ *listener << "whose element #" << i << " matches, " << s;
+ reason_printed = true;
+ }
+ }
+ }
+ return true;
+ }
+
+ private:
+ static Message Elements(size_t count) {
+ return Message() << count << (count == 1 ? " element" : " elements");
+ }
+
+ size_t count() const { return matchers_.size(); }
+
+ ::std::vector<Matcher<const Element&> > matchers_;
+
+ GTEST_DISALLOW_ASSIGN_(ElementsAreMatcherImpl);
+};
+
+// Connectivity matrix of (elements X matchers), in element-major order.
+// Initially, there are no edges.
+// Use NextGraph() to iterate over all possible edge configurations.
+// Use Randomize() to generate a random edge configuration.
+class GTEST_API_ MatchMatrix {
+ public:
+ MatchMatrix(size_t num_elements, size_t num_matchers)
+ : num_elements_(num_elements),
+ num_matchers_(num_matchers),
+ matched_(num_elements_* num_matchers_, 0) {
+ }
+
+ size_t LhsSize() const { return num_elements_; }
+ size_t RhsSize() const { return num_matchers_; }
+ bool HasEdge(size_t ilhs, size_t irhs) const {
+ return matched_[SpaceIndex(ilhs, irhs)] == 1;
+ }
+ void SetEdge(size_t ilhs, size_t irhs, bool b) {
+ matched_[SpaceIndex(ilhs, irhs)] = b ? 1 : 0;
+ }
+
+ // Treating the connectivity matrix as a (LhsSize()*RhsSize())-bit number,
+ // adds 1 to that number; returns false if incrementing the graph left it
+ // empty.
+ bool NextGraph();
+
+ void Randomize();
+
+ string DebugString() const;
+
+ private:
+ size_t SpaceIndex(size_t ilhs, size_t irhs) const {
+ return ilhs * num_matchers_ + irhs;
+ }
+
+ size_t num_elements_;
+ size_t num_matchers_;
+
+ // Each element is a char interpreted as bool. They are stored as a
+ // flattened array in lhs-major order, use 'SpaceIndex()' to translate
+ // a (ilhs, irhs) matrix coordinate into an offset.
+ ::std::vector<char> matched_;
+};
+
+typedef ::std::pair<size_t, size_t> ElementMatcherPair;
+typedef ::std::vector<ElementMatcherPair> ElementMatcherPairs;
+
+// Returns a maximum bipartite matching for the specified graph 'g'.
+// The matching is represented as a vector of {element, matcher} pairs.
+GTEST_API_ ElementMatcherPairs
+FindMaxBipartiteMatching(const MatchMatrix& g);
+
+GTEST_API_ bool FindPairing(const MatchMatrix& matrix,
+ MatchResultListener* listener);
+
+// Untyped base class for implementing UnorderedElementsAre. By
+// putting logic that's not specific to the element type here, we
+// reduce binary bloat and increase compilation speed.
+class GTEST_API_ UnorderedElementsAreMatcherImplBase {
+ protected:
+ // A vector of matcher describers, one for each element matcher.
+ // Does not own the describers (and thus can be used only when the
+ // element matchers are alive).
+ typedef ::std::vector<const MatcherDescriberInterface*> MatcherDescriberVec;
+
+ // Describes this UnorderedElementsAre matcher.
+ void DescribeToImpl(::std::ostream* os) const;
+
+ // Describes the negation of this UnorderedElementsAre matcher.
+ void DescribeNegationToImpl(::std::ostream* os) const;
+
+ bool VerifyAllElementsAndMatchersAreMatched(
+ const ::std::vector<string>& element_printouts,
+ const MatchMatrix& matrix,
+ MatchResultListener* listener) const;
+
+ MatcherDescriberVec& matcher_describers() {
+ return matcher_describers_;
+ }
+
+ static Message Elements(size_t n) {
+ return Message() << n << " element" << (n == 1 ? "" : "s");
+ }
+
+ private:
+ MatcherDescriberVec matcher_describers_;
+
+ GTEST_DISALLOW_ASSIGN_(UnorderedElementsAreMatcherImplBase);
+};
+
+// Implements unordered ElementsAre and unordered ElementsAreArray.
+template <typename Container>
+class UnorderedElementsAreMatcherImpl
+ : public MatcherInterface<Container>,
+ public UnorderedElementsAreMatcherImplBase {
+ public:
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(Container) RawContainer;
+ typedef internal::StlContainerView<RawContainer> View;
+ typedef typename View::type StlContainer;
+ typedef typename View::const_reference StlContainerReference;
+ typedef typename StlContainer::const_iterator StlContainerConstIterator;
+ typedef typename StlContainer::value_type Element;
+
+ // Constructs the matcher from a sequence of element values or
+ // element matchers.
+ template <typename InputIter>
+ UnorderedElementsAreMatcherImpl(InputIter first, InputIter last) {
+ for (; first != last; ++first) {
+ matchers_.push_back(MatcherCast<const Element&>(*first));
+ matcher_describers().push_back(matchers_.back().GetDescriber());
+ }
+ }
+
+ // Describes what this matcher does.
+ virtual void DescribeTo(::std::ostream* os) const {
+ return UnorderedElementsAreMatcherImplBase::DescribeToImpl(os);
+ }
+
+ // Describes what the negation of this matcher does.
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ return UnorderedElementsAreMatcherImplBase::DescribeNegationToImpl(os);
+ }
+
+ virtual bool MatchAndExplain(Container container,
+ MatchResultListener* listener) const {
+ StlContainerReference stl_container = View::ConstReference(container);
+ ::std::vector<string> element_printouts;
+ MatchMatrix matrix = AnalyzeElements(stl_container.begin(),
+ stl_container.end(),
+ &element_printouts,
+ listener);
+
+ const size_t actual_count = matrix.LhsSize();
+ if (actual_count == 0 && matchers_.empty()) {
+ return true;
+ }
+ if (actual_count != matchers_.size()) {
+ // The element count doesn't match. If the container is empty,
+ // there's no need to explain anything as Google Mock already
+ // prints the empty container. Otherwise we just need to show
+ // how many elements there actually are.
+ if (actual_count != 0 && listener->IsInterested()) {
+ *listener << "which has " << Elements(actual_count);
+ }
+ return false;
+ }
+
+ return VerifyAllElementsAndMatchersAreMatched(element_printouts,
+ matrix, listener) &&
+ FindPairing(matrix, listener);
+ }
+
+ private:
+ typedef ::std::vector<Matcher<const Element&> > MatcherVec;
+
+ template <typename ElementIter>
+ MatchMatrix AnalyzeElements(ElementIter elem_first, ElementIter elem_last,
+ ::std::vector<string>* element_printouts,
+ MatchResultListener* listener) const {
+ element_printouts->clear();
+ ::std::vector<char> did_match;
+ size_t num_elements = 0;
+ for (; elem_first != elem_last; ++num_elements, ++elem_first) {
+ if (listener->IsInterested()) {
+ element_printouts->push_back(PrintToString(*elem_first));
+ }
+ for (size_t irhs = 0; irhs != matchers_.size(); ++irhs) {
+ did_match.push_back(Matches(matchers_[irhs])(*elem_first));
+ }
+ }
+
+ MatchMatrix matrix(num_elements, matchers_.size());
+ ::std::vector<char>::const_iterator did_match_iter = did_match.begin();
+ for (size_t ilhs = 0; ilhs != num_elements; ++ilhs) {
+ for (size_t irhs = 0; irhs != matchers_.size(); ++irhs) {
+ matrix.SetEdge(ilhs, irhs, *did_match_iter++ != 0);
+ }
+ }
+ return matrix;
+ }
+
+ MatcherVec matchers_;
+
+ GTEST_DISALLOW_ASSIGN_(UnorderedElementsAreMatcherImpl);
+};
+
+// Functor for use in TransformTuple.
+// Performs MatcherCast<Target> on an input argument of any type.
+template <typename Target>
+struct CastAndAppendTransform {
+ template <typename Arg>
+ Matcher<Target> operator()(const Arg& a) const {
+ return MatcherCast<Target>(a);
+ }
+};
+
+// Implements UnorderedElementsAre.
+template <typename MatcherTuple>
+class UnorderedElementsAreMatcher {
+ public:
+ explicit UnorderedElementsAreMatcher(const MatcherTuple& args)
+ : matchers_(args) {}
+
+ template <typename Container>
+ operator Matcher<Container>() const {
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(Container) RawContainer;
+ typedef typename internal::StlContainerView<RawContainer>::type View;
+ typedef typename View::value_type Element;
+ typedef ::std::vector<Matcher<const Element&> > MatcherVec;
+ MatcherVec matchers;
+ matchers.reserve(::std::tr1::tuple_size<MatcherTuple>::value);
+ TransformTupleValues(CastAndAppendTransform<const Element&>(), matchers_,
+ ::std::back_inserter(matchers));
+ return MakeMatcher(new UnorderedElementsAreMatcherImpl<Container>(
+ matchers.begin(), matchers.end()));
+ }
+
+ private:
+ const MatcherTuple matchers_;
+ GTEST_DISALLOW_ASSIGN_(UnorderedElementsAreMatcher);
+};
+
+// Implements ElementsAre.
+template <typename MatcherTuple>
+class ElementsAreMatcher {
+ public:
+ explicit ElementsAreMatcher(const MatcherTuple& args) : matchers_(args) {}
+
+ template <typename Container>
+ operator Matcher<Container>() const {
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(Container) RawContainer;
+ typedef typename internal::StlContainerView<RawContainer>::type View;
+ typedef typename View::value_type Element;
+ typedef ::std::vector<Matcher<const Element&> > MatcherVec;
+ MatcherVec matchers;
+ matchers.reserve(::std::tr1::tuple_size<MatcherTuple>::value);
+ TransformTupleValues(CastAndAppendTransform<const Element&>(), matchers_,
+ ::std::back_inserter(matchers));
+ return MakeMatcher(new ElementsAreMatcherImpl<Container>(
+ matchers.begin(), matchers.end()));
+ }
+
+ private:
+ const MatcherTuple matchers_;
+ GTEST_DISALLOW_ASSIGN_(ElementsAreMatcher);
+};
+
+// Implements UnorderedElementsAreArray().
+template <typename T>
+class UnorderedElementsAreArrayMatcher {
+ public:
+ UnorderedElementsAreArrayMatcher() {}
+
+ template <typename Iter>
+ UnorderedElementsAreArrayMatcher(Iter first, Iter last)
+ : matchers_(first, last) {}
+
+ template <typename Container>
+ operator Matcher<Container>() const {
+ return MakeMatcher(
+ new UnorderedElementsAreMatcherImpl<Container>(matchers_.begin(),
+ matchers_.end()));
+ }
+
+ private:
+ ::std::vector<T> matchers_;
+
+ GTEST_DISALLOW_ASSIGN_(UnorderedElementsAreArrayMatcher);
+};
+
+// Implements ElementsAreArray().
+template <typename T>
+class ElementsAreArrayMatcher {
+ public:
+ template <typename Iter>
+ ElementsAreArrayMatcher(Iter first, Iter last) : matchers_(first, last) {}
+
+ template <typename Container>
+ operator Matcher<Container>() const {
+ return MakeMatcher(new ElementsAreMatcherImpl<Container>(
+ matchers_.begin(), matchers_.end()));
+ }
+
+ private:
+ const ::std::vector<T> matchers_;
+
+ GTEST_DISALLOW_ASSIGN_(ElementsAreArrayMatcher);
+};
+
+// Returns the description for a matcher defined using the MATCHER*()
+// macro where the user-supplied description string is "", if
+// 'negation' is false; otherwise returns the description of the
+// negation of the matcher. 'param_values' contains a list of strings
+// that are the print-out of the matcher's parameters.
+GTEST_API_ string FormatMatcherDescription(bool negation,
+ const char* matcher_name,
+ const Strings& param_values);
+
+} // namespace internal
+
+// ElementsAreArray(first, last)
+// ElementsAreArray(pointer, count)
+// ElementsAreArray(array)
+// ElementsAreArray(vector)
+// ElementsAreArray({ e1, e2, ..., en })
+//
+// The ElementsAreArray() functions are like ElementsAre(...), except
+// that they are given a homogeneous sequence rather than taking each
+// element as a function argument. The sequence can be specified as an
+// array, a pointer and count, a vector, an initializer list, or an
+// STL iterator range. In each of these cases, the underlying sequence
+// can be either a sequence of values or a sequence of matchers.
+//
+// All forms of ElementsAreArray() make a copy of the input matcher sequence.
+
+template <typename Iter>
+inline internal::ElementsAreArrayMatcher<
+ typename ::std::iterator_traits<Iter>::value_type>
+ElementsAreArray(Iter first, Iter last) {
+ typedef typename ::std::iterator_traits<Iter>::value_type T;
+ return internal::ElementsAreArrayMatcher<T>(first, last);
+}
+
+template <typename T>
+inline internal::ElementsAreArrayMatcher<T> ElementsAreArray(
+ const T* pointer, size_t count) {
+ return ElementsAreArray(pointer, pointer + count);
+}
+
+template <typename T, size_t N>
+inline internal::ElementsAreArrayMatcher<T> ElementsAreArray(
+ const T (&array)[N]) {
+ return ElementsAreArray(array, N);
+}
+
+template <typename T, typename A>
+inline internal::ElementsAreArrayMatcher<T> ElementsAreArray(
+ const ::std::vector<T, A>& vec) {
+ return ElementsAreArray(vec.begin(), vec.end());
+}
+
+#if GTEST_LANG_CXX11
+template <typename T>
+inline internal::ElementsAreArrayMatcher<T>
+ElementsAreArray(::std::initializer_list<T> xs) {
+ return ElementsAreArray(xs.begin(), xs.end());
+}
+#endif
+
+// UnorderedElementsAreArray(first, last)
+// UnorderedElementsAreArray(pointer, count)
+// UnorderedElementsAreArray(array)
+// UnorderedElementsAreArray(vector)
+// UnorderedElementsAreArray({ e1, e2, ..., en })
+//
+// The UnorderedElementsAreArray() functions are like
+// ElementsAreArray(...), but allow matching the elements in any order.
+template <typename Iter>
+inline internal::UnorderedElementsAreArrayMatcher<
+ typename ::std::iterator_traits<Iter>::value_type>
+UnorderedElementsAreArray(Iter first, Iter last) {
+ typedef typename ::std::iterator_traits<Iter>::value_type T;
+ return internal::UnorderedElementsAreArrayMatcher<T>(first, last);
+}
+
+template <typename T>
+inline internal::UnorderedElementsAreArrayMatcher<T>
+UnorderedElementsAreArray(const T* pointer, size_t count) {
+ return UnorderedElementsAreArray(pointer, pointer + count);
+}
+
+template <typename T, size_t N>
+inline internal::UnorderedElementsAreArrayMatcher<T>
+UnorderedElementsAreArray(const T (&array)[N]) {
+ return UnorderedElementsAreArray(array, N);
+}
+
+template <typename T, typename A>
+inline internal::UnorderedElementsAreArrayMatcher<T>
+UnorderedElementsAreArray(const ::std::vector<T, A>& vec) {
+ return UnorderedElementsAreArray(vec.begin(), vec.end());
+}
+
+#if GTEST_LANG_CXX11
+template <typename T>
+inline internal::UnorderedElementsAreArrayMatcher<T>
+UnorderedElementsAreArray(::std::initializer_list<T> xs) {
+ return UnorderedElementsAreArray(xs.begin(), xs.end());
+}
+#endif
+
+// _ is a matcher that matches anything of any type.
+//
+// This definition is fine as:
+//
+// 1. The C++ standard permits using the name _ in a namespace that
+// is not the global namespace or ::std.
+// 2. The AnythingMatcher class has no data member or constructor,
+// so it's OK to create global variables of this type.
+// 3. c-style has approved of using _ in this case.
+const internal::AnythingMatcher _ = {};
+// Creates a matcher that matches any value of the given type T.
+template <typename T>
+inline Matcher<T> A() { return MakeMatcher(new internal::AnyMatcherImpl<T>()); }
+
+// Creates a matcher that matches any value of the given type T.
+template <typename T>
+inline Matcher<T> An() { return A<T>(); }
+
+// Creates a polymorphic matcher that matches anything equal to x.
+// Note: if the parameter of Eq() were declared as const T&, Eq("foo")
+// wouldn't compile.
+template <typename T>
+inline internal::EqMatcher<T> Eq(T x) { return internal::EqMatcher<T>(x); }
+
+// Constructs a Matcher<T> from a 'value' of type T. The constructed
+// matcher matches any value that's equal to 'value'.
+template <typename T>
+Matcher<T>::Matcher(T value) { *this = Eq(value); }
+
+// Creates a monomorphic matcher that matches anything with type Lhs
+// and equal to rhs. A user may need to use this instead of Eq(...)
+// in order to resolve an overloading ambiguity.
+//
+// TypedEq<T>(x) is just a convenient short-hand for Matcher<T>(Eq(x))
+// or Matcher<T>(x), but more readable than the latter.
+//
+// We could define similar monomorphic matchers for other comparison
+// operations (e.g. TypedLt, TypedGe, and etc), but decided not to do
+// it yet as those are used much less than Eq() in practice. A user
+// can always write Matcher<T>(Lt(5)) to be explicit about the type,
+// for example.
+template <typename Lhs, typename Rhs>
+inline Matcher<Lhs> TypedEq(const Rhs& rhs) { return Eq(rhs); }
+
+// Creates a polymorphic matcher that matches anything >= x.
+template <typename Rhs>
+inline internal::GeMatcher<Rhs> Ge(Rhs x) {
+ return internal::GeMatcher<Rhs>(x);
+}
+
+// Creates a polymorphic matcher that matches anything > x.
+template <typename Rhs>
+inline internal::GtMatcher<Rhs> Gt(Rhs x) {
+ return internal::GtMatcher<Rhs>(x);
+}
+
+// Creates a polymorphic matcher that matches anything <= x.
+template <typename Rhs>
+inline internal::LeMatcher<Rhs> Le(Rhs x) {
+ return internal::LeMatcher<Rhs>(x);
+}
+
+// Creates a polymorphic matcher that matches anything < x.
+template <typename Rhs>
+inline internal::LtMatcher<Rhs> Lt(Rhs x) {
+ return internal::LtMatcher<Rhs>(x);
+}
+
+// Creates a polymorphic matcher that matches anything != x.
+template <typename Rhs>
+inline internal::NeMatcher<Rhs> Ne(Rhs x) {
+ return internal::NeMatcher<Rhs>(x);
+}
+
+// Creates a polymorphic matcher that matches any NULL pointer.
+inline PolymorphicMatcher<internal::IsNullMatcher > IsNull() {
+ return MakePolymorphicMatcher(internal::IsNullMatcher());
+}
+
+// Creates a polymorphic matcher that matches any non-NULL pointer.
+// This is convenient as Not(NULL) doesn't compile (the compiler
+// thinks that that expression is comparing a pointer with an integer).
+inline PolymorphicMatcher<internal::NotNullMatcher > NotNull() {
+ return MakePolymorphicMatcher(internal::NotNullMatcher());
+}
+
+// Creates a polymorphic matcher that matches any argument that
+// references variable x.
+template <typename T>
+inline internal::RefMatcher<T&> Ref(T& x) { // NOLINT
+ return internal::RefMatcher<T&>(x);
+}
+
+// Creates a matcher that matches any double argument approximately
+// equal to rhs, where two NANs are considered unequal.
+inline internal::FloatingEqMatcher<double> DoubleEq(double rhs) {
+ return internal::FloatingEqMatcher<double>(rhs, false);
+}
+
+// Creates a matcher that matches any double argument approximately
+// equal to rhs, including NaN values when rhs is NaN.
+inline internal::FloatingEqMatcher<double> NanSensitiveDoubleEq(double rhs) {
+ return internal::FloatingEqMatcher<double>(rhs, true);
+}
+
+// Creates a matcher that matches any double argument approximately equal to
+// rhs, up to the specified max absolute error bound, where two NANs are
+// considered unequal. The max absolute error bound must be non-negative.
+inline internal::FloatingEqMatcher<double> DoubleNear(
+ double rhs, double max_abs_error) {
+ return internal::FloatingEqMatcher<double>(rhs, false, max_abs_error);
+}
+
+// Creates a matcher that matches any double argument approximately equal to
+// rhs, up to the specified max absolute error bound, including NaN values when
+// rhs is NaN. The max absolute error bound must be non-negative.
+inline internal::FloatingEqMatcher<double> NanSensitiveDoubleNear(
+ double rhs, double max_abs_error) {
+ return internal::FloatingEqMatcher<double>(rhs, true, max_abs_error);
+}
+
+// Creates a matcher that matches any float argument approximately
+// equal to rhs, where two NANs are considered unequal.
+inline internal::FloatingEqMatcher<float> FloatEq(float rhs) {
+ return internal::FloatingEqMatcher<float>(rhs, false);
+}
+
+// Creates a matcher that matches any float argument approximately
+// equal to rhs, including NaN values when rhs is NaN.
+inline internal::FloatingEqMatcher<float> NanSensitiveFloatEq(float rhs) {
+ return internal::FloatingEqMatcher<float>(rhs, true);
+}
+
+// Creates a matcher that matches any float argument approximately equal to
+// rhs, up to the specified max absolute error bound, where two NANs are
+// considered unequal. The max absolute error bound must be non-negative.
+inline internal::FloatingEqMatcher<float> FloatNear(
+ float rhs, float max_abs_error) {
+ return internal::FloatingEqMatcher<float>(rhs, false, max_abs_error);
+}
+
+// Creates a matcher that matches any float argument approximately equal to
+// rhs, up to the specified max absolute error bound, including NaN values when
+// rhs is NaN. The max absolute error bound must be non-negative.
+inline internal::FloatingEqMatcher<float> NanSensitiveFloatNear(
+ float rhs, float max_abs_error) {
+ return internal::FloatingEqMatcher<float>(rhs, true, max_abs_error);
+}
+
+// Creates a matcher that matches a pointer (raw or smart) that points
+// to a value that matches inner_matcher.
+template <typename InnerMatcher>
+inline internal::PointeeMatcher<InnerMatcher> Pointee(
+ const InnerMatcher& inner_matcher) {
+ return internal::PointeeMatcher<InnerMatcher>(inner_matcher);
+}
+
+// Creates a matcher that matches an object whose given field matches
+// 'matcher'. For example,
+// Field(&Foo::number, Ge(5))
+// matches a Foo object x iff x.number >= 5.
+template <typename Class, typename FieldType, typename FieldMatcher>
+inline PolymorphicMatcher<
+ internal::FieldMatcher<Class, FieldType> > Field(
+ FieldType Class::*field, const FieldMatcher& matcher) {
+ return MakePolymorphicMatcher(
+ internal::FieldMatcher<Class, FieldType>(
+ field, MatcherCast<const FieldType&>(matcher)));
+ // The call to MatcherCast() is required for supporting inner
+ // matchers of compatible types. For example, it allows
+ // Field(&Foo::bar, m)
+ // to compile where bar is an int32 and m is a matcher for int64.
+}
+
+// Creates a matcher that matches an object whose given property
+// matches 'matcher'. For example,
+// Property(&Foo::str, StartsWith("hi"))
+// matches a Foo object x iff x.str() starts with "hi".
+template <typename Class, typename PropertyType, typename PropertyMatcher>
+inline PolymorphicMatcher<
+ internal::PropertyMatcher<Class, PropertyType> > Property(
+ PropertyType (Class::*property)() const, const PropertyMatcher& matcher) {
+ return MakePolymorphicMatcher(
+ internal::PropertyMatcher<Class, PropertyType>(
+ property,
+ MatcherCast<GTEST_REFERENCE_TO_CONST_(PropertyType)>(matcher)));
+ // The call to MatcherCast() is required for supporting inner
+ // matchers of compatible types. For example, it allows
+ // Property(&Foo::bar, m)
+ // to compile where bar() returns an int32 and m is a matcher for int64.
+}
+
+// Creates a matcher that matches an object iff the result of applying
+// a callable to x matches 'matcher'.
+// For example,
+// ResultOf(f, StartsWith("hi"))
+// matches a Foo object x iff f(x) starts with "hi".
+// callable parameter can be a function, function pointer, or a functor.
+// Callable has to satisfy the following conditions:
+// * It is required to keep no state affecting the results of
+// the calls on it and make no assumptions about how many calls
+// will be made. Any state it keeps must be protected from the
+// concurrent access.
+// * If it is a function object, it has to define type result_type.
+// We recommend deriving your functor classes from std::unary_function.
+template <typename Callable, typename ResultOfMatcher>
+internal::ResultOfMatcher<Callable> ResultOf(
+ Callable callable, const ResultOfMatcher& matcher) {
+ return internal::ResultOfMatcher<Callable>(
+ callable,
+ MatcherCast<typename internal::CallableTraits<Callable>::ResultType>(
+ matcher));
+ // The call to MatcherCast() is required for supporting inner
+ // matchers of compatible types. For example, it allows
+ // ResultOf(Function, m)
+ // to compile where Function() returns an int32 and m is a matcher for int64.
+}
+
+// String matchers.
+
+// Matches a string equal to str.
+inline PolymorphicMatcher<internal::StrEqualityMatcher<internal::string> >
+ StrEq(const internal::string& str) {
+ return MakePolymorphicMatcher(internal::StrEqualityMatcher<internal::string>(
+ str, true, true));
+}
+
+// Matches a string not equal to str.
+inline PolymorphicMatcher<internal::StrEqualityMatcher<internal::string> >
+ StrNe(const internal::string& str) {
+ return MakePolymorphicMatcher(internal::StrEqualityMatcher<internal::string>(
+ str, false, true));
+}
+
+// Matches a string equal to str, ignoring case.
+inline PolymorphicMatcher<internal::StrEqualityMatcher<internal::string> >
+ StrCaseEq(const internal::string& str) {
+ return MakePolymorphicMatcher(internal::StrEqualityMatcher<internal::string>(
+ str, true, false));
+}
+
+// Matches a string not equal to str, ignoring case.
+inline PolymorphicMatcher<internal::StrEqualityMatcher<internal::string> >
+ StrCaseNe(const internal::string& str) {
+ return MakePolymorphicMatcher(internal::StrEqualityMatcher<internal::string>(
+ str, false, false));
+}
+
+// Creates a matcher that matches any string, std::string, or C string
+// that contains the given substring.
+inline PolymorphicMatcher<internal::HasSubstrMatcher<internal::string> >
+ HasSubstr(const internal::string& substring) {
+ return MakePolymorphicMatcher(internal::HasSubstrMatcher<internal::string>(
+ substring));
+}
+
+// Matches a string that starts with 'prefix' (case-sensitive).
+inline PolymorphicMatcher<internal::StartsWithMatcher<internal::string> >
+ StartsWith(const internal::string& prefix) {
+ return MakePolymorphicMatcher(internal::StartsWithMatcher<internal::string>(
+ prefix));
+}
+
+// Matches a string that ends with 'suffix' (case-sensitive).
+inline PolymorphicMatcher<internal::EndsWithMatcher<internal::string> >
+ EndsWith(const internal::string& suffix) {
+ return MakePolymorphicMatcher(internal::EndsWithMatcher<internal::string>(
+ suffix));
+}
+
+// Matches a string that fully matches regular expression 'regex'.
+// The matcher takes ownership of 'regex'.
+inline PolymorphicMatcher<internal::MatchesRegexMatcher> MatchesRegex(
+ const internal::RE* regex) {
+ return MakePolymorphicMatcher(internal::MatchesRegexMatcher(regex, true));
+}
+inline PolymorphicMatcher<internal::MatchesRegexMatcher> MatchesRegex(
+ const internal::string& regex) {
+ return MatchesRegex(new internal::RE(regex));
+}
+
+// Matches a string that contains regular expression 'regex'.
+// The matcher takes ownership of 'regex'.
+inline PolymorphicMatcher<internal::MatchesRegexMatcher> ContainsRegex(
+ const internal::RE* regex) {
+ return MakePolymorphicMatcher(internal::MatchesRegexMatcher(regex, false));
+}
+inline PolymorphicMatcher<internal::MatchesRegexMatcher> ContainsRegex(
+ const internal::string& regex) {
+ return ContainsRegex(new internal::RE(regex));
+}
+
+#if GTEST_HAS_GLOBAL_WSTRING || GTEST_HAS_STD_WSTRING
+// Wide string matchers.
+
+// Matches a string equal to str.
+inline PolymorphicMatcher<internal::StrEqualityMatcher<internal::wstring> >
+ StrEq(const internal::wstring& str) {
+ return MakePolymorphicMatcher(internal::StrEqualityMatcher<internal::wstring>(
+ str, true, true));
+}
+
+// Matches a string not equal to str.
+inline PolymorphicMatcher<internal::StrEqualityMatcher<internal::wstring> >
+ StrNe(const internal::wstring& str) {
+ return MakePolymorphicMatcher(internal::StrEqualityMatcher<internal::wstring>(
+ str, false, true));
+}
+
+// Matches a string equal to str, ignoring case.
+inline PolymorphicMatcher<internal::StrEqualityMatcher<internal::wstring> >
+ StrCaseEq(const internal::wstring& str) {
+ return MakePolymorphicMatcher(internal::StrEqualityMatcher<internal::wstring>(
+ str, true, false));
+}
+
+// Matches a string not equal to str, ignoring case.
+inline PolymorphicMatcher<internal::StrEqualityMatcher<internal::wstring> >
+ StrCaseNe(const internal::wstring& str) {
+ return MakePolymorphicMatcher(internal::StrEqualityMatcher<internal::wstring>(
+ str, false, false));
+}
+
+// Creates a matcher that matches any wstring, std::wstring, or C wide string
+// that contains the given substring.
+inline PolymorphicMatcher<internal::HasSubstrMatcher<internal::wstring> >
+ HasSubstr(const internal::wstring& substring) {
+ return MakePolymorphicMatcher(internal::HasSubstrMatcher<internal::wstring>(
+ substring));
+}
+
+// Matches a string that starts with 'prefix' (case-sensitive).
+inline PolymorphicMatcher<internal::StartsWithMatcher<internal::wstring> >
+ StartsWith(const internal::wstring& prefix) {
+ return MakePolymorphicMatcher(internal::StartsWithMatcher<internal::wstring>(
+ prefix));
+}
+
+// Matches a string that ends with 'suffix' (case-sensitive).
+inline PolymorphicMatcher<internal::EndsWithMatcher<internal::wstring> >
+ EndsWith(const internal::wstring& suffix) {
+ return MakePolymorphicMatcher(internal::EndsWithMatcher<internal::wstring>(
+ suffix));
+}
+
+#endif // GTEST_HAS_GLOBAL_WSTRING || GTEST_HAS_STD_WSTRING
+
+// Creates a polymorphic matcher that matches a 2-tuple where the
+// first field == the second field.
+inline internal::Eq2Matcher Eq() { return internal::Eq2Matcher(); }
+
+// Creates a polymorphic matcher that matches a 2-tuple where the
+// first field >= the second field.
+inline internal::Ge2Matcher Ge() { return internal::Ge2Matcher(); }
+
+// Creates a polymorphic matcher that matches a 2-tuple where the
+// first field > the second field.
+inline internal::Gt2Matcher Gt() { return internal::Gt2Matcher(); }
+
+// Creates a polymorphic matcher that matches a 2-tuple where the
+// first field <= the second field.
+inline internal::Le2Matcher Le() { return internal::Le2Matcher(); }
+
+// Creates a polymorphic matcher that matches a 2-tuple where the
+// first field < the second field.
+inline internal::Lt2Matcher Lt() { return internal::Lt2Matcher(); }
+
+// Creates a polymorphic matcher that matches a 2-tuple where the
+// first field != the second field.
+inline internal::Ne2Matcher Ne() { return internal::Ne2Matcher(); }
+
+// Creates a matcher that matches any value of type T that m doesn't
+// match.
+template <typename InnerMatcher>
+inline internal::NotMatcher<InnerMatcher> Not(InnerMatcher m) {
+ return internal::NotMatcher<InnerMatcher>(m);
+}
+
+// Returns a matcher that matches anything that satisfies the given
+// predicate. The predicate can be any unary function or functor
+// whose return type can be implicitly converted to bool.
+template <typename Predicate>
+inline PolymorphicMatcher<internal::TrulyMatcher<Predicate> >
+Truly(Predicate pred) {
+ return MakePolymorphicMatcher(internal::TrulyMatcher<Predicate>(pred));
+}
+
+// Returns a matcher that matches the container size. The container must
+// support both size() and size_type which all STL-like containers provide.
+// Note that the parameter 'size' can be a value of type size_type as well as
+// matcher. For instance:
+// EXPECT_THAT(container, SizeIs(2)); // Checks container has 2 elements.
+// EXPECT_THAT(container, SizeIs(Le(2)); // Checks container has at most 2.
+template <typename SizeMatcher>
+inline internal::SizeIsMatcher<SizeMatcher>
+SizeIs(const SizeMatcher& size_matcher) {
+ return internal::SizeIsMatcher<SizeMatcher>(size_matcher);
+}
+
+// Returns a matcher that matches an equal container.
+// This matcher behaves like Eq(), but in the event of mismatch lists the
+// values that are included in one container but not the other. (Duplicate
+// values and order differences are not explained.)
+template <typename Container>
+inline PolymorphicMatcher<internal::ContainerEqMatcher< // NOLINT
+ GTEST_REMOVE_CONST_(Container)> >
+ ContainerEq(const Container& rhs) {
+ // This following line is for working around a bug in MSVC 8.0,
+ // which causes Container to be a const type sometimes.
+ typedef GTEST_REMOVE_CONST_(Container) RawContainer;
+ return MakePolymorphicMatcher(
+ internal::ContainerEqMatcher<RawContainer>(rhs));
+}
+
+// Returns a matcher that matches a container that, when sorted using
+// the given comparator, matches container_matcher.
+template <typename Comparator, typename ContainerMatcher>
+inline internal::WhenSortedByMatcher<Comparator, ContainerMatcher>
+WhenSortedBy(const Comparator& comparator,
+ const ContainerMatcher& container_matcher) {
+ return internal::WhenSortedByMatcher<Comparator, ContainerMatcher>(
+ comparator, container_matcher);
+}
+
+// Returns a matcher that matches a container that, when sorted using
+// the < operator, matches container_matcher.
+template <typename ContainerMatcher>
+inline internal::WhenSortedByMatcher<internal::LessComparator, ContainerMatcher>
+WhenSorted(const ContainerMatcher& container_matcher) {
+ return
+ internal::WhenSortedByMatcher<internal::LessComparator, ContainerMatcher>(
+ internal::LessComparator(), container_matcher);
+}
+
+// Matches an STL-style container or a native array that contains the
+// same number of elements as in rhs, where its i-th element and rhs's
+// i-th element (as a pair) satisfy the given pair matcher, for all i.
+// TupleMatcher must be able to be safely cast to Matcher<tuple<const
+// T1&, const T2&> >, where T1 and T2 are the types of elements in the
+// LHS container and the RHS container respectively.
+template <typename TupleMatcher, typename Container>
+inline internal::PointwiseMatcher<TupleMatcher,
+ GTEST_REMOVE_CONST_(Container)>
+Pointwise(const TupleMatcher& tuple_matcher, const Container& rhs) {
+ // This following line is for working around a bug in MSVC 8.0,
+ // which causes Container to be a const type sometimes.
+ typedef GTEST_REMOVE_CONST_(Container) RawContainer;
+ return internal::PointwiseMatcher<TupleMatcher, RawContainer>(
+ tuple_matcher, rhs);
+}
+
+// Matches an STL-style container or a native array that contains at
+// least one element matching the given value or matcher.
+//
+// Examples:
+// ::std::set<int> page_ids;
+// page_ids.insert(3);
+// page_ids.insert(1);
+// EXPECT_THAT(page_ids, Contains(1));
+// EXPECT_THAT(page_ids, Contains(Gt(2)));
+// EXPECT_THAT(page_ids, Not(Contains(4)));
+//
+// ::std::map<int, size_t> page_lengths;
+// page_lengths[1] = 100;
+// EXPECT_THAT(page_lengths,
+// Contains(::std::pair<const int, size_t>(1, 100)));
+//
+// const char* user_ids[] = { "joe", "mike", "tom" };
+// EXPECT_THAT(user_ids, Contains(Eq(::std::string("tom"))));
+template <typename M>
+inline internal::ContainsMatcher<M> Contains(M matcher) {
+ return internal::ContainsMatcher<M>(matcher);
+}
+
+// Matches an STL-style container or a native array that contains only
+// elements matching the given value or matcher.
+//
+// Each(m) is semantically equivalent to Not(Contains(Not(m))). Only
+// the messages are different.
+//
+// Examples:
+// ::std::set<int> page_ids;
+// // Each(m) matches an empty container, regardless of what m is.
+// EXPECT_THAT(page_ids, Each(Eq(1)));
+// EXPECT_THAT(page_ids, Each(Eq(77)));
+//
+// page_ids.insert(3);
+// EXPECT_THAT(page_ids, Each(Gt(0)));
+// EXPECT_THAT(page_ids, Not(Each(Gt(4))));
+// page_ids.insert(1);
+// EXPECT_THAT(page_ids, Not(Each(Lt(2))));
+//
+// ::std::map<int, size_t> page_lengths;
+// page_lengths[1] = 100;
+// page_lengths[2] = 200;
+// page_lengths[3] = 300;
+// EXPECT_THAT(page_lengths, Not(Each(Pair(1, 100))));
+// EXPECT_THAT(page_lengths, Each(Key(Le(3))));
+//
+// const char* user_ids[] = { "joe", "mike", "tom" };
+// EXPECT_THAT(user_ids, Not(Each(Eq(::std::string("tom")))));
+template <typename M>
+inline internal::EachMatcher<M> Each(M matcher) {
+ return internal::EachMatcher<M>(matcher);
+}
+
+// Key(inner_matcher) matches an std::pair whose 'first' field matches
+// inner_matcher. For example, Contains(Key(Ge(5))) can be used to match an
+// std::map that contains at least one element whose key is >= 5.
+template <typename M>
+inline internal::KeyMatcher<M> Key(M inner_matcher) {
+ return internal::KeyMatcher<M>(inner_matcher);
+}
+
+// Pair(first_matcher, second_matcher) matches a std::pair whose 'first' field
+// matches first_matcher and whose 'second' field matches second_matcher. For
+// example, EXPECT_THAT(map_type, ElementsAre(Pair(Ge(5), "foo"))) can be used
+// to match a std::map<int, string> that contains exactly one element whose key
+// is >= 5 and whose value equals "foo".
+template <typename FirstMatcher, typename SecondMatcher>
+inline internal::PairMatcher<FirstMatcher, SecondMatcher>
+Pair(FirstMatcher first_matcher, SecondMatcher second_matcher) {
+ return internal::PairMatcher<FirstMatcher, SecondMatcher>(
+ first_matcher, second_matcher);
+}
+
+// Returns a predicate that is satisfied by anything that matches the
+// given matcher.
+template <typename M>
+inline internal::MatcherAsPredicate<M> Matches(M matcher) {
+ return internal::MatcherAsPredicate<M>(matcher);
+}
+
+// Returns true iff the value matches the matcher.
+template <typename T, typename M>
+inline bool Value(const T& value, M matcher) {
+ return testing::Matches(matcher)(value);
+}
+
+// Matches the value against the given matcher and explains the match
+// result to listener.
+template <typename T, typename M>
+inline bool ExplainMatchResult(
+ M matcher, const T& value, MatchResultListener* listener) {
+ return SafeMatcherCast<const T&>(matcher).MatchAndExplain(value, listener);
+}
+
+#if GTEST_LANG_CXX11
+// Define variadic matcher versions. They are overloaded in
+// gmock-generated-matchers.h for the cases supported by pre C++11 compilers.
+template <typename... Args>
+inline internal::AllOfMatcher<Args...> AllOf(const Args&... matchers) {
+ return internal::AllOfMatcher<Args...>(matchers...);
+}
+
+template <typename... Args>
+inline internal::AnyOfMatcher<Args...> AnyOf(const Args&... matchers) {
+ return internal::AnyOfMatcher<Args...>(matchers...);
+}
+
+#endif // GTEST_LANG_CXX11
+
+// AllArgs(m) is a synonym of m. This is useful in
+//
+// EXPECT_CALL(foo, Bar(_, _)).With(AllArgs(Eq()));
+//
+// which is easier to read than
+//
+// EXPECT_CALL(foo, Bar(_, _)).With(Eq());
+template <typename InnerMatcher>
+inline InnerMatcher AllArgs(const InnerMatcher& matcher) { return matcher; }
+
+// These macros allow using matchers to check values in Google Test
+// tests. ASSERT_THAT(value, matcher) and EXPECT_THAT(value, matcher)
+// succeed iff the value matches the matcher. If the assertion fails,
+// the value and the description of the matcher will be printed.
+#define ASSERT_THAT(value, matcher) ASSERT_PRED_FORMAT1(\
+ ::testing::internal::MakePredicateFormatterFromMatcher(matcher), value)
+#define EXPECT_THAT(value, matcher) EXPECT_PRED_FORMAT1(\
+ ::testing::internal::MakePredicateFormatterFromMatcher(matcher), value)
+
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_MATCHERS_H_
+
+namespace testing {
+
+// An abstract handle of an expectation.
+class Expectation;
+
+// A set of expectation handles.
+class ExpectationSet;
+
+// Anything inside the 'internal' namespace IS INTERNAL IMPLEMENTATION
+// and MUST NOT BE USED IN USER CODE!!!
+namespace internal {
+
+// Implements a mock function.
+template <typename F> class FunctionMocker;
+
+// Base class for expectations.
+class ExpectationBase;
+
+// Implements an expectation.
+template <typename F> class TypedExpectation;
+
+// Helper class for testing the Expectation class template.
+class ExpectationTester;
+
+// Base class for function mockers.
+template <typename F> class FunctionMockerBase;
+
+// Protects the mock object registry (in class Mock), all function
+// mockers, and all expectations.
+//
+// The reason we don't use more fine-grained protection is: when a
+// mock function Foo() is called, it needs to consult its expectations
+// to see which one should be picked. If another thread is allowed to
+// call a mock function (either Foo() or a different one) at the same
+// time, it could affect the "retired" attributes of Foo()'s
+// expectations when InSequence() is used, and thus affect which
+// expectation gets picked. Therefore, we sequence all mock function
+// calls to ensure the integrity of the mock objects' states.
+GTEST_API_ GTEST_DECLARE_STATIC_MUTEX_(g_gmock_mutex);
+
+// Untyped base class for ActionResultHolder<R>.
+class UntypedActionResultHolderBase;
+
+// Abstract base class of FunctionMockerBase. This is the
+// type-agnostic part of the function mocker interface. Its pure
+// virtual methods are implemented by FunctionMockerBase.
+class GTEST_API_ UntypedFunctionMockerBase {
+ public:
+ UntypedFunctionMockerBase();
+ virtual ~UntypedFunctionMockerBase();
+
+ // Verifies that all expectations on this mock function have been
+ // satisfied. Reports one or more Google Test non-fatal failures
+ // and returns false if not.
+ bool VerifyAndClearExpectationsLocked()
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex);
+
+ // Clears the ON_CALL()s set on this mock function.
+ virtual void ClearDefaultActionsLocked()
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) = 0;
+
+ // In all of the following Untyped* functions, it's the caller's
+ // responsibility to guarantee the correctness of the arguments'
+ // types.
+
+ // Performs the default action with the given arguments and returns
+ // the action's result. The call description string will be used in
+ // the error message to describe the call in the case the default
+ // action fails.
+ // L = *
+ virtual UntypedActionResultHolderBase* UntypedPerformDefaultAction(
+ const void* untyped_args,
+ const string& call_description) const = 0;
+
+ // Performs the given action with the given arguments and returns
+ // the action's result.
+ // L = *
+ virtual UntypedActionResultHolderBase* UntypedPerformAction(
+ const void* untyped_action,
+ const void* untyped_args) const = 0;
+
+ // Writes a message that the call is uninteresting (i.e. neither
+ // explicitly expected nor explicitly unexpected) to the given
+ // ostream.
+ virtual void UntypedDescribeUninterestingCall(
+ const void* untyped_args,
+ ::std::ostream* os) const
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) = 0;
+
+ // Returns the expectation that matches the given function arguments
+ // (or NULL is there's no match); when a match is found,
+ // untyped_action is set to point to the action that should be
+ // performed (or NULL if the action is "do default"), and
+ // is_excessive is modified to indicate whether the call exceeds the
+ // expected number.
+ virtual const ExpectationBase* UntypedFindMatchingExpectation(
+ const void* untyped_args,
+ const void** untyped_action, bool* is_excessive,
+ ::std::ostream* what, ::std::ostream* why)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) = 0;
+
+ // Prints the given function arguments to the ostream.
+ virtual void UntypedPrintArgs(const void* untyped_args,
+ ::std::ostream* os) const = 0;
+
+ // Sets the mock object this mock method belongs to, and registers
+ // this information in the global mock registry. Will be called
+ // whenever an EXPECT_CALL() or ON_CALL() is executed on this mock
+ // method.
+ // TODO(wan at google.com): rename to SetAndRegisterOwner().
+ void RegisterOwner(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex);
+
+ // Sets the mock object this mock method belongs to, and sets the
+ // name of the mock function. Will be called upon each invocation
+ // of this mock function.
+ void SetOwnerAndName(const void* mock_obj, const char* name)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex);
+
+ // Returns the mock object this mock method belongs to. Must be
+ // called after RegisterOwner() or SetOwnerAndName() has been
+ // called.
+ const void* MockObject() const
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex);
+
+ // Returns the name of this mock method. Must be called after
+ // SetOwnerAndName() has been called.
+ const char* Name() const
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex);
+
+ // Returns the result of invoking this mock function with the given
+ // arguments. This function can be safely called from multiple
+ // threads concurrently. The caller is responsible for deleting the
+ // result.
+ const UntypedActionResultHolderBase* UntypedInvokeWith(
+ const void* untyped_args)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex);
+
+ protected:
+ typedef std::vector<const void*> UntypedOnCallSpecs;
+
+ typedef std::vector<internal::linked_ptr<ExpectationBase> >
+ UntypedExpectations;
+
+ // Returns an Expectation object that references and co-owns exp,
+ // which must be an expectation on this mock function.
+ Expectation GetHandleOf(ExpectationBase* exp);
+
+ // Address of the mock object this mock method belongs to. Only
+ // valid after this mock method has been called or
+ // ON_CALL/EXPECT_CALL has been invoked on it.
+ const void* mock_obj_; // Protected by g_gmock_mutex.
+
+ // Name of the function being mocked. Only valid after this mock
+ // method has been called.
+ const char* name_; // Protected by g_gmock_mutex.
+
+ // All default action specs for this function mocker.
+ UntypedOnCallSpecs untyped_on_call_specs_;
+
+ // All expectations for this function mocker.
+ UntypedExpectations untyped_expectations_;
+}; // class UntypedFunctionMockerBase
+
+// Untyped base class for OnCallSpec<F>.
+class UntypedOnCallSpecBase {
+ public:
+ // The arguments are the location of the ON_CALL() statement.
+ UntypedOnCallSpecBase(const char* a_file, int a_line)
+ : file_(a_file), line_(a_line), last_clause_(kNone) {}
+
+ // Where in the source file was the default action spec defined?
+ const char* file() const { return file_; }
+ int line() const { return line_; }
+
+ protected:
+ // Gives each clause in the ON_CALL() statement a name.
+ enum Clause {
+ // Do not change the order of the enum members! The run-time
+ // syntax checking relies on it.
+ kNone,
+ kWith,
+ kWillByDefault
+ };
+
+ // Asserts that the ON_CALL() statement has a certain property.
+ void AssertSpecProperty(bool property, const string& failure_message) const {
+ Assert(property, file_, line_, failure_message);
+ }
+
+ // Expects that the ON_CALL() statement has a certain property.
+ void ExpectSpecProperty(bool property, const string& failure_message) const {
+ Expect(property, file_, line_, failure_message);
+ }
+
+ const char* file_;
+ int line_;
+
+ // The last clause in the ON_CALL() statement as seen so far.
+ // Initially kNone and changes as the statement is parsed.
+ Clause last_clause_;
+}; // class UntypedOnCallSpecBase
+
+// This template class implements an ON_CALL spec.
+template <typename F>
+class OnCallSpec : public UntypedOnCallSpecBase {
+ public:
+ typedef typename Function<F>::ArgumentTuple ArgumentTuple;
+ typedef typename Function<F>::ArgumentMatcherTuple ArgumentMatcherTuple;
+
+ // Constructs an OnCallSpec object from the information inside
+ // the parenthesis of an ON_CALL() statement.
+ OnCallSpec(const char* a_file, int a_line,
+ const ArgumentMatcherTuple& matchers)
+ : UntypedOnCallSpecBase(a_file, a_line),
+ matchers_(matchers),
+ // By default, extra_matcher_ should match anything. However,
+ // we cannot initialize it with _ as that triggers a compiler
+ // bug in Symbian's C++ compiler (cannot decide between two
+ // overloaded constructors of Matcher<const ArgumentTuple&>).
+ extra_matcher_(A<const ArgumentTuple&>()) {
+ }
+
+ // Implements the .With() clause.
+ OnCallSpec& With(const Matcher<const ArgumentTuple&>& m) {
+ // Makes sure this is called at most once.
+ ExpectSpecProperty(last_clause_ < kWith,
+ ".With() cannot appear "
+ "more than once in an ON_CALL().");
+ last_clause_ = kWith;
+
+ extra_matcher_ = m;
+ return *this;
+ }
+
+ // Implements the .WillByDefault() clause.
+ OnCallSpec& WillByDefault(const Action<F>& action) {
+ ExpectSpecProperty(last_clause_ < kWillByDefault,
+ ".WillByDefault() must appear "
+ "exactly once in an ON_CALL().");
+ last_clause_ = kWillByDefault;
+
+ ExpectSpecProperty(!action.IsDoDefault(),
+ "DoDefault() cannot be used in ON_CALL().");
+ action_ = action;
+ return *this;
+ }
+
+ // Returns true iff the given arguments match the matchers.
+ bool Matches(const ArgumentTuple& args) const {
+ return TupleMatches(matchers_, args) && extra_matcher_.Matches(args);
+ }
+
+ // Returns the action specified by the user.
+ const Action<F>& GetAction() const {
+ AssertSpecProperty(last_clause_ == kWillByDefault,
+ ".WillByDefault() must appear exactly "
+ "once in an ON_CALL().");
+ return action_;
+ }
+
+ private:
+ // The information in statement
+ //
+ // ON_CALL(mock_object, Method(matchers))
+ // .With(multi-argument-matcher)
+ // .WillByDefault(action);
+ //
+ // is recorded in the data members like this:
+ //
+ // source file that contains the statement => file_
+ // line number of the statement => line_
+ // matchers => matchers_
+ // multi-argument-matcher => extra_matcher_
+ // action => action_
+ ArgumentMatcherTuple matchers_;
+ Matcher<const ArgumentTuple&> extra_matcher_;
+ Action<F> action_;
+}; // class OnCallSpec
+
+// Possible reactions on uninteresting calls.
+enum CallReaction {
+ kAllow,
+ kWarn,
+ kFail,
+ kDefault = kWarn // By default, warn about uninteresting calls.
+};
+
+} // namespace internal
+
+// Utilities for manipulating mock objects.
+class GTEST_API_ Mock {
+ public:
+ // The following public methods can be called concurrently.
+
+ // Tells Google Mock to ignore mock_obj when checking for leaked
+ // mock objects.
+ static void AllowLeak(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ // Verifies and clears all expectations on the given mock object.
+ // If the expectations aren't satisfied, generates one or more
+ // Google Test non-fatal failures and returns false.
+ static bool VerifyAndClearExpectations(void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ // Verifies all expectations on the given mock object and clears its
+ // default actions and expectations. Returns true iff the
+ // verification was successful.
+ static bool VerifyAndClear(void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ private:
+ friend class internal::UntypedFunctionMockerBase;
+
+ // Needed for a function mocker to register itself (so that we know
+ // how to clear a mock object).
+ template <typename F>
+ friend class internal::FunctionMockerBase;
+
+ template <typename M>
+ friend class NiceMock;
+
+ template <typename M>
+ friend class NaggyMock;
+
+ template <typename M>
+ friend class StrictMock;
+
+ // Tells Google Mock to allow uninteresting calls on the given mock
+ // object.
+ static void AllowUninterestingCalls(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ // Tells Google Mock to warn the user about uninteresting calls on
+ // the given mock object.
+ static void WarnUninterestingCalls(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ // Tells Google Mock to fail uninteresting calls on the given mock
+ // object.
+ static void FailUninterestingCalls(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ // Tells Google Mock the given mock object is being destroyed and
+ // its entry in the call-reaction table should be removed.
+ static void UnregisterCallReaction(const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ // Returns the reaction Google Mock will have on uninteresting calls
+ // made on the given mock object.
+ static internal::CallReaction GetReactionOnUninterestingCalls(
+ const void* mock_obj)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ // Verifies that all expectations on the given mock object have been
+ // satisfied. Reports one or more Google Test non-fatal failures
+ // and returns false if not.
+ static bool VerifyAndClearExpectationsLocked(void* mock_obj)
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(internal::g_gmock_mutex);
+
+ // Clears all ON_CALL()s set on the given mock object.
+ static void ClearDefaultActionsLocked(void* mock_obj)
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(internal::g_gmock_mutex);
+
+ // Registers a mock object and a mock method it owns.
+ static void Register(
+ const void* mock_obj,
+ internal::UntypedFunctionMockerBase* mocker)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ // Tells Google Mock where in the source code mock_obj is used in an
+ // ON_CALL or EXPECT_CALL. In case mock_obj is leaked, this
+ // information helps the user identify which object it is.
+ static void RegisterUseByOnCallOrExpectCall(
+ const void* mock_obj, const char* file, int line)
+ GTEST_LOCK_EXCLUDED_(internal::g_gmock_mutex);
+
+ // Unregisters a mock method; removes the owning mock object from
+ // the registry when the last mock method associated with it has
+ // been unregistered. This is called only in the destructor of
+ // FunctionMockerBase.
+ static void UnregisterLocked(internal::UntypedFunctionMockerBase* mocker)
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(internal::g_gmock_mutex);
+}; // class Mock
+
+// An abstract handle of an expectation. Useful in the .After()
+// clause of EXPECT_CALL() for setting the (partial) order of
+// expectations. The syntax:
+//
+// Expectation e1 = EXPECT_CALL(...)...;
+// EXPECT_CALL(...).After(e1)...;
+//
+// sets two expectations where the latter can only be matched after
+// the former has been satisfied.
+//
+// Notes:
+// - This class is copyable and has value semantics.
+// - Constness is shallow: a const Expectation object itself cannot
+// be modified, but the mutable methods of the ExpectationBase
+// object it references can be called via expectation_base().
+// - The constructors and destructor are defined out-of-line because
+// the Symbian WINSCW compiler wants to otherwise instantiate them
+// when it sees this class definition, at which point it doesn't have
+// ExpectationBase available yet, leading to incorrect destruction
+// in the linked_ptr (or compilation errors if using a checking
+// linked_ptr).
+class GTEST_API_ Expectation {
+ public:
+ // Constructs a null object that doesn't reference any expectation.
+ Expectation();
+
+ ~Expectation();
+
+ // This single-argument ctor must not be explicit, in order to support the
+ // Expectation e = EXPECT_CALL(...);
+ // syntax.
+ //
+ // A TypedExpectation object stores its pre-requisites as
+ // Expectation objects, and needs to call the non-const Retire()
+ // method on the ExpectationBase objects they reference. Therefore
+ // Expectation must receive a *non-const* reference to the
+ // ExpectationBase object.
+ Expectation(internal::ExpectationBase& exp); // NOLINT
+
+ // The compiler-generated copy ctor and operator= work exactly as
+ // intended, so we don't need to define our own.
+
+ // Returns true iff rhs references the same expectation as this object does.
+ bool operator==(const Expectation& rhs) const {
+ return expectation_base_ == rhs.expectation_base_;
+ }
+
+ bool operator!=(const Expectation& rhs) const { return !(*this == rhs); }
+
+ private:
+ friend class ExpectationSet;
+ friend class Sequence;
+ friend class ::testing::internal::ExpectationBase;
+ friend class ::testing::internal::UntypedFunctionMockerBase;
+
+ template <typename F>
+ friend class ::testing::internal::FunctionMockerBase;
+
+ template <typename F>
+ friend class ::testing::internal::TypedExpectation;
+
+ // This comparator is needed for putting Expectation objects into a set.
+ class Less {
+ public:
+ bool operator()(const Expectation& lhs, const Expectation& rhs) const {
+ return lhs.expectation_base_.get() < rhs.expectation_base_.get();
+ }
+ };
+
+ typedef ::std::set<Expectation, Less> Set;
+
+ Expectation(
+ const internal::linked_ptr<internal::ExpectationBase>& expectation_base);
+
+ // Returns the expectation this object references.
+ const internal::linked_ptr<internal::ExpectationBase>&
+ expectation_base() const {
+ return expectation_base_;
+ }
+
+ // A linked_ptr that co-owns the expectation this handle references.
+ internal::linked_ptr<internal::ExpectationBase> expectation_base_;
+};
+
+// A set of expectation handles. Useful in the .After() clause of
+// EXPECT_CALL() for setting the (partial) order of expectations. The
+// syntax:
+//
+// ExpectationSet es;
+// es += EXPECT_CALL(...)...;
+// es += EXPECT_CALL(...)...;
+// EXPECT_CALL(...).After(es)...;
+//
+// sets three expectations where the last one can only be matched
+// after the first two have both been satisfied.
+//
+// This class is copyable and has value semantics.
+class ExpectationSet {
+ public:
+ // A bidirectional iterator that can read a const element in the set.
+ typedef Expectation::Set::const_iterator const_iterator;
+
+ // An object stored in the set. This is an alias of Expectation.
+ typedef Expectation::Set::value_type value_type;
+
+ // Constructs an empty set.
+ ExpectationSet() {}
+
+ // This single-argument ctor must not be explicit, in order to support the
+ // ExpectationSet es = EXPECT_CALL(...);
+ // syntax.
+ ExpectationSet(internal::ExpectationBase& exp) { // NOLINT
+ *this += Expectation(exp);
+ }
+
+ // This single-argument ctor implements implicit conversion from
+ // Expectation and thus must not be explicit. This allows either an
+ // Expectation or an ExpectationSet to be used in .After().
+ ExpectationSet(const Expectation& e) { // NOLINT
+ *this += e;
+ }
+
+ // The compiler-generator ctor and operator= works exactly as
+ // intended, so we don't need to define our own.
+
+ // Returns true iff rhs contains the same set of Expectation objects
+ // as this does.
+ bool operator==(const ExpectationSet& rhs) const {
+ return expectations_ == rhs.expectations_;
+ }
+
+ bool operator!=(const ExpectationSet& rhs) const { return !(*this == rhs); }
+
+ // Implements the syntax
+ // expectation_set += EXPECT_CALL(...);
+ ExpectationSet& operator+=(const Expectation& e) {
+ expectations_.insert(e);
+ return *this;
+ }
+
+ int size() const { return static_cast<int>(expectations_.size()); }
+
+ const_iterator begin() const { return expectations_.begin(); }
+ const_iterator end() const { return expectations_.end(); }
+
+ private:
+ Expectation::Set expectations_;
+};
+
+
+// Sequence objects are used by a user to specify the relative order
+// in which the expectations should match. They are copyable (we rely
+// on the compiler-defined copy constructor and assignment operator).
+class GTEST_API_ Sequence {
+ public:
+ // Constructs an empty sequence.
+ Sequence() : last_expectation_(new Expectation) {}
+
+ // Adds an expectation to this sequence. The caller must ensure
+ // that no other thread is accessing this Sequence object.
+ void AddExpectation(const Expectation& expectation) const;
+
+ private:
+ // The last expectation in this sequence. We use a linked_ptr here
+ // because Sequence objects are copyable and we want the copies to
+ // be aliases. The linked_ptr allows the copies to co-own and share
+ // the same Expectation object.
+ internal::linked_ptr<Expectation> last_expectation_;
+}; // class Sequence
+
+// An object of this type causes all EXPECT_CALL() statements
+// encountered in its scope to be put in an anonymous sequence. The
+// work is done in the constructor and destructor. You should only
+// create an InSequence object on the stack.
+//
+// The sole purpose for this class is to support easy definition of
+// sequential expectations, e.g.
+//
+// {
+// InSequence dummy; // The name of the object doesn't matter.
+//
+// // The following expectations must match in the order they appear.
+// EXPECT_CALL(a, Bar())...;
+// EXPECT_CALL(a, Baz())...;
+// ...
+// EXPECT_CALL(b, Xyz())...;
+// }
+//
+// You can create InSequence objects in multiple threads, as long as
+// they are used to affect different mock objects. The idea is that
+// each thread can create and set up its own mocks as if it's the only
+// thread. However, for clarity of your tests we recommend you to set
+// up mocks in the main thread unless you have a good reason not to do
+// so.
+class GTEST_API_ InSequence {
+ public:
+ InSequence();
+ ~InSequence();
+ private:
+ bool sequence_created_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(InSequence); // NOLINT
+} GTEST_ATTRIBUTE_UNUSED_;
+
+namespace internal {
+
+// Points to the implicit sequence introduced by a living InSequence
+// object (if any) in the current thread or NULL.
+GTEST_API_ extern ThreadLocal<Sequence*> g_gmock_implicit_sequence;
+
+// Base class for implementing expectations.
+//
+// There are two reasons for having a type-agnostic base class for
+// Expectation:
+//
+// 1. We need to store collections of expectations of different
+// types (e.g. all pre-requisites of a particular expectation, all
+// expectations in a sequence). Therefore these expectation objects
+// must share a common base class.
+//
+// 2. We can avoid binary code bloat by moving methods not depending
+// on the template argument of Expectation to the base class.
+//
+// This class is internal and mustn't be used by user code directly.
+class GTEST_API_ ExpectationBase {
+ public:
+ // source_text is the EXPECT_CALL(...) source that created this Expectation.
+ ExpectationBase(const char* file, int line, const string& source_text);
+
+ virtual ~ExpectationBase();
+
+ // Where in the source file was the expectation spec defined?
+ const char* file() const { return file_; }
+ int line() const { return line_; }
+ const char* source_text() const { return source_text_.c_str(); }
+ // Returns the cardinality specified in the expectation spec.
+ const Cardinality& cardinality() const { return cardinality_; }
+
+ // Describes the source file location of this expectation.
+ void DescribeLocationTo(::std::ostream* os) const {
+ *os << FormatFileLocation(file(), line()) << " ";
+ }
+
+ // Describes how many times a function call matching this
+ // expectation has occurred.
+ void DescribeCallCountTo(::std::ostream* os) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex);
+
+ // If this mock method has an extra matcher (i.e. .With(matcher)),
+ // describes it to the ostream.
+ virtual void MaybeDescribeExtraMatcherTo(::std::ostream* os) = 0;
+
+ protected:
+ friend class ::testing::Expectation;
+ friend class UntypedFunctionMockerBase;
+
+ enum Clause {
+ // Don't change the order of the enum members!
+ kNone,
+ kWith,
+ kTimes,
+ kInSequence,
+ kAfter,
+ kWillOnce,
+ kWillRepeatedly,
+ kRetiresOnSaturation
+ };
+
+ typedef std::vector<const void*> UntypedActions;
+
+ // Returns an Expectation object that references and co-owns this
+ // expectation.
+ virtual Expectation GetHandle() = 0;
+
+ // Asserts that the EXPECT_CALL() statement has the given property.
+ void AssertSpecProperty(bool property, const string& failure_message) const {
+ Assert(property, file_, line_, failure_message);
+ }
+
+ // Expects that the EXPECT_CALL() statement has the given property.
+ void ExpectSpecProperty(bool property, const string& failure_message) const {
+ Expect(property, file_, line_, failure_message);
+ }
+
+ // Explicitly specifies the cardinality of this expectation. Used
+ // by the subclasses to implement the .Times() clause.
+ void SpecifyCardinality(const Cardinality& cardinality);
+
+ // Returns true iff the user specified the cardinality explicitly
+ // using a .Times().
+ bool cardinality_specified() const { return cardinality_specified_; }
+
+ // Sets the cardinality of this expectation spec.
+ void set_cardinality(const Cardinality& a_cardinality) {
+ cardinality_ = a_cardinality;
+ }
+
+ // The following group of methods should only be called after the
+ // EXPECT_CALL() statement, and only when g_gmock_mutex is held by
+ // the current thread.
+
+ // Retires all pre-requisites of this expectation.
+ void RetireAllPreRequisites()
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex);
+
+ // Returns true iff this expectation is retired.
+ bool is_retired() const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ return retired_;
+ }
+
+ // Retires this expectation.
+ void Retire()
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ retired_ = true;
+ }
+
+ // Returns true iff this expectation is satisfied.
+ bool IsSatisfied() const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ return cardinality().IsSatisfiedByCallCount(call_count_);
+ }
+
+ // Returns true iff this expectation is saturated.
+ bool IsSaturated() const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ return cardinality().IsSaturatedByCallCount(call_count_);
+ }
+
+ // Returns true iff this expectation is over-saturated.
+ bool IsOverSaturated() const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ return cardinality().IsOverSaturatedByCallCount(call_count_);
+ }
+
+ // Returns true iff all pre-requisites of this expectation are satisfied.
+ bool AllPrerequisitesAreSatisfied() const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex);
+
+ // Adds unsatisfied pre-requisites of this expectation to 'result'.
+ void FindUnsatisfiedPrerequisites(ExpectationSet* result) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex);
+
+ // Returns the number this expectation has been invoked.
+ int call_count() const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ return call_count_;
+ }
+
+ // Increments the number this expectation has been invoked.
+ void IncrementCallCount()
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ call_count_++;
+ }
+
+ // Checks the action count (i.e. the number of WillOnce() and
+ // WillRepeatedly() clauses) against the cardinality if this hasn't
+ // been done before. Prints a warning if there are too many or too
+ // few actions.
+ void CheckActionCountIfNotDone() const
+ GTEST_LOCK_EXCLUDED_(mutex_);
+
+ friend class ::testing::Sequence;
+ friend class ::testing::internal::ExpectationTester;
+
+ template <typename Function>
+ friend class TypedExpectation;
+
+ // Implements the .Times() clause.
+ void UntypedTimes(const Cardinality& a_cardinality);
+
+ // This group of fields are part of the spec and won't change after
+ // an EXPECT_CALL() statement finishes.
+ const char* file_; // The file that contains the expectation.
+ int line_; // The line number of the expectation.
+ const string source_text_; // The EXPECT_CALL(...) source text.
+ // True iff the cardinality is specified explicitly.
+ bool cardinality_specified_;
+ Cardinality cardinality_; // The cardinality of the expectation.
+ // The immediate pre-requisites (i.e. expectations that must be
+ // satisfied before this expectation can be matched) of this
+ // expectation. We use linked_ptr in the set because we want an
+ // Expectation object to be co-owned by its FunctionMocker and its
+ // successors. This allows multiple mock objects to be deleted at
+ // different times.
+ ExpectationSet immediate_prerequisites_;
+
+ // This group of fields are the current state of the expectation,
+ // and can change as the mock function is called.
+ int call_count_; // How many times this expectation has been invoked.
+ bool retired_; // True iff this expectation has retired.
+ UntypedActions untyped_actions_;
+ bool extra_matcher_specified_;
+ bool repeated_action_specified_; // True if a WillRepeatedly() was specified.
+ bool retires_on_saturation_;
+ Clause last_clause_;
+ mutable bool action_count_checked_; // Under mutex_.
+ mutable Mutex mutex_; // Protects action_count_checked_.
+
+ GTEST_DISALLOW_ASSIGN_(ExpectationBase);
+}; // class ExpectationBase
+
+// Impements an expectation for the given function type.
+template <typename F>
+class TypedExpectation : public ExpectationBase {
+ public:
+ typedef typename Function<F>::ArgumentTuple ArgumentTuple;
+ typedef typename Function<F>::ArgumentMatcherTuple ArgumentMatcherTuple;
+ typedef typename Function<F>::Result Result;
+
+ TypedExpectation(FunctionMockerBase<F>* owner,
+ const char* a_file, int a_line, const string& a_source_text,
+ const ArgumentMatcherTuple& m)
+ : ExpectationBase(a_file, a_line, a_source_text),
+ owner_(owner),
+ matchers_(m),
+ // By default, extra_matcher_ should match anything. However,
+ // we cannot initialize it with _ as that triggers a compiler
+ // bug in Symbian's C++ compiler (cannot decide between two
+ // overloaded constructors of Matcher<const ArgumentTuple&>).
+ extra_matcher_(A<const ArgumentTuple&>()),
+ repeated_action_(DoDefault()) {}
+
+ virtual ~TypedExpectation() {
+ // Check the validity of the action count if it hasn't been done
+ // yet (for example, if the expectation was never used).
+ CheckActionCountIfNotDone();
+ for (UntypedActions::const_iterator it = untyped_actions_.begin();
+ it != untyped_actions_.end(); ++it) {
+ delete static_cast<const Action<F>*>(*it);
+ }
+ }
+
+ // Implements the .With() clause.
+ TypedExpectation& With(const Matcher<const ArgumentTuple&>& m) {
+ if (last_clause_ == kWith) {
+ ExpectSpecProperty(false,
+ ".With() cannot appear "
+ "more than once in an EXPECT_CALL().");
+ } else {
+ ExpectSpecProperty(last_clause_ < kWith,
+ ".With() must be the first "
+ "clause in an EXPECT_CALL().");
+ }
+ last_clause_ = kWith;
+
+ extra_matcher_ = m;
+ extra_matcher_specified_ = true;
+ return *this;
+ }
+
+ // Implements the .Times() clause.
+ TypedExpectation& Times(const Cardinality& a_cardinality) {
+ ExpectationBase::UntypedTimes(a_cardinality);
+ return *this;
+ }
+
+ // Implements the .Times() clause.
+ TypedExpectation& Times(int n) {
+ return Times(Exactly(n));
+ }
+
+ // Implements the .InSequence() clause.
+ TypedExpectation& InSequence(const Sequence& s) {
+ ExpectSpecProperty(last_clause_ <= kInSequence,
+ ".InSequence() cannot appear after .After(),"
+ " .WillOnce(), .WillRepeatedly(), or "
+ ".RetiresOnSaturation().");
+ last_clause_ = kInSequence;
+
+ s.AddExpectation(GetHandle());
+ return *this;
+ }
+ TypedExpectation& InSequence(const Sequence& s1, const Sequence& s2) {
+ return InSequence(s1).InSequence(s2);
+ }
+ TypedExpectation& InSequence(const Sequence& s1, const Sequence& s2,
+ const Sequence& s3) {
+ return InSequence(s1, s2).InSequence(s3);
+ }
+ TypedExpectation& InSequence(const Sequence& s1, const Sequence& s2,
+ const Sequence& s3, const Sequence& s4) {
+ return InSequence(s1, s2, s3).InSequence(s4);
+ }
+ TypedExpectation& InSequence(const Sequence& s1, const Sequence& s2,
+ const Sequence& s3, const Sequence& s4,
+ const Sequence& s5) {
+ return InSequence(s1, s2, s3, s4).InSequence(s5);
+ }
+
+ // Implements that .After() clause.
+ TypedExpectation& After(const ExpectationSet& s) {
+ ExpectSpecProperty(last_clause_ <= kAfter,
+ ".After() cannot appear after .WillOnce(),"
+ " .WillRepeatedly(), or "
+ ".RetiresOnSaturation().");
+ last_clause_ = kAfter;
+
+ for (ExpectationSet::const_iterator it = s.begin(); it != s.end(); ++it) {
+ immediate_prerequisites_ += *it;
+ }
+ return *this;
+ }
+ TypedExpectation& After(const ExpectationSet& s1, const ExpectationSet& s2) {
+ return After(s1).After(s2);
+ }
+ TypedExpectation& After(const ExpectationSet& s1, const ExpectationSet& s2,
+ const ExpectationSet& s3) {
+ return After(s1, s2).After(s3);
+ }
+ TypedExpectation& After(const ExpectationSet& s1, const ExpectationSet& s2,
+ const ExpectationSet& s3, const ExpectationSet& s4) {
+ return After(s1, s2, s3).After(s4);
+ }
+ TypedExpectation& After(const ExpectationSet& s1, const ExpectationSet& s2,
+ const ExpectationSet& s3, const ExpectationSet& s4,
+ const ExpectationSet& s5) {
+ return After(s1, s2, s3, s4).After(s5);
+ }
+
+ // Implements the .WillOnce() clause.
+ TypedExpectation& WillOnce(const Action<F>& action) {
+ ExpectSpecProperty(last_clause_ <= kWillOnce,
+ ".WillOnce() cannot appear after "
+ ".WillRepeatedly() or .RetiresOnSaturation().");
+ last_clause_ = kWillOnce;
+
+ untyped_actions_.push_back(new Action<F>(action));
+ if (!cardinality_specified()) {
+ set_cardinality(Exactly(static_cast<int>(untyped_actions_.size())));
+ }
+ return *this;
+ }
+
+ // Implements the .WillRepeatedly() clause.
+ TypedExpectation& WillRepeatedly(const Action<F>& action) {
+ if (last_clause_ == kWillRepeatedly) {
+ ExpectSpecProperty(false,
+ ".WillRepeatedly() cannot appear "
+ "more than once in an EXPECT_CALL().");
+ } else {
+ ExpectSpecProperty(last_clause_ < kWillRepeatedly,
+ ".WillRepeatedly() cannot appear "
+ "after .RetiresOnSaturation().");
+ }
+ last_clause_ = kWillRepeatedly;
+ repeated_action_specified_ = true;
+
+ repeated_action_ = action;
+ if (!cardinality_specified()) {
+ set_cardinality(AtLeast(static_cast<int>(untyped_actions_.size())));
+ }
+
+ // Now that no more action clauses can be specified, we check
+ // whether their count makes sense.
+ CheckActionCountIfNotDone();
+ return *this;
+ }
+
+ // Implements the .RetiresOnSaturation() clause.
+ TypedExpectation& RetiresOnSaturation() {
+ ExpectSpecProperty(last_clause_ < kRetiresOnSaturation,
+ ".RetiresOnSaturation() cannot appear "
+ "more than once.");
+ last_clause_ = kRetiresOnSaturation;
+ retires_on_saturation_ = true;
+
+ // Now that no more action clauses can be specified, we check
+ // whether their count makes sense.
+ CheckActionCountIfNotDone();
+ return *this;
+ }
+
+ // Returns the matchers for the arguments as specified inside the
+ // EXPECT_CALL() macro.
+ const ArgumentMatcherTuple& matchers() const {
+ return matchers_;
+ }
+
+ // Returns the matcher specified by the .With() clause.
+ const Matcher<const ArgumentTuple&>& extra_matcher() const {
+ return extra_matcher_;
+ }
+
+ // Returns the action specified by the .WillRepeatedly() clause.
+ const Action<F>& repeated_action() const { return repeated_action_; }
+
+ // If this mock method has an extra matcher (i.e. .With(matcher)),
+ // describes it to the ostream.
+ virtual void MaybeDescribeExtraMatcherTo(::std::ostream* os) {
+ if (extra_matcher_specified_) {
+ *os << " Expected args: ";
+ extra_matcher_.DescribeTo(os);
+ *os << "\n";
+ }
+ }
+
+ private:
+ template <typename Function>
+ friend class FunctionMockerBase;
+
+ // Returns an Expectation object that references and co-owns this
+ // expectation.
+ virtual Expectation GetHandle() {
+ return owner_->GetHandleOf(this);
+ }
+
+ // The following methods will be called only after the EXPECT_CALL()
+ // statement finishes and when the current thread holds
+ // g_gmock_mutex.
+
+ // Returns true iff this expectation matches the given arguments.
+ bool Matches(const ArgumentTuple& args) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ return TupleMatches(matchers_, args) && extra_matcher_.Matches(args);
+ }
+
+ // Returns true iff this expectation should handle the given arguments.
+ bool ShouldHandleArguments(const ArgumentTuple& args) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+
+ // In case the action count wasn't checked when the expectation
+ // was defined (e.g. if this expectation has no WillRepeatedly()
+ // or RetiresOnSaturation() clause), we check it when the
+ // expectation is used for the first time.
+ CheckActionCountIfNotDone();
+ return !is_retired() && AllPrerequisitesAreSatisfied() && Matches(args);
+ }
+
+ // Describes the result of matching the arguments against this
+ // expectation to the given ostream.
+ void ExplainMatchResultTo(
+ const ArgumentTuple& args,
+ ::std::ostream* os) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+
+ if (is_retired()) {
+ *os << " Expected: the expectation is active\n"
+ << " Actual: it is retired\n";
+ } else if (!Matches(args)) {
+ if (!TupleMatches(matchers_, args)) {
+ ExplainMatchFailureTupleTo(matchers_, args, os);
+ }
+ StringMatchResultListener listener;
+ if (!extra_matcher_.MatchAndExplain(args, &listener)) {
+ *os << " Expected args: ";
+ extra_matcher_.DescribeTo(os);
+ *os << "\n Actual: don't match";
+
+ internal::PrintIfNotEmpty(listener.str(), os);
+ *os << "\n";
+ }
+ } else if (!AllPrerequisitesAreSatisfied()) {
+ *os << " Expected: all pre-requisites are satisfied\n"
+ << " Actual: the following immediate pre-requisites "
+ << "are not satisfied:\n";
+ ExpectationSet unsatisfied_prereqs;
+ FindUnsatisfiedPrerequisites(&unsatisfied_prereqs);
+ int i = 0;
+ for (ExpectationSet::const_iterator it = unsatisfied_prereqs.begin();
+ it != unsatisfied_prereqs.end(); ++it) {
+ it->expectation_base()->DescribeLocationTo(os);
+ *os << "pre-requisite #" << i++ << "\n";
+ }
+ *os << " (end of pre-requisites)\n";
+ } else {
+ // This line is here just for completeness' sake. It will never
+ // be executed as currently the ExplainMatchResultTo() function
+ // is called only when the mock function call does NOT match the
+ // expectation.
+ *os << "The call matches the expectation.\n";
+ }
+ }
+
+ // Returns the action that should be taken for the current invocation.
+ const Action<F>& GetCurrentAction(
+ const FunctionMockerBase<F>* mocker,
+ const ArgumentTuple& args) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ const int count = call_count();
+ Assert(count >= 1, __FILE__, __LINE__,
+ "call_count() is <= 0 when GetCurrentAction() is "
+ "called - this should never happen.");
+
+ const int action_count = static_cast<int>(untyped_actions_.size());
+ if (action_count > 0 && !repeated_action_specified_ &&
+ count > action_count) {
+ // If there is at least one WillOnce() and no WillRepeatedly(),
+ // we warn the user when the WillOnce() clauses ran out.
+ ::std::stringstream ss;
+ DescribeLocationTo(&ss);
+ ss << "Actions ran out in " << source_text() << "...\n"
+ << "Called " << count << " times, but only "
+ << action_count << " WillOnce()"
+ << (action_count == 1 ? " is" : "s are") << " specified - ";
+ mocker->DescribeDefaultActionTo(args, &ss);
+ Log(kWarning, ss.str(), 1);
+ }
+
+ return count <= action_count ?
+ *static_cast<const Action<F>*>(untyped_actions_[count - 1]) :
+ repeated_action();
+ }
+
+ // Given the arguments of a mock function call, if the call will
+ // over-saturate this expectation, returns the default action;
+ // otherwise, returns the next action in this expectation. Also
+ // describes *what* happened to 'what', and explains *why* Google
+ // Mock does it to 'why'. This method is not const as it calls
+ // IncrementCallCount(). A return value of NULL means the default
+ // action.
+ const Action<F>* GetActionForArguments(
+ const FunctionMockerBase<F>* mocker,
+ const ArgumentTuple& args,
+ ::std::ostream* what,
+ ::std::ostream* why)
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ if (IsSaturated()) {
+ // We have an excessive call.
+ IncrementCallCount();
+ *what << "Mock function called more times than expected - ";
+ mocker->DescribeDefaultActionTo(args, what);
+ DescribeCallCountTo(why);
+
+ // TODO(wan at google.com): allow the user to control whether
+ // unexpected calls should fail immediately or continue using a
+ // flag --gmock_unexpected_calls_are_fatal.
+ return NULL;
+ }
+
+ IncrementCallCount();
+ RetireAllPreRequisites();
+
+ if (retires_on_saturation_ && IsSaturated()) {
+ Retire();
+ }
+
+ // Must be done after IncrementCount()!
+ *what << "Mock function call matches " << source_text() <<"...\n";
+ return &(GetCurrentAction(mocker, args));
+ }
+
+ // All the fields below won't change once the EXPECT_CALL()
+ // statement finishes.
+ FunctionMockerBase<F>* const owner_;
+ ArgumentMatcherTuple matchers_;
+ Matcher<const ArgumentTuple&> extra_matcher_;
+ Action<F> repeated_action_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(TypedExpectation);
+}; // class TypedExpectation
+
+// A MockSpec object is used by ON_CALL() or EXPECT_CALL() for
+// specifying the default behavior of, or expectation on, a mock
+// function.
+
+// Note: class MockSpec really belongs to the ::testing namespace.
+// However if we define it in ::testing, MSVC will complain when
+// classes in ::testing::internal declare it as a friend class
+// template. To workaround this compiler bug, we define MockSpec in
+// ::testing::internal and import it into ::testing.
+
+// Logs a message including file and line number information.
+GTEST_API_ void LogWithLocation(testing::internal::LogSeverity severity,
+ const char* file, int line,
+ const string& message);
+
+template <typename F>
+class MockSpec {
+ public:
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+ typedef typename internal::Function<F>::ArgumentMatcherTuple
+ ArgumentMatcherTuple;
+
+ // Constructs a MockSpec object, given the function mocker object
+ // that the spec is associated with.
+ explicit MockSpec(internal::FunctionMockerBase<F>* function_mocker)
+ : function_mocker_(function_mocker) {}
+
+ // Adds a new default action spec to the function mocker and returns
+ // the newly created spec.
+ internal::OnCallSpec<F>& InternalDefaultActionSetAt(
+ const char* file, int line, const char* obj, const char* call) {
+ LogWithLocation(internal::kInfo, file, line,
+ string("ON_CALL(") + obj + ", " + call + ") invoked");
+ return function_mocker_->AddNewOnCallSpec(file, line, matchers_);
+ }
+
+ // Adds a new expectation spec to the function mocker and returns
+ // the newly created spec.
+ internal::TypedExpectation<F>& InternalExpectedAt(
+ const char* file, int line, const char* obj, const char* call) {
+ const string source_text(string("EXPECT_CALL(") + obj + ", " + call + ")");
+ LogWithLocation(internal::kInfo, file, line, source_text + " invoked");
+ return function_mocker_->AddNewExpectation(
+ file, line, source_text, matchers_);
+ }
+
+ private:
+ template <typename Function>
+ friend class internal::FunctionMocker;
+
+ void SetMatchers(const ArgumentMatcherTuple& matchers) {
+ matchers_ = matchers;
+ }
+
+ // The function mocker that owns this spec.
+ internal::FunctionMockerBase<F>* const function_mocker_;
+ // The argument matchers specified in the spec.
+ ArgumentMatcherTuple matchers_;
+
+ GTEST_DISALLOW_ASSIGN_(MockSpec);
+}; // class MockSpec
+
+// MSVC warns about using 'this' in base member initializer list, so
+// we need to temporarily disable the warning. We have to do it for
+// the entire class to suppress the warning, even though it's about
+// the constructor only.
+
+#ifdef _MSC_VER
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4355) // Temporarily disables warning 4355.
+#endif // _MSV_VER
+
+// C++ treats the void type specially. For example, you cannot define
+// a void-typed variable or pass a void value to a function.
+// ActionResultHolder<T> holds a value of type T, where T must be a
+// copyable type or void (T doesn't need to be default-constructable).
+// It hides the syntactic difference between void and other types, and
+// is used to unify the code for invoking both void-returning and
+// non-void-returning mock functions.
+
+// Untyped base class for ActionResultHolder<T>.
+class UntypedActionResultHolderBase {
+ public:
+ virtual ~UntypedActionResultHolderBase() {}
+
+ // Prints the held value as an action's result to os.
+ virtual void PrintAsActionResult(::std::ostream* os) const = 0;
+};
+
+// This generic definition is used when T is not void.
+template <typename T>
+class ActionResultHolder : public UntypedActionResultHolderBase {
+ public:
+ explicit ActionResultHolder(T a_value) : value_(a_value) {}
+
+ // The compiler-generated copy constructor and assignment operator
+ // are exactly what we need, so we don't need to define them.
+
+ // Returns the held value and deletes this object.
+ T GetValueAndDelete() const {
+ T retval(value_);
+ delete this;
+ return retval;
+ }
+
+ // Prints the held value as an action's result to os.
+ virtual void PrintAsActionResult(::std::ostream* os) const {
+ *os << "\n Returns: ";
+ // T may be a reference type, so we don't use UniversalPrint().
+ UniversalPrinter<T>::Print(value_, os);
+ }
+
+ // Performs the given mock function's default action and returns the
+ // result in a new-ed ActionResultHolder.
+ template <typename F>
+ static ActionResultHolder* PerformDefaultAction(
+ const FunctionMockerBase<F>* func_mocker,
+ const typename Function<F>::ArgumentTuple& args,
+ const string& call_description) {
+ return new ActionResultHolder(
+ func_mocker->PerformDefaultAction(args, call_description));
+ }
+
+ // Performs the given action and returns the result in a new-ed
+ // ActionResultHolder.
+ template <typename F>
+ static ActionResultHolder*
+ PerformAction(const Action<F>& action,
+ const typename Function<F>::ArgumentTuple& args) {
+ return new ActionResultHolder(action.Perform(args));
+ }
+
+ private:
+ T value_;
+
+ // T could be a reference type, so = isn't supported.
+ GTEST_DISALLOW_ASSIGN_(ActionResultHolder);
+};
+
+// Specialization for T = void.
+template <>
+class ActionResultHolder<void> : public UntypedActionResultHolderBase {
+ public:
+ void GetValueAndDelete() const { delete this; }
+
+ virtual void PrintAsActionResult(::std::ostream* /* os */) const {}
+
+ // Performs the given mock function's default action and returns NULL;
+ template <typename F>
+ static ActionResultHolder* PerformDefaultAction(
+ const FunctionMockerBase<F>* func_mocker,
+ const typename Function<F>::ArgumentTuple& args,
+ const string& call_description) {
+ func_mocker->PerformDefaultAction(args, call_description);
+ return NULL;
+ }
+
+ // Performs the given action and returns NULL.
+ template <typename F>
+ static ActionResultHolder* PerformAction(
+ const Action<F>& action,
+ const typename Function<F>::ArgumentTuple& args) {
+ action.Perform(args);
+ return NULL;
+ }
+};
+
+// The base of the function mocker class for the given function type.
+// We put the methods in this class instead of its child to avoid code
+// bloat.
+template <typename F>
+class FunctionMockerBase : public UntypedFunctionMockerBase {
+ public:
+ typedef typename Function<F>::Result Result;
+ typedef typename Function<F>::ArgumentTuple ArgumentTuple;
+ typedef typename Function<F>::ArgumentMatcherTuple ArgumentMatcherTuple;
+
+ FunctionMockerBase() : current_spec_(this) {}
+
+ // The destructor verifies that all expectations on this mock
+ // function have been satisfied. If not, it will report Google Test
+ // non-fatal failures for the violations.
+ virtual ~FunctionMockerBase()
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ MutexLock l(&g_gmock_mutex);
+ VerifyAndClearExpectationsLocked();
+ Mock::UnregisterLocked(this);
+ ClearDefaultActionsLocked();
+ }
+
+ // Returns the ON_CALL spec that matches this mock function with the
+ // given arguments; returns NULL if no matching ON_CALL is found.
+ // L = *
+ const OnCallSpec<F>* FindOnCallSpec(
+ const ArgumentTuple& args) const {
+ for (UntypedOnCallSpecs::const_reverse_iterator it
+ = untyped_on_call_specs_.rbegin();
+ it != untyped_on_call_specs_.rend(); ++it) {
+ const OnCallSpec<F>* spec = static_cast<const OnCallSpec<F>*>(*it);
+ if (spec->Matches(args))
+ return spec;
+ }
+
+ return NULL;
+ }
+
+ // Performs the default action of this mock function on the given
+ // arguments and returns the result. Asserts (or throws if
+ // exceptions are enabled) with a helpful call descrption if there
+ // is no valid return value. This method doesn't depend on the
+ // mutable state of this object, and thus can be called concurrently
+ // without locking.
+ // L = *
+ Result PerformDefaultAction(const ArgumentTuple& args,
+ const string& call_description) const {
+ const OnCallSpec<F>* const spec =
+ this->FindOnCallSpec(args);
+ if (spec != NULL) {
+ return spec->GetAction().Perform(args);
+ }
+ const string message = call_description +
+ "\n The mock function has no default action "
+ "set, and its return type has no default value set.";
+#if GTEST_HAS_EXCEPTIONS
+ if (!DefaultValue<Result>::Exists()) {
+ throw std::runtime_error(message);
+ }
+#else
+ Assert(DefaultValue<Result>::Exists(), "", -1, message);
+#endif
+ return DefaultValue<Result>::Get();
+ }
+
+ // Performs the default action with the given arguments and returns
+ // the action's result. The call description string will be used in
+ // the error message to describe the call in the case the default
+ // action fails. The caller is responsible for deleting the result.
+ // L = *
+ virtual UntypedActionResultHolderBase* UntypedPerformDefaultAction(
+ const void* untyped_args, // must point to an ArgumentTuple
+ const string& call_description) const {
+ const ArgumentTuple& args =
+ *static_cast<const ArgumentTuple*>(untyped_args);
+ return ResultHolder::PerformDefaultAction(this, args, call_description);
+ }
+
+ // Performs the given action with the given arguments and returns
+ // the action's result. The caller is responsible for deleting the
+ // result.
+ // L = *
+ virtual UntypedActionResultHolderBase* UntypedPerformAction(
+ const void* untyped_action, const void* untyped_args) const {
+ // Make a copy of the action before performing it, in case the
+ // action deletes the mock object (and thus deletes itself).
+ const Action<F> action = *static_cast<const Action<F>*>(untyped_action);
+ const ArgumentTuple& args =
+ *static_cast<const ArgumentTuple*>(untyped_args);
+ return ResultHolder::PerformAction(action, args);
+ }
+
+ // Implements UntypedFunctionMockerBase::ClearDefaultActionsLocked():
+ // clears the ON_CALL()s set on this mock function.
+ virtual void ClearDefaultActionsLocked()
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+
+ // Deleting our default actions may trigger other mock objects to be
+ // deleted, for example if an action contains a reference counted smart
+ // pointer to that mock object, and that is the last reference. So if we
+ // delete our actions within the context of the global mutex we may deadlock
+ // when this method is called again. Instead, make a copy of the set of
+ // actions to delete, clear our set within the mutex, and then delete the
+ // actions outside of the mutex.
+ UntypedOnCallSpecs specs_to_delete;
+ untyped_on_call_specs_.swap(specs_to_delete);
+
+ g_gmock_mutex.Unlock();
+ for (UntypedOnCallSpecs::const_iterator it =
+ specs_to_delete.begin();
+ it != specs_to_delete.end(); ++it) {
+ delete static_cast<const OnCallSpec<F>*>(*it);
+ }
+
+ // Lock the mutex again, since the caller expects it to be locked when we
+ // return.
+ g_gmock_mutex.Lock();
+ }
+
+ protected:
+ template <typename Function>
+ friend class MockSpec;
+
+ typedef ActionResultHolder<Result> ResultHolder;
+
+ // Returns the result of invoking this mock function with the given
+ // arguments. This function can be safely called from multiple
+ // threads concurrently.
+ Result InvokeWith(const ArgumentTuple& args)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ return static_cast<const ResultHolder*>(
+ this->UntypedInvokeWith(&args))->GetValueAndDelete();
+ }
+
+ // Adds and returns a default action spec for this mock function.
+ OnCallSpec<F>& AddNewOnCallSpec(
+ const char* file, int line,
+ const ArgumentMatcherTuple& m)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ Mock::RegisterUseByOnCallOrExpectCall(MockObject(), file, line);
+ OnCallSpec<F>* const on_call_spec = new OnCallSpec<F>(file, line, m);
+ untyped_on_call_specs_.push_back(on_call_spec);
+ return *on_call_spec;
+ }
+
+ // Adds and returns an expectation spec for this mock function.
+ TypedExpectation<F>& AddNewExpectation(
+ const char* file,
+ int line,
+ const string& source_text,
+ const ArgumentMatcherTuple& m)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ Mock::RegisterUseByOnCallOrExpectCall(MockObject(), file, line);
+ TypedExpectation<F>* const expectation =
+ new TypedExpectation<F>(this, file, line, source_text, m);
+ const linked_ptr<ExpectationBase> untyped_expectation(expectation);
+ untyped_expectations_.push_back(untyped_expectation);
+
+ // Adds this expectation into the implicit sequence if there is one.
+ Sequence* const implicit_sequence = g_gmock_implicit_sequence.get();
+ if (implicit_sequence != NULL) {
+ implicit_sequence->AddExpectation(Expectation(untyped_expectation));
+ }
+
+ return *expectation;
+ }
+
+ // The current spec (either default action spec or expectation spec)
+ // being described on this function mocker.
+ MockSpec<F>& current_spec() { return current_spec_; }
+
+ private:
+ template <typename Func> friend class TypedExpectation;
+
+ // Some utilities needed for implementing UntypedInvokeWith().
+
+ // Describes what default action will be performed for the given
+ // arguments.
+ // L = *
+ void DescribeDefaultActionTo(const ArgumentTuple& args,
+ ::std::ostream* os) const {
+ const OnCallSpec<F>* const spec = FindOnCallSpec(args);
+
+ if (spec == NULL) {
+ *os << (internal::type_equals<Result, void>::value ?
+ "returning directly.\n" :
+ "returning default value.\n");
+ } else {
+ *os << "taking default action specified at:\n"
+ << FormatFileLocation(spec->file(), spec->line()) << "\n";
+ }
+ }
+
+ // Writes a message that the call is uninteresting (i.e. neither
+ // explicitly expected nor explicitly unexpected) to the given
+ // ostream.
+ virtual void UntypedDescribeUninterestingCall(
+ const void* untyped_args,
+ ::std::ostream* os) const
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ const ArgumentTuple& args =
+ *static_cast<const ArgumentTuple*>(untyped_args);
+ *os << "Uninteresting mock function call - ";
+ DescribeDefaultActionTo(args, os);
+ *os << " Function call: " << Name();
+ UniversalPrint(args, os);
+ }
+
+ // Returns the expectation that matches the given function arguments
+ // (or NULL is there's no match); when a match is found,
+ // untyped_action is set to point to the action that should be
+ // performed (or NULL if the action is "do default"), and
+ // is_excessive is modified to indicate whether the call exceeds the
+ // expected number.
+ //
+ // Critical section: We must find the matching expectation and the
+ // corresponding action that needs to be taken in an ATOMIC
+ // transaction. Otherwise another thread may call this mock
+ // method in the middle and mess up the state.
+ //
+ // However, performing the action has to be left out of the critical
+ // section. The reason is that we have no control on what the
+ // action does (it can invoke an arbitrary user function or even a
+ // mock function) and excessive locking could cause a dead lock.
+ virtual const ExpectationBase* UntypedFindMatchingExpectation(
+ const void* untyped_args,
+ const void** untyped_action, bool* is_excessive,
+ ::std::ostream* what, ::std::ostream* why)
+ GTEST_LOCK_EXCLUDED_(g_gmock_mutex) {
+ const ArgumentTuple& args =
+ *static_cast<const ArgumentTuple*>(untyped_args);
+ MutexLock l(&g_gmock_mutex);
+ TypedExpectation<F>* exp = this->FindMatchingExpectationLocked(args);
+ if (exp == NULL) { // A match wasn't found.
+ this->FormatUnexpectedCallMessageLocked(args, what, why);
+ return NULL;
+ }
+
+ // This line must be done before calling GetActionForArguments(),
+ // which will increment the call count for *exp and thus affect
+ // its saturation status.
+ *is_excessive = exp->IsSaturated();
+ const Action<F>* action = exp->GetActionForArguments(this, args, what, why);
+ if (action != NULL && action->IsDoDefault())
+ action = NULL; // Normalize "do default" to NULL.
+ *untyped_action = action;
+ return exp;
+ }
+
+ // Prints the given function arguments to the ostream.
+ virtual void UntypedPrintArgs(const void* untyped_args,
+ ::std::ostream* os) const {
+ const ArgumentTuple& args =
+ *static_cast<const ArgumentTuple*>(untyped_args);
+ UniversalPrint(args, os);
+ }
+
+ // Returns the expectation that matches the arguments, or NULL if no
+ // expectation matches them.
+ TypedExpectation<F>* FindMatchingExpectationLocked(
+ const ArgumentTuple& args) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ for (typename UntypedExpectations::const_reverse_iterator it =
+ untyped_expectations_.rbegin();
+ it != untyped_expectations_.rend(); ++it) {
+ TypedExpectation<F>* const exp =
+ static_cast<TypedExpectation<F>*>(it->get());
+ if (exp->ShouldHandleArguments(args)) {
+ return exp;
+ }
+ }
+ return NULL;
+ }
+
+ // Returns a message that the arguments don't match any expectation.
+ void FormatUnexpectedCallMessageLocked(
+ const ArgumentTuple& args,
+ ::std::ostream* os,
+ ::std::ostream* why) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ *os << "\nUnexpected mock function call - ";
+ DescribeDefaultActionTo(args, os);
+ PrintTriedExpectationsLocked(args, why);
+ }
+
+ // Prints a list of expectations that have been tried against the
+ // current mock function call.
+ void PrintTriedExpectationsLocked(
+ const ArgumentTuple& args,
+ ::std::ostream* why) const
+ GTEST_EXCLUSIVE_LOCK_REQUIRED_(g_gmock_mutex) {
+ g_gmock_mutex.AssertHeld();
+ const int count = static_cast<int>(untyped_expectations_.size());
+ *why << "Google Mock tried the following " << count << " "
+ << (count == 1 ? "expectation, but it didn't match" :
+ "expectations, but none matched")
+ << ":\n";
+ for (int i = 0; i < count; i++) {
+ TypedExpectation<F>* const expectation =
+ static_cast<TypedExpectation<F>*>(untyped_expectations_[i].get());
+ *why << "\n";
+ expectation->DescribeLocationTo(why);
+ if (count > 1) {
+ *why << "tried expectation #" << i << ": ";
+ }
+ *why << expectation->source_text() << "...\n";
+ expectation->ExplainMatchResultTo(args, why);
+ expectation->DescribeCallCountTo(why);
+ }
+ }
+
+ // The current spec (either default action spec or expectation spec)
+ // being described on this function mocker.
+ MockSpec<F> current_spec_;
+
+ // There is no generally useful and implementable semantics of
+ // copying a mock object, so copying a mock is usually a user error.
+ // Thus we disallow copying function mockers. If the user really
+ // wants to copy a mock object, he should implement his own copy
+ // operation, for example:
+ //
+ // class MockFoo : public Foo {
+ // public:
+ // // Defines a copy constructor explicitly.
+ // MockFoo(const MockFoo& src) {}
+ // ...
+ // };
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(FunctionMockerBase);
+}; // class FunctionMockerBase
+
+#ifdef _MSC_VER
+# pragma warning(pop) // Restores the warning state.
+#endif // _MSV_VER
+
+// Implements methods of FunctionMockerBase.
+
+// Verifies that all expectations on this mock function have been
+// satisfied. Reports one or more Google Test non-fatal failures and
+// returns false if not.
+
+// Reports an uninteresting call (whose description is in msg) in the
+// manner specified by 'reaction'.
+void ReportUninterestingCall(CallReaction reaction, const string& msg);
+
+} // namespace internal
+
+// The style guide prohibits "using" statements in a namespace scope
+// inside a header file. However, the MockSpec class template is
+// meant to be defined in the ::testing namespace. The following line
+// is just a trick for working around a bug in MSVC 8.0, which cannot
+// handle it if we define MockSpec in ::testing.
+using internal::MockSpec;
+
+// Const(x) is a convenient function for obtaining a const reference
+// to x. This is useful for setting expectations on an overloaded
+// const mock method, e.g.
+//
+// class MockFoo : public FooInterface {
+// public:
+// MOCK_METHOD0(Bar, int());
+// MOCK_CONST_METHOD0(Bar, int&());
+// };
+//
+// MockFoo foo;
+// // Expects a call to non-const MockFoo::Bar().
+// EXPECT_CALL(foo, Bar());
+// // Expects a call to const MockFoo::Bar().
+// EXPECT_CALL(Const(foo), Bar());
+template <typename T>
+inline const T& Const(const T& x) { return x; }
+
+// Constructs an Expectation object that references and co-owns exp.
+inline Expectation::Expectation(internal::ExpectationBase& exp) // NOLINT
+ : expectation_base_(exp.GetHandle().expectation_base()) {}
+
+} // namespace testing
+
+// A separate macro is required to avoid compile errors when the name
+// of the method used in call is a result of macro expansion.
+// See CompilesWithMethodNameExpandedFromMacro tests in
+// internal/gmock-spec-builders_test.cc for more details.
+#define GMOCK_ON_CALL_IMPL_(obj, call) \
+ ((obj).gmock_##call).InternalDefaultActionSetAt(__FILE__, __LINE__, \
+ #obj, #call)
+#define ON_CALL(obj, call) GMOCK_ON_CALL_IMPL_(obj, call)
+
+#define GMOCK_EXPECT_CALL_IMPL_(obj, call) \
+ ((obj).gmock_##call).InternalExpectedAt(__FILE__, __LINE__, #obj, #call)
+#define EXPECT_CALL(obj, call) GMOCK_EXPECT_CALL_IMPL_(obj, call)
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_SPEC_BUILDERS_H_
+
+namespace testing {
+namespace internal {
+
+template <typename F>
+class FunctionMockerBase;
+
+// Note: class FunctionMocker really belongs to the ::testing
+// namespace. However if we define it in ::testing, MSVC will
+// complain when classes in ::testing::internal declare it as a
+// friend class template. To workaround this compiler bug, we define
+// FunctionMocker in ::testing::internal and import it into ::testing.
+template <typename F>
+class FunctionMocker;
+
+template <typename R>
+class FunctionMocker<R()> : public
+ internal::FunctionMockerBase<R()> {
+ public:
+ typedef R F();
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With() {
+ return this->current_spec();
+ }
+
+ R Invoke() {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple());
+ }
+};
+
+template <typename R, typename A1>
+class FunctionMocker<R(A1)> : public
+ internal::FunctionMockerBase<R(A1)> {
+ public:
+ typedef R F(A1);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1));
+ }
+};
+
+template <typename R, typename A1, typename A2>
+class FunctionMocker<R(A1, A2)> : public
+ internal::FunctionMockerBase<R(A1, A2)> {
+ public:
+ typedef R F(A1, A2);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1, const Matcher<A2>& m2) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1, m2));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1, A2 a2) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1, a2));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3>
+class FunctionMocker<R(A1, A2, A3)> : public
+ internal::FunctionMockerBase<R(A1, A2, A3)> {
+ public:
+ typedef R F(A1, A2, A3);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1, const Matcher<A2>& m2,
+ const Matcher<A3>& m3) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1, m2, m3));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1, A2 a2, A3 a3) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1, a2, a3));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4>
+class FunctionMocker<R(A1, A2, A3, A4)> : public
+ internal::FunctionMockerBase<R(A1, A2, A3, A4)> {
+ public:
+ typedef R F(A1, A2, A3, A4);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1, const Matcher<A2>& m2,
+ const Matcher<A3>& m3, const Matcher<A4>& m4) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1, m2, m3, m4));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1, A2 a2, A3 a3, A4 a4) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1, a2, a3, a4));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5>
+class FunctionMocker<R(A1, A2, A3, A4, A5)> : public
+ internal::FunctionMockerBase<R(A1, A2, A3, A4, A5)> {
+ public:
+ typedef R F(A1, A2, A3, A4, A5);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1, const Matcher<A2>& m2,
+ const Matcher<A3>& m3, const Matcher<A4>& m4, const Matcher<A5>& m5) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1, m2, m3, m4,
+ m5));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1, A2 a2, A3 a3, A4 a4, A5 a5) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1, a2, a3, a4, a5));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6>
+class FunctionMocker<R(A1, A2, A3, A4, A5, A6)> : public
+ internal::FunctionMockerBase<R(A1, A2, A3, A4, A5, A6)> {
+ public:
+ typedef R F(A1, A2, A3, A4, A5, A6);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1, const Matcher<A2>& m2,
+ const Matcher<A3>& m3, const Matcher<A4>& m4, const Matcher<A5>& m5,
+ const Matcher<A6>& m6) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1, m2, m3, m4, m5,
+ m6));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1, a2, a3, a4, a5, a6));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7>
+class FunctionMocker<R(A1, A2, A3, A4, A5, A6, A7)> : public
+ internal::FunctionMockerBase<R(A1, A2, A3, A4, A5, A6, A7)> {
+ public:
+ typedef R F(A1, A2, A3, A4, A5, A6, A7);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1, const Matcher<A2>& m2,
+ const Matcher<A3>& m3, const Matcher<A4>& m4, const Matcher<A5>& m5,
+ const Matcher<A6>& m6, const Matcher<A7>& m7) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1, m2, m3, m4, m5,
+ m6, m7));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6, A7 a7) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1, a2, a3, a4, a5, a6, a7));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8>
+class FunctionMocker<R(A1, A2, A3, A4, A5, A6, A7, A8)> : public
+ internal::FunctionMockerBase<R(A1, A2, A3, A4, A5, A6, A7, A8)> {
+ public:
+ typedef R F(A1, A2, A3, A4, A5, A6, A7, A8);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1, const Matcher<A2>& m2,
+ const Matcher<A3>& m3, const Matcher<A4>& m4, const Matcher<A5>& m5,
+ const Matcher<A6>& m6, const Matcher<A7>& m7, const Matcher<A8>& m8) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1, m2, m3, m4, m5,
+ m6, m7, m8));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6, A7 a7, A8 a8) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1, a2, a3, a4, a5, a6, a7, a8));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8, typename A9>
+class FunctionMocker<R(A1, A2, A3, A4, A5, A6, A7, A8, A9)> : public
+ internal::FunctionMockerBase<R(A1, A2, A3, A4, A5, A6, A7, A8, A9)> {
+ public:
+ typedef R F(A1, A2, A3, A4, A5, A6, A7, A8, A9);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1, const Matcher<A2>& m2,
+ const Matcher<A3>& m3, const Matcher<A4>& m4, const Matcher<A5>& m5,
+ const Matcher<A6>& m6, const Matcher<A7>& m7, const Matcher<A8>& m8,
+ const Matcher<A9>& m9) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1, m2, m3, m4, m5,
+ m6, m7, m8, m9));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6, A7 a7, A8 a8, A9 a9) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1, a2, a3, a4, a5, a6, a7, a8, a9));
+ }
+};
+
+template <typename R, typename A1, typename A2, typename A3, typename A4,
+ typename A5, typename A6, typename A7, typename A8, typename A9,
+ typename A10>
+class FunctionMocker<R(A1, A2, A3, A4, A5, A6, A7, A8, A9, A10)> : public
+ internal::FunctionMockerBase<R(A1, A2, A3, A4, A5, A6, A7, A8, A9, A10)> {
+ public:
+ typedef R F(A1, A2, A3, A4, A5, A6, A7, A8, A9, A10);
+ typedef typename internal::Function<F>::ArgumentTuple ArgumentTuple;
+
+ MockSpec<F>& With(const Matcher<A1>& m1, const Matcher<A2>& m2,
+ const Matcher<A3>& m3, const Matcher<A4>& m4, const Matcher<A5>& m5,
+ const Matcher<A6>& m6, const Matcher<A7>& m7, const Matcher<A8>& m8,
+ const Matcher<A9>& m9, const Matcher<A10>& m10) {
+ this->current_spec().SetMatchers(::std::tr1::make_tuple(m1, m2, m3, m4, m5,
+ m6, m7, m8, m9, m10));
+ return this->current_spec();
+ }
+
+ R Invoke(A1 a1, A2 a2, A3 a3, A4 a4, A5 a5, A6 a6, A7 a7, A8 a8, A9 a9,
+ A10 a10) {
+ // Even though gcc and MSVC don't enforce it, 'this->' is required
+ // by the C++ standard [14.6.4] here, as the base class type is
+ // dependent on the template argument (and thus shouldn't be
+ // looked into when resolving InvokeWith).
+ return this->InvokeWith(ArgumentTuple(a1, a2, a3, a4, a5, a6, a7, a8, a9,
+ a10));
+ }
+};
+
+} // namespace internal
+
+// The style guide prohibits "using" statements in a namespace scope
+// inside a header file. However, the FunctionMocker class template
+// is meant to be defined in the ::testing namespace. The following
+// line is just a trick for working around a bug in MSVC 8.0, which
+// cannot handle it if we define FunctionMocker in ::testing.
+using internal::FunctionMocker;
+
+// GMOCK_RESULT_(tn, F) expands to the result type of function type F.
+// We define this as a variadic macro in case F contains unprotected
+// commas (the same reason that we use variadic macros in other places
+// in this file).
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_RESULT_(tn, ...) \
+ tn ::testing::internal::Function<__VA_ARGS__>::Result
+
+// The type of argument N of the given function type.
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_ARG_(tn, N, ...) \
+ tn ::testing::internal::Function<__VA_ARGS__>::Argument##N
+
+// The matcher type for argument N of the given function type.
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_MATCHER_(tn, N, ...) \
+ const ::testing::Matcher<GMOCK_ARG_(tn, N, __VA_ARGS__)>&
+
+// The variable for mocking the given method.
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_MOCKER_(arity, constness, Method) \
+ GTEST_CONCAT_TOKEN_(gmock##constness##arity##_##Method##_, __LINE__)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD0_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ ) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 0), \
+ this_method_does_not_take_0_arguments); \
+ GMOCK_MOCKER_(0, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(0, constness, Method).Invoke(); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method() constness { \
+ GMOCK_MOCKER_(0, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(0, constness, Method).With(); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(0, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD1_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 1), \
+ this_method_does_not_take_1_argument); \
+ GMOCK_MOCKER_(1, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(1, constness, Method).Invoke(gmock_a1); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1) constness { \
+ GMOCK_MOCKER_(1, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(1, constness, Method).With(gmock_a1); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(1, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD2_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_ARG_(tn, 2, __VA_ARGS__) gmock_a2) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 2), \
+ this_method_does_not_take_2_arguments); \
+ GMOCK_MOCKER_(2, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(2, constness, Method).Invoke(gmock_a1, gmock_a2); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_MATCHER_(tn, 2, __VA_ARGS__) gmock_a2) constness { \
+ GMOCK_MOCKER_(2, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(2, constness, Method).With(gmock_a1, gmock_a2); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(2, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD3_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_ARG_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_ARG_(tn, 3, __VA_ARGS__) gmock_a3) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 3), \
+ this_method_does_not_take_3_arguments); \
+ GMOCK_MOCKER_(3, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(3, constness, Method).Invoke(gmock_a1, gmock_a2, \
+ gmock_a3); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_MATCHER_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_MATCHER_(tn, 3, __VA_ARGS__) gmock_a3) constness { \
+ GMOCK_MOCKER_(3, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(3, constness, Method).With(gmock_a1, gmock_a2, \
+ gmock_a3); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(3, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD4_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_ARG_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_ARG_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_ARG_(tn, 4, __VA_ARGS__) gmock_a4) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 4), \
+ this_method_does_not_take_4_arguments); \
+ GMOCK_MOCKER_(4, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(4, constness, Method).Invoke(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_MATCHER_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_MATCHER_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_MATCHER_(tn, 4, __VA_ARGS__) gmock_a4) constness { \
+ GMOCK_MOCKER_(4, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(4, constness, Method).With(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(4, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD5_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_ARG_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_ARG_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_ARG_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_ARG_(tn, 5, __VA_ARGS__) gmock_a5) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 5), \
+ this_method_does_not_take_5_arguments); \
+ GMOCK_MOCKER_(5, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(5, constness, Method).Invoke(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_MATCHER_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_MATCHER_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_MATCHER_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_MATCHER_(tn, 5, __VA_ARGS__) gmock_a5) constness { \
+ GMOCK_MOCKER_(5, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(5, constness, Method).With(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(5, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD6_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_ARG_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_ARG_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_ARG_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_ARG_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_ARG_(tn, 6, __VA_ARGS__) gmock_a6) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 6), \
+ this_method_does_not_take_6_arguments); \
+ GMOCK_MOCKER_(6, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(6, constness, Method).Invoke(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_MATCHER_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_MATCHER_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_MATCHER_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_MATCHER_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_MATCHER_(tn, 6, __VA_ARGS__) gmock_a6) constness { \
+ GMOCK_MOCKER_(6, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(6, constness, Method).With(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(6, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD7_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_ARG_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_ARG_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_ARG_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_ARG_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_ARG_(tn, 6, __VA_ARGS__) gmock_a6, \
+ GMOCK_ARG_(tn, 7, __VA_ARGS__) gmock_a7) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 7), \
+ this_method_does_not_take_7_arguments); \
+ GMOCK_MOCKER_(7, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(7, constness, Method).Invoke(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6, gmock_a7); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_MATCHER_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_MATCHER_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_MATCHER_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_MATCHER_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_MATCHER_(tn, 6, __VA_ARGS__) gmock_a6, \
+ GMOCK_MATCHER_(tn, 7, __VA_ARGS__) gmock_a7) constness { \
+ GMOCK_MOCKER_(7, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(7, constness, Method).With(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6, gmock_a7); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(7, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD8_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_ARG_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_ARG_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_ARG_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_ARG_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_ARG_(tn, 6, __VA_ARGS__) gmock_a6, \
+ GMOCK_ARG_(tn, 7, __VA_ARGS__) gmock_a7, \
+ GMOCK_ARG_(tn, 8, __VA_ARGS__) gmock_a8) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 8), \
+ this_method_does_not_take_8_arguments); \
+ GMOCK_MOCKER_(8, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(8, constness, Method).Invoke(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6, gmock_a7, gmock_a8); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_MATCHER_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_MATCHER_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_MATCHER_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_MATCHER_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_MATCHER_(tn, 6, __VA_ARGS__) gmock_a6, \
+ GMOCK_MATCHER_(tn, 7, __VA_ARGS__) gmock_a7, \
+ GMOCK_MATCHER_(tn, 8, __VA_ARGS__) gmock_a8) constness { \
+ GMOCK_MOCKER_(8, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(8, constness, Method).With(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6, gmock_a7, gmock_a8); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(8, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD9_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_ARG_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_ARG_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_ARG_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_ARG_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_ARG_(tn, 6, __VA_ARGS__) gmock_a6, \
+ GMOCK_ARG_(tn, 7, __VA_ARGS__) gmock_a7, \
+ GMOCK_ARG_(tn, 8, __VA_ARGS__) gmock_a8, \
+ GMOCK_ARG_(tn, 9, __VA_ARGS__) gmock_a9) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 9), \
+ this_method_does_not_take_9_arguments); \
+ GMOCK_MOCKER_(9, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(9, constness, Method).Invoke(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6, gmock_a7, gmock_a8, \
+ gmock_a9); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_MATCHER_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_MATCHER_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_MATCHER_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_MATCHER_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_MATCHER_(tn, 6, __VA_ARGS__) gmock_a6, \
+ GMOCK_MATCHER_(tn, 7, __VA_ARGS__) gmock_a7, \
+ GMOCK_MATCHER_(tn, 8, __VA_ARGS__) gmock_a8, \
+ GMOCK_MATCHER_(tn, 9, __VA_ARGS__) gmock_a9) constness { \
+ GMOCK_MOCKER_(9, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(9, constness, Method).With(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6, gmock_a7, gmock_a8, \
+ gmock_a9); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(9, constness, \
+ Method)
+
+// INTERNAL IMPLEMENTATION - DON'T USE IN USER CODE!!!
+#define GMOCK_METHOD10_(tn, constness, ct, Method, ...) \
+ GMOCK_RESULT_(tn, __VA_ARGS__) ct Method( \
+ GMOCK_ARG_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_ARG_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_ARG_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_ARG_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_ARG_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_ARG_(tn, 6, __VA_ARGS__) gmock_a6, \
+ GMOCK_ARG_(tn, 7, __VA_ARGS__) gmock_a7, \
+ GMOCK_ARG_(tn, 8, __VA_ARGS__) gmock_a8, \
+ GMOCK_ARG_(tn, 9, __VA_ARGS__) gmock_a9, \
+ GMOCK_ARG_(tn, 10, __VA_ARGS__) gmock_a10) constness { \
+ GTEST_COMPILE_ASSERT_((::std::tr1::tuple_size< \
+ tn ::testing::internal::Function<__VA_ARGS__>::ArgumentTuple>::value \
+ == 10), \
+ this_method_does_not_take_10_arguments); \
+ GMOCK_MOCKER_(10, constness, Method).SetOwnerAndName(this, #Method); \
+ return GMOCK_MOCKER_(10, constness, Method).Invoke(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6, gmock_a7, gmock_a8, gmock_a9, \
+ gmock_a10); \
+ } \
+ ::testing::MockSpec<__VA_ARGS__>& \
+ gmock_##Method(GMOCK_MATCHER_(tn, 1, __VA_ARGS__) gmock_a1, \
+ GMOCK_MATCHER_(tn, 2, __VA_ARGS__) gmock_a2, \
+ GMOCK_MATCHER_(tn, 3, __VA_ARGS__) gmock_a3, \
+ GMOCK_MATCHER_(tn, 4, __VA_ARGS__) gmock_a4, \
+ GMOCK_MATCHER_(tn, 5, __VA_ARGS__) gmock_a5, \
+ GMOCK_MATCHER_(tn, 6, __VA_ARGS__) gmock_a6, \
+ GMOCK_MATCHER_(tn, 7, __VA_ARGS__) gmock_a7, \
+ GMOCK_MATCHER_(tn, 8, __VA_ARGS__) gmock_a8, \
+ GMOCK_MATCHER_(tn, 9, __VA_ARGS__) gmock_a9, \
+ GMOCK_MATCHER_(tn, 10, \
+ __VA_ARGS__) gmock_a10) constness { \
+ GMOCK_MOCKER_(10, constness, Method).RegisterOwner(this); \
+ return GMOCK_MOCKER_(10, constness, Method).With(gmock_a1, gmock_a2, \
+ gmock_a3, gmock_a4, gmock_a5, gmock_a6, gmock_a7, gmock_a8, gmock_a9, \
+ gmock_a10); \
+ } \
+ mutable ::testing::FunctionMocker<__VA_ARGS__> GMOCK_MOCKER_(10, constness, \
+ Method)
+
+#define MOCK_METHOD0(m, ...) GMOCK_METHOD0_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD1(m, ...) GMOCK_METHOD1_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD2(m, ...) GMOCK_METHOD2_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD3(m, ...) GMOCK_METHOD3_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD4(m, ...) GMOCK_METHOD4_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD5(m, ...) GMOCK_METHOD5_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD6(m, ...) GMOCK_METHOD6_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD7(m, ...) GMOCK_METHOD7_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD8(m, ...) GMOCK_METHOD8_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD9(m, ...) GMOCK_METHOD9_(, , , m, __VA_ARGS__)
+#define MOCK_METHOD10(m, ...) GMOCK_METHOD10_(, , , m, __VA_ARGS__)
+
+#define MOCK_CONST_METHOD0(m, ...) GMOCK_METHOD0_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD1(m, ...) GMOCK_METHOD1_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD2(m, ...) GMOCK_METHOD2_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD3(m, ...) GMOCK_METHOD3_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD4(m, ...) GMOCK_METHOD4_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD5(m, ...) GMOCK_METHOD5_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD6(m, ...) GMOCK_METHOD6_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD7(m, ...) GMOCK_METHOD7_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD8(m, ...) GMOCK_METHOD8_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD9(m, ...) GMOCK_METHOD9_(, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD10(m, ...) GMOCK_METHOD10_(, const, , m, __VA_ARGS__)
+
+#define MOCK_METHOD0_T(m, ...) GMOCK_METHOD0_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD1_T(m, ...) GMOCK_METHOD1_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD2_T(m, ...) GMOCK_METHOD2_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD3_T(m, ...) GMOCK_METHOD3_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD4_T(m, ...) GMOCK_METHOD4_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD5_T(m, ...) GMOCK_METHOD5_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD6_T(m, ...) GMOCK_METHOD6_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD7_T(m, ...) GMOCK_METHOD7_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD8_T(m, ...) GMOCK_METHOD8_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD9_T(m, ...) GMOCK_METHOD9_(typename, , , m, __VA_ARGS__)
+#define MOCK_METHOD10_T(m, ...) GMOCK_METHOD10_(typename, , , m, __VA_ARGS__)
+
+#define MOCK_CONST_METHOD0_T(m, ...) \
+ GMOCK_METHOD0_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD1_T(m, ...) \
+ GMOCK_METHOD1_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD2_T(m, ...) \
+ GMOCK_METHOD2_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD3_T(m, ...) \
+ GMOCK_METHOD3_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD4_T(m, ...) \
+ GMOCK_METHOD4_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD5_T(m, ...) \
+ GMOCK_METHOD5_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD6_T(m, ...) \
+ GMOCK_METHOD6_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD7_T(m, ...) \
+ GMOCK_METHOD7_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD8_T(m, ...) \
+ GMOCK_METHOD8_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD9_T(m, ...) \
+ GMOCK_METHOD9_(typename, const, , m, __VA_ARGS__)
+#define MOCK_CONST_METHOD10_T(m, ...) \
+ GMOCK_METHOD10_(typename, const, , m, __VA_ARGS__)
+
+#define MOCK_METHOD0_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD0_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD1_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD1_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD2_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD2_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD3_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD3_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD4_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD4_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD5_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD5_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD6_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD6_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD7_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD7_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD8_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD8_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD9_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD9_(, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD10_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD10_(, , ct, m, __VA_ARGS__)
+
+#define MOCK_CONST_METHOD0_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD0_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD1_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD1_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD2_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD2_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD3_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD3_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD4_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD4_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD5_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD5_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD6_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD6_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD7_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD7_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD8_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD8_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD9_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD9_(, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD10_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD10_(, const, ct, m, __VA_ARGS__)
+
+#define MOCK_METHOD0_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD0_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD1_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD1_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD2_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD2_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD3_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD3_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD4_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD4_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD5_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD5_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD6_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD6_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD7_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD7_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD8_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD8_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD9_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD9_(typename, , ct, m, __VA_ARGS__)
+#define MOCK_METHOD10_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD10_(typename, , ct, m, __VA_ARGS__)
+
+#define MOCK_CONST_METHOD0_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD0_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD1_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD1_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD2_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD2_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD3_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD3_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD4_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD4_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD5_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD5_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD6_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD6_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD7_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD7_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD8_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD8_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD9_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD9_(typename, const, ct, m, __VA_ARGS__)
+#define MOCK_CONST_METHOD10_T_WITH_CALLTYPE(ct, m, ...) \
+ GMOCK_METHOD10_(typename, const, ct, m, __VA_ARGS__)
+
+// A MockFunction<F> class has one mock method whose type is F. It is
+// useful when you just want your test code to emit some messages and
+// have Google Mock verify the right messages are sent (and perhaps at
+// the right times). For example, if you are exercising code:
+//
+// Foo(1);
+// Foo(2);
+// Foo(3);
+//
+// and want to verify that Foo(1) and Foo(3) both invoke
+// mock.Bar("a"), but Foo(2) doesn't invoke anything, you can write:
+//
+// TEST(FooTest, InvokesBarCorrectly) {
+// MyMock mock;
+// MockFunction<void(string check_point_name)> check;
+// {
+// InSequence s;
+//
+// EXPECT_CALL(mock, Bar("a"));
+// EXPECT_CALL(check, Call("1"));
+// EXPECT_CALL(check, Call("2"));
+// EXPECT_CALL(mock, Bar("a"));
+// }
+// Foo(1);
+// check.Call("1");
+// Foo(2);
+// check.Call("2");
+// Foo(3);
+// }
+//
+// The expectation spec says that the first Bar("a") must happen
+// before check point "1", the second Bar("a") must happen after check
+// point "2", and nothing should happen between the two check
+// points. The explicit check points make it easy to tell which
+// Bar("a") is called by which call to Foo().
+template <typename F>
+class MockFunction;
+
+template <typename R>
+class MockFunction<R()> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD0_T(Call, R());
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0>
+class MockFunction<R(A0)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD1_T(Call, R(A0));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0, typename A1>
+class MockFunction<R(A0, A1)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD2_T(Call, R(A0, A1));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0, typename A1, typename A2>
+class MockFunction<R(A0, A1, A2)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD3_T(Call, R(A0, A1, A2));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0, typename A1, typename A2, typename A3>
+class MockFunction<R(A0, A1, A2, A3)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD4_T(Call, R(A0, A1, A2, A3));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0, typename A1, typename A2, typename A3,
+ typename A4>
+class MockFunction<R(A0, A1, A2, A3, A4)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD5_T(Call, R(A0, A1, A2, A3, A4));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0, typename A1, typename A2, typename A3,
+ typename A4, typename A5>
+class MockFunction<R(A0, A1, A2, A3, A4, A5)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD6_T(Call, R(A0, A1, A2, A3, A4, A5));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0, typename A1, typename A2, typename A3,
+ typename A4, typename A5, typename A6>
+class MockFunction<R(A0, A1, A2, A3, A4, A5, A6)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD7_T(Call, R(A0, A1, A2, A3, A4, A5, A6));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0, typename A1, typename A2, typename A3,
+ typename A4, typename A5, typename A6, typename A7>
+class MockFunction<R(A0, A1, A2, A3, A4, A5, A6, A7)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD8_T(Call, R(A0, A1, A2, A3, A4, A5, A6, A7));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0, typename A1, typename A2, typename A3,
+ typename A4, typename A5, typename A6, typename A7, typename A8>
+class MockFunction<R(A0, A1, A2, A3, A4, A5, A6, A7, A8)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD9_T(Call, R(A0, A1, A2, A3, A4, A5, A6, A7, A8));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+template <typename R, typename A0, typename A1, typename A2, typename A3,
+ typename A4, typename A5, typename A6, typename A7, typename A8,
+ typename A9>
+class MockFunction<R(A0, A1, A2, A3, A4, A5, A6, A7, A8, A9)> {
+ public:
+ MockFunction() {}
+
+ MOCK_METHOD10_T(Call, R(A0, A1, A2, A3, A4, A5, A6, A7, A8, A9));
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(MockFunction);
+};
+
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_FUNCTION_MOCKERS_H_
+// This file was GENERATED by command:
+// pump.py gmock-generated-nice-strict.h.pump
+// DO NOT EDIT BY HAND!!!
+
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Implements class templates NiceMock, NaggyMock, and StrictMock.
+//
+// Given a mock class MockFoo that is created using Google Mock,
+// NiceMock<MockFoo> is a subclass of MockFoo that allows
+// uninteresting calls (i.e. calls to mock methods that have no
+// EXPECT_CALL specs), NaggyMock<MockFoo> is a subclass of MockFoo
+// that prints a warning when an uninteresting call occurs, and
+// StrictMock<MockFoo> is a subclass of MockFoo that treats all
+// uninteresting calls as errors.
+//
+// Currently a mock is naggy by default, so MockFoo and
+// NaggyMock<MockFoo> behave like the same. However, we will soon
+// switch the default behavior of mocks to be nice, as that in general
+// leads to more maintainable tests. When that happens, MockFoo will
+// stop behaving like NaggyMock<MockFoo> and start behaving like
+// NiceMock<MockFoo>.
+//
+// NiceMock, NaggyMock, and StrictMock "inherit" the constructors of
+// their respective base class, with up-to 10 arguments. Therefore
+// you can write NiceMock<MockFoo>(5, "a") to construct a nice mock
+// where MockFoo has a constructor that accepts (int, const char*),
+// for example.
+//
+// A known limitation is that NiceMock<MockFoo>, NaggyMock<MockFoo>,
+// and StrictMock<MockFoo> only works for mock methods defined using
+// the MOCK_METHOD* family of macros DIRECTLY in the MockFoo class.
+// If a mock method is defined in a base class of MockFoo, the "nice"
+// or "strict" modifier may not affect it, depending on the compiler.
+// In particular, nesting NiceMock, NaggyMock, and StrictMock is NOT
+// supported.
+//
+// Another known limitation is that the constructors of the base mock
+// cannot have arguments passed by non-const reference, which are
+// banned by the Google C++ style guide anyway.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_NICE_STRICT_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_NICE_STRICT_H_
+
+
+namespace testing {
+
+template <class MockClass>
+class NiceMock : public MockClass {
+ public:
+ // We don't factor out the constructor body to a common method, as
+ // we have to avoid a possible clash with members of MockClass.
+ NiceMock() {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ // C++ doesn't (yet) allow inheritance of constructors, so we have
+ // to define it for each arity.
+ template <typename A1>
+ explicit NiceMock(const A1& a1) : MockClass(a1) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+ template <typename A1, typename A2>
+ NiceMock(const A1& a1, const A2& a2) : MockClass(a1, a2) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3>
+ NiceMock(const A1& a1, const A2& a2, const A3& a3) : MockClass(a1, a2, a3) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4>
+ NiceMock(const A1& a1, const A2& a2, const A3& a3,
+ const A4& a4) : MockClass(a1, a2, a3, a4) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5>
+ NiceMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5) : MockClass(a1, a2, a3, a4, a5) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6>
+ NiceMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6) : MockClass(a1, a2, a3, a4, a5, a6) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7>
+ NiceMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7) : MockClass(a1, a2, a3, a4, a5,
+ a6, a7) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8>
+ NiceMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7, const A8& a8) : MockClass(a1,
+ a2, a3, a4, a5, a6, a7, a8) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8, typename A9>
+ NiceMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7, const A8& a8,
+ const A9& a9) : MockClass(a1, a2, a3, a4, a5, a6, a7, a8, a9) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8, typename A9, typename A10>
+ NiceMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7, const A8& a8, const A9& a9,
+ const A10& a10) : MockClass(a1, a2, a3, a4, a5, a6, a7, a8, a9, a10) {
+ ::testing::Mock::AllowUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ virtual ~NiceMock() {
+ ::testing::Mock::UnregisterCallReaction(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(NiceMock);
+};
+
+template <class MockClass>
+class NaggyMock : public MockClass {
+ public:
+ // We don't factor out the constructor body to a common method, as
+ // we have to avoid a possible clash with members of MockClass.
+ NaggyMock() {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ // C++ doesn't (yet) allow inheritance of constructors, so we have
+ // to define it for each arity.
+ template <typename A1>
+ explicit NaggyMock(const A1& a1) : MockClass(a1) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+ template <typename A1, typename A2>
+ NaggyMock(const A1& a1, const A2& a2) : MockClass(a1, a2) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3>
+ NaggyMock(const A1& a1, const A2& a2, const A3& a3) : MockClass(a1, a2, a3) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4>
+ NaggyMock(const A1& a1, const A2& a2, const A3& a3,
+ const A4& a4) : MockClass(a1, a2, a3, a4) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5>
+ NaggyMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5) : MockClass(a1, a2, a3, a4, a5) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6>
+ NaggyMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6) : MockClass(a1, a2, a3, a4, a5, a6) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7>
+ NaggyMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7) : MockClass(a1, a2, a3, a4, a5,
+ a6, a7) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8>
+ NaggyMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7, const A8& a8) : MockClass(a1,
+ a2, a3, a4, a5, a6, a7, a8) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8, typename A9>
+ NaggyMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7, const A8& a8,
+ const A9& a9) : MockClass(a1, a2, a3, a4, a5, a6, a7, a8, a9) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8, typename A9, typename A10>
+ NaggyMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7, const A8& a8, const A9& a9,
+ const A10& a10) : MockClass(a1, a2, a3, a4, a5, a6, a7, a8, a9, a10) {
+ ::testing::Mock::WarnUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ virtual ~NaggyMock() {
+ ::testing::Mock::UnregisterCallReaction(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(NaggyMock);
+};
+
+template <class MockClass>
+class StrictMock : public MockClass {
+ public:
+ // We don't factor out the constructor body to a common method, as
+ // we have to avoid a possible clash with members of MockClass.
+ StrictMock() {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ // C++ doesn't (yet) allow inheritance of constructors, so we have
+ // to define it for each arity.
+ template <typename A1>
+ explicit StrictMock(const A1& a1) : MockClass(a1) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+ template <typename A1, typename A2>
+ StrictMock(const A1& a1, const A2& a2) : MockClass(a1, a2) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3>
+ StrictMock(const A1& a1, const A2& a2, const A3& a3) : MockClass(a1, a2, a3) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4>
+ StrictMock(const A1& a1, const A2& a2, const A3& a3,
+ const A4& a4) : MockClass(a1, a2, a3, a4) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5>
+ StrictMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5) : MockClass(a1, a2, a3, a4, a5) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6>
+ StrictMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6) : MockClass(a1, a2, a3, a4, a5, a6) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7>
+ StrictMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7) : MockClass(a1, a2, a3, a4, a5,
+ a6, a7) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8>
+ StrictMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7, const A8& a8) : MockClass(a1,
+ a2, a3, a4, a5, a6, a7, a8) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8, typename A9>
+ StrictMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7, const A8& a8,
+ const A9& a9) : MockClass(a1, a2, a3, a4, a5, a6, a7, a8, a9) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ template <typename A1, typename A2, typename A3, typename A4, typename A5,
+ typename A6, typename A7, typename A8, typename A9, typename A10>
+ StrictMock(const A1& a1, const A2& a2, const A3& a3, const A4& a4,
+ const A5& a5, const A6& a6, const A7& a7, const A8& a8, const A9& a9,
+ const A10& a10) : MockClass(a1, a2, a3, a4, a5, a6, a7, a8, a9, a10) {
+ ::testing::Mock::FailUninterestingCalls(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ virtual ~StrictMock() {
+ ::testing::Mock::UnregisterCallReaction(
+ internal::ImplicitCast_<MockClass*>(this));
+ }
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(StrictMock);
+};
+
+// The following specializations catch some (relatively more common)
+// user errors of nesting nice and strict mocks. They do NOT catch
+// all possible errors.
+
+// These specializations are declared but not defined, as NiceMock,
+// NaggyMock, and StrictMock cannot be nested.
+
+template <typename MockClass>
+class NiceMock<NiceMock<MockClass> >;
+template <typename MockClass>
+class NiceMock<NaggyMock<MockClass> >;
+template <typename MockClass>
+class NiceMock<StrictMock<MockClass> >;
+
+template <typename MockClass>
+class NaggyMock<NiceMock<MockClass> >;
+template <typename MockClass>
+class NaggyMock<NaggyMock<MockClass> >;
+template <typename MockClass>
+class NaggyMock<StrictMock<MockClass> >;
+
+template <typename MockClass>
+class StrictMock<NiceMock<MockClass> >;
+template <typename MockClass>
+class StrictMock<NaggyMock<MockClass> >;
+template <typename MockClass>
+class StrictMock<StrictMock<MockClass> >;
+
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_NICE_STRICT_H_
+// This file was GENERATED by command:
+// pump.py gmock-generated-matchers.h.pump
+// DO NOT EDIT BY HAND!!!
+
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements some commonly used variadic matchers.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_MATCHERS_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_MATCHERS_H_
+
+#include <iterator>
+#include <sstream>
+#include <string>
+#include <vector>
+
+namespace testing {
+namespace internal {
+
+// The type of the i-th (0-based) field of Tuple.
+#define GMOCK_FIELD_TYPE_(Tuple, i) \
+ typename ::std::tr1::tuple_element<i, Tuple>::type
+
+// TupleFields<Tuple, k0, ..., kn> is for selecting fields from a
+// tuple of type Tuple. It has two members:
+//
+// type: a tuple type whose i-th field is the ki-th field of Tuple.
+// GetSelectedFields(t): returns fields k0, ..., and kn of t as a tuple.
+//
+// For example, in class TupleFields<tuple<bool, char, int>, 2, 0>, we have:
+//
+// type is tuple<int, bool>, and
+// GetSelectedFields(make_tuple(true, 'a', 42)) is (42, true).
+
+template <class Tuple, int k0 = -1, int k1 = -1, int k2 = -1, int k3 = -1,
+ int k4 = -1, int k5 = -1, int k6 = -1, int k7 = -1, int k8 = -1,
+ int k9 = -1>
+class TupleFields;
+
+// This generic version is used when there are 10 selectors.
+template <class Tuple, int k0, int k1, int k2, int k3, int k4, int k5, int k6,
+ int k7, int k8, int k9>
+class TupleFields {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0),
+ GMOCK_FIELD_TYPE_(Tuple, k1), GMOCK_FIELD_TYPE_(Tuple, k2),
+ GMOCK_FIELD_TYPE_(Tuple, k3), GMOCK_FIELD_TYPE_(Tuple, k4),
+ GMOCK_FIELD_TYPE_(Tuple, k5), GMOCK_FIELD_TYPE_(Tuple, k6),
+ GMOCK_FIELD_TYPE_(Tuple, k7), GMOCK_FIELD_TYPE_(Tuple, k8),
+ GMOCK_FIELD_TYPE_(Tuple, k9)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t), get<k1>(t), get<k2>(t), get<k3>(t), get<k4>(t),
+ get<k5>(t), get<k6>(t), get<k7>(t), get<k8>(t), get<k9>(t));
+ }
+};
+
+// The following specialization is used for 0 ~ 9 selectors.
+
+template <class Tuple>
+class TupleFields<Tuple, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef ::std::tr1::tuple<> type;
+ static type GetSelectedFields(const Tuple& /* t */) {
+ using ::std::tr1::get;
+ return type();
+ }
+};
+
+template <class Tuple, int k0>
+class TupleFields<Tuple, k0, -1, -1, -1, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t));
+ }
+};
+
+template <class Tuple, int k0, int k1>
+class TupleFields<Tuple, k0, k1, -1, -1, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0),
+ GMOCK_FIELD_TYPE_(Tuple, k1)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t), get<k1>(t));
+ }
+};
+
+template <class Tuple, int k0, int k1, int k2>
+class TupleFields<Tuple, k0, k1, k2, -1, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0),
+ GMOCK_FIELD_TYPE_(Tuple, k1), GMOCK_FIELD_TYPE_(Tuple, k2)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t), get<k1>(t), get<k2>(t));
+ }
+};
+
+template <class Tuple, int k0, int k1, int k2, int k3>
+class TupleFields<Tuple, k0, k1, k2, k3, -1, -1, -1, -1, -1, -1> {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0),
+ GMOCK_FIELD_TYPE_(Tuple, k1), GMOCK_FIELD_TYPE_(Tuple, k2),
+ GMOCK_FIELD_TYPE_(Tuple, k3)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t), get<k1>(t), get<k2>(t), get<k3>(t));
+ }
+};
+
+template <class Tuple, int k0, int k1, int k2, int k3, int k4>
+class TupleFields<Tuple, k0, k1, k2, k3, k4, -1, -1, -1, -1, -1> {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0),
+ GMOCK_FIELD_TYPE_(Tuple, k1), GMOCK_FIELD_TYPE_(Tuple, k2),
+ GMOCK_FIELD_TYPE_(Tuple, k3), GMOCK_FIELD_TYPE_(Tuple, k4)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t), get<k1>(t), get<k2>(t), get<k3>(t), get<k4>(t));
+ }
+};
+
+template <class Tuple, int k0, int k1, int k2, int k3, int k4, int k5>
+class TupleFields<Tuple, k0, k1, k2, k3, k4, k5, -1, -1, -1, -1> {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0),
+ GMOCK_FIELD_TYPE_(Tuple, k1), GMOCK_FIELD_TYPE_(Tuple, k2),
+ GMOCK_FIELD_TYPE_(Tuple, k3), GMOCK_FIELD_TYPE_(Tuple, k4),
+ GMOCK_FIELD_TYPE_(Tuple, k5)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t), get<k1>(t), get<k2>(t), get<k3>(t), get<k4>(t),
+ get<k5>(t));
+ }
+};
+
+template <class Tuple, int k0, int k1, int k2, int k3, int k4, int k5, int k6>
+class TupleFields<Tuple, k0, k1, k2, k3, k4, k5, k6, -1, -1, -1> {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0),
+ GMOCK_FIELD_TYPE_(Tuple, k1), GMOCK_FIELD_TYPE_(Tuple, k2),
+ GMOCK_FIELD_TYPE_(Tuple, k3), GMOCK_FIELD_TYPE_(Tuple, k4),
+ GMOCK_FIELD_TYPE_(Tuple, k5), GMOCK_FIELD_TYPE_(Tuple, k6)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t), get<k1>(t), get<k2>(t), get<k3>(t), get<k4>(t),
+ get<k5>(t), get<k6>(t));
+ }
+};
+
+template <class Tuple, int k0, int k1, int k2, int k3, int k4, int k5, int k6,
+ int k7>
+class TupleFields<Tuple, k0, k1, k2, k3, k4, k5, k6, k7, -1, -1> {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0),
+ GMOCK_FIELD_TYPE_(Tuple, k1), GMOCK_FIELD_TYPE_(Tuple, k2),
+ GMOCK_FIELD_TYPE_(Tuple, k3), GMOCK_FIELD_TYPE_(Tuple, k4),
+ GMOCK_FIELD_TYPE_(Tuple, k5), GMOCK_FIELD_TYPE_(Tuple, k6),
+ GMOCK_FIELD_TYPE_(Tuple, k7)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t), get<k1>(t), get<k2>(t), get<k3>(t), get<k4>(t),
+ get<k5>(t), get<k6>(t), get<k7>(t));
+ }
+};
+
+template <class Tuple, int k0, int k1, int k2, int k3, int k4, int k5, int k6,
+ int k7, int k8>
+class TupleFields<Tuple, k0, k1, k2, k3, k4, k5, k6, k7, k8, -1> {
+ public:
+ typedef ::std::tr1::tuple<GMOCK_FIELD_TYPE_(Tuple, k0),
+ GMOCK_FIELD_TYPE_(Tuple, k1), GMOCK_FIELD_TYPE_(Tuple, k2),
+ GMOCK_FIELD_TYPE_(Tuple, k3), GMOCK_FIELD_TYPE_(Tuple, k4),
+ GMOCK_FIELD_TYPE_(Tuple, k5), GMOCK_FIELD_TYPE_(Tuple, k6),
+ GMOCK_FIELD_TYPE_(Tuple, k7), GMOCK_FIELD_TYPE_(Tuple, k8)> type;
+ static type GetSelectedFields(const Tuple& t) {
+ using ::std::tr1::get;
+ return type(get<k0>(t), get<k1>(t), get<k2>(t), get<k3>(t), get<k4>(t),
+ get<k5>(t), get<k6>(t), get<k7>(t), get<k8>(t));
+ }
+};
+
+#undef GMOCK_FIELD_TYPE_
+
+// Implements the Args() matcher.
+template <class ArgsTuple, int k0 = -1, int k1 = -1, int k2 = -1, int k3 = -1,
+ int k4 = -1, int k5 = -1, int k6 = -1, int k7 = -1, int k8 = -1,
+ int k9 = -1>
+class ArgsMatcherImpl : public MatcherInterface<ArgsTuple> {
+ public:
+ // ArgsTuple may have top-level const or reference modifiers.
+ typedef GTEST_REMOVE_REFERENCE_AND_CONST_(ArgsTuple) RawArgsTuple;
+ typedef typename internal::TupleFields<RawArgsTuple, k0, k1, k2, k3, k4, k5,
+ k6, k7, k8, k9>::type SelectedArgs;
+ typedef Matcher<const SelectedArgs&> MonomorphicInnerMatcher;
+
+ template <typename InnerMatcher>
+ explicit ArgsMatcherImpl(const InnerMatcher& inner_matcher)
+ : inner_matcher_(SafeMatcherCast<const SelectedArgs&>(inner_matcher)) {}
+
+ virtual bool MatchAndExplain(ArgsTuple args,
+ MatchResultListener* listener) const {
+ const SelectedArgs& selected_args = GetSelectedArgs(args);
+ if (!listener->IsInterested())
+ return inner_matcher_.Matches(selected_args);
+
+ PrintIndices(listener->stream());
+ *listener << "are " << PrintToString(selected_args);
+
+ StringMatchResultListener inner_listener;
+ const bool match = inner_matcher_.MatchAndExplain(selected_args,
+ &inner_listener);
+ PrintIfNotEmpty(inner_listener.str(), listener->stream());
+ return match;
+ }
+
+ virtual void DescribeTo(::std::ostream* os) const {
+ *os << "are a tuple ";
+ PrintIndices(os);
+ inner_matcher_.DescribeTo(os);
+ }
+
+ virtual void DescribeNegationTo(::std::ostream* os) const {
+ *os << "are a tuple ";
+ PrintIndices(os);
+ inner_matcher_.DescribeNegationTo(os);
+ }
+
+ private:
+ static SelectedArgs GetSelectedArgs(ArgsTuple args) {
+ return TupleFields<RawArgsTuple, k0, k1, k2, k3, k4, k5, k6, k7, k8,
+ k9>::GetSelectedFields(args);
+ }
+
+ // Prints the indices of the selected fields.
+ static void PrintIndices(::std::ostream* os) {
+ *os << "whose fields (";
+ const int indices[10] = { k0, k1, k2, k3, k4, k5, k6, k7, k8, k9 };
+ for (int i = 0; i < 10; i++) {
+ if (indices[i] < 0)
+ break;
+
+ if (i >= 1)
+ *os << ", ";
+
+ *os << "#" << indices[i];
+ }
+ *os << ") ";
+ }
+
+ const MonomorphicInnerMatcher inner_matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(ArgsMatcherImpl);
+};
+
+template <class InnerMatcher, int k0 = -1, int k1 = -1, int k2 = -1,
+ int k3 = -1, int k4 = -1, int k5 = -1, int k6 = -1, int k7 = -1,
+ int k8 = -1, int k9 = -1>
+class ArgsMatcher {
+ public:
+ explicit ArgsMatcher(const InnerMatcher& inner_matcher)
+ : inner_matcher_(inner_matcher) {}
+
+ template <typename ArgsTuple>
+ operator Matcher<ArgsTuple>() const {
+ return MakeMatcher(new ArgsMatcherImpl<ArgsTuple, k0, k1, k2, k3, k4, k5,
+ k6, k7, k8, k9>(inner_matcher_));
+ }
+
+ private:
+ const InnerMatcher inner_matcher_;
+
+ GTEST_DISALLOW_ASSIGN_(ArgsMatcher);
+};
+
+// A set of metafunctions for computing the result type of AllOf.
+// AllOf(m1, ..., mN) returns
+// AllOfResultN<decltype(m1), ..., decltype(mN)>::type.
+
+// Although AllOf isn't defined for one argument, AllOfResult1 is defined
+// to simplify the implementation.
+template <typename M1>
+struct AllOfResult1 {
+ typedef M1 type;
+};
+
+template <typename M1, typename M2>
+struct AllOfResult2 {
+ typedef BothOfMatcher<
+ typename AllOfResult1<M1>::type,
+ typename AllOfResult1<M2>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3>
+struct AllOfResult3 {
+ typedef BothOfMatcher<
+ typename AllOfResult1<M1>::type,
+ typename AllOfResult2<M2, M3>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4>
+struct AllOfResult4 {
+ typedef BothOfMatcher<
+ typename AllOfResult2<M1, M2>::type,
+ typename AllOfResult2<M3, M4>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5>
+struct AllOfResult5 {
+ typedef BothOfMatcher<
+ typename AllOfResult2<M1, M2>::type,
+ typename AllOfResult3<M3, M4, M5>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6>
+struct AllOfResult6 {
+ typedef BothOfMatcher<
+ typename AllOfResult3<M1, M2, M3>::type,
+ typename AllOfResult3<M4, M5, M6>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7>
+struct AllOfResult7 {
+ typedef BothOfMatcher<
+ typename AllOfResult3<M1, M2, M3>::type,
+ typename AllOfResult4<M4, M5, M6, M7>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8>
+struct AllOfResult8 {
+ typedef BothOfMatcher<
+ typename AllOfResult4<M1, M2, M3, M4>::type,
+ typename AllOfResult4<M5, M6, M7, M8>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8, typename M9>
+struct AllOfResult9 {
+ typedef BothOfMatcher<
+ typename AllOfResult4<M1, M2, M3, M4>::type,
+ typename AllOfResult5<M5, M6, M7, M8, M9>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8, typename M9, typename M10>
+struct AllOfResult10 {
+ typedef BothOfMatcher<
+ typename AllOfResult5<M1, M2, M3, M4, M5>::type,
+ typename AllOfResult5<M6, M7, M8, M9, M10>::type
+ > type;
+};
+
+// A set of metafunctions for computing the result type of AnyOf.
+// AnyOf(m1, ..., mN) returns
+// AnyOfResultN<decltype(m1), ..., decltype(mN)>::type.
+
+// Although AnyOf isn't defined for one argument, AnyOfResult1 is defined
+// to simplify the implementation.
+template <typename M1>
+struct AnyOfResult1 {
+ typedef M1 type;
+};
+
+template <typename M1, typename M2>
+struct AnyOfResult2 {
+ typedef EitherOfMatcher<
+ typename AnyOfResult1<M1>::type,
+ typename AnyOfResult1<M2>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3>
+struct AnyOfResult3 {
+ typedef EitherOfMatcher<
+ typename AnyOfResult1<M1>::type,
+ typename AnyOfResult2<M2, M3>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4>
+struct AnyOfResult4 {
+ typedef EitherOfMatcher<
+ typename AnyOfResult2<M1, M2>::type,
+ typename AnyOfResult2<M3, M4>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5>
+struct AnyOfResult5 {
+ typedef EitherOfMatcher<
+ typename AnyOfResult2<M1, M2>::type,
+ typename AnyOfResult3<M3, M4, M5>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6>
+struct AnyOfResult6 {
+ typedef EitherOfMatcher<
+ typename AnyOfResult3<M1, M2, M3>::type,
+ typename AnyOfResult3<M4, M5, M6>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7>
+struct AnyOfResult7 {
+ typedef EitherOfMatcher<
+ typename AnyOfResult3<M1, M2, M3>::type,
+ typename AnyOfResult4<M4, M5, M6, M7>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8>
+struct AnyOfResult8 {
+ typedef EitherOfMatcher<
+ typename AnyOfResult4<M1, M2, M3, M4>::type,
+ typename AnyOfResult4<M5, M6, M7, M8>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8, typename M9>
+struct AnyOfResult9 {
+ typedef EitherOfMatcher<
+ typename AnyOfResult4<M1, M2, M3, M4>::type,
+ typename AnyOfResult5<M5, M6, M7, M8, M9>::type
+ > type;
+};
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8, typename M9, typename M10>
+struct AnyOfResult10 {
+ typedef EitherOfMatcher<
+ typename AnyOfResult5<M1, M2, M3, M4, M5>::type,
+ typename AnyOfResult5<M6, M7, M8, M9, M10>::type
+ > type;
+};
+
+} // namespace internal
+
+// Args<N1, N2, ..., Nk>(a_matcher) matches a tuple if the selected
+// fields of it matches a_matcher. C++ doesn't support default
+// arguments for function templates, so we have to overload it.
+template <typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher>(matcher);
+}
+
+template <int k1, typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1>(matcher);
+}
+
+template <int k1, int k2, typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1, k2>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1, k2>(matcher);
+}
+
+template <int k1, int k2, int k3, typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1, k2, k3>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1, k2, k3>(matcher);
+}
+
+template <int k1, int k2, int k3, int k4, typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4>(matcher);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5>(matcher);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6>(matcher);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, int k7,
+ typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6, k7>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6,
+ k7>(matcher);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, int k7, int k8,
+ typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6, k7, k8>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6, k7,
+ k8>(matcher);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, int k7, int k8,
+ int k9, typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6, k7, k8, k9>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6, k7, k8,
+ k9>(matcher);
+}
+
+template <int k1, int k2, int k3, int k4, int k5, int k6, int k7, int k8,
+ int k9, int k10, typename InnerMatcher>
+inline internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6, k7, k8, k9,
+ k10>
+Args(const InnerMatcher& matcher) {
+ return internal::ArgsMatcher<InnerMatcher, k1, k2, k3, k4, k5, k6, k7, k8,
+ k9, k10>(matcher);
+}
+
+// ElementsAre(e_1, e_2, ... e_n) matches an STL-style container with
+// n elements, where the i-th element in the container must
+// match the i-th argument in the list. Each argument of
+// ElementsAre() can be either a value or a matcher. We support up to
+// 10 arguments.
+//
+// The use of DecayArray in the implementation allows ElementsAre()
+// to accept string literals, whose type is const char[N], but we
+// want to treat them as const char*.
+//
+// NOTE: Since ElementsAre() cares about the order of the elements, it
+// must not be used with containers whose elements's order is
+// undefined (e.g. hash_map).
+
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<> >
+ElementsAre() {
+ typedef std::tr1::tuple<> Args;
+ return internal::ElementsAreMatcher<Args>(Args());
+}
+
+template <typename T1>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type> >
+ElementsAre(const T1& e1) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1));
+}
+
+template <typename T1, typename T2>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type> >
+ElementsAre(const T1& e1, const T2& e2) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1, e2));
+}
+
+template <typename T1, typename T2, typename T3>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type> >
+ElementsAre(const T1& e1, const T2& e2, const T3& e3) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1, e2, e3));
+}
+
+template <typename T1, typename T2, typename T3, typename T4>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type> >
+ElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1, e2, e3, e4));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type> >
+ElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type> >
+ElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5, e6));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type> >
+ElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6, const T7& e7) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5, e6, e7));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type> >
+ElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6, const T7& e7, const T8& e8) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5, e6, e7,
+ e8));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type,
+ typename internal::DecayArray<T9>::type> >
+ElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6, const T7& e7, const T8& e8, const T9& e9) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type,
+ typename internal::DecayArray<T9>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5, e6, e7,
+ e8, e9));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10>
+inline internal::ElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type,
+ typename internal::DecayArray<T9>::type,
+ typename internal::DecayArray<T10>::type> >
+ElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6, const T7& e7, const T8& e8, const T9& e9,
+ const T10& e10) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type,
+ typename internal::DecayArray<T9>::type,
+ typename internal::DecayArray<T10>::type> Args;
+ return internal::ElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5, e6, e7,
+ e8, e9, e10));
+}
+
+// UnorderedElementsAre(e_1, e_2, ..., e_n) is an ElementsAre extension
+// that matches n elements in any order. We support up to n=10 arguments.
+
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<> >
+UnorderedElementsAre() {
+ typedef std::tr1::tuple<> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args());
+}
+
+template <typename T1>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type> >
+UnorderedElementsAre(const T1& e1) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1));
+}
+
+template <typename T1, typename T2>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type> >
+UnorderedElementsAre(const T1& e1, const T2& e2) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1, e2));
+}
+
+template <typename T1, typename T2, typename T3>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type> >
+UnorderedElementsAre(const T1& e1, const T2& e2, const T3& e3) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1, e2, e3));
+}
+
+template <typename T1, typename T2, typename T3, typename T4>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type> >
+UnorderedElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1, e2, e3, e4));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type> >
+UnorderedElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type> >
+UnorderedElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5,
+ e6));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type> >
+UnorderedElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6, const T7& e7) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5,
+ e6, e7));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type> >
+UnorderedElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6, const T7& e7, const T8& e8) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5,
+ e6, e7, e8));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type,
+ typename internal::DecayArray<T9>::type> >
+UnorderedElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6, const T7& e7, const T8& e8, const T9& e9) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type,
+ typename internal::DecayArray<T9>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5,
+ e6, e7, e8, e9));
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10>
+inline internal::UnorderedElementsAreMatcher<
+ std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type,
+ typename internal::DecayArray<T9>::type,
+ typename internal::DecayArray<T10>::type> >
+UnorderedElementsAre(const T1& e1, const T2& e2, const T3& e3, const T4& e4,
+ const T5& e5, const T6& e6, const T7& e7, const T8& e8, const T9& e9,
+ const T10& e10) {
+ typedef std::tr1::tuple<
+ typename internal::DecayArray<T1>::type,
+ typename internal::DecayArray<T2>::type,
+ typename internal::DecayArray<T3>::type,
+ typename internal::DecayArray<T4>::type,
+ typename internal::DecayArray<T5>::type,
+ typename internal::DecayArray<T6>::type,
+ typename internal::DecayArray<T7>::type,
+ typename internal::DecayArray<T8>::type,
+ typename internal::DecayArray<T9>::type,
+ typename internal::DecayArray<T10>::type> Args;
+ return internal::UnorderedElementsAreMatcher<Args>(Args(e1, e2, e3, e4, e5,
+ e6, e7, e8, e9, e10));
+}
+
+// AllOf(m1, m2, ..., mk) matches any value that matches all of the given
+// sub-matchers. AllOf is called fully qualified to prevent ADL from firing.
+
+template <typename M1, typename M2>
+inline typename internal::AllOfResult2<M1, M2>::type
+AllOf(M1 m1, M2 m2) {
+ return typename internal::AllOfResult2<M1, M2>::type(
+ m1,
+ m2);
+}
+
+template <typename M1, typename M2, typename M3>
+inline typename internal::AllOfResult3<M1, M2, M3>::type
+AllOf(M1 m1, M2 m2, M3 m3) {
+ return typename internal::AllOfResult3<M1, M2, M3>::type(
+ m1,
+ ::testing::AllOf(m2, m3));
+}
+
+template <typename M1, typename M2, typename M3, typename M4>
+inline typename internal::AllOfResult4<M1, M2, M3, M4>::type
+AllOf(M1 m1, M2 m2, M3 m3, M4 m4) {
+ return typename internal::AllOfResult4<M1, M2, M3, M4>::type(
+ ::testing::AllOf(m1, m2),
+ ::testing::AllOf(m3, m4));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5>
+inline typename internal::AllOfResult5<M1, M2, M3, M4, M5>::type
+AllOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5) {
+ return typename internal::AllOfResult5<M1, M2, M3, M4, M5>::type(
+ ::testing::AllOf(m1, m2),
+ ::testing::AllOf(m3, m4, m5));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6>
+inline typename internal::AllOfResult6<M1, M2, M3, M4, M5, M6>::type
+AllOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6) {
+ return typename internal::AllOfResult6<M1, M2, M3, M4, M5, M6>::type(
+ ::testing::AllOf(m1, m2, m3),
+ ::testing::AllOf(m4, m5, m6));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7>
+inline typename internal::AllOfResult7<M1, M2, M3, M4, M5, M6, M7>::type
+AllOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6, M7 m7) {
+ return typename internal::AllOfResult7<M1, M2, M3, M4, M5, M6, M7>::type(
+ ::testing::AllOf(m1, m2, m3),
+ ::testing::AllOf(m4, m5, m6, m7));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8>
+inline typename internal::AllOfResult8<M1, M2, M3, M4, M5, M6, M7, M8>::type
+AllOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6, M7 m7, M8 m8) {
+ return typename internal::AllOfResult8<M1, M2, M3, M4, M5, M6, M7, M8>::type(
+ ::testing::AllOf(m1, m2, m3, m4),
+ ::testing::AllOf(m5, m6, m7, m8));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8, typename M9>
+inline typename internal::AllOfResult9<M1, M2, M3, M4, M5, M6, M7, M8, M9>::type
+AllOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6, M7 m7, M8 m8, M9 m9) {
+ return typename internal::AllOfResult9<M1, M2, M3, M4, M5, M6, M7, M8,
+ M9>::type(
+ ::testing::AllOf(m1, m2, m3, m4),
+ ::testing::AllOf(m5, m6, m7, m8, m9));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8, typename M9, typename M10>
+inline typename internal::AllOfResult10<M1, M2, M3, M4, M5, M6, M7, M8, M9,
+ M10>::type
+AllOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6, M7 m7, M8 m8, M9 m9, M10 m10) {
+ return typename internal::AllOfResult10<M1, M2, M3, M4, M5, M6, M7, M8, M9,
+ M10>::type(
+ ::testing::AllOf(m1, m2, m3, m4, m5),
+ ::testing::AllOf(m6, m7, m8, m9, m10));
+}
+
+// AnyOf(m1, m2, ..., mk) matches any value that matches any of the given
+// sub-matchers. AnyOf is called fully qualified to prevent ADL from firing.
+
+template <typename M1, typename M2>
+inline typename internal::AnyOfResult2<M1, M2>::type
+AnyOf(M1 m1, M2 m2) {
+ return typename internal::AnyOfResult2<M1, M2>::type(
+ m1,
+ m2);
+}
+
+template <typename M1, typename M2, typename M3>
+inline typename internal::AnyOfResult3<M1, M2, M3>::type
+AnyOf(M1 m1, M2 m2, M3 m3) {
+ return typename internal::AnyOfResult3<M1, M2, M3>::type(
+ m1,
+ ::testing::AnyOf(m2, m3));
+}
+
+template <typename M1, typename M2, typename M3, typename M4>
+inline typename internal::AnyOfResult4<M1, M2, M3, M4>::type
+AnyOf(M1 m1, M2 m2, M3 m3, M4 m4) {
+ return typename internal::AnyOfResult4<M1, M2, M3, M4>::type(
+ ::testing::AnyOf(m1, m2),
+ ::testing::AnyOf(m3, m4));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5>
+inline typename internal::AnyOfResult5<M1, M2, M3, M4, M5>::type
+AnyOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5) {
+ return typename internal::AnyOfResult5<M1, M2, M3, M4, M5>::type(
+ ::testing::AnyOf(m1, m2),
+ ::testing::AnyOf(m3, m4, m5));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6>
+inline typename internal::AnyOfResult6<M1, M2, M3, M4, M5, M6>::type
+AnyOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6) {
+ return typename internal::AnyOfResult6<M1, M2, M3, M4, M5, M6>::type(
+ ::testing::AnyOf(m1, m2, m3),
+ ::testing::AnyOf(m4, m5, m6));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7>
+inline typename internal::AnyOfResult7<M1, M2, M3, M4, M5, M6, M7>::type
+AnyOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6, M7 m7) {
+ return typename internal::AnyOfResult7<M1, M2, M3, M4, M5, M6, M7>::type(
+ ::testing::AnyOf(m1, m2, m3),
+ ::testing::AnyOf(m4, m5, m6, m7));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8>
+inline typename internal::AnyOfResult8<M1, M2, M3, M4, M5, M6, M7, M8>::type
+AnyOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6, M7 m7, M8 m8) {
+ return typename internal::AnyOfResult8<M1, M2, M3, M4, M5, M6, M7, M8>::type(
+ ::testing::AnyOf(m1, m2, m3, m4),
+ ::testing::AnyOf(m5, m6, m7, m8));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8, typename M9>
+inline typename internal::AnyOfResult9<M1, M2, M3, M4, M5, M6, M7, M8, M9>::type
+AnyOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6, M7 m7, M8 m8, M9 m9) {
+ return typename internal::AnyOfResult9<M1, M2, M3, M4, M5, M6, M7, M8,
+ M9>::type(
+ ::testing::AnyOf(m1, m2, m3, m4),
+ ::testing::AnyOf(m5, m6, m7, m8, m9));
+}
+
+template <typename M1, typename M2, typename M3, typename M4, typename M5,
+ typename M6, typename M7, typename M8, typename M9, typename M10>
+inline typename internal::AnyOfResult10<M1, M2, M3, M4, M5, M6, M7, M8, M9,
+ M10>::type
+AnyOf(M1 m1, M2 m2, M3 m3, M4 m4, M5 m5, M6 m6, M7 m7, M8 m8, M9 m9, M10 m10) {
+ return typename internal::AnyOfResult10<M1, M2, M3, M4, M5, M6, M7, M8, M9,
+ M10>::type(
+ ::testing::AnyOf(m1, m2, m3, m4, m5),
+ ::testing::AnyOf(m6, m7, m8, m9, m10));
+}
+
+} // namespace testing
+
+
+// The MATCHER* family of macros can be used in a namespace scope to
+// define custom matchers easily.
+//
+// Basic Usage
+// ===========
+//
+// The syntax
+//
+// MATCHER(name, description_string) { statements; }
+//
+// defines a matcher with the given name that executes the statements,
+// which must return a bool to indicate if the match succeeds. Inside
+// the statements, you can refer to the value being matched by 'arg',
+// and refer to its type by 'arg_type'.
+//
+// The description string documents what the matcher does, and is used
+// to generate the failure message when the match fails. Since a
+// MATCHER() is usually defined in a header file shared by multiple
+// C++ source files, we require the description to be a C-string
+// literal to avoid possible side effects. It can be empty, in which
+// case we'll use the sequence of words in the matcher name as the
+// description.
+//
+// For example:
+//
+// MATCHER(IsEven, "") { return (arg % 2) == 0; }
+//
+// allows you to write
+//
+// // Expects mock_foo.Bar(n) to be called where n is even.
+// EXPECT_CALL(mock_foo, Bar(IsEven()));
+//
+// or,
+//
+// // Verifies that the value of some_expression is even.
+// EXPECT_THAT(some_expression, IsEven());
+//
+// If the above assertion fails, it will print something like:
+//
+// Value of: some_expression
+// Expected: is even
+// Actual: 7
+//
+// where the description "is even" is automatically calculated from the
+// matcher name IsEven.
+//
+// Argument Type
+// =============
+//
+// Note that the type of the value being matched (arg_type) is
+// determined by the context in which you use the matcher and is
+// supplied to you by the compiler, so you don't need to worry about
+// declaring it (nor can you). This allows the matcher to be
+// polymorphic. For example, IsEven() can be used to match any type
+// where the value of "(arg % 2) == 0" can be implicitly converted to
+// a bool. In the "Bar(IsEven())" example above, if method Bar()
+// takes an int, 'arg_type' will be int; if it takes an unsigned long,
+// 'arg_type' will be unsigned long; and so on.
+//
+// Parameterizing Matchers
+// =======================
+//
+// Sometimes you'll want to parameterize the matcher. For that you
+// can use another macro:
+//
+// MATCHER_P(name, param_name, description_string) { statements; }
+//
+// For example:
+//
+// MATCHER_P(HasAbsoluteValue, value, "") { return abs(arg) == value; }
+//
+// will allow you to write:
+//
+// EXPECT_THAT(Blah("a"), HasAbsoluteValue(n));
+//
+// which may lead to this message (assuming n is 10):
+//
+// Value of: Blah("a")
+// Expected: has absolute value 10
+// Actual: -9
+//
+// Note that both the matcher description and its parameter are
+// printed, making the message human-friendly.
+//
+// In the matcher definition body, you can write 'foo_type' to
+// reference the type of a parameter named 'foo'. For example, in the
+// body of MATCHER_P(HasAbsoluteValue, value) above, you can write
+// 'value_type' to refer to the type of 'value'.
+//
+// We also provide MATCHER_P2, MATCHER_P3, ..., up to MATCHER_P10 to
+// support multi-parameter matchers.
+//
+// Describing Parameterized Matchers
+// =================================
+//
+// The last argument to MATCHER*() is a string-typed expression. The
+// expression can reference all of the matcher's parameters and a
+// special bool-typed variable named 'negation'. When 'negation' is
+// false, the expression should evaluate to the matcher's description;
+// otherwise it should evaluate to the description of the negation of
+// the matcher. For example,
+//
+// using testing::PrintToString;
+//
+// MATCHER_P2(InClosedRange, low, hi,
+// string(negation ? "is not" : "is") + " in range [" +
+// PrintToString(low) + ", " + PrintToString(hi) + "]") {
+// return low <= arg && arg <= hi;
+// }
+// ...
+// EXPECT_THAT(3, InClosedRange(4, 6));
+// EXPECT_THAT(3, Not(InClosedRange(2, 4)));
+//
+// would generate two failures that contain the text:
+//
+// Expected: is in range [4, 6]
+// ...
+// Expected: is not in range [2, 4]
+//
+// If you specify "" as the description, the failure message will
+// contain the sequence of words in the matcher name followed by the
+// parameter values printed as a tuple. For example,
+//
+// MATCHER_P2(InClosedRange, low, hi, "") { ... }
+// ...
+// EXPECT_THAT(3, InClosedRange(4, 6));
+// EXPECT_THAT(3, Not(InClosedRange(2, 4)));
+//
+// would generate two failures that contain the text:
+//
+// Expected: in closed range (4, 6)
+// ...
+// Expected: not (in closed range (2, 4))
+//
+// Types of Matcher Parameters
+// ===========================
+//
+// For the purpose of typing, you can view
+//
+// MATCHER_Pk(Foo, p1, ..., pk, description_string) { ... }
+//
+// as shorthand for
+//
+// template <typename p1_type, ..., typename pk_type>
+// FooMatcherPk<p1_type, ..., pk_type>
+// Foo(p1_type p1, ..., pk_type pk) { ... }
+//
+// When you write Foo(v1, ..., vk), the compiler infers the types of
+// the parameters v1, ..., and vk for you. If you are not happy with
+// the result of the type inference, you can specify the types by
+// explicitly instantiating the template, as in Foo<long, bool>(5,
+// false). As said earlier, you don't get to (or need to) specify
+// 'arg_type' as that's determined by the context in which the matcher
+// is used. You can assign the result of expression Foo(p1, ..., pk)
+// to a variable of type FooMatcherPk<p1_type, ..., pk_type>. This
+// can be useful when composing matchers.
+//
+// While you can instantiate a matcher template with reference types,
+// passing the parameters by pointer usually makes your code more
+// readable. If, however, you still want to pass a parameter by
+// reference, be aware that in the failure message generated by the
+// matcher you will see the value of the referenced object but not its
+// address.
+//
+// Explaining Match Results
+// ========================
+//
+// Sometimes the matcher description alone isn't enough to explain why
+// the match has failed or succeeded. For example, when expecting a
+// long string, it can be very helpful to also print the diff between
+// the expected string and the actual one. To achieve that, you can
+// optionally stream additional information to a special variable
+// named result_listener, whose type is a pointer to class
+// MatchResultListener:
+//
+// MATCHER_P(EqualsLongString, str, "") {
+// if (arg == str) return true;
+//
+// *result_listener << "the difference: "
+/// << DiffStrings(str, arg);
+// return false;
+// }
+//
+// Overloading Matchers
+// ====================
+//
+// You can overload matchers with different numbers of parameters:
+//
+// MATCHER_P(Blah, a, description_string1) { ... }
+// MATCHER_P2(Blah, a, b, description_string2) { ... }
+//
+// Caveats
+// =======
+//
+// When defining a new matcher, you should also consider implementing
+// MatcherInterface or using MakePolymorphicMatcher(). These
+// approaches require more work than the MATCHER* macros, but also
+// give you more control on the types of the value being matched and
+// the matcher parameters, which may leads to better compiler error
+// messages when the matcher is used wrong. They also allow
+// overloading matchers based on parameter types (as opposed to just
+// based on the number of parameters).
+//
+// MATCHER*() can only be used in a namespace scope. The reason is
+// that C++ doesn't yet allow function-local types to be used to
+// instantiate templates. The up-coming C++0x standard will fix this.
+// Once that's done, we'll consider supporting using MATCHER*() inside
+// a function.
+//
+// More Information
+// ================
+//
+// To learn more about using these macros, please search for 'MATCHER'
+// on http://code.google.com/p/googlemock/wiki/CookBook.
+
+#define MATCHER(name, description)\
+ class name##Matcher {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl()\
+ {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<>()));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>());\
+ }\
+ name##Matcher() {\
+ }\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##Matcher);\
+ };\
+ inline name##Matcher name() {\
+ return name##Matcher();\
+ }\
+ template <typename arg_type>\
+ bool name##Matcher::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P(name, p0, description)\
+ template <typename p0##_type>\
+ class name##MatcherP {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ explicit gmock_Impl(p0##_type gmock_p0)\
+ : p0(gmock_p0) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type>(p0)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0));\
+ }\
+ name##MatcherP(p0##_type gmock_p0) : p0(gmock_p0) {\
+ }\
+ p0##_type p0;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP);\
+ };\
+ template <typename p0##_type>\
+ inline name##MatcherP<p0##_type> name(p0##_type p0) {\
+ return name##MatcherP<p0##_type>(p0);\
+ }\
+ template <typename p0##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP<p0##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P2(name, p0, p1, description)\
+ template <typename p0##_type, typename p1##_type>\
+ class name##MatcherP2 {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1)\
+ : p0(gmock_p0), p1(gmock_p1) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type, p1##_type>(p0, p1)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0, p1));\
+ }\
+ name##MatcherP2(p0##_type gmock_p0, p1##_type gmock_p1) : p0(gmock_p0), \
+ p1(gmock_p1) {\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP2);\
+ };\
+ template <typename p0##_type, typename p1##_type>\
+ inline name##MatcherP2<p0##_type, p1##_type> name(p0##_type p0, \
+ p1##_type p1) {\
+ return name##MatcherP2<p0##_type, p1##_type>(p0, p1);\
+ }\
+ template <typename p0##_type, typename p1##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP2<p0##_type, \
+ p1##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P3(name, p0, p1, p2, description)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type>\
+ class name##MatcherP3 {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2)\
+ : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type, p1##_type, p2##_type>(p0, p1, \
+ p2)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0, p1, p2));\
+ }\
+ name##MatcherP3(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2) {\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP3);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type>\
+ inline name##MatcherP3<p0##_type, p1##_type, p2##_type> name(p0##_type p0, \
+ p1##_type p1, p2##_type p2) {\
+ return name##MatcherP3<p0##_type, p1##_type, p2##_type>(p0, p1, p2);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP3<p0##_type, p1##_type, \
+ p2##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P4(name, p0, p1, p2, p3, description)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type>\
+ class name##MatcherP4 {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3)\
+ : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), p3(gmock_p3) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type, p1##_type, p2##_type, \
+ p3##_type>(p0, p1, p2, p3)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0, p1, p2, p3));\
+ }\
+ name##MatcherP4(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3) : p0(gmock_p0), p1(gmock_p1), \
+ p2(gmock_p2), p3(gmock_p3) {\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP4);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type>\
+ inline name##MatcherP4<p0##_type, p1##_type, p2##_type, \
+ p3##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, \
+ p3##_type p3) {\
+ return name##MatcherP4<p0##_type, p1##_type, p2##_type, p3##_type>(p0, \
+ p1, p2, p3);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP4<p0##_type, p1##_type, p2##_type, \
+ p3##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P5(name, p0, p1, p2, p3, p4, description)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type>\
+ class name##MatcherP5 {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4)\
+ : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), p3(gmock_p3), \
+ p4(gmock_p4) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type>(p0, p1, p2, p3, p4)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0, p1, p2, p3, p4));\
+ }\
+ name##MatcherP5(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, \
+ p4##_type gmock_p4) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4) {\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP5);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type>\
+ inline name##MatcherP5<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, \
+ p4##_type p4) {\
+ return name##MatcherP5<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type>(p0, p1, p2, p3, p4);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP5<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P6(name, p0, p1, p2, p3, p4, p5, description)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type>\
+ class name##MatcherP6 {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5)\
+ : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), p3(gmock_p3), \
+ p4(gmock_p4), p5(gmock_p5) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type>(p0, p1, p2, p3, p4, p5)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0, p1, p2, p3, p4, p5));\
+ }\
+ name##MatcherP6(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5) {\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP6);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type>\
+ inline name##MatcherP6<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, \
+ p3##_type p3, p4##_type p4, p5##_type p5) {\
+ return name##MatcherP6<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type>(p0, p1, p2, p3, p4, p5);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP6<p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P7(name, p0, p1, p2, p3, p4, p5, p6, description)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type>\
+ class name##MatcherP7 {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6)\
+ : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), p3(gmock_p3), \
+ p4(gmock_p4), p5(gmock_p5), p6(gmock_p6) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type>(p0, p1, p2, p3, p4, p5, \
+ p6)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0, p1, p2, p3, p4, p5, p6));\
+ }\
+ name##MatcherP7(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5, p6##_type gmock_p6) : p0(gmock_p0), p1(gmock_p1), \
+ p2(gmock_p2), p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), \
+ p6(gmock_p6) {\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP7);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type>\
+ inline name##MatcherP7<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type> name(p0##_type p0, p1##_type p1, \
+ p2##_type p2, p3##_type p3, p4##_type p4, p5##_type p5, \
+ p6##_type p6) {\
+ return name##MatcherP7<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type>(p0, p1, p2, p3, p4, p5, p6);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP7<p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P8(name, p0, p1, p2, p3, p4, p5, p6, p7, description)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type>\
+ class name##MatcherP8 {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6, p7##_type gmock_p7)\
+ : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), p3(gmock_p3), \
+ p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), p7(gmock_p7) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type>(p0, p1, p2, \
+ p3, p4, p5, p6, p7)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0, p1, p2, p3, p4, p5, p6, p7));\
+ }\
+ name##MatcherP8(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5, p6##_type gmock_p6, \
+ p7##_type gmock_p7) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), \
+ p7(gmock_p7) {\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP8);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type>\
+ inline name##MatcherP8<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type> name(p0##_type p0, \
+ p1##_type p1, p2##_type p2, p3##_type p3, p4##_type p4, p5##_type p5, \
+ p6##_type p6, p7##_type p7) {\
+ return name##MatcherP8<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type>(p0, p1, p2, p3, p4, p5, \
+ p6, p7);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP8<p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type, \
+ p7##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P9(name, p0, p1, p2, p3, p4, p5, p6, p7, p8, description)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type>\
+ class name##MatcherP9 {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6, p7##_type gmock_p7, p8##_type gmock_p8)\
+ : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), p3(gmock_p3), \
+ p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), p7(gmock_p7), \
+ p8(gmock_p8) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ p8##_type p8;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, \
+ p8##_type>(p0, p1, p2, p3, p4, p5, p6, p7, p8)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0, p1, p2, p3, p4, p5, p6, p7, p8));\
+ }\
+ name##MatcherP9(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5, p6##_type gmock_p6, p7##_type gmock_p7, \
+ p8##_type gmock_p8) : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), \
+ p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), p7(gmock_p7), \
+ p8(gmock_p8) {\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ p8##_type p8;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP9);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type>\
+ inline name##MatcherP9<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, \
+ p8##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, \
+ p4##_type p4, p5##_type p5, p6##_type p6, p7##_type p7, \
+ p8##_type p8) {\
+ return name##MatcherP9<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, p8##_type>(p0, p1, p2, \
+ p3, p4, p5, p6, p7, p8);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP9<p0##_type, p1##_type, p2##_type, p3##_type, p4##_type, \
+ p5##_type, p6##_type, p7##_type, \
+ p8##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#define MATCHER_P10(name, p0, p1, p2, p3, p4, p5, p6, p7, p8, p9, description)\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type, \
+ typename p9##_type>\
+ class name##MatcherP10 {\
+ public:\
+ template <typename arg_type>\
+ class gmock_Impl : public ::testing::MatcherInterface<arg_type> {\
+ public:\
+ gmock_Impl(p0##_type gmock_p0, p1##_type gmock_p1, p2##_type gmock_p2, \
+ p3##_type gmock_p3, p4##_type gmock_p4, p5##_type gmock_p5, \
+ p6##_type gmock_p6, p7##_type gmock_p7, p8##_type gmock_p8, \
+ p9##_type gmock_p9)\
+ : p0(gmock_p0), p1(gmock_p1), p2(gmock_p2), p3(gmock_p3), \
+ p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), p7(gmock_p7), \
+ p8(gmock_p8), p9(gmock_p9) {}\
+ virtual bool MatchAndExplain(\
+ arg_type arg, ::testing::MatchResultListener* result_listener) const;\
+ virtual void DescribeTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(false);\
+ }\
+ virtual void DescribeNegationTo(::std::ostream* gmock_os) const {\
+ *gmock_os << FormatDescription(true);\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ p8##_type p8;\
+ p9##_type p9;\
+ private:\
+ ::testing::internal::string FormatDescription(bool negation) const {\
+ const ::testing::internal::string gmock_description = (description);\
+ if (!gmock_description.empty())\
+ return gmock_description;\
+ return ::testing::internal::FormatMatcherDescription(\
+ negation, #name, \
+ ::testing::internal::UniversalTersePrintTupleFieldsToStrings(\
+ ::std::tr1::tuple<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, p8##_type, \
+ p9##_type>(p0, p1, p2, p3, p4, p5, p6, p7, p8, p9)));\
+ }\
+ GTEST_DISALLOW_ASSIGN_(gmock_Impl);\
+ };\
+ template <typename arg_type>\
+ operator ::testing::Matcher<arg_type>() const {\
+ return ::testing::Matcher<arg_type>(\
+ new gmock_Impl<arg_type>(p0, p1, p2, p3, p4, p5, p6, p7, p8, p9));\
+ }\
+ name##MatcherP10(p0##_type gmock_p0, p1##_type gmock_p1, \
+ p2##_type gmock_p2, p3##_type gmock_p3, p4##_type gmock_p4, \
+ p5##_type gmock_p5, p6##_type gmock_p6, p7##_type gmock_p7, \
+ p8##_type gmock_p8, p9##_type gmock_p9) : p0(gmock_p0), p1(gmock_p1), \
+ p2(gmock_p2), p3(gmock_p3), p4(gmock_p4), p5(gmock_p5), p6(gmock_p6), \
+ p7(gmock_p7), p8(gmock_p8), p9(gmock_p9) {\
+ }\
+ p0##_type p0;\
+ p1##_type p1;\
+ p2##_type p2;\
+ p3##_type p3;\
+ p4##_type p4;\
+ p5##_type p5;\
+ p6##_type p6;\
+ p7##_type p7;\
+ p8##_type p8;\
+ p9##_type p9;\
+ private:\
+ GTEST_DISALLOW_ASSIGN_(name##MatcherP10);\
+ };\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type, \
+ typename p9##_type>\
+ inline name##MatcherP10<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, p8##_type, \
+ p9##_type> name(p0##_type p0, p1##_type p1, p2##_type p2, p3##_type p3, \
+ p4##_type p4, p5##_type p5, p6##_type p6, p7##_type p7, p8##_type p8, \
+ p9##_type p9) {\
+ return name##MatcherP10<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, p8##_type, p9##_type>(p0, \
+ p1, p2, p3, p4, p5, p6, p7, p8, p9);\
+ }\
+ template <typename p0##_type, typename p1##_type, typename p2##_type, \
+ typename p3##_type, typename p4##_type, typename p5##_type, \
+ typename p6##_type, typename p7##_type, typename p8##_type, \
+ typename p9##_type>\
+ template <typename arg_type>\
+ bool name##MatcherP10<p0##_type, p1##_type, p2##_type, p3##_type, \
+ p4##_type, p5##_type, p6##_type, p7##_type, p8##_type, \
+ p9##_type>::gmock_Impl<arg_type>::MatchAndExplain(\
+ arg_type arg, \
+ ::testing::MatchResultListener* result_listener GTEST_ATTRIBUTE_UNUSED_)\
+ const
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_GENERATED_MATCHERS_H_
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements some actions that depend on gmock-generated-actions.h.
+
+#ifndef GMOCK_INCLUDE_GMOCK_GMOCK_MORE_ACTIONS_H_
+#define GMOCK_INCLUDE_GMOCK_GMOCK_MORE_ACTIONS_H_
+
+#include <algorithm>
+
+
+namespace testing {
+namespace internal {
+
+// Implements the Invoke(f) action. The template argument
+// FunctionImpl is the implementation type of f, which can be either a
+// function pointer or a functor. Invoke(f) can be used as an
+// Action<F> as long as f's type is compatible with F (i.e. f can be
+// assigned to a tr1::function<F>).
+template <typename FunctionImpl>
+class InvokeAction {
+ public:
+ // The c'tor makes a copy of function_impl (either a function
+ // pointer or a functor).
+ explicit InvokeAction(FunctionImpl function_impl)
+ : function_impl_(function_impl) {}
+
+ template <typename Result, typename ArgumentTuple>
+ Result Perform(const ArgumentTuple& args) {
+ return InvokeHelper<Result, ArgumentTuple>::Invoke(function_impl_, args);
+ }
+
+ private:
+ FunctionImpl function_impl_;
+
+ GTEST_DISALLOW_ASSIGN_(InvokeAction);
+};
+
+// Implements the Invoke(object_ptr, &Class::Method) action.
+template <class Class, typename MethodPtr>
+class InvokeMethodAction {
+ public:
+ InvokeMethodAction(Class* obj_ptr, MethodPtr method_ptr)
+ : obj_ptr_(obj_ptr), method_ptr_(method_ptr) {}
+
+ template <typename Result, typename ArgumentTuple>
+ Result Perform(const ArgumentTuple& args) const {
+ return InvokeHelper<Result, ArgumentTuple>::InvokeMethod(
+ obj_ptr_, method_ptr_, args);
+ }
+
+ private:
+ Class* const obj_ptr_;
+ const MethodPtr method_ptr_;
+
+ GTEST_DISALLOW_ASSIGN_(InvokeMethodAction);
+};
+
+} // namespace internal
+
+// Various overloads for Invoke().
+
+// Creates an action that invokes 'function_impl' with the mock
+// function's arguments.
+template <typename FunctionImpl>
+PolymorphicAction<internal::InvokeAction<FunctionImpl> > Invoke(
+ FunctionImpl function_impl) {
+ return MakePolymorphicAction(
+ internal::InvokeAction<FunctionImpl>(function_impl));
+}
+
+// Creates an action that invokes the given method on the given object
+// with the mock function's arguments.
+template <class Class, typename MethodPtr>
+PolymorphicAction<internal::InvokeMethodAction<Class, MethodPtr> > Invoke(
+ Class* obj_ptr, MethodPtr method_ptr) {
+ return MakePolymorphicAction(
+ internal::InvokeMethodAction<Class, MethodPtr>(obj_ptr, method_ptr));
+}
+
+// WithoutArgs(inner_action) can be used in a mock function with a
+// non-empty argument list to perform inner_action, which takes no
+// argument. In other words, it adapts an action accepting no
+// argument to one that accepts (and ignores) arguments.
+template <typename InnerAction>
+inline internal::WithArgsAction<InnerAction>
+WithoutArgs(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction>(action);
+}
+
+// WithArg<k>(an_action) creates an action that passes the k-th
+// (0-based) argument of the mock function to an_action and performs
+// it. It adapts an action accepting one argument to one that accepts
+// multiple arguments. For convenience, we also provide
+// WithArgs<k>(an_action) (defined below) as a synonym.
+template <int k, typename InnerAction>
+inline internal::WithArgsAction<InnerAction, k>
+WithArg(const InnerAction& action) {
+ return internal::WithArgsAction<InnerAction, k>(action);
+}
+
+// The ACTION*() macros trigger warning C4100 (unreferenced formal
+// parameter) in MSVC with -W4. Unfortunately they cannot be fixed in
+// the macro definition, as the warnings are generated when the macro
+// is expanded and macro expansion cannot contain #pragma. Therefore
+// we suppress them here.
+#ifdef _MSC_VER
+# pragma warning(push)
+# pragma warning(disable:4100)
+#endif
+
+// Action ReturnArg<k>() returns the k-th argument of the mock function.
+ACTION_TEMPLATE(ReturnArg,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_0_VALUE_PARAMS()) {
+ return std::tr1::get<k>(args);
+}
+
+// Action SaveArg<k>(pointer) saves the k-th (0-based) argument of the
+// mock function to *pointer.
+ACTION_TEMPLATE(SaveArg,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_1_VALUE_PARAMS(pointer)) {
+ *pointer = ::std::tr1::get<k>(args);
+}
+
+// Action SaveArgPointee<k>(pointer) saves the value pointed to
+// by the k-th (0-based) argument of the mock function to *pointer.
+ACTION_TEMPLATE(SaveArgPointee,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_1_VALUE_PARAMS(pointer)) {
+ *pointer = *::std::tr1::get<k>(args);
+}
+
+// Action SetArgReferee<k>(value) assigns 'value' to the variable
+// referenced by the k-th (0-based) argument of the mock function.
+ACTION_TEMPLATE(SetArgReferee,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_1_VALUE_PARAMS(value)) {
+ typedef typename ::std::tr1::tuple_element<k, args_type>::type argk_type;
+ // Ensures that argument #k is a reference. If you get a compiler
+ // error on the next line, you are using SetArgReferee<k>(value) in
+ // a mock function whose k-th (0-based) argument is not a reference.
+ GTEST_COMPILE_ASSERT_(internal::is_reference<argk_type>::value,
+ SetArgReferee_must_be_used_with_a_reference_argument);
+ ::std::tr1::get<k>(args) = value;
+}
+
+// Action SetArrayArgument<k>(first, last) copies the elements in
+// source range [first, last) to the array pointed to by the k-th
+// (0-based) argument, which can be either a pointer or an
+// iterator. The action does not take ownership of the elements in the
+// source range.
+ACTION_TEMPLATE(SetArrayArgument,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_2_VALUE_PARAMS(first, last)) {
+ // Microsoft compiler deprecates ::std::copy, so we want to suppress warning
+ // 4996 (Function call with parameters that may be unsafe) there.
+#ifdef _MSC_VER
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4996) // Temporarily disables warning 4996.
+#endif
+ ::std::copy(first, last, ::std::tr1::get<k>(args));
+#ifdef _MSC_VER
+# pragma warning(pop) // Restores the warning state.
+#endif
+}
+
+// Action DeleteArg<k>() deletes the k-th (0-based) argument of the mock
+// function.
+ACTION_TEMPLATE(DeleteArg,
+ HAS_1_TEMPLATE_PARAMS(int, k),
+ AND_0_VALUE_PARAMS()) {
+ delete ::std::tr1::get<k>(args);
+}
+
+// This action returns the value pointed to by 'pointer'.
+ACTION_P(ReturnPointee, pointer) { return *pointer; }
+
+// Action Throw(exception) can be used in a mock function of any type
+// to throw the given exception. Any copyable value can be thrown.
+#if GTEST_HAS_EXCEPTIONS
+
+// Suppresses the 'unreachable code' warning that VC generates in opt modes.
+# ifdef _MSC_VER
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4702) // Temporarily disables warning 4702.
+# endif
+ACTION_P(Throw, exception) { throw exception; }
+# ifdef _MSC_VER
+# pragma warning(pop) // Restores the warning state.
+# endif
+
+#endif // GTEST_HAS_EXCEPTIONS
+
+#ifdef _MSC_VER
+# pragma warning(pop)
+#endif
+
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_MORE_ACTIONS_H_
+// Copyright 2013, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: marcus.boerger at google.com (Marcus Boerger)
+
+// Google Mock - a framework for writing C++ mock classes.
+//
+// This file implements some matchers that depend on gmock-generated-matchers.h.
+//
+// Note that tests are implemented in gmock-matchers_test.cc rather than
+// gmock-more-matchers-test.cc.
+
+#ifndef GMOCK_GMOCK_MORE_MATCHERS_H_
+#define GMOCK_GMOCK_MORE_MATCHERS_H_
+
+
+namespace testing {
+
+// Defines a matcher that matches an empty container. The container must
+// support both size() and empty(), which all STL-like containers provide.
+MATCHER(IsEmpty, negation ? "isn't empty" : "is empty") {
+ if (arg.empty()) {
+ return true;
+ }
+ *result_listener << "whose size is " << arg.size();
+ return false;
+}
+
+} // namespace testing
+
+#endif // GMOCK_GMOCK_MORE_MATCHERS_H_
+
+namespace testing {
+
+// Declares Google Mock flags that we want a user to use programmatically.
+GMOCK_DECLARE_bool_(catch_leaked_mocks);
+GMOCK_DECLARE_string_(verbose);
+
+// Initializes Google Mock. This must be called before running the
+// tests. In particular, it parses the command line for the flags
+// that Google Mock recognizes. Whenever a Google Mock flag is seen,
+// it is removed from argv, and *argc is decremented.
+//
+// No value is returned. Instead, the Google Mock flag variables are
+// updated.
+//
+// Since Google Test is needed for Google Mock to work, this function
+// also initializes Google Test and parses its flags, if that hasn't
+// been done.
+GTEST_API_ void InitGoogleMock(int* argc, char** argv);
+
+// This overloaded version can be used in Windows programs compiled in
+// UNICODE mode.
+GTEST_API_ void InitGoogleMock(int* argc, wchar_t** argv);
+
+} // namespace testing
+
+#endif // GMOCK_INCLUDE_GMOCK_GMOCK_H_
diff --git a/third-party/gmock-1.7.0/gmock_main.cc b/third-party/gmock-1.7.0/gmock_main.cc
new file mode 100644
index 0000000..bd5be03
--- /dev/null
+++ b/third-party/gmock-1.7.0/gmock_main.cc
@@ -0,0 +1,54 @@
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+#include <iostream>
+#include "gmock/gmock.h"
+#include "gtest/gtest.h"
+
+// MS C++ compiler/linker has a bug on Windows (not on Windows CE), which
+// causes a link error when _tmain is defined in a static library and UNICODE
+// is enabled. For this reason instead of _tmain, main function is used on
+// Windows. See the following link to track the current status of this bug:
+// http://connect.microsoft.com/VisualStudio/feedback/ViewFeedback.aspx?FeedbackID=394464 // NOLINT
+#if GTEST_OS_WINDOWS_MOBILE
+# include <tchar.h> // NOLINT
+
+GTEST_API_ int _tmain(int argc, TCHAR** argv) {
+#else
+GTEST_API_ int main(int argc, char** argv) {
+#endif // GTEST_OS_WINDOWS_MOBILE
+ std::cout << "Running main() from gmock_main.cc\n";
+ // Since Google Mock depends on Google Test, InitGoogleMock() is
+ // also responsible for initializing Google Test. Therefore there's
+ // no need for calling testing::InitGoogleTest() separately.
+ testing::InitGoogleMock(&argc, argv);
+ return RUN_ALL_TESTS();
+}
diff --git a/third-party/gmock-1.7.0/gtest/gtest.h b/third-party/gmock-1.7.0/gtest/gtest.h
new file mode 100644
index 0000000..4f3804f
--- /dev/null
+++ b/third-party/gmock-1.7.0/gtest/gtest.h
@@ -0,0 +1,20061 @@
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+//
+// The Google C++ Testing Framework (Google Test)
+//
+// This header file defines the public API for Google Test. It should be
+// included by any test program that uses Google Test.
+//
+// IMPORTANT NOTE: Due to limitation of the C++ language, we have to
+// leave some internal implementation details in this header file.
+// They are clearly marked by comments like this:
+//
+// // INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+//
+// Such code is NOT meant to be used by a user directly, and is subject
+// to CHANGE WITHOUT NOTICE. Therefore DO NOT DEPEND ON IT in a user
+// program!
+//
+// Acknowledgment: Google Test borrowed the idea of automatic test
+// registration from Barthelemy Dagenais' (barthelemy at prologique.com)
+// easyUnit framework.
+
+#ifndef GTEST_INCLUDE_GTEST_GTEST_H_
+#define GTEST_INCLUDE_GTEST_GTEST_H_
+
+#include <limits>
+#include <ostream>
+#include <vector>
+
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Authors: wan at google.com (Zhanyong Wan), eefacm at gmail.com (Sean Mcafee)
+//
+// The Google C++ Testing Framework (Google Test)
+//
+// This header file declares functions and macros used internally by
+// Google Test. They are subject to change without notice.
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_INTERNAL_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_INTERNAL_H_
+
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Authors: wan at google.com (Zhanyong Wan)
+//
+// Low-level types and utilities for porting Google Test to various
+// platforms. They are subject to change without notice. DO NOT USE
+// THEM IN USER CODE.
+//
+// This file is fundamental to Google Test. All other Google Test source
+// files are expected to #include this. Therefore, it cannot #include
+// any other Google Test header.
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_PORT_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_PORT_H_
+
+// The user can define the following macros in the build script to
+// control Google Test's behavior. If the user doesn't define a macro
+// in this list, Google Test will define it.
+//
+// GTEST_HAS_CLONE - Define it to 1/0 to indicate that clone(2)
+// is/isn't available.
+// GTEST_HAS_EXCEPTIONS - Define it to 1/0 to indicate that exceptions
+// are enabled.
+// GTEST_HAS_GLOBAL_STRING - Define it to 1/0 to indicate that ::string
+// is/isn't available (some systems define
+// ::string, which is different to std::string).
+// GTEST_HAS_GLOBAL_WSTRING - Define it to 1/0 to indicate that ::string
+// is/isn't available (some systems define
+// ::wstring, which is different to std::wstring).
+// GTEST_HAS_POSIX_RE - Define it to 1/0 to indicate that POSIX regular
+// expressions are/aren't available.
+// GTEST_HAS_PTHREAD - Define it to 1/0 to indicate that <pthread.h>
+// is/isn't available.
+// GTEST_HAS_RTTI - Define it to 1/0 to indicate that RTTI is/isn't
+// enabled.
+// GTEST_HAS_STD_WSTRING - Define it to 1/0 to indicate that
+// std::wstring does/doesn't work (Google Test can
+// be used where std::wstring is unavailable).
+// GTEST_HAS_TR1_TUPLE - Define it to 1/0 to indicate tr1::tuple
+// is/isn't available.
+// GTEST_HAS_SEH - Define it to 1/0 to indicate whether the
+// compiler supports Microsoft's "Structured
+// Exception Handling".
+// GTEST_HAS_STREAM_REDIRECTION
+// - Define it to 1/0 to indicate whether the
+// platform supports I/O stream redirection using
+// dup() and dup2().
+// GTEST_USE_OWN_TR1_TUPLE - Define it to 1/0 to indicate whether Google
+// Test's own tr1 tuple implementation should be
+// used. Unused when the user sets
+// GTEST_HAS_TR1_TUPLE to 0.
+// GTEST_LANG_CXX11 - Define it to 1/0 to indicate that Google Test
+// is building in C++11/C++98 mode.
+// GTEST_LINKED_AS_SHARED_LIBRARY
+// - Define to 1 when compiling tests that use
+// Google Test as a shared library (known as
+// DLL on Windows).
+// GTEST_CREATE_SHARED_LIBRARY
+// - Define to 1 when compiling Google Test itself
+// as a shared library.
+
+// This header defines the following utilities:
+//
+// Macros indicating the current platform (defined to 1 if compiled on
+// the given platform; otherwise undefined):
+// GTEST_OS_AIX - IBM AIX
+// GTEST_OS_CYGWIN - Cygwin
+// GTEST_OS_HPUX - HP-UX
+// GTEST_OS_LINUX - Linux
+// GTEST_OS_LINUX_ANDROID - Google Android
+// GTEST_OS_MAC - Mac OS X
+// GTEST_OS_IOS - iOS
+// GTEST_OS_IOS_SIMULATOR - iOS simulator
+// GTEST_OS_NACL - Google Native Client (NaCl)
+// GTEST_OS_OPENBSD - OpenBSD
+// GTEST_OS_QNX - QNX
+// GTEST_OS_SOLARIS - Sun Solaris
+// GTEST_OS_SYMBIAN - Symbian
+// GTEST_OS_WINDOWS - Windows (Desktop, MinGW, or Mobile)
+// GTEST_OS_WINDOWS_DESKTOP - Windows Desktop
+// GTEST_OS_WINDOWS_MINGW - MinGW
+// GTEST_OS_WINDOWS_MOBILE - Windows Mobile
+// GTEST_OS_ZOS - z/OS
+//
+// Among the platforms, Cygwin, Linux, Max OS X, and Windows have the
+// most stable support. Since core members of the Google Test project
+// don't have access to other platforms, support for them may be less
+// stable. If you notice any problems on your platform, please notify
+// googletestframework at googlegroups.com (patches for fixing them are
+// even more welcome!).
+//
+// Note that it is possible that none of the GTEST_OS_* macros are defined.
+//
+// Macros indicating available Google Test features (defined to 1 if
+// the corresponding feature is supported; otherwise undefined):
+// GTEST_HAS_COMBINE - the Combine() function (for value-parameterized
+// tests)
+// GTEST_HAS_DEATH_TEST - death tests
+// GTEST_HAS_PARAM_TEST - value-parameterized tests
+// GTEST_HAS_TYPED_TEST - typed tests
+// GTEST_HAS_TYPED_TEST_P - type-parameterized tests
+// GTEST_USES_POSIX_RE - enhanced POSIX regex is used. Do not confuse with
+// GTEST_HAS_POSIX_RE (see above) which users can
+// define themselves.
+// GTEST_USES_SIMPLE_RE - our own simple regex is used;
+// the above two are mutually exclusive.
+// GTEST_CAN_COMPARE_NULL - accepts untyped NULL in EXPECT_EQ().
+//
+// Macros for basic C++ coding:
+// GTEST_AMBIGUOUS_ELSE_BLOCKER_ - for disabling a gcc warning.
+// GTEST_ATTRIBUTE_UNUSED_ - declares that a class' instances or a
+// variable don't have to be used.
+// GTEST_DISALLOW_ASSIGN_ - disables operator=.
+// GTEST_DISALLOW_COPY_AND_ASSIGN_ - disables copy ctor and operator=.
+// GTEST_MUST_USE_RESULT_ - declares that a function's result must be used.
+//
+// Synchronization:
+// Mutex, MutexLock, ThreadLocal, GetThreadCount()
+// - synchronization primitives.
+// GTEST_IS_THREADSAFE - defined to 1 to indicate that the above
+// synchronization primitives have real implementations
+// and Google Test is thread-safe; or 0 otherwise.
+//
+// Template meta programming:
+// is_pointer - as in TR1; needed on Symbian and IBM XL C/C++ only.
+// IteratorTraits - partial implementation of std::iterator_traits, which
+// is not available in libCstd when compiled with Sun C++.
+//
+// Smart pointers:
+// scoped_ptr - as in TR2.
+//
+// Regular expressions:
+// RE - a simple regular expression class using the POSIX
+// Extended Regular Expression syntax on UNIX-like
+// platforms, or a reduced regular exception syntax on
+// other platforms, including Windows.
+//
+// Logging:
+// GTEST_LOG_() - logs messages at the specified severity level.
+// LogToStderr() - directs all log messages to stderr.
+// FlushInfoLog() - flushes informational log messages.
+//
+// Stdout and stderr capturing:
+// CaptureStdout() - starts capturing stdout.
+// GetCapturedStdout() - stops capturing stdout and returns the captured
+// string.
+// CaptureStderr() - starts capturing stderr.
+// GetCapturedStderr() - stops capturing stderr and returns the captured
+// string.
+//
+// Integer types:
+// TypeWithSize - maps an integer to a int type.
+// Int32, UInt32, Int64, UInt64, TimeInMillis
+// - integers of known sizes.
+// BiggestInt - the biggest signed integer type.
+//
+// Command-line utilities:
+// GTEST_FLAG() - references a flag.
+// GTEST_DECLARE_*() - declares a flag.
+// GTEST_DEFINE_*() - defines a flag.
+// GetInjectableArgvs() - returns the command line as a vector of strings.
+//
+// Environment variable utilities:
+// GetEnv() - gets the value of an environment variable.
+// BoolFromGTestEnv() - parses a bool environment variable.
+// Int32FromGTestEnv() - parses an Int32 environment variable.
+// StringFromGTestEnv() - parses a string environment variable.
+
+#include <ctype.h> // for isspace, etc
+#include <stddef.h> // for ptrdiff_t
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#ifndef _WIN32_WCE
+# include <sys/types.h>
+# include <sys/stat.h>
+#endif // !_WIN32_WCE
+
+#if defined __APPLE__
+# include <AvailabilityMacros.h>
+# include <TargetConditionals.h>
+#endif
+
+#include <iostream> // NOLINT
+#include <sstream> // NOLINT
+#include <string> // NOLINT
+
+#define GTEST_DEV_EMAIL_ "googletestframework@@googlegroups.com"
+#define GTEST_FLAG_PREFIX_ "gtest_"
+#define GTEST_FLAG_PREFIX_DASH_ "gtest-"
+#define GTEST_FLAG_PREFIX_UPPER_ "GTEST_"
+#define GTEST_NAME_ "Google Test"
+#define GTEST_PROJECT_URL_ "http://code.google.com/p/googletest/"
+
+// Determines the version of gcc that is used to compile this.
+#ifdef __GNUC__
+// 40302 means version 4.3.2.
+# define GTEST_GCC_VER_ \
+ (__GNUC__*10000 + __GNUC_MINOR__*100 + __GNUC_PATCHLEVEL__)
+#endif // __GNUC__
+
+// Determines the platform on which Google Test is compiled.
+#ifdef __CYGWIN__
+# define GTEST_OS_CYGWIN 1
+#elif defined __SYMBIAN32__
+# define GTEST_OS_SYMBIAN 1
+#elif defined _WIN32
+# define GTEST_OS_WINDOWS 1
+# ifdef _WIN32_WCE
+# define GTEST_OS_WINDOWS_MOBILE 1
+# elif defined(__MINGW__) || defined(__MINGW32__)
+# define GTEST_OS_WINDOWS_MINGW 1
+# else
+# define GTEST_OS_WINDOWS_DESKTOP 1
+# endif // _WIN32_WCE
+#elif defined __APPLE__
+# define GTEST_OS_MAC 1
+# if TARGET_OS_IPHONE
+# define GTEST_OS_IOS 1
+# if TARGET_IPHONE_SIMULATOR
+# define GTEST_OS_IOS_SIMULATOR 1
+# endif
+# endif
+#elif defined __linux__
+# define GTEST_OS_LINUX 1
+# if defined __ANDROID__
+# define GTEST_OS_LINUX_ANDROID 1
+# endif
+#elif defined __MVS__
+# define GTEST_OS_ZOS 1
+#elif defined(__sun) && defined(__SVR4)
+# define GTEST_OS_SOLARIS 1
+#elif defined(_AIX)
+# define GTEST_OS_AIX 1
+#elif defined(__hpux)
+# define GTEST_OS_HPUX 1
+#elif defined __native_client__
+# define GTEST_OS_NACL 1
+#elif defined __OpenBSD__
+# define GTEST_OS_OPENBSD 1
+#elif defined __QNX__
+# define GTEST_OS_QNX 1
+#endif // __CYGWIN__
+
+#ifndef GTEST_LANG_CXX11
+// gcc and clang define __GXX_EXPERIMENTAL_CXX0X__ when
+// -std={c,gnu}++{0x,11} is passed. The C++11 standard specifies a
+// value for __cplusplus, and recent versions of clang, gcc, and
+// probably other compilers set that too in C++11 mode.
+# if __GXX_EXPERIMENTAL_CXX0X__ || __cplusplus >= 201103L
+// Compiling in at least C++11 mode.
+# define GTEST_LANG_CXX11 1
+# else
+# define GTEST_LANG_CXX11 0
+# endif
+#endif
+
+// Brings in definitions for functions used in the testing::internal::posix
+// namespace (read, write, close, chdir, isatty, stat). We do not currently
+// use them on Windows Mobile.
+#if !GTEST_OS_WINDOWS
+// This assumes that non-Windows OSes provide unistd.h. For OSes where this
+// is not the case, we need to include headers that provide the functions
+// mentioned above.
+# include <unistd.h>
+# include <strings.h>
+#elif !GTEST_OS_WINDOWS_MOBILE
+# include <direct.h>
+# include <io.h>
+#endif
+
+#if GTEST_OS_LINUX_ANDROID
+// Used to define __ANDROID_API__ matching the target NDK API level.
+# include <android/api-level.h> // NOLINT
+#endif
+
+// Defines this to true iff Google Test can use POSIX regular expressions.
+#ifndef GTEST_HAS_POSIX_RE
+# if GTEST_OS_LINUX_ANDROID
+// On Android, <regex.h> is only available starting with Gingerbread.
+# define GTEST_HAS_POSIX_RE (__ANDROID_API__ >= 9)
+# else
+# define GTEST_HAS_POSIX_RE (!GTEST_OS_WINDOWS)
+# endif
+#endif
+
+#if GTEST_HAS_POSIX_RE
+
+// On some platforms, <regex.h> needs someone to define size_t, and
+// won't compile otherwise. We can #include it here as we already
+// included <stdlib.h>, which is guaranteed to define size_t through
+// <stddef.h>.
+# include <regex.h> // NOLINT
+
+# define GTEST_USES_POSIX_RE 1
+
+#elif GTEST_OS_WINDOWS
+
+// <regex.h> is not available on Windows. Use our own simple regex
+// implementation instead.
+# define GTEST_USES_SIMPLE_RE 1
+
+#else
+
+// <regex.h> may not be available on this platform. Use our own
+// simple regex implementation instead.
+# define GTEST_USES_SIMPLE_RE 1
+
+#endif // GTEST_HAS_POSIX_RE
+
+#ifndef GTEST_HAS_EXCEPTIONS
+// The user didn't tell us whether exceptions are enabled, so we need
+// to figure it out.
+# if defined(_MSC_VER) || defined(__BORLANDC__)
+// MSVC's and C++Builder's implementations of the STL use the _HAS_EXCEPTIONS
+// macro to enable exceptions, so we'll do the same.
+// Assumes that exceptions are enabled by default.
+# ifndef _HAS_EXCEPTIONS
+# define _HAS_EXCEPTIONS 1
+# endif // _HAS_EXCEPTIONS
+# define GTEST_HAS_EXCEPTIONS _HAS_EXCEPTIONS
+# elif defined(__GNUC__) && __EXCEPTIONS
+// gcc defines __EXCEPTIONS to 1 iff exceptions are enabled.
+# define GTEST_HAS_EXCEPTIONS 1
+# elif defined(__SUNPRO_CC)
+// Sun Pro CC supports exceptions. However, there is no compile-time way of
+// detecting whether they are enabled or not. Therefore, we assume that
+// they are enabled unless the user tells us otherwise.
+# define GTEST_HAS_EXCEPTIONS 1
+# elif defined(__IBMCPP__) && __EXCEPTIONS
+// xlC defines __EXCEPTIONS to 1 iff exceptions are enabled.
+# define GTEST_HAS_EXCEPTIONS 1
+# elif defined(__HP_aCC)
+// Exception handling is in effect by default in HP aCC compiler. It has to
+// be turned of by +noeh compiler option if desired.
+# define GTEST_HAS_EXCEPTIONS 1
+# else
+// For other compilers, we assume exceptions are disabled to be
+// conservative.
+# define GTEST_HAS_EXCEPTIONS 0
+# endif // defined(_MSC_VER) || defined(__BORLANDC__)
+#endif // GTEST_HAS_EXCEPTIONS
+
+#if !defined(GTEST_HAS_STD_STRING)
+// Even though we don't use this macro any longer, we keep it in case
+// some clients still depend on it.
+# define GTEST_HAS_STD_STRING 1
+#elif !GTEST_HAS_STD_STRING
+// The user told us that ::std::string isn't available.
+# error "Google Test cannot be used where ::std::string isn't available."
+#endif // !defined(GTEST_HAS_STD_STRING)
+
+#ifndef GTEST_HAS_GLOBAL_STRING
+// The user didn't tell us whether ::string is available, so we need
+// to figure it out.
+
+# define GTEST_HAS_GLOBAL_STRING 0
+
+#endif // GTEST_HAS_GLOBAL_STRING
+
+#ifndef GTEST_HAS_STD_WSTRING
+// The user didn't tell us whether ::std::wstring is available, so we need
+// to figure it out.
+// TODO(wan at google.com): uses autoconf to detect whether ::std::wstring
+// is available.
+
+// Cygwin 1.7 and below doesn't support ::std::wstring.
+// Solaris' libc++ doesn't support it either. Android has
+// no support for it at least as recent as Froyo (2.2).
+# define GTEST_HAS_STD_WSTRING \
+ (!(GTEST_OS_LINUX_ANDROID || GTEST_OS_CYGWIN || GTEST_OS_SOLARIS))
+
+#endif // GTEST_HAS_STD_WSTRING
+
+#ifndef GTEST_HAS_GLOBAL_WSTRING
+// The user didn't tell us whether ::wstring is available, so we need
+// to figure it out.
+# define GTEST_HAS_GLOBAL_WSTRING \
+ (GTEST_HAS_STD_WSTRING && GTEST_HAS_GLOBAL_STRING)
+#endif // GTEST_HAS_GLOBAL_WSTRING
+
+// Determines whether RTTI is available.
+#ifndef GTEST_HAS_RTTI
+// The user didn't tell us whether RTTI is enabled, so we need to
+// figure it out.
+
+# ifdef _MSC_VER
+
+# ifdef _CPPRTTI // MSVC defines this macro iff RTTI is enabled.
+# define GTEST_HAS_RTTI 1
+# else
+# define GTEST_HAS_RTTI 0
+# endif
+
+// Starting with version 4.3.2, gcc defines __GXX_RTTI iff RTTI is enabled.
+# elif defined(__GNUC__) && (GTEST_GCC_VER_ >= 40302)
+
+# ifdef __GXX_RTTI
+// When building against STLport with the Android NDK and with
+// -frtti -fno-exceptions, the build fails at link time with undefined
+// references to __cxa_bad_typeid. Note sure if STL or toolchain bug,
+// so disable RTTI when detected.
+# if GTEST_OS_LINUX_ANDROID && defined(_STLPORT_MAJOR) && \
+ !defined(__EXCEPTIONS)
+# define GTEST_HAS_RTTI 0
+# else
+# define GTEST_HAS_RTTI 1
+# endif // GTEST_OS_LINUX_ANDROID && __STLPORT_MAJOR && !__EXCEPTIONS
+# else
+# define GTEST_HAS_RTTI 0
+# endif // __GXX_RTTI
+
+// Clang defines __GXX_RTTI starting with version 3.0, but its manual recommends
+// using has_feature instead. has_feature(cxx_rtti) is supported since 2.7, the
+// first version with C++ support.
+# elif defined(__clang__)
+
+# define GTEST_HAS_RTTI __has_feature(cxx_rtti)
+
+// Starting with version 9.0 IBM Visual Age defines __RTTI_ALL__ to 1 if
+// both the typeid and dynamic_cast features are present.
+# elif defined(__IBMCPP__) && (__IBMCPP__ >= 900)
+
+# ifdef __RTTI_ALL__
+# define GTEST_HAS_RTTI 1
+# else
+# define GTEST_HAS_RTTI 0
+# endif
+
+# else
+
+// For all other compilers, we assume RTTI is enabled.
+# define GTEST_HAS_RTTI 1
+
+# endif // _MSC_VER
+
+#endif // GTEST_HAS_RTTI
+
+// It's this header's responsibility to #include <typeinfo> when RTTI
+// is enabled.
+#if GTEST_HAS_RTTI
+# include <typeinfo>
+#endif
+
+// Determines whether Google Test can use the pthreads library.
+#ifndef GTEST_HAS_PTHREAD
+// The user didn't tell us explicitly, so we assume pthreads support is
+// available on Linux and Mac.
+//
+// To disable threading support in Google Test, add -DGTEST_HAS_PTHREAD=0
+// to your compiler flags.
+# define GTEST_HAS_PTHREAD (GTEST_OS_LINUX || GTEST_OS_MAC || GTEST_OS_HPUX \
+ || GTEST_OS_QNX)
+#endif // GTEST_HAS_PTHREAD
+
+#if GTEST_HAS_PTHREAD
+// gtest-port.h guarantees to #include <pthread.h> when GTEST_HAS_PTHREAD is
+// true.
+# include <pthread.h> // NOLINT
+
+// For timespec and nanosleep, used below.
+# include <time.h> // NOLINT
+#endif
+
+// Determines whether Google Test can use tr1/tuple. You can define
+// this macro to 0 to prevent Google Test from using tuple (any
+// feature depending on tuple with be disabled in this mode).
+#ifndef GTEST_HAS_TR1_TUPLE
+# if GTEST_OS_LINUX_ANDROID && defined(_STLPORT_MAJOR)
+// STLport, provided with the Android NDK, has neither <tr1/tuple> or <tuple>.
+# define GTEST_HAS_TR1_TUPLE 0
+# else
+// The user didn't tell us not to do it, so we assume it's OK.
+# define GTEST_HAS_TR1_TUPLE 1
+# endif
+#endif // GTEST_HAS_TR1_TUPLE
+
+// Determines whether Google Test's own tr1 tuple implementation
+// should be used.
+#ifndef GTEST_USE_OWN_TR1_TUPLE
+// The user didn't tell us, so we need to figure it out.
+
+// We use our own TR1 tuple if we aren't sure the user has an
+// implementation of it already. At this time, libstdc++ 4.0.0+ and
+// MSVC 2010 are the only mainstream standard libraries that come
+// with a TR1 tuple implementation. NVIDIA's CUDA NVCC compiler
+// pretends to be GCC by defining __GNUC__ and friends, but cannot
+// compile GCC's tuple implementation. MSVC 2008 (9.0) provides TR1
+// tuple in a 323 MB Feature Pack download, which we cannot assume the
+// user has. QNX's QCC compiler is a modified GCC but it doesn't
+// support TR1 tuple. libc++ only provides std::tuple, in C++11 mode,
+// and it can be used with some compilers that define __GNUC__.
+# if (defined(__GNUC__) && !defined(__CUDACC__) && (GTEST_GCC_VER_ >= 40000) \
+ && !GTEST_OS_QNX && !defined(_LIBCPP_VERSION)) || _MSC_VER >= 1600
+# define GTEST_ENV_HAS_TR1_TUPLE_ 1
+# endif
+
+// C++11 specifies that <tuple> provides std::tuple. Use that if gtest is used
+// in C++11 mode and libstdc++ isn't very old (binaries targeting OS X 10.6
+// can build with clang but need to use gcc4.2's libstdc++).
+# if GTEST_LANG_CXX11 && (!defined(__GLIBCXX__) || __GLIBCXX__ > 20110325)
+# define GTEST_ENV_HAS_STD_TUPLE_ 1
+# endif
+
+# if GTEST_ENV_HAS_TR1_TUPLE_ || GTEST_ENV_HAS_STD_TUPLE_
+# define GTEST_USE_OWN_TR1_TUPLE 0
+# else
+# define GTEST_USE_OWN_TR1_TUPLE 1
+# endif
+
+#endif // GTEST_USE_OWN_TR1_TUPLE
+
+// To avoid conditional compilation everywhere, we make it
+// gtest-port.h's responsibility to #include the header implementing
+// tr1/tuple.
+#if GTEST_HAS_TR1_TUPLE
+
+# if GTEST_USE_OWN_TR1_TUPLE
+// This file was GENERATED by command:
+// pump.py gtest-tuple.h.pump
+// DO NOT EDIT BY HAND!!!
+
+// Copyright 2009 Google Inc.
+// All Rights Reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Implements a subset of TR1 tuple needed by Google Test and Google Mock.
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_TUPLE_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_TUPLE_H_
+
+#include <utility> // For ::std::pair.
+
+// The compiler used in Symbian has a bug that prevents us from declaring the
+// tuple template as a friend (it complains that tuple is redefined). This
+// hack bypasses the bug by declaring the members that should otherwise be
+// private as public.
+// Sun Studio versions < 12 also have the above bug.
+#if defined(__SYMBIAN32__) || (defined(__SUNPRO_CC) && __SUNPRO_CC < 0x590)
+# define GTEST_DECLARE_TUPLE_AS_FRIEND_ public:
+#else
+# define GTEST_DECLARE_TUPLE_AS_FRIEND_ \
+ template <GTEST_10_TYPENAMES_(U)> friend class tuple; \
+ private:
+#endif
+
+// GTEST_n_TUPLE_(T) is the type of an n-tuple.
+#define GTEST_0_TUPLE_(T) tuple<>
+#define GTEST_1_TUPLE_(T) tuple<T##0, void, void, void, void, void, void, \
+ void, void, void>
+#define GTEST_2_TUPLE_(T) tuple<T##0, T##1, void, void, void, void, void, \
+ void, void, void>
+#define GTEST_3_TUPLE_(T) tuple<T##0, T##1, T##2, void, void, void, void, \
+ void, void, void>
+#define GTEST_4_TUPLE_(T) tuple<T##0, T##1, T##2, T##3, void, void, void, \
+ void, void, void>
+#define GTEST_5_TUPLE_(T) tuple<T##0, T##1, T##2, T##3, T##4, void, void, \
+ void, void, void>
+#define GTEST_6_TUPLE_(T) tuple<T##0, T##1, T##2, T##3, T##4, T##5, void, \
+ void, void, void>
+#define GTEST_7_TUPLE_(T) tuple<T##0, T##1, T##2, T##3, T##4, T##5, T##6, \
+ void, void, void>
+#define GTEST_8_TUPLE_(T) tuple<T##0, T##1, T##2, T##3, T##4, T##5, T##6, \
+ T##7, void, void>
+#define GTEST_9_TUPLE_(T) tuple<T##0, T##1, T##2, T##3, T##4, T##5, T##6, \
+ T##7, T##8, void>
+#define GTEST_10_TUPLE_(T) tuple<T##0, T##1, T##2, T##3, T##4, T##5, T##6, \
+ T##7, T##8, T##9>
+
+// GTEST_n_TYPENAMES_(T) declares a list of n typenames.
+#define GTEST_0_TYPENAMES_(T)
+#define GTEST_1_TYPENAMES_(T) typename T##0
+#define GTEST_2_TYPENAMES_(T) typename T##0, typename T##1
+#define GTEST_3_TYPENAMES_(T) typename T##0, typename T##1, typename T##2
+#define GTEST_4_TYPENAMES_(T) typename T##0, typename T##1, typename T##2, \
+ typename T##3
+#define GTEST_5_TYPENAMES_(T) typename T##0, typename T##1, typename T##2, \
+ typename T##3, typename T##4
+#define GTEST_6_TYPENAMES_(T) typename T##0, typename T##1, typename T##2, \
+ typename T##3, typename T##4, typename T##5
+#define GTEST_7_TYPENAMES_(T) typename T##0, typename T##1, typename T##2, \
+ typename T##3, typename T##4, typename T##5, typename T##6
+#define GTEST_8_TYPENAMES_(T) typename T##0, typename T##1, typename T##2, \
+ typename T##3, typename T##4, typename T##5, typename T##6, typename T##7
+#define GTEST_9_TYPENAMES_(T) typename T##0, typename T##1, typename T##2, \
+ typename T##3, typename T##4, typename T##5, typename T##6, \
+ typename T##7, typename T##8
+#define GTEST_10_TYPENAMES_(T) typename T##0, typename T##1, typename T##2, \
+ typename T##3, typename T##4, typename T##5, typename T##6, \
+ typename T##7, typename T##8, typename T##9
+
+// In theory, defining stuff in the ::std namespace is undefined
+// behavior. We can do this as we are playing the role of a standard
+// library vendor.
+namespace std {
+namespace tr1 {
+
+template <typename T0 = void, typename T1 = void, typename T2 = void,
+ typename T3 = void, typename T4 = void, typename T5 = void,
+ typename T6 = void, typename T7 = void, typename T8 = void,
+ typename T9 = void>
+class tuple;
+
+// Anything in namespace gtest_internal is Google Test's INTERNAL
+// IMPLEMENTATION DETAIL and MUST NOT BE USED DIRECTLY in user code.
+namespace gtest_internal {
+
+// ByRef<T>::type is T if T is a reference; otherwise it's const T&.
+template <typename T>
+struct ByRef { typedef const T& type; }; // NOLINT
+template <typename T>
+struct ByRef<T&> { typedef T& type; }; // NOLINT
+
+// A handy wrapper for ByRef.
+#define GTEST_BY_REF_(T) typename ::std::tr1::gtest_internal::ByRef<T>::type
+
+// AddRef<T>::type is T if T is a reference; otherwise it's T&. This
+// is the same as tr1::add_reference<T>::type.
+template <typename T>
+struct AddRef { typedef T& type; }; // NOLINT
+template <typename T>
+struct AddRef<T&> { typedef T& type; }; // NOLINT
+
+// A handy wrapper for AddRef.
+#define GTEST_ADD_REF_(T) typename ::std::tr1::gtest_internal::AddRef<T>::type
+
+// A helper for implementing get<k>().
+template <int k> class Get;
+
+// A helper for implementing tuple_element<k, T>. kIndexValid is true
+// iff k < the number of fields in tuple type T.
+template <bool kIndexValid, int kIndex, class Tuple>
+struct TupleElement;
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 0, GTEST_10_TUPLE_(T) > {
+ typedef T0 type;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 1, GTEST_10_TUPLE_(T) > {
+ typedef T1 type;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 2, GTEST_10_TUPLE_(T) > {
+ typedef T2 type;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 3, GTEST_10_TUPLE_(T) > {
+ typedef T3 type;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 4, GTEST_10_TUPLE_(T) > {
+ typedef T4 type;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 5, GTEST_10_TUPLE_(T) > {
+ typedef T5 type;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 6, GTEST_10_TUPLE_(T) > {
+ typedef T6 type;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 7, GTEST_10_TUPLE_(T) > {
+ typedef T7 type;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 8, GTEST_10_TUPLE_(T) > {
+ typedef T8 type;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct TupleElement<true, 9, GTEST_10_TUPLE_(T) > {
+ typedef T9 type;
+};
+
+} // namespace gtest_internal
+
+template <>
+class tuple<> {
+ public:
+ tuple() {}
+ tuple(const tuple& /* t */) {}
+ tuple& operator=(const tuple& /* t */) { return *this; }
+};
+
+template <GTEST_1_TYPENAMES_(T)>
+class GTEST_1_TUPLE_(T) {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0) : f0_(f0) {}
+
+ tuple(const tuple& t) : f0_(t.f0_) {}
+
+ template <GTEST_1_TYPENAMES_(U)>
+ tuple(const GTEST_1_TUPLE_(U)& t) : f0_(t.f0_) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_1_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_1_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_1_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_1_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ return *this;
+ }
+
+ T0 f0_;
+};
+
+template <GTEST_2_TYPENAMES_(T)>
+class GTEST_2_TUPLE_(T) {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_(), f1_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0, GTEST_BY_REF_(T1) f1) : f0_(f0),
+ f1_(f1) {}
+
+ tuple(const tuple& t) : f0_(t.f0_), f1_(t.f1_) {}
+
+ template <GTEST_2_TYPENAMES_(U)>
+ tuple(const GTEST_2_TUPLE_(U)& t) : f0_(t.f0_), f1_(t.f1_) {}
+ template <typename U0, typename U1>
+ tuple(const ::std::pair<U0, U1>& p) : f0_(p.first), f1_(p.second) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_2_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_2_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+ template <typename U0, typename U1>
+ tuple& operator=(const ::std::pair<U0, U1>& p) {
+ f0_ = p.first;
+ f1_ = p.second;
+ return *this;
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_2_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_2_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ f1_ = t.f1_;
+ return *this;
+ }
+
+ T0 f0_;
+ T1 f1_;
+};
+
+template <GTEST_3_TYPENAMES_(T)>
+class GTEST_3_TUPLE_(T) {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_(), f1_(), f2_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0, GTEST_BY_REF_(T1) f1,
+ GTEST_BY_REF_(T2) f2) : f0_(f0), f1_(f1), f2_(f2) {}
+
+ tuple(const tuple& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_) {}
+
+ template <GTEST_3_TYPENAMES_(U)>
+ tuple(const GTEST_3_TUPLE_(U)& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_3_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_3_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_3_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_3_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ f1_ = t.f1_;
+ f2_ = t.f2_;
+ return *this;
+ }
+
+ T0 f0_;
+ T1 f1_;
+ T2 f2_;
+};
+
+template <GTEST_4_TYPENAMES_(T)>
+class GTEST_4_TUPLE_(T) {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_(), f1_(), f2_(), f3_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0, GTEST_BY_REF_(T1) f1,
+ GTEST_BY_REF_(T2) f2, GTEST_BY_REF_(T3) f3) : f0_(f0), f1_(f1), f2_(f2),
+ f3_(f3) {}
+
+ tuple(const tuple& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_), f3_(t.f3_) {}
+
+ template <GTEST_4_TYPENAMES_(U)>
+ tuple(const GTEST_4_TUPLE_(U)& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_),
+ f3_(t.f3_) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_4_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_4_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_4_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_4_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ f1_ = t.f1_;
+ f2_ = t.f2_;
+ f3_ = t.f3_;
+ return *this;
+ }
+
+ T0 f0_;
+ T1 f1_;
+ T2 f2_;
+ T3 f3_;
+};
+
+template <GTEST_5_TYPENAMES_(T)>
+class GTEST_5_TUPLE_(T) {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_(), f1_(), f2_(), f3_(), f4_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0, GTEST_BY_REF_(T1) f1,
+ GTEST_BY_REF_(T2) f2, GTEST_BY_REF_(T3) f3,
+ GTEST_BY_REF_(T4) f4) : f0_(f0), f1_(f1), f2_(f2), f3_(f3), f4_(f4) {}
+
+ tuple(const tuple& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_), f3_(t.f3_),
+ f4_(t.f4_) {}
+
+ template <GTEST_5_TYPENAMES_(U)>
+ tuple(const GTEST_5_TUPLE_(U)& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_),
+ f3_(t.f3_), f4_(t.f4_) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_5_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_5_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_5_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_5_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ f1_ = t.f1_;
+ f2_ = t.f2_;
+ f3_ = t.f3_;
+ f4_ = t.f4_;
+ return *this;
+ }
+
+ T0 f0_;
+ T1 f1_;
+ T2 f2_;
+ T3 f3_;
+ T4 f4_;
+};
+
+template <GTEST_6_TYPENAMES_(T)>
+class GTEST_6_TUPLE_(T) {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_(), f1_(), f2_(), f3_(), f4_(), f5_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0, GTEST_BY_REF_(T1) f1,
+ GTEST_BY_REF_(T2) f2, GTEST_BY_REF_(T3) f3, GTEST_BY_REF_(T4) f4,
+ GTEST_BY_REF_(T5) f5) : f0_(f0), f1_(f1), f2_(f2), f3_(f3), f4_(f4),
+ f5_(f5) {}
+
+ tuple(const tuple& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_), f3_(t.f3_),
+ f4_(t.f4_), f5_(t.f5_) {}
+
+ template <GTEST_6_TYPENAMES_(U)>
+ tuple(const GTEST_6_TUPLE_(U)& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_),
+ f3_(t.f3_), f4_(t.f4_), f5_(t.f5_) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_6_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_6_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_6_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_6_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ f1_ = t.f1_;
+ f2_ = t.f2_;
+ f3_ = t.f3_;
+ f4_ = t.f4_;
+ f5_ = t.f5_;
+ return *this;
+ }
+
+ T0 f0_;
+ T1 f1_;
+ T2 f2_;
+ T3 f3_;
+ T4 f4_;
+ T5 f5_;
+};
+
+template <GTEST_7_TYPENAMES_(T)>
+class GTEST_7_TUPLE_(T) {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_(), f1_(), f2_(), f3_(), f4_(), f5_(), f6_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0, GTEST_BY_REF_(T1) f1,
+ GTEST_BY_REF_(T2) f2, GTEST_BY_REF_(T3) f3, GTEST_BY_REF_(T4) f4,
+ GTEST_BY_REF_(T5) f5, GTEST_BY_REF_(T6) f6) : f0_(f0), f1_(f1), f2_(f2),
+ f3_(f3), f4_(f4), f5_(f5), f6_(f6) {}
+
+ tuple(const tuple& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_), f3_(t.f3_),
+ f4_(t.f4_), f5_(t.f5_), f6_(t.f6_) {}
+
+ template <GTEST_7_TYPENAMES_(U)>
+ tuple(const GTEST_7_TUPLE_(U)& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_),
+ f3_(t.f3_), f4_(t.f4_), f5_(t.f5_), f6_(t.f6_) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_7_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_7_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_7_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_7_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ f1_ = t.f1_;
+ f2_ = t.f2_;
+ f3_ = t.f3_;
+ f4_ = t.f4_;
+ f5_ = t.f5_;
+ f6_ = t.f6_;
+ return *this;
+ }
+
+ T0 f0_;
+ T1 f1_;
+ T2 f2_;
+ T3 f3_;
+ T4 f4_;
+ T5 f5_;
+ T6 f6_;
+};
+
+template <GTEST_8_TYPENAMES_(T)>
+class GTEST_8_TUPLE_(T) {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_(), f1_(), f2_(), f3_(), f4_(), f5_(), f6_(), f7_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0, GTEST_BY_REF_(T1) f1,
+ GTEST_BY_REF_(T2) f2, GTEST_BY_REF_(T3) f3, GTEST_BY_REF_(T4) f4,
+ GTEST_BY_REF_(T5) f5, GTEST_BY_REF_(T6) f6,
+ GTEST_BY_REF_(T7) f7) : f0_(f0), f1_(f1), f2_(f2), f3_(f3), f4_(f4),
+ f5_(f5), f6_(f6), f7_(f7) {}
+
+ tuple(const tuple& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_), f3_(t.f3_),
+ f4_(t.f4_), f5_(t.f5_), f6_(t.f6_), f7_(t.f7_) {}
+
+ template <GTEST_8_TYPENAMES_(U)>
+ tuple(const GTEST_8_TUPLE_(U)& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_),
+ f3_(t.f3_), f4_(t.f4_), f5_(t.f5_), f6_(t.f6_), f7_(t.f7_) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_8_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_8_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_8_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_8_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ f1_ = t.f1_;
+ f2_ = t.f2_;
+ f3_ = t.f3_;
+ f4_ = t.f4_;
+ f5_ = t.f5_;
+ f6_ = t.f6_;
+ f7_ = t.f7_;
+ return *this;
+ }
+
+ T0 f0_;
+ T1 f1_;
+ T2 f2_;
+ T3 f3_;
+ T4 f4_;
+ T5 f5_;
+ T6 f6_;
+ T7 f7_;
+};
+
+template <GTEST_9_TYPENAMES_(T)>
+class GTEST_9_TUPLE_(T) {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_(), f1_(), f2_(), f3_(), f4_(), f5_(), f6_(), f7_(), f8_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0, GTEST_BY_REF_(T1) f1,
+ GTEST_BY_REF_(T2) f2, GTEST_BY_REF_(T3) f3, GTEST_BY_REF_(T4) f4,
+ GTEST_BY_REF_(T5) f5, GTEST_BY_REF_(T6) f6, GTEST_BY_REF_(T7) f7,
+ GTEST_BY_REF_(T8) f8) : f0_(f0), f1_(f1), f2_(f2), f3_(f3), f4_(f4),
+ f5_(f5), f6_(f6), f7_(f7), f8_(f8) {}
+
+ tuple(const tuple& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_), f3_(t.f3_),
+ f4_(t.f4_), f5_(t.f5_), f6_(t.f6_), f7_(t.f7_), f8_(t.f8_) {}
+
+ template <GTEST_9_TYPENAMES_(U)>
+ tuple(const GTEST_9_TUPLE_(U)& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_),
+ f3_(t.f3_), f4_(t.f4_), f5_(t.f5_), f6_(t.f6_), f7_(t.f7_), f8_(t.f8_) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_9_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_9_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_9_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_9_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ f1_ = t.f1_;
+ f2_ = t.f2_;
+ f3_ = t.f3_;
+ f4_ = t.f4_;
+ f5_ = t.f5_;
+ f6_ = t.f6_;
+ f7_ = t.f7_;
+ f8_ = t.f8_;
+ return *this;
+ }
+
+ T0 f0_;
+ T1 f1_;
+ T2 f2_;
+ T3 f3_;
+ T4 f4_;
+ T5 f5_;
+ T6 f6_;
+ T7 f7_;
+ T8 f8_;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+class tuple {
+ public:
+ template <int k> friend class gtest_internal::Get;
+
+ tuple() : f0_(), f1_(), f2_(), f3_(), f4_(), f5_(), f6_(), f7_(), f8_(),
+ f9_() {}
+
+ explicit tuple(GTEST_BY_REF_(T0) f0, GTEST_BY_REF_(T1) f1,
+ GTEST_BY_REF_(T2) f2, GTEST_BY_REF_(T3) f3, GTEST_BY_REF_(T4) f4,
+ GTEST_BY_REF_(T5) f5, GTEST_BY_REF_(T6) f6, GTEST_BY_REF_(T7) f7,
+ GTEST_BY_REF_(T8) f8, GTEST_BY_REF_(T9) f9) : f0_(f0), f1_(f1), f2_(f2),
+ f3_(f3), f4_(f4), f5_(f5), f6_(f6), f7_(f7), f8_(f8), f9_(f9) {}
+
+ tuple(const tuple& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_), f3_(t.f3_),
+ f4_(t.f4_), f5_(t.f5_), f6_(t.f6_), f7_(t.f7_), f8_(t.f8_), f9_(t.f9_) {}
+
+ template <GTEST_10_TYPENAMES_(U)>
+ tuple(const GTEST_10_TUPLE_(U)& t) : f0_(t.f0_), f1_(t.f1_), f2_(t.f2_),
+ f3_(t.f3_), f4_(t.f4_), f5_(t.f5_), f6_(t.f6_), f7_(t.f7_), f8_(t.f8_),
+ f9_(t.f9_) {}
+
+ tuple& operator=(const tuple& t) { return CopyFrom(t); }
+
+ template <GTEST_10_TYPENAMES_(U)>
+ tuple& operator=(const GTEST_10_TUPLE_(U)& t) {
+ return CopyFrom(t);
+ }
+
+ GTEST_DECLARE_TUPLE_AS_FRIEND_
+
+ template <GTEST_10_TYPENAMES_(U)>
+ tuple& CopyFrom(const GTEST_10_TUPLE_(U)& t) {
+ f0_ = t.f0_;
+ f1_ = t.f1_;
+ f2_ = t.f2_;
+ f3_ = t.f3_;
+ f4_ = t.f4_;
+ f5_ = t.f5_;
+ f6_ = t.f6_;
+ f7_ = t.f7_;
+ f8_ = t.f8_;
+ f9_ = t.f9_;
+ return *this;
+ }
+
+ T0 f0_;
+ T1 f1_;
+ T2 f2_;
+ T3 f3_;
+ T4 f4_;
+ T5 f5_;
+ T6 f6_;
+ T7 f7_;
+ T8 f8_;
+ T9 f9_;
+};
+
+// 6.1.3.2 Tuple creation functions.
+
+// Known limitations: we don't support passing an
+// std::tr1::reference_wrapper<T> to make_tuple(). And we don't
+// implement tie().
+
+inline tuple<> make_tuple() { return tuple<>(); }
+
+template <GTEST_1_TYPENAMES_(T)>
+inline GTEST_1_TUPLE_(T) make_tuple(const T0& f0) {
+ return GTEST_1_TUPLE_(T)(f0);
+}
+
+template <GTEST_2_TYPENAMES_(T)>
+inline GTEST_2_TUPLE_(T) make_tuple(const T0& f0, const T1& f1) {
+ return GTEST_2_TUPLE_(T)(f0, f1);
+}
+
+template <GTEST_3_TYPENAMES_(T)>
+inline GTEST_3_TUPLE_(T) make_tuple(const T0& f0, const T1& f1, const T2& f2) {
+ return GTEST_3_TUPLE_(T)(f0, f1, f2);
+}
+
+template <GTEST_4_TYPENAMES_(T)>
+inline GTEST_4_TUPLE_(T) make_tuple(const T0& f0, const T1& f1, const T2& f2,
+ const T3& f3) {
+ return GTEST_4_TUPLE_(T)(f0, f1, f2, f3);
+}
+
+template <GTEST_5_TYPENAMES_(T)>
+inline GTEST_5_TUPLE_(T) make_tuple(const T0& f0, const T1& f1, const T2& f2,
+ const T3& f3, const T4& f4) {
+ return GTEST_5_TUPLE_(T)(f0, f1, f2, f3, f4);
+}
+
+template <GTEST_6_TYPENAMES_(T)>
+inline GTEST_6_TUPLE_(T) make_tuple(const T0& f0, const T1& f1, const T2& f2,
+ const T3& f3, const T4& f4, const T5& f5) {
+ return GTEST_6_TUPLE_(T)(f0, f1, f2, f3, f4, f5);
+}
+
+template <GTEST_7_TYPENAMES_(T)>
+inline GTEST_7_TUPLE_(T) make_tuple(const T0& f0, const T1& f1, const T2& f2,
+ const T3& f3, const T4& f4, const T5& f5, const T6& f6) {
+ return GTEST_7_TUPLE_(T)(f0, f1, f2, f3, f4, f5, f6);
+}
+
+template <GTEST_8_TYPENAMES_(T)>
+inline GTEST_8_TUPLE_(T) make_tuple(const T0& f0, const T1& f1, const T2& f2,
+ const T3& f3, const T4& f4, const T5& f5, const T6& f6, const T7& f7) {
+ return GTEST_8_TUPLE_(T)(f0, f1, f2, f3, f4, f5, f6, f7);
+}
+
+template <GTEST_9_TYPENAMES_(T)>
+inline GTEST_9_TUPLE_(T) make_tuple(const T0& f0, const T1& f1, const T2& f2,
+ const T3& f3, const T4& f4, const T5& f5, const T6& f6, const T7& f7,
+ const T8& f8) {
+ return GTEST_9_TUPLE_(T)(f0, f1, f2, f3, f4, f5, f6, f7, f8);
+}
+
+template <GTEST_10_TYPENAMES_(T)>
+inline GTEST_10_TUPLE_(T) make_tuple(const T0& f0, const T1& f1, const T2& f2,
+ const T3& f3, const T4& f4, const T5& f5, const T6& f6, const T7& f7,
+ const T8& f8, const T9& f9) {
+ return GTEST_10_TUPLE_(T)(f0, f1, f2, f3, f4, f5, f6, f7, f8, f9);
+}
+
+// 6.1.3.3 Tuple helper classes.
+
+template <typename Tuple> struct tuple_size;
+
+template <GTEST_0_TYPENAMES_(T)>
+struct tuple_size<GTEST_0_TUPLE_(T) > {
+ static const int value = 0;
+};
+
+template <GTEST_1_TYPENAMES_(T)>
+struct tuple_size<GTEST_1_TUPLE_(T) > {
+ static const int value = 1;
+};
+
+template <GTEST_2_TYPENAMES_(T)>
+struct tuple_size<GTEST_2_TUPLE_(T) > {
+ static const int value = 2;
+};
+
+template <GTEST_3_TYPENAMES_(T)>
+struct tuple_size<GTEST_3_TUPLE_(T) > {
+ static const int value = 3;
+};
+
+template <GTEST_4_TYPENAMES_(T)>
+struct tuple_size<GTEST_4_TUPLE_(T) > {
+ static const int value = 4;
+};
+
+template <GTEST_5_TYPENAMES_(T)>
+struct tuple_size<GTEST_5_TUPLE_(T) > {
+ static const int value = 5;
+};
+
+template <GTEST_6_TYPENAMES_(T)>
+struct tuple_size<GTEST_6_TUPLE_(T) > {
+ static const int value = 6;
+};
+
+template <GTEST_7_TYPENAMES_(T)>
+struct tuple_size<GTEST_7_TUPLE_(T) > {
+ static const int value = 7;
+};
+
+template <GTEST_8_TYPENAMES_(T)>
+struct tuple_size<GTEST_8_TUPLE_(T) > {
+ static const int value = 8;
+};
+
+template <GTEST_9_TYPENAMES_(T)>
+struct tuple_size<GTEST_9_TUPLE_(T) > {
+ static const int value = 9;
+};
+
+template <GTEST_10_TYPENAMES_(T)>
+struct tuple_size<GTEST_10_TUPLE_(T) > {
+ static const int value = 10;
+};
+
+template <int k, class Tuple>
+struct tuple_element {
+ typedef typename gtest_internal::TupleElement<
+ k < (tuple_size<Tuple>::value), k, Tuple>::type type;
+};
+
+#define GTEST_TUPLE_ELEMENT_(k, Tuple) typename tuple_element<k, Tuple >::type
+
+// 6.1.3.4 Element access.
+
+namespace gtest_internal {
+
+template <>
+class Get<0> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(0, Tuple))
+ Field(Tuple& t) { return t.f0_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(0, Tuple))
+ ConstField(const Tuple& t) { return t.f0_; }
+};
+
+template <>
+class Get<1> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(1, Tuple))
+ Field(Tuple& t) { return t.f1_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(1, Tuple))
+ ConstField(const Tuple& t) { return t.f1_; }
+};
+
+template <>
+class Get<2> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(2, Tuple))
+ Field(Tuple& t) { return t.f2_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(2, Tuple))
+ ConstField(const Tuple& t) { return t.f2_; }
+};
+
+template <>
+class Get<3> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(3, Tuple))
+ Field(Tuple& t) { return t.f3_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(3, Tuple))
+ ConstField(const Tuple& t) { return t.f3_; }
+};
+
+template <>
+class Get<4> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(4, Tuple))
+ Field(Tuple& t) { return t.f4_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(4, Tuple))
+ ConstField(const Tuple& t) { return t.f4_; }
+};
+
+template <>
+class Get<5> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(5, Tuple))
+ Field(Tuple& t) { return t.f5_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(5, Tuple))
+ ConstField(const Tuple& t) { return t.f5_; }
+};
+
+template <>
+class Get<6> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(6, Tuple))
+ Field(Tuple& t) { return t.f6_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(6, Tuple))
+ ConstField(const Tuple& t) { return t.f6_; }
+};
+
+template <>
+class Get<7> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(7, Tuple))
+ Field(Tuple& t) { return t.f7_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(7, Tuple))
+ ConstField(const Tuple& t) { return t.f7_; }
+};
+
+template <>
+class Get<8> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(8, Tuple))
+ Field(Tuple& t) { return t.f8_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(8, Tuple))
+ ConstField(const Tuple& t) { return t.f8_; }
+};
+
+template <>
+class Get<9> {
+ public:
+ template <class Tuple>
+ static GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(9, Tuple))
+ Field(Tuple& t) { return t.f9_; } // NOLINT
+
+ template <class Tuple>
+ static GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(9, Tuple))
+ ConstField(const Tuple& t) { return t.f9_; }
+};
+
+} // namespace gtest_internal
+
+template <int k, GTEST_10_TYPENAMES_(T)>
+GTEST_ADD_REF_(GTEST_TUPLE_ELEMENT_(k, GTEST_10_TUPLE_(T)))
+get(GTEST_10_TUPLE_(T)& t) {
+ return gtest_internal::Get<k>::Field(t);
+}
+
+template <int k, GTEST_10_TYPENAMES_(T)>
+GTEST_BY_REF_(GTEST_TUPLE_ELEMENT_(k, GTEST_10_TUPLE_(T)))
+get(const GTEST_10_TUPLE_(T)& t) {
+ return gtest_internal::Get<k>::ConstField(t);
+}
+
+// 6.1.3.5 Relational operators
+
+// We only implement == and !=, as we don't have a need for the rest yet.
+
+namespace gtest_internal {
+
+// SameSizeTuplePrefixComparator<k, k>::Eq(t1, t2) returns true if the
+// first k fields of t1 equals the first k fields of t2.
+// SameSizeTuplePrefixComparator(k1, k2) would be a compiler error if
+// k1 != k2.
+template <int kSize1, int kSize2>
+struct SameSizeTuplePrefixComparator;
+
+template <>
+struct SameSizeTuplePrefixComparator<0, 0> {
+ template <class Tuple1, class Tuple2>
+ static bool Eq(const Tuple1& /* t1 */, const Tuple2& /* t2 */) {
+ return true;
+ }
+};
+
+template <int k>
+struct SameSizeTuplePrefixComparator<k, k> {
+ template <class Tuple1, class Tuple2>
+ static bool Eq(const Tuple1& t1, const Tuple2& t2) {
+ return SameSizeTuplePrefixComparator<k - 1, k - 1>::Eq(t1, t2) &&
+ ::std::tr1::get<k - 1>(t1) == ::std::tr1::get<k - 1>(t2);
+ }
+};
+
+} // namespace gtest_internal
+
+template <GTEST_10_TYPENAMES_(T), GTEST_10_TYPENAMES_(U)>
+inline bool operator==(const GTEST_10_TUPLE_(T)& t,
+ const GTEST_10_TUPLE_(U)& u) {
+ return gtest_internal::SameSizeTuplePrefixComparator<
+ tuple_size<GTEST_10_TUPLE_(T) >::value,
+ tuple_size<GTEST_10_TUPLE_(U) >::value>::Eq(t, u);
+}
+
+template <GTEST_10_TYPENAMES_(T), GTEST_10_TYPENAMES_(U)>
+inline bool operator!=(const GTEST_10_TUPLE_(T)& t,
+ const GTEST_10_TUPLE_(U)& u) { return !(t == u); }
+
+// 6.1.4 Pairs.
+// Unimplemented.
+
+} // namespace tr1
+} // namespace std
+
+#undef GTEST_0_TUPLE_
+#undef GTEST_1_TUPLE_
+#undef GTEST_2_TUPLE_
+#undef GTEST_3_TUPLE_
+#undef GTEST_4_TUPLE_
+#undef GTEST_5_TUPLE_
+#undef GTEST_6_TUPLE_
+#undef GTEST_7_TUPLE_
+#undef GTEST_8_TUPLE_
+#undef GTEST_9_TUPLE_
+#undef GTEST_10_TUPLE_
+
+#undef GTEST_0_TYPENAMES_
+#undef GTEST_1_TYPENAMES_
+#undef GTEST_2_TYPENAMES_
+#undef GTEST_3_TYPENAMES_
+#undef GTEST_4_TYPENAMES_
+#undef GTEST_5_TYPENAMES_
+#undef GTEST_6_TYPENAMES_
+#undef GTEST_7_TYPENAMES_
+#undef GTEST_8_TYPENAMES_
+#undef GTEST_9_TYPENAMES_
+#undef GTEST_10_TYPENAMES_
+
+#undef GTEST_DECLARE_TUPLE_AS_FRIEND_
+#undef GTEST_BY_REF_
+#undef GTEST_ADD_REF_
+#undef GTEST_TUPLE_ELEMENT_
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_TUPLE_H_
+# elif GTEST_ENV_HAS_STD_TUPLE_
+# include <tuple>
+// C++11 puts its tuple into the ::std namespace rather than
+// ::std::tr1. gtest expects tuple to live in ::std::tr1, so put it there.
+// This causes undefined behavior, but supported compilers react in
+// the way we intend.
+namespace std {
+namespace tr1 {
+using ::std::get;
+using ::std::make_tuple;
+using ::std::tuple;
+using ::std::tuple_element;
+using ::std::tuple_size;
+}
+}
+
+# elif GTEST_OS_SYMBIAN
+
+// On Symbian, BOOST_HAS_TR1_TUPLE causes Boost's TR1 tuple library to
+// use STLport's tuple implementation, which unfortunately doesn't
+// work as the copy of STLport distributed with Symbian is incomplete.
+// By making sure BOOST_HAS_TR1_TUPLE is undefined, we force Boost to
+// use its own tuple implementation.
+# ifdef BOOST_HAS_TR1_TUPLE
+# undef BOOST_HAS_TR1_TUPLE
+# endif // BOOST_HAS_TR1_TUPLE
+
+// This prevents <boost/tr1/detail/config.hpp>, which defines
+// BOOST_HAS_TR1_TUPLE, from being #included by Boost's <tuple>.
+# define BOOST_TR1_DETAIL_CONFIG_HPP_INCLUDED
+# include <tuple>
+
+# elif defined(__GNUC__) && (GTEST_GCC_VER_ >= 40000)
+// GCC 4.0+ implements tr1/tuple in the <tr1/tuple> header. This does
+// not conform to the TR1 spec, which requires the header to be <tuple>.
+
+# if !GTEST_HAS_RTTI && GTEST_GCC_VER_ < 40302
+// Until version 4.3.2, gcc has a bug that causes <tr1/functional>,
+// which is #included by <tr1/tuple>, to not compile when RTTI is
+// disabled. _TR1_FUNCTIONAL is the header guard for
+// <tr1/functional>. Hence the following #define is a hack to prevent
+// <tr1/functional> from being included.
+# define _TR1_FUNCTIONAL 1
+# include <tr1/tuple>
+# undef _TR1_FUNCTIONAL // Allows the user to #include
+ // <tr1/functional> if he chooses to.
+# else
+# include <tr1/tuple> // NOLINT
+# endif // !GTEST_HAS_RTTI && GTEST_GCC_VER_ < 40302
+
+# else
+// If the compiler is not GCC 4.0+, we assume the user is using a
+// spec-conforming TR1 implementation.
+# include <tuple> // NOLINT
+# endif // GTEST_USE_OWN_TR1_TUPLE
+
+#endif // GTEST_HAS_TR1_TUPLE
+
+// Determines whether clone(2) is supported.
+// Usually it will only be available on Linux, excluding
+// Linux on the Itanium architecture.
+// Also see http://linux.die.net/man/2/clone.
+#ifndef GTEST_HAS_CLONE
+// The user didn't tell us, so we need to figure it out.
+
+# if GTEST_OS_LINUX && !defined(__ia64__)
+# if GTEST_OS_LINUX_ANDROID
+// On Android, clone() is only available on ARM starting with Gingerbread.
+# if defined(__arm__) && __ANDROID_API__ >= 9
+# define GTEST_HAS_CLONE 1
+# else
+# define GTEST_HAS_CLONE 0
+# endif
+# else
+# define GTEST_HAS_CLONE 1
+# endif
+# else
+# define GTEST_HAS_CLONE 0
+# endif // GTEST_OS_LINUX && !defined(__ia64__)
+
+#endif // GTEST_HAS_CLONE
+
+// Determines whether to support stream redirection. This is used to test
+// output correctness and to implement death tests.
+#ifndef GTEST_HAS_STREAM_REDIRECTION
+// By default, we assume that stream redirection is supported on all
+// platforms except known mobile ones.
+# if GTEST_OS_WINDOWS_MOBILE || GTEST_OS_SYMBIAN
+# define GTEST_HAS_STREAM_REDIRECTION 0
+# else
+# define GTEST_HAS_STREAM_REDIRECTION 1
+# endif // !GTEST_OS_WINDOWS_MOBILE && !GTEST_OS_SYMBIAN
+#endif // GTEST_HAS_STREAM_REDIRECTION
+
+// Determines whether to support death tests.
+// Google Test does not support death tests for VC 7.1 and earlier as
+// abort() in a VC 7.1 application compiled as GUI in debug config
+// pops up a dialog window that cannot be suppressed programmatically.
+#if (GTEST_OS_LINUX || GTEST_OS_CYGWIN || GTEST_OS_SOLARIS || \
+ (GTEST_OS_MAC && !GTEST_OS_IOS) || GTEST_OS_IOS_SIMULATOR || \
+ (GTEST_OS_WINDOWS_DESKTOP && _MSC_VER >= 1400) || \
+ GTEST_OS_WINDOWS_MINGW || GTEST_OS_AIX || GTEST_OS_HPUX || \
+ GTEST_OS_OPENBSD || GTEST_OS_QNX)
+# define GTEST_HAS_DEATH_TEST 1
+# include <vector> // NOLINT
+#endif
+
+// We don't support MSVC 7.1 with exceptions disabled now. Therefore
+// all the compilers we care about are adequate for supporting
+// value-parameterized tests.
+#define GTEST_HAS_PARAM_TEST 1
+
+// Determines whether to support type-driven tests.
+
+// Typed tests need <typeinfo> and variadic macros, which GCC, VC++ 8.0,
+// Sun Pro CC, IBM Visual Age, and HP aCC support.
+#if defined(__GNUC__) || (_MSC_VER >= 1400) || defined(__SUNPRO_CC) || \
+ defined(__IBMCPP__) || defined(__HP_aCC)
+# define GTEST_HAS_TYPED_TEST 1
+# define GTEST_HAS_TYPED_TEST_P 1
+#endif
+
+// Determines whether to support Combine(). This only makes sense when
+// value-parameterized tests are enabled. The implementation doesn't
+// work on Sun Studio since it doesn't understand templated conversion
+// operators.
+#if GTEST_HAS_PARAM_TEST && GTEST_HAS_TR1_TUPLE && !defined(__SUNPRO_CC)
+# define GTEST_HAS_COMBINE 1
+#endif
+
+// Determines whether the system compiler uses UTF-16 for encoding wide strings.
+#define GTEST_WIDE_STRING_USES_UTF16_ \
+ (GTEST_OS_WINDOWS || GTEST_OS_CYGWIN || GTEST_OS_SYMBIAN || GTEST_OS_AIX)
+
+// Determines whether test results can be streamed to a socket.
+#if GTEST_OS_LINUX
+# define GTEST_CAN_STREAM_RESULTS_ 1
+#endif
+
+// Defines some utility macros.
+
+// The GNU compiler emits a warning if nested "if" statements are followed by
+// an "else" statement and braces are not used to explicitly disambiguate the
+// "else" binding. This leads to problems with code like:
+//
+// if (gate)
+// ASSERT_*(condition) << "Some message";
+//
+// The "switch (0) case 0:" idiom is used to suppress this.
+#ifdef __INTEL_COMPILER
+# define GTEST_AMBIGUOUS_ELSE_BLOCKER_
+#else
+# define GTEST_AMBIGUOUS_ELSE_BLOCKER_ switch (0) case 0: default: // NOLINT
+#endif
+
+// Use this annotation at the end of a struct/class definition to
+// prevent the compiler from optimizing away instances that are never
+// used. This is useful when all interesting logic happens inside the
+// c'tor and / or d'tor. Example:
+//
+// struct Foo {
+// Foo() { ... }
+// } GTEST_ATTRIBUTE_UNUSED_;
+//
+// Also use it after a variable or parameter declaration to tell the
+// compiler the variable/parameter does not have to be used.
+#if defined(__GNUC__) && !defined(COMPILER_ICC)
+# define GTEST_ATTRIBUTE_UNUSED_ __attribute__ ((unused))
+#else
+# define GTEST_ATTRIBUTE_UNUSED_
+#endif
+
+// A macro to disallow operator=
+// This should be used in the private: declarations for a class.
+#define GTEST_DISALLOW_ASSIGN_(type)\
+ void operator=(type const &)
+
+// A macro to disallow copy constructor and operator=
+// This should be used in the private: declarations for a class.
+#define GTEST_DISALLOW_COPY_AND_ASSIGN_(type)\
+ type(type const &);\
+ GTEST_DISALLOW_ASSIGN_(type)
+
+// Tell the compiler to warn about unused return values for functions declared
+// with this macro. The macro should be used on function declarations
+// following the argument list:
+//
+// Sprocket* AllocateSprocket() GTEST_MUST_USE_RESULT_;
+#if defined(__GNUC__) && (GTEST_GCC_VER_ >= 30400) && !defined(COMPILER_ICC)
+# define GTEST_MUST_USE_RESULT_ __attribute__ ((warn_unused_result))
+#else
+# define GTEST_MUST_USE_RESULT_
+#endif // __GNUC__ && (GTEST_GCC_VER_ >= 30400) && !COMPILER_ICC
+
+// Determine whether the compiler supports Microsoft's Structured Exception
+// Handling. This is supported by several Windows compilers but generally
+// does not exist on any other system.
+#ifndef GTEST_HAS_SEH
+// The user didn't tell us, so we need to figure it out.
+
+# if defined(_MSC_VER) || defined(__BORLANDC__)
+// These two compilers are known to support SEH.
+# define GTEST_HAS_SEH 1
+# else
+// Assume no SEH.
+# define GTEST_HAS_SEH 0
+# endif
+
+#endif // GTEST_HAS_SEH
+
+#ifdef _MSC_VER
+
+# if GTEST_LINKED_AS_SHARED_LIBRARY
+# define GTEST_API_ __declspec(dllimport)
+# elif GTEST_CREATE_SHARED_LIBRARY
+# define GTEST_API_ __declspec(dllexport)
+# endif
+
+#endif // _MSC_VER
+
+#ifndef GTEST_API_
+# define GTEST_API_
+#endif
+
+#ifdef __GNUC__
+// Ask the compiler to never inline a given function.
+# define GTEST_NO_INLINE_ __attribute__((noinline))
+#else
+# define GTEST_NO_INLINE_
+#endif
+
+// _LIBCPP_VERSION is defined by the libc++ library from the LLVM project.
+#if defined(__GLIBCXX__) || defined(_LIBCPP_VERSION)
+# define GTEST_HAS_CXXABI_H_ 1
+#else
+# define GTEST_HAS_CXXABI_H_ 0
+#endif
+
+namespace testing {
+
+class Message;
+
+namespace internal {
+
+// A secret type that Google Test users don't know about. It has no
+// definition on purpose. Therefore it's impossible to create a
+// Secret object, which is what we want.
+class Secret;
+
+// The GTEST_COMPILE_ASSERT_ macro can be used to verify that a compile time
+// expression is true. For example, you could use it to verify the
+// size of a static array:
+//
+// GTEST_COMPILE_ASSERT_(ARRAYSIZE(content_type_names) == CONTENT_NUM_TYPES,
+// content_type_names_incorrect_size);
+//
+// or to make sure a struct is smaller than a certain size:
+//
+// GTEST_COMPILE_ASSERT_(sizeof(foo) < 128, foo_too_large);
+//
+// The second argument to the macro is the name of the variable. If
+// the expression is false, most compilers will issue a warning/error
+// containing the name of the variable.
+
+template <bool>
+struct CompileAssert {
+};
+
+#define GTEST_COMPILE_ASSERT_(expr, msg) \
+ typedef ::testing::internal::CompileAssert<(static_cast<bool>(expr))> \
+ msg[static_cast<bool>(expr) ? 1 : -1] GTEST_ATTRIBUTE_UNUSED_
+
+// Implementation details of GTEST_COMPILE_ASSERT_:
+//
+// - GTEST_COMPILE_ASSERT_ works by defining an array type that has -1
+// elements (and thus is invalid) when the expression is false.
+//
+// - The simpler definition
+//
+// #define GTEST_COMPILE_ASSERT_(expr, msg) typedef char msg[(expr) ? 1 : -1]
+//
+// does not work, as gcc supports variable-length arrays whose sizes
+// are determined at run-time (this is gcc's extension and not part
+// of the C++ standard). As a result, gcc fails to reject the
+// following code with the simple definition:
+//
+// int foo;
+// GTEST_COMPILE_ASSERT_(foo, msg); // not supposed to compile as foo is
+// // not a compile-time constant.
+//
+// - By using the type CompileAssert<(bool(expr))>, we ensures that
+// expr is a compile-time constant. (Template arguments must be
+// determined at compile-time.)
+//
+// - The outter parentheses in CompileAssert<(bool(expr))> are necessary
+// to work around a bug in gcc 3.4.4 and 4.0.1. If we had written
+//
+// CompileAssert<bool(expr)>
+//
+// instead, these compilers will refuse to compile
+//
+// GTEST_COMPILE_ASSERT_(5 > 0, some_message);
+//
+// (They seem to think the ">" in "5 > 0" marks the end of the
+// template argument list.)
+//
+// - The array size is (bool(expr) ? 1 : -1), instead of simply
+//
+// ((expr) ? 1 : -1).
+//
+// This is to avoid running into a bug in MS VC 7.1, which
+// causes ((0.0) ? 1 : -1) to incorrectly evaluate to 1.
+
+// StaticAssertTypeEqHelper is used by StaticAssertTypeEq defined in gtest.h.
+//
+// This template is declared, but intentionally undefined.
+template <typename T1, typename T2>
+struct StaticAssertTypeEqHelper;
+
+template <typename T>
+struct StaticAssertTypeEqHelper<T, T> {};
+
+#if GTEST_HAS_GLOBAL_STRING
+typedef ::string string;
+#else
+typedef ::std::string string;
+#endif // GTEST_HAS_GLOBAL_STRING
+
+#if GTEST_HAS_GLOBAL_WSTRING
+typedef ::wstring wstring;
+#elif GTEST_HAS_STD_WSTRING
+typedef ::std::wstring wstring;
+#endif // GTEST_HAS_GLOBAL_WSTRING
+
+// A helper for suppressing warnings on constant condition. It just
+// returns 'condition'.
+GTEST_API_ bool IsTrue(bool condition);
+
+// Defines scoped_ptr.
+
+// This implementation of scoped_ptr is PARTIAL - it only contains
+// enough stuff to satisfy Google Test's need.
+template <typename T>
+class scoped_ptr {
+ public:
+ typedef T element_type;
+
+ explicit scoped_ptr(T* p = NULL) : ptr_(p) {}
+ ~scoped_ptr() { reset(); }
+
+ T& operator*() const { return *ptr_; }
+ T* operator->() const { return ptr_; }
+ T* get() const { return ptr_; }
+
+ T* release() {
+ T* const ptr = ptr_;
+ ptr_ = NULL;
+ return ptr;
+ }
+
+ void reset(T* p = NULL) {
+ if (p != ptr_) {
+ if (IsTrue(sizeof(T) > 0)) { // Makes sure T is a complete type.
+ delete ptr_;
+ }
+ ptr_ = p;
+ }
+ }
+
+ private:
+ T* ptr_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(scoped_ptr);
+};
+
+// Defines RE.
+
+// A simple C++ wrapper for <regex.h>. It uses the POSIX Extended
+// Regular Expression syntax.
+class GTEST_API_ RE {
+ public:
+ // A copy constructor is required by the Standard to initialize object
+ // references from r-values.
+ RE(const RE& other) { Init(other.pattern()); }
+
+ // Constructs an RE from a string.
+ RE(const ::std::string& regex) { Init(regex.c_str()); } // NOLINT
+
+#if GTEST_HAS_GLOBAL_STRING
+
+ RE(const ::string& regex) { Init(regex.c_str()); } // NOLINT
+
+#endif // GTEST_HAS_GLOBAL_STRING
+
+ RE(const char* regex) { Init(regex); } // NOLINT
+ ~RE();
+
+ // Returns the string representation of the regex.
+ const char* pattern() const { return pattern_; }
+
+ // FullMatch(str, re) returns true iff regular expression re matches
+ // the entire str.
+ // PartialMatch(str, re) returns true iff regular expression re
+ // matches a substring of str (including str itself).
+ //
+ // TODO(wan at google.com): make FullMatch() and PartialMatch() work
+ // when str contains NUL characters.
+ static bool FullMatch(const ::std::string& str, const RE& re) {
+ return FullMatch(str.c_str(), re);
+ }
+ static bool PartialMatch(const ::std::string& str, const RE& re) {
+ return PartialMatch(str.c_str(), re);
+ }
+
+#if GTEST_HAS_GLOBAL_STRING
+
+ static bool FullMatch(const ::string& str, const RE& re) {
+ return FullMatch(str.c_str(), re);
+ }
+ static bool PartialMatch(const ::string& str, const RE& re) {
+ return PartialMatch(str.c_str(), re);
+ }
+
+#endif // GTEST_HAS_GLOBAL_STRING
+
+ static bool FullMatch(const char* str, const RE& re);
+ static bool PartialMatch(const char* str, const RE& re);
+
+ private:
+ void Init(const char* regex);
+
+ // We use a const char* instead of an std::string, as Google Test used to be
+ // used where std::string is not available. TODO(wan at google.com): change to
+ // std::string.
+ const char* pattern_;
+ bool is_valid_;
+
+#if GTEST_USES_POSIX_RE
+
+ regex_t full_regex_; // For FullMatch().
+ regex_t partial_regex_; // For PartialMatch().
+
+#else // GTEST_USES_SIMPLE_RE
+
+ const char* full_pattern_; // For FullMatch();
+
+#endif
+
+ GTEST_DISALLOW_ASSIGN_(RE);
+};
+
+// Formats a source file path and a line number as they would appear
+// in an error message from the compiler used to compile this code.
+GTEST_API_ ::std::string FormatFileLocation(const char* file, int line);
+
+// Formats a file location for compiler-independent XML output.
+// Although this function is not platform dependent, we put it next to
+// FormatFileLocation in order to contrast the two functions.
+GTEST_API_ ::std::string FormatCompilerIndependentFileLocation(const char* file,
+ int line);
+
+// Defines logging utilities:
+// GTEST_LOG_(severity) - logs messages at the specified severity level. The
+// message itself is streamed into the macro.
+// LogToStderr() - directs all log messages to stderr.
+// FlushInfoLog() - flushes informational log messages.
+
+enum GTestLogSeverity {
+ GTEST_INFO,
+ GTEST_WARNING,
+ GTEST_ERROR,
+ GTEST_FATAL
+};
+
+// Formats log entry severity, provides a stream object for streaming the
+// log message, and terminates the message with a newline when going out of
+// scope.
+class GTEST_API_ GTestLog {
+ public:
+ GTestLog(GTestLogSeverity severity, const char* file, int line);
+
+ // Flushes the buffers and, if severity is GTEST_FATAL, aborts the program.
+ ~GTestLog();
+
+ ::std::ostream& GetStream() { return ::std::cerr; }
+
+ private:
+ const GTestLogSeverity severity_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(GTestLog);
+};
+
+#define GTEST_LOG_(severity) \
+ ::testing::internal::GTestLog(::testing::internal::GTEST_##severity, \
+ __FILE__, __LINE__).GetStream()
+
+inline void LogToStderr() {}
+inline void FlushInfoLog() { fflush(NULL); }
+
+// INTERNAL IMPLEMENTATION - DO NOT USE.
+//
+// GTEST_CHECK_ is an all-mode assert. It aborts the program if the condition
+// is not satisfied.
+// Synopsys:
+// GTEST_CHECK_(boolean_condition);
+// or
+// GTEST_CHECK_(boolean_condition) << "Additional message";
+//
+// This checks the condition and if the condition is not satisfied
+// it prints message about the condition violation, including the
+// condition itself, plus additional message streamed into it, if any,
+// and then it aborts the program. It aborts the program irrespective of
+// whether it is built in the debug mode or not.
+#define GTEST_CHECK_(condition) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (::testing::internal::IsTrue(condition)) \
+ ; \
+ else \
+ GTEST_LOG_(FATAL) << "Condition " #condition " failed. "
+
+// An all-mode assert to verify that the given POSIX-style function
+// call returns 0 (indicating success). Known limitation: this
+// doesn't expand to a balanced 'if' statement, so enclose the macro
+// in {} if you need to use it as the only statement in an 'if'
+// branch.
+#define GTEST_CHECK_POSIX_SUCCESS_(posix_call) \
+ if (const int gtest_error = (posix_call)) \
+ GTEST_LOG_(FATAL) << #posix_call << "failed with error " \
+ << gtest_error
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// Use ImplicitCast_ as a safe version of static_cast for upcasting in
+// the type hierarchy (e.g. casting a Foo* to a SuperclassOfFoo* or a
+// const Foo*). When you use ImplicitCast_, the compiler checks that
+// the cast is safe. Such explicit ImplicitCast_s are necessary in
+// surprisingly many situations where C++ demands an exact type match
+// instead of an argument type convertable to a target type.
+//
+// The syntax for using ImplicitCast_ is the same as for static_cast:
+//
+// ImplicitCast_<ToType>(expr)
+//
+// ImplicitCast_ would have been part of the C++ standard library,
+// but the proposal was submitted too late. It will probably make
+// its way into the language in the future.
+//
+// This relatively ugly name is intentional. It prevents clashes with
+// similar functions users may have (e.g., implicit_cast). The internal
+// namespace alone is not enough because the function can be found by ADL.
+template<typename To>
+inline To ImplicitCast_(To x) { return x; }
+
+// When you upcast (that is, cast a pointer from type Foo to type
+// SuperclassOfFoo), it's fine to use ImplicitCast_<>, since upcasts
+// always succeed. When you downcast (that is, cast a pointer from
+// type Foo to type SubclassOfFoo), static_cast<> isn't safe, because
+// how do you know the pointer is really of type SubclassOfFoo? It
+// could be a bare Foo, or of type DifferentSubclassOfFoo. Thus,
+// when you downcast, you should use this macro. In debug mode, we
+// use dynamic_cast<> to double-check the downcast is legal (we die
+// if it's not). In normal mode, we do the efficient static_cast<>
+// instead. Thus, it's important to test in debug mode to make sure
+// the cast is legal!
+// This is the only place in the code we should use dynamic_cast<>.
+// In particular, you SHOULDN'T be using dynamic_cast<> in order to
+// do RTTI (eg code like this:
+// if (dynamic_cast<Subclass1>(foo)) HandleASubclass1Object(foo);
+// if (dynamic_cast<Subclass2>(foo)) HandleASubclass2Object(foo);
+// You should design the code some other way not to need this.
+//
+// This relatively ugly name is intentional. It prevents clashes with
+// similar functions users may have (e.g., down_cast). The internal
+// namespace alone is not enough because the function can be found by ADL.
+template<typename To, typename From> // use like this: DownCast_<T*>(foo);
+inline To DownCast_(From* f) { // so we only accept pointers
+ // Ensures that To is a sub-type of From *. This test is here only
+ // for compile-time type checking, and has no overhead in an
+ // optimized build at run-time, as it will be optimized away
+ // completely.
+ if (false) {
+ const To to = NULL;
+ ::testing::internal::ImplicitCast_<From*>(to);
+ }
+
+#if GTEST_HAS_RTTI
+ // RTTI: debug mode only!
+ GTEST_CHECK_(f == NULL || dynamic_cast<To>(f) != NULL);
+#endif
+ return static_cast<To>(f);
+}
+
+// Downcasts the pointer of type Base to Derived.
+// Derived must be a subclass of Base. The parameter MUST
+// point to a class of type Derived, not any subclass of it.
+// When RTTI is available, the function performs a runtime
+// check to enforce this.
+template <class Derived, class Base>
+Derived* CheckedDowncastToActualType(Base* base) {
+#if GTEST_HAS_RTTI
+ GTEST_CHECK_(typeid(*base) == typeid(Derived));
+ return dynamic_cast<Derived*>(base); // NOLINT
+#else
+ return static_cast<Derived*>(base); // Poor man's downcast.
+#endif
+}
+
+#if GTEST_HAS_STREAM_REDIRECTION
+
+// Defines the stderr capturer:
+// CaptureStdout - starts capturing stdout.
+// GetCapturedStdout - stops capturing stdout and returns the captured string.
+// CaptureStderr - starts capturing stderr.
+// GetCapturedStderr - stops capturing stderr and returns the captured string.
+//
+GTEST_API_ void CaptureStdout();
+GTEST_API_ std::string GetCapturedStdout();
+GTEST_API_ void CaptureStderr();
+GTEST_API_ std::string GetCapturedStderr();
+
+#endif // GTEST_HAS_STREAM_REDIRECTION
+
+
+#if GTEST_HAS_DEATH_TEST
+
+const ::std::vector<testing::internal::string>& GetInjectableArgvs();
+void SetInjectableArgvs(const ::std::vector<testing::internal::string>*
+ new_argvs);
+
+// A copy of all command line arguments. Set by InitGoogleTest().
+extern ::std::vector<testing::internal::string> g_argvs;
+
+#endif // GTEST_HAS_DEATH_TEST
+
+// Defines synchronization primitives.
+
+#if GTEST_HAS_PTHREAD
+
+// Sleeps for (roughly) n milli-seconds. This function is only for
+// testing Google Test's own constructs. Don't use it in user tests,
+// either directly or indirectly.
+inline void SleepMilliseconds(int n) {
+ const timespec time = {
+ 0, // 0 seconds.
+ n * 1000L * 1000L, // And n ms.
+ };
+ nanosleep(&time, NULL);
+}
+
+// Allows a controller thread to pause execution of newly created
+// threads until notified. Instances of this class must be created
+// and destroyed in the controller thread.
+//
+// This class is only for testing Google Test's own constructs. Do not
+// use it in user tests, either directly or indirectly.
+class Notification {
+ public:
+ Notification() : notified_(false) {
+ GTEST_CHECK_POSIX_SUCCESS_(pthread_mutex_init(&mutex_, NULL));
+ }
+ ~Notification() {
+ pthread_mutex_destroy(&mutex_);
+ }
+
+ // Notifies all threads created with this notification to start. Must
+ // be called from the controller thread.
+ void Notify() {
+ pthread_mutex_lock(&mutex_);
+ notified_ = true;
+ pthread_mutex_unlock(&mutex_);
+ }
+
+ // Blocks until the controller thread notifies. Must be called from a test
+ // thread.
+ void WaitForNotification() {
+ for (;;) {
+ pthread_mutex_lock(&mutex_);
+ const bool notified = notified_;
+ pthread_mutex_unlock(&mutex_);
+ if (notified)
+ break;
+ SleepMilliseconds(10);
+ }
+ }
+
+ private:
+ pthread_mutex_t mutex_;
+ bool notified_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(Notification);
+};
+
+// As a C-function, ThreadFuncWithCLinkage cannot be templated itself.
+// Consequently, it cannot select a correct instantiation of ThreadWithParam
+// in order to call its Run(). Introducing ThreadWithParamBase as a
+// non-templated base class for ThreadWithParam allows us to bypass this
+// problem.
+class ThreadWithParamBase {
+ public:
+ virtual ~ThreadWithParamBase() {}
+ virtual void Run() = 0;
+};
+
+// pthread_create() accepts a pointer to a function type with the C linkage.
+// According to the Standard (7.5/1), function types with different linkages
+// are different even if they are otherwise identical. Some compilers (for
+// example, SunStudio) treat them as different types. Since class methods
+// cannot be defined with C-linkage we need to define a free C-function to
+// pass into pthread_create().
+extern "C" inline void* ThreadFuncWithCLinkage(void* thread) {
+ static_cast<ThreadWithParamBase*>(thread)->Run();
+ return NULL;
+}
+
+// Helper class for testing Google Test's multi-threading constructs.
+// To use it, write:
+//
+// void ThreadFunc(int param) { /* Do things with param */ }
+// Notification thread_can_start;
+// ...
+// // The thread_can_start parameter is optional; you can supply NULL.
+// ThreadWithParam<int> thread(&ThreadFunc, 5, &thread_can_start);
+// thread_can_start.Notify();
+//
+// These classes are only for testing Google Test's own constructs. Do
+// not use them in user tests, either directly or indirectly.
+template <typename T>
+class ThreadWithParam : public ThreadWithParamBase {
+ public:
+ typedef void (*UserThreadFunc)(T);
+
+ ThreadWithParam(
+ UserThreadFunc func, T param, Notification* thread_can_start)
+ : func_(func),
+ param_(param),
+ thread_can_start_(thread_can_start),
+ finished_(false) {
+ ThreadWithParamBase* const base = this;
+ // The thread can be created only after all fields except thread_
+ // have been initialized.
+ GTEST_CHECK_POSIX_SUCCESS_(
+ pthread_create(&thread_, 0, &ThreadFuncWithCLinkage, base));
+ }
+ ~ThreadWithParam() { Join(); }
+
+ void Join() {
+ if (!finished_) {
+ GTEST_CHECK_POSIX_SUCCESS_(pthread_join(thread_, 0));
+ finished_ = true;
+ }
+ }
+
+ virtual void Run() {
+ if (thread_can_start_ != NULL)
+ thread_can_start_->WaitForNotification();
+ func_(param_);
+ }
+
+ private:
+ const UserThreadFunc func_; // User-supplied thread function.
+ const T param_; // User-supplied parameter to the thread function.
+ // When non-NULL, used to block execution until the controller thread
+ // notifies.
+ Notification* const thread_can_start_;
+ bool finished_; // true iff we know that the thread function has finished.
+ pthread_t thread_; // The native thread object.
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ThreadWithParam);
+};
+
+// MutexBase and Mutex implement mutex on pthreads-based platforms. They
+// are used in conjunction with class MutexLock:
+//
+// Mutex mutex;
+// ...
+// MutexLock lock(&mutex); // Acquires the mutex and releases it at the end
+// // of the current scope.
+//
+// MutexBase implements behavior for both statically and dynamically
+// allocated mutexes. Do not use MutexBase directly. Instead, write
+// the following to define a static mutex:
+//
+// GTEST_DEFINE_STATIC_MUTEX_(g_some_mutex);
+//
+// You can forward declare a static mutex like this:
+//
+// GTEST_DECLARE_STATIC_MUTEX_(g_some_mutex);
+//
+// To create a dynamic mutex, just define an object of type Mutex.
+class MutexBase {
+ public:
+ // Acquires this mutex.
+ void Lock() {
+ GTEST_CHECK_POSIX_SUCCESS_(pthread_mutex_lock(&mutex_));
+ owner_ = pthread_self();
+ has_owner_ = true;
+ }
+
+ // Releases this mutex.
+ void Unlock() {
+ // Since the lock is being released the owner_ field should no longer be
+ // considered valid. We don't protect writing to has_owner_ here, as it's
+ // the caller's responsibility to ensure that the current thread holds the
+ // mutex when this is called.
+ has_owner_ = false;
+ GTEST_CHECK_POSIX_SUCCESS_(pthread_mutex_unlock(&mutex_));
+ }
+
+ // Does nothing if the current thread holds the mutex. Otherwise, crashes
+ // with high probability.
+ void AssertHeld() const {
+ GTEST_CHECK_(has_owner_ && pthread_equal(owner_, pthread_self()))
+ << "The current thread is not holding the mutex @" << this;
+ }
+
+ // A static mutex may be used before main() is entered. It may even
+ // be used before the dynamic initialization stage. Therefore we
+ // must be able to initialize a static mutex object at link time.
+ // This means MutexBase has to be a POD and its member variables
+ // have to be public.
+ public:
+ pthread_mutex_t mutex_; // The underlying pthread mutex.
+ // has_owner_ indicates whether the owner_ field below contains a valid thread
+ // ID and is therefore safe to inspect (e.g., to use in pthread_equal()). All
+ // accesses to the owner_ field should be protected by a check of this field.
+ // An alternative might be to memset() owner_ to all zeros, but there's no
+ // guarantee that a zero'd pthread_t is necessarily invalid or even different
+ // from pthread_self().
+ bool has_owner_;
+ pthread_t owner_; // The thread holding the mutex.
+};
+
+// Forward-declares a static mutex.
+# define GTEST_DECLARE_STATIC_MUTEX_(mutex) \
+ extern ::testing::internal::MutexBase mutex
+
+// Defines and statically (i.e. at link time) initializes a static mutex.
+// The initialization list here does not explicitly initialize each field,
+// instead relying on default initialization for the unspecified fields. In
+// particular, the owner_ field (a pthread_t) is not explicitly initialized.
+// This allows initialization to work whether pthread_t is a scalar or struct.
+// The flag -Wmissing-field-initializers must not be specified for this to work.
+# define GTEST_DEFINE_STATIC_MUTEX_(mutex) \
+ ::testing::internal::MutexBase mutex = { PTHREAD_MUTEX_INITIALIZER, false }
+
+// The Mutex class can only be used for mutexes created at runtime. It
+// shares its API with MutexBase otherwise.
+class Mutex : public MutexBase {
+ public:
+ Mutex() {
+ GTEST_CHECK_POSIX_SUCCESS_(pthread_mutex_init(&mutex_, NULL));
+ has_owner_ = false;
+ }
+ ~Mutex() {
+ GTEST_CHECK_POSIX_SUCCESS_(pthread_mutex_destroy(&mutex_));
+ }
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(Mutex);
+};
+
+// We cannot name this class MutexLock as the ctor declaration would
+// conflict with a macro named MutexLock, which is defined on some
+// platforms. Hence the typedef trick below.
+class GTestMutexLock {
+ public:
+ explicit GTestMutexLock(MutexBase* mutex)
+ : mutex_(mutex) { mutex_->Lock(); }
+
+ ~GTestMutexLock() { mutex_->Unlock(); }
+
+ private:
+ MutexBase* const mutex_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(GTestMutexLock);
+};
+
+typedef GTestMutexLock MutexLock;
+
+// Helpers for ThreadLocal.
+
+// pthread_key_create() requires DeleteThreadLocalValue() to have
+// C-linkage. Therefore it cannot be templatized to access
+// ThreadLocal<T>. Hence the need for class
+// ThreadLocalValueHolderBase.
+class ThreadLocalValueHolderBase {
+ public:
+ virtual ~ThreadLocalValueHolderBase() {}
+};
+
+// Called by pthread to delete thread-local data stored by
+// pthread_setspecific().
+extern "C" inline void DeleteThreadLocalValue(void* value_holder) {
+ delete static_cast<ThreadLocalValueHolderBase*>(value_holder);
+}
+
+// Implements thread-local storage on pthreads-based systems.
+//
+// // Thread 1
+// ThreadLocal<int> tl(100); // 100 is the default value for each thread.
+//
+// // Thread 2
+// tl.set(150); // Changes the value for thread 2 only.
+// EXPECT_EQ(150, tl.get());
+//
+// // Thread 1
+// EXPECT_EQ(100, tl.get()); // In thread 1, tl has the original value.
+// tl.set(200);
+// EXPECT_EQ(200, tl.get());
+//
+// The template type argument T must have a public copy constructor.
+// In addition, the default ThreadLocal constructor requires T to have
+// a public default constructor.
+//
+// An object managed for a thread by a ThreadLocal instance is deleted
+// when the thread exits. Or, if the ThreadLocal instance dies in
+// that thread, when the ThreadLocal dies. It's the user's
+// responsibility to ensure that all other threads using a ThreadLocal
+// have exited when it dies, or the per-thread objects for those
+// threads will not be deleted.
+//
+// Google Test only uses global ThreadLocal objects. That means they
+// will die after main() has returned. Therefore, no per-thread
+// object managed by Google Test will be leaked as long as all threads
+// using Google Test have exited when main() returns.
+template <typename T>
+class ThreadLocal {
+ public:
+ ThreadLocal() : key_(CreateKey()),
+ default_() {}
+ explicit ThreadLocal(const T& value) : key_(CreateKey()),
+ default_(value) {}
+
+ ~ThreadLocal() {
+ // Destroys the managed object for the current thread, if any.
+ DeleteThreadLocalValue(pthread_getspecific(key_));
+
+ // Releases resources associated with the key. This will *not*
+ // delete managed objects for other threads.
+ GTEST_CHECK_POSIX_SUCCESS_(pthread_key_delete(key_));
+ }
+
+ T* pointer() { return GetOrCreateValue(); }
+ const T* pointer() const { return GetOrCreateValue(); }
+ const T& get() const { return *pointer(); }
+ void set(const T& value) { *pointer() = value; }
+
+ private:
+ // Holds a value of type T.
+ class ValueHolder : public ThreadLocalValueHolderBase {
+ public:
+ explicit ValueHolder(const T& value) : value_(value) {}
+
+ T* pointer() { return &value_; }
+
+ private:
+ T value_;
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ValueHolder);
+ };
+
+ static pthread_key_t CreateKey() {
+ pthread_key_t key;
+ // When a thread exits, DeleteThreadLocalValue() will be called on
+ // the object managed for that thread.
+ GTEST_CHECK_POSIX_SUCCESS_(
+ pthread_key_create(&key, &DeleteThreadLocalValue));
+ return key;
+ }
+
+ T* GetOrCreateValue() const {
+ ThreadLocalValueHolderBase* const holder =
+ static_cast<ThreadLocalValueHolderBase*>(pthread_getspecific(key_));
+ if (holder != NULL) {
+ return CheckedDowncastToActualType<ValueHolder>(holder)->pointer();
+ }
+
+ ValueHolder* const new_holder = new ValueHolder(default_);
+ ThreadLocalValueHolderBase* const holder_base = new_holder;
+ GTEST_CHECK_POSIX_SUCCESS_(pthread_setspecific(key_, holder_base));
+ return new_holder->pointer();
+ }
+
+ // A key pthreads uses for looking up per-thread values.
+ const pthread_key_t key_;
+ const T default_; // The default value for each thread.
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ThreadLocal);
+};
+
+# define GTEST_IS_THREADSAFE 1
+
+#else // GTEST_HAS_PTHREAD
+
+// A dummy implementation of synchronization primitives (mutex, lock,
+// and thread-local variable). Necessary for compiling Google Test where
+// mutex is not supported - using Google Test in multiple threads is not
+// supported on such platforms.
+
+class Mutex {
+ public:
+ Mutex() {}
+ void Lock() {}
+ void Unlock() {}
+ void AssertHeld() const {}
+};
+
+# define GTEST_DECLARE_STATIC_MUTEX_(mutex) \
+ extern ::testing::internal::Mutex mutex
+
+# define GTEST_DEFINE_STATIC_MUTEX_(mutex) ::testing::internal::Mutex mutex
+
+class GTestMutexLock {
+ public:
+ explicit GTestMutexLock(Mutex*) {} // NOLINT
+};
+
+typedef GTestMutexLock MutexLock;
+
+template <typename T>
+class ThreadLocal {
+ public:
+ ThreadLocal() : value_() {}
+ explicit ThreadLocal(const T& value) : value_(value) {}
+ T* pointer() { return &value_; }
+ const T* pointer() const { return &value_; }
+ const T& get() const { return value_; }
+ void set(const T& value) { value_ = value; }
+ private:
+ T value_;
+};
+
+// The above synchronization primitives have dummy implementations.
+// Therefore Google Test is not thread-safe.
+# define GTEST_IS_THREADSAFE 0
+
+#endif // GTEST_HAS_PTHREAD
+
+// Returns the number of threads running in the process, or 0 to indicate that
+// we cannot detect it.
+GTEST_API_ size_t GetThreadCount();
+
+// Passing non-POD classes through ellipsis (...) crashes the ARM
+// compiler and generates a warning in Sun Studio. The Nokia Symbian
+// and the IBM XL C/C++ compiler try to instantiate a copy constructor
+// for objects passed through ellipsis (...), failing for uncopyable
+// objects. We define this to ensure that only POD is passed through
+// ellipsis on these systems.
+#if defined(__SYMBIAN32__) || defined(__IBMCPP__) || defined(__SUNPRO_CC)
+// We lose support for NULL detection where the compiler doesn't like
+// passing non-POD classes through ellipsis (...).
+# define GTEST_ELLIPSIS_NEEDS_POD_ 1
+#else
+# define GTEST_CAN_COMPARE_NULL 1
+#endif
+
+// The Nokia Symbian and IBM XL C/C++ compilers cannot decide between
+// const T& and const T* in a function template. These compilers
+// _can_ decide between class template specializations for T and T*,
+// so a tr1::type_traits-like is_pointer works.
+#if defined(__SYMBIAN32__) || defined(__IBMCPP__)
+# define GTEST_NEEDS_IS_POINTER_ 1
+#endif
+
+template <bool bool_value>
+struct bool_constant {
+ typedef bool_constant<bool_value> type;
+ static const bool value = bool_value;
+};
+template <bool bool_value> const bool bool_constant<bool_value>::value;
+
+typedef bool_constant<false> false_type;
+typedef bool_constant<true> true_type;
+
+template <typename T>
+struct is_pointer : public false_type {};
+
+template <typename T>
+struct is_pointer<T*> : public true_type {};
+
+template <typename Iterator>
+struct IteratorTraits {
+ typedef typename Iterator::value_type value_type;
+};
+
+template <typename T>
+struct IteratorTraits<T*> {
+ typedef T value_type;
+};
+
+template <typename T>
+struct IteratorTraits<const T*> {
+ typedef T value_type;
+};
+
+#if GTEST_OS_WINDOWS
+# define GTEST_PATH_SEP_ "\\"
+# define GTEST_HAS_ALT_PATH_SEP_ 1
+// The biggest signed integer type the compiler supports.
+typedef __int64 BiggestInt;
+#else
+# define GTEST_PATH_SEP_ "/"
+# define GTEST_HAS_ALT_PATH_SEP_ 0
+typedef long long BiggestInt; // NOLINT
+#endif // GTEST_OS_WINDOWS
+
+// Utilities for char.
+
+// isspace(int ch) and friends accept an unsigned char or EOF. char
+// may be signed, depending on the compiler (or compiler flags).
+// Therefore we need to cast a char to unsigned char before calling
+// isspace(), etc.
+
+inline bool IsAlpha(char ch) {
+ return isalpha(static_cast<unsigned char>(ch)) != 0;
+}
+inline bool IsAlNum(char ch) {
+ return isalnum(static_cast<unsigned char>(ch)) != 0;
+}
+inline bool IsDigit(char ch) {
+ return isdigit(static_cast<unsigned char>(ch)) != 0;
+}
+inline bool IsLower(char ch) {
+ return islower(static_cast<unsigned char>(ch)) != 0;
+}
+inline bool IsSpace(char ch) {
+ return isspace(static_cast<unsigned char>(ch)) != 0;
+}
+inline bool IsUpper(char ch) {
+ return isupper(static_cast<unsigned char>(ch)) != 0;
+}
+inline bool IsXDigit(char ch) {
+ return isxdigit(static_cast<unsigned char>(ch)) != 0;
+}
+inline bool IsXDigit(wchar_t ch) {
+ const unsigned char low_byte = static_cast<unsigned char>(ch);
+ return ch == low_byte && isxdigit(low_byte) != 0;
+}
+
+inline char ToLower(char ch) {
+ return static_cast<char>(tolower(static_cast<unsigned char>(ch)));
+}
+inline char ToUpper(char ch) {
+ return static_cast<char>(toupper(static_cast<unsigned char>(ch)));
+}
+
+// The testing::internal::posix namespace holds wrappers for common
+// POSIX functions. These wrappers hide the differences between
+// Windows/MSVC and POSIX systems. Since some compilers define these
+// standard functions as macros, the wrapper cannot have the same name
+// as the wrapped function.
+
+namespace posix {
+
+// Functions with a different name on Windows.
+
+#if GTEST_OS_WINDOWS
+
+typedef struct _stat StatStruct;
+
+# ifdef __BORLANDC__
+inline int IsATTY(int fd) { return isatty(fd); }
+inline int StrCaseCmp(const char* s1, const char* s2) {
+ return stricmp(s1, s2);
+}
+inline char* StrDup(const char* src) { return strdup(src); }
+# else // !__BORLANDC__
+# if GTEST_OS_WINDOWS_MOBILE
+inline int IsATTY(int /* fd */) { return 0; }
+# else
+inline int IsATTY(int fd) { return _isatty(fd); }
+# endif // GTEST_OS_WINDOWS_MOBILE
+inline int StrCaseCmp(const char* s1, const char* s2) {
+ return _stricmp(s1, s2);
+}
+inline char* StrDup(const char* src) { return _strdup(src); }
+# endif // __BORLANDC__
+
+# if GTEST_OS_WINDOWS_MOBILE
+inline int FileNo(FILE* file) { return reinterpret_cast<int>(_fileno(file)); }
+// Stat(), RmDir(), and IsDir() are not needed on Windows CE at this
+// time and thus not defined there.
+# else
+inline int FileNo(FILE* file) { return _fileno(file); }
+inline int Stat(const char* path, StatStruct* buf) { return _stat(path, buf); }
+inline int RmDir(const char* dir) { return _rmdir(dir); }
+inline bool IsDir(const StatStruct& st) {
+ return (_S_IFDIR & st.st_mode) != 0;
+}
+# endif // GTEST_OS_WINDOWS_MOBILE
+
+#else
+
+typedef struct stat StatStruct;
+
+inline int FileNo(FILE* file) { return fileno(file); }
+inline int IsATTY(int fd) { return isatty(fd); }
+inline int Stat(const char* path, StatStruct* buf) { return stat(path, buf); }
+inline int StrCaseCmp(const char* s1, const char* s2) {
+ return strcasecmp(s1, s2);
+}
+inline char* StrDup(const char* src) { return strdup(src); }
+inline int RmDir(const char* dir) { return rmdir(dir); }
+inline bool IsDir(const StatStruct& st) { return S_ISDIR(st.st_mode); }
+
+#endif // GTEST_OS_WINDOWS
+
+// Functions deprecated by MSVC 8.0.
+
+#ifdef _MSC_VER
+// Temporarily disable warning 4996 (deprecated function).
+# pragma warning(push)
+# pragma warning(disable:4996)
+#endif
+
+inline const char* StrNCpy(char* dest, const char* src, size_t n) {
+ return strncpy(dest, src, n);
+}
+
+// ChDir(), FReopen(), FDOpen(), Read(), Write(), Close(), and
+// StrError() aren't needed on Windows CE at this time and thus not
+// defined there.
+
+#if !GTEST_OS_WINDOWS_MOBILE
+inline int ChDir(const char* dir) { return chdir(dir); }
+#endif
+inline FILE* FOpen(const char* path, const char* mode) {
+ return fopen(path, mode);
+}
+#if !GTEST_OS_WINDOWS_MOBILE
+inline FILE *FReopen(const char* path, const char* mode, FILE* stream) {
+ return freopen(path, mode, stream);
+}
+inline FILE* FDOpen(int fd, const char* mode) { return fdopen(fd, mode); }
+#endif
+inline int FClose(FILE* fp) { return fclose(fp); }
+#if !GTEST_OS_WINDOWS_MOBILE
+inline int Read(int fd, void* buf, unsigned int count) {
+ return static_cast<int>(read(fd, buf, count));
+}
+inline int Write(int fd, const void* buf, unsigned int count) {
+ return static_cast<int>(write(fd, buf, count));
+}
+inline int Close(int fd) { return close(fd); }
+inline const char* StrError(int errnum) { return strerror(errnum); }
+#endif
+inline const char* GetEnv(const char* name) {
+#if GTEST_OS_WINDOWS_MOBILE
+ // We are on Windows CE, which has no environment variables.
+ return NULL;
+#elif defined(__BORLANDC__) || defined(__SunOS_5_8) || defined(__SunOS_5_9)
+ // Environment variables which we programmatically clear will be set to the
+ // empty string rather than unset (NULL). Handle that case.
+ const char* const env = getenv(name);
+ return (env != NULL && env[0] != '\0') ? env : NULL;
+#else
+ return getenv(name);
+#endif
+}
+
+#ifdef _MSC_VER
+# pragma warning(pop) // Restores the warning state.
+#endif
+
+#if GTEST_OS_WINDOWS_MOBILE
+// Windows CE has no C library. The abort() function is used in
+// several places in Google Test. This implementation provides a reasonable
+// imitation of standard behaviour.
+void Abort();
+#else
+inline void Abort() { abort(); }
+#endif // GTEST_OS_WINDOWS_MOBILE
+
+} // namespace posix
+
+// MSVC "deprecates" snprintf and issues warnings wherever it is used. In
+// order to avoid these warnings, we need to use _snprintf or _snprintf_s on
+// MSVC-based platforms. We map the GTEST_SNPRINTF_ macro to the appropriate
+// function in order to achieve that. We use macro definition here because
+// snprintf is a variadic function.
+#if _MSC_VER >= 1400 && !GTEST_OS_WINDOWS_MOBILE
+// MSVC 2005 and above support variadic macros.
+# define GTEST_SNPRINTF_(buffer, size, format, ...) \
+ _snprintf_s(buffer, size, size, format, __VA_ARGS__)
+#elif defined(_MSC_VER)
+// Windows CE does not define _snprintf_s and MSVC prior to 2005 doesn't
+// complain about _snprintf.
+# define GTEST_SNPRINTF_ _snprintf
+#else
+# define GTEST_SNPRINTF_ snprintf
+#endif
+
+// The maximum number a BiggestInt can represent. This definition
+// works no matter BiggestInt is represented in one's complement or
+// two's complement.
+//
+// We cannot rely on numeric_limits in STL, as __int64 and long long
+// are not part of standard C++ and numeric_limits doesn't need to be
+// defined for them.
+const BiggestInt kMaxBiggestInt =
+ ~(static_cast<BiggestInt>(1) << (8*sizeof(BiggestInt) - 1));
+
+// This template class serves as a compile-time function from size to
+// type. It maps a size in bytes to a primitive type with that
+// size. e.g.
+//
+// TypeWithSize<4>::UInt
+//
+// is typedef-ed to be unsigned int (unsigned integer made up of 4
+// bytes).
+//
+// Such functionality should belong to STL, but I cannot find it
+// there.
+//
+// Google Test uses this class in the implementation of floating-point
+// comparison.
+//
+// For now it only handles UInt (unsigned int) as that's all Google Test
+// needs. Other types can be easily added in the future if need
+// arises.
+template <size_t size>
+class TypeWithSize {
+ public:
+ // This prevents the user from using TypeWithSize<N> with incorrect
+ // values of N.
+ typedef void UInt;
+};
+
+// The specialization for size 4.
+template <>
+class TypeWithSize<4> {
+ public:
+ // unsigned int has size 4 in both gcc and MSVC.
+ //
+ // As base/basictypes.h doesn't compile on Windows, we cannot use
+ // uint32, uint64, and etc here.
+ typedef int Int;
+ typedef unsigned int UInt;
+};
+
+// The specialization for size 8.
+template <>
+class TypeWithSize<8> {
+ public:
+#if GTEST_OS_WINDOWS
+ typedef __int64 Int;
+ typedef unsigned __int64 UInt;
+#else
+ typedef long long Int; // NOLINT
+ typedef unsigned long long UInt; // NOLINT
+#endif // GTEST_OS_WINDOWS
+};
+
+// Integer types of known sizes.
+typedef TypeWithSize<4>::Int Int32;
+typedef TypeWithSize<4>::UInt UInt32;
+typedef TypeWithSize<8>::Int Int64;
+typedef TypeWithSize<8>::UInt UInt64;
+typedef TypeWithSize<8>::Int TimeInMillis; // Represents time in milliseconds.
+
+// Utilities for command line flags and environment variables.
+
+// Macro for referencing flags.
+#define GTEST_FLAG(name) FLAGS_gtest_##name
+
+// Macros for declaring flags.
+#define GTEST_DECLARE_bool_(name) GTEST_API_ extern bool GTEST_FLAG(name)
+#define GTEST_DECLARE_int32_(name) \
+ GTEST_API_ extern ::testing::internal::Int32 GTEST_FLAG(name)
+#define GTEST_DECLARE_string_(name) \
+ GTEST_API_ extern ::std::string GTEST_FLAG(name)
+
+// Macros for defining flags.
+#define GTEST_DEFINE_bool_(name, default_val, doc) \
+ GTEST_API_ bool GTEST_FLAG(name) = (default_val)
+#define GTEST_DEFINE_int32_(name, default_val, doc) \
+ GTEST_API_ ::testing::internal::Int32 GTEST_FLAG(name) = (default_val)
+#define GTEST_DEFINE_string_(name, default_val, doc) \
+ GTEST_API_ ::std::string GTEST_FLAG(name) = (default_val)
+
+// Thread annotations
+#define GTEST_EXCLUSIVE_LOCK_REQUIRED_(locks)
+#define GTEST_LOCK_EXCLUDED_(locks)
+
+// Parses 'str' for a 32-bit signed integer. If successful, writes the result
+// to *value and returns true; otherwise leaves *value unchanged and returns
+// false.
+// TODO(chandlerc): Find a better way to refactor flag and environment parsing
+// out of both gtest-port.cc and gtest.cc to avoid exporting this utility
+// function.
+bool ParseInt32(const Message& src_text, const char* str, Int32* value);
+
+// Parses a bool/Int32/string from the environment variable
+// corresponding to the given Google Test flag.
+bool BoolFromGTestEnv(const char* flag, bool default_val);
+GTEST_API_ Int32 Int32FromGTestEnv(const char* flag, Int32 default_val);
+const char* StringFromGTestEnv(const char* flag, const char* default_val);
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_PORT_H_
+
+#if GTEST_OS_LINUX
+# include <stdlib.h>
+# include <sys/types.h>
+# include <sys/wait.h>
+# include <unistd.h>
+#endif // GTEST_OS_LINUX
+
+#if GTEST_HAS_EXCEPTIONS
+# include <stdexcept>
+#endif
+
+#include <ctype.h>
+#include <float.h>
+#include <string.h>
+#include <iomanip>
+#include <limits>
+#include <set>
+
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+//
+// The Google C++ Testing Framework (Google Test)
+//
+// This header file defines the Message class.
+//
+// IMPORTANT NOTE: Due to limitation of the C++ language, we have to
+// leave some internal implementation details in this header file.
+// They are clearly marked by comments like this:
+//
+// // INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+//
+// Such code is NOT meant to be used by a user directly, and is subject
+// to CHANGE WITHOUT NOTICE. Therefore DO NOT DEPEND ON IT in a user
+// program!
+
+#ifndef GTEST_INCLUDE_GTEST_GTEST_MESSAGE_H_
+#define GTEST_INCLUDE_GTEST_GTEST_MESSAGE_H_
+
+#include <limits>
+
+
+// Ensures that there is at least one operator<< in the global namespace.
+// See Message& operator<<(...) below for why.
+void operator<<(const testing::internal::Secret&, int);
+
+namespace testing {
+
+// The Message class works like an ostream repeater.
+//
+// Typical usage:
+//
+// 1. You stream a bunch of values to a Message object.
+// It will remember the text in a stringstream.
+// 2. Then you stream the Message object to an ostream.
+// This causes the text in the Message to be streamed
+// to the ostream.
+//
+// For example;
+//
+// testing::Message foo;
+// foo << 1 << " != " << 2;
+// std::cout << foo;
+//
+// will print "1 != 2".
+//
+// Message is not intended to be inherited from. In particular, its
+// destructor is not virtual.
+//
+// Note that stringstream behaves differently in gcc and in MSVC. You
+// can stream a NULL char pointer to it in the former, but not in the
+// latter (it causes an access violation if you do). The Message
+// class hides this difference by treating a NULL char pointer as
+// "(null)".
+class GTEST_API_ Message {
+ private:
+ // The type of basic IO manipulators (endl, ends, and flush) for
+ // narrow streams.
+ typedef std::ostream& (*BasicNarrowIoManip)(std::ostream&);
+
+ public:
+ // Constructs an empty Message.
+ Message();
+
+ // Copy constructor.
+ Message(const Message& msg) : ss_(new ::std::stringstream) { // NOLINT
+ *ss_ << msg.GetString();
+ }
+
+ // Constructs a Message from a C-string.
+ explicit Message(const char* str) : ss_(new ::std::stringstream) {
+ *ss_ << str;
+ }
+
+#if GTEST_OS_SYMBIAN
+ // Streams a value (either a pointer or not) to this object.
+ template <typename T>
+ inline Message& operator <<(const T& value) {
+ StreamHelper(typename internal::is_pointer<T>::type(), value);
+ return *this;
+ }
+#else
+ // Streams a non-pointer value to this object.
+ template <typename T>
+ inline Message& operator <<(const T& val) {
+ // Some libraries overload << for STL containers. These
+ // overloads are defined in the global namespace instead of ::std.
+ //
+ // C++'s symbol lookup rule (i.e. Koenig lookup) says that these
+ // overloads are visible in either the std namespace or the global
+ // namespace, but not other namespaces, including the testing
+ // namespace which Google Test's Message class is in.
+ //
+ // To allow STL containers (and other types that has a << operator
+ // defined in the global namespace) to be used in Google Test
+ // assertions, testing::Message must access the custom << operator
+ // from the global namespace. With this using declaration,
+ // overloads of << defined in the global namespace and those
+ // visible via Koenig lookup are both exposed in this function.
+ using ::operator <<;
+ *ss_ << val;
+ return *this;
+ }
+
+ // Streams a pointer value to this object.
+ //
+ // This function is an overload of the previous one. When you
+ // stream a pointer to a Message, this definition will be used as it
+ // is more specialized. (The C++ Standard, section
+ // [temp.func.order].) If you stream a non-pointer, then the
+ // previous definition will be used.
+ //
+ // The reason for this overload is that streaming a NULL pointer to
+ // ostream is undefined behavior. Depending on the compiler, you
+ // may get "0", "(nil)", "(null)", or an access violation. To
+ // ensure consistent result across compilers, we always treat NULL
+ // as "(null)".
+ template <typename T>
+ inline Message& operator <<(T* const& pointer) { // NOLINT
+ if (pointer == NULL) {
+ *ss_ << "(null)";
+ } else {
+ *ss_ << pointer;
+ }
+ return *this;
+ }
+#endif // GTEST_OS_SYMBIAN
+
+ // Since the basic IO manipulators are overloaded for both narrow
+ // and wide streams, we have to provide this specialized definition
+ // of operator <<, even though its body is the same as the
+ // templatized version above. Without this definition, streaming
+ // endl or other basic IO manipulators to Message will confuse the
+ // compiler.
+ Message& operator <<(BasicNarrowIoManip val) {
+ *ss_ << val;
+ return *this;
+ }
+
+ // Instead of 1/0, we want to see true/false for bool values.
+ Message& operator <<(bool b) {
+ return *this << (b ? "true" : "false");
+ }
+
+ // These two overloads allow streaming a wide C string to a Message
+ // using the UTF-8 encoding.
+ Message& operator <<(const wchar_t* wide_c_str);
+ Message& operator <<(wchar_t* wide_c_str);
+
+#if GTEST_HAS_STD_WSTRING
+ // Converts the given wide string to a narrow string using the UTF-8
+ // encoding, and streams the result to this Message object.
+ Message& operator <<(const ::std::wstring& wstr);
+#endif // GTEST_HAS_STD_WSTRING
+
+#if GTEST_HAS_GLOBAL_WSTRING
+ // Converts the given wide string to a narrow string using the UTF-8
+ // encoding, and streams the result to this Message object.
+ Message& operator <<(const ::wstring& wstr);
+#endif // GTEST_HAS_GLOBAL_WSTRING
+
+ // Gets the text streamed to this object so far as an std::string.
+ // Each '\0' character in the buffer is replaced with "\\0".
+ //
+ // INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+ std::string GetString() const;
+
+ private:
+
+#if GTEST_OS_SYMBIAN
+ // These are needed as the Nokia Symbian Compiler cannot decide between
+ // const T& and const T* in a function template. The Nokia compiler _can_
+ // decide between class template specializations for T and T*, so a
+ // tr1::type_traits-like is_pointer works, and we can overload on that.
+ template <typename T>
+ inline void StreamHelper(internal::true_type /*is_pointer*/, T* pointer) {
+ if (pointer == NULL) {
+ *ss_ << "(null)";
+ } else {
+ *ss_ << pointer;
+ }
+ }
+ template <typename T>
+ inline void StreamHelper(internal::false_type /*is_pointer*/,
+ const T& value) {
+ // See the comments in Message& operator <<(const T&) above for why
+ // we need this using statement.
+ using ::operator <<;
+ *ss_ << value;
+ }
+#endif // GTEST_OS_SYMBIAN
+
+ // We'll hold the text streamed to this object here.
+ const internal::scoped_ptr< ::std::stringstream> ss_;
+
+ // We declare (but don't implement) this to prevent the compiler
+ // from implementing the assignment operator.
+ void operator=(const Message&);
+};
+
+// Streams a Message to an ostream.
+inline std::ostream& operator <<(std::ostream& os, const Message& sb) {
+ return os << sb.GetString();
+}
+
+namespace internal {
+
+// Converts a streamable value to an std::string. A NULL pointer is
+// converted to "(null)". When the input value is a ::string,
+// ::std::string, ::wstring, or ::std::wstring object, each NUL
+// character in it is replaced with "\\0".
+template <typename T>
+std::string StreamableToString(const T& streamable) {
+ return (Message() << streamable).GetString();
+}
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_MESSAGE_H_
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Authors: wan at google.com (Zhanyong Wan), eefacm at gmail.com (Sean Mcafee)
+//
+// The Google C++ Testing Framework (Google Test)
+//
+// This header file declares the String class and functions used internally by
+// Google Test. They are subject to change without notice. They should not used
+// by code external to Google Test.
+//
+// This header file is #included by <gtest/internal/gtest-internal.h>.
+// It should not be #included by other files.
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_STRING_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_STRING_H_
+
+#ifdef __BORLANDC__
+// string.h is not guaranteed to provide strcpy on C++ Builder.
+# include <mem.h>
+#endif
+
+#include <string.h>
+#include <string>
+
+
+namespace testing {
+namespace internal {
+
+// String - an abstract class holding static string utilities.
+class GTEST_API_ String {
+ public:
+ // Static utility methods
+
+ // Clones a 0-terminated C string, allocating memory using new. The
+ // caller is responsible for deleting the return value using
+ // delete[]. Returns the cloned string, or NULL if the input is
+ // NULL.
+ //
+ // This is different from strdup() in string.h, which allocates
+ // memory using malloc().
+ static const char* CloneCString(const char* c_str);
+
+#if GTEST_OS_WINDOWS_MOBILE
+ // Windows CE does not have the 'ANSI' versions of Win32 APIs. To be
+ // able to pass strings to Win32 APIs on CE we need to convert them
+ // to 'Unicode', UTF-16.
+
+ // Creates a UTF-16 wide string from the given ANSI string, allocating
+ // memory using new. The caller is responsible for deleting the return
+ // value using delete[]. Returns the wide string, or NULL if the
+ // input is NULL.
+ //
+ // The wide string is created using the ANSI codepage (CP_ACP) to
+ // match the behaviour of the ANSI versions of Win32 calls and the
+ // C runtime.
+ static LPCWSTR AnsiToUtf16(const char* c_str);
+
+ // Creates an ANSI string from the given wide string, allocating
+ // memory using new. The caller is responsible for deleting the return
+ // value using delete[]. Returns the ANSI string, or NULL if the
+ // input is NULL.
+ //
+ // The returned string is created using the ANSI codepage (CP_ACP) to
+ // match the behaviour of the ANSI versions of Win32 calls and the
+ // C runtime.
+ static const char* Utf16ToAnsi(LPCWSTR utf16_str);
+#endif
+
+ // Compares two C strings. Returns true iff they have the same content.
+ //
+ // Unlike strcmp(), this function can handle NULL argument(s). A
+ // NULL C string is considered different to any non-NULL C string,
+ // including the empty string.
+ static bool CStringEquals(const char* lhs, const char* rhs);
+
+ // Converts a wide C string to a String using the UTF-8 encoding.
+ // NULL will be converted to "(null)". If an error occurred during
+ // the conversion, "(failed to convert from wide string)" is
+ // returned.
+ static std::string ShowWideCString(const wchar_t* wide_c_str);
+
+ // Compares two wide C strings. Returns true iff they have the same
+ // content.
+ //
+ // Unlike wcscmp(), this function can handle NULL argument(s). A
+ // NULL C string is considered different to any non-NULL C string,
+ // including the empty string.
+ static bool WideCStringEquals(const wchar_t* lhs, const wchar_t* rhs);
+
+ // Compares two C strings, ignoring case. Returns true iff they
+ // have the same content.
+ //
+ // Unlike strcasecmp(), this function can handle NULL argument(s).
+ // A NULL C string is considered different to any non-NULL C string,
+ // including the empty string.
+ static bool CaseInsensitiveCStringEquals(const char* lhs,
+ const char* rhs);
+
+ // Compares two wide C strings, ignoring case. Returns true iff they
+ // have the same content.
+ //
+ // Unlike wcscasecmp(), this function can handle NULL argument(s).
+ // A NULL C string is considered different to any non-NULL wide C string,
+ // including the empty string.
+ // NB: The implementations on different platforms slightly differ.
+ // On windows, this method uses _wcsicmp which compares according to LC_CTYPE
+ // environment variable. On GNU platform this method uses wcscasecmp
+ // which compares according to LC_CTYPE category of the current locale.
+ // On MacOS X, it uses towlower, which also uses LC_CTYPE category of the
+ // current locale.
+ static bool CaseInsensitiveWideCStringEquals(const wchar_t* lhs,
+ const wchar_t* rhs);
+
+ // Returns true iff the given string ends with the given suffix, ignoring
+ // case. Any string is considered to end with an empty suffix.
+ static bool EndsWithCaseInsensitive(
+ const std::string& str, const std::string& suffix);
+
+ // Formats an int value as "%02d".
+ static std::string FormatIntWidth2(int value); // "%02d" for width == 2
+
+ // Formats an int value as "%X".
+ static std::string FormatHexInt(int value);
+
+ // Formats a byte as "%02X".
+ static std::string FormatByte(unsigned char value);
+
+ private:
+ String(); // Not meant to be instantiated.
+}; // class String
+
+// Gets the content of the stringstream's buffer as an std::string. Each '\0'
+// character in the buffer is replaced with "\\0".
+GTEST_API_ std::string StringStreamToString(::std::stringstream* stream);
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_STRING_H_
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: keith.ray at gmail.com (Keith Ray)
+//
+// Google Test filepath utilities
+//
+// This header file declares classes and functions used internally by
+// Google Test. They are subject to change without notice.
+//
+// This file is #included in <gtest/internal/gtest-internal.h>.
+// Do not include this header file separately!
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_FILEPATH_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_FILEPATH_H_
+
+
+namespace testing {
+namespace internal {
+
+// FilePath - a class for file and directory pathname manipulation which
+// handles platform-specific conventions (like the pathname separator).
+// Used for helper functions for naming files in a directory for xml output.
+// Except for Set methods, all methods are const or static, which provides an
+// "immutable value object" -- useful for peace of mind.
+// A FilePath with a value ending in a path separator ("like/this/") represents
+// a directory, otherwise it is assumed to represent a file. In either case,
+// it may or may not represent an actual file or directory in the file system.
+// Names are NOT checked for syntax correctness -- no checking for illegal
+// characters, malformed paths, etc.
+
+class GTEST_API_ FilePath {
+ public:
+ FilePath() : pathname_("") { }
+ FilePath(const FilePath& rhs) : pathname_(rhs.pathname_) { }
+
+ explicit FilePath(const std::string& pathname) : pathname_(pathname) {
+ Normalize();
+ }
+
+ FilePath& operator=(const FilePath& rhs) {
+ Set(rhs);
+ return *this;
+ }
+
+ void Set(const FilePath& rhs) {
+ pathname_ = rhs.pathname_;
+ }
+
+ const std::string& string() const { return pathname_; }
+ const char* c_str() const { return pathname_.c_str(); }
+
+ // Returns the current working directory, or "" if unsuccessful.
+ static FilePath GetCurrentDir();
+
+ // Given directory = "dir", base_name = "test", number = 0,
+ // extension = "xml", returns "dir/test.xml". If number is greater
+ // than zero (e.g., 12), returns "dir/test_12.xml".
+ // On Windows platform, uses \ as the separator rather than /.
+ static FilePath MakeFileName(const FilePath& directory,
+ const FilePath& base_name,
+ int number,
+ const char* extension);
+
+ // Given directory = "dir", relative_path = "test.xml",
+ // returns "dir/test.xml".
+ // On Windows, uses \ as the separator rather than /.
+ static FilePath ConcatPaths(const FilePath& directory,
+ const FilePath& relative_path);
+
+ // Returns a pathname for a file that does not currently exist. The pathname
+ // will be directory/base_name.extension or
+ // directory/base_name_<number>.extension if directory/base_name.extension
+ // already exists. The number will be incremented until a pathname is found
+ // that does not already exist.
+ // Examples: 'dir/foo_test.xml' or 'dir/foo_test_1.xml'.
+ // There could be a race condition if two or more processes are calling this
+ // function at the same time -- they could both pick the same filename.
+ static FilePath GenerateUniqueFileName(const FilePath& directory,
+ const FilePath& base_name,
+ const char* extension);
+
+ // Returns true iff the path is "".
+ bool IsEmpty() const { return pathname_.empty(); }
+
+ // If input name has a trailing separator character, removes it and returns
+ // the name, otherwise return the name string unmodified.
+ // On Windows platform, uses \ as the separator, other platforms use /.
+ FilePath RemoveTrailingPathSeparator() const;
+
+ // Returns a copy of the FilePath with the directory part removed.
+ // Example: FilePath("path/to/file").RemoveDirectoryName() returns
+ // FilePath("file"). If there is no directory part ("just_a_file"), it returns
+ // the FilePath unmodified. If there is no file part ("just_a_dir/") it
+ // returns an empty FilePath ("").
+ // On Windows platform, '\' is the path separator, otherwise it is '/'.
+ FilePath RemoveDirectoryName() const;
+
+ // RemoveFileName returns the directory path with the filename removed.
+ // Example: FilePath("path/to/file").RemoveFileName() returns "path/to/".
+ // If the FilePath is "a_file" or "/a_file", RemoveFileName returns
+ // FilePath("./") or, on Windows, FilePath(".\\"). If the filepath does
+ // not have a file, like "just/a/dir/", it returns the FilePath unmodified.
+ // On Windows platform, '\' is the path separator, otherwise it is '/'.
+ FilePath RemoveFileName() const;
+
+ // Returns a copy of the FilePath with the case-insensitive extension removed.
+ // Example: FilePath("dir/file.exe").RemoveExtension("EXE") returns
+ // FilePath("dir/file"). If a case-insensitive extension is not
+ // found, returns a copy of the original FilePath.
+ FilePath RemoveExtension(const char* extension) const;
+
+ // Creates directories so that path exists. Returns true if successful or if
+ // the directories already exist; returns false if unable to create
+ // directories for any reason. Will also return false if the FilePath does
+ // not represent a directory (that is, it doesn't end with a path separator).
+ bool CreateDirectoriesRecursively() const;
+
+ // Create the directory so that path exists. Returns true if successful or
+ // if the directory already exists; returns false if unable to create the
+ // directory for any reason, including if the parent directory does not
+ // exist. Not named "CreateDirectory" because that's a macro on Windows.
+ bool CreateFolder() const;
+
+ // Returns true if FilePath describes something in the file-system,
+ // either a file, directory, or whatever, and that something exists.
+ bool FileOrDirectoryExists() const;
+
+ // Returns true if pathname describes a directory in the file-system
+ // that exists.
+ bool DirectoryExists() const;
+
+ // Returns true if FilePath ends with a path separator, which indicates that
+ // it is intended to represent a directory. Returns false otherwise.
+ // This does NOT check that a directory (or file) actually exists.
+ bool IsDirectory() const;
+
+ // Returns true if pathname describes a root directory. (Windows has one
+ // root directory per disk drive.)
+ bool IsRootDirectory() const;
+
+ // Returns true if pathname describes an absolute path.
+ bool IsAbsolutePath() const;
+
+ private:
+ // Replaces multiple consecutive separators with a single separator.
+ // For example, "bar///foo" becomes "bar/foo". Does not eliminate other
+ // redundancies that might be in a pathname involving "." or "..".
+ //
+ // A pathname with multiple consecutive separators may occur either through
+ // user error or as a result of some scripts or APIs that generate a pathname
+ // with a trailing separator. On other platforms the same API or script
+ // may NOT generate a pathname with a trailing "/". Then elsewhere that
+ // pathname may have another "/" and pathname components added to it,
+ // without checking for the separator already being there.
+ // The script language and operating system may allow paths like "foo//bar"
+ // but some of the functions in FilePath will not handle that correctly. In
+ // particular, RemoveTrailingPathSeparator() only removes one separator, and
+ // it is called in CreateDirectoriesRecursively() assuming that it will change
+ // a pathname from directory syntax (trailing separator) to filename syntax.
+ //
+ // On Windows this method also replaces the alternate path separator '/' with
+ // the primary path separator '\\', so that for example "bar\\/\\foo" becomes
+ // "bar\\foo".
+
+ void Normalize();
+
+ // Returns a pointer to the last occurence of a valid path separator in
+ // the FilePath. On Windows, for example, both '/' and '\' are valid path
+ // separators. Returns NULL if no path separator was found.
+ const char* FindLastPathSeparator() const;
+
+ std::string pathname_;
+}; // class FilePath
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_FILEPATH_H_
+// This file was GENERATED by command:
+// pump.py gtest-type-util.h.pump
+// DO NOT EDIT BY HAND!!!
+
+// Copyright 2008 Google Inc.
+// All Rights Reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Type utilities needed for implementing typed and type-parameterized
+// tests. This file is generated by a SCRIPT. DO NOT EDIT BY HAND!
+//
+// Currently we support at most 50 types in a list, and at most 50
+// type-parameterized tests in one type-parameterized test case.
+// Please contact googletestframework at googlegroups.com if you need
+// more.
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_TYPE_UTIL_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_TYPE_UTIL_H_
+
+
+// #ifdef __GNUC__ is too general here. It is possible to use gcc without using
+// libstdc++ (which is where cxxabi.h comes from).
+# if GTEST_HAS_CXXABI_H_
+# include <cxxabi.h>
+# elif defined(__HP_aCC)
+# include <acxx_demangle.h>
+# endif // GTEST_HASH_CXXABI_H_
+
+namespace testing {
+namespace internal {
+
+// GetTypeName<T>() returns a human-readable name of type T.
+// NB: This function is also used in Google Mock, so don't move it inside of
+// the typed-test-only section below.
+template <typename T>
+std::string GetTypeName() {
+# if GTEST_HAS_RTTI
+
+ const char* const name = typeid(T).name();
+# if GTEST_HAS_CXXABI_H_ || defined(__HP_aCC)
+ int status = 0;
+ // gcc's implementation of typeid(T).name() mangles the type name,
+ // so we have to demangle it.
+# if GTEST_HAS_CXXABI_H_
+ using abi::__cxa_demangle;
+# endif // GTEST_HAS_CXXABI_H_
+ char* const readable_name = __cxa_demangle(name, 0, 0, &status);
+ const std::string name_str(status == 0 ? readable_name : name);
+ free(readable_name);
+ return name_str;
+# else
+ return name;
+# endif // GTEST_HAS_CXXABI_H_ || __HP_aCC
+
+# else
+
+ return "<type>";
+
+# endif // GTEST_HAS_RTTI
+}
+
+#if GTEST_HAS_TYPED_TEST || GTEST_HAS_TYPED_TEST_P
+
+// AssertyTypeEq<T1, T2>::type is defined iff T1 and T2 are the same
+// type. This can be used as a compile-time assertion to ensure that
+// two types are equal.
+
+template <typename T1, typename T2>
+struct AssertTypeEq;
+
+template <typename T>
+struct AssertTypeEq<T, T> {
+ typedef bool type;
+};
+
+// A unique type used as the default value for the arguments of class
+// template Types. This allows us to simulate variadic templates
+// (e.g. Types<int>, Type<int, double>, and etc), which C++ doesn't
+// support directly.
+struct None {};
+
+// The following family of struct and struct templates are used to
+// represent type lists. In particular, TypesN<T1, T2, ..., TN>
+// represents a type list with N types (T1, T2, ..., and TN) in it.
+// Except for Types0, every struct in the family has two member types:
+// Head for the first type in the list, and Tail for the rest of the
+// list.
+
+// The empty type list.
+struct Types0 {};
+
+// Type lists of length 1, 2, 3, and so on.
+
+template <typename T1>
+struct Types1 {
+ typedef T1 Head;
+ typedef Types0 Tail;
+};
+template <typename T1, typename T2>
+struct Types2 {
+ typedef T1 Head;
+ typedef Types1<T2> Tail;
+};
+
+template <typename T1, typename T2, typename T3>
+struct Types3 {
+ typedef T1 Head;
+ typedef Types2<T2, T3> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4>
+struct Types4 {
+ typedef T1 Head;
+ typedef Types3<T2, T3, T4> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5>
+struct Types5 {
+ typedef T1 Head;
+ typedef Types4<T2, T3, T4, T5> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6>
+struct Types6 {
+ typedef T1 Head;
+ typedef Types5<T2, T3, T4, T5, T6> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7>
+struct Types7 {
+ typedef T1 Head;
+ typedef Types6<T2, T3, T4, T5, T6, T7> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8>
+struct Types8 {
+ typedef T1 Head;
+ typedef Types7<T2, T3, T4, T5, T6, T7, T8> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9>
+struct Types9 {
+ typedef T1 Head;
+ typedef Types8<T2, T3, T4, T5, T6, T7, T8, T9> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10>
+struct Types10 {
+ typedef T1 Head;
+ typedef Types9<T2, T3, T4, T5, T6, T7, T8, T9, T10> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11>
+struct Types11 {
+ typedef T1 Head;
+ typedef Types10<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12>
+struct Types12 {
+ typedef T1 Head;
+ typedef Types11<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13>
+struct Types13 {
+ typedef T1 Head;
+ typedef Types12<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14>
+struct Types14 {
+ typedef T1 Head;
+ typedef Types13<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15>
+struct Types15 {
+ typedef T1 Head;
+ typedef Types14<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16>
+struct Types16 {
+ typedef T1 Head;
+ typedef Types15<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17>
+struct Types17 {
+ typedef T1 Head;
+ typedef Types16<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18>
+struct Types18 {
+ typedef T1 Head;
+ typedef Types17<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19>
+struct Types19 {
+ typedef T1 Head;
+ typedef Types18<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20>
+struct Types20 {
+ typedef T1 Head;
+ typedef Types19<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21>
+struct Types21 {
+ typedef T1 Head;
+ typedef Types20<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22>
+struct Types22 {
+ typedef T1 Head;
+ typedef Types21<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23>
+struct Types23 {
+ typedef T1 Head;
+ typedef Types22<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24>
+struct Types24 {
+ typedef T1 Head;
+ typedef Types23<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25>
+struct Types25 {
+ typedef T1 Head;
+ typedef Types24<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26>
+struct Types26 {
+ typedef T1 Head;
+ typedef Types25<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27>
+struct Types27 {
+ typedef T1 Head;
+ typedef Types26<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28>
+struct Types28 {
+ typedef T1 Head;
+ typedef Types27<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29>
+struct Types29 {
+ typedef T1 Head;
+ typedef Types28<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30>
+struct Types30 {
+ typedef T1 Head;
+ typedef Types29<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31>
+struct Types31 {
+ typedef T1 Head;
+ typedef Types30<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32>
+struct Types32 {
+ typedef T1 Head;
+ typedef Types31<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33>
+struct Types33 {
+ typedef T1 Head;
+ typedef Types32<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34>
+struct Types34 {
+ typedef T1 Head;
+ typedef Types33<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35>
+struct Types35 {
+ typedef T1 Head;
+ typedef Types34<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36>
+struct Types36 {
+ typedef T1 Head;
+ typedef Types35<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37>
+struct Types37 {
+ typedef T1 Head;
+ typedef Types36<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38>
+struct Types38 {
+ typedef T1 Head;
+ typedef Types37<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39>
+struct Types39 {
+ typedef T1 Head;
+ typedef Types38<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40>
+struct Types40 {
+ typedef T1 Head;
+ typedef Types39<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41>
+struct Types41 {
+ typedef T1 Head;
+ typedef Types40<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42>
+struct Types42 {
+ typedef T1 Head;
+ typedef Types41<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43>
+struct Types43 {
+ typedef T1 Head;
+ typedef Types42<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44>
+struct Types44 {
+ typedef T1 Head;
+ typedef Types43<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45>
+struct Types45 {
+ typedef T1 Head;
+ typedef Types44<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46>
+struct Types46 {
+ typedef T1 Head;
+ typedef Types45<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47>
+struct Types47 {
+ typedef T1 Head;
+ typedef Types46<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46, T47> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48>
+struct Types48 {
+ typedef T1 Head;
+ typedef Types47<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46, T47, T48> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48, typename T49>
+struct Types49 {
+ typedef T1 Head;
+ typedef Types48<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46, T47, T48, T49> Tail;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48, typename T49, typename T50>
+struct Types50 {
+ typedef T1 Head;
+ typedef Types49<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46, T47, T48, T49, T50> Tail;
+};
+
+
+} // namespace internal
+
+// We don't want to require the users to write TypesN<...> directly,
+// as that would require them to count the length. Types<...> is much
+// easier to write, but generates horrible messages when there is a
+// compiler error, as gcc insists on printing out each template
+// argument, even if it has the default value (this means Types<int>
+// will appear as Types<int, None, None, ..., None> in the compiler
+// errors).
+//
+// Our solution is to combine the best part of the two approaches: a
+// user would write Types<T1, ..., TN>, and Google Test will translate
+// that to TypesN<T1, ..., TN> internally to make error messages
+// readable. The translation is done by the 'type' member of the
+// Types template.
+template <typename T1 = internal::None, typename T2 = internal::None,
+ typename T3 = internal::None, typename T4 = internal::None,
+ typename T5 = internal::None, typename T6 = internal::None,
+ typename T7 = internal::None, typename T8 = internal::None,
+ typename T9 = internal::None, typename T10 = internal::None,
+ typename T11 = internal::None, typename T12 = internal::None,
+ typename T13 = internal::None, typename T14 = internal::None,
+ typename T15 = internal::None, typename T16 = internal::None,
+ typename T17 = internal::None, typename T18 = internal::None,
+ typename T19 = internal::None, typename T20 = internal::None,
+ typename T21 = internal::None, typename T22 = internal::None,
+ typename T23 = internal::None, typename T24 = internal::None,
+ typename T25 = internal::None, typename T26 = internal::None,
+ typename T27 = internal::None, typename T28 = internal::None,
+ typename T29 = internal::None, typename T30 = internal::None,
+ typename T31 = internal::None, typename T32 = internal::None,
+ typename T33 = internal::None, typename T34 = internal::None,
+ typename T35 = internal::None, typename T36 = internal::None,
+ typename T37 = internal::None, typename T38 = internal::None,
+ typename T39 = internal::None, typename T40 = internal::None,
+ typename T41 = internal::None, typename T42 = internal::None,
+ typename T43 = internal::None, typename T44 = internal::None,
+ typename T45 = internal::None, typename T46 = internal::None,
+ typename T47 = internal::None, typename T48 = internal::None,
+ typename T49 = internal::None, typename T50 = internal::None>
+struct Types {
+ typedef internal::Types50<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42, T43, T44, T45, T46, T47, T48, T49, T50> type;
+};
+
+template <>
+struct Types<internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types0 type;
+};
+template <typename T1>
+struct Types<T1, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types1<T1> type;
+};
+template <typename T1, typename T2>
+struct Types<T1, T2, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types2<T1, T2> type;
+};
+template <typename T1, typename T2, typename T3>
+struct Types<T1, T2, T3, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types3<T1, T2, T3> type;
+};
+template <typename T1, typename T2, typename T3, typename T4>
+struct Types<T1, T2, T3, T4, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types4<T1, T2, T3, T4> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5>
+struct Types<T1, T2, T3, T4, T5, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types5<T1, T2, T3, T4, T5> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6>
+struct Types<T1, T2, T3, T4, T5, T6, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types6<T1, T2, T3, T4, T5, T6> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7>
+struct Types<T1, T2, T3, T4, T5, T6, T7, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types7<T1, T2, T3, T4, T5, T6, T7> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types8<T1, T2, T3, T4, T5, T6, T7, T8> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types9<T1, T2, T3, T4, T5, T6, T7, T8, T9> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types10<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types11<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types12<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types13<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types14<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types15<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types16<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types17<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types18<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types19<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types20<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types21<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types22<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types23<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types24<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types25<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types26<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types27<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types28<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types29<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types30<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types31<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types32<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types33<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types34<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types35<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types36<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types37<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types38<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types39<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types40<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types41<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, internal::None,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types42<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None, internal::None> {
+ typedef internal::Types43<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42, T43> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None, internal::None> {
+ typedef internal::Types44<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42, T43, T44> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44, T45,
+ internal::None, internal::None, internal::None, internal::None,
+ internal::None> {
+ typedef internal::Types45<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42, T43, T44, T45> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44, T45,
+ T46, internal::None, internal::None, internal::None, internal::None> {
+ typedef internal::Types46<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42, T43, T44, T45, T46> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44, T45,
+ T46, T47, internal::None, internal::None, internal::None> {
+ typedef internal::Types47<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42, T43, T44, T45, T46, T47> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44, T45,
+ T46, T47, T48, internal::None, internal::None> {
+ typedef internal::Types48<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42, T43, T44, T45, T46, T47, T48> type;
+};
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48, typename T49>
+struct Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15,
+ T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29, T30,
+ T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44, T45,
+ T46, T47, T48, T49, internal::None> {
+ typedef internal::Types49<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42, T43, T44, T45, T46, T47, T48, T49> type;
+};
+
+namespace internal {
+
+# define GTEST_TEMPLATE_ template <typename T> class
+
+// The template "selector" struct TemplateSel<Tmpl> is used to
+// represent Tmpl, which must be a class template with one type
+// parameter, as a type. TemplateSel<Tmpl>::Bind<T>::type is defined
+// as the type Tmpl<T>. This allows us to actually instantiate the
+// template "selected" by TemplateSel<Tmpl>.
+//
+// This trick is necessary for simulating typedef for class templates,
+// which C++ doesn't support directly.
+template <GTEST_TEMPLATE_ Tmpl>
+struct TemplateSel {
+ template <typename T>
+ struct Bind {
+ typedef Tmpl<T> type;
+ };
+};
+
+# define GTEST_BIND_(TmplSel, T) \
+ TmplSel::template Bind<T>::type
+
+// A unique struct template used as the default value for the
+// arguments of class template Templates. This allows us to simulate
+// variadic templates (e.g. Templates<int>, Templates<int, double>,
+// and etc), which C++ doesn't support directly.
+template <typename T>
+struct NoneT {};
+
+// The following family of struct and struct templates are used to
+// represent template lists. In particular, TemplatesN<T1, T2, ...,
+// TN> represents a list of N templates (T1, T2, ..., and TN). Except
+// for Templates0, every struct in the family has two member types:
+// Head for the selector of the first template in the list, and Tail
+// for the rest of the list.
+
+// The empty template list.
+struct Templates0 {};
+
+// Template lists of length 1, 2, 3, and so on.
+
+template <GTEST_TEMPLATE_ T1>
+struct Templates1 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates0 Tail;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2>
+struct Templates2 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates1<T2> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3>
+struct Templates3 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates2<T2, T3> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4>
+struct Templates4 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates3<T2, T3, T4> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5>
+struct Templates5 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates4<T2, T3, T4, T5> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6>
+struct Templates6 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates5<T2, T3, T4, T5, T6> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7>
+struct Templates7 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates6<T2, T3, T4, T5, T6, T7> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8>
+struct Templates8 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates7<T2, T3, T4, T5, T6, T7, T8> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9>
+struct Templates9 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates8<T2, T3, T4, T5, T6, T7, T8, T9> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10>
+struct Templates10 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates9<T2, T3, T4, T5, T6, T7, T8, T9, T10> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11>
+struct Templates11 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates10<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12>
+struct Templates12 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates11<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13>
+struct Templates13 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates12<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14>
+struct Templates14 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates13<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15>
+struct Templates15 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates14<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16>
+struct Templates16 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates15<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17>
+struct Templates17 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates16<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18>
+struct Templates18 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates17<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19>
+struct Templates19 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates18<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20>
+struct Templates20 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates19<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21>
+struct Templates21 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates20<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22>
+struct Templates22 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates21<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23>
+struct Templates23 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates22<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24>
+struct Templates24 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates23<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25>
+struct Templates25 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates24<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26>
+struct Templates26 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates25<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27>
+struct Templates27 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates26<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28>
+struct Templates28 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates27<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29>
+struct Templates29 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates28<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30>
+struct Templates30 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates29<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31>
+struct Templates31 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates30<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32>
+struct Templates32 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates31<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33>
+struct Templates33 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates32<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34>
+struct Templates34 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates33<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35>
+struct Templates35 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates34<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36>
+struct Templates36 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates35<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37>
+struct Templates37 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates36<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38>
+struct Templates38 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates37<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39>
+struct Templates39 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates38<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40>
+struct Templates40 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates39<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41>
+struct Templates41 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates40<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42>
+struct Templates42 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates41<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43>
+struct Templates43 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates42<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44>
+struct Templates44 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates43<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43, T44> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45>
+struct Templates45 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates44<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43, T44, T45> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45,
+ GTEST_TEMPLATE_ T46>
+struct Templates46 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates45<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43, T44, T45, T46> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45,
+ GTEST_TEMPLATE_ T46, GTEST_TEMPLATE_ T47>
+struct Templates47 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates46<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43, T44, T45, T46, T47> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45,
+ GTEST_TEMPLATE_ T46, GTEST_TEMPLATE_ T47, GTEST_TEMPLATE_ T48>
+struct Templates48 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates47<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43, T44, T45, T46, T47, T48> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45,
+ GTEST_TEMPLATE_ T46, GTEST_TEMPLATE_ T47, GTEST_TEMPLATE_ T48,
+ GTEST_TEMPLATE_ T49>
+struct Templates49 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates48<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43, T44, T45, T46, T47, T48, T49> Tail;
+};
+
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45,
+ GTEST_TEMPLATE_ T46, GTEST_TEMPLATE_ T47, GTEST_TEMPLATE_ T48,
+ GTEST_TEMPLATE_ T49, GTEST_TEMPLATE_ T50>
+struct Templates50 {
+ typedef TemplateSel<T1> Head;
+ typedef Templates49<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43, T44, T45, T46, T47, T48, T49, T50> Tail;
+};
+
+
+// We don't want to require the users to write TemplatesN<...> directly,
+// as that would require them to count the length. Templates<...> is much
+// easier to write, but generates horrible messages when there is a
+// compiler error, as gcc insists on printing out each template
+// argument, even if it has the default value (this means Templates<list>
+// will appear as Templates<list, NoneT, NoneT, ..., NoneT> in the compiler
+// errors).
+//
+// Our solution is to combine the best part of the two approaches: a
+// user would write Templates<T1, ..., TN>, and Google Test will translate
+// that to TemplatesN<T1, ..., TN> internally to make error messages
+// readable. The translation is done by the 'type' member of the
+// Templates template.
+template <GTEST_TEMPLATE_ T1 = NoneT, GTEST_TEMPLATE_ T2 = NoneT,
+ GTEST_TEMPLATE_ T3 = NoneT, GTEST_TEMPLATE_ T4 = NoneT,
+ GTEST_TEMPLATE_ T5 = NoneT, GTEST_TEMPLATE_ T6 = NoneT,
+ GTEST_TEMPLATE_ T7 = NoneT, GTEST_TEMPLATE_ T8 = NoneT,
+ GTEST_TEMPLATE_ T9 = NoneT, GTEST_TEMPLATE_ T10 = NoneT,
+ GTEST_TEMPLATE_ T11 = NoneT, GTEST_TEMPLATE_ T12 = NoneT,
+ GTEST_TEMPLATE_ T13 = NoneT, GTEST_TEMPLATE_ T14 = NoneT,
+ GTEST_TEMPLATE_ T15 = NoneT, GTEST_TEMPLATE_ T16 = NoneT,
+ GTEST_TEMPLATE_ T17 = NoneT, GTEST_TEMPLATE_ T18 = NoneT,
+ GTEST_TEMPLATE_ T19 = NoneT, GTEST_TEMPLATE_ T20 = NoneT,
+ GTEST_TEMPLATE_ T21 = NoneT, GTEST_TEMPLATE_ T22 = NoneT,
+ GTEST_TEMPLATE_ T23 = NoneT, GTEST_TEMPLATE_ T24 = NoneT,
+ GTEST_TEMPLATE_ T25 = NoneT, GTEST_TEMPLATE_ T26 = NoneT,
+ GTEST_TEMPLATE_ T27 = NoneT, GTEST_TEMPLATE_ T28 = NoneT,
+ GTEST_TEMPLATE_ T29 = NoneT, GTEST_TEMPLATE_ T30 = NoneT,
+ GTEST_TEMPLATE_ T31 = NoneT, GTEST_TEMPLATE_ T32 = NoneT,
+ GTEST_TEMPLATE_ T33 = NoneT, GTEST_TEMPLATE_ T34 = NoneT,
+ GTEST_TEMPLATE_ T35 = NoneT, GTEST_TEMPLATE_ T36 = NoneT,
+ GTEST_TEMPLATE_ T37 = NoneT, GTEST_TEMPLATE_ T38 = NoneT,
+ GTEST_TEMPLATE_ T39 = NoneT, GTEST_TEMPLATE_ T40 = NoneT,
+ GTEST_TEMPLATE_ T41 = NoneT, GTEST_TEMPLATE_ T42 = NoneT,
+ GTEST_TEMPLATE_ T43 = NoneT, GTEST_TEMPLATE_ T44 = NoneT,
+ GTEST_TEMPLATE_ T45 = NoneT, GTEST_TEMPLATE_ T46 = NoneT,
+ GTEST_TEMPLATE_ T47 = NoneT, GTEST_TEMPLATE_ T48 = NoneT,
+ GTEST_TEMPLATE_ T49 = NoneT, GTEST_TEMPLATE_ T50 = NoneT>
+struct Templates {
+ typedef Templates50<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42, T43, T44, T45, T46, T47, T48, T49, T50> type;
+};
+
+template <>
+struct Templates<NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT> {
+ typedef Templates0 type;
+};
+template <GTEST_TEMPLATE_ T1>
+struct Templates<T1, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT> {
+ typedef Templates1<T1> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2>
+struct Templates<T1, T2, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT> {
+ typedef Templates2<T1, T2> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3>
+struct Templates<T1, T2, T3, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates3<T1, T2, T3> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4>
+struct Templates<T1, T2, T3, T4, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates4<T1, T2, T3, T4> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5>
+struct Templates<T1, T2, T3, T4, T5, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates5<T1, T2, T3, T4, T5> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6>
+struct Templates<T1, T2, T3, T4, T5, T6, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates6<T1, T2, T3, T4, T5, T6> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates7<T1, T2, T3, T4, T5, T6, T7> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates8<T1, T2, T3, T4, T5, T6, T7, T8> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates9<T1, T2, T3, T4, T5, T6, T7, T8, T9> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates10<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates11<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates12<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates13<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates14<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates15<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates16<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates17<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates18<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates19<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates20<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates21<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT> {
+ typedef Templates22<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT> {
+ typedef Templates23<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT> {
+ typedef Templates24<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT> {
+ typedef Templates25<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT> {
+ typedef Templates26<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT> {
+ typedef Templates27<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT> {
+ typedef Templates28<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT> {
+ typedef Templates29<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates30<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates31<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates32<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates33<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates34<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates35<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates36<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, NoneT, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates37<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, NoneT, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates38<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates39<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, NoneT, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates40<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, NoneT, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates41<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, NoneT,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates42<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates43<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42, T43> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44,
+ NoneT, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates44<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42, T43, T44> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44,
+ T45, NoneT, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates45<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42, T43, T44, T45> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45,
+ GTEST_TEMPLATE_ T46>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44,
+ T45, T46, NoneT, NoneT, NoneT, NoneT> {
+ typedef Templates46<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42, T43, T44, T45, T46> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45,
+ GTEST_TEMPLATE_ T46, GTEST_TEMPLATE_ T47>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44,
+ T45, T46, T47, NoneT, NoneT, NoneT> {
+ typedef Templates47<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42, T43, T44, T45, T46, T47> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45,
+ GTEST_TEMPLATE_ T46, GTEST_TEMPLATE_ T47, GTEST_TEMPLATE_ T48>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44,
+ T45, T46, T47, T48, NoneT, NoneT> {
+ typedef Templates48<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42, T43, T44, T45, T46, T47, T48> type;
+};
+template <GTEST_TEMPLATE_ T1, GTEST_TEMPLATE_ T2, GTEST_TEMPLATE_ T3,
+ GTEST_TEMPLATE_ T4, GTEST_TEMPLATE_ T5, GTEST_TEMPLATE_ T6,
+ GTEST_TEMPLATE_ T7, GTEST_TEMPLATE_ T8, GTEST_TEMPLATE_ T9,
+ GTEST_TEMPLATE_ T10, GTEST_TEMPLATE_ T11, GTEST_TEMPLATE_ T12,
+ GTEST_TEMPLATE_ T13, GTEST_TEMPLATE_ T14, GTEST_TEMPLATE_ T15,
+ GTEST_TEMPLATE_ T16, GTEST_TEMPLATE_ T17, GTEST_TEMPLATE_ T18,
+ GTEST_TEMPLATE_ T19, GTEST_TEMPLATE_ T20, GTEST_TEMPLATE_ T21,
+ GTEST_TEMPLATE_ T22, GTEST_TEMPLATE_ T23, GTEST_TEMPLATE_ T24,
+ GTEST_TEMPLATE_ T25, GTEST_TEMPLATE_ T26, GTEST_TEMPLATE_ T27,
+ GTEST_TEMPLATE_ T28, GTEST_TEMPLATE_ T29, GTEST_TEMPLATE_ T30,
+ GTEST_TEMPLATE_ T31, GTEST_TEMPLATE_ T32, GTEST_TEMPLATE_ T33,
+ GTEST_TEMPLATE_ T34, GTEST_TEMPLATE_ T35, GTEST_TEMPLATE_ T36,
+ GTEST_TEMPLATE_ T37, GTEST_TEMPLATE_ T38, GTEST_TEMPLATE_ T39,
+ GTEST_TEMPLATE_ T40, GTEST_TEMPLATE_ T41, GTEST_TEMPLATE_ T42,
+ GTEST_TEMPLATE_ T43, GTEST_TEMPLATE_ T44, GTEST_TEMPLATE_ T45,
+ GTEST_TEMPLATE_ T46, GTEST_TEMPLATE_ T47, GTEST_TEMPLATE_ T48,
+ GTEST_TEMPLATE_ T49>
+struct Templates<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14,
+ T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28, T29,
+ T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43, T44,
+ T45, T46, T47, T48, T49, NoneT> {
+ typedef Templates49<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42, T43, T44, T45, T46, T47, T48, T49> type;
+};
+
+// The TypeList template makes it possible to use either a single type
+// or a Types<...> list in TYPED_TEST_CASE() and
+// INSTANTIATE_TYPED_TEST_CASE_P().
+
+template <typename T>
+struct TypeList {
+ typedef Types1<T> type;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48, typename T49, typename T50>
+struct TypeList<Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46, T47, T48, T49, T50> > {
+ typedef typename Types<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41, T42, T43, T44, T45, T46, T47, T48, T49, T50>::type type;
+};
+
+#endif // GTEST_HAS_TYPED_TEST || GTEST_HAS_TYPED_TEST_P
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_TYPE_UTIL_H_
+
+// Due to C++ preprocessor weirdness, we need double indirection to
+// concatenate two tokens when one of them is __LINE__. Writing
+//
+// foo ## __LINE__
+//
+// will result in the token foo__LINE__, instead of foo followed by
+// the current line number. For more details, see
+// http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.6
+#define GTEST_CONCAT_TOKEN_(foo, bar) GTEST_CONCAT_TOKEN_IMPL_(foo, bar)
+#define GTEST_CONCAT_TOKEN_IMPL_(foo, bar) foo ## bar
+
+class ProtocolMessage;
+namespace proto2 { class Message; }
+
+namespace testing {
+
+// Forward declarations.
+
+class AssertionResult; // Result of an assertion.
+class Message; // Represents a failure message.
+class Test; // Represents a test.
+class TestInfo; // Information about a test.
+class TestPartResult; // Result of a test part.
+class UnitTest; // A collection of test cases.
+
+template <typename T>
+::std::string PrintToString(const T& value);
+
+namespace internal {
+
+struct TraceInfo; // Information about a trace point.
+class ScopedTrace; // Implements scoped trace.
+class TestInfoImpl; // Opaque implementation of TestInfo
+class UnitTestImpl; // Opaque implementation of UnitTest
+
+// How many times InitGoogleTest() has been called.
+GTEST_API_ extern int g_init_gtest_count;
+
+// The text used in failure messages to indicate the start of the
+// stack trace.
+GTEST_API_ extern const char kStackTraceMarker[];
+
+// Two overloaded helpers for checking at compile time whether an
+// expression is a null pointer literal (i.e. NULL or any 0-valued
+// compile-time integral constant). Their return values have
+// different sizes, so we can use sizeof() to test which version is
+// picked by the compiler. These helpers have no implementations, as
+// we only need their signatures.
+//
+// Given IsNullLiteralHelper(x), the compiler will pick the first
+// version if x can be implicitly converted to Secret*, and pick the
+// second version otherwise. Since Secret is a secret and incomplete
+// type, the only expression a user can write that has type Secret* is
+// a null pointer literal. Therefore, we know that x is a null
+// pointer literal if and only if the first version is picked by the
+// compiler.
+char IsNullLiteralHelper(Secret* p);
+char (&IsNullLiteralHelper(...))[2]; // NOLINT
+
+// A compile-time bool constant that is true if and only if x is a
+// null pointer literal (i.e. NULL or any 0-valued compile-time
+// integral constant).
+#ifdef GTEST_ELLIPSIS_NEEDS_POD_
+// We lose support for NULL detection where the compiler doesn't like
+// passing non-POD classes through ellipsis (...).
+# define GTEST_IS_NULL_LITERAL_(x) false
+#else
+# define GTEST_IS_NULL_LITERAL_(x) \
+ (sizeof(::testing::internal::IsNullLiteralHelper(x)) == 1)
+#endif // GTEST_ELLIPSIS_NEEDS_POD_
+
+// Appends the user-supplied message to the Google-Test-generated message.
+GTEST_API_ std::string AppendUserMessage(
+ const std::string& gtest_msg, const Message& user_msg);
+
+#if GTEST_HAS_EXCEPTIONS
+
+// This exception is thrown by (and only by) a failed Google Test
+// assertion when GTEST_FLAG(throw_on_failure) is true (if exceptions
+// are enabled). We derive it from std::runtime_error, which is for
+// errors presumably detectable only at run time. Since
+// std::runtime_error inherits from std::exception, many testing
+// frameworks know how to extract and print the message inside it.
+class GTEST_API_ GoogleTestFailureException : public ::std::runtime_error {
+ public:
+ explicit GoogleTestFailureException(const TestPartResult& failure);
+};
+
+#endif // GTEST_HAS_EXCEPTIONS
+
+// A helper class for creating scoped traces in user programs.
+class GTEST_API_ ScopedTrace {
+ public:
+ // The c'tor pushes the given source file location and message onto
+ // a trace stack maintained by Google Test.
+ ScopedTrace(const char* file, int line, const Message& message);
+
+ // The d'tor pops the info pushed by the c'tor.
+ //
+ // Note that the d'tor is not virtual in order to be efficient.
+ // Don't inherit from ScopedTrace!
+ ~ScopedTrace();
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ScopedTrace);
+} GTEST_ATTRIBUTE_UNUSED_; // A ScopedTrace object does its job in its
+ // c'tor and d'tor. Therefore it doesn't
+ // need to be used otherwise.
+
+// Constructs and returns the message for an equality assertion
+// (e.g. ASSERT_EQ, EXPECT_STREQ, etc) failure.
+//
+// The first four parameters are the expressions used in the assertion
+// and their values, as strings. For example, for ASSERT_EQ(foo, bar)
+// where foo is 5 and bar is 6, we have:
+//
+// expected_expression: "foo"
+// actual_expression: "bar"
+// expected_value: "5"
+// actual_value: "6"
+//
+// The ignoring_case parameter is true iff the assertion is a
+// *_STRCASEEQ*. When it's true, the string " (ignoring case)" will
+// be inserted into the message.
+GTEST_API_ AssertionResult EqFailure(const char* expected_expression,
+ const char* actual_expression,
+ const std::string& expected_value,
+ const std::string& actual_value,
+ bool ignoring_case);
+
+// Constructs a failure message for Boolean assertions such as EXPECT_TRUE.
+GTEST_API_ std::string GetBoolAssertionFailureMessage(
+ const AssertionResult& assertion_result,
+ const char* expression_text,
+ const char* actual_predicate_value,
+ const char* expected_predicate_value);
+
+// This template class represents an IEEE floating-point number
+// (either single-precision or double-precision, depending on the
+// template parameters).
+//
+// The purpose of this class is to do more sophisticated number
+// comparison. (Due to round-off error, etc, it's very unlikely that
+// two floating-points will be equal exactly. Hence a naive
+// comparison by the == operation often doesn't work.)
+//
+// Format of IEEE floating-point:
+//
+// The most-significant bit being the leftmost, an IEEE
+// floating-point looks like
+//
+// sign_bit exponent_bits fraction_bits
+//
+// Here, sign_bit is a single bit that designates the sign of the
+// number.
+//
+// For float, there are 8 exponent bits and 23 fraction bits.
+//
+// For double, there are 11 exponent bits and 52 fraction bits.
+//
+// More details can be found at
+// http://en.wikipedia.org/wiki/IEEE_floating-point_standard.
+//
+// Template parameter:
+//
+// RawType: the raw floating-point type (either float or double)
+template <typename RawType>
+class FloatingPoint {
+ public:
+ // Defines the unsigned integer type that has the same size as the
+ // floating point number.
+ typedef typename TypeWithSize<sizeof(RawType)>::UInt Bits;
+
+ // Constants.
+
+ // # of bits in a number.
+ static const size_t kBitCount = 8*sizeof(RawType);
+
+ // # of fraction bits in a number.
+ static const size_t kFractionBitCount =
+ std::numeric_limits<RawType>::digits - 1;
+
+ // # of exponent bits in a number.
+ static const size_t kExponentBitCount = kBitCount - 1 - kFractionBitCount;
+
+ // The mask for the sign bit.
+ static const Bits kSignBitMask = static_cast<Bits>(1) << (kBitCount - 1);
+
+ // The mask for the fraction bits.
+ static const Bits kFractionBitMask =
+ ~static_cast<Bits>(0) >> (kExponentBitCount + 1);
+
+ // The mask for the exponent bits.
+ static const Bits kExponentBitMask = ~(kSignBitMask | kFractionBitMask);
+
+ // How many ULP's (Units in the Last Place) we want to tolerate when
+ // comparing two numbers. The larger the value, the more error we
+ // allow. A 0 value means that two numbers must be exactly the same
+ // to be considered equal.
+ //
+ // The maximum error of a single floating-point operation is 0.5
+ // units in the last place. On Intel CPU's, all floating-point
+ // calculations are done with 80-bit precision, while double has 64
+ // bits. Therefore, 4 should be enough for ordinary use.
+ //
+ // See the following article for more details on ULP:
+ // http://randomascii.wordpress.com/2012/02/25/comparing-floating-point-numbers-2012-edition/
+ static const size_t kMaxUlps = 4;
+
+ // Constructs a FloatingPoint from a raw floating-point number.
+ //
+ // On an Intel CPU, passing a non-normalized NAN (Not a Number)
+ // around may change its bits, although the new value is guaranteed
+ // to be also a NAN. Therefore, don't expect this constructor to
+ // preserve the bits in x when x is a NAN.
+ explicit FloatingPoint(const RawType& x) { u_.value_ = x; }
+
+ // Static methods
+
+ // Reinterprets a bit pattern as a floating-point number.
+ //
+ // This function is needed to test the AlmostEquals() method.
+ static RawType ReinterpretBits(const Bits bits) {
+ FloatingPoint fp(0);
+ fp.u_.bits_ = bits;
+ return fp.u_.value_;
+ }
+
+ // Returns the floating-point number that represent positive infinity.
+ static RawType Infinity() {
+ return ReinterpretBits(kExponentBitMask);
+ }
+
+ // Returns the maximum representable finite floating-point number.
+ static RawType Max();
+
+ // Non-static methods
+
+ // Returns the bits that represents this number.
+ const Bits &bits() const { return u_.bits_; }
+
+ // Returns the exponent bits of this number.
+ Bits exponent_bits() const { return kExponentBitMask & u_.bits_; }
+
+ // Returns the fraction bits of this number.
+ Bits fraction_bits() const { return kFractionBitMask & u_.bits_; }
+
+ // Returns the sign bit of this number.
+ Bits sign_bit() const { return kSignBitMask & u_.bits_; }
+
+ // Returns true iff this is NAN (not a number).
+ bool is_nan() const {
+ // It's a NAN if the exponent bits are all ones and the fraction
+ // bits are not entirely zeros.
+ return (exponent_bits() == kExponentBitMask) && (fraction_bits() != 0);
+ }
+
+ // Returns true iff this number is at most kMaxUlps ULP's away from
+ // rhs. In particular, this function:
+ //
+ // - returns false if either number is (or both are) NAN.
+ // - treats really large numbers as almost equal to infinity.
+ // - thinks +0.0 and -0.0 are 0 DLP's apart.
+ bool AlmostEquals(const FloatingPoint& rhs) const {
+ // The IEEE standard says that any comparison operation involving
+ // a NAN must return false.
+ if (is_nan() || rhs.is_nan()) return false;
+
+ return DistanceBetweenSignAndMagnitudeNumbers(u_.bits_, rhs.u_.bits_)
+ <= kMaxUlps;
+ }
+
+ private:
+ // The data type used to store the actual floating-point number.
+ union FloatingPointUnion {
+ RawType value_; // The raw floating-point number.
+ Bits bits_; // The bits that represent the number.
+ };
+
+ // Converts an integer from the sign-and-magnitude representation to
+ // the biased representation. More precisely, let N be 2 to the
+ // power of (kBitCount - 1), an integer x is represented by the
+ // unsigned number x + N.
+ //
+ // For instance,
+ //
+ // -N + 1 (the most negative number representable using
+ // sign-and-magnitude) is represented by 1;
+ // 0 is represented by N; and
+ // N - 1 (the biggest number representable using
+ // sign-and-magnitude) is represented by 2N - 1.
+ //
+ // Read http://en.wikipedia.org/wiki/Signed_number_representations
+ // for more details on signed number representations.
+ static Bits SignAndMagnitudeToBiased(const Bits &sam) {
+ if (kSignBitMask & sam) {
+ // sam represents a negative number.
+ return ~sam + 1;
+ } else {
+ // sam represents a positive number.
+ return kSignBitMask | sam;
+ }
+ }
+
+ // Given two numbers in the sign-and-magnitude representation,
+ // returns the distance between them as an unsigned number.
+ static Bits DistanceBetweenSignAndMagnitudeNumbers(const Bits &sam1,
+ const Bits &sam2) {
+ const Bits biased1 = SignAndMagnitudeToBiased(sam1);
+ const Bits biased2 = SignAndMagnitudeToBiased(sam2);
+ return (biased1 >= biased2) ? (biased1 - biased2) : (biased2 - biased1);
+ }
+
+ FloatingPointUnion u_;
+};
+
+// We cannot use std::numeric_limits<T>::max() as it clashes with the max()
+// macro defined by <windows.h>.
+template <>
+inline float FloatingPoint<float>::Max() { return FLT_MAX; }
+template <>
+inline double FloatingPoint<double>::Max() { return DBL_MAX; }
+
+// Typedefs the instances of the FloatingPoint template class that we
+// care to use.
+typedef FloatingPoint<float> Float;
+typedef FloatingPoint<double> Double;
+
+// In order to catch the mistake of putting tests that use different
+// test fixture classes in the same test case, we need to assign
+// unique IDs to fixture classes and compare them. The TypeId type is
+// used to hold such IDs. The user should treat TypeId as an opaque
+// type: the only operation allowed on TypeId values is to compare
+// them for equality using the == operator.
+typedef const void* TypeId;
+
+template <typename T>
+class TypeIdHelper {
+ public:
+ // dummy_ must not have a const type. Otherwise an overly eager
+ // compiler (e.g. MSVC 7.1 & 8.0) may try to merge
+ // TypeIdHelper<T>::dummy_ for different Ts as an "optimization".
+ static bool dummy_;
+};
+
+template <typename T>
+bool TypeIdHelper<T>::dummy_ = false;
+
+// GetTypeId<T>() returns the ID of type T. Different values will be
+// returned for different types. Calling the function twice with the
+// same type argument is guaranteed to return the same ID.
+template <typename T>
+TypeId GetTypeId() {
+ // The compiler is required to allocate a different
+ // TypeIdHelper<T>::dummy_ variable for each T used to instantiate
+ // the template. Therefore, the address of dummy_ is guaranteed to
+ // be unique.
+ return &(TypeIdHelper<T>::dummy_);
+}
+
+// Returns the type ID of ::testing::Test. Always call this instead
+// of GetTypeId< ::testing::Test>() to get the type ID of
+// ::testing::Test, as the latter may give the wrong result due to a
+// suspected linker bug when compiling Google Test as a Mac OS X
+// framework.
+GTEST_API_ TypeId GetTestTypeId();
+
+// Defines the abstract factory interface that creates instances
+// of a Test object.
+class TestFactoryBase {
+ public:
+ virtual ~TestFactoryBase() {}
+
+ // Creates a test instance to run. The instance is both created and destroyed
+ // within TestInfoImpl::Run()
+ virtual Test* CreateTest() = 0;
+
+ protected:
+ TestFactoryBase() {}
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(TestFactoryBase);
+};
+
+// This class provides implementation of TeastFactoryBase interface.
+// It is used in TEST and TEST_F macros.
+template <class TestClass>
+class TestFactoryImpl : public TestFactoryBase {
+ public:
+ virtual Test* CreateTest() { return new TestClass; }
+};
+
+#if GTEST_OS_WINDOWS
+
+// Predicate-formatters for implementing the HRESULT checking macros
+// {ASSERT|EXPECT}_HRESULT_{SUCCEEDED|FAILED}
+// We pass a long instead of HRESULT to avoid causing an
+// include dependency for the HRESULT type.
+GTEST_API_ AssertionResult IsHRESULTSuccess(const char* expr,
+ long hr); // NOLINT
+GTEST_API_ AssertionResult IsHRESULTFailure(const char* expr,
+ long hr); // NOLINT
+
+#endif // GTEST_OS_WINDOWS
+
+// Types of SetUpTestCase() and TearDownTestCase() functions.
+typedef void (*SetUpTestCaseFunc)();
+typedef void (*TearDownTestCaseFunc)();
+
+// Creates a new TestInfo object and registers it with Google Test;
+// returns the created object.
+//
+// Arguments:
+//
+// test_case_name: name of the test case
+// name: name of the test
+// type_param the name of the test's type parameter, or NULL if
+// this is not a typed or a type-parameterized test.
+// value_param text representation of the test's value parameter,
+// or NULL if this is not a type-parameterized test.
+// fixture_class_id: ID of the test fixture class
+// set_up_tc: pointer to the function that sets up the test case
+// tear_down_tc: pointer to the function that tears down the test case
+// factory: pointer to the factory that creates a test object.
+// The newly created TestInfo instance will assume
+// ownership of the factory object.
+GTEST_API_ TestInfo* MakeAndRegisterTestInfo(
+ const char* test_case_name,
+ const char* name,
+ const char* type_param,
+ const char* value_param,
+ TypeId fixture_class_id,
+ SetUpTestCaseFunc set_up_tc,
+ TearDownTestCaseFunc tear_down_tc,
+ TestFactoryBase* factory);
+
+// If *pstr starts with the given prefix, modifies *pstr to be right
+// past the prefix and returns true; otherwise leaves *pstr unchanged
+// and returns false. None of pstr, *pstr, and prefix can be NULL.
+GTEST_API_ bool SkipPrefix(const char* prefix, const char** pstr);
+
+#if GTEST_HAS_TYPED_TEST || GTEST_HAS_TYPED_TEST_P
+
+// State of the definition of a type-parameterized test case.
+class GTEST_API_ TypedTestCasePState {
+ public:
+ TypedTestCasePState() : registered_(false) {}
+
+ // Adds the given test name to defined_test_names_ and return true
+ // if the test case hasn't been registered; otherwise aborts the
+ // program.
+ bool AddTestName(const char* file, int line, const char* case_name,
+ const char* test_name) {
+ if (registered_) {
+ fprintf(stderr, "%s Test %s must be defined before "
+ "REGISTER_TYPED_TEST_CASE_P(%s, ...).\n",
+ FormatFileLocation(file, line).c_str(), test_name, case_name);
+ fflush(stderr);
+ posix::Abort();
+ }
+ defined_test_names_.insert(test_name);
+ return true;
+ }
+
+ // Verifies that registered_tests match the test names in
+ // defined_test_names_; returns registered_tests if successful, or
+ // aborts the program otherwise.
+ const char* VerifyRegisteredTestNames(
+ const char* file, int line, const char* registered_tests);
+
+ private:
+ bool registered_;
+ ::std::set<const char*> defined_test_names_;
+};
+
+// Skips to the first non-space char after the first comma in 'str';
+// returns NULL if no comma is found in 'str'.
+inline const char* SkipComma(const char* str) {
+ const char* comma = strchr(str, ',');
+ if (comma == NULL) {
+ return NULL;
+ }
+ while (IsSpace(*(++comma))) {}
+ return comma;
+}
+
+// Returns the prefix of 'str' before the first comma in it; returns
+// the entire string if it contains no comma.
+inline std::string GetPrefixUntilComma(const char* str) {
+ const char* comma = strchr(str, ',');
+ return comma == NULL ? str : std::string(str, comma);
+}
+
+// TypeParameterizedTest<Fixture, TestSel, Types>::Register()
+// registers a list of type-parameterized tests with Google Test. The
+// return value is insignificant - we just need to return something
+// such that we can call this function in a namespace scope.
+//
+// Implementation note: The GTEST_TEMPLATE_ macro declares a template
+// template parameter. It's defined in gtest-type-util.h.
+template <GTEST_TEMPLATE_ Fixture, class TestSel, typename Types>
+class TypeParameterizedTest {
+ public:
+ // 'index' is the index of the test in the type list 'Types'
+ // specified in INSTANTIATE_TYPED_TEST_CASE_P(Prefix, TestCase,
+ // Types). Valid values for 'index' are [0, N - 1] where N is the
+ // length of Types.
+ static bool Register(const char* prefix, const char* case_name,
+ const char* test_names, int index) {
+ typedef typename Types::Head Type;
+ typedef Fixture<Type> FixtureClass;
+ typedef typename GTEST_BIND_(TestSel, Type) TestClass;
+
+ // First, registers the first type-parameterized test in the type
+ // list.
+ MakeAndRegisterTestInfo(
+ (std::string(prefix) + (prefix[0] == '\0' ? "" : "/") + case_name + "/"
+ + StreamableToString(index)).c_str(),
+ GetPrefixUntilComma(test_names).c_str(),
+ GetTypeName<Type>().c_str(),
+ NULL, // No value parameter.
+ GetTypeId<FixtureClass>(),
+ TestClass::SetUpTestCase,
+ TestClass::TearDownTestCase,
+ new TestFactoryImpl<TestClass>);
+
+ // Next, recurses (at compile time) with the tail of the type list.
+ return TypeParameterizedTest<Fixture, TestSel, typename Types::Tail>
+ ::Register(prefix, case_name, test_names, index + 1);
+ }
+};
+
+// The base case for the compile time recursion.
+template <GTEST_TEMPLATE_ Fixture, class TestSel>
+class TypeParameterizedTest<Fixture, TestSel, Types0> {
+ public:
+ static bool Register(const char* /*prefix*/, const char* /*case_name*/,
+ const char* /*test_names*/, int /*index*/) {
+ return true;
+ }
+};
+
+// TypeParameterizedTestCase<Fixture, Tests, Types>::Register()
+// registers *all combinations* of 'Tests' and 'Types' with Google
+// Test. The return value is insignificant - we just need to return
+// something such that we can call this function in a namespace scope.
+template <GTEST_TEMPLATE_ Fixture, typename Tests, typename Types>
+class TypeParameterizedTestCase {
+ public:
+ static bool Register(const char* prefix, const char* case_name,
+ const char* test_names) {
+ typedef typename Tests::Head Head;
+
+ // First, register the first test in 'Test' for each type in 'Types'.
+ TypeParameterizedTest<Fixture, Head, Types>::Register(
+ prefix, case_name, test_names, 0);
+
+ // Next, recurses (at compile time) with the tail of the test list.
+ return TypeParameterizedTestCase<Fixture, typename Tests::Tail, Types>
+ ::Register(prefix, case_name, SkipComma(test_names));
+ }
+};
+
+// The base case for the compile time recursion.
+template <GTEST_TEMPLATE_ Fixture, typename Types>
+class TypeParameterizedTestCase<Fixture, Templates0, Types> {
+ public:
+ static bool Register(const char* /*prefix*/, const char* /*case_name*/,
+ const char* /*test_names*/) {
+ return true;
+ }
+};
+
+#endif // GTEST_HAS_TYPED_TEST || GTEST_HAS_TYPED_TEST_P
+
+// Returns the current OS stack trace as an std::string.
+//
+// The maximum number of stack frames to be included is specified by
+// the gtest_stack_trace_depth flag. The skip_count parameter
+// specifies the number of top frames to be skipped, which doesn't
+// count against the number of frames to be included.
+//
+// For example, if Foo() calls Bar(), which in turn calls
+// GetCurrentOsStackTraceExceptTop(..., 1), Foo() will be included in
+// the trace but Bar() and GetCurrentOsStackTraceExceptTop() won't.
+GTEST_API_ std::string GetCurrentOsStackTraceExceptTop(
+ UnitTest* unit_test, int skip_count);
+
+// Helpers for suppressing warnings on unreachable code or constant
+// condition.
+
+// Always returns true.
+GTEST_API_ bool AlwaysTrue();
+
+// Always returns false.
+inline bool AlwaysFalse() { return !AlwaysTrue(); }
+
+// Helper for suppressing false warning from Clang on a const char*
+// variable declared in a conditional expression always being NULL in
+// the else branch.
+struct GTEST_API_ ConstCharPtr {
+ ConstCharPtr(const char* str) : value(str) {}
+ operator bool() const { return true; }
+ const char* value;
+};
+
+// A simple Linear Congruential Generator for generating random
+// numbers with a uniform distribution. Unlike rand() and srand(), it
+// doesn't use global state (and therefore can't interfere with user
+// code). Unlike rand_r(), it's portable. An LCG isn't very random,
+// but it's good enough for our purposes.
+class GTEST_API_ Random {
+ public:
+ static const UInt32 kMaxRange = 1u << 31;
+
+ explicit Random(UInt32 seed) : state_(seed) {}
+
+ void Reseed(UInt32 seed) { state_ = seed; }
+
+ // Generates a random number from [0, range). Crashes if 'range' is
+ // 0 or greater than kMaxRange.
+ UInt32 Generate(UInt32 range);
+
+ private:
+ UInt32 state_;
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(Random);
+};
+
+// Defining a variable of type CompileAssertTypesEqual<T1, T2> will cause a
+// compiler error iff T1 and T2 are different types.
+template <typename T1, typename T2>
+struct CompileAssertTypesEqual;
+
+template <typename T>
+struct CompileAssertTypesEqual<T, T> {
+};
+
+// Removes the reference from a type if it is a reference type,
+// otherwise leaves it unchanged. This is the same as
+// tr1::remove_reference, which is not widely available yet.
+template <typename T>
+struct RemoveReference { typedef T type; }; // NOLINT
+template <typename T>
+struct RemoveReference<T&> { typedef T type; }; // NOLINT
+
+// A handy wrapper around RemoveReference that works when the argument
+// T depends on template parameters.
+#define GTEST_REMOVE_REFERENCE_(T) \
+ typename ::testing::internal::RemoveReference<T>::type
+
+// Removes const from a type if it is a const type, otherwise leaves
+// it unchanged. This is the same as tr1::remove_const, which is not
+// widely available yet.
+template <typename T>
+struct RemoveConst { typedef T type; }; // NOLINT
+template <typename T>
+struct RemoveConst<const T> { typedef T type; }; // NOLINT
+
+// MSVC 8.0, Sun C++, and IBM XL C++ have a bug which causes the above
+// definition to fail to remove the const in 'const int[3]' and 'const
+// char[3][4]'. The following specialization works around the bug.
+template <typename T, size_t N>
+struct RemoveConst<const T[N]> {
+ typedef typename RemoveConst<T>::type type[N];
+};
+
+#if defined(_MSC_VER) && _MSC_VER < 1400
+// This is the only specialization that allows VC++ 7.1 to remove const in
+// 'const int[3] and 'const int[3][4]'. However, it causes trouble with GCC
+// and thus needs to be conditionally compiled.
+template <typename T, size_t N>
+struct RemoveConst<T[N]> {
+ typedef typename RemoveConst<T>::type type[N];
+};
+#endif
+
+// A handy wrapper around RemoveConst that works when the argument
+// T depends on template parameters.
+#define GTEST_REMOVE_CONST_(T) \
+ typename ::testing::internal::RemoveConst<T>::type
+
+// Turns const U&, U&, const U, and U all into U.
+#define GTEST_REMOVE_REFERENCE_AND_CONST_(T) \
+ GTEST_REMOVE_CONST_(GTEST_REMOVE_REFERENCE_(T))
+
+// Adds reference to a type if it is not a reference type,
+// otherwise leaves it unchanged. This is the same as
+// tr1::add_reference, which is not widely available yet.
+template <typename T>
+struct AddReference { typedef T& type; }; // NOLINT
+template <typename T>
+struct AddReference<T&> { typedef T& type; }; // NOLINT
+
+// A handy wrapper around AddReference that works when the argument T
+// depends on template parameters.
+#define GTEST_ADD_REFERENCE_(T) \
+ typename ::testing::internal::AddReference<T>::type
+
+// Adds a reference to const on top of T as necessary. For example,
+// it transforms
+//
+// char ==> const char&
+// const char ==> const char&
+// char& ==> const char&
+// const char& ==> const char&
+//
+// The argument T must depend on some template parameters.
+#define GTEST_REFERENCE_TO_CONST_(T) \
+ GTEST_ADD_REFERENCE_(const GTEST_REMOVE_REFERENCE_(T))
+
+// ImplicitlyConvertible<From, To>::value is a compile-time bool
+// constant that's true iff type From can be implicitly converted to
+// type To.
+template <typename From, typename To>
+class ImplicitlyConvertible {
+ private:
+ // We need the following helper functions only for their types.
+ // They have no implementations.
+
+ // MakeFrom() is an expression whose type is From. We cannot simply
+ // use From(), as the type From may not have a public default
+ // constructor.
+ static From MakeFrom();
+
+ // These two functions are overloaded. Given an expression
+ // Helper(x), the compiler will pick the first version if x can be
+ // implicitly converted to type To; otherwise it will pick the
+ // second version.
+ //
+ // The first version returns a value of size 1, and the second
+ // version returns a value of size 2. Therefore, by checking the
+ // size of Helper(x), which can be done at compile time, we can tell
+ // which version of Helper() is used, and hence whether x can be
+ // implicitly converted to type To.
+ static char Helper(To);
+ static char (&Helper(...))[2]; // NOLINT
+
+ // We have to put the 'public' section after the 'private' section,
+ // or MSVC refuses to compile the code.
+ public:
+ // MSVC warns about implicitly converting from double to int for
+ // possible loss of data, so we need to temporarily disable the
+ // warning.
+#ifdef _MSC_VER
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4244) // Temporarily disables warning 4244.
+
+ static const bool value =
+ sizeof(Helper(ImplicitlyConvertible::MakeFrom())) == 1;
+# pragma warning(pop) // Restores the warning state.
+#elif defined(__BORLANDC__)
+ // C++Builder cannot use member overload resolution during template
+ // instantiation. The simplest workaround is to use its C++0x type traits
+ // functions (C++Builder 2009 and above only).
+ static const bool value = __is_convertible(From, To);
+#else
+ static const bool value =
+ sizeof(Helper(ImplicitlyConvertible::MakeFrom())) == 1;
+#endif // _MSV_VER
+};
+template <typename From, typename To>
+const bool ImplicitlyConvertible<From, To>::value;
+
+// IsAProtocolMessage<T>::value is a compile-time bool constant that's
+// true iff T is type ProtocolMessage, proto2::Message, or a subclass
+// of those.
+template <typename T>
+struct IsAProtocolMessage
+ : public bool_constant<
+ ImplicitlyConvertible<const T*, const ::ProtocolMessage*>::value ||
+ ImplicitlyConvertible<const T*, const ::proto2::Message*>::value> {
+};
+
+// When the compiler sees expression IsContainerTest<C>(0), if C is an
+// STL-style container class, the first overload of IsContainerTest
+// will be viable (since both C::iterator* and C::const_iterator* are
+// valid types and NULL can be implicitly converted to them). It will
+// be picked over the second overload as 'int' is a perfect match for
+// the type of argument 0. If C::iterator or C::const_iterator is not
+// a valid type, the first overload is not viable, and the second
+// overload will be picked. Therefore, we can determine whether C is
+// a container class by checking the type of IsContainerTest<C>(0).
+// The value of the expression is insignificant.
+//
+// Note that we look for both C::iterator and C::const_iterator. The
+// reason is that C++ injects the name of a class as a member of the
+// class itself (e.g. you can refer to class iterator as either
+// 'iterator' or 'iterator::iterator'). If we look for C::iterator
+// only, for example, we would mistakenly think that a class named
+// iterator is an STL container.
+//
+// Also note that the simpler approach of overloading
+// IsContainerTest(typename C::const_iterator*) and
+// IsContainerTest(...) doesn't work with Visual Age C++ and Sun C++.
+typedef int IsContainer;
+template <class C>
+IsContainer IsContainerTest(int /* dummy */,
+ typename C::iterator* /* it */ = NULL,
+ typename C::const_iterator* /* const_it */ = NULL) {
+ return 0;
+}
+
+typedef char IsNotContainer;
+template <class C>
+IsNotContainer IsContainerTest(long /* dummy */) { return '\0'; }
+
+// EnableIf<condition>::type is void when 'Cond' is true, and
+// undefined when 'Cond' is false. To use SFINAE to make a function
+// overload only apply when a particular expression is true, add
+// "typename EnableIf<expression>::type* = 0" as the last parameter.
+template<bool> struct EnableIf;
+template<> struct EnableIf<true> { typedef void type; }; // NOLINT
+
+// Utilities for native arrays.
+
+// ArrayEq() compares two k-dimensional native arrays using the
+// elements' operator==, where k can be any integer >= 0. When k is
+// 0, ArrayEq() degenerates into comparing a single pair of values.
+
+template <typename T, typename U>
+bool ArrayEq(const T* lhs, size_t size, const U* rhs);
+
+// This generic version is used when k is 0.
+template <typename T, typename U>
+inline bool ArrayEq(const T& lhs, const U& rhs) { return lhs == rhs; }
+
+// This overload is used when k >= 1.
+template <typename T, typename U, size_t N>
+inline bool ArrayEq(const T(&lhs)[N], const U(&rhs)[N]) {
+ return internal::ArrayEq(lhs, N, rhs);
+}
+
+// This helper reduces code bloat. If we instead put its logic inside
+// the previous ArrayEq() function, arrays with different sizes would
+// lead to different copies of the template code.
+template <typename T, typename U>
+bool ArrayEq(const T* lhs, size_t size, const U* rhs) {
+ for (size_t i = 0; i != size; i++) {
+ if (!internal::ArrayEq(lhs[i], rhs[i]))
+ return false;
+ }
+ return true;
+}
+
+// Finds the first element in the iterator range [begin, end) that
+// equals elem. Element may be a native array type itself.
+template <typename Iter, typename Element>
+Iter ArrayAwareFind(Iter begin, Iter end, const Element& elem) {
+ for (Iter it = begin; it != end; ++it) {
+ if (internal::ArrayEq(*it, elem))
+ return it;
+ }
+ return end;
+}
+
+// CopyArray() copies a k-dimensional native array using the elements'
+// operator=, where k can be any integer >= 0. When k is 0,
+// CopyArray() degenerates into copying a single value.
+
+template <typename T, typename U>
+void CopyArray(const T* from, size_t size, U* to);
+
+// This generic version is used when k is 0.
+template <typename T, typename U>
+inline void CopyArray(const T& from, U* to) { *to = from; }
+
+// This overload is used when k >= 1.
+template <typename T, typename U, size_t N>
+inline void CopyArray(const T(&from)[N], U(*to)[N]) {
+ internal::CopyArray(from, N, *to);
+}
+
+// This helper reduces code bloat. If we instead put its logic inside
+// the previous CopyArray() function, arrays with different sizes
+// would lead to different copies of the template code.
+template <typename T, typename U>
+void CopyArray(const T* from, size_t size, U* to) {
+ for (size_t i = 0; i != size; i++) {
+ internal::CopyArray(from[i], to + i);
+ }
+}
+
+// The relation between an NativeArray object (see below) and the
+// native array it represents.
+enum RelationToSource {
+ kReference, // The NativeArray references the native array.
+ kCopy // The NativeArray makes a copy of the native array and
+ // owns the copy.
+};
+
+// Adapts a native array to a read-only STL-style container. Instead
+// of the complete STL container concept, this adaptor only implements
+// members useful for Google Mock's container matchers. New members
+// should be added as needed. To simplify the implementation, we only
+// support Element being a raw type (i.e. having no top-level const or
+// reference modifier). It's the client's responsibility to satisfy
+// this requirement. Element can be an array type itself (hence
+// multi-dimensional arrays are supported).
+template <typename Element>
+class NativeArray {
+ public:
+ // STL-style container typedefs.
+ typedef Element value_type;
+ typedef Element* iterator;
+ typedef const Element* const_iterator;
+
+ // Constructs from a native array.
+ NativeArray(const Element* array, size_t count, RelationToSource relation) {
+ Init(array, count, relation);
+ }
+
+ // Copy constructor.
+ NativeArray(const NativeArray& rhs) {
+ Init(rhs.array_, rhs.size_, rhs.relation_to_source_);
+ }
+
+ ~NativeArray() {
+ // Ensures that the user doesn't instantiate NativeArray with a
+ // const or reference type.
+ static_cast<void>(StaticAssertTypeEqHelper<Element,
+ GTEST_REMOVE_REFERENCE_AND_CONST_(Element)>());
+ if (relation_to_source_ == kCopy)
+ delete[] array_;
+ }
+
+ // STL-style container methods.
+ size_t size() const { return size_; }
+ const_iterator begin() const { return array_; }
+ const_iterator end() const { return array_ + size_; }
+ bool operator==(const NativeArray& rhs) const {
+ return size() == rhs.size() &&
+ ArrayEq(begin(), size(), rhs.begin());
+ }
+
+ private:
+ // Initializes this object; makes a copy of the input array if
+ // 'relation' is kCopy.
+ void Init(const Element* array, size_t a_size, RelationToSource relation) {
+ if (relation == kReference) {
+ array_ = array;
+ } else {
+ Element* const copy = new Element[a_size];
+ CopyArray(array, a_size, copy);
+ array_ = copy;
+ }
+ size_ = a_size;
+ relation_to_source_ = relation;
+ }
+
+ const Element* array_;
+ size_t size_;
+ RelationToSource relation_to_source_;
+
+ GTEST_DISALLOW_ASSIGN_(NativeArray);
+};
+
+} // namespace internal
+} // namespace testing
+
+#define GTEST_MESSAGE_AT_(file, line, message, result_type) \
+ ::testing::internal::AssertHelper(result_type, file, line, message) \
+ = ::testing::Message()
+
+#define GTEST_MESSAGE_(message, result_type) \
+ GTEST_MESSAGE_AT_(__FILE__, __LINE__, message, result_type)
+
+#define GTEST_FATAL_FAILURE_(message) \
+ return GTEST_MESSAGE_(message, ::testing::TestPartResult::kFatalFailure)
+
+#define GTEST_NONFATAL_FAILURE_(message) \
+ GTEST_MESSAGE_(message, ::testing::TestPartResult::kNonFatalFailure)
+
+#define GTEST_SUCCESS_(message) \
+ GTEST_MESSAGE_(message, ::testing::TestPartResult::kSuccess)
+
+// Suppresses MSVC warnings 4072 (unreachable code) for the code following
+// statement if it returns or throws (or doesn't return or throw in some
+// situations).
+#define GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement) \
+ if (::testing::internal::AlwaysTrue()) { statement; }
+
+#define GTEST_TEST_THROW_(statement, expected_exception, fail) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (::testing::internal::ConstCharPtr gtest_msg = "") { \
+ bool gtest_caught_expected = false; \
+ try { \
+ GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement); \
+ } \
+ catch (expected_exception const&) { \
+ gtest_caught_expected = true; \
+ } \
+ catch (...) { \
+ gtest_msg.value = \
+ "Expected: " #statement " throws an exception of type " \
+ #expected_exception ".\n Actual: it throws a different type."; \
+ goto GTEST_CONCAT_TOKEN_(gtest_label_testthrow_, __LINE__); \
+ } \
+ if (!gtest_caught_expected) { \
+ gtest_msg.value = \
+ "Expected: " #statement " throws an exception of type " \
+ #expected_exception ".\n Actual: it throws nothing."; \
+ goto GTEST_CONCAT_TOKEN_(gtest_label_testthrow_, __LINE__); \
+ } \
+ } else \
+ GTEST_CONCAT_TOKEN_(gtest_label_testthrow_, __LINE__): \
+ fail(gtest_msg.value)
+
+#define GTEST_TEST_NO_THROW_(statement, fail) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (::testing::internal::AlwaysTrue()) { \
+ try { \
+ GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement); \
+ } \
+ catch (...) { \
+ goto GTEST_CONCAT_TOKEN_(gtest_label_testnothrow_, __LINE__); \
+ } \
+ } else \
+ GTEST_CONCAT_TOKEN_(gtest_label_testnothrow_, __LINE__): \
+ fail("Expected: " #statement " doesn't throw an exception.\n" \
+ " Actual: it throws.")
+
+#define GTEST_TEST_ANY_THROW_(statement, fail) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (::testing::internal::AlwaysTrue()) { \
+ bool gtest_caught_any = false; \
+ try { \
+ GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement); \
+ } \
+ catch (...) { \
+ gtest_caught_any = true; \
+ } \
+ if (!gtest_caught_any) { \
+ goto GTEST_CONCAT_TOKEN_(gtest_label_testanythrow_, __LINE__); \
+ } \
+ } else \
+ GTEST_CONCAT_TOKEN_(gtest_label_testanythrow_, __LINE__): \
+ fail("Expected: " #statement " throws an exception.\n" \
+ " Actual: it doesn't.")
+
+
+// Implements Boolean test assertions such as EXPECT_TRUE. expression can be
+// either a boolean expression or an AssertionResult. text is a textual
+// represenation of expression as it was passed into the EXPECT_TRUE.
+#define GTEST_TEST_BOOLEAN_(expression, text, actual, expected, fail) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (const ::testing::AssertionResult gtest_ar_ = \
+ ::testing::AssertionResult(expression)) \
+ ; \
+ else \
+ fail(::testing::internal::GetBoolAssertionFailureMessage(\
+ gtest_ar_, text, #actual, #expected).c_str())
+
+#define GTEST_TEST_NO_FATAL_FAILURE_(statement, fail) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (::testing::internal::AlwaysTrue()) { \
+ ::testing::internal::HasNewFatalFailureHelper gtest_fatal_failure_checker; \
+ GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement); \
+ if (gtest_fatal_failure_checker.has_new_fatal_failure()) { \
+ goto GTEST_CONCAT_TOKEN_(gtest_label_testnofatal_, __LINE__); \
+ } \
+ } else \
+ GTEST_CONCAT_TOKEN_(gtest_label_testnofatal_, __LINE__): \
+ fail("Expected: " #statement " doesn't generate new fatal " \
+ "failures in the current thread.\n" \
+ " Actual: it does.")
+
+// Expands to the name of the class that implements the given test.
+#define GTEST_TEST_CLASS_NAME_(test_case_name, test_name) \
+ test_case_name##_##test_name##_Test
+
+// Helper macro for defining tests.
+#define GTEST_TEST_(test_case_name, test_name, parent_class, parent_id)\
+class GTEST_TEST_CLASS_NAME_(test_case_name, test_name) : public parent_class {\
+ public:\
+ GTEST_TEST_CLASS_NAME_(test_case_name, test_name)() {}\
+ private:\
+ virtual void TestBody();\
+ static ::testing::TestInfo* const test_info_ GTEST_ATTRIBUTE_UNUSED_;\
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(\
+ GTEST_TEST_CLASS_NAME_(test_case_name, test_name));\
+};\
+\
+::testing::TestInfo* const GTEST_TEST_CLASS_NAME_(test_case_name, test_name)\
+ ::test_info_ =\
+ ::testing::internal::MakeAndRegisterTestInfo(\
+ #test_case_name, #test_name, NULL, NULL, \
+ (parent_id), \
+ parent_class::SetUpTestCase, \
+ parent_class::TearDownTestCase, \
+ new ::testing::internal::TestFactoryImpl<\
+ GTEST_TEST_CLASS_NAME_(test_case_name, test_name)>);\
+void GTEST_TEST_CLASS_NAME_(test_case_name, test_name)::TestBody()
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_INTERNAL_H_
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+//
+// The Google C++ Testing Framework (Google Test)
+//
+// This header file defines the public API for death tests. It is
+// #included by gtest.h so a user doesn't need to include this
+// directly.
+
+#ifndef GTEST_INCLUDE_GTEST_GTEST_DEATH_TEST_H_
+#define GTEST_INCLUDE_GTEST_GTEST_DEATH_TEST_H_
+
+// Copyright 2005, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Authors: wan at google.com (Zhanyong Wan), eefacm at gmail.com (Sean Mcafee)
+//
+// The Google C++ Testing Framework (Google Test)
+//
+// This header file defines internal utilities needed for implementing
+// death tests. They are subject to change without notice.
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_DEATH_TEST_INTERNAL_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_DEATH_TEST_INTERNAL_H_
+
+
+#include <stdio.h>
+
+namespace testing {
+namespace internal {
+
+GTEST_DECLARE_string_(internal_run_death_test);
+
+// Names of the flags (needed for parsing Google Test flags).
+const char kDeathTestStyleFlag[] = "death_test_style";
+const char kDeathTestUseFork[] = "death_test_use_fork";
+const char kInternalRunDeathTestFlag[] = "internal_run_death_test";
+
+#if GTEST_HAS_DEATH_TEST
+
+// DeathTest is a class that hides much of the complexity of the
+// GTEST_DEATH_TEST_ macro. It is abstract; its static Create method
+// returns a concrete class that depends on the prevailing death test
+// style, as defined by the --gtest_death_test_style and/or
+// --gtest_internal_run_death_test flags.
+
+// In describing the results of death tests, these terms are used with
+// the corresponding definitions:
+//
+// exit status: The integer exit information in the format specified
+// by wait(2)
+// exit code: The integer code passed to exit(3), _exit(2), or
+// returned from main()
+class GTEST_API_ DeathTest {
+ public:
+ // Create returns false if there was an error determining the
+ // appropriate action to take for the current death test; for example,
+ // if the gtest_death_test_style flag is set to an invalid value.
+ // The LastMessage method will return a more detailed message in that
+ // case. Otherwise, the DeathTest pointer pointed to by the "test"
+ // argument is set. If the death test should be skipped, the pointer
+ // is set to NULL; otherwise, it is set to the address of a new concrete
+ // DeathTest object that controls the execution of the current test.
+ static bool Create(const char* statement, const RE* regex,
+ const char* file, int line, DeathTest** test);
+ DeathTest();
+ virtual ~DeathTest() { }
+
+ // A helper class that aborts a death test when it's deleted.
+ class ReturnSentinel {
+ public:
+ explicit ReturnSentinel(DeathTest* test) : test_(test) { }
+ ~ReturnSentinel() { test_->Abort(TEST_ENCOUNTERED_RETURN_STATEMENT); }
+ private:
+ DeathTest* const test_;
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ReturnSentinel);
+ } GTEST_ATTRIBUTE_UNUSED_;
+
+ // An enumeration of possible roles that may be taken when a death
+ // test is encountered. EXECUTE means that the death test logic should
+ // be executed immediately. OVERSEE means that the program should prepare
+ // the appropriate environment for a child process to execute the death
+ // test, then wait for it to complete.
+ enum TestRole { OVERSEE_TEST, EXECUTE_TEST };
+
+ // An enumeration of the three reasons that a test might be aborted.
+ enum AbortReason {
+ TEST_ENCOUNTERED_RETURN_STATEMENT,
+ TEST_THREW_EXCEPTION,
+ TEST_DID_NOT_DIE
+ };
+
+ // Assumes one of the above roles.
+ virtual TestRole AssumeRole() = 0;
+
+ // Waits for the death test to finish and returns its status.
+ virtual int Wait() = 0;
+
+ // Returns true if the death test passed; that is, the test process
+ // exited during the test, its exit status matches a user-supplied
+ // predicate, and its stderr output matches a user-supplied regular
+ // expression.
+ // The user-supplied predicate may be a macro expression rather
+ // than a function pointer or functor, or else Wait and Passed could
+ // be combined.
+ virtual bool Passed(bool exit_status_ok) = 0;
+
+ // Signals that the death test did not die as expected.
+ virtual void Abort(AbortReason reason) = 0;
+
+ // Returns a human-readable outcome message regarding the outcome of
+ // the last death test.
+ static const char* LastMessage();
+
+ static void set_last_death_test_message(const std::string& message);
+
+ private:
+ // A string containing a description of the outcome of the last death test.
+ static std::string last_death_test_message_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(DeathTest);
+};
+
+// Factory interface for death tests. May be mocked out for testing.
+class DeathTestFactory {
+ public:
+ virtual ~DeathTestFactory() { }
+ virtual bool Create(const char* statement, const RE* regex,
+ const char* file, int line, DeathTest** test) = 0;
+};
+
+// A concrete DeathTestFactory implementation for normal use.
+class DefaultDeathTestFactory : public DeathTestFactory {
+ public:
+ virtual bool Create(const char* statement, const RE* regex,
+ const char* file, int line, DeathTest** test);
+};
+
+// Returns true if exit_status describes a process that was terminated
+// by a signal, or exited normally with a nonzero exit code.
+GTEST_API_ bool ExitedUnsuccessfully(int exit_status);
+
+// Traps C++ exceptions escaping statement and reports them as test
+// failures. Note that trapping SEH exceptions is not implemented here.
+# if GTEST_HAS_EXCEPTIONS
+# define GTEST_EXECUTE_DEATH_TEST_STATEMENT_(statement, death_test) \
+ try { \
+ GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement); \
+ } catch (const ::std::exception& gtest_exception) { \
+ fprintf(\
+ stderr, \
+ "\n%s: Caught std::exception-derived exception escaping the " \
+ "death test statement. Exception message: %s\n", \
+ ::testing::internal::FormatFileLocation(__FILE__, __LINE__).c_str(), \
+ gtest_exception.what()); \
+ fflush(stderr); \
+ death_test->Abort(::testing::internal::DeathTest::TEST_THREW_EXCEPTION); \
+ } catch (...) { \
+ death_test->Abort(::testing::internal::DeathTest::TEST_THREW_EXCEPTION); \
+ }
+
+# else
+# define GTEST_EXECUTE_DEATH_TEST_STATEMENT_(statement, death_test) \
+ GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement)
+
+# endif
+
+// This macro is for implementing ASSERT_DEATH*, EXPECT_DEATH*,
+// ASSERT_EXIT*, and EXPECT_EXIT*.
+# define GTEST_DEATH_TEST_(statement, predicate, regex, fail) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (::testing::internal::AlwaysTrue()) { \
+ const ::testing::internal::RE& gtest_regex = (regex); \
+ ::testing::internal::DeathTest* gtest_dt; \
+ if (!::testing::internal::DeathTest::Create(#statement, >est_regex, \
+ __FILE__, __LINE__, >est_dt)) { \
+ goto GTEST_CONCAT_TOKEN_(gtest_label_, __LINE__); \
+ } \
+ if (gtest_dt != NULL) { \
+ ::testing::internal::scoped_ptr< ::testing::internal::DeathTest> \
+ gtest_dt_ptr(gtest_dt); \
+ switch (gtest_dt->AssumeRole()) { \
+ case ::testing::internal::DeathTest::OVERSEE_TEST: \
+ if (!gtest_dt->Passed(predicate(gtest_dt->Wait()))) { \
+ goto GTEST_CONCAT_TOKEN_(gtest_label_, __LINE__); \
+ } \
+ break; \
+ case ::testing::internal::DeathTest::EXECUTE_TEST: { \
+ ::testing::internal::DeathTest::ReturnSentinel \
+ gtest_sentinel(gtest_dt); \
+ GTEST_EXECUTE_DEATH_TEST_STATEMENT_(statement, gtest_dt); \
+ gtest_dt->Abort(::testing::internal::DeathTest::TEST_DID_NOT_DIE); \
+ break; \
+ } \
+ default: \
+ break; \
+ } \
+ } \
+ } else \
+ GTEST_CONCAT_TOKEN_(gtest_label_, __LINE__): \
+ fail(::testing::internal::DeathTest::LastMessage())
+// The symbol "fail" here expands to something into which a message
+// can be streamed.
+
+// This macro is for implementing ASSERT/EXPECT_DEBUG_DEATH when compiled in
+// NDEBUG mode. In this case we need the statements to be executed, the regex is
+// ignored, and the macro must accept a streamed message even though the message
+// is never printed.
+# define GTEST_EXECUTE_STATEMENT_(statement, regex) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (::testing::internal::AlwaysTrue()) { \
+ GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement); \
+ } else \
+ ::testing::Message()
+
+// A class representing the parsed contents of the
+// --gtest_internal_run_death_test flag, as it existed when
+// RUN_ALL_TESTS was called.
+class InternalRunDeathTestFlag {
+ public:
+ InternalRunDeathTestFlag(const std::string& a_file,
+ int a_line,
+ int an_index,
+ int a_write_fd)
+ : file_(a_file), line_(a_line), index_(an_index),
+ write_fd_(a_write_fd) {}
+
+ ~InternalRunDeathTestFlag() {
+ if (write_fd_ >= 0)
+ posix::Close(write_fd_);
+ }
+
+ const std::string& file() const { return file_; }
+ int line() const { return line_; }
+ int index() const { return index_; }
+ int write_fd() const { return write_fd_; }
+
+ private:
+ std::string file_;
+ int line_;
+ int index_;
+ int write_fd_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(InternalRunDeathTestFlag);
+};
+
+// Returns a newly created InternalRunDeathTestFlag object with fields
+// initialized from the GTEST_FLAG(internal_run_death_test) flag if
+// the flag is specified; otherwise returns NULL.
+InternalRunDeathTestFlag* ParseInternalRunDeathTestFlag();
+
+#else // GTEST_HAS_DEATH_TEST
+
+// This macro is used for implementing macros such as
+// EXPECT_DEATH_IF_SUPPORTED and ASSERT_DEATH_IF_SUPPORTED on systems where
+// death tests are not supported. Those macros must compile on such systems
+// iff EXPECT_DEATH and ASSERT_DEATH compile with the same parameters on
+// systems that support death tests. This allows one to write such a macro
+// on a system that does not support death tests and be sure that it will
+// compile on a death-test supporting system.
+//
+// Parameters:
+// statement - A statement that a macro such as EXPECT_DEATH would test
+// for program termination. This macro has to make sure this
+// statement is compiled but not executed, to ensure that
+// EXPECT_DEATH_IF_SUPPORTED compiles with a certain
+// parameter iff EXPECT_DEATH compiles with it.
+// regex - A regex that a macro such as EXPECT_DEATH would use to test
+// the output of statement. This parameter has to be
+// compiled but not evaluated by this macro, to ensure that
+// this macro only accepts expressions that a macro such as
+// EXPECT_DEATH would accept.
+// terminator - Must be an empty statement for EXPECT_DEATH_IF_SUPPORTED
+// and a return statement for ASSERT_DEATH_IF_SUPPORTED.
+// This ensures that ASSERT_DEATH_IF_SUPPORTED will not
+// compile inside functions where ASSERT_DEATH doesn't
+// compile.
+//
+// The branch that has an always false condition is used to ensure that
+// statement and regex are compiled (and thus syntactically correct) but
+// never executed. The unreachable code macro protects the terminator
+// statement from generating an 'unreachable code' warning in case
+// statement unconditionally returns or throws. The Message constructor at
+// the end allows the syntax of streaming additional messages into the
+// macro, for compilational compatibility with EXPECT_DEATH/ASSERT_DEATH.
+# define GTEST_UNSUPPORTED_DEATH_TEST_(statement, regex, terminator) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (::testing::internal::AlwaysTrue()) { \
+ GTEST_LOG_(WARNING) \
+ << "Death tests are not supported on this platform.\n" \
+ << "Statement '" #statement "' cannot be verified."; \
+ } else if (::testing::internal::AlwaysFalse()) { \
+ ::testing::internal::RE::PartialMatch(".*", (regex)); \
+ GTEST_SUPPRESS_UNREACHABLE_CODE_WARNING_BELOW_(statement); \
+ terminator; \
+ } else \
+ ::testing::Message()
+
+#endif // GTEST_HAS_DEATH_TEST
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_DEATH_TEST_INTERNAL_H_
+
+namespace testing {
+
+// This flag controls the style of death tests. Valid values are "threadsafe",
+// meaning that the death test child process will re-execute the test binary
+// from the start, running only a single death test, or "fast",
+// meaning that the child process will execute the test logic immediately
+// after forking.
+GTEST_DECLARE_string_(death_test_style);
+
+#if GTEST_HAS_DEATH_TEST
+
+namespace internal {
+
+// Returns a Boolean value indicating whether the caller is currently
+// executing in the context of the death test child process. Tools such as
+// Valgrind heap checkers may need this to modify their behavior in death
+// tests. IMPORTANT: This is an internal utility. Using it may break the
+// implementation of death tests. User code MUST NOT use it.
+GTEST_API_ bool InDeathTestChild();
+
+} // namespace internal
+
+// The following macros are useful for writing death tests.
+
+// Here's what happens when an ASSERT_DEATH* or EXPECT_DEATH* is
+// executed:
+//
+// 1. It generates a warning if there is more than one active
+// thread. This is because it's safe to fork() or clone() only
+// when there is a single thread.
+//
+// 2. The parent process clone()s a sub-process and runs the death
+// test in it; the sub-process exits with code 0 at the end of the
+// death test, if it hasn't exited already.
+//
+// 3. The parent process waits for the sub-process to terminate.
+//
+// 4. The parent process checks the exit code and error message of
+// the sub-process.
+//
+// Examples:
+//
+// ASSERT_DEATH(server.SendMessage(56, "Hello"), "Invalid port number");
+// for (int i = 0; i < 5; i++) {
+// EXPECT_DEATH(server.ProcessRequest(i),
+// "Invalid request .* in ProcessRequest()")
+// << "Failed to die on request " << i;
+// }
+//
+// ASSERT_EXIT(server.ExitNow(), ::testing::ExitedWithCode(0), "Exiting");
+//
+// bool KilledBySIGHUP(int exit_code) {
+// return WIFSIGNALED(exit_code) && WTERMSIG(exit_code) == SIGHUP;
+// }
+//
+// ASSERT_EXIT(client.HangUpServer(), KilledBySIGHUP, "Hanging up!");
+//
+// On the regular expressions used in death tests:
+//
+// On POSIX-compliant systems (*nix), we use the <regex.h> library,
+// which uses the POSIX extended regex syntax.
+//
+// On other platforms (e.g. Windows), we only support a simple regex
+// syntax implemented as part of Google Test. This limited
+// implementation should be enough most of the time when writing
+// death tests; though it lacks many features you can find in PCRE
+// or POSIX extended regex syntax. For example, we don't support
+// union ("x|y"), grouping ("(xy)"), brackets ("[xy]"), and
+// repetition count ("x{5,7}"), among others.
+//
+// Below is the syntax that we do support. We chose it to be a
+// subset of both PCRE and POSIX extended regex, so it's easy to
+// learn wherever you come from. In the following: 'A' denotes a
+// literal character, period (.), or a single \\ escape sequence;
+// 'x' and 'y' denote regular expressions; 'm' and 'n' are for
+// natural numbers.
+//
+// c matches any literal character c
+// \\d matches any decimal digit
+// \\D matches any character that's not a decimal digit
+// \\f matches \f
+// \\n matches \n
+// \\r matches \r
+// \\s matches any ASCII whitespace, including \n
+// \\S matches any character that's not a whitespace
+// \\t matches \t
+// \\v matches \v
+// \\w matches any letter, _, or decimal digit
+// \\W matches any character that \\w doesn't match
+// \\c matches any literal character c, which must be a punctuation
+// . matches any single character except \n
+// A? matches 0 or 1 occurrences of A
+// A* matches 0 or many occurrences of A
+// A+ matches 1 or many occurrences of A
+// ^ matches the beginning of a string (not that of each line)
+// $ matches the end of a string (not that of each line)
+// xy matches x followed by y
+//
+// If you accidentally use PCRE or POSIX extended regex features
+// not implemented by us, you will get a run-time failure. In that
+// case, please try to rewrite your regular expression within the
+// above syntax.
+//
+// This implementation is *not* meant to be as highly tuned or robust
+// as a compiled regex library, but should perform well enough for a
+// death test, which already incurs significant overhead by launching
+// a child process.
+//
+// Known caveats:
+//
+// A "threadsafe" style death test obtains the path to the test
+// program from argv[0] and re-executes it in the sub-process. For
+// simplicity, the current implementation doesn't search the PATH
+// when launching the sub-process. This means that the user must
+// invoke the test program via a path that contains at least one
+// path separator (e.g. path/to/foo_test and
+// /absolute/path/to/bar_test are fine, but foo_test is not). This
+// is rarely a problem as people usually don't put the test binary
+// directory in PATH.
+//
+// TODO(wan at google.com): make thread-safe death tests search the PATH.
+
+// Asserts that a given statement causes the program to exit, with an
+// integer exit status that satisfies predicate, and emitting error output
+// that matches regex.
+# define ASSERT_EXIT(statement, predicate, regex) \
+ GTEST_DEATH_TEST_(statement, predicate, regex, GTEST_FATAL_FAILURE_)
+
+// Like ASSERT_EXIT, but continues on to successive tests in the
+// test case, if any:
+# define EXPECT_EXIT(statement, predicate, regex) \
+ GTEST_DEATH_TEST_(statement, predicate, regex, GTEST_NONFATAL_FAILURE_)
+
+// Asserts that a given statement causes the program to exit, either by
+// explicitly exiting with a nonzero exit code or being killed by a
+// signal, and emitting error output that matches regex.
+# define ASSERT_DEATH(statement, regex) \
+ ASSERT_EXIT(statement, ::testing::internal::ExitedUnsuccessfully, regex)
+
+// Like ASSERT_DEATH, but continues on to successive tests in the
+// test case, if any:
+# define EXPECT_DEATH(statement, regex) \
+ EXPECT_EXIT(statement, ::testing::internal::ExitedUnsuccessfully, regex)
+
+// Two predicate classes that can be used in {ASSERT,EXPECT}_EXIT*:
+
+// Tests that an exit code describes a normal exit with a given exit code.
+class GTEST_API_ ExitedWithCode {
+ public:
+ explicit ExitedWithCode(int exit_code);
+ bool operator()(int exit_status) const;
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ExitedWithCode& other);
+
+ const int exit_code_;
+};
+
+# if !GTEST_OS_WINDOWS
+// Tests that an exit code describes an exit due to termination by a
+// given signal.
+class GTEST_API_ KilledBySignal {
+ public:
+ explicit KilledBySignal(int signum);
+ bool operator()(int exit_status) const;
+ private:
+ const int signum_;
+};
+# endif // !GTEST_OS_WINDOWS
+
+// EXPECT_DEBUG_DEATH asserts that the given statements die in debug mode.
+// The death testing framework causes this to have interesting semantics,
+// since the sideeffects of the call are only visible in opt mode, and not
+// in debug mode.
+//
+// In practice, this can be used to test functions that utilize the
+// LOG(DFATAL) macro using the following style:
+//
+// int DieInDebugOr12(int* sideeffect) {
+// if (sideeffect) {
+// *sideeffect = 12;
+// }
+// LOG(DFATAL) << "death";
+// return 12;
+// }
+//
+// TEST(TestCase, TestDieOr12WorksInDgbAndOpt) {
+// int sideeffect = 0;
+// // Only asserts in dbg.
+// EXPECT_DEBUG_DEATH(DieInDebugOr12(&sideeffect), "death");
+//
+// #ifdef NDEBUG
+// // opt-mode has sideeffect visible.
+// EXPECT_EQ(12, sideeffect);
+// #else
+// // dbg-mode no visible sideeffect.
+// EXPECT_EQ(0, sideeffect);
+// #endif
+// }
+//
+// This will assert that DieInDebugReturn12InOpt() crashes in debug
+// mode, usually due to a DCHECK or LOG(DFATAL), but returns the
+// appropriate fallback value (12 in this case) in opt mode. If you
+// need to test that a function has appropriate side-effects in opt
+// mode, include assertions against the side-effects. A general
+// pattern for this is:
+//
+// EXPECT_DEBUG_DEATH({
+// // Side-effects here will have an effect after this statement in
+// // opt mode, but none in debug mode.
+// EXPECT_EQ(12, DieInDebugOr12(&sideeffect));
+// }, "death");
+//
+# ifdef NDEBUG
+
+# define EXPECT_DEBUG_DEATH(statement, regex) \
+ GTEST_EXECUTE_STATEMENT_(statement, regex)
+
+# define ASSERT_DEBUG_DEATH(statement, regex) \
+ GTEST_EXECUTE_STATEMENT_(statement, regex)
+
+# else
+
+# define EXPECT_DEBUG_DEATH(statement, regex) \
+ EXPECT_DEATH(statement, regex)
+
+# define ASSERT_DEBUG_DEATH(statement, regex) \
+ ASSERT_DEATH(statement, regex)
+
+# endif // NDEBUG for EXPECT_DEBUG_DEATH
+#endif // GTEST_HAS_DEATH_TEST
+
+// EXPECT_DEATH_IF_SUPPORTED(statement, regex) and
+// ASSERT_DEATH_IF_SUPPORTED(statement, regex) expand to real death tests if
+// death tests are supported; otherwise they just issue a warning. This is
+// useful when you are combining death test assertions with normal test
+// assertions in one test.
+#if GTEST_HAS_DEATH_TEST
+# define EXPECT_DEATH_IF_SUPPORTED(statement, regex) \
+ EXPECT_DEATH(statement, regex)
+# define ASSERT_DEATH_IF_SUPPORTED(statement, regex) \
+ ASSERT_DEATH(statement, regex)
+#else
+# define EXPECT_DEATH_IF_SUPPORTED(statement, regex) \
+ GTEST_UNSUPPORTED_DEATH_TEST_(statement, regex, )
+# define ASSERT_DEATH_IF_SUPPORTED(statement, regex) \
+ GTEST_UNSUPPORTED_DEATH_TEST_(statement, regex, return)
+#endif
+
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_DEATH_TEST_H_
+// This file was GENERATED by command:
+// pump.py gtest-param-test.h.pump
+// DO NOT EDIT BY HAND!!!
+
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Authors: vladl at google.com (Vlad Losev)
+//
+// Macros and functions for implementing parameterized tests
+// in Google C++ Testing Framework (Google Test)
+//
+// This file is generated by a SCRIPT. DO NOT EDIT BY HAND!
+//
+#ifndef GTEST_INCLUDE_GTEST_GTEST_PARAM_TEST_H_
+#define GTEST_INCLUDE_GTEST_GTEST_PARAM_TEST_H_
+
+
+// Value-parameterized tests allow you to test your code with different
+// parameters without writing multiple copies of the same test.
+//
+// Here is how you use value-parameterized tests:
+
+#if 0
+
+// To write value-parameterized tests, first you should define a fixture
+// class. It is usually derived from testing::TestWithParam<T> (see below for
+// another inheritance scheme that's sometimes useful in more complicated
+// class hierarchies), where the type of your parameter values.
+// TestWithParam<T> is itself derived from testing::Test. T can be any
+// copyable type. If it's a raw pointer, you are responsible for managing the
+// lifespan of the pointed values.
+
+class FooTest : public ::testing::TestWithParam<const char*> {
+ // You can implement all the usual class fixture members here.
+};
+
+// Then, use the TEST_P macro to define as many parameterized tests
+// for this fixture as you want. The _P suffix is for "parameterized"
+// or "pattern", whichever you prefer to think.
+
+TEST_P(FooTest, DoesBlah) {
+ // Inside a test, access the test parameter with the GetParam() method
+ // of the TestWithParam<T> class:
+ EXPECT_TRUE(foo.Blah(GetParam()));
+ ...
+}
+
+TEST_P(FooTest, HasBlahBlah) {
+ ...
+}
+
+// Finally, you can use INSTANTIATE_TEST_CASE_P to instantiate the test
+// case with any set of parameters you want. Google Test defines a number
+// of functions for generating test parameters. They return what we call
+// (surprise!) parameter generators. Here is a summary of them, which
+// are all in the testing namespace:
+//
+//
+// Range(begin, end [, step]) - Yields values {begin, begin+step,
+// begin+step+step, ...}. The values do not
+// include end. step defaults to 1.
+// Values(v1, v2, ..., vN) - Yields values {v1, v2, ..., vN}.
+// ValuesIn(container) - Yields values from a C-style array, an STL
+// ValuesIn(begin,end) container, or an iterator range [begin, end).
+// Bool() - Yields sequence {false, true}.
+// Combine(g1, g2, ..., gN) - Yields all combinations (the Cartesian product
+// for the math savvy) of the values generated
+// by the N generators.
+//
+// For more details, see comments at the definitions of these functions below
+// in this file.
+//
+// The following statement will instantiate tests from the FooTest test case
+// each with parameter values "meeny", "miny", and "moe".
+
+INSTANTIATE_TEST_CASE_P(InstantiationName,
+ FooTest,
+ Values("meeny", "miny", "moe"));
+
+// To distinguish different instances of the pattern, (yes, you
+// can instantiate it more then once) the first argument to the
+// INSTANTIATE_TEST_CASE_P macro is a prefix that will be added to the
+// actual test case name. Remember to pick unique prefixes for different
+// instantiations. The tests from the instantiation above will have
+// these names:
+//
+// * InstantiationName/FooTest.DoesBlah/0 for "meeny"
+// * InstantiationName/FooTest.DoesBlah/1 for "miny"
+// * InstantiationName/FooTest.DoesBlah/2 for "moe"
+// * InstantiationName/FooTest.HasBlahBlah/0 for "meeny"
+// * InstantiationName/FooTest.HasBlahBlah/1 for "miny"
+// * InstantiationName/FooTest.HasBlahBlah/2 for "moe"
+//
+// You can use these names in --gtest_filter.
+//
+// This statement will instantiate all tests from FooTest again, each
+// with parameter values "cat" and "dog":
+
+const char* pets[] = {"cat", "dog"};
+INSTANTIATE_TEST_CASE_P(AnotherInstantiationName, FooTest, ValuesIn(pets));
+
+// The tests from the instantiation above will have these names:
+//
+// * AnotherInstantiationName/FooTest.DoesBlah/0 for "cat"
+// * AnotherInstantiationName/FooTest.DoesBlah/1 for "dog"
+// * AnotherInstantiationName/FooTest.HasBlahBlah/0 for "cat"
+// * AnotherInstantiationName/FooTest.HasBlahBlah/1 for "dog"
+//
+// Please note that INSTANTIATE_TEST_CASE_P will instantiate all tests
+// in the given test case, whether their definitions come before or
+// AFTER the INSTANTIATE_TEST_CASE_P statement.
+//
+// Please also note that generator expressions (including parameters to the
+// generators) are evaluated in InitGoogleTest(), after main() has started.
+// This allows the user on one hand, to adjust generator parameters in order
+// to dynamically determine a set of tests to run and on the other hand,
+// give the user a chance to inspect the generated tests with Google Test
+// reflection API before RUN_ALL_TESTS() is executed.
+//
+// You can see samples/sample7_unittest.cc and samples/sample8_unittest.cc
+// for more examples.
+//
+// In the future, we plan to publish the API for defining new parameter
+// generators. But for now this interface remains part of the internal
+// implementation and is subject to change.
+//
+//
+// A parameterized test fixture must be derived from testing::Test and from
+// testing::WithParamInterface<T>, where T is the type of the parameter
+// values. Inheriting from TestWithParam<T> satisfies that requirement because
+// TestWithParam<T> inherits from both Test and WithParamInterface. In more
+// complicated hierarchies, however, it is occasionally useful to inherit
+// separately from Test and WithParamInterface. For example:
+
+class BaseTest : public ::testing::Test {
+ // You can inherit all the usual members for a non-parameterized test
+ // fixture here.
+};
+
+class DerivedTest : public BaseTest, public ::testing::WithParamInterface<int> {
+ // The usual test fixture members go here too.
+};
+
+TEST_F(BaseTest, HasFoo) {
+ // This is an ordinary non-parameterized test.
+}
+
+TEST_P(DerivedTest, DoesBlah) {
+ // GetParam works just the same here as if you inherit from TestWithParam.
+ EXPECT_TRUE(foo.Blah(GetParam()));
+}
+
+#endif // 0
+
+
+#if !GTEST_OS_SYMBIAN
+# include <utility>
+#endif
+
+// scripts/fuse_gtest.py depends on gtest's own header being #included
+// *unconditionally*. Therefore these #includes cannot be moved
+// inside #if GTEST_HAS_PARAM_TEST.
+// Copyright 2008 Google Inc.
+// All Rights Reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: vladl at google.com (Vlad Losev)
+
+// Type and function utilities for implementing parameterized tests.
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_PARAM_UTIL_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_PARAM_UTIL_H_
+
+#include <iterator>
+#include <utility>
+#include <vector>
+
+// scripts/fuse_gtest.py depends on gtest's own header being #included
+// *unconditionally*. Therefore these #includes cannot be moved
+// inside #if GTEST_HAS_PARAM_TEST.
+// Copyright 2003 Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Authors: Dan Egnor (egnor at google.com)
+//
+// A "smart" pointer type with reference tracking. Every pointer to a
+// particular object is kept on a circular linked list. When the last pointer
+// to an object is destroyed or reassigned, the object is deleted.
+//
+// Used properly, this deletes the object when the last reference goes away.
+// There are several caveats:
+// - Like all reference counting schemes, cycles lead to leaks.
+// - Each smart pointer is actually two pointers (8 bytes instead of 4).
+// - Every time a pointer is assigned, the entire list of pointers to that
+// object is traversed. This class is therefore NOT SUITABLE when there
+// will often be more than two or three pointers to a particular object.
+// - References are only tracked as long as linked_ptr<> objects are copied.
+// If a linked_ptr<> is converted to a raw pointer and back, BAD THINGS
+// will happen (double deletion).
+//
+// A good use of this class is storing object references in STL containers.
+// You can safely put linked_ptr<> in a vector<>.
+// Other uses may not be as good.
+//
+// Note: If you use an incomplete type with linked_ptr<>, the class
+// *containing* linked_ptr<> must have a constructor and destructor (even
+// if they do nothing!).
+//
+// Bill Gibbons suggested we use something like this.
+//
+// Thread Safety:
+// Unlike other linked_ptr implementations, in this implementation
+// a linked_ptr object is thread-safe in the sense that:
+// - it's safe to copy linked_ptr objects concurrently,
+// - it's safe to copy *from* a linked_ptr and read its underlying
+// raw pointer (e.g. via get()) concurrently, and
+// - it's safe to write to two linked_ptrs that point to the same
+// shared object concurrently.
+// TODO(wan at google.com): rename this to safe_linked_ptr to avoid
+// confusion with normal linked_ptr.
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_LINKED_PTR_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_LINKED_PTR_H_
+
+#include <stdlib.h>
+#include <assert.h>
+
+
+namespace testing {
+namespace internal {
+
+// Protects copying of all linked_ptr objects.
+GTEST_API_ GTEST_DECLARE_STATIC_MUTEX_(g_linked_ptr_mutex);
+
+// This is used internally by all instances of linked_ptr<>. It needs to be
+// a non-template class because different types of linked_ptr<> can refer to
+// the same object (linked_ptr<Superclass>(obj) vs linked_ptr<Subclass>(obj)).
+// So, it needs to be possible for different types of linked_ptr to participate
+// in the same circular linked list, so we need a single class type here.
+//
+// DO NOT USE THIS CLASS DIRECTLY YOURSELF. Use linked_ptr<T>.
+class linked_ptr_internal {
+ public:
+ // Create a new circle that includes only this instance.
+ void join_new() {
+ next_ = this;
+ }
+
+ // Many linked_ptr operations may change p.link_ for some linked_ptr
+ // variable p in the same circle as this object. Therefore we need
+ // to prevent two such operations from occurring concurrently.
+ //
+ // Note that different types of linked_ptr objects can coexist in a
+ // circle (e.g. linked_ptr<Base>, linked_ptr<Derived1>, and
+ // linked_ptr<Derived2>). Therefore we must use a single mutex to
+ // protect all linked_ptr objects. This can create serious
+ // contention in production code, but is acceptable in a testing
+ // framework.
+
+ // Join an existing circle.
+ void join(linked_ptr_internal const* ptr)
+ GTEST_LOCK_EXCLUDED_(g_linked_ptr_mutex) {
+ MutexLock lock(&g_linked_ptr_mutex);
+
+ linked_ptr_internal const* p = ptr;
+ while (p->next_ != ptr) p = p->next_;
+ p->next_ = this;
+ next_ = ptr;
+ }
+
+ // Leave whatever circle we're part of. Returns true if we were the
+ // last member of the circle. Once this is done, you can join() another.
+ bool depart()
+ GTEST_LOCK_EXCLUDED_(g_linked_ptr_mutex) {
+ MutexLock lock(&g_linked_ptr_mutex);
+
+ if (next_ == this) return true;
+ linked_ptr_internal const* p = next_;
+ while (p->next_ != this) p = p->next_;
+ p->next_ = next_;
+ return false;
+ }
+
+ private:
+ mutable linked_ptr_internal const* next_;
+};
+
+template <typename T>
+class linked_ptr {
+ public:
+ typedef T element_type;
+
+ // Take over ownership of a raw pointer. This should happen as soon as
+ // possible after the object is created.
+ explicit linked_ptr(T* ptr = NULL) { capture(ptr); }
+ ~linked_ptr() { depart(); }
+
+ // Copy an existing linked_ptr<>, adding ourselves to the list of references.
+ template <typename U> linked_ptr(linked_ptr<U> const& ptr) { copy(&ptr); }
+ linked_ptr(linked_ptr const& ptr) { // NOLINT
+ assert(&ptr != this);
+ copy(&ptr);
+ }
+
+ // Assignment releases the old value and acquires the new.
+ template <typename U> linked_ptr& operator=(linked_ptr<U> const& ptr) {
+ depart();
+ copy(&ptr);
+ return *this;
+ }
+
+ linked_ptr& operator=(linked_ptr const& ptr) {
+ if (&ptr != this) {
+ depart();
+ copy(&ptr);
+ }
+ return *this;
+ }
+
+ // Smart pointer members.
+ void reset(T* ptr = NULL) {
+ depart();
+ capture(ptr);
+ }
+ T* get() const { return value_; }
+ T* operator->() const { return value_; }
+ T& operator*() const { return *value_; }
+
+ bool operator==(T* p) const { return value_ == p; }
+ bool operator!=(T* p) const { return value_ != p; }
+ template <typename U>
+ bool operator==(linked_ptr<U> const& ptr) const {
+ return value_ == ptr.get();
+ }
+ template <typename U>
+ bool operator!=(linked_ptr<U> const& ptr) const {
+ return value_ != ptr.get();
+ }
+
+ private:
+ template <typename U>
+ friend class linked_ptr;
+
+ T* value_;
+ linked_ptr_internal link_;
+
+ void depart() {
+ if (link_.depart()) delete value_;
+ }
+
+ void capture(T* ptr) {
+ value_ = ptr;
+ link_.join_new();
+ }
+
+ template <typename U> void copy(linked_ptr<U> const* ptr) {
+ value_ = ptr->get();
+ if (value_)
+ link_.join(&ptr->link_);
+ else
+ link_.join_new();
+ }
+};
+
+template<typename T> inline
+bool operator==(T* ptr, const linked_ptr<T>& x) {
+ return ptr == x.get();
+}
+
+template<typename T> inline
+bool operator!=(T* ptr, const linked_ptr<T>& x) {
+ return ptr != x.get();
+}
+
+// A function to convert T* into linked_ptr<T>
+// Doing e.g. make_linked_ptr(new FooBarBaz<type>(arg)) is a shorter notation
+// for linked_ptr<FooBarBaz<type> >(new FooBarBaz<type>(arg))
+template <typename T>
+linked_ptr<T> make_linked_ptr(T* ptr) {
+ return linked_ptr<T>(ptr);
+}
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_LINKED_PTR_H_
+// Copyright 2007, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+// Google Test - The Google C++ Testing Framework
+//
+// This file implements a universal value printer that can print a
+// value of any type T:
+//
+// void ::testing::internal::UniversalPrinter<T>::Print(value, ostream_ptr);
+//
+// A user can teach this function how to print a class type T by
+// defining either operator<<() or PrintTo() in the namespace that
+// defines T. More specifically, the FIRST defined function in the
+// following list will be used (assuming T is defined in namespace
+// foo):
+//
+// 1. foo::PrintTo(const T&, ostream*)
+// 2. operator<<(ostream&, const T&) defined in either foo or the
+// global namespace.
+//
+// If none of the above is defined, it will print the debug string of
+// the value if it is a protocol buffer, or print the raw bytes in the
+// value otherwise.
+//
+// To aid debugging: when T is a reference type, the address of the
+// value is also printed; when T is a (const) char pointer, both the
+// pointer value and the NUL-terminated string it points to are
+// printed.
+//
+// We also provide some convenient wrappers:
+//
+// // Prints a value to a string. For a (const or not) char
+// // pointer, the NUL-terminated string (but not the pointer) is
+// // printed.
+// std::string ::testing::PrintToString(const T& value);
+//
+// // Prints a value tersely: for a reference type, the referenced
+// // value (but not the address) is printed; for a (const or not) char
+// // pointer, the NUL-terminated string (but not the pointer) is
+// // printed.
+// void ::testing::internal::UniversalTersePrint(const T& value, ostream*);
+//
+// // Prints value using the type inferred by the compiler. The difference
+// // from UniversalTersePrint() is that this function prints both the
+// // pointer and the NUL-terminated string for a (const or not) char pointer.
+// void ::testing::internal::UniversalPrint(const T& value, ostream*);
+//
+// // Prints the fields of a tuple tersely to a string vector, one
+// // element for each field. Tuple support must be enabled in
+// // gtest-port.h.
+// std::vector<string> UniversalTersePrintTupleFieldsToStrings(
+// const Tuple& value);
+//
+// Known limitation:
+//
+// The print primitives print the elements of an STL-style container
+// using the compiler-inferred type of *iter where iter is a
+// const_iterator of the container. When const_iterator is an input
+// iterator but not a forward iterator, this inferred type may not
+// match value_type, and the print output may be incorrect. In
+// practice, this is rarely a problem as for most containers
+// const_iterator is a forward iterator. We'll fix this if there's an
+// actual need for it. Note that this fix cannot rely on value_type
+// being defined as many user-defined container types don't have
+// value_type.
+
+#ifndef GTEST_INCLUDE_GTEST_GTEST_PRINTERS_H_
+#define GTEST_INCLUDE_GTEST_GTEST_PRINTERS_H_
+
+#include <ostream> // NOLINT
+#include <sstream>
+#include <string>
+#include <utility>
+#include <vector>
+
+namespace testing {
+
+// Definitions in the 'internal' and 'internal2' name spaces are
+// subject to change without notice. DO NOT USE THEM IN USER CODE!
+namespace internal2 {
+
+// Prints the given number of bytes in the given object to the given
+// ostream.
+GTEST_API_ void PrintBytesInObjectTo(const unsigned char* obj_bytes,
+ size_t count,
+ ::std::ostream* os);
+
+// For selecting which printer to use when a given type has neither <<
+// nor PrintTo().
+enum TypeKind {
+ kProtobuf, // a protobuf type
+ kConvertibleToInteger, // a type implicitly convertible to BiggestInt
+ // (e.g. a named or unnamed enum type)
+ kOtherType // anything else
+};
+
+// TypeWithoutFormatter<T, kTypeKind>::PrintValue(value, os) is called
+// by the universal printer to print a value of type T when neither
+// operator<< nor PrintTo() is defined for T, where kTypeKind is the
+// "kind" of T as defined by enum TypeKind.
+template <typename T, TypeKind kTypeKind>
+class TypeWithoutFormatter {
+ public:
+ // This default version is called when kTypeKind is kOtherType.
+ static void PrintValue(const T& value, ::std::ostream* os) {
+ PrintBytesInObjectTo(reinterpret_cast<const unsigned char*>(&value),
+ sizeof(value), os);
+ }
+};
+
+// We print a protobuf using its ShortDebugString() when the string
+// doesn't exceed this many characters; otherwise we print it using
+// DebugString() for better readability.
+const size_t kProtobufOneLinerMaxLength = 50;
+
+template <typename T>
+class TypeWithoutFormatter<T, kProtobuf> {
+ public:
+ static void PrintValue(const T& value, ::std::ostream* os) {
+ const ::testing::internal::string short_str = value.ShortDebugString();
+ const ::testing::internal::string pretty_str =
+ short_str.length() <= kProtobufOneLinerMaxLength ?
+ short_str : ("\n" + value.DebugString());
+ *os << ("<" + pretty_str + ">");
+ }
+};
+
+template <typename T>
+class TypeWithoutFormatter<T, kConvertibleToInteger> {
+ public:
+ // Since T has no << operator or PrintTo() but can be implicitly
+ // converted to BiggestInt, we print it as a BiggestInt.
+ //
+ // Most likely T is an enum type (either named or unnamed), in which
+ // case printing it as an integer is the desired behavior. In case
+ // T is not an enum, printing it as an integer is the best we can do
+ // given that it has no user-defined printer.
+ static void PrintValue(const T& value, ::std::ostream* os) {
+ const internal::BiggestInt kBigInt = value;
+ *os << kBigInt;
+ }
+};
+
+// Prints the given value to the given ostream. If the value is a
+// protocol message, its debug string is printed; if it's an enum or
+// of a type implicitly convertible to BiggestInt, it's printed as an
+// integer; otherwise the bytes in the value are printed. This is
+// what UniversalPrinter<T>::Print() does when it knows nothing about
+// type T and T has neither << operator nor PrintTo().
+//
+// A user can override this behavior for a class type Foo by defining
+// a << operator in the namespace where Foo is defined.
+//
+// We put this operator in namespace 'internal2' instead of 'internal'
+// to simplify the implementation, as much code in 'internal' needs to
+// use << in STL, which would conflict with our own << were it defined
+// in 'internal'.
+//
+// Note that this operator<< takes a generic std::basic_ostream<Char,
+// CharTraits> type instead of the more restricted std::ostream. If
+// we define it to take an std::ostream instead, we'll get an
+// "ambiguous overloads" compiler error when trying to print a type
+// Foo that supports streaming to std::basic_ostream<Char,
+// CharTraits>, as the compiler cannot tell whether
+// operator<<(std::ostream&, const T&) or
+// operator<<(std::basic_stream<Char, CharTraits>, const Foo&) is more
+// specific.
+template <typename Char, typename CharTraits, typename T>
+::std::basic_ostream<Char, CharTraits>& operator<<(
+ ::std::basic_ostream<Char, CharTraits>& os, const T& x) {
+ TypeWithoutFormatter<T,
+ (internal::IsAProtocolMessage<T>::value ? kProtobuf :
+ internal::ImplicitlyConvertible<const T&, internal::BiggestInt>::value ?
+ kConvertibleToInteger : kOtherType)>::PrintValue(x, &os);
+ return os;
+}
+
+} // namespace internal2
+} // namespace testing
+
+// This namespace MUST NOT BE NESTED IN ::testing, or the name look-up
+// magic needed for implementing UniversalPrinter won't work.
+namespace testing_internal {
+
+// Used to print a value that is not an STL-style container when the
+// user doesn't define PrintTo() for it.
+template <typename T>
+void DefaultPrintNonContainerTo(const T& value, ::std::ostream* os) {
+ // With the following statement, during unqualified name lookup,
+ // testing::internal2::operator<< appears as if it was declared in
+ // the nearest enclosing namespace that contains both
+ // ::testing_internal and ::testing::internal2, i.e. the global
+ // namespace. For more details, refer to the C++ Standard section
+ // 7.3.4-1 [namespace.udir]. This allows us to fall back onto
+ // testing::internal2::operator<< in case T doesn't come with a <<
+ // operator.
+ //
+ // We cannot write 'using ::testing::internal2::operator<<;', which
+ // gcc 3.3 fails to compile due to a compiler bug.
+ using namespace ::testing::internal2; // NOLINT
+
+ // Assuming T is defined in namespace foo, in the next statement,
+ // the compiler will consider all of:
+ //
+ // 1. foo::operator<< (thanks to Koenig look-up),
+ // 2. ::operator<< (as the current namespace is enclosed in ::),
+ // 3. testing::internal2::operator<< (thanks to the using statement above).
+ //
+ // The operator<< whose type matches T best will be picked.
+ //
+ // We deliberately allow #2 to be a candidate, as sometimes it's
+ // impossible to define #1 (e.g. when foo is ::std, defining
+ // anything in it is undefined behavior unless you are a compiler
+ // vendor.).
+ *os << value;
+}
+
+} // namespace testing_internal
+
+namespace testing {
+namespace internal {
+
+// UniversalPrinter<T>::Print(value, ostream_ptr) prints the given
+// value to the given ostream. The caller must ensure that
+// 'ostream_ptr' is not NULL, or the behavior is undefined.
+//
+// We define UniversalPrinter as a class template (as opposed to a
+// function template), as we need to partially specialize it for
+// reference types, which cannot be done with function templates.
+template <typename T>
+class UniversalPrinter;
+
+template <typename T>
+void UniversalPrint(const T& value, ::std::ostream* os);
+
+// Used to print an STL-style container when the user doesn't define
+// a PrintTo() for it.
+template <typename C>
+void DefaultPrintTo(IsContainer /* dummy */,
+ false_type /* is not a pointer */,
+ const C& container, ::std::ostream* os) {
+ const size_t kMaxCount = 32; // The maximum number of elements to print.
+ *os << '{';
+ size_t count = 0;
+ for (typename C::const_iterator it = container.begin();
+ it != container.end(); ++it, ++count) {
+ if (count > 0) {
+ *os << ',';
+ if (count == kMaxCount) { // Enough has been printed.
+ *os << " ...";
+ break;
+ }
+ }
+ *os << ' ';
+ // We cannot call PrintTo(*it, os) here as PrintTo() doesn't
+ // handle *it being a native array.
+ internal::UniversalPrint(*it, os);
+ }
+
+ if (count > 0) {
+ *os << ' ';
+ }
+ *os << '}';
+}
+
+// Used to print a pointer that is neither a char pointer nor a member
+// pointer, when the user doesn't define PrintTo() for it. (A member
+// variable pointer or member function pointer doesn't really point to
+// a location in the address space. Their representation is
+// implementation-defined. Therefore they will be printed as raw
+// bytes.)
+template <typename T>
+void DefaultPrintTo(IsNotContainer /* dummy */,
+ true_type /* is a pointer */,
+ T* p, ::std::ostream* os) {
+ if (p == NULL) {
+ *os << "NULL";
+ } else {
+ // C++ doesn't allow casting from a function pointer to any object
+ // pointer.
+ //
+ // IsTrue() silences warnings: "Condition is always true",
+ // "unreachable code".
+ if (IsTrue(ImplicitlyConvertible<T*, const void*>::value)) {
+ // T is not a function type. We just call << to print p,
+ // relying on ADL to pick up user-defined << for their pointer
+ // types, if any.
+ *os << p;
+ } else {
+ // T is a function type, so '*os << p' doesn't do what we want
+ // (it just prints p as bool). We want to print p as a const
+ // void*. However, we cannot cast it to const void* directly,
+ // even using reinterpret_cast, as earlier versions of gcc
+ // (e.g. 3.4.5) cannot compile the cast when p is a function
+ // pointer. Casting to UInt64 first solves the problem.
+ *os << reinterpret_cast<const void*>(
+ reinterpret_cast<internal::UInt64>(p));
+ }
+ }
+}
+
+// Used to print a non-container, non-pointer value when the user
+// doesn't define PrintTo() for it.
+template <typename T>
+void DefaultPrintTo(IsNotContainer /* dummy */,
+ false_type /* is not a pointer */,
+ const T& value, ::std::ostream* os) {
+ ::testing_internal::DefaultPrintNonContainerTo(value, os);
+}
+
+// Prints the given value using the << operator if it has one;
+// otherwise prints the bytes in it. This is what
+// UniversalPrinter<T>::Print() does when PrintTo() is not specialized
+// or overloaded for type T.
+//
+// A user can override this behavior for a class type Foo by defining
+// an overload of PrintTo() in the namespace where Foo is defined. We
+// give the user this option as sometimes defining a << operator for
+// Foo is not desirable (e.g. the coding style may prevent doing it,
+// or there is already a << operator but it doesn't do what the user
+// wants).
+template <typename T>
+void PrintTo(const T& value, ::std::ostream* os) {
+ // DefaultPrintTo() is overloaded. The type of its first two
+ // arguments determine which version will be picked. If T is an
+ // STL-style container, the version for container will be called; if
+ // T is a pointer, the pointer version will be called; otherwise the
+ // generic version will be called.
+ //
+ // Note that we check for container types here, prior to we check
+ // for protocol message types in our operator<<. The rationale is:
+ //
+ // For protocol messages, we want to give people a chance to
+ // override Google Mock's format by defining a PrintTo() or
+ // operator<<. For STL containers, other formats can be
+ // incompatible with Google Mock's format for the container
+ // elements; therefore we check for container types here to ensure
+ // that our format is used.
+ //
+ // The second argument of DefaultPrintTo() is needed to bypass a bug
+ // in Symbian's C++ compiler that prevents it from picking the right
+ // overload between:
+ //
+ // PrintTo(const T& x, ...);
+ // PrintTo(T* x, ...);
+ DefaultPrintTo(IsContainerTest<T>(0), is_pointer<T>(), value, os);
+}
+
+// The following list of PrintTo() overloads tells
+// UniversalPrinter<T>::Print() how to print standard types (built-in
+// types, strings, plain arrays, and pointers).
+
+// Overloads for various char types.
+GTEST_API_ void PrintTo(unsigned char c, ::std::ostream* os);
+GTEST_API_ void PrintTo(signed char c, ::std::ostream* os);
+inline void PrintTo(char c, ::std::ostream* os) {
+ // When printing a plain char, we always treat it as unsigned. This
+ // way, the output won't be affected by whether the compiler thinks
+ // char is signed or not.
+ PrintTo(static_cast<unsigned char>(c), os);
+}
+
+// Overloads for other simple built-in types.
+inline void PrintTo(bool x, ::std::ostream* os) {
+ *os << (x ? "true" : "false");
+}
+
+// Overload for wchar_t type.
+// Prints a wchar_t as a symbol if it is printable or as its internal
+// code otherwise and also as its decimal code (except for L'\0').
+// The L'\0' char is printed as "L'\\0'". The decimal code is printed
+// as signed integer when wchar_t is implemented by the compiler
+// as a signed type and is printed as an unsigned integer when wchar_t
+// is implemented as an unsigned type.
+GTEST_API_ void PrintTo(wchar_t wc, ::std::ostream* os);
+
+// Overloads for C strings.
+GTEST_API_ void PrintTo(const char* s, ::std::ostream* os);
+inline void PrintTo(char* s, ::std::ostream* os) {
+ PrintTo(ImplicitCast_<const char*>(s), os);
+}
+
+// signed/unsigned char is often used for representing binary data, so
+// we print pointers to it as void* to be safe.
+inline void PrintTo(const signed char* s, ::std::ostream* os) {
+ PrintTo(ImplicitCast_<const void*>(s), os);
+}
+inline void PrintTo(signed char* s, ::std::ostream* os) {
+ PrintTo(ImplicitCast_<const void*>(s), os);
+}
+inline void PrintTo(const unsigned char* s, ::std::ostream* os) {
+ PrintTo(ImplicitCast_<const void*>(s), os);
+}
+inline void PrintTo(unsigned char* s, ::std::ostream* os) {
+ PrintTo(ImplicitCast_<const void*>(s), os);
+}
+
+// MSVC can be configured to define wchar_t as a typedef of unsigned
+// short. It defines _NATIVE_WCHAR_T_DEFINED when wchar_t is a native
+// type. When wchar_t is a typedef, defining an overload for const
+// wchar_t* would cause unsigned short* be printed as a wide string,
+// possibly causing invalid memory accesses.
+#if !defined(_MSC_VER) || defined(_NATIVE_WCHAR_T_DEFINED)
+// Overloads for wide C strings
+GTEST_API_ void PrintTo(const wchar_t* s, ::std::ostream* os);
+inline void PrintTo(wchar_t* s, ::std::ostream* os) {
+ PrintTo(ImplicitCast_<const wchar_t*>(s), os);
+}
+#endif
+
+// Overload for C arrays. Multi-dimensional arrays are printed
+// properly.
+
+// Prints the given number of elements in an array, without printing
+// the curly braces.
+template <typename T>
+void PrintRawArrayTo(const T a[], size_t count, ::std::ostream* os) {
+ UniversalPrint(a[0], os);
+ for (size_t i = 1; i != count; i++) {
+ *os << ", ";
+ UniversalPrint(a[i], os);
+ }
+}
+
+// Overloads for ::string and ::std::string.
+#if GTEST_HAS_GLOBAL_STRING
+GTEST_API_ void PrintStringTo(const ::string&s, ::std::ostream* os);
+inline void PrintTo(const ::string& s, ::std::ostream* os) {
+ PrintStringTo(s, os);
+}
+#endif // GTEST_HAS_GLOBAL_STRING
+
+GTEST_API_ void PrintStringTo(const ::std::string&s, ::std::ostream* os);
+inline void PrintTo(const ::std::string& s, ::std::ostream* os) {
+ PrintStringTo(s, os);
+}
+
+// Overloads for ::wstring and ::std::wstring.
+#if GTEST_HAS_GLOBAL_WSTRING
+GTEST_API_ void PrintWideStringTo(const ::wstring&s, ::std::ostream* os);
+inline void PrintTo(const ::wstring& s, ::std::ostream* os) {
+ PrintWideStringTo(s, os);
+}
+#endif // GTEST_HAS_GLOBAL_WSTRING
+
+#if GTEST_HAS_STD_WSTRING
+GTEST_API_ void PrintWideStringTo(const ::std::wstring&s, ::std::ostream* os);
+inline void PrintTo(const ::std::wstring& s, ::std::ostream* os) {
+ PrintWideStringTo(s, os);
+}
+#endif // GTEST_HAS_STD_WSTRING
+
+#if GTEST_HAS_TR1_TUPLE
+// Overload for ::std::tr1::tuple. Needed for printing function arguments,
+// which are packed as tuples.
+
+// Helper function for printing a tuple. T must be instantiated with
+// a tuple type.
+template <typename T>
+void PrintTupleTo(const T& t, ::std::ostream* os);
+
+// Overloaded PrintTo() for tuples of various arities. We support
+// tuples of up-to 10 fields. The following implementation works
+// regardless of whether tr1::tuple is implemented using the
+// non-standard variadic template feature or not.
+
+inline void PrintTo(const ::std::tr1::tuple<>& t, ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1>
+void PrintTo(const ::std::tr1::tuple<T1>& t, ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1, typename T2>
+void PrintTo(const ::std::tr1::tuple<T1, T2>& t, ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1, typename T2, typename T3>
+void PrintTo(const ::std::tr1::tuple<T1, T2, T3>& t, ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1, typename T2, typename T3, typename T4>
+void PrintTo(const ::std::tr1::tuple<T1, T2, T3, T4>& t, ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5>
+void PrintTo(const ::std::tr1::tuple<T1, T2, T3, T4, T5>& t,
+ ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6>
+void PrintTo(const ::std::tr1::tuple<T1, T2, T3, T4, T5, T6>& t,
+ ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7>
+void PrintTo(const ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7>& t,
+ ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8>
+void PrintTo(const ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8>& t,
+ ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9>
+void PrintTo(const ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8, T9>& t,
+ ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10>
+void PrintTo(
+ const ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10>& t,
+ ::std::ostream* os) {
+ PrintTupleTo(t, os);
+}
+#endif // GTEST_HAS_TR1_TUPLE
+
+// Overload for std::pair.
+template <typename T1, typename T2>
+void PrintTo(const ::std::pair<T1, T2>& value, ::std::ostream* os) {
+ *os << '(';
+ // We cannot use UniversalPrint(value.first, os) here, as T1 may be
+ // a reference type. The same for printing value.second.
+ UniversalPrinter<T1>::Print(value.first, os);
+ *os << ", ";
+ UniversalPrinter<T2>::Print(value.second, os);
+ *os << ')';
+}
+
+// Implements printing a non-reference type T by letting the compiler
+// pick the right overload of PrintTo() for T.
+template <typename T>
+class UniversalPrinter {
+ public:
+ // MSVC warns about adding const to a function type, so we want to
+ // disable the warning.
+#ifdef _MSC_VER
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4180) // Temporarily disables warning 4180.
+#endif // _MSC_VER
+
+ // Note: we deliberately don't call this PrintTo(), as that name
+ // conflicts with ::testing::internal::PrintTo in the body of the
+ // function.
+ static void Print(const T& value, ::std::ostream* os) {
+ // By default, ::testing::internal::PrintTo() is used for printing
+ // the value.
+ //
+ // Thanks to Koenig look-up, if T is a class and has its own
+ // PrintTo() function defined in its namespace, that function will
+ // be visible here. Since it is more specific than the generic ones
+ // in ::testing::internal, it will be picked by the compiler in the
+ // following statement - exactly what we want.
+ PrintTo(value, os);
+ }
+
+#ifdef _MSC_VER
+# pragma warning(pop) // Restores the warning state.
+#endif // _MSC_VER
+};
+
+// UniversalPrintArray(begin, len, os) prints an array of 'len'
+// elements, starting at address 'begin'.
+template <typename T>
+void UniversalPrintArray(const T* begin, size_t len, ::std::ostream* os) {
+ if (len == 0) {
+ *os << "{}";
+ } else {
+ *os << "{ ";
+ const size_t kThreshold = 18;
+ const size_t kChunkSize = 8;
+ // If the array has more than kThreshold elements, we'll have to
+ // omit some details by printing only the first and the last
+ // kChunkSize elements.
+ // TODO(wan at google.com): let the user control the threshold using a flag.
+ if (len <= kThreshold) {
+ PrintRawArrayTo(begin, len, os);
+ } else {
+ PrintRawArrayTo(begin, kChunkSize, os);
+ *os << ", ..., ";
+ PrintRawArrayTo(begin + len - kChunkSize, kChunkSize, os);
+ }
+ *os << " }";
+ }
+}
+// This overload prints a (const) char array compactly.
+GTEST_API_ void UniversalPrintArray(
+ const char* begin, size_t len, ::std::ostream* os);
+
+// This overload prints a (const) wchar_t array compactly.
+GTEST_API_ void UniversalPrintArray(
+ const wchar_t* begin, size_t len, ::std::ostream* os);
+
+// Implements printing an array type T[N].
+template <typename T, size_t N>
+class UniversalPrinter<T[N]> {
+ public:
+ // Prints the given array, omitting some elements when there are too
+ // many.
+ static void Print(const T (&a)[N], ::std::ostream* os) {
+ UniversalPrintArray(a, N, os);
+ }
+};
+
+// Implements printing a reference type T&.
+template <typename T>
+class UniversalPrinter<T&> {
+ public:
+ // MSVC warns about adding const to a function type, so we want to
+ // disable the warning.
+#ifdef _MSC_VER
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4180) // Temporarily disables warning 4180.
+#endif // _MSC_VER
+
+ static void Print(const T& value, ::std::ostream* os) {
+ // Prints the address of the value. We use reinterpret_cast here
+ // as static_cast doesn't compile when T is a function type.
+ *os << "@" << reinterpret_cast<const void*>(&value) << " ";
+
+ // Then prints the value itself.
+ UniversalPrint(value, os);
+ }
+
+#ifdef _MSC_VER
+# pragma warning(pop) // Restores the warning state.
+#endif // _MSC_VER
+};
+
+// Prints a value tersely: for a reference type, the referenced value
+// (but not the address) is printed; for a (const) char pointer, the
+// NUL-terminated string (but not the pointer) is printed.
+
+template <typename T>
+class UniversalTersePrinter {
+ public:
+ static void Print(const T& value, ::std::ostream* os) {
+ UniversalPrint(value, os);
+ }
+};
+template <typename T>
+class UniversalTersePrinter<T&> {
+ public:
+ static void Print(const T& value, ::std::ostream* os) {
+ UniversalPrint(value, os);
+ }
+};
+template <typename T, size_t N>
+class UniversalTersePrinter<T[N]> {
+ public:
+ static void Print(const T (&value)[N], ::std::ostream* os) {
+ UniversalPrinter<T[N]>::Print(value, os);
+ }
+};
+template <>
+class UniversalTersePrinter<const char*> {
+ public:
+ static void Print(const char* str, ::std::ostream* os) {
+ if (str == NULL) {
+ *os << "NULL";
+ } else {
+ UniversalPrint(string(str), os);
+ }
+ }
+};
+template <>
+class UniversalTersePrinter<char*> {
+ public:
+ static void Print(char* str, ::std::ostream* os) {
+ UniversalTersePrinter<const char*>::Print(str, os);
+ }
+};
+
+#if GTEST_HAS_STD_WSTRING
+template <>
+class UniversalTersePrinter<const wchar_t*> {
+ public:
+ static void Print(const wchar_t* str, ::std::ostream* os) {
+ if (str == NULL) {
+ *os << "NULL";
+ } else {
+ UniversalPrint(::std::wstring(str), os);
+ }
+ }
+};
+#endif
+
+template <>
+class UniversalTersePrinter<wchar_t*> {
+ public:
+ static void Print(wchar_t* str, ::std::ostream* os) {
+ UniversalTersePrinter<const wchar_t*>::Print(str, os);
+ }
+};
+
+template <typename T>
+void UniversalTersePrint(const T& value, ::std::ostream* os) {
+ UniversalTersePrinter<T>::Print(value, os);
+}
+
+// Prints a value using the type inferred by the compiler. The
+// difference between this and UniversalTersePrint() is that for a
+// (const) char pointer, this prints both the pointer and the
+// NUL-terminated string.
+template <typename T>
+void UniversalPrint(const T& value, ::std::ostream* os) {
+ // A workarond for the bug in VC++ 7.1 that prevents us from instantiating
+ // UniversalPrinter with T directly.
+ typedef T T1;
+ UniversalPrinter<T1>::Print(value, os);
+}
+
+#if GTEST_HAS_TR1_TUPLE
+typedef ::std::vector<string> Strings;
+
+// This helper template allows PrintTo() for tuples and
+// UniversalTersePrintTupleFieldsToStrings() to be defined by
+// induction on the number of tuple fields. The idea is that
+// TuplePrefixPrinter<N>::PrintPrefixTo(t, os) prints the first N
+// fields in tuple t, and can be defined in terms of
+// TuplePrefixPrinter<N - 1>.
+
+// The inductive case.
+template <size_t N>
+struct TuplePrefixPrinter {
+ // Prints the first N fields of a tuple.
+ template <typename Tuple>
+ static void PrintPrefixTo(const Tuple& t, ::std::ostream* os) {
+ TuplePrefixPrinter<N - 1>::PrintPrefixTo(t, os);
+ *os << ", ";
+ UniversalPrinter<typename ::std::tr1::tuple_element<N - 1, Tuple>::type>
+ ::Print(::std::tr1::get<N - 1>(t), os);
+ }
+
+ // Tersely prints the first N fields of a tuple to a string vector,
+ // one element for each field.
+ template <typename Tuple>
+ static void TersePrintPrefixToStrings(const Tuple& t, Strings* strings) {
+ TuplePrefixPrinter<N - 1>::TersePrintPrefixToStrings(t, strings);
+ ::std::stringstream ss;
+ UniversalTersePrint(::std::tr1::get<N - 1>(t), &ss);
+ strings->push_back(ss.str());
+ }
+};
+
+// Base cases.
+template <>
+struct TuplePrefixPrinter<0> {
+ template <typename Tuple>
+ static void PrintPrefixTo(const Tuple&, ::std::ostream*) {}
+
+ template <typename Tuple>
+ static void TersePrintPrefixToStrings(const Tuple&, Strings*) {}
+};
+// We have to specialize the entire TuplePrefixPrinter<> class
+// template here, even though the definition of
+// TersePrintPrefixToStrings() is the same as the generic version, as
+// Embarcadero (formerly CodeGear, formerly Borland) C++ doesn't
+// support specializing a method template of a class template.
+template <>
+struct TuplePrefixPrinter<1> {
+ template <typename Tuple>
+ static void PrintPrefixTo(const Tuple& t, ::std::ostream* os) {
+ UniversalPrinter<typename ::std::tr1::tuple_element<0, Tuple>::type>::
+ Print(::std::tr1::get<0>(t), os);
+ }
+
+ template <typename Tuple>
+ static void TersePrintPrefixToStrings(const Tuple& t, Strings* strings) {
+ ::std::stringstream ss;
+ UniversalTersePrint(::std::tr1::get<0>(t), &ss);
+ strings->push_back(ss.str());
+ }
+};
+
+// Helper function for printing a tuple. T must be instantiated with
+// a tuple type.
+template <typename T>
+void PrintTupleTo(const T& t, ::std::ostream* os) {
+ *os << "(";
+ TuplePrefixPrinter< ::std::tr1::tuple_size<T>::value>::
+ PrintPrefixTo(t, os);
+ *os << ")";
+}
+
+// Prints the fields of a tuple tersely to a string vector, one
+// element for each field. See the comment before
+// UniversalTersePrint() for how we define "tersely".
+template <typename Tuple>
+Strings UniversalTersePrintTupleFieldsToStrings(const Tuple& value) {
+ Strings result;
+ TuplePrefixPrinter< ::std::tr1::tuple_size<Tuple>::value>::
+ TersePrintPrefixToStrings(value, &result);
+ return result;
+}
+#endif // GTEST_HAS_TR1_TUPLE
+
+} // namespace internal
+
+template <typename T>
+::std::string PrintToString(const T& value) {
+ ::std::stringstream ss;
+ internal::UniversalTersePrinter<T>::Print(value, &ss);
+ return ss.str();
+}
+
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_PRINTERS_H_
+
+#if GTEST_HAS_PARAM_TEST
+
+namespace testing {
+namespace internal {
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// Outputs a message explaining invalid registration of different
+// fixture class for the same test case. This may happen when
+// TEST_P macro is used to define two tests with the same name
+// but in different namespaces.
+GTEST_API_ void ReportInvalidTestCaseType(const char* test_case_name,
+ const char* file, int line);
+
+template <typename> class ParamGeneratorInterface;
+template <typename> class ParamGenerator;
+
+// Interface for iterating over elements provided by an implementation
+// of ParamGeneratorInterface<T>.
+template <typename T>
+class ParamIteratorInterface {
+ public:
+ virtual ~ParamIteratorInterface() {}
+ // A pointer to the base generator instance.
+ // Used only for the purposes of iterator comparison
+ // to make sure that two iterators belong to the same generator.
+ virtual const ParamGeneratorInterface<T>* BaseGenerator() const = 0;
+ // Advances iterator to point to the next element
+ // provided by the generator. The caller is responsible
+ // for not calling Advance() on an iterator equal to
+ // BaseGenerator()->End().
+ virtual void Advance() = 0;
+ // Clones the iterator object. Used for implementing copy semantics
+ // of ParamIterator<T>.
+ virtual ParamIteratorInterface* Clone() const = 0;
+ // Dereferences the current iterator and provides (read-only) access
+ // to the pointed value. It is the caller's responsibility not to call
+ // Current() on an iterator equal to BaseGenerator()->End().
+ // Used for implementing ParamGenerator<T>::operator*().
+ virtual const T* Current() const = 0;
+ // Determines whether the given iterator and other point to the same
+ // element in the sequence generated by the generator.
+ // Used for implementing ParamGenerator<T>::operator==().
+ virtual bool Equals(const ParamIteratorInterface& other) const = 0;
+};
+
+// Class iterating over elements provided by an implementation of
+// ParamGeneratorInterface<T>. It wraps ParamIteratorInterface<T>
+// and implements the const forward iterator concept.
+template <typename T>
+class ParamIterator {
+ public:
+ typedef T value_type;
+ typedef const T& reference;
+ typedef ptrdiff_t difference_type;
+
+ // ParamIterator assumes ownership of the impl_ pointer.
+ ParamIterator(const ParamIterator& other) : impl_(other.impl_->Clone()) {}
+ ParamIterator& operator=(const ParamIterator& other) {
+ if (this != &other)
+ impl_.reset(other.impl_->Clone());
+ return *this;
+ }
+
+ const T& operator*() const { return *impl_->Current(); }
+ const T* operator->() const { return impl_->Current(); }
+ // Prefix version of operator++.
+ ParamIterator& operator++() {
+ impl_->Advance();
+ return *this;
+ }
+ // Postfix version of operator++.
+ ParamIterator operator++(int /*unused*/) {
+ ParamIteratorInterface<T>* clone = impl_->Clone();
+ impl_->Advance();
+ return ParamIterator(clone);
+ }
+ bool operator==(const ParamIterator& other) const {
+ return impl_.get() == other.impl_.get() || impl_->Equals(*other.impl_);
+ }
+ bool operator!=(const ParamIterator& other) const {
+ return !(*this == other);
+ }
+
+ private:
+ friend class ParamGenerator<T>;
+ explicit ParamIterator(ParamIteratorInterface<T>* impl) : impl_(impl) {}
+ scoped_ptr<ParamIteratorInterface<T> > impl_;
+};
+
+// ParamGeneratorInterface<T> is the binary interface to access generators
+// defined in other translation units.
+template <typename T>
+class ParamGeneratorInterface {
+ public:
+ typedef T ParamType;
+
+ virtual ~ParamGeneratorInterface() {}
+
+ // Generator interface definition
+ virtual ParamIteratorInterface<T>* Begin() const = 0;
+ virtual ParamIteratorInterface<T>* End() const = 0;
+};
+
+// Wraps ParamGeneratorInterface<T> and provides general generator syntax
+// compatible with the STL Container concept.
+// This class implements copy initialization semantics and the contained
+// ParamGeneratorInterface<T> instance is shared among all copies
+// of the original object. This is possible because that instance is immutable.
+template<typename T>
+class ParamGenerator {
+ public:
+ typedef ParamIterator<T> iterator;
+
+ explicit ParamGenerator(ParamGeneratorInterface<T>* impl) : impl_(impl) {}
+ ParamGenerator(const ParamGenerator& other) : impl_(other.impl_) {}
+
+ ParamGenerator& operator=(const ParamGenerator& other) {
+ impl_ = other.impl_;
+ return *this;
+ }
+
+ iterator begin() const { return iterator(impl_->Begin()); }
+ iterator end() const { return iterator(impl_->End()); }
+
+ private:
+ linked_ptr<const ParamGeneratorInterface<T> > impl_;
+};
+
+// Generates values from a range of two comparable values. Can be used to
+// generate sequences of user-defined types that implement operator+() and
+// operator<().
+// This class is used in the Range() function.
+template <typename T, typename IncrementT>
+class RangeGenerator : public ParamGeneratorInterface<T> {
+ public:
+ RangeGenerator(T begin, T end, IncrementT step)
+ : begin_(begin), end_(end),
+ step_(step), end_index_(CalculateEndIndex(begin, end, step)) {}
+ virtual ~RangeGenerator() {}
+
+ virtual ParamIteratorInterface<T>* Begin() const {
+ return new Iterator(this, begin_, 0, step_);
+ }
+ virtual ParamIteratorInterface<T>* End() const {
+ return new Iterator(this, end_, end_index_, step_);
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<T> {
+ public:
+ Iterator(const ParamGeneratorInterface<T>* base, T value, int index,
+ IncrementT step)
+ : base_(base), value_(value), index_(index), step_(step) {}
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<T>* BaseGenerator() const {
+ return base_;
+ }
+ virtual void Advance() {
+ value_ = value_ + step_;
+ index_++;
+ }
+ virtual ParamIteratorInterface<T>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const T* Current() const { return &value_; }
+ virtual bool Equals(const ParamIteratorInterface<T>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const int other_index =
+ CheckedDowncastToActualType<const Iterator>(&other)->index_;
+ return index_ == other_index;
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : ParamIteratorInterface<T>(),
+ base_(other.base_), value_(other.value_), index_(other.index_),
+ step_(other.step_) {}
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<T>* const base_;
+ T value_;
+ int index_;
+ const IncrementT step_;
+ }; // class RangeGenerator::Iterator
+
+ static int CalculateEndIndex(const T& begin,
+ const T& end,
+ const IncrementT& step) {
+ int end_index = 0;
+ for (T i = begin; i < end; i = i + step)
+ end_index++;
+ return end_index;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const RangeGenerator& other);
+
+ const T begin_;
+ const T end_;
+ const IncrementT step_;
+ // The index for the end() iterator. All the elements in the generated
+ // sequence are indexed (0-based) to aid iterator comparison.
+ const int end_index_;
+}; // class RangeGenerator
+
+
+// Generates values from a pair of STL-style iterators. Used in the
+// ValuesIn() function. The elements are copied from the source range
+// since the source can be located on the stack, and the generator
+// is likely to persist beyond that stack frame.
+template <typename T>
+class ValuesInIteratorRangeGenerator : public ParamGeneratorInterface<T> {
+ public:
+ template <typename ForwardIterator>
+ ValuesInIteratorRangeGenerator(ForwardIterator begin, ForwardIterator end)
+ : container_(begin, end) {}
+ virtual ~ValuesInIteratorRangeGenerator() {}
+
+ virtual ParamIteratorInterface<T>* Begin() const {
+ return new Iterator(this, container_.begin());
+ }
+ virtual ParamIteratorInterface<T>* End() const {
+ return new Iterator(this, container_.end());
+ }
+
+ private:
+ typedef typename ::std::vector<T> ContainerType;
+
+ class Iterator : public ParamIteratorInterface<T> {
+ public:
+ Iterator(const ParamGeneratorInterface<T>* base,
+ typename ContainerType::const_iterator iterator)
+ : base_(base), iterator_(iterator) {}
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<T>* BaseGenerator() const {
+ return base_;
+ }
+ virtual void Advance() {
+ ++iterator_;
+ value_.reset();
+ }
+ virtual ParamIteratorInterface<T>* Clone() const {
+ return new Iterator(*this);
+ }
+ // We need to use cached value referenced by iterator_ because *iterator_
+ // can return a temporary object (and of type other then T), so just
+ // having "return &*iterator_;" doesn't work.
+ // value_ is updated here and not in Advance() because Advance()
+ // can advance iterator_ beyond the end of the range, and we cannot
+ // detect that fact. The client code, on the other hand, is
+ // responsible for not calling Current() on an out-of-range iterator.
+ virtual const T* Current() const {
+ if (value_.get() == NULL)
+ value_.reset(new T(*iterator_));
+ return value_.get();
+ }
+ virtual bool Equals(const ParamIteratorInterface<T>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ return iterator_ ==
+ CheckedDowncastToActualType<const Iterator>(&other)->iterator_;
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ // The explicit constructor call suppresses a false warning
+ // emitted by gcc when supplied with the -Wextra option.
+ : ParamIteratorInterface<T>(),
+ base_(other.base_),
+ iterator_(other.iterator_) {}
+
+ const ParamGeneratorInterface<T>* const base_;
+ typename ContainerType::const_iterator iterator_;
+ // A cached value of *iterator_. We keep it here to allow access by
+ // pointer in the wrapping iterator's operator->().
+ // value_ needs to be mutable to be accessed in Current().
+ // Use of scoped_ptr helps manage cached value's lifetime,
+ // which is bound by the lifespan of the iterator itself.
+ mutable scoped_ptr<const T> value_;
+ }; // class ValuesInIteratorRangeGenerator::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const ValuesInIteratorRangeGenerator& other);
+
+ const ContainerType container_;
+}; // class ValuesInIteratorRangeGenerator
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// Stores a parameter value and later creates tests parameterized with that
+// value.
+template <class TestClass>
+class ParameterizedTestFactory : public TestFactoryBase {
+ public:
+ typedef typename TestClass::ParamType ParamType;
+ explicit ParameterizedTestFactory(ParamType parameter) :
+ parameter_(parameter) {}
+ virtual Test* CreateTest() {
+ TestClass::SetParam(¶meter_);
+ return new TestClass();
+ }
+
+ private:
+ const ParamType parameter_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestFactory);
+};
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// TestMetaFactoryBase is a base class for meta-factories that create
+// test factories for passing into MakeAndRegisterTestInfo function.
+template <class ParamType>
+class TestMetaFactoryBase {
+ public:
+ virtual ~TestMetaFactoryBase() {}
+
+ virtual TestFactoryBase* CreateTestFactory(ParamType parameter) = 0;
+};
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// TestMetaFactory creates test factories for passing into
+// MakeAndRegisterTestInfo function. Since MakeAndRegisterTestInfo receives
+// ownership of test factory pointer, same factory object cannot be passed
+// into that method twice. But ParameterizedTestCaseInfo is going to call
+// it for each Test/Parameter value combination. Thus it needs meta factory
+// creator class.
+template <class TestCase>
+class TestMetaFactory
+ : public TestMetaFactoryBase<typename TestCase::ParamType> {
+ public:
+ typedef typename TestCase::ParamType ParamType;
+
+ TestMetaFactory() {}
+
+ virtual TestFactoryBase* CreateTestFactory(ParamType parameter) {
+ return new ParameterizedTestFactory<TestCase>(parameter);
+ }
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(TestMetaFactory);
+};
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// ParameterizedTestCaseInfoBase is a generic interface
+// to ParameterizedTestCaseInfo classes. ParameterizedTestCaseInfoBase
+// accumulates test information provided by TEST_P macro invocations
+// and generators provided by INSTANTIATE_TEST_CASE_P macro invocations
+// and uses that information to register all resulting test instances
+// in RegisterTests method. The ParameterizeTestCaseRegistry class holds
+// a collection of pointers to the ParameterizedTestCaseInfo objects
+// and calls RegisterTests() on each of them when asked.
+class ParameterizedTestCaseInfoBase {
+ public:
+ virtual ~ParameterizedTestCaseInfoBase() {}
+
+ // Base part of test case name for display purposes.
+ virtual const string& GetTestCaseName() const = 0;
+ // Test case id to verify identity.
+ virtual TypeId GetTestCaseTypeId() const = 0;
+ // UnitTest class invokes this method to register tests in this
+ // test case right before running them in RUN_ALL_TESTS macro.
+ // This method should not be called more then once on any single
+ // instance of a ParameterizedTestCaseInfoBase derived class.
+ virtual void RegisterTests() = 0;
+
+ protected:
+ ParameterizedTestCaseInfoBase() {}
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestCaseInfoBase);
+};
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// ParameterizedTestCaseInfo accumulates tests obtained from TEST_P
+// macro invocations for a particular test case and generators
+// obtained from INSTANTIATE_TEST_CASE_P macro invocations for that
+// test case. It registers tests with all values generated by all
+// generators when asked.
+template <class TestCase>
+class ParameterizedTestCaseInfo : public ParameterizedTestCaseInfoBase {
+ public:
+ // ParamType and GeneratorCreationFunc are private types but are required
+ // for declarations of public methods AddTestPattern() and
+ // AddTestCaseInstantiation().
+ typedef typename TestCase::ParamType ParamType;
+ // A function that returns an instance of appropriate generator type.
+ typedef ParamGenerator<ParamType>(GeneratorCreationFunc)();
+
+ explicit ParameterizedTestCaseInfo(const char* name)
+ : test_case_name_(name) {}
+
+ // Test case base name for display purposes.
+ virtual const string& GetTestCaseName() const { return test_case_name_; }
+ // Test case id to verify identity.
+ virtual TypeId GetTestCaseTypeId() const { return GetTypeId<TestCase>(); }
+ // TEST_P macro uses AddTestPattern() to record information
+ // about a single test in a LocalTestInfo structure.
+ // test_case_name is the base name of the test case (without invocation
+ // prefix). test_base_name is the name of an individual test without
+ // parameter index. For the test SequenceA/FooTest.DoBar/1 FooTest is
+ // test case base name and DoBar is test base name.
+ void AddTestPattern(const char* test_case_name,
+ const char* test_base_name,
+ TestMetaFactoryBase<ParamType>* meta_factory) {
+ tests_.push_back(linked_ptr<TestInfo>(new TestInfo(test_case_name,
+ test_base_name,
+ meta_factory)));
+ }
+ // INSTANTIATE_TEST_CASE_P macro uses AddGenerator() to record information
+ // about a generator.
+ int AddTestCaseInstantiation(const string& instantiation_name,
+ GeneratorCreationFunc* func,
+ const char* /* file */,
+ int /* line */) {
+ instantiations_.push_back(::std::make_pair(instantiation_name, func));
+ return 0; // Return value used only to run this method in namespace scope.
+ }
+ // UnitTest class invokes this method to register tests in this test case
+ // test cases right before running tests in RUN_ALL_TESTS macro.
+ // This method should not be called more then once on any single
+ // instance of a ParameterizedTestCaseInfoBase derived class.
+ // UnitTest has a guard to prevent from calling this method more then once.
+ virtual void RegisterTests() {
+ for (typename TestInfoContainer::iterator test_it = tests_.begin();
+ test_it != tests_.end(); ++test_it) {
+ linked_ptr<TestInfo> test_info = *test_it;
+ for (typename InstantiationContainer::iterator gen_it =
+ instantiations_.begin(); gen_it != instantiations_.end();
+ ++gen_it) {
+ const string& instantiation_name = gen_it->first;
+ ParamGenerator<ParamType> generator((*gen_it->second)());
+
+ string test_case_name;
+ if ( !instantiation_name.empty() )
+ test_case_name = instantiation_name + "/";
+ test_case_name += test_info->test_case_base_name;
+
+ int i = 0;
+ for (typename ParamGenerator<ParamType>::iterator param_it =
+ generator.begin();
+ param_it != generator.end(); ++param_it, ++i) {
+ Message test_name_stream;
+ test_name_stream << test_info->test_base_name << "/" << i;
+ MakeAndRegisterTestInfo(
+ test_case_name.c_str(),
+ test_name_stream.GetString().c_str(),
+ NULL, // No type parameter.
+ PrintToString(*param_it).c_str(),
+ GetTestCaseTypeId(),
+ TestCase::SetUpTestCase,
+ TestCase::TearDownTestCase,
+ test_info->test_meta_factory->CreateTestFactory(*param_it));
+ } // for param_it
+ } // for gen_it
+ } // for test_it
+ } // RegisterTests
+
+ private:
+ // LocalTestInfo structure keeps information about a single test registered
+ // with TEST_P macro.
+ struct TestInfo {
+ TestInfo(const char* a_test_case_base_name,
+ const char* a_test_base_name,
+ TestMetaFactoryBase<ParamType>* a_test_meta_factory) :
+ test_case_base_name(a_test_case_base_name),
+ test_base_name(a_test_base_name),
+ test_meta_factory(a_test_meta_factory) {}
+
+ const string test_case_base_name;
+ const string test_base_name;
+ const scoped_ptr<TestMetaFactoryBase<ParamType> > test_meta_factory;
+ };
+ typedef ::std::vector<linked_ptr<TestInfo> > TestInfoContainer;
+ // Keeps pairs of <Instantiation name, Sequence generator creation function>
+ // received from INSTANTIATE_TEST_CASE_P macros.
+ typedef ::std::vector<std::pair<string, GeneratorCreationFunc*> >
+ InstantiationContainer;
+
+ const string test_case_name_;
+ TestInfoContainer tests_;
+ InstantiationContainer instantiations_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestCaseInfo);
+}; // class ParameterizedTestCaseInfo
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// ParameterizedTestCaseRegistry contains a map of ParameterizedTestCaseInfoBase
+// classes accessed by test case names. TEST_P and INSTANTIATE_TEST_CASE_P
+// macros use it to locate their corresponding ParameterizedTestCaseInfo
+// descriptors.
+class ParameterizedTestCaseRegistry {
+ public:
+ ParameterizedTestCaseRegistry() {}
+ ~ParameterizedTestCaseRegistry() {
+ for (TestCaseInfoContainer::iterator it = test_case_infos_.begin();
+ it != test_case_infos_.end(); ++it) {
+ delete *it;
+ }
+ }
+
+ // Looks up or creates and returns a structure containing information about
+ // tests and instantiations of a particular test case.
+ template <class TestCase>
+ ParameterizedTestCaseInfo<TestCase>* GetTestCasePatternHolder(
+ const char* test_case_name,
+ const char* file,
+ int line) {
+ ParameterizedTestCaseInfo<TestCase>* typed_test_info = NULL;
+ for (TestCaseInfoContainer::iterator it = test_case_infos_.begin();
+ it != test_case_infos_.end(); ++it) {
+ if ((*it)->GetTestCaseName() == test_case_name) {
+ if ((*it)->GetTestCaseTypeId() != GetTypeId<TestCase>()) {
+ // Complain about incorrect usage of Google Test facilities
+ // and terminate the program since we cannot guaranty correct
+ // test case setup and tear-down in this case.
+ ReportInvalidTestCaseType(test_case_name, file, line);
+ posix::Abort();
+ } else {
+ // At this point we are sure that the object we found is of the same
+ // type we are looking for, so we downcast it to that type
+ // without further checks.
+ typed_test_info = CheckedDowncastToActualType<
+ ParameterizedTestCaseInfo<TestCase> >(*it);
+ }
+ break;
+ }
+ }
+ if (typed_test_info == NULL) {
+ typed_test_info = new ParameterizedTestCaseInfo<TestCase>(test_case_name);
+ test_case_infos_.push_back(typed_test_info);
+ }
+ return typed_test_info;
+ }
+ void RegisterTests() {
+ for (TestCaseInfoContainer::iterator it = test_case_infos_.begin();
+ it != test_case_infos_.end(); ++it) {
+ (*it)->RegisterTests();
+ }
+ }
+
+ private:
+ typedef ::std::vector<ParameterizedTestCaseInfoBase*> TestCaseInfoContainer;
+
+ TestCaseInfoContainer test_case_infos_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestCaseRegistry);
+};
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_HAS_PARAM_TEST
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_PARAM_UTIL_H_
+// This file was GENERATED by command:
+// pump.py gtest-param-util-generated.h.pump
+// DO NOT EDIT BY HAND!!!
+
+// Copyright 2008 Google Inc.
+// All Rights Reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: vladl at google.com (Vlad Losev)
+
+// Type and function utilities for implementing parameterized tests.
+// This file is generated by a SCRIPT. DO NOT EDIT BY HAND!
+//
+// Currently Google Test supports at most 50 arguments in Values,
+// and at most 10 arguments in Combine. Please contact
+// googletestframework at googlegroups.com if you need more.
+// Please note that the number of arguments to Combine is limited
+// by the maximum arity of the implementation of tr1::tuple which is
+// currently set at 10.
+
+#ifndef GTEST_INCLUDE_GTEST_INTERNAL_GTEST_PARAM_UTIL_GENERATED_H_
+#define GTEST_INCLUDE_GTEST_INTERNAL_GTEST_PARAM_UTIL_GENERATED_H_
+
+// scripts/fuse_gtest.py depends on gtest's own header being #included
+// *unconditionally*. Therefore these #includes cannot be moved
+// inside #if GTEST_HAS_PARAM_TEST.
+
+#if GTEST_HAS_PARAM_TEST
+
+namespace testing {
+
+// Forward declarations of ValuesIn(), which is implemented in
+// include/gtest/gtest-param-test.h.
+template <typename ForwardIterator>
+internal::ParamGenerator<
+ typename ::testing::internal::IteratorTraits<ForwardIterator>::value_type>
+ValuesIn(ForwardIterator begin, ForwardIterator end);
+
+template <typename T, size_t N>
+internal::ParamGenerator<T> ValuesIn(const T (&array)[N]);
+
+template <class Container>
+internal::ParamGenerator<typename Container::value_type> ValuesIn(
+ const Container& container);
+
+namespace internal {
+
+// Used in the Values() function to provide polymorphic capabilities.
+template <typename T1>
+class ValueArray1 {
+ public:
+ explicit ValueArray1(T1 v1) : v1_(v1) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const { return ValuesIn(&v1_, &v1_ + 1); }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray1& other);
+
+ const T1 v1_;
+};
+
+template <typename T1, typename T2>
+class ValueArray2 {
+ public:
+ ValueArray2(T1 v1, T2 v2) : v1_(v1), v2_(v2) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray2& other);
+
+ const T1 v1_;
+ const T2 v2_;
+};
+
+template <typename T1, typename T2, typename T3>
+class ValueArray3 {
+ public:
+ ValueArray3(T1 v1, T2 v2, T3 v3) : v1_(v1), v2_(v2), v3_(v3) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray3& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4>
+class ValueArray4 {
+ public:
+ ValueArray4(T1 v1, T2 v2, T3 v3, T4 v4) : v1_(v1), v2_(v2), v3_(v3),
+ v4_(v4) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray4& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5>
+class ValueArray5 {
+ public:
+ ValueArray5(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5) : v1_(v1), v2_(v2), v3_(v3),
+ v4_(v4), v5_(v5) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray5& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6>
+class ValueArray6 {
+ public:
+ ValueArray6(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6) : v1_(v1), v2_(v2),
+ v3_(v3), v4_(v4), v5_(v5), v6_(v6) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray6& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7>
+class ValueArray7 {
+ public:
+ ValueArray7(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7) : v1_(v1),
+ v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray7& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8>
+class ValueArray8 {
+ public:
+ ValueArray8(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7,
+ T8 v8) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray8& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9>
+class ValueArray9 {
+ public:
+ ValueArray9(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8,
+ T9 v9) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray9& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10>
+class ValueArray10 {
+ public:
+ ValueArray10(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray10& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11>
+class ValueArray11 {
+ public:
+ ValueArray11(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6),
+ v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray11& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12>
+class ValueArray12 {
+ public:
+ ValueArray12(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5),
+ v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray12& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13>
+class ValueArray13 {
+ public:
+ ValueArray13(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13) : v1_(v1), v2_(v2), v3_(v3), v4_(v4),
+ v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11),
+ v12_(v12), v13_(v13) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray13& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14>
+class ValueArray14 {
+ public:
+ ValueArray14(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14) : v1_(v1), v2_(v2), v3_(v3),
+ v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray14& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15>
+class ValueArray15 {
+ public:
+ ValueArray15(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15) : v1_(v1), v2_(v2),
+ v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray15& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16>
+class ValueArray16 {
+ public:
+ ValueArray16(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16) : v1_(v1),
+ v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9),
+ v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15),
+ v16_(v16) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray16& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17>
+class ValueArray17 {
+ public:
+ ValueArray17(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16,
+ T17 v17) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray17& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18>
+class ValueArray18 {
+ public:
+ ValueArray18(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17), v18_(v18) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray18& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19>
+class ValueArray19 {
+ public:
+ ValueArray19(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6),
+ v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13),
+ v14_(v14), v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray19& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20>
+class ValueArray20 {
+ public:
+ ValueArray20(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5),
+ v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12),
+ v13_(v13), v14_(v14), v15_(v15), v16_(v16), v17_(v17), v18_(v18),
+ v19_(v19), v20_(v20) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray20& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21>
+class ValueArray21 {
+ public:
+ ValueArray21(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21) : v1_(v1), v2_(v2), v3_(v3), v4_(v4),
+ v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11),
+ v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16), v17_(v17),
+ v18_(v18), v19_(v19), v20_(v20), v21_(v21) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray21& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22>
+class ValueArray22 {
+ public:
+ ValueArray22(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22) : v1_(v1), v2_(v2), v3_(v3),
+ v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16),
+ v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray22& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23>
+class ValueArray23 {
+ public:
+ ValueArray23(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23) : v1_(v1), v2_(v2),
+ v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16),
+ v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22),
+ v23_(v23) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray23& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24>
+class ValueArray24 {
+ public:
+ ValueArray24(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24) : v1_(v1),
+ v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9),
+ v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15),
+ v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21),
+ v22_(v22), v23_(v23), v24_(v24) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray24& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25>
+class ValueArray25 {
+ public:
+ ValueArray25(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24,
+ T25 v25) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20),
+ v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray25& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26>
+class ValueArray26 {
+ public:
+ ValueArray26(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20),
+ v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray26& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27>
+class ValueArray27 {
+ public:
+ ValueArray27(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6),
+ v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13),
+ v14_(v14), v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19),
+ v20_(v20), v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25),
+ v26_(v26), v27_(v27) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray27& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28>
+class ValueArray28 {
+ public:
+ ValueArray28(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5),
+ v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12),
+ v13_(v13), v14_(v14), v15_(v15), v16_(v16), v17_(v17), v18_(v18),
+ v19_(v19), v20_(v20), v21_(v21), v22_(v22), v23_(v23), v24_(v24),
+ v25_(v25), v26_(v26), v27_(v27), v28_(v28) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray28& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29>
+class ValueArray29 {
+ public:
+ ValueArray29(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29) : v1_(v1), v2_(v2), v3_(v3), v4_(v4),
+ v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11),
+ v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16), v17_(v17),
+ v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22), v23_(v23),
+ v24_(v24), v25_(v25), v26_(v26), v27_(v27), v28_(v28), v29_(v29) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray29& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30>
+class ValueArray30 {
+ public:
+ ValueArray30(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30) : v1_(v1), v2_(v2), v3_(v3),
+ v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16),
+ v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22),
+ v23_(v23), v24_(v24), v25_(v25), v26_(v26), v27_(v27), v28_(v28),
+ v29_(v29), v30_(v30) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray30& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31>
+class ValueArray31 {
+ public:
+ ValueArray31(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31) : v1_(v1), v2_(v2),
+ v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16),
+ v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22),
+ v23_(v23), v24_(v24), v25_(v25), v26_(v26), v27_(v27), v28_(v28),
+ v29_(v29), v30_(v30), v31_(v31) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray31& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32>
+class ValueArray32 {
+ public:
+ ValueArray32(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32) : v1_(v1),
+ v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9),
+ v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15),
+ v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21),
+ v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26), v27_(v27),
+ v28_(v28), v29_(v29), v30_(v30), v31_(v31), v32_(v32) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray32& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33>
+class ValueArray33 {
+ public:
+ ValueArray33(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32,
+ T33 v33) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20),
+ v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26),
+ v27_(v27), v28_(v28), v29_(v29), v30_(v30), v31_(v31), v32_(v32),
+ v33_(v33) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray33& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34>
+class ValueArray34 {
+ public:
+ ValueArray34(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20),
+ v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26),
+ v27_(v27), v28_(v28), v29_(v29), v30_(v30), v31_(v31), v32_(v32),
+ v33_(v33), v34_(v34) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray34& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35>
+class ValueArray35 {
+ public:
+ ValueArray35(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6),
+ v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13),
+ v14_(v14), v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19),
+ v20_(v20), v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25),
+ v26_(v26), v27_(v27), v28_(v28), v29_(v29), v30_(v30), v31_(v31),
+ v32_(v32), v33_(v33), v34_(v34), v35_(v35) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray35& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36>
+class ValueArray36 {
+ public:
+ ValueArray36(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5),
+ v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12),
+ v13_(v13), v14_(v14), v15_(v15), v16_(v16), v17_(v17), v18_(v18),
+ v19_(v19), v20_(v20), v21_(v21), v22_(v22), v23_(v23), v24_(v24),
+ v25_(v25), v26_(v26), v27_(v27), v28_(v28), v29_(v29), v30_(v30),
+ v31_(v31), v32_(v32), v33_(v33), v34_(v34), v35_(v35), v36_(v36) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray36& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37>
+class ValueArray37 {
+ public:
+ ValueArray37(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37) : v1_(v1), v2_(v2), v3_(v3), v4_(v4),
+ v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11),
+ v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16), v17_(v17),
+ v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22), v23_(v23),
+ v24_(v24), v25_(v25), v26_(v26), v27_(v27), v28_(v28), v29_(v29),
+ v30_(v30), v31_(v31), v32_(v32), v33_(v33), v34_(v34), v35_(v35),
+ v36_(v36), v37_(v37) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray37& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38>
+class ValueArray38 {
+ public:
+ ValueArray38(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38) : v1_(v1), v2_(v2), v3_(v3),
+ v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16),
+ v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22),
+ v23_(v23), v24_(v24), v25_(v25), v26_(v26), v27_(v27), v28_(v28),
+ v29_(v29), v30_(v30), v31_(v31), v32_(v32), v33_(v33), v34_(v34),
+ v35_(v35), v36_(v36), v37_(v37), v38_(v38) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray38& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39>
+class ValueArray39 {
+ public:
+ ValueArray39(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39) : v1_(v1), v2_(v2),
+ v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16),
+ v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22),
+ v23_(v23), v24_(v24), v25_(v25), v26_(v26), v27_(v27), v28_(v28),
+ v29_(v29), v30_(v30), v31_(v31), v32_(v32), v33_(v33), v34_(v34),
+ v35_(v35), v36_(v36), v37_(v37), v38_(v38), v39_(v39) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray39& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40>
+class ValueArray40 {
+ public:
+ ValueArray40(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40) : v1_(v1),
+ v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9),
+ v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15),
+ v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21),
+ v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26), v27_(v27),
+ v28_(v28), v29_(v29), v30_(v30), v31_(v31), v32_(v32), v33_(v33),
+ v34_(v34), v35_(v35), v36_(v36), v37_(v37), v38_(v38), v39_(v39),
+ v40_(v40) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray40& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41>
+class ValueArray41 {
+ public:
+ ValueArray41(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40,
+ T41 v41) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20),
+ v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26),
+ v27_(v27), v28_(v28), v29_(v29), v30_(v30), v31_(v31), v32_(v32),
+ v33_(v33), v34_(v34), v35_(v35), v36_(v36), v37_(v37), v38_(v38),
+ v39_(v39), v40_(v40), v41_(v41) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray41& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42>
+class ValueArray42 {
+ public:
+ ValueArray42(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20),
+ v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26),
+ v27_(v27), v28_(v28), v29_(v29), v30_(v30), v31_(v31), v32_(v32),
+ v33_(v33), v34_(v34), v35_(v35), v36_(v36), v37_(v37), v38_(v38),
+ v39_(v39), v40_(v40), v41_(v41), v42_(v42) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_),
+ static_cast<T>(v42_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray42& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+ const T42 v42_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43>
+class ValueArray43 {
+ public:
+ ValueArray43(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6),
+ v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13),
+ v14_(v14), v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19),
+ v20_(v20), v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25),
+ v26_(v26), v27_(v27), v28_(v28), v29_(v29), v30_(v30), v31_(v31),
+ v32_(v32), v33_(v33), v34_(v34), v35_(v35), v36_(v36), v37_(v37),
+ v38_(v38), v39_(v39), v40_(v40), v41_(v41), v42_(v42), v43_(v43) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_),
+ static_cast<T>(v42_), static_cast<T>(v43_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray43& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+ const T42 v42_;
+ const T43 v43_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44>
+class ValueArray44 {
+ public:
+ ValueArray44(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43, T44 v44) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5),
+ v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12),
+ v13_(v13), v14_(v14), v15_(v15), v16_(v16), v17_(v17), v18_(v18),
+ v19_(v19), v20_(v20), v21_(v21), v22_(v22), v23_(v23), v24_(v24),
+ v25_(v25), v26_(v26), v27_(v27), v28_(v28), v29_(v29), v30_(v30),
+ v31_(v31), v32_(v32), v33_(v33), v34_(v34), v35_(v35), v36_(v36),
+ v37_(v37), v38_(v38), v39_(v39), v40_(v40), v41_(v41), v42_(v42),
+ v43_(v43), v44_(v44) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_),
+ static_cast<T>(v42_), static_cast<T>(v43_), static_cast<T>(v44_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray44& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+ const T42 v42_;
+ const T43 v43_;
+ const T44 v44_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45>
+class ValueArray45 {
+ public:
+ ValueArray45(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43, T44 v44, T45 v45) : v1_(v1), v2_(v2), v3_(v3), v4_(v4),
+ v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10), v11_(v11),
+ v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16), v17_(v17),
+ v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22), v23_(v23),
+ v24_(v24), v25_(v25), v26_(v26), v27_(v27), v28_(v28), v29_(v29),
+ v30_(v30), v31_(v31), v32_(v32), v33_(v33), v34_(v34), v35_(v35),
+ v36_(v36), v37_(v37), v38_(v38), v39_(v39), v40_(v40), v41_(v41),
+ v42_(v42), v43_(v43), v44_(v44), v45_(v45) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_),
+ static_cast<T>(v42_), static_cast<T>(v43_), static_cast<T>(v44_),
+ static_cast<T>(v45_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray45& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+ const T42 v42_;
+ const T43 v43_;
+ const T44 v44_;
+ const T45 v45_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46>
+class ValueArray46 {
+ public:
+ ValueArray46(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43, T44 v44, T45 v45, T46 v46) : v1_(v1), v2_(v2), v3_(v3),
+ v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16),
+ v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22),
+ v23_(v23), v24_(v24), v25_(v25), v26_(v26), v27_(v27), v28_(v28),
+ v29_(v29), v30_(v30), v31_(v31), v32_(v32), v33_(v33), v34_(v34),
+ v35_(v35), v36_(v36), v37_(v37), v38_(v38), v39_(v39), v40_(v40),
+ v41_(v41), v42_(v42), v43_(v43), v44_(v44), v45_(v45), v46_(v46) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_),
+ static_cast<T>(v42_), static_cast<T>(v43_), static_cast<T>(v44_),
+ static_cast<T>(v45_), static_cast<T>(v46_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray46& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+ const T42 v42_;
+ const T43 v43_;
+ const T44 v44_;
+ const T45 v45_;
+ const T46 v46_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47>
+class ValueArray47 {
+ public:
+ ValueArray47(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43, T44 v44, T45 v45, T46 v46, T47 v47) : v1_(v1), v2_(v2),
+ v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9), v10_(v10),
+ v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15), v16_(v16),
+ v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21), v22_(v22),
+ v23_(v23), v24_(v24), v25_(v25), v26_(v26), v27_(v27), v28_(v28),
+ v29_(v29), v30_(v30), v31_(v31), v32_(v32), v33_(v33), v34_(v34),
+ v35_(v35), v36_(v36), v37_(v37), v38_(v38), v39_(v39), v40_(v40),
+ v41_(v41), v42_(v42), v43_(v43), v44_(v44), v45_(v45), v46_(v46),
+ v47_(v47) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_),
+ static_cast<T>(v42_), static_cast<T>(v43_), static_cast<T>(v44_),
+ static_cast<T>(v45_), static_cast<T>(v46_), static_cast<T>(v47_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray47& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+ const T42 v42_;
+ const T43 v43_;
+ const T44 v44_;
+ const T45 v45_;
+ const T46 v46_;
+ const T47 v47_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48>
+class ValueArray48 {
+ public:
+ ValueArray48(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43, T44 v44, T45 v45, T46 v46, T47 v47, T48 v48) : v1_(v1),
+ v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7), v8_(v8), v9_(v9),
+ v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14), v15_(v15),
+ v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20), v21_(v21),
+ v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26), v27_(v27),
+ v28_(v28), v29_(v29), v30_(v30), v31_(v31), v32_(v32), v33_(v33),
+ v34_(v34), v35_(v35), v36_(v36), v37_(v37), v38_(v38), v39_(v39),
+ v40_(v40), v41_(v41), v42_(v42), v43_(v43), v44_(v44), v45_(v45),
+ v46_(v46), v47_(v47), v48_(v48) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_),
+ static_cast<T>(v42_), static_cast<T>(v43_), static_cast<T>(v44_),
+ static_cast<T>(v45_), static_cast<T>(v46_), static_cast<T>(v47_),
+ static_cast<T>(v48_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray48& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+ const T42 v42_;
+ const T43 v43_;
+ const T44 v44_;
+ const T45 v45_;
+ const T46 v46_;
+ const T47 v47_;
+ const T48 v48_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48, typename T49>
+class ValueArray49 {
+ public:
+ ValueArray49(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43, T44 v44, T45 v45, T46 v46, T47 v47, T48 v48,
+ T49 v49) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20),
+ v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26),
+ v27_(v27), v28_(v28), v29_(v29), v30_(v30), v31_(v31), v32_(v32),
+ v33_(v33), v34_(v34), v35_(v35), v36_(v36), v37_(v37), v38_(v38),
+ v39_(v39), v40_(v40), v41_(v41), v42_(v42), v43_(v43), v44_(v44),
+ v45_(v45), v46_(v46), v47_(v47), v48_(v48), v49_(v49) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_),
+ static_cast<T>(v42_), static_cast<T>(v43_), static_cast<T>(v44_),
+ static_cast<T>(v45_), static_cast<T>(v46_), static_cast<T>(v47_),
+ static_cast<T>(v48_), static_cast<T>(v49_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray49& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+ const T42 v42_;
+ const T43 v43_;
+ const T44 v44_;
+ const T45 v45_;
+ const T46 v46_;
+ const T47 v47_;
+ const T48 v48_;
+ const T49 v49_;
+};
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48, typename T49, typename T50>
+class ValueArray50 {
+ public:
+ ValueArray50(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43, T44 v44, T45 v45, T46 v46, T47 v47, T48 v48, T49 v49,
+ T50 v50) : v1_(v1), v2_(v2), v3_(v3), v4_(v4), v5_(v5), v6_(v6), v7_(v7),
+ v8_(v8), v9_(v9), v10_(v10), v11_(v11), v12_(v12), v13_(v13), v14_(v14),
+ v15_(v15), v16_(v16), v17_(v17), v18_(v18), v19_(v19), v20_(v20),
+ v21_(v21), v22_(v22), v23_(v23), v24_(v24), v25_(v25), v26_(v26),
+ v27_(v27), v28_(v28), v29_(v29), v30_(v30), v31_(v31), v32_(v32),
+ v33_(v33), v34_(v34), v35_(v35), v36_(v36), v37_(v37), v38_(v38),
+ v39_(v39), v40_(v40), v41_(v41), v42_(v42), v43_(v43), v44_(v44),
+ v45_(v45), v46_(v46), v47_(v47), v48_(v48), v49_(v49), v50_(v50) {}
+
+ template <typename T>
+ operator ParamGenerator<T>() const {
+ const T array[] = {static_cast<T>(v1_), static_cast<T>(v2_),
+ static_cast<T>(v3_), static_cast<T>(v4_), static_cast<T>(v5_),
+ static_cast<T>(v6_), static_cast<T>(v7_), static_cast<T>(v8_),
+ static_cast<T>(v9_), static_cast<T>(v10_), static_cast<T>(v11_),
+ static_cast<T>(v12_), static_cast<T>(v13_), static_cast<T>(v14_),
+ static_cast<T>(v15_), static_cast<T>(v16_), static_cast<T>(v17_),
+ static_cast<T>(v18_), static_cast<T>(v19_), static_cast<T>(v20_),
+ static_cast<T>(v21_), static_cast<T>(v22_), static_cast<T>(v23_),
+ static_cast<T>(v24_), static_cast<T>(v25_), static_cast<T>(v26_),
+ static_cast<T>(v27_), static_cast<T>(v28_), static_cast<T>(v29_),
+ static_cast<T>(v30_), static_cast<T>(v31_), static_cast<T>(v32_),
+ static_cast<T>(v33_), static_cast<T>(v34_), static_cast<T>(v35_),
+ static_cast<T>(v36_), static_cast<T>(v37_), static_cast<T>(v38_),
+ static_cast<T>(v39_), static_cast<T>(v40_), static_cast<T>(v41_),
+ static_cast<T>(v42_), static_cast<T>(v43_), static_cast<T>(v44_),
+ static_cast<T>(v45_), static_cast<T>(v46_), static_cast<T>(v47_),
+ static_cast<T>(v48_), static_cast<T>(v49_), static_cast<T>(v50_)};
+ return ValuesIn(array);
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const ValueArray50& other);
+
+ const T1 v1_;
+ const T2 v2_;
+ const T3 v3_;
+ const T4 v4_;
+ const T5 v5_;
+ const T6 v6_;
+ const T7 v7_;
+ const T8 v8_;
+ const T9 v9_;
+ const T10 v10_;
+ const T11 v11_;
+ const T12 v12_;
+ const T13 v13_;
+ const T14 v14_;
+ const T15 v15_;
+ const T16 v16_;
+ const T17 v17_;
+ const T18 v18_;
+ const T19 v19_;
+ const T20 v20_;
+ const T21 v21_;
+ const T22 v22_;
+ const T23 v23_;
+ const T24 v24_;
+ const T25 v25_;
+ const T26 v26_;
+ const T27 v27_;
+ const T28 v28_;
+ const T29 v29_;
+ const T30 v30_;
+ const T31 v31_;
+ const T32 v32_;
+ const T33 v33_;
+ const T34 v34_;
+ const T35 v35_;
+ const T36 v36_;
+ const T37 v37_;
+ const T38 v38_;
+ const T39 v39_;
+ const T40 v40_;
+ const T41 v41_;
+ const T42 v42_;
+ const T43 v43_;
+ const T44 v44_;
+ const T45 v45_;
+ const T46 v46_;
+ const T47 v47_;
+ const T48 v48_;
+ const T49 v49_;
+ const T50 v50_;
+};
+
+# if GTEST_HAS_COMBINE
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// Generates values from the Cartesian product of values produced
+// by the argument generators.
+//
+template <typename T1, typename T2>
+class CartesianProductGenerator2
+ : public ParamGeneratorInterface< ::std::tr1::tuple<T1, T2> > {
+ public:
+ typedef ::std::tr1::tuple<T1, T2> ParamType;
+
+ CartesianProductGenerator2(const ParamGenerator<T1>& g1,
+ const ParamGenerator<T2>& g2)
+ : g1_(g1), g2_(g2) {}
+ virtual ~CartesianProductGenerator2() {}
+
+ virtual ParamIteratorInterface<ParamType>* Begin() const {
+ return new Iterator(this, g1_, g1_.begin(), g2_, g2_.begin());
+ }
+ virtual ParamIteratorInterface<ParamType>* End() const {
+ return new Iterator(this, g1_, g1_.end(), g2_, g2_.end());
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<ParamType> {
+ public:
+ Iterator(const ParamGeneratorInterface<ParamType>* base,
+ const ParamGenerator<T1>& g1,
+ const typename ParamGenerator<T1>::iterator& current1,
+ const ParamGenerator<T2>& g2,
+ const typename ParamGenerator<T2>::iterator& current2)
+ : base_(base),
+ begin1_(g1.begin()), end1_(g1.end()), current1_(current1),
+ begin2_(g2.begin()), end2_(g2.end()), current2_(current2) {
+ ComputeCurrentValue();
+ }
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<ParamType>* BaseGenerator() const {
+ return base_;
+ }
+ // Advance should not be called on beyond-of-range iterators
+ // so no component iterators must be beyond end of range, either.
+ virtual void Advance() {
+ assert(!AtEnd());
+ ++current2_;
+ if (current2_ == end2_) {
+ current2_ = begin2_;
+ ++current1_;
+ }
+ ComputeCurrentValue();
+ }
+ virtual ParamIteratorInterface<ParamType>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const ParamType* Current() const { return ¤t_value_; }
+ virtual bool Equals(const ParamIteratorInterface<ParamType>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const Iterator* typed_other =
+ CheckedDowncastToActualType<const Iterator>(&other);
+ // We must report iterators equal if they both point beyond their
+ // respective ranges. That can happen in a variety of fashions,
+ // so we have to consult AtEnd().
+ return (AtEnd() && typed_other->AtEnd()) ||
+ (
+ current1_ == typed_other->current1_ &&
+ current2_ == typed_other->current2_);
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : base_(other.base_),
+ begin1_(other.begin1_),
+ end1_(other.end1_),
+ current1_(other.current1_),
+ begin2_(other.begin2_),
+ end2_(other.end2_),
+ current2_(other.current2_) {
+ ComputeCurrentValue();
+ }
+
+ void ComputeCurrentValue() {
+ if (!AtEnd())
+ current_value_ = ParamType(*current1_, *current2_);
+ }
+ bool AtEnd() const {
+ // We must report iterator past the end of the range when either of the
+ // component iterators has reached the end of its range.
+ return
+ current1_ == end1_ ||
+ current2_ == end2_;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<ParamType>* const base_;
+ // begin[i]_ and end[i]_ define the i-th range that Iterator traverses.
+ // current[i]_ is the actual traversing iterator.
+ const typename ParamGenerator<T1>::iterator begin1_;
+ const typename ParamGenerator<T1>::iterator end1_;
+ typename ParamGenerator<T1>::iterator current1_;
+ const typename ParamGenerator<T2>::iterator begin2_;
+ const typename ParamGenerator<T2>::iterator end2_;
+ typename ParamGenerator<T2>::iterator current2_;
+ ParamType current_value_;
+ }; // class CartesianProductGenerator2::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductGenerator2& other);
+
+ const ParamGenerator<T1> g1_;
+ const ParamGenerator<T2> g2_;
+}; // class CartesianProductGenerator2
+
+
+template <typename T1, typename T2, typename T3>
+class CartesianProductGenerator3
+ : public ParamGeneratorInterface< ::std::tr1::tuple<T1, T2, T3> > {
+ public:
+ typedef ::std::tr1::tuple<T1, T2, T3> ParamType;
+
+ CartesianProductGenerator3(const ParamGenerator<T1>& g1,
+ const ParamGenerator<T2>& g2, const ParamGenerator<T3>& g3)
+ : g1_(g1), g2_(g2), g3_(g3) {}
+ virtual ~CartesianProductGenerator3() {}
+
+ virtual ParamIteratorInterface<ParamType>* Begin() const {
+ return new Iterator(this, g1_, g1_.begin(), g2_, g2_.begin(), g3_,
+ g3_.begin());
+ }
+ virtual ParamIteratorInterface<ParamType>* End() const {
+ return new Iterator(this, g1_, g1_.end(), g2_, g2_.end(), g3_, g3_.end());
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<ParamType> {
+ public:
+ Iterator(const ParamGeneratorInterface<ParamType>* base,
+ const ParamGenerator<T1>& g1,
+ const typename ParamGenerator<T1>::iterator& current1,
+ const ParamGenerator<T2>& g2,
+ const typename ParamGenerator<T2>::iterator& current2,
+ const ParamGenerator<T3>& g3,
+ const typename ParamGenerator<T3>::iterator& current3)
+ : base_(base),
+ begin1_(g1.begin()), end1_(g1.end()), current1_(current1),
+ begin2_(g2.begin()), end2_(g2.end()), current2_(current2),
+ begin3_(g3.begin()), end3_(g3.end()), current3_(current3) {
+ ComputeCurrentValue();
+ }
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<ParamType>* BaseGenerator() const {
+ return base_;
+ }
+ // Advance should not be called on beyond-of-range iterators
+ // so no component iterators must be beyond end of range, either.
+ virtual void Advance() {
+ assert(!AtEnd());
+ ++current3_;
+ if (current3_ == end3_) {
+ current3_ = begin3_;
+ ++current2_;
+ }
+ if (current2_ == end2_) {
+ current2_ = begin2_;
+ ++current1_;
+ }
+ ComputeCurrentValue();
+ }
+ virtual ParamIteratorInterface<ParamType>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const ParamType* Current() const { return ¤t_value_; }
+ virtual bool Equals(const ParamIteratorInterface<ParamType>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const Iterator* typed_other =
+ CheckedDowncastToActualType<const Iterator>(&other);
+ // We must report iterators equal if they both point beyond their
+ // respective ranges. That can happen in a variety of fashions,
+ // so we have to consult AtEnd().
+ return (AtEnd() && typed_other->AtEnd()) ||
+ (
+ current1_ == typed_other->current1_ &&
+ current2_ == typed_other->current2_ &&
+ current3_ == typed_other->current3_);
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : base_(other.base_),
+ begin1_(other.begin1_),
+ end1_(other.end1_),
+ current1_(other.current1_),
+ begin2_(other.begin2_),
+ end2_(other.end2_),
+ current2_(other.current2_),
+ begin3_(other.begin3_),
+ end3_(other.end3_),
+ current3_(other.current3_) {
+ ComputeCurrentValue();
+ }
+
+ void ComputeCurrentValue() {
+ if (!AtEnd())
+ current_value_ = ParamType(*current1_, *current2_, *current3_);
+ }
+ bool AtEnd() const {
+ // We must report iterator past the end of the range when either of the
+ // component iterators has reached the end of its range.
+ return
+ current1_ == end1_ ||
+ current2_ == end2_ ||
+ current3_ == end3_;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<ParamType>* const base_;
+ // begin[i]_ and end[i]_ define the i-th range that Iterator traverses.
+ // current[i]_ is the actual traversing iterator.
+ const typename ParamGenerator<T1>::iterator begin1_;
+ const typename ParamGenerator<T1>::iterator end1_;
+ typename ParamGenerator<T1>::iterator current1_;
+ const typename ParamGenerator<T2>::iterator begin2_;
+ const typename ParamGenerator<T2>::iterator end2_;
+ typename ParamGenerator<T2>::iterator current2_;
+ const typename ParamGenerator<T3>::iterator begin3_;
+ const typename ParamGenerator<T3>::iterator end3_;
+ typename ParamGenerator<T3>::iterator current3_;
+ ParamType current_value_;
+ }; // class CartesianProductGenerator3::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductGenerator3& other);
+
+ const ParamGenerator<T1> g1_;
+ const ParamGenerator<T2> g2_;
+ const ParamGenerator<T3> g3_;
+}; // class CartesianProductGenerator3
+
+
+template <typename T1, typename T2, typename T3, typename T4>
+class CartesianProductGenerator4
+ : public ParamGeneratorInterface< ::std::tr1::tuple<T1, T2, T3, T4> > {
+ public:
+ typedef ::std::tr1::tuple<T1, T2, T3, T4> ParamType;
+
+ CartesianProductGenerator4(const ParamGenerator<T1>& g1,
+ const ParamGenerator<T2>& g2, const ParamGenerator<T3>& g3,
+ const ParamGenerator<T4>& g4)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4) {}
+ virtual ~CartesianProductGenerator4() {}
+
+ virtual ParamIteratorInterface<ParamType>* Begin() const {
+ return new Iterator(this, g1_, g1_.begin(), g2_, g2_.begin(), g3_,
+ g3_.begin(), g4_, g4_.begin());
+ }
+ virtual ParamIteratorInterface<ParamType>* End() const {
+ return new Iterator(this, g1_, g1_.end(), g2_, g2_.end(), g3_, g3_.end(),
+ g4_, g4_.end());
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<ParamType> {
+ public:
+ Iterator(const ParamGeneratorInterface<ParamType>* base,
+ const ParamGenerator<T1>& g1,
+ const typename ParamGenerator<T1>::iterator& current1,
+ const ParamGenerator<T2>& g2,
+ const typename ParamGenerator<T2>::iterator& current2,
+ const ParamGenerator<T3>& g3,
+ const typename ParamGenerator<T3>::iterator& current3,
+ const ParamGenerator<T4>& g4,
+ const typename ParamGenerator<T4>::iterator& current4)
+ : base_(base),
+ begin1_(g1.begin()), end1_(g1.end()), current1_(current1),
+ begin2_(g2.begin()), end2_(g2.end()), current2_(current2),
+ begin3_(g3.begin()), end3_(g3.end()), current3_(current3),
+ begin4_(g4.begin()), end4_(g4.end()), current4_(current4) {
+ ComputeCurrentValue();
+ }
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<ParamType>* BaseGenerator() const {
+ return base_;
+ }
+ // Advance should not be called on beyond-of-range iterators
+ // so no component iterators must be beyond end of range, either.
+ virtual void Advance() {
+ assert(!AtEnd());
+ ++current4_;
+ if (current4_ == end4_) {
+ current4_ = begin4_;
+ ++current3_;
+ }
+ if (current3_ == end3_) {
+ current3_ = begin3_;
+ ++current2_;
+ }
+ if (current2_ == end2_) {
+ current2_ = begin2_;
+ ++current1_;
+ }
+ ComputeCurrentValue();
+ }
+ virtual ParamIteratorInterface<ParamType>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const ParamType* Current() const { return ¤t_value_; }
+ virtual bool Equals(const ParamIteratorInterface<ParamType>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const Iterator* typed_other =
+ CheckedDowncastToActualType<const Iterator>(&other);
+ // We must report iterators equal if they both point beyond their
+ // respective ranges. That can happen in a variety of fashions,
+ // so we have to consult AtEnd().
+ return (AtEnd() && typed_other->AtEnd()) ||
+ (
+ current1_ == typed_other->current1_ &&
+ current2_ == typed_other->current2_ &&
+ current3_ == typed_other->current3_ &&
+ current4_ == typed_other->current4_);
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : base_(other.base_),
+ begin1_(other.begin1_),
+ end1_(other.end1_),
+ current1_(other.current1_),
+ begin2_(other.begin2_),
+ end2_(other.end2_),
+ current2_(other.current2_),
+ begin3_(other.begin3_),
+ end3_(other.end3_),
+ current3_(other.current3_),
+ begin4_(other.begin4_),
+ end4_(other.end4_),
+ current4_(other.current4_) {
+ ComputeCurrentValue();
+ }
+
+ void ComputeCurrentValue() {
+ if (!AtEnd())
+ current_value_ = ParamType(*current1_, *current2_, *current3_,
+ *current4_);
+ }
+ bool AtEnd() const {
+ // We must report iterator past the end of the range when either of the
+ // component iterators has reached the end of its range.
+ return
+ current1_ == end1_ ||
+ current2_ == end2_ ||
+ current3_ == end3_ ||
+ current4_ == end4_;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<ParamType>* const base_;
+ // begin[i]_ and end[i]_ define the i-th range that Iterator traverses.
+ // current[i]_ is the actual traversing iterator.
+ const typename ParamGenerator<T1>::iterator begin1_;
+ const typename ParamGenerator<T1>::iterator end1_;
+ typename ParamGenerator<T1>::iterator current1_;
+ const typename ParamGenerator<T2>::iterator begin2_;
+ const typename ParamGenerator<T2>::iterator end2_;
+ typename ParamGenerator<T2>::iterator current2_;
+ const typename ParamGenerator<T3>::iterator begin3_;
+ const typename ParamGenerator<T3>::iterator end3_;
+ typename ParamGenerator<T3>::iterator current3_;
+ const typename ParamGenerator<T4>::iterator begin4_;
+ const typename ParamGenerator<T4>::iterator end4_;
+ typename ParamGenerator<T4>::iterator current4_;
+ ParamType current_value_;
+ }; // class CartesianProductGenerator4::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductGenerator4& other);
+
+ const ParamGenerator<T1> g1_;
+ const ParamGenerator<T2> g2_;
+ const ParamGenerator<T3> g3_;
+ const ParamGenerator<T4> g4_;
+}; // class CartesianProductGenerator4
+
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5>
+class CartesianProductGenerator5
+ : public ParamGeneratorInterface< ::std::tr1::tuple<T1, T2, T3, T4, T5> > {
+ public:
+ typedef ::std::tr1::tuple<T1, T2, T3, T4, T5> ParamType;
+
+ CartesianProductGenerator5(const ParamGenerator<T1>& g1,
+ const ParamGenerator<T2>& g2, const ParamGenerator<T3>& g3,
+ const ParamGenerator<T4>& g4, const ParamGenerator<T5>& g5)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5) {}
+ virtual ~CartesianProductGenerator5() {}
+
+ virtual ParamIteratorInterface<ParamType>* Begin() const {
+ return new Iterator(this, g1_, g1_.begin(), g2_, g2_.begin(), g3_,
+ g3_.begin(), g4_, g4_.begin(), g5_, g5_.begin());
+ }
+ virtual ParamIteratorInterface<ParamType>* End() const {
+ return new Iterator(this, g1_, g1_.end(), g2_, g2_.end(), g3_, g3_.end(),
+ g4_, g4_.end(), g5_, g5_.end());
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<ParamType> {
+ public:
+ Iterator(const ParamGeneratorInterface<ParamType>* base,
+ const ParamGenerator<T1>& g1,
+ const typename ParamGenerator<T1>::iterator& current1,
+ const ParamGenerator<T2>& g2,
+ const typename ParamGenerator<T2>::iterator& current2,
+ const ParamGenerator<T3>& g3,
+ const typename ParamGenerator<T3>::iterator& current3,
+ const ParamGenerator<T4>& g4,
+ const typename ParamGenerator<T4>::iterator& current4,
+ const ParamGenerator<T5>& g5,
+ const typename ParamGenerator<T5>::iterator& current5)
+ : base_(base),
+ begin1_(g1.begin()), end1_(g1.end()), current1_(current1),
+ begin2_(g2.begin()), end2_(g2.end()), current2_(current2),
+ begin3_(g3.begin()), end3_(g3.end()), current3_(current3),
+ begin4_(g4.begin()), end4_(g4.end()), current4_(current4),
+ begin5_(g5.begin()), end5_(g5.end()), current5_(current5) {
+ ComputeCurrentValue();
+ }
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<ParamType>* BaseGenerator() const {
+ return base_;
+ }
+ // Advance should not be called on beyond-of-range iterators
+ // so no component iterators must be beyond end of range, either.
+ virtual void Advance() {
+ assert(!AtEnd());
+ ++current5_;
+ if (current5_ == end5_) {
+ current5_ = begin5_;
+ ++current4_;
+ }
+ if (current4_ == end4_) {
+ current4_ = begin4_;
+ ++current3_;
+ }
+ if (current3_ == end3_) {
+ current3_ = begin3_;
+ ++current2_;
+ }
+ if (current2_ == end2_) {
+ current2_ = begin2_;
+ ++current1_;
+ }
+ ComputeCurrentValue();
+ }
+ virtual ParamIteratorInterface<ParamType>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const ParamType* Current() const { return ¤t_value_; }
+ virtual bool Equals(const ParamIteratorInterface<ParamType>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const Iterator* typed_other =
+ CheckedDowncastToActualType<const Iterator>(&other);
+ // We must report iterators equal if they both point beyond their
+ // respective ranges. That can happen in a variety of fashions,
+ // so we have to consult AtEnd().
+ return (AtEnd() && typed_other->AtEnd()) ||
+ (
+ current1_ == typed_other->current1_ &&
+ current2_ == typed_other->current2_ &&
+ current3_ == typed_other->current3_ &&
+ current4_ == typed_other->current4_ &&
+ current5_ == typed_other->current5_);
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : base_(other.base_),
+ begin1_(other.begin1_),
+ end1_(other.end1_),
+ current1_(other.current1_),
+ begin2_(other.begin2_),
+ end2_(other.end2_),
+ current2_(other.current2_),
+ begin3_(other.begin3_),
+ end3_(other.end3_),
+ current3_(other.current3_),
+ begin4_(other.begin4_),
+ end4_(other.end4_),
+ current4_(other.current4_),
+ begin5_(other.begin5_),
+ end5_(other.end5_),
+ current5_(other.current5_) {
+ ComputeCurrentValue();
+ }
+
+ void ComputeCurrentValue() {
+ if (!AtEnd())
+ current_value_ = ParamType(*current1_, *current2_, *current3_,
+ *current4_, *current5_);
+ }
+ bool AtEnd() const {
+ // We must report iterator past the end of the range when either of the
+ // component iterators has reached the end of its range.
+ return
+ current1_ == end1_ ||
+ current2_ == end2_ ||
+ current3_ == end3_ ||
+ current4_ == end4_ ||
+ current5_ == end5_;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<ParamType>* const base_;
+ // begin[i]_ and end[i]_ define the i-th range that Iterator traverses.
+ // current[i]_ is the actual traversing iterator.
+ const typename ParamGenerator<T1>::iterator begin1_;
+ const typename ParamGenerator<T1>::iterator end1_;
+ typename ParamGenerator<T1>::iterator current1_;
+ const typename ParamGenerator<T2>::iterator begin2_;
+ const typename ParamGenerator<T2>::iterator end2_;
+ typename ParamGenerator<T2>::iterator current2_;
+ const typename ParamGenerator<T3>::iterator begin3_;
+ const typename ParamGenerator<T3>::iterator end3_;
+ typename ParamGenerator<T3>::iterator current3_;
+ const typename ParamGenerator<T4>::iterator begin4_;
+ const typename ParamGenerator<T4>::iterator end4_;
+ typename ParamGenerator<T4>::iterator current4_;
+ const typename ParamGenerator<T5>::iterator begin5_;
+ const typename ParamGenerator<T5>::iterator end5_;
+ typename ParamGenerator<T5>::iterator current5_;
+ ParamType current_value_;
+ }; // class CartesianProductGenerator5::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductGenerator5& other);
+
+ const ParamGenerator<T1> g1_;
+ const ParamGenerator<T2> g2_;
+ const ParamGenerator<T3> g3_;
+ const ParamGenerator<T4> g4_;
+ const ParamGenerator<T5> g5_;
+}; // class CartesianProductGenerator5
+
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6>
+class CartesianProductGenerator6
+ : public ParamGeneratorInterface< ::std::tr1::tuple<T1, T2, T3, T4, T5,
+ T6> > {
+ public:
+ typedef ::std::tr1::tuple<T1, T2, T3, T4, T5, T6> ParamType;
+
+ CartesianProductGenerator6(const ParamGenerator<T1>& g1,
+ const ParamGenerator<T2>& g2, const ParamGenerator<T3>& g3,
+ const ParamGenerator<T4>& g4, const ParamGenerator<T5>& g5,
+ const ParamGenerator<T6>& g6)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6) {}
+ virtual ~CartesianProductGenerator6() {}
+
+ virtual ParamIteratorInterface<ParamType>* Begin() const {
+ return new Iterator(this, g1_, g1_.begin(), g2_, g2_.begin(), g3_,
+ g3_.begin(), g4_, g4_.begin(), g5_, g5_.begin(), g6_, g6_.begin());
+ }
+ virtual ParamIteratorInterface<ParamType>* End() const {
+ return new Iterator(this, g1_, g1_.end(), g2_, g2_.end(), g3_, g3_.end(),
+ g4_, g4_.end(), g5_, g5_.end(), g6_, g6_.end());
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<ParamType> {
+ public:
+ Iterator(const ParamGeneratorInterface<ParamType>* base,
+ const ParamGenerator<T1>& g1,
+ const typename ParamGenerator<T1>::iterator& current1,
+ const ParamGenerator<T2>& g2,
+ const typename ParamGenerator<T2>::iterator& current2,
+ const ParamGenerator<T3>& g3,
+ const typename ParamGenerator<T3>::iterator& current3,
+ const ParamGenerator<T4>& g4,
+ const typename ParamGenerator<T4>::iterator& current4,
+ const ParamGenerator<T5>& g5,
+ const typename ParamGenerator<T5>::iterator& current5,
+ const ParamGenerator<T6>& g6,
+ const typename ParamGenerator<T6>::iterator& current6)
+ : base_(base),
+ begin1_(g1.begin()), end1_(g1.end()), current1_(current1),
+ begin2_(g2.begin()), end2_(g2.end()), current2_(current2),
+ begin3_(g3.begin()), end3_(g3.end()), current3_(current3),
+ begin4_(g4.begin()), end4_(g4.end()), current4_(current4),
+ begin5_(g5.begin()), end5_(g5.end()), current5_(current5),
+ begin6_(g6.begin()), end6_(g6.end()), current6_(current6) {
+ ComputeCurrentValue();
+ }
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<ParamType>* BaseGenerator() const {
+ return base_;
+ }
+ // Advance should not be called on beyond-of-range iterators
+ // so no component iterators must be beyond end of range, either.
+ virtual void Advance() {
+ assert(!AtEnd());
+ ++current6_;
+ if (current6_ == end6_) {
+ current6_ = begin6_;
+ ++current5_;
+ }
+ if (current5_ == end5_) {
+ current5_ = begin5_;
+ ++current4_;
+ }
+ if (current4_ == end4_) {
+ current4_ = begin4_;
+ ++current3_;
+ }
+ if (current3_ == end3_) {
+ current3_ = begin3_;
+ ++current2_;
+ }
+ if (current2_ == end2_) {
+ current2_ = begin2_;
+ ++current1_;
+ }
+ ComputeCurrentValue();
+ }
+ virtual ParamIteratorInterface<ParamType>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const ParamType* Current() const { return ¤t_value_; }
+ virtual bool Equals(const ParamIteratorInterface<ParamType>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const Iterator* typed_other =
+ CheckedDowncastToActualType<const Iterator>(&other);
+ // We must report iterators equal if they both point beyond their
+ // respective ranges. That can happen in a variety of fashions,
+ // so we have to consult AtEnd().
+ return (AtEnd() && typed_other->AtEnd()) ||
+ (
+ current1_ == typed_other->current1_ &&
+ current2_ == typed_other->current2_ &&
+ current3_ == typed_other->current3_ &&
+ current4_ == typed_other->current4_ &&
+ current5_ == typed_other->current5_ &&
+ current6_ == typed_other->current6_);
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : base_(other.base_),
+ begin1_(other.begin1_),
+ end1_(other.end1_),
+ current1_(other.current1_),
+ begin2_(other.begin2_),
+ end2_(other.end2_),
+ current2_(other.current2_),
+ begin3_(other.begin3_),
+ end3_(other.end3_),
+ current3_(other.current3_),
+ begin4_(other.begin4_),
+ end4_(other.end4_),
+ current4_(other.current4_),
+ begin5_(other.begin5_),
+ end5_(other.end5_),
+ current5_(other.current5_),
+ begin6_(other.begin6_),
+ end6_(other.end6_),
+ current6_(other.current6_) {
+ ComputeCurrentValue();
+ }
+
+ void ComputeCurrentValue() {
+ if (!AtEnd())
+ current_value_ = ParamType(*current1_, *current2_, *current3_,
+ *current4_, *current5_, *current6_);
+ }
+ bool AtEnd() const {
+ // We must report iterator past the end of the range when either of the
+ // component iterators has reached the end of its range.
+ return
+ current1_ == end1_ ||
+ current2_ == end2_ ||
+ current3_ == end3_ ||
+ current4_ == end4_ ||
+ current5_ == end5_ ||
+ current6_ == end6_;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<ParamType>* const base_;
+ // begin[i]_ and end[i]_ define the i-th range that Iterator traverses.
+ // current[i]_ is the actual traversing iterator.
+ const typename ParamGenerator<T1>::iterator begin1_;
+ const typename ParamGenerator<T1>::iterator end1_;
+ typename ParamGenerator<T1>::iterator current1_;
+ const typename ParamGenerator<T2>::iterator begin2_;
+ const typename ParamGenerator<T2>::iterator end2_;
+ typename ParamGenerator<T2>::iterator current2_;
+ const typename ParamGenerator<T3>::iterator begin3_;
+ const typename ParamGenerator<T3>::iterator end3_;
+ typename ParamGenerator<T3>::iterator current3_;
+ const typename ParamGenerator<T4>::iterator begin4_;
+ const typename ParamGenerator<T4>::iterator end4_;
+ typename ParamGenerator<T4>::iterator current4_;
+ const typename ParamGenerator<T5>::iterator begin5_;
+ const typename ParamGenerator<T5>::iterator end5_;
+ typename ParamGenerator<T5>::iterator current5_;
+ const typename ParamGenerator<T6>::iterator begin6_;
+ const typename ParamGenerator<T6>::iterator end6_;
+ typename ParamGenerator<T6>::iterator current6_;
+ ParamType current_value_;
+ }; // class CartesianProductGenerator6::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductGenerator6& other);
+
+ const ParamGenerator<T1> g1_;
+ const ParamGenerator<T2> g2_;
+ const ParamGenerator<T3> g3_;
+ const ParamGenerator<T4> g4_;
+ const ParamGenerator<T5> g5_;
+ const ParamGenerator<T6> g6_;
+}; // class CartesianProductGenerator6
+
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7>
+class CartesianProductGenerator7
+ : public ParamGeneratorInterface< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6,
+ T7> > {
+ public:
+ typedef ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7> ParamType;
+
+ CartesianProductGenerator7(const ParamGenerator<T1>& g1,
+ const ParamGenerator<T2>& g2, const ParamGenerator<T3>& g3,
+ const ParamGenerator<T4>& g4, const ParamGenerator<T5>& g5,
+ const ParamGenerator<T6>& g6, const ParamGenerator<T7>& g7)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6), g7_(g7) {}
+ virtual ~CartesianProductGenerator7() {}
+
+ virtual ParamIteratorInterface<ParamType>* Begin() const {
+ return new Iterator(this, g1_, g1_.begin(), g2_, g2_.begin(), g3_,
+ g3_.begin(), g4_, g4_.begin(), g5_, g5_.begin(), g6_, g6_.begin(), g7_,
+ g7_.begin());
+ }
+ virtual ParamIteratorInterface<ParamType>* End() const {
+ return new Iterator(this, g1_, g1_.end(), g2_, g2_.end(), g3_, g3_.end(),
+ g4_, g4_.end(), g5_, g5_.end(), g6_, g6_.end(), g7_, g7_.end());
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<ParamType> {
+ public:
+ Iterator(const ParamGeneratorInterface<ParamType>* base,
+ const ParamGenerator<T1>& g1,
+ const typename ParamGenerator<T1>::iterator& current1,
+ const ParamGenerator<T2>& g2,
+ const typename ParamGenerator<T2>::iterator& current2,
+ const ParamGenerator<T3>& g3,
+ const typename ParamGenerator<T3>::iterator& current3,
+ const ParamGenerator<T4>& g4,
+ const typename ParamGenerator<T4>::iterator& current4,
+ const ParamGenerator<T5>& g5,
+ const typename ParamGenerator<T5>::iterator& current5,
+ const ParamGenerator<T6>& g6,
+ const typename ParamGenerator<T6>::iterator& current6,
+ const ParamGenerator<T7>& g7,
+ const typename ParamGenerator<T7>::iterator& current7)
+ : base_(base),
+ begin1_(g1.begin()), end1_(g1.end()), current1_(current1),
+ begin2_(g2.begin()), end2_(g2.end()), current2_(current2),
+ begin3_(g3.begin()), end3_(g3.end()), current3_(current3),
+ begin4_(g4.begin()), end4_(g4.end()), current4_(current4),
+ begin5_(g5.begin()), end5_(g5.end()), current5_(current5),
+ begin6_(g6.begin()), end6_(g6.end()), current6_(current6),
+ begin7_(g7.begin()), end7_(g7.end()), current7_(current7) {
+ ComputeCurrentValue();
+ }
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<ParamType>* BaseGenerator() const {
+ return base_;
+ }
+ // Advance should not be called on beyond-of-range iterators
+ // so no component iterators must be beyond end of range, either.
+ virtual void Advance() {
+ assert(!AtEnd());
+ ++current7_;
+ if (current7_ == end7_) {
+ current7_ = begin7_;
+ ++current6_;
+ }
+ if (current6_ == end6_) {
+ current6_ = begin6_;
+ ++current5_;
+ }
+ if (current5_ == end5_) {
+ current5_ = begin5_;
+ ++current4_;
+ }
+ if (current4_ == end4_) {
+ current4_ = begin4_;
+ ++current3_;
+ }
+ if (current3_ == end3_) {
+ current3_ = begin3_;
+ ++current2_;
+ }
+ if (current2_ == end2_) {
+ current2_ = begin2_;
+ ++current1_;
+ }
+ ComputeCurrentValue();
+ }
+ virtual ParamIteratorInterface<ParamType>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const ParamType* Current() const { return ¤t_value_; }
+ virtual bool Equals(const ParamIteratorInterface<ParamType>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const Iterator* typed_other =
+ CheckedDowncastToActualType<const Iterator>(&other);
+ // We must report iterators equal if they both point beyond their
+ // respective ranges. That can happen in a variety of fashions,
+ // so we have to consult AtEnd().
+ return (AtEnd() && typed_other->AtEnd()) ||
+ (
+ current1_ == typed_other->current1_ &&
+ current2_ == typed_other->current2_ &&
+ current3_ == typed_other->current3_ &&
+ current4_ == typed_other->current4_ &&
+ current5_ == typed_other->current5_ &&
+ current6_ == typed_other->current6_ &&
+ current7_ == typed_other->current7_);
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : base_(other.base_),
+ begin1_(other.begin1_),
+ end1_(other.end1_),
+ current1_(other.current1_),
+ begin2_(other.begin2_),
+ end2_(other.end2_),
+ current2_(other.current2_),
+ begin3_(other.begin3_),
+ end3_(other.end3_),
+ current3_(other.current3_),
+ begin4_(other.begin4_),
+ end4_(other.end4_),
+ current4_(other.current4_),
+ begin5_(other.begin5_),
+ end5_(other.end5_),
+ current5_(other.current5_),
+ begin6_(other.begin6_),
+ end6_(other.end6_),
+ current6_(other.current6_),
+ begin7_(other.begin7_),
+ end7_(other.end7_),
+ current7_(other.current7_) {
+ ComputeCurrentValue();
+ }
+
+ void ComputeCurrentValue() {
+ if (!AtEnd())
+ current_value_ = ParamType(*current1_, *current2_, *current3_,
+ *current4_, *current5_, *current6_, *current7_);
+ }
+ bool AtEnd() const {
+ // We must report iterator past the end of the range when either of the
+ // component iterators has reached the end of its range.
+ return
+ current1_ == end1_ ||
+ current2_ == end2_ ||
+ current3_ == end3_ ||
+ current4_ == end4_ ||
+ current5_ == end5_ ||
+ current6_ == end6_ ||
+ current7_ == end7_;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<ParamType>* const base_;
+ // begin[i]_ and end[i]_ define the i-th range that Iterator traverses.
+ // current[i]_ is the actual traversing iterator.
+ const typename ParamGenerator<T1>::iterator begin1_;
+ const typename ParamGenerator<T1>::iterator end1_;
+ typename ParamGenerator<T1>::iterator current1_;
+ const typename ParamGenerator<T2>::iterator begin2_;
+ const typename ParamGenerator<T2>::iterator end2_;
+ typename ParamGenerator<T2>::iterator current2_;
+ const typename ParamGenerator<T3>::iterator begin3_;
+ const typename ParamGenerator<T3>::iterator end3_;
+ typename ParamGenerator<T3>::iterator current3_;
+ const typename ParamGenerator<T4>::iterator begin4_;
+ const typename ParamGenerator<T4>::iterator end4_;
+ typename ParamGenerator<T4>::iterator current4_;
+ const typename ParamGenerator<T5>::iterator begin5_;
+ const typename ParamGenerator<T5>::iterator end5_;
+ typename ParamGenerator<T5>::iterator current5_;
+ const typename ParamGenerator<T6>::iterator begin6_;
+ const typename ParamGenerator<T6>::iterator end6_;
+ typename ParamGenerator<T6>::iterator current6_;
+ const typename ParamGenerator<T7>::iterator begin7_;
+ const typename ParamGenerator<T7>::iterator end7_;
+ typename ParamGenerator<T7>::iterator current7_;
+ ParamType current_value_;
+ }; // class CartesianProductGenerator7::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductGenerator7& other);
+
+ const ParamGenerator<T1> g1_;
+ const ParamGenerator<T2> g2_;
+ const ParamGenerator<T3> g3_;
+ const ParamGenerator<T4> g4_;
+ const ParamGenerator<T5> g5_;
+ const ParamGenerator<T6> g6_;
+ const ParamGenerator<T7> g7_;
+}; // class CartesianProductGenerator7
+
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8>
+class CartesianProductGenerator8
+ : public ParamGeneratorInterface< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6,
+ T7, T8> > {
+ public:
+ typedef ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8> ParamType;
+
+ CartesianProductGenerator8(const ParamGenerator<T1>& g1,
+ const ParamGenerator<T2>& g2, const ParamGenerator<T3>& g3,
+ const ParamGenerator<T4>& g4, const ParamGenerator<T5>& g5,
+ const ParamGenerator<T6>& g6, const ParamGenerator<T7>& g7,
+ const ParamGenerator<T8>& g8)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6), g7_(g7),
+ g8_(g8) {}
+ virtual ~CartesianProductGenerator8() {}
+
+ virtual ParamIteratorInterface<ParamType>* Begin() const {
+ return new Iterator(this, g1_, g1_.begin(), g2_, g2_.begin(), g3_,
+ g3_.begin(), g4_, g4_.begin(), g5_, g5_.begin(), g6_, g6_.begin(), g7_,
+ g7_.begin(), g8_, g8_.begin());
+ }
+ virtual ParamIteratorInterface<ParamType>* End() const {
+ return new Iterator(this, g1_, g1_.end(), g2_, g2_.end(), g3_, g3_.end(),
+ g4_, g4_.end(), g5_, g5_.end(), g6_, g6_.end(), g7_, g7_.end(), g8_,
+ g8_.end());
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<ParamType> {
+ public:
+ Iterator(const ParamGeneratorInterface<ParamType>* base,
+ const ParamGenerator<T1>& g1,
+ const typename ParamGenerator<T1>::iterator& current1,
+ const ParamGenerator<T2>& g2,
+ const typename ParamGenerator<T2>::iterator& current2,
+ const ParamGenerator<T3>& g3,
+ const typename ParamGenerator<T3>::iterator& current3,
+ const ParamGenerator<T4>& g4,
+ const typename ParamGenerator<T4>::iterator& current4,
+ const ParamGenerator<T5>& g5,
+ const typename ParamGenerator<T5>::iterator& current5,
+ const ParamGenerator<T6>& g6,
+ const typename ParamGenerator<T6>::iterator& current6,
+ const ParamGenerator<T7>& g7,
+ const typename ParamGenerator<T7>::iterator& current7,
+ const ParamGenerator<T8>& g8,
+ const typename ParamGenerator<T8>::iterator& current8)
+ : base_(base),
+ begin1_(g1.begin()), end1_(g1.end()), current1_(current1),
+ begin2_(g2.begin()), end2_(g2.end()), current2_(current2),
+ begin3_(g3.begin()), end3_(g3.end()), current3_(current3),
+ begin4_(g4.begin()), end4_(g4.end()), current4_(current4),
+ begin5_(g5.begin()), end5_(g5.end()), current5_(current5),
+ begin6_(g6.begin()), end6_(g6.end()), current6_(current6),
+ begin7_(g7.begin()), end7_(g7.end()), current7_(current7),
+ begin8_(g8.begin()), end8_(g8.end()), current8_(current8) {
+ ComputeCurrentValue();
+ }
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<ParamType>* BaseGenerator() const {
+ return base_;
+ }
+ // Advance should not be called on beyond-of-range iterators
+ // so no component iterators must be beyond end of range, either.
+ virtual void Advance() {
+ assert(!AtEnd());
+ ++current8_;
+ if (current8_ == end8_) {
+ current8_ = begin8_;
+ ++current7_;
+ }
+ if (current7_ == end7_) {
+ current7_ = begin7_;
+ ++current6_;
+ }
+ if (current6_ == end6_) {
+ current6_ = begin6_;
+ ++current5_;
+ }
+ if (current5_ == end5_) {
+ current5_ = begin5_;
+ ++current4_;
+ }
+ if (current4_ == end4_) {
+ current4_ = begin4_;
+ ++current3_;
+ }
+ if (current3_ == end3_) {
+ current3_ = begin3_;
+ ++current2_;
+ }
+ if (current2_ == end2_) {
+ current2_ = begin2_;
+ ++current1_;
+ }
+ ComputeCurrentValue();
+ }
+ virtual ParamIteratorInterface<ParamType>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const ParamType* Current() const { return ¤t_value_; }
+ virtual bool Equals(const ParamIteratorInterface<ParamType>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const Iterator* typed_other =
+ CheckedDowncastToActualType<const Iterator>(&other);
+ // We must report iterators equal if they both point beyond their
+ // respective ranges. That can happen in a variety of fashions,
+ // so we have to consult AtEnd().
+ return (AtEnd() && typed_other->AtEnd()) ||
+ (
+ current1_ == typed_other->current1_ &&
+ current2_ == typed_other->current2_ &&
+ current3_ == typed_other->current3_ &&
+ current4_ == typed_other->current4_ &&
+ current5_ == typed_other->current5_ &&
+ current6_ == typed_other->current6_ &&
+ current7_ == typed_other->current7_ &&
+ current8_ == typed_other->current8_);
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : base_(other.base_),
+ begin1_(other.begin1_),
+ end1_(other.end1_),
+ current1_(other.current1_),
+ begin2_(other.begin2_),
+ end2_(other.end2_),
+ current2_(other.current2_),
+ begin3_(other.begin3_),
+ end3_(other.end3_),
+ current3_(other.current3_),
+ begin4_(other.begin4_),
+ end4_(other.end4_),
+ current4_(other.current4_),
+ begin5_(other.begin5_),
+ end5_(other.end5_),
+ current5_(other.current5_),
+ begin6_(other.begin6_),
+ end6_(other.end6_),
+ current6_(other.current6_),
+ begin7_(other.begin7_),
+ end7_(other.end7_),
+ current7_(other.current7_),
+ begin8_(other.begin8_),
+ end8_(other.end8_),
+ current8_(other.current8_) {
+ ComputeCurrentValue();
+ }
+
+ void ComputeCurrentValue() {
+ if (!AtEnd())
+ current_value_ = ParamType(*current1_, *current2_, *current3_,
+ *current4_, *current5_, *current6_, *current7_, *current8_);
+ }
+ bool AtEnd() const {
+ // We must report iterator past the end of the range when either of the
+ // component iterators has reached the end of its range.
+ return
+ current1_ == end1_ ||
+ current2_ == end2_ ||
+ current3_ == end3_ ||
+ current4_ == end4_ ||
+ current5_ == end5_ ||
+ current6_ == end6_ ||
+ current7_ == end7_ ||
+ current8_ == end8_;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<ParamType>* const base_;
+ // begin[i]_ and end[i]_ define the i-th range that Iterator traverses.
+ // current[i]_ is the actual traversing iterator.
+ const typename ParamGenerator<T1>::iterator begin1_;
+ const typename ParamGenerator<T1>::iterator end1_;
+ typename ParamGenerator<T1>::iterator current1_;
+ const typename ParamGenerator<T2>::iterator begin2_;
+ const typename ParamGenerator<T2>::iterator end2_;
+ typename ParamGenerator<T2>::iterator current2_;
+ const typename ParamGenerator<T3>::iterator begin3_;
+ const typename ParamGenerator<T3>::iterator end3_;
+ typename ParamGenerator<T3>::iterator current3_;
+ const typename ParamGenerator<T4>::iterator begin4_;
+ const typename ParamGenerator<T4>::iterator end4_;
+ typename ParamGenerator<T4>::iterator current4_;
+ const typename ParamGenerator<T5>::iterator begin5_;
+ const typename ParamGenerator<T5>::iterator end5_;
+ typename ParamGenerator<T5>::iterator current5_;
+ const typename ParamGenerator<T6>::iterator begin6_;
+ const typename ParamGenerator<T6>::iterator end6_;
+ typename ParamGenerator<T6>::iterator current6_;
+ const typename ParamGenerator<T7>::iterator begin7_;
+ const typename ParamGenerator<T7>::iterator end7_;
+ typename ParamGenerator<T7>::iterator current7_;
+ const typename ParamGenerator<T8>::iterator begin8_;
+ const typename ParamGenerator<T8>::iterator end8_;
+ typename ParamGenerator<T8>::iterator current8_;
+ ParamType current_value_;
+ }; // class CartesianProductGenerator8::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductGenerator8& other);
+
+ const ParamGenerator<T1> g1_;
+ const ParamGenerator<T2> g2_;
+ const ParamGenerator<T3> g3_;
+ const ParamGenerator<T4> g4_;
+ const ParamGenerator<T5> g5_;
+ const ParamGenerator<T6> g6_;
+ const ParamGenerator<T7> g7_;
+ const ParamGenerator<T8> g8_;
+}; // class CartesianProductGenerator8
+
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9>
+class CartesianProductGenerator9
+ : public ParamGeneratorInterface< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6,
+ T7, T8, T9> > {
+ public:
+ typedef ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8, T9> ParamType;
+
+ CartesianProductGenerator9(const ParamGenerator<T1>& g1,
+ const ParamGenerator<T2>& g2, const ParamGenerator<T3>& g3,
+ const ParamGenerator<T4>& g4, const ParamGenerator<T5>& g5,
+ const ParamGenerator<T6>& g6, const ParamGenerator<T7>& g7,
+ const ParamGenerator<T8>& g8, const ParamGenerator<T9>& g9)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6), g7_(g7), g8_(g8),
+ g9_(g9) {}
+ virtual ~CartesianProductGenerator9() {}
+
+ virtual ParamIteratorInterface<ParamType>* Begin() const {
+ return new Iterator(this, g1_, g1_.begin(), g2_, g2_.begin(), g3_,
+ g3_.begin(), g4_, g4_.begin(), g5_, g5_.begin(), g6_, g6_.begin(), g7_,
+ g7_.begin(), g8_, g8_.begin(), g9_, g9_.begin());
+ }
+ virtual ParamIteratorInterface<ParamType>* End() const {
+ return new Iterator(this, g1_, g1_.end(), g2_, g2_.end(), g3_, g3_.end(),
+ g4_, g4_.end(), g5_, g5_.end(), g6_, g6_.end(), g7_, g7_.end(), g8_,
+ g8_.end(), g9_, g9_.end());
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<ParamType> {
+ public:
+ Iterator(const ParamGeneratorInterface<ParamType>* base,
+ const ParamGenerator<T1>& g1,
+ const typename ParamGenerator<T1>::iterator& current1,
+ const ParamGenerator<T2>& g2,
+ const typename ParamGenerator<T2>::iterator& current2,
+ const ParamGenerator<T3>& g3,
+ const typename ParamGenerator<T3>::iterator& current3,
+ const ParamGenerator<T4>& g4,
+ const typename ParamGenerator<T4>::iterator& current4,
+ const ParamGenerator<T5>& g5,
+ const typename ParamGenerator<T5>::iterator& current5,
+ const ParamGenerator<T6>& g6,
+ const typename ParamGenerator<T6>::iterator& current6,
+ const ParamGenerator<T7>& g7,
+ const typename ParamGenerator<T7>::iterator& current7,
+ const ParamGenerator<T8>& g8,
+ const typename ParamGenerator<T8>::iterator& current8,
+ const ParamGenerator<T9>& g9,
+ const typename ParamGenerator<T9>::iterator& current9)
+ : base_(base),
+ begin1_(g1.begin()), end1_(g1.end()), current1_(current1),
+ begin2_(g2.begin()), end2_(g2.end()), current2_(current2),
+ begin3_(g3.begin()), end3_(g3.end()), current3_(current3),
+ begin4_(g4.begin()), end4_(g4.end()), current4_(current4),
+ begin5_(g5.begin()), end5_(g5.end()), current5_(current5),
+ begin6_(g6.begin()), end6_(g6.end()), current6_(current6),
+ begin7_(g7.begin()), end7_(g7.end()), current7_(current7),
+ begin8_(g8.begin()), end8_(g8.end()), current8_(current8),
+ begin9_(g9.begin()), end9_(g9.end()), current9_(current9) {
+ ComputeCurrentValue();
+ }
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<ParamType>* BaseGenerator() const {
+ return base_;
+ }
+ // Advance should not be called on beyond-of-range iterators
+ // so no component iterators must be beyond end of range, either.
+ virtual void Advance() {
+ assert(!AtEnd());
+ ++current9_;
+ if (current9_ == end9_) {
+ current9_ = begin9_;
+ ++current8_;
+ }
+ if (current8_ == end8_) {
+ current8_ = begin8_;
+ ++current7_;
+ }
+ if (current7_ == end7_) {
+ current7_ = begin7_;
+ ++current6_;
+ }
+ if (current6_ == end6_) {
+ current6_ = begin6_;
+ ++current5_;
+ }
+ if (current5_ == end5_) {
+ current5_ = begin5_;
+ ++current4_;
+ }
+ if (current4_ == end4_) {
+ current4_ = begin4_;
+ ++current3_;
+ }
+ if (current3_ == end3_) {
+ current3_ = begin3_;
+ ++current2_;
+ }
+ if (current2_ == end2_) {
+ current2_ = begin2_;
+ ++current1_;
+ }
+ ComputeCurrentValue();
+ }
+ virtual ParamIteratorInterface<ParamType>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const ParamType* Current() const { return ¤t_value_; }
+ virtual bool Equals(const ParamIteratorInterface<ParamType>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const Iterator* typed_other =
+ CheckedDowncastToActualType<const Iterator>(&other);
+ // We must report iterators equal if they both point beyond their
+ // respective ranges. That can happen in a variety of fashions,
+ // so we have to consult AtEnd().
+ return (AtEnd() && typed_other->AtEnd()) ||
+ (
+ current1_ == typed_other->current1_ &&
+ current2_ == typed_other->current2_ &&
+ current3_ == typed_other->current3_ &&
+ current4_ == typed_other->current4_ &&
+ current5_ == typed_other->current5_ &&
+ current6_ == typed_other->current6_ &&
+ current7_ == typed_other->current7_ &&
+ current8_ == typed_other->current8_ &&
+ current9_ == typed_other->current9_);
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : base_(other.base_),
+ begin1_(other.begin1_),
+ end1_(other.end1_),
+ current1_(other.current1_),
+ begin2_(other.begin2_),
+ end2_(other.end2_),
+ current2_(other.current2_),
+ begin3_(other.begin3_),
+ end3_(other.end3_),
+ current3_(other.current3_),
+ begin4_(other.begin4_),
+ end4_(other.end4_),
+ current4_(other.current4_),
+ begin5_(other.begin5_),
+ end5_(other.end5_),
+ current5_(other.current5_),
+ begin6_(other.begin6_),
+ end6_(other.end6_),
+ current6_(other.current6_),
+ begin7_(other.begin7_),
+ end7_(other.end7_),
+ current7_(other.current7_),
+ begin8_(other.begin8_),
+ end8_(other.end8_),
+ current8_(other.current8_),
+ begin9_(other.begin9_),
+ end9_(other.end9_),
+ current9_(other.current9_) {
+ ComputeCurrentValue();
+ }
+
+ void ComputeCurrentValue() {
+ if (!AtEnd())
+ current_value_ = ParamType(*current1_, *current2_, *current3_,
+ *current4_, *current5_, *current6_, *current7_, *current8_,
+ *current9_);
+ }
+ bool AtEnd() const {
+ // We must report iterator past the end of the range when either of the
+ // component iterators has reached the end of its range.
+ return
+ current1_ == end1_ ||
+ current2_ == end2_ ||
+ current3_ == end3_ ||
+ current4_ == end4_ ||
+ current5_ == end5_ ||
+ current6_ == end6_ ||
+ current7_ == end7_ ||
+ current8_ == end8_ ||
+ current9_ == end9_;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<ParamType>* const base_;
+ // begin[i]_ and end[i]_ define the i-th range that Iterator traverses.
+ // current[i]_ is the actual traversing iterator.
+ const typename ParamGenerator<T1>::iterator begin1_;
+ const typename ParamGenerator<T1>::iterator end1_;
+ typename ParamGenerator<T1>::iterator current1_;
+ const typename ParamGenerator<T2>::iterator begin2_;
+ const typename ParamGenerator<T2>::iterator end2_;
+ typename ParamGenerator<T2>::iterator current2_;
+ const typename ParamGenerator<T3>::iterator begin3_;
+ const typename ParamGenerator<T3>::iterator end3_;
+ typename ParamGenerator<T3>::iterator current3_;
+ const typename ParamGenerator<T4>::iterator begin4_;
+ const typename ParamGenerator<T4>::iterator end4_;
+ typename ParamGenerator<T4>::iterator current4_;
+ const typename ParamGenerator<T5>::iterator begin5_;
+ const typename ParamGenerator<T5>::iterator end5_;
+ typename ParamGenerator<T5>::iterator current5_;
+ const typename ParamGenerator<T6>::iterator begin6_;
+ const typename ParamGenerator<T6>::iterator end6_;
+ typename ParamGenerator<T6>::iterator current6_;
+ const typename ParamGenerator<T7>::iterator begin7_;
+ const typename ParamGenerator<T7>::iterator end7_;
+ typename ParamGenerator<T7>::iterator current7_;
+ const typename ParamGenerator<T8>::iterator begin8_;
+ const typename ParamGenerator<T8>::iterator end8_;
+ typename ParamGenerator<T8>::iterator current8_;
+ const typename ParamGenerator<T9>::iterator begin9_;
+ const typename ParamGenerator<T9>::iterator end9_;
+ typename ParamGenerator<T9>::iterator current9_;
+ ParamType current_value_;
+ }; // class CartesianProductGenerator9::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductGenerator9& other);
+
+ const ParamGenerator<T1> g1_;
+ const ParamGenerator<T2> g2_;
+ const ParamGenerator<T3> g3_;
+ const ParamGenerator<T4> g4_;
+ const ParamGenerator<T5> g5_;
+ const ParamGenerator<T6> g6_;
+ const ParamGenerator<T7> g7_;
+ const ParamGenerator<T8> g8_;
+ const ParamGenerator<T9> g9_;
+}; // class CartesianProductGenerator9
+
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10>
+class CartesianProductGenerator10
+ : public ParamGeneratorInterface< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6,
+ T7, T8, T9, T10> > {
+ public:
+ typedef ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10> ParamType;
+
+ CartesianProductGenerator10(const ParamGenerator<T1>& g1,
+ const ParamGenerator<T2>& g2, const ParamGenerator<T3>& g3,
+ const ParamGenerator<T4>& g4, const ParamGenerator<T5>& g5,
+ const ParamGenerator<T6>& g6, const ParamGenerator<T7>& g7,
+ const ParamGenerator<T8>& g8, const ParamGenerator<T9>& g9,
+ const ParamGenerator<T10>& g10)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6), g7_(g7), g8_(g8),
+ g9_(g9), g10_(g10) {}
+ virtual ~CartesianProductGenerator10() {}
+
+ virtual ParamIteratorInterface<ParamType>* Begin() const {
+ return new Iterator(this, g1_, g1_.begin(), g2_, g2_.begin(), g3_,
+ g3_.begin(), g4_, g4_.begin(), g5_, g5_.begin(), g6_, g6_.begin(), g7_,
+ g7_.begin(), g8_, g8_.begin(), g9_, g9_.begin(), g10_, g10_.begin());
+ }
+ virtual ParamIteratorInterface<ParamType>* End() const {
+ return new Iterator(this, g1_, g1_.end(), g2_, g2_.end(), g3_, g3_.end(),
+ g4_, g4_.end(), g5_, g5_.end(), g6_, g6_.end(), g7_, g7_.end(), g8_,
+ g8_.end(), g9_, g9_.end(), g10_, g10_.end());
+ }
+
+ private:
+ class Iterator : public ParamIteratorInterface<ParamType> {
+ public:
+ Iterator(const ParamGeneratorInterface<ParamType>* base,
+ const ParamGenerator<T1>& g1,
+ const typename ParamGenerator<T1>::iterator& current1,
+ const ParamGenerator<T2>& g2,
+ const typename ParamGenerator<T2>::iterator& current2,
+ const ParamGenerator<T3>& g3,
+ const typename ParamGenerator<T3>::iterator& current3,
+ const ParamGenerator<T4>& g4,
+ const typename ParamGenerator<T4>::iterator& current4,
+ const ParamGenerator<T5>& g5,
+ const typename ParamGenerator<T5>::iterator& current5,
+ const ParamGenerator<T6>& g6,
+ const typename ParamGenerator<T6>::iterator& current6,
+ const ParamGenerator<T7>& g7,
+ const typename ParamGenerator<T7>::iterator& current7,
+ const ParamGenerator<T8>& g8,
+ const typename ParamGenerator<T8>::iterator& current8,
+ const ParamGenerator<T9>& g9,
+ const typename ParamGenerator<T9>::iterator& current9,
+ const ParamGenerator<T10>& g10,
+ const typename ParamGenerator<T10>::iterator& current10)
+ : base_(base),
+ begin1_(g1.begin()), end1_(g1.end()), current1_(current1),
+ begin2_(g2.begin()), end2_(g2.end()), current2_(current2),
+ begin3_(g3.begin()), end3_(g3.end()), current3_(current3),
+ begin4_(g4.begin()), end4_(g4.end()), current4_(current4),
+ begin5_(g5.begin()), end5_(g5.end()), current5_(current5),
+ begin6_(g6.begin()), end6_(g6.end()), current6_(current6),
+ begin7_(g7.begin()), end7_(g7.end()), current7_(current7),
+ begin8_(g8.begin()), end8_(g8.end()), current8_(current8),
+ begin9_(g9.begin()), end9_(g9.end()), current9_(current9),
+ begin10_(g10.begin()), end10_(g10.end()), current10_(current10) {
+ ComputeCurrentValue();
+ }
+ virtual ~Iterator() {}
+
+ virtual const ParamGeneratorInterface<ParamType>* BaseGenerator() const {
+ return base_;
+ }
+ // Advance should not be called on beyond-of-range iterators
+ // so no component iterators must be beyond end of range, either.
+ virtual void Advance() {
+ assert(!AtEnd());
+ ++current10_;
+ if (current10_ == end10_) {
+ current10_ = begin10_;
+ ++current9_;
+ }
+ if (current9_ == end9_) {
+ current9_ = begin9_;
+ ++current8_;
+ }
+ if (current8_ == end8_) {
+ current8_ = begin8_;
+ ++current7_;
+ }
+ if (current7_ == end7_) {
+ current7_ = begin7_;
+ ++current6_;
+ }
+ if (current6_ == end6_) {
+ current6_ = begin6_;
+ ++current5_;
+ }
+ if (current5_ == end5_) {
+ current5_ = begin5_;
+ ++current4_;
+ }
+ if (current4_ == end4_) {
+ current4_ = begin4_;
+ ++current3_;
+ }
+ if (current3_ == end3_) {
+ current3_ = begin3_;
+ ++current2_;
+ }
+ if (current2_ == end2_) {
+ current2_ = begin2_;
+ ++current1_;
+ }
+ ComputeCurrentValue();
+ }
+ virtual ParamIteratorInterface<ParamType>* Clone() const {
+ return new Iterator(*this);
+ }
+ virtual const ParamType* Current() const { return ¤t_value_; }
+ virtual bool Equals(const ParamIteratorInterface<ParamType>& other) const {
+ // Having the same base generator guarantees that the other
+ // iterator is of the same type and we can downcast.
+ GTEST_CHECK_(BaseGenerator() == other.BaseGenerator())
+ << "The program attempted to compare iterators "
+ << "from different generators." << std::endl;
+ const Iterator* typed_other =
+ CheckedDowncastToActualType<const Iterator>(&other);
+ // We must report iterators equal if they both point beyond their
+ // respective ranges. That can happen in a variety of fashions,
+ // so we have to consult AtEnd().
+ return (AtEnd() && typed_other->AtEnd()) ||
+ (
+ current1_ == typed_other->current1_ &&
+ current2_ == typed_other->current2_ &&
+ current3_ == typed_other->current3_ &&
+ current4_ == typed_other->current4_ &&
+ current5_ == typed_other->current5_ &&
+ current6_ == typed_other->current6_ &&
+ current7_ == typed_other->current7_ &&
+ current8_ == typed_other->current8_ &&
+ current9_ == typed_other->current9_ &&
+ current10_ == typed_other->current10_);
+ }
+
+ private:
+ Iterator(const Iterator& other)
+ : base_(other.base_),
+ begin1_(other.begin1_),
+ end1_(other.end1_),
+ current1_(other.current1_),
+ begin2_(other.begin2_),
+ end2_(other.end2_),
+ current2_(other.current2_),
+ begin3_(other.begin3_),
+ end3_(other.end3_),
+ current3_(other.current3_),
+ begin4_(other.begin4_),
+ end4_(other.end4_),
+ current4_(other.current4_),
+ begin5_(other.begin5_),
+ end5_(other.end5_),
+ current5_(other.current5_),
+ begin6_(other.begin6_),
+ end6_(other.end6_),
+ current6_(other.current6_),
+ begin7_(other.begin7_),
+ end7_(other.end7_),
+ current7_(other.current7_),
+ begin8_(other.begin8_),
+ end8_(other.end8_),
+ current8_(other.current8_),
+ begin9_(other.begin9_),
+ end9_(other.end9_),
+ current9_(other.current9_),
+ begin10_(other.begin10_),
+ end10_(other.end10_),
+ current10_(other.current10_) {
+ ComputeCurrentValue();
+ }
+
+ void ComputeCurrentValue() {
+ if (!AtEnd())
+ current_value_ = ParamType(*current1_, *current2_, *current3_,
+ *current4_, *current5_, *current6_, *current7_, *current8_,
+ *current9_, *current10_);
+ }
+ bool AtEnd() const {
+ // We must report iterator past the end of the range when either of the
+ // component iterators has reached the end of its range.
+ return
+ current1_ == end1_ ||
+ current2_ == end2_ ||
+ current3_ == end3_ ||
+ current4_ == end4_ ||
+ current5_ == end5_ ||
+ current6_ == end6_ ||
+ current7_ == end7_ ||
+ current8_ == end8_ ||
+ current9_ == end9_ ||
+ current10_ == end10_;
+ }
+
+ // No implementation - assignment is unsupported.
+ void operator=(const Iterator& other);
+
+ const ParamGeneratorInterface<ParamType>* const base_;
+ // begin[i]_ and end[i]_ define the i-th range that Iterator traverses.
+ // current[i]_ is the actual traversing iterator.
+ const typename ParamGenerator<T1>::iterator begin1_;
+ const typename ParamGenerator<T1>::iterator end1_;
+ typename ParamGenerator<T1>::iterator current1_;
+ const typename ParamGenerator<T2>::iterator begin2_;
+ const typename ParamGenerator<T2>::iterator end2_;
+ typename ParamGenerator<T2>::iterator current2_;
+ const typename ParamGenerator<T3>::iterator begin3_;
+ const typename ParamGenerator<T3>::iterator end3_;
+ typename ParamGenerator<T3>::iterator current3_;
+ const typename ParamGenerator<T4>::iterator begin4_;
+ const typename ParamGenerator<T4>::iterator end4_;
+ typename ParamGenerator<T4>::iterator current4_;
+ const typename ParamGenerator<T5>::iterator begin5_;
+ const typename ParamGenerator<T5>::iterator end5_;
+ typename ParamGenerator<T5>::iterator current5_;
+ const typename ParamGenerator<T6>::iterator begin6_;
+ const typename ParamGenerator<T6>::iterator end6_;
+ typename ParamGenerator<T6>::iterator current6_;
+ const typename ParamGenerator<T7>::iterator begin7_;
+ const typename ParamGenerator<T7>::iterator end7_;
+ typename ParamGenerator<T7>::iterator current7_;
+ const typename ParamGenerator<T8>::iterator begin8_;
+ const typename ParamGenerator<T8>::iterator end8_;
+ typename ParamGenerator<T8>::iterator current8_;
+ const typename ParamGenerator<T9>::iterator begin9_;
+ const typename ParamGenerator<T9>::iterator end9_;
+ typename ParamGenerator<T9>::iterator current9_;
+ const typename ParamGenerator<T10>::iterator begin10_;
+ const typename ParamGenerator<T10>::iterator end10_;
+ typename ParamGenerator<T10>::iterator current10_;
+ ParamType current_value_;
+ }; // class CartesianProductGenerator10::Iterator
+
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductGenerator10& other);
+
+ const ParamGenerator<T1> g1_;
+ const ParamGenerator<T2> g2_;
+ const ParamGenerator<T3> g3_;
+ const ParamGenerator<T4> g4_;
+ const ParamGenerator<T5> g5_;
+ const ParamGenerator<T6> g6_;
+ const ParamGenerator<T7> g7_;
+ const ParamGenerator<T8> g8_;
+ const ParamGenerator<T9> g9_;
+ const ParamGenerator<T10> g10_;
+}; // class CartesianProductGenerator10
+
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// Helper classes providing Combine() with polymorphic features. They allow
+// casting CartesianProductGeneratorN<T> to ParamGenerator<U> if T is
+// convertible to U.
+//
+template <class Generator1, class Generator2>
+class CartesianProductHolder2 {
+ public:
+CartesianProductHolder2(const Generator1& g1, const Generator2& g2)
+ : g1_(g1), g2_(g2) {}
+ template <typename T1, typename T2>
+ operator ParamGenerator< ::std::tr1::tuple<T1, T2> >() const {
+ return ParamGenerator< ::std::tr1::tuple<T1, T2> >(
+ new CartesianProductGenerator2<T1, T2>(
+ static_cast<ParamGenerator<T1> >(g1_),
+ static_cast<ParamGenerator<T2> >(g2_)));
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductHolder2& other);
+
+ const Generator1 g1_;
+ const Generator2 g2_;
+}; // class CartesianProductHolder2
+
+template <class Generator1, class Generator2, class Generator3>
+class CartesianProductHolder3 {
+ public:
+CartesianProductHolder3(const Generator1& g1, const Generator2& g2,
+ const Generator3& g3)
+ : g1_(g1), g2_(g2), g3_(g3) {}
+ template <typename T1, typename T2, typename T3>
+ operator ParamGenerator< ::std::tr1::tuple<T1, T2, T3> >() const {
+ return ParamGenerator< ::std::tr1::tuple<T1, T2, T3> >(
+ new CartesianProductGenerator3<T1, T2, T3>(
+ static_cast<ParamGenerator<T1> >(g1_),
+ static_cast<ParamGenerator<T2> >(g2_),
+ static_cast<ParamGenerator<T3> >(g3_)));
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductHolder3& other);
+
+ const Generator1 g1_;
+ const Generator2 g2_;
+ const Generator3 g3_;
+}; // class CartesianProductHolder3
+
+template <class Generator1, class Generator2, class Generator3,
+ class Generator4>
+class CartesianProductHolder4 {
+ public:
+CartesianProductHolder4(const Generator1& g1, const Generator2& g2,
+ const Generator3& g3, const Generator4& g4)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4) {}
+ template <typename T1, typename T2, typename T3, typename T4>
+ operator ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4> >() const {
+ return ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4> >(
+ new CartesianProductGenerator4<T1, T2, T3, T4>(
+ static_cast<ParamGenerator<T1> >(g1_),
+ static_cast<ParamGenerator<T2> >(g2_),
+ static_cast<ParamGenerator<T3> >(g3_),
+ static_cast<ParamGenerator<T4> >(g4_)));
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductHolder4& other);
+
+ const Generator1 g1_;
+ const Generator2 g2_;
+ const Generator3 g3_;
+ const Generator4 g4_;
+}; // class CartesianProductHolder4
+
+template <class Generator1, class Generator2, class Generator3,
+ class Generator4, class Generator5>
+class CartesianProductHolder5 {
+ public:
+CartesianProductHolder5(const Generator1& g1, const Generator2& g2,
+ const Generator3& g3, const Generator4& g4, const Generator5& g5)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5) {}
+ template <typename T1, typename T2, typename T3, typename T4, typename T5>
+ operator ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5> >() const {
+ return ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5> >(
+ new CartesianProductGenerator5<T1, T2, T3, T4, T5>(
+ static_cast<ParamGenerator<T1> >(g1_),
+ static_cast<ParamGenerator<T2> >(g2_),
+ static_cast<ParamGenerator<T3> >(g3_),
+ static_cast<ParamGenerator<T4> >(g4_),
+ static_cast<ParamGenerator<T5> >(g5_)));
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductHolder5& other);
+
+ const Generator1 g1_;
+ const Generator2 g2_;
+ const Generator3 g3_;
+ const Generator4 g4_;
+ const Generator5 g5_;
+}; // class CartesianProductHolder5
+
+template <class Generator1, class Generator2, class Generator3,
+ class Generator4, class Generator5, class Generator6>
+class CartesianProductHolder6 {
+ public:
+CartesianProductHolder6(const Generator1& g1, const Generator2& g2,
+ const Generator3& g3, const Generator4& g4, const Generator5& g5,
+ const Generator6& g6)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6) {}
+ template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6>
+ operator ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6> >() const {
+ return ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6> >(
+ new CartesianProductGenerator6<T1, T2, T3, T4, T5, T6>(
+ static_cast<ParamGenerator<T1> >(g1_),
+ static_cast<ParamGenerator<T2> >(g2_),
+ static_cast<ParamGenerator<T3> >(g3_),
+ static_cast<ParamGenerator<T4> >(g4_),
+ static_cast<ParamGenerator<T5> >(g5_),
+ static_cast<ParamGenerator<T6> >(g6_)));
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductHolder6& other);
+
+ const Generator1 g1_;
+ const Generator2 g2_;
+ const Generator3 g3_;
+ const Generator4 g4_;
+ const Generator5 g5_;
+ const Generator6 g6_;
+}; // class CartesianProductHolder6
+
+template <class Generator1, class Generator2, class Generator3,
+ class Generator4, class Generator5, class Generator6, class Generator7>
+class CartesianProductHolder7 {
+ public:
+CartesianProductHolder7(const Generator1& g1, const Generator2& g2,
+ const Generator3& g3, const Generator4& g4, const Generator5& g5,
+ const Generator6& g6, const Generator7& g7)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6), g7_(g7) {}
+ template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7>
+ operator ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6,
+ T7> >() const {
+ return ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7> >(
+ new CartesianProductGenerator7<T1, T2, T3, T4, T5, T6, T7>(
+ static_cast<ParamGenerator<T1> >(g1_),
+ static_cast<ParamGenerator<T2> >(g2_),
+ static_cast<ParamGenerator<T3> >(g3_),
+ static_cast<ParamGenerator<T4> >(g4_),
+ static_cast<ParamGenerator<T5> >(g5_),
+ static_cast<ParamGenerator<T6> >(g6_),
+ static_cast<ParamGenerator<T7> >(g7_)));
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductHolder7& other);
+
+ const Generator1 g1_;
+ const Generator2 g2_;
+ const Generator3 g3_;
+ const Generator4 g4_;
+ const Generator5 g5_;
+ const Generator6 g6_;
+ const Generator7 g7_;
+}; // class CartesianProductHolder7
+
+template <class Generator1, class Generator2, class Generator3,
+ class Generator4, class Generator5, class Generator6, class Generator7,
+ class Generator8>
+class CartesianProductHolder8 {
+ public:
+CartesianProductHolder8(const Generator1& g1, const Generator2& g2,
+ const Generator3& g3, const Generator4& g4, const Generator5& g5,
+ const Generator6& g6, const Generator7& g7, const Generator8& g8)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6), g7_(g7),
+ g8_(g8) {}
+ template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8>
+ operator ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7,
+ T8> >() const {
+ return ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8> >(
+ new CartesianProductGenerator8<T1, T2, T3, T4, T5, T6, T7, T8>(
+ static_cast<ParamGenerator<T1> >(g1_),
+ static_cast<ParamGenerator<T2> >(g2_),
+ static_cast<ParamGenerator<T3> >(g3_),
+ static_cast<ParamGenerator<T4> >(g4_),
+ static_cast<ParamGenerator<T5> >(g5_),
+ static_cast<ParamGenerator<T6> >(g6_),
+ static_cast<ParamGenerator<T7> >(g7_),
+ static_cast<ParamGenerator<T8> >(g8_)));
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductHolder8& other);
+
+ const Generator1 g1_;
+ const Generator2 g2_;
+ const Generator3 g3_;
+ const Generator4 g4_;
+ const Generator5 g5_;
+ const Generator6 g6_;
+ const Generator7 g7_;
+ const Generator8 g8_;
+}; // class CartesianProductHolder8
+
+template <class Generator1, class Generator2, class Generator3,
+ class Generator4, class Generator5, class Generator6, class Generator7,
+ class Generator8, class Generator9>
+class CartesianProductHolder9 {
+ public:
+CartesianProductHolder9(const Generator1& g1, const Generator2& g2,
+ const Generator3& g3, const Generator4& g4, const Generator5& g5,
+ const Generator6& g6, const Generator7& g7, const Generator8& g8,
+ const Generator9& g9)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6), g7_(g7), g8_(g8),
+ g9_(g9) {}
+ template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9>
+ operator ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8,
+ T9> >() const {
+ return ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8,
+ T9> >(
+ new CartesianProductGenerator9<T1, T2, T3, T4, T5, T6, T7, T8, T9>(
+ static_cast<ParamGenerator<T1> >(g1_),
+ static_cast<ParamGenerator<T2> >(g2_),
+ static_cast<ParamGenerator<T3> >(g3_),
+ static_cast<ParamGenerator<T4> >(g4_),
+ static_cast<ParamGenerator<T5> >(g5_),
+ static_cast<ParamGenerator<T6> >(g6_),
+ static_cast<ParamGenerator<T7> >(g7_),
+ static_cast<ParamGenerator<T8> >(g8_),
+ static_cast<ParamGenerator<T9> >(g9_)));
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductHolder9& other);
+
+ const Generator1 g1_;
+ const Generator2 g2_;
+ const Generator3 g3_;
+ const Generator4 g4_;
+ const Generator5 g5_;
+ const Generator6 g6_;
+ const Generator7 g7_;
+ const Generator8 g8_;
+ const Generator9 g9_;
+}; // class CartesianProductHolder9
+
+template <class Generator1, class Generator2, class Generator3,
+ class Generator4, class Generator5, class Generator6, class Generator7,
+ class Generator8, class Generator9, class Generator10>
+class CartesianProductHolder10 {
+ public:
+CartesianProductHolder10(const Generator1& g1, const Generator2& g2,
+ const Generator3& g3, const Generator4& g4, const Generator5& g5,
+ const Generator6& g6, const Generator7& g7, const Generator8& g8,
+ const Generator9& g9, const Generator10& g10)
+ : g1_(g1), g2_(g2), g3_(g3), g4_(g4), g5_(g5), g6_(g6), g7_(g7), g8_(g8),
+ g9_(g9), g10_(g10) {}
+ template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10>
+ operator ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8,
+ T9, T10> >() const {
+ return ParamGenerator< ::std::tr1::tuple<T1, T2, T3, T4, T5, T6, T7, T8,
+ T9, T10> >(
+ new CartesianProductGenerator10<T1, T2, T3, T4, T5, T6, T7, T8, T9,
+ T10>(
+ static_cast<ParamGenerator<T1> >(g1_),
+ static_cast<ParamGenerator<T2> >(g2_),
+ static_cast<ParamGenerator<T3> >(g3_),
+ static_cast<ParamGenerator<T4> >(g4_),
+ static_cast<ParamGenerator<T5> >(g5_),
+ static_cast<ParamGenerator<T6> >(g6_),
+ static_cast<ParamGenerator<T7> >(g7_),
+ static_cast<ParamGenerator<T8> >(g8_),
+ static_cast<ParamGenerator<T9> >(g9_),
+ static_cast<ParamGenerator<T10> >(g10_)));
+ }
+
+ private:
+ // No implementation - assignment is unsupported.
+ void operator=(const CartesianProductHolder10& other);
+
+ const Generator1 g1_;
+ const Generator2 g2_;
+ const Generator3 g3_;
+ const Generator4 g4_;
+ const Generator5 g5_;
+ const Generator6 g6_;
+ const Generator7 g7_;
+ const Generator8 g8_;
+ const Generator9 g9_;
+ const Generator10 g10_;
+}; // class CartesianProductHolder10
+
+# endif // GTEST_HAS_COMBINE
+
+} // namespace internal
+} // namespace testing
+
+#endif // GTEST_HAS_PARAM_TEST
+
+#endif // GTEST_INCLUDE_GTEST_INTERNAL_GTEST_PARAM_UTIL_GENERATED_H_
+
+#if GTEST_HAS_PARAM_TEST
+
+namespace testing {
+
+// Functions producing parameter generators.
+//
+// Google Test uses these generators to produce parameters for value-
+// parameterized tests. When a parameterized test case is instantiated
+// with a particular generator, Google Test creates and runs tests
+// for each element in the sequence produced by the generator.
+//
+// In the following sample, tests from test case FooTest are instantiated
+// each three times with parameter values 3, 5, and 8:
+//
+// class FooTest : public TestWithParam<int> { ... };
+//
+// TEST_P(FooTest, TestThis) {
+// }
+// TEST_P(FooTest, TestThat) {
+// }
+// INSTANTIATE_TEST_CASE_P(TestSequence, FooTest, Values(3, 5, 8));
+//
+
+// Range() returns generators providing sequences of values in a range.
+//
+// Synopsis:
+// Range(start, end)
+// - returns a generator producing a sequence of values {start, start+1,
+// start+2, ..., }.
+// Range(start, end, step)
+// - returns a generator producing a sequence of values {start, start+step,
+// start+step+step, ..., }.
+// Notes:
+// * The generated sequences never include end. For example, Range(1, 5)
+// returns a generator producing a sequence {1, 2, 3, 4}. Range(1, 9, 2)
+// returns a generator producing {1, 3, 5, 7}.
+// * start and end must have the same type. That type may be any integral or
+// floating-point type or a user defined type satisfying these conditions:
+// * It must be assignable (have operator=() defined).
+// * It must have operator+() (operator+(int-compatible type) for
+// two-operand version).
+// * It must have operator<() defined.
+// Elements in the resulting sequences will also have that type.
+// * Condition start < end must be satisfied in order for resulting sequences
+// to contain any elements.
+//
+template <typename T, typename IncrementT>
+internal::ParamGenerator<T> Range(T start, T end, IncrementT step) {
+ return internal::ParamGenerator<T>(
+ new internal::RangeGenerator<T, IncrementT>(start, end, step));
+}
+
+template <typename T>
+internal::ParamGenerator<T> Range(T start, T end) {
+ return Range(start, end, 1);
+}
+
+// ValuesIn() function allows generation of tests with parameters coming from
+// a container.
+//
+// Synopsis:
+// ValuesIn(const T (&array)[N])
+// - returns a generator producing sequences with elements from
+// a C-style array.
+// ValuesIn(const Container& container)
+// - returns a generator producing sequences with elements from
+// an STL-style container.
+// ValuesIn(Iterator begin, Iterator end)
+// - returns a generator producing sequences with elements from
+// a range [begin, end) defined by a pair of STL-style iterators. These
+// iterators can also be plain C pointers.
+//
+// Please note that ValuesIn copies the values from the containers
+// passed in and keeps them to generate tests in RUN_ALL_TESTS().
+//
+// Examples:
+//
+// This instantiates tests from test case StringTest
+// each with C-string values of "foo", "bar", and "baz":
+//
+// const char* strings[] = {"foo", "bar", "baz"};
+// INSTANTIATE_TEST_CASE_P(StringSequence, SrtingTest, ValuesIn(strings));
+//
+// This instantiates tests from test case StlStringTest
+// each with STL strings with values "a" and "b":
+//
+// ::std::vector< ::std::string> GetParameterStrings() {
+// ::std::vector< ::std::string> v;
+// v.push_back("a");
+// v.push_back("b");
+// return v;
+// }
+//
+// INSTANTIATE_TEST_CASE_P(CharSequence,
+// StlStringTest,
+// ValuesIn(GetParameterStrings()));
+//
+//
+// This will also instantiate tests from CharTest
+// each with parameter values 'a' and 'b':
+//
+// ::std::list<char> GetParameterChars() {
+// ::std::list<char> list;
+// list.push_back('a');
+// list.push_back('b');
+// return list;
+// }
+// ::std::list<char> l = GetParameterChars();
+// INSTANTIATE_TEST_CASE_P(CharSequence2,
+// CharTest,
+// ValuesIn(l.begin(), l.end()));
+//
+template <typename ForwardIterator>
+internal::ParamGenerator<
+ typename ::testing::internal::IteratorTraits<ForwardIterator>::value_type>
+ValuesIn(ForwardIterator begin, ForwardIterator end) {
+ typedef typename ::testing::internal::IteratorTraits<ForwardIterator>
+ ::value_type ParamType;
+ return internal::ParamGenerator<ParamType>(
+ new internal::ValuesInIteratorRangeGenerator<ParamType>(begin, end));
+}
+
+template <typename T, size_t N>
+internal::ParamGenerator<T> ValuesIn(const T (&array)[N]) {
+ return ValuesIn(array, array + N);
+}
+
+template <class Container>
+internal::ParamGenerator<typename Container::value_type> ValuesIn(
+ const Container& container) {
+ return ValuesIn(container.begin(), container.end());
+}
+
+// Values() allows generating tests from explicitly specified list of
+// parameters.
+//
+// Synopsis:
+// Values(T v1, T v2, ..., T vN)
+// - returns a generator producing sequences with elements v1, v2, ..., vN.
+//
+// For example, this instantiates tests from test case BarTest each
+// with values "one", "two", and "three":
+//
+// INSTANTIATE_TEST_CASE_P(NumSequence, BarTest, Values("one", "two", "three"));
+//
+// This instantiates tests from test case BazTest each with values 1, 2, 3.5.
+// The exact type of values will depend on the type of parameter in BazTest.
+//
+// INSTANTIATE_TEST_CASE_P(FloatingNumbers, BazTest, Values(1, 2, 3.5));
+//
+// Currently, Values() supports from 1 to 50 parameters.
+//
+template <typename T1>
+internal::ValueArray1<T1> Values(T1 v1) {
+ return internal::ValueArray1<T1>(v1);
+}
+
+template <typename T1, typename T2>
+internal::ValueArray2<T1, T2> Values(T1 v1, T2 v2) {
+ return internal::ValueArray2<T1, T2>(v1, v2);
+}
+
+template <typename T1, typename T2, typename T3>
+internal::ValueArray3<T1, T2, T3> Values(T1 v1, T2 v2, T3 v3) {
+ return internal::ValueArray3<T1, T2, T3>(v1, v2, v3);
+}
+
+template <typename T1, typename T2, typename T3, typename T4>
+internal::ValueArray4<T1, T2, T3, T4> Values(T1 v1, T2 v2, T3 v3, T4 v4) {
+ return internal::ValueArray4<T1, T2, T3, T4>(v1, v2, v3, v4);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5>
+internal::ValueArray5<T1, T2, T3, T4, T5> Values(T1 v1, T2 v2, T3 v3, T4 v4,
+ T5 v5) {
+ return internal::ValueArray5<T1, T2, T3, T4, T5>(v1, v2, v3, v4, v5);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6>
+internal::ValueArray6<T1, T2, T3, T4, T5, T6> Values(T1 v1, T2 v2, T3 v3,
+ T4 v4, T5 v5, T6 v6) {
+ return internal::ValueArray6<T1, T2, T3, T4, T5, T6>(v1, v2, v3, v4, v5, v6);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7>
+internal::ValueArray7<T1, T2, T3, T4, T5, T6, T7> Values(T1 v1, T2 v2, T3 v3,
+ T4 v4, T5 v5, T6 v6, T7 v7) {
+ return internal::ValueArray7<T1, T2, T3, T4, T5, T6, T7>(v1, v2, v3, v4, v5,
+ v6, v7);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8>
+internal::ValueArray8<T1, T2, T3, T4, T5, T6, T7, T8> Values(T1 v1, T2 v2,
+ T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8) {
+ return internal::ValueArray8<T1, T2, T3, T4, T5, T6, T7, T8>(v1, v2, v3, v4,
+ v5, v6, v7, v8);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9>
+internal::ValueArray9<T1, T2, T3, T4, T5, T6, T7, T8, T9> Values(T1 v1, T2 v2,
+ T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9) {
+ return internal::ValueArray9<T1, T2, T3, T4, T5, T6, T7, T8, T9>(v1, v2, v3,
+ v4, v5, v6, v7, v8, v9);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10>
+internal::ValueArray10<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10> Values(T1 v1,
+ T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10) {
+ return internal::ValueArray10<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10>(v1,
+ v2, v3, v4, v5, v6, v7, v8, v9, v10);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11>
+internal::ValueArray11<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10,
+ T11> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11) {
+ return internal::ValueArray11<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10,
+ T11>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12>
+internal::ValueArray12<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12) {
+ return internal::ValueArray12<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13>
+internal::ValueArray13<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
+ T13> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13) {
+ return internal::ValueArray13<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14>
+internal::ValueArray14<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14) {
+ return internal::ValueArray14<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13,
+ v14);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15>
+internal::ValueArray15<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8,
+ T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15) {
+ return internal::ValueArray15<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12,
+ v13, v14, v15);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16>
+internal::ValueArray16<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7,
+ T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15,
+ T16 v16) {
+ return internal::ValueArray16<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11,
+ v12, v13, v14, v15, v16);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17>
+internal::ValueArray17<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7,
+ T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15,
+ T16 v16, T17 v17) {
+ return internal::ValueArray17<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10,
+ v11, v12, v13, v14, v15, v16, v17);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18>
+internal::ValueArray18<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6,
+ T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15,
+ T16 v16, T17 v17, T18 v18) {
+ return internal::ValueArray18<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18>(v1, v2, v3, v4, v5, v6, v7, v8, v9,
+ v10, v11, v12, v13, v14, v15, v16, v17, v18);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19>
+internal::ValueArray19<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5,
+ T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14,
+ T15 v15, T16 v16, T17 v17, T18 v18, T19 v19) {
+ return internal::ValueArray19<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19>(v1, v2, v3, v4, v5, v6, v7, v8,
+ v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20>
+internal::ValueArray20<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20> Values(T1 v1, T2 v2, T3 v3, T4 v4,
+ T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13,
+ T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20) {
+ return internal::ValueArray20<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20>(v1, v2, v3, v4, v5, v6, v7,
+ v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21>
+internal::ValueArray21<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21> Values(T1 v1, T2 v2, T3 v3, T4 v4,
+ T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13,
+ T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21) {
+ return internal::ValueArray21<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21>(v1, v2, v3, v4, v5, v6,
+ v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22>
+internal::ValueArray22<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22> Values(T1 v1, T2 v2, T3 v3,
+ T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12,
+ T13 v13, T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20,
+ T21 v21, T22 v22) {
+ return internal::ValueArray22<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22>(v1, v2, v3, v4,
+ v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19,
+ v20, v21, v22);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23>
+internal::ValueArray23<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23> Values(T1 v1, T2 v2,
+ T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12,
+ T13 v13, T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20,
+ T21 v21, T22 v22, T23 v23) {
+ return internal::ValueArray23<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23>(v1, v2, v3,
+ v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19,
+ v20, v21, v22, v23);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24>
+internal::ValueArray24<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24> Values(T1 v1, T2 v2,
+ T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12,
+ T13 v13, T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20,
+ T21 v21, T22 v22, T23 v23, T24 v24) {
+ return internal::ValueArray24<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24>(v1, v2,
+ v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18,
+ v19, v20, v21, v22, v23, v24);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25>
+internal::ValueArray25<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25> Values(T1 v1,
+ T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11,
+ T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19,
+ T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25) {
+ return internal::ValueArray25<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25>(v1,
+ v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17,
+ v18, v19, v20, v21, v22, v23, v24, v25);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26>
+internal::ValueArray26<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26) {
+ return internal::ValueArray26<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15,
+ v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27>
+internal::ValueArray27<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26,
+ T27> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27) {
+ return internal::ValueArray27<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14,
+ v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28>
+internal::ValueArray28<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27,
+ T28> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28) {
+ return internal::ValueArray28<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13,
+ v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27,
+ v28);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29>
+internal::ValueArray29<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29) {
+ return internal::ValueArray29<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12,
+ v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26,
+ v27, v28, v29);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30>
+internal::ValueArray30<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8,
+ T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16,
+ T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24,
+ T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30) {
+ return internal::ValueArray30<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11,
+ v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25,
+ v26, v27, v28, v29, v30);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31>
+internal::ValueArray31<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7,
+ T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15,
+ T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23,
+ T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31) {
+ return internal::ValueArray31<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10,
+ v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24,
+ v25, v26, v27, v28, v29, v30, v31);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32>
+internal::ValueArray32<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7,
+ T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15,
+ T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23,
+ T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31,
+ T32 v32) {
+ return internal::ValueArray32<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32>(v1, v2, v3, v4, v5, v6, v7, v8, v9,
+ v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23,
+ v24, v25, v26, v27, v28, v29, v30, v31, v32);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33>
+internal::ValueArray33<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6,
+ T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15,
+ T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23,
+ T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31,
+ T32 v32, T33 v33) {
+ return internal::ValueArray33<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33>(v1, v2, v3, v4, v5, v6, v7, v8,
+ v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23,
+ v24, v25, v26, v27, v28, v29, v30, v31, v32, v33);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34>
+internal::ValueArray34<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5,
+ T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14,
+ T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22,
+ T23 v23, T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30,
+ T31 v31, T32 v32, T33 v33, T34 v34) {
+ return internal::ValueArray34<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34>(v1, v2, v3, v4, v5, v6, v7,
+ v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22,
+ v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35>
+internal::ValueArray35<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35> Values(T1 v1, T2 v2, T3 v3, T4 v4,
+ T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13,
+ T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21,
+ T22 v22, T23 v23, T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29,
+ T30 v30, T31 v31, T32 v32, T33 v33, T34 v34, T35 v35) {
+ return internal::ValueArray35<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35>(v1, v2, v3, v4, v5, v6,
+ v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21,
+ v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36>
+internal::ValueArray36<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36> Values(T1 v1, T2 v2, T3 v3, T4 v4,
+ T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13,
+ T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21,
+ T22 v22, T23 v23, T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29,
+ T30 v30, T31 v31, T32 v32, T33 v33, T34 v34, T35 v35, T36 v36) {
+ return internal::ValueArray36<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36>(v1, v2, v3, v4,
+ v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19,
+ v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33,
+ v34, v35, v36);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37>
+internal::ValueArray37<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37> Values(T1 v1, T2 v2, T3 v3,
+ T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12,
+ T13 v13, T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20,
+ T21 v21, T22 v22, T23 v23, T24 v24, T25 v25, T26 v26, T27 v27, T28 v28,
+ T29 v29, T30 v30, T31 v31, T32 v32, T33 v33, T34 v34, T35 v35, T36 v36,
+ T37 v37) {
+ return internal::ValueArray37<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37>(v1, v2, v3,
+ v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19,
+ v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33,
+ v34, v35, v36, v37);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38>
+internal::ValueArray38<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38> Values(T1 v1, T2 v2,
+ T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12,
+ T13 v13, T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20,
+ T21 v21, T22 v22, T23 v23, T24 v24, T25 v25, T26 v26, T27 v27, T28 v28,
+ T29 v29, T30 v30, T31 v31, T32 v32, T33 v33, T34 v34, T35 v35, T36 v36,
+ T37 v37, T38 v38) {
+ return internal::ValueArray38<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38>(v1, v2,
+ v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18,
+ v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32,
+ v33, v34, v35, v36, v37, v38);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39>
+internal::ValueArray39<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39> Values(T1 v1, T2 v2,
+ T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12,
+ T13 v13, T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20,
+ T21 v21, T22 v22, T23 v23, T24 v24, T25 v25, T26 v26, T27 v27, T28 v28,
+ T29 v29, T30 v30, T31 v31, T32 v32, T33 v33, T34 v34, T35 v35, T36 v36,
+ T37 v37, T38 v38, T39 v39) {
+ return internal::ValueArray39<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39>(v1,
+ v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17,
+ v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31,
+ v32, v33, v34, v35, v36, v37, v38, v39);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40>
+internal::ValueArray40<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40> Values(T1 v1,
+ T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11,
+ T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19,
+ T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25, T26 v26, T27 v27,
+ T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33, T34 v34, T35 v35,
+ T36 v36, T37 v37, T38 v38, T39 v39, T40 v40) {
+ return internal::ValueArray40<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15,
+ v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29,
+ v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41>
+internal::ValueArray41<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40,
+ T41> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41) {
+ return internal::ValueArray41<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14,
+ v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28,
+ v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42>
+internal::ValueArray42<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41,
+ T42> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42) {
+ return internal::ValueArray42<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41, T42>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13,
+ v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27,
+ v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41,
+ v42);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43>
+internal::ValueArray43<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42,
+ T43> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43) {
+ return internal::ValueArray43<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41, T42, T43>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12,
+ v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26,
+ v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40,
+ v41, v42, v43);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44>
+internal::ValueArray44<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8, T9 v9,
+ T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16, T17 v17,
+ T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24, T25 v25,
+ T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32, T33 v33,
+ T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40, T41 v41,
+ T42 v42, T43 v43, T44 v44) {
+ return internal::ValueArray44<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41, T42, T43, T44>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11,
+ v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25,
+ v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39,
+ v40, v41, v42, v43, v44);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45>
+internal::ValueArray45<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7, T8 v8,
+ T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15, T16 v16,
+ T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23, T24 v24,
+ T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31, T32 v32,
+ T33 v33, T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39, T40 v40,
+ T41 v41, T42 v42, T43 v43, T44 v44, T45 v45) {
+ return internal::ValueArray45<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41, T42, T43, T44, T45>(v1, v2, v3, v4, v5, v6, v7, v8, v9, v10,
+ v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24,
+ v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38,
+ v39, v40, v41, v42, v43, v44, v45);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46>
+internal::ValueArray46<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7,
+ T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15,
+ T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23,
+ T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31,
+ T32 v32, T33 v33, T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39,
+ T40 v40, T41 v41, T42 v42, T43 v43, T44 v44, T45 v45, T46 v46) {
+ return internal::ValueArray46<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41, T42, T43, T44, T45, T46>(v1, v2, v3, v4, v5, v6, v7, v8, v9,
+ v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23,
+ v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37,
+ v38, v39, v40, v41, v42, v43, v44, v45, v46);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47>
+internal::ValueArray47<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46, T47> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6, T7 v7,
+ T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15,
+ T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23,
+ T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31,
+ T32 v32, T33 v33, T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39,
+ T40 v40, T41 v41, T42 v42, T43 v43, T44 v44, T45 v45, T46 v46, T47 v47) {
+ return internal::ValueArray47<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41, T42, T43, T44, T45, T46, T47>(v1, v2, v3, v4, v5, v6, v7, v8,
+ v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23,
+ v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37,
+ v38, v39, v40, v41, v42, v43, v44, v45, v46, v47);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48>
+internal::ValueArray48<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46, T47, T48> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5, T6 v6,
+ T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14, T15 v15,
+ T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22, T23 v23,
+ T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30, T31 v31,
+ T32 v32, T33 v33, T34 v34, T35 v35, T36 v36, T37 v37, T38 v38, T39 v39,
+ T40 v40, T41 v41, T42 v42, T43 v43, T44 v44, T45 v45, T46 v46, T47 v47,
+ T48 v48) {
+ return internal::ValueArray48<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41, T42, T43, T44, T45, T46, T47, T48>(v1, v2, v3, v4, v5, v6, v7,
+ v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22,
+ v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36,
+ v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48, typename T49>
+internal::ValueArray49<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46, T47, T48, T49> Values(T1 v1, T2 v2, T3 v3, T4 v4, T5 v5,
+ T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13, T14 v14,
+ T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21, T22 v22,
+ T23 v23, T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29, T30 v30,
+ T31 v31, T32 v32, T33 v33, T34 v34, T35 v35, T36 v36, T37 v37, T38 v38,
+ T39 v39, T40 v40, T41 v41, T42 v42, T43 v43, T44 v44, T45 v45, T46 v46,
+ T47 v47, T48 v48, T49 v49) {
+ return internal::ValueArray49<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41, T42, T43, T44, T45, T46, T47, T48, T49>(v1, v2, v3, v4, v5, v6,
+ v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21,
+ v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35,
+ v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49);
+}
+
+template <typename T1, typename T2, typename T3, typename T4, typename T5,
+ typename T6, typename T7, typename T8, typename T9, typename T10,
+ typename T11, typename T12, typename T13, typename T14, typename T15,
+ typename T16, typename T17, typename T18, typename T19, typename T20,
+ typename T21, typename T22, typename T23, typename T24, typename T25,
+ typename T26, typename T27, typename T28, typename T29, typename T30,
+ typename T31, typename T32, typename T33, typename T34, typename T35,
+ typename T36, typename T37, typename T38, typename T39, typename T40,
+ typename T41, typename T42, typename T43, typename T44, typename T45,
+ typename T46, typename T47, typename T48, typename T49, typename T50>
+internal::ValueArray50<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13,
+ T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25, T26, T27, T28,
+ T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39, T40, T41, T42, T43,
+ T44, T45, T46, T47, T48, T49, T50> Values(T1 v1, T2 v2, T3 v3, T4 v4,
+ T5 v5, T6 v6, T7 v7, T8 v8, T9 v9, T10 v10, T11 v11, T12 v12, T13 v13,
+ T14 v14, T15 v15, T16 v16, T17 v17, T18 v18, T19 v19, T20 v20, T21 v21,
+ T22 v22, T23 v23, T24 v24, T25 v25, T26 v26, T27 v27, T28 v28, T29 v29,
+ T30 v30, T31 v31, T32 v32, T33 v33, T34 v34, T35 v35, T36 v36, T37 v37,
+ T38 v38, T39 v39, T40 v40, T41 v41, T42 v42, T43 v43, T44 v44, T45 v45,
+ T46 v46, T47 v47, T48 v48, T49 v49, T50 v50) {
+ return internal::ValueArray50<T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11,
+ T12, T13, T14, T15, T16, T17, T18, T19, T20, T21, T22, T23, T24, T25,
+ T26, T27, T28, T29, T30, T31, T32, T33, T34, T35, T36, T37, T38, T39,
+ T40, T41, T42, T43, T44, T45, T46, T47, T48, T49, T50>(v1, v2, v3, v4,
+ v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19,
+ v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33,
+ v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47,
+ v48, v49, v50);
+}
+
+// Bool() allows generating tests with parameters in a set of (false, true).
+//
+// Synopsis:
+// Bool()
+// - returns a generator producing sequences with elements {false, true}.
+//
+// It is useful when testing code that depends on Boolean flags. Combinations
+// of multiple flags can be tested when several Bool()'s are combined using
+// Combine() function.
+//
+// In the following example all tests in the test case FlagDependentTest
+// will be instantiated twice with parameters false and true.
+//
+// class FlagDependentTest : public testing::TestWithParam<bool> {
+// virtual void SetUp() {
+// external_flag = GetParam();
+// }
+// }
+// INSTANTIATE_TEST_CASE_P(BoolSequence, FlagDependentTest, Bool());
+//
+inline internal::ParamGenerator<bool> Bool() {
+ return Values(false, true);
+}
+
+# if GTEST_HAS_COMBINE
+// Combine() allows the user to combine two or more sequences to produce
+// values of a Cartesian product of those sequences' elements.
+//
+// Synopsis:
+// Combine(gen1, gen2, ..., genN)
+// - returns a generator producing sequences with elements coming from
+// the Cartesian product of elements from the sequences generated by
+// gen1, gen2, ..., genN. The sequence elements will have a type of
+// tuple<T1, T2, ..., TN> where T1, T2, ..., TN are the types
+// of elements from sequences produces by gen1, gen2, ..., genN.
+//
+// Combine can have up to 10 arguments. This number is currently limited
+// by the maximum number of elements in the tuple implementation used by Google
+// Test.
+//
+// Example:
+//
+// This will instantiate tests in test case AnimalTest each one with
+// the parameter values tuple("cat", BLACK), tuple("cat", WHITE),
+// tuple("dog", BLACK), and tuple("dog", WHITE):
+//
+// enum Color { BLACK, GRAY, WHITE };
+// class AnimalTest
+// : public testing::TestWithParam<tuple<const char*, Color> > {...};
+//
+// TEST_P(AnimalTest, AnimalLooksNice) {...}
+//
+// INSTANTIATE_TEST_CASE_P(AnimalVariations, AnimalTest,
+// Combine(Values("cat", "dog"),
+// Values(BLACK, WHITE)));
+//
+// This will instantiate tests in FlagDependentTest with all variations of two
+// Boolean flags:
+//
+// class FlagDependentTest
+// : public testing::TestWithParam<tuple<bool, bool> > {
+// virtual void SetUp() {
+// // Assigns external_flag_1 and external_flag_2 values from the tuple.
+// tie(external_flag_1, external_flag_2) = GetParam();
+// }
+// };
+//
+// TEST_P(FlagDependentTest, TestFeature1) {
+// // Test your code using external_flag_1 and external_flag_2 here.
+// }
+// INSTANTIATE_TEST_CASE_P(TwoBoolSequence, FlagDependentTest,
+// Combine(Bool(), Bool()));
+//
+template <typename Generator1, typename Generator2>
+internal::CartesianProductHolder2<Generator1, Generator2> Combine(
+ const Generator1& g1, const Generator2& g2) {
+ return internal::CartesianProductHolder2<Generator1, Generator2>(
+ g1, g2);
+}
+
+template <typename Generator1, typename Generator2, typename Generator3>
+internal::CartesianProductHolder3<Generator1, Generator2, Generator3> Combine(
+ const Generator1& g1, const Generator2& g2, const Generator3& g3) {
+ return internal::CartesianProductHolder3<Generator1, Generator2, Generator3>(
+ g1, g2, g3);
+}
+
+template <typename Generator1, typename Generator2, typename Generator3,
+ typename Generator4>
+internal::CartesianProductHolder4<Generator1, Generator2, Generator3,
+ Generator4> Combine(
+ const Generator1& g1, const Generator2& g2, const Generator3& g3,
+ const Generator4& g4) {
+ return internal::CartesianProductHolder4<Generator1, Generator2, Generator3,
+ Generator4>(
+ g1, g2, g3, g4);
+}
+
+template <typename Generator1, typename Generator2, typename Generator3,
+ typename Generator4, typename Generator5>
+internal::CartesianProductHolder5<Generator1, Generator2, Generator3,
+ Generator4, Generator5> Combine(
+ const Generator1& g1, const Generator2& g2, const Generator3& g3,
+ const Generator4& g4, const Generator5& g5) {
+ return internal::CartesianProductHolder5<Generator1, Generator2, Generator3,
+ Generator4, Generator5>(
+ g1, g2, g3, g4, g5);
+}
+
+template <typename Generator1, typename Generator2, typename Generator3,
+ typename Generator4, typename Generator5, typename Generator6>
+internal::CartesianProductHolder6<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6> Combine(
+ const Generator1& g1, const Generator2& g2, const Generator3& g3,
+ const Generator4& g4, const Generator5& g5, const Generator6& g6) {
+ return internal::CartesianProductHolder6<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6>(
+ g1, g2, g3, g4, g5, g6);
+}
+
+template <typename Generator1, typename Generator2, typename Generator3,
+ typename Generator4, typename Generator5, typename Generator6,
+ typename Generator7>
+internal::CartesianProductHolder7<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6, Generator7> Combine(
+ const Generator1& g1, const Generator2& g2, const Generator3& g3,
+ const Generator4& g4, const Generator5& g5, const Generator6& g6,
+ const Generator7& g7) {
+ return internal::CartesianProductHolder7<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6, Generator7>(
+ g1, g2, g3, g4, g5, g6, g7);
+}
+
+template <typename Generator1, typename Generator2, typename Generator3,
+ typename Generator4, typename Generator5, typename Generator6,
+ typename Generator7, typename Generator8>
+internal::CartesianProductHolder8<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6, Generator7, Generator8> Combine(
+ const Generator1& g1, const Generator2& g2, const Generator3& g3,
+ const Generator4& g4, const Generator5& g5, const Generator6& g6,
+ const Generator7& g7, const Generator8& g8) {
+ return internal::CartesianProductHolder8<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6, Generator7, Generator8>(
+ g1, g2, g3, g4, g5, g6, g7, g8);
+}
+
+template <typename Generator1, typename Generator2, typename Generator3,
+ typename Generator4, typename Generator5, typename Generator6,
+ typename Generator7, typename Generator8, typename Generator9>
+internal::CartesianProductHolder9<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6, Generator7, Generator8,
+ Generator9> Combine(
+ const Generator1& g1, const Generator2& g2, const Generator3& g3,
+ const Generator4& g4, const Generator5& g5, const Generator6& g6,
+ const Generator7& g7, const Generator8& g8, const Generator9& g9) {
+ return internal::CartesianProductHolder9<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6, Generator7, Generator8, Generator9>(
+ g1, g2, g3, g4, g5, g6, g7, g8, g9);
+}
+
+template <typename Generator1, typename Generator2, typename Generator3,
+ typename Generator4, typename Generator5, typename Generator6,
+ typename Generator7, typename Generator8, typename Generator9,
+ typename Generator10>
+internal::CartesianProductHolder10<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6, Generator7, Generator8, Generator9,
+ Generator10> Combine(
+ const Generator1& g1, const Generator2& g2, const Generator3& g3,
+ const Generator4& g4, const Generator5& g5, const Generator6& g6,
+ const Generator7& g7, const Generator8& g8, const Generator9& g9,
+ const Generator10& g10) {
+ return internal::CartesianProductHolder10<Generator1, Generator2, Generator3,
+ Generator4, Generator5, Generator6, Generator7, Generator8, Generator9,
+ Generator10>(
+ g1, g2, g3, g4, g5, g6, g7, g8, g9, g10);
+}
+# endif // GTEST_HAS_COMBINE
+
+
+
+# define TEST_P(test_case_name, test_name) \
+ class GTEST_TEST_CLASS_NAME_(test_case_name, test_name) \
+ : public test_case_name { \
+ public: \
+ GTEST_TEST_CLASS_NAME_(test_case_name, test_name)() {} \
+ virtual void TestBody(); \
+ private: \
+ static int AddToRegistry() { \
+ ::testing::UnitTest::GetInstance()->parameterized_test_registry(). \
+ GetTestCasePatternHolder<test_case_name>(\
+ #test_case_name, __FILE__, __LINE__)->AddTestPattern(\
+ #test_case_name, \
+ #test_name, \
+ new ::testing::internal::TestMetaFactory< \
+ GTEST_TEST_CLASS_NAME_(test_case_name, test_name)>()); \
+ return 0; \
+ } \
+ static int gtest_registering_dummy_; \
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(\
+ GTEST_TEST_CLASS_NAME_(test_case_name, test_name)); \
+ }; \
+ int GTEST_TEST_CLASS_NAME_(test_case_name, \
+ test_name)::gtest_registering_dummy_ = \
+ GTEST_TEST_CLASS_NAME_(test_case_name, test_name)::AddToRegistry(); \
+ void GTEST_TEST_CLASS_NAME_(test_case_name, test_name)::TestBody()
+
+# define INSTANTIATE_TEST_CASE_P(prefix, test_case_name, generator) \
+ ::testing::internal::ParamGenerator<test_case_name::ParamType> \
+ gtest_##prefix##test_case_name##_EvalGenerator_() { return generator; } \
+ int gtest_##prefix##test_case_name##_dummy_ = \
+ ::testing::UnitTest::GetInstance()->parameterized_test_registry(). \
+ GetTestCasePatternHolder<test_case_name>(\
+ #test_case_name, __FILE__, __LINE__)->AddTestCaseInstantiation(\
+ #prefix, \
+ >est_##prefix##test_case_name##_EvalGenerator_, \
+ __FILE__, __LINE__)
+
+} // namespace testing
+
+#endif // GTEST_HAS_PARAM_TEST
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_PARAM_TEST_H_
+// Copyright 2006, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+//
+// Google C++ Testing Framework definitions useful in production code.
+
+#ifndef GTEST_INCLUDE_GTEST_GTEST_PROD_H_
+#define GTEST_INCLUDE_GTEST_GTEST_PROD_H_
+
+// When you need to test the private or protected members of a class,
+// use the FRIEND_TEST macro to declare your tests as friends of the
+// class. For example:
+//
+// class MyClass {
+// private:
+// void MyMethod();
+// FRIEND_TEST(MyClassTest, MyMethod);
+// };
+//
+// class MyClassTest : public testing::Test {
+// // ...
+// };
+//
+// TEST_F(MyClassTest, MyMethod) {
+// // Can call MyClass::MyMethod() here.
+// }
+
+#define FRIEND_TEST(test_case_name, test_name)\
+friend class test_case_name##_##test_name##_Test
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_PROD_H_
+// Copyright 2008, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: mheule at google.com (Markus Heule)
+//
+
+#ifndef GTEST_INCLUDE_GTEST_GTEST_TEST_PART_H_
+#define GTEST_INCLUDE_GTEST_GTEST_TEST_PART_H_
+
+#include <iosfwd>
+#include <vector>
+
+namespace testing {
+
+// A copyable object representing the result of a test part (i.e. an
+// assertion or an explicit FAIL(), ADD_FAILURE(), or SUCCESS()).
+//
+// Don't inherit from TestPartResult as its destructor is not virtual.
+class GTEST_API_ TestPartResult {
+ public:
+ // The possible outcomes of a test part (i.e. an assertion or an
+ // explicit SUCCEED(), FAIL(), or ADD_FAILURE()).
+ enum Type {
+ kSuccess, // Succeeded.
+ kNonFatalFailure, // Failed but the test can continue.
+ kFatalFailure // Failed and the test should be terminated.
+ };
+
+ // C'tor. TestPartResult does NOT have a default constructor.
+ // Always use this constructor (with parameters) to create a
+ // TestPartResult object.
+ TestPartResult(Type a_type,
+ const char* a_file_name,
+ int a_line_number,
+ const char* a_message)
+ : type_(a_type),
+ file_name_(a_file_name == NULL ? "" : a_file_name),
+ line_number_(a_line_number),
+ summary_(ExtractSummary(a_message)),
+ message_(a_message) {
+ }
+
+ // Gets the outcome of the test part.
+ Type type() const { return type_; }
+
+ // Gets the name of the source file where the test part took place, or
+ // NULL if it's unknown.
+ const char* file_name() const {
+ return file_name_.empty() ? NULL : file_name_.c_str();
+ }
+
+ // Gets the line in the source file where the test part took place,
+ // or -1 if it's unknown.
+ int line_number() const { return line_number_; }
+
+ // Gets the summary of the failure message.
+ const char* summary() const { return summary_.c_str(); }
+
+ // Gets the message associated with the test part.
+ const char* message() const { return message_.c_str(); }
+
+ // Returns true iff the test part passed.
+ bool passed() const { return type_ == kSuccess; }
+
+ // Returns true iff the test part failed.
+ bool failed() const { return type_ != kSuccess; }
+
+ // Returns true iff the test part non-fatally failed.
+ bool nonfatally_failed() const { return type_ == kNonFatalFailure; }
+
+ // Returns true iff the test part fatally failed.
+ bool fatally_failed() const { return type_ == kFatalFailure; }
+
+ private:
+ Type type_;
+
+ // Gets the summary of the failure message by omitting the stack
+ // trace in it.
+ static std::string ExtractSummary(const char* message);
+
+ // The name of the source file where the test part took place, or
+ // "" if the source file is unknown.
+ std::string file_name_;
+ // The line in the source file where the test part took place, or -1
+ // if the line number is unknown.
+ int line_number_;
+ std::string summary_; // The test failure summary.
+ std::string message_; // The test failure message.
+};
+
+// Prints a TestPartResult object.
+std::ostream& operator<<(std::ostream& os, const TestPartResult& result);
+
+// An array of TestPartResult objects.
+//
+// Don't inherit from TestPartResultArray as its destructor is not
+// virtual.
+class GTEST_API_ TestPartResultArray {
+ public:
+ TestPartResultArray() {}
+
+ // Appends the given TestPartResult to the array.
+ void Append(const TestPartResult& result);
+
+ // Returns the TestPartResult at the given index (0-based).
+ const TestPartResult& GetTestPartResult(int index) const;
+
+ // Returns the number of TestPartResult objects in the array.
+ int size() const;
+
+ private:
+ std::vector<TestPartResult> array_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(TestPartResultArray);
+};
+
+// This interface knows how to report a test part result.
+class TestPartResultReporterInterface {
+ public:
+ virtual ~TestPartResultReporterInterface() {}
+
+ virtual void ReportTestPartResult(const TestPartResult& result) = 0;
+};
+
+namespace internal {
+
+// This helper class is used by {ASSERT|EXPECT}_NO_FATAL_FAILURE to check if a
+// statement generates new fatal failures. To do so it registers itself as the
+// current test part result reporter. Besides checking if fatal failures were
+// reported, it only delegates the reporting to the former result reporter.
+// The original result reporter is restored in the destructor.
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+class GTEST_API_ HasNewFatalFailureHelper
+ : public TestPartResultReporterInterface {
+ public:
+ HasNewFatalFailureHelper();
+ virtual ~HasNewFatalFailureHelper();
+ virtual void ReportTestPartResult(const TestPartResult& result);
+ bool has_new_fatal_failure() const { return has_new_fatal_failure_; }
+ private:
+ bool has_new_fatal_failure_;
+ TestPartResultReporterInterface* original_reporter_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(HasNewFatalFailureHelper);
+};
+
+} // namespace internal
+
+} // namespace testing
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_TEST_PART_H_
+// Copyright 2008 Google Inc.
+// All Rights Reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: wan at google.com (Zhanyong Wan)
+
+#ifndef GTEST_INCLUDE_GTEST_GTEST_TYPED_TEST_H_
+#define GTEST_INCLUDE_GTEST_GTEST_TYPED_TEST_H_
+
+// This header implements typed tests and type-parameterized tests.
+
+// Typed (aka type-driven) tests repeat the same test for types in a
+// list. You must know which types you want to test with when writing
+// typed tests. Here's how you do it:
+
+#if 0
+
+// First, define a fixture class template. It should be parameterized
+// by a type. Remember to derive it from testing::Test.
+template <typename T>
+class FooTest : public testing::Test {
+ public:
+ ...
+ typedef std::list<T> List;
+ static T shared_;
+ T value_;
+};
+
+// Next, associate a list of types with the test case, which will be
+// repeated for each type in the list. The typedef is necessary for
+// the macro to parse correctly.
+typedef testing::Types<char, int, unsigned int> MyTypes;
+TYPED_TEST_CASE(FooTest, MyTypes);
+
+// If the type list contains only one type, you can write that type
+// directly without Types<...>:
+// TYPED_TEST_CASE(FooTest, int);
+
+// Then, use TYPED_TEST() instead of TEST_F() to define as many typed
+// tests for this test case as you want.
+TYPED_TEST(FooTest, DoesBlah) {
+ // Inside a test, refer to TypeParam to get the type parameter.
+ // Since we are inside a derived class template, C++ requires use to
+ // visit the members of FooTest via 'this'.
+ TypeParam n = this->value_;
+
+ // To visit static members of the fixture, add the TestFixture::
+ // prefix.
+ n += TestFixture::shared_;
+
+ // To refer to typedefs in the fixture, add the "typename
+ // TestFixture::" prefix.
+ typename TestFixture::List values;
+ values.push_back(n);
+ ...
+}
+
+TYPED_TEST(FooTest, HasPropertyA) { ... }
+
+#endif // 0
+
+// Type-parameterized tests are abstract test patterns parameterized
+// by a type. Compared with typed tests, type-parameterized tests
+// allow you to define the test pattern without knowing what the type
+// parameters are. The defined pattern can be instantiated with
+// different types any number of times, in any number of translation
+// units.
+//
+// If you are designing an interface or concept, you can define a
+// suite of type-parameterized tests to verify properties that any
+// valid implementation of the interface/concept should have. Then,
+// each implementation can easily instantiate the test suite to verify
+// that it conforms to the requirements, without having to write
+// similar tests repeatedly. Here's an example:
+
+#if 0
+
+// First, define a fixture class template. It should be parameterized
+// by a type. Remember to derive it from testing::Test.
+template <typename T>
+class FooTest : public testing::Test {
+ ...
+};
+
+// Next, declare that you will define a type-parameterized test case
+// (the _P suffix is for "parameterized" or "pattern", whichever you
+// prefer):
+TYPED_TEST_CASE_P(FooTest);
+
+// Then, use TYPED_TEST_P() to define as many type-parameterized tests
+// for this type-parameterized test case as you want.
+TYPED_TEST_P(FooTest, DoesBlah) {
+ // Inside a test, refer to TypeParam to get the type parameter.
+ TypeParam n = 0;
+ ...
+}
+
+TYPED_TEST_P(FooTest, HasPropertyA) { ... }
+
+// Now the tricky part: you need to register all test patterns before
+// you can instantiate them. The first argument of the macro is the
+// test case name; the rest are the names of the tests in this test
+// case.
+REGISTER_TYPED_TEST_CASE_P(FooTest,
+ DoesBlah, HasPropertyA);
+
+// Finally, you are free to instantiate the pattern with the types you
+// want. If you put the above code in a header file, you can #include
+// it in multiple C++ source files and instantiate it multiple times.
+//
+// To distinguish different instances of the pattern, the first
+// argument to the INSTANTIATE_* macro is a prefix that will be added
+// to the actual test case name. Remember to pick unique prefixes for
+// different instances.
+typedef testing::Types<char, int, unsigned int> MyTypes;
+INSTANTIATE_TYPED_TEST_CASE_P(My, FooTest, MyTypes);
+
+// If the type list contains only one type, you can write that type
+// directly without Types<...>:
+// INSTANTIATE_TYPED_TEST_CASE_P(My, FooTest, int);
+
+#endif // 0
+
+
+// Implements typed tests.
+
+#if GTEST_HAS_TYPED_TEST
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// Expands to the name of the typedef for the type parameters of the
+// given test case.
+# define GTEST_TYPE_PARAMS_(TestCaseName) gtest_type_params_##TestCaseName##_
+
+// The 'Types' template argument below must have spaces around it
+// since some compilers may choke on '>>' when passing a template
+// instance (e.g. Types<int>)
+# define TYPED_TEST_CASE(CaseName, Types) \
+ typedef ::testing::internal::TypeList< Types >::type \
+ GTEST_TYPE_PARAMS_(CaseName)
+
+# define TYPED_TEST(CaseName, TestName) \
+ template <typename gtest_TypeParam_> \
+ class GTEST_TEST_CLASS_NAME_(CaseName, TestName) \
+ : public CaseName<gtest_TypeParam_> { \
+ private: \
+ typedef CaseName<gtest_TypeParam_> TestFixture; \
+ typedef gtest_TypeParam_ TypeParam; \
+ virtual void TestBody(); \
+ }; \
+ bool gtest_##CaseName##_##TestName##_registered_ GTEST_ATTRIBUTE_UNUSED_ = \
+ ::testing::internal::TypeParameterizedTest< \
+ CaseName, \
+ ::testing::internal::TemplateSel< \
+ GTEST_TEST_CLASS_NAME_(CaseName, TestName)>, \
+ GTEST_TYPE_PARAMS_(CaseName)>::Register(\
+ "", #CaseName, #TestName, 0); \
+ template <typename gtest_TypeParam_> \
+ void GTEST_TEST_CLASS_NAME_(CaseName, TestName)<gtest_TypeParam_>::TestBody()
+
+#endif // GTEST_HAS_TYPED_TEST
+
+// Implements type-parameterized tests.
+
+#if GTEST_HAS_TYPED_TEST_P
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// Expands to the namespace name that the type-parameterized tests for
+// the given type-parameterized test case are defined in. The exact
+// name of the namespace is subject to change without notice.
+# define GTEST_CASE_NAMESPACE_(TestCaseName) \
+ gtest_case_##TestCaseName##_
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+//
+// Expands to the name of the variable used to remember the names of
+// the defined tests in the given test case.
+# define GTEST_TYPED_TEST_CASE_P_STATE_(TestCaseName) \
+ gtest_typed_test_case_p_state_##TestCaseName##_
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE DIRECTLY.
+//
+// Expands to the name of the variable used to remember the names of
+// the registered tests in the given test case.
+# define GTEST_REGISTERED_TEST_NAMES_(TestCaseName) \
+ gtest_registered_test_names_##TestCaseName##_
+
+// The variables defined in the type-parameterized test macros are
+// static as typically these macros are used in a .h file that can be
+// #included in multiple translation units linked together.
+# define TYPED_TEST_CASE_P(CaseName) \
+ static ::testing::internal::TypedTestCasePState \
+ GTEST_TYPED_TEST_CASE_P_STATE_(CaseName)
+
+# define TYPED_TEST_P(CaseName, TestName) \
+ namespace GTEST_CASE_NAMESPACE_(CaseName) { \
+ template <typename gtest_TypeParam_> \
+ class TestName : public CaseName<gtest_TypeParam_> { \
+ private: \
+ typedef CaseName<gtest_TypeParam_> TestFixture; \
+ typedef gtest_TypeParam_ TypeParam; \
+ virtual void TestBody(); \
+ }; \
+ static bool gtest_##TestName##_defined_ GTEST_ATTRIBUTE_UNUSED_ = \
+ GTEST_TYPED_TEST_CASE_P_STATE_(CaseName).AddTestName(\
+ __FILE__, __LINE__, #CaseName, #TestName); \
+ } \
+ template <typename gtest_TypeParam_> \
+ void GTEST_CASE_NAMESPACE_(CaseName)::TestName<gtest_TypeParam_>::TestBody()
+
+# define REGISTER_TYPED_TEST_CASE_P(CaseName, ...) \
+ namespace GTEST_CASE_NAMESPACE_(CaseName) { \
+ typedef ::testing::internal::Templates<__VA_ARGS__>::type gtest_AllTests_; \
+ } \
+ static const char* const GTEST_REGISTERED_TEST_NAMES_(CaseName) = \
+ GTEST_TYPED_TEST_CASE_P_STATE_(CaseName).VerifyRegisteredTestNames(\
+ __FILE__, __LINE__, #__VA_ARGS__)
+
+// The 'Types' template argument below must have spaces around it
+// since some compilers may choke on '>>' when passing a template
+// instance (e.g. Types<int>)
+# define INSTANTIATE_TYPED_TEST_CASE_P(Prefix, CaseName, Types) \
+ bool gtest_##Prefix##_##CaseName GTEST_ATTRIBUTE_UNUSED_ = \
+ ::testing::internal::TypeParameterizedTestCase<CaseName, \
+ GTEST_CASE_NAMESPACE_(CaseName)::gtest_AllTests_, \
+ ::testing::internal::TypeList< Types >::type>::Register(\
+ #Prefix, #CaseName, GTEST_REGISTERED_TEST_NAMES_(CaseName))
+
+#endif // GTEST_HAS_TYPED_TEST_P
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_TYPED_TEST_H_
+
+// Depending on the platform, different string classes are available.
+// On Linux, in addition to ::std::string, Google also makes use of
+// class ::string, which has the same interface as ::std::string, but
+// has a different implementation.
+//
+// The user can define GTEST_HAS_GLOBAL_STRING to 1 to indicate that
+// ::string is available AND is a distinct type to ::std::string, or
+// define it to 0 to indicate otherwise.
+//
+// If the user's ::std::string and ::string are the same class due to
+// aliasing, he should define GTEST_HAS_GLOBAL_STRING to 0.
+//
+// If the user doesn't define GTEST_HAS_GLOBAL_STRING, it is defined
+// heuristically.
+
+namespace testing {
+
+// Declares the flags.
+
+// This flag temporary enables the disabled tests.
+GTEST_DECLARE_bool_(also_run_disabled_tests);
+
+// This flag brings the debugger on an assertion failure.
+GTEST_DECLARE_bool_(break_on_failure);
+
+// This flag controls whether Google Test catches all test-thrown exceptions
+// and logs them as failures.
+GTEST_DECLARE_bool_(catch_exceptions);
+
+// This flag enables using colors in terminal output. Available values are
+// "yes" to enable colors, "no" (disable colors), or "auto" (the default)
+// to let Google Test decide.
+GTEST_DECLARE_string_(color);
+
+// This flag sets up the filter to select by name using a glob pattern
+// the tests to run. If the filter is not given all tests are executed.
+GTEST_DECLARE_string_(filter);
+
+// This flag causes the Google Test to list tests. None of the tests listed
+// are actually run if the flag is provided.
+GTEST_DECLARE_bool_(list_tests);
+
+// This flag controls whether Google Test emits a detailed XML report to a file
+// in addition to its normal textual output.
+GTEST_DECLARE_string_(output);
+
+// This flags control whether Google Test prints the elapsed time for each
+// test.
+GTEST_DECLARE_bool_(print_time);
+
+// This flag specifies the random number seed.
+GTEST_DECLARE_int32_(random_seed);
+
+// This flag sets how many times the tests are repeated. The default value
+// is 1. If the value is -1 the tests are repeating forever.
+GTEST_DECLARE_int32_(repeat);
+
+// This flag controls whether Google Test includes Google Test internal
+// stack frames in failure stack traces.
+GTEST_DECLARE_bool_(show_internal_stack_frames);
+
+// When this flag is specified, tests' order is randomized on every iteration.
+GTEST_DECLARE_bool_(shuffle);
+
+// This flag specifies the maximum number of stack frames to be
+// printed in a failure message.
+GTEST_DECLARE_int32_(stack_trace_depth);
+
+// When this flag is specified, a failed assertion will throw an
+// exception if exceptions are enabled, or exit the program with a
+// non-zero code otherwise.
+GTEST_DECLARE_bool_(throw_on_failure);
+
+// When this flag is set with a "host:port" string, on supported
+// platforms test results are streamed to the specified port on
+// the specified host machine.
+GTEST_DECLARE_string_(stream_result_to);
+
+// The upper limit for valid stack trace depths.
+const int kMaxStackTraceDepth = 100;
+
+namespace internal {
+
+class AssertHelper;
+class DefaultGlobalTestPartResultReporter;
+class ExecDeathTest;
+class NoExecDeathTest;
+class FinalSuccessChecker;
+class GTestFlagSaver;
+class StreamingListenerTest;
+class TestResultAccessor;
+class TestEventListenersAccessor;
+class TestEventRepeater;
+class UnitTestRecordPropertyTestHelper;
+class WindowsDeathTest;
+class UnitTestImpl* GetUnitTestImpl();
+void ReportFailureInUnknownLocation(TestPartResult::Type result_type,
+ const std::string& message);
+
+} // namespace internal
+
+// The friend relationship of some of these classes is cyclic.
+// If we don't forward declare them the compiler might confuse the classes
+// in friendship clauses with same named classes on the scope.
+class Test;
+class TestCase;
+class TestInfo;
+class UnitTest;
+
+// A class for indicating whether an assertion was successful. When
+// the assertion wasn't successful, the AssertionResult object
+// remembers a non-empty message that describes how it failed.
+//
+// To create an instance of this class, use one of the factory functions
+// (AssertionSuccess() and AssertionFailure()).
+//
+// This class is useful for two purposes:
+// 1. Defining predicate functions to be used with Boolean test assertions
+// EXPECT_TRUE/EXPECT_FALSE and their ASSERT_ counterparts
+// 2. Defining predicate-format functions to be
+// used with predicate assertions (ASSERT_PRED_FORMAT*, etc).
+//
+// For example, if you define IsEven predicate:
+//
+// testing::AssertionResult IsEven(int n) {
+// if ((n % 2) == 0)
+// return testing::AssertionSuccess();
+// else
+// return testing::AssertionFailure() << n << " is odd";
+// }
+//
+// Then the failed expectation EXPECT_TRUE(IsEven(Fib(5)))
+// will print the message
+//
+// Value of: IsEven(Fib(5))
+// Actual: false (5 is odd)
+// Expected: true
+//
+// instead of a more opaque
+//
+// Value of: IsEven(Fib(5))
+// Actual: false
+// Expected: true
+//
+// in case IsEven is a simple Boolean predicate.
+//
+// If you expect your predicate to be reused and want to support informative
+// messages in EXPECT_FALSE and ASSERT_FALSE (negative assertions show up
+// about half as often as positive ones in our tests), supply messages for
+// both success and failure cases:
+//
+// testing::AssertionResult IsEven(int n) {
+// if ((n % 2) == 0)
+// return testing::AssertionSuccess() << n << " is even";
+// else
+// return testing::AssertionFailure() << n << " is odd";
+// }
+//
+// Then a statement EXPECT_FALSE(IsEven(Fib(6))) will print
+//
+// Value of: IsEven(Fib(6))
+// Actual: true (8 is even)
+// Expected: false
+//
+// NB: Predicates that support negative Boolean assertions have reduced
+// performance in positive ones so be careful not to use them in tests
+// that have lots (tens of thousands) of positive Boolean assertions.
+//
+// To use this class with EXPECT_PRED_FORMAT assertions such as:
+//
+// // Verifies that Foo() returns an even number.
+// EXPECT_PRED_FORMAT1(IsEven, Foo());
+//
+// you need to define:
+//
+// testing::AssertionResult IsEven(const char* expr, int n) {
+// if ((n % 2) == 0)
+// return testing::AssertionSuccess();
+// else
+// return testing::AssertionFailure()
+// << "Expected: " << expr << " is even\n Actual: it's " << n;
+// }
+//
+// If Foo() returns 5, you will see the following message:
+//
+// Expected: Foo() is even
+// Actual: it's 5
+//
+class GTEST_API_ AssertionResult {
+ public:
+ // Copy constructor.
+ // Used in EXPECT_TRUE/FALSE(assertion_result).
+ AssertionResult(const AssertionResult& other);
+ // Used in the EXPECT_TRUE/FALSE(bool_expression).
+ explicit AssertionResult(bool success) : success_(success) {}
+
+ // Returns true iff the assertion succeeded.
+ operator bool() const { return success_; } // NOLINT
+
+ // Returns the assertion's negation. Used with EXPECT/ASSERT_FALSE.
+ AssertionResult operator!() const;
+
+ // Returns the text streamed into this AssertionResult. Test assertions
+ // use it when they fail (i.e., the predicate's outcome doesn't match the
+ // assertion's expectation). When nothing has been streamed into the
+ // object, returns an empty string.
+ const char* message() const {
+ return message_.get() != NULL ? message_->c_str() : "";
+ }
+ // TODO(vladl at google.com): Remove this after making sure no clients use it.
+ // Deprecated; please use message() instead.
+ const char* failure_message() const { return message(); }
+
+ // Streams a custom failure message into this object.
+ template <typename T> AssertionResult& operator<<(const T& value) {
+ AppendMessage(Message() << value);
+ return *this;
+ }
+
+ // Allows streaming basic output manipulators such as endl or flush into
+ // this object.
+ AssertionResult& operator<<(
+ ::std::ostream& (*basic_manipulator)(::std::ostream& stream)) {
+ AppendMessage(Message() << basic_manipulator);
+ return *this;
+ }
+
+ private:
+ // Appends the contents of message to message_.
+ void AppendMessage(const Message& a_message) {
+ if (message_.get() == NULL)
+ message_.reset(new ::std::string);
+ message_->append(a_message.GetString().c_str());
+ }
+
+ // Stores result of the assertion predicate.
+ bool success_;
+ // Stores the message describing the condition in case the expectation
+ // construct is not satisfied with the predicate's outcome.
+ // Referenced via a pointer to avoid taking too much stack frame space
+ // with test assertions.
+ internal::scoped_ptr< ::std::string> message_;
+
+ GTEST_DISALLOW_ASSIGN_(AssertionResult);
+};
+
+// Makes a successful assertion result.
+GTEST_API_ AssertionResult AssertionSuccess();
+
+// Makes a failed assertion result.
+GTEST_API_ AssertionResult AssertionFailure();
+
+// Makes a failed assertion result with the given failure message.
+// Deprecated; use AssertionFailure() << msg.
+GTEST_API_ AssertionResult AssertionFailure(const Message& msg);
+
+// The abstract class that all tests inherit from.
+//
+// In Google Test, a unit test program contains one or many TestCases, and
+// each TestCase contains one or many Tests.
+//
+// When you define a test using the TEST macro, you don't need to
+// explicitly derive from Test - the TEST macro automatically does
+// this for you.
+//
+// The only time you derive from Test is when defining a test fixture
+// to be used a TEST_F. For example:
+//
+// class FooTest : public testing::Test {
+// protected:
+// virtual void SetUp() { ... }
+// virtual void TearDown() { ... }
+// ...
+// };
+//
+// TEST_F(FooTest, Bar) { ... }
+// TEST_F(FooTest, Baz) { ... }
+//
+// Test is not copyable.
+class GTEST_API_ Test {
+ public:
+ friend class TestInfo;
+
+ // Defines types for pointers to functions that set up and tear down
+ // a test case.
+ typedef internal::SetUpTestCaseFunc SetUpTestCaseFunc;
+ typedef internal::TearDownTestCaseFunc TearDownTestCaseFunc;
+
+ // The d'tor is virtual as we intend to inherit from Test.
+ virtual ~Test();
+
+ // Sets up the stuff shared by all tests in this test case.
+ //
+ // Google Test will call Foo::SetUpTestCase() before running the first
+ // test in test case Foo. Hence a sub-class can define its own
+ // SetUpTestCase() method to shadow the one defined in the super
+ // class.
+ static void SetUpTestCase() {}
+
+ // Tears down the stuff shared by all tests in this test case.
+ //
+ // Google Test will call Foo::TearDownTestCase() after running the last
+ // test in test case Foo. Hence a sub-class can define its own
+ // TearDownTestCase() method to shadow the one defined in the super
+ // class.
+ static void TearDownTestCase() {}
+
+ // Returns true iff the current test has a fatal failure.
+ static bool HasFatalFailure();
+
+ // Returns true iff the current test has a non-fatal failure.
+ static bool HasNonfatalFailure();
+
+ // Returns true iff the current test has a (either fatal or
+ // non-fatal) failure.
+ static bool HasFailure() { return HasFatalFailure() || HasNonfatalFailure(); }
+
+ // Logs a property for the current test, test case, or for the entire
+ // invocation of the test program when used outside of the context of a
+ // test case. Only the last value for a given key is remembered. These
+ // are public static so they can be called from utility functions that are
+ // not members of the test fixture. Calls to RecordProperty made during
+ // lifespan of the test (from the moment its constructor starts to the
+ // moment its destructor finishes) will be output in XML as attributes of
+ // the <testcase> element. Properties recorded from fixture's
+ // SetUpTestCase or TearDownTestCase are logged as attributes of the
+ // corresponding <testsuite> element. Calls to RecordProperty made in the
+ // global context (before or after invocation of RUN_ALL_TESTS and from
+ // SetUp/TearDown method of Environment objects registered with Google
+ // Test) will be output as attributes of the <testsuites> element.
+ static void RecordProperty(const std::string& key, const std::string& value);
+ static void RecordProperty(const std::string& key, int value);
+
+ protected:
+ // Creates a Test object.
+ Test();
+
+ // Sets up the test fixture.
+ virtual void SetUp();
+
+ // Tears down the test fixture.
+ virtual void TearDown();
+
+ private:
+ // Returns true iff the current test has the same fixture class as
+ // the first test in the current test case.
+ static bool HasSameFixtureClass();
+
+ // Runs the test after the test fixture has been set up.
+ //
+ // A sub-class must implement this to define the test logic.
+ //
+ // DO NOT OVERRIDE THIS FUNCTION DIRECTLY IN A USER PROGRAM.
+ // Instead, use the TEST or TEST_F macro.
+ virtual void TestBody() = 0;
+
+ // Sets up, executes, and tears down the test.
+ void Run();
+
+ // Deletes self. We deliberately pick an unusual name for this
+ // internal method to avoid clashing with names used in user TESTs.
+ void DeleteSelf_() { delete this; }
+
+ // Uses a GTestFlagSaver to save and restore all Google Test flags.
+ const internal::GTestFlagSaver* const gtest_flag_saver_;
+
+ // Often a user mis-spells SetUp() as Setup() and spends a long time
+ // wondering why it is never called by Google Test. The declaration of
+ // the following method is solely for catching such an error at
+ // compile time:
+ //
+ // - The return type is deliberately chosen to be not void, so it
+ // will be a conflict if a user declares void Setup() in his test
+ // fixture.
+ //
+ // - This method is private, so it will be another compiler error
+ // if a user calls it from his test fixture.
+ //
+ // DO NOT OVERRIDE THIS FUNCTION.
+ //
+ // If you see an error about overriding the following function or
+ // about it being private, you have mis-spelled SetUp() as Setup().
+ struct Setup_should_be_spelled_SetUp {};
+ virtual Setup_should_be_spelled_SetUp* Setup() { return NULL; }
+
+ // We disallow copying Tests.
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(Test);
+};
+
+typedef internal::TimeInMillis TimeInMillis;
+
+// A copyable object representing a user specified test property which can be
+// output as a key/value string pair.
+//
+// Don't inherit from TestProperty as its destructor is not virtual.
+class TestProperty {
+ public:
+ // C'tor. TestProperty does NOT have a default constructor.
+ // Always use this constructor (with parameters) to create a
+ // TestProperty object.
+ TestProperty(const std::string& a_key, const std::string& a_value) :
+ key_(a_key), value_(a_value) {
+ }
+
+ // Gets the user supplied key.
+ const char* key() const {
+ return key_.c_str();
+ }
+
+ // Gets the user supplied value.
+ const char* value() const {
+ return value_.c_str();
+ }
+
+ // Sets a new value, overriding the one supplied in the constructor.
+ void SetValue(const std::string& new_value) {
+ value_ = new_value;
+ }
+
+ private:
+ // The key supplied by the user.
+ std::string key_;
+ // The value supplied by the user.
+ std::string value_;
+};
+
+// The result of a single Test. This includes a list of
+// TestPartResults, a list of TestProperties, a count of how many
+// death tests there are in the Test, and how much time it took to run
+// the Test.
+//
+// TestResult is not copyable.
+class GTEST_API_ TestResult {
+ public:
+ // Creates an empty TestResult.
+ TestResult();
+
+ // D'tor. Do not inherit from TestResult.
+ ~TestResult();
+
+ // Gets the number of all test parts. This is the sum of the number
+ // of successful test parts and the number of failed test parts.
+ int total_part_count() const;
+
+ // Returns the number of the test properties.
+ int test_property_count() const;
+
+ // Returns true iff the test passed (i.e. no test part failed).
+ bool Passed() const { return !Failed(); }
+
+ // Returns true iff the test failed.
+ bool Failed() const;
+
+ // Returns true iff the test fatally failed.
+ bool HasFatalFailure() const;
+
+ // Returns true iff the test has a non-fatal failure.
+ bool HasNonfatalFailure() const;
+
+ // Returns the elapsed time, in milliseconds.
+ TimeInMillis elapsed_time() const { return elapsed_time_; }
+
+ // Returns the i-th test part result among all the results. i can range
+ // from 0 to test_property_count() - 1. If i is not in that range, aborts
+ // the program.
+ const TestPartResult& GetTestPartResult(int i) const;
+
+ // Returns the i-th test property. i can range from 0 to
+ // test_property_count() - 1. If i is not in that range, aborts the
+ // program.
+ const TestProperty& GetTestProperty(int i) const;
+
+ private:
+ friend class TestInfo;
+ friend class TestCase;
+ friend class UnitTest;
+ friend class internal::DefaultGlobalTestPartResultReporter;
+ friend class internal::ExecDeathTest;
+ friend class internal::TestResultAccessor;
+ friend class internal::UnitTestImpl;
+ friend class internal::WindowsDeathTest;
+
+ // Gets the vector of TestPartResults.
+ const std::vector<TestPartResult>& test_part_results() const {
+ return test_part_results_;
+ }
+
+ // Gets the vector of TestProperties.
+ const std::vector<TestProperty>& test_properties() const {
+ return test_properties_;
+ }
+
+ // Sets the elapsed time.
+ void set_elapsed_time(TimeInMillis elapsed) { elapsed_time_ = elapsed; }
+
+ // Adds a test property to the list. The property is validated and may add
+ // a non-fatal failure if invalid (e.g., if it conflicts with reserved
+ // key names). If a property is already recorded for the same key, the
+ // value will be updated, rather than storing multiple values for the same
+ // key. xml_element specifies the element for which the property is being
+ // recorded and is used for validation.
+ void RecordProperty(const std::string& xml_element,
+ const TestProperty& test_property);
+
+ // Adds a failure if the key is a reserved attribute of Google Test
+ // testcase tags. Returns true if the property is valid.
+ // TODO(russr): Validate attribute names are legal and human readable.
+ static bool ValidateTestProperty(const std::string& xml_element,
+ const TestProperty& test_property);
+
+ // Adds a test part result to the list.
+ void AddTestPartResult(const TestPartResult& test_part_result);
+
+ // Returns the death test count.
+ int death_test_count() const { return death_test_count_; }
+
+ // Increments the death test count, returning the new count.
+ int increment_death_test_count() { return ++death_test_count_; }
+
+ // Clears the test part results.
+ void ClearTestPartResults();
+
+ // Clears the object.
+ void Clear();
+
+ // Protects mutable state of the property vector and of owned
+ // properties, whose values may be updated.
+ internal::Mutex test_properites_mutex_;
+
+ // The vector of TestPartResults
+ std::vector<TestPartResult> test_part_results_;
+ // The vector of TestProperties
+ std::vector<TestProperty> test_properties_;
+ // Running count of death tests.
+ int death_test_count_;
+ // The elapsed time, in milliseconds.
+ TimeInMillis elapsed_time_;
+
+ // We disallow copying TestResult.
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(TestResult);
+}; // class TestResult
+
+// A TestInfo object stores the following information about a test:
+//
+// Test case name
+// Test name
+// Whether the test should be run
+// A function pointer that creates the test object when invoked
+// Test result
+//
+// The constructor of TestInfo registers itself with the UnitTest
+// singleton such that the RUN_ALL_TESTS() macro knows which tests to
+// run.
+class GTEST_API_ TestInfo {
+ public:
+ // Destructs a TestInfo object. This function is not virtual, so
+ // don't inherit from TestInfo.
+ ~TestInfo();
+
+ // Returns the test case name.
+ const char* test_case_name() const { return test_case_name_.c_str(); }
+
+ // Returns the test name.
+ const char* name() const { return name_.c_str(); }
+
+ // Returns the name of the parameter type, or NULL if this is not a typed
+ // or a type-parameterized test.
+ const char* type_param() const {
+ if (type_param_.get() != NULL)
+ return type_param_->c_str();
+ return NULL;
+ }
+
+ // Returns the text representation of the value parameter, or NULL if this
+ // is not a value-parameterized test.
+ const char* value_param() const {
+ if (value_param_.get() != NULL)
+ return value_param_->c_str();
+ return NULL;
+ }
+
+ // Returns true if this test should run, that is if the test is not
+ // disabled (or it is disabled but the also_run_disabled_tests flag has
+ // been specified) and its full name matches the user-specified filter.
+ //
+ // Google Test allows the user to filter the tests by their full names.
+ // The full name of a test Bar in test case Foo is defined as
+ // "Foo.Bar". Only the tests that match the filter will run.
+ //
+ // A filter is a colon-separated list of glob (not regex) patterns,
+ // optionally followed by a '-' and a colon-separated list of
+ // negative patterns (tests to exclude). A test is run if it
+ // matches one of the positive patterns and does not match any of
+ // the negative patterns.
+ //
+ // For example, *A*:Foo.* is a filter that matches any string that
+ // contains the character 'A' or starts with "Foo.".
+ bool should_run() const { return should_run_; }
+
+ // Returns true iff this test will appear in the XML report.
+ bool is_reportable() const {
+ // For now, the XML report includes all tests matching the filter.
+ // In the future, we may trim tests that are excluded because of
+ // sharding.
+ return matches_filter_;
+ }
+
+ // Returns the result of the test.
+ const TestResult* result() const { return &result_; }
+
+ private:
+#if GTEST_HAS_DEATH_TEST
+ friend class internal::DefaultDeathTestFactory;
+#endif // GTEST_HAS_DEATH_TEST
+ friend class Test;
+ friend class TestCase;
+ friend class internal::UnitTestImpl;
+ friend class internal::StreamingListenerTest;
+ friend TestInfo* internal::MakeAndRegisterTestInfo(
+ const char* test_case_name,
+ const char* name,
+ const char* type_param,
+ const char* value_param,
+ internal::TypeId fixture_class_id,
+ Test::SetUpTestCaseFunc set_up_tc,
+ Test::TearDownTestCaseFunc tear_down_tc,
+ internal::TestFactoryBase* factory);
+
+ // Constructs a TestInfo object. The newly constructed instance assumes
+ // ownership of the factory object.
+ TestInfo(const std::string& test_case_name,
+ const std::string& name,
+ const char* a_type_param, // NULL if not a type-parameterized test
+ const char* a_value_param, // NULL if not a value-parameterized test
+ internal::TypeId fixture_class_id,
+ internal::TestFactoryBase* factory);
+
+ // Increments the number of death tests encountered in this test so
+ // far.
+ int increment_death_test_count() {
+ return result_.increment_death_test_count();
+ }
+
+ // Creates the test object, runs it, records its result, and then
+ // deletes it.
+ void Run();
+
+ static void ClearTestResult(TestInfo* test_info) {
+ test_info->result_.Clear();
+ }
+
+ // These fields are immutable properties of the test.
+ const std::string test_case_name_; // Test case name
+ const std::string name_; // Test name
+ // Name of the parameter type, or NULL if this is not a typed or a
+ // type-parameterized test.
+ const internal::scoped_ptr<const ::std::string> type_param_;
+ // Text representation of the value parameter, or NULL if this is not a
+ // value-parameterized test.
+ const internal::scoped_ptr<const ::std::string> value_param_;
+ const internal::TypeId fixture_class_id_; // ID of the test fixture class
+ bool should_run_; // True iff this test should run
+ bool is_disabled_; // True iff this test is disabled
+ bool matches_filter_; // True if this test matches the
+ // user-specified filter.
+ internal::TestFactoryBase* const factory_; // The factory that creates
+ // the test object
+
+ // This field is mutable and needs to be reset before running the
+ // test for the second time.
+ TestResult result_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(TestInfo);
+};
+
+// A test case, which consists of a vector of TestInfos.
+//
+// TestCase is not copyable.
+class GTEST_API_ TestCase {
+ public:
+ // Creates a TestCase with the given name.
+ //
+ // TestCase does NOT have a default constructor. Always use this
+ // constructor to create a TestCase object.
+ //
+ // Arguments:
+ //
+ // name: name of the test case
+ // a_type_param: the name of the test's type parameter, or NULL if
+ // this is not a type-parameterized test.
+ // set_up_tc: pointer to the function that sets up the test case
+ // tear_down_tc: pointer to the function that tears down the test case
+ TestCase(const char* name, const char* a_type_param,
+ Test::SetUpTestCaseFunc set_up_tc,
+ Test::TearDownTestCaseFunc tear_down_tc);
+
+ // Destructor of TestCase.
+ virtual ~TestCase();
+
+ // Gets the name of the TestCase.
+ const char* name() const { return name_.c_str(); }
+
+ // Returns the name of the parameter type, or NULL if this is not a
+ // type-parameterized test case.
+ const char* type_param() const {
+ if (type_param_.get() != NULL)
+ return type_param_->c_str();
+ return NULL;
+ }
+
+ // Returns true if any test in this test case should run.
+ bool should_run() const { return should_run_; }
+
+ // Gets the number of successful tests in this test case.
+ int successful_test_count() const;
+
+ // Gets the number of failed tests in this test case.
+ int failed_test_count() const;
+
+ // Gets the number of disabled tests that will be reported in the XML report.
+ int reportable_disabled_test_count() const;
+
+ // Gets the number of disabled tests in this test case.
+ int disabled_test_count() const;
+
+ // Gets the number of tests to be printed in the XML report.
+ int reportable_test_count() const;
+
+ // Get the number of tests in this test case that should run.
+ int test_to_run_count() const;
+
+ // Gets the number of all tests in this test case.
+ int total_test_count() const;
+
+ // Returns true iff the test case passed.
+ bool Passed() const { return !Failed(); }
+
+ // Returns true iff the test case failed.
+ bool Failed() const { return failed_test_count() > 0; }
+
+ // Returns the elapsed time, in milliseconds.
+ TimeInMillis elapsed_time() const { return elapsed_time_; }
+
+ // Returns the i-th test among all the tests. i can range from 0 to
+ // total_test_count() - 1. If i is not in that range, returns NULL.
+ const TestInfo* GetTestInfo(int i) const;
+
+ // Returns the TestResult that holds test properties recorded during
+ // execution of SetUpTestCase and TearDownTestCase.
+ const TestResult& ad_hoc_test_result() const { return ad_hoc_test_result_; }
+
+ private:
+ friend class Test;
+ friend class internal::UnitTestImpl;
+
+ // Gets the (mutable) vector of TestInfos in this TestCase.
+ std::vector<TestInfo*>& test_info_list() { return test_info_list_; }
+
+ // Gets the (immutable) vector of TestInfos in this TestCase.
+ const std::vector<TestInfo*>& test_info_list() const {
+ return test_info_list_;
+ }
+
+ // Returns the i-th test among all the tests. i can range from 0 to
+ // total_test_count() - 1. If i is not in that range, returns NULL.
+ TestInfo* GetMutableTestInfo(int i);
+
+ // Sets the should_run member.
+ void set_should_run(bool should) { should_run_ = should; }
+
+ // Adds a TestInfo to this test case. Will delete the TestInfo upon
+ // destruction of the TestCase object.
+ void AddTestInfo(TestInfo * test_info);
+
+ // Clears the results of all tests in this test case.
+ void ClearResult();
+
+ // Clears the results of all tests in the given test case.
+ static void ClearTestCaseResult(TestCase* test_case) {
+ test_case->ClearResult();
+ }
+
+ // Runs every test in this TestCase.
+ void Run();
+
+ // Runs SetUpTestCase() for this TestCase. This wrapper is needed
+ // for catching exceptions thrown from SetUpTestCase().
+ void RunSetUpTestCase() { (*set_up_tc_)(); }
+
+ // Runs TearDownTestCase() for this TestCase. This wrapper is
+ // needed for catching exceptions thrown from TearDownTestCase().
+ void RunTearDownTestCase() { (*tear_down_tc_)(); }
+
+ // Returns true iff test passed.
+ static bool TestPassed(const TestInfo* test_info) {
+ return test_info->should_run() && test_info->result()->Passed();
+ }
+
+ // Returns true iff test failed.
+ static bool TestFailed(const TestInfo* test_info) {
+ return test_info->should_run() && test_info->result()->Failed();
+ }
+
+ // Returns true iff the test is disabled and will be reported in the XML
+ // report.
+ static bool TestReportableDisabled(const TestInfo* test_info) {
+ return test_info->is_reportable() && test_info->is_disabled_;
+ }
+
+ // Returns true iff test is disabled.
+ static bool TestDisabled(const TestInfo* test_info) {
+ return test_info->is_disabled_;
+ }
+
+ // Returns true iff this test will appear in the XML report.
+ static bool TestReportable(const TestInfo* test_info) {
+ return test_info->is_reportable();
+ }
+
+ // Returns true if the given test should run.
+ static bool ShouldRunTest(const TestInfo* test_info) {
+ return test_info->should_run();
+ }
+
+ // Shuffles the tests in this test case.
+ void ShuffleTests(internal::Random* random);
+
+ // Restores the test order to before the first shuffle.
+ void UnshuffleTests();
+
+ // Name of the test case.
+ std::string name_;
+ // Name of the parameter type, or NULL if this is not a typed or a
+ // type-parameterized test.
+ const internal::scoped_ptr<const ::std::string> type_param_;
+ // The vector of TestInfos in their original order. It owns the
+ // elements in the vector.
+ std::vector<TestInfo*> test_info_list_;
+ // Provides a level of indirection for the test list to allow easy
+ // shuffling and restoring the test order. The i-th element in this
+ // vector is the index of the i-th test in the shuffled test list.
+ std::vector<int> test_indices_;
+ // Pointer to the function that sets up the test case.
+ Test::SetUpTestCaseFunc set_up_tc_;
+ // Pointer to the function that tears down the test case.
+ Test::TearDownTestCaseFunc tear_down_tc_;
+ // True iff any test in this test case should run.
+ bool should_run_;
+ // Elapsed time, in milliseconds.
+ TimeInMillis elapsed_time_;
+ // Holds test properties recorded during execution of SetUpTestCase and
+ // TearDownTestCase.
+ TestResult ad_hoc_test_result_;
+
+ // We disallow copying TestCases.
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(TestCase);
+};
+
+// An Environment object is capable of setting up and tearing down an
+// environment. The user should subclass this to define his own
+// environment(s).
+//
+// An Environment object does the set-up and tear-down in virtual
+// methods SetUp() and TearDown() instead of the constructor and the
+// destructor, as:
+//
+// 1. You cannot safely throw from a destructor. This is a problem
+// as in some cases Google Test is used where exceptions are enabled, and
+// we may want to implement ASSERT_* using exceptions where they are
+// available.
+// 2. You cannot use ASSERT_* directly in a constructor or
+// destructor.
+class Environment {
+ public:
+ // The d'tor is virtual as we need to subclass Environment.
+ virtual ~Environment() {}
+
+ // Override this to define how to set up the environment.
+ virtual void SetUp() {}
+
+ // Override this to define how to tear down the environment.
+ virtual void TearDown() {}
+ private:
+ // If you see an error about overriding the following function or
+ // about it being private, you have mis-spelled SetUp() as Setup().
+ struct Setup_should_be_spelled_SetUp {};
+ virtual Setup_should_be_spelled_SetUp* Setup() { return NULL; }
+};
+
+// The interface for tracing execution of tests. The methods are organized in
+// the order the corresponding events are fired.
+class TestEventListener {
+ public:
+ virtual ~TestEventListener() {}
+
+ // Fired before any test activity starts.
+ virtual void OnTestProgramStart(const UnitTest& unit_test) = 0;
+
+ // Fired before each iteration of tests starts. There may be more than
+ // one iteration if GTEST_FLAG(repeat) is set. iteration is the iteration
+ // index, starting from 0.
+ virtual void OnTestIterationStart(const UnitTest& unit_test,
+ int iteration) = 0;
+
+ // Fired before environment set-up for each iteration of tests starts.
+ virtual void OnEnvironmentsSetUpStart(const UnitTest& unit_test) = 0;
+
+ // Fired after environment set-up for each iteration of tests ends.
+ virtual void OnEnvironmentsSetUpEnd(const UnitTest& unit_test) = 0;
+
+ // Fired before the test case starts.
+ virtual void OnTestCaseStart(const TestCase& test_case) = 0;
+
+ // Fired before the test starts.
+ virtual void OnTestStart(const TestInfo& test_info) = 0;
+
+ // Fired after a failed assertion or a SUCCEED() invocation.
+ virtual void OnTestPartResult(const TestPartResult& test_part_result) = 0;
+
+ // Fired after the test ends.
+ virtual void OnTestEnd(const TestInfo& test_info) = 0;
+
+ // Fired after the test case ends.
+ virtual void OnTestCaseEnd(const TestCase& test_case) = 0;
+
+ // Fired before environment tear-down for each iteration of tests starts.
+ virtual void OnEnvironmentsTearDownStart(const UnitTest& unit_test) = 0;
+
+ // Fired after environment tear-down for each iteration of tests ends.
+ virtual void OnEnvironmentsTearDownEnd(const UnitTest& unit_test) = 0;
+
+ // Fired after each iteration of tests finishes.
+ virtual void OnTestIterationEnd(const UnitTest& unit_test,
+ int iteration) = 0;
+
+ // Fired after all test activities have ended.
+ virtual void OnTestProgramEnd(const UnitTest& unit_test) = 0;
+};
+
+// The convenience class for users who need to override just one or two
+// methods and are not concerned that a possible change to a signature of
+// the methods they override will not be caught during the build. For
+// comments about each method please see the definition of TestEventListener
+// above.
+class EmptyTestEventListener : public TestEventListener {
+ public:
+ virtual void OnTestProgramStart(const UnitTest& /*unit_test*/) {}
+ virtual void OnTestIterationStart(const UnitTest& /*unit_test*/,
+ int /*iteration*/) {}
+ virtual void OnEnvironmentsSetUpStart(const UnitTest& /*unit_test*/) {}
+ virtual void OnEnvironmentsSetUpEnd(const UnitTest& /*unit_test*/) {}
+ virtual void OnTestCaseStart(const TestCase& /*test_case*/) {}
+ virtual void OnTestStart(const TestInfo& /*test_info*/) {}
+ virtual void OnTestPartResult(const TestPartResult& /*test_part_result*/) {}
+ virtual void OnTestEnd(const TestInfo& /*test_info*/) {}
+ virtual void OnTestCaseEnd(const TestCase& /*test_case*/) {}
+ virtual void OnEnvironmentsTearDownStart(const UnitTest& /*unit_test*/) {}
+ virtual void OnEnvironmentsTearDownEnd(const UnitTest& /*unit_test*/) {}
+ virtual void OnTestIterationEnd(const UnitTest& /*unit_test*/,
+ int /*iteration*/) {}
+ virtual void OnTestProgramEnd(const UnitTest& /*unit_test*/) {}
+};
+
+// TestEventListeners lets users add listeners to track events in Google Test.
+class GTEST_API_ TestEventListeners {
+ public:
+ TestEventListeners();
+ ~TestEventListeners();
+
+ // Appends an event listener to the end of the list. Google Test assumes
+ // the ownership of the listener (i.e. it will delete the listener when
+ // the test program finishes).
+ void Append(TestEventListener* listener);
+
+ // Removes the given event listener from the list and returns it. It then
+ // becomes the caller's responsibility to delete the listener. Returns
+ // NULL if the listener is not found in the list.
+ TestEventListener* Release(TestEventListener* listener);
+
+ // Returns the standard listener responsible for the default console
+ // output. Can be removed from the listeners list to shut down default
+ // console output. Note that removing this object from the listener list
+ // with Release transfers its ownership to the caller and makes this
+ // function return NULL the next time.
+ TestEventListener* default_result_printer() const {
+ return default_result_printer_;
+ }
+
+ // Returns the standard listener responsible for the default XML output
+ // controlled by the --gtest_output=xml flag. Can be removed from the
+ // listeners list by users who want to shut down the default XML output
+ // controlled by this flag and substitute it with custom one. Note that
+ // removing this object from the listener list with Release transfers its
+ // ownership to the caller and makes this function return NULL the next
+ // time.
+ TestEventListener* default_xml_generator() const {
+ return default_xml_generator_;
+ }
+
+ private:
+ friend class TestCase;
+ friend class TestInfo;
+ friend class internal::DefaultGlobalTestPartResultReporter;
+ friend class internal::NoExecDeathTest;
+ friend class internal::TestEventListenersAccessor;
+ friend class internal::UnitTestImpl;
+
+ // Returns repeater that broadcasts the TestEventListener events to all
+ // subscribers.
+ TestEventListener* repeater();
+
+ // Sets the default_result_printer attribute to the provided listener.
+ // The listener is also added to the listener list and previous
+ // default_result_printer is removed from it and deleted. The listener can
+ // also be NULL in which case it will not be added to the list. Does
+ // nothing if the previous and the current listener objects are the same.
+ void SetDefaultResultPrinter(TestEventListener* listener);
+
+ // Sets the default_xml_generator attribute to the provided listener. The
+ // listener is also added to the listener list and previous
+ // default_xml_generator is removed from it and deleted. The listener can
+ // also be NULL in which case it will not be added to the list. Does
+ // nothing if the previous and the current listener objects are the same.
+ void SetDefaultXmlGenerator(TestEventListener* listener);
+
+ // Controls whether events will be forwarded by the repeater to the
+ // listeners in the list.
+ bool EventForwardingEnabled() const;
+ void SuppressEventForwarding();
+
+ // The actual list of listeners.
+ internal::TestEventRepeater* repeater_;
+ // Listener responsible for the standard result output.
+ TestEventListener* default_result_printer_;
+ // Listener responsible for the creation of the XML output file.
+ TestEventListener* default_xml_generator_;
+
+ // We disallow copying TestEventListeners.
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(TestEventListeners);
+};
+
+// A UnitTest consists of a vector of TestCases.
+//
+// This is a singleton class. The only instance of UnitTest is
+// created when UnitTest::GetInstance() is first called. This
+// instance is never deleted.
+//
+// UnitTest is not copyable.
+//
+// This class is thread-safe as long as the methods are called
+// according to their specification.
+class GTEST_API_ UnitTest {
+ public:
+ // Gets the singleton UnitTest object. The first time this method
+ // is called, a UnitTest object is constructed and returned.
+ // Consecutive calls will return the same object.
+ static UnitTest* GetInstance();
+
+ // Runs all tests in this UnitTest object and prints the result.
+ // Returns 0 if successful, or 1 otherwise.
+ //
+ // This method can only be called from the main thread.
+ //
+ // INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+ int Run() GTEST_MUST_USE_RESULT_;
+
+ // Returns the working directory when the first TEST() or TEST_F()
+ // was executed. The UnitTest object owns the string.
+ const char* original_working_dir() const;
+
+ // Returns the TestCase object for the test that's currently running,
+ // or NULL if no test is running.
+ const TestCase* current_test_case() const
+ GTEST_LOCK_EXCLUDED_(mutex_);
+
+ // Returns the TestInfo object for the test that's currently running,
+ // or NULL if no test is running.
+ const TestInfo* current_test_info() const
+ GTEST_LOCK_EXCLUDED_(mutex_);
+
+ // Returns the random seed used at the start of the current test run.
+ int random_seed() const;
+
+#if GTEST_HAS_PARAM_TEST
+ // Returns the ParameterizedTestCaseRegistry object used to keep track of
+ // value-parameterized tests and instantiate and register them.
+ //
+ // INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+ internal::ParameterizedTestCaseRegistry& parameterized_test_registry()
+ GTEST_LOCK_EXCLUDED_(mutex_);
+#endif // GTEST_HAS_PARAM_TEST
+
+ // Gets the number of successful test cases.
+ int successful_test_case_count() const;
+
+ // Gets the number of failed test cases.
+ int failed_test_case_count() const;
+
+ // Gets the number of all test cases.
+ int total_test_case_count() const;
+
+ // Gets the number of all test cases that contain at least one test
+ // that should run.
+ int test_case_to_run_count() const;
+
+ // Gets the number of successful tests.
+ int successful_test_count() const;
+
+ // Gets the number of failed tests.
+ int failed_test_count() const;
+
+ // Gets the number of disabled tests that will be reported in the XML report.
+ int reportable_disabled_test_count() const;
+
+ // Gets the number of disabled tests.
+ int disabled_test_count() const;
+
+ // Gets the number of tests to be printed in the XML report.
+ int reportable_test_count() const;
+
+ // Gets the number of all tests.
+ int total_test_count() const;
+
+ // Gets the number of tests that should run.
+ int test_to_run_count() const;
+
+ // Gets the time of the test program start, in ms from the start of the
+ // UNIX epoch.
+ TimeInMillis start_timestamp() const;
+
+ // Gets the elapsed time, in milliseconds.
+ TimeInMillis elapsed_time() const;
+
+ // Returns true iff the unit test passed (i.e. all test cases passed).
+ bool Passed() const;
+
+ // Returns true iff the unit test failed (i.e. some test case failed
+ // or something outside of all tests failed).
+ bool Failed() const;
+
+ // Gets the i-th test case among all the test cases. i can range from 0 to
+ // total_test_case_count() - 1. If i is not in that range, returns NULL.
+ const TestCase* GetTestCase(int i) const;
+
+ // Returns the TestResult containing information on test failures and
+ // properties logged outside of individual test cases.
+ const TestResult& ad_hoc_test_result() const;
+
+ // Returns the list of event listeners that can be used to track events
+ // inside Google Test.
+ TestEventListeners& listeners();
+
+ private:
+ // Registers and returns a global test environment. When a test
+ // program is run, all global test environments will be set-up in
+ // the order they were registered. After all tests in the program
+ // have finished, all global test environments will be torn-down in
+ // the *reverse* order they were registered.
+ //
+ // The UnitTest object takes ownership of the given environment.
+ //
+ // This method can only be called from the main thread.
+ Environment* AddEnvironment(Environment* env);
+
+ // Adds a TestPartResult to the current TestResult object. All
+ // Google Test assertion macros (e.g. ASSERT_TRUE, EXPECT_EQ, etc)
+ // eventually call this to report their results. The user code
+ // should use the assertion macros instead of calling this directly.
+ void AddTestPartResult(TestPartResult::Type result_type,
+ const char* file_name,
+ int line_number,
+ const std::string& message,
+ const std::string& os_stack_trace)
+ GTEST_LOCK_EXCLUDED_(mutex_);
+
+ // Adds a TestProperty to the current TestResult object when invoked from
+ // inside a test, to current TestCase's ad_hoc_test_result_ when invoked
+ // from SetUpTestCase or TearDownTestCase, or to the global property set
+ // when invoked elsewhere. If the result already contains a property with
+ // the same key, the value will be updated.
+ void RecordProperty(const std::string& key, const std::string& value);
+
+ // Gets the i-th test case among all the test cases. i can range from 0 to
+ // total_test_case_count() - 1. If i is not in that range, returns NULL.
+ TestCase* GetMutableTestCase(int i);
+
+ // Accessors for the implementation object.
+ internal::UnitTestImpl* impl() { return impl_; }
+ const internal::UnitTestImpl* impl() const { return impl_; }
+
+ // These classes and funcions are friends as they need to access private
+ // members of UnitTest.
+ friend class Test;
+ friend class internal::AssertHelper;
+ friend class internal::ScopedTrace;
+ friend class internal::StreamingListenerTest;
+ friend class internal::UnitTestRecordPropertyTestHelper;
+ friend Environment* AddGlobalTestEnvironment(Environment* env);
+ friend internal::UnitTestImpl* internal::GetUnitTestImpl();
+ friend void internal::ReportFailureInUnknownLocation(
+ TestPartResult::Type result_type,
+ const std::string& message);
+
+ // Creates an empty UnitTest.
+ UnitTest();
+
+ // D'tor
+ virtual ~UnitTest();
+
+ // Pushes a trace defined by SCOPED_TRACE() on to the per-thread
+ // Google Test trace stack.
+ void PushGTestTrace(const internal::TraceInfo& trace)
+ GTEST_LOCK_EXCLUDED_(mutex_);
+
+ // Pops a trace from the per-thread Google Test trace stack.
+ void PopGTestTrace()
+ GTEST_LOCK_EXCLUDED_(mutex_);
+
+ // Protects mutable state in *impl_. This is mutable as some const
+ // methods need to lock it too.
+ mutable internal::Mutex mutex_;
+
+ // Opaque implementation object. This field is never changed once
+ // the object is constructed. We don't mark it as const here, as
+ // doing so will cause a warning in the constructor of UnitTest.
+ // Mutable state in *impl_ is protected by mutex_.
+ internal::UnitTestImpl* impl_;
+
+ // We disallow copying UnitTest.
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(UnitTest);
+};
+
+// A convenient wrapper for adding an environment for the test
+// program.
+//
+// You should call this before RUN_ALL_TESTS() is called, probably in
+// main(). If you use gtest_main, you need to call this before main()
+// starts for it to take effect. For example, you can define a global
+// variable like this:
+//
+// testing::Environment* const foo_env =
+// testing::AddGlobalTestEnvironment(new FooEnvironment);
+//
+// However, we strongly recommend you to write your own main() and
+// call AddGlobalTestEnvironment() there, as relying on initialization
+// of global variables makes the code harder to read and may cause
+// problems when you register multiple environments from different
+// translation units and the environments have dependencies among them
+// (remember that the compiler doesn't guarantee the order in which
+// global variables from different translation units are initialized).
+inline Environment* AddGlobalTestEnvironment(Environment* env) {
+ return UnitTest::GetInstance()->AddEnvironment(env);
+}
+
+// Initializes Google Test. This must be called before calling
+// RUN_ALL_TESTS(). In particular, it parses a command line for the
+// flags that Google Test recognizes. Whenever a Google Test flag is
+// seen, it is removed from argv, and *argc is decremented.
+//
+// No value is returned. Instead, the Google Test flag variables are
+// updated.
+//
+// Calling the function for the second time has no user-visible effect.
+GTEST_API_ void InitGoogleTest(int* argc, char** argv);
+
+// This overloaded version can be used in Windows programs compiled in
+// UNICODE mode.
+GTEST_API_ void InitGoogleTest(int* argc, wchar_t** argv);
+
+namespace internal {
+
+// FormatForComparison<ToPrint, OtherOperand>::Format(value) formats a
+// value of type ToPrint that is an operand of a comparison assertion
+// (e.g. ASSERT_EQ). OtherOperand is the type of the other operand in
+// the comparison, and is used to help determine the best way to
+// format the value. In particular, when the value is a C string
+// (char pointer) and the other operand is an STL string object, we
+// want to format the C string as a string, since we know it is
+// compared by value with the string object. If the value is a char
+// pointer but the other operand is not an STL string object, we don't
+// know whether the pointer is supposed to point to a NUL-terminated
+// string, and thus want to print it as a pointer to be safe.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+
+// The default case.
+template <typename ToPrint, typename OtherOperand>
+class FormatForComparison {
+ public:
+ static ::std::string Format(const ToPrint& value) {
+ return ::testing::PrintToString(value);
+ }
+};
+
+// Array.
+template <typename ToPrint, size_t N, typename OtherOperand>
+class FormatForComparison<ToPrint[N], OtherOperand> {
+ public:
+ static ::std::string Format(const ToPrint* value) {
+ return FormatForComparison<const ToPrint*, OtherOperand>::Format(value);
+ }
+};
+
+// By default, print C string as pointers to be safe, as we don't know
+// whether they actually point to a NUL-terminated string.
+
+#define GTEST_IMPL_FORMAT_C_STRING_AS_POINTER_(CharType) \
+ template <typename OtherOperand> \
+ class FormatForComparison<CharType*, OtherOperand> { \
+ public: \
+ static ::std::string Format(CharType* value) { \
+ return ::testing::PrintToString(static_cast<const void*>(value)); \
+ } \
+ }
+
+GTEST_IMPL_FORMAT_C_STRING_AS_POINTER_(char);
+GTEST_IMPL_FORMAT_C_STRING_AS_POINTER_(const char);
+GTEST_IMPL_FORMAT_C_STRING_AS_POINTER_(wchar_t);
+GTEST_IMPL_FORMAT_C_STRING_AS_POINTER_(const wchar_t);
+
+#undef GTEST_IMPL_FORMAT_C_STRING_AS_POINTER_
+
+// If a C string is compared with an STL string object, we know it's meant
+// to point to a NUL-terminated string, and thus can print it as a string.
+
+#define GTEST_IMPL_FORMAT_C_STRING_AS_STRING_(CharType, OtherStringType) \
+ template <> \
+ class FormatForComparison<CharType*, OtherStringType> { \
+ public: \
+ static ::std::string Format(CharType* value) { \
+ return ::testing::PrintToString(value); \
+ } \
+ }
+
+GTEST_IMPL_FORMAT_C_STRING_AS_STRING_(char, ::std::string);
+GTEST_IMPL_FORMAT_C_STRING_AS_STRING_(const char, ::std::string);
+
+#if GTEST_HAS_GLOBAL_STRING
+GTEST_IMPL_FORMAT_C_STRING_AS_STRING_(char, ::string);
+GTEST_IMPL_FORMAT_C_STRING_AS_STRING_(const char, ::string);
+#endif
+
+#if GTEST_HAS_GLOBAL_WSTRING
+GTEST_IMPL_FORMAT_C_STRING_AS_STRING_(wchar_t, ::wstring);
+GTEST_IMPL_FORMAT_C_STRING_AS_STRING_(const wchar_t, ::wstring);
+#endif
+
+#if GTEST_HAS_STD_WSTRING
+GTEST_IMPL_FORMAT_C_STRING_AS_STRING_(wchar_t, ::std::wstring);
+GTEST_IMPL_FORMAT_C_STRING_AS_STRING_(const wchar_t, ::std::wstring);
+#endif
+
+#undef GTEST_IMPL_FORMAT_C_STRING_AS_STRING_
+
+// Formats a comparison assertion (e.g. ASSERT_EQ, EXPECT_LT, and etc)
+// operand to be used in a failure message. The type (but not value)
+// of the other operand may affect the format. This allows us to
+// print a char* as a raw pointer when it is compared against another
+// char* or void*, and print it as a C string when it is compared
+// against an std::string object, for example.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+template <typename T1, typename T2>
+std::string FormatForComparisonFailureMessage(
+ const T1& value, const T2& /* other_operand */) {
+ return FormatForComparison<T1, T2>::Format(value);
+}
+
+// The helper function for {ASSERT|EXPECT}_EQ.
+template <typename T1, typename T2>
+AssertionResult CmpHelperEQ(const char* expected_expression,
+ const char* actual_expression,
+ const T1& expected,
+ const T2& actual) {
+#ifdef _MSC_VER
+# pragma warning(push) // Saves the current warning state.
+# pragma warning(disable:4389) // Temporarily disables warning on
+ // signed/unsigned mismatch.
+#endif
+
+ if (expected == actual) {
+ return AssertionSuccess();
+ }
+
+#ifdef _MSC_VER
+# pragma warning(pop) // Restores the warning state.
+#endif
+
+ return EqFailure(expected_expression,
+ actual_expression,
+ FormatForComparisonFailureMessage(expected, actual),
+ FormatForComparisonFailureMessage(actual, expected),
+ false);
+}
+
+// With this overloaded version, we allow anonymous enums to be used
+// in {ASSERT|EXPECT}_EQ when compiled with gcc 4, as anonymous enums
+// can be implicitly cast to BiggestInt.
+GTEST_API_ AssertionResult CmpHelperEQ(const char* expected_expression,
+ const char* actual_expression,
+ BiggestInt expected,
+ BiggestInt actual);
+
+// The helper class for {ASSERT|EXPECT}_EQ. The template argument
+// lhs_is_null_literal is true iff the first argument to ASSERT_EQ()
+// is a null pointer literal. The following default implementation is
+// for lhs_is_null_literal being false.
+template <bool lhs_is_null_literal>
+class EqHelper {
+ public:
+ // This templatized version is for the general case.
+ template <typename T1, typename T2>
+ static AssertionResult Compare(const char* expected_expression,
+ const char* actual_expression,
+ const T1& expected,
+ const T2& actual) {
+ return CmpHelperEQ(expected_expression, actual_expression, expected,
+ actual);
+ }
+
+ // With this overloaded version, we allow anonymous enums to be used
+ // in {ASSERT|EXPECT}_EQ when compiled with gcc 4, as anonymous
+ // enums can be implicitly cast to BiggestInt.
+ //
+ // Even though its body looks the same as the above version, we
+ // cannot merge the two, as it will make anonymous enums unhappy.
+ static AssertionResult Compare(const char* expected_expression,
+ const char* actual_expression,
+ BiggestInt expected,
+ BiggestInt actual) {
+ return CmpHelperEQ(expected_expression, actual_expression, expected,
+ actual);
+ }
+};
+
+// This specialization is used when the first argument to ASSERT_EQ()
+// is a null pointer literal, like NULL, false, or 0.
+template <>
+class EqHelper<true> {
+ public:
+ // We define two overloaded versions of Compare(). The first
+ // version will be picked when the second argument to ASSERT_EQ() is
+ // NOT a pointer, e.g. ASSERT_EQ(0, AnIntFunction()) or
+ // EXPECT_EQ(false, a_bool).
+ template <typename T1, typename T2>
+ static AssertionResult Compare(
+ const char* expected_expression,
+ const char* actual_expression,
+ const T1& expected,
+ const T2& actual,
+ // The following line prevents this overload from being considered if T2
+ // is not a pointer type. We need this because ASSERT_EQ(NULL, my_ptr)
+ // expands to Compare("", "", NULL, my_ptr), which requires a conversion
+ // to match the Secret* in the other overload, which would otherwise make
+ // this template match better.
+ typename EnableIf<!is_pointer<T2>::value>::type* = 0) {
+ return CmpHelperEQ(expected_expression, actual_expression, expected,
+ actual);
+ }
+
+ // This version will be picked when the second argument to ASSERT_EQ() is a
+ // pointer, e.g. ASSERT_EQ(NULL, a_pointer).
+ template <typename T>
+ static AssertionResult Compare(
+ const char* expected_expression,
+ const char* actual_expression,
+ // We used to have a second template parameter instead of Secret*. That
+ // template parameter would deduce to 'long', making this a better match
+ // than the first overload even without the first overload's EnableIf.
+ // Unfortunately, gcc with -Wconversion-null warns when "passing NULL to
+ // non-pointer argument" (even a deduced integral argument), so the old
+ // implementation caused warnings in user code.
+ Secret* /* expected (NULL) */,
+ T* actual) {
+ // We already know that 'expected' is a null pointer.
+ return CmpHelperEQ(expected_expression, actual_expression,
+ static_cast<T*>(NULL), actual);
+ }
+};
+
+// A macro for implementing the helper functions needed to implement
+// ASSERT_?? and EXPECT_??. It is here just to avoid copy-and-paste
+// of similar code.
+//
+// For each templatized helper function, we also define an overloaded
+// version for BiggestInt in order to reduce code bloat and allow
+// anonymous enums to be used with {ASSERT|EXPECT}_?? when compiled
+// with gcc 4.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+#define GTEST_IMPL_CMP_HELPER_(op_name, op)\
+template <typename T1, typename T2>\
+AssertionResult CmpHelper##op_name(const char* expr1, const char* expr2, \
+ const T1& val1, const T2& val2) {\
+ if (val1 op val2) {\
+ return AssertionSuccess();\
+ } else {\
+ return AssertionFailure() \
+ << "Expected: (" << expr1 << ") " #op " (" << expr2\
+ << "), actual: " << FormatForComparisonFailureMessage(val1, val2)\
+ << " vs " << FormatForComparisonFailureMessage(val2, val1);\
+ }\
+}\
+GTEST_API_ AssertionResult CmpHelper##op_name(\
+ const char* expr1, const char* expr2, BiggestInt val1, BiggestInt val2)
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+
+// Implements the helper function for {ASSERT|EXPECT}_NE
+GTEST_IMPL_CMP_HELPER_(NE, !=);
+// Implements the helper function for {ASSERT|EXPECT}_LE
+GTEST_IMPL_CMP_HELPER_(LE, <=);
+// Implements the helper function for {ASSERT|EXPECT}_LT
+GTEST_IMPL_CMP_HELPER_(LT, <);
+// Implements the helper function for {ASSERT|EXPECT}_GE
+GTEST_IMPL_CMP_HELPER_(GE, >=);
+// Implements the helper function for {ASSERT|EXPECT}_GT
+GTEST_IMPL_CMP_HELPER_(GT, >);
+
+#undef GTEST_IMPL_CMP_HELPER_
+
+// The helper function for {ASSERT|EXPECT}_STREQ.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+GTEST_API_ AssertionResult CmpHelperSTREQ(const char* expected_expression,
+ const char* actual_expression,
+ const char* expected,
+ const char* actual);
+
+// The helper function for {ASSERT|EXPECT}_STRCASEEQ.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+GTEST_API_ AssertionResult CmpHelperSTRCASEEQ(const char* expected_expression,
+ const char* actual_expression,
+ const char* expected,
+ const char* actual);
+
+// The helper function for {ASSERT|EXPECT}_STRNE.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+GTEST_API_ AssertionResult CmpHelperSTRNE(const char* s1_expression,
+ const char* s2_expression,
+ const char* s1,
+ const char* s2);
+
+// The helper function for {ASSERT|EXPECT}_STRCASENE.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+GTEST_API_ AssertionResult CmpHelperSTRCASENE(const char* s1_expression,
+ const char* s2_expression,
+ const char* s1,
+ const char* s2);
+
+
+// Helper function for *_STREQ on wide strings.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+GTEST_API_ AssertionResult CmpHelperSTREQ(const char* expected_expression,
+ const char* actual_expression,
+ const wchar_t* expected,
+ const wchar_t* actual);
+
+// Helper function for *_STRNE on wide strings.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+GTEST_API_ AssertionResult CmpHelperSTRNE(const char* s1_expression,
+ const char* s2_expression,
+ const wchar_t* s1,
+ const wchar_t* s2);
+
+} // namespace internal
+
+// IsSubstring() and IsNotSubstring() are intended to be used as the
+// first argument to {EXPECT,ASSERT}_PRED_FORMAT2(), not by
+// themselves. They check whether needle is a substring of haystack
+// (NULL is considered a substring of itself only), and return an
+// appropriate error message when they fail.
+//
+// The {needle,haystack}_expr arguments are the stringified
+// expressions that generated the two real arguments.
+GTEST_API_ AssertionResult IsSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const char* needle, const char* haystack);
+GTEST_API_ AssertionResult IsSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const wchar_t* needle, const wchar_t* haystack);
+GTEST_API_ AssertionResult IsNotSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const char* needle, const char* haystack);
+GTEST_API_ AssertionResult IsNotSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const wchar_t* needle, const wchar_t* haystack);
+GTEST_API_ AssertionResult IsSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const ::std::string& needle, const ::std::string& haystack);
+GTEST_API_ AssertionResult IsNotSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const ::std::string& needle, const ::std::string& haystack);
+
+#if GTEST_HAS_STD_WSTRING
+GTEST_API_ AssertionResult IsSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const ::std::wstring& needle, const ::std::wstring& haystack);
+GTEST_API_ AssertionResult IsNotSubstring(
+ const char* needle_expr, const char* haystack_expr,
+ const ::std::wstring& needle, const ::std::wstring& haystack);
+#endif // GTEST_HAS_STD_WSTRING
+
+namespace internal {
+
+// Helper template function for comparing floating-points.
+//
+// Template parameter:
+//
+// RawType: the raw floating-point type (either float or double)
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+template <typename RawType>
+AssertionResult CmpHelperFloatingPointEQ(const char* expected_expression,
+ const char* actual_expression,
+ RawType expected,
+ RawType actual) {
+ const FloatingPoint<RawType> lhs(expected), rhs(actual);
+
+ if (lhs.AlmostEquals(rhs)) {
+ return AssertionSuccess();
+ }
+
+ ::std::stringstream expected_ss;
+ expected_ss << std::setprecision(std::numeric_limits<RawType>::digits10 + 2)
+ << expected;
+
+ ::std::stringstream actual_ss;
+ actual_ss << std::setprecision(std::numeric_limits<RawType>::digits10 + 2)
+ << actual;
+
+ return EqFailure(expected_expression,
+ actual_expression,
+ StringStreamToString(&expected_ss),
+ StringStreamToString(&actual_ss),
+ false);
+}
+
+// Helper function for implementing ASSERT_NEAR.
+//
+// INTERNAL IMPLEMENTATION - DO NOT USE IN A USER PROGRAM.
+GTEST_API_ AssertionResult DoubleNearPredFormat(const char* expr1,
+ const char* expr2,
+ const char* abs_error_expr,
+ double val1,
+ double val2,
+ double abs_error);
+
+// INTERNAL IMPLEMENTATION - DO NOT USE IN USER CODE.
+// A class that enables one to stream messages to assertion macros
+class GTEST_API_ AssertHelper {
+ public:
+ // Constructor.
+ AssertHelper(TestPartResult::Type type,
+ const char* file,
+ int line,
+ const char* message);
+ ~AssertHelper();
+
+ // Message assignment is a semantic trick to enable assertion
+ // streaming; see the GTEST_MESSAGE_ macro below.
+ void operator=(const Message& message) const;
+
+ private:
+ // We put our data in a struct so that the size of the AssertHelper class can
+ // be as small as possible. This is important because gcc is incapable of
+ // re-using stack space even for temporary variables, so every EXPECT_EQ
+ // reserves stack space for another AssertHelper.
+ struct AssertHelperData {
+ AssertHelperData(TestPartResult::Type t,
+ const char* srcfile,
+ int line_num,
+ const char* msg)
+ : type(t), file(srcfile), line(line_num), message(msg) { }
+
+ TestPartResult::Type const type;
+ const char* const file;
+ int const line;
+ std::string const message;
+
+ private:
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(AssertHelperData);
+ };
+
+ AssertHelperData* const data_;
+
+ GTEST_DISALLOW_COPY_AND_ASSIGN_(AssertHelper);
+};
+
+} // namespace internal
+
+#if GTEST_HAS_PARAM_TEST
+// The pure interface class that all value-parameterized tests inherit from.
+// A value-parameterized class must inherit from both ::testing::Test and
+// ::testing::WithParamInterface. In most cases that just means inheriting
+// from ::testing::TestWithParam, but more complicated test hierarchies
+// may need to inherit from Test and WithParamInterface at different levels.
+//
+// This interface has support for accessing the test parameter value via
+// the GetParam() method.
+//
+// Use it with one of the parameter generator defining functions, like Range(),
+// Values(), ValuesIn(), Bool(), and Combine().
+//
+// class FooTest : public ::testing::TestWithParam<int> {
+// protected:
+// FooTest() {
+// // Can use GetParam() here.
+// }
+// virtual ~FooTest() {
+// // Can use GetParam() here.
+// }
+// virtual void SetUp() {
+// // Can use GetParam() here.
+// }
+// virtual void TearDown {
+// // Can use GetParam() here.
+// }
+// };
+// TEST_P(FooTest, DoesBar) {
+// // Can use GetParam() method here.
+// Foo foo;
+// ASSERT_TRUE(foo.DoesBar(GetParam()));
+// }
+// INSTANTIATE_TEST_CASE_P(OneToTenRange, FooTest, ::testing::Range(1, 10));
+
+template <typename T>
+class WithParamInterface {
+ public:
+ typedef T ParamType;
+ virtual ~WithParamInterface() {}
+
+ // The current parameter value. Is also available in the test fixture's
+ // constructor. This member function is non-static, even though it only
+ // references static data, to reduce the opportunity for incorrect uses
+ // like writing 'WithParamInterface<bool>::GetParam()' for a test that
+ // uses a fixture whose parameter type is int.
+ const ParamType& GetParam() const {
+ GTEST_CHECK_(parameter_ != NULL)
+ << "GetParam() can only be called inside a value-parameterized test "
+ << "-- did you intend to write TEST_P instead of TEST_F?";
+ return *parameter_;
+ }
+
+ private:
+ // Sets parameter value. The caller is responsible for making sure the value
+ // remains alive and unchanged throughout the current test.
+ static void SetParam(const ParamType* parameter) {
+ parameter_ = parameter;
+ }
+
+ // Static value used for accessing parameter during a test lifetime.
+ static const ParamType* parameter_;
+
+ // TestClass must be a subclass of WithParamInterface<T> and Test.
+ template <class TestClass> friend class internal::ParameterizedTestFactory;
+};
+
+template <typename T>
+const T* WithParamInterface<T>::parameter_ = NULL;
+
+// Most value-parameterized classes can ignore the existence of
+// WithParamInterface, and can just inherit from ::testing::TestWithParam.
+
+template <typename T>
+class TestWithParam : public Test, public WithParamInterface<T> {
+};
+
+#endif // GTEST_HAS_PARAM_TEST
+
+// Macros for indicating success/failure in test code.
+
+// ADD_FAILURE unconditionally adds a failure to the current test.
+// SUCCEED generates a success - it doesn't automatically make the
+// current test successful, as a test is only successful when it has
+// no failure.
+//
+// EXPECT_* verifies that a certain condition is satisfied. If not,
+// it behaves like ADD_FAILURE. In particular:
+//
+// EXPECT_TRUE verifies that a Boolean condition is true.
+// EXPECT_FALSE verifies that a Boolean condition is false.
+//
+// FAIL and ASSERT_* are similar to ADD_FAILURE and EXPECT_*, except
+// that they will also abort the current function on failure. People
+// usually want the fail-fast behavior of FAIL and ASSERT_*, but those
+// writing data-driven tests often find themselves using ADD_FAILURE
+// and EXPECT_* more.
+
+// Generates a nonfatal failure with a generic message.
+#define ADD_FAILURE() GTEST_NONFATAL_FAILURE_("Failed")
+
+// Generates a nonfatal failure at the given source file location with
+// a generic message.
+#define ADD_FAILURE_AT(file, line) \
+ GTEST_MESSAGE_AT_(file, line, "Failed", \
+ ::testing::TestPartResult::kNonFatalFailure)
+
+// Generates a fatal failure with a generic message.
+#define GTEST_FAIL() GTEST_FATAL_FAILURE_("Failed")
+
+// Define this macro to 1 to omit the definition of FAIL(), which is a
+// generic name and clashes with some other libraries.
+#if !GTEST_DONT_DEFINE_FAIL
+# define FAIL() GTEST_FAIL()
+#endif
+
+// Generates a success with a generic message.
+#define GTEST_SUCCEED() GTEST_SUCCESS_("Succeeded")
+
+// Define this macro to 1 to omit the definition of SUCCEED(), which
+// is a generic name and clashes with some other libraries.
+#if !GTEST_DONT_DEFINE_SUCCEED
+# define SUCCEED() GTEST_SUCCEED()
+#endif
+
+// Macros for testing exceptions.
+//
+// * {ASSERT|EXPECT}_THROW(statement, expected_exception):
+// Tests that the statement throws the expected exception.
+// * {ASSERT|EXPECT}_NO_THROW(statement):
+// Tests that the statement doesn't throw any exception.
+// * {ASSERT|EXPECT}_ANY_THROW(statement):
+// Tests that the statement throws an exception.
+
+#define EXPECT_THROW(statement, expected_exception) \
+ GTEST_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
+#define EXPECT_NO_THROW(statement) \
+ GTEST_TEST_NO_THROW_(statement, GTEST_NONFATAL_FAILURE_)
+#define EXPECT_ANY_THROW(statement) \
+ GTEST_TEST_ANY_THROW_(statement, GTEST_NONFATAL_FAILURE_)
+#define ASSERT_THROW(statement, expected_exception) \
+ GTEST_TEST_THROW_(statement, expected_exception, GTEST_FATAL_FAILURE_)
+#define ASSERT_NO_THROW(statement) \
+ GTEST_TEST_NO_THROW_(statement, GTEST_FATAL_FAILURE_)
+#define ASSERT_ANY_THROW(statement) \
+ GTEST_TEST_ANY_THROW_(statement, GTEST_FATAL_FAILURE_)
+
+// Boolean assertions. Condition can be either a Boolean expression or an
+// AssertionResult. For more information on how to use AssertionResult with
+// these macros see comments on that class.
+#define EXPECT_TRUE(condition) \
+ GTEST_TEST_BOOLEAN_(condition, #condition, false, true, \
+ GTEST_NONFATAL_FAILURE_)
+#define EXPECT_FALSE(condition) \
+ GTEST_TEST_BOOLEAN_(!(condition), #condition, true, false, \
+ GTEST_NONFATAL_FAILURE_)
+#define ASSERT_TRUE(condition) \
+ GTEST_TEST_BOOLEAN_(condition, #condition, false, true, \
+ GTEST_FATAL_FAILURE_)
+#define ASSERT_FALSE(condition) \
+ GTEST_TEST_BOOLEAN_(!(condition), #condition, true, false, \
+ GTEST_FATAL_FAILURE_)
+
+// Includes the auto-generated header that implements a family of
+// generic predicate assertion macros.
+// Copyright 2006, Google Inc.
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+// This file is AUTOMATICALLY GENERATED on 10/31/2011 by command
+// 'gen_gtest_pred_impl.py 5'. DO NOT EDIT BY HAND!
+//
+// Implements a family of generic predicate assertion macros.
+
+#ifndef GTEST_INCLUDE_GTEST_GTEST_PRED_IMPL_H_
+#define GTEST_INCLUDE_GTEST_GTEST_PRED_IMPL_H_
+
+// Makes sure this header is not included before gtest.h.
+#ifndef GTEST_INCLUDE_GTEST_GTEST_H_
+# error Do not include gtest_pred_impl.h directly. Include gtest.h instead.
+#endif // GTEST_INCLUDE_GTEST_GTEST_H_
+
+// This header implements a family of generic predicate assertion
+// macros:
+//
+// ASSERT_PRED_FORMAT1(pred_format, v1)
+// ASSERT_PRED_FORMAT2(pred_format, v1, v2)
+// ...
+//
+// where pred_format is a function or functor that takes n (in the
+// case of ASSERT_PRED_FORMATn) values and their source expression
+// text, and returns a testing::AssertionResult. See the definition
+// of ASSERT_EQ in gtest.h for an example.
+//
+// If you don't care about formatting, you can use the more
+// restrictive version:
+//
+// ASSERT_PRED1(pred, v1)
+// ASSERT_PRED2(pred, v1, v2)
+// ...
+//
+// where pred is an n-ary function or functor that returns bool,
+// and the values v1, v2, ..., must support the << operator for
+// streaming to std::ostream.
+//
+// We also define the EXPECT_* variations.
+//
+// For now we only support predicates whose arity is at most 5.
+// Please email googletestframework at googlegroups.com if you need
+// support for higher arities.
+
+// GTEST_ASSERT_ is the basic statement to which all of the assertions
+// in this file reduce. Don't use this in your code.
+
+#define GTEST_ASSERT_(expression, on_failure) \
+ GTEST_AMBIGUOUS_ELSE_BLOCKER_ \
+ if (const ::testing::AssertionResult gtest_ar = (expression)) \
+ ; \
+ else \
+ on_failure(gtest_ar.failure_message())
+
+
+// Helper function for implementing {EXPECT|ASSERT}_PRED1. Don't use
+// this in your code.
+template <typename Pred,
+ typename T1>
+AssertionResult AssertPred1Helper(const char* pred_text,
+ const char* e1,
+ Pred pred,
+ const T1& v1) {
+ if (pred(v1)) return AssertionSuccess();
+
+ return AssertionFailure() << pred_text << "("
+ << e1 << ") evaluates to false, where"
+ << "\n" << e1 << " evaluates to " << v1;
+}
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED_FORMAT1.
+// Don't use this in your code.
+#define GTEST_PRED_FORMAT1_(pred_format, v1, on_failure)\
+ GTEST_ASSERT_(pred_format(#v1, v1), \
+ on_failure)
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED1. Don't use
+// this in your code.
+#define GTEST_PRED1_(pred, v1, on_failure)\
+ GTEST_ASSERT_(::testing::AssertPred1Helper(#pred, \
+ #v1, \
+ pred, \
+ v1), on_failure)
+
+// Unary predicate assertion macros.
+#define EXPECT_PRED_FORMAT1(pred_format, v1) \
+ GTEST_PRED_FORMAT1_(pred_format, v1, GTEST_NONFATAL_FAILURE_)
+#define EXPECT_PRED1(pred, v1) \
+ GTEST_PRED1_(pred, v1, GTEST_NONFATAL_FAILURE_)
+#define ASSERT_PRED_FORMAT1(pred_format, v1) \
+ GTEST_PRED_FORMAT1_(pred_format, v1, GTEST_FATAL_FAILURE_)
+#define ASSERT_PRED1(pred, v1) \
+ GTEST_PRED1_(pred, v1, GTEST_FATAL_FAILURE_)
+
+
+
+// Helper function for implementing {EXPECT|ASSERT}_PRED2. Don't use
+// this in your code.
+template <typename Pred,
+ typename T1,
+ typename T2>
+AssertionResult AssertPred2Helper(const char* pred_text,
+ const char* e1,
+ const char* e2,
+ Pred pred,
+ const T1& v1,
+ const T2& v2) {
+ if (pred(v1, v2)) return AssertionSuccess();
+
+ return AssertionFailure() << pred_text << "("
+ << e1 << ", "
+ << e2 << ") evaluates to false, where"
+ << "\n" << e1 << " evaluates to " << v1
+ << "\n" << e2 << " evaluates to " << v2;
+}
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED_FORMAT2.
+// Don't use this in your code.
+#define GTEST_PRED_FORMAT2_(pred_format, v1, v2, on_failure)\
+ GTEST_ASSERT_(pred_format(#v1, #v2, v1, v2), \
+ on_failure)
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED2. Don't use
+// this in your code.
+#define GTEST_PRED2_(pred, v1, v2, on_failure)\
+ GTEST_ASSERT_(::testing::AssertPred2Helper(#pred, \
+ #v1, \
+ #v2, \
+ pred, \
+ v1, \
+ v2), on_failure)
+
+// Binary predicate assertion macros.
+#define EXPECT_PRED_FORMAT2(pred_format, v1, v2) \
+ GTEST_PRED_FORMAT2_(pred_format, v1, v2, GTEST_NONFATAL_FAILURE_)
+#define EXPECT_PRED2(pred, v1, v2) \
+ GTEST_PRED2_(pred, v1, v2, GTEST_NONFATAL_FAILURE_)
+#define ASSERT_PRED_FORMAT2(pred_format, v1, v2) \
+ GTEST_PRED_FORMAT2_(pred_format, v1, v2, GTEST_FATAL_FAILURE_)
+#define ASSERT_PRED2(pred, v1, v2) \
+ GTEST_PRED2_(pred, v1, v2, GTEST_FATAL_FAILURE_)
+
+
+
+// Helper function for implementing {EXPECT|ASSERT}_PRED3. Don't use
+// this in your code.
+template <typename Pred,
+ typename T1,
+ typename T2,
+ typename T3>
+AssertionResult AssertPred3Helper(const char* pred_text,
+ const char* e1,
+ const char* e2,
+ const char* e3,
+ Pred pred,
+ const T1& v1,
+ const T2& v2,
+ const T3& v3) {
+ if (pred(v1, v2, v3)) return AssertionSuccess();
+
+ return AssertionFailure() << pred_text << "("
+ << e1 << ", "
+ << e2 << ", "
+ << e3 << ") evaluates to false, where"
+ << "\n" << e1 << " evaluates to " << v1
+ << "\n" << e2 << " evaluates to " << v2
+ << "\n" << e3 << " evaluates to " << v3;
+}
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED_FORMAT3.
+// Don't use this in your code.
+#define GTEST_PRED_FORMAT3_(pred_format, v1, v2, v3, on_failure)\
+ GTEST_ASSERT_(pred_format(#v1, #v2, #v3, v1, v2, v3), \
+ on_failure)
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED3. Don't use
+// this in your code.
+#define GTEST_PRED3_(pred, v1, v2, v3, on_failure)\
+ GTEST_ASSERT_(::testing::AssertPred3Helper(#pred, \
+ #v1, \
+ #v2, \
+ #v3, \
+ pred, \
+ v1, \
+ v2, \
+ v3), on_failure)
+
+// Ternary predicate assertion macros.
+#define EXPECT_PRED_FORMAT3(pred_format, v1, v2, v3) \
+ GTEST_PRED_FORMAT3_(pred_format, v1, v2, v3, GTEST_NONFATAL_FAILURE_)
+#define EXPECT_PRED3(pred, v1, v2, v3) \
+ GTEST_PRED3_(pred, v1, v2, v3, GTEST_NONFATAL_FAILURE_)
+#define ASSERT_PRED_FORMAT3(pred_format, v1, v2, v3) \
+ GTEST_PRED_FORMAT3_(pred_format, v1, v2, v3, GTEST_FATAL_FAILURE_)
+#define ASSERT_PRED3(pred, v1, v2, v3) \
+ GTEST_PRED3_(pred, v1, v2, v3, GTEST_FATAL_FAILURE_)
+
+
+
+// Helper function for implementing {EXPECT|ASSERT}_PRED4. Don't use
+// this in your code.
+template <typename Pred,
+ typename T1,
+ typename T2,
+ typename T3,
+ typename T4>
+AssertionResult AssertPred4Helper(const char* pred_text,
+ const char* e1,
+ const char* e2,
+ const char* e3,
+ const char* e4,
+ Pred pred,
+ const T1& v1,
+ const T2& v2,
+ const T3& v3,
+ const T4& v4) {
+ if (pred(v1, v2, v3, v4)) return AssertionSuccess();
+
+ return AssertionFailure() << pred_text << "("
+ << e1 << ", "
+ << e2 << ", "
+ << e3 << ", "
+ << e4 << ") evaluates to false, where"
+ << "\n" << e1 << " evaluates to " << v1
+ << "\n" << e2 << " evaluates to " << v2
+ << "\n" << e3 << " evaluates to " << v3
+ << "\n" << e4 << " evaluates to " << v4;
+}
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED_FORMAT4.
+// Don't use this in your code.
+#define GTEST_PRED_FORMAT4_(pred_format, v1, v2, v3, v4, on_failure)\
+ GTEST_ASSERT_(pred_format(#v1, #v2, #v3, #v4, v1, v2, v3, v4), \
+ on_failure)
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED4. Don't use
+// this in your code.
+#define GTEST_PRED4_(pred, v1, v2, v3, v4, on_failure)\
+ GTEST_ASSERT_(::testing::AssertPred4Helper(#pred, \
+ #v1, \
+ #v2, \
+ #v3, \
+ #v4, \
+ pred, \
+ v1, \
+ v2, \
+ v3, \
+ v4), on_failure)
+
+// 4-ary predicate assertion macros.
+#define EXPECT_PRED_FORMAT4(pred_format, v1, v2, v3, v4) \
+ GTEST_PRED_FORMAT4_(pred_format, v1, v2, v3, v4, GTEST_NONFATAL_FAILURE_)
+#define EXPECT_PRED4(pred, v1, v2, v3, v4) \
+ GTEST_PRED4_(pred, v1, v2, v3, v4, GTEST_NONFATAL_FAILURE_)
+#define ASSERT_PRED_FORMAT4(pred_format, v1, v2, v3, v4) \
+ GTEST_PRED_FORMAT4_(pred_format, v1, v2, v3, v4, GTEST_FATAL_FAILURE_)
+#define ASSERT_PRED4(pred, v1, v2, v3, v4) \
+ GTEST_PRED4_(pred, v1, v2, v3, v4, GTEST_FATAL_FAILURE_)
+
+
+
+// Helper function for implementing {EXPECT|ASSERT}_PRED5. Don't use
+// this in your code.
+template <typename Pred,
+ typename T1,
+ typename T2,
+ typename T3,
+ typename T4,
+ typename T5>
+AssertionResult AssertPred5Helper(const char* pred_text,
+ const char* e1,
+ const char* e2,
+ const char* e3,
+ const char* e4,
+ const char* e5,
+ Pred pred,
+ const T1& v1,
+ const T2& v2,
+ const T3& v3,
+ const T4& v4,
+ const T5& v5) {
+ if (pred(v1, v2, v3, v4, v5)) return AssertionSuccess();
+
+ return AssertionFailure() << pred_text << "("
+ << e1 << ", "
+ << e2 << ", "
+ << e3 << ", "
+ << e4 << ", "
+ << e5 << ") evaluates to false, where"
+ << "\n" << e1 << " evaluates to " << v1
+ << "\n" << e2 << " evaluates to " << v2
+ << "\n" << e3 << " evaluates to " << v3
+ << "\n" << e4 << " evaluates to " << v4
+ << "\n" << e5 << " evaluates to " << v5;
+}
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED_FORMAT5.
+// Don't use this in your code.
+#define GTEST_PRED_FORMAT5_(pred_format, v1, v2, v3, v4, v5, on_failure)\
+ GTEST_ASSERT_(pred_format(#v1, #v2, #v3, #v4, #v5, v1, v2, v3, v4, v5), \
+ on_failure)
+
+// Internal macro for implementing {EXPECT|ASSERT}_PRED5. Don't use
+// this in your code.
+#define GTEST_PRED5_(pred, v1, v2, v3, v4, v5, on_failure)\
+ GTEST_ASSERT_(::testing::AssertPred5Helper(#pred, \
+ #v1, \
+ #v2, \
+ #v3, \
+ #v4, \
+ #v5, \
+ pred, \
+ v1, \
+ v2, \
+ v3, \
+ v4, \
+ v5), on_failure)
+
+// 5-ary predicate assertion macros.
+#define EXPECT_PRED_FORMAT5(pred_format, v1, v2, v3, v4, v5) \
+ GTEST_PRED_FORMAT5_(pred_format, v1, v2, v3, v4, v5, GTEST_NONFATAL_FAILURE_)
+#define EXPECT_PRED5(pred, v1, v2, v3, v4, v5) \
+ GTEST_PRED5_(pred, v1, v2, v3, v4, v5, GTEST_NONFATAL_FAILURE_)
+#define ASSERT_PRED_FORMAT5(pred_format, v1, v2, v3, v4, v5) \
+ GTEST_PRED_FORMAT5_(pred_format, v1, v2, v3, v4, v5, GTEST_FATAL_FAILURE_)
+#define ASSERT_PRED5(pred, v1, v2, v3, v4, v5) \
+ GTEST_PRED5_(pred, v1, v2, v3, v4, v5, GTEST_FATAL_FAILURE_)
+
+
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_PRED_IMPL_H_
+
+// Macros for testing equalities and inequalities.
+//
+// * {ASSERT|EXPECT}_EQ(expected, actual): Tests that expected == actual
+// * {ASSERT|EXPECT}_NE(v1, v2): Tests that v1 != v2
+// * {ASSERT|EXPECT}_LT(v1, v2): Tests that v1 < v2
+// * {ASSERT|EXPECT}_LE(v1, v2): Tests that v1 <= v2
+// * {ASSERT|EXPECT}_GT(v1, v2): Tests that v1 > v2
+// * {ASSERT|EXPECT}_GE(v1, v2): Tests that v1 >= v2
+//
+// When they are not, Google Test prints both the tested expressions and
+// their actual values. The values must be compatible built-in types,
+// or you will get a compiler error. By "compatible" we mean that the
+// values can be compared by the respective operator.
+//
+// Note:
+//
+// 1. It is possible to make a user-defined type work with
+// {ASSERT|EXPECT}_??(), but that requires overloading the
+// comparison operators and is thus discouraged by the Google C++
+// Usage Guide. Therefore, you are advised to use the
+// {ASSERT|EXPECT}_TRUE() macro to assert that two objects are
+// equal.
+//
+// 2. The {ASSERT|EXPECT}_??() macros do pointer comparisons on
+// pointers (in particular, C strings). Therefore, if you use it
+// with two C strings, you are testing how their locations in memory
+// are related, not how their content is related. To compare two C
+// strings by content, use {ASSERT|EXPECT}_STR*().
+//
+// 3. {ASSERT|EXPECT}_EQ(expected, actual) is preferred to
+// {ASSERT|EXPECT}_TRUE(expected == actual), as the former tells you
+// what the actual value is when it fails, and similarly for the
+// other comparisons.
+//
+// 4. Do not depend on the order in which {ASSERT|EXPECT}_??()
+// evaluate their arguments, which is undefined.
+//
+// 5. These macros evaluate their arguments exactly once.
+//
+// Examples:
+//
+// EXPECT_NE(5, Foo());
+// EXPECT_EQ(NULL, a_pointer);
+// ASSERT_LT(i, array_size);
+// ASSERT_GT(records.size(), 0) << "There is no record left.";
+
+#define EXPECT_EQ(expected, actual) \
+ EXPECT_PRED_FORMAT2(::testing::internal:: \
+ EqHelper<GTEST_IS_NULL_LITERAL_(expected)>::Compare, \
+ expected, actual)
+#define EXPECT_NE(expected, actual) \
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperNE, expected, actual)
+#define EXPECT_LE(val1, val2) \
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperLE, val1, val2)
+#define EXPECT_LT(val1, val2) \
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperLT, val1, val2)
+#define EXPECT_GE(val1, val2) \
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperGE, val1, val2)
+#define EXPECT_GT(val1, val2) \
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperGT, val1, val2)
+
+#define GTEST_ASSERT_EQ(expected, actual) \
+ ASSERT_PRED_FORMAT2(::testing::internal:: \
+ EqHelper<GTEST_IS_NULL_LITERAL_(expected)>::Compare, \
+ expected, actual)
+#define GTEST_ASSERT_NE(val1, val2) \
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperNE, val1, val2)
+#define GTEST_ASSERT_LE(val1, val2) \
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperLE, val1, val2)
+#define GTEST_ASSERT_LT(val1, val2) \
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperLT, val1, val2)
+#define GTEST_ASSERT_GE(val1, val2) \
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperGE, val1, val2)
+#define GTEST_ASSERT_GT(val1, val2) \
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperGT, val1, val2)
+
+// Define macro GTEST_DONT_DEFINE_ASSERT_XY to 1 to omit the definition of
+// ASSERT_XY(), which clashes with some users' own code.
+
+#if !GTEST_DONT_DEFINE_ASSERT_EQ
+# define ASSERT_EQ(val1, val2) GTEST_ASSERT_EQ(val1, val2)
+#endif
+
+#if !GTEST_DONT_DEFINE_ASSERT_NE
+# define ASSERT_NE(val1, val2) GTEST_ASSERT_NE(val1, val2)
+#endif
+
+#if !GTEST_DONT_DEFINE_ASSERT_LE
+# define ASSERT_LE(val1, val2) GTEST_ASSERT_LE(val1, val2)
+#endif
+
+#if !GTEST_DONT_DEFINE_ASSERT_LT
+# define ASSERT_LT(val1, val2) GTEST_ASSERT_LT(val1, val2)
+#endif
+
+#if !GTEST_DONT_DEFINE_ASSERT_GE
+# define ASSERT_GE(val1, val2) GTEST_ASSERT_GE(val1, val2)
+#endif
+
+#if !GTEST_DONT_DEFINE_ASSERT_GT
+# define ASSERT_GT(val1, val2) GTEST_ASSERT_GT(val1, val2)
+#endif
+
+// C-string Comparisons. All tests treat NULL and any non-NULL string
+// as different. Two NULLs are equal.
+//
+// * {ASSERT|EXPECT}_STREQ(s1, s2): Tests that s1 == s2
+// * {ASSERT|EXPECT}_STRNE(s1, s2): Tests that s1 != s2
+// * {ASSERT|EXPECT}_STRCASEEQ(s1, s2): Tests that s1 == s2, ignoring case
+// * {ASSERT|EXPECT}_STRCASENE(s1, s2): Tests that s1 != s2, ignoring case
+//
+// For wide or narrow string objects, you can use the
+// {ASSERT|EXPECT}_??() macros.
+//
+// Don't depend on the order in which the arguments are evaluated,
+// which is undefined.
+//
+// These macros evaluate their arguments exactly once.
+
+#define EXPECT_STREQ(expected, actual) \
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperSTREQ, expected, actual)
+#define EXPECT_STRNE(s1, s2) \
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperSTRNE, s1, s2)
+#define EXPECT_STRCASEEQ(expected, actual) \
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperSTRCASEEQ, expected, actual)
+#define EXPECT_STRCASENE(s1, s2)\
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperSTRCASENE, s1, s2)
+
+#define ASSERT_STREQ(expected, actual) \
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperSTREQ, expected, actual)
+#define ASSERT_STRNE(s1, s2) \
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperSTRNE, s1, s2)
+#define ASSERT_STRCASEEQ(expected, actual) \
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperSTRCASEEQ, expected, actual)
+#define ASSERT_STRCASENE(s1, s2)\
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperSTRCASENE, s1, s2)
+
+// Macros for comparing floating-point numbers.
+//
+// * {ASSERT|EXPECT}_FLOAT_EQ(expected, actual):
+// Tests that two float values are almost equal.
+// * {ASSERT|EXPECT}_DOUBLE_EQ(expected, actual):
+// Tests that two double values are almost equal.
+// * {ASSERT|EXPECT}_NEAR(v1, v2, abs_error):
+// Tests that v1 and v2 are within the given distance to each other.
+//
+// Google Test uses ULP-based comparison to automatically pick a default
+// error bound that is appropriate for the operands. See the
+// FloatingPoint template class in gtest-internal.h if you are
+// interested in the implementation details.
+
+#define EXPECT_FLOAT_EQ(expected, actual)\
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperFloatingPointEQ<float>, \
+ expected, actual)
+
+#define EXPECT_DOUBLE_EQ(expected, actual)\
+ EXPECT_PRED_FORMAT2(::testing::internal::CmpHelperFloatingPointEQ<double>, \
+ expected, actual)
+
+#define ASSERT_FLOAT_EQ(expected, actual)\
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperFloatingPointEQ<float>, \
+ expected, actual)
+
+#define ASSERT_DOUBLE_EQ(expected, actual)\
+ ASSERT_PRED_FORMAT2(::testing::internal::CmpHelperFloatingPointEQ<double>, \
+ expected, actual)
+
+#define EXPECT_NEAR(val1, val2, abs_error)\
+ EXPECT_PRED_FORMAT3(::testing::internal::DoubleNearPredFormat, \
+ val1, val2, abs_error)
+
+#define ASSERT_NEAR(val1, val2, abs_error)\
+ ASSERT_PRED_FORMAT3(::testing::internal::DoubleNearPredFormat, \
+ val1, val2, abs_error)
+
+// These predicate format functions work on floating-point values, and
+// can be used in {ASSERT|EXPECT}_PRED_FORMAT2*(), e.g.
+//
+// EXPECT_PRED_FORMAT2(testing::DoubleLE, Foo(), 5.0);
+
+// Asserts that val1 is less than, or almost equal to, val2. Fails
+// otherwise. In particular, it fails if either val1 or val2 is NaN.
+GTEST_API_ AssertionResult FloatLE(const char* expr1, const char* expr2,
+ float val1, float val2);
+GTEST_API_ AssertionResult DoubleLE(const char* expr1, const char* expr2,
+ double val1, double val2);
+
+
+#if GTEST_OS_WINDOWS
+
+// Macros that test for HRESULT failure and success, these are only useful
+// on Windows, and rely on Windows SDK macros and APIs to compile.
+//
+// * {ASSERT|EXPECT}_HRESULT_{SUCCEEDED|FAILED}(expr)
+//
+// When expr unexpectedly fails or succeeds, Google Test prints the
+// expected result and the actual result with both a human-readable
+// string representation of the error, if available, as well as the
+// hex result code.
+# define EXPECT_HRESULT_SUCCEEDED(expr) \
+ EXPECT_PRED_FORMAT1(::testing::internal::IsHRESULTSuccess, (expr))
+
+# define ASSERT_HRESULT_SUCCEEDED(expr) \
+ ASSERT_PRED_FORMAT1(::testing::internal::IsHRESULTSuccess, (expr))
+
+# define EXPECT_HRESULT_FAILED(expr) \
+ EXPECT_PRED_FORMAT1(::testing::internal::IsHRESULTFailure, (expr))
+
+# define ASSERT_HRESULT_FAILED(expr) \
+ ASSERT_PRED_FORMAT1(::testing::internal::IsHRESULTFailure, (expr))
+
+#endif // GTEST_OS_WINDOWS
+
+// Macros that execute statement and check that it doesn't generate new fatal
+// failures in the current thread.
+//
+// * {ASSERT|EXPECT}_NO_FATAL_FAILURE(statement);
+//
+// Examples:
+//
+// EXPECT_NO_FATAL_FAILURE(Process());
+// ASSERT_NO_FATAL_FAILURE(Process()) << "Process() failed";
+//
+#define ASSERT_NO_FATAL_FAILURE(statement) \
+ GTEST_TEST_NO_FATAL_FAILURE_(statement, GTEST_FATAL_FAILURE_)
+#define EXPECT_NO_FATAL_FAILURE(statement) \
+ GTEST_TEST_NO_FATAL_FAILURE_(statement, GTEST_NONFATAL_FAILURE_)
+
+// Causes a trace (including the source file path, the current line
+// number, and the given message) to be included in every test failure
+// message generated by code in the current scope. The effect is
+// undone when the control leaves the current scope.
+//
+// The message argument can be anything streamable to std::ostream.
+//
+// In the implementation, we include the current line number as part
+// of the dummy variable name, thus allowing multiple SCOPED_TRACE()s
+// to appear in the same block - as long as they are on different
+// lines.
+#define SCOPED_TRACE(message) \
+ ::testing::internal::ScopedTrace GTEST_CONCAT_TOKEN_(gtest_trace_, __LINE__)(\
+ __FILE__, __LINE__, ::testing::Message() << (message))
+
+// Compile-time assertion for type equality.
+// StaticAssertTypeEq<type1, type2>() compiles iff type1 and type2 are
+// the same type. The value it returns is not interesting.
+//
+// Instead of making StaticAssertTypeEq a class template, we make it a
+// function template that invokes a helper class template. This
+// prevents a user from misusing StaticAssertTypeEq<T1, T2> by
+// defining objects of that type.
+//
+// CAVEAT:
+//
+// When used inside a method of a class template,
+// StaticAssertTypeEq<T1, T2>() is effective ONLY IF the method is
+// instantiated. For example, given:
+//
+// template <typename T> class Foo {
+// public:
+// void Bar() { testing::StaticAssertTypeEq<int, T>(); }
+// };
+//
+// the code:
+//
+// void Test1() { Foo<bool> foo; }
+//
+// will NOT generate a compiler error, as Foo<bool>::Bar() is never
+// actually instantiated. Instead, you need:
+//
+// void Test2() { Foo<bool> foo; foo.Bar(); }
+//
+// to cause a compiler error.
+template <typename T1, typename T2>
+bool StaticAssertTypeEq() {
+ (void)internal::StaticAssertTypeEqHelper<T1, T2>();
+ return true;
+}
+
+// Defines a test.
+//
+// The first parameter is the name of the test case, and the second
+// parameter is the name of the test within the test case.
+//
+// The convention is to end the test case name with "Test". For
+// example, a test case for the Foo class can be named FooTest.
+//
+// The user should put his test code between braces after using this
+// macro. Example:
+//
+// TEST(FooTest, InitializesCorrectly) {
+// Foo foo;
+// EXPECT_TRUE(foo.StatusIsOK());
+// }
+
+// Note that we call GetTestTypeId() instead of GetTypeId<
+// ::testing::Test>() here to get the type ID of testing::Test. This
+// is to work around a suspected linker bug when using Google Test as
+// a framework on Mac OS X. The bug causes GetTypeId<
+// ::testing::Test>() to return different values depending on whether
+// the call is from the Google Test framework itself or from user test
+// code. GetTestTypeId() is guaranteed to always return the same
+// value, as it always calls GetTypeId<>() from the Google Test
+// framework.
+#define GTEST_TEST(test_case_name, test_name)\
+ GTEST_TEST_(test_case_name, test_name, \
+ ::testing::Test, ::testing::internal::GetTestTypeId())
+
+// Define this macro to 1 to omit the definition of TEST(), which
+// is a generic name and clashes with some other libraries.
+#if !GTEST_DONT_DEFINE_TEST
+# define TEST(test_case_name, test_name) GTEST_TEST(test_case_name, test_name)
+#endif
+
+// Defines a test that uses a test fixture.
+//
+// The first parameter is the name of the test fixture class, which
+// also doubles as the test case name. The second parameter is the
+// name of the test within the test case.
+//
+// A test fixture class must be declared earlier. The user should put
+// his test code between braces after using this macro. Example:
+//
+// class FooTest : public testing::Test {
+// protected:
+// virtual void SetUp() { b_.AddElement(3); }
+//
+// Foo a_;
+// Foo b_;
+// };
+//
+// TEST_F(FooTest, InitializesCorrectly) {
+// EXPECT_TRUE(a_.StatusIsOK());
+// }
+//
+// TEST_F(FooTest, ReturnsElementCountCorrectly) {
+// EXPECT_EQ(0, a_.size());
+// EXPECT_EQ(1, b_.size());
+// }
+
+#define TEST_F(test_fixture, test_name)\
+ GTEST_TEST_(test_fixture, test_name, test_fixture, \
+ ::testing::internal::GetTypeId<test_fixture>())
+
+} // namespace testing
+
+// Use this function in main() to run all tests. It returns 0 if all
+// tests are successful, or 1 otherwise.
+//
+// RUN_ALL_TESTS() should be invoked after the command line has been
+// parsed by InitGoogleTest().
+//
+// This function was formerly a macro; thus, it is in the global
+// namespace and has an all-caps name.
+int RUN_ALL_TESTS() GTEST_MUST_USE_RESULT_;
+
+inline int RUN_ALL_TESTS() {
+ return ::testing::UnitTest::GetInstance()->Run();
+}
+
+#endif // GTEST_INCLUDE_GTEST_GTEST_H_
diff --git a/tools/Darwin/clang-format b/tools/Darwin/clang-format
new file mode 100755
index 0000000..33201aa
Binary files /dev/null and b/tools/Darwin/clang-format differ
diff --git a/tools/Linux/clang-format b/tools/Linux/clang-format
new file mode 100755
index 0000000..c450691
Binary files /dev/null and b/tools/Linux/clang-format differ
diff --git a/tools/check-formatting b/tools/check-formatting
new file mode 100755
index 0000000..dccf458
--- /dev/null
+++ b/tools/check-formatting
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+PLATFORM=$(uname)
+CLANGFORMAT="./tools/${PLATFORM}/clang-format -style=file"
+
+if [ "$1" == "--all" ]
+then
+ find include src tests/unit \( -name *.cpp -or -name *.h \) -print0 \
+ | xargs -n1 -0 ${CLANGFORMAT} -output-replacements-xml \
+ | grep -c "<replacement " > /dev/null
+ grepCode=$?
+elif [ "$1" == "--staged" ]
+then
+ git diff --cached --name-only --diff-filter=ACMRT | grep -e '.*\.h' -e '.*\.cpp' \
+ | xargs -n1 ${CLANGFORMAT} -output-replacements-xml \
+ | grep -c "<replacement " >/dev/null
+ grepCode=$?
+else
+ echo "Please specify --all or --staged"
+ exit 1
+fi
+
+# grep exits 0 => found needed formatting changes
+if [ $grepCode -ne 0 ]
+then
+ echo "Formatting looks good!"
+ exit 0
+else
+ echo "****************************************************"
+ echo "Code needs formatting! Please use 'tools/format-all'"
+ echo "****************************************************"
+ exit 1
+fi
diff --git a/tools/format-all b/tools/format-all
new file mode 100755
index 0000000..919f82f
--- /dev/null
+++ b/tools/format-all
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# This command can be run by the user to clang-format everything.
+
+PLATFORM=$(uname)
+CLANGFORMAT="./tools/${PLATFORM}/clang-format -style=file"
+
+find include src tests/unit \( -name *.cpp -or -name *.h \) -print0 | xargs -n1 -0 ${CLANGFORMAT} -i
diff --git a/tools/git-clang-format b/tools/git-clang-format
new file mode 100755
index 0000000..0c45762
--- /dev/null
+++ b/tools/git-clang-format
@@ -0,0 +1,485 @@
+#!/usr/bin/env python
+#
+#===- git-clang-format - ClangFormat Git Integration ---------*- python -*--===#
+#
+# The LLVM Compiler Infrastructure
+#
+# This file is distributed under the University of Illinois Open Source
+# License. See LICENSE.TXT for details.
+#
+#===------------------------------------------------------------------------===#
+
+r"""
+clang-format git integration
+============================
+
+This file provides a clang-format integration for git. Put it somewhere in your
+path and ensure that it is executable. Then, "git clang-format" will invoke
+clang-format on the changes in current files or a specific commit.
+
+For further details, run:
+git clang-format -h
+
+Requires Python 2.7
+"""
+
+import argparse
+import collections
+import contextlib
+import errno
+import os
+import re
+import subprocess
+import sys
+
+usage = 'git clang-format [OPTIONS] [<commit>] [--] [<file>...]'
+
+desc = '''
+Run clang-format on all lines that differ between the working directory
+and <commit>, which defaults to HEAD. Changes are only applied to the working
+directory.
+
+The following git-config settings set the default of the corresponding option:
+ clangFormat.binary
+ clangFormat.commit
+ clangFormat.extension
+ clangFormat.style
+'''
+
+# Name of the temporary index file in which save the output of clang-format.
+# This file is created within the .git directory.
+temp_index_basename = 'clang-format-index'
+
+
+Range = collections.namedtuple('Range', 'start, count')
+
+
+def main():
+ config = load_git_config()
+
+ # In order to keep '--' yet allow options after positionals, we need to
+ # check for '--' ourselves. (Setting nargs='*' throws away the '--', while
+ # nargs=argparse.REMAINDER disallows options after positionals.)
+ argv = sys.argv[1:]
+ try:
+ idx = argv.index('--')
+ except ValueError:
+ dash_dash = []
+ else:
+ dash_dash = argv[idx:]
+ argv = argv[:idx]
+
+ default_extensions = ','.join([
+ # From clang/lib/Frontend/FrontendOptions.cpp, all lower case
+ 'c', 'h', # C
+ 'm', # ObjC
+ 'mm', # ObjC++
+ 'cc', 'cp', 'cpp', 'c++', 'cxx', 'hpp', # C++
+ # Other languages that clang-format supports
+ 'proto', 'protodevel', # Protocol Buffers
+ 'js', # JavaScript
+ 'ts', # TypeScript
+ ])
+
+ p = argparse.ArgumentParser(
+ usage=usage, formatter_class=argparse.RawDescriptionHelpFormatter,
+ description=desc)
+ p.add_argument('--binary',
+ default=config.get('clangformat.binary', 'clang-format'),
+ help='path to clang-format'),
+ p.add_argument('--commit',
+ default=config.get('clangformat.commit', 'HEAD'),
+ help='default commit to use if none is specified'),
+ p.add_argument('--diff', action='store_true',
+ help='print a diff instead of applying the changes')
+ p.add_argument('--extensions',
+ default=config.get('clangformat.extensions',
+ default_extensions),
+ help=('comma-separated list of file extensions to format, '
+ 'excluding the period and case-insensitive')),
+ p.add_argument('-f', '--force', action='store_true',
+ help='allow changes to unstaged files')
+ p.add_argument('-p', '--patch', action='store_true',
+ help='select hunks interactively')
+ p.add_argument('-q', '--quiet', action='count', default=0,
+ help='print less information')
+ p.add_argument('--style',
+ default=config.get('clangformat.style', None),
+ help='passed to clang-format'),
+ p.add_argument('-v', '--verbose', action='count', default=0,
+ help='print extra information')
+ # We gather all the remaining positional arguments into 'args' since we need
+ # to use some heuristics to determine whether or not <commit> was present.
+ # However, to print pretty messages, we make use of metavar and help.
+ p.add_argument('args', nargs='*', metavar='<commit>',
+ help='revision from which to compute the diff')
+ p.add_argument('ignored', nargs='*', metavar='<file>...',
+ help='if specified, only consider differences in these files')
+ opts = p.parse_args(argv)
+
+ opts.verbose -= opts.quiet
+ del opts.quiet
+
+ commit, files = interpret_args(opts.args, dash_dash, opts.commit)
+ changed_lines = compute_diff_and_extract_lines(commit, files)
+ if opts.verbose >= 1:
+ ignored_files = set(changed_lines)
+ filter_by_extension(changed_lines, opts.extensions.lower().split(','))
+ if opts.verbose >= 1:
+ ignored_files.difference_update(changed_lines)
+ if ignored_files:
+ print 'Ignoring changes in the following files (wrong extension):'
+ for filename in ignored_files:
+ print ' ', filename
+ if changed_lines:
+ print 'Running clang-format on the following files:'
+ for filename in changed_lines:
+ print ' ', filename
+ if not changed_lines:
+ print 'no modified files to format'
+ return
+ # The computed diff outputs absolute paths, so we must cd before accessing
+ # those files.
+ cd_to_toplevel()
+ old_tree = create_tree_from_workdir(changed_lines)
+ new_tree = run_clang_format_and_save_to_tree(changed_lines,
+ binary=opts.binary,
+ style=opts.style)
+ if opts.verbose >= 1:
+ print 'old tree:', old_tree
+ print 'new tree:', new_tree
+ if old_tree == new_tree:
+ if opts.verbose >= 0:
+ print 'clang-format did not modify any files'
+ elif opts.diff:
+ print_diff(old_tree, new_tree)
+ else:
+ changed_files = apply_changes(old_tree, new_tree, force=opts.force,
+ patch_mode=opts.patch)
+ if (opts.verbose >= 0 and not opts.patch) or opts.verbose >= 1:
+ print 'changed files:'
+ for filename in changed_files:
+ print ' ', filename
+
+
+def load_git_config(non_string_options=None):
+ """Return the git configuration as a dictionary.
+
+ All options are assumed to be strings unless in `non_string_options`, in which
+ is a dictionary mapping option name (in lower case) to either "--bool" or
+ "--int"."""
+ if non_string_options is None:
+ non_string_options = {}
+ out = {}
+ for entry in run('git', 'config', '--list', '--null').split('\0'):
+ if entry:
+ name, value = entry.split('\n', 1)
+ if name in non_string_options:
+ value = run('git', 'config', non_string_options[name], name)
+ out[name] = value
+ return out
+
+
+def interpret_args(args, dash_dash, default_commit):
+ """Interpret `args` as "[commit] [--] [files...]" and return (commit, files).
+
+ It is assumed that "--" and everything that follows has been removed from
+ args and placed in `dash_dash`.
+
+ If "--" is present (i.e., `dash_dash` is non-empty), the argument to its
+ left (if present) is taken as commit. Otherwise, the first argument is
+ checked if it is a commit or a file. If commit is not given,
+ `default_commit` is used."""
+ if dash_dash:
+ if len(args) == 0:
+ commit = default_commit
+ elif len(args) > 1:
+ die('at most one commit allowed; %d given' % len(args))
+ else:
+ commit = args[0]
+ object_type = get_object_type(commit)
+ if object_type not in ('commit', 'tag'):
+ if object_type is None:
+ die("'%s' is not a commit" % commit)
+ else:
+ die("'%s' is a %s, but a commit was expected" % (commit, object_type))
+ files = dash_dash[1:]
+ elif args:
+ if disambiguate_revision(args[0]):
+ commit = args[0]
+ files = args[1:]
+ else:
+ commit = default_commit
+ files = args
+ else:
+ commit = default_commit
+ files = []
+ return commit, files
+
+
+def disambiguate_revision(value):
+ """Returns True if `value` is a revision, False if it is a file, or dies."""
+ # If `value` is ambiguous (neither a commit nor a file), the following
+ # command will die with an appropriate error message.
+ run('git', 'rev-parse', value, verbose=False)
+ object_type = get_object_type(value)
+ if object_type is None:
+ return False
+ if object_type in ('commit', 'tag'):
+ return True
+ die('`%s` is a %s, but a commit or filename was expected' %
+ (value, object_type))
+
+
+def get_object_type(value):
+ """Returns a string description of an object's type, or None if it is not
+ a valid git object."""
+ cmd = ['git', 'cat-file', '-t', value]
+ p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ stdout, stderr = p.communicate()
+ if p.returncode != 0:
+ return None
+ return stdout.strip()
+
+
+def compute_diff_and_extract_lines(commit, files):
+ """Calls compute_diff() followed by extract_lines()."""
+ diff_process = compute_diff(commit, files)
+ changed_lines = extract_lines(diff_process.stdout)
+ diff_process.stdout.close()
+ diff_process.wait()
+ if diff_process.returncode != 0:
+ # Assume error was already printed to stderr.
+ sys.exit(2)
+ return changed_lines
+
+
+def compute_diff(commit, files):
+ """Return a subprocess object producing the diff from `commit`.
+
+ The return value's `stdin` file object will produce a patch with the
+ differences between the working directory and `commit`, filtered on `files`
+ (if non-empty). Zero context lines are used in the patch."""
+ cmd = ['git', 'diff-index', '-p', '-U0', commit, '--']
+ cmd.extend(files)
+ p = subprocess.Popen(cmd, stdin=subprocess.PIPE, stdout=subprocess.PIPE)
+ p.stdin.close()
+ return p
+
+
+def extract_lines(patch_file):
+ """Extract the changed lines in `patch_file`.
+
+ The return value is a dictionary mapping filename to a list of (start_line,
+ line_count) pairs.
+
+ The input must have been produced with ``-U0``, meaning unidiff format with
+ zero lines of context. The return value is a dict mapping filename to a
+ list of line `Range`s."""
+ matches = {}
+ for line in patch_file:
+ match = re.search(r'^\+\+\+\ [^/]+/(.*)', line)
+ if match:
+ filename = match.group(1).rstrip('\r\n')
+ match = re.search(r'^@@ -[0-9,]+ \+(\d+)(,(\d+))?', line)
+ if match:
+ start_line = int(match.group(1))
+ line_count = 1
+ if match.group(3):
+ line_count = int(match.group(3))
+ if line_count > 0:
+ matches.setdefault(filename, []).append(Range(start_line, line_count))
+ return matches
+
+
+def filter_by_extension(dictionary, allowed_extensions):
+ """Delete every key in `dictionary` that doesn't have an allowed extension.
+
+ `allowed_extensions` must be a collection of lowercase file extensions,
+ excluding the period."""
+ allowed_extensions = frozenset(allowed_extensions)
+ for filename in dictionary.keys():
+ base_ext = filename.rsplit('.', 1)
+ if len(base_ext) == 1 or base_ext[1].lower() not in allowed_extensions:
+ del dictionary[filename]
+
+
+def cd_to_toplevel():
+ """Change to the top level of the git repository."""
+ toplevel = run('git', 'rev-parse', '--show-toplevel')
+ os.chdir(toplevel)
+
+
+def create_tree_from_workdir(filenames):
+ """Create a new git tree with the given files from the working directory.
+
+ Returns the object ID (SHA-1) of the created tree."""
+ return create_tree(filenames, '--stdin')
+
+
+def run_clang_format_and_save_to_tree(changed_lines, binary='clang-format',
+ style=None):
+ """Run clang-format on each file and save the result to a git tree.
+
+ Returns the object ID (SHA-1) of the created tree."""
+ def index_info_generator():
+ for filename, line_ranges in changed_lines.iteritems():
+ mode = oct(os.stat(filename).st_mode)
+ blob_id = clang_format_to_blob(filename, line_ranges, binary=binary,
+ style=style)
+ yield '%s %s\t%s' % (mode, blob_id, filename)
+ return create_tree(index_info_generator(), '--index-info')
+
+
+def create_tree(input_lines, mode):
+ """Create a tree object from the given input.
+
+ If mode is '--stdin', it must be a list of filenames. If mode is
+ '--index-info' is must be a list of values suitable for "git update-index
+ --index-info", such as "<mode> <SP> <sha1> <TAB> <filename>". Any other mode
+ is invalid."""
+ assert mode in ('--stdin', '--index-info')
+ cmd = ['git', 'update-index', '--add', '-z', mode]
+ with temporary_index_file():
+ p = subprocess.Popen(cmd, stdin=subprocess.PIPE)
+ for line in input_lines:
+ p.stdin.write('%s\0' % line)
+ p.stdin.close()
+ if p.wait() != 0:
+ die('`%s` failed' % ' '.join(cmd))
+ tree_id = run('git', 'write-tree')
+ return tree_id
+
+
+def clang_format_to_blob(filename, line_ranges, binary='clang-format',
+ style=None):
+ """Run clang-format on the given file and save the result to a git blob.
+
+ Returns the object ID (SHA-1) of the created blob."""
+ clang_format_cmd = [binary, filename]
+ if style:
+ clang_format_cmd.extend(['-style='+style])
+ clang_format_cmd.extend([
+ '-lines=%s:%s' % (start_line, start_line+line_count-1)
+ for start_line, line_count in line_ranges])
+ try:
+ clang_format = subprocess.Popen(clang_format_cmd, stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE)
+ except OSError as e:
+ if e.errno == errno.ENOENT:
+ die('cannot find executable "%s"' % binary)
+ else:
+ raise
+ clang_format.stdin.close()
+ hash_object_cmd = ['git', 'hash-object', '-w', '--path='+filename, '--stdin']
+ hash_object = subprocess.Popen(hash_object_cmd, stdin=clang_format.stdout,
+ stdout=subprocess.PIPE)
+ clang_format.stdout.close()
+ stdout = hash_object.communicate()[0]
+ if hash_object.returncode != 0:
+ die('`%s` failed' % ' '.join(hash_object_cmd))
+ if clang_format.wait() != 0:
+ die('`%s` failed' % ' '.join(clang_format_cmd))
+ return stdout.rstrip('\r\n')
+
+
+ at contextlib.contextmanager
+def temporary_index_file(tree=None):
+ """Context manager for setting GIT_INDEX_FILE to a temporary file and deleting
+ the file afterward."""
+ index_path = create_temporary_index(tree)
+ old_index_path = os.environ.get('GIT_INDEX_FILE')
+ os.environ['GIT_INDEX_FILE'] = index_path
+ try:
+ yield
+ finally:
+ if old_index_path is None:
+ del os.environ['GIT_INDEX_FILE']
+ else:
+ os.environ['GIT_INDEX_FILE'] = old_index_path
+ os.remove(index_path)
+
+
+def create_temporary_index(tree=None):
+ """Create a temporary index file and return the created file's path.
+
+ If `tree` is not None, use that as the tree to read in. Otherwise, an
+ empty index is created."""
+ gitdir = run('git', 'rev-parse', '--git-dir')
+ path = os.path.join(gitdir, temp_index_basename)
+ if tree is None:
+ tree = '--empty'
+ run('git', 'read-tree', '--index-output='+path, tree)
+ return path
+
+
+def print_diff(old_tree, new_tree):
+ """Print the diff between the two trees to stdout."""
+ # We use the porcelain 'diff' and not plumbing 'diff-tree' because the output
+ # is expected to be viewed by the user, and only the former does nice things
+ # like color and pagination.
+ subprocess.check_call(['git', 'diff', old_tree, new_tree, '--'])
+
+
+def apply_changes(old_tree, new_tree, force=False, patch_mode=False):
+ """Apply the changes in `new_tree` to the working directory.
+
+ Bails if there are local changes in those files and not `force`. If
+ `patch_mode`, runs `git checkout --patch` to select hunks interactively."""
+ changed_files = run('git', 'diff-tree', '-r', '-z', '--name-only', old_tree,
+ new_tree).rstrip('\0').split('\0')
+ if not force:
+ unstaged_files = run('git', 'diff-files', '--name-status', *changed_files)
+ if unstaged_files:
+ print >>sys.stderr, ('The following files would be modified but '
+ 'have unstaged changes:')
+ print >>sys.stderr, unstaged_files
+ print >>sys.stderr, 'Please commit, stage, or stash them first.'
+ sys.exit(2)
+ if patch_mode:
+ # In patch mode, we could just as well create an index from the new tree
+ # and checkout from that, but then the user will be presented with a
+ # message saying "Discard ... from worktree". Instead, we use the old
+ # tree as the index and checkout from new_tree, which gives the slightly
+ # better message, "Apply ... to index and worktree". This is not quite
+ # right, since it won't be applied to the user's index, but oh well.
+ with temporary_index_file(old_tree):
+ subprocess.check_call(['git', 'checkout', '--patch', new_tree])
+ index_tree = old_tree
+ else:
+ with temporary_index_file(new_tree):
+ run('git', 'checkout-index', '-a', '-f')
+ return changed_files
+
+
+def run(*args, **kwargs):
+ stdin = kwargs.pop('stdin', '')
+ verbose = kwargs.pop('verbose', True)
+ strip = kwargs.pop('strip', True)
+ for name in kwargs:
+ raise TypeError("run() got an unexpected keyword argument '%s'" % name)
+ p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
+ stdin=subprocess.PIPE)
+ stdout, stderr = p.communicate(input=stdin)
+ if p.returncode == 0:
+ if stderr:
+ if verbose:
+ print >>sys.stderr, '`%s` printed to stderr:' % ' '.join(args)
+ print >>sys.stderr, stderr.rstrip()
+ if strip:
+ stdout = stdout.rstrip('\r\n')
+ return stdout
+ if verbose:
+ print >>sys.stderr, '`%s` returned %s' % (' '.join(args), p.returncode)
+ if stderr:
+ print >>sys.stderr, stderr.rstrip()
+ sys.exit(2)
+
+
+def die(message):
+ print >>sys.stderr, 'error:', message
+ sys.exit(2)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/tools/win32/clang-format.exe b/tools/win32/clang-format.exe
new file mode 100644
index 0000000..d42fb80
Binary files /dev/null and b/tools/win32/clang-format.exe differ
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