[med-svn] [libbpp-seq] 01/02: Imported Upstream version 2.1.0
Andreas Tille
tille at debian.org
Sat Apr 9 06:00:14 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libbpp-seq.
commit c5e2fe5956dfcf9e66a55bd1e8ab72654faefc63
Author: Andreas Tille <tille at debian.org>
Date: Sat Apr 9 07:50:29 2016 +0200
Imported Upstream version 2.1.0
---
AUTHORS.txt | 24 +
CMakeLists.txt | 186 ++
COPYING.txt | 340 +++
ChangeLog | 422 ++++
Doxyfile | 1888 ++++++++++++++
INSTALL.txt | 12 +
bpp-seq.spec | 200 ++
debian/changelog | 64 +
debian/compat | 1 +
debian/control | 25 +
debian/copyright | 66 +
debian/docs | 0
debian/libbpp-seq-dev.install | 3 +
debian/libbpp-seq9.install | 1 +
debian/postinst | 43 +
debian/postrm | 45 +
debian/prerm | 27 +
debian/rules | 120 +
debian/source/format | 1 +
src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp | 276 +++
src/Bpp/Seq/Alphabet/AbstractAlphabet.h | 220 ++
src/Bpp/Seq/Alphabet/Alphabet.h | 390 +++
src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp | 92 +
src/Bpp/Seq/Alphabet/AlphabetExceptions.h | 213 ++
src/Bpp/Seq/Alphabet/AlphabetState.h | 132 +
src/Bpp/Seq/Alphabet/AlphabetTools.cpp | 126 +
src/Bpp/Seq/Alphabet/AlphabetTools.h | 231 ++
src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp | 62 +
src/Bpp/Seq/Alphabet/BinaryAlphabet.h | 78 +
src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp | 97 +
src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h | 117 +
src/Bpp/Seq/Alphabet/CodonAlphabet.cpp | 127 +
src/Bpp/Seq/Alphabet/CodonAlphabet.h | 241 ++
src/Bpp/Seq/Alphabet/DNA.cpp | 150 ++
src/Bpp/Seq/Alphabet/DNA.h | 82 +
src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp | 62 +
src/Bpp/Seq/Alphabet/DefaultAlphabet.h | 83 +
.../EchinodermMitochondrialCodonAlphabet.cpp | 75 +
.../EchinodermMitochondrialCodonAlphabet.h | 72 +
.../InvertebrateMitochondrialCodonAlphabet.cpp | 74 +
.../InvertebrateMitochondrialCodonAlphabet.h | 75 +
src/Bpp/Seq/Alphabet/LetterAlphabet.h | 106 +
src/Bpp/Seq/Alphabet/NucleicAlphabet.h | 259 ++
src/Bpp/Seq/Alphabet/NucleicAlphabetState.h | 116 +
src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp | 212 ++
src/Bpp/Seq/Alphabet/ProteicAlphabet.h | 137 ++
src/Bpp/Seq/Alphabet/ProteicAlphabetState.h | 82 +
src/Bpp/Seq/Alphabet/RNA.cpp | 148 ++
src/Bpp/Seq/Alphabet/RNA.h | 79 +
src/Bpp/Seq/Alphabet/RNY.cpp | 515 ++++
src/Bpp/Seq/Alphabet/RNY.h | 111 +
src/Bpp/Seq/Alphabet/StandardCodonAlphabet.cpp | 75 +
src/Bpp/Seq/Alphabet/StandardCodonAlphabet.h | 71 +
.../VertebrateMitochondrialCodonAlphabet.cpp | 76 +
.../VertebrateMitochondrialCodonAlphabet.h | 71 +
src/Bpp/Seq/Alphabet/WordAlphabet.cpp | 345 +++
src/Bpp/Seq/Alphabet/WordAlphabet.h | 330 +++
.../Alphabet/YeastMitochondrialCodonAlphabet.cpp | 72 +
.../Seq/Alphabet/YeastMitochondrialCodonAlphabet.h | 75 +
src/Bpp/Seq/AlphabetIndex/AAChargeIndex.h | 151 ++
.../AAChenGuHuangHydrophobicityIndex.h | 122 +
.../Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h | 111 +
.../Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h | 111 +
src/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h | 111 +
src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp | 85 +
src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h | 102 +
src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp | 101 +
src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h | 108 +
src/Bpp/Seq/AlphabetIndex/AAMassIndex.h | 110 +
src/Bpp/Seq/AlphabetIndex/AASEA1030Index.h | 111 +
src/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h | 111 +
src/Bpp/Seq/AlphabetIndex/AASEASup30Index.h | 111 +
src/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h | 111 +
src/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h | 111 +
src/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h | 97 +
src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h | 97 +
src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp | 78 +
src/Bpp/Seq/AlphabetIndex/BLOSUM50.h | 104 +
.../Seq/AlphabetIndex/DefaultNucleotideScore.cpp | 109 +
src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h | 108 +
.../AlphabetIndex/GranthamAAChemicalDistance.cpp | 110 +
.../Seq/AlphabetIndex/GranthamAAChemicalDistance.h | 158 ++
.../Seq/AlphabetIndex/GranthamAAPolarityIndex.h | 123 +
src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h | 126 +
src/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h | 124 +
.../Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp | 92 +
.../Seq/AlphabetIndex/MiyataAAChemicalDistance.h | 118 +
src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h | 134 +
src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp | 84 +
src/Bpp/Seq/AlphabetIndex/SimpleScore.h | 105 +
src/Bpp/Seq/AlphabetIndex/__BLOSUM50MatrixCode | 400 +++
src/Bpp/Seq/AlphabetIndex/__GranthamMatrixCode | 827 +++++++
src/Bpp/Seq/AlphabetIndex/__MiyataMatrixCode | 400 +++
src/Bpp/Seq/App/SequenceApplicationTools.cpp | 539 ++++
src/Bpp/Seq/App/SequenceApplicationTools.h | 269 ++
src/Bpp/Seq/CodonSiteTools.cpp | 846 +++++++
src/Bpp/Seq/CodonSiteTools.h | 331 +++
.../Seq/Container/AbstractSequenceContainer.cpp | 56 +
src/Bpp/Seq/Container/AbstractSequenceContainer.h | 190 ++
src/Bpp/Seq/Container/AlignedSequenceContainer.cpp | 521 ++++
src/Bpp/Seq/Container/AlignedSequenceContainer.h | 201 ++
.../Container/CompressedVectorSiteContainer.cpp | 597 +++++
.../Seq/Container/CompressedVectorSiteContainer.h | 290 +++
src/Bpp/Seq/Container/MapSequenceContainer.cpp | 466 ++++
src/Bpp/Seq/Container/MapSequenceContainer.h | 240 ++
src/Bpp/Seq/Container/OrderedSequenceContainer.h | 242 ++
src/Bpp/Seq/Container/SequenceContainer.h | 316 +++
.../Seq/Container/SequenceContainerExceptions.h | 149 ++
.../Seq/Container/SequenceContainerIterator.cpp | 75 +
src/Bpp/Seq/Container/SequenceContainerIterator.h | 97 +
src/Bpp/Seq/Container/SequenceContainerTools.cpp | 223 ++
src/Bpp/Seq/Container/SequenceContainerTools.h | 299 +++
src/Bpp/Seq/Container/SiteContainer.h | 183 ++
src/Bpp/Seq/Container/SiteContainerExceptions.cpp | 60 +
src/Bpp/Seq/Container/SiteContainerExceptions.h | 100 +
src/Bpp/Seq/Container/SiteContainerIterator.cpp | 144 ++
src/Bpp/Seq/Container/SiteContainerIterator.h | 128 +
src/Bpp/Seq/Container/SiteContainerTools.cpp | 1050 ++++++++
src/Bpp/Seq/Container/SiteContainerTools.h | 474 ++++
src/Bpp/Seq/Container/VectorSequenceContainer.cpp | 399 +++
src/Bpp/Seq/Container/VectorSequenceContainer.h | 306 +++
src/Bpp/Seq/Container/VectorSiteContainer.cpp | 862 +++++++
src/Bpp/Seq/Container/VectorSiteContainer.h | 240 ++
src/Bpp/Seq/DNAToRNA.cpp | 78 +
src/Bpp/Seq/DNAToRNA.h | 100 +
src/Bpp/Seq/DistanceMatrix.cpp | 53 +
src/Bpp/Seq/DistanceMatrix.h | 237 ++
.../EchinodermMitochondrialGeneticCode.cpp | 167 ++
.../EchinodermMitochondrialGeneticCode.h | 74 +
src/Bpp/Seq/GeneticCode/GeneticCode.cpp | 192 ++
src/Bpp/Seq/GeneticCode/GeneticCode.h | 174 ++
.../InvertebrateMitochondrialGeneticCode.cpp | 170 ++
.../InvertebrateMitochondrialGeneticCode.h | 75 +
src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp | 172 ++
src/Bpp/Seq/GeneticCode/StandardGeneticCode.h | 73 +
.../VertebrateMitochondrialGeneticCode.cpp | 172 ++
.../VertebrateMitochondrialGeneticCode.h | 73 +
.../GeneticCode/YeastMitochondrialGeneticCode.cpp | 170 ++
.../GeneticCode/YeastMitochondrialGeneticCode.h | 75 +
src/Bpp/Seq/Io/AbstractIAlignment.h | 185 ++
src/Bpp/Seq/Io/AbstractISequence.h | 182 ++
src/Bpp/Seq/Io/AbstractOAlignment.h | 86 +
src/Bpp/Seq/Io/AbstractOSequence.h | 107 +
src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp | 134 +
src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h | 95 +
src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp | 127 +
src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h | 95 +
src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp | 155 ++
src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h | 114 +
src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp | 125 +
src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h | 114 +
src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp | 139 ++
src/Bpp/Seq/Io/BppOSequenceReaderFormat.h | 95 +
src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp | 70 +
src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h | 96 +
src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp | 74 +
src/Bpp/Seq/Io/BppOSequenceWriterFormat.h | 95 +
src/Bpp/Seq/Io/Clustal.cpp | 138 ++
src/Bpp/Seq/Io/Clustal.h | 146 ++
src/Bpp/Seq/Io/Dcse.cpp | 97 +
src/Bpp/Seq/Io/Dcse.h | 109 +
src/Bpp/Seq/Io/Fasta.cpp | 291 +++
src/Bpp/Seq/Io/Fasta.h | 214 ++
src/Bpp/Seq/Io/GenBank.cpp | 86 +
src/Bpp/Seq/Io/GenBank.h | 94 +
src/Bpp/Seq/Io/ISequence.h | 132 +
src/Bpp/Seq/Io/ISequenceStream.h | 82 +
src/Bpp/Seq/Io/IoSequence.h | 72 +
src/Bpp/Seq/Io/IoSequenceFactory.cpp | 109 +
src/Bpp/Seq/Io/IoSequenceFactory.h | 124 +
src/Bpp/Seq/Io/IoSequenceStream.h | 66 +
src/Bpp/Seq/Io/Mase.cpp | 313 +++
src/Bpp/Seq/Io/Mase.h | 256 ++
src/Bpp/Seq/Io/MaseTools.cpp | 306 +++
src/Bpp/Seq/Io/MaseTools.h | 146 ++
src/Bpp/Seq/Io/NexusIoSequence.cpp | 209 ++
src/Bpp/Seq/Io/NexusIoSequence.h | 150 ++
src/Bpp/Seq/Io/NexusTools.cpp | 119 +
src/Bpp/Seq/Io/NexusTools.h | 84 +
src/Bpp/Seq/Io/OSequence.h | 128 +
src/Bpp/Seq/Io/OSequenceStream.h | 81 +
src/Bpp/Seq/Io/PhredPhd.cpp | 138 ++
src/Bpp/Seq/Io/PhredPhd.h | 156 ++
src/Bpp/Seq/Io/PhredPoly.cpp | 97 +
src/Bpp/Seq/Io/PhredPoly.h | 91 +
src/Bpp/Seq/Io/Phylip.cpp | 304 +++
src/Bpp/Seq/Io/Phylip.h | 196 ++
src/Bpp/Seq/Io/SequenceFileIndex.h | 75 +
src/Bpp/Seq/Io/Stockholm.cpp | 83 +
src/Bpp/Seq/Io/Stockholm.h | 120 +
src/Bpp/Seq/Io/StreamSequenceIterator.cpp | 97 +
src/Bpp/Seq/Io/StreamSequenceIterator.h | 138 ++
src/Bpp/Seq/NucleicAcidsReplication.cpp | 120 +
src/Bpp/Seq/NucleicAcidsReplication.h | 105 +
src/Bpp/Seq/Sequence.cpp | 222 ++
src/Bpp/Seq/Sequence.h | 465 ++++
src/Bpp/Seq/SequenceExceptions.cpp | 68 +
src/Bpp/Seq/SequenceExceptions.h | 161 ++
src/Bpp/Seq/SequenceIterator.h | 108 +
src/Bpp/Seq/SequencePositionIterators.cpp | 146 ++
src/Bpp/Seq/SequencePositionIterators.h | 210 ++
src/Bpp/Seq/SequenceTools.cpp | 699 ++++++
src/Bpp/Seq/SequenceTools.h | 410 +++
src/Bpp/Seq/SequenceWalker.cpp | 107 +
src/Bpp/Seq/SequenceWalker.h | 88 +
src/Bpp/Seq/SequenceWithAnnotation.cpp | 303 +++
src/Bpp/Seq/SequenceWithAnnotation.h | 443 ++++
src/Bpp/Seq/SequenceWithAnnotationTools.cpp | 89 +
src/Bpp/Seq/SequenceWithAnnotationTools.h | 205 ++
src/Bpp/Seq/SequenceWithQuality.cpp | 76 +
src/Bpp/Seq/SequenceWithQuality.h | 781 ++++++
src/Bpp/Seq/SequenceWithQualityTools.cpp | 194 ++
src/Bpp/Seq/SequenceWithQualityTools.h | 175 ++
src/Bpp/Seq/Site.cpp | 101 +
src/Bpp/Seq/Site.h | 179 ++
src/Bpp/Seq/SiteExceptions.cpp | 52 +
src/Bpp/Seq/SiteExceptions.h | 124 +
src/Bpp/Seq/SiteIterator.h | 80 +
src/Bpp/Seq/SiteTools.cpp | 426 ++++
src/Bpp/Seq/SiteTools.h | 259 ++
src/Bpp/Seq/StringSequenceTools.cpp | 344 +++
src/Bpp/Seq/StringSequenceTools.h | 204 ++
src/Bpp/Seq/SymbolList.cpp | 442 ++++
src/Bpp/Seq/SymbolList.h | 745 ++++++
src/Bpp/Seq/SymbolListTools.cpp | 197 ++
src/Bpp/Seq/SymbolListTools.h | 207 ++
src/Bpp/Seq/Transliterator.cpp | 72 +
src/Bpp/Seq/Transliterator.h | 187 ++
src/CMakeLists.txt | 246 ++
test/CMakeLists.txt | 66 +
test/example.aln | 2143 ++++++++++++++++
test/example.fasta | 1702 +++++++++++++
test/example.fastq | 12 +
test/example.gff | 25 +
test/example.mase | 1500 +++++++++++
test/example.ph | 2526 +++++++++++++++++++
test/example.ph3 | 2601 ++++++++++++++++++++
test/test_alignment_scores.cpp | 102 +
test/test_alphabets.cpp | 77 +
test/test_bowker.cpp | 101 +
test/test_containers.cpp | 68 +
test/test_io.cpp | 96 +
test/test_sequences.cpp | 92 +
test/test_walker.cpp | 119 +
244 files changed, 53837 insertions(+)
diff --git a/AUTHORS.txt b/AUTHORS.txt
new file mode 100644
index 0000000..2e617ee
--- /dev/null
+++ b/AUTHORS.txt
@@ -0,0 +1,24 @@
+Julien Dutheil <julien.dutheil at univ-montp2.fr>
+Sylvain Gaillard <sylvain.gaillard at angers.inra.fr>
+Khalid Belkhir <belkhir at univ-montp2.fr>
+Laurent Gueguen <gueguen at biomserv.univ-lyon1.fr>
+Sylvain Glémin <glemin at univ-montp2.fr>
+Guillaume Deuchst
+Eric Bazin
+Vincent Cahais
+
+Contributed code to Bio++ was enabled thanks to the following institutions and resources:
+
+2002 - 2006 Laboratoire GPIA - UMR CNRS 5171 Université Montpellier 2 (Eric Bazin, Khalid Belkhir, Guillaume Deuchst, Julien Dutheil, Sylvain Gaillard, Nicolas Galtier, Sylvain Glémin)
+2005 - ISE-M UMR CNRS 5554 Université Montpellier 2 (Vincent Ranwez, Céline Scornavacca)
+2006 - ISE-M UMR CNRS 5554 Université Montpellier 2 (Khalid Belkhir, Nicolas Galtier, Sylvain Glémin)
+2006 - 2007 ISE-M UMR CNRS 5554 Université Montpellier 2 (Julien Dutheil)
+2007 - 2010 Bioinformatics Research Center, University of Aarhus (Julien Dutheil).
+ Funded by European research Area on Plant Genomics (ERA-PG) ARelatives.
+2010 - ISE-M UMR CNRS 5554 Université Montpellier 2 (Julien Dutheil)
+2010 - ISE-M UMR CNRS 5554 Université Montpellier 2 (Vincent Cahais)
+2007 - Genetics and Horticulture UMR INRA 1259 Angers-Nantes INRA Center (Sylvain Gaillard)
+2008 - 2009 Laboratoire BBE - UMR CNRS 5558 Université Lyon 1 (Bastien Boussau)
+2009 - 2010 Berkeley University (Bastien Boussau)
+2010 - Laboratoire BBE - UMR CNRS 5558 Université Lyon 1 (Bastien Boussau)
+2008 - Laboratoire BBE - UMR CNRS 5558 Université Lyon 1 (Laurent Guéguen)
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..bf03ce6
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,186 @@
+# CMake script for Bio++ Sequence library
+# Author: Sylvain Gaillard and Julien Dutheil
+# Created: 20/08/2009
+
+# Global parameters
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+PROJECT(bpp-seq CXX)
+IF(NOT CMAKE_BUILD_TYPE)
+ SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
+ "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
+ FORCE)
+ENDIF(NOT CMAKE_BUILD_TYPE)
+
+SET(CMAKE_CXX_FLAGS "-Wall -Weffc++ -Wshadow -Wconversion")
+IF(NOT NO_VIRTUAL_COV)
+ SET(NO_VIRTUAL_COV FALSE CACHE BOOL
+ "Disable covariant return type with virtual inheritance, for compilers that do not support it."
+ FORCE)
+ENDIF(NOT NO_VIRTUAL_COV)
+
+IF(NO_VIRTUAL_COV)
+ MESSAGE("-- Covariant return with virtual inheritance disabled.")
+ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNO_VIRTUAL_COV=1")
+ENDIF(NO_VIRTUAL_COV)
+
+IF(NOT NO_DEP_CHECK)
+ SET(NO_DEP_CHECK FALSE CACHE BOOL
+ "Disable dependencies check for building distribution only."
+ FORCE)
+ENDIF(NOT NO_DEP_CHECK)
+
+IF(NO_DEP_CHECK)
+ MESSAGE("-- Dependencies checking disabled. Only distribution can be built.")
+ELSE(NO_DEP_CHECK)
+
+# Libtool-like version number
+# CURRENT:REVISION:AGE => file.so.(C-A).A.R
+# current: The most recent interface number that this library implements.
+# revision: The implementation number of the current interface.
+# age: The difference between the newest and oldest interfaces that this
+# library implements.
+# In other words, the library implements all the interface numbers in the
+# range from number current - age to current.
+SET(BPPSEQ_VERSION_CURRENT "10")
+SET(BPPSEQ_VERSION_REVISION "3")
+SET(BPPSEQ_VERSION_AGE "1")
+
+# Effective version number computation
+math(EXPR BPPSEQ_VERSION_MAJOR "${BPPSEQ_VERSION_CURRENT} - ${BPPSEQ_VERSION_AGE}")
+SET(BPPSEQ_VERSION_MINOR ${BPPSEQ_VERSION_AGE})
+SET(BPPSEQ_VERSION_PATCH ${BPPSEQ_VERSION_REVISION})
+SET(BPPSEQ_VERSION "${BPPSEQ_VERSION_MAJOR}.${BPPSEQ_VERSION_MINOR}.${BPPSEQ_VERSION_PATCH}")
+
+# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
+# standard install location
+IF(CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
+ENDIF(CMAKE_INSTALL_PREFIX)
+
+MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
+ #start:
+ FIND_PATH(${lib_name}_INCLUDE_DIR ${include_to_find})
+ SET(${lib_name}_NAMES ${lib_name} ${lib_name}lib ${lib_name}dll)
+ FIND_LIBRARY(${lib_name}_LIBRARY NAMES ${${lib_name}_NAMES} PATH_SUFFIXES lib${LIB_SUFFIX})
+
+ IF(${lib_name}_LIBRARY)
+ MESSAGE("-- Library ${lib_name} found here:")
+ MESSAGE(" includes : ${${lib_name}_INCLUDE_DIR}")
+ MESSAGE(" libraries: ${${lib_name}_LIBRARY}")
+ ELSE(${lib_name}_LIBRARY)
+ MESSAGE(FATAL_ERROR "${lib_name} required but not found.")
+ ENDIF(${lib_name}_LIBRARY)
+
+ #add the dependency:
+ INCLUDE_DIRECTORIES(${${lib_name}_INCLUDE_DIR})
+ SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_LIBRARY})
+ENDMACRO(IMPROVED_FIND_LIBRARY)
+
+#Find the Bio++ libraries:
+IMPROVED_FIND_LIBRARY(LIBS bpp-core Bpp/Clonable.h)
+
+# Subdirectories
+ADD_SUBDIRECTORY(src)
+
+# Doxygen
+FIND_PACKAGE(Doxygen)
+IF (DOXYGEN_FOUND)
+ ADD_CUSTOM_TARGET (apidoc cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-build
+ COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-build
+ COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-build
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+ ADD_CUSTOM_TARGET (apidoc-stable cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ COMMAND echo "HTML_HEADER=header.html" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+ENDIF (DOXYGEN_FOUND)
+
+ENDIF(NO_DEP_CHECK)
+
+# Packager
+SET(CPACK_PACKAGE_NAME "libbpp-seq")
+SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
+SET(CPACK_PACKAGE_VERSION "2.1.0")
+SET(CPACK_PACKAGE_VERSION_MAJOR "2")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Sequence library")
+SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
+SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
+SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt")
+SET(CPACK_SOURCE_GENERATOR "TGZ")
+SET(CPACK_SOURCE_IGNORE_FILES
+ "CMakeFiles"
+ "Makefile"
+ "_CPack_Packages"
+ "CMakeCache.txt"
+ ".*\\\\.cmake"
+ ".*\\\\.git"
+ ".*\\\\.gz"
+ ".*\\\\.deb"
+ ".*\\\\.rpm"
+ ".*\\\\.dmg"
+ ".*\\\\.sh"
+ ".*\\\\..*\\\\.swp"
+ "src/\\\\..*"
+ "src/libbpp*"
+ "debian/tmp"
+ "debian/libbpp.*/"
+ "debian/libbpp.*\\\\.so.*"
+ "debian/libbpp.*\\\\.a"
+ "debian/libbpp.*\\\\.substvars"
+ "debian/libbpp.*\\\\.debhelper"
+ "debian/debhelper\\\\.log"
+ "html"
+ "Seq.tag"
+ "Testing"
+ "build-stamp"
+ "install_manifest.txt"
+ "DartConfiguration.tcl"
+ ${CPACK_SOURCE_IGNORE_FILES}
+)
+IF (MACOS)
+ SET(CPACK_GENERATOR "Bundle")
+ENDIF()
+
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
+SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "lib${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig")
+INCLUDE(CPack)
+
+#This adds the 'dist' target
+ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
+# 'clean' is not (yet) a first class target. However, we need to clean the directories before building the sources:
+IF("${CMAKE_GENERATOR}" MATCHES "Make")
+ ADD_CUSTOM_TARGET(make_clean
+ COMMAND ${CMAKE_MAKE_PROGRAM} clean
+ WORKING_DIRECTORY ${CMAKE_CURRENT_DIR}
+ )
+ ADD_DEPENDENCIES(dist make_clean)
+ENDIF()
+
+IF(NOT NO_DEP_CHECK)
+IF (UNIX)
+#This creates deb packages:
+ADD_CUSTOM_TARGET(origdist COMMAND cp ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz ../${CPACK_DEBSOURCE_PACKAGE_FILE_NAME}.tar.gz)
+ADD_DEPENDENCIES(origdist dist)
+ADD_CUSTOM_TARGET(deb dpkg-buildpackage -uc -us -i${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
+ADD_DEPENDENCIES(deb origdist)
+
+#This creates rpm packages:
+ADD_CUSTOM_TARGET(rpm rpmbuild -ta ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
+ADD_DEPENDENCIES(rpm dist)
+
+ENDIF()
+
+SET(CTEST_UPDATE_TYPE git)
+SET(UPDATE_COMMAND "git")
+SET(UPDATE_OPTIONS "")
+
+ENABLE_TESTING()
+INCLUDE(CTest)
+IF (BUILD_TESTING)
+ ADD_SUBDIRECTORY(test)
+ENDIF(BUILD_TESTING)
+
+ENDIF(NOT NO_DEP_CHECK)
diff --git a/COPYING.txt b/COPYING.txt
new file mode 100644
index 0000000..623b625
--- /dev/null
+++ b/COPYING.txt
@@ -0,0 +1,340 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
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+
+ When we speak of free software, we are referring to freedom, not
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+
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+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
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+ 0. This License applies to any program or other work which contains
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+ 10. If you wish to incorporate parts of the Program into other free
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+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
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+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
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+free software which everyone can redistribute and change under these terms.
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+ To do so, attach the following notices to the program. It is safest
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+the "copyright" line and a pointer to where the full notice is found.
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+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+
+Also add information on how to contact you by electronic and paper mail.
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+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
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+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
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+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..433ca47
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,422 @@
+05/03/13 -*- Version 2.1.0 -*-
+
+07/02/13 Julien Dutheil
+* StateProperties => Alphabet index (dir renamed).
+* New BppO classes forAlphabet Index 1 and 2, and corresponding methods in SequenceApplicationTools.
+
+19/01/13 Julien Dutheil
+* Compiles with -Wconversion.
+
+09/01/13 Julien Dutheil
+* Use size_t instead of unsigned int for indexes in containers.
+
+17/09/12 Julien Dutheil
+* Reorganized IO classes.
+
+11/09/12 Julien Dutheil
+* Added generic container converter function.
+
+30/07/12 Julien Dutheil
+* Moved features, fastq and maf to new bpp-seq-omics library.
+
+18/07/12 Julien Dutheil
+* Bug fixed in merge maf iterator, in case a sequence is missing in one of the two blocks.
+
+25/06/12 Julien Dutheil
+* Extended maf tools and reorganization of the code.
+* Extended GFF output.
+* New [] operator in SequenceFeatureSet.
+
+18/06/12 Julien Dutheil
+* Fixed bug in Maf parser: scores are now parsed correctly.
+
+08/03/12 Julien Dutheil
+* Added support for '*' character in proteins (stop codon)
+
+09/02/12 -*- Version 2.0.3 -*-
+
+16/01/12 Julien Dutheil
+* Bug #42 solved, new support for extended fasta parser in application tools.
+* Added contribution from Benoit Nabholz and Annabelle Haudry on 4-fold degenerated sites.
+
+06/01/12 Julien Dutheil
+* Added support for "!" state in nucleic alphabet, which can be either a gap or an unknown character.
+
+24/11/11 Julien Dutheil
+* Added SequenceWalker class and test.
+
+22/11/11 Sylvain Gaillard
+* Added support for FastQ
+
+21/11/11 Julien Dutheil
+* Added support for GFF3.
+
+21/11/11 Sylvain Gaillard
+* Bug #35 solved.
+
+18/11/11 Julien Dutheil
+* New MafIterators: SequenceStatistics and PairwiseSequenceStatistics.
+* Function SequenceTools::getPercentIdentity now allows to exclude gaps.
+
+15/09/11 Julien Dutheil
+* Merge function of SequenceWithAnnotation now also merges annotations properly.
+
+17/06/11 Julien Dutheil
+* Bug #39 solved.
+
+09/06/11 -*- Version 2.0.2 -*-
+
+08/06/11 Julien Dutheil
+* Fixed several Maf iterators.
+
+28/02/11 -*- Version 2.0.1 -*-
+
+* Fixed debian packaging.
+
+07/02/11 -*- Version 2.0.0 -*-
+
+19/11/10 Julien Dutheil
+* Solved bug 0000016 (General comments not copied in containers).
+* A few more code cleaning.
+
+01/11/10 Julien Dutheil
+* Solved bug 0000005 (Clustal parser).
+* Added unit testing for sequence input format.
+* Solved bug 0000004 (Remove gap sites in SiteContainer).
+
+12/10/10 Benoît Nabholz
+* Added yeast mitochondrial codon alphabet and genetic code.
+
+20/09/10 Julien Dutheil
+* Reorganization of the code for version 2.0.
+
+06/09/10 Julien Dutheil
+* Added support for masked sequences in SequenceWithAnnotationTools and MafParser.
+
+05/09/10 Julien Dutheil
+* First draft of CaseMaskedAlphabet, for dealing with repeat-masked sequences for instance.
+
+21/07/10 Julien Dutheil
+* Added method hasSequence(name) in SequenceContainer interface.
+
+20/07/10 Julien Dutheil
+* New Sequence interface design.
+* Maf parser now reads quality scores if there are some.
+
+19/07/10 Julien Dutheil
+* New method isInit in CodonAlphabet.
+* New method getCDS in SequenceTools.
+
+28/04/10 Julien Dutheil
+* New MAF genome alignment parser.
+
+22/04/10 Sylvain Gaillard
+* Break SequenceTools interface:
+ - renamed invert -> getInvert
+ - renamed complement -> getComplement
+ now invert and complement methods deals with sequence ref
+ - New method invertComplement
+
+16/04/10 Julien Dutheil
+* New Stockholm sequence format (output only).
+* Refactoring of class ISequence2 => IAlignment + new interface OAlignment.
+
+24/03/10 -*- Version 1.7.0 -*-
+
+11/03/10 Julien Dutheil
+* Nexus format now deals with lower case keywords.
+
+17/12/09 Julien Dutheil
+* Code cleaning for VectorSiteContainer
+* New class CompressedVectorSiteContainer using less memory than
+ VectorSiteContainer, but more restricted.
+
+16/11/09 Sylvain Gaillard
+* No more "using namespace" in header files.
+
+04/11/09 Julien Dutheil
+* Remove SymbolListTools::randomizeContent to a more efficient SymbolList::shuffle
+method.
+
+12/10/09 Julien Dutheil
+* Now SeqLib compiles with -Weffc++ and -Wshadow without any warning :)
+
+22/09/09 Julien Dutheil
+* Finally added 'addSequence' method in SequenceContainer.
+* MapSequenceContainer now has a addSequence method that uses the name of the
+ sequence as a key by default.
+* Several methods in Sequence/SiteContainerTools are not templated anymore and
+ have been improved.
+
+09/09/09 Sylvain Gaillard
+* Fixed white space skip in Fasta sequence
+
+20/08/09 Julien Dutheil
+* Added config files for CMake.
+
+19/08/09 Sylvain Gaillard
+* Introduced 3 new interfaces IOSequenceStream, ISequenceStream and
+ OSequenceStream. These interfaces are intended to be used by IOFormat
+ dealing with Sequence and not SequenceContainers. They are actually
+ implemented by the Fasta class.
+
+17/08/09 Adam Smith
+* Bug fixed in DefaultAlphabet: unknow state is 37 not 38.
+
+04/08/09 Sylvain Gaillard
+* Introduced new classes for Alphabet States
+
+23/07/09 Sylvain Gaillard
+* Added SequenceTools::getPutativeHaplotypes
+
+22/07/09 Sylvain Gaillard
+* Added SequenceTools::getNumberOfUnresolvedSites
+* Updated SequenceTools::getNumberOfSites,
+ SequenceTools::getNumberOfCompleteSites and SequenceTools::removeGaps to be
+ Alphabet implementation independant.
+
+07/07/07 Julien Dutheil
+* Updated GranthamAAChemicalDistance, with a new signed, non-symmetric,
+ option.
+
+26/06/09 Sylvain Gaillard
+* Added new SequencePositionIterators classes.
+
+23/06/09 Julien Dutheil
+* Actualization of the Container classes: now returns references and not
+pointer. Several code updates, including copy contructors.
+
+17/06/09 Sylvain Gaillard (Glasgow Workshop)
+* Fix DNA/RNA/ProteicAlphabet::getAlias: works now with lower case states.
+* Fix SiteTools::isConstant test gap or unknown
+* Turning SequenceContainerTools::getFrequencies into void function.
+
+21/07/08 -*- Version 1.6.0 -*-
+
+28/05/09 Julien Dutheil
+* Added basic support for the Nexus format.
+
+22/05/09 Julien Dutheil
+* Improved Clustal format (solves bug found by Emmanuel M.)
+* SequenceApplicationTools uses the keyval syntax for format description.
+
+27/04/09 Julien Dutheil
+* Added site randomization method.
+
+28/02/09 Julien Dutheil
+* Added mutual information calculation.
+* Added pairwise counting methods.
+* Frequencies counting methods have been improved (avoid useless copy of maps).
+
+16/01/09 Julien Dutheil
+* max_gap_allowed option in SequenceApplicationTools is now a included bound:
+ 0 or 0% will keep all complete sites, and 'n=number of sequences' or 100%
+ will keep all sites.
+
+13/01/09 Sylvain Gaillard
+* Little optimization in Fasta::write() method.
+
+12/01/09 Sylvain Gaillard
+* Added support for comments (HUPO-PSI like) in Fasta.
+
+08/01/09 Julien Dutheil
+* SequenceTools::reverse method has been deprecated in favor of the
+ SequenceTools::inverse method, of witch it is now an alias.
+
+07/01/09 Julien Dutheil
+* Code improvement in Vector containers.
+
+21/12/08 Julien Dutheil
+* Return type for clone() methods corrected (Sequence, Site, SiteContainer and derivated classes).
+* Bug fixed in SequenceApplicationTools::get[Sequence/Site]Container, phylip format.
+
+21/07/08 -*- Version 1.5.0 -*-
+
+05/12/08 Julien Dutheil
+* VectorSiteContainer::getSite() faster (more than 10 times faster on a ~500
+ sequences data set!)
+
+04/12/08 Julien Dutheil
+* Fixed missing redefinition of translate and reverse methods in class DNAToRNA.
+* Made inheritance virtual.
+
+01/12/08 Julien Dutheil
+* New methods getSupportedInts and getSupportedChars in Alphabet classes.
+
+18/11/08 Julien Dutheil
+* biopp-help-forum 91 (by Stephen Smith): Fasta, Mase, Clustal and Phylip now
+ have an option to turn off the name checking and decrease loading time.
+* biopp-help-forum 93 (by Stephen Smith): Phylip format now supports any
+ delimiter when reading/writing files in extended format.
+
+14/11/08 Sylvain Gaillard
+* New method SequenceTools::subtractHaplotype(Sequence, Sequence, string,
+ unsigned int).
+
+07/11/08 Julien Dutheil
+* New contructor in VectorSiteContainer now as a tag to disable position
+ checking, which can turn to be quite slow.
+
+06/11/08 Sylvain Gaillard
+* New class PhredPhd to read sequence from phd files produced by the phred
+ program
+* Removed an unused method in PhredPoly
+
+05/11/08 Sylvain Gaillard
+* New methods Alphabet::getGeneric(states) implemented in AbstractAlphabet,
+ DefaultAlphabet, DNA, RNA and ProteicAlphabet.
+* New alphabet exception CharStateNotSupportedException.
+* New class PhredPoly to read sequence from poly files produced by the phred
+ program.
+* Fixed heterozygous site read in PhredPoly.
+
+09/10/08 Julien Dutheil
+* New method SequenceTools::invert(Sequence).
+
+24/09/08 Bastien Boussau & Julien Dutheil
+* Memory leak fixed in Fasta and Mase readers.
+
+21/07/08 -*- Version 1.4.1 -*-
+
+26/06/08 Julien Dutheil
+* Bug fixed in Clustal format.
+
+20/04/08 Julien Dutheil
+* New interface ISequence2 for reading alignments.
+
+18/03/08 Julien Dutheil and Bastien Boussau
+* Bowker's test for homogeneity implemented in SequenceTools.
+
+08/02/08 Julien Dutheil
+* Bug fixed in VectorSequenceContainer: method addSequence is now virtual!
+ (thanks to Laurent Gueguen for pointing out this bug)!.
+
+07/02/08 Julien Dutheil
+* Added function isDNAAlphabet and isRNAAlphabet in AlphabetTools.
+* Bug fixed in getAlphabetFromSequence method.
+* Method getContent in Sequence and Site now outputs a reference.
+
+18/01/08 -*- Version 1.4.0 -*-
+
+09/01/08 Julien Dutheil
+* All classes included in the new 'bpp' namespace.
+
+06/11/07 Julien Dutheil
+* New function SequenceContainerTools::merge.
+
+02/10/07 Julien Dutheil
+* New class GenBank, enabling GenBank sequence format support for input.
+* Added new copy constructors from SequenceContainer in
+ Vector[Site/Sequence]Container.
+* New methods changeUnresolvedCharacterToGaps and changeGapsToUnknownCharacters in SymbolListTools.
+* Bug fixed in changeUnresolvedCharacterToGaps in SiteContainerTools.
+
+06/07/07 -*- Version 1.3.0 -*-
+
+12/06/07 Julien Dutheil
+* More tools in class alphabet (isGap, isUnresolved, etc.)
+* New class DistanceMatrix, previously in phyllib.
+* New similarity measures in SiteContainerTools.
+
+04/06/07 Julien Dutheil
+* New constructor from sequence names in VectorSiteContainer.
+
+01/06/07 Julien Dutheil
+* New method SiteContainerTools::boostrapSites to bootstrap an alignment.
+
+21/05/07 Julien Dutheil
+* New method SequenceContainerTools::getSequenceContainer to read non-aligned
+ sequences.
+
+04/05/07 Julien Dutheil
+* Bug fixed in global alignment with gap opening and extending penalties.
+* New generic score scheme.
+* Compatibility update (NumCalc)
+
+24/04/07 Benoît Nabholz & Julien Dutheil
+* GeneticCode classes can now translate unknow codons to unknown amino acids.
+
+02/04/07 Julien Dutheil
+* VIRTUAL_COV variable changed to NO_VIRTUAL_COV. configure.ac file updated.
+ => Default behaviour is now /really/ to use covariant return type with
+ virtual inheritence, even when importing the files in an IDE. To use the old
+ compilers behaviour, one must set the NO_VIRTUAL_COV preproc variable.
+* this modification also solves a problem with the old configure.ac which
+ was not correctly updated in version 1.2.0 :(
+* Bug fixed in SymbolListTools::getCounts.
+
+02/04/07 Julien Dutheil
+* New method getAlphabetIndex1() in class SimpleIndexDistance.
+
+24/02/07 Julien Dutheil
+* New pairwise alignment algorithm: gap opening and extending penalties.
+
+22/02/07 Julien Dutheil
+* GeneticCode derivated classes now properly redefine the translate(Sequence&)
+ method.
+
+19/01/07 -*- Version 1.2.0 -*-
+
+19/01/07 Julien Dutheil
+* Functions AlphabetTools::getType() and StringSequenceTools::getAlphabetFromSequence() rewritten.
+* New DefaultNucleotideScore matrix.
+* New AAIndex1Entry and AAIndex2Entry classes which create AlphabetIndex1 and
+AlphabetIndex2 objects from AAIndex1 and AAIndex2 entries, respectively.
+
+18/12/06 Julien Dutheil
+* New alignment tools in SiteContainerTools, including the Needleman and
+Wunsch alogrithm.
+* BLOSUM50 matrix available.
+* Bug fixed in Sequence.h: method setContent is now properly redefined.
+* Bug fixed in ProteicAlphabet->getAbbr(int). The returned result is now
+correct!!!
+
+06/12/06 Julien Dutheil
+* DefaultAlphabet now accepts "." characters.
+* New AlphabetTools::isDefaultAlphabet(const Alphabet *) method.
+* New SiteContainerTools::resolveDottedAlignment(const Sitecontainer &, const Alphabet *) method.
+
+30/08/06 Julien Dutheil
+* Bug fixed in phylip sequential reader, + duplicated sequence in container
+now throws sequence name. (included in 1.1.1 release).
+
+28/08/06 -*- Version 1.1.1 -*-
+
+08/08/06 Julien Dutheil
+* Bug fixed in Phylip sequential read method.
+
+15/06/06 Julien Dutheil
+* Method changeGapsToUnknownCharacters() moved from SequenceContainerTools to
+SiteContainerTools, and is really faster!
+* New removeGapOnlySites() method in SiteContainerTools.
+* New method SiteTools::isGapOnly().
+* new 'sequence.max_gap_allowed' option in SequenceApplicationTools::getSitesToAnalyse().
+
+13/06/06 Julien Dutheil
+* Phylip sequential format improved, no more empty line between sequences
+needed.
+
+12/06/06 Julien Dutheil
+* SiteTools::isConstant() method now has a 'ignoreUnknown' option.
+
+01/01/06 Julien Dutheil
+* VectorSiteContainer and AlignedSequenceContainer now number sites from 1 (and not 0).
+
+17/05/06 Benoît Nabholz, Sylvain Glémin & Julien Dutheil
+* Bug fixed in SiteContainerTools::getConsensus(), + SymbolListTools::getFrequencies() and getCounts() improved.
+
+15/05/06 Julien Dutheil
+* Bug fixed: Added getUnknownCharacterCode() method in DefaultAlphabet.
+
+09/05/06 Julien Dutheil
+* New AAChargeIndex class.
+* Bug fixed in SiteTools::hasUnknown(Site).
+
+18/04/06 -*- Version 1.1.0 -*-
+
+18/04/06 Julien Dutheil
+* New IOSequenceFactory class.
+
+06/04/06 Julien Dutheil
+* New () function operators defined on SequenceContainers.
+
diff --git a/Doxyfile b/Doxyfile
new file mode 100644
index 0000000..86feefb
--- /dev/null
+++ b/Doxyfile
@@ -0,0 +1,1888 @@
+# Doxyfile 1.8.3.1-20130209
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+# TAG = value [value, ...]
+# For lists items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or sequence of words) that should
+# identify the project. Note that if you do not use Doxywizard you need
+# to put quotes around the project name if it contains spaces.
+
+PROJECT_NAME = bpp-seq
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# This could be handy for archiving the generated documentation or
+# if some version control system is used.
+
+PROJECT_NUMBER = 2.1.0
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer
+# a quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF =
+
+# With the PROJECT_LOGO tag one can specify an logo or icon that is
+# included in the documentation. The maximum height of the logo should not
+# exceed 55 pixels and the maximum width should not exceed 200 pixels.
+# Doxygen will copy the logo to the output directory.
+
+PROJECT_LOGO =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY =
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
+# 4096 sub-directories (in 2 levels) under the output directory of each output
+# format and will distribute the generated files over these directories.
+# Enabling this option can be useful when feeding doxygen a huge amount of
+# source files, where putting all generated files in the same directory would
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# The default language is English, other supported languages are:
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
+# messages), Korean, Korean-en, Latvian, Lithuanian, Norwegian, Macedonian, Persian,
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+
+OUTPUT_LANGUAGE = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# include brief member descriptions after the members that are listed in
+# the file and class documentation (similar to JavaDoc).
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+# the brief description of a member or function before the detailed description.
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator
+# that is used to form the text in various listings. Each string
+# in this list, if found as the leading text of the brief description, will be
+# stripped from the text and the result after processing the whole list, is
+# used as the annotated text. Otherwise, the brief description is used as-is.
+# If left blank, the following values are used ("$name" is automatically
+# replaced with the name of the entity): "The $name class" "The $name widget"
+# "The $name file" "is" "provides" "specifies" "contains"
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# Doxygen will generate a detailed section even if there is only a brief
+# description.
+
+ALWAYS_DETAILED_SEC = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user-defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the
+# path to strip. Note that you specify absolute paths here, but also
+# relative paths, which will be relative from the directory where doxygen is
+# started.
+
+STRIP_FROM_PATH = ./src/
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
+# the path mentioned in the documentation of a class, which tells
+# the reader which header file to include in order to use a class.
+# If left blank only the name of the header file containing the class
+# definition is used. Otherwise one should specify the include paths that
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH = ./src/
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+# (but less readable) file names. This can be useful if your file system
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like regular Qt-style comments
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
+# interpret the first line (until the first dot) of a Qt-style
+# comment as the brief description. If set to NO, the comments
+# will behave just like regular Qt-style comments (thus requiring
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
+# comments) as a brief description. This used to be the default behaviour.
+# The new default is to treat a multi-line C++ comment block as a detailed
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+# member inherits the documentation from any documented member that it
+# re-implements.
+
+INHERIT_DOCS = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
+# a new page for each member. If set to NO, the documentation of a member will
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE = 2
+
+# This tag can be used to specify a number of aliases that acts
+# as commands in the documentation. An alias has the form "name=value".
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+# put the command \sideeffect (or @sideeffect) in the documentation, which
+# will result in a user-defined paragraph with heading "Side Effects:".
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding
+# "class=itcl::class" will allow you to use the command class in the
+# itcl::class meaning.
+
+TCL_SUBST =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
+# sources only. Doxygen will then generate output that is more tailored for C.
+# For instance, some of the names that are used will be different. The list
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
+# sources only. Doxygen will then generate output that is more tailored for
+# Java. For instance, namespaces will be presented as packages, qualified
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources only. Doxygen will then generate output that is more tailored for
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension,
+# and language is one of the parsers supported by doxygen: IDL, Java,
+# Javascript, CSharp, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL, C,
+# C++. For instance to make doxygen treat .inc files as Fortran files (default
+# is PHP), and .f files as C (default is Fortran), use: inc=Fortran f=C. Note
+# that for custom extensions you also need to set FILE_PATTERNS otherwise the
+# files are not read by doxygen.
+
+EXTENSION_MAPPING =
+
+# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
+# comments according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you
+# can mix doxygen, HTML, and XML commands with Markdown formatting.
+# Disable only in case of backward compatibilities issues.
+
+MARKDOWN_SUPPORT = YES
+
+# When enabled doxygen tries to link words that correspond to documented classes,
+# or namespaces to their corresponding documentation. Such a link can be
+# prevented in individual cases by by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+
+AUTOLINK_SUPPORT = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should
+# set this tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
+# func(std::string) {}). This also makes the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT = YES
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+# Doxygen will parse them like normal C++ but will assume all classes use public
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES (the
+# default) will make doxygen replace the get and set methods by a property in
+# the documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
+# the same type (for instance a group of public functions) to be put as a
+# subgroup of that type (e.g. under the Public Functions section). Set it to
+# NO to prevent subgrouping. Alternatively, this can be done per class using
+# the \nosubgrouping command.
+
+SUBGROUPING = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
+# unions are shown inside the group in which they are included (e.g. using
+# @ingroup) instead of on a separate page (for HTML and Man pages) or
+# section (for LaTeX and RTF).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
+# unions with only public data fields or simple typedef fields will be shown
+# inline in the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO (the default), structs, classes, and unions are shown on a separate
+# page (for HTML and Man pages) or section (for LaTeX and RTF).
+
+INLINE_SIMPLE_STRUCTS = NO
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penalty.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will roughly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+SYMBOL_CACHE_SIZE = 0
+
+# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
+# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
+# their name and scope. Since this can be an expensive process and often the
+# same symbol appear multiple times in the code, doxygen keeps a cache of
+# pre-resolved symbols. If the cache is too small doxygen will become slower.
+# If the cache is too large, memory is wasted. The cache size is given by this
+# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+LOOKUP_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = YES
+
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
+# scope will be included in the documentation.
+
+EXTRACT_PACKAGE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespaces are hidden.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put a list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
+# will list include files with double quotes in the documentation
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
+# will sort the (brief and detailed) documentation of class members so that
+# constructors and destructors are listed first. If set to NO (the default)
+# the constructors will appear in the respective orders defined by
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+# sorted by fully-qualified names, including namespaces. If set to
+# NO (the default), the class list will be sorted only by class name,
+# not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# do proper type resolution of all parameters of a function it will reject a
+# match between the prototype and the implementation of a member function even
+# if there is only one candidate or it is obvious which candidate to choose
+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
+# will still accept a match between prototype and implementation in such cases.
+
+STRICT_PROTO_MATCHING = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = NO
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST = NO
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if section-label ... \endif
+# and \cond section-label ... \endcond blocks.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or macro consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and macros in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page. This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option.
+# You can optionally specify a file name after the option, if omitted
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files
+# containing the references data. This must be a list of .bib files. The
+# .bib extension is automatically appended if omitted. Using this command
+# requires the bibtex tool to be installed. See also
+# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
+# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
+# feature you need bibtex and perl available in the search path. Do not use
+# file names with spaces, bibtex cannot handle them.
+
+CITE_BIB_FILES =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR = YES
+
+# The WARN_NO_PARAMDOC option can be enabled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT = src
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
+# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
+# *.f90 *.f *.for *.vhd *.vhdl
+
+FILE_PATTERNS = *.h \
+ *.cpp
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. Note that the wildcards are matched
+# against the file with absolute path, so to exclude all test directories
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output. If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty or if
+# non of the patterns match the file name, INPUT_FILTER is applied.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
+# and it is also possible to disable source filtering for a specific pattern
+# using *.ext= (so without naming a filter). This option only has effect when
+# FILTER_SOURCE_FILES is enabled.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page (index.html).
+# This can be useful if you have a project on for instance GitHub and want reuse
+# the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C, C++ and Fortran comments will always remain visible.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES
+# then for each documented function all documented
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = YES
+
+# If the REFERENCES_RELATION tag is set to YES
+# then for each documented function all documented entities
+# called/used by that function will be listed.
+
+REFERENCES_RELATION = YES
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code. Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code
+# will point to the HTML generated by the htags(1) tool instead of doxygen
+# built-in source browser. The htags tool is part of GNU's global source
+# tagging system (see http://www.gnu.org/software/global/global.html). You
+# will need version 4.8.6 or higher.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header. Note that when using a custom header you are responsible
+# for the proper inclusion of any scripts and style sheets that doxygen
+# needs, which is dependent on the configuration options used.
+# It is advised to generate a default header using "doxygen -w html
+# header.html footer.html stylesheet.css YourConfigFile" and then modify
+# that header. Note that the header is subject to change so you typically
+# have to redo this when upgrading to a newer version of doxygen or when
+# changing the value of configuration settings such as GENERATE_TREEVIEW!
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If left blank doxygen will
+# generate a default style sheet. Note that it is recommended to use
+# HTML_EXTRA_STYLESHEET instead of this one, as it is more robust and this
+# tag will in the future become obsolete.
+
+HTML_STYLESHEET =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional
+# user-defined cascading style sheet that is included after the standard
+# style sheets created by doxygen. Using this option one can overrule
+# certain style aspects. This is preferred over using HTML_STYLESHEET
+# since it does not replace the standard style sheet and is therefor more
+# robust against future updates. Doxygen will copy the style sheet file to
+# the output directory.
+
+HTML_EXTRA_STYLESHEET =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that
+# the files will be copied as-is; there are no commands or markers available.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
+# Doxygen will adjust the colors in the style sheet and background images
+# according to this color. Hue is specified as an angle on a colorwheel,
+# see http://en.wikipedia.org/wiki/Hue for more information.
+# For instance the value 0 represents red, 60 is yellow, 120 is green,
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
+# The allowed range is 0 to 359.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
+# the colors in the HTML output. For a value of 0 the output will use
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
+# the luminance component of the colors in the HTML output. Values below
+# 100 gradually make the output lighter, whereas values above 100 make
+# the output darker. The value divided by 100 is the actual gamma applied,
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting
+# this to NO can help when comparing the output of multiple runs.
+
+HTML_TIMESTAMP = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+
+HTML_DYNAMIC_SECTIONS = YES
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+
+GENERATE_DOCSET = YES
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Bio++ Sequence Library"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = bpp.seq
+
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely
+# identify the documentation publisher. This should be a reverse domain-name
+# style string, e.g. com.mycompany.MyDocSet.documentation.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
+# that can be used as input for Qt's qhelpgenerator to generate a
+# Qt Compressed Help (.qch) of the generated HTML documentation.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
+# add. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
+# Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
+# Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
+# will be generated, which together with the HTML files, form an Eclipse help
+# plugin. To install this plugin and make it available under the help contents
+# menu in Eclipse, the contents of the directory containing the HTML and XML
+# files needs to be copied into the plugins directory of eclipse. The name of
+# the directory within the plugins directory should be the same as
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
+# the help appears.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
+# at top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it. Since the tabs have the same information as the
+# navigation tree you can set this option to NO if you already set
+# GENERATE_TREEVIEW to YES.
+
+DISABLE_INDEX = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to YES, a side panel will be generated
+# containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
+# Windows users are probably better off using the HTML help feature.
+# Since the tree basically has the same information as the tab index you
+# could consider to set DISABLE_INDEX to NO when enabling this option.
+
+GENERATE_TREEVIEW = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
+# (range [0,1..20]) that doxygen will group on one line in the generated HTML
+# documentation. Note that a value of 0 will completely suppress the enum
+# values from appearing in the overview section.
+
+ENUM_VALUES_PER_LINE = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH = 250
+
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
+# links to external symbols imported via tag files in a separate window.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are
+# not supported properly for IE 6.0, but are supported on all modern browsers.
+# Note that when changing this option you need to delete any form_*.png files
+# in the HTML output before the changes have effect.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
+# (see http://www.mathjax.org) which uses client side Javascript for the
+# rendering instead of using prerendered bitmaps. Use this if you do not
+# have LaTeX installed or if you want to formulas look prettier in the HTML
+# output. When enabled you may also need to install MathJax separately and
+# configure the path to it using the MATHJAX_RELPATH option.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# thA MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and
+# SVG. The default value is HTML-CSS, which is slower, but has the best
+# compatibility.
+
+MATHJAX_FORMAT = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the
+# HTML output directory using the MATHJAX_RELPATH option. The destination
+# directory should contain the MathJax.js script. For instance, if the mathjax
+# directory is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to
+# the MathJax Content Delivery Network so you can quickly see the result without
+# installing MathJax. However, it is strongly recommended to install a local
+# copy of MathJax from http://www.mathjax.org before deployment.
+
+MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
+# names that should be enabled during MathJax rendering.
+
+MATHJAX_EXTENSIONS =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
+# for the HTML output. The underlying search engine uses javascript
+# and DHTML and should work on any modern browser. Note that when using
+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
+# (GENERATE_DOCSET) there is already a search function so this one should
+# typically be disabled. For large projects the javascript based search engine
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript.
+# There are two flavours of web server based search depending on the
+# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for
+# searching and an index file used by the script. When EXTERNAL_SEARCH is
+# enabled the indexing and searching needs to be provided by external tools.
+# See the manual for details.
+
+SERVER_BASED_SEARCH = NO
+
+# When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain
+# the search results. Doxygen ships with an example indexer (doxyindexer) and
+# search engine (doxysearch.cgi) which are based on the open source search engine
+# library Xapian. See the manual for configuration details.
+
+EXTERNAL_SEARCH = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will returned the search results when EXTERNAL_SEARCH is enabled.
+# Doxygen ships with an example search engine (doxysearch) which is based on
+# the open source search engine library Xapian. See the manual for configuration
+# details.
+
+SEARCHENGINE_URL =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+
+SEARCHDATA_FILE = searchdata.xml
+
+# When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+
+EXTERNAL_SEARCH_ID =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id
+# of to a relative location where the documentation can be found.
+# The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ...
+
+EXTRA_SEARCH_MAPPINGS =
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked. If left blank `latex' will be used as the default command name.
+# Note that when enabling USE_PDFLATEX this option is only used for
+# generating bitmaps for formulas in the HTML output, but not in the
+# Makefile that is written to the output directory.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+# generate index for LaTeX. If left blank `makeindex' will be used as the
+# default command name.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES = amsmath
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
+# the generated latex document. The footer should contain everything after
+# the last chapter. If it is left blank doxygen will generate a
+# standard footer. Notice: only use this tag if you know what you are doing!
+
+LATEX_FOOTER =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images
+# or other source files which should be copied to the LaTeX output directory.
+# Note that the files will be copied as-is; there are no commands or markers
+# available.
+
+LATEX_EXTRA_FILES =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS = NO
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+# include the index chapters (such as File Index, Compound Index, etc.)
+# in the output.
+
+LATEX_HIDE_INDICES = NO
+
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
+# source code with syntax highlighting in the LaTeX output.
+# Note that which sources are shown also depends on other settings
+# such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
+# http://en.wikipedia.org/wiki/BibTeX for more info.
+
+LATEX_BIB_STYLE = plain
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimized for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using WORD or other
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS = NO
+
+# Load style sheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an rtf document.
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+# then it will generate one additional man file for each entity
+# documented in the real man page(s). These additional files
+# only source the real man page, but without them the man command
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_SCHEMA =
+
+# The XML_DTD tag can be used to specify an XML DTD,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_DTD =
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+# dump the program listings (including syntax highlighting
+# and cross-referencing information) to the XML output. Note that
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files
+# that can be used to generate PDF.
+
+GENERATE_DOCBOOK = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the DOCBOOK pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it. If left blank docbook will be used as the default path.
+
+DOCBOOK_OUTPUT = docbook
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+# generate an AutoGen Definitions (see autogen.sf.net) file
+# that captures the structure of the code including all
+# documentation. Note that this feature is still experimental
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+# generate a Perl module file that captures the structure of
+# the code including all documentation. Note that this
+# feature is still experimental and incomplete at the
+# moment.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+# nicely formatted so it can be parsed by a human reader. This is useful
+# if you want to understand what is going on. On the other hand, if this
+# tag is set to NO the size of the Perl module output will be much smaller
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+# This is useful so different doxyrules.make files included by the same
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# pointed to by INCLUDE_PATH will be searched when a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition that
+# overrules the definition found in the source code.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all references to function-like macros
+# that are alone on a line, have an all uppercase name, and do not end with a
+# semicolon, because these will confuse the parser if not removed.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles. For each
+# tag file the location of the external documentation should be added. The
+# format of a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths
+# or URLs. Note that each tag file must have a unique name (where the name does
+# NOT include the path). If a tag file is not located in the directory in which
+# doxygen is run, you must also specify the path to the tagfile here.
+
+TAGFILES = ../bpp-core/BppCore.tag=../../bpp-core/html/
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE = BppSeq.tag
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will
+# be listed.
+
+EXTERNAL_GROUPS = YES
+
+# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed
+# in the related pages index. If set to NO, only the current project's
+# pages will be listed.
+
+EXTERNAL_PAGES = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option also works with HAVE_DOT disabled, but it is recommended to
+# install and use dot, since it yields more powerful graphs.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT = YES
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
+# allowed to run in parallel. When set to 0 (the default) doxygen will
+# base this on the number of processors available in the system. You can set it
+# explicitly to a value larger than 0 to get control over the balance
+# between CPU load and processing speed.
+
+DOT_NUM_THREADS = 0
+
+# By default doxygen will use the Helvetica font for all dot files that
+# doxygen generates. When you want a differently looking font you can specify
+# the font name using DOT_FONTNAME. You need to make sure dot is able to find
+# the font, which can be done by putting it in a standard location or by setting
+# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
+# directory containing the font.
+
+DOT_FONTNAME = FreeSans
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the Helvetica font.
+# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
+# set the path where dot can find it.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
+UML_LOOK = NO
+
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside
+# the class node. If there are many fields or methods and many nodes the
+# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
+# threshold limits the number of items for each type to make the size more
+# managable. Set this to 0 for no limit. Note that the threshold may be
+# exceeded by 50% before the limit is enforced.
+
+UML_LIMIT_NUM_FIELDS = 10
+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
+INCLUDE_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will generate a graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
+# in a graphical way. The dependency relations are determined by the #include
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. Possible values are svg, png, jpg, or gif.
+# If left blank png will be used. If you choose svg you need to set
+# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
+# visible in IE 9+ (other browsers do not have this requirement).
+
+DOT_IMAGE_FORMAT = png
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+# Note that this requires a modern browser other than Internet Explorer.
+# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
+# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
+# visible. Older versions of IE do not have SVG support.
+
+INTERACTIVE_SVG = NO
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the
+# \dotfile command).
+
+DOTFILE_DIRS =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the
+# \mscfile command).
+
+MSCFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# nodes that will be shown in the graph. If the number of nodes in a graph
+# becomes larger than this value, doxygen will truncate the graph, which is
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+# graphs generated by dot. A depth value of 3 means that only nodes reachable
+# from the root by following a path via at most 3 edges will be shown. Nodes
+# that lay further from the root node will be omitted. Note that setting this
+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS = YES
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+# remove the intermediate dot files that are used to generate
+# the various graphs.
+
+DOT_CLEANUP = YES
diff --git a/INSTALL.txt b/INSTALL.txt
new file mode 100644
index 0000000..c8859da
--- /dev/null
+++ b/INSTALL.txt
@@ -0,0 +1,12 @@
+This software needs cmake >= 2.6 to build.
+
+After installing cmake, run it with the following command:
+cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] .
+
+If available, you can also use ccmake instead of cmake for a more user-friendly interface.
+
+Then compile and install the software with
+make install
+
+You may also consider installing and using the software checkinstall for easier system administration.
+
diff --git a/bpp-seq.spec b/bpp-seq.spec
new file mode 100644
index 0000000..c8eb8fa
--- /dev/null
+++ b/bpp-seq.spec
@@ -0,0 +1,200 @@
+%define _basename bpp-seq
+%define _version 2.1.0
+%define _release 1
+%define _prefix /usr
+
+URL: http://biopp.univ-montp2.fr/
+
+Name: %{_basename}
+Version: %{_version}
+Release: %{_release}
+License: CECILL-2.0
+Vendor: The Bio++ Project
+Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
+Summary: Bio++ Sequence library
+Group: Development/Libraries/C and C++
+Requires: bpp-core = %{_version}
+
+BuildRoot: %{_builddir}/%{_basename}-root
+BuildRequires: cmake >= 2.6.0
+BuildRequires: gcc-c++ >= 4.0.0
+BuildRequires: libbpp-core2 = %{_version}
+BuildRequires: libbpp-core-devel = %{_version}
+AutoReq: yes
+AutoProv: yes
+
+%description
+This library contains utilitary and classes for bio-sequence analysis.
+It is part of the Bio++ project.
+
+%package -n libbpp-seq9
+Summary: Bio++ Sequence library
+Group: Development/Libraries/C and C++
+
+%description -n libbpp-seq9
+This library contains utilitary and classes for bio-sequence analysis.
+It is part of the Bio++ project.
+
+%package -n libbpp-seq-devel
+Summary: Libraries, includes to develop applications with %{_basename}
+Group: Development/Libraries/C and C++
+Requires: libbpp-seq9 = %{_version}
+Requires: libbpp-core2 = %{_version}
+Requires: libbpp-core-devel = %{_version}
+
+%description -n libbpp-seq-devel
+The libbpp-seq-devel package contains the header files and static libraries for
+building applications which use %{_basename}.
+
+%prep
+%setup -q
+
+%build
+CFLAGS="$RPM_OPT_FLAGS"
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix} -DBUILD_TESTING=OFF"
+if [ %{_lib} == 'lib64' ] ; then
+ CMAKE_FLAGS="$CMAKE_FLAGS -DLIB_SUFFIX=64"
+fi
+cmake $CMAKE_FLAGS .
+make
+
+%install
+make DESTDIR=$RPM_BUILD_ROOT install
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+%post -n libbpp-seq9 -p /sbin/ldconfig
+
+%post -n libbpp-seq-devel
+createGeneric() {
+ echo "-- Creating generic include file: $1.all"
+ #Make sure we run into subdirectories first:
+ dirs=()
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ dirs+=( "$file" )
+ fi
+ done
+ for dir in ${dirs[@]}
+ do
+ createGeneric $dir
+ done
+ #Now list all files, including newly created .all files:
+ if [ -f $1.all ]
+ then
+ rm $1.all
+ fi
+ dir=`basename $1`
+ for file in "$1"/*
+ do
+ if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
+ then
+ file=`basename $file`
+ echo "#include \"$dir/$file\"" >> $1.all
+ fi
+ done;
+}
+# Actualize .all files
+createGeneric %{_prefix}/include/Bpp
+exit 0
+
+%preun -n libbpp-seq-devel
+removeGeneric() {
+ if [ -f $1.all ]
+ then
+ echo "-- Remove generic include file: $1.all"
+ rm $1.all
+ fi
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ removeGeneric $file
+ fi
+ done
+}
+# Actualize .all files
+removeGeneric %{_prefix}/include/Bpp
+exit 0
+
+%postun -n libbpp-seq9 -p /sbin/ldconfig
+
+%postun -n libbpp-seq-devel
+createGeneric() {
+ echo "-- Creating generic include file: $1.all"
+ #Make sure we run into subdirectories first:
+ dirs=()
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ dirs+=( "$file" )
+ fi
+ done
+ for dir in ${dirs[@]}
+ do
+ createGeneric $dir
+ done
+ #Now list all files, including newly created .all files:
+ if [ -f $1.all ]
+ then
+ rm $1.all
+ fi
+ dir=`basename $1`
+ for file in "$1"/*
+ do
+ if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
+ then
+ file=`basename $file`
+ echo "#include \"$dir/$file\"" >> $1.all
+ fi
+ done;
+}
+# Actualize .all files
+createGeneric %{_prefix}/include/Bpp
+exit 0
+
+%files -n libbpp-seq9
+%defattr(-,root,root)
+%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
+%{_prefix}/%{_lib}/lib*.so.*
+
+%files -n libbpp-seq-devel
+%defattr(-,root,root)
+%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
+%{_prefix}/%{_lib}/lib*.so
+%{_prefix}/%{_lib}/lib*.a
+%{_prefix}/include/*
+
+%changelog
+* Tue Mar 05 2013 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.1.0-1
+- 'omics' tools now in bpp-seq-omics
+- Extended BppO support
+- StateProperties renamed to AlphabetIndex
+* Thu Feb 09 2012 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.0.3-1
+- Improved maf tools + new iterators
+- Added support for GFF
+- Added support for FastQ
+- Several bugs fixed.
+* Thu Jun 09 2011 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.0.2-1
+- Improved maf tools, several bugs fixed.
+* Mon Feb 28 2011 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.0.1-1
+* Mon Feb 07 2011 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.0.0-1
+* Thu Mar 25 2010 Julien Dutheil <julien.dutheil at univ-montp2.fr> 1.7.0-1
+* Wed Jun 10 2009 Julien Dutheil <jdutheil at birc.au.dk> 1.6.0-1
+* Thu Dec 11 2008 Julien Dutheil <jdutheil at birc.au.dk> 1.5.0-1
+* Mon Jul 21 2008 Julien Dutheil <jdutheil at birc.au.dk> 1.4.1-1
+* Fri Jan 18 2008 Julien Dutheil <Julien.Dutheil at univ-montp2.fr> 1.4.0-1
+* Fri Jul 06 2007 Julien Dutheil <Julien.Dutheil at univ-montp2.fr> 1.3.0-1
+* Fri Jan 19 2007 Julien Dutheil <Julien.Dutheil at univ-montp2.fr> 1.2.0-1
+* Mon Aug 28 2006 Julien Dutheil <Julien.Dutheil at univ-montp2.fr> 1.1.1-1
+* Tue Apr 18 2006 Julien Dutheil <Julien.Dutheil at univ-montp2.fr> 1.1.0-1
+* Fri Nov 16 2005 Julien Dutheil <Julien.Dutheil at univ-montp2.fr> 1.0.0-1
+- First draft of the spec file
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..660977c
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,64 @@
+libbpp-seq (2.1.0-1) unstable; urgency=low
+
+ * 'omics' tools now in bpp-seq-omics
+ * Extended BppO support
+ * StateProperties renamed to AlphabetIndex
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Tue, 05 Mar 2013 14:31:00 +0100
+
+libbpp-seq (2.0.3-1) unstable; urgency=low
+
+ * Bugs fixed in maf parser + new iterators
+ * Added support for GFF
+ * Added support for FastQ
+ * Several bugs fixed
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Thu, 09 Feb 2012 14:00:00 +0100
+
+libbpp-seq (2.0.2-1) unstable; urgency=low
+
+ * RFP: Bio++ -- The Bio++ bioinformatics libraries. (Closes: #616373).
+ * Packages are now non-native.
+ * Bugs fixed in maf parser.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Thu, 09 Jun 2011 11:00:00 +0100
+
+libbpp-seq (2.0.1) unstable; urgency=low
+
+ * Fixed copyright and rules file.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Mon, 28 Feb 2011 09:00:00 +0100
+
+libbpp-seq (2.0.0) unstable; urgency=low
+
+ * New source files organization.
+ * More NGS tools: sequence annotations, quality scores, file parsers, etc.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Mon, 07 Feb 2011 09:00:00 +0100
+
+libbpp-seq (1.7.0) unstable; urgency=low
+
+ * Several bug fixed. Compilation with -Weffc++.
+ * New compressed sites container.
+ * Improved security by changing several pointers to references.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Thu, 25 Mar 2010 10:02:50 +0100
+
+libbpp-seq (1.6.0) unstable; urgency=low
+
+ * New support for Nexus sequence files.
+ * Update for version 1.8 of Bio++.
+
+ -- Julien Dutheil <jdutheil at birc.au.dk> Wed, 10 Jun 2009 11:28:58 +0100
+
+libbpp-seq (1.5.0) unstable; urgency=low
+
+ * Several bugs fixed, new Phred sequence format, speed improvements.
+
+ -- Julien Dutheil <jdutheil at birc.au.dk> Thu, 11 Dec 2008 12:21:37 +0100
+
+libbpp-seq (1.4.1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Julien Dutheil <jdutheil at birc.au.dk> Mon, 21 Jul 2008 15:17:26 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7ed6ff8
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+5
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..8e2765b
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,25 @@
+Source: libbpp-seq
+Section: libs
+Priority: optional
+Maintainer: Loic Dachary <loic at dachary.org>
+Uploaders: Julien Dutheil <julien.dutheil at univ-montp2.fr>
+Build-Depends: debhelper (>= 5), cmake (>= 2.6),
+ libbpp-core-dev (>= 2.1.0)
+Standards-Version: 3.9.1
+
+Package: libbpp-seq-dev
+Section: libdevel
+Architecture: any
+Depends: libbpp-seq9 (= ${binary:Version}), ${misc:Depends},
+ libbpp-core-dev (>= 2.1.0)
+Description: Bio++ Sequence library development files.
+ Contains the Bio++ classes for sequence analysis.
+
+Package: libbpp-seq9
+Section: libs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libbpp-core2 (>= 2.1.0)
+Description: Bio++ Sequence library.
+ Contains the Bio++ classes for sequence analysis.
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..e589092
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,66 @@
+This package was debianized by Julien Dutheil <julien.dutheil at univ-montp2.fr> on
+Tue, 05 Mar 2013 14:34:00 +0100.
+
+It was downloaded from <http://biopp.univ-montp2.fr/Repositories/sources>
+
+Upstream Author:
+
+ Julien Dutheil <julien.dutheil at univ-montp2.fr>
+
+Copyright:
+
+ Copyright (C) 2013 Bio++ Development Team
+
+License:
+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
+The Debian packaging is (C) 2013, Julien Dutheil <julien.dutheil at univ-montp2.fr> and
+is licensed under the GPL, see above.
+
+The provided software is distributed under the CeCILL license:
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+
+The complete text of the license may be found here:
+http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
+
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e69de29
diff --git a/debian/libbpp-seq-dev.install b/debian/libbpp-seq-dev.install
new file mode 100644
index 0000000..0f5727e
--- /dev/null
+++ b/debian/libbpp-seq-dev.install
@@ -0,0 +1,3 @@
+debian/tmp/usr/include/*
+debian/tmp/usr/lib/*.a
+debian/tmp/usr/lib/*.so
diff --git a/debian/libbpp-seq9.install b/debian/libbpp-seq9.install
new file mode 100644
index 0000000..c45ebcf
--- /dev/null
+++ b/debian/libbpp-seq9.install
@@ -0,0 +1 @@
+debian/tmp/usr/lib/lib*.so.*
diff --git a/debian/postinst b/debian/postinst
new file mode 100755
index 0000000..cf9e925
--- /dev/null
+++ b/debian/postinst
@@ -0,0 +1,43 @@
+#! /bin/bash
+
+# Abort if any command returns an error value
+set -e
+
+createGeneric() {
+ echo "-- Creating generic include file: $1.all"
+ #Make sure we run into subdirectories first:
+ dirs=()
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ dirs+=( "$file" )
+ fi
+ done
+ for dir in ${dirs[@]}
+ do
+ createGeneric $dir
+ done
+ #Now list all files, including newly created .all files:
+ if [ -f $1.all ]
+ then
+ rm $1.all
+ fi
+ dir=`basename $1`
+ for file in "$1"/*
+ do
+ if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
+ then
+ file=`basename $file`
+ echo "#include \"$dir/$file\"" >> $1.all
+ fi
+ done;
+}
+
+if [ "$1" = "configure" ]; then
+ # Actualize .all files
+ createGeneric /usr/include/Bpp
+fi
+
+exit 0
diff --git a/debian/postrm b/debian/postrm
new file mode 100755
index 0000000..3931669
--- /dev/null
+++ b/debian/postrm
@@ -0,0 +1,45 @@
+#! /bin/bash
+
+# Abort if any command returns an error value
+set -e
+
+createGeneric() {
+ echo "-- Creating generic include file: $1.all"
+ #Make sure we run into subdirectories first:
+ dirs=()
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ dirs+=( "$file" )
+ fi
+ done
+ for dir in ${dirs[@]}
+ do
+ createGeneric $dir
+ done
+ #Now list all files, including newly created .all files:
+ if [ -f $1.all ]
+ then
+ rm $1.all
+ fi
+ dir=`basename $1`
+ for file in "$1"/*
+ do
+ if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
+ then
+ file=`basename $file`
+ echo "#include \"$dir/$file\"" >> $1.all
+ fi
+ done;
+}
+
+if [ "$1" = "remove" ]; then
+ # Automatically added by dh_makeshlibs
+ ldconfig
+ # Actualize .all files
+ createGeneric /usr/include/Bpp
+fi
+
+exit 0
diff --git a/debian/prerm b/debian/prerm
new file mode 100755
index 0000000..5aefd24
--- /dev/null
+++ b/debian/prerm
@@ -0,0 +1,27 @@
+#! /bin/bash
+
+# Abort if any command returns an error value
+set -e
+
+removeGeneric() {
+ if [ -f $1.all ]
+ then
+ echo "-- Remove generic include file: $1.all"
+ rm $1.all
+ fi
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ removeGeneric $file
+ fi
+ done
+}
+
+if [ "$1" = "remove" ]; then
+ # Actualize .all files
+ removeGeneric /usr/include/Bpp
+fi
+
+exit 0
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..92c389e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,120 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# 24/01/10 Modification for use with CMake by Julien Dutheil.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+# shared library versions
+version=`ls src/lib*.so.* | \
+ awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'`
+major=`ls src/lib*.so.* | \
+ awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'`
+
+configure:
+ cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_TESTING=OFF .
+
+config.status: configure
+ dh_testdir
+
+build: build-stamp
+build-stamp: config.status
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+
+ # Add here commands to clean up after the build process.
+ [ ! -f Makefile ] || $(MAKE) clean;
+ [ ! -f Makefile ] || rm Makefile;
+ [ ! -f src/Makefile ] || rm src/Makefile;
+ [ ! -f test/Makefile ] || rm test/Makefile;
+ rm -f config.sub config.guess
+ rm -f build-stamp
+ rm -f CMakeCache.txt
+ rm -f *.cmake
+ rm -f src/*.cmake
+ rm -f test/*.cmake
+ rm -rf CMakeFiles
+ rm -rf src/CMakeFiles
+ rm -rf test/CMakeFiles
+ rm -rf _CPack_Packages
+ rm -rf Testing
+ rm -f DartConfiguration.tcl
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_prep
+ dh_installdirs
+
+ # Add here commands to install the package into debian/tmp
+ $(MAKE) DESTDIR=$(CURDIR)/debian/tmp install
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs ChangeLog
+ dh_installdocs
+ dh_installexamples
+ dh_install
+# dh_installmenu
+# dh_installdebconf
+# dh_installlogrotate
+# dh_installemacsen
+# dh_installpam
+# dh_installmime
+# dh_installinit
+# dh_installcron
+# dh_installinfo
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+# dh_python
+ dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp b/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp
new file mode 100644
index 0000000..1c970bd
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp
@@ -0,0 +1,276 @@
+//
+// File: AbstractAlphabet.cpp
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created on: Tue Jul 22 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "AbstractAlphabet.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Utils/MapTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <ctype.h>
+#include <map>
+
+using namespace std;
+
+/******************************************************************************/
+
+void AbstractAlphabet::updateMaps_(size_t pos, const AlphabetState& st) {
+ if (letters_.find(st.getLetter()) == letters_.end())
+ letters_[st.getLetter()] = pos;
+ if (nums_.find(st.getNum()) == nums_.end())
+ nums_[st.getNum()] = pos;
+}
+
+/******************************************************************************/
+
+void AbstractAlphabet::registerState(const AlphabetState& st) {
+ // Add the state to the vector
+ alphabet_.push_back(st.clone());
+ // Update the maps
+ updateMaps_(alphabet_.size(), st);
+}
+
+/******************************************************************************/
+
+void AbstractAlphabet::setState(size_t pos, const AlphabetState& st)
+ throw (IndexOutOfBoundsException) {
+ if (pos > alphabet_.size())
+ throw IndexOutOfBoundsException("AbstractAlphabet::setState: incorect position", pos, 0, alphabet_.size());
+ // Delete the state if not empty
+ if (alphabet_[pos] != 0)
+ delete alphabet_[pos];
+ // Put the state in the vector
+ alphabet_[pos] = st.clone();
+ // Update the maps
+ updateMaps_(pos, st);
+ }
+
+/******************************************************************************/
+
+const AlphabetState& AbstractAlphabet::getState(const std::string& letter) const throw (BadCharException) {
+ map<string, size_t>::const_iterator it = letters_.find(letter);
+ if (it == letters_.end())
+ throw BadCharException(letter, "AbstractAlphabet::getState(string): Specified base unknown", this);
+ return * (alphabet_[it->second]);
+}
+
+/******************************************************************************/
+
+const AlphabetState& AbstractAlphabet::getState(int num) const throw (BadIntException) {
+ map<int, size_t>::const_iterator it = nums_.find(num);
+ if (it == nums_.end())
+ throw BadIntException(num, "AbstractAlphabet::getState(int): Specified base unknown", this);
+ return * (alphabet_[it->second]);
+}
+
+/******************************************************************************/
+
+AlphabetState& AbstractAlphabet::getStateAt(size_t pos) throw (IndexOutOfBoundsException) {
+ if (pos > alphabet_.size())
+ throw IndexOutOfBoundsException("AbstractAlphabet::getStateAt: incorect position", pos, 0, alphabet_.size());
+ return * (alphabet_[pos]);
+}
+
+/******************************************************************************/
+
+const AlphabetState& AbstractAlphabet::getStateAt(size_t pos) const throw (IndexOutOfBoundsException) {
+ if (pos > alphabet_.size())
+ throw IndexOutOfBoundsException("AbstractAlphabet::getStateAt: incorect position", pos, 0, alphabet_.size());
+ return * (alphabet_[pos]);
+}
+
+/******************************************************************************/
+
+std::string AbstractAlphabet::getName(const std::string& state) const throw (BadCharException)
+{
+ return (getState(state)).getName();
+}
+
+/******************************************************************************/
+
+std::string AbstractAlphabet::getName(int state) const throw (BadIntException)
+{
+ return (getState(state)).getName();
+}
+
+/******************************************************************************/
+
+int AbstractAlphabet::charToInt(const std::string& state) const throw (BadCharException)
+{
+ return getState(state).getNum();
+}
+
+/******************************************************************************/
+
+std::string AbstractAlphabet::intToChar(int state) const throw (BadIntException)
+{
+ return (getState(state)).getLetter();
+}
+
+/******************************************************************************/
+
+bool AbstractAlphabet::isIntInAlphabet(int state) const
+{
+ map<int, size_t>::const_iterator it = nums_.find(state);
+ if (it != nums_.end())
+ return true;
+ return false;
+}
+
+/******************************************************************************/
+
+bool AbstractAlphabet::isCharInAlphabet(const std::string& state) const
+{
+ map<string, size_t>::const_iterator it = letters_.find(state);
+ if (it != letters_.end())
+ return true;
+ return false;
+}
+
+/******************************************************************************/
+
+std::vector<int> AbstractAlphabet::getAlias(int state) const throw (BadIntException)
+{
+ if (!isIntInAlphabet(state)) throw BadIntException(state, "AbstractAlphabet::getAlias(int): Specified base unknown.");
+ vector<int> v(1);
+ v[0] = state;
+ return v;
+}
+
+/******************************************************************************/
+
+std::vector<std::string> AbstractAlphabet::getAlias(const std::string& state) const throw (BadCharException)
+{
+ if (!isCharInAlphabet(state)) throw BadCharException(state, "AbstractAlphabet::getAlias(char): Specified base unknown.");
+ vector<string> v(1);
+ v[0] = state;
+ return v;
+}
+
+/******************************************************************************/
+
+int AbstractAlphabet::getGeneric(const std::vector<int>& states) const throw (BadIntException) {
+ map<int, int> m;
+ for (unsigned int i = 0 ; i < states.size() ; ++i) {
+ vector<int> tmp_s = this->getAlias(states[i]); // get the states for generic characters
+ for (unsigned int j = 0 ; j < tmp_s.size() ; ++j) {
+ m[tmp_s[j]] ++; // add each state to the list
+ }
+ }
+ vector<int> ve = MapTools::getKeys(m);
+
+ string key;
+ for (unsigned int i = 0 ; i < ve.size() ; ++i) {
+ if (!isIntInAlphabet(ve[i])) throw BadIntException(ve[i], "AbstractAlphabet::getGeneric(const vector<int>): Specified base unknown.");
+ key += "_" + TextTools::toString(ve[i]);
+ }
+ int v;
+ if (ve.size() == 1) {
+ v = ve[0];
+ } else {
+ v = this->getUnknownCharacterCode();
+ }
+ return v;
+}
+
+/******************************************************************************/
+
+std::string AbstractAlphabet::getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) {
+ map <string, int> m;
+ for (unsigned int i = 0 ; i < states.size() ; ++i) {
+ vector<string> tmp_s = this->getAlias(states[i]); // get the states for generic characters
+ for (unsigned int j = 0 ; j < tmp_s.size() ; ++j) {
+ m[tmp_s[j]] ++; // add each state to the list
+ }
+ }
+ vector<string> ve = MapTools::getKeys(m);
+
+ string key;
+ for (unsigned int i = 0 ; i < ve.size() ; ++i) {
+ if (!isCharInAlphabet(ve[i])) throw BadCharException(ve[i], "AbstractAlphabet::getAlias(const vector<string>): Specified base unknown.");
+ key += TextTools::toString(ve[i]);
+ }
+ string v;
+ if (ve.size() == 1) {
+ v = ve[0];
+ } else {
+ throw CharStateNotSupportedException("AbstractAlphabet::getAlias(const vector<string>): No generic char state.");
+ }
+ return v;
+}
+
+/******************************************************************************/
+
+const std::vector<int>& AbstractAlphabet::getSupportedInts() const
+{
+ if(intList_.size() == 0)
+ {
+ intList_.resize(alphabet_.size());
+ charList_.resize(alphabet_.size());
+ for(unsigned int i = 0; i < alphabet_.size(); i++)
+ {
+ intList_[i] = alphabet_[i]->getNum();
+ charList_[i] = alphabet_[i]->getLetter();
+ }
+ }
+ return intList_;
+}
+
+/******************************************************************************/
+
+const std::vector<std::string>& AbstractAlphabet::getSupportedChars() const
+{
+ if(charList_.size() == 0)
+ {
+ intList_.resize(alphabet_.size());
+ charList_.resize(alphabet_.size());
+ for(unsigned int i = 0; i < alphabet_.size(); i++)
+ {
+ intList_[i] = alphabet_[i]->getNum();
+ charList_[i] = alphabet_[i]->getLetter();
+ }
+ }
+ return charList_;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Alphabet/AbstractAlphabet.h b/src/Bpp/Seq/Alphabet/AbstractAlphabet.h
new file mode 100644
index 0000000..f32ab45
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/AbstractAlphabet.h
@@ -0,0 +1,220 @@
+//
+// File: AbstractAlphabet.h
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created on: Tue Jul 22 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ABSTRACTALPHABET_H_
+#define _ABSTRACTALPHABET_H_
+
+#include "Alphabet.h"
+#include "AlphabetState.h"
+#include <Bpp/Exceptions.h>
+
+// From the STL:
+#include <string>
+#include <vector>
+#include <map>
+
+namespace bpp
+{
+
+ /**
+ * @brief A partial implementation of the Alphabet interface.
+ *
+ * It contains a vector of AlphabetState.
+ * All methods are based uppon this vector
+ * but do not provide any method to initialize it.
+ * This is up to each constructor of the derived classes.
+ *
+ * @see Alphabet
+ */
+ class AbstractAlphabet:
+ public Alphabet
+ {
+ private:
+
+ /**
+ * @brief Alphabet: vector of AlphabetState.
+ */
+ std::vector<AlphabetState*> alphabet_;
+ /**
+ * @name maps used to quick search for letter and num.
+ * @{
+ */
+ std::map<std::string, size_t> letters_;
+ std::map<int, size_t> nums_;
+ /** @} */
+ /**
+ * @brief Update the private maps letters_ and nums_ when adding a state.
+ *
+ * @param pos The index of the state in the alphabet_ vector.
+ * @param st The state that have been added or modified
+ */
+ void updateMaps_(size_t pos, const AlphabetState& st);
+
+ protected:
+ /**
+ * @name Available codes
+ *
+ * These vectors will be computed the first time you call the getAvailableInts or getAvailableChars method.
+ *
+ * @{
+ */
+ mutable std::vector<std::string> charList_;
+ mutable std::vector<int> intList_;
+ /** @} */
+
+ public:
+
+ AbstractAlphabet(): alphabet_(), letters_(), nums_(), charList_(), intList_() {}
+
+ virtual ~AbstractAlphabet()
+ {
+ for (unsigned int i = 0 ; i < alphabet_.size() ; i++)
+ delete alphabet_[i];
+ }
+
+ public:
+ /**
+ * @name Implement these methods from the Alphabet interface.
+ *
+ * @{
+ */
+ unsigned int getNumberOfChars() const { return static_cast<unsigned int>(alphabet_.size()); }
+ std::string getName(const std::string& state) const throw (BadCharException);
+ std::string getName(int state) const throw (BadIntException);
+ int charToInt(const std::string& state) const throw (BadCharException);
+ std::string intToChar(int state) const throw (BadIntException);
+ bool isIntInAlphabet(int state) const;
+ bool isCharInAlphabet(const std::string& state) const;
+ std::vector<int> getAlias(int state) const throw (BadIntException);
+ std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
+ int getGeneric(const std::vector<int>& states) const throw (BadIntException);
+ std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
+ const std::vector<int>& getSupportedInts() const;
+ const std::vector<std::string>& getSupportedChars() const;
+ int getGapCharacterCode() const { return -1; }
+ bool isGap(int state) const { return state == -1; }
+ bool isGap(const std::string& state) const { return charToInt(state) == -1; }
+ /** @} */
+
+ /**
+ * @name Specific methods to access AlphabetState
+ * @{
+ */
+ /**
+ * @brief Get a state by its letter.
+ *
+ * This method must be overloaded in specialized classes to send back
+ * a reference of the corect type.
+ *
+ * @param letter The letter of the state to find.
+ * @throw BadCharException If the letter is not in the Alphabet.
+ */
+ const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
+ /**
+ * @brief Get a state by its num.
+ *
+ * This method must be overloaded in specialized classes to send back
+ * a reference of the corect type.
+ *
+ * @param num The num of the state to find.
+ * @throw BadIntException If the num is not in the Alphabet.
+ */
+ const AlphabetState& getState(int num) const throw (BadIntException);
+ /** @} */
+
+ protected:
+ /**
+ * @brief Add a state to the Alphabet.
+ *
+ * @param st The state to add.
+ */
+ virtual void registerState(const AlphabetState& st);
+ /**
+ * @brief Set a state in the Alphabet.
+ *
+ * @param pos The index of the state in the alphabet_ vector.
+ * @param st The new state to put in the Alphabet.
+ */
+ virtual void setState(size_t pos, const AlphabetState& st) throw (IndexOutOfBoundsException);
+ /**
+ * @brief Resize the private alphabet_ vector.
+ *
+ * @param size The new size of the Alphabet.
+ */
+ void resize(unsigned int size) { alphabet_.resize(size); }
+ /**
+ * @brief Get a state at a position in the alphabet_ vector.
+ *
+ * This method must be overloaded in specialized classes to send back
+ * a reference of the corect type.
+ *
+ * @param pos The index of the state in the alphabet_ vector.
+ * @throw IndexOutOfBoundsException If pos is out of the vector.
+ */
+ virtual AlphabetState& getStateAt(size_t pos) throw (IndexOutOfBoundsException);
+ /**
+ * @brief Get a state at a position in the alphabet_ vector.
+ *
+ * This method must be overloaded in specialized classes to send back
+ * a reference of the corect type.
+ *
+ * @param pos The index of the state in the alphabet_ vector.
+ * @throw IndexOutOfBoundsException If pos is out of the vector.
+ */
+ virtual const AlphabetState& getStateAt(size_t pos) const throw (IndexOutOfBoundsException);
+
+ /**
+ * @brief Re-update the maps using the alphabet_ vector content.
+ */
+ void remap() {
+ for (size_t i = 0 ; i < alphabet_.size() ; i++) {
+ updateMaps_(i, * alphabet_[i]);
+ }
+ }
+
+ unsigned int getStateCodingSize() const { return 1; }
+
+ };
+
+} //end of namespace bpp.
+
+#endif // _ABSTRACTALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/Alphabet.h b/src/Bpp/Seq/Alphabet/Alphabet.h
new file mode 100644
index 0000000..d61ae1d
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/Alphabet.h
@@ -0,0 +1,390 @@
+//
+// File: Alphabet.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: Tue Jul 22 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ALPHABET_H_
+#define _ALPHABET_H_
+
+#include <string>
+#include <vector>
+
+#include "AlphabetExceptions.h"
+#include "AlphabetState.h"
+
+/**
+ * @mainpage
+ *
+ * @par
+ * This library provides classes to store and analyse biological sequences.
+ * Each position in a sequences is coded by a int. An object implementing the bpp::Alphabet
+ * interface is used to make the relation between the int code and its more common character
+ * representation. Support for DNA, RNA, protein and codon sequences is provided. The
+ * bpp::AlphabetTools provides tools to deal with Alphabet objects.
+ * The basic bpp::Sequence class contains the code sequence, a name for the sequence
+ * and optionally comments. More elaborated classes can be built by inheriting this class.
+ * The bpp::SequenceTools static class provides simple analysis tools, like base frequencies measures,
+ * concatenation, etc.
+ *
+ * @par
+ * SeqLib also provides tools to perform <i>in silico</i> molecular biology, like complementation,
+ * transcription, translation, etc. All these methods are particular cases of alphabet translation, and are implemented
+ * via the interface bpp::Translator. Of particular interest are the classes bpp::NucleicAcidsReplication,
+ * bpp::DNAToRNA and bpp::GeneticCode + derivatives.
+ *
+ * @par
+ * Sequence collections are stored as <em>containers</em>. The simplest container implements the
+ * bpp::SequenceContainer interface, providing access to sequences by their name.
+ * The bpp::OrderedSequenceContainer adds access by position in the container.
+ * The simplest implementation of this interface is the bpp::VectorSequenceContainer, which stores the sequences
+ * as a vector of bpp::Sequence objects (or instances inheriting from this class).
+ * Input/output from various file formats is provided, including fasta (bpp::Fasta), GenBank (bpp::GenBank) and Mase (bpp::Mase).
+ * Tools dealing with containers can be found in the bpp::SequenceContainerTools static class.
+ *
+ * @par
+ * Support for alignments is provided via the bpp::SiteContainer interface, which enables site access.
+ * Sites are stored as a distinct class, similar to a "vertical" sequence, called bpp::Site.
+ * It shares several methods with the bpp::Sequence object, although it does not contain a name but
+ * a position attribute. This attribute can be used to track the position of sites when handling
+ * alignments (for instance after removing all gap-containing sites).
+ * There are currently two implementations of the bpp::SiteContainer interface:
+ * - bpp::AlignedSequenceContainer, inheriting from bpp::VectorSequenceContainer and adding the site access.
+ * Sequence access is hence in @f$o(1)@f$ and site access in @f$o(n)@f$, n being the total number of sites.
+ * - bpp::VectorSiteContainer is a symmetric implementation, storing the data as a vector of bpp::Site objects,
+ * providing site access in @f$o(1)@f$ but sequence access in @f$o(m)@f$, m being the total number of sequences.
+ * The static classes bpp::SiteTools and bpp::SiteContainerTools provide some tools (for instance: pairwise alignment) to deal respectively with
+ * bpp::Site and bpp::SiteContainer objects. I/O is provided for several formats, including Clustal (bpp::Clustal) and Phylip (bpp::Phylip).
+ *
+ * @par
+ * Bio++ SeqLib also contains support for sequence properties, like amino-acids biochemical properties.
+ * The interfaces bpp::AlphabetIndex1 and bpp::AlphabetIndex2 provides methods to deal with indices in 1 and 2 dimensions
+ * respectively. Several basic properties are provided, together with input from the AAIndex databases.
+ */
+
+namespace bpp
+{
+
+/**
+ * @brief The Alphabet interface.
+ *
+ * An alphabet object defines all the states allowed for a particular type of
+ * sequence. These states are coded as a string and an integer.
+ * The string description is the one found in the text (human comprehensive)
+ * description of sequences, typically in sequence files.
+ * However, for computionnal needs, this is often more efficient to store the sequences as
+ * a vector of integers.
+ * The link between the two descriptions is made <i>via</i>
+ * the Alphabet classes, and the two methods intToChar() and charToInt().
+ * The Alphabet interface also provides other methods, like getting the full name
+ * of the states and so on.
+ *
+ * The alphabet objects may throw several exceptions derived of the AlphabetException
+ * class.
+ *
+ * @see AlphabetException, BadCharException, BadIntException
+ */
+class Alphabet
+{
+ public:
+ Alphabet() {}
+ virtual ~Alphabet() {}
+
+ public:
+
+ /**
+ * @brief Get the complete name of a state given its int description.
+ *
+ * In case of several states with identical number (i.e. N and X for nucleic alphabets),
+ * this method returns the name of the first found in the vector.
+ *
+ * @param state The int description of the given state.
+ * @return The name of the state.
+ * @throw BadIntException When state is not a valid integer.
+ */
+ virtual std::string getName(int state) const throw (BadIntException) = 0;
+
+ /**
+ * @brief Get the complete name of a state given its string description.
+ *
+ * In case of several states with identical number (i.e. N and X for nucleic alphabets),
+ * this method will return the name of the first found in the vector.
+ *
+ * @param state The string description of the given state.
+ * @return The name of the state.
+ * @throw BadCharException When state is not a valid char description.
+ */
+ virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
+
+ /**
+ * @name = Tests
+ *
+ * @{
+ */
+
+ /**
+ * @brief Tell if a state (specified by its int description) is allowed by the
+ * the alphabet.
+ *
+ * @param state The int description.
+ * @return 'true' if the state in known.
+ */
+ virtual bool isIntInAlphabet(int state) const = 0;
+
+ /**
+ * @brief Tell if a state (specified by its string description) is allowed by the
+ * the alphabet.
+ *
+ * @param state The string description.
+ * @return 'true' if the state in known.
+ */
+ virtual bool isCharInAlphabet(const std::string& state) const = 0;
+ /** @} */
+
+ /**
+ * @name State access
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get a state given its int description.
+ *
+ * @param state The int description.
+ * @return The AlphabetState.
+ * @throw BadIntException When state is not a valid integer.
+ */
+ virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
+
+ /**
+ * @brief Get a state given its string description.
+ *
+ * @param state The string description.
+ * @return The AlphabetState.
+ * @throw BadCharException When state is not a valid string.
+ */
+ virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
+
+ /** @} */
+
+ /**
+ * @name Conversion methods
+ *
+ * @{
+ */
+
+ /**
+ * @brief Give the string description of a state given its int description.
+ *
+ * @param state The int description.
+ * @return The string description.
+ * @throw BadIntException When state is not a valid integer.
+ */
+ virtual std::string intToChar(int state) const throw (BadIntException) = 0;
+
+ /**
+ * @brief Give the int description of a state given its string description.
+ *
+ * @param state The string description.
+ * @return The int description.
+ * @throw BadCharException When state is not a valid char description.
+ */
+ virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
+ /** @} */
+
+ /**
+ * @name Sizes.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the number of supported characters in this alphabet,
+ * including generic characters (e.g. return 20 for DNA alphabet).
+ *
+ * @return The total number of supported character descriptions.
+ */
+ virtual unsigned int getNumberOfChars() const = 0;
+
+ /**
+ * @brief Get the number of <strong>distinct</strong> states in alphabet (e.g. return 15 for DNA alphabet).
+ * This is the number of integers used for state description.
+ *
+ * @return The number of distinct states.
+ */
+ virtual unsigned int getNumberOfTypes() const = 0;
+
+ /**
+ * @brief Get the number of <strong>resolved</strong> states in the alphabet (e.g. return 4 for DNA alphabet).
+ * This is the method you'll need in most cases.
+ *
+ * @return The number of resolved states.
+ */
+ virtual unsigned int getSize() const = 0;
+
+ /** @} */
+
+ /**
+ * @name Utilitary methods
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get all resolved states that match a generic state.
+ *
+ * If the given state is not a generic code then the output vector will contain this unique code.
+ *
+ * @param state The alias to resolve.
+ * @return A vector of resolved states.
+ * @throw BadIntException When state is not a valid integer.
+ */
+ virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
+
+ /**
+ * @brief Get all resolved states that match a generic state.
+ *
+ * If the given state is not a generic code then the output vector will contain this unique code.
+ *
+ * @param state The alias to resolve.
+ * @return A vector of resolved states.
+ * @throw BadCharException When state is not a valid char description.
+ */
+ virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
+
+ /**
+ * @brief Get the generic state that match a set of states.
+ *
+ * If the given states contain generic code, each generic code is first resolved and then the new generic state is returned.
+ * If only a single resolved state is given the function return this state.
+ *
+ * @param states A vector of states to resolve.
+ * @return A int code for the computed state.
+ * @throw BadIntException When a state is not a valid integer.
+ */
+ virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
+
+ /**
+ * @brief Get the generic state that match a set of states.
+ *
+ * If the given states contain generic code, each generic code is first resolved and then the new generic state is returned.
+ * If only a single resolved state is given the function return this state.
+ *
+ * @param states A vector of states to resolve.
+ * @return A string code for the computed state.
+ * @throw BadCharException when a state is not a valid char description.
+ * @throw CharStateNotSupportedException when the alphabet does not support Char state for unresolved state.
+ */
+ virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
+
+ /**
+ * @return A list of all supported int codes.
+ *
+ * Note for developers of new alphabets:
+ * we return a const reference here since the list is supposed to be
+ * stored within the class and should not be modified outside the class.
+ */
+ virtual const std::vector<int>& getSupportedInts() const = 0;
+
+ /**
+ * @return A list of all supported character codes.
+ *
+ * Note for developers of new alphabets:
+ * we return a const reference here since the list is supposed to be
+ * stored within the class and should not be modified outside the class.
+ */
+ virtual const std::vector<std::string>& getSupportedChars() const = 0;
+
+ /**
+ * @return The int code for unknown characters.
+ */
+ virtual int getUnknownCharacterCode() const = 0;
+
+ /**
+ * @return The int code for gap characters.
+ */
+ virtual int getGapCharacterCode() const = 0;
+
+ /**
+ * @param state The state to test.
+ * @return 'True' if the state is a gap.
+ */
+ virtual bool isGap(int state) const = 0;
+
+ /**
+ * @param state The state to test.
+ * @return 'True' if the state is a gap.
+ */
+ virtual bool isGap(const std::string& state) const = 0;
+
+ /**
+ * @param state The state to test.
+ * @return 'True' if the state is unresolved.
+ */
+ virtual bool isUnresolved(int state) const = 0;
+
+ /**
+ * @param state The state to test.
+ * @return 'True' if the state is unresolved.
+ */
+ virtual bool isUnresolved(const std::string& state) const = 0;
+
+ /** @} */
+
+ /**
+ * @brief Identification method.
+ *
+ * Used to tell if two alphabets describe the same type of sequences.
+ * For instance, this method is used by sequence containers to compare two alphabets and
+ * allow or deny addition of sequences.
+ *
+ * @return A text describing the alphabet.
+ */
+ virtual std::string getAlphabetType() const = 0;
+
+ /**
+ * @brief Get the size of the string coding a state.
+ * @return The size of the tring coding each states in the Alphabet.
+ * @author Sylvain Gaillard
+ */
+ virtual unsigned int getStateCodingSize() const = 0;
+};
+
+} //end of namespace bpp.
+
+#endif // _ALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp b/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp
new file mode 100644
index 0000000..05a36b1
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp
@@ -0,0 +1,92 @@
+//
+// File: AlphabetExceptions.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Nov 3 16:41:53 2003
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "AlphabetExceptions.h"
+#include "Alphabet.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+using namespace std;
+
+/******************************************************************************
+ * Alphabet exceptions: *
+ ******************************************************************************/
+
+AlphabetException::AlphabetException(const std::string& text, const Alphabet* alpha) :
+ Exception("AlphabetException: " + text + (alpha ? "(" + (alpha->getAlphabetType()) + ")" : string(""))),
+ alphabet_(alpha) {}
+
+/******************************************************************************/
+
+BadCharException::BadCharException(const std::string& badChar, const std::string& text, const Alphabet* alpha) :
+ AlphabetException("BadCharException: " + badChar + ". " + text, alpha),
+ c_(badChar) {}
+
+string BadCharException::getBadChar() const { return c_; }
+
+/******************************************************************************/
+
+BadIntException::BadIntException(int badInt, const std::string& text, const Alphabet* alpha) :
+ AlphabetException("BadIntException: " + TextTools::toString(badInt) + ". " + text, alpha),
+ i_(badInt) {}
+
+int BadIntException::getBadInt() const { return i_; }
+
+/******************************************************************************/
+
+AlphabetMismatchException::AlphabetMismatchException(const std::string& text, const Alphabet* alpha1, const Alphabet* alpha2) :
+ Exception("AlphabetMismatchException: " + text + (alpha1 != 0 && alpha2 != 0 ? "(" + alpha1->getAlphabetType() + ", " + alpha2->getAlphabetType() + ")" : string(""))),
+ alphabet1_(alpha1),
+ alphabet2_(alpha2) {}
+
+vector<const Alphabet*> AlphabetMismatchException::getAlphabets() const
+{
+ vector<const Alphabet*> v(2);
+ v[0] = alphabet1_;
+ v[1] = alphabet2_;
+ return v;
+}
+
+/******************************************************************************/
+
+CharStateNotSupportedException::CharStateNotSupportedException(const string & text, const Alphabet * alpha) :
+ AlphabetException("CharStateNotSupportedException: " + text, alpha) {};
+
+/******************************************************************************/
diff --git a/src/Bpp/Seq/Alphabet/AlphabetExceptions.h b/src/Bpp/Seq/Alphabet/AlphabetExceptions.h
new file mode 100644
index 0000000..1f04a37
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/AlphabetExceptions.h
@@ -0,0 +1,213 @@
+//
+// File: AlphabetExceptions.h
+// Created by: Julien Dutheil
+// Created on: Mon Nov 3 16:41:53 2003
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ALPHABETEXCEPTIONS_H_
+#define _ALPHABETEXCEPTIONS_H_
+
+#include <Bpp/Exceptions.h>
+
+// From the STL:
+#include <vector>
+
+namespace bpp
+{
+
+class Alphabet;
+
+/**
+ * @brief The alphabet exception base class.
+ *
+ * @see Alphabet, Exception
+ */
+class AlphabetException:
+ public Exception
+{
+ private:
+ const Alphabet* alphabet_;
+
+ public:
+ /**
+ * @brief Build a new AlphabetException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param alpha A const pointer toward the alphabet that threw the exception.
+ */
+ AlphabetException(const std::string& text, const Alphabet* alpha = 0);
+
+ AlphabetException(const AlphabetException& ae): Exception(ae), alphabet_(ae.alphabet_) {}
+ AlphabetException& operator=(const AlphabetException& ae)
+ {
+ Exception::operator=(ae);
+ alphabet_ = ae.alphabet_;
+ return *this;
+ }
+
+ virtual ~AlphabetException() throw () {}
+
+ public:
+ /**
+ * @brief Get the alphabet that threw the exception.
+ *
+ * @return a const pointer toward the alphabet.
+ */
+ virtual const Alphabet* getAlphabet() const { return alphabet_; }
+};
+
+/**
+ * @brief An alphabet exception thrown when trying to specify a bad char to the alphabet.
+ */
+class BadCharException:
+ public AlphabetException
+{
+ protected:
+ std::string c_;
+
+ public:
+ /**
+ * @brief Build a new BadCharException.
+ *
+ * @param badChar The faulty character.
+ * @param text A message to be passed to the exception hierarchy.
+ * @param alpha A const pointer toward the alphabet that threw the exception.
+ */
+ BadCharException(const std::string & badChar, const std::string & text = "", const Alphabet * alpha = 0);
+
+ virtual ~BadCharException() throw() {};
+
+ public:
+ /**
+ * @brief Get the character that threw the exception.
+ *
+ * @return the faulty character.
+ */
+ virtual std::string getBadChar() const;
+};
+
+/**
+ * @brief An alphabet exception thrown when trying to specify a bad int to the alphabet.
+ */
+class BadIntException:
+ public AlphabetException
+{
+ protected:
+ int i_;
+
+ public:
+ /**
+ * @brief Build a new BadIntException.
+ * @param badInt The faulty integer.
+ * @param text A message to be passed to the exception hierarchy.
+ * @param alpha A const pointer toward the alphabet that threw the exception.
+ */
+ BadIntException(int badInt, const std::string& text = "", const Alphabet* alpha = 0);
+
+ virtual ~BadIntException() throw() {}
+
+ public:
+ /**
+ * @brief Get the integer that threw the exception.
+ *
+ * @return the faulty integer.
+ */
+ virtual int getBadInt() const;
+};
+
+/**
+ * @brief Exception thrown when two alphabets do not match.
+ *
+ * Typically, this may occur when you try to add a bad sequence to a container,
+ * or concatenate two kinds of sequences, and so on.
+ */
+class AlphabetMismatchException : public Exception
+{
+ private:
+ const Alphabet* alphabet1_, * alphabet2_;
+
+ public:
+
+ /**
+ * @brief Build a new AlphabetMismatchException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param alpha1 A const pointer toward the first alphabet.
+ * @param alpha2 A const pointer toward the second alphabet, i.e. the one which does not match with the first.
+ */
+ AlphabetMismatchException(const std::string& text = "", const Alphabet* alpha1 = 0, const Alphabet* alpha2 = 0);
+
+ AlphabetMismatchException(const AlphabetMismatchException& ame): Exception(ame), alphabet1_(ame.alphabet1_), alphabet2_(ame.alphabet2_) {}
+ AlphabetMismatchException& operator=(const AlphabetMismatchException& ame)
+ {
+ Exception::operator=(ame);
+ alphabet1_ = ame.alphabet1_;
+ alphabet2_ = ame.alphabet2_;
+ return *this;
+ }
+
+ virtual ~AlphabetMismatchException() throw() {}
+
+ public:
+ /**
+ * @brief Get the alphabets that do not match.
+ *
+ * @return a vector of pointers toward the alphabets.
+ */
+ std::vector<const Alphabet *> getAlphabets() const;
+};
+
+/**
+ * @brief Exception thrown in case no character is available for a certain state in an alphabet.
+ */
+class CharStateNotSupportedException : public AlphabetException
+{
+ public:
+ /**
+ * @brief Build a new CharStateNotSupportedException.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param alpha A const pointer toward the alphabet that threw the exception.
+ */
+ CharStateNotSupportedException(const std::string & text = "", const Alphabet * alpha = 0);
+
+ virtual ~CharStateNotSupportedException() throw() {};
+};
+
+} //end of namespace bpp.
+
+#endif //_ALPHABETEXCEPTIONS_H_
+
diff --git a/src/Bpp/Seq/Alphabet/AlphabetState.h b/src/Bpp/Seq/Alphabet/AlphabetState.h
new file mode 100644
index 0000000..8893add
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/AlphabetState.h
@@ -0,0 +1,132 @@
+//
+// File: AlphabetState.h
+// Author: Sylvain Gaillard
+// Created: 29/07/2009 13:56:01
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (July 29, 2009)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ALPHABETSTATE_H_
+#define _ALPHABETSTATE_H_
+
+#include <Bpp/Clonable.h>
+
+// From the STL
+#include <string>
+
+namespace bpp {
+ /**
+ * @brief This is the base class to describe states in an Alphabet.
+ *
+ * @author Sylvain Gaillard
+ */
+ class AlphabetState: public virtual Clonable {
+ private:
+ int num_;
+ std::string letter_;
+ std::string name_;
+
+ public:
+ AlphabetState(int num, const std::string& letter, const std::string& name): num_(num), letter_(letter), name_(name) {}
+
+ // Class destructor
+ virtual ~AlphabetState() {}
+
+ public:
+ /**
+ * @name The Clonable interface.
+ * @{
+ */
+#ifdef NO_VIRTUAL_COV
+ Clonable*
+#else
+ AlphabetState*
+#endif
+ clone() const { return new AlphabetState(* this); }
+ /** @} */
+ /**
+ * @brief Get the state's number.
+ *
+ * @return The state's number (i.e. -1 for gap (-)).
+ */
+ int getNum() const { return num_; }
+ /**
+ * @brief Set the state's number.
+ *
+ * @param num The state's number.
+ */
+ void setNum(int num) { num_ = num; }
+
+ /**
+ * @brief Get the letter(s) corresponding to the state.
+ *
+ * The letter is a string because it may more than one char
+ * (for instance: codon).
+ *
+ * @return The state's letter.
+ */
+ const std::string& getLetter() const { return letter_; }
+ /**
+ * @brief Set the letter(s) of the state.
+ *
+ * @param letter The state's letter.
+ */
+ void setLetter(const std::string& letter) { letter_ = letter; }
+
+ /**
+ * @brief Get the name of the state.
+ *
+ * @return The full name of the state (i.e. Adenine).
+ */
+ const std::string& getName() const { return name_; }
+ /**
+ * @brief Set the name of the state.
+ *
+ * @param name The state's name
+ */
+ void setName(const std::string& name) { name_ = name; }
+
+ /**
+ * @brief operator ==
+ *
+ * Comparison is done on state num
+ */
+ bool operator == (AlphabetState& l2) {
+ return getNum() == l2.getNum();
+ }
+ };
+}
+
+#endif // _ALPHABETSTATE_H_
+
diff --git a/src/Bpp/Seq/Alphabet/AlphabetTools.cpp b/src/Bpp/Seq/Alphabet/AlphabetTools.cpp
new file mode 100644
index 0000000..90f42f5
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/AlphabetTools.cpp
@@ -0,0 +1,126 @@
+//
+// File: AlphabetTools.cpp
+// Created by: Julien Dutheil
+// Created on: Fri Oct 10 17:27:39 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "AlphabetTools.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <ctype.h>
+#include <iostream>
+
+using namespace std;
+
+/**********************************************************************************************/
+
+const DNA AlphabetTools::DNA_ALPHABET;
+const RNA AlphabetTools::RNA_ALPHABET;
+const ProteicAlphabet AlphabetTools::PROTEIN_ALPHABET;
+const DefaultAlphabet AlphabetTools::DEFAULT_ALPHABET;
+
+/**********************************************************************************************/
+
+int AlphabetTools::getType(char state)
+{
+ if (state == '-')
+ return -1;
+ state = static_cast<char>(toupper(static_cast<int>(state))); // toupper works on int
+ bool d = DNA_ALPHABET.isCharInAlphabet(TextTools::toString(state));
+ bool r = RNA_ALPHABET.isCharInAlphabet(TextTools::toString(state));
+ bool p = PROTEIN_ALPHABET.isCharInAlphabet(TextTools::toString(state));
+
+ if (!d && !r && !p)
+ return 0; // Unknown character
+ else if (d && !r && !p)
+ return 1; // DNA specific
+ else if (!d && r && !p)
+ return 2; // RNA specific
+ else if (!d && !r && p)
+ return 3; // Protein specific
+ else if (d && r && !p)
+ return 4; // Nucleotide specific
+ else if (d && !r && p)
+ return 5; // DNA or Protein specific
+ else if (!d && r && p)
+ return 6; // RNA or Protein specific
+ else
+ return 7; // Non-specific character
+}
+
+/**********************************************************************************************/
+
+bool AlphabetTools::checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
+{
+ if (alphabet.getNumberOfChars() == 0)
+ return true; // Will this really happen?
+ size_t size = alphabet.intToChar(0).size();
+ for (unsigned int i = 1; i < alphabet.getNumberOfTypes(); i++)
+ {
+ if (alphabet.intToChar(i).size() != size)
+ return false;
+ }
+ return true;
+}
+
+/**********************************************************************************************/
+
+bool AlphabetTools::checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException)
+{
+ return checkAlphabetCodingSize(*alphabet);
+}
+
+/**********************************************************************************************/
+
+unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
+{
+ if (!checkAlphabetCodingSize(alphabet))
+ throw AlphabetException("Bad alphabet in function Alphabet::getAlphabetCodingSize().");
+ return static_cast<unsigned int>(alphabet.intToChar(0).size());
+}
+
+/**********************************************************************************************/
+
+unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException)
+{
+ return getAlphabetCodingSize(*alphabet);
+}
+
+/**********************************************************************************************/
+
diff --git a/src/Bpp/Seq/Alphabet/AlphabetTools.h b/src/Bpp/Seq/Alphabet/AlphabetTools.h
new file mode 100644
index 0000000..3d3b356
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/AlphabetTools.h
@@ -0,0 +1,231 @@
+//
+// File: AlphabetTools.h
+// Created by: Julien Dutheil
+// Created on: Fri Oct 10 17:27:39 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _ALPHABETTOOLS_H_
+#define _ALPHABETTOOLS_H_
+
+#include "DNA.h"
+#include "RNA.h"
+#include "ProteicAlphabet.h"
+#include "DefaultAlphabet.h"
+#include "CodonAlphabet.h"
+#include "RNY.h"
+#include "BinaryAlphabet.h"
+#include <Bpp/Numeric/VectorTools.h>
+
+#include <typeinfo>
+
+namespace bpp
+{
+/**
+ * @brief Utilitary functions dealing with alphabets.
+ */
+class AlphabetTools
+{
+public:
+ static const DNA DNA_ALPHABET;
+ static const RNA RNA_ALPHABET;
+ static const ProteicAlphabet PROTEIN_ALPHABET;
+ static const DefaultAlphabet DEFAULT_ALPHABET;
+
+public:
+ AlphabetTools() {}
+ virtual ~AlphabetTools() {}
+
+public:
+ /**
+ * @brief Character identification method for sequence's alphabet identification
+ *
+ * Return :
+ * - -1 gap
+ * - 1 DNA specific (no character!)
+ * - 2 RNA specific (U)
+ * - 3 Protein specific (characters E, F, I, L, P, Q)
+ * - 4 Nucleotide specific (no character)
+ * - 5 DNA or Protein specific (T)
+ * - 6 RNA or Protein specific (no character)
+ * - 7 Any alphabet (A, B, C, D, G, H, J, K, M, N, O, R, S, V, W, X, Y, Z, 0)
+ * - 0 Unknown character
+ *
+ * @param state The character to test.
+ * @return The type code.
+ */
+ static int getType(char state);
+
+ /**
+ * @brief This checks that all characters in the alphabet are coded by a string of same length.
+ *
+ * This method is used when states are coded by more than one character, typically: codon alphabets.
+ *
+ * @param alphabet The alphabet to check.
+ * @return True if all text description have the same length (e.g. 3 for codon alphabet).
+ */
+ static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
+
+ /**
+ * @brief This checks that all characters in the alphabet are coded by a string of same length.
+ *
+ * This function performs the same work as the previous one, but deals with pointers
+ * instead of reference. This may be more convenient since we often use pointers on alphabets.
+ *
+ * @param alphabet a pointer toward the alphabet to check.
+ * @return True if all text description have the same length (e.g. 3 for codon alphabet).
+ */
+ static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
+
+ /**
+ * @brief In case that all states in the given alphabet have a string description of same length,
+ * send this length; e.g. 3 for codon alphabets.
+ *
+ * @param alphabet The alphabet to analyse.
+ * @return The common size of all text descriptionif there is one. Else throws an AlphabetException.
+ */
+ static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
+
+ /**
+ * @brief In case that all states in the given alphabet have a string description of same length,
+ * send this length; e.g. 3 for codon alphabets.
+ *
+ * This function performs the same work as the previous one, but deals with pointers
+ * instead of reference. This may be more convenient since we often use pointers on alphabets.
+ *
+ * @param alphabet a pointer toward the alphabet to analyse.
+ * @return The common size of all text descriptionif there is one. Else throws an AlphabetException.
+ */
+ static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
+
+ /**
+ * @return True if the alphabet is an instanciation of the NucleicAlphabet class.
+ * @param alphabet The alphabet to check.
+ */
+ static bool isNucleicAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<NucleicAlphabet>(alphabet); }
+
+ /**
+ * @return True if the alphabet is an instanciation of the DNA class.
+ * @param alphabet The alphabet to check.
+ */
+ static bool isDNAAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<DNA>(alphabet); }
+
+ /**
+ * @return True if the alphabet is an instanciation of the RNA class.
+ * @param alphabet The alphabet to check.
+ */
+ static bool isRNAAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<RNA>(alphabet); }
+
+ /**
+ * @return True if the alphabet is an instanciation of the ProteicAlphabet class.
+ * @param alphabet The alphabet to check.
+ */
+ static bool isProteicAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<ProteicAlphabet>(alphabet); }
+
+ /**
+ * @return True if the alphabet is an instanciation of the Codon class.
+ * @param alphabet The alphabet to check.
+ */
+ static bool isCodonAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<CodonAlphabet>(alphabet); }
+
+ /**
+ * @return True if the alphabet is an instanciation of the WordAlphabet class.
+ * @param alphabet The alphabet to check.
+ */
+ static bool isWordAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<WordAlphabet>(alphabet); }
+
+ /**
+ * @return True if the alphabet is an instanciation of the RNY class.
+ * @param alphabet The alphabet to check.
+ */
+ static bool isRNYAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<RNY>(alphabet); }
+
+ /**
+ * @return True if the alphabet is an instanciation of the BinaryAlphabet class.
+ * @param alphabet The alphabet to check.
+ */
+ static bool isBinaryAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<BinaryAlphabet>(alphabet); }
+
+ /**
+ * @return True if the alphabet is an instanciation of the DefaultAlphabet class.
+ * @param alphabet The alphabet to check.
+ */
+ static bool isDefaultAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<DefaultAlphabet>(alphabet); }
+
+ /**
+ * @brief Tell if two characters match according to a given alphabet.
+ *
+ * Example (DNA):
+ * @verbatim
+ * A,T: false
+ * A,A: true
+ * A,N: true
+ * A,Y: false
+ * N,Y: true
+ * N,N: true
+ * @endverbatim
+ *
+ * @return True if the two characters are identical, or are compatible if at least one of them is a generic character.
+ * @param alphabet The alphabet to use.
+ * @param i First character to check.
+ * @param j Secondt character to check.
+ */
+ static bool match(const Alphabet* alphabet, int i, int j)
+ {
+ std::vector<int> a = alphabet->getAlias(i);
+ std::vector<int> b = alphabet->getAlias(j);
+ std::vector<int> u = VectorTools::vectorIntersection(a, b);
+ return u.size() > 0;
+ }
+
+private:
+ template<class Y>
+ static bool alphabetInheritsFrom(const Alphabet* alphabet)
+ {
+ try
+ {
+ const Y* t = dynamic_cast<const Y*>(alphabet);
+ return t != 0; // Solves strange behavior in new gcc?
+ }
+ catch (std::exception& e)
+ {
+ return false;
+ }
+ }
+};
+} // end of namespace bpp.
+
+#endif // _ALPHABETTOOLS_H_
+
diff --git a/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp b/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp
new file mode 100644
index 0000000..0a51ddd
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp
@@ -0,0 +1,62 @@
+//
+// File: BinaryAlphabet.cpp
+// Authors: Laurent Gueguen
+// Created on: 2009
+//
+
+/*
+ Copyright or � or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+
+#include "BinaryAlphabet.h"
+#include "AlphabetState.h"
+
+// From Utils:
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+BinaryAlphabet::BinaryAlphabet()
+{
+ // Alphabet size definition
+ resize(3);
+
+ // Alphabet content definition
+ setState(0, AlphabetState(-1, "-", "Gap"));
+
+ for (unsigned int i = 0; i < 2; i++)
+ {
+ setState(i + 1, AlphabetState(i, TextTools::toString(i), ""));
+ }
+}
+
diff --git a/src/Bpp/Seq/Alphabet/BinaryAlphabet.h b/src/Bpp/Seq/Alphabet/BinaryAlphabet.h
new file mode 100644
index 0000000..dbb05a8
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/BinaryAlphabet.h
@@ -0,0 +1,78 @@
+//
+// File: BinaryAlphabet.h
+// Author: L Gueguen
+//
+
+/*
+ Copyright or � or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _BINARYALPHABET_H_
+#define _BINARYALPHABET_H_
+
+#include "AbstractAlphabet.h"
+
+namespace bpp
+{
+/**
+ * @brief The BinaryAlphabet class, letters are 0 and 1.
+ * @author Laurent Gueguen
+ *
+ */
+class BinaryAlphabet :
+ public AbstractAlphabet
+{
+protected:
+ void registerState(const AlphabetState& st)
+ {
+ AbstractAlphabet::registerState(*(st.clone()));
+ }
+
+public:
+ // class constructor
+ BinaryAlphabet();
+
+ // class destructor
+ virtual ~BinaryAlphabet() {}
+
+public:
+ unsigned int getSize() const { return 2; }
+ unsigned int getNumberOfTypes() const { return 2; }
+ std::string getAlphabetType() const { return "Binary alphabet"; }
+ int getUnknownCharacterCode() const { return 3; }
+ bool isUnresolved(int state) const { return state == 3; }
+ bool isUnresolved(const std::string& state) const { return false; }
+};
+} // end of namespace bpp.
+
+#endif // _BINARYALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp b/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp
new file mode 100644
index 0000000..024336f
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp
@@ -0,0 +1,97 @@
+//
+// File: CaseMaskedAlphabet.cpp
+// Created by: Julien Dutheil
+// Created on: Sun Sep 05 2010
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "CaseMaskedAlphabet.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+//From the STL:
+#include <vector>
+#include <iostream>
+
+using namespace std;
+
+CaseMaskedAlphabet::CaseMaskedAlphabet(const LetterAlphabet* nocaseAlphabet) :
+ LetterAlphabet(true),
+ nocaseAlphabet_(nocaseAlphabet)
+{
+ vector<string> chars = nocaseAlphabet_->getSupportedChars();
+ for (unsigned int i = 0; i < chars.size(); ++i) {
+ AlphabetState state = nocaseAlphabet_->getState(chars[i]);
+ registerState(state);
+ char c = *chars[i].c_str();
+ if (isalpha(c)) {
+ if (isupper(c)) {
+ registerState(AlphabetState(state.getNum() + 100, TextTools::toLower(state.getLetter()), string("Masked ") + state.getName()));
+ }
+ }
+ }
+}
+
+int CaseMaskedAlphabet::getMaskedEquivalentState(int state) const
+ throw (BadIntException)
+{
+ if (!isIntInAlphabet(state))
+ throw BadIntException(state, "CaseMaskedAlphabet::getMaskedEquivalentState. Unsupported state code.");
+ if (state >= 100) return state;
+ else {
+ state += 100;
+ if (!isIntInAlphabet(state))
+ throw BadIntException(state, "CaseMaskedAlphabet::getMaskedEquivalentState. State has masked equivalent.");
+ return state;
+ }
+}
+
+const string CaseMaskedAlphabet::getMaskedEquivalentState(const string& state) const
+ throw (BadCharException, BadIntException)
+{
+ if (!isCharInAlphabet(state))
+ throw BadCharException(state, "CaseMaskedAlphabet::getMaskedEquivalentState. Unsupported state code.");
+ int code = charToInt(state);
+ if (code >= 100) return state;
+ else {
+ code += 100;
+ if (!isIntInAlphabet(code))
+ throw BadIntException(code, "CaseMaskedAlphabet::getMaskedEquivalentState. State has masked equivalent.");
+ return intToChar(code);
+ }
+}
+
+
diff --git a/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h b/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h
new file mode 100644
index 0000000..225d6ce
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h
@@ -0,0 +1,117 @@
+//
+// File: CaseMaskedAlphabet.h
+// Created by: Julien Dutheil
+// Created on: Sun Sep 05 2010
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _CASEMASKEDALPHABET_H_
+#define _CASEMASKEDALPHABET_H_
+
+#include "LetterAlphabet.h"
+
+//From the STL:
+#include <string>
+
+namespace bpp
+{
+
+/**
+ * @brief Case-sensitive letter alphabet.
+ *
+ * This alphabet is used for parsing comodity.
+ * It takes as input another LetterAlphabet and will create duplicate any aphanumerical and upper case state,
+ * by creating a lower case version of the state, also named "masked" state.
+ * Helper functions are provided to determine whether a given state is masked or unmasked.
+ */
+class CaseMaskedAlphabet :
+ public LetterAlphabet
+{
+ public:
+ const LetterAlphabet* nocaseAlphabet_;
+
+ public:
+ CaseMaskedAlphabet(const LetterAlphabet* nocaseAlphabet);
+ CaseMaskedAlphabet(const CaseMaskedAlphabet& cma) :
+ LetterAlphabet(cma), nocaseAlphabet_(cma.nocaseAlphabet_) {}
+ CaseMaskedAlphabet& operator=(const CaseMaskedAlphabet& cma) {
+ LetterAlphabet::operator=(cma);
+ nocaseAlphabet_ = cma.nocaseAlphabet_;
+ return *this;
+ }
+
+ public:
+ unsigned int getSize() const { return nocaseAlphabet_->getSize(); }
+ unsigned int getNumberOfTypes() const { return nocaseAlphabet_->getNumberOfTypes(); }
+ std::string getAlphabetType() const { return "Default alphabet"; }
+ int getUnknownCharacterCode() const { return nocaseAlphabet_->getUnknownCharacterCode(); }
+ bool isUnresolved(int state) const { return nocaseAlphabet_->isUnresolved(state); }
+ bool isUnresolved(const std::string& state) const { return nocaseAlphabet_->isUnresolved(state); }
+
+ const Alphabet* getUnmaskedAlphabet() const { return nocaseAlphabet_; }
+
+ bool isMasked(int state) const { return state >= 100; }
+ bool isMasked(const std::string& state) const {
+ char c = state.c_str()[0];
+ return isMasked(c);
+ }
+ bool isMasked(char state) const {
+ return isalpha(state) && !isupper(state);
+ }
+
+ /**
+ * @brief Get the masked state equivalent to the input one.
+ *
+ * If the input state is masked, returns it "as is".
+ * @param state The input state.
+ * @throw BadIntException if the input state is not supported, or if there is no quivallent masked state.
+ */
+ int getMaskedEquivalentState(int state) const throw (BadIntException);
+ /**
+ * @brief Get the masked state equivalent to the input one.
+ *
+ * If the input state is masked, returns it "as is".
+ * @param state The input state.
+ * @throw BadCharException if the input state is not supported.
+ * @throw BadIntException if there is no equivalent masked state.
+ */
+ const std::string getMaskedEquivalentState(const std::string& state) const throw (BadCharException, BadIntException);
+
+};
+
+} // end of namespace bpp
+
+#endif //_CASEMASKEDALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp b/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp
new file mode 100644
index 0000000..15522c2
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp
@@ -0,0 +1,127 @@
+//
+// File: CodonAlphabet.h
+// Created by: Julien Dutheil
+// Created on: Sun Oct 12 17:41:56 2003
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "CodonAlphabet.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+
+using namespace std;
+
+const string CodonAlphabet::STOP = "Stop";
+
+/******************************************************************************/
+
+unsigned int CodonAlphabet::numberOfStopCodons() const
+{
+ return static_cast<unsigned int>(stopCodons_.size());
+}
+
+int CodonAlphabet::getCodon(int pos1, int pos2, int pos3) const
+throw (BadIntException)
+{
+ vector<int> vint;
+ vint.push_back(pos1);
+ vint.push_back(pos2);
+ vint.push_back(pos3);
+
+ return getWord(vint);
+}
+
+/******************************************************************************/
+
+string CodonAlphabet::getCodon(const string & pos1, const string & pos2, const string & pos3) const
+throw (BadCharException)
+{
+ vector<string> vint;
+ vint.push_back(pos1);
+ vint.push_back(pos2);
+ vint.push_back(pos3);
+
+ return getWord(vint);
+}
+
+/******************************************************************************/
+
+int CodonAlphabet::getFirstPosition (int codon) const throw (BadIntException)
+{
+ return getNPosition(codon,0);
+}
+
+/******************************************************************************/
+
+int CodonAlphabet::getSecondPosition(int codon) const throw (BadIntException)
+{
+ return getNPosition(codon,1);
+}
+
+/******************************************************************************/
+
+int CodonAlphabet::getThirdPosition (int codon) const throw (BadIntException)
+{
+ return getNPosition(codon,2);
+}
+
+/******************************************************************************/
+
+string CodonAlphabet::getFirstPosition (const string & codon) const
+throw (BadCharException)
+{
+ return getNPosition(codon,0);
+}
+
+/******************************************************************************/
+
+string CodonAlphabet::getSecondPosition(const string & codon) const
+throw (BadCharException)
+{
+ return getNPosition(codon,1);
+}
+
+/******************************************************************************/
+
+string CodonAlphabet::getThirdPosition (const string & codon) const
+throw (BadCharException)
+{
+ return getNPosition(codon,2);
+}
+
diff --git a/src/Bpp/Seq/Alphabet/CodonAlphabet.h b/src/Bpp/Seq/Alphabet/CodonAlphabet.h
new file mode 100644
index 0000000..a0f37b8
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/CodonAlphabet.h
@@ -0,0 +1,241 @@
+//
+// File: CodonAlphabet.h
+// Created by: Julien Dutheil
+// Created on: Sun Oct 12 17:41:56 2003
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided
+only with a limited warranty and the software's author, the holder of
+the economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards
+their requirements in conditions enabling the security of their
+systems and/or data to be ensured and, more generally, to use and
+operate it in the same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _CODONALPHABET_H_
+#define _CODONALPHABET_H_
+
+#include "WordAlphabet.h"
+#include "NucleicAlphabet.h"
+
+// From the STL:
+#include <string>
+
+
+namespace bpp
+{
+
+/**
+ * @brief The abstract base class for codon alphabets.
+ * @author Laurent Guéguen
+ *
+ * Since codons are made of 3 nucleic bases (RNA or DNA), this class
+ * has a NucleicAlphabet field used to check char description. This
+ * nucleic alphabet is passed to the constructor. This class also adds
+ * some methods specific to codon manipulation.
+ */
+class CodonAlphabet:
+ public WordAlphabet
+{
+protected:
+ /**
+ *@brief the vector of the numbers of the stop codon states.
+ */
+ std::vector<int> stopCodons_;
+
+ //Constant used for init codon:
+ int initCodon_;
+
+
+public:
+ //Constant used for stop codons:
+ static const std::string STOP;
+
+public: // Constructor and destructor.
+
+ /**
+ * @brief Builds a new codon alphabet from a nucleic alphabet.
+ *
+ * @param alpha The nucleic alphabet to be used.
+ */
+ CodonAlphabet(const NucleicAlphabet* alpha) : WordAlphabet(alpha, 3), stopCodons_(), initCodon_() {}
+
+ virtual ~CodonAlphabet() {}
+
+ virtual std::string getAlphabetType() const = 0;
+
+public:
+
+ /**
+ * @name Codon specific methods
+ *
+ * @{
+ */
+
+ /**
+ * @brief Returns the number of stop codons
+ */
+
+ unsigned int numberOfStopCodons() const;
+
+ /**
+ * @brief Returns the vector of the numbers of the stop codon states.
+ */
+
+ const std::vector<int>& stopCodons() const { return stopCodons_;}
+
+ /**
+ * @brief Get the int code for a codon given the int code of the three underlying positions.
+ *
+ * The int code of each position must match the nucleic alphabet specified for this alphabet.
+ * @param pos1 Int description for position 1.
+ * @param pos2 Int description for position 2.
+ * @param pos3 Int description for position 3.
+ * @return The int code of the codon.
+ */
+ virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
+
+ /**
+ * @brief Get the char code for a codon given the char code of the three underlying positions.
+ *
+ * The char code of each position must match the nucleic alphabet specified for this alphabet.
+ * NB: This performs pos1 + pos2 + pos3 after checking for each position validity.
+ * @param pos1 Char description for position 1.
+ * @param pos2 Char description for position 2.
+ * @param pos3 Char description for position 3.
+ * @return The Char code of the codon.
+ */
+ virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
+
+ /**
+ * @brief Get the int code of the first position of a codon given its int description.
+ *
+ * @param codon The int description of the codon.
+ * @return The int description of the first position of the codon.
+ */
+ virtual int getFirstPosition(int codon) const throw (BadIntException);
+
+ /**
+ * @brief Get the int code of the second position of a codon given its int description.
+ *
+ * @param codon The int description of the codon.
+ * @return The int description of the second position of the codon.
+ */
+ virtual int getSecondPosition(int codon) const throw (BadIntException);
+
+ /**
+ * @brief Get the int code of the third position of a codon given its int description.
+ *
+ * @param codon The int description of the codon.
+ * @return The int description of the third position of the codon.
+ */
+ virtual int getThirdPosition(int codon) const throw (BadIntException);
+
+ /**
+ * @brief Get the char code of the first position of a codon given its char description.
+ *
+ * @param codon The char description of the codon.
+ * @return The char description of the first position of the codon.
+ */
+ virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
+
+ /**
+ * @brief Get the char code of the second position of a codon given its char description.
+ *
+ * @param codon The char description of the codon.
+ * @return The char description of the second position of the codon.
+ */
+ virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
+
+ /**
+ * @brief Get the char code of the third position of a codon given its char description.
+ *
+ * @param codon The char description of the codon.
+ * @return The char description of the third position of the codon.
+ */
+ virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
+
+ /**
+ * @brief Tell whether a particular codon is a stop codon.
+ *
+ * @param codon The int description of the codon to test.
+ * @return True if the codon is a stop codon.
+ */
+ bool isStop(int codon) const
+ {
+ return (getName(intToChar(codon)) == STOP);
+ }
+
+ /**
+ * @brief Tell whether a particular codon is a stop codon.
+ *
+ * @param codon The char description of the codon to test.
+ * @return True if the codon is a stop codon.
+ */
+ bool isStop(const std::string& codon) const
+ {
+ return (getName(codon) == STOP);
+ }
+
+ /**
+ * @brief Tell whether a particular codon is the init codon.
+ *
+ * @param codon The int description of the codon to test.
+ * @return True if the codon is the init codon.
+ */
+ bool isInit(int codon) const
+ {
+ return (codon == initCodon_);
+ }
+
+ /**
+ * @brief Tell whether a particular codon is the init codon.
+ *
+ * @param codon The char description of the codon to test.
+ * @return True if the codon is a init codon.
+ */
+ bool isInit(const std::string& codon) const
+ {
+ return (charToInt(codon) == initCodon_);
+ }
+
+ /**
+ * @return The nucleic alphabet associated to this codon alphabet.
+ */
+ virtual const NucleicAlphabet* const getNucleicAlphabet() const
+ {
+ return dynamic_cast<const NucleicAlphabet*>(vAbsAlph_[0]);
+ }
+
+ /** @} */
+};
+
+} //end of namespace bpp.
+
+#endif //_CODONALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/DNA.cpp b/src/Bpp/Seq/Alphabet/DNA.cpp
new file mode 100644
index 0000000..3eac3e9
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/DNA.cpp
@@ -0,0 +1,150 @@
+//
+// File: DNA.cpp
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created on: Tue Jul 22 2003
+//
+
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "DNA.h"
+#include "AlphabetState.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Utils/MapTools.h>
+
+using namespace bpp;
+
+// From STL:
+#include <map>
+
+using namespace std;
+
+/******************************************************************************/
+
+DNA::DNA(bool exclamationMarkCountsAsGap)
+{
+ // Alphabet size definition
+ resize(21);
+
+ // Alphabet content definition
+ // all unresolved bases use n°14
+ setState( 0, NucleicAlphabetState(-1, "-", 0, "Gap"));
+ setState( 1, NucleicAlphabetState( 0, "A", 1, "Adenine"));
+ setState( 2, NucleicAlphabetState( 1, "C", 2, "Cytosine"));
+ setState( 3, NucleicAlphabetState( 2, "G", 4, "Guanine"));
+ setState( 4, NucleicAlphabetState( 3, "T", 8, "Thymine"));
+ setState( 5, NucleicAlphabetState( 4, "M", 3, "Adenine or Cytosine"));
+ setState( 6, NucleicAlphabetState( 5, "R", 5, "Purine (Adenine or Guanine)"));
+ setState( 7, NucleicAlphabetState( 6, "W", 9, "Adenine or Thymine"));
+ setState( 8, NucleicAlphabetState( 7, "S", 6, "Cytosine or Guanine"));
+ setState( 9, NucleicAlphabetState( 8, "Y", 10, "Pyrimidine (Cytosine or Thymine)"));
+ setState(10, NucleicAlphabetState( 9, "K", 12, "Guanine or Thymine"));
+ setState(11, NucleicAlphabetState(10, "V", 7, "Adenine or Cytosine or Guanine"));
+ setState(12, NucleicAlphabetState(11, "H", 11, "Adenine or Cytosine or Thymine"));
+ setState(13, NucleicAlphabetState(12, "D", 13, "Adenine or Guanine or Thymine"));
+ setState(14, NucleicAlphabetState(13, "B", 14, "Cytosine or Guanine or Thymine"));
+ setState(15, NucleicAlphabetState(14, "N", 15, "Unresolved base"));
+ setState(16, NucleicAlphabetState(14, "X", 15, "Unresolved base"));
+ setState(17, NucleicAlphabetState(14, "O", 15, "Unresolved base"));
+ setState(18, NucleicAlphabetState(14, "0", 15, "Unresolved base"));
+ setState(19, NucleicAlphabetState(14, "?", 15, "Unresolved base"));
+ if (exclamationMarkCountsAsGap)
+ setState(20, NucleicAlphabetState(-1, "!", 0, "Unresolved base"));
+ else
+ setState(20, NucleicAlphabetState(14, "!", 15, "Unresolved base"));
+}
+
+/******************************************************************************/
+
+std::vector<int> DNA::getAlias(int state) const throw (BadIntException)
+{
+ if (!isIntInAlphabet(state))
+ throw BadIntException(state, "DNA::getAlias(int): Specified base unknown.");
+ vector<int> v;
+ const NucleicAlphabetState& st = getState(state);
+ if (state == -1)
+ v.push_back(-1);
+ if (st.getBinaryCode() & 1)
+ v.push_back(0);
+ if (st.getBinaryCode() & 2)
+ v.push_back(1);
+ if (st.getBinaryCode() & 4)
+ v.push_back(2);
+ if (st.getBinaryCode() & 8)
+ v.push_back(3);
+ return v;
+}
+
+
+/******************************************************************************/
+
+std::vector<std::string> DNA::getAlias(const std::string& state) const throw (BadCharException)
+{
+ string locstate = TextTools::toUpper(state);
+ if(!isCharInAlphabet(locstate)) throw BadCharException(locstate, "DNA::getAlias(int): Specified base unknown.");
+ vector<int> vi = this->getAlias(this->charToInt(state));
+ vector<string> v;
+ for (unsigned int i = 0 ; i < vi.size() ; i++)
+ v.push_back(this->intToChar(vi[i]));
+ return v;
+}
+
+/******************************************************************************/
+
+int DNA::getGeneric(const std::vector<int>& states) const throw (BadIntException)
+{
+ int v = 0;
+ for (size_t i = 0 ; i < states.size() ; ++i) {
+ if (!isIntInAlphabet(states[i])) throw BadIntException(states[i], "DNA::getGeneric(const vector<int>& states): Specified base unknown.");
+ v |= getState(states[i]).getBinaryCode();
+ }
+ return getStateByBinCode(v).getNum();
+}
+
+/******************************************************************************/
+
+std::string DNA::getGeneric(const std::vector<std::string>& states) const throw (BadCharException)
+{
+ vector<int> vi;
+ for (unsigned int i = 0 ; i < states.size() ; ++i) {
+ if (!isCharInAlphabet(states[i])) throw BadCharException(states[i], "DNA::getGeneric(const vector<string>& states): Specified base unknown.");
+ vi.push_back(this->charToInt(states[i]));
+ }
+ return intToChar(getGeneric(vi));
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Alphabet/DNA.h b/src/Bpp/Seq/Alphabet/DNA.h
new file mode 100644
index 0000000..b11c9d9
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/DNA.h
@@ -0,0 +1,82 @@
+//
+// File: DNA.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: Tue Jul 22 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _DNA_H_
+#define _DNA_H_
+
+#include "NucleicAlphabet.h"
+
+//From the STL:
+#include <string>
+#include <vector>
+
+namespace bpp
+{
+
+/**
+ * @brief This alphabet is used to deal with DNA sequences.
+ *
+ * It supports all 4 nucleotides (A, T, G and C) with their standard denomination.
+ * Gaps are coded by '-', unresolved characters are coded by 'X, N, O, 0 or ?'.
+ * Extensive support for generic characters (e.g. 'P', 'Y', etc.) is provided.
+ */
+class DNA:
+ public NucleicAlphabet
+{
+ public:
+ /**
+ * @param exclamationMarkCountsAsGap If yes, '!' characters are replaced by gaps.
+ * Otherwise, they are counted as unknown characters.
+ */
+ DNA(bool exclamationMarkCountsAsGap = false);
+ virtual ~DNA() {}
+
+ public:
+ std::vector<int> getAlias(int state) const throw (BadIntException);
+ std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
+ int getGeneric(const std::vector<int>& states) const throw (BadIntException);
+ std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
+ std::string getAlphabetType() const { return "DNA alphabet"; }
+};
+
+} //end of namespace bpp.
+
+#endif // _DNA_H_
+
diff --git a/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp b/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp
new file mode 100644
index 0000000..3b48611
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp
@@ -0,0 +1,62 @@
+//
+// File: DefaultAlphabet.cpp
+// Authors: Julien Dutheil
+// Sylvain Gaillard
+// Created on: 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+
+#include "DefaultAlphabet.h"
+#include "AlphabetState.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+DefaultAlphabet::DefaultAlphabet():
+ chars_("ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890.?")
+{
+ // Alphabet size definition
+ resize(static_cast<unsigned int>(chars_.size()) + 1);
+
+ // Alphabet content definition
+ setState(0, AlphabetState(-1, "-", "Gap"));
+
+ for (size_t i = 0; i < chars_.size(); i++)
+ {
+ setState(i + 1, AlphabetState(static_cast<int>(i), TextTools::toString(chars_[i]), ""));
+ }
+}
+
diff --git a/src/Bpp/Seq/Alphabet/DefaultAlphabet.h b/src/Bpp/Seq/Alphabet/DefaultAlphabet.h
new file mode 100644
index 0000000..f88edf9
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/DefaultAlphabet.h
@@ -0,0 +1,83 @@
+//
+// File: DefaultAlphabet.h
+// Author: Julien Dutheil
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _DEFAULTALPHABET_H_
+#define _DEFAULTALPHABET_H_
+
+#include "LetterAlphabet.h"
+#include <Bpp/Text/TextTools.h>
+
+namespace bpp
+{
+
+/**
+ * @brief The DefaultAlphabet class.
+ *
+ * This alphabet should match virtually any type of sequences.
+ * This should be used by who does not care of the sequence type.
+ */
+class DefaultAlphabet:
+ public LetterAlphabet
+{
+ protected:
+ void registerState(const AlphabetState& st) {
+ AbstractAlphabet::registerState(* (st.clone()));
+ }
+ const std::string chars_;
+
+ public:
+ // class constructor
+ DefaultAlphabet();
+
+ // class destructor
+ virtual ~DefaultAlphabet() {}
+
+ public:
+ unsigned int getSize() const { return 26; }
+ unsigned int getNumberOfTypes() const { return 27; }
+ std::string getAlphabetType() const { return "Default alphabet"; }
+ int getUnknownCharacterCode() const { return 37; }
+ bool isUnresolved(int state) const { return state == 37; }
+ bool isUnresolved(const std::string& state) const { return false; }
+
+ };
+
+} //end of namespace bpp.
+
+#endif // _DEFAULTALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.cpp b/src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.cpp
new file mode 100644
index 0000000..bd5953b
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.cpp
@@ -0,0 +1,75 @@
+//
+// File: EchinodermMitochondrialCodonAlphabet.h
+// Authors: Eric Bazin
+// Sylvain Gaillard
+// Created on: 14 11:31:27 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "EchinodermMitochondrialCodonAlphabet.h"
+
+using namespace bpp;
+using namespace std;
+
+EchinodermMitochondrialCodonAlphabet::EchinodermMitochondrialCodonAlphabet(const NucleicAlphabet* alpha) :
+ CodonAlphabet(alpha)
+{
+ string A = alpha->intToChar(0);
+ string G = alpha->intToChar(2);
+ string T = alpha->intToChar(3);
+
+ vector<string> vstop;
+
+ vstop.push_back(T + A + A);
+ vstop.push_back(T + A + G);
+
+ int istop;
+ unsigned int j;
+ for (unsigned int i = 0 ; i < vstop.size() ; i++) {
+ istop = charToInt(vstop[i]);
+ stopCodons_.push_back(istop);
+
+ j = 0;
+ while (j < getNumberOfChars()) {
+ if (getStateAt(j).getNum() == istop) {
+ getStateAt(j).setName(STOP);
+ break;
+ }
+ j++;
+ }
+ }
+ initCodon_ = charToInt(A + T + G);
+}
+
diff --git a/src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.h b/src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.h
new file mode 100644
index 0000000..7bfc395
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.h
@@ -0,0 +1,72 @@
+//
+// File: EchinodermMitochondrialCodonAlphabet.h
+// Created by: Eric Bazin
+// Created on: 14 11:31:27 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ECHINODERMMITOCHONDRIALCODONALPHABET_H_
+#define _ECHINODERMMITOCHONDRIALCODONALPHABET_H_
+
+
+#include "CodonAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the Echinoderm and Faltworms
+ * Mitochondrial codon alphabet as describe on the NCBI website:
+ * http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG9
+ * @author Laurent Guéguen
+ */
+
+class EchinodermMitochondrialCodonAlphabet : public CodonAlphabet
+{
+public:
+ EchinodermMitochondrialCodonAlphabet(const NucleicAlphabet * alpha);
+ virtual ~EchinodermMitochondrialCodonAlphabet() {};
+
+public:
+ std::string getAlphabetType() const
+ {
+ return "Codon alphabet: EchinodermMitochondrialCodonAlphabet(" + vAbsAlph_[0]->getAlphabetType() + ")";
+ }
+
+};
+
+} //end of namespace bpp.
+
+#endif //_ECHINODERMMITOCHONDRIALCODONALPHABET_H_
diff --git a/src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.cpp b/src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.cpp
new file mode 100644
index 0000000..548c5e7
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.cpp
@@ -0,0 +1,74 @@
+//
+// File: InvertebrateMitochondrialCodonAlphabet.h
+// Authors: Eric Bazin
+// Sylvain Gaillard
+// Created on: thu mar 1 14:25:09 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "InvertebrateMitochondrialCodonAlphabet.h"
+
+using namespace bpp;
+using namespace std;
+
+InvertebrateMitochondrialCodonAlphabet::InvertebrateMitochondrialCodonAlphabet(const NucleicAlphabet* alpha) : CodonAlphabet(alpha)
+{
+ string A = alpha->intToChar(0);
+ string G = alpha->intToChar(2);
+ string T = alpha->intToChar(3);
+
+ vector<string> vstop;
+
+ vstop.push_back(T + A + A);
+ vstop.push_back(T + A + G);
+
+ int istop;
+ unsigned int j;
+ for (unsigned int i = 0 ; i < vstop.size() ; i++) {
+ istop = charToInt(vstop[i]);
+ stopCodons_.push_back(istop);
+
+ j = 0;
+ while (j < getNumberOfChars()) {
+ if (getStateAt(j).getNum() == istop) {
+ getStateAt(j).setName(STOP);
+ break;
+ }
+ j++;
+ }
+ }
+ initCodon_ = charToInt(A + T + G);
+}
+
diff --git a/src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.h b/src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.h
new file mode 100644
index 0000000..a24fda3
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.h
@@ -0,0 +1,75 @@
+//
+// File: InvertebrateMitochondrialCodonAlphabet.h
+// Created by: Eric Bazin
+// Created on: thu mar 1 14:25:09 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _INVERTEBRATEMITOCHONDRIALCODONALPHABET_H_
+#define _INVERTEBRATEMITOCHONDRIALCODONALPHABET_H_
+
+
+#include "CodonAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the Invertebrate
+ * @author Laurent Guéguen
+ *
+ * Mitochondrial codon alphabet as describe on the NCBI website:
+ * http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG5
+ */
+class InvertebrateMitochondrialCodonAlphabet:
+ public CodonAlphabet
+{
+public:
+ InvertebrateMitochondrialCodonAlphabet(const NucleicAlphabet * alpha);
+ virtual ~InvertebrateMitochondrialCodonAlphabet() {};
+
+public:
+
+ std::string getAlphabetType() const
+ {
+ return "Codon alphabet: InvertebrateMitochondrial(" + vAbsAlph_[0]->getAlphabetType() + ")";
+ }
+
+};
+
+} //end of namespace bpp.
+
+#endif //_INVERTEBRATEMITOCHONDRIALCODONALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/LetterAlphabet.h b/src/Bpp/Seq/Alphabet/LetterAlphabet.h
new file mode 100644
index 0000000..4bbd359
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/LetterAlphabet.h
@@ -0,0 +1,106 @@
+//
+// File: LetterAlphabet.h
+// Author: Sylvain Gaillard
+// Created: 11/09/2009 14:31:05
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (September 11, 2009)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _LETTERALPHABET_
+#define _LETTERALPHABET_
+
+// From the STL
+#include <string>
+#include <vector>
+#include <iostream>
+
+// From Seq
+#include "AbstractAlphabet.h"
+
+namespace bpp {
+ /**
+ * @brief Specialized partial implementation of Alphabet using single letters.
+ *
+ * @author Sylvain Gaillard
+ */
+ class LetterAlphabet:
+ public AbstractAlphabet
+ {
+ private:
+ static const int LETTER_UNDEF_VALUE = -99;
+ std::vector<int> letters_;
+ bool caseSensitive_;
+
+ public:
+ LetterAlphabet(bool caseSensitive = false): letters_(256, LETTER_UNDEF_VALUE), caseSensitive_(caseSensitive) {}
+ virtual ~LetterAlphabet() {}
+
+ public:
+ bool isCharInAlphabet(char state) const {
+ return letters_[static_cast<unsigned int>(state)] != LETTER_UNDEF_VALUE;
+ }
+ bool isCharInAlphabet(const std::string& state) const {
+ return isCharInAlphabet(state[0]);
+ }
+ int charToInt(const std::string &state) const throw (BadCharException) {
+ if (!isCharInAlphabet(state))
+ throw BadCharException(state, "LetterAlphabet::charToInt: Unknown state", this);
+ return letters_[static_cast<unsigned int>(state[0])];
+ }
+
+ protected:
+ void registerState(const AlphabetState& st) {
+ AbstractAlphabet::registerState(st);
+ if (caseSensitive_) {
+ letters_[static_cast<unsigned int>(st.getLetter()[0])] = st.getNum();
+ } else {
+ letters_[static_cast<unsigned int>(tolower(st.getLetter()[0]))] = st.getNum();
+ letters_[static_cast<unsigned int>(toupper(st.getLetter()[0]))] = st.getNum();
+ }
+ }
+
+ void setState(size_t pos, const AlphabetState& st) throw (IndexOutOfBoundsException) {
+ AbstractAlphabet::setState(pos, st);
+ if (caseSensitive_) {
+ letters_[static_cast<unsigned int>(st.getLetter()[0])] = st.getNum();
+ } else {
+ letters_[static_cast<unsigned int>(tolower(st.getLetter()[0]))] = st.getNum();
+ letters_[static_cast<unsigned int>(toupper(st.getLetter()[0]))] = st.getNum();
+ }
+ }
+
+ };
+}
+
+#endif // _LETTERALPHABET_
diff --git a/src/Bpp/Seq/Alphabet/NucleicAlphabet.h b/src/Bpp/Seq/Alphabet/NucleicAlphabet.h
new file mode 100644
index 0000000..8eca540
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/NucleicAlphabet.h
@@ -0,0 +1,259 @@
+//
+// File: NucleicAlphabet.h
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created on: Tue Jul 22 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _NUCLEICALPHABET_H_
+#define _NUCLEICALPHABET_H_
+
+#include "LetterAlphabet.h"
+#include "NucleicAlphabetState.h"
+
+#include <map>
+#include <iostream>
+
+namespace bpp
+{
+
+/**
+ * @brief The abstract base class for nucleic alphabets.
+ *
+ * This class only implements a few methods, it is mainly designed for methods/classes
+ * that will require to work with both RNA and DNA.
+ */
+class NucleicAlphabet :
+ public LetterAlphabet
+{
+ private:
+ std::map<int, unsigned int> binCodes_;
+ void updateMaps_(int pos, const NucleicAlphabetState& st) {
+ if (binCodes_.find(st.getBinaryCode()) == binCodes_.end())
+ binCodes_[st.getBinaryCode()] = pos;
+ }
+
+ public:
+ NucleicAlphabet(): binCodes_() {}
+
+ virtual ~NucleicAlphabet() {}
+
+ protected:
+ /**
+ * @name Overloaded methods from AbstractAlphabet
+ * @{
+ */
+ void registerState(const NucleicAlphabetState& st) {
+ LetterAlphabet::registerState(st);
+ updateMaps_(getNumberOfChars(), st);
+ }
+ void setState(unsigned int pos, const NucleicAlphabetState& st) {
+ LetterAlphabet::setState(pos, st);
+ updateMaps_(pos, st);
+ }
+ const NucleicAlphabetState& getStateAt(unsigned int pos) const
+ throw (IndexOutOfBoundsException) {
+ return dynamic_cast<const NucleicAlphabetState&>(
+ AbstractAlphabet::getStateAt(pos)
+ );
+ }
+ NucleicAlphabetState& getStateAt(unsigned int pos)
+ throw (IndexOutOfBoundsException) {
+ return dynamic_cast<NucleicAlphabetState&>(
+ AbstractAlphabet::getStateAt(pos)
+ );
+ }
+ /** @} */
+
+ public:
+ /**
+ * @name Overloaded methods from AbstractAlphabet
+ * @{
+ */
+ const NucleicAlphabetState& getState(const std::string& letter) const
+ throw (BadCharException) {
+ return dynamic_cast<const NucleicAlphabetState&>(
+ AbstractAlphabet::getState(letter)
+ );
+ }
+ const NucleicAlphabetState& getState(int num) const
+ throw (BadIntException) {
+ return dynamic_cast<const NucleicAlphabetState&>(
+ AbstractAlphabet::getState(num)
+ );
+ }
+ /** @} */
+
+ /**
+ * @name Specific methods
+ * @{
+ */
+
+ /**
+ * @brief Get a state by its binary representation.
+ *
+ * @param code The binary representation as an unsigned char.
+ * @return The NucleicAlphabetState.
+ * @throw BadIntException If the code is not a valide state.
+ * @author Sylvain Gaillard
+ */
+ const NucleicAlphabetState& getStateByBinCode(int code) const
+ throw (BadIntException) {
+ std::map<int, unsigned int>::const_iterator it = binCodes_.find(code);
+ if (it == binCodes_.end())
+ throw BadIntException(code, "NucleicAlphabet::getState(unsigned char): Binary code not in alphabet", this);
+ return getStateAt(it->second);
+ }
+
+ /**
+ * @brief Subtract states
+ *
+ * Get the remaining state when subtracting one state to another.
+ *
+ * @code
+ * int a = alpha->charToInt("A");
+ * int m = alpha->charToInt("M");
+ * int c = alpha->subtract(m, a);
+ *
+ * cout << alpha->intToChar(c) << endl;
+ *
+ * // should print C because M - A = C
+ * @endcode
+ *
+ * @param s1 the first state as an int
+ * @param s2 the second state as an int
+ * @throw BadIntException if one of the states is not valide.
+ * @return The remaining state as an int
+ * @author Sylvain Gaillard
+ */
+ int subtract(int s1, int s2) const throw (BadIntException) {
+ return getStateByBinCode(getState(s1).getBinaryCode() & ~ getState(s2).getBinaryCode()).getNum();
+ }
+
+ /**
+ * @brief Subtract states
+ *
+ * Get the remaining state when subtracting one state to another.
+ *
+ * @code
+ * string a = "A";
+ * string m = "M";
+ *
+ * cout << alpha->subtract(m, a) << endl;
+ *
+ * // should print C because M - A = C
+ * @endcode
+ *
+ * @param s1 the first state as a string
+ * @param s2 the second state as a string
+ * @throw BadCharException if one of the states is not valide.
+ * @return The remaining state as a string
+ * @author Sylvain Gaillard
+ */
+ std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
+ return intToChar(subtract(charToInt(s1), charToInt(s2)));
+ }
+
+ /**
+ * @brief Get the overlap between to states
+ *
+ * Get the overlapping states between two steps.
+ *
+ * @code
+ * int m = alpha->charToInt("M");
+ * int r = alpha->charToInt("R");
+ * int a = alpha->getOverlap(m, r);
+ *
+ * cout << alpha->intToChar(a) << endl;
+ *
+ * // should print A because M = A/C and R = A/G
+ * @endcode
+ *
+ * @param s1 the first state as an int
+ * @param s2 the second state as an int
+ * @throw BadIntException if one of the states is not valid
+ * @return The overlapping state
+ * @author Sylvain Gaillard
+ */
+ int getOverlap(int s1, int s2) const throw (BadIntException) {
+ return getStateByBinCode(getState(s1).getBinaryCode() & getState(s2).getBinaryCode()).getNum();
+ }
+
+ /**
+ * @brief Get the overlap between to states
+ *
+ * Get the overlapping states between two steps.
+ *
+ * @code
+ * string m = "M";
+ * string r = R;
+ *
+ * cout << alpha->getOverlap(m, r) << endl;
+ *
+ * // should print A because M = A/C and R = A/G
+ * @endcode
+ *
+ * @param s1 the first state as a string
+ * @param s2 the second state as a string
+ * @throw BadCharException if one of the states is not valid
+ * @return The overlapping state
+ * @author Sylvain Gaillard
+ */
+ std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
+ return intToChar(getOverlap(charToInt(s1), charToInt(s2)));
+ }
+
+ /** @} */
+
+ public:
+ // return 4 : A, C, G, T (or U)
+ unsigned int getSize() const { return 4; }
+
+ // return 15 : gap isn't included, generic unresolved bases (N, X, ?, O, 0) count for one
+ unsigned int getNumberOfTypes() const { return 15; }
+
+ int getUnknownCharacterCode() const { return 14; }
+
+ bool isUnresolved(int state) const { return state > 3; }
+ bool isUnresolved(const std::string& state) const { return charToInt(state) > 3; }
+
+};
+
+} //end of namespace bpp.
+
+#endif // _NUCLEICALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/NucleicAlphabetState.h b/src/Bpp/Seq/Alphabet/NucleicAlphabetState.h
new file mode 100644
index 0000000..c275d82
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/NucleicAlphabetState.h
@@ -0,0 +1,116 @@
+//
+// File: NucleicAlphabetState.h
+// Author: Sylvain Gaillard
+// Created: 31/07/2009
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (July 29, 2009)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _NUCLEICALPHABETSTATE_H_
+#define _NUCLEICALPHABETSTATE_H_
+
+// From the STL
+#include <string>
+#include <bitset>
+
+namespace bpp {
+ /**
+ * @brief This is the base class to describe states in a NucleicAlphabet.
+ *
+ * This class store a binary code for each state.
+ * This binary code is of length 4, one bit per nucleotid.
+ * For DNA alphabet, this code looks like this:
+ * <table>
+ * <tr><th>Letter</th><th>Binary code</th><th>int value</th></tr>
+ * <tr><td>-</td><td>0000</td><td>0</td></tr>
+ * <tr><td>A</td><td>0001</td><td>1</td></tr>
+ * <tr><td>C</td><td>0010</td><td>2</td></tr>
+ * <tr><td>G</td><td>0100</td><td>4</td></tr>
+ * <tr><td>T</td><td>1000</td><td>8</td></tr>
+ * <tr><td>N</td><td>1111</td><td>15</td></tr>
+ * <tr><td>...</td><td></td><td></td></tr>
+ * <tr><td>M</td><td>0011</td><td>3</td></tr>
+ * <tr><td>W</td><td>1001</td><td>9</td></tr>
+ * <tr><td>...</td><td></td><td></td></tr>
+ * <tr><td>V</td><td>0111</td><td>7</td></tr>
+ * </table>
+ * This notation allows the use of bitwize operations like:
+ * - build a generic state from to states
+ * @code
+ * A | G = R <=> 0001 | 0100 = 0101
+ * @endcode
+ * - extract a state from an unresolved one by subtraction of an other state
+ * @code
+ * S & ~ C = G <=> 0110 & ~ 0010 = 0100
+ * @endcode
+ *
+ * The binary code is stored as a char because it's the smallest memory word
+ * that can be allocated. A char is 8 bits long allowing the use of this
+ * class with Alphabet of at least 8 resolved states (enough for known
+ * nucleic alphabets!).
+ *
+ * @author Sylvain Gaillard
+ */
+ class NucleicAlphabetState: public AlphabetState {
+ private:
+ int binCode_;
+
+ public:
+ NucleicAlphabetState(int num, const std::string& letter, unsigned char code, const std::string& name):
+ AlphabetState(num, letter, name), binCode_(code) {}
+
+ // Class destructor
+ virtual ~NucleicAlphabetState() {}
+
+ public:
+ NucleicAlphabetState* clone() const {
+ return new NucleicAlphabetState(* this);
+ }
+ /**
+ * @brief Get the state's binary representation.
+ *
+ * @return The state's binary representation.
+ */
+ int getBinaryCode() const { return binCode_; }
+ /**
+ * @brief Set the state's binary representation.
+ *
+ * @param code The state's binary representation.
+ */
+ void setBinaryCode(int code) { binCode_ = code; }
+ };
+}
+
+#endif // _NUCLEICALPHABETSTATE_H_
+
diff --git a/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp b/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp
new file mode 100644
index 0000000..003299e
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp
@@ -0,0 +1,212 @@
+//
+// File: ProteicAlphabet.cpp
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created on: Tue Jul 22 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "ProteicAlphabet.h"
+#include "ProteicAlphabetState.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Utils/MapTools.h>
+
+using namespace bpp;
+using namespace std;
+
+// From STL:
+#include <map>
+
+/******************************************************************************/
+
+ProteicAlphabet::ProteicAlphabet()
+{
+ // Alphabet size definition
+ resize(28);
+
+ // Alphabet content definition
+ setState( 0, ProteicAlphabetState(-1, "-", "GAP", "Gap"));
+ setState( 1, ProteicAlphabetState( 0, "A", "ALA", "Alanine"));
+ setState( 2, ProteicAlphabetState( 1, "R", "ARG", "Arginine"));
+ setState( 3, ProteicAlphabetState( 2, "N", "ASN", "Asparagine"));
+ setState( 4, ProteicAlphabetState( 3, "D", "ASP", "Asparatic Acid"));
+ setState( 5, ProteicAlphabetState( 4, "C", "CYS", "Cysteine"));
+ setState( 6, ProteicAlphabetState( 5, "Q", "GLN", "Glutamine"));
+ setState( 7, ProteicAlphabetState( 6, "E", "GLU", "Glutamic acid"));
+ setState( 8, ProteicAlphabetState( 7, "G", "GLY", "Glycine"));
+ setState( 9, ProteicAlphabetState( 8, "H", "HIS", "Histidine"));
+ setState(10, ProteicAlphabetState( 9, "I", "ILE", "Isoleucine"));
+ setState(11, ProteicAlphabetState(10, "L", "LEU", "Leucine"));
+ setState(12, ProteicAlphabetState(11, "K", "LYS", "Lysine"));
+ setState(13, ProteicAlphabetState(12, "M", "MET", "Methionine"));
+ setState(14, ProteicAlphabetState(13, "F", "PHE", "Phenylalanine"));
+ setState(15, ProteicAlphabetState(14, "P", "PRO", "Proline"));
+ setState(16, ProteicAlphabetState(15, "S", "SER", "Serine"));
+ setState(17, ProteicAlphabetState(16, "T", "THR", "Threonine"));
+ setState(18, ProteicAlphabetState(17, "W", "TRP", "Tryptophan"));
+ setState(19, ProteicAlphabetState(18, "Y", "TYR", "Tyrosine"));
+ setState(20, ProteicAlphabetState(19, "V", "VAL", "Valine"));
+ setState(21, ProteicAlphabetState(20, "B", "B", "N or D"));
+ setState(22, ProteicAlphabetState(21, "Z", "Z", "Q or E"));
+ setState(23, ProteicAlphabetState(22, "X", "X", "Unresolved amino acid"));
+ setState(24, ProteicAlphabetState(22, "O", "O", "Unresolved amino acid"));
+ setState(25, ProteicAlphabetState(22, "0", "0", "Unresolved amino acid"));
+ setState(26, ProteicAlphabetState(22, "?", "?", "Unresolved amino acid"));
+ setState(27, ProteicAlphabetState(-2, "*", "STOP", "Stop"));
+}
+
+/******************************************************************************/
+
+string ProteicAlphabet::getAbbr(const string& aa) const throw (AlphabetException)
+{
+ string AA = TextTools::toUpper(aa);
+ return (getState(aa).getAbbreviation());
+}
+
+/******************************************************************************/
+
+string ProteicAlphabet::getAbbr(int aa) const throw (AlphabetException)
+{
+ return (getState(aa).getAbbreviation());
+}
+
+/******************************************************************************/
+
+vector<int> ProteicAlphabet::getAlias(int state) const throw (BadIntException)
+{
+ if(!isIntInAlphabet(state)) throw BadIntException(state, "ProteicAlphabet::getAlias(int): Specified base unknown.");
+ vector<int> v;
+ if(state == 20) {// N or D
+ v.resize(2); v[0] = 2; v[1] = 3;
+ } else if(state == 21) {// Q or E
+ v.resize(2); v[0] = 5; v[1] = 6;
+ } else if(state == 22) {// all!
+ v.resize(20);
+ for(unsigned int i = 0; i < 20; i++) v[i] = i;
+ } else {
+ v.resize(1); v[0] = state;
+ }
+ return v;
+}
+
+/******************************************************************************/
+
+vector<string> ProteicAlphabet::getAlias(const string & state) const throw (BadCharException)
+{
+ string locstate = TextTools::toUpper(state);
+ if(!isCharInAlphabet(locstate)) throw BadCharException(locstate, "ProteicAlphabet::getAlias(int): Specified base unknown.");
+ vector<string> v;
+ if(locstate == "B") {// N or D
+ v.resize(2); v[0] = "N"; v[1] = "D";
+ } else if(locstate == "Z") {// Q or E
+ v.resize(2); v[0] = "Q"; v[1] = "E";
+ } else if(locstate == "X"
+ || locstate == "O"
+ || locstate == "0"
+ || locstate == "?") {// all!
+ v.resize(20);
+ for(unsigned int i = 0; i < 20; i++) v[i] = getState(i).getLetter();
+ } else {
+ v.resize(1); v[0] = locstate;
+ }
+ return v;
+}
+
+/******************************************************************************/
+
+int ProteicAlphabet::getGeneric(const vector<int> & states) const throw (BadIntException) {
+ map<int, int> m;
+ for (unsigned int i = 0 ; i < states.size() ; ++i) {
+ vector<int> tmp_s = this->getAlias(states[i]); // get the states for generic characters
+ for (unsigned int j = 0 ; j < tmp_s.size() ; ++j) {
+ m[tmp_s[j]] ++; // add each state to the list
+ }
+ }
+ vector<int> ve = MapTools::getKeys(m);
+
+ string key;
+ for (unsigned int i = 0 ; i < ve.size() ; ++i) {
+ if (!isIntInAlphabet(ve[i])) throw BadIntException(ve[i], "ProteicAlphabet::getGeneric(const vector<int>): Specified base unknown.");
+ key += "_" + TextTools::toString(ve[i]);
+ }
+ map<string, int> g;
+ g["_2_3"] = 20;
+ g["_5_6"] = 21;
+ int v;
+ map<string, int>::iterator it = g.find(key);
+ if (ve.size() == 1) {
+ v = ve[0];
+ } else if (it != g.end()) {
+ v = it->second;
+ } else {
+ v = 22;
+ }
+ return v;
+}
+
+/******************************************************************************/
+
+string ProteicAlphabet::getGeneric(const vector<string> & states) const throw (BadCharException) {
+ map <string, int> m;
+ for (unsigned int i = 0 ; i < states.size() ; ++i) {
+ vector<string> tmp_s = this->getAlias(states[i]); // get the states for generic characters
+ for (unsigned int j = 0 ; j < tmp_s.size() ; ++j) {
+ m[tmp_s[j]] ++; // add each state to the list
+ }
+ }
+ vector<string> ve = MapTools::getKeys(m);
+
+ string key;
+ for (unsigned int i = 0 ; i < ve.size() ; ++i) {
+ if (!isCharInAlphabet(ve[i])) throw BadCharException(ve[i], "ProteicAlphabet::getAlias(const vector<string>): Specified base unknown.");
+ key += TextTools::toString(ve[i]);
+ }
+ map<string, string> g;
+ g["DN"] = "B";
+ g["EQ"] = "Z";
+ string v;
+ map<string, string>::iterator it = g.find(key);
+ if (ve.size() == 1) {
+ v = ve[0];
+ } else if (it != g.end()) {
+ v = it->second;
+ } else {
+ v = "?";
+ }
+ return v;
+}
+
+/******************************************************************************/
diff --git a/src/Bpp/Seq/Alphabet/ProteicAlphabet.h b/src/Bpp/Seq/Alphabet/ProteicAlphabet.h
new file mode 100644
index 0000000..48d2071
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/ProteicAlphabet.h
@@ -0,0 +1,137 @@
+//
+// File: ProteicAlphabet.h
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created on: Tue Jul 22 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+
+#ifndef _PROTEICALPHABET_H_
+#define _PROTEICALPHABET_H_
+
+#include "LetterAlphabet.h"
+#include "ProteicAlphabetState.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This alphabet is used to deal with proteins.
+ *
+ * It supports all 20 amino-acids with their standard denomination.
+ * Gaps are coded by '-', unresolved characters are coded by 'X'.
+ */
+
+class ProteicAlphabet:
+ public LetterAlphabet
+{
+ /**
+ * @name Overloaded methods from AbstractAlphabet
+ * @{
+ */
+ public:
+ const ProteicAlphabetState& getState(const std::string& letter) const
+ throw (BadCharException) {
+ return dynamic_cast<const ProteicAlphabetState&>(
+ AbstractAlphabet::getState(letter)
+ );
+ }
+ const ProteicAlphabetState& getState(int num) const
+ throw (BadIntException) {
+ return dynamic_cast<const ProteicAlphabetState&>(
+ AbstractAlphabet::getState(num)
+ );
+ }
+ protected:
+ const ProteicAlphabetState& getStateAt(unsigned int pos) const
+ throw (IndexOutOfBoundsException) {
+ return dynamic_cast<const ProteicAlphabetState&>(
+ AbstractAlphabet::getStateAt(pos)
+ );
+ }
+ ProteicAlphabetState& getStateAt(unsigned int pos)
+ throw (IndexOutOfBoundsException) {
+ return dynamic_cast<ProteicAlphabetState&>(
+ AbstractAlphabet::getStateAt(pos)
+ );
+ }
+ /** @} */
+ public:
+ ProteicAlphabet();
+ virtual ~ProteicAlphabet() {}
+
+ public:
+ unsigned int getSize() const { return 20; }
+ unsigned int getNumberOfTypes() const { return 23; }
+ int getUnknownCharacterCode() const { return 22; }
+ std::vector<int> getAlias(int state) const throw (BadIntException);
+ std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
+ int getGeneric(const std::vector<int>& states) const throw (BadIntException);
+ std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
+ bool isUnresolved(int state) const { return state > 19; }
+ bool isUnresolved(const std::string& state) const { return charToInt(state) > 19; }
+ std::string getAlphabetType() const { return "Proteic alphabet"; }
+
+ public:
+
+ /**
+ * @name Specific methods
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the abbreviation (3 letter code) for a state coded as char.
+ *
+ * @param aa Char description of the amino-acid to analyse.
+ */
+ std::string getAbbr(const std::string & aa) const throw (AlphabetException);
+
+ /**
+ * @brief Get the abbreviation (3 letter code) for a state coded as int.
+ *
+ * @param aa Int description of the amino-acid to analyse.
+ */
+ std::string getAbbr(int aa) const throw (AlphabetException);
+ /** @} */
+
+};
+
+} //end of namespace bpp.
+
+#endif // _PROTEICALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/ProteicAlphabetState.h b/src/Bpp/Seq/Alphabet/ProteicAlphabetState.h
new file mode 100644
index 0000000..9b6d735
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/ProteicAlphabetState.h
@@ -0,0 +1,82 @@
+//
+// File: ProteicAlphabetState.h
+// Author: Sylvain Gaillard
+// Created: 29/07/2009 13:56:01
+//
+
+/*
+Copyright or © or Copr. CNRS, (July 29, 2009)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _PROTEICALPHABETSTATE_H_
+#define _PROTEICALPHABETSTATE_H_
+
+// From the STL
+#include <string>
+
+namespace bpp {
+ /**
+ * @brief This is the base class to describe states in a ProteicAlphabet.
+ *
+ * @author Sylvain Gaillard
+ */
+ class ProteicAlphabetState: public AlphabetState {
+ private:
+ std::string abbr_;
+
+ public:
+ ProteicAlphabetState(int num, const std::string & letter, const std::string & abbr, const std::string & name): AlphabetState(num, letter, name), abbr_(abbr) {}
+
+ // Class destructor
+ virtual ~ProteicAlphabetState() {}
+
+ public:
+ ProteicAlphabetState * clone() const {
+ return new ProteicAlphabetState(* this);
+ }
+ /**
+ * @brief Get the state's abbreviation.
+ *
+ * @return The state's abbreviation.
+ */
+ const std::string & getAbbreviation() const { return abbr_; }
+ /**
+ * @brief Set the state's abbreviation.
+ *
+ * @param abbr The state's abbreviation.
+ */
+ void setAbbreviation(const std::string & abbr) { abbr_ = abbr; }
+ };
+}
+
+#endif // _PROTEICALPHABETSTATE_H_
+
diff --git a/src/Bpp/Seq/Alphabet/RNA.cpp b/src/Bpp/Seq/Alphabet/RNA.cpp
new file mode 100644
index 0000000..53f065e
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/RNA.cpp
@@ -0,0 +1,148 @@
+//
+// File: RNA.cpp
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created on: Tue Jul 22 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "RNA.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Utils/MapTools.h>
+
+using namespace bpp;
+
+// From STL:
+#include <map>
+
+using namespace std;
+
+/******************************************************************************/
+// class constructor
+RNA::RNA(bool exclamationMarkCountsAsGap)
+{
+ // Alphabet size definition
+ resize(21);
+
+ // Alphabet content definition
+ // all unresolved bases use n°14
+ setState( 0, NucleicAlphabetState(-1, "-", 0, "Gap"));
+ setState( 1, NucleicAlphabetState( 0, "A", 1, "Adenine"));
+ setState( 2, NucleicAlphabetState( 1, "C", 2, "Cytosine"));
+ setState( 3, NucleicAlphabetState( 2, "G", 4, "Guanine"));
+ setState( 4, NucleicAlphabetState( 3, "U", 8, "Uracile"));
+ setState( 5, NucleicAlphabetState( 4, "M", 3, "Adenine or Cytosine"));
+ setState( 6, NucleicAlphabetState( 5, "R", 5, "Purine (Adenine or Guanine)"));
+ setState( 7, NucleicAlphabetState( 6, "W", 9, "Adenine or Uracile"));
+ setState( 8, NucleicAlphabetState( 7, "S", 6, "Cytosine or Guanine"));
+ setState( 9, NucleicAlphabetState( 8, "Y", 10, "Pyrimidine (Cytosine or Uracile)"));
+ setState(10, NucleicAlphabetState( 9, "K", 12, "Guanine or Uracile"));
+ setState(11, NucleicAlphabetState(10, "V", 7, "Adenine or Cytosine or Guanine"));
+ setState(12, NucleicAlphabetState(11, "H", 11, "Adenine or Cytosine or Uracile"));
+ setState(13, NucleicAlphabetState(12, "D", 13, "Adenine or Guanine or Uracile"));
+ setState(14, NucleicAlphabetState(13, "B", 14, "Cytosine or Guanine or Uracile"));
+ setState(15, NucleicAlphabetState(14, "N", 15, "Unresolved base"));
+ setState(16, NucleicAlphabetState(14, "X", 15, "Unresolved base"));
+ setState(17, NucleicAlphabetState(14, "O", 15, "Unresolved base"));
+ setState(18, NucleicAlphabetState(14, "0", 15, "Unresolved base"));
+ setState(19, NucleicAlphabetState(14, "?", 15, "Unresolved base"));
+ if (exclamationMarkCountsAsGap)
+ setState(20, NucleicAlphabetState(-1, "!", 0, "Unresolved base"));
+ else
+ setState(20, NucleicAlphabetState(14, "!", 15, "Unresolved base"));
+}
+
+/******************************************************************************/
+
+std::vector<int> RNA::getAlias(int state) const throw (BadIntException)
+{
+ if (!isIntInAlphabet(state))
+ throw BadIntException(state, "DNA::getAlias(int): Specified base unknown.");
+ vector<int> v;
+ const NucleicAlphabetState& st = getState(state);
+ if (state == -1)
+ v.push_back(-1);
+ if (st.getBinaryCode() & 1)
+ v.push_back(0);
+ if (st.getBinaryCode() & 2)
+ v.push_back(1);
+ if (st.getBinaryCode() & 4)
+ v.push_back(2);
+ if (st.getBinaryCode() & 8)
+ v.push_back(3);
+ return v;
+}
+
+
+/******************************************************************************/
+
+std::vector<std::string> RNA::getAlias(const std::string & state) const throw (BadCharException)
+{
+ string locstate = TextTools::toUpper(state);
+ if(!isCharInAlphabet(locstate)) throw BadCharException(locstate, "RNA::getAlias(int): Specified base unknown.");
+ vector<int> vi = this->getAlias(this->charToInt(state));
+ vector<string> v;
+ for (unsigned int i = 0 ; i < vi.size() ; i++)
+ v.push_back(this->intToChar(vi[i]));
+ return v;
+}
+
+/******************************************************************************/
+
+int RNA::getGeneric(const std::vector<int> & states) const throw (BadIntException)
+{
+ int v = 0;
+ for (size_t i = 0 ; i < states.size() ; ++i) {
+ if (!isIntInAlphabet(states[i])) throw BadIntException(states[i], "RNA::getGeneric(const vector<int>& states): Specified base unknown.");
+ v |= getState(states[i]).getBinaryCode();
+ }
+ return getStateByBinCode(v).getNum();
+}
+
+/******************************************************************************/
+
+std::string RNA::getGeneric(const std::vector<std::string> & states) const throw (BadCharException)
+{
+ vector<int> vi;
+ for (unsigned int i = 0 ; i < states.size() ; ++i) {
+ if (!isCharInAlphabet(states[i])) throw BadCharException(states[i], "DNA::getGeneric(const vector<string>& states): Specified base unknown.");
+ vi.push_back(this->charToInt(states[i]));
+ }
+ return intToChar(getGeneric(vi));
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Alphabet/RNA.h b/src/Bpp/Seq/Alphabet/RNA.h
new file mode 100644
index 0000000..068bde5
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/RNA.h
@@ -0,0 +1,79 @@
+//
+// File: RNA.h
+// Created by: Guillaume Deuchst
+// Created on: Tue Jul 22 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _RNA_H_
+#define _RNA_H_
+
+#include "NucleicAlphabet.h"
+
+//From the STL:
+#include <string>
+
+namespace bpp
+{
+
+/**
+ * @brief This alphabet is used to deal with RNA sequences.
+ *
+ * It supports all 4 nucleotides (A, U, G and C) with their standard denomination.
+ * Gaps are coded by '-', unresolved characters are coded by 'X, N, O, 0 or ?'.
+ * Extensive support for generic characters (e.g. 'P', 'Y', etc.) is provided.
+ */
+class RNA:
+ public NucleicAlphabet
+{
+ public:
+ /**
+ * @param exclamationMarkCountsAsGap If yes, '!' characters are replaced by gaps.
+ * Otherwise, they are counted as unknown characters.
+ */
+ RNA(bool exclamationMarkCountsAsGap = false);
+ virtual ~RNA() {}
+
+ public:
+ std::vector<int> getAlias(int state) const throw (BadIntException);
+ std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
+ int getGeneric(const std::vector<int> & states) const throw (BadIntException);
+ std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
+ std::string getAlphabetType() const { return "RNA alphabet"; }
+};
+
+} //end of namespace bpp.
+
+#endif // _RNA_H_
diff --git a/src/Bpp/Seq/Alphabet/RNY.cpp b/src/Bpp/Seq/Alphabet/RNY.cpp
new file mode 100644
index 0000000..0df099d
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/RNY.cpp
@@ -0,0 +1,515 @@
+//
+// File: RNY.cpp
+// Created by: Laurent Gueguen
+// Created on: Tue Jul 31 2007
+//
+
+/*
+ Copyright or � or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide
+ classes for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided
+ only with a limited warranty and the software's author, the holder of
+ the economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards
+ their requirements in conditions enabling the security of their
+ systems and/or data to be ensured and, more generally, to use and
+ operate it in the same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "RNY.h" // class's header file
+
+// From Utils:
+#include <Bpp/Text/TextTools.h>
+
+#include <iostream>
+using namespace std;
+using namespace bpp;
+
+/****************************************************************************************/
+
+RNY::RNY(const NucleicAlphabet& na) : nuclalph_(na)
+{
+ // Alphabet size definition
+ resize(351);
+ int i,j,k,l;
+
+ for (i = 0; i < 351; i++)
+ {
+ setState(i,AlphabetState(i,"",""));
+ }
+
+ // Alphabet content definition
+
+ // / changer pour ARN
+
+ string s1 = "RCT-";
+ string s2 = "AGCT-";
+ string s3 = "AGY-";
+ string s = " ";
+
+
+ // NNN (0->35)
+
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 4; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ l = i * 12 + j * 3 + k;
+ s[0] = s1[i];
+ s[1] = s2[j];
+ s[2] = s3[k];
+ setState(l, AlphabetState(l,s,s));
+ }
+ }
+ }
+
+ // NN- (50->83)
+
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 4; j++)
+ {
+ l = 50 + 12 * i + j * 3;
+ s[0] = s1[i];
+ s[1] = s2[j];
+ s[2] = s3[3];
+ setState(l, AlphabetState(l,s,s));
+ }
+ }
+
+ // N-N (100->126)
+
+ for (i = 0; i < 3; i++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ l = 100 + 12 * i + k;
+ s[0] = s1[i];
+ s[1] = s2[4];
+ s[2] = s3[k];
+ setState(l, AlphabetState(l,s,s));
+ }
+ }
+
+ // N-- (150->152)
+
+ for (i = 0; i < 3; i++)
+ {
+ l = 150 + 12 * i;
+ s[0] = s1[i];
+ s[1] = s2[4];
+ s[2] = s3[3];
+ setState(l, AlphabetState(l,s,s));
+ }
+
+ // -NN (200->211)
+
+ for (j = 0; j < 4; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ l = 200 + j * 3 + k;
+ s[0] = s1[3];
+ s[1] = s2[j];
+ s[2] = s3[k];
+ setState(l, AlphabetState(l,s,s));
+ }
+ }
+
+
+ // -N- (250->253)
+
+ for (j = 0; j < 4; j++)
+ {
+ l = 250 + 3 * j;
+ s[0] = s1[3];
+ s[1] = s2[j];
+ s[2] = s3[3];
+ setState(l, AlphabetState(l,s,s));
+ }
+
+ // --N (300->302)
+
+ for (k = 0; k < 3; k++)
+ {
+ l = 300 + k;
+ s[0] = s1[3];
+ s[1] = s2[4];
+ s[2] = s3[k];
+ setState(l, AlphabetState(l,s,s));
+ }
+
+
+ // --- (350)
+
+ l = 350;
+ s[0] = s1[3];
+ s[1] = s2[4];
+ s[2] = s3[3];
+ setState(l, AlphabetState(l,s,s));
+}
+
+/****************************************************************************************/
+
+vector<int> RNY::getAlias(int state) const throw (BadIntException)
+{
+ if (!isIntInAlphabet(state)) throw BadIntException(state, "RNY::getAlias(int): Specified base unknown.");
+ vector<int> v;
+
+ int qs = state / 50;
+ int rs = state % 50;
+ int i,j,k;
+
+ switch (qs)
+ {
+ case 0: // NNN
+ v.resize(1);
+ v[0] = rs;
+ break;
+ case 1: // NN-
+ v.resize(3);
+ for (k = 0; k < 3; k++)
+ {
+ v[k] = k + rs;
+ }
+ break;
+ case 2: // N-N
+ v.resize(4);
+ for (j = 0; j < 4; j++)
+ {
+ v[j] = 3 * j + rs;
+ }
+ break;
+ case 3: // N--
+ v.resize(12);
+ for (j = 0; j < 4; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ v[3 * j + k] = rs + 3 * j + k;
+ }
+ }
+ break;
+ case 4: // -NN
+ v.resize(3);
+ for (i = 0; i < 3; i++)
+ {
+ v[i] = 12 * i + rs;
+ }
+ break;
+ case 5: // -N-
+ v.resize(9);
+ for (i = 0; i < 3; i++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ v[3 * i + k] = rs + 12 * i + k;
+ }
+ }
+ break;
+ case 6: // --N
+ v.resize(12);
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 4; j++)
+ {
+ v[4 * i + j] = rs + 12 * i + 3 * j;
+ }
+ }
+ break;
+ case 7: // ---
+ v.resize(36);
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 4; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ v[12 * i + 3 * j + k] = 12 * i + 3 * j + k;
+ }
+ }
+ }
+ break;
+ }
+ return v;
+}
+
+const NucleicAlphabet& RNY::getLetterAlphabet() const
+{
+ return nuclalph_;
+}
+
+/****************************************************************************************/
+
+vector<string> RNY::getAlias(const string& state) const throw (BadCharException)
+{
+ if (!isCharInAlphabet(state)) throw BadCharException(state, "RNY::getAlias(int): Specified base unknown.");
+
+ vector<int> v = getAlias(charToInt(state));
+ vector<string> s;
+ size_t size = v.size();
+ s.resize(size);
+
+ for (size_t i = 0; i < size; i++)
+ {
+ s[i] = AbstractAlphabet::intToChar(v[i]);
+ }
+ return s;
+}
+
+/****************************************************************************************/
+
+string RNY::getRNY(const string& pos1, const string& pos2, const string& pos3) const throw (BadCharException)
+{
+ string tr;
+
+ if (pos1 == "A" || pos1 == "G")
+ tr = "R";
+ else
+ tr = pos1;
+
+ tr += pos2;
+
+ if (pos3 == "T" || pos3 == "C")
+ tr += "Y";
+ else
+ tr += pos3;
+
+ // teste triplet;
+ charToInt(tr);
+ return tr;
+}
+
+/**************************************************************************************/
+int RNY::getRNY(int i, int j, int k, const Alphabet& alph) const throw (BadCharException)
+{
+ if (alph.getAlphabetType() != "DNA alphabet")
+ {
+ throw AlphabetException ("RNY::getRNY : Sequence must be DNA",
+ &alph);
+ }
+
+ char li = alph.intToChar(i)[0];
+ char lj = alph.intToChar(j)[0];
+ char lk = alph.intToChar(k)[0];
+
+ int r = 0;
+ int s = 0;
+
+ switch (li)
+ {
+ case 'A':
+ case 'G':
+ r += 0;
+ break;
+ case 'C':
+ r += 1;
+ break;
+ case 'T':
+ r += 2;
+ break;
+ case '-':
+ case 'N':
+ s += 1;
+ break;
+ default:
+ throw BadCharException(&li, "RNY::getRNY(int,int;int,alph): Specified base unknown.");
+ }
+
+ r *= 4;
+ s *= 2;
+
+ switch (lj)
+ {
+ case 'A':
+ r += 0;
+ break;
+ case 'G':
+ r += 1;
+ break;
+ case 'C':
+ r += 2;
+ break;
+ case 'T':
+ r += 3;
+ break;
+ case '-':
+ case 'N':
+ s += 1;
+ break;
+ default:
+ throw BadCharException(&lj, "RNY::getRNY(int,int;int,alph): Specified base unknown.");
+ }
+
+ r *= 3;
+ s *= 2;
+
+ switch (lk)
+ {
+ case 'A':
+ r += 0;
+ break;
+ case 'G':
+ r += 1;
+ break;
+ case 'C':
+ case 'T':
+ r += 2;
+ break;
+ case '-':
+ case 'N':
+ s += 1;
+ break;
+ default:
+ throw BadCharException(&lk, "RNY::getRNY(int,int;int,alph): Specified base unknown.");
+ }
+
+ return 50 * s + r;
+}
+
+/****************************************************************************************/
+bool RNY::isGap(int state) const
+{
+ return state==350;
+}
+
+bool RNY::containsGap(const string& state) const throw (BadCharException)
+{
+ return (state.find("-")!=string::npos);
+}
+
+bool RNY::isUnresolved(const string& state) const
+{
+ return containsGap(state);
+}
+
+bool RNY::isUnresolved(int state) const
+{
+ return (state>=50 && state!=350);
+}
+
+/****************************************************************************************/
+
+int RNY::charToInt(const string& state) const throw (BadCharException)
+{
+ if (state.size() != 3) throw BadCharException(state, "RNY::charToInt", this);
+ else
+ return AbstractAlphabet::charToInt(state);
+}
+
+
+/************************************************************/
+
+string RNY::intToChar(int state) const throw (BadIntException)
+{
+ unsigned int i,j,k,l;
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 4; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ l = i * 12 + j * 3 + k;
+ if (getState(l).getNum() == state)
+ return getState(l).getLetter();
+ }
+ }
+ }
+
+ // NN- (50->83)
+
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 4; j++)
+ {
+ l = 50 + 12 * i + j * 3;
+ if (getState(l).getNum() == state)
+ return getState(l).getLetter();
+ }
+ }
+
+ // N-N (100->126)
+
+ for (i = 0; i < 3; i++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ l = 100 + 12 * i + k;
+ if (getState(l).getNum() == state)
+ return getState(l).getLetter();
+ }
+ }
+
+ // N-- (150->152)
+
+ for (i = 0; i < 3; i++)
+ {
+ l = 150 + 12 * i;
+ if (getState(l).getNum() == state)
+ return getState(l).getLetter();
+ }
+
+ // -NN (200->211)
+
+ for (j = 0; j < 4; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ l = 200 + j * 3 + k;
+ if (getState(l).getNum() == state)
+ return getState(l).getLetter();
+ }
+ }
+
+
+ // -N- (250->253)
+
+ for (j = 0; j < 4; j++)
+ {
+ l = 250 + 3 * j;
+ if (getState(l).getNum() == state)
+ return getState(l).getLetter();
+ }
+
+ // --N (300->302)
+
+ for (k = 0; k < 3; k++)
+ {
+ l = 300 + k;
+ if (getState(l).getNum() == state)
+ return getState(l).getLetter();
+ }
+
+
+ // --- (350)
+
+ l = 350;
+ if (getState(l).getNum() == state)
+ return getState(l).getLetter();
+
+ throw BadIntException(state, "RNY::intToChar: Specified base unknown", this);
+ return "XXX";
+}
diff --git a/src/Bpp/Seq/Alphabet/RNY.h b/src/Bpp/Seq/Alphabet/RNY.h
new file mode 100644
index 0000000..8fd713c
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/RNY.h
@@ -0,0 +1,111 @@
+//
+// File: RNY.h
+// Created by: Laurent Gueguen
+// Created on: Tue Jul 31 2007
+//
+
+/*
+ Copyright or � or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided
+ only with a limited warranty and the software's author, the holder of
+ the economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards
+ their requirements in conditions enabling the security of their
+ systems and/or data to be ensured and, more generally, to use and
+ operate it in the same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+
+#ifndef _RNY_H_
+#define _RNY_H_
+
+#include "AbstractAlphabet.h"
+#include "NucleicAlphabet.h"
+
+#include <string>
+
+/**
+ * @brief This alphabet is used to deal quotiented triplet RNY +
+ * combinations with "-".
+ *
+ * More explicitly, a quotiented triplet RNY is defined on the alphabet
+ *
+ * @f\{C,T,R\} x \{A,C,G,T\} x \{ A,G,Y\}@f.
+ *
+ * Triplet "---" is the only triplet defined as gap. Other triplets
+ * with "-" are defined as unresolved.
+ *
+ * @author Laurent Gu�guen
+ */
+
+namespace bpp
+{
+class RNY : public AbstractAlphabet
+{
+private:
+ const NucleicAlphabet& nuclalph_;
+
+public:
+ RNY(const NucleicAlphabet&);
+ ~RNY() {}
+
+public:
+ int charToInt(const std::string& state) const throw (BadCharException);
+ std::string intToChar(int state) const throw (BadIntException);
+
+ bool containsGap(const std::string& state) const throw (BadCharException);
+
+ unsigned int getSize() const { return 36; }
+ unsigned int getNumberOfTypes() const { return 80; }
+ int getUnknownCharacterCode() const { return 350; }
+ bool isGap(int state) const;
+ std::vector<int > getAlias( int state) const throw (BadIntException);
+ std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
+ bool isUnresolved(int state) const;
+ bool isUnresolved(const std::string& state) const;
+
+ std::string getAlphabetType() const { return "RNY alphabet"; }
+
+ const NucleicAlphabet& getLetterAlphabet() const;
+
+public:
+ /**
+ * @brief Get the char code for a triplet given the char code of the three underlying positions.
+ *
+ * The char code of each position must match the nucleic alphabet specified for this alphabet.
+ * NB: This performs pos1 + pos2 + pos3 after checking for each position validity.
+ * @param pos1 Char description for position 1.
+ * @param pos2 Char description for position 2.
+ * @param pos3 Char description for position 3.
+ * @return The Char code of the triplet.
+ */
+ std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
+
+ int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
+};
+}
+
+#endif // _RNY_H_
+
diff --git a/src/Bpp/Seq/Alphabet/StandardCodonAlphabet.cpp b/src/Bpp/Seq/Alphabet/StandardCodonAlphabet.cpp
new file mode 100644
index 0000000..42f6617
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/StandardCodonAlphabet.cpp
@@ -0,0 +1,75 @@
+//
+// File: StandardCodonAlphabet.h
+// Authors: Julien Dutheil
+// Sylvain Gaillard
+// Created on: Sun Oct 12 17:51:36 2003
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "StandardCodonAlphabet.h"
+
+using namespace bpp;
+using namespace std;
+
+StandardCodonAlphabet::StandardCodonAlphabet(const NucleicAlphabet* alpha) :
+ CodonAlphabet(alpha)
+{
+ string A = alpha->intToChar(0);
+ string G = alpha->intToChar(2);
+ string T = alpha->intToChar(3);
+
+ vector<string> vstop;
+
+ vstop.push_back(T + A + A);
+ vstop.push_back(T + A + G);
+ vstop.push_back(T + G + A);
+
+ int istop;
+ unsigned int j;
+ for (unsigned int i = 0 ; i < vstop.size() ; i++) {
+ istop = charToInt(vstop[i]);
+ stopCodons_.push_back(istop);
+ j = 0;
+ while (j < getNumberOfChars()) {
+ if (getStateAt(j).getNum() == istop) {
+ getStateAt(j).setName(STOP);
+ break;
+ }
+ j++;
+ }
+ }
+ initCodon_ = charToInt(A + T + G);
+}
+
diff --git a/src/Bpp/Seq/Alphabet/StandardCodonAlphabet.h b/src/Bpp/Seq/Alphabet/StandardCodonAlphabet.h
new file mode 100644
index 0000000..7a011d2
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/StandardCodonAlphabet.h
@@ -0,0 +1,71 @@
+//
+// File: StandardCodonAlphabet.h
+// Created by: Julien Dutheil
+// Created on: Sun Oct 12 17:51:36 2003
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _STANDARDCODONALPHABET_H_
+#define _STANDARDCODONALPHABET_H_
+
+#include "CodonAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the standard codon alphabet as describe on the NCBI
+ * web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
+ */
+class StandardCodonAlphabet : public CodonAlphabet
+{
+public:
+ StandardCodonAlphabet(const NucleicAlphabet * alpha);
+
+ virtual ~StandardCodonAlphabet() {}
+
+public:
+
+ std::string getAlphabetType() const
+ {
+ return "Codon alphabet: Standard("+ vAbsAlph_[0]->getAlphabetType() + ")";
+ }
+
+};
+
+} //end of namespace bpp.
+
+#endif //_STANDARDCODONALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.cpp b/src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.cpp
new file mode 100644
index 0000000..a261c92
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.cpp
@@ -0,0 +1,76 @@
+//
+// File: VertebrateMitochondrialCodonAlphabet.h
+// Authors: Eric Bazin
+// Sylvain Gaillard
+// Created on: thu mar 1 14:25:09 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "VertebrateMitochondrialCodonAlphabet.h"
+
+using namespace bpp;
+using namespace std;
+
+VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(const NucleicAlphabet* alpha) : CodonAlphabet(alpha)
+{
+ string A = alpha->intToChar(0);
+ string G = alpha->intToChar(2);
+ string T = alpha->intToChar(3);
+
+ vector<string> vstop;
+
+ vstop.push_back(T + A + A);
+ vstop.push_back(T + A + G);
+ vstop.push_back(A + G + G);
+ vstop.push_back(A + G + A);
+
+ int istop;
+ unsigned int j;
+ for (unsigned int i = 0 ; i < vstop.size() ; i++) {
+ istop = charToInt(vstop[i]);
+ stopCodons_.push_back(istop);
+
+ j = 0;
+ while (j < getNumberOfChars()) {
+ if (getStateAt(j).getNum() == istop) {
+ getStateAt(j).setName(STOP);
+ break;
+ }
+ j++;
+ }
+ }
+ initCodon_ = charToInt(A + T + G);
+}
+
diff --git a/src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.h b/src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.h
new file mode 100644
index 0000000..e241c5d
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.h
@@ -0,0 +1,71 @@
+//
+// File: VertebrateMitochondrialCodonAlphabet.h
+// Created by: Eric Bazin
+// Created on: wen mar 2 16:01:59 CET 2005
+///
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _VERTEBRATEMITOCHONDRIALCODONALPHABET_H_
+#define _VERTEBRATEMITOCHONDRIALCODONALPHABET_H_
+
+#include "CodonAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the vertebrate mitochondrial codon alphabet as describe on the NCBI
+ * web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2
+ * @author Laurent Guéguen
+ */
+
+class VertebrateMitochondrialCodonAlphabet : public CodonAlphabet
+{
+public:
+ VertebrateMitochondrialCodonAlphabet(const NucleicAlphabet * alpha);
+ virtual ~VertebrateMitochondrialCodonAlphabet() {};
+
+public:
+
+ std::string getAlphabetType() const
+ {
+ return "Codon alphabet: VertebrateMitochondrial(" + vAbsAlph_[0]->getAlphabetType() + ")";
+ }
+};
+
+} //end of namespace bpp.
+
+#endif //_VERTEBRATEMITOCHONDRIALCODONALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/WordAlphabet.cpp b/src/Bpp/Seq/Alphabet/WordAlphabet.cpp
new file mode 100644
index 0000000..cb78f32
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/WordAlphabet.cpp
@@ -0,0 +1,345 @@
+//
+// File: WordAlphabet.h
+// Authors: Laurent Gueguen
+// Sylvain Gaillard
+// Created on: Sun Dec 28 2008
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "WordAlphabet.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+
+using namespace std;
+
+WordAlphabet::WordAlphabet(const vector<const Alphabet*>& vAlpha) :
+ AbstractAlphabet(),
+ vAbsAlph_(vAlpha)
+{
+ build_();
+}
+
+WordAlphabet::WordAlphabet(const Alphabet* pAlpha, unsigned int num) :
+ AbstractAlphabet(),
+ vAbsAlph_(0)
+{
+ for (unsigned int i = 0; i < num; i++)
+ {
+ vAbsAlph_.push_back(pAlpha);
+ }
+
+ build_();
+}
+
+void WordAlphabet::build_()
+{
+ unsigned int size = 1;
+
+ for (unsigned int i = 0; i < vAbsAlph_.size(); i++)
+ {
+ size *= vAbsAlph_[i]->getSize();
+ }
+
+ resize(size + 2);
+
+ string s = "";
+ for (unsigned int i = 0; i < vAbsAlph_.size(); i++)
+ {
+ s += "-";
+ }
+
+ setState(0, AlphabetState(-1, s, "gap"));
+
+ for (unsigned int i = 0; i < size; i++)
+ {
+ setState(i + 1, AlphabetState(i, "", ""));
+ }
+
+ unsigned lr = size;
+ char c;
+ for (unsigned int na = 0; na < vAbsAlph_.size(); na++)
+ {
+ lr /= vAbsAlph_[na]->getSize();
+ unsigned int j = 1;
+ unsigned int i = 0;
+ while (j <= size)
+ {
+ c = vAbsAlph_[na]->intToChar(i)[0];
+
+ for (unsigned int k = 0; k < lr; k++)
+ {
+ getStateAt(j).setLetter(getStateAt(j).getLetter() + c);
+ j++;
+ // alphabet[j++].letter += c;
+ }
+
+ if (++i == vAbsAlph_[na]->getSize())
+ i = 0;
+ }
+ }
+
+ s = "";
+ for (unsigned i = 0; i < vAbsAlph_.size(); i++)
+ {
+ s += "N";
+ }
+
+ setState(size + 1, AlphabetState(size, s, "Unresolved"));
+ remap();
+}
+
+/******************************************************************************/
+
+std::string WordAlphabet::getAlphabetType() const
+{
+ string s = "Word alphabet:";
+ for (unsigned int i = 0; i < vAbsAlph_.size(); i++)
+ {
+ s += " " + vAbsAlph_[i]->getAlphabetType();
+ }
+
+ return s;
+}
+
+bool WordAlphabet::hasUniqueAlphabet() const
+{
+ string s = vAbsAlph_[0]->getAlphabetType();
+ for (unsigned int i = 1; i < vAbsAlph_.size(); i++)
+ {
+ if (vAbsAlph_[i]->getAlphabetType() != s)
+ return false;
+ }
+ return true;
+}
+
+bool WordAlphabet::containsUnresolved(const std::string& state) const throw (BadCharException)
+{
+ size_t s = vAbsAlph_.size();
+ if (state.length() != s)
+ throw BadCharException(state, "WordAlphabet::containsUnresolved", this);
+
+ for (size_t i = 0; i < vAbsAlph_.size(); i++)
+ {
+ if (vAbsAlph_[i]->isUnresolved(state.substr(i, 1)))
+ {
+ return true;
+ }
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+bool WordAlphabet::containsGap(const std::string& state) const throw (BadCharException)
+{
+ size_t s = vAbsAlph_.size();
+ if (state.length() != s)
+ throw BadCharException(state, "WordAlphabet::containsGap", this);
+
+ for (size_t i = 0; i < vAbsAlph_.size(); i++)
+ {
+ if (vAbsAlph_[i]->isGap(state.substr(i, 1)))
+ return true;
+ }
+
+ return false;
+}
+
+/******************************************************************************/
+
+std::string WordAlphabet::getName(const std::string& state) const throw (BadCharException)
+{
+ if (state.size() != vAbsAlph_.size())
+ throw BadCharException(state, "WordAlphabet::getName", this);
+ if (containsUnresolved(state))
+ return getStateAt(getSize() + 1).getName();
+ if (containsGap(state))
+ return getStateAt(0).getName();
+ else
+ return AbstractAlphabet::getName(state);
+}
+
+/******************************************************************************/
+
+std::vector<int> WordAlphabet::getAlias(int state) const throw (BadIntException)
+{
+ if (!isIntInAlphabet(state))
+ throw BadIntException(state, "WordAlphabet::getAlias(int): Specified base unknown.");
+ vector<int> v;
+ int i, s = getSize();
+
+ if (state == s)
+ {
+ v.resize(s);
+ for (i = 0; i < s; i++)
+ {
+ v[i] = i;
+ }
+ }
+ else
+ {
+ v.resize(1); v[0] = state;
+ }
+ return v;
+}
+
+/******************************************************************************/
+
+std::vector<std::string> WordAlphabet::getAlias(const std::string& state) const throw (BadCharException)
+{
+ string locstate = TextTools::toUpper(state);
+ if (!isCharInAlphabet(locstate))
+ throw BadCharException(locstate, "WordAlphabet::getAlias(string): Specified base unknown.");
+ vector<string> v;
+
+ unsigned int i, s = getSize();
+
+ string st = "";
+ for (i = 0; i < vAbsAlph_.size(); i++)
+ {
+ st += "N";
+ }
+
+ if (locstate == st)
+ {
+ v.resize(s);
+ for (i = 0; i < s; i++)
+ {
+ v[i] = intToChar(i);
+ }
+ }
+ else
+ {
+ v.resize(1); v[0] = state;
+ }
+ return v;
+}
+
+/******************************************************************************/
+
+int WordAlphabet::getGeneric(const std::vector<int>& states) const throw (BadIntException)
+{
+ return states[0];
+}
+
+/******************************************************************************/
+
+std::string WordAlphabet::getGeneric(const std::vector<std::string>& states) const throw (BadCharException)
+{
+ return states[0];
+}
+
+/******************************************************************************/
+
+int WordAlphabet::getWord(const std::vector<int>& vint, size_t pos) const throw (IndexOutOfBoundsException)
+{
+ if (vint.size() < pos + vAbsAlph_.size())
+ throw IndexOutOfBoundsException("WordAlphabet::getWord", pos, 0, vint.size() - vAbsAlph_.size());
+
+ vector<string> vs;
+ for (size_t i = 0; i < vAbsAlph_.size(); i++)
+ {
+ vs.push_back(vAbsAlph_[i]->intToChar(vint[i + pos]));
+ }
+
+ return charToInt(getWord(vs)); // This can't throw a BadCharException!
+}
+
+/****************************************************************************************/
+
+std::string WordAlphabet::getWord(const std::vector<string>& vpos, size_t pos) const throw (IndexOutOfBoundsException, BadCharException)
+{
+ if (vpos.size() < pos + vAbsAlph_.size())
+ throw IndexOutOfBoundsException("WordAlphabet::getWord", pos, 0, vpos.size() - vAbsAlph_.size());
+
+ string s = "";
+ for (size_t i = 0; i < vAbsAlph_.size(); i++)
+ {
+ s += vpos[pos + i];
+ }
+ // test
+ charToInt(s);
+ return s;
+}
+
+/****************************************************************************************/
+
+Sequence* WordAlphabet::translate(const Sequence& sequence, size_t pos) const throw (AlphabetMismatchException, Exception)
+{
+ if ((!hasUniqueAlphabet()) or
+ (sequence.getAlphabet()->getAlphabetType() != vAbsAlph_[0]->getAlphabetType()))
+ throw AlphabetMismatchException("No matching alphabets", sequence.getAlphabet(), vAbsAlph_[0]);
+
+ vector<int> v1 = sequence.getContent();
+ vector<int> v2;
+
+ size_t s = sequence.size();
+ unsigned int l = getLength();
+ size_t i = pos;
+
+ while (i + l < s)
+ {
+ v2.push_back(getWord(v1, i));
+ i += l;
+ }
+
+ return new BasicSequence(sequence.getName(), v2, this);
+}
+
+/****************************************************************************************/
+
+Sequence* WordAlphabet::reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
+{
+ if ((!hasUniqueAlphabet()) or
+ (sequence.getAlphabet()->getAlphabetType() != getAlphabetType()))
+ throw AlphabetMismatchException("No matching alphabets");
+
+ Sequence* pseq = new BasicSequence(sequence.getName(), "", getNAlphabet(0));
+
+ size_t s = sequence.size();
+ for (size_t i = 0; i < s; i++)
+ {
+ pseq->append(getPositions(sequence[i]));
+ }
+
+ return pseq;
+}
+
+/****************************************************************************************/
+
diff --git a/src/Bpp/Seq/Alphabet/WordAlphabet.h b/src/Bpp/Seq/Alphabet/WordAlphabet.h
new file mode 100644
index 0000000..5bec05c
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/WordAlphabet.h
@@ -0,0 +1,330 @@
+//
+// File: WordAlphabet.h
+// Created by: Laurent Gueguen
+// Created on: Sun Dec 28 2008
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided
+ only with a limited warranty and the software's author, the holder of
+ the economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards
+ their requirements in conditions enabling the security of their
+ systems and/or data to be ensured and, more generally, to use and
+ operate it in the same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _WORDALPHABET_H_
+#define _WORDALPHABET_H_
+
+#include "AbstractAlphabet.h"
+
+// From the STL:
+#include <string>
+#include <vector>
+
+#include "../Sequence.h"
+
+namespace bpp
+{
+/**
+ * @brief The base class for word alphabets.
+ *
+ * These alphabets are compounds of several alphabets. The only
+ * constraint on these alphabets is that their words have length one
+ * (so it is not possible to make WordAlphabets from other
+ * WordAlphabets). The construction is made from a vector of pointers
+ * to AbstractAlphabets.
+ *
+ * The strings of the WordAlphabet are concatenations of the strings
+ * of the Alphabets. They are made from the resolved letters of the
+ * Alphabets.
+ */
+class WordAlphabet :
+ public AbstractAlphabet
+{
+protected:
+ std::vector<const Alphabet* > vAbsAlph_;
+
+public:
+ // Constructor and destructor.
+ /**
+ * @brief Builds a new word alphabet from a vector of Alphabets.
+ *
+ * The unit alphabets are not owned by the world alphabet, and won't
+ * be destroyed when this instance is destroyed.
+ *
+ * @param vAlpha The vector of Alphabets to be used.
+ */
+ WordAlphabet(const std::vector<const Alphabet*>& vAlpha);
+
+ /**
+ * @brief Builds a new word alphabet from a pointer to number of
+ * Alphabets.
+ *
+ * @param pAlpha The Pointer to the Alphabet to be used.
+ * @param num the length of the words.
+ */
+ WordAlphabet(const Alphabet* pAlpha, unsigned int num);
+
+ virtual ~WordAlphabet() {}
+
+public:
+ /**
+ * @name Methods redefined from Alphabet
+ *
+ * @{
+ */
+ /**
+ * @brief Get the complete name of a state given its string description.
+ *
+ * In case of undefined characters (i.e. N and X for nucleic alphabets),
+ * this method will return the name of the undefined word.
+ *
+ * @param state The string description of the given state.
+ * @return The name of the state.
+ * @throw BadCharException When state is not a valid char description.
+ */
+ std::string getName(const std::string& state) const throw (BadCharException);
+
+ int charToInt(const std::string& state) const throw (BadCharException)
+ {
+ if (state.size() != vAbsAlph_.size())
+ throw BadCharException(state, "WordAlphabet::charToInt", this);
+ if (containsUnresolved(state))
+ return getSize();
+ if (containsGap(state))
+ return -1;
+ else return AbstractAlphabet::charToInt(state);
+ }
+
+ unsigned int getSize() const
+ {
+ return getNumberOfChars() - 2;
+ }
+
+ /** @} */
+
+ /**
+ * @brief Returns True if the Alphabet of the letters in the word
+ * are the same type.
+ *
+ */
+ bool hasUniqueAlphabet() const;
+
+ /**
+ * @brief Returns the length of the word
+ *
+ */
+ unsigned int getLength() const
+ {
+ return static_cast<unsigned int>(vAbsAlph_.size());
+ }
+
+
+ /**
+ * @brief Returns the number of resolved states + one for unresolved
+ *
+ */
+ unsigned int getNumberOfTypes() const
+ {
+ return getNumberOfChars() - 1;
+ }
+
+ std::string getAlphabetType() const;
+ int getUnknownCharacterCode() const
+ {
+ return getSize();
+ }
+
+ bool isUnresolved(int state) const { return state == getUnknownCharacterCode(); }
+ bool isUnresolved(const std::string& state) const { return charToInt(state) == getUnknownCharacterCode(); }
+
+ std::vector<int> getAlias(int state) const throw (BadIntException);
+ std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
+ int getGeneric(const std::vector<int>& states) const throw (BadIntException);
+ std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
+
+private:
+ /**
+ * @name Inner utilitary functions
+ *
+ * @{
+ */
+ bool containsUnresolved(const std::string& state) const throw (BadCharException);
+ bool containsGap(const std::string& state) const throw (BadCharException);
+ void build_();
+ /** @} */
+
+public:
+ /**
+ * @name Word specific methods
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the pointer to the Alphabet of the n-position.
+ *
+ * @param n The position in the word (starting at 0).
+ * @return The pointer to the Alphabet of the n-position.
+ */
+ const Alphabet* getNAlphabet(size_t n) const
+ {
+ if (n >= vAbsAlph_.size())
+ throw IndexOutOfBoundsException("WordAlphabet::getNPosition", n, 0, vAbsAlph_.size());
+
+ return vAbsAlph_[n];
+ }
+
+ /**
+ * @brief Get the int code for a word given the int code of the underlying positions.
+ *
+ * The int code of each position must match the corresponding alphabet specified at this position.
+ * @param vint description for all the positions.
+ * @param pos the start position to match in the vector.
+ * @return The int code of the word.
+ * @throw IndexOutOfBoundsException In case of wrong position.
+ */
+ virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
+
+ /**
+ * @brief Get the char code for a word given the char code of the
+ * underlying positions.
+ *
+ * The char code of each position must match the corresponding alphabet specified at this position.
+ * @param vpos vector description for all the positions.
+ * @param pos the start position to match in the vector.
+ * @return The string of the word.
+ * @throw IndexOutOfBoundsException In case of wrong position.
+ */
+ virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
+
+ /**
+ * @brief Get the int code of the n-position of a word given its int description.
+ *
+ * @param word The int description of the word.
+ * @param n The position in the word (starting at 0).
+ * @return The int description of the n-position of the word.
+ */
+ int getNPosition(int word, size_t n) const throw (BadIntException)
+ {
+ if (n >= vAbsAlph_.size())
+ throw IndexOutOfBoundsException("WordAlphabet::getNPosition", n, 0, vAbsAlph_.size());
+
+ std::string s = intToChar(word);
+ return vAbsAlph_[n]->charToInt(s.substr(n, 1));
+ }
+
+ /**
+ * @brief Get the int codes of each position of a word given its int description.
+ *
+ * @param word The int description of the word.
+ * @return The int description of the positions of the codon.
+ */
+
+ std::vector<int> getPositions(int word) const throw (BadIntException)
+ {
+ std::string s = intToChar(word);
+ std::vector<int> positions;
+ for (size_t i = 0; i < s.size(); i++)
+ {
+ positions.push_back(vAbsAlph_[i]->charToInt(s.substr(i, 1)));
+ }
+
+ return positions;
+ }
+ /**
+ * @brief Get the char code of the n-position of a word given its char description.
+ *
+ * @param word The char description of the word.
+ * @param n The position in the word (starting at 0).
+ * @return The char description of the n-position of the word.
+ */
+ std::string getNPosition (const std::string& word, size_t n) const throw (BadCharException)
+ {
+ if (n > vAbsAlph_.size())
+ throw BadCharException("", "WordAlphabet::getNPosition", this);
+ // Test:
+ charToInt(word);
+
+ return "" + word.substr(n, 1);
+ }
+
+
+ /**
+ * @brief Get the char codes of each position of a word given its char description.
+ *
+ * @param word The char description of the word.
+ * @return The char description of the three positions of the word.
+ */
+
+ std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
+ {
+ charToInt(word);
+ std::vector<std::string> positions;
+ for (size_t i = 0; i < word.size(); i++)
+ {
+ positions.push_back(word.substr(i, 1));
+ }
+
+ return positions;
+ }
+
+ /**
+ * @brief Translate a whole sequence from letters alphabet to words alphabet.
+ *
+ * @param sequence A sequence in letters alphabet.
+ * @param pos the start postion (default 0)
+ * @return The corresponding sequence in words alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the source alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+ Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
+
+ /**
+ * @brief Translate a whole sequence from words alphabet to letters alphabet.
+ *
+ * @param sequence A sequence in words alphabet.
+ * @return The corresponding sequence in letters alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the target alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+ Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
+
+ /** @} */
+
+ /**
+ * @name Overloaded AbstractAlphabet methods.
+ * @{
+ */
+ unsigned int getStateCodingSize() const { return static_cast<unsigned int>(vAbsAlph_.size()); }
+ /** @} */
+};
+} // end of namespace bpp.
+
+#endif // _WORDALPHABET_H_
+
diff --git a/src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.cpp b/src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.cpp
new file mode 100644
index 0000000..e4c26a9
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.cpp
@@ -0,0 +1,72 @@
+//
+// File: YeastbrateMitochondrialCodonAlphabet.cpp
+// Created by: Benoit Nabholz
+// Created on: Sun Oct 10 14:33 CET 2010
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "YeastMitochondrialCodonAlphabet.h"
+
+using namespace bpp;
+using namespace std;
+
+YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet(const NucleicAlphabet * alpha) : CodonAlphabet(alpha)
+{
+ string A = alpha->intToChar(0);
+ string G = alpha->intToChar(2);
+ string T = alpha->intToChar(3);
+
+ vector<string> vstop;
+
+ vstop.push_back(T + A + A);
+ vstop.push_back(T + A + G);
+
+ int istop;
+ unsigned int j;
+ for (unsigned int i = 0 ; i < vstop.size() ; i++) {
+ istop = charToInt(vstop[i]);
+ stopCodons_.push_back(istop);
+
+ j = 0;
+ while (j < getNumberOfChars()) {
+ if (getStateAt(j).getNum() == istop) {
+ getStateAt(j).setName(STOP);
+ break;
+ }
+ j++;
+ }
+ }
+}
+
diff --git a/src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.h b/src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.h
new file mode 100644
index 0000000..ce67912
--- /dev/null
+++ b/src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.h
@@ -0,0 +1,75 @@
+//
+// File: YeastbrateMitochondrialCodonAlphabet.h
+// Created by: Benoit Nabholz
+// Created on: Sun Oct 10 14:33 CET 2010
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _YEASTMITOCHONDRIALCODONALPHABET_H_
+#define _YEASTMITOCHONDRIALCODONALPHABET_H_
+
+
+#include "CodonAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the Yeast
+ * @author Laurent Guéguen
+ *
+ * Mitochondrial codon alphabet as describe on the NCBI website:
+ * http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG3
+ */
+class YeastMitochondrialCodonAlphabet:
+ public CodonAlphabet
+{
+public:
+ YeastMitochondrialCodonAlphabet(const NucleicAlphabet * alpha);
+ virtual ~YeastMitochondrialCodonAlphabet() {};
+
+public:
+
+ std::string getAlphabetType() const
+ {
+ return "Codon alphabet: YeastMitochondrial(" + vAbsAlph_[0]->getAlphabetType() + ")";
+ }
+
+};
+
+} //end of namespace bpp.
+
+#endif //_YEASTMITOCHONDRIALCODONALPHABET_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAChargeIndex.h b/src/Bpp/Seq/AlphabetIndex/AAChargeIndex.h
new file mode 100644
index 0000000..a388987
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAChargeIndex.h
@@ -0,0 +1,151 @@
+//
+// File: AAChargeIndex.h
+// Created by: Julien Dutheil
+// Created on: Tue May 02 13:34 2006
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AACHARGEINDEX_H_
+#define _AACHARGEINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief Charge of each amino acid.
+ *
+ * @code
+ * Database: AAindex1
+ * Entry: FAUJ880111
+ *
+ * H FAUJ880111
+ * D Positive charge (Fauchere et al., 1988)
+ * R LIT:1414114 PMID:3209351
+ * A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+ * T Amino acid side chain parameters for correlation studies in biology and
+ * pharmacology
+ * J Int. J. Peptide Protein Res. 32, 269-278 (1988)
+ * C ZIMJ680104 0.813
+ * I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ * 0. 1. 0. 0. 0. 0. 0. 0. 1. 0.
+ * 0. 1. 0. 0. 0. 0. 0. 0. 0. 0.
+ * //
+ * @endcode
+ *
+ * @code
+ * Database: AAindex1
+ * Entry: FAUJ880111
+ *
+ * H FAUJ880112
+ * D Negative charge (Fauchere et al., 1988)
+ * R LIT:1414114 PMID:3209351
+ * A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+ * T Amino acid side chain parameters for correlation studies in biology and
+ * pharmacology
+ * J Int. J. Peptide Protein Res. 32, 269-278 (1988)
+ * C RICJ880106 0.849
+ * I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ * 0. 0. 0. 1. 0. 0. 1. 0. 0. 0.
+ * 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. * Soit:
+ * //
+ * @endcode
+ *
+ * Hence, combining the two:
+ * @code
+ * I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ * 0. 1. 0. -1. 0. 0. -1. 0. 1. 0.
+ * 0. 1. 0. 0. 0. 0. 0. 0. 0. 0.
+ * @endcode
+ */
+class AAChargeIndex :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> charge_;
+
+public:
+ AAChargeIndex() :
+ charge_()
+ {
+ charge_.resize(20);
+ charge_[ 0] = 0.; // A
+ charge_[ 1] = 1.; // R
+ charge_[ 2] = 0.; // N
+ charge_[ 3] = -1.; // D
+ charge_[ 4] = 0.; // C
+ charge_[ 5] = 0.; // Q
+ charge_[ 6] = -1.; // E
+ charge_[ 7] = 0.; // G
+ charge_[ 8] = 1.; // H
+ charge_[ 9] = 0.; // I
+ charge_[10] = 0.; // L
+ charge_[11] = 1.; // K
+ charge_[12] = 0.; // M
+ charge_[13] = 0.; // F
+ charge_[14] = 0.; // P
+ charge_[15] = 0.; // S
+ charge_[16] = 0.; // T
+ charge_[17] = 0.; // W
+ charge_[18] = 0.; // Y
+ charge_[19] = 0.; // V
+ }
+
+ virtual ~AAChargeIndex() {}
+
+ AAChargeIndex* clone() const { return new AAChargeIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AAChargeIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return charge_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return charge_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(charge_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AACHARGEINDEX_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h b/src/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h
new file mode 100644
index 0000000..2c43615
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h
@@ -0,0 +1,122 @@
+//
+// File: AAChenGuHuangHydrophobicityIndex.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AACHENGUHUANGHYDROPHOBICITYINDEX_H_
+#define _AACHENGUHUANGHYDROPHOBICITYINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 2006.
+ *
+ * @code
+ * Database: AAChenGuHuangHydrophobicity
+ * Entry: CHENH06
+ *
+ * H FAUJ880111
+ * D Hydrophobicity (Chen et al., 2006)
+ * R PMCID:PMC1780123 PMID:17217506
+ * A Hang Chen, Fei Gu, and Zhengge Huang.
+ * T Improved Chou-Fasman method for protein secondary structure prediction
+ * J BMC Bioinformatics. 2006; 7(Suppl 4): S14. (2006)
+ * //
+ * @endcode
+ *
+ */
+class AAChenGuHuangHydrophobicityIndex :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> hydrophobicity_;
+
+public:
+ AAChenGuHuangHydrophobicityIndex() :
+ hydrophobicity_()
+ {
+ hydrophobicity_.resize(20);
+ hydrophobicity_[ 0] = 0.87; // A
+ hydrophobicity_[ 1] = 0.85; // R
+ hydrophobicity_[ 2] = 0.09; // N
+ hydrophobicity_[ 3] = 0.66; // D
+ hydrophobicity_[ 4] = 1.52; // C
+ hydrophobicity_[ 5] = 0.00; // Q
+ hydrophobicity_[ 6] = 0.67; // E
+ hydrophobicity_[ 7] = 0.00; // G
+ hydrophobicity_[ 8] = 0.87; // H
+ hydrophobicity_[ 9] = 3.15; // I
+ hydrophobicity_[10] = 2.17; // L
+ hydrophobicity_[11] = 1.64; // K
+ hydrophobicity_[12] = 1.67; // M
+ hydrophobicity_[13] = 2.87; // F
+ hydrophobicity_[14] = 2.77; // P
+ hydrophobicity_[15] = 0.07; // S
+ hydrophobicity_[16] = 0.07; // T
+ hydrophobicity_[17] = 3.77; // W
+ hydrophobicity_[18] = 2.76; // Y
+ hydrophobicity_[19] = 1.87; // V
+ }
+
+ virtual ~AAChenGuHuangHydrophobicityIndex() {}
+
+ AAChenGuHuangHydrophobicityIndex* clone() const { return new AAChenGuHuangHydrophobicityIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AAChenGuHuangHydrophobicityIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return hydrophobicity_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return hydrophobicity_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(hydrophobicity_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AACHENGUHUANGHYDROPHOBICITYINDEX_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h b/src/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h
new file mode 100644
index 0000000..dc2ade5
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h
@@ -0,0 +1,111 @@
+//
+// File: AAChouFasmanAHelixIndex.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AACHUFASMANAHELIXINDEX_H_
+#define _AACHUFASMANAHELIXINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief A-Helix score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm
+ *
+ *
+ */
+class AAChouFasmanAHelixIndex :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> aHelix_;
+
+public:
+ AAChouFasmanAHelixIndex() :
+ aHelix_()
+ {
+ aHelix_.resize(20);
+ aHelix_[ 0] = 142; // A
+ aHelix_[ 1] = 98; // R
+ aHelix_[ 2] = 67; // N
+ aHelix_[ 3] = 101; // D
+ aHelix_[ 4] = 70; // C
+ aHelix_[ 5] = 111; // Q
+ aHelix_[ 6] = 151; // E
+ aHelix_[ 7] = 57; // G
+ aHelix_[ 8] = 100; // H
+ aHelix_[ 9] = 108; // I
+ aHelix_[10] = 121; // L
+ aHelix_[11] = 114; // K
+ aHelix_[12] = 145; // M
+ aHelix_[13] = 113; // F
+ aHelix_[14] = 57; // P
+ aHelix_[15] = 77; // S
+ aHelix_[16] = 83; // T
+ aHelix_[17] = 108; // W
+ aHelix_[18] = 69; // Y
+ aHelix_[19] = 106; // V
+ }
+
+ virtual ~AAChouFasmanAHelixIndex() {}
+
+ AAChouFasmanAHelixIndex* clone() const { return new AAChouFasmanAHelixIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AAChouFasmanAHelixIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return aHelix_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return aHelix_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(aHelix_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AACHUFASMANAHELIXINDEX_H_
+
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h b/src/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h
new file mode 100644
index 0000000..7747860
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h
@@ -0,0 +1,111 @@
+//
+// File: AAChouFasmanBSheetIndex.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AACHUFASMANBSHEETINDEX_H_
+#define _AACHUFASMANBSHEETINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief B-sheet score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm
+ *
+ *
+ */
+class AAChouFasmanBSheetIndex :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> bSheet_;
+
+public:
+ AAChouFasmanBSheetIndex() :
+ bSheet_()
+ {
+ bSheet_.resize(20);
+ bSheet_[ 0] = 83; // A
+ bSheet_[ 1] = 93; // R
+ bSheet_[ 2] = 89; // N
+ bSheet_[ 3] = 54; // D
+ bSheet_[ 4] = 119; // C
+ bSheet_[ 5] = 110; // Q
+ bSheet_[ 6] = 37; // E
+ bSheet_[ 7] = 75; // G
+ bSheet_[ 8] = 87; // H
+ bSheet_[ 9] = 160; // I
+ bSheet_[10] = 130; // L
+ bSheet_[11] = 74; // K
+ bSheet_[12] = 105; // M
+ bSheet_[13] = 138; // F
+ bSheet_[14] = 55; // P
+ bSheet_[15] = 75; // S
+ bSheet_[16] = 119; // T
+ bSheet_[17] = 137; // W
+ bSheet_[18] = 147; // Y
+ bSheet_[19] = 170; // V
+ }
+
+ virtual ~AAChouFasmanBSheetIndex() {}
+
+ AAChouFasmanBSheetIndex* clone() const { return new AAChouFasmanBSheetIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AAChouFasmanBSheetIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return bSheet_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return bSheet_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(bSheet_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AACHUFASMANBSHEETINDEX_H_
+
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h b/src/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h
new file mode 100644
index 0000000..a0bbbd7
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h
@@ -0,0 +1,111 @@
+//
+// File: AAChouFasmanTurnIndex.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AACHUFASMANTURNINDEX_H_
+#define _AACHUFASMANTURNINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief Turn score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm
+ *
+ *
+ */
+class AAChouFasmanTurnIndex :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> turn_;
+
+public:
+ AAChouFasmanTurnIndex() :
+ turn_()
+ {
+ turn_.resize(20);
+ turn_[ 0] = 66; // A
+ turn_[ 1] = 95; // R
+ turn_[ 2] = 156; // N
+ turn_[ 3] = 146; // D
+ turn_[ 4] = 119; // C
+ turn_[ 5] = 98; // Q
+ turn_[ 6] = 74; // E
+ turn_[ 7] = 156; // G
+ turn_[ 8] = 95; // H
+ turn_[ 9] = 47; // I
+ turn_[10] = 59; // L
+ turn_[11] = 101; // K
+ turn_[12] = 60; // M
+ turn_[13] = 60; // F
+ turn_[14] = 152; // P
+ turn_[15] = 143; // S
+ turn_[16] = 96; // T
+ turn_[17] = 96; // W
+ turn_[18] = 114; // Y
+ turn_[19] = 50; // V
+ }
+
+ virtual ~AAChouFasmanTurnIndex() {}
+
+ AAChouFasmanTurnIndex* clone() const { return new AAChouFasmanTurnIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AAChouFasmanTurnIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return turn_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return turn_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(turn_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AACHUFASMANTURNINDEX_H_
+
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp b/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp
new file mode 100644
index 0000000..07a7725
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp
@@ -0,0 +1,85 @@
+//
+// File: AAIndex1Entry.cpp
+// Created by: Julien Dutheil
+// Created on: Fri Jan 19 17:07 2007
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "AAIndex1Entry.h"
+#include "../Alphabet/AlphabetTools.h"
+#include <Bpp/Io/FileTools.h>
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+
+using namespace bpp;
+using namespace std;
+
+AAIndex1Entry::AAIndex1Entry(std::istream& input) throw (IOException) :
+ property_(20),
+ alpha_(&AlphabetTools::PROTEIN_ALPHABET)
+{
+ // Parse entry:
+ string line;
+ bool ok = false;
+ do
+ {
+ line = FileTools::getNextLine(input);
+ if (line[0] == 'I')
+ {
+ string line1 = FileTools::getNextLine(input);
+ string line2 = FileTools::getNextLine(input);
+ StringTokenizer st1(line1, " ");
+ StringTokenizer st2(line2, " ");
+ if (st1.numberOfRemainingTokens() != 10 || st1.numberOfRemainingTokens() != 10)
+ break;
+ // Amino acids are in the same order in the AAIndex1 database than in the ProteicAlphabet class:
+ for (unsigned int i = 0; i < 10; i++)
+ {
+ property_[i] = TextTools::toDouble(st1.nextToken());
+ }
+ for (unsigned int i = 10; i < 20; i++)
+ {
+ property_[i] = TextTools::toDouble(st2.nextToken());
+ }
+ // Jump to next entry...
+ FileTools::getNextLine(input);
+ ok = true;
+ }
+ }
+ while (!ok);
+ if (!ok)
+ throw IOException("AAIndex1Entry: invalid AAIndex1 entry.");
+}
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h b/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h
new file mode 100644
index 0000000..1e12f00
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h
@@ -0,0 +1,102 @@
+//
+// File: AAIndex1Entry.h
+// Created by: Julien Dutheil
+// Created on: Fri Jan 19 17:07 2007
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AAINDEX1ENTRY_H_
+#define _AAINDEX1ENTRY_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+
+namespace bpp
+{
+/**
+ * @brief Create a AlphabetIndex1 object from an AAIndex2 entry.
+ */
+class AAIndex1Entry :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> property_;
+ const ProteicAlphabet* alpha_;
+
+public:
+ /**
+ * @brief Create a new AAIndex1Entry from an input stream.
+ *
+ * @param input The input stream to use.
+ * @throw IOException if the stream content does not follow the AAIndex1 database entry format.
+ */
+ AAIndex1Entry(std::istream& input) throw (IOException);
+
+ AAIndex1Entry(const AAIndex1Entry& index) :
+ property_(index.property_),
+ alpha_(index.alpha_)
+ {}
+
+ AAIndex1Entry& operator=(const AAIndex1Entry& index)
+ {
+ property_ = index.property_;
+ alpha_ = index.alpha_;
+ return *this;
+ }
+
+ virtual ~AAIndex1Entry() {}
+
+ AAIndex1Entry* clone() const { return new AAIndex1Entry(*this); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "KleinAANetChargeIndex::getIndex(). Invalid state.", alpha_);
+ return property_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return property_[alpha_->charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(property_); }
+
+ const Alphabet* getAlphabet() const { return alpha_; }
+};
+} // end of namespace bpp.
+
+#endif // _AAINDEX1ENTRY_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp b/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp
new file mode 100644
index 0000000..5daf635
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp
@@ -0,0 +1,101 @@
+//
+// File: AAIndex2Entry.cpp
+// Created by: Julien Dutheil
+// Created on: Fri Jan 19 17:07 2007
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "AAIndex2Entry.h"
+#include "../Alphabet/AlphabetTools.h"
+
+using namespace bpp;
+using namespace std;
+
+#include <Bpp/Io/FileTools.h>
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+
+AAIndex2Entry::AAIndex2Entry(std::istream& input, bool sym) throw (IOException) :
+ property_(20, 20),
+ alpha_(&AlphabetTools::PROTEIN_ALPHABET)
+{
+ // Parse entry:
+ string line;
+ bool ok = false;
+ bool diag = false;
+ do
+ {
+ line = FileTools::getNextLine(input);
+ if (line[0] == 'M')
+ {
+ for (unsigned int i = 0; i < 20; i++)
+ {
+ line = FileTools::getNextLine(input);
+ StringTokenizer st1(line, " ");
+ if (i == 0 && st1.numberOfRemainingTokens() == 1)
+ {
+ // Lower triangle only:
+ diag = true;
+ }
+ // Amino acids are in the same order in the AAIndex1 database than in the ProteicAlphabet class:
+ if (diag)
+ {
+ if (st1.numberOfRemainingTokens() != i + 1)
+ break;
+ for (unsigned int j = 0; j <= i; j++)
+ {
+ property_(i, j) = TextTools::toDouble(st1.nextToken());
+ }
+ }
+ else
+ {
+ if (st1.numberOfRemainingTokens() != 20)
+ break;
+ for (unsigned int j = 0; j < 20; j++)
+ {
+ property_(i, j) = TextTools::toDouble(st1.nextToken());
+ }
+ }
+ }
+ // Jump to next entry...
+ FileTools::getNextLine(input);
+ ok = true;
+ }
+ }
+ while (!ok);
+ if (!ok)
+ throw IOException("AAIndex2Entry: invalid AAIndex2 entry.");
+}
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h b/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h
new file mode 100644
index 0000000..2398e0b
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h
@@ -0,0 +1,108 @@
+//
+// File: AAIndex2Entry.h
+// Created by: Julien Dutheil
+// Created on: Fri Jan 19 17:07 2007
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AAINDEX2ENTRY_H_
+#define _AAINDEX2ENTRY_H_
+
+#include "AlphabetIndex2.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+namespace bpp
+{
+/**
+ * @brief Create a AlphabetIndex2 object from an AAIndex2 entry.
+ */
+class AAIndex2Entry :
+ public virtual AlphabetIndex2
+{
+private:
+ LinearMatrix<double> property_;
+ const ProteicAlphabet* alpha_;
+
+public:
+ /**
+ * @brief Create a new AAIndex2Entry from an input stream.
+ *
+ * @param input The input stream to use.
+ * @param sym Tell if the matrix is symmetric.
+ * This option as an effect only if the matrix is specified as a triangle in the entry.
+ * If sym==true, the oher triangle will be built by symmetry.
+ * If sym==false, the other triangle will be set to (-) the given triangle.
+ * @throw IOException if the stream content does not follow the AAIndex2 database entry format.
+ */
+ AAIndex2Entry(std::istream& input, bool sym = true) throw (IOException);
+
+ AAIndex2Entry(const AAIndex2Entry& index) :
+ property_(index.property_),
+ alpha_(index.alpha_)
+ {}
+
+ AAIndex2Entry& operator=(const AAIndex2Entry& index)
+ {
+ property_ = index.property_;
+ alpha_ = index.alpha_;
+ return *this;
+ }
+
+ virtual ~AAIndex2Entry() {}
+
+public:
+ const Alphabet* getAlphabet() const { return alpha_; }
+
+ AAIndex2Entry* clone() const { return new AAIndex2Entry(*this); }
+
+ double getIndex(int state1, int state2) const throw (BadIntException)
+ {
+ if (state1 < 0 || state1 > 19) throw BadIntException(state1, "AAIndex2Entry::getIndex(). Invalid state1.", alpha_);
+ if (state2 < 0 || state2 > 19) throw BadIntException(state2, "AAIndex2Entry::getIndex(). Invalid state2.", alpha_);
+ return property_(state1, state2);
+ }
+
+ double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
+ {
+ return property_(alpha_->charToInt(state1), alpha_->charToInt(state2));
+ }
+
+ LinearMatrix<double>* getIndexMatrix() const { return new LinearMatrix<double>(property_); }
+};
+} // end of namespace bpp.
+
+#endif // _AAINDEX2ENTRY_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAMassIndex.h b/src/Bpp/Seq/AlphabetIndex/AAMassIndex.h
new file mode 100644
index 0000000..e71c634
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAMassIndex.h
@@ -0,0 +1,110 @@
+//
+// File: AAMassIndex.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AAMASSINDEX_H_
+#define _AAMASSINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief Mass (dalton) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html.
+ *
+ *
+ */
+class AAMassIndex :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> mass_;
+
+public:
+ AAMassIndex() :
+ mass_()
+ {
+ mass_.resize(20);
+ mass_[ 0] = 71.09; // A
+ mass_[ 1] = 156.19; // R
+ mass_[ 2] = 114.11; // N
+ mass_[ 3] = 115.09; // D
+ mass_[ 4] = 103.15; // C
+ mass_[ 5] = 128.14; // Q
+ mass_[ 6] = 129.12; // E
+ mass_[ 7] = 57.05; // G
+ mass_[ 8] = 137.14; // H
+ mass_[ 9] = 113.16; // I
+ mass_[10] = 113.16; // L
+ mass_[11] = 128.17; // K
+ mass_[12] = 131.19; // M
+ mass_[13] = 147.18; // F
+ mass_[14] = 97.12; // P
+ mass_[15] = 87.08; // S
+ mass_[16] = 101.11; // T
+ mass_[17] = 186.12; // W
+ mass_[18] = 163.18; // Y
+ mass_[19] = 99.14; // V
+ }
+
+ virtual ~AAMassIndex() {}
+
+ AAMassIndex* clone() const { return new AAMassIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AAMassIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return mass_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return mass_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(mass_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AAMASSINDEX_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AASEA1030Index.h b/src/Bpp/Seq/AlphabetIndex/AASEA1030Index.h
new file mode 100644
index 0000000..5a295a1
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AASEA1030Index.h
@@ -0,0 +1,111 @@
+//
+// File: AASEA1030Index.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AASEA1030INDEX_H_
+#define _AASEA1030INDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief Percentage of amino acids having a Solvent Exposed Area between 10 and 30 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm.
+ *
+ *
+ */
+class AASEA1030Index :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> sea1030_;
+
+public:
+ AASEA1030Index() :
+ sea1030_()
+ {
+ sea1030_.resize(20);
+ sea1030_[ 0] = 0.17; // A
+ sea1030_[ 1] = 0.11; // R
+ sea1030_[ 2] = 0.08; // N
+ sea1030_[ 3] = 0.10; // D
+ sea1030_[ 4] = 0.14; // C
+ sea1030_[ 5] = 0.09; // Q
+ sea1030_[ 6] = 0.03; // E
+ sea1030_[ 7] = 0.13; // G
+ sea1030_[ 8] = 0.15; // H
+ sea1030_[ 9] = 0.14; // I
+ sea1030_[10] = 0.10; // L
+ sea1030_[11] = 0.05; // K
+ sea1030_[12] = 0.36; // M
+ sea1030_[13] = 0.16; // F
+ sea1030_[14] = 0.09; // P
+ sea1030_[15] = 0.10; // S
+ sea1030_[16] = 0.13; // T
+ sea1030_[17] = 0.07; // W
+ sea1030_[18] = 0.13; // Y
+ sea1030_[19] = 0.10; // V
+ }
+
+ virtual ~AASEA1030Index() {}
+
+ AASEA1030Index* clone() const { return new AASEA1030Index(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AASEA1030Index::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return sea1030_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return sea1030_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(sea1030_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AASEA1030INDEX_H_
+
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h b/src/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h
new file mode 100644
index 0000000..915f975
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h
@@ -0,0 +1,111 @@
+//
+// File: AASEAInf10Index.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AASEAINF10INDEX_H_
+#define _AASEAINF10INDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief Percentage of amino acids having a Solvent Exposed Area below 10 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm.
+ *
+ *
+ */
+class AASEAInf10Index :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> seaInf10_;
+
+public:
+ AASEAInf10Index() :
+ seaInf10_()
+ {
+ seaInf10_.resize(20);
+ seaInf10_[ 0] = 0.35; // A
+ seaInf10_[ 1] = 0.05; // R
+ seaInf10_[ 2] = 0.10; // N
+ seaInf10_[ 3] = 0.09; // D
+ seaInf10_[ 4] = 0.54; // C
+ seaInf10_[ 5] = 0.10; // Q
+ seaInf10_[ 6] = 0.04; // E
+ seaInf10_[ 7] = 0.36; // G
+ seaInf10_[ 8] = 0.19; // H
+ seaInf10_[ 9] = 0.47; // I
+ seaInf10_[10] = 0.49; // L
+ seaInf10_[11] = 0.02; // K
+ seaInf10_[12] = 0.20; // M
+ seaInf10_[13] = 0.42; // F
+ seaInf10_[14] = 0.13; // P
+ seaInf10_[15] = 0.20; // S
+ seaInf10_[16] = 0.16; // T
+ seaInf10_[17] = 0.44; // W
+ seaInf10_[18] = 0.20; // Y
+ seaInf10_[19] = 0.50; // V
+ }
+
+ virtual ~AASEAInf10Index() {}
+
+ AASEAInf10Index* clone() const { return new AASEAInf10Index(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AASEAInf10Index::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return seaInf10_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return seaInf10_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(seaInf10_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AASEAINF10INDEX_H_
+
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AASEASup30Index.h b/src/Bpp/Seq/AlphabetIndex/AASEASup30Index.h
new file mode 100644
index 0000000..cfc6ad5
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AASEASup30Index.h
@@ -0,0 +1,111 @@
+//
+// File: AASEASup30Index.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AASEASUP30INDEX_H_
+#define _AASEASUP30INDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief Percentage of amino acids having a Solvent Exposed Area above 30 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm
+ *
+ *
+ */
+class AASEASup30Index :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> seaSup30_;
+
+public:
+ AASEASup30Index() :
+ seaSup30_()
+ {
+ seaSup30_.resize(20);
+ seaSup30_[ 0] = 0.48; // A
+ seaSup30_[ 1] = 0.84; // R
+ seaSup30_[ 2] = 0.82; // N
+ seaSup30_[ 3] = 0.81; // D
+ seaSup30_[ 4] = 0.32; // C
+ seaSup30_[ 5] = 0.81; // Q
+ seaSup30_[ 6] = 0.93; // E
+ seaSup30_[ 7] = 0.51; // G
+ seaSup30_[ 8] = 0.66; // H
+ seaSup30_[ 9] = 0.39; // I
+ seaSup30_[10] = 0.41; // L
+ seaSup30_[11] = 0.93; // K
+ seaSup30_[12] = 0.44; // M
+ seaSup30_[13] = 0.42; // F
+ seaSup30_[14] = 0.78; // P
+ seaSup30_[15] = 0.70; // S
+ seaSup30_[16] = 0.71; // T
+ seaSup30_[17] = 0.49; // W
+ seaSup30_[18] = 0.67; // Y
+ seaSup30_[19] = 0.40; // V
+ }
+
+ virtual ~AASEASup30Index() {}
+
+ AASEASup30Index* clone() const { return new AASEASup30Index(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AASEASup30Index::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return seaSup30_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return seaSup30_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(seaSup30_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AASEASUP30INDEX_H_
+
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h b/src/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h
new file mode 100644
index 0000000..a259915
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h
@@ -0,0 +1,111 @@
+//
+// File: AASurfaceIndex.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AASURFACEINDEX_H_
+#define _AASURFACEINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief Surface (Angström^2) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html
+ *
+ *
+ */
+class AASurfaceIndex :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> surface_;
+
+public:
+ AASurfaceIndex() :
+ surface_()
+ {
+ surface_.resize(20);
+ surface_[ 0] = 115; // A
+ surface_[ 1] = 225; // R
+ surface_[ 2] = 160; // N
+ surface_[ 3] = 150; // D
+ surface_[ 4] = 135; // C
+ surface_[ 5] = 180; // Q
+ surface_[ 6] = 190; // E
+ surface_[ 7] = 75; // G
+ surface_[ 8] = 195; // H
+ surface_[ 9] = 175; // I
+ surface_[10] = 170; // L
+ surface_[11] = 200; // K
+ surface_[12] = 185; // M
+ surface_[13] = 210; // F
+ surface_[14] = 145; // P
+ surface_[15] = 115; // S
+ surface_[16] = 140; // T
+ surface_[17] = 255; // W
+ surface_[18] = 230; // Y
+ surface_[19] = 155; // V
+ }
+
+ virtual ~AASurfaceIndex() {}
+
+ AASurfaceIndex* clone() const { return new AASurfaceIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AASurfaceIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return surface_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return surface_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(surface_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AASURFACEINDEX_H_
+
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h b/src/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h
new file mode 100644
index 0000000..4cedd45
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h
@@ -0,0 +1,111 @@
+//
+// File: AAVolumeIndex.h
+// Created by: Bastien Boussau
+// Created on: Fri Jan 14 10:31 2011
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _AAVOLUMEINDEX_H_
+#define _AAVOLUMEINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+/**
+ * @brief Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html
+ *
+ *
+ */
+class AAVolumeIndex :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> volume_;
+
+public:
+ AAVolumeIndex() :
+ volume_()
+ {
+ volume_.resize(20);
+ volume_[ 0] = 115; // A
+ volume_[ 1] = 225; // R
+ volume_[ 2] = 160; // N
+ volume_[ 3] = 150; // D
+ volume_[ 4] = 135; // C
+ volume_[ 5] = 180; // Q
+ volume_[ 6] = 190; // E
+ volume_[ 7] = 75; // G
+ volume_[ 8] = 195; // H
+ volume_[ 9] = 175; // I
+ volume_[10] = 170; // L
+ volume_[11] = 200; // K
+ volume_[12] = 185; // M
+ volume_[13] = 210; // F
+ volume_[14] = 145; // P
+ volume_[15] = 115; // S
+ volume_[16] = 140; // T
+ volume_[17] = 255; // W
+ volume_[18] = 230; // Y
+ volume_[19] = 155; // V
+ }
+
+ virtual ~AAVolumeIndex() {}
+
+ AAVolumeIndex* clone() const { return new AAVolumeIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "AAVolumeIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return volume_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return volume_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(volume_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _AAVOLUMEINDEX_H_
+
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h b/src/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h
new file mode 100644
index 0000000..7578ff1
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h
@@ -0,0 +1,97 @@
+//
+// File: AlphabetIndex1.h
+// Created by: Julien Dutheil
+// Created on: Mon Feb 21 17:42 2005
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ Julien.Dutheil at univ-montp2.fr
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _ALPHABETINDEX1_H_
+#define _ALPHABETINDEX1_H_
+
+#include "../Alphabet/Alphabet.h"
+#include <Bpp/Clonable.h>
+
+// From the STL:
+#include <string>
+
+namespace bpp
+{
+/**
+ * @brief One dimensionnal alphabet index interface.
+ *
+ * Derivatives of this interface implement properties for a single state.
+ */
+class AlphabetIndex1 :
+ public virtual Clonable
+{
+public:
+ AlphabetIndex1() {}
+ virtual ~AlphabetIndex1() {}
+
+public:
+ /**
+ * @brief Get the index associated to a state.
+ *
+ * @param state The state to consider, as a int value.
+ * @return The index associated to the state
+ */
+ virtual double getIndex(int state) const = 0;
+
+ /**
+ * @brief Get the index associated to a state.
+ *
+ * @param state The state to consider, as a string value.
+ * @return The index associated to the state
+ */
+ virtual double getIndex(const std::string& state) const = 0;
+
+ /**
+ * @brief Get the alphabet associated to this index.
+ *
+ * @return Alphabet The alphabet associated to this index.
+ */
+ virtual const Alphabet* getAlphabet() const = 0;
+
+ /**
+ * @return A vector object with all indices.
+ */
+ virtual std::vector<double>* getIndexVector() const = 0;
+};
+} // end of namespace bpp.
+
+#endif // _ALPHABETINDEX1_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h b/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h
new file mode 100644
index 0000000..bf7b29d
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h
@@ -0,0 +1,97 @@
+//
+// File: AlphabetIndex2.h
+// Created by: Julien Dutheil
+// Created on: Mon Feb 21 17:42 2005
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _ALPHABETINDEX2_H_
+#define _ALPHABETINDEX2_H_
+
+#include "../Alphabet/Alphabet.h"
+#include <Bpp/Clonable.h>
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+// From the STL:
+#include <string>
+
+namespace bpp
+{
+/**
+ * @brief Two dimensionnal alphabet index interface.
+ *
+ * Derivatives of this interface implement distances between two states.
+ */
+class AlphabetIndex2 : public Clonable
+{
+public:
+ AlphabetIndex2() {}
+ virtual ~AlphabetIndex2() {}
+
+public:
+ /**
+ * @brief Get the index associated to a pair of states.
+ *
+ * @param state1 First state to consider, as a int value.
+ * @param state2 Second state to consider, as a int value.
+ * @return The index associated to the pair of states
+ */
+ virtual double getIndex(int state1, int state2) const = 0;
+
+ /**
+ * @brief Get the index associated to a pair of states.
+ *
+ * @param state1 First state to consider, as a string value.
+ * @param state2 Second state to consider, as a string value.
+ * @return The index associated to the pair of states
+ */
+ virtual double getIndex(const std::string& state1, const std::string& state2) const = 0;
+
+ /**
+ * @brief Get the alphabet associated to this index.
+ *
+ * @return Alphabet The alphabet associated to this index.
+ */
+ virtual const Alphabet* getAlphabet() const = 0;
+
+ /**
+ * @return A matrix object with all indices.
+ */
+ virtual Matrix<double>* getIndexMatrix() const = 0;
+};
+} // end of namespace bpp.
+
+#endif // _ALPHABETINDEX2_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp b/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp
new file mode 100644
index 0000000..146e328
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp
@@ -0,0 +1,78 @@
+//
+// File: BLOSUM50.cpp
+// Created by: Julien Dutheil
+// Created on: Tue Jan 18 10:28 2007
+//
+
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "BLOSUM50.h"
+
+#include "../Alphabet/AlphabetTools.h"
+
+// from the STL:
+#include <string>
+
+using namespace std;
+using namespace bpp;
+
+BLOSUM50::BLOSUM50() :
+ distanceMatrix_(20, 20),
+ alpha_(&AlphabetTools::PROTEIN_ALPHABET)
+{
+ #include "__BLOSUM50MatrixCode"
+}
+
+double BLOSUM50::getIndex(int state1, int state2) const
+throw (BadIntException)
+{
+ if (state1 < 0 || state1 > 19)
+ throw BadIntException(state1, "BLOSUM50::getIndex(). Invalid state1.", alpha_);
+ if (state2 < 0 || state2 > 19)
+ throw BadIntException(state2, "BLOSUM50::getIndex(). Invalid state2.", alpha_);
+ return distanceMatrix_(state1, state2);
+}
+
+double BLOSUM50::getIndex(const std::string& state1, const std::string& state2) const
+throw (BadCharException)
+{
+ return distanceMatrix_(alpha_->charToInt(state1), alpha_->charToInt(state2));
+}
+
+LinearMatrix<double>* BLOSUM50::getIndexMatrix() const
+{
+ return new LinearMatrix<double>(distanceMatrix_);
+}
+
diff --git a/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h b/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h
new file mode 100644
index 0000000..ea0b5fc
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h
@@ -0,0 +1,104 @@
+//
+// File: BLOSUM50.h
+// Created by: Julien Dutheil
+// Created on: Tue Jan 18 10:28 2007
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _BLOSUM50_H_
+#define _BLOSUM50_H_
+
+// from the STL:
+#include <string>
+
+#include "AlphabetIndex2.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetExceptions.h"
+#include <Bpp/Exceptions.h>
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+namespace bpp
+{
+/**
+ * @brief BLOSUM 50 Substitution Matrix.
+ *
+ * Reference:
+ * Henikoff, S. and Henikoff, J.G.
+ * Amino acid substitution matrices from protein blocks
+ * Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
+ *
+ * Data from AAIndex2 database, Accession Number HENS920104.
+ */
+class BLOSUM50 :
+ public virtual AlphabetIndex2
+{
+private:
+ LinearMatrix<double> distanceMatrix_;
+ const ProteicAlphabet* alpha_;
+
+public:
+ BLOSUM50();
+
+ BLOSUM50(const BLOSUM50& blosum) :
+ distanceMatrix_(blosum.distanceMatrix_),
+ alpha_(blosum.alpha_)
+ {}
+
+ BLOSUM50& operator=(const BLOSUM50& blosum)
+ {
+ distanceMatrix_ = blosum.distanceMatrix_;
+ alpha_ = blosum.alpha_;
+ return *this;
+ }
+
+ virtual ~BLOSUM50() {}
+
+public:
+ /**
+ * @name Methods from the AlphabetIndex2 interface.
+ *
+ * @{
+ */
+ double getIndex(int state1, int state2) const throw (BadIntException);
+ double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
+ const Alphabet* getAlphabet() const { return alpha_; }
+ BLOSUM50* clone() const { return new BLOSUM50(); }
+ LinearMatrix<double>* getIndexMatrix() const;
+ /** @} */
+};
+} // end of namespace bpp.
+
+#endif // _BLOSUM50_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp b/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp
new file mode 100644
index 0000000..0265983
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp
@@ -0,0 +1,109 @@
+//
+// File: DefaultNucleotideScore.cpp
+// Created by: Julien Dutheil
+// Created on: Fri Jan 19 10:30 2007
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "DefaultNucleotideScore.h"
+
+// from the STL:
+#include <string>
+
+using namespace std;
+using namespace bpp;
+
+DefaultNucleotideScore::DefaultNucleotideScore(const NucleicAlphabet* alphabet) :
+ distanceMatrix_(4, 4),
+ alpha_(alphabet)
+{
+ // Load the matrix:
+ distanceMatrix_(0, 0) = 10;
+ distanceMatrix_(0, 1) = -3;
+ distanceMatrix_(0, 2) = -1;
+ distanceMatrix_(0, 3) = -4;
+
+ distanceMatrix_(1, 0) = -3;
+ distanceMatrix_(1, 1) = 9;
+ distanceMatrix_(1, 2) = -5;
+ distanceMatrix_(1, 3) = 0;
+
+ distanceMatrix_(2, 0) = -1;
+ distanceMatrix_(2, 1) = -5;
+ distanceMatrix_(2, 2) = 7;
+ distanceMatrix_(2, 3) = -3;
+
+ distanceMatrix_(3, 0) = -4;
+ distanceMatrix_(3, 1) = 0;
+ distanceMatrix_(3, 2) = -3;
+ distanceMatrix_(3, 3) = 8;
+}
+
+double DefaultNucleotideScore::getIndex(int state1, int state2) const
+throw (BadIntException)
+{
+ if (alpha_->isGap(state1) || !alpha_->isIntInAlphabet(state1))
+ throw BadIntException(state1, "DefaultNucleotideScore::getIndex(). Invalid state1.", alpha_);
+ if (alpha_->isGap(state2) || !alpha_->isIntInAlphabet(state2))
+ throw BadIntException(state2, "DefaultNucleotideScore::getIndex(). Invalid state1.", alpha_);
+ if (!alpha_->isUnresolved(state1) && !alpha_->isUnresolved(state2))
+ return distanceMatrix_(state1, state2);
+ vector<int> states1 = alpha_->getAlias(state1);
+ vector<int> states2 = alpha_->getAlias(state2);
+ double score = -5;
+ double tmp_score;
+ for (size_t i = 0; i < states1.size(); i++)
+ {
+ for (size_t j = 0; j < states2.size(); j++)
+ {
+ tmp_score = getIndex(states1[i], states2[j]);
+ if (tmp_score > score)
+ score = tmp_score;
+ }
+ }
+ return score / static_cast<double>(states1.size() + states2.size() - 1);
+}
+
+double DefaultNucleotideScore::getIndex(const std::string& state1, const std::string& state2) const
+throw (BadCharException)
+{
+ return distanceMatrix_(alpha_->charToInt(state1), alpha_->charToInt(state2));
+}
+
+LinearMatrix<double>* DefaultNucleotideScore::getIndexMatrix() const
+{
+ return new LinearMatrix<double>(distanceMatrix_);
+}
+
diff --git a/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h b/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h
new file mode 100644
index 0000000..b431bbf
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h
@@ -0,0 +1,108 @@
+//
+// File: DefaultNucleotideScore.h
+// Created by: Julien Dutheil
+// Created on: Fri Jan 19 10:30 2007
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _DEFAULTNUCLEOTIDESCORE_H_
+#define _DEFAULTNUCLEOTIDESCORE_H_
+
+// from the STL:
+#include <string>
+
+#include "AlphabetIndex2.h"
+#include "../Alphabet/NucleicAlphabet.h"
+#include "../Alphabet/AlphabetExceptions.h"
+#include <Bpp/Exceptions.h>
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+namespace bpp
+{
+/**
+ * @brief Default Substitution Matrix for nucleotide alignments.
+ */
+class DefaultNucleotideScore :
+ public virtual AlphabetIndex2
+{
+private:
+ LinearMatrix<double> distanceMatrix_;
+ const NucleicAlphabet* alpha_;
+
+public:
+ /**
+ * @brief Build a new DefaultNucleotideScore object.
+ *
+ * @param alphabet The alphabet to use.
+ */
+ DefaultNucleotideScore(const NucleicAlphabet* alphabet);
+
+ DefaultNucleotideScore(const DefaultNucleotideScore& dns) :
+ distanceMatrix_(dns.distanceMatrix_),
+ alpha_(dns.alpha_) {}
+
+ DefaultNucleotideScore& operator=(const DefaultNucleotideScore& dns)
+ {
+ distanceMatrix_ = dns.distanceMatrix_;
+ alpha_ = dns.alpha_;
+ return *this;
+ }
+
+ virtual ~DefaultNucleotideScore() {}
+
+public:
+ /**
+ * @name Methods from the AlphabetIndex2 interface.
+ *
+ * @{
+ */
+ /**
+ * @copydoc bpp::AlphabetIndex2::getIndex()
+ *
+ * If states are unresolved, takes the best score of all possible matches
+ * and divides it by the number of different states.
+ * @author Sylvain Gaillard
+ */
+ double getIndex(int state1, int state2) const throw (BadIntException);
+ double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
+ const Alphabet* getAlphabet() const { return alpha_; }
+ DefaultNucleotideScore* clone() const { return new DefaultNucleotideScore(*this); }
+ LinearMatrix<double>* getIndexMatrix() const;
+ /** @} */
+};
+} // end of namespace bpp.
+
+#endif // _DEFAULTNUCLEOTIDESCORE_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp b/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp
new file mode 100644
index 0000000..702246f
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp
@@ -0,0 +1,110 @@
+//
+// File: GranthamAAChemicalDistance.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Feb 21 17:42 2005
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+// from the STL:
+#include <string>
+
+#include "GranthamAAChemicalDistance.h"
+#include "../Alphabet/AlphabetTools.h"
+#include <Bpp/Numeric/NumTools.h>
+
+using namespace bpp;
+
+short int GranthamAAChemicalDistance::SIGN_NONE = 0;
+short int GranthamAAChemicalDistance::SIGN_ARBITRARY = 1;
+short int GranthamAAChemicalDistance::SIGN_PC1 = 2;
+
+GranthamAAChemicalDistance::GranthamAAChemicalDistance() :
+ distanceMatrix_(20, 20),
+ signMatrix_(20, 20),
+ alpha_(&AlphabetTools::PROTEIN_ALPHABET),
+ sign_(0)
+{
+ // Load the matrix:
+ #include "__GranthamMatrixCode"
+}
+GranthamAAChemicalDistance::~GranthamAAChemicalDistance() {}
+
+double GranthamAAChemicalDistance::getIndex(int state1, int state2) const
+throw (BadIntException)
+{
+ if (state1 < 0 || state1 > 19)
+ throw BadIntException(state1, "GranthamAAChemicalDistance::getIndex(). Invalid state1.", alpha_);
+ if (state2 < 0 || state2 > 19)
+ throw BadIntException(state2, "GranthamAAChemicalDistance::getIndex(). Invalid state2.", alpha_);
+ double d = distanceMatrix_(state1, state2);
+ if (sign_ == SIGN_NONE)
+ return NumTools::abs<double>(d);
+ if (sign_ == SIGN_PC1)
+ return signMatrix_(state1, state2) * NumTools::abs<double>(d);
+ return d;
+}
+
+double GranthamAAChemicalDistance::getIndex(const std::string& state1, const std::string& state2) const
+throw (BadCharException)
+{
+ return getIndex(alpha_->charToInt(state1), alpha_->charToInt(state2));
+}
+
+Matrix<double>* GranthamAAChemicalDistance::getIndexMatrix() const
+{
+ RowMatrix<double>* m = new RowMatrix<double>(distanceMatrix_);
+ if (sign_ == SIGN_NONE)
+ {
+ for (unsigned int i = 0; i < 20; i++)
+ {
+ for (unsigned int j = 0; j < 20; j++)
+ {
+ (*m)(i, j) = NumTools::abs<double>((*m)(i, j));
+ }
+ }
+ }
+ else if (sign_ == SIGN_PC1)
+ {
+ for (unsigned int i = 0; i < 20; i++)
+ {
+ for (unsigned int j = 0; j < 20; j++)
+ {
+ (*m)(i, j) = signMatrix_(i, j) * NumTools::abs<double>((*m)(i, j));
+ }
+ }
+ }
+ return m;
+}
+
diff --git a/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h b/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h
new file mode 100644
index 0000000..aaa9d51
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h
@@ -0,0 +1,158 @@
+//
+// File: GranthamAAChemicalDistance.h
+// Created by: Julien Dutheil
+// Created on: Mon Feb 21 17:42 2005
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _GRANTHAMAACHEMICALDISTANCE_H_
+#define _GRANTHAMAACHEMICALDISTANCE_H_
+
+// from the STL:
+#include <string>
+
+#include "AlphabetIndex2.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetExceptions.h"
+#include <Bpp/Exceptions.h>
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+namespace bpp
+{
+/**
+ * @brief Grantham (1974) Amino-Acid chemical distance.
+ *
+ * Two kinds of matrix can be built:
+ * - a symmetric one, with \f$I_{i,j} = I_{i,j}\f$,
+ * - or a non-symmetric one, with \f$I_{i,j} = -I_{i,j}\f$.
+ * In the second case, which one of the two entries between \f$I_{i,j}\f$ and \f$I_{i,j}\f$ is positive is arbitrary by default.
+ * It is also possible to use the coordinate on a principal component analysis between the elementary propoerties of the distance instead (setPC1Sign(true)).
+ * The following R code was use in order to get those signs:
+ * @code
+ * library(seqinr)
+ * data(aaindex)
+ * data<-data.frame(composition=aaindex[["GRAR740101"]]$I,
+ * polarity=aaindex[["GRAR740102"]]$I,
+ * volume=aaindex[["GRAR740103"]]$I)
+ * library(ade4)
+ * pca<-dudi.pca(data)
+ *
+ * plot(pca$li[, 1:2], type="n")
+ * text(pca$li[, 1:2], rownames(data))
+ *
+ * s.corcircle(pca$co)
+ * layout(matrix(1:3,nrow=1))
+ * a1<-pca$li[,1]; names(a1)<-rownames(data); dotchart(sort(a1))
+ * a2<-pca$li[,2]; names(a2)<-rownames(data); dotchart(sort(a2))
+ * a3<-pca$li[,3]; names(a3)<-rownames(data); dotchart(sort(a3))
+ *
+ * x<-pca$li[,1] #Contains the coordinates on the first axis.
+ * m<-matrix(nrow=20, ncol=20)
+ * for(i in 1:length(x))
+ * for(j in 1:length(x))
+ * m[i,j]<-sign(x[j] - x[i])
+ *
+ * @endcode
+ *
+ * Reference:
+ * Grantham, R.
+ * Amino acid difference formula to help explain protein evolution
+ * Science 185, 862-864 (1974)
+ *
+ * Data from AAIndex2 database, Accession Number GRAR740104.
+ */
+class GranthamAAChemicalDistance :
+ public virtual AlphabetIndex2
+{
+private:
+ LinearMatrix<double> distanceMatrix_;
+ LinearMatrix<double> signMatrix_;
+ const ProteicAlphabet* alpha_;
+ short int sign_;
+
+public:
+ GranthamAAChemicalDistance();
+
+ GranthamAAChemicalDistance(const GranthamAAChemicalDistance& gd) :
+ distanceMatrix_(gd.distanceMatrix_),
+ signMatrix_(gd.signMatrix_),
+ alpha_(gd.alpha_),
+ sign_(gd.sign_)
+ {}
+
+ GranthamAAChemicalDistance& operator=(const GranthamAAChemicalDistance& gd)
+ {
+ distanceMatrix_ = gd.distanceMatrix_;
+ signMatrix_ = gd.signMatrix_;
+ alpha_ = gd.alpha_;
+ sign_ = gd.sign_;
+ return *this;
+ }
+
+ virtual ~GranthamAAChemicalDistance();
+
+public:
+ /**
+ * @name Methods from the AlphabetIndex2 interface.
+ *
+ * @{
+ */
+ double getIndex(int state1, int state2) const throw (BadIntException);
+ double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
+ const Alphabet* getAlphabet() const { return alpha_; }
+ GranthamAAChemicalDistance* clone() const { return new GranthamAAChemicalDistance(); }
+ Matrix<double>* getIndexMatrix() const;
+ /** @} */
+
+public:
+ void setSymmetric(bool yn) { sign_ = (yn ? SIGN_NONE : SIGN_ARBITRARY); }
+ bool isSymmetric() const { return sign_ == SIGN_NONE; }
+ /**
+ * @brief The sign of the distance is computed using the coordinate on the first axis
+ * of a principal component analysis with the 3 elementary properties (Volume, Polarity, Composition).
+ * Otherwise, use the default arbitrary sign. Using this option will lead isSymmetric to return false.
+ *
+ * @param yn Tell is the PC1-based sign should be used instead of the arbitrary one.
+ */
+ void setPC1Sign(bool yn) { sign_ = (yn ? SIGN_PC1 : SIGN_ARBITRARY); }
+
+ static short int SIGN_ARBITRARY;
+ static short int SIGN_PC1;
+ static short int SIGN_NONE;
+};
+} // end of namespace bpp.
+
+#endif // _GRANTHAMAACHEMICALDISTANCE_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h b/src/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h
new file mode 100644
index 0000000..7dcc1a4
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h
@@ -0,0 +1,123 @@
+//
+// File: GranthamAAPolarityIndex.h
+// Created by: Julien Dutheil
+// Created on: Tue Apr 21 2005
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _GRANTHAMAAPOLARITYINDEX_H_
+#define _GRANTHAMAAPOLARITYINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+
+namespace bpp
+{
+/**
+ * @brief Polarity index used in Grantham (1974).
+ *
+ * @code
+ * Database: AAindex1
+ * Entry: GRAR740102
+ *
+ * H GRAR740102
+ * D Polarity (Grantham, 1974)
+ * R LIT:2004143b PMID:4843792
+ * A Grantham, R.
+ * T Amino acid difference formula to help explain protein evolution
+ * J Science 185, 862-864 (1974)
+ * I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ * 8.1 10.5 11.6 13.0 5.5 10.5 12.3 9.0 10.4 5.2
+ * 4.9 11.3 5.7 5.2 8.0 9.2 8.6 5.4 6.2 5.9
+ * //
+ * @endcode
+ */
+class GranthamAAPolarityIndex :
+ public virtual AlphabetIndex1
+{
+private:
+ std::vector<double> polarity_;
+
+public:
+ GranthamAAPolarityIndex() :
+ polarity_()
+ {
+ polarity_.resize(20);
+ polarity_[ 0] = 8.1; // A
+ polarity_[ 1] = 10.5; // R
+ polarity_[ 2] = 11.6; // N
+ polarity_[ 3] = 13.0; // D
+ polarity_[ 4] = 5.5; // C
+ polarity_[ 5] = 10.5; // Q
+ polarity_[ 6] = 12.3; // E
+ polarity_[ 7] = 9.0; // G
+ polarity_[ 8] = 10.4; // H
+ polarity_[ 9] = 5.2; // I
+ polarity_[10] = 4.9; // L
+ polarity_[11] = 11.3; // K
+ polarity_[12] = 5.7; // M
+ polarity_[13] = 5.2; // F
+ polarity_[14] = 8.0; // P
+ polarity_[15] = 9.2; // S
+ polarity_[16] = 8.6; // T
+ polarity_[17] = 5.4; // W
+ polarity_[18] = 6.2; // Y
+ polarity_[19] = 5.9; // V
+ }
+
+ virtual ~GranthamAAPolarityIndex() {}
+
+ GranthamAAPolarityIndex* clone() const { return new GranthamAAPolarityIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "GranthamAAPolarityIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return polarity_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return polarity_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(polarity_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _GRANTHAMAAPOLARITYINDEX_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h b/src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h
new file mode 100644
index 0000000..75ad954
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h
@@ -0,0 +1,126 @@
+//
+// File: GranthamAAVolumeIndex.h
+// Created by: Julien Dutheil
+// Created on: Tue Apr 21 2005
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _GRANTHAMAAVOLUMEINDEX_H_
+#define _GRANTHAMAAVOLUMEINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+
+// From the STL:
+#include <vector>
+
+namespace bpp
+{
+/**
+ * @brief Volume index used in Grantham (1974).
+ *
+ * @code
+ * Database: AAindex1
+ * Entry: GRAR740103
+ *
+ * H GRAR740103
+ * D Volume (Grantham, 1974)
+ * R LIT:2004143b PMID:4843792
+ * A Grantham, R.
+ * T Amino acid difference formula to help explain protein evolution
+ * J Science 185, 862-864 (1974)
+ * I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ * 31. 124. 56. 54. 55. 85. 83. 3. 96. 111.
+ * 111. 119. 105. 132. 32.5 32. 61. 170. 136. 84.
+ * //
+ * @endcode
+ */
+class GranthamAAVolumeIndex :
+ public virtual AlphabetIndex1
+{
+private:
+ std::vector<double> volume_;
+
+public:
+ GranthamAAVolumeIndex() :
+ volume_()
+ {
+ volume_.resize(20);
+ volume_[ 0] = 31.; // A
+ volume_[ 1] = 124.; // R
+ volume_[ 2] = 56.; // N
+ volume_[ 3] = 54.; // D
+ volume_[ 4] = 55.; // C
+ volume_[ 5] = 85.; // Q
+ volume_[ 6] = 83.; // E
+ volume_[ 7] = 3.; // G
+ volume_[ 8] = 96.; // H
+ volume_[ 9] = 111.; // I
+ volume_[10] = 111.; // L
+ volume_[11] = 119.; // K
+ volume_[12] = 105.; // M
+ volume_[13] = 132.; // F
+ volume_[14] = 32.5; // P
+ volume_[15] = 32.; // S
+ volume_[16] = 61.; // T
+ volume_[17] = 170.; // W
+ volume_[18] = 136.; // Y
+ volume_[19] = 84.; // V
+ }
+
+ virtual ~GranthamAAVolumeIndex() {}
+
+ GranthamAAVolumeIndex* clone() const { return new GranthamAAVolumeIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "GranthamAAVolumeIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return volume_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return volume_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(volume_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _GRANTHAMAAVOLUMEINDEX_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h b/src/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h
new file mode 100644
index 0000000..76c3d2b
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h
@@ -0,0 +1,124 @@
+//
+// File: KleinAANetChargeIndex.h
+// Created by: Julien Dutheil
+// Created on: Wed Aug 31 17:48 2005
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _KLEINAANETCHARGEINDEX_H_
+#define _KLEINAANETCHARGEINDEX_H_
+
+#include "AlphabetIndex1.h"
+#include "../Alphabet/ProteicAlphabet.h"
+
+namespace bpp
+{
+/**
+ * @brief Charge of each amino acid.
+ *
+ * @code
+ * Database: AAindex
+ * Entry: KLEP840101
+ *
+ * H KLEP840101
+ * D Net charge (Klein et al., 1984)
+ * R LIT:1008055 PMID:6547351
+ * A Klein, P., Kanehisa, M. and DeLisi, C.
+ * T Prediction of protein function from sequence properties: Discriminant
+ * analysis of a data base
+ * J Biochim. Biophys. Acta 787, 221-226 (1984)
+ * C ZIMJ680104 0.941
+ * I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ * 0. 1. 0. -1. 0. 0. -1. 0. 0. 0.
+ * 0. 1. 0. 0. 0. 0. 0. 0. 0. 0.
+ * //
+ * @endcode
+ */
+class KleinAANetChargeIndex :
+ public AlphabetIndex1
+{
+private:
+ std::vector<double> charge_;
+
+public:
+ KleinAANetChargeIndex() : charge_()
+ {
+ charge_.resize(20);
+ charge_[ 0] = 0.; // A
+ charge_[ 1] = 1.; // R
+ charge_[ 2] = 0.; // N
+ charge_[ 3] = -1.; // D
+ charge_[ 4] = 0.; // C
+ charge_[ 5] = 0.; // Q
+ charge_[ 6] = -1.; // E
+ charge_[ 7] = 0.; // G
+ charge_[ 8] = 0.; // H
+ charge_[ 9] = 0.; // I
+ charge_[10] = 0.; // L
+ charge_[11] = 1.; // K
+ charge_[12] = 0.; // M
+ charge_[13] = 0.; // F
+ charge_[14] = 0.; // P
+ charge_[15] = 0.; // S
+ charge_[16] = 0.; // T
+ charge_[17] = 0.; // W
+ charge_[18] = 0.; // Y
+ charge_[19] = 0.; // V
+ }
+
+ virtual ~KleinAANetChargeIndex() {}
+
+ KleinAANetChargeIndex* clone() const { return new KleinAANetChargeIndex(); }
+
+public:
+ double getIndex(int state) const throw (BadIntException)
+ {
+ if (state < 0 || state > 19) throw BadIntException(state, "KleinAANetChargeIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
+ return charge_[state];
+ }
+
+ double getIndex(const std::string& state) const throw (BadCharException)
+ {
+ return charge_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
+ }
+
+ std::vector<double>* getIndexVector() const { return new std::vector<double>(charge_); }
+
+ const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
+};
+} // end of namespace bpp.
+
+#endif // _KLEINAANETCHARGEINDEX_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp b/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp
new file mode 100644
index 0000000..9d56acd
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp
@@ -0,0 +1,92 @@
+//
+// File: MiyataAAChemicalDistance.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Feb 21 17:42 2005
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+// from the STL:
+#include <string>
+
+using namespace std;
+
+#include "MiyataAAChemicalDistance.h"
+#include "../Alphabet/AlphabetTools.h"
+#include <Bpp/Numeric/NumTools.h>
+
+using namespace bpp;
+
+MiyataAAChemicalDistance::MiyataAAChemicalDistance() :
+ distanceMatrix_(20, 20),
+ alpha_(&AlphabetTools::PROTEIN_ALPHABET),
+ sym_(true)
+{
+ #include "__MiyataMatrixCode"
+}
+
+double MiyataAAChemicalDistance::getIndex(int state1, int state2) const
+throw (BadIntException)
+{
+ if (state1 < 0 || state1 > 19)
+ throw BadIntException(state1, "MiyataAAChemicalDistance::getIndex(). Invalid state1.", alpha_);
+ if (state2 < 0 || state2 > 19)
+ throw BadIntException(state2, "MiyataAAChemicalDistance::getIndex(). Invalid state2.", alpha_);
+ double d = distanceMatrix_(state1, state2);
+ return sym_ ? NumTools::abs<double>(d) : d;
+}
+
+double MiyataAAChemicalDistance::getIndex(const string& state1, const string& state2) const
+throw (BadCharException)
+{
+ double d = distanceMatrix_(alpha_->charToInt(state1), alpha_->charToInt(state2));
+ return sym_ ? NumTools::abs(d) : d;
+}
+
+Matrix<double>* MiyataAAChemicalDistance::getIndexMatrix() const
+{
+ RowMatrix<double>* m = new RowMatrix<double>(distanceMatrix_);
+ if (sym_)
+ {
+ for (unsigned int i = 0; i < 20; i++)
+ {
+ for (unsigned int j = 0; j < 20; j++)
+ {
+ (*m)(i, j) = NumTools::abs<double>((*m)(i, j));
+ }
+ }
+ }
+ return m;
+}
+
diff --git a/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h b/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h
new file mode 100644
index 0000000..3bfaede
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h
@@ -0,0 +1,118 @@
+//
+// File: MiyataAAChemicalDistance.h
+// Created by: jdutheil <Julien.Dutheil at univ-montp2.fr>
+// Created on: Mon Feb 21 17:42 2005
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ Julien.Dutheil at univ-montp2.fr
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _MIYATAAACHEMICALDISTANCE_H_
+#define _MIYATAAACHEMICALDISTANCE_H_
+
+// from the STL:
+#include <string>
+
+#include "AlphabetIndex2.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetExceptions.h"
+#include <Bpp/Exceptions.h>
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+namespace bpp
+{
+/**
+ * @brief Miyata et al. (1979) Amino-Acid chemical distance.
+ *
+ * Two kinds of matrix can be built:
+ * - a symmetric one, with \f$I_{i,j} = I_{i,j}\f$,
+ * - or a non-symmetric one, with \f$I_{i,j} = -I_{i,j}\f$.
+ *
+ * Reference:
+ * Miyata, T., Miyazawa, S. and Yasunaga, T.
+ * Two types of amino acid substitutions in protein evolution
+ * J. Mol. Evol. 12, 219-236 (1979)
+ *
+ * Data from AAIndex2 database, Accession Number MIYT790101.
+ */
+class MiyataAAChemicalDistance :
+ public virtual AlphabetIndex2
+{
+private:
+ LinearMatrix<double> distanceMatrix_;
+ const ProteicAlphabet* alpha_;
+ bool sym_;
+
+public:
+ MiyataAAChemicalDistance();
+
+ MiyataAAChemicalDistance(const MiyataAAChemicalDistance& md) :
+ distanceMatrix_(md.distanceMatrix_),
+ alpha_(md.alpha_),
+ sym_(md.sym_)
+ {}
+
+ MiyataAAChemicalDistance& operator=(const MiyataAAChemicalDistance& md)
+ {
+ distanceMatrix_ = md.distanceMatrix_;
+ alpha_ = md.alpha_;
+ sym_ = md.sym_;
+ return *this;
+ }
+
+ virtual ~MiyataAAChemicalDistance() {}
+
+ MiyataAAChemicalDistance* clone() const { return new MiyataAAChemicalDistance(); }
+
+public:
+ /**
+ * @name Methods from the AlphabetIndex2 interface.
+ *
+ * @{
+ */
+ double getIndex(int state1, int state2) const throw (BadIntException);
+ double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
+ const Alphabet* getAlphabet() const { return alpha_; }
+ Matrix<double>* getIndexMatrix() const;
+ /** @} */
+
+public:
+ void setSymmetric(bool yn) { sym_ = yn; }
+ bool isSymmetric() const { return sym_; }
+};
+} // end of namespace bpp.
+
+#endif // _MIYATAAACHEMICALDISTANCE_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h b/src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h
new file mode 100644
index 0000000..35a4247
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h
@@ -0,0 +1,134 @@
+//
+// File: SimpleIndexDistance.h
+// Created by: Julien Dutheil
+// Created on: Tue Apr 21 2005
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _SIMPLEINDEXDISTANCE_H_
+#define _SIMPLEINDEXDISTANCE_H_
+
+// from the STL:
+#include <string>
+
+#include "AlphabetIndex1.h"
+#include "AlphabetIndex2.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include "../Alphabet/AlphabetExceptions.h"
+#include <Bpp/Exceptions.h>
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+namespace bpp
+{
+/**
+ * @brief Simple dissimilarity distance.
+ *
+ * Take a one-dimensional index end return the difference between the
+ * indexes of two states.
+ */
+class SimpleIndexDistance :
+ public virtual AlphabetIndex2
+{
+private:
+ std::auto_ptr<AlphabetIndex1> index_;
+ bool sym_;
+
+public:
+ SimpleIndexDistance(AlphabetIndex1* index) :
+ index_(index),
+ sym_(false)
+ {}
+
+ SimpleIndexDistance(const SimpleIndexDistance& sid) :
+ index_(dynamic_cast<AlphabetIndex1*>(sid.index_->clone())),
+ sym_(sid.sym_)
+ {}
+
+ SimpleIndexDistance& operator=(const SimpleIndexDistance& sid)
+ {
+ index_.reset(dynamic_cast<AlphabetIndex1*>(sid.index_->clone()));
+ sym_ = sid.sym_;
+ return *this;
+ }
+
+ virtual ~SimpleIndexDistance() {}
+
+public:
+ double getIndex(int state1, int state2) const throw (BadIntException)
+ {
+ double d = index_->getIndex(state2) - index_->getIndex(state1);
+ return sym_ ? NumTools::abs<double>(d) : d;
+ }
+
+ double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
+ {
+ double d = index_->getIndex(state2) - index_->getIndex(state1);
+ return sym_ ? NumTools::abs<double>(d) : d;
+ }
+
+ const Alphabet* getAlphabet() const { return index_->getAlphabet(); }
+
+ Clonable* clone() const { return new SimpleIndexDistance(*this); }
+
+ Matrix<double>* getIndexMatrix() const
+ {
+ size_t n = index_->getAlphabet()->getSize(); //We should change to "supported ints" there...
+ RowMatrix<double>* m = new RowMatrix<double>(n, n);
+ for (int i = 0; i < static_cast<int>(n); i++)
+ {
+ for (int j = 0; j < static_cast<int>(n); j++)
+ {
+ (*m)(i, j) = getIndex(i, j);
+ }
+ }
+ return m;
+ }
+
+public:
+ void setSymmetric(bool yn) { sym_ = yn; }
+ bool isSymmetric() const { return sym_; }
+ /**
+ * @return The AlphabetIndex1 object associated to this object.
+ */
+ const AlphabetIndex1& getAlphabetIndex1() const { return *index_; }
+ /**
+ * @return The AlphabetIndex1 object associated to this object.
+ */
+ AlphabetIndex1& getAlphabetIndex1() { return *index_; }
+};
+} // end of namespace bpp.
+
+#endif // _SIMPLEINDEXDISTANCE_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp b/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp
new file mode 100644
index 0000000..00cf000
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp
@@ -0,0 +1,84 @@
+//
+// File: SimpleScore.cpp
+// Created by: Julien Dutheil
+// Created on: Fri May 04 09:35 2007
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+// from the STL:
+#include <string>
+
+using namespace std;
+
+#include "SimpleScore.h"
+
+using namespace bpp;
+
+SimpleScore::SimpleScore(const Alphabet* alphabet, double match, double mismatch) :
+ distanceMatrix_(alphabet->getSize(), alphabet->getSize()),
+ alphabet_(alphabet)
+{
+ // Load the matrix:
+ unsigned int n = alphabet_->getSize();
+ for (unsigned int i = 0; i < n; i++)
+ {
+ for (unsigned int j = 0; j < n; j++)
+ {
+ distanceMatrix_(i, j) = (i == j ? match : mismatch);
+ }
+ }
+}
+
+double SimpleScore::getIndex(int state1, int state2) const
+throw (BadIntException)
+{
+ if (state1 < 0 || state1 > (int)alphabet_->getSize())
+ throw BadIntException(state1, "SimpleScore::getIndex(). Invalid state1.", alphabet_);
+ if (state2 < 0 || state2 > (int)alphabet_->getSize())
+ throw BadIntException(state2, "SimpleScore::getIndex(). Invalid state2.", alphabet_);
+ return distanceMatrix_(state1, state2);
+}
+
+double SimpleScore::getIndex(const std::string& state1, const std::string& state2) const
+throw (BadCharException)
+{
+ return distanceMatrix_(alphabet_->charToInt(state1), alphabet_->charToInt(state2));
+}
+
+LinearMatrix<double>* SimpleScore::getIndexMatrix() const
+{
+ return new LinearMatrix<double>(distanceMatrix_);
+}
+
diff --git a/src/Bpp/Seq/AlphabetIndex/SimpleScore.h b/src/Bpp/Seq/AlphabetIndex/SimpleScore.h
new file mode 100644
index 0000000..3dbc5f0
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/SimpleScore.h
@@ -0,0 +1,105 @@
+//
+// File: SimpleScore.h
+// Created by: Julien Dutheil
+// Created on: Fri May 04 09:35 2007
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _SIMPLESCORE_H_
+#define _SIMPLESCORE_H_
+
+// from the STL:
+#include <string>
+
+#include "AlphabetIndex2.h"
+#include "../Alphabet/Alphabet.h"
+#include "../Alphabet/AlphabetExceptions.h"
+#include <Bpp/Exceptions.h>
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+namespace bpp
+{
+/**
+ * @brief Simple Substitution Matrix, with match and mismatch penalties.
+ */
+class SimpleScore :
+ public virtual AlphabetIndex2
+{
+private:
+ LinearMatrix<double> distanceMatrix_;
+ const Alphabet* alphabet_;
+
+public:
+ /**
+ * @brief Build a new simpleScore object.
+ *
+ * @param alphabet The alphabet to use.
+ * @param match Matching score.
+ * @param mismatch Mismatching penalty.
+ */
+ SimpleScore(const Alphabet* alphabet, double match, double mismatch);
+
+ SimpleScore(const SimpleScore& sc) :
+ distanceMatrix_(sc.distanceMatrix_),
+ alphabet_(sc.alphabet_)
+ {}
+
+ SimpleScore& operator=(const SimpleScore& sc)
+ {
+ distanceMatrix_ = sc.distanceMatrix_;
+ alphabet_ = sc.alphabet_;
+ return *this;
+ }
+
+ virtual ~SimpleScore() {}
+
+ SimpleScore* clone() const { return new SimpleScore(*this); }
+
+public:
+ /**
+ * @name Methods from the AlphabetIndex2 interface.
+ *
+ * @{
+ */
+ double getIndex(int state1, int state2) const throw (BadIntException);
+ double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
+ const Alphabet* getAlphabet() const { return alphabet_; }
+ LinearMatrix<double>* getIndexMatrix() const;
+ /** @} */
+};
+} // end of namespace bpp.
+
+#endif // _SIMPLESCORE_H_
+
diff --git a/src/Bpp/Seq/AlphabetIndex/__BLOSUM50MatrixCode b/src/Bpp/Seq/AlphabetIndex/__BLOSUM50MatrixCode
new file mode 100644
index 0000000..39923fd
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/__BLOSUM50MatrixCode
@@ -0,0 +1,400 @@
+distanceMatrix_(0,0) = 5;
+distanceMatrix_(0,1) = -2;
+distanceMatrix_(0,2) = -1;
+distanceMatrix_(0,3) = -2;
+distanceMatrix_(0,4) = -1;
+distanceMatrix_(0,5) = -1;
+distanceMatrix_(0,6) = -1;
+distanceMatrix_(0,7) = 0;
+distanceMatrix_(0,8) = -2;
+distanceMatrix_(0,9) = -1;
+distanceMatrix_(0,10) = -2;
+distanceMatrix_(0,11) = -1;
+distanceMatrix_(0,12) = -1;
+distanceMatrix_(0,13) = -3;
+distanceMatrix_(0,14) = -1;
+distanceMatrix_(0,15) = 1;
+distanceMatrix_(0,16) = 0;
+distanceMatrix_(0,17) = -3;
+distanceMatrix_(0,18) = -2;
+distanceMatrix_(0,19) = 0;
+distanceMatrix_(1,0) = -2;
+distanceMatrix_(1,1) = 7;
+distanceMatrix_(1,2) = -1;
+distanceMatrix_(1,3) = -2;
+distanceMatrix_(1,4) = -4;
+distanceMatrix_(1,5) = 1;
+distanceMatrix_(1,6) = 0;
+distanceMatrix_(1,7) = -3;
+distanceMatrix_(1,8) = 0;
+distanceMatrix_(1,9) = -4;
+distanceMatrix_(1,10) = -3;
+distanceMatrix_(1,11) = 3;
+distanceMatrix_(1,12) = -2;
+distanceMatrix_(1,13) = -3;
+distanceMatrix_(1,14) = -3;
+distanceMatrix_(1,15) = -1;
+distanceMatrix_(1,16) = -1;
+distanceMatrix_(1,17) = -3;
+distanceMatrix_(1,18) = -1;
+distanceMatrix_(1,19) = -3;
+distanceMatrix_(2,0) = -1;
+distanceMatrix_(2,1) = -1;
+distanceMatrix_(2,2) = 7;
+distanceMatrix_(2,3) = 2;
+distanceMatrix_(2,4) = -2;
+distanceMatrix_(2,5) = 0;
+distanceMatrix_(2,6) = 0;
+distanceMatrix_(2,7) = 0;
+distanceMatrix_(2,8) = 1;
+distanceMatrix_(2,9) = -3;
+distanceMatrix_(2,10) = -4;
+distanceMatrix_(2,11) = 0;
+distanceMatrix_(2,12) = -2;
+distanceMatrix_(2,13) = -4;
+distanceMatrix_(2,14) = -2;
+distanceMatrix_(2,15) = 1;
+distanceMatrix_(2,16) = 0;
+distanceMatrix_(2,17) = -4;
+distanceMatrix_(2,18) = -2;
+distanceMatrix_(2,19) = -3;
+distanceMatrix_(3,0) = -2;
+distanceMatrix_(3,1) = -2;
+distanceMatrix_(3,2) = 2;
+distanceMatrix_(3,3) = 8;
+distanceMatrix_(3,4) = -4;
+distanceMatrix_(3,5) = 0;
+distanceMatrix_(3,6) = 2;
+distanceMatrix_(3,7) = -1;
+distanceMatrix_(3,8) = -1;
+distanceMatrix_(3,9) = -4;
+distanceMatrix_(3,10) = -4;
+distanceMatrix_(3,11) = -1;
+distanceMatrix_(3,12) = -4;
+distanceMatrix_(3,13) = -5;
+distanceMatrix_(3,14) = -1;
+distanceMatrix_(3,15) = 0;
+distanceMatrix_(3,16) = -1;
+distanceMatrix_(3,17) = -5;
+distanceMatrix_(3,18) = -3;
+distanceMatrix_(3,19) = -4;
+distanceMatrix_(4,0) = -1;
+distanceMatrix_(4,1) = -4;
+distanceMatrix_(4,2) = -2;
+distanceMatrix_(4,3) = -4;
+distanceMatrix_(4,4) = 13;
+distanceMatrix_(4,5) = -3;
+distanceMatrix_(4,6) = -3;
+distanceMatrix_(4,7) = -3;
+distanceMatrix_(4,8) = -3;
+distanceMatrix_(4,9) = -2;
+distanceMatrix_(4,10) = -2;
+distanceMatrix_(4,11) = -3;
+distanceMatrix_(4,12) = -2;
+distanceMatrix_(4,13) = -2;
+distanceMatrix_(4,14) = -4;
+distanceMatrix_(4,15) = -1;
+distanceMatrix_(4,16) = -1;
+distanceMatrix_(4,17) = -5;
+distanceMatrix_(4,18) = -3;
+distanceMatrix_(4,19) = -1;
+distanceMatrix_(5,0) = -1;
+distanceMatrix_(5,1) = 1;
+distanceMatrix_(5,2) = 0;
+distanceMatrix_(5,3) = 0;
+distanceMatrix_(5,4) = -3;
+distanceMatrix_(5,5) = 7;
+distanceMatrix_(5,6) = 2;
+distanceMatrix_(5,7) = -2;
+distanceMatrix_(5,8) = 1;
+distanceMatrix_(5,9) = -3;
+distanceMatrix_(5,10) = -2;
+distanceMatrix_(5,11) = 2;
+distanceMatrix_(5,12) = 0;
+distanceMatrix_(5,13) = -4;
+distanceMatrix_(5,14) = -1;
+distanceMatrix_(5,15) = 0;
+distanceMatrix_(5,16) = -1;
+distanceMatrix_(5,17) = -1;
+distanceMatrix_(5,18) = -1;
+distanceMatrix_(5,19) = -3;
+distanceMatrix_(6,0) = -1;
+distanceMatrix_(6,1) = 0;
+distanceMatrix_(6,2) = 0;
+distanceMatrix_(6,3) = 2;
+distanceMatrix_(6,4) = -3;
+distanceMatrix_(6,5) = 2;
+distanceMatrix_(6,6) = 6;
+distanceMatrix_(6,7) = -3;
+distanceMatrix_(6,8) = 0;
+distanceMatrix_(6,9) = -4;
+distanceMatrix_(6,10) = -3;
+distanceMatrix_(6,11) = 1;
+distanceMatrix_(6,12) = -2;
+distanceMatrix_(6,13) = -3;
+distanceMatrix_(6,14) = -1;
+distanceMatrix_(6,15) = -1;
+distanceMatrix_(6,16) = -1;
+distanceMatrix_(6,17) = -3;
+distanceMatrix_(6,18) = -2;
+distanceMatrix_(6,19) = -3;
+distanceMatrix_(7,0) = 0;
+distanceMatrix_(7,1) = -3;
+distanceMatrix_(7,2) = 0;
+distanceMatrix_(7,3) = -1;
+distanceMatrix_(7,4) = -3;
+distanceMatrix_(7,5) = -2;
+distanceMatrix_(7,6) = -3;
+distanceMatrix_(7,7) = 8;
+distanceMatrix_(7,8) = -2;
+distanceMatrix_(7,9) = -4;
+distanceMatrix_(7,10) = -4;
+distanceMatrix_(7,11) = -2;
+distanceMatrix_(7,12) = -3;
+distanceMatrix_(7,13) = -4;
+distanceMatrix_(7,14) = -2;
+distanceMatrix_(7,15) = 0;
+distanceMatrix_(7,16) = -2;
+distanceMatrix_(7,17) = -3;
+distanceMatrix_(7,18) = -3;
+distanceMatrix_(7,19) = -4;
+distanceMatrix_(8,0) = -2;
+distanceMatrix_(8,1) = 0;
+distanceMatrix_(8,2) = 1;
+distanceMatrix_(8,3) = -1;
+distanceMatrix_(8,4) = -3;
+distanceMatrix_(8,5) = 1;
+distanceMatrix_(8,6) = 0;
+distanceMatrix_(8,7) = -2;
+distanceMatrix_(8,8) = 10;
+distanceMatrix_(8,9) = -4;
+distanceMatrix_(8,10) = -3;
+distanceMatrix_(8,11) = 0;
+distanceMatrix_(8,12) = -1;
+distanceMatrix_(8,13) = -1;
+distanceMatrix_(8,14) = -2;
+distanceMatrix_(8,15) = -1;
+distanceMatrix_(8,16) = -2;
+distanceMatrix_(8,17) = -3;
+distanceMatrix_(8,18) = 2;
+distanceMatrix_(8,19) = -4;
+distanceMatrix_(9,0) = -1;
+distanceMatrix_(9,1) = -4;
+distanceMatrix_(9,2) = -3;
+distanceMatrix_(9,3) = -4;
+distanceMatrix_(9,4) = -2;
+distanceMatrix_(9,5) = -3;
+distanceMatrix_(9,6) = -4;
+distanceMatrix_(9,7) = -4;
+distanceMatrix_(9,8) = -4;
+distanceMatrix_(9,9) = 5;
+distanceMatrix_(9,10) = 2;
+distanceMatrix_(9,11) = -3;
+distanceMatrix_(9,12) = 2;
+distanceMatrix_(9,13) = 0;
+distanceMatrix_(9,14) = -3;
+distanceMatrix_(9,15) = -3;
+distanceMatrix_(9,16) = -1;
+distanceMatrix_(9,17) = -3;
+distanceMatrix_(9,18) = -1;
+distanceMatrix_(9,19) = 4;
+distanceMatrix_(10,0) = -2;
+distanceMatrix_(10,1) = -3;
+distanceMatrix_(10,2) = -4;
+distanceMatrix_(10,3) = -4;
+distanceMatrix_(10,4) = -2;
+distanceMatrix_(10,5) = -2;
+distanceMatrix_(10,6) = -3;
+distanceMatrix_(10,7) = -4;
+distanceMatrix_(10,8) = -3;
+distanceMatrix_(10,9) = 2;
+distanceMatrix_(10,10) = 5;
+distanceMatrix_(10,11) = -3;
+distanceMatrix_(10,12) = 3;
+distanceMatrix_(10,13) = 1;
+distanceMatrix_(10,14) = -4;
+distanceMatrix_(10,15) = -3;
+distanceMatrix_(10,16) = -1;
+distanceMatrix_(10,17) = -2;
+distanceMatrix_(10,18) = -1;
+distanceMatrix_(10,19) = 1;
+distanceMatrix_(11,0) = -1;
+distanceMatrix_(11,1) = 3;
+distanceMatrix_(11,2) = 0;
+distanceMatrix_(11,3) = -1;
+distanceMatrix_(11,4) = -3;
+distanceMatrix_(11,5) = 2;
+distanceMatrix_(11,6) = 1;
+distanceMatrix_(11,7) = -2;
+distanceMatrix_(11,8) = 0;
+distanceMatrix_(11,9) = -3;
+distanceMatrix_(11,10) = -3;
+distanceMatrix_(11,11) = 6;
+distanceMatrix_(11,12) = -2;
+distanceMatrix_(11,13) = -4;
+distanceMatrix_(11,14) = -1;
+distanceMatrix_(11,15) = 0;
+distanceMatrix_(11,16) = -1;
+distanceMatrix_(11,17) = -3;
+distanceMatrix_(11,18) = -2;
+distanceMatrix_(11,19) = -3;
+distanceMatrix_(12,0) = -1;
+distanceMatrix_(12,1) = -2;
+distanceMatrix_(12,2) = -2;
+distanceMatrix_(12,3) = -4;
+distanceMatrix_(12,4) = -2;
+distanceMatrix_(12,5) = 0;
+distanceMatrix_(12,6) = -2;
+distanceMatrix_(12,7) = -3;
+distanceMatrix_(12,8) = -1;
+distanceMatrix_(12,9) = 2;
+distanceMatrix_(12,10) = 3;
+distanceMatrix_(12,11) = -2;
+distanceMatrix_(12,12) = 7;
+distanceMatrix_(12,13) = 0;
+distanceMatrix_(12,14) = -3;
+distanceMatrix_(12,15) = -2;
+distanceMatrix_(12,16) = -1;
+distanceMatrix_(12,17) = -1;
+distanceMatrix_(12,18) = 0;
+distanceMatrix_(12,19) = 1;
+distanceMatrix_(13,0) = -3;
+distanceMatrix_(13,1) = -3;
+distanceMatrix_(13,2) = -4;
+distanceMatrix_(13,3) = -5;
+distanceMatrix_(13,4) = -2;
+distanceMatrix_(13,5) = -4;
+distanceMatrix_(13,6) = -3;
+distanceMatrix_(13,7) = -4;
+distanceMatrix_(13,8) = -1;
+distanceMatrix_(13,9) = 0;
+distanceMatrix_(13,10) = 1;
+distanceMatrix_(13,11) = -4;
+distanceMatrix_(13,12) = 0;
+distanceMatrix_(13,13) = 8;
+distanceMatrix_(13,14) = -4;
+distanceMatrix_(13,15) = -3;
+distanceMatrix_(13,16) = -2;
+distanceMatrix_(13,17) = 1;
+distanceMatrix_(13,18) = 4;
+distanceMatrix_(13,19) = -1;
+distanceMatrix_(14,0) = -1;
+distanceMatrix_(14,1) = -3;
+distanceMatrix_(14,2) = -2;
+distanceMatrix_(14,3) = -1;
+distanceMatrix_(14,4) = -4;
+distanceMatrix_(14,5) = -1;
+distanceMatrix_(14,6) = -1;
+distanceMatrix_(14,7) = -2;
+distanceMatrix_(14,8) = -2;
+distanceMatrix_(14,9) = -3;
+distanceMatrix_(14,10) = -4;
+distanceMatrix_(14,11) = -1;
+distanceMatrix_(14,12) = -3;
+distanceMatrix_(14,13) = -4;
+distanceMatrix_(14,14) = 10;
+distanceMatrix_(14,15) = -1;
+distanceMatrix_(14,16) = -1;
+distanceMatrix_(14,17) = -4;
+distanceMatrix_(14,18) = -3;
+distanceMatrix_(14,19) = -3;
+distanceMatrix_(15,0) = 1;
+distanceMatrix_(15,1) = -1;
+distanceMatrix_(15,2) = 1;
+distanceMatrix_(15,3) = 0;
+distanceMatrix_(15,4) = -1;
+distanceMatrix_(15,5) = 0;
+distanceMatrix_(15,6) = -1;
+distanceMatrix_(15,7) = 0;
+distanceMatrix_(15,8) = -1;
+distanceMatrix_(15,9) = -3;
+distanceMatrix_(15,10) = -3;
+distanceMatrix_(15,11) = 0;
+distanceMatrix_(15,12) = -2;
+distanceMatrix_(15,13) = -3;
+distanceMatrix_(15,14) = -1;
+distanceMatrix_(15,15) = 5;
+distanceMatrix_(15,16) = 2;
+distanceMatrix_(15,17) = -4;
+distanceMatrix_(15,18) = -2;
+distanceMatrix_(15,19) = -2;
+distanceMatrix_(16,0) = 0;
+distanceMatrix_(16,1) = -1;
+distanceMatrix_(16,2) = 0;
+distanceMatrix_(16,3) = -1;
+distanceMatrix_(16,4) = -1;
+distanceMatrix_(16,5) = -1;
+distanceMatrix_(16,6) = -1;
+distanceMatrix_(16,7) = -2;
+distanceMatrix_(16,8) = -2;
+distanceMatrix_(16,9) = -1;
+distanceMatrix_(16,10) = -1;
+distanceMatrix_(16,11) = -1;
+distanceMatrix_(16,12) = -1;
+distanceMatrix_(16,13) = -2;
+distanceMatrix_(16,14) = -1;
+distanceMatrix_(16,15) = 2;
+distanceMatrix_(16,16) = 5;
+distanceMatrix_(16,17) = -3;
+distanceMatrix_(16,18) = -2;
+distanceMatrix_(16,19) = 0;
+distanceMatrix_(17,0) = -3;
+distanceMatrix_(17,1) = -3;
+distanceMatrix_(17,2) = -4;
+distanceMatrix_(17,3) = -5;
+distanceMatrix_(17,4) = -5;
+distanceMatrix_(17,5) = -1;
+distanceMatrix_(17,6) = -3;
+distanceMatrix_(17,7) = -3;
+distanceMatrix_(17,8) = -3;
+distanceMatrix_(17,9) = -3;
+distanceMatrix_(17,10) = -2;
+distanceMatrix_(17,11) = -3;
+distanceMatrix_(17,12) = -1;
+distanceMatrix_(17,13) = 1;
+distanceMatrix_(17,14) = -4;
+distanceMatrix_(17,15) = -4;
+distanceMatrix_(17,16) = -3;
+distanceMatrix_(17,17) = 15;
+distanceMatrix_(17,18) = 2;
+distanceMatrix_(17,19) = -3;
+distanceMatrix_(18,0) = -2;
+distanceMatrix_(18,1) = -1;
+distanceMatrix_(18,2) = -2;
+distanceMatrix_(18,3) = -3;
+distanceMatrix_(18,4) = -3;
+distanceMatrix_(18,5) = -1;
+distanceMatrix_(18,6) = -2;
+distanceMatrix_(18,7) = -3;
+distanceMatrix_(18,8) = 2;
+distanceMatrix_(18,9) = -1;
+distanceMatrix_(18,10) = -1;
+distanceMatrix_(18,11) = -2;
+distanceMatrix_(18,12) = 0;
+distanceMatrix_(18,13) = 4;
+distanceMatrix_(18,14) = -3;
+distanceMatrix_(18,15) = -2;
+distanceMatrix_(18,16) = -2;
+distanceMatrix_(18,17) = 2;
+distanceMatrix_(18,18) = 8;
+distanceMatrix_(18,19) = -1;
+distanceMatrix_(19,0) = 0;
+distanceMatrix_(19,1) = -3;
+distanceMatrix_(19,2) = -3;
+distanceMatrix_(19,3) = -4;
+distanceMatrix_(19,4) = -1;
+distanceMatrix_(19,5) = -3;
+distanceMatrix_(19,6) = -3;
+distanceMatrix_(19,7) = -4;
+distanceMatrix_(19,8) = -4;
+distanceMatrix_(19,9) = 4;
+distanceMatrix_(19,10) = 1;
+distanceMatrix_(19,11) = -3;
+distanceMatrix_(19,12) = 1;
+distanceMatrix_(19,13) = -1;
+distanceMatrix_(19,14) = -3;
+distanceMatrix_(19,15) = -2;
+distanceMatrix_(19,16) = 0;
+distanceMatrix_(19,17) = -3;
+distanceMatrix_(19,18) = -1;
+distanceMatrix_(19,19) = 5;
diff --git a/src/Bpp/Seq/AlphabetIndex/__GranthamMatrixCode b/src/Bpp/Seq/AlphabetIndex/__GranthamMatrixCode
new file mode 100644
index 0000000..b1f9dcf
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/__GranthamMatrixCode
@@ -0,0 +1,827 @@
+//library(seqinr)
+//data(aaindex)
+
+distanceMatrix_(0,0) = 0;
+distanceMatrix_(1,0) = 112;
+distanceMatrix_(1,1) = 0;
+distanceMatrix_(2,0) = 111;
+distanceMatrix_(2,1) = 86;
+distanceMatrix_(2,2) = 0;
+distanceMatrix_(3,0) = 126;
+distanceMatrix_(3,1) = 96;
+distanceMatrix_(3,2) = 23;
+distanceMatrix_(3,3) = 0;
+distanceMatrix_(4,0) = 195;
+distanceMatrix_(4,1) = 180;
+distanceMatrix_(4,2) = 139;
+distanceMatrix_(4,3) = 154;
+distanceMatrix_(4,4) = 0;
+distanceMatrix_(5,0) = 91;
+distanceMatrix_(5,1) = 43;
+distanceMatrix_(5,2) = 46;
+distanceMatrix_(5,3) = 61;
+distanceMatrix_(5,4) = 154;
+distanceMatrix_(5,5) = 0;
+distanceMatrix_(6,0) = 107;
+distanceMatrix_(6,1) = 54;
+distanceMatrix_(6,2) = 42;
+distanceMatrix_(6,3) = 45;
+distanceMatrix_(6,4) = 170;
+distanceMatrix_(6,5) = 29;
+distanceMatrix_(6,6) = 0;
+distanceMatrix_(7,0) = 60;
+distanceMatrix_(7,1) = 125;
+distanceMatrix_(7,2) = 80;
+distanceMatrix_(7,3) = 94;
+distanceMatrix_(7,4) = 159;
+distanceMatrix_(7,5) = 87;
+distanceMatrix_(7,6) = 98;
+distanceMatrix_(7,7) = 0;
+distanceMatrix_(8,0) = 86;
+distanceMatrix_(8,1) = 29;
+distanceMatrix_(8,2) = 68;
+distanceMatrix_(8,3) = 81;
+distanceMatrix_(8,4) = 174;
+distanceMatrix_(8,5) = 24;
+distanceMatrix_(8,6) = 40;
+distanceMatrix_(8,7) = 98;
+distanceMatrix_(8,8) = 0;
+distanceMatrix_(9,0) = 94;
+distanceMatrix_(9,1) = 97;
+distanceMatrix_(9,2) = 149;
+distanceMatrix_(9,3) = 168;
+distanceMatrix_(9,4) = 198;
+distanceMatrix_(9,5) = 109;
+distanceMatrix_(9,6) = 134;
+distanceMatrix_(9,7) = 135;
+distanceMatrix_(9,8) = 94;
+distanceMatrix_(9,9) = 0;
+distanceMatrix_(10,0) = 96;
+distanceMatrix_(10,1) = 102;
+distanceMatrix_(10,2) = 153;
+distanceMatrix_(10,3) = 172;
+distanceMatrix_(10,4) = 198;
+distanceMatrix_(10,5) = 113;
+distanceMatrix_(10,6) = 138;
+distanceMatrix_(10,7) = 138;
+distanceMatrix_(10,8) = 99;
+distanceMatrix_(10,9) = 5;
+distanceMatrix_(10,10) = 0;
+distanceMatrix_(11,0) = 106;
+distanceMatrix_(11,1) = 26;
+distanceMatrix_(11,2) = 94;
+distanceMatrix_(11,3) = 101;
+distanceMatrix_(11,4) = 202;
+distanceMatrix_(11,5) = 53;
+distanceMatrix_(11,6) = 56;
+distanceMatrix_(11,7) = 127;
+distanceMatrix_(11,8) = 32;
+distanceMatrix_(11,9) = 102;
+distanceMatrix_(11,10) = 107;
+distanceMatrix_(11,11) = 0;
+distanceMatrix_(12,0) = 84;
+distanceMatrix_(12,1) = 91;
+distanceMatrix_(12,2) = 142;
+distanceMatrix_(12,3) = 160;
+distanceMatrix_(12,4) = 196;
+distanceMatrix_(12,5) = 101;
+distanceMatrix_(12,6) = 126;
+distanceMatrix_(12,7) = 127;
+distanceMatrix_(12,8) = 87;
+distanceMatrix_(12,9) = 10;
+distanceMatrix_(12,10) = 15;
+distanceMatrix_(12,11) = 95;
+distanceMatrix_(12,12) = 0;
+distanceMatrix_(13,0) = 113;
+distanceMatrix_(13,1) = 97;
+distanceMatrix_(13,2) = 158;
+distanceMatrix_(13,3) = 177;
+distanceMatrix_(13,4) = 205;
+distanceMatrix_(13,5) = 116;
+distanceMatrix_(13,6) = 140;
+distanceMatrix_(13,7) = 153;
+distanceMatrix_(13,8) = 100;
+distanceMatrix_(13,9) = 21;
+distanceMatrix_(13,10) = 22;
+distanceMatrix_(13,11) = 102;
+distanceMatrix_(13,12) = 28;
+distanceMatrix_(13,13) = 0;
+distanceMatrix_(14,0) = 27;
+distanceMatrix_(14,1) = 103;
+distanceMatrix_(14,2) = 91;
+distanceMatrix_(14,3) = 108;
+distanceMatrix_(14,4) = 169;
+distanceMatrix_(14,5) = 76;
+distanceMatrix_(14,6) = 93;
+distanceMatrix_(14,7) = 42;
+distanceMatrix_(14,8) = 77;
+distanceMatrix_(14,9) = 95;
+distanceMatrix_(14,10) = 98;
+distanceMatrix_(14,11) = 103;
+distanceMatrix_(14,12) = 87;
+distanceMatrix_(14,13) = 114;
+distanceMatrix_(14,14) = 0;
+distanceMatrix_(15,0) = 99;
+distanceMatrix_(15,1) = 110;
+distanceMatrix_(15,2) = 46;
+distanceMatrix_(15,3) = 65;
+distanceMatrix_(15,4) = 112;
+distanceMatrix_(15,5) = 68;
+distanceMatrix_(15,6) = 80;
+distanceMatrix_(15,7) = 56;
+distanceMatrix_(15,8) = 89;
+distanceMatrix_(15,9) = 142;
+distanceMatrix_(15,10) = 145;
+distanceMatrix_(15,11) = 121;
+distanceMatrix_(15,12) = 135;
+distanceMatrix_(15,13) = 155;
+distanceMatrix_(15,14) = 74;
+distanceMatrix_(15,15) = 0;
+distanceMatrix_(16,0) = 58;
+distanceMatrix_(16,1) = 71;
+distanceMatrix_(16,2) = 65;
+distanceMatrix_(16,3) = 85;
+distanceMatrix_(16,4) = 149;
+distanceMatrix_(16,5) = 42;
+distanceMatrix_(16,6) = 65;
+distanceMatrix_(16,7) = 59;
+distanceMatrix_(16,8) = 47;
+distanceMatrix_(16,9) = 89;
+distanceMatrix_(16,10) = 92;
+distanceMatrix_(16,11) = 78;
+distanceMatrix_(16,12) = 81;
+distanceMatrix_(16,13) = 103;
+distanceMatrix_(16,14) = 38;
+distanceMatrix_(16,15) = 58;
+distanceMatrix_(16,16) = 0;
+distanceMatrix_(17,0) = 148;
+distanceMatrix_(17,1) = 101;
+distanceMatrix_(17,2) = 174;
+distanceMatrix_(17,3) = 181;
+distanceMatrix_(17,4) = 215;
+distanceMatrix_(17,5) = 130;
+distanceMatrix_(17,6) = 152;
+distanceMatrix_(17,7) = 184;
+distanceMatrix_(17,8) = 115;
+distanceMatrix_(17,9) = 61;
+distanceMatrix_(17,10) = 61;
+distanceMatrix_(17,11) = 110;
+distanceMatrix_(17,12) = 67;
+distanceMatrix_(17,13) = 40;
+distanceMatrix_(17,14) = 147;
+distanceMatrix_(17,15) = 177;
+distanceMatrix_(17,16) = 128;
+distanceMatrix_(17,17) = 0;
+distanceMatrix_(18,0) = 112;
+distanceMatrix_(18,1) = 77;
+distanceMatrix_(18,2) = 143;
+distanceMatrix_(18,3) = 160;
+distanceMatrix_(18,4) = 194;
+distanceMatrix_(18,5) = 99;
+distanceMatrix_(18,6) = 122;
+distanceMatrix_(18,7) = 147;
+distanceMatrix_(18,8) = 83;
+distanceMatrix_(18,9) = 33;
+distanceMatrix_(18,10) = 36;
+distanceMatrix_(18,11) = 85;
+distanceMatrix_(18,12) = 36;
+distanceMatrix_(18,13) = 22;
+distanceMatrix_(18,14) = 110;
+distanceMatrix_(18,15) = 144;
+distanceMatrix_(18,16) = 92;
+distanceMatrix_(18,17) = 37;
+distanceMatrix_(18,18) = 0;
+distanceMatrix_(19,0) = 64;
+distanceMatrix_(19,1) = 96;
+distanceMatrix_(19,2) = 133;
+distanceMatrix_(19,3) = 152;
+distanceMatrix_(19,4) = 192;
+distanceMatrix_(19,5) = 96;
+distanceMatrix_(19,6) = 121;
+distanceMatrix_(19,7) = 109;
+distanceMatrix_(19,8) = 84;
+distanceMatrix_(19,9) = 29;
+distanceMatrix_(19,10) = 32;
+distanceMatrix_(19,11) = 97;
+distanceMatrix_(19,12) = 21;
+distanceMatrix_(19,13) = 50;
+distanceMatrix_(19,14) = 68;
+distanceMatrix_(19,15) = 124;
+distanceMatrix_(19,16) = 69;
+distanceMatrix_(19,17) = 88;
+distanceMatrix_(19,18) = 55;
+distanceMatrix_(19,19) = 0;
+distanceMatrix_(0,1) = -112;
+distanceMatrix_(0,2) = -111;
+distanceMatrix_(0,3) = -126;
+distanceMatrix_(0,4) = -195;
+distanceMatrix_(0,5) = -91;
+distanceMatrix_(0,6) = -107;
+distanceMatrix_(0,7) = -60;
+distanceMatrix_(0,8) = -86;
+distanceMatrix_(0,9) = -94;
+distanceMatrix_(0,10) = -96;
+distanceMatrix_(0,11) = -106;
+distanceMatrix_(0,12) = -84;
+distanceMatrix_(0,13) = -113;
+distanceMatrix_(0,14) = -27;
+distanceMatrix_(0,15) = -99;
+distanceMatrix_(0,16) = -58;
+distanceMatrix_(0,17) = -148;
+distanceMatrix_(0,18) = -112;
+distanceMatrix_(0,19) = -64;
+distanceMatrix_(1,2) = -86;
+distanceMatrix_(1,3) = -96;
+distanceMatrix_(1,4) = -180;
+distanceMatrix_(1,5) = -43;
+distanceMatrix_(1,6) = -54;
+distanceMatrix_(1,7) = -125;
+distanceMatrix_(1,8) = -29;
+distanceMatrix_(1,9) = -97;
+distanceMatrix_(1,10) = -102;
+distanceMatrix_(1,11) = -26;
+distanceMatrix_(1,12) = -91;
+distanceMatrix_(1,13) = -97;
+distanceMatrix_(1,14) = -103;
+distanceMatrix_(1,15) = -110;
+distanceMatrix_(1,16) = -71;
+distanceMatrix_(1,17) = -101;
+distanceMatrix_(1,18) = -77;
+distanceMatrix_(1,19) = -96;
+distanceMatrix_(2,3) = -23;
+distanceMatrix_(2,4) = -139;
+distanceMatrix_(2,5) = -46;
+distanceMatrix_(2,6) = -42;
+distanceMatrix_(2,7) = -80;
+distanceMatrix_(2,8) = -68;
+distanceMatrix_(2,9) = -149;
+distanceMatrix_(2,10) = -153;
+distanceMatrix_(2,11) = -94;
+distanceMatrix_(2,12) = -142;
+distanceMatrix_(2,13) = -158;
+distanceMatrix_(2,14) = -91;
+distanceMatrix_(2,15) = -46;
+distanceMatrix_(2,16) = -65;
+distanceMatrix_(2,17) = -174;
+distanceMatrix_(2,18) = -143;
+distanceMatrix_(2,19) = -133;
+distanceMatrix_(3,4) = -154;
+distanceMatrix_(3,5) = -61;
+distanceMatrix_(3,6) = -45;
+distanceMatrix_(3,7) = -94;
+distanceMatrix_(3,8) = -81;
+distanceMatrix_(3,9) = -168;
+distanceMatrix_(3,10) = -172;
+distanceMatrix_(3,11) = -101;
+distanceMatrix_(3,12) = -160;
+distanceMatrix_(3,13) = -177;
+distanceMatrix_(3,14) = -108;
+distanceMatrix_(3,15) = -65;
+distanceMatrix_(3,16) = -85;
+distanceMatrix_(3,17) = -181;
+distanceMatrix_(3,18) = -160;
+distanceMatrix_(3,19) = -152;
+distanceMatrix_(4,5) = -154;
+distanceMatrix_(4,6) = -170;
+distanceMatrix_(4,7) = -159;
+distanceMatrix_(4,8) = -174;
+distanceMatrix_(4,9) = -198;
+distanceMatrix_(4,10) = -198;
+distanceMatrix_(4,11) = -202;
+distanceMatrix_(4,12) = -196;
+distanceMatrix_(4,13) = -205;
+distanceMatrix_(4,14) = -169;
+distanceMatrix_(4,15) = -112;
+distanceMatrix_(4,16) = -149;
+distanceMatrix_(4,17) = -215;
+distanceMatrix_(4,18) = -194;
+distanceMatrix_(4,19) = -192;
+distanceMatrix_(5,6) = -29;
+distanceMatrix_(5,7) = -87;
+distanceMatrix_(5,8) = -24;
+distanceMatrix_(5,9) = -109;
+distanceMatrix_(5,10) = -113;
+distanceMatrix_(5,11) = -53;
+distanceMatrix_(5,12) = -101;
+distanceMatrix_(5,13) = -116;
+distanceMatrix_(5,14) = -76;
+distanceMatrix_(5,15) = -68;
+distanceMatrix_(5,16) = -42;
+distanceMatrix_(5,17) = -130;
+distanceMatrix_(5,18) = -99;
+distanceMatrix_(5,19) = -96;
+distanceMatrix_(6,7) = -98;
+distanceMatrix_(6,8) = -40;
+distanceMatrix_(6,9) = -134;
+distanceMatrix_(6,10) = -138;
+distanceMatrix_(6,11) = -56;
+distanceMatrix_(6,12) = -126;
+distanceMatrix_(6,13) = -140;
+distanceMatrix_(6,14) = -93;
+distanceMatrix_(6,15) = -80;
+distanceMatrix_(6,16) = -65;
+distanceMatrix_(6,17) = -152;
+distanceMatrix_(6,18) = -122;
+distanceMatrix_(6,19) = -121;
+distanceMatrix_(7,8) = -98;
+distanceMatrix_(7,9) = -135;
+distanceMatrix_(7,10) = -138;
+distanceMatrix_(7,11) = -127;
+distanceMatrix_(7,12) = -127;
+distanceMatrix_(7,13) = -153;
+distanceMatrix_(7,14) = -42;
+distanceMatrix_(7,15) = -56;
+distanceMatrix_(7,16) = -59;
+distanceMatrix_(7,17) = -184;
+distanceMatrix_(7,18) = -147;
+distanceMatrix_(7,19) = -109;
+distanceMatrix_(8,9) = -94;
+distanceMatrix_(8,10) = -99;
+distanceMatrix_(8,11) = -32;
+distanceMatrix_(8,12) = -87;
+distanceMatrix_(8,13) = -100;
+distanceMatrix_(8,14) = -77;
+distanceMatrix_(8,15) = -89;
+distanceMatrix_(8,16) = -47;
+distanceMatrix_(8,17) = -115;
+distanceMatrix_(8,18) = -83;
+distanceMatrix_(8,19) = -84;
+distanceMatrix_(9,10) = -5;
+distanceMatrix_(9,11) = -102;
+distanceMatrix_(9,12) = -10;
+distanceMatrix_(9,13) = -21;
+distanceMatrix_(9,14) = -95;
+distanceMatrix_(9,15) = -142;
+distanceMatrix_(9,16) = -89;
+distanceMatrix_(9,17) = -61;
+distanceMatrix_(9,18) = -33;
+distanceMatrix_(9,19) = -29;
+distanceMatrix_(10,11) = -107;
+distanceMatrix_(10,12) = -15;
+distanceMatrix_(10,13) = -22;
+distanceMatrix_(10,14) = -98;
+distanceMatrix_(10,15) = -145;
+distanceMatrix_(10,16) = -92;
+distanceMatrix_(10,17) = -61;
+distanceMatrix_(10,18) = -36;
+distanceMatrix_(10,19) = -32;
+distanceMatrix_(11,12) = -95;
+distanceMatrix_(11,13) = -102;
+distanceMatrix_(11,14) = -103;
+distanceMatrix_(11,15) = -121;
+distanceMatrix_(11,16) = -78;
+distanceMatrix_(11,17) = -110;
+distanceMatrix_(11,18) = -85;
+distanceMatrix_(11,19) = -97;
+distanceMatrix_(12,13) = -28;
+distanceMatrix_(12,14) = -87;
+distanceMatrix_(12,15) = -135;
+distanceMatrix_(12,16) = -81;
+distanceMatrix_(12,17) = -67;
+distanceMatrix_(12,18) = -36;
+distanceMatrix_(12,19) = -21;
+distanceMatrix_(13,14) = -114;
+distanceMatrix_(13,15) = -155;
+distanceMatrix_(13,16) = -103;
+distanceMatrix_(13,17) = -40;
+distanceMatrix_(13,18) = -22;
+distanceMatrix_(13,19) = -50;
+distanceMatrix_(14,15) = -74;
+distanceMatrix_(14,16) = -38;
+distanceMatrix_(14,17) = -147;
+distanceMatrix_(14,18) = -110;
+distanceMatrix_(14,19) = -68;
+distanceMatrix_(15,16) = -58;
+distanceMatrix_(15,17) = -177;
+distanceMatrix_(15,18) = -144;
+distanceMatrix_(15,19) = -124;
+distanceMatrix_(16,17) = -128;
+distanceMatrix_(16,18) = -92;
+distanceMatrix_(16,19) = -69;
+distanceMatrix_(17,18) = -37;
+distanceMatrix_(17,19) = -88;
+distanceMatrix_(18,19) = -55;
+
+//data<-data.frame(composition=aaindex[["GRAR740101"]]$I,polarity=aaindex[["GRAR740102"]]$I,volume=aaindex[["GRAR740103"]]$I)
+//library(ade4)
+//pca<-dudi.pca(data)
+//
+//plot(pca$li[,1:2],type="n")
+//text(pca$li[,1:2],rownames(data))
+//
+//s.corcircle(pca$co)
+//layout(matrix(1:3,nrow=1))
+//a1<-pca$li[,1]; names(a1)<-rownames(data); dotchart(sort(a1))
+//a2<-pca$li[,2]; names(a2)<-rownames(data); dotchart(sort(a2))
+//a3<-pca$li[,3]; names(a3)<-rownames(data); dotchart(sort(a3))
+//
+//x<-pca$li[,1]
+//m<-matrix(nrow=20, ncol=20)
+//unlink("tmp.cpp")
+//for(i in 1:length(x))
+// for(j in 1:length(x))
+// {
+// m[i,j]<-sign(x[j] - x[i])
+// cat("signMatrix_(",(i-1),", ",(j-1),") = ", m[i,j], ";\n",sep="",file="tmp.cpp",append=TRUE)
+// }
+
+signMatrix_(0, 0) = 0;
+signMatrix_(0, 1) = 1;
+signMatrix_(0, 2) = -1;
+signMatrix_(0, 3) = -1;
+signMatrix_(0, 4) = -1;
+signMatrix_(0, 5) = -1;
+signMatrix_(0, 6) = -1;
+signMatrix_(0, 7) = -1;
+signMatrix_(0, 8) = -1;
+signMatrix_(0, 9) = 1;
+signMatrix_(0, 10) = 1;
+signMatrix_(0, 11) = 1;
+signMatrix_(0, 12) = 1;
+signMatrix_(0, 13) = 1;
+signMatrix_(0, 14) = -1;
+signMatrix_(0, 15) = -1;
+signMatrix_(0, 16) = -1;
+signMatrix_(0, 17) = 1;
+signMatrix_(0, 18) = 1;
+signMatrix_(0, 19) = 1;
+signMatrix_(1, 0) = -1;
+signMatrix_(1, 1) = 0;
+signMatrix_(1, 2) = -1;
+signMatrix_(1, 3) = -1;
+signMatrix_(1, 4) = -1;
+signMatrix_(1, 5) = -1;
+signMatrix_(1, 6) = -1;
+signMatrix_(1, 7) = -1;
+signMatrix_(1, 8) = -1;
+signMatrix_(1, 9) = 1;
+signMatrix_(1, 10) = 1;
+signMatrix_(1, 11) = 1;
+signMatrix_(1, 12) = 1;
+signMatrix_(1, 13) = 1;
+signMatrix_(1, 14) = -1;
+signMatrix_(1, 15) = -1;
+signMatrix_(1, 16) = -1;
+signMatrix_(1, 17) = 1;
+signMatrix_(1, 18) = 1;
+signMatrix_(1, 19) = 1;
+signMatrix_(2, 0) = 1;
+signMatrix_(2, 1) = 1;
+signMatrix_(2, 2) = 0;
+signMatrix_(2, 3) = -1;
+signMatrix_(2, 4) = -1;
+signMatrix_(2, 5) = 1;
+signMatrix_(2, 6) = 1;
+signMatrix_(2, 7) = 1;
+signMatrix_(2, 8) = 1;
+signMatrix_(2, 9) = 1;
+signMatrix_(2, 10) = 1;
+signMatrix_(2, 11) = 1;
+signMatrix_(2, 12) = 1;
+signMatrix_(2, 13) = 1;
+signMatrix_(2, 14) = 1;
+signMatrix_(2, 15) = 1;
+signMatrix_(2, 16) = 1;
+signMatrix_(2, 17) = 1;
+signMatrix_(2, 18) = 1;
+signMatrix_(2, 19) = 1;
+signMatrix_(3, 0) = 1;
+signMatrix_(3, 1) = 1;
+signMatrix_(3, 2) = 1;
+signMatrix_(3, 3) = 0;
+signMatrix_(3, 4) = 1;
+signMatrix_(3, 5) = 1;
+signMatrix_(3, 6) = 1;
+signMatrix_(3, 7) = 1;
+signMatrix_(3, 8) = 1;
+signMatrix_(3, 9) = 1;
+signMatrix_(3, 10) = 1;
+signMatrix_(3, 11) = 1;
+signMatrix_(3, 12) = 1;
+signMatrix_(3, 13) = 1;
+signMatrix_(3, 14) = 1;
+signMatrix_(3, 15) = 1;
+signMatrix_(3, 16) = 1;
+signMatrix_(3, 17) = 1;
+signMatrix_(3, 18) = 1;
+signMatrix_(3, 19) = 1;
+signMatrix_(4, 0) = 1;
+signMatrix_(4, 1) = 1;
+signMatrix_(4, 2) = 1;
+signMatrix_(4, 3) = -1;
+signMatrix_(4, 4) = 0;
+signMatrix_(4, 5) = 1;
+signMatrix_(4, 6) = 1;
+signMatrix_(4, 7) = 1;
+signMatrix_(4, 8) = 1;
+signMatrix_(4, 9) = 1;
+signMatrix_(4, 10) = 1;
+signMatrix_(4, 11) = 1;
+signMatrix_(4, 12) = 1;
+signMatrix_(4, 13) = 1;
+signMatrix_(4, 14) = 1;
+signMatrix_(4, 15) = 1;
+signMatrix_(4, 16) = 1;
+signMatrix_(4, 17) = 1;
+signMatrix_(4, 18) = 1;
+signMatrix_(4, 19) = 1;
+signMatrix_(5, 0) = 1;
+signMatrix_(5, 1) = 1;
+signMatrix_(5, 2) = -1;
+signMatrix_(5, 3) = -1;
+signMatrix_(5, 4) = -1;
+signMatrix_(5, 5) = 0;
+signMatrix_(5, 6) = -1;
+signMatrix_(5, 7) = -1;
+signMatrix_(5, 8) = 1;
+signMatrix_(5, 9) = 1;
+signMatrix_(5, 10) = 1;
+signMatrix_(5, 11) = 1;
+signMatrix_(5, 12) = 1;
+signMatrix_(5, 13) = 1;
+signMatrix_(5, 14) = 1;
+signMatrix_(5, 15) = -1;
+signMatrix_(5, 16) = 1;
+signMatrix_(5, 17) = 1;
+signMatrix_(5, 18) = 1;
+signMatrix_(5, 19) = 1;
+signMatrix_(6, 0) = 1;
+signMatrix_(6, 1) = 1;
+signMatrix_(6, 2) = -1;
+signMatrix_(6, 3) = -1;
+signMatrix_(6, 4) = -1;
+signMatrix_(6, 5) = 1;
+signMatrix_(6, 6) = 0;
+signMatrix_(6, 7) = -1;
+signMatrix_(6, 8) = 1;
+signMatrix_(6, 9) = 1;
+signMatrix_(6, 10) = 1;
+signMatrix_(6, 11) = 1;
+signMatrix_(6, 12) = 1;
+signMatrix_(6, 13) = 1;
+signMatrix_(6, 14) = 1;
+signMatrix_(6, 15) = -1;
+signMatrix_(6, 16) = 1;
+signMatrix_(6, 17) = 1;
+signMatrix_(6, 18) = 1;
+signMatrix_(6, 19) = 1;
+signMatrix_(7, 0) = 1;
+signMatrix_(7, 1) = 1;
+signMatrix_(7, 2) = -1;
+signMatrix_(7, 3) = -1;
+signMatrix_(7, 4) = -1;
+signMatrix_(7, 5) = 1;
+signMatrix_(7, 6) = 1;
+signMatrix_(7, 7) = 0;
+signMatrix_(7, 8) = 1;
+signMatrix_(7, 9) = 1;
+signMatrix_(7, 10) = 1;
+signMatrix_(7, 11) = 1;
+signMatrix_(7, 12) = 1;
+signMatrix_(7, 13) = 1;
+signMatrix_(7, 14) = 1;
+signMatrix_(7, 15) = -1;
+signMatrix_(7, 16) = 1;
+signMatrix_(7, 17) = 1;
+signMatrix_(7, 18) = 1;
+signMatrix_(7, 19) = 1;
+signMatrix_(8, 0) = 1;
+signMatrix_(8, 1) = 1;
+signMatrix_(8, 2) = -1;
+signMatrix_(8, 3) = -1;
+signMatrix_(8, 4) = -1;
+signMatrix_(8, 5) = -1;
+signMatrix_(8, 6) = -1;
+signMatrix_(8, 7) = -1;
+signMatrix_(8, 8) = 0;
+signMatrix_(8, 9) = 1;
+signMatrix_(8, 10) = 1;
+signMatrix_(8, 11) = 1;
+signMatrix_(8, 12) = 1;
+signMatrix_(8, 13) = 1;
+signMatrix_(8, 14) = -1;
+signMatrix_(8, 15) = -1;
+signMatrix_(8, 16) = -1;
+signMatrix_(8, 17) = 1;
+signMatrix_(8, 18) = 1;
+signMatrix_(8, 19) = 1;
+signMatrix_(9, 0) = -1;
+signMatrix_(9, 1) = -1;
+signMatrix_(9, 2) = -1;
+signMatrix_(9, 3) = -1;
+signMatrix_(9, 4) = -1;
+signMatrix_(9, 5) = -1;
+signMatrix_(9, 6) = -1;
+signMatrix_(9, 7) = -1;
+signMatrix_(9, 8) = -1;
+signMatrix_(9, 9) = 0;
+signMatrix_(9, 10) = 1;
+signMatrix_(9, 11) = -1;
+signMatrix_(9, 12) = -1;
+signMatrix_(9, 13) = 1;
+signMatrix_(9, 14) = -1;
+signMatrix_(9, 15) = -1;
+signMatrix_(9, 16) = -1;
+signMatrix_(9, 17) = 1;
+signMatrix_(9, 18) = -1;
+signMatrix_(9, 19) = -1;
+signMatrix_(10, 0) = -1;
+signMatrix_(10, 1) = -1;
+signMatrix_(10, 2) = -1;
+signMatrix_(10, 3) = -1;
+signMatrix_(10, 4) = -1;
+signMatrix_(10, 5) = -1;
+signMatrix_(10, 6) = -1;
+signMatrix_(10, 7) = -1;
+signMatrix_(10, 8) = -1;
+signMatrix_(10, 9) = -1;
+signMatrix_(10, 10) = 0;
+signMatrix_(10, 11) = -1;
+signMatrix_(10, 12) = -1;
+signMatrix_(10, 13) = 1;
+signMatrix_(10, 14) = -1;
+signMatrix_(10, 15) = -1;
+signMatrix_(10, 16) = -1;
+signMatrix_(10, 17) = 1;
+signMatrix_(10, 18) = -1;
+signMatrix_(10, 19) = -1;
+signMatrix_(11, 0) = -1;
+signMatrix_(11, 1) = -1;
+signMatrix_(11, 2) = -1;
+signMatrix_(11, 3) = -1;
+signMatrix_(11, 4) = -1;
+signMatrix_(11, 5) = -1;
+signMatrix_(11, 6) = -1;
+signMatrix_(11, 7) = -1;
+signMatrix_(11, 8) = -1;
+signMatrix_(11, 9) = 1;
+signMatrix_(11, 10) = 1;
+signMatrix_(11, 11) = 0;
+signMatrix_(11, 12) = 1;
+signMatrix_(11, 13) = 1;
+signMatrix_(11, 14) = -1;
+signMatrix_(11, 15) = -1;
+signMatrix_(11, 16) = -1;
+signMatrix_(11, 17) = 1;
+signMatrix_(11, 18) = 1;
+signMatrix_(11, 19) = 1;
+signMatrix_(12, 0) = -1;
+signMatrix_(12, 1) = -1;
+signMatrix_(12, 2) = -1;
+signMatrix_(12, 3) = -1;
+signMatrix_(12, 4) = -1;
+signMatrix_(12, 5) = -1;
+signMatrix_(12, 6) = -1;
+signMatrix_(12, 7) = -1;
+signMatrix_(12, 8) = -1;
+signMatrix_(12, 9) = 1;
+signMatrix_(12, 10) = 1;
+signMatrix_(12, 11) = -1;
+signMatrix_(12, 12) = 0;
+signMatrix_(12, 13) = 1;
+signMatrix_(12, 14) = -1;
+signMatrix_(12, 15) = -1;
+signMatrix_(12, 16) = -1;
+signMatrix_(12, 17) = 1;
+signMatrix_(12, 18) = 1;
+signMatrix_(12, 19) = -1;
+signMatrix_(13, 0) = -1;
+signMatrix_(13, 1) = -1;
+signMatrix_(13, 2) = -1;
+signMatrix_(13, 3) = -1;
+signMatrix_(13, 4) = -1;
+signMatrix_(13, 5) = -1;
+signMatrix_(13, 6) = -1;
+signMatrix_(13, 7) = -1;
+signMatrix_(13, 8) = -1;
+signMatrix_(13, 9) = -1;
+signMatrix_(13, 10) = -1;
+signMatrix_(13, 11) = -1;
+signMatrix_(13, 12) = -1;
+signMatrix_(13, 13) = 0;
+signMatrix_(13, 14) = -1;
+signMatrix_(13, 15) = -1;
+signMatrix_(13, 16) = -1;
+signMatrix_(13, 17) = 1;
+signMatrix_(13, 18) = -1;
+signMatrix_(13, 19) = -1;
+signMatrix_(14, 0) = 1;
+signMatrix_(14, 1) = 1;
+signMatrix_(14, 2) = -1;
+signMatrix_(14, 3) = -1;
+signMatrix_(14, 4) = -1;
+signMatrix_(14, 5) = -1;
+signMatrix_(14, 6) = -1;
+signMatrix_(14, 7) = -1;
+signMatrix_(14, 8) = 1;
+signMatrix_(14, 9) = 1;
+signMatrix_(14, 10) = 1;
+signMatrix_(14, 11) = 1;
+signMatrix_(14, 12) = 1;
+signMatrix_(14, 13) = 1;
+signMatrix_(14, 14) = 0;
+signMatrix_(14, 15) = -1;
+signMatrix_(14, 16) = -1;
+signMatrix_(14, 17) = 1;
+signMatrix_(14, 18) = 1;
+signMatrix_(14, 19) = 1;
+signMatrix_(15, 0) = 1;
+signMatrix_(15, 1) = 1;
+signMatrix_(15, 2) = -1;
+signMatrix_(15, 3) = -1;
+signMatrix_(15, 4) = -1;
+signMatrix_(15, 5) = 1;
+signMatrix_(15, 6) = 1;
+signMatrix_(15, 7) = 1;
+signMatrix_(15, 8) = 1;
+signMatrix_(15, 9) = 1;
+signMatrix_(15, 10) = 1;
+signMatrix_(15, 11) = 1;
+signMatrix_(15, 12) = 1;
+signMatrix_(15, 13) = 1;
+signMatrix_(15, 14) = 1;
+signMatrix_(15, 15) = 0;
+signMatrix_(15, 16) = 1;
+signMatrix_(15, 17) = 1;
+signMatrix_(15, 18) = 1;
+signMatrix_(15, 19) = 1;
+signMatrix_(16, 0) = 1;
+signMatrix_(16, 1) = 1;
+signMatrix_(16, 2) = -1;
+signMatrix_(16, 3) = -1;
+signMatrix_(16, 4) = -1;
+signMatrix_(16, 5) = -1;
+signMatrix_(16, 6) = -1;
+signMatrix_(16, 7) = -1;
+signMatrix_(16, 8) = 1;
+signMatrix_(16, 9) = 1;
+signMatrix_(16, 10) = 1;
+signMatrix_(16, 11) = 1;
+signMatrix_(16, 12) = 1;
+signMatrix_(16, 13) = 1;
+signMatrix_(16, 14) = 1;
+signMatrix_(16, 15) = -1;
+signMatrix_(16, 16) = 0;
+signMatrix_(16, 17) = 1;
+signMatrix_(16, 18) = 1;
+signMatrix_(16, 19) = 1;
+signMatrix_(17, 0) = -1;
+signMatrix_(17, 1) = -1;
+signMatrix_(17, 2) = -1;
+signMatrix_(17, 3) = -1;
+signMatrix_(17, 4) = -1;
+signMatrix_(17, 5) = -1;
+signMatrix_(17, 6) = -1;
+signMatrix_(17, 7) = -1;
+signMatrix_(17, 8) = -1;
+signMatrix_(17, 9) = -1;
+signMatrix_(17, 10) = -1;
+signMatrix_(17, 11) = -1;
+signMatrix_(17, 12) = -1;
+signMatrix_(17, 13) = -1;
+signMatrix_(17, 14) = -1;
+signMatrix_(17, 15) = -1;
+signMatrix_(17, 16) = -1;
+signMatrix_(17, 17) = 0;
+signMatrix_(17, 18) = -1;
+signMatrix_(17, 19) = -1;
+signMatrix_(18, 0) = -1;
+signMatrix_(18, 1) = -1;
+signMatrix_(18, 2) = -1;
+signMatrix_(18, 3) = -1;
+signMatrix_(18, 4) = -1;
+signMatrix_(18, 5) = -1;
+signMatrix_(18, 6) = -1;
+signMatrix_(18, 7) = -1;
+signMatrix_(18, 8) = -1;
+signMatrix_(18, 9) = 1;
+signMatrix_(18, 10) = 1;
+signMatrix_(18, 11) = -1;
+signMatrix_(18, 12) = -1;
+signMatrix_(18, 13) = 1;
+signMatrix_(18, 14) = -1;
+signMatrix_(18, 15) = -1;
+signMatrix_(18, 16) = -1;
+signMatrix_(18, 17) = 1;
+signMatrix_(18, 18) = 0;
+signMatrix_(18, 19) = -1;
+signMatrix_(19, 0) = -1;
+signMatrix_(19, 1) = -1;
+signMatrix_(19, 2) = -1;
+signMatrix_(19, 3) = -1;
+signMatrix_(19, 4) = -1;
+signMatrix_(19, 5) = -1;
+signMatrix_(19, 6) = -1;
+signMatrix_(19, 7) = -1;
+signMatrix_(19, 8) = -1;
+signMatrix_(19, 9) = 1;
+signMatrix_(19, 10) = 1;
+signMatrix_(19, 11) = -1;
+signMatrix_(19, 12) = 1;
+signMatrix_(19, 13) = 1;
+signMatrix_(19, 14) = -1;
+signMatrix_(19, 15) = -1;
+signMatrix_(19, 16) = -1;
+signMatrix_(19, 17) = 1;
+signMatrix_(19, 18) = 1;
+signMatrix_(19, 19) = 0;
diff --git a/src/Bpp/Seq/AlphabetIndex/__MiyataMatrixCode b/src/Bpp/Seq/AlphabetIndex/__MiyataMatrixCode
new file mode 100644
index 0000000..9929985
--- /dev/null
+++ b/src/Bpp/Seq/AlphabetIndex/__MiyataMatrixCode
@@ -0,0 +1,400 @@
+distanceMatrix_(0,0) = 0;
+distanceMatrix_(1,0) = 2.92;
+distanceMatrix_(1,1) = 0;
+distanceMatrix_(2,0) = 1.78;
+distanceMatrix_(2,1) = 2.04;
+distanceMatrix_(2,2) = 0;
+distanceMatrix_(3,0) = 2.37;
+distanceMatrix_(3,1) = 2.34;
+distanceMatrix_(3,2) = 0.65;
+distanceMatrix_(3,3) = 0;
+distanceMatrix_(4,0) = 1.39;
+distanceMatrix_(4,1) = 3.06;
+distanceMatrix_(4,2) = 2.83;
+distanceMatrix_(4,3) = 3.48;
+distanceMatrix_(4,4) = 0;
+distanceMatrix_(5,0) = 1.92;
+distanceMatrix_(5,1) = 1.13;
+distanceMatrix_(5,2) = 0.99;
+distanceMatrix_(5,3) = 1.47;
+distanceMatrix_(5,4) = 2.48;
+distanceMatrix_(5,5) = 0;
+distanceMatrix_(6,0) = 2.46;
+distanceMatrix_(6,1) = 1.45;
+distanceMatrix_(6,2) = 0.85;
+distanceMatrix_(6,3) = 0.9;
+distanceMatrix_(6,4) = 3.26;
+distanceMatrix_(6,5) = 0.84;
+distanceMatrix_(6,6) = 0;
+distanceMatrix_(7,0) = 0.91;
+distanceMatrix_(7,1) = 3.58;
+distanceMatrix_(7,2) = 1.96;
+distanceMatrix_(7,3) = 2.37;
+distanceMatrix_(7,4) = 2.22;
+distanceMatrix_(7,5) = 2.48;
+distanceMatrix_(7,6) = 2.78;
+distanceMatrix_(7,7) = 0;
+distanceMatrix_(8,0) = 2.17;
+distanceMatrix_(8,1) = 0.82;
+distanceMatrix_(8,2) = 1.29;
+distanceMatrix_(8,3) = 1.72;
+distanceMatrix_(8,4) = 2.56;
+distanceMatrix_(8,5) = 0.32;
+distanceMatrix_(8,6) = 0.96;
+distanceMatrix_(8,7) = 2.78;
+distanceMatrix_(8,8) = 0;
+distanceMatrix_(9,0) = 2.69;
+distanceMatrix_(9,1) = 2.49;
+distanceMatrix_(9,2) = 3.37;
+distanceMatrix_(9,3) = 3.98;
+distanceMatrix_(9,4) = 1.63;
+distanceMatrix_(9,5) = 2.57;
+distanceMatrix_(9,6) = 3.39;
+distanceMatrix_(9,7) = 3.6;
+distanceMatrix_(9,8) = 2.45;
+distanceMatrix_(9,9) = 0;
+distanceMatrix_(10,0) = 2.76;
+distanceMatrix_(10,1) = 2.62;
+distanceMatrix_(10,2) = 3.49;
+distanceMatrix_(10,3) = 4.1;
+distanceMatrix_(10,4) = 1.65;
+distanceMatrix_(10,5) = 2.7;
+distanceMatrix_(10,6) = 3.53;
+distanceMatrix_(10,7) = 3.67;
+distanceMatrix_(10,8) = 2.59;
+distanceMatrix_(10,9) = 0.14;
+distanceMatrix_(10,10) = 0;
+distanceMatrix_(11,0) = 2.96;
+distanceMatrix_(11,1) = 0.4;
+distanceMatrix_(11,2) = 1.84;
+distanceMatrix_(11,3) = 2.05;
+distanceMatrix_(11,4) = 3.27;
+distanceMatrix_(11,5) = 1.06;
+distanceMatrix_(11,6) = 1.14;
+distanceMatrix_(11,7) = 3.54;
+distanceMatrix_(11,8) = 0.79;
+distanceMatrix_(11,9) = 2.84;
+distanceMatrix_(11,10) = 2.98;
+distanceMatrix_(11,11) = 0;
+distanceMatrix_(12,0) = 2.42;
+distanceMatrix_(12,1) = 2.29;
+distanceMatrix_(12,2) = 3.08;
+distanceMatrix_(12,3) = 3.69;
+distanceMatrix_(12,4) = 1.46;
+distanceMatrix_(12,5) = 2.3;
+distanceMatrix_(12,6) = 3.13;
+distanceMatrix_(12,7) = 3.34;
+distanceMatrix_(12,8) = 2.19;
+distanceMatrix_(12,9) = 0.29;
+distanceMatrix_(12,10) = 0.41;
+distanceMatrix_(12,11) = 2.63;
+distanceMatrix_(12,12) = 0;
+distanceMatrix_(13,0) = 3.23;
+distanceMatrix_(13,1) = 2.47;
+distanceMatrix_(13,2) = 3.7;
+distanceMatrix_(13,3) = 4.27;
+distanceMatrix_(13,4) = 2.24;
+distanceMatrix_(13,5) = 2.81;
+distanceMatrix_(13,6) = 3.59;
+distanceMatrix_(13,7) = 4.14;
+distanceMatrix_(13,8) = 2.63;
+distanceMatrix_(13,9) = 0.61;
+distanceMatrix_(13,10) = 0.63;
+distanceMatrix_(13,11) = 2.85;
+distanceMatrix_(13,12) = 0.82;
+distanceMatrix_(13,13) = 0;
+distanceMatrix_(14,0) = 0.06;
+distanceMatrix_(14,1) = 2.9;
+distanceMatrix_(14,2) = 1.8;
+distanceMatrix_(14,3) = 2.4;
+distanceMatrix_(14,4) = 1.33;
+distanceMatrix_(14,5) = 1.92;
+distanceMatrix_(14,6) = 2.48;
+distanceMatrix_(14,7) = 0.97;
+distanceMatrix_(14,8) = 2.15;
+distanceMatrix_(14,9) = 2.62;
+distanceMatrix_(14,10) = 2.7;
+distanceMatrix_(14,11) = 2.94;
+distanceMatrix_(14,12) = 2.36;
+distanceMatrix_(14,13) = 3.17;
+distanceMatrix_(14,14) = 0;
+distanceMatrix_(15,0) = 0.51;
+distanceMatrix_(15,1) = 2.74;
+distanceMatrix_(15,2) = 1.31;
+distanceMatrix_(15,3) = 1.87;
+distanceMatrix_(15,4) = 1.84;
+distanceMatrix_(15,5) = 1.65;
+distanceMatrix_(15,6) = 2.06;
+distanceMatrix_(15,7) = 0.85;
+distanceMatrix_(15,8) = 1.94;
+distanceMatrix_(15,9) = 2.95;
+distanceMatrix_(15,10) = 3.04;
+distanceMatrix_(15,11) = 2.71;
+distanceMatrix_(15,12) = 2.67;
+distanceMatrix_(15,13) = 3.45;
+distanceMatrix_(15,14) = 0.56;
+distanceMatrix_(15,15) = 0;
+distanceMatrix_(16,0) = 0.9;
+distanceMatrix_(16,1) = 2.03;
+distanceMatrix_(16,2) = 1.4;
+distanceMatrix_(16,3) = 2.05;
+distanceMatrix_(16,4) = 1.45;
+distanceMatrix_(16,5) = 1.12;
+distanceMatrix_(16,6) = 1.83;
+distanceMatrix_(16,7) = 1.7;
+distanceMatrix_(16,8) = 1.32;
+distanceMatrix_(16,9) = 2.14;
+distanceMatrix_(16,10) = 2.25;
+distanceMatrix_(16,11) = 2.1;
+distanceMatrix_(16,12) = 1.86;
+distanceMatrix_(16,13) = 2.6;
+distanceMatrix_(16,14) = 0.87;
+distanceMatrix_(16,15) = 0.89;
+distanceMatrix_(16,16) = 0;
+distanceMatrix_(17,0) = 4.23;
+distanceMatrix_(17,1) = 2.72;
+distanceMatrix_(17,2) = 4.39;
+distanceMatrix_(17,3) = 4.88;
+distanceMatrix_(17,4) = 3.34;
+distanceMatrix_(17,5) = 3.42;
+distanceMatrix_(17,6) = 4.08;
+distanceMatrix_(17,7) = 5.13;
+distanceMatrix_(17,8) = 3.16;
+distanceMatrix_(17,9) = 1.72;
+distanceMatrix_(17,10) = 1.73;
+distanceMatrix_(17,11) = 3.11;
+distanceMatrix_(17,12) = 1.89;
+distanceMatrix_(17,13) = 1.11;
+distanceMatrix_(17,14) = 4.17;
+distanceMatrix_(17,15) = 4.38;
+distanceMatrix_(17,16) = 3.5;
+distanceMatrix_(17,17) = 0;
+distanceMatrix_(18,0) = 3.18;
+distanceMatrix_(18,1) = 2.02;
+distanceMatrix_(18,2) = 3.42;
+distanceMatrix_(18,3) = 3.95;
+distanceMatrix_(18,4) = 2.38;
+distanceMatrix_(18,5) = 2.48;
+distanceMatrix_(18,6) = 3.22;
+distanceMatrix_(18,7) = 4.08;
+distanceMatrix_(18,8) = 2.27;
+distanceMatrix_(18,9) = 0.86;
+distanceMatrix_(18,10) = 0.94;
+distanceMatrix_(18,11) = 2.42;
+distanceMatrix_(18,12) = 0.93;
+distanceMatrix_(18,13) = 0.48;
+distanceMatrix_(18,14) = 3.12;
+distanceMatrix_(18,15) = 3.33;
+distanceMatrix_(18,16) = 2.45;
+distanceMatrix_(18,17) = 1.06;
+distanceMatrix_(18,18) = 0;
+distanceMatrix_(19,0) = 1.85;
+distanceMatrix_(19,1) = 2.43;
+distanceMatrix_(19,2) = 2.76;
+distanceMatrix_(19,3) = 3.4;
+distanceMatrix_(19,4) = 0.86;
+distanceMatrix_(19,5) = 2.13;
+distanceMatrix_(19,6) = 2.97;
+distanceMatrix_(19,7) = 2.76;
+distanceMatrix_(19,8) = 2.11;
+distanceMatrix_(19,9) = 0.85;
+distanceMatrix_(19,10) = 0.91;
+distanceMatrix_(19,11) = 2.7;
+distanceMatrix_(19,12) = 0.62;
+distanceMatrix_(19,13) = 1.43;
+distanceMatrix_(19,14) = 1.79;
+distanceMatrix_(19,15) = 2.15;
+distanceMatrix_(19,16) = 1.42;
+distanceMatrix_(19,17) = 2.51;
+distanceMatrix_(19,18) = 1.52;
+distanceMatrix_(19,19) = 0;
+distanceMatrix_(0,1) = -2.92;
+distanceMatrix_(0,2) = -1.78;
+distanceMatrix_(0,3) = -2.37;
+distanceMatrix_(0,4) = -1.39;
+distanceMatrix_(0,5) = -1.92;
+distanceMatrix_(0,6) = -2.46;
+distanceMatrix_(0,7) = -0.91;
+distanceMatrix_(0,8) = -2.17;
+distanceMatrix_(0,9) = -2.69;
+distanceMatrix_(0,10) = -2.76;
+distanceMatrix_(0,11) = -2.96;
+distanceMatrix_(0,12) = -2.42;
+distanceMatrix_(0,13) = -3.23;
+distanceMatrix_(0,14) = -0.06;
+distanceMatrix_(0,15) = -0.51;
+distanceMatrix_(0,16) = -0.9;
+distanceMatrix_(0,17) = -4.23;
+distanceMatrix_(0,18) = -3.18;
+distanceMatrix_(0,19) = -1.85;
+distanceMatrix_(1,2) = -2.04;
+distanceMatrix_(1,3) = -2.34;
+distanceMatrix_(1,4) = -3.06;
+distanceMatrix_(1,5) = -1.13;
+distanceMatrix_(1,6) = -1.45;
+distanceMatrix_(1,7) = -3.58;
+distanceMatrix_(1,8) = -0.82;
+distanceMatrix_(1,9) = -2.49;
+distanceMatrix_(1,10) = -2.62;
+distanceMatrix_(1,11) = -0.4;
+distanceMatrix_(1,12) = -2.29;
+distanceMatrix_(1,13) = -2.47;
+distanceMatrix_(1,14) = -2.9;
+distanceMatrix_(1,15) = -2.74;
+distanceMatrix_(1,16) = -2.03;
+distanceMatrix_(1,17) = -2.72;
+distanceMatrix_(1,18) = -2.02;
+distanceMatrix_(1,19) = -2.43;
+distanceMatrix_(2,3) = -0.65;
+distanceMatrix_(2,4) = -2.83;
+distanceMatrix_(2,5) = -0.99;
+distanceMatrix_(2,6) = -0.85;
+distanceMatrix_(2,7) = -1.96;
+distanceMatrix_(2,8) = -1.29;
+distanceMatrix_(2,9) = -3.37;
+distanceMatrix_(2,10) = -3.49;
+distanceMatrix_(2,11) = -1.84;
+distanceMatrix_(2,12) = -3.08;
+distanceMatrix_(2,13) = -3.7;
+distanceMatrix_(2,14) = -1.8;
+distanceMatrix_(2,15) = -1.31;
+distanceMatrix_(2,16) = -1.4;
+distanceMatrix_(2,17) = -4.39;
+distanceMatrix_(2,18) = -3.42;
+distanceMatrix_(2,19) = -2.76;
+distanceMatrix_(3,4) = -3.48;
+distanceMatrix_(3,5) = -1.47;
+distanceMatrix_(3,6) = -0.9;
+distanceMatrix_(3,7) = -2.37;
+distanceMatrix_(3,8) = -1.72;
+distanceMatrix_(3,9) = -3.98;
+distanceMatrix_(3,10) = -4.1;
+distanceMatrix_(3,11) = -2.05;
+distanceMatrix_(3,12) = -3.69;
+distanceMatrix_(3,13) = -4.27;
+distanceMatrix_(3,14) = -2.4;
+distanceMatrix_(3,15) = -1.87;
+distanceMatrix_(3,16) = -2.05;
+distanceMatrix_(3,17) = -4.88;
+distanceMatrix_(3,18) = -3.95;
+distanceMatrix_(3,19) = -3.4;
+distanceMatrix_(4,5) = -2.48;
+distanceMatrix_(4,6) = -3.26;
+distanceMatrix_(4,7) = -2.22;
+distanceMatrix_(4,8) = -2.56;
+distanceMatrix_(4,9) = -1.63;
+distanceMatrix_(4,10) = -1.65;
+distanceMatrix_(4,11) = -3.27;
+distanceMatrix_(4,12) = -1.46;
+distanceMatrix_(4,13) = -2.24;
+distanceMatrix_(4,14) = -1.33;
+distanceMatrix_(4,15) = -1.84;
+distanceMatrix_(4,16) = -1.45;
+distanceMatrix_(4,17) = -3.34;
+distanceMatrix_(4,18) = -2.38;
+distanceMatrix_(4,19) = -0.86;
+distanceMatrix_(5,6) = -0.84;
+distanceMatrix_(5,7) = -2.48;
+distanceMatrix_(5,8) = -0.32;
+distanceMatrix_(5,9) = -2.57;
+distanceMatrix_(5,10) = -2.7;
+distanceMatrix_(5,11) = -1.06;
+distanceMatrix_(5,12) = -2.3;
+distanceMatrix_(5,13) = -2.81;
+distanceMatrix_(5,14) = -1.92;
+distanceMatrix_(5,15) = -1.65;
+distanceMatrix_(5,16) = -1.12;
+distanceMatrix_(5,17) = -3.42;
+distanceMatrix_(5,18) = -2.48;
+distanceMatrix_(5,19) = -2.13;
+distanceMatrix_(6,7) = -2.78;
+distanceMatrix_(6,8) = -0.96;
+distanceMatrix_(6,9) = -3.39;
+distanceMatrix_(6,10) = -3.53;
+distanceMatrix_(6,11) = -1.14;
+distanceMatrix_(6,12) = -3.13;
+distanceMatrix_(6,13) = -3.59;
+distanceMatrix_(6,14) = -2.48;
+distanceMatrix_(6,15) = -2.06;
+distanceMatrix_(6,16) = -1.83;
+distanceMatrix_(6,17) = -4.08;
+distanceMatrix_(6,18) = -3.22;
+distanceMatrix_(6,19) = -2.97;
+distanceMatrix_(7,8) = -2.78;
+distanceMatrix_(7,9) = -3.6;
+distanceMatrix_(7,10) = -3.67;
+distanceMatrix_(7,11) = -3.54;
+distanceMatrix_(7,12) = -3.34;
+distanceMatrix_(7,13) = -4.14;
+distanceMatrix_(7,14) = -0.97;
+distanceMatrix_(7,15) = -0.85;
+distanceMatrix_(7,16) = -1.7;
+distanceMatrix_(7,17) = -5.13;
+distanceMatrix_(7,18) = -4.08;
+distanceMatrix_(7,19) = -2.76;
+distanceMatrix_(8,9) = -2.45;
+distanceMatrix_(8,10) = -2.59;
+distanceMatrix_(8,11) = -0.79;
+distanceMatrix_(8,12) = -2.19;
+distanceMatrix_(8,13) = -2.63;
+distanceMatrix_(8,14) = -2.15;
+distanceMatrix_(8,15) = -1.94;
+distanceMatrix_(8,16) = -1.32;
+distanceMatrix_(8,17) = -3.16;
+distanceMatrix_(8,18) = -2.27;
+distanceMatrix_(8,19) = -2.11;
+distanceMatrix_(9,10) = -0.14;
+distanceMatrix_(9,11) = -2.84;
+distanceMatrix_(9,12) = -0.29;
+distanceMatrix_(9,13) = -0.61;
+distanceMatrix_(9,14) = -2.62;
+distanceMatrix_(9,15) = -2.95;
+distanceMatrix_(9,16) = -2.14;
+distanceMatrix_(9,17) = -1.72;
+distanceMatrix_(9,18) = -0.86;
+distanceMatrix_(9,19) = -0.85;
+distanceMatrix_(10,11) = -2.98;
+distanceMatrix_(10,12) = -0.41;
+distanceMatrix_(10,13) = -0.63;
+distanceMatrix_(10,14) = -2.7;
+distanceMatrix_(10,15) = -3.04;
+distanceMatrix_(10,16) = -2.25;
+distanceMatrix_(10,17) = -1.73;
+distanceMatrix_(10,18) = -0.94;
+distanceMatrix_(10,19) = -0.91;
+distanceMatrix_(11,12) = -2.63;
+distanceMatrix_(11,13) = -2.85;
+distanceMatrix_(11,14) = -2.94;
+distanceMatrix_(11,15) = -2.71;
+distanceMatrix_(11,16) = -2.1;
+distanceMatrix_(11,17) = -3.11;
+distanceMatrix_(11,18) = -2.42;
+distanceMatrix_(11,19) = -2.7;
+distanceMatrix_(12,13) = -0.82;
+distanceMatrix_(12,14) = -2.36;
+distanceMatrix_(12,15) = -2.67;
+distanceMatrix_(12,16) = -1.86;
+distanceMatrix_(12,17) = -1.89;
+distanceMatrix_(12,18) = -0.93;
+distanceMatrix_(12,19) = -0.62;
+distanceMatrix_(13,14) = -3.17;
+distanceMatrix_(13,15) = -3.45;
+distanceMatrix_(13,16) = -2.6;
+distanceMatrix_(13,17) = -1.11;
+distanceMatrix_(13,18) = -0.48;
+distanceMatrix_(13,19) = -1.43;
+distanceMatrix_(14,15) = -0.56;
+distanceMatrix_(14,16) = -0.87;
+distanceMatrix_(14,17) = -4.17;
+distanceMatrix_(14,18) = -3.12;
+distanceMatrix_(14,19) = -1.79;
+distanceMatrix_(15,16) = -0.89;
+distanceMatrix_(15,17) = -4.38;
+distanceMatrix_(15,18) = -3.33;
+distanceMatrix_(15,19) = -2.15;
+distanceMatrix_(16,17) = -3.5;
+distanceMatrix_(16,18) = -2.45;
+distanceMatrix_(16,19) = -1.42;
+distanceMatrix_(17,18) = -1.06;
+distanceMatrix_(17,19) = -2.51;
+distanceMatrix_(18,19) = -1.52;
diff --git a/src/Bpp/Seq/App/SequenceApplicationTools.cpp b/src/Bpp/Seq/App/SequenceApplicationTools.cpp
new file mode 100644
index 0000000..e7502d4
--- /dev/null
+++ b/src/Bpp/Seq/App/SequenceApplicationTools.cpp
@@ -0,0 +1,539 @@
+//
+// File: SequenceApplicationTools.cpp
+// Created by: Julien Dutheil
+// Created on: Fri Oct 21 13:13
+// from file old ApplicationTools.h created on Sun Dec 14 09:36:26 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "SequenceApplicationTools.h"
+#include "../Alphabet/BinaryAlphabet.h"
+#include "../Alphabet/DefaultAlphabet.h"
+#include "../Alphabet/EchinodermMitochondrialCodonAlphabet.h"
+#include "../Alphabet/InvertebrateMitochondrialCodonAlphabet.h"
+#include "../Alphabet/StandardCodonAlphabet.h"
+#include "../Alphabet/VertebrateMitochondrialCodonAlphabet.h"
+#include "../Alphabet/YeastMitochondrialCodonAlphabet.h"
+#include "../Alphabet/AlphabetTools.h"
+#include "../GeneticCode/EchinodermMitochondrialGeneticCode.h"
+#include "../GeneticCode/InvertebrateMitochondrialGeneticCode.h"
+#include "../GeneticCode/StandardGeneticCode.h"
+#include "../GeneticCode/VertebrateMitochondrialGeneticCode.h"
+#include "../GeneticCode/YeastMitochondrialGeneticCode.h"
+#include "../Io/BppOSequenceReaderFormat.h"
+#include "../Io/BppOAlignmentReaderFormat.h"
+#include "../Io/BppOSequenceWriterFormat.h"
+#include "../Io/BppOAlignmentWriterFormat.h"
+#include "../Io/BppOAlphabetIndex1Format.h"
+#include "../Io/BppOAlphabetIndex2Format.h"
+#include "../Io/MaseTools.h"
+#include "../SiteTools.h"
+#include "../SequenceTools.h"
+#include <Bpp/App/ApplicationTools.h>
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/KeyvalTools.h>
+
+using namespace bpp;
+using namespace std;
+
+/******************************************************************************/
+
+Alphabet* SequenceApplicationTools::getAlphabet(
+ map<string, string>& params,
+ const string& suffix,
+ bool suffixIsOptional,
+ bool verbose,
+ bool allowGeneric) throw (Exception)
+{
+ Alphabet* chars;
+ string alphtt = ApplicationTools::getStringParameter("alphabet", params, "DNA", suffix, suffixIsOptional);
+
+ string alphabet = "";
+ map<string, string> args;
+ int flag = 0;
+
+ KeyvalTools::parseProcedure(alphtt, alphabet, args);
+ unsigned int lg = 1;
+
+ if (alphabet == "Word")
+ {
+ if (args.find("length") == args.end())
+ throw Exception("Missing length parameter for Word alphabet");
+ lg = TextTools::to<unsigned int>(args["length"]);
+ if (args.find("letter") == args.end())
+ throw Exception("Missing letter alphabet for Word alphabet");
+ alphabet = args["letter"];
+ flag = 1;
+ }
+ else if (alphabet == "RNY")
+ {
+ if (args.find("letter") == args.end())
+ throw Exception("Missing letter alphabet for RNY alphabet");
+ alphabet = args["letter"];
+ flag = 2;
+ }
+
+
+ if (alphabet == "Binary")
+ chars = new BinaryAlphabet();
+ else if (alphabet == "DNA")
+ {
+ bool mark = ApplicationTools::getBooleanParameter("bangAsGap", args, false, "", true, false);
+ chars = new DNA(mark);
+ }
+ else if (alphabet == "RNA")
+ {
+ bool mark = ApplicationTools::getBooleanParameter("bangAsGap", args, false, "", true, false);
+ chars = new RNA(mark);
+ }
+ else if (alphabet == "Protein")
+ chars = new ProteicAlphabet();
+ else if (allowGeneric && alphabet == "Generic")
+ chars = new DefaultAlphabet();
+ else if (alphabet == "Codon")
+ {
+ if (args.find("letter") == args.end())
+ throw Exception("Missing 'letter' argument in Codon :" + alphabet);
+
+ string alphnDesc = ApplicationTools::getStringParameter("letter", args, "RNA");
+ string alphn;
+ map<string, string> alphnArgs;
+ KeyvalTools::parseProcedure(alphnDesc, alphn, alphnArgs);
+
+ NucleicAlphabet* pnalph;
+ if (alphn == "RNA")
+ {
+ bool mark = ApplicationTools::getBooleanParameter("bangAsGap", alphnArgs, false, "", true, false);
+ pnalph = new RNA(mark);
+ }
+ else if (alphn == "DNA")
+ {
+ bool mark = ApplicationTools::getBooleanParameter("bangAsGap", alphnArgs, false, "", true, false);
+ pnalph = new DNA(mark);
+ }
+ else
+ throw Exception("Alphabet not known in Codon : " + alphn);
+
+ string type = ApplicationTools::getStringParameter("type", args, "Standard");
+
+ if (type == "EchinodermMitochondrial")
+ chars = new EchinodermMitochondrialCodonAlphabet(pnalph);
+ else if (type == "InvertebrateMitochondrial")
+ chars = new InvertebrateMitochondrialCodonAlphabet(pnalph);
+ else if (type == "Standard")
+ chars = new StandardCodonAlphabet(pnalph);
+ else if (type == "VertebrateMitochondrial")
+ chars = new VertebrateMitochondrialCodonAlphabet(pnalph);
+ else if (type == "YeastMitochondrial")
+ chars = new YeastMitochondrialCodonAlphabet(pnalph);
+ else
+ throw Exception("Unknown Alphabet : " + alphabet);
+ alphabet = alphabet + "(" + alphn + ")";
+ }
+ else
+ throw Exception("Alphabet not known: " + alphabet);
+
+ if (flag == 1)
+ {
+ chars = new WordAlphabet(chars, lg);
+ string al = " ";
+ for (unsigned i = 0; i < lg; i++)
+ {
+ al += alphabet + " ";
+ }
+ alphabet = "Word(" + al + ")";
+ }
+ else if (flag == 2)
+ {
+ if (AlphabetTools::isNucleicAlphabet(chars))
+ {
+ chars = new RNY(*(dynamic_cast<NucleicAlphabet*>(chars)));
+ alphabet = "RNY(" + alphabet + ")";
+ }
+ else
+ throw Exception("RNY needs a Nucleic Alphabet, instead of " + alphabet);
+ }
+
+
+ if (verbose)
+ ApplicationTools::displayResult("Alphabet type ", alphabet);
+ return chars;
+}
+
+/******************************************************************************/
+
+GeneticCode* SequenceApplicationTools::getGeneticCode(
+ const NucleicAlphabet* alphabet,
+ const string& description) throw (Exception)
+{
+ GeneticCode* geneCode;
+ if (description.find("EchinodermMitochondrial") != string::npos)
+ geneCode = new EchinodermMitochondrialGeneticCode(alphabet);
+ else if (description.find("InvertebrateMitochondrial") != string::npos)
+ geneCode = new InvertebrateMitochondrialGeneticCode(alphabet);
+ else if (description.find("Standard") != string::npos)
+ geneCode = new StandardGeneticCode(alphabet);
+ else if (description.find("VertebrateMitochondrial") != string::npos)
+ geneCode = new VertebrateMitochondrialGeneticCode(alphabet);
+ else if (description.find("YeastMitochondrial") != string::npos)
+ geneCode = new YeastMitochondrialGeneticCode(alphabet);
+ else
+ throw Exception("Unknown GeneticCode: " + description);
+ return geneCode;
+}
+
+/******************************************************************************/
+
+AlphabetIndex1* SequenceApplicationTools::getAlphabetIndex1(const Alphabet* alphabet, const string& description, const string& message, bool verbose)
+throw (Exception)
+{
+ BppOAlphabetIndex1Format reader(alphabet, message, verbose);
+ return reader.read(description);
+}
+
+AlphabetIndex2* SequenceApplicationTools::getAlphabetIndex2(const Alphabet* alphabet, const string& description, const string& message, bool verbose)
+throw (Exception)
+{
+ BppOAlphabetIndex2Format reader(alphabet, message, verbose);
+ return reader.read(description);
+}
+
+/******************************************************************************/
+SequenceContainer* SequenceApplicationTools::getSequenceContainer(
+ const Alphabet* alpha,
+ map<string, string>& params,
+ const string& suffix,
+ bool suffixIsOptional,
+ bool verbose)
+{
+ string sequenceFilePath = ApplicationTools::getAFilePath("input.sequence.file", params, true, true, suffix, suffixIsOptional);
+ string sequenceFormat = ApplicationTools::getStringParameter("input.sequence.format", params, "Fasta()", suffix, suffixIsOptional);
+ BppOSequenceReaderFormat bppoReader(verbose);
+ auto_ptr<ISequence> iSeq(bppoReader.read(sequenceFormat));
+ if (verbose)
+ {
+ ApplicationTools::displayResult("Sequence file " + suffix, sequenceFilePath);
+ ApplicationTools::displayResult("Sequence format " + suffix, iSeq->getFormatName());
+ }
+ SequenceContainer* sequences = iSeq->readSequences(sequenceFilePath, alpha);
+
+ return sequences;
+}
+
+/******************************************************************************/
+
+VectorSiteContainer* SequenceApplicationTools::getSiteContainer(
+ const Alphabet* alpha,
+ map<string, string>& params,
+ const string& suffix,
+ bool suffixIsOptional,
+ bool verbose)
+{
+ string sequenceFilePath = ApplicationTools::getAFilePath("input.sequence.file", params, true, true, suffix, suffixIsOptional);
+ string sequenceFormat = ApplicationTools::getStringParameter("input.sequence.format", params, "Fasta()", suffix, suffixIsOptional);
+ BppOAlignmentReaderFormat bppoReader(verbose);
+ auto_ptr<IAlignment> iAln(bppoReader.read(sequenceFormat));
+ map<string, string> args(bppoReader.getUnparsedArguments());
+ if (verbose)
+ {
+ ApplicationTools::displayResult("Sequence file " + suffix, sequenceFilePath);
+ ApplicationTools::displayResult("Sequence format " + suffix, iAln->getFormatName());
+ }
+
+ const Alphabet* alpha2;
+ if (AlphabetTools::isRNYAlphabet(alpha))
+ alpha2 = &dynamic_cast<const RNY*>(alpha)->getLetterAlphabet();
+ else
+ alpha2 = alpha;
+
+ const SequenceContainer* seqCont = iAln->readAlignment(sequenceFilePath, alpha2);
+
+ VectorSiteContainer* sites2 = new VectorSiteContainer(*dynamic_cast<const OrderedSequenceContainer*>(seqCont));
+ delete seqCont;
+
+ VectorSiteContainer* sites;
+
+ if (AlphabetTools::isRNYAlphabet(alpha))
+ {
+ const SequenceTools ST;
+ sites = new VectorSiteContainer(alpha);
+ for (unsigned int i = 0; i < sites2->getNumberOfSequences(); i++)
+ {
+ sites->addSequence(*(ST.RNYslice(sites2->getSequence(i))));
+ }
+ delete sites2;
+ }
+ else
+ sites = sites2;
+
+ // Look for site selection:
+ if (iAln->getFormatName() == "MASE file")
+ {
+ // getting site set:
+ string siteSet = ApplicationTools::getStringParameter("siteSelection", args, "none", suffix, suffixIsOptional, false);
+ if (siteSet != "none")
+ {
+ VectorSiteContainer* selectedSites;
+ try
+ {
+ selectedSites = dynamic_cast<VectorSiteContainer*>(MaseTools::getSelectedSites(*sites, siteSet));
+ if (verbose)
+ ApplicationTools::displayResult("Set found", TextTools::toString(siteSet) + " sites.");
+ }
+ catch (IOException& ioe)
+ {
+ throw ioe;
+ }
+ if (selectedSites->getNumberOfSites() == 0)
+ {
+ throw Exception("Site set '" + siteSet + "' is empty.");
+ }
+ delete sites;
+ sites = selectedSites;
+ }
+ }
+ return sites;
+}
+
+/******************************************************************************/
+
+VectorSiteContainer* SequenceApplicationTools::getSitesToAnalyse(
+ const SiteContainer& allSites,
+ map<string, string>& params,
+ string suffix,
+ bool suffixIsOptional,
+ bool gapAsUnknown,
+ bool verbose)
+{
+ // Fully resolved sites, i.e. without jokers and gaps:
+ SiteContainer* sitesToAnalyse;
+ VectorSiteContainer* sitesToAnalyse2;
+
+ string option = ApplicationTools::getStringParameter("input.sequence.sites_to_use", params, "complete", suffix, suffixIsOptional);
+ if (verbose)
+ ApplicationTools::displayResult("Sites to use", option);
+ if (option == "all")
+ {
+ sitesToAnalyse = new VectorSiteContainer(allSites);
+ string maxGapOption = ApplicationTools::getStringParameter("input.sequence.max_gap_allowed", params, "100%", suffix, suffixIsOptional);
+
+ if (maxGapOption[maxGapOption.size() - 1] == '%')
+ {
+ double gapFreq = TextTools::toDouble(maxGapOption.substr(0, maxGapOption.size() - 1)) / 100.;
+ if (gapFreq < 1)
+ {
+ if (verbose)
+ ApplicationTools::displayTask("Remove sites with gaps", true);
+ for (size_t i = sitesToAnalyse->getNumberOfSites(); i > 0; --i)
+ {
+ if (verbose)
+ ApplicationTools::displayGauge(sitesToAnalyse->getNumberOfSites() - i, sitesToAnalyse->getNumberOfSites() - 1, '=');
+ map<int, double> freq;
+ SiteTools::getFrequencies(sitesToAnalyse->getSite(i - 1), freq);
+ if (freq[-1] > gapFreq)
+ sitesToAnalyse->deleteSite(i - 1);
+ }
+ if (verbose)
+ ApplicationTools::displayTaskDone();
+ }
+ }
+ else
+ {
+ size_t gapNum = TextTools::to<size_t>(maxGapOption);
+ if (gapNum < sitesToAnalyse->getNumberOfSequences())
+ {
+ if (verbose)
+ ApplicationTools::displayTask("Remove sites with gaps", true);
+ for (size_t i = sitesToAnalyse->getNumberOfSites(); i > 0; i--)
+ {
+ if (verbose)
+ ApplicationTools::displayGauge(sitesToAnalyse->getNumberOfSites() - i, sitesToAnalyse->getNumberOfSites() - 1, '=');
+ map<int, size_t> counts;
+ SiteTools::getCounts(sitesToAnalyse->getSite(i - 1), counts);
+ if (counts[-1] > gapNum)
+ sitesToAnalyse->deleteSite(i - 1);
+ }
+ if (verbose)
+ ApplicationTools::displayTaskDone();
+ }
+ }
+
+ string maxUnresolvedOption = ApplicationTools::getStringParameter("input.sequence.max_unresolved_allowed", params, "100%", suffix, suffixIsOptional);
+
+ size_t sAlph = sitesToAnalyse->getAlphabet()->getSize();
+
+ if (maxUnresolvedOption[maxUnresolvedOption.size() - 1] == '%')
+ {
+ double unresolvedFreq = TextTools::toDouble(maxUnresolvedOption.substr(0, maxUnresolvedOption.size() - 1)) / 100.;
+ if (unresolvedFreq < 1)
+ {
+ if (verbose)
+ ApplicationTools::displayTask("Remove unresolved sites", true);
+ for (size_t i = sitesToAnalyse->getNumberOfSites(); i > 0; --i)
+ {
+ if (verbose)
+ ApplicationTools::displayGauge(sitesToAnalyse->getNumberOfSites() - i, sitesToAnalyse->getNumberOfSites() - 1, '=');
+ map<int, double> freq;
+ SiteTools::getFrequencies(sitesToAnalyse->getSite(i - 1), freq);
+ double x = 0;
+ for (unsigned int l = 0; l < sAlph; l++)
+ {
+ x += freq[l];
+ }
+ if (1 - x > unresolvedFreq)
+ sitesToAnalyse->deleteSite(i - 1);
+ }
+ if (verbose)
+ ApplicationTools::displayTaskDone();
+ }
+ }
+ else
+ {
+ size_t nbSeq = sitesToAnalyse->getNumberOfSequences();
+ size_t unresolvedNum = TextTools::to<size_t>(maxUnresolvedOption);
+ if (unresolvedNum < nbSeq)
+ {
+ if (verbose)
+ ApplicationTools::displayTask("Remove sites with gaps", true);
+ for (size_t i = sitesToAnalyse->getNumberOfSites(); i > 0; i--)
+ {
+ if (verbose)
+ ApplicationTools::displayGauge(sitesToAnalyse->getNumberOfSites() - i, sitesToAnalyse->getNumberOfSites() - 1, '=');
+ map<int, size_t> counts;
+ SiteTools::getCounts(sitesToAnalyse->getSite(i - 1), counts);
+ size_t x = 0;
+ for (int l = 0; l < static_cast<int>(sAlph); l++)
+ {
+ x += counts[l];
+ }
+
+ if (nbSeq - x > unresolvedNum)
+ sitesToAnalyse->deleteSite(i - 1);
+ }
+ if (verbose)
+ ApplicationTools::displayTaskDone();
+ }
+ }
+
+ if (gapAsUnknown)
+ {
+ SiteContainerTools::changeGapsToUnknownCharacters(*sitesToAnalyse);
+ }
+ }
+ else if (option == "complete")
+ {
+ sitesToAnalyse = SiteContainerTools::getCompleteSites(allSites);
+ size_t nbSites = sitesToAnalyse->getNumberOfSites();
+ if (verbose)
+ ApplicationTools::displayResult("Complete sites", TextTools::toString(nbSites));
+ }
+ else if (option == "nogap")
+ {
+ sitesToAnalyse = SiteContainerTools::getSitesWithoutGaps(allSites);
+ size_t nbSites = sitesToAnalyse->getNumberOfSites();
+ if (verbose)
+ ApplicationTools::displayResult("Sites without gap", TextTools::toString(nbSites));
+ }
+ else
+ {
+ throw Exception("Option '" + option + "' unknown in parameter 'sequence.sites_to_use'.");
+ }
+
+ if (AlphabetTools::isCodonAlphabet(sitesToAnalyse->getAlphabet()))
+ {
+ option = ApplicationTools::getStringParameter("input.sequence.remove_stop_codons", params, "no", suffix, true);
+ if ((option != "") && verbose)
+ ApplicationTools::displayResult("Remove Stop Codons", option);
+
+ if (option == "yes")
+ {
+ sitesToAnalyse2 = dynamic_cast<VectorSiteContainer*>(SiteContainerTools::removeStopCodonSites(*sitesToAnalyse));
+ delete sitesToAnalyse;
+ }
+ else
+ sitesToAnalyse2 = dynamic_cast<VectorSiteContainer*>(sitesToAnalyse);
+ }
+ else
+ sitesToAnalyse2 = dynamic_cast<VectorSiteContainer*>(sitesToAnalyse);
+
+ return sitesToAnalyse2;
+}
+
+/******************************************************************************/
+
+void SequenceApplicationTools::writeSequenceFile(
+ const SequenceContainer& sequences,
+ map<string, string>& params,
+ const string& suffix,
+ bool verbose)
+{
+ string sequenceFilePath = ApplicationTools::getAFilePath("output.sequence.file", params, true, false, suffix, false);
+ string sequenceFormat = ApplicationTools::getStringParameter("output.sequence.format", params, "Fasta", suffix, false, true);
+ BppOSequenceWriterFormat bppoWriter(verbose);
+ auto_ptr<OSequence> oSeq(bppoWriter.read(sequenceFormat));
+ if (verbose)
+ {
+ ApplicationTools::displayResult("Output sequence file " + suffix, sequenceFilePath);
+ ApplicationTools::displayResult("Output sequence format " + suffix, oSeq->getFormatName());
+ }
+
+ // Write sequences:
+ oSeq->writeSequences(sequenceFilePath, sequences, true);
+}
+
+/******************************************************************************/
+
+void SequenceApplicationTools::writeAlignmentFile(
+ const SiteContainer& sequences,
+ map<string, string>& params,
+ const string& suffix,
+ bool verbose)
+{
+ string sequenceFilePath = ApplicationTools::getAFilePath("output.sequence.file", params, true, false, suffix, false);
+ string sequenceFormat = ApplicationTools::getStringParameter("output.sequence.format", params, "Fasta", suffix, false, true);
+ BppOAlignmentWriterFormat bppoWriter(verbose);
+ auto_ptr<OAlignment> oAln(bppoWriter.read(sequenceFormat));
+ if (verbose)
+ {
+ ApplicationTools::displayResult("Output alignment file " + suffix, sequenceFilePath);
+ ApplicationTools::displayResult("Output alignment format " + suffix, oAln->getFormatName());
+ }
+
+ // Write sequences:
+ oAln->writeAlignment(sequenceFilePath, sequences, true);
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/App/SequenceApplicationTools.h b/src/Bpp/Seq/App/SequenceApplicationTools.h
new file mode 100644
index 0000000..d94920b
--- /dev/null
+++ b/src/Bpp/Seq/App/SequenceApplicationTools.h
@@ -0,0 +1,269 @@
+//
+// File: SequenceApplicationTools.h
+// Created by: Julien Dutheil
+// Created on: Fri Oct 21 13:13
+// from file old ApplicationTools.h created on Sun Dec 14 09:36:26 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _SEQUENCEAPPLICATIONTOOLS_H_
+#define _SEQUENCEAPPLICATIONTOOLS_H_
+
+#include "../Alphabet/Alphabet.h"
+#include "../GeneticCode/GeneticCode.h"
+#include "../AlphabetIndex/AlphabetIndex1.h"
+#include "../AlphabetIndex/AlphabetIndex2.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/VectorSiteContainer.h"
+
+#include <map>
+#include <string>
+
+namespace bpp
+{
+/**
+ * @brief This class provides some common tools for applications.
+ *
+ * The functions parse some option file, create corresponding objects and send
+ * a pointer toward it.
+ *
+ * The option files are supposed to follow this simple format:
+ * @code
+ * parameterName = parameterContent
+ * @endcode
+ * with one parameter per line.
+ *
+ * @see ApplicationTools
+ */
+class SequenceApplicationTools
+{
+public:
+ SequenceApplicationTools() {}
+ virtual ~SequenceApplicationTools() {}
+
+public:
+ /**
+ * @brief Build an Alphabet object according to options.
+ *
+ * Options used are:
+ * - alphabet = [DNA|RNA|Protein], the alphabet type to use.
+ * = [DNA|RNA|Protein](length=n) a word-alphabet of
+ * words with length n
+ * = [EchinodermMitochondrialCodonAlphabet
+ * | InvertebrateMitochondrialCodonAlphabet
+ * | InvertebrateMitochondrialCodonAlphabet
+ * | StandardCodonAlphabet
+ * | VertebrateMitochondrialCodonAlphabet]([alphn=NA|RNA])
+ * a codon-alphabet
+ *
+ * @param params The attribute map where options may be found.
+ * @param suffix A suffix to be applied to each attribute name.
+ * @param suffixIsOptional Tell if the suffix is absolutely required.
+ * @param verbose Print some info to the 'message' output stream.
+ * @param allowGeneric Tell if generic alphabets can be used.
+ * @return A new Alphabet object according to options specified.
+ */
+ static Alphabet* getAlphabet(
+ std::map<std::string, std::string>& params,
+ const std::string& suffix = "",
+ bool suffixIsOptional = true,
+ bool verbose = true,
+ bool allowGeneric = false) throw (Exception);
+
+ /**
+ * @brief Build a GeneticCode object according to options.
+ *
+ * @param alphabet pointer to the NucleicAlphabet
+ * @param description for the name of the GeneticCode:
+ * [EchinodermMitochondrialGeneticCode
+ * | InvertebrateMitochondrialGeneticCode
+ * | InvertebrateMitochondrialGeneticCode
+ * | StandardGeneticCode
+ * | VertebrateMitochondrialGeneticCode]
+ * @return A new GeneticCode object
+ * @throw Exception in case of bad description.
+ */
+ static GeneticCode* getGeneticCode(const NucleicAlphabet* alphabet, const std::string& description) throw (Exception);
+
+
+ /**
+ * @brief Build a AlphabetIndex1 object for a given alphabet.
+ *
+ * @param alphabet The alphabet to use. This is currently only used for assessing the type of distance allowed.
+ * @param description Which distance to use. See the Bio++ Program Suite reference manual for a description of the syntax.
+ * @param message To be displayed when parsing.
+ * @param verbose Tell if some info should be displayed while parsing.
+ * @return A new AlphabetIndex1 object.
+ * @throw Exception in case of bad description.
+ */
+ static AlphabetIndex1* getAlphabetIndex1(const Alphabet* alphabet, const std::string& description, const std::string& message = "Alphabet distance:", bool verbose = true) throw (Exception);
+
+
+ /**
+ * @brief Build a AlphabetIndex2 object for a given alphabet.
+ *
+ * @param alphabet The alphabet to use. This is currently only used for assessing the type of distance allowed.
+ * @param description Which distance to use. See the Bio++ Program Suite reference manual for a description of the syntax.
+ * @param message To be displayed when parsing.
+ * @return A new AlphabetIndex2 object.
+ * @param verbose Tell if some info should be displayed while parsing.
+ * @throw Exception in case of bad description.
+ */
+ static AlphabetIndex2* getAlphabetIndex2(const Alphabet* alphabet, const std::string& description, const std::string& message = "Alphabet distance:", bool verbose = true) throw (Exception);
+
+
+ /**
+ * @brief Build a SequenceContainer object according to options.
+ *
+ * The sequences do not have to be aligned.
+ * The supported sequence formats are Fasta, DCSE, Clustal, Mase, Phylip and GenBank.
+ *
+ * See the Bio++ program suite manual for a full description of the syntax.
+ *
+ * @param alpha The alphabet to use in the container.
+ * @param params The attribute map where options may be found.
+ * @param suffix A suffix to be applied to each attribute name.
+ * @param suffixIsOptional Tell if the suffix is absolutely required.
+ * @param verbose Print some info to the 'message' output stream.
+ * @return A new VectorSequenceContainer object according to options specified.
+ * @see getSiteContainer to read an alignment.
+ */
+
+ static SequenceContainer* getSequenceContainer(
+ const Alphabet* alpha,
+ std::map<std::string, std::string>& params,
+ const std::string& suffix = "",
+ bool suffixIsOptional = true,
+ bool verbose = true);
+
+ /**
+ * @brief Build a SiteContainer object according to options.
+ *
+ * Sequences in file must be aligned.
+ * The supported sequence formats are Fasta, DCSE, Clustal, Mase and Phylip.
+ *
+ * See the Bio++ program suite manual for a full description of the syntax.
+ *
+ * @param alpha The alphabet to use in the container.
+ * @param params The attribute map where options may be found.
+ * @param suffix A suffix to be applied to each attribute name.
+ * @param suffixIsOptional Tell if the suffix is absolutely required.
+ * @param verbose Print some info to the 'message' output stream.
+ * @return A new VectorSiteContainer object according to options specified.
+ */
+ static VectorSiteContainer* getSiteContainer(
+ const Alphabet* alpha,
+ std::map<std::string, std::string>& params,
+ const std::string& suffix = "",
+ bool suffixIsOptional = true,
+ bool verbose = true);
+
+ /**
+ * @brief Retrieves sites suitable for the analysis.
+ *
+ * Options used are:
+ * - sequence.sites_to_use = [all|complete|nogap].
+ *
+ * If the 'complete' option is used, only fully resolve site will be taken
+ * into account.
+ * If the 'nogap' option is used, only sites without gap will be taken into
+ * account.
+ * If 'gapAsUnknown' is set to true and the all option is selected, gaps will
+ * be changed to 'unknown' character is sequences.
+ *
+ * - sequence.max_gap_allowed = [57%|30]
+ * If a % sign fallow the number, it is taken to be a frequence (in percent).
+ * This specify the maximum amount of gaps allowed for each site.
+ * Sites not satisfying this amount will be removed.
+ * A value of 100% will remove all gap-only sites, a value >100% will keep all sites.
+ *
+ * @param allSites The site container from which sites must be retrieved.
+ * @param params The attribute map where options may be found.
+ * @param suffix A suffix to be applied to each attribute name.
+ * @param suffixIsOptional Tell if the suffix is absolutely required.
+ * @param gapAsUnknown Convert gaps to unknown characters.
+ * @param verbose Print some info to the 'message' output stream.
+ * @return A new VectorSiteContainer object containing sites of interest.
+ */
+ static VectorSiteContainer* getSitesToAnalyse(
+ const SiteContainer& allSites,
+ std::map<std::string, std::string>& params,
+ std::string suffix = "",
+ bool suffixIsOptional = true,
+ bool gapAsUnknown = true,
+ bool verbose = true);
+
+ /**
+ * @brief Write a sequence file according to options.
+ *
+ * The supported sequence formats are Fasta and Mase.
+ *
+ * See the Bio++ program suite manual for a full description of the syntax.
+ *
+ * @see writeSequenceFile(SiteContainer) for writing alignments, with more output formats.
+ *
+ * @param sequences The sequences to write.
+ * @param params The attribute map where options may be found.
+ * @param suffix A suffix to be applied to each attribute name.
+ * @param verbose Print some info to the 'message' output stream.
+ */
+ static void writeSequenceFile(
+ const SequenceContainer& sequences,
+ std::map<std::string, std::string>& params,
+ const std::string& suffix = "",
+ bool verbose = true);
+
+ /**
+ * @brief Write a sequence alignment file according to options.
+ *
+ * The supported sequence formats are Fasta, Mase and Phylip.
+ *
+ * See the Bio++ program suite manual for a full description of the syntax.
+ *
+ * @param sequences The aligned sequences to write.
+ * @param params The attribute map where options may be found.
+ * @param suffix A suffix to be applied to each attribute name.
+ * @param verbose Print some info to the 'message' output stream.
+ */
+ static void writeAlignmentFile(
+ const SiteContainer& sequences,
+ std::map<std::string, std::string>& params,
+ const std::string& suffix = "",
+ bool verbose = true);
+};
+} // end of namespace bpp.
+
+#endif // _SEQUENCEAPPLICATIONTOOLS_H_
+
diff --git a/src/Bpp/Seq/CodonSiteTools.cpp b/src/Bpp/Seq/CodonSiteTools.cpp
new file mode 100644
index 0000000..9b7007f
--- /dev/null
+++ b/src/Bpp/Seq/CodonSiteTools.cpp
@@ -0,0 +1,846 @@
+//
+// File CodonSiteTools.cpp
+// Author : Sylvain Glémin
+// Last modification : October 2004
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "CodonSiteTools.h"
+#include "Alphabet/StandardCodonAlphabet.h"
+#include "Alphabet/CodonAlphabet.h"
+#include "Alphabet/DNA.h"
+#include "Alphabet/AlphabetTools.h"
+#include "SiteTools.h"
+#include "GeneticCode/GeneticCode.h"
+#include "GeneticCode/StandardGeneticCode.h"
+#include <Bpp/Utils/MapTools.h>
+#include <Bpp/Numeric/NumTools.h>
+#include <Bpp/Numeric/VectorTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <cmath>
+
+using namespace std;
+
+/******************************************************************************/
+
+bool CodonSiteTools::hasGapOrStop(const Site& site) throw (AlphabetException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::hasGapOrStop: alphabet is not CodonAlphabet", site.getAlphabet());
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (site[i] < 0)
+ return true;
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+bool CodonSiteTools::hasStop(const Site& site) throw (AlphabetException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::hasStop: alphabet is not CodonAlphabet", site.getAlphabet());
+ const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(site.getAlphabet());
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (ca->isStop(site[i]))
+ return true;
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+bool CodonSiteTools::isMonoSitePolymorphic(const Site& site) throw (AlphabetException, EmptySiteException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::isMonoSitePolymorphic: alphabet is not CodonAlphabet", site.getAlphabet());
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("CodonSiteTools::isMonoSitePolymorphic: Incorrect specified site", &site);
+
+ // Global polymorphism checking
+ if (SiteTools::isConstant(site))
+ return false;
+ // initialisation of the 3 sub-sites ot the codon
+ vector<int> pos1, pos2, pos3;
+ const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(site.getAlphabet());
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ pos1.push_back(ca->getFirstPosition(site[i]));
+ pos2.push_back(ca->getSecondPosition(site[i]));
+ pos3.push_back(ca->getThirdPosition(site[i]));
+ }
+ const NucleicAlphabet* na = ca->getNucleicAlphabet();
+ Site s1(pos1, na), s2(pos2, na), s3(pos3, na);
+ // polymorphism checking for each sub-sites
+ size_t nbpol = 0;
+ if (!SiteTools::isConstant(s1))
+ nbpol++;
+ if (!SiteTools::isConstant(s2))
+ nbpol++;
+ if (!SiteTools::isConstant(s3))
+ nbpol++;
+ if (nbpol > 1)
+ return false;
+ return true;
+}
+
+/******************************************************************************/
+
+bool CodonSiteTools::isSynonymousPolymorphic(const Site& site, const GeneticCode& gc)
+throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::isSynonymousPolymorphic: alphabet is not CodonAlphabet", site.getAlphabet());
+ if (typeid(site.getAlphabet()) != typeid(gc.getSourceAlphabet()))
+ throw AlphabetMismatchException("CodonSiteTools::isSynonymousPolymorphic: site and genetic code have not the same codon alphabet.", site.getAlphabet(), gc.getSourceAlphabet());
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("CodonSiteTools::isSynonymousPolymorphic: Incorrect specified site", &site);
+
+ // Global polymorphism checking
+ if (SiteTools::isConstant(site))
+ return false;
+
+ // Synonymous polymorphism checking
+ vector<int> prot;
+ int first_aa = gc.translate(site[0]);
+ for (size_t i = 1; i < site.size(); i++)
+ {
+ int aa = gc.translate(site[i]);
+ if (aa != first_aa)
+ return false;
+ }
+ return true;
+}
+
+/******************************************************************************/
+
+Site* CodonSiteTools::generateCodonSiteWithoutRareVariant(const Site& site, double freqmin)
+throw (AlphabetException, EmptySiteException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::generateCodonSiteWithoutRareVariant: alphabet is not CodonAlphabet", site.getAlphabet());
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("CodonSiteTools::generateCodonSiteWithoutRareVariant: Incorrect specified site", &site);
+
+ if (SiteTools::isConstant(site))
+ {
+ Site* noRareVariant = new Site(site);
+ return noRareVariant;
+ }
+ else
+ {
+ // Computation
+ map<int, double> freqcodon;
+ SiteTools::getFrequencies(site, freqcodon);
+ const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(site.getAlphabet());
+ const NucleicAlphabet* na = ca->getNucleicAlphabet();
+ int newcodon = -1;
+ for (map<int, double>::iterator it = freqcodon.begin(); it != freqcodon.end(); it++)
+ {
+ if (it->second > freqmin && !ca->isStop(it->first))
+ {
+ newcodon = it->first;
+ break;
+ }
+ }
+ vector<int> pos1, pos2, pos3;
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ pos1.push_back(ca->getFirstPosition(site[i]));
+ pos2.push_back(ca->getSecondPosition(site[i]));
+ pos3.push_back(ca->getThirdPosition(site[i]));
+ }
+ Site s1(pos1, na), s2(pos2, na), s3(pos3, na);
+ map<int, double> freq1;
+ SiteTools::getFrequencies(s1, freq1);
+ map<int, double> freq2;
+ SiteTools::getFrequencies(s2, freq2);
+ map<int, double> freq3;
+ SiteTools::getFrequencies(s3, freq3);
+ vector<int> codon;
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (freq1[s1.getValue(i)] > freqmin && freq2[s2.getValue(i)] > freqmin && freq3[s3.getValue(i)] > freqmin)
+ {
+ codon.push_back(site.getValue(i));
+ }
+ else
+ codon.push_back(newcodon);
+ }
+ Site* noRareVariant = new Site(codon, ca);
+ return noRareVariant;
+ }
+}
+
+/******************************************************************************/
+
+size_t CodonSiteTools::numberOfDifferences(int i, int j, const CodonAlphabet& ca)
+{
+ size_t nbdif = 0;
+ if (ca.getFirstPosition(i) != ca.getFirstPosition(j))
+ nbdif++;
+ if (ca.getSecondPosition(i) != ca.getSecondPosition(j))
+ nbdif++;
+ if (ca.getThirdPosition(i) != ca.getThirdPosition(j))
+ nbdif++;
+ return nbdif;
+}
+
+/******************************************************************************/
+
+double CodonSiteTools::numberOfSynonymousDifferences(int i, int j, const GeneticCode& gc, bool minchange)
+{
+ const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(gc.getSourceAlphabet());
+ vector<int> ci = ca->getPositions(i);
+ vector<int> cj = ca->getPositions(j);
+
+ switch (numberOfDifferences(i, j, *ca))
+ {
+ case 0: return 0;
+ case 1:
+ {
+ if (gc.areSynonymous(i, j))
+ return 1;
+ return 0;
+ }
+ case 2:
+ {
+ if (gc.areSynonymous(i, j))
+ return 2;
+ vector<double> path(2, 0); // Vector of number of synonymous changes per path (2 here)
+ vector<double> weight(2, 1); // Weight to exclude path through stop codon
+ if (ci[0] == cj[0])
+ {
+ int trans1 = ca->getCodon(ci[0], cj[1], ci[2]); // transitory codon between NcNiNi et NcNjNj: NcNjNi, Nc = identical site
+ int trans2 = ca->getCodon(ci[0], ci[1], cj[2]); // transitory codon between NcNiNi et NcNjNj: NcNiNj, Nc = identical site
+ if (!ca->isStop(trans1))
+ {
+ if (gc.areSynonymous(i, trans1))
+ path[0]++;
+ if (gc.areSynonymous(trans1, j))
+ path[0]++;
+ }
+ else
+ weight[0] = 0;
+ if (!ca->isStop(trans2))
+ {
+ if (gc.areSynonymous(i, trans2))
+ path[1]++;
+ if (gc.areSynonymous(trans2, j))
+ path[1]++;
+ }
+ else
+ weight[1] = 0;
+ }
+ if (ci[1] == cj[1])
+ {
+ int trans1 = ca->getCodon(cj[0], ci[1], ci[2]); // transitory codon between NiNcNi et NjNcNj: NjNcNi, Nc = identical site
+ int trans2 = ca->getCodon(ci[0], ci[1], cj[2]); // transitory codon between NiNcNi et NjNcNj: NiNcNj, Nc = identical site
+ if (!ca->isStop(trans1))
+ {
+ if (gc.areSynonymous(i, trans1))
+ path[0]++;
+ if (gc.areSynonymous(trans1, j))
+ path[0]++;
+ }
+ else
+ weight[0] = 0;
+ if (!ca->isStop(trans2))
+ {
+ if (gc.areSynonymous(i, trans2))
+ path[1]++;
+ if (gc.areSynonymous(trans2, j))
+ path[1]++;
+ }
+ else
+ weight[1] = 0;
+ }
+ if (ci[2] == cj[2])
+ {
+ int trans1 = ca->getCodon(cj[0], ci[1], ci[2]); // transitory codon between NiNiNc et NjNjNc: NjNiNc, Nc = identical site
+ int trans2 = ca->getCodon(ci[0], cj[1], ci[2]); // transitory codon between NiNiNc et NjNjNc: NiNjNc, Nc = identical site
+ if (!ca->isStop(trans1))
+ {
+ if (gc.areSynonymous(i, trans1))
+ path[0]++;
+ if (gc.areSynonymous(trans1, j))
+ path[0]++;
+ }
+ else
+ weight[0] = 0;
+ if (!ca->isStop(trans2))
+ {
+ if (gc.areSynonymous(i, trans2))
+ path[1]++;
+ if (gc.areSynonymous(trans2, j))
+ path[1]++;
+ }
+ else
+ weight[1] = 0;
+ }
+ if (minchange)
+ return VectorTools::max(path);
+
+ double nbdif = 0;
+ for (size_t k = 0; k < 2; k++)
+ {
+ nbdif += path[k] * weight[k];
+ }
+
+ return nbdif / VectorTools::sum(weight);
+ }
+ case 3:
+ {
+ vector<double> path(6, 0);
+ vector<double> weight(6, 1);
+ // First transitory codons
+ int trans100 = ca->getCodon(cj[0], ci[1], ci[2]);
+ int trans010 = ca->getCodon(ci[0], cj[1], ci[2]);
+ int trans001 = ca->getCodon(ci[0], ci[1], cj[2]);
+ // Second transitory codons
+ int trans110 = ca->getCodon(cj[0], cj[1], ci[2]);
+ int trans101 = ca->getCodon(cj[0], ci[1], cj[2]);
+ int trans011 = ca->getCodon(ci[0], cj[1], cj[2]);
+ // Paths
+ if (!ca->isStop(trans100))
+ {
+ if (gc.areSynonymous(i, trans100))
+ {
+ path[0]++; path[1]++;
+ }
+ if (!ca->isStop(trans110))
+ {
+ if (gc.areSynonymous(trans100, trans110))
+ path[0]++;
+ if (gc.areSynonymous(trans110, j))
+ path[0]++;
+ }
+ else
+ weight[0] = 0;
+ if (!ca->isStop(trans101))
+ {
+ if (gc.areSynonymous(trans100, trans101))
+ path[1]++;
+ if (gc.areSynonymous(trans101, j))
+ path[1]++;
+ }
+ else
+ weight[1] = 0;
+ }
+ else
+ {
+ weight[0] = 0; weight[1] = 0;
+ }
+ if (!ca->isStop(trans010))
+ {
+ if (gc.areSynonymous(i, trans010))
+ {
+ path[2]++; path[3]++;
+ }
+ if (!ca->isStop(trans110))
+ {
+ if (gc.areSynonymous(trans010, trans110))
+ path[2]++;
+ if (gc.areSynonymous(trans110, j))
+ path[2]++;
+ }
+ else
+ weight[2] = 0;
+ if (!ca->isStop(trans011))
+ {
+ if (gc.areSynonymous(trans010, trans011))
+ path[3]++;
+ if (gc.areSynonymous(trans011, j))
+ path[3]++;
+ }
+ else
+ weight[3] = 0;
+ }
+ else
+ {
+ weight[2] = 0; weight[3] = 0;
+ }
+ if (!ca->isStop(trans001))
+ {
+ if (gc.areSynonymous(i, trans001))
+ {
+ path[4]++; path[5]++;
+ }
+ if (!ca->isStop(trans101))
+ {
+ if (gc.areSynonymous(trans001, trans101))
+ path[4]++;
+ if (gc.areSynonymous(trans101, j))
+ path[4]++;
+ }
+ else
+ weight[4] = 0;
+ if (!ca->isStop(trans011))
+ {
+ if (gc.areSynonymous(trans001, trans011))
+ path[5]++;
+ if (gc.areSynonymous(trans011, j))
+ path[5]++;
+ }
+ else
+ weight[5] = 0;
+ }
+ else
+ {
+ weight[4] = 0; weight[5] = 0;
+ }
+ if (minchange)
+ return VectorTools::max(path);
+
+ double nbdif = 0;
+ for (size_t k = 0; k < 6; k++)
+ {
+ nbdif += path[k] * weight[k];
+ }
+
+ return nbdif / VectorTools::sum(weight);
+ }
+ }
+ // This line is never reached but sends a warning if not there:
+ return 0.;
+}
+
+/******************************************************************************/
+
+double CodonSiteTools::piSynonymous(const Site& site, const GeneticCode& gc, bool minchange)
+throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::piSynonymous: alphabet is not CodonAlphabet", site.getAlphabet());
+ if (typeid(site.getAlphabet()) != typeid(gc.getSourceAlphabet()))
+ throw AlphabetMismatchException("CodonSiteTools::piSynonymous: site and genetic code have not the same codon alphabet.", site.getAlphabet(), gc.getSourceAlphabet());
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("CodonSiteTools::piSynonymous: Incorrect specified site", &site);
+
+ // General polymorphism checking
+ if (SiteTools::isConstant(site))
+ return 0;
+ // Computation
+ map<int, double> freq;
+ SiteTools::getFrequencies(site, freq);
+ double pi = 0;
+ for (map<int, double>::iterator it1 = freq.begin(); it1 != freq.end(); it1++)
+ {
+ for (map<int, double>::iterator it2 = freq.begin(); it2 != freq.end(); it2++)
+ {
+ pi += (it1->second) * (it2->second) * (numberOfSynonymousDifferences(it1->first, it2->first, gc, minchange));
+ }
+ }
+ size_t n = site.size();
+ return pi * static_cast<double>(n / (n - 1));
+}
+
+/******************************************************************************/
+
+double CodonSiteTools::piNonSynonymous(const Site& site, const GeneticCode& gc, bool minchange)
+throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::piNonSynonymous: alphabet is not CodonAlphabet", site.getAlphabet());
+ if (typeid(site.getAlphabet()) != typeid(gc.getSourceAlphabet()))
+ throw AlphabetMismatchException("CodonSiteTools::piNonSynonymous: site and genetic code have not the same codon alphabet.", site.getAlphabet(), gc.getSourceAlphabet());
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("CodonSiteTools::piSynonymous: Incorrect specified site", &site);
+
+ // General polymorphism checking
+ if (SiteTools::isConstant(site))
+ return 0;
+ if (isSynonymousPolymorphic(site, gc))
+ return 0;
+ // Computation
+ map<int, double> freq;
+ SiteTools::getFrequencies(site, freq);
+ const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(site.getAlphabet());
+ double pi = 0;
+ for (map<int, double>::iterator it1 = freq.begin(); it1 != freq.end(); it1++)
+ {
+ for (map<int, double>::iterator it2 = freq.begin(); it2 != freq.end(); it2++)
+ {
+ double nbtot = static_cast<double>(numberOfDifferences(it1->first, it2->first, *ca));
+ double nbsyn = numberOfSynonymousDifferences(it1->first, it2->first, gc, minchange);
+ pi += (it1->second) * (it2->second) * (nbtot - nbsyn);
+ }
+ }
+ size_t n = site.size();
+ return pi * static_cast<double>(n / (n - 1));
+}
+
+/******************************************************************************/
+
+double CodonSiteTools::numberOfSynonymousPositions(int i, const GeneticCode& gc, double ratio) throw (Exception)
+{
+ try
+ {
+ const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(gc.getSourceAlphabet());
+ if (ca->isStop(i))
+ return 0;
+ if (ca->isUnresolved(i))
+ return 0;
+ double nbsynpos = 0.0;
+ vector<int> codon = ca->getPositions(i);
+ int acid = gc.translate(i);
+ for (int pos = 0; pos < 3; pos++)
+ {
+ for (int an = 0; an < 4; an++)
+ {
+ if (an == codon[pos])
+ continue;
+ vector<int> mutcodon = codon;
+ mutcodon[pos] = an;
+ int intcodon = ca->getCodon(mutcodon[0], mutcodon[1], mutcodon[2]);
+ if (ca->isStop(intcodon))
+ continue;
+ int altacid = gc.translate(intcodon);
+ if (altacid == acid) // if synonymous
+ {
+ if (((codon[pos] == 0 || codon[pos] == 2) && (mutcodon[pos] == 1 || mutcodon[pos] == 3)) ||
+ ((codon[pos] == 1 || codon[pos] == 3) && (mutcodon[pos] == 0 || mutcodon[pos] == 2))) // if it is a transversion
+ {
+ nbsynpos = nbsynpos + 1 / (ratio + 2);
+ }
+ else // if transition
+ {
+ nbsynpos = nbsynpos + ratio / (ratio + 2);
+ }
+ }
+ }
+ }
+ return nbsynpos;
+ }
+ catch (...)
+ {} // !!!!! en cas d'exception, plante! il faudrait forwarder l'exception
+ // This line is never reached but sends a warning if not there:
+ return 0.;
+}
+
+/******************************************************************************/
+
+double CodonSiteTools::meanNumberOfSynonymousPositions(const Site& site, const GeneticCode& gc, double ratio)
+throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::meanNumberOfSynonymousPositions: alphabet is not CodonAlphabet", site.getAlphabet());
+ if (typeid(site.getAlphabet()) != typeid(gc.getSourceAlphabet()))
+ throw AlphabetMismatchException("CodonSiteTools::meanNumberOfSynonymousPositions: site and genetic code have not the same codon alphabet.", site.getAlphabet(), gc.getSourceAlphabet());
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("CodonSiteTools::meanNumberOfSynonymousPositions: Incorrect specified site", &site);
+
+ // Computation
+ double NbSyn = 0;
+ map<int, double> freq;
+ SiteTools::getFrequencies(site, freq);
+ for (map<int, double>::iterator it = freq.begin(); it != freq.end(); it++)
+ {
+ NbSyn += (it->second) * numberOfSynonymousPositions(it->first, gc, ratio);
+ }
+ return NbSyn;
+}
+
+/******************************************************************************/
+
+size_t CodonSiteTools::numberOfSubsitutions(const Site& site, double freqmin)
+throw (AlphabetException, EmptySiteException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::numberOfSubsitutions: alphabet is not CodonAlphabet", site.getAlphabet());
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("CodonSiteTools::numberOfSubsitutions: Incorrect specified site", &site);
+
+ if (SiteTools::isConstant(site))
+ return 0;
+ Site* newsite;
+ if (freqmin > 1. / static_cast<double>(site.size()))
+ newsite = CodonSiteTools::generateCodonSiteWithoutRareVariant(site, freqmin);
+ else
+ newsite = new Site(site);
+ // Computation
+ if (SiteTools::hasGap(*newsite))
+ return 0;
+ vector<int> pos1, pos2, pos3;
+
+ const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(site.getAlphabet());
+
+ for (size_t i = 0; i < newsite->size(); i++)
+ {
+ pos1.push_back(ca->getFirstPosition(newsite->getValue(i)));
+ pos2.push_back(ca->getSecondPosition(newsite->getValue(i)));
+ pos3.push_back(ca->getThirdPosition(newsite->getValue(i)));
+ }
+
+ const NucleicAlphabet* na = ca->getNucleicAlphabet();
+
+ Site s1(pos1, na), s2(pos2, na), s3(pos3, na);
+ size_t Scodon = SiteTools::getNumberOfDistinctCharacters(*newsite) - 1;
+ size_t Sbase = SiteTools::getNumberOfDistinctCharacters(s1) + SiteTools::getNumberOfDistinctCharacters(s2) + SiteTools::getNumberOfDistinctCharacters(s3) - 3;
+ delete newsite;
+ if (Scodon >= Sbase)
+ return Scodon;
+ else
+ return Sbase;
+}
+
+/******************************************************************************/
+
+size_t CodonSiteTools::numberOfNonSynonymousSubstitutions(const Site& site, const GeneticCode& gc, double freqmin)
+throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::numberOfNonSynonymousSubstitutions: alphabet is not CodonAlphabet", site.getAlphabet());
+ if (typeid(site.getAlphabet()) != typeid(gc.getSourceAlphabet()))
+ throw AlphabetMismatchException("CodonSiteTools::numberOfNonSynonymousSubstitutions: site and genetic code have not the same codon alphabet.", site.getAlphabet(), gc.getSourceAlphabet());
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("CodonSiteTools::numberOfNonSynonymousSubstitutions: Incorrect specified site", &site);
+
+ if (SiteTools::isConstant(site))
+ return 0;
+ Site* newsite;
+ if (freqmin > 1. / static_cast<double>(site.size()))
+ newsite = generateCodonSiteWithoutRareVariant(site, freqmin);
+ else
+ newsite = new Site(site);
+ if (SiteTools::hasGap(*newsite))
+ return 0;
+ // computation
+ map<int, size_t> count;
+ SiteTools::getCounts(*newsite, count);
+ size_t NaSup = 0;
+ size_t Nminmin = 10;
+
+ const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(site.getAlphabet());
+
+ for (map<int, size_t>::iterator it1 = count.begin(); it1 != count.end(); it1++)
+ {
+ size_t Nmin = 10;
+ for (map<int, size_t>::iterator it2 = count.begin(); it2 != count.end(); it2++)
+ {
+ size_t Ntot = numberOfDifferences(it1->first, it2->first, *ca);
+ size_t Ns = (size_t)numberOfSynonymousDifferences(it1->first, it2->first, gc, true);
+ if (Nmin > Ntot - Ns && it1->first != it2->first)
+ Nmin = Ntot - Ns;
+ }
+ NaSup += Nmin;
+ if (Nmin < Nminmin)
+ Nminmin = Nmin;
+ }
+ delete newsite;
+ return NaSup - Nminmin;
+}
+
+/******************************************************************************/
+
+vector<size_t> CodonSiteTools::fixedDifferences(const Site& siteIn, const Site& siteOut, int i, int j, const GeneticCode& gc)
+throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
+{
+ // Alphabet checking
+ if (!AlphabetTools::isCodonAlphabet(siteIn.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::fixedDifferences: alphabet is not CodonAlphabet (siteIn)", siteIn.getAlphabet());
+ if (!AlphabetTools::isCodonAlphabet(siteOut.getAlphabet()))
+ throw AlphabetException("CodonSiteTools::fixedDifferences: alphabet is not CodonAlphabet (siteOut)", siteOut.getAlphabet());
+ if (typeid(siteIn.getAlphabet()) != typeid(gc.getSourceAlphabet()))
+ throw AlphabetMismatchException("CodonSiteTools::fixedDifferences: siteIn and genetic code have not the same codon alphabet.", siteIn.getAlphabet(), gc.getSourceAlphabet());
+ if (typeid(siteOut.getAlphabet()) != typeid(gc.getSourceAlphabet()))
+ throw AlphabetMismatchException("CodonSiteTools::fixedDifferences: siteOut and genetic code have not the same codon alphabet.", siteOut.getAlphabet(), gc.getSourceAlphabet());
+ // Empty site checking
+ if (siteIn.size() == 0)
+ throw EmptySiteException("CodonSiteTools::getFixedDifferences Incorrect specified site", &siteIn);
+ if (siteOut.size() == 0)
+ throw EmptySiteException("CodonSiteTools::getFixedDifferences Incorrect specified site", &siteOut);
+
+ const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(gc.getSourceAlphabet());
+
+ size_t Ntot = numberOfDifferences(i, j, *ca);
+ size_t Ns = (size_t) numberOfSynonymousDifferences(i, j, gc, true);
+ size_t Na = Ntot - Ns;
+ size_t Nfix = Ntot;
+ vector<int> pos1in, pos2in, pos3in, pos1out, pos2out, pos3out;
+
+ for (size_t k = 0; k < siteIn.size(); k++)
+ {
+ pos1in.push_back(ca->getFirstPosition(siteIn[k]));
+ pos2in.push_back(ca->getSecondPosition(siteIn[k]));
+ pos3in.push_back(ca->getThirdPosition(siteIn[k]));
+ pos1out.push_back(ca->getFirstPosition(siteOut[k]));
+ pos2out.push_back(ca->getSecondPosition(siteOut[k]));
+ pos3out.push_back(ca->getThirdPosition(siteOut[k]));
+ }
+ const NucleicAlphabet* na = ca->getNucleicAlphabet();
+
+ Site s1in(pos1in, na), s2in(pos2in, na), s3in(pos3in, na);
+ Site s1out(pos1out, na), s2out(pos2out, na), s3out(pos3out, na);
+ bool test1 = false;
+ bool test2 = false;
+ bool test3 = false;
+ if ( (!SiteTools::isConstant(s1in) || !SiteTools::isConstant(s1out)) && ca->getFirstPosition(i) != ca->getFirstPosition(j) )
+ {
+ test1 = true;
+ Nfix--;
+ }
+ if ( (!SiteTools::isConstant(s2in) || !SiteTools::isConstant(s2out)) && ca->getSecondPosition(i) != ca->getSecondPosition(j) )
+ {
+ test2 = true;
+ Nfix--;
+ }
+ if ( (!SiteTools::isConstant(s3in) || !SiteTools::isConstant(s3out)) && ca->getThirdPosition(i) != ca->getThirdPosition(j) )
+ {
+ test3 = true;
+ Nfix--;
+ }
+ // Suppression of differences when not fixed
+ vector<size_t> v(2);
+ if (Nfix == 0)
+ {
+ v[0] = 0;
+ v[1] = 0;
+ return v;
+ }
+ if (Nfix < Ntot)
+ {
+ if (Na == 0)
+ Ns = Nfix;
+ if (Ns == 0)
+ Na = Nfix;
+ else
+ {
+ if (Ntot == 3)
+ {
+ if (Nfix == 1)
+ {
+ if (test1 && test2)
+ {
+ Na = 0; Ns = 1;
+ }
+ if (test1 && test3)
+ {
+ Na = 1; Ns = 0;
+ }
+ if (test2 && test3)
+ {
+ Na--; Ns--;
+ }
+ }
+ }
+ if (Nfix == 2)
+ {
+ if (test1)
+ {
+ Na = 1; Ns = 1;
+ }
+ if (test2)
+ Na--;
+ if (test3)
+ Ns--;
+ }
+ }
+ if (Ntot == 2)
+ {
+ if (test1)
+ {
+ if (ca->getSecondPosition(i) == ca->getSecondPosition(j))
+ Na--;
+ else
+ Ns--;
+ }
+ if (test2)
+ Na--;
+ if (test3)
+ Ns--;
+ }
+ }
+ v[0] = Ns;
+ v[1] = Na;
+ return v;
+}
+
+/******************************************************************************/
+
+bool CodonSiteTools::isFourFoldDegenerated(const Site& site, const GeneticCode& gc)
+{
+ if (!SiteTools::isConstant(site, true))
+ {
+ /** If non-synonymous mutation **/
+ if (!(CodonSiteTools::isSynonymousPolymorphic(site, gc)))
+ return false;
+
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (!(gc.isFourFoldDegenerated(site.getValue(i))))
+ {
+ return false;
+ }
+ }
+ }
+ else
+ {
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (!(gc.isFourFoldDegenerated(site.getValue(i))))
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/CodonSiteTools.h b/src/Bpp/Seq/CodonSiteTools.h
new file mode 100644
index 0000000..bb7cd2a
--- /dev/null
+++ b/src/Bpp/Seq/CodonSiteTools.h
@@ -0,0 +1,331 @@
+//
+// File CodonSiteTools.h
+// Author : Sylvain Glémin
+// Last modification : November 2005
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _CODONSITETOOLS_H_
+#define _CODONSITETOOLS_H_
+
+#include "SymbolListTools.h"
+#include "Site.h"
+#include "Alphabet/CodonAlphabet.h"
+#include "GeneticCode/GeneticCode.h"
+
+#include <Bpp/Exceptions.h>
+
+// From the STL:
+#include <map>
+
+namespace bpp
+{
+
+/**
+ * @brief Utilitary functions for codon sites.
+ */
+
+class CodonSiteTools:
+ public SymbolListTools
+{
+ public:
+ CodonSiteTools() {}
+ virtual ~CodonSiteTools() {}
+
+ public:
+
+ /**
+ * @brief Method to know if a codon site contains gap(s) or stop codons.
+ *
+ * @param site a Site
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ */
+ static bool hasGapOrStop(const Site & site) throw (AlphabetException);
+
+ /**
+ * @brief Method to know if a codon site contains stop codon or not
+ *
+ * @param site a Site
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ */
+ static bool hasStop(const Site & site) throw (AlphabetException);
+
+ /**
+ * @brief Method to know if a polymorphic codon site is polymorphic at only one site
+ *
+ * @param site a Site
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static bool isMonoSitePolymorphic(const Site & site) throw (AlphabetException, EmptySiteException);
+
+ /**
+ * @brief Method to know if polymorphism at a codon site is synonymous
+ *
+ * @param site a Site
+ * @param gc a GeneticCode
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ * @throw AlphabetMismatchException If the codon alphabet of the site do not match the codon alphabet of the genetic code.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static bool isSynonymousPolymorphic(const Site & site, const GeneticCode & gc)
+ throw (AlphabetException, AlphabetMismatchException, EmptySiteException);
+
+ /**
+ * @brief generate a codon site without rare variants
+ *
+ * Rare variants are replaced by the most frequent allele.
+ * This method is used to exclude rare variants in some analyses as in McDonald-Kreitman Test
+ * (McDonald & Kreitman, 1991, Nature 351 pp652-654).
+ * For an application, see for example (Fay et al. 2001, Genetics 158 pp 1227-1234).
+ *
+ * @param site a Site
+ * @param freqmin a double, allele in frequency stricly lower than freqmin are replaced
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ * @throw EmptySiteException If the site has size 0.
+ *
+ */
+ static Site * generateCodonSiteWithoutRareVariant(const Site & site, double freqmin)
+ throw(AlphabetException, EmptySiteException);
+
+
+ /**
+ * @brief Compute the number of differences between two codons
+ *
+ * @param i a int
+ * @param j a int
+ * @param ca a CodonAlphabet
+ */
+ static size_t numberOfDifferences(int i, int j, const CodonAlphabet & ca);
+
+ /**
+ * @brief Compute the number of synonymous differences between two codons
+ *
+ * For complex codon:
+ * If minchange = false (default option) the different paths are equally weighted.
+ * If minchange = true the path with the minimum number of non-synonymous change is chosen.
+ * Paths included stop codons are excluded.
+ * @param i a int
+ * @param j a int
+ * @param gc a GeneticCode
+ * @param minchange a boolean set by default to false
+ */
+ static double numberOfSynonymousDifferences(int i, int j, const GeneticCode & gc, bool minchange=false);
+
+ /**
+ * @brief Compute the synonymous pi per codon site
+ *
+ * The following formula is used:
+ * @f[
+ * pi = frac{n}{n-1}\sum_{i,j}x_{i}x_{j}P_{ij}
+ * @f]
+ * where n is the number of sequence, \f$x_i\f$ and \f$x_j\f$ the frequencies of each codon type occuring at the site
+ * \f$P_{i,j}\f$ the number of synonymous difference between these codons.
+ * Be careful: here, pi is not normalized by the number of synonymous sites.
+ *
+ * If minchange = false (default option) the different paths are equally weighted.
+ * If minchange = true the path with the minimum number of non-synonymous change is chosen.
+ *
+ * @param site a Site
+ * @param gc a GeneticCode
+ * @param minchange a boolean set by default to false
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ * @throw AlphabetMismatchException If the codon alphabet of the site do not match the codon alphabet of the genetic code.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static double piSynonymous(const Site & site, const GeneticCode & gc, bool minchange=false)
+ throw (AlphabetException, AlphabetMismatchException, EmptySiteException);
+
+ /**
+ * @brief Compute the non-synonymous pi per codon site
+ *
+ * The following formula is used:
+ * @f[
+ * pi = frac{n}{n-1}\sum_{i,j}x_{i}x_{j}P_{ij}
+ * @f]
+ * where n is the number of sequence, \f$x_i\f$ and \f$x_j\f$ the frequencies of each codon type occuring at the site
+ * \f$P_{i,j}\f$ the number of nonsynonymous difference between these codons.
+ * Be careful: here, pi is not normalized by the number of non-synonymous sites.
+ * If minchange = false (default option) the different paths are equally weighted.
+ * If minchange = true the path with the minimum number of non-synonymous change is chosen.
+ *
+ * @param site a Site
+ * @param gc a GeneticCode
+ * @param minchange a boolean set by default to false
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ * @throw AlphabetMismatchException If the codon alphabet of the site do not match the codon alphabet of the genetic code.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static double piNonSynonymous(const Site & site, const GeneticCode & gc, bool minchange = false)
+ throw (AlphabetException, AlphabetMismatchException, EmptySiteException);
+
+
+ /**
+ * @brief Return the number of synonymous positions of a codon
+ *
+ * A site is consider as x% synonymous if x% of the possible mutations are synonymous
+ * Transition/transversion ratio can be taken into account (use the variable ratio)
+ *
+ * Unresolved codons and stop codon will return a value of 0.
+ *
+ * @param i a int
+ * @param gc a GeneticCode
+ * @param ratio a double set by default to 1
+ */
+ static double numberOfSynonymousPositions(int i, const GeneticCode & gc, double ratio=1.0) throw (Exception);
+
+ /**
+ * @brief Return the mean number of synonymous positions per codon site
+ *
+ * A site is consider as x% synonymous if x% of the possible mutations are synonymous
+ * Transition/transversion ratio can be taken into account (use the variable ratio)
+ * The mean is computed over the VectorSite.
+ *
+ * Unresolved and stop codons are counted as 0.
+ *
+ * @param site a Site
+ * @param gc a GeneticCode
+ * @param ratio a double Set by default to 1
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ * @throw AlphabetMismatchException If the codon alphabet of the site do not match the codon alphabet of the genetic code.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static double meanNumberOfSynonymousPositions(const Site & site, const GeneticCode & gc, double ratio=1)
+ throw (AlphabetException, AlphabetMismatchException, EmptySiteException);
+
+ /**
+ * @brief Return the number of subsitutions per codon site
+ *
+ * No recombination is assumed, that is in complex codon homoplasy is assumed.
+ * Example:
+ * @code
+ * ATT
+ * ATT
+ * ATT
+ * ATC
+ * ATC
+ * AGT
+ * AGT
+ * AGC
+ * @endcode
+ * Here, 3 substitutions are counted. Assuming that the last codon (AGC) is a recombinant between ATC and AGT
+ * would have lead to counting only 2 subsitutions.
+ *
+ * Rare variants (<= freqmin) can be excluded.
+ *
+ * @param site a Site
+ * @param freqmin a double To exclude snp in frequency strictly lower than freqmin (by default freqmin = 0)
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static size_t numberOfSubsitutions(const Site & site, double freqmin = 0.)
+ throw(AlphabetException, EmptySiteException);
+
+ /**
+ * @brief Return the number of Non Synonymous subsitutions per codon site.
+ *
+ * It is assumed that the path linking amino acids only involved one substitution by step.
+ *
+ * Rare variants (<= freqmin) can be excluded.
+ * In case of complex codon, the path that gives the minimum number of non-synonymous changes
+ * is chosen. The argument minchange=true is sent to numberOfSynonymousDifferences used in this method.
+ * Otherwise, a non-integer number could be return.
+ *
+ * @param site a Site
+ * @param gc a GeneticCode
+ * @param freqmin a double To exclude snp in frequency strictly lower than freqmin (by default freqmin = 0).
+ * @throw AlphabetException If the alphabet associated to the site is not a codon alphabet.
+ * @throw AlphabetMismatchException If the codon alphabet of the site do not match the codon alphabet of the genetic code.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static size_t numberOfNonSynonymousSubstitutions(const Site & site, const GeneticCode & gc, double freqmin = 0.)
+ throw (AlphabetException, AlphabetMismatchException, EmptySiteException);
+
+
+ /**
+ * @brief Return a vector with the number of fixed synonymous and non-synonymous differences per codon site
+ *
+ * Compute the number of synonymous and non-synonymous differences between
+ * the concensus codon of SiteIn (i) and SiteOut (j), which are fixed within each alignement.
+ * Example:
+ * @code
+ * SiteIn
+ * ATT
+ * ATT
+ * ATC
+ * @endcode
+ * @code
+ * SiteOut
+ * CTA
+ * CTA
+ * CTA
+ * @endcode
+ * Here, the first position is non-synonymous different and fixed,
+ * the third position is synonymous different but not fixed (polymorphic in SiteIn).
+ * The return vector is thus [0,1].
+ * In case of complex codon, the path that gives the minimum number of non-synonymous changes
+ * is chosen. The argument minchange=true is sent to numberOfSynonymousDifferences used in this method.
+ * Otherwise, a non-integer number could be return.
+ *
+ * Rare variants (<= freqmin) can be excluded.
+ *
+ * @param siteIn a Site
+ * @param siteOut a Site
+ * @param i an integer
+ * @param j an integer
+ * @param gc a GeneticCode
+ * @throw AlphabetException If the alphabet associated to one of the sites is not a codon alphabet.
+ * @throw AlphabetMismatchException If the codon alphabet each the site do not match the codon alphabet of the genetic code.
+ * @throw EmptySiteException If one of the sites has size 0.
+ */
+ static std::vector<size_t> fixedDifferences(const Site & siteIn, const Site & siteOut, int i, int j, const GeneticCode & gc)
+ throw (AlphabetException, AlphabetMismatchException, EmptySiteException);
+
+
+ /**
+ * @return True if all sequences have a fourfold degenerated codon in the site
+ * (that is, if a mutation in the fourth position does not change the aminoacid).
+ * @author Benoit Nabholz, Annabelle Haudry
+ * @param site The site to analyze.
+ * @param gc The genetic code to use.
+ */
+ static bool isFourFoldDegenerated(const Site& site, const GeneticCode& gc);
+
+};
+
+} //end of namespace bpp.
+
+#endif //_CONDONSITETOOLS_H_
+
diff --git a/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp b/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp
new file mode 100644
index 0000000..f9e7820
--- /dev/null
+++ b/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp
@@ -0,0 +1,56 @@
+//
+// File: AbstractSequenceContainer.cpp
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: Wednesday July 30 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info". uu
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "AbstractSequenceContainer.h"
+
+using namespace bpp;
+using namespace std;
+
+/**************************************************************************************************/
+
+void AbstractSequenceContainer::setComments(const string& name, const Comments& comments)
+throw (SequenceNotFoundException)
+{
+ size_t pos = getSequencePosition(name);
+ setComments(pos, comments);
+}
+
+/**************************************************************************************************/
+
diff --git a/src/Bpp/Seq/Container/AbstractSequenceContainer.h b/src/Bpp/Seq/Container/AbstractSequenceContainer.h
new file mode 100644
index 0000000..d0718d9
--- /dev/null
+++ b/src/Bpp/Seq/Container/AbstractSequenceContainer.h
@@ -0,0 +1,190 @@
+//
+// File AbstractSequenceContainer.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ABSTRACTSEQUENCECONTAINER_H_
+#define _ABSTRACTSEQUENCECONTAINER_H_
+
+#include "../Alphabet/Alphabet.h"
+#include "../Sequence.h"
+#include "SequenceContainer.h"
+#include "OrderedSequenceContainer.h"
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+/**
+ * @brief Partial implementation of the OrderedSequenceContainer interface.
+ *
+ * This abstract class provides an alphabet and comments, with associated methods.
+ */
+class AbstractSequenceContainer:
+ public virtual OrderedSequenceContainer
+{
+ private:
+
+ /**
+ * @brief The container's alphabet.
+ */
+ const Alphabet* alphabet_;
+
+ /**
+ * @brief The container's comments.
+ */
+ Comments comments_;
+
+ public:
+
+ /**
+ * @brief This constructor initialize the alphabet pointer.
+ *
+ * This constructor is to be called by constructors of derived classes.
+ *
+ * @param alpha The alphabet to be associated to this container.
+ */
+ AbstractSequenceContainer(const Alphabet* alpha):
+ alphabet_(alpha), comments_() {}
+
+ AbstractSequenceContainer(const AbstractSequenceContainer& sc):
+ alphabet_(sc.alphabet_), comments_(sc.comments_) {}
+
+ AbstractSequenceContainer& operator=(const AbstractSequenceContainer& sc)
+ {
+ alphabet_ = sc.alphabet_;
+ comments_ = sc.comments_;
+ return *this;
+ }
+
+ /**
+ * @brief Copy constructor from any SequenceContainer object.
+ *
+ * @param sc Another sequence container.
+ */
+ AbstractSequenceContainer(const SequenceContainer& sc):
+ alphabet_(sc.getAlphabet()), comments_(sc.getGeneralComments()) {}
+
+ /**
+ * @brief Assignation operator from any SequenceContainer object.
+ *
+ * @param sc Another sequence container.
+ */
+ AbstractSequenceContainer& operator=(const SequenceContainer& sc)
+ {
+ alphabet_ = sc.getAlphabet();
+ comments_ = sc.getGeneralComments();
+ return *this;
+ }
+
+ virtual ~AbstractSequenceContainer() {}
+
+ public:
+
+ /**
+ * @name From the SequenceContainer interface
+ *
+ * @{
+ */
+ const Alphabet* getAlphabet() const { return alphabet_; }
+ const std::vector<int>& getContent(const std::string& name) const throw (SequenceNotFoundException)
+ {
+ return getSequence(name).getContent();
+ }
+
+ std::string toString(const std::string& name) const throw (SequenceNotFoundException)
+ {
+ return getSequence(name).toString();
+ }
+
+ const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
+ {
+ return getSequence(name).getComments();
+ }
+
+ void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
+ const Comments& getGeneralComments() const
+ {
+ return comments_;
+ }
+
+ void setGeneralComments(const Comments& comments)
+ {
+ comments_ = comments;
+ }
+
+ void deleteGeneralComments()
+ {
+ comments_.clear();
+ }
+
+ /** @} */
+
+ /**
+ * @name From the OrderedSequenceContainer interface
+ *
+ * @{
+ */
+ virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
+ {
+ return getSequence(sequenceIndex).getName();
+ }
+
+ virtual const std::vector<int>& getContent(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
+ {
+ return getSequence(sequenceIndex).getContent();
+ }
+
+ virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
+ {
+ return getSequence(sequenceIndex).toString();
+ }
+
+ virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
+ {
+ return getSequence(sequenceIndex).getComments();
+ }
+
+ virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
+ /** @} */
+
+};
+
+} //end of namespace bpp.
+
+#endif // _ABSTRACTSEQUENCECONTAINER_H_
+
diff --git a/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp b/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp
new file mode 100644
index 0000000..5ae8aa4
--- /dev/null
+++ b/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp
@@ -0,0 +1,521 @@
+//
+// File: AlignedSequenceContainer.cpp
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: Friday August 22 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "AlignedSequenceContainer.h"
+
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+
+using namespace std;
+
+/***************************************************************************/
+
+AlignedSequenceContainer::AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException) :
+ VectorSequenceContainer(osc.getAlphabet()),
+ // We can't call the copy constructor because we want to use the overloaded addSequence method !!!
+ positions_(),
+ length_(),
+ sites_()
+{
+ // Initializing
+ for (unsigned int i = 0; i < osc.getNumberOfSequences(); i++)
+ {
+ addSequence(osc.getSequence(i), true);
+ }
+
+ if (osc.getNumberOfSequences() > 0)
+ length_ = getSequence(0).size(); // the overloaded
+ else
+ length_ = 0;
+
+ reindexSites();
+ sites_.resize(length_);
+ setGeneralComments(osc.getGeneralComments());
+}
+
+/***************************************************************************/
+
+AlignedSequenceContainer& AlignedSequenceContainer::operator=(const AlignedSequenceContainer& asc)
+{
+ VectorSequenceContainer::operator=(asc);
+
+ // Initializing
+ length_ = asc.getNumberOfSites();
+ positions_ = asc.getSitePositions();
+ sites_.resize(length_);
+
+ return *this;
+}
+
+/***************************************************************************/
+
+AlignedSequenceContainer& AlignedSequenceContainer::operator=(const SiteContainer& sc)
+{
+ VectorSequenceContainer::operator=(sc);
+
+ // Initializing
+ length_ = sc.getNumberOfSites();
+ positions_ = sc.getSitePositions();
+ sites_.resize(length_);
+
+ return *this;
+}
+
+/***************************************************************************/
+
+AlignedSequenceContainer& AlignedSequenceContainer::operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException)
+{
+ VectorSequenceContainer::operator=(osc);
+
+ // Initializing
+ length_ = 0;
+ reindexSites();
+ sites_.resize(length_);
+
+ return *this;
+}
+
+/** Class destructor: *********************************************************/
+
+AlignedSequenceContainer::~AlignedSequenceContainer()
+{
+ // delete all sites:
+ for (unsigned int i = 0; i < sites_.size(); i++)
+ {
+ if (sites_[i])
+ delete sites_[i];
+ }
+}
+
+/***************************************************************************/
+
+const Site& AlignedSequenceContainer::getSite(size_t i) const throw (IndexOutOfBoundsException)
+{
+ if (i >= length_)
+ throw IndexOutOfBoundsException("AlignedSequenceContainer::getSite", i, 0, getNumberOfSites() - 1);
+
+ // Main loop : for all sequences
+ size_t n = getNumberOfSequences();
+ std::vector<int> site(n);
+ for (size_t j = 0; j < n; j++)
+ {
+ site[j] = getSequence(j)[i];
+ }
+
+ if (sites_[i])
+ delete sites_[i];
+ sites_[i] = new Site(site, getAlphabet(), positions_[i]);
+ return *sites_[i];
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
+{
+ // New site's alphabet and site container's alphabet matching verification
+ if (pos >= getNumberOfSites())
+ throw IndexOutOfBoundsException("AlignedSequenceContainer::setSite", pos, 0, getNumberOfSites() - 1);
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("AlignedSequenceContainer::setSite", getAlphabet(), site.getAlphabet());
+
+ std::vector<int> s = site.getContent();
+
+ // Check size:
+ if (s.size() != getNumberOfSequences())
+ throw SiteException("AlignedSequenceContainer::setSite, site does not have the appropriate length", &site);
+
+ // Check position:
+ int position = site.getPosition();
+ if (checkPositions)
+ {
+ // For all positions in vector : throw exception if position already exists
+ for (size_t i = 0; i < positions_.size(); i++)
+ {
+ if (positions_[i] == position)
+ throw SiteException("AlignedSequenceContainer::setSite: Site position already exists in container", &site);
+ }
+ }
+
+ // For all sequences
+ for (size_t j = 0; j < getNumberOfSequences(); j++)
+ {
+ getSequence_(j).setElement(pos, s[j]);
+ }
+ positions_[pos] = site.getPosition();
+}
+
+/******************************************************************************/
+
+Site* AlignedSequenceContainer::removeSite(size_t pos) throw (IndexOutOfBoundsException)
+{
+ if (pos >= getNumberOfSites())
+ throw IndexOutOfBoundsException("AlignedSequenceContainer::removeSite", pos, 0, getNumberOfSites() - 1);
+
+ // Get old site
+ getSite(pos); // Creates the site!
+ Site* old = sites_[pos];
+
+ // For all sequences
+ for (size_t j = 0; j < getNumberOfSequences(); j++)
+ {
+ getSequence_(j).deleteElement(pos);
+ }
+
+ // Delete site's position
+ positions_.erase(positions_.begin() + pos);
+ length_--;
+
+ // Actualizes the 'sites' vector:
+ if (sites_[pos])
+ delete sites_[pos];
+ sites_.erase(sites_.begin() + pos);
+
+ // Send result
+ return old;
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::deleteSite(size_t pos) throw (IndexOutOfBoundsException)
+{
+ if (pos >= getNumberOfSites())
+ throw IndexOutOfBoundsException("AlignedSequenceContainer::deleteSite", pos, 0, getNumberOfSites() - 1);
+
+ // For all sequences
+ for (size_t j = 0; j < getNumberOfSequences(); j++)
+ {
+ getSequence_(j).deleteElement(pos);
+ }
+
+ // Delete site's position
+ positions_.erase(positions_.begin() + pos);
+ length_--;
+
+ // Actualizes the 'sites' vector:
+ if (sites_[pos])
+ delete sites_[pos];
+ sites_.erase(sites_.begin() + pos);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception)
+{
+ if (siteIndex + length > getNumberOfSites())
+ throw IndexOutOfBoundsException("AlignedSequenceContainer::deleteSites", siteIndex + length, 0, getNumberOfSites() - 1);
+
+ // For all sequences
+ for (size_t j = 0; j < getNumberOfSequences(); j++)
+ {
+ getSequence_(j).deleteElements(siteIndex, length);
+ }
+
+ // Delete site's siteIndexition
+ positions_.erase(positions_.begin() + siteIndex, positions_.begin() + siteIndex + length);
+ length_ -= length;
+
+ // Actualizes the 'sites' vector:
+ for (size_t i = siteIndex; i < siteIndex + length; ++i)
+ {
+ if (sites_[i])
+ delete sites_[i];
+ }
+ sites_.erase(sites_.begin() + siteIndex, sites_.begin() + siteIndex + length);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
+{
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("AlignedSequenceContainer::addSite");
+
+ // Initializing
+ std::vector<int> s = site.getContent();
+
+ // Check size:
+ if (s.size() != getNumberOfSequences())
+ throw SiteException("AlignedSequenceContainer::addSite, site does not have the appropriate length", &site);
+
+ // Check position:
+
+ int position = site.getPosition();
+ if (checkPositions)
+ {
+ // For all positions in vector : throw exception if position already exists
+ for (unsigned int i = 0; i < positions_.size(); i++)
+ {
+ if (positions_[i] == position)
+ throw SiteException("AlignedSequenceContainer::addSite: Site position already exists in container", &site);
+ }
+ }
+
+ // For all sequences
+ for (unsigned int j = 0; j < getNumberOfSequences(); j++)
+ {
+ getSequence_(j).addElement(s[j]);
+ }
+
+ length_++;
+ positions_.push_back(position);
+
+ // Actualizes the 'sites' vector:
+ sites_.push_back(0);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::addSite(const Site& site, int position, bool checkPositions) throw (Exception)
+{
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("AlignedSequenceContainer::addSite");
+
+ // Initializing
+ std::vector<int> s = site.getContent();
+
+ // Check size:
+ if (s.size() != getNumberOfSequences())
+ throw SiteException("AlignedSequenceContainer::addSite, site does not have the appropriate length", &site);
+
+ // Check position:
+
+ if (checkPositions)
+ {
+ // For all positions in vector : throw exception if position already exists
+ for (unsigned int i = 0; i < positions_.size(); i++)
+ {
+ if (positions_[i] == position)
+ throw SiteException("AlignedSequenceContainer::addSite: Site position already exists in container", &site);
+ }
+ }
+
+ // For all sequences
+ for (unsigned int j = 0; j < getNumberOfSequences(); j++)
+ {
+ getSequence_(j).addElement(s[j]);
+ }
+
+ length_++;
+ positions_.push_back(position);
+
+ // Actualizes the 'sites' vector:
+ sites_.push_back(0);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::addSite(const Site& site, size_t siteIndex, bool checkPositions) throw (Exception)
+{
+ if (siteIndex >= getNumberOfSites())
+ throw IndexOutOfBoundsException("AlignedSequenceContainer::addSite", siteIndex, 0, getNumberOfSites() - 1);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("AlignedSequenceContainer::addSite", getAlphabet(), site.getAlphabet());
+
+ std::vector<int> s = site.getContent();
+
+ // Check size:
+ if (s.size() != getNumberOfSequences())
+ throw SiteException("AlignedSequenceContainer::addSite, site does not have the appropriate length", &site);
+
+ // Check position:
+ int position = site.getPosition();
+ if (checkPositions)
+ {
+ // For all positions in vector : throw exception if position already exists
+ for (size_t i = 0; i < positions_.size(); i++)
+ {
+ if (positions_[i] == position)
+ throw SiteException("AlignedSequenceContainer::addSite: Site position already exists in container", &site);
+ }
+ }
+
+ // For all sequences
+ for (size_t j = 0; j < getNumberOfSequences(); j++)
+ {
+ getSequence_(j).addElement(siteIndex, site[j]);
+ }
+
+ length_++;
+ positions_.insert(positions_.begin() + siteIndex, position);
+
+ // Actualizes the 'sites' vector:
+ sites_.insert(sites_.begin() + siteIndex, 0);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::addSite(const Site& site, size_t siteIndex, int position, bool checkPositions) throw (Exception)
+{
+ if (siteIndex >= getNumberOfSites())
+ throw IndexOutOfBoundsException("AlignedSequenceContainer::addSite", siteIndex, 0, getNumberOfSites() - 1);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("AlignedSequenceContainer::addSite", getAlphabet(), site.getAlphabet());
+
+ std::vector<int> s = site.getContent();
+
+ // Check size:
+ if (s.size() != getNumberOfSequences())
+ throw SiteException("AlignedSequenceContainer::addSite, site does not have the appropriate length", &site);
+
+ // Check position:
+ if (checkPositions)
+ {
+ // For all positions in vector : throw exception if position already exists
+ for (size_t i = 0; i < positions_.size(); i++)
+ {
+ if (positions_[i] == position)
+ throw SiteException("AlignedSequenceContainer::addSite: Site position already exists in container", &site);
+ }
+ }
+
+ // For all sequences
+ for (size_t j = 0; j < getNumberOfSequences(); j++)
+ {
+ getSequence_(j).addElement(siteIndex, site[j]);
+ }
+
+ length_++;
+ positions_.insert(positions_.begin() + siteIndex, position);
+
+ // Actualizes the 'sites' vector:
+ sites_.insert(sites_.begin() + siteIndex, 0);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::reindexSites()
+{
+ positions_.resize(length_);
+ for (size_t i = 0; i < length_; i++)
+ {
+ positions_[i] = static_cast<int>(i + 1); // start with 1.
+ }
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::setSequence(size_t i, const Sequence& sequence, bool checkName) throw (Exception)
+{
+ if (i >= getNumberOfSequences())
+ throw IndexOutOfBoundsException("AlignedSequenceContainer::setSequence", i, 0, getNumberOfSequences() - 1);
+ // if container has only one sequence
+ if (getNumberOfSequences() == 1)
+ length_ = sequence.size();
+ if (checkSize_(sequence))
+ VectorSequenceContainer::setSequence(i, sequence, checkName);
+ else
+ throw SequenceNotAlignedException("AlignedSequenceContainer::setSequence", &sequence);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::setSequence(const string& name, const Sequence& sequence, bool checkName) throw (Exception)
+{
+ // if container has only one sequence
+ if (getNumberOfSequences() == 1)
+ length_ = sequence.size();
+ if (checkSize_(sequence))
+ VectorSequenceContainer::setSequence(name, sequence, checkName);
+ else
+ throw SequenceNotAlignedException("AlignedSequenceContainer::setSequence", &sequence);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::addSequence(const Sequence& sequence, bool checkName) throw (Exception)
+{
+ // if container has only one sequence
+ if (length_ == 0)
+ {
+ length_ = sequence.size();
+ sites_.resize(length_);
+ reindexSites();
+ }
+ if (checkSize_(sequence))
+ VectorSequenceContainer::addSequence(sequence, checkName);
+ else
+ throw SequenceNotAlignedException("AlignedSequenceContainer::addSequence", &sequence);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::addSequence(const Sequence& sequence, size_t i, bool checkName) throw (Exception)
+{
+ if (i >= getNumberOfSequences())
+ throw IndexOutOfBoundsException("AlignedSequenceContainer::addSequence", i, 0, getNumberOfSequences() - 1);
+ // if container has only one sequence
+ if (length_ == 0)
+ length_ = sequence.size();
+ if (checkSize_(sequence))
+ VectorSequenceContainer::addSequence(sequence, i, checkName);
+ else
+ throw SequenceNotAlignedException("AlignedSequenceContainer::addSequence", &sequence);
+}
+
+/******************************************************************************/
+
+void AlignedSequenceContainer::clear()
+{
+ length_ = 0;
+ VectorSequenceContainer::clear();
+}
+
+/******************************************************************************/
+
+AlignedSequenceContainer* AlignedSequenceContainer::createEmptyContainer() const
+{
+ AlignedSequenceContainer* asc = new AlignedSequenceContainer(getAlphabet());
+ asc->setGeneralComments(getGeneralComments());
+ return asc;
+}
+
+/******************************************************************************/
+
+
diff --git a/src/Bpp/Seq/Container/AlignedSequenceContainer.h b/src/Bpp/Seq/Container/AlignedSequenceContainer.h
new file mode 100644
index 0000000..57a2f05
--- /dev/null
+++ b/src/Bpp/Seq/Container/AlignedSequenceContainer.h
@@ -0,0 +1,201 @@
+//
+// File AlignedSequenceContainer.h
+// Created by: Guillaume Deuchst
+// // Julien Dutheil
+// Last modification : Friday August 22 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ALIGNEDSEQUENCECONTAINER_H_
+#define _ALIGNEDSEQUENCECONTAINER_H_
+
+#include "../Site.h"
+#include "SiteContainer.h"
+#include "OrderedSequenceContainer.h"
+#include "VectorSequenceContainer.h"
+#include <Bpp/Exceptions.h>
+
+// From the STL:
+#include <string>
+
+namespace bpp
+{
+
+/**
+ * @brief Aligned sequences container.
+ *
+ * This class inherits from the VectorSequenceContainer and add site access.
+ * Sequence addition methods are re-defined to check for sequence lengths.
+ * Sequence access is in \f$O(1)\f$, and site access in \f$O(n)\f$, where
+ * \f$n\f$ is the number of sequences in the container.
+ *
+ * See VectorSiteContainer for an alternative implementation.
+ *
+ * @see VectorSequenceContainer, Sequence, Site, VectorSiteContainer
+ */
+class AlignedSequenceContainer:
+ public virtual VectorSequenceContainer,
+ public virtual SiteContainer
+{
+ private:
+ // Integer std::vector that contains sites's positions
+ std::vector<int> positions_;
+
+ size_t length_; // Number of sites for verifications before sequence's insertion in sequence container
+
+ /**
+ * This is used in order to implement the SiteContainer interface.
+ * A SiteContainer is expected to work on Site objects, but this class
+ * -- since it is a VectorSequenceContainer -- has its data sored as
+ * Sequence object. When the SiteContainer method getSite() is invoked
+ * it creates a new Site object and send the address of it.
+ * To avoid memory leaks, this object is put into a std::vector so that it can be
+ * destroyed when the container is destroyed.
+ */
+ mutable std::vector<Site*> sites_;
+
+ public:
+ /**
+ * @brief Build a new empty container with the specified alphabet.
+ *
+ * @param alpha The alphabet to use.
+ */
+ AlignedSequenceContainer(const Alphabet* alpha):
+ VectorSequenceContainer(alpha),
+ positions_(),
+ length_(0),
+ sites_()
+ {
+ reindexSites();
+ }
+ /**
+ * @brief Copy constructor.
+ *
+ * @param asc The container to copy.
+ */
+ AlignedSequenceContainer(const AlignedSequenceContainer& asc):
+ VectorSequenceContainer(asc),
+ positions_(asc.getSitePositions()),
+ length_(asc.getNumberOfSites()),
+ sites_(asc.getNumberOfSites())
+ {}
+
+ /**
+ * @brief Convert any SiteContainer object into a AlignedSequenceContainer object.
+ *
+ * @param sc The container to copy.
+ */
+ AlignedSequenceContainer(const SiteContainer& sc):
+ VectorSequenceContainer(sc),
+ positions_(sc.getSitePositions()),
+ length_(sc.getNumberOfSites()),
+ sites_(sc.getNumberOfSites())
+ {}
+
+ /**
+ * @brief Try to coerce an OrderedSequenceContainer object into an AlignedSequenceContainer object.
+ *
+ * Sequences in osc will be considered alligned, and have the same number of sites.
+ *
+ * @param osc The ordered container to coerce.
+ * @throw SequenceNotAlignedException If sequences in osc do not have the same length.
+ */
+ AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
+
+ AlignedSequenceContainer& operator=(const AlignedSequenceContainer& asc);
+ AlignedSequenceContainer& operator=(const SiteContainer& sc);
+ AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
+
+ virtual ~AlignedSequenceContainer();
+
+ public:
+
+ /**
+ * @name The Clonable interface.
+ *
+ * @{
+ */
+ AlignedSequenceContainer* clone() const { return new AlignedSequenceContainer(*this); }
+ /** @} */
+
+ /**
+ * @name The SiteContainer interface implementation:
+ *
+ * @{
+ */
+ const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
+ void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
+ Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
+ void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
+ void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
+ void addSite(const Site& site, bool checkPosition = true) throw (Exception);
+ void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
+ void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
+ void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
+ size_t getNumberOfSites() const { return length_; }
+ Vint getSitePositions() const { return positions_; }
+ void reindexSites();
+ void clear();
+ AlignedSequenceContainer* createEmptyContainer() const;
+ /** @} */
+
+ /**
+ * @name Redefinition of VectorSequenceContainer methods, to check for sequence lengths.
+ *
+ * @{
+ */
+ void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
+ void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
+
+ void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
+ void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
+ /** @} */
+
+
+ protected:
+ /**
+ * @brief Check sequence's size before insertion in sequence container.
+ *
+ * @param sequence The sequence to check.
+ * @return True if sequence length = number of sites in container.
+ */
+ bool checkSize_(const Sequence& sequence) { return (sequence.size() == length_); }
+
+};
+
+} //end of namespace bpp.
+
+#endif // _ALIGNEDSEQUENCECONTAINER_H_
+
diff --git a/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp b/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp
new file mode 100644
index 0000000..4c8cb67
--- /dev/null
+++ b/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp
@@ -0,0 +1,597 @@
+//
+// File: CompressedCompressedVectorSiteContainer.cpp
+// Created by: Julien Dutheil
+// Created on: Wed Dec 16 12:08 2009
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "CompressedVectorSiteContainer.h"
+#include <Bpp/Text/TextTools.h>
+
+#include <iostream>
+
+using namespace std;
+
+using namespace bpp;
+
+/** Class constructors: *******************************************************/
+
+CompressedVectorSiteContainer::CompressedVectorSiteContainer(
+ const std::vector<const Site*>& vs,
+ const Alphabet* alpha)
+throw (Exception) :
+ AbstractSequenceContainer(alpha),
+ sites_(0),
+ index_(0),
+ names_(0),
+ comments_(0),
+ sequences_(0)
+{
+ if (vs.size() == 0) throw Exception("CompressedVectorSiteContainer::CompressedVectorSiteContainer. Empty site set.");
+ // Seq names and comments:
+ size_t nbSeq = vs[0]->size();
+ names_.resize(nbSeq);
+ comments_.resize(nbSeq);
+ for (size_t i = 0; i < nbSeq; i++)
+ {
+ names_[i] = "Seq_" + TextTools::toString(i);
+ comments_[i] = new Comments();
+ }
+ // Now try to add each site:
+ for (size_t i = 0; i < vs.size(); i++)
+ {
+ addSite(*vs[i]); // This may throw an exception if position argument already exists or is size is not valid.
+ }
+
+ sequences_.resize(nbSeq);
+}
+
+/******************************************************************************/
+
+CompressedVectorSiteContainer::CompressedVectorSiteContainer(size_t size, const Alphabet* alpha) :
+ AbstractSequenceContainer(alpha),
+ sites_(0),
+ index_(0),
+ names_(size),
+ comments_(size),
+ sequences_(size)
+{
+ // Seq names and comments:
+ for (size_t i = 0; i < size; i++)
+ {
+ names_[i] = "Seq_" + i;
+ comments_[i] = new Comments();
+ }
+}
+
+/******************************************************************************/
+
+CompressedVectorSiteContainer::CompressedVectorSiteContainer(const std::vector<std::string>& names, const Alphabet* alpha) :
+ AbstractSequenceContainer(alpha),
+ sites_(0),
+ index_(0),
+ names_(names.size()),
+ comments_(names.size()),
+ sequences_(names.size())
+{
+ // Seq names and comments:
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ names_[i] = names[i];
+ comments_[i] = new Comments();
+ }
+}
+
+/******************************************************************************/
+
+CompressedVectorSiteContainer::CompressedVectorSiteContainer(const Alphabet* alpha) :
+ AbstractSequenceContainer(alpha),
+ sites_(0),
+ index_(0),
+ names_(0),
+ comments_(0),
+ sequences_(0)
+{}
+
+/******************************************************************************/
+
+CompressedVectorSiteContainer::CompressedVectorSiteContainer(const CompressedVectorSiteContainer& vsc) :
+ AbstractSequenceContainer(vsc),
+ sites_(vsc.sites_.size()),
+ index_(vsc.index_),
+ names_(vsc.names_),
+ comments_(vsc.getNumberOfSequences()),
+ sequences_(vsc.getNumberOfSequences())
+{
+ // Now try to add each site:
+ sites_.resize(vsc.sites_.size());
+ for (size_t i = 0; i < vsc.sites_.size(); i++)
+ {
+ sites_[i] = dynamic_cast<Site*>(vsc.sites_[i]->clone());
+ }
+ for (size_t i = 0; i < vsc.getNumberOfSites(); i++)
+ {
+ addSite(vsc.getSite(i), false); // We assume that positions are correct.
+ }
+ // Seq comments:
+ for (size_t i = 0; i < vsc.getNumberOfSequences(); i++)
+ {
+ comments_[i] = new Comments(vsc.getComments(i));
+ }
+}
+
+/******************************************************************************/
+
+CompressedVectorSiteContainer::CompressedVectorSiteContainer(const SiteContainer& sc) :
+ AbstractSequenceContainer(sc.getAlphabet()),
+ sites_(0),
+ index_(0),
+ names_(sc.getSequencesNames()),
+ comments_(sc.getNumberOfSequences()),
+ sequences_(sc.getNumberOfSequences())
+{
+ // Now try to add each site:
+ for (size_t i = 0; i < sc.getNumberOfSites(); i++)
+ {
+ addSite(sc.getSite(i), false); // We assume that positions are correct.
+ }
+ // Seq comments:
+ for (size_t i = 0; i < sc.getNumberOfSequences(); i++)
+ {
+ comments_[i] = new Comments(sc.getComments(i));
+ }
+}
+
+/******************************************************************************/
+
+CompressedVectorSiteContainer& CompressedVectorSiteContainer::operator=(const CompressedVectorSiteContainer& vsc)
+{
+ AbstractSequenceContainer::operator=(vsc);
+ // Seq names:
+ names_ = vsc.names_;
+ // Now try to add each site:
+ sites_.resize(vsc.sites_.size());
+ for (size_t i = 0; i < vsc.sites_.size(); i++)
+ {
+ sites_[i] = dynamic_cast<Site*>(vsc.sites_[i]->clone());
+ }
+ index_ = vsc.index_;
+ // Seq comments:
+ size_t nbSeq = vsc.getNumberOfSequences();
+ comments_.resize(nbSeq);
+ for (size_t i = 0; i < nbSeq; i++)
+ {
+ comments_[i] = new Comments(vsc.getComments(i));
+ }
+ sequences_.resize(nbSeq);
+
+ return *this;
+}
+
+/******************************************************************************/
+
+CompressedVectorSiteContainer& CompressedVectorSiteContainer::operator=(const SiteContainer& sc)
+{
+ clear();
+ AbstractSequenceContainer::operator=(sc);
+ // Seq names:
+ names_ = sc.getSequencesNames();
+ // Now try to add each site:
+ for (size_t i = 0; i < sc.getNumberOfSites(); i++)
+ {
+ addSite(sc.getSite(i), false); // We assume that positions are correct.
+ }
+ // Seq comments:
+ size_t nbSeq = sc.getNumberOfSequences();
+ comments_.resize(nbSeq);
+ for (size_t i = 0; i < nbSeq; i++)
+ {
+ comments_[i] = new Comments(sc.getComments(i));
+ }
+ sequences_.resize(nbSeq);
+
+ return *this;
+}
+
+/******************************************************************************/
+
+const Site& CompressedVectorSiteContainer::getSite(size_t i) const throw (IndexOutOfBoundsException)
+{
+ if (i >= getNumberOfSites())
+ throw IndexOutOfBoundsException("CompressedVectorSiteContainer::getSite.", i, 0, getNumberOfSites() - 1);
+ return *sites_[index_[i]];
+}
+
+/******************************************************************************/
+
+void CompressedVectorSiteContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
+{
+ if (pos >= getNumberOfSites()) throw IndexOutOfBoundsException("CompressedVectorSiteContainer::setSite.", pos, 0, getNumberOfSites() - 1);
+
+ // Check size:
+ if (site.size() != getNumberOfSequences()) throw SiteException("AlignedSequenceContainer::addSite. Site does not have the appropriate length", &site);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("CompressedVectorSiteContainer::setSite", getAlphabet(), site.getAlphabet());
+
+ size_t current = index_[pos];
+ size_t siteIndex = getSiteIndex_(site);
+ if (siteIndex == current)
+ {
+ //Nothing to do here, this is the same site.
+ }
+ else if (siteIndex < sites_.size())
+ {
+ //The new site is already in the list, si we just update the index:
+ index_[pos] = siteIndex;
+
+ //We have to check if the previous pattern was unique, and if so, remove it and update indices:
+ bool test = true;
+ for (size_t i = 0; test && i < index_.size(); ++i)
+ {
+ if (index_[i] == current)
+ {
+ //There is another site, so nothing to do...
+ test = false;
+ }
+ }
+ if (test)
+ {
+ //There was no other site pointing toward this pattern, so we remove it.
+ delete sites_[current];
+ sites_.erase(sites_.begin() + current);
+ //Now we have to correct all indices:
+ for (size_t i = 0; i < index_.size(); ++i)
+ {
+ if (index_[i] > current) index_[i]--;
+ }
+ }
+ }
+ else
+ {
+ //This is a new pattern, and we have to add it to the list...
+ Site* copy = dynamic_cast<Site*>(site.clone());
+
+ //Now we have to check if the previous pattern was unique, and if so,
+ //replace it with the new one. Otherwise, add the new site at the end of the list.
+ bool test = true;
+ for (size_t i = 0; test && i < index_.size(); ++i)
+ {
+ if (i != pos && index_[i] == current)
+ {
+ //There is another site, so nothing to do...
+ test = false;
+ }
+ }
+ if (test)
+ {
+ //There was no other site pointing toward this pattern, so we remove it.
+ delete sites_[current];
+ sites_[current] = copy;
+ }
+ else
+ {
+ //We add the site at the end:
+ sites_.push_back(copy);
+ index_[pos] = siteIndex;
+ }
+ }
+}
+
+/******************************************************************************/
+
+Site* CompressedVectorSiteContainer::removeSite(size_t i) throw (IndexOutOfBoundsException)
+{
+ if (i >= getNumberOfSites()) throw IndexOutOfBoundsException("CompressedVectorSiteContainer::removeSite.", i, 0, getNumberOfSites() - 1);
+ //Here we return a copy of the site, as it will not necessarily be removed from the set, so we don't want to delete it.
+ Site* site = dynamic_cast<Site *>(sites_[index_[i]]->clone());
+ deleteSite(i);
+ return site;
+}
+
+/******************************************************************************/
+
+void CompressedVectorSiteContainer::deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException)
+{
+ if (siteIndex >= getNumberOfSites())
+ throw IndexOutOfBoundsException("CompressedVectorSiteContainer::deleteSite.", siteIndex, 0, getNumberOfSites() - 1);
+ //Here we need to check whether the pattern corresponding to this site is unique:
+ size_t current = index_[siteIndex];
+ bool test = true;
+ for (size_t j = 0; test && j < index_.size(); ++j)
+ {
+ if (j != siteIndex && index_[j] == current)
+ {
+ //There is a nother site, so nothing to...
+ test = false;
+ }
+ }
+ if (test)
+ {
+ //There was no other site pointing toward this pattern, so we remove it.
+ delete sites_[current];
+ sites_.erase(sites_.begin() + current);
+ //Now we have to correct all indices:
+ for (size_t j = 0; j < index_.size(); ++j)
+ {
+ if (index_[j] > current) index_[j]--;
+ }
+ }
+ index_.erase(index_.begin() + siteIndex);
+}
+
+/******************************************************************************/
+
+void CompressedVectorSiteContainer::deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException)
+{
+ //This may be optimized later:
+ for (size_t i = 0; i < length; ++i) {
+ deleteSite(siteIndex + i);
+ }
+}
+
+/******************************************************************************/
+
+void CompressedVectorSiteContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
+{
+ // Check size:
+ if (site.size() != getNumberOfSequences()) throw SiteException("CompressedVectorSiteContainer::addSite. Site does not have the appropriate length", &site);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ {
+ throw AlphabetMismatchException("CompressedVectorSiteContainer::addSite", getAlphabet(), site.getAlphabet());
+ }
+
+ size_t siteIndex = getSiteIndex_(site);
+ if (siteIndex == sites_.size())
+ {
+ //This is a new pattern:
+ Site* copy = dynamic_cast<Site*>(site.clone());
+ sites_.push_back(copy);
+ }
+ index_.push_back(siteIndex);
+}
+
+/******************************************************************************/
+
+void CompressedVectorSiteContainer::addSite(const Site& site, size_t siteIndex, bool checkPositions) throw (Exception)
+{
+ if (siteIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("CompressedVectorSiteContainer::addSite", siteIndex, 0, getNumberOfSites() - 1);
+
+ // Check size:
+ if (site.size() != getNumberOfSequences()) throw SiteException("CompressedVectorSiteContainer::addSite. Site does not have the appropriate length", &site);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ {
+ throw AlphabetMismatchException("CompressedVectorSiteContainer::addSite", getAlphabet(), site.getAlphabet());
+ }
+
+ size_t index = getSiteIndex_(site);
+ if (index == sites_.size())
+ {
+ //This is a new pattern:
+ Site* copy = dynamic_cast<Site*>(site.clone());
+ sites_.push_back(copy);
+ }
+ index_.insert(index_.begin() + siteIndex, index);
+}
+
+/******************************************************************************/
+
+void CompressedVectorSiteContainer::reindexSites()
+{
+ int pos = 1; // first position is 1.
+ for (vector<Site*>::iterator i = sites_.begin(); i < sites_.end(); i++)
+ {
+ (*i)->setPosition(pos++);
+ }
+}
+
+/******************************************************************************/
+
+Vint CompressedVectorSiteContainer::getSitePositions() const
+{
+ size_t n = getNumberOfSites();
+ Vint positions(n);
+ for (size_t i = 0; i < n; i++)
+ {
+ positions[i] = sites_[index_[i]]->getPosition();
+ }
+ return positions;
+}
+
+/******************************************************************************/
+
+const Sequence& CompressedVectorSiteContainer::getSequence(size_t i) const throw (IndexOutOfBoundsException)
+{
+ if (i >= getNumberOfSequences()) throw IndexOutOfBoundsException("CompressedVectorSiteContainer::getSequence.", i, 0, getNumberOfSequences() - 1);
+
+ // Main loop : for all sites
+ size_t n = getNumberOfSites();
+ vector<int> sequence(n);
+ for (size_t j = 0; j < n; j++)
+ {
+ sequence[j] = sites_[index_[j]]->getContent()[i];
+ }
+ if (sequences_[i]) delete sequences_[i];
+ sequences_[i] = new BasicSequence(names_[i], sequence, *comments_[i], getAlphabet());
+ return *sequences_[i];
+}
+
+/******************************************************************************/
+
+const Sequence& CompressedVectorSiteContainer::getSequence(const std::string& name) const throw (SequenceNotFoundException)
+{
+ // Look for sequence name:
+ size_t pos = getSequencePosition(name);
+ return getSequence(pos);
+}
+
+/******************************************************************************/
+
+bool CompressedVectorSiteContainer::hasSequence(const string& name) const
+{
+ //Look for sequence name:
+ for (size_t pos = 0; pos < names_.size(); pos++) {
+ if (names_[pos] == name) return true;
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+size_t CompressedVectorSiteContainer::getSequencePosition(const std::string& name) const throw (SequenceNotFoundException)
+{
+ // Look for sequence name:
+ for (size_t pos = 0; pos < names_.size(); pos++)
+ {
+ if (names_[pos] == name) return pos;
+ }
+ throw SequenceNotFoundException("CompressedVectorSiteContainer::getSequencePosition().", name);
+}
+
+/******************************************************************************/
+
+void CompressedVectorSiteContainer::clear()
+{
+ // Must delete all sites in the container:
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ delete sites_[i];
+ }
+
+ // must delete all comments too:
+ for (size_t i = 0; i < comments_.size(); i++)
+ {
+ if (comments_[i]) delete comments_[i];
+ }
+
+ // Delete all sequences retrieved:
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ if (sequences_[i]) delete (sequences_[i]);
+ }
+
+ // Delete all sites pointers
+ sites_.clear();
+ index_.clear();
+ names_.clear();
+ comments_.clear();
+ sequences_.clear();
+}
+
+/******************************************************************************/
+
+vector<string> CompressedVectorSiteContainer::getSequencesNames() const
+{
+ vector<string> seqnames(names_.size());
+ for (size_t i = 0; i < names_.size(); i++)
+ {
+ seqnames[i] = names_[i];
+ }
+ return seqnames;
+}
+
+/******************************************************************************/
+
+void CompressedVectorSiteContainer::setSequencesNames(
+ const vector<string>& names,
+ bool checkNames)
+throw (Exception)
+{
+ if (names.size() != getNumberOfSequences())
+ throw IndexOutOfBoundsException("CompressedVectorSiteContainer::setSequenceNames: bad number of names.", names.size(), getNumberOfSequences(), getNumberOfSequences());
+ if (checkNames)
+ {
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ // For all names in vector : throw exception if name already exists
+ for (size_t j = 0; j < i; j++)
+ {
+ if (names[j] == names[i])
+ throw Exception("CompressedVectorSiteContainer::setSequencesNames : Sequence's name already exists in container");
+ }
+ }
+ }
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ names_[i] = names[i];
+ }
+}
+
+/******************************************************************************/
+
+void CompressedVectorSiteContainer::setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException)
+{
+ comments_[sequenceIndex] = new Comments(comments);
+}
+
+/******************************************************************************/
+
+CompressedVectorSiteContainer* CompressedVectorSiteContainer::createEmptyContainer() const
+{
+ CompressedVectorSiteContainer* vsc = new CompressedVectorSiteContainer(getAlphabet());
+ vsc->setGeneralComments(getGeneralComments());
+ return vsc;
+}
+
+/******************************************************************************/
+
+size_t CompressedVectorSiteContainer::getSiteIndex_(const Site& site)
+{
+ size_t pos = sites_.size();
+ bool test;
+ for (size_t i = 0; i < sites_.size(); ++i)
+ {
+ test = true;
+ for (size_t j = 0; test && j < site.size(); ++j) //site is supposed to have the correct size, that is the same as all the ones in the container.
+ {
+ if (site[j] != (*sites_[i])[j])
+ test = false;
+ }
+ if (test)
+ {
+ pos = i;
+ break;
+ }
+ }
+ return pos;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h b/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h
new file mode 100644
index 0000000..b720583
--- /dev/null
+++ b/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h
@@ -0,0 +1,290 @@
+//
+// File: CompressedVectorSiteContainer.h
+// Created by: Julien Dutheil
+// Created on: Wed Dec 16 12:08 2009
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _COMPRESSEDVECTORSITECONTAINER_H_
+#define _COMPRESSEDVECTORSITECONTAINER_H_
+
+#include "../Site.h"
+#include "SiteContainer.h"
+#include "AbstractSequenceContainer.h"
+#include "AlignedSequenceContainer.h"
+#include "OrderedSequenceContainer.h"
+#include <Bpp/Numeric/VectorTools.h>
+
+// From the STL library:
+#include <string>
+#include <vector>
+#include <iostream>
+
+namespace bpp
+{
+/**
+ * @brief A low memory, yet restricted, version of the VectorSiteContainer class.
+ *
+ * This implementation is very similar to VectorSiteContainer, but identical sites
+ * are stored only once, which significantly reduce memory usage in the case of
+ * containers where the number of sites is large compared to the number of sequences.
+ * site access is as fast as in the standard VectorSiteContainer class, but site
+ * addition takes more time, as the new site must be first compared to the existing set.
+ * A major restriction of this container is that you can't add or remove sequences.
+ * The number of sequences is fixed after the first site has been added.
+ *
+ * @warning Since the data is compressed, the sites given as input are modified. The
+ * major pratical consequence is that the 'position' attribute of sites will be lost.
+ * Instead, the position will correspond to the position in the compressed container.
+ * In addition, this container may lead to unexpected behavior if used with derived
+ * classes of Site. Use with care then...
+ *
+ * @see Sequence, Site, VectorSiteContainer
+ */
+class CompressedVectorSiteContainer :
+ public AbstractSequenceContainer,
+ // This container implements the SequenceContainer interface
+ // and use the AbstractSequenceContainer adapter.
+ public virtual SiteContainer // This container is a SiteContainer.
+{
+protected:
+ std::vector<Site*> sites_; //A set of unique sites.
+ std::vector<size_t> index_; //For all sites, give the actual position in the set.
+ std::vector<std::string> names_;
+ std::vector<Comments*> comments_; // Sequences comments.
+ mutable std::vector<Sequence*> sequences_; // To store pointer toward sequences retrieved (cf. AlignedSequenceContainer).
+
+public:
+ /**
+ * @brief Build a new container from a set of sites.
+ *
+ * @param vs A std::vector of sites.
+ * @param alpha The common alphabet for all sites.
+ * @throw Exception If sites differ in size or in alphabet.
+ */
+ CompressedVectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha) throw (Exception);
+ /**
+ * @brief Build a new empty container with specified size.
+ *
+ * @param size Number of sequences in the container.
+ * @param alpha The alphabet for this container.
+ */
+ CompressedVectorSiteContainer(size_t size, const Alphabet* alpha);
+ /**
+ * @brief Build a new empty container with specified sequence names.
+ *
+ * @param names Sequence names. This will set the number of sequences in the container.
+ * @param alpha The alphabet for this container.
+ */
+ CompressedVectorSiteContainer(const std::vector<std::string>& names, const Alphabet* alpha);
+
+ /**
+ * @brief Build a new empty container.
+ *
+ * @param alpha The alphabet for this container.
+ */
+ CompressedVectorSiteContainer(const Alphabet* alpha);
+
+ CompressedVectorSiteContainer(const CompressedVectorSiteContainer& vsc);
+ CompressedVectorSiteContainer(const SiteContainer& sc);
+
+ CompressedVectorSiteContainer& operator=(const CompressedVectorSiteContainer& vsc);
+ CompressedVectorSiteContainer& operator=(const SiteContainer& sc);
+
+ virtual ~CompressedVectorSiteContainer() { clear(); }
+
+public:
+ /**
+ * @name The Clonable interface.
+ *
+ * @{
+ */
+ CompressedVectorSiteContainer* clone() const { return new CompressedVectorSiteContainer(*this); }
+ /** @} */
+
+ /**
+ * @name The SiteContainer interface implementation:
+ *
+ * @{
+ */
+ const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
+ void setSite(size_t siteIndex, const Site& site, bool checkPosition = false) throw (Exception);
+ Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
+ void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
+ void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
+ void addSite(const Site& site, bool checkPosition = false) throw (Exception);
+ void addSite(const Site& site, int position, bool checkPosition = false) throw (Exception)
+ {
+ addSite(site, checkPosition);
+ }
+ void addSite(const Site& site, size_t siteIndex, bool checkPosition = false) throw (Exception);
+ void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = false) throw (Exception)
+ {
+ addSite(site, siteIndex, checkPosition);
+ }
+ size_t getNumberOfSites() const { return index_.size(); }
+ void reindexSites();
+ Vint getSitePositions() const;
+ /** @} */
+
+ // Theses methods are implemented for this class:
+
+ /**
+ * @name The SequenceContainer interface.
+ *
+ * @{
+ */
+ void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
+
+ // Method to get a sequence object from sequence container
+ const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
+ const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
+ bool hasSequence(const std::string& name) const;
+
+ // Methods to get position of a sequence in sequence container from his name
+ // This method is used by delete and remove methods
+ size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
+
+ Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, NotImplementedException)
+ {
+ //Implementing this function would involve (partially) decompressing the data...
+ throw NotImplementedException("CompressedVectorSiteContainer::removeSequence.");
+ }
+
+ Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, NotImplementedException)
+ {
+ //Implementing this function would involve (partially) decompressing the data...
+ throw NotImplementedException("CompressedVectorSiteContainer::removeSequence.");
+ }
+
+ void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, NotImplementedException)
+ {
+ //Implementing this function would involve (partially) decompressing the data...
+ throw NotImplementedException("CompressedVectorSiteContainer::deleteSequence.");
+ }
+
+ void deleteSequence(const std::string& name) throw (SequenceNotFoundException, NotImplementedException)
+ {
+ //Implementing this function would involve (partially) decompressing the data...
+ throw NotImplementedException("CompressedVectorSiteContainer::deleteSequence.");
+ }
+
+ size_t getNumberOfSequences() const { return names_.size(); }
+
+ std::vector<std::string> getSequencesNames() const;
+
+ void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
+
+ void clear();
+
+ CompressedVectorSiteContainer* createEmptyContainer() const;
+
+ int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
+ {
+ if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(std::string, size_t).", elementIndex, 0, getNumberOfSites() - 1);
+ return (*sites_[index_[elementIndex]])[getSequencePosition(sequenceName)];
+ }
+ const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
+ {
+ if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(std::string, size_t).", elementIndex, 0, getNumberOfSites() - 1);
+ return (*sites_[index_[elementIndex]])[getSequencePosition(sequenceName)];
+ }
+ int& operator()(const std::string& sequenceName, size_t elementIndex)
+ {
+ return (*sites_[index_[elementIndex]])[getSequencePosition(sequenceName)];
+ }
+ const int& operator()(const std::string& sequenceName, size_t elementIndex) const
+ {
+ return (*sites_[index_[elementIndex]])[getSequencePosition(sequenceName)];
+ }
+
+ int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
+ {
+ if (sequenceIndex >= getNumberOfSequences()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(size_t, size_t).", sequenceIndex, 0, getNumberOfSequences() - 1);
+ if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(size_t, size_t).", elementIndex, 0, getNumberOfSites() - 1);
+ return (*sites_[index_[elementIndex]])[sequenceIndex];
+ }
+ const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
+ {
+ if (sequenceIndex >= getNumberOfSequences()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(size_t, size_t).", sequenceIndex, 0, getNumberOfSequences() - 1);
+ if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(size_t, size_t).", elementIndex, 0, getNumberOfSites() - 1);
+ return (*sites_[index_[elementIndex]])[sequenceIndex];
+ }
+ int& operator()(size_t sequenceIndex, size_t elementIndex)
+ {
+ return (*sites_[index_[elementIndex]])[sequenceIndex];
+ }
+ const int& operator()(size_t sequenceIndex, size_t elementIndex) const
+ {
+ return (*sites_[index_[elementIndex]])[sequenceIndex];
+ }
+ /** @} */
+
+ void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception, NotImplementedException)
+ {
+ //Implementing this function would involve (partially) decompressing the data...
+ throw NotImplementedException("CompressedVectorSiteContainer::addSequence.");
+ }
+
+ void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception, NotImplementedException)
+ {
+ //Implementing this function would involve (partially) decompressing the data...
+ throw NotImplementedException("CompressedVectorSiteContainer::addSequence.");
+ }
+
+ void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception, NotImplementedException)
+ {
+ //Implementing this function would involve (partially) decompressing the data...
+ throw NotImplementedException("CompressedVectorSiteContainer::setSequence.");
+ }
+
+ void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception, NotImplementedException)
+ {
+ //Implementing this function would involve (partially) decompressing the data...
+ throw NotImplementedException("CompressedVectorSiteContainer::setSequence.");
+ }
+
+protected:
+ /**
+ * @return The position of the site in the compressed set. If the site is not found,
+ * this will return the number of sites in the compressed set.
+ */
+ size_t getSiteIndex_(const Site& site);
+};
+
+} // end of namespace bpp.
+
+#endif // _COMPRESSEDVECTORSITECONTAINER_H_
+
diff --git a/src/Bpp/Seq/Container/MapSequenceContainer.cpp b/src/Bpp/Seq/Container/MapSequenceContainer.cpp
new file mode 100644
index 0000000..a79340e
--- /dev/null
+++ b/src/Bpp/Seq/Container/MapSequenceContainer.cpp
@@ -0,0 +1,466 @@
+//
+// File MapSequenceContainer.cpp
+// Authors : Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Last modification : Monday July 19 2004
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "MapSequenceContainer.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+using namespace std;
+
+/******************************************************************************/
+
+MapSequenceContainer::MapSequenceContainer(const map<string, Sequence*>& ms, const Alphabet* alpha) :
+ AbstractSequenceContainer(alpha), sequences_()
+{
+ for (map<string, Sequence*>::const_iterator it = ms.begin(); it != ms.end(); it++)
+ {
+ addSequence(it->first, *it->second);
+ }
+}
+
+/******************************************************************************/
+
+MapSequenceContainer::MapSequenceContainer(const MapSequenceContainer& msc) :
+ AbstractSequenceContainer(msc.getAlphabet()), sequences_()
+{
+ for (unsigned int i = 0; i < msc.getNumberOfSequences(); i++)
+ addSequence(msc.getKey(i), msc.getSequence(i), false);
+}
+
+/******************************************************************************/
+
+MapSequenceContainer& MapSequenceContainer::operator=(const MapSequenceContainer& msc)
+{
+ clear();
+ AbstractSequenceContainer::operator=(msc);
+
+ // Sequences insertion
+ vector<string> keys = msc.getKeys();
+ for (unsigned int i = 0 ; i < getNumberOfSequences(); i++)
+ {
+ addSequence(keys[i], msc.getSequence(i), false);
+ }
+
+ return * this;
+}
+
+/******************************************************************************/
+
+MapSequenceContainer::~MapSequenceContainer()
+{
+ clear();
+}
+
+/******************************************************************************/
+
+const Sequence& MapSequenceContainer::getSequence(size_t i) const throw (IndexOutOfBoundsException)
+{
+ // Specified sequence existence verification
+ if (i < sequences_.size())
+ {
+ map<string, Sequence*>::const_iterator it = sequences_.begin();
+ for (unsigned int j = 0; j < i; j++) it++;
+ return *it->second;
+ }
+ throw IndexOutOfBoundsException("MapSequenceContainer::getSequence", i, 0, sequences_.size() - 1);
+}
+
+/******************************************************************************/
+
+const Sequence& MapSequenceContainer::getSequence(const string& name) const throw (SequenceNotFoundException)
+{
+ // Specified sequence name research into all sequences
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ if (it->second->getName() == name)
+ return *it->second;
+ throw SequenceNotFoundException("MapSequenceContainer::getSequence", name);
+}
+
+/******************************************************************************/
+
+bool MapSequenceContainer::hasSequence(const string& name) const
+{
+ // Specified sequence name research into all sequences
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ if (it->second->getName() == name)
+ return true;
+ return false;
+}
+
+/******************************************************************************/
+
+Sequence& MapSequenceContainer::getSequence_(size_t i) throw (IndexOutOfBoundsException)
+{
+ if (i >= sequences_.size())
+ throw IndexOutOfBoundsException("MapSequenceContainer::getSequence", i, 0, sequences_.size() - 1);
+ map<string, Sequence*>::iterator it = sequences_.begin();
+ for (size_t j = 0; j < i; j++) it++;
+ return *it->second;
+}
+
+/******************************************************************************/
+
+Sequence& MapSequenceContainer::getSequence_(const string& name) throw (SequenceNotFoundException)
+{
+ // Specified sequence name research into all sequences
+ for (map<string, Sequence*>::iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ if (it->second->getName() == name)
+ return *it->second;
+ throw SequenceNotFoundException("MapSequenceContainer::getSequence", name);
+}
+
+/******************************************************************************/
+
+const Sequence& MapSequenceContainer::getSequenceByKey(const string& key) const
+ throw (SequenceNotFoundException)
+{
+ map<string, Sequence*>::const_iterator it = sequences_.find(key);
+ if (it == sequences_.end())
+ throw SequenceNotFoundException("MapSequenceContainer::getSequenceByKey", key);
+ return *it->second;
+}
+
+/******************************************************************************/
+
+size_t MapSequenceContainer::getSequencePosition(const string& name)
+ const throw (SequenceNotFoundException)
+{
+ // Specified sequence name research into all sequences
+ int pos = 0;
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ {
+ if (it->second->getName() == name) return pos;
+ pos++;
+ }
+
+ throw SequenceNotFoundException("MapSequenceContainer::getSequencePosition", name);
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::setSequence(size_t i, const Sequence& sequence, bool checkNames)
+ throw (IndexOutOfBoundsException)
+{
+ // Sequence's name existence checking
+ if (checkNames)
+ {
+ size_t j = 0;
+ // For all names in map : throw exception if name already exists
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ {
+ if (it->second->getName() == sequence.getName())
+ if (j != i) throw Exception("MapSequenceContainer::setSequence : Sequence's name already exists in container");
+ j++;
+ }
+ }
+
+ // New sequence's alphabet and sequence container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() == getAlphabet()->getAlphabetType())
+ {
+ // Delete old sequence
+ delete sequences_[getKey(i)];
+ // New sequence insertion in sequence container
+ sequences_[getKey(i)] = dynamic_cast<Sequence*>(sequence.clone());
+ }
+ else
+ throw AlphabetMismatchException("MapSequenceContainer::setSequence", getAlphabet(), sequence.getAlphabet());
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::setSequence(const string& name, const Sequence& sequence, bool checkNames) throw (SequenceNotFoundException)
+{
+ // Sequence's name existence checking
+ if (checkNames)
+ {
+ // For all names in map : throw exception if name already exists
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ {
+ if (it->second->getName() == name)
+ if (it->second->getName() != name)
+ throw Exception("MapSequenceContainer::setSequence : Sequence's name already exists in container");
+ }
+ }
+
+ // New sequence's alphabet and sequence container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() == getAlphabet()->getAlphabetType())
+ {
+ // Delete old sequence
+ delete sequences_[name];
+ // New sequence insertion in sequence container
+ sequences_[name] = dynamic_cast<Sequence*>(sequence.clone());
+ }
+ else
+ throw AlphabetMismatchException("MapSequenceContainer::setSequence", getAlphabet(), sequence.getAlphabet());
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::setSequenceByKey(const string& key, const Sequence& sequence, bool checkNames) throw (SequenceNotFoundException)
+{
+ // Sequence's name existence checking
+ if (checkNames)
+ {
+ // For all names in map : throw exception if name already exists
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ {
+ if (it->second->getName() == sequence.getName())
+ if (it->first != key)
+ throw Exception("MapSequenceContainer::setSequenceByKey : Sequence's name already exists in container");
+ }
+ }
+
+ // New sequence's alphabet and sequence container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() == getAlphabet()->getAlphabetType())
+ {
+ // Delete old sequence
+ delete sequences_[key];
+ // New sequence insertion in sequence container
+ sequences_[key] = dynamic_cast<Sequence*>(sequence.clone());
+ }
+ else
+ throw AlphabetMismatchException("MapSequenceContainer::setSequenceByKey", getAlphabet(), sequence.getAlphabet());
+}
+
+/******************************************************************************/
+
+Sequence* MapSequenceContainer::removeSequence(size_t i) throw (IndexOutOfBoundsException)
+{
+ if (i >= sequences_.size())
+ throw IndexOutOfBoundsException("MapSequenceContainer::removeSequence", i, 0, sequences_.size() - 1);
+ map<string, Sequence*>::iterator it = sequences_.begin();
+ for (size_t j = 0; j < i; j++) it++;
+ Sequence* old = it->second;
+ sequences_.erase(it);
+ return old;
+}
+
+/******************************************************************************/
+
+Sequence* MapSequenceContainer::removeSequence(const string& name) throw (SequenceNotFoundException)
+{
+ for (map<string, Sequence*>::iterator it = sequences_.begin(); it != sequences_.end(); it++) {
+ if (it->second->getName() == name)
+ {
+ Sequence* old = it->second;
+ sequences_.erase(it);
+ return old;
+ }
+ }
+ throw SequenceNotFoundException("MapSequenceContainer::removeSequence", name);
+}
+
+/******************************************************************************/
+
+Sequence* MapSequenceContainer::removeSequenceByKey(const string& key)throw (SequenceNotFoundException)
+{
+ map<string, Sequence*>::iterator it = sequences_.find(key);
+ if (it == sequences_.end())
+ throw SequenceNotFoundException("MapSequenceContainer::removeSequenceByKey", key);
+
+ Sequence* old = it->second;
+ sequences_.erase(key);
+ return old;
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::deleteSequence(size_t i) throw (IndexOutOfBoundsException)
+{
+ if (i >= sequences_.size())
+ throw IndexOutOfBoundsException("MapSequenceContainer::deleteSequence", i, 0, sequences_.size() - 1);
+ map<string, Sequence*>::iterator it = sequences_.begin();
+ for (size_t j = 0; j < i; j++) it++;
+ delete it->second;
+ sequences_.erase(it);
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::deleteSequence(const string& name) throw (SequenceNotFoundException)
+{
+ for (map<string, Sequence*>::iterator it = sequences_.begin(); it != sequences_.end(); it++) {
+ if (it->second->getName() == name)
+ {
+ delete it->second;
+ sequences_.erase(it);
+ return;
+ }
+ }
+ throw SequenceNotFoundException("MapSequenceContainer::deleteSequence", name);
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::deleteSequenceByKey(const string& key) throw (SequenceNotFoundException)
+{
+ map<string, Sequence*>::iterator it = sequences_.find(key);
+ if (it == sequences_.end())
+ throw SequenceNotFoundException("MapSequenceContainer::deleteSequenceByKey", key);
+ delete it->second;
+ sequences_.erase(key);
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::addSequence(const string& key, const Sequence& sequence, bool checkNames) throw (Exception)
+{
+ // Sequence's name existence checking
+ if (checkNames)
+ {
+ // For all names in map : throw exception if name already exists
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ {
+ if (it->second->getName() == sequence.getName())
+ throw Exception("MapSequenceContainer::addSequence: Sequence '" + sequence.getName() + ", already exists in container");
+ }
+ }
+
+ // Check if the key is not used
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ if (key == it->first)
+ throw Exception("MapSequenceContainer::addSequence: key already in use. (" + key + ")");
+
+ // New sequence's alphabet and sequence container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() == getAlphabet()->getAlphabetType())
+ sequences_.insert(make_pair(key, dynamic_cast<Sequence*>(sequence.clone())));
+ else throw AlphabetMismatchException("MapSequenceContainer::addSequence", getAlphabet(), sequence.getAlphabet());
+}
+
+/******************************************************************************/
+
+vector<string> MapSequenceContainer::getKeys() const
+{
+ vector<string> keys;
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ keys.push_back(it->first);
+ return keys;
+}
+
+/******************************************************************************/
+
+string MapSequenceContainer::getKey(size_t pos) const throw (IndexOutOfBoundsException)
+{
+ if (pos >= getNumberOfSequences())
+ throw IndexOutOfBoundsException("MapSequenceContainer::getKey", pos, 0, sequences_.size() - 1);
+ map<string, Sequence*>::const_iterator it = sequences_.begin();
+ for (size_t i = 0; i < pos; i++) it++;
+ return it->first;
+}
+
+/******************************************************************************/
+
+string MapSequenceContainer::getKey(const string& name) const throw (SequenceNotFoundException)
+{
+ try
+ {
+ return getKey(getSequencePosition(name));
+ }
+ catch (SequenceNotFoundException & snfe)
+ {
+ throw SequenceNotFoundException("MapSequenceContainer::getKey", snfe.getSequenceId());
+ }
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::setComments(size_t pos, const Comments& comments) throw (IndexOutOfBoundsException)
+{
+ if (pos >= getNumberOfSequences())
+ throw IndexOutOfBoundsException("MapSequenceContainer::setComments", pos, 0, sequences_.size() - 1);
+ map<string, Sequence*>::iterator it = sequences_.begin();
+ for (size_t i = 0 ; i < pos ; i++) it++;
+ it->second->setComments(comments);
+}
+
+/******************************************************************************/
+
+vector<string> MapSequenceContainer::getSequencesNames() const
+{
+ vector<string> names;
+ for (map<string, Sequence*>::const_iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ names.push_back(it->second->getName());
+ return names;
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::setSequencesNames(const vector<string>& names, bool checkNames) throw (Exception)
+{
+ if (names.size() != getNumberOfSequences())
+ throw IndexOutOfBoundsException("MapSequenceContainer::setSequenceNames : bad number of names", names.size(), getNumberOfSequences(), getNumberOfSequences());
+ if (checkNames) {
+ // check if there is no repeat names in teh vector
+ for (size_t i = 0 ; i < names.size() ; i++)
+ for (unsigned int j = 0 ; j < i ; j++)
+ if (names[j] == names[i])
+ throw Exception("MapSequenceContainer::setSequencesNames: Sequence's name already exists in container");
+ }
+ map<string, Sequence*>::iterator it = sequences_.begin();
+ for (size_t i = 0 ; i < names.size() ; i++)
+ {
+ it->second->setName(names[i]);
+ it++;
+ }
+}
+
+/******************************************************************************/
+
+void MapSequenceContainer::clear()
+{
+ // Delete sequences
+ for (map<string, Sequence *>::iterator it = sequences_.begin(); it != sequences_.end(); it++)
+ delete it->second;
+ // Delete all sequence pointers
+ sequences_.clear();
+}
+
+/******************************************************************************/
+
+MapSequenceContainer* MapSequenceContainer::createEmptyContainer() const
+{
+ MapSequenceContainer* msc = new MapSequenceContainer(getAlphabet());
+ msc->setGeneralComments(getGeneralComments());
+ return msc;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Container/MapSequenceContainer.h b/src/Bpp/Seq/Container/MapSequenceContainer.h
new file mode 100644
index 0000000..d75e1f4
--- /dev/null
+++ b/src/Bpp/Seq/Container/MapSequenceContainer.h
@@ -0,0 +1,240 @@
+//
+// File MapSequenceContainer.h
+// Authors : Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Last modification : Friday June 25 2004
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _MAPSEQUENCECONTAINER_H_
+#define _MAPSEQUENCECONTAINER_H_
+
+#include "../Alphabet/Alphabet.h"
+#include "../Sequence.h"
+#include "AbstractSequenceContainer.h"
+
+#include <string>
+#include <map>
+
+namespace bpp
+{
+
+/**
+ * @brief MapSequenceContainer class
+ *
+ * Sequences are stored using a key std::string, in a map object.
+ * Sequences are ordered according to the key order (defined by the < operator).
+ *
+ */
+
+class MapSequenceContainer:
+ public AbstractSequenceContainer
+{
+ private:
+ std::map<std::string, Sequence*> sequences_;
+
+ public:
+ MapSequenceContainer(const std::map<std::string, Sequence*>& ms, const Alphabet* alpha);
+ MapSequenceContainer(const Alphabet* alpha):
+ AbstractSequenceContainer(alpha), sequences_() {}
+
+ MapSequenceContainer(const MapSequenceContainer& msc);
+ MapSequenceContainer& operator=(const MapSequenceContainer& msc);
+
+ virtual ~MapSequenceContainer();
+
+ public:
+ /**
+ * @brief Get a sequence.
+ *
+ * @param key The key of the sequence to retrieve.
+ * @return The sequence associated to the given key.
+ * @throw SequenceNotFoundException If no sequence is associated to the given key.
+ */
+ const Sequence& getSequenceByKey(const std::string& key) const throw (SequenceNotFoundException);
+
+ /**
+ * @brief Set a sequence.
+ *
+ * @param key The key of the sequence.
+ * @param sequence The new sequence that will be associated to the key.
+ * @param checkNames Tell is the sequence name must be checked.
+ * @throw SequenceNotFoundException If no sequence is associated to the given key.
+ */
+ void setSequenceByKey(const std::string& key , const Sequence& sequence, bool checkNames = true) throw (SequenceNotFoundException);
+
+ /**
+ * @brief Remove a sequence.
+ *
+ * @param key The key of the sequence.
+ * @return The sequence previously associated to the given key.
+ * @throw SequenceNotFoundException If no sequence is associated to the given key.
+ */
+ Sequence* removeSequenceByKey(const std::string& key) throw (SequenceNotFoundException);
+
+ /**
+ * @brief Delete a sequence.
+ *
+ * @param key The key of the sequence.
+ * @throw SequenceNotFoundException If no sequence is associated to the given key.
+ */
+ void deleteSequenceByKey(const std::string& key) throw (SequenceNotFoundException);
+
+ /**
+ * @brief Add a sequence and key.
+ *
+ * @param key The key of the new sequence.
+ * @param sequence The new sequence that will be associated to the key.
+ * @param checkNames Tell is the sequence name must be checked.
+ */
+ void addSequence(const std::string& key, const Sequence& sequence, bool checkNames = true) throw (Exception);
+
+ /**
+ * @return All sequences keys.
+ */
+ std::vector<std::string> getKeys() const;
+
+ /**
+ * @return The key of a given sequence specified by its position in the container.
+ * @param pos The index of the sequence.
+ * @throw IndexOutOfBoundsException If pos is not a valid index.
+ */
+ std::string getKey(size_t pos) const throw (IndexOutOfBoundsException);
+
+ /**
+ * @return The key of a given sequence specified by its name.
+ * @param name The name of the sequence.
+ * @throw SequenceNotFoundException If no sequence was found with the given name.
+ */
+ std::string getKey(const std::string& name) const throw (SequenceNotFoundException);
+
+ /**
+ * @name The clonable interface
+ *
+ * @{
+ */
+ MapSequenceContainer* clone() const { return new MapSequenceContainer(*this); }
+ /**
+ * @}
+ */
+
+ /**
+ * @name The SequenceContainer interface implementation:
+ *
+ * @{
+ */
+ const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
+
+ bool hasSequence(const std::string& name) const;
+
+ /**
+ * @brief The SequenceContainer method. Calls the addSeqeucne(key, Sequence) method while using the resut of sequence.getName() as a key.
+ */
+ void addSequence(const Sequence& sequence, bool checkNames = true) throw (Exception)
+ {
+ addSequence(sequence.getName(), sequence, checkNames);
+ }
+ void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (SequenceNotFoundException);
+ Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
+ void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
+ size_t getNumberOfSequences() const { return sequences_.size(); }
+ void clear();
+ MapSequenceContainer* createEmptyContainer() const;
+
+ int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
+ {
+ return getSequence_(sequenceName)[elementIndex];
+ }
+ const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
+ {
+ return getSequence(sequenceName)[elementIndex];
+ }
+ int& operator()(const std::string& sequenceName, size_t elementIndex)
+ {
+ return getSequence_(sequenceName)[elementIndex];
+ }
+ const int& operator()(const std::string & sequenceName, size_t elementIndex) const
+ {
+ return getSequence(sequenceName)[elementIndex];
+ }
+
+ int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
+ {
+ return getSequence_(sequenceIndex)[elementIndex];
+ }
+ const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
+ {
+ return getSequence(sequenceIndex)[elementIndex];
+ }
+ int& operator()(size_t sequenceIndex, size_t elementIndex)
+ {
+ return getSequence_(sequenceIndex)[elementIndex];
+ }
+ const int& operator()(size_t sequenceIndex, size_t elementIndex) const
+ {
+ return getSequence(sequenceIndex)[elementIndex];
+ }
+ /** @} */
+
+ /**
+ * @name The OrderedSequenceContainer interface implementation:
+ *
+ * @{
+ */
+ const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
+ size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
+ void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (IndexOutOfBoundsException);
+ Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
+ void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
+ void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
+ std::vector<std::string> getSequencesNames() const;
+ void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception);
+ /** @} */
+
+ /**
+ * @name AbstractSequenceContainer methods.
+ *
+ * @{
+ */
+ Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
+ Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
+ /** @} */
+};
+
+} //end of namespace bpp.
+
+#endif // _MAPSEQUENCECONTAINER_H_
+
diff --git a/src/Bpp/Seq/Container/OrderedSequenceContainer.h b/src/Bpp/Seq/Container/OrderedSequenceContainer.h
new file mode 100644
index 0000000..95903a4
--- /dev/null
+++ b/src/Bpp/Seq/Container/OrderedSequenceContainer.h
@@ -0,0 +1,242 @@
+//
+// File OrderedSequenceContainer.h
+// Author: Guillaume Deuchst
+// Julien Dutheil
+// Last modification : Tuesday August 7 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ORDEREDSEQUENCECONTAINER_H_
+#define _ORDEREDSEQUENCECONTAINER_H_
+
+#include "../Sequence.h"
+#include "SequenceContainer.h"
+
+namespace bpp
+{
+
+/**
+ * @brief The OrderedSequenceContainer interface.
+ *
+ * Interface to manage indexed containers.
+ * Sequences may be accessed via their indice, <i>i.e.</i> their position in the container.
+ */
+class OrderedSequenceContainer:
+ public virtual SequenceContainer
+{
+ public:
+ OrderedSequenceContainer() {}
+ virtual ~OrderedSequenceContainer() {}
+
+ public:
+ /**
+ * @brief Get the content of a sequence.
+ *
+ * @param sequenceIndex The position of the sequence.
+ * @return The content of the sequence as a vector of integers.
+ * @throw IndexOutOfBoundsException If the position does not match any sequence in the container.
+ */
+ virtual const std::vector<int>& getContent(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Convert a particular sequence to a string.
+ *
+ * @param sequenceIndex The position of the sequence.
+ * @return A string describing the content of the sequence.
+ * @throw IndexOutOfBoundsException If the position does not match any sequence in the container.
+ */
+ virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Retrieve a sequence object from the container.
+
+ *
+ * @param sequenceIndex The position of the sequence.
+ * @return A reference toward the Sequence object with corresponding name.
+ * @throw IndexOutOfBoundsException If the position does not match any sequence in the container.
+ */
+ virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Replace a sequence in the container.
+ *
+ * @param sequenceIndex The position of the sequence.
+ * @param sequence The sequence to add.
+ * @param checkName Tell if the container must check if the name of the sequence
+ * is already used in the container before adding it.
+ * @throw IndexOutOfBoundsException If the position does not match any sequence in the container.
+ * @throw Exception Any other kind of exception.
+ */
+ virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
+
+ /**
+ * @brief Extract (and remove) a sequence from the container.
+ *
+ * @param sequenceIndex The position of the sequence.
+ * @throw IndexOutOfBoundsException If the name does not match any sequence in
+ * the container.
+ */
+ virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
+
+ /**
+ * @brief Delete a sequence of the container.
+ *
+ * @param sequenceIndex The position of the sequence.
+ * @throw IndexOutOfBoundsException If the position does not match any sequence in
+ * the container.
+ */
+ virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
+
+ /**
+ * @brief Get the name of a particular sequence.
+ *
+ * @param sequenceIndex The position of the sequence.
+ * @return The name of the sequence at position 'sequenceIndex'.
+ * @throw IndexOutOfBoundsException If the position does not match any sequence in
+ * the container.
+ */
+ virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Get comments of a particular sequence.
+ *
+ * @param sequenceIndex The position of the sequence.
+ * @return The comments associated to sequence at position 'sequenceIndex'.
+ * @throw IndexOutOfBoundsException If the position does not match any sequence in
+ * the container.
+ */
+ virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Set the comments of a particular sequence.
+ *
+ * @param sequenceIndex The position of the sequence.
+ * @param comments The comments to set to sequence with position 'i'.
+ * @throw IndexOutOfBoundsException If the position does not match any sequence in
+ * the container.
+ */
+ virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Get the position of a sequence in sequence container from its name.
+ *
+ * @param name The name of the sequence.
+ * @return The position of the sequence with name 'name', if it exists.
+ * @throw SequenceNotFoundException If no sequence with name 'name' could be found.
+ */
+ virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
+
+ /**
+ * @name Provide direct access to sequences content.
+ *
+ * @warning These operators allow you to modifiy the content of the sequences.
+ * No checking is performed for your modifications, so use with care, or
+ * consider using the setContent() methods.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Element access operator.
+ *
+ * Allows direct access to the data stored in the container.
+ *
+ * @param sequenceIndex The sequence position.
+ * @param elementIndex The element position within the sequence.
+ * @throw IndexOutOfBoundsException If a position is not valid.
+ */
+ virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Element access operator.
+ *
+ * Allows direct access to the data stored in the container.
+ *
+ * @param sequenceIndex The sequence position.
+ * @param elementIndex The element position within the sequence.
+ * @throw IndexOutOfBoundsException If a position is not valid.
+ */
+ virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Element access operator.
+ *
+ * Allows direct access to the data stored in the container.
+ * This method is faster then the valueAt function, but input
+ * parameters are not checked!
+ *
+ * @param sequenceIndex The sequence position.
+ * @param elementIndex The element position within the sequence.
+ */
+ virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0;
+
+ /**
+ * @brief Element access operator.
+ *
+ * Allows direct access to the data stored in the container.
+ * This method is faster then the valueAt function, but input
+ * parameters are not checked!
+ *
+ * @param sequenceIndex The sequence position.
+ * @param elementIndex The element position within the sequence.
+ */
+ virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0;
+ /** @} */
+
+ public:
+
+ /**
+ * @name SequenceContainer methods.
+ *
+ * @{
+ */
+ virtual const std::vector<int>& getContent(const std::string& name) const throw (SequenceNotFoundException) = 0;
+ virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
+ virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
+ virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
+ virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
+ virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
+ virtual size_t getNumberOfSequences() const = 0;
+ virtual std::vector<std::string> getSequencesNames() const = 0;
+ virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
+ virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
+ virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
+ /** @} */
+};
+
+} //end of namespace bpp.
+
+#endif //_ORDEREDSEQUENCECONTAINER_H_
+
diff --git a/src/Bpp/Seq/Container/SequenceContainer.h b/src/Bpp/Seq/Container/SequenceContainer.h
new file mode 100644
index 0000000..85294a7
--- /dev/null
+++ b/src/Bpp/Seq/Container/SequenceContainer.h
@@ -0,0 +1,316 @@
+//
+// File: SequenceContainer.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: Fri Jul 25 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCECONTAINER_H_
+#define _SEQUENCECONTAINER_H_
+
+#include "../Alphabet/Alphabet.h"
+#include "../Sequence.h"
+#include "SequenceContainerExceptions.h"
+#include <Bpp/Clonable.h>
+
+// From the STL:
+#include <string>
+
+namespace bpp
+{
+
+/**
+ * @brief The SequenceContainer interface.
+ *
+ * This interface is the most general one in the container hierarchy.
+ * No assumption is made on the sequences in the container (no ordering, no alignment).
+ * Sequences may be retrieved using their names, which must be unique.
+ *
+ * The container is the only one responsible for the allocation/destruction of sequences it
+ * contains. This means that any sequence passed to it will be <strong>copied</strong> into the container.
+ * The container also provides methods that send const pointers towards these sequences
+ * (without performing any copy of the underlying objects).
+ *
+ * Notes :
+ * 1. methods for adding sequences to the container are not declared here
+ * (so they can't be used throught this interface),
+ * because these methods take sequence container's type specific parameters
+ * (i.e. a key for map sequence containers);
+ * 2. to delete a sequence from a container, one must use the appropriate method
+ * (removeSequence() and deleteSequence()).
+ * These methods performs a few check, and properly update pointers.
+ * You should never delete a sequence from a container by yourself.
+ *
+ * @see Sequence
+ */
+
+class SequenceContainer:
+ public virtual Clonable
+{
+ public:
+ SequenceContainer() {}
+ virtual ~SequenceContainer() {}
+
+ public:
+ /**
+ * @brief Get sequence container's alphabet.
+ *
+ * @return The alphabet associated to this container.
+ */
+ virtual const Alphabet* getAlphabet() const = 0;
+
+ /**
+ * @brief Get the content of a sequence.
+ *
+ * @param name The name of the sequence.
+ * @return The content of the sequence as a vector of integers.
+ * @throw SequenceNotFoundException If the name does not match any sequence in the container.
+ */
+ virtual const std::vector<int>& getContent(const std::string& name) const throw (SequenceNotFoundException) = 0;
+
+ /**
+ * @brief Convert a particular sequence to a string.
+ *
+ * @param name The name of the sequence.
+ * @return A string describing the content of the sequence.
+ * @throw SequenceNotFoundException If the name does not match any sequence in the container.
+ */
+ virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
+
+ /**
+ * @brief Retrieve a sequence object from the container.
+ *
+ * @param name The name of the sequence.
+ * @return A reference toward the Sequence with corresponding name.
+ * @throw SequenceNotFoundException If the name does not match any sequence in the container.
+ */
+ virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
+
+ /**
+ * @brief Check if a sequence with a given name is present in the container.
+ *
+ * @param name The name of the sequence.
+ * @return True if a sequence with the given name is present in the container.
+ */
+ virtual bool hasSequence(const std::string& name) const = 0;
+
+ /**
+ * @brief Add a sequence to the container.
+ *
+ * @param sequence The sequence to add.
+ * @param checkName Tell if the container must check if the name of the sequence
+ * is already used in the container before adding it.
+ * @throw Exception Any other kind of exception, if the name of the sequence is
+ * already used, are whatever else depending on the implementation.
+ */
+ virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
+
+ /**
+ * @brief Replace a sequence in the container.
+ *
+ * @param name The name of the sequence.
+ * @param sequence The sequence to add.
+ * @param checkName Tell if the container must check if the name of the sequence
+ * is already used in the container before adding it.
+ * @throw SequenceNotFoundException If the name does not match any sequence in
+ * the container.
+ * @throw Exception Any other kind of exception, if the name of the sequence is
+ * already used, are whatever else depending on the implementation.
+ */
+ virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
+
+ /**
+ * @brief Extract (and remove) a sequence from the container.
+ *
+ * @param name The name of the sequence.
+ * @throw SequenceNotFoundException If the name does not match any sequence in
+ * the container.
+ */
+ virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
+
+ /**
+ * @brief Delete a sequence of the container.
+ *
+ * @param name The name of the sequence.
+ * @throw SequenceNotFoundException If the name does not match any sequence in
+ * the container.
+ */
+ virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
+
+ /**
+ * @brief Get the number of sequences in the container.
+ *
+ * @return The number of sequences in the container.
+ */
+ virtual size_t getNumberOfSequences() const = 0;
+
+ /**
+ * @brief Get all the names of the sequences in the container.
+ *
+ * @return A vector of strings with all sequence names.
+ */
+ virtual std::vector<std::string> getSequencesNames() const = 0;
+
+ /**
+ * @brief Set all sequence names.
+ *
+ * @param names A vector of strings with all sequence names.
+ * Its size must be strictly equal to the the size of the container (the number of
+ * sequences).
+ * @param checkNames Tell if the container must check if the name of the sequence
+ * is already used in the container before adding it.
+ * @throw Exception If there are redundant names in the input vector.
+ */
+ virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
+
+ /**
+ * @brief Get comments of a particular sequence.
+ *
+ * @param name The name of the sequence.
+ * @return The comments associated to sequence with name 'name'.
+ * @throw SequenceNotFoundException If the name does not match any sequence in
+ * the container.
+ */
+ virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
+
+ /**
+ * @brief Set the comments of a particular sequence.
+ *
+ * @param name The name of the sequence.
+ * @param comments The comments to set to sequence with name 'name'.
+ * @throw SequenceNotFoundException If the name does not match any sequence in
+ * the container.
+ */
+ virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
+
+ /**
+ * @brief Get the comments of this container.
+ *
+ * @return The comments associated to this container.
+ */
+ virtual const Comments& getGeneralComments() const = 0;
+
+ /**
+ * @brief Set the comments of this container.
+ *
+ * @param comments The comments to be associated to this container.
+ */
+ virtual void setGeneralComments(const Comments& comments) = 0;
+
+ /**
+ * @brief Delete the comments associated to this container.
+ */
+ virtual void deleteGeneralComments() = 0;
+
+ /**
+ * @brief Delete all sequences in the container.
+ */
+ virtual void clear() = 0;
+
+ /**
+ * @brief Return a copy of this container, but with no sequence inside.
+ *
+ * This method creates a new SequenceContainer objet.
+ * The class of this container depends on the derivative class.
+ *
+ * @return A new empty container, with the same alphabet as this one.
+ */
+ virtual SequenceContainer* createEmptyContainer() const = 0;
+
+ /**
+ * @name Provide direct access to sequences content.
+ *
+ * @warning These operators allow you to modifiy the content of the sequences.
+ * No checking is performed for your modifications, so use with care, or
+ * consider using the setContent() methods.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Element access function.
+ *
+ * Allows direct access to the data stored in the container.
+ *
+ * @param sequenceName The sequence name.
+ * @param elementIndex The element position within the sequence.
+ * @throw SequenceNotFoundException If no corresponding sequence is found in the container.
+ * @throw IndexOutOfBoundsException If the element position is not valid.
+ */
+ virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Element access function.
+ *
+ * Allows direct access to the data stored in the container.
+ *
+ * @param sequenceName The sequence name.
+ * @param elementIndex The element position within the sequence.
+ * @throw SequenceNotFoundException If no corresponding sequence is found in the container.
+ * @throw IndexOutOfBoundsException If the element position is not valid.
+ */
+ virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Element access operator.
+ *
+ * Allows direct access to the data stored in the container.
+ * This method is faster then the valueAt function, but input
+ * parameters are not checked!
+ *
+ * @param sequenceName The sequence name.
+ * @param elementIndex The element position within the sequence.
+ */
+ virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0;
+
+ /**
+ * @brief Element access operator.
+ *
+ * Allows direct access to the data stored in the container.
+ * This method is faster then the valueAt function, but input
+ * parameters are not checked!
+ *
+ * @param sequenceName The sequence name.
+ * @param elementIndex The element position within the sequence.
+ */
+ virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0;
+ /** @} */
+};
+
+} //end of namespace bpp.
+
+#endif // _SEQUENCECONTAINER_H_
+
diff --git a/src/Bpp/Seq/Container/SequenceContainerExceptions.h b/src/Bpp/Seq/Container/SequenceContainerExceptions.h
new file mode 100644
index 0000000..c4f612d
--- /dev/null
+++ b/src/Bpp/Seq/Container/SequenceContainerExceptions.h
@@ -0,0 +1,149 @@
+//
+// File: SequenceContainerExceptions.h
+// Created by: Julien Dutheil
+// Created on: Mon Nov 3 17:00:05 2003
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCECONTAINEREXCEPTIONS_H_
+#define _SEQUENCECONTAINEREXCEPTIONS_H_
+
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+class SequenceContainer;
+
+/**
+ * @brief Exception thrown when a sequence is not found The sequence not found exception base class.
+ */
+class SequenceNotFoundException :
+ public Exception
+{
+
+ protected:
+
+ /**
+ * @brief The id of the sequence that was to be found.
+ */
+ const std::string id;
+
+ public:
+
+ /**
+ * @brief Build a new SequenceNotFoundException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param seqId A the id of the sequence that was to be found.
+ */
+ SequenceNotFoundException(const char * text, const char * seqId = "") :
+ Exception("SequenceNotFoundException: " + std::string(text) + "(" + seqId + ")"),
+ id(seqId) {};
+
+ /**
+ * @brief Build a new SequenceNotFoundException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param seqId A the id of the sequence that was to be found.
+ */
+ SequenceNotFoundException(const std::string & text, const std::string & seqId = "") :
+ Exception("SequenceNotFoundException: " + text + "(" + seqId + ")"),
+ id(seqId) {};
+
+ // Class destructor
+ virtual ~SequenceNotFoundException() throw() {}
+
+ public:
+
+ /**
+ * @brief Get the id of the sequence that was to be found.
+ *
+ * @return The id of the sequence that was to be found.
+ */
+ virtual const std::string getSequenceId() const { return id; }
+};
+
+/**
+ * @brief Exception thrown when an empty container is found.
+ */
+class EmptyContainerException :
+ public Exception
+{
+
+ private:
+
+ /**
+ * @brief The empty container.
+ */
+ const SequenceContainer *container_;
+
+ public:
+
+ /**
+ * @brief Build a new EmptyContainerException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param container The empty container.
+ */
+ EmptyContainerException(const std::string& text, const SequenceContainer* container) :
+ Exception("EmptyContainerException: " + text),
+ container_(container) {};
+
+ EmptyContainerException(const EmptyContainerException& ece):
+ Exception(ece), container_(ece.container_) {}
+
+ EmptyContainerException& operator=(const EmptyContainerException& ece)
+ {
+ Exception::operator=(ece);
+ container_ = ece.container_;
+ return *this;
+ }
+
+ // Class destructor
+ virtual ~EmptyContainerException() throw() {}
+
+ public:
+
+ /**
+ * @return The empty container.
+ */
+ virtual const SequenceContainer* getContainer() const { return container_; }
+};
+
+} //end of namespace bpp.
+
+#endif //_SEQUENCECONTAINEREXCEPTIONS_H_
+
diff --git a/src/Bpp/Seq/Container/SequenceContainerIterator.cpp b/src/Bpp/Seq/Container/SequenceContainerIterator.cpp
new file mode 100644
index 0000000..140fa3a
--- /dev/null
+++ b/src/Bpp/Seq/Container/SequenceContainerIterator.cpp
@@ -0,0 +1,75 @@
+//
+// File: SequenceContainerIterator.cpp
+// Created by: Julien Dutheil
+// Created on: Tue Feb 26 14:44 2013
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SequenceContainerIterator.h"
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+
+using namespace std;
+
+/******************************************************************************/
+
+AbstractSequenceContainerIterator::AbstractSequenceContainerIterator(const OrderedSequenceContainer& sequences) :
+ sequences_(&sequences),
+ currentPosition_(0)
+{}
+
+/******************************************************************************/
+
+SimpleSequenceContainerIterator::SimpleSequenceContainerIterator(const OrderedSequenceContainer& sequences):
+ AbstractSequenceContainerIterator(sequences) {}
+
+const Sequence* SimpleSequenceContainerIterator::nextSequence()
+{
+ const Sequence* s = &sequences_->getSequence(currentPosition_);
+ currentPosition_++;
+ return s;
+}
+
+bool SimpleSequenceContainerIterator::hasMoreSequences() const
+{
+ return currentPosition_ < static_cast<int>(sequences_->getNumberOfSequences());
+}
+
+/******************************************************************************/
+
+
diff --git a/src/Bpp/Seq/Container/SequenceContainerIterator.h b/src/Bpp/Seq/Container/SequenceContainerIterator.h
new file mode 100644
index 0000000..fc10feb
--- /dev/null
+++ b/src/Bpp/Seq/Container/SequenceContainerIterator.h
@@ -0,0 +1,97 @@
+//
+// File: SequenceContainerIterator.h
+// Created by: Julien Dutheil
+// Created on: Tue Feb 26 14:34 2013
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCECONTAINERITERATOR_H_
+#define _SEQUENCECONTAINERITERATOR_H_
+
+#include "../Sequence.h"
+#include "../SequenceIterator.h"
+#include "OrderedSequenceContainer.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Partial implementation of the SequenceIterator interface, allowing to loop over an ordered sequence container.
+ */
+class AbstractSequenceContainerIterator :
+ public virtual ConstSequenceIterator
+{
+ protected:
+ const OrderedSequenceContainer* sequences_;
+ int currentPosition_;
+
+ public:
+ AbstractSequenceContainerIterator(const OrderedSequenceContainer& sites);
+
+ AbstractSequenceContainerIterator(const AbstractSequenceContainerIterator& asi) :
+ sequences_(asi.sequences_),
+ currentPosition_(asi.currentPosition_)
+ {}
+
+ AbstractSequenceContainerIterator& operator=(const AbstractSequenceContainerIterator& asi)
+ {
+ sequences_ = asi.sequences_;
+ currentPosition_ = asi.currentPosition_;
+ return *this;
+ }
+
+ virtual ~AbstractSequenceContainerIterator() {}
+
+};
+
+/**
+ * @brief Loop over all sequences in a SequenceContainer.
+ */
+class SimpleSequenceContainerIterator:
+ public AbstractSequenceContainerIterator
+{
+ public:
+ SimpleSequenceContainerIterator(const OrderedSequenceContainer& sites);
+ virtual ~SimpleSequenceContainerIterator() {}
+
+ public:
+ const Sequence* nextSequence();
+ bool hasMoreSequences() const;
+};
+
+} //end of namespace bpp.
+
+#endif //_SEQUENCEITERATOR_H_
+
diff --git a/src/Bpp/Seq/Container/SequenceContainerTools.cpp b/src/Bpp/Seq/Container/SequenceContainerTools.cpp
new file mode 100644
index 0000000..72c2d9c
--- /dev/null
+++ b/src/Bpp/Seq/Container/SequenceContainerTools.cpp
@@ -0,0 +1,223 @@
+//
+// File: SequenceContainerTools.cpp
+// Created by: Julien Dutheil
+// Created on: Sat Oct 4 09:18:34 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "SequenceContainerTools.h"
+#include "VectorSequenceContainer.h"
+#include "../Alphabet/CodonAlphabet.h"
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+
+using namespace std;
+
+/******************************************************************************/
+
+SequenceContainer* SequenceContainerTools::createContainerOfSpecifiedSize(const Alphabet* alphabet, size_t size)
+{
+ VectorSequenceContainer* vsc = new VectorSequenceContainer(alphabet);
+ for (size_t i = 0; i < size; ++i)
+ {
+ vsc->addSequence(BasicSequence("" + i, "", alphabet), false);
+ }
+ return vsc;
+}
+
+/******************************************************************************/
+
+SequenceContainer* SequenceContainerTools::createContainerWithSequenceNames(
+ const Alphabet* alphabet,
+ const vector<string>& seqNames)
+throw (Exception)
+{
+ SequenceContainer* sc = createContainerOfSpecifiedSize(alphabet, seqNames.size());
+ sc->setSequencesNames(seqNames, true);
+ return sc;
+}
+
+/******************************************************************************/
+
+void SequenceContainerTools::getSelectedSequences(
+ const OrderedSequenceContainer& sequences,
+ const SequenceSelection& selection,
+ SequenceContainer& outputCont) throw (Exception)
+{
+ bool checkNames = outputCont.getNumberOfSequences() > 0;
+ for (size_t i = 0; i < selection.size(); i++)
+ {
+ outputCont.addSequence(sequences.getSequence(selection[i]), checkNames);
+ }
+}
+
+/******************************************************************************/
+
+void SequenceContainerTools::getSelectedSequences(
+ const SequenceContainer& sequences,
+ const std::vector<std::string>& selection,
+ SequenceContainer& outputCont, bool strict) throw (Exception)
+{
+ bool checkNames = outputCont.getNumberOfSequences() > 0;
+ for (size_t i = 0; i < selection.size(); i++)
+ {
+ if (strict)
+ {
+ outputCont.addSequence(sequences.getSequence(selection[i]), checkNames);
+ }
+ else
+ {
+ if (sequences.hasSequence(selection[i]))
+ outputCont.addSequence(sequences.getSequence(selection[i]), checkNames);
+ }
+ }
+}
+
+/******************************************************************************/
+
+void SequenceContainerTools::keepOnlySelectedSequences(
+ OrderedSequenceContainer& sequences,
+ const SequenceSelection& selection)
+{
+ vector<string> names = sequences.getSequencesNames();
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ // We need to do this because after removal the indices will not be the same!
+ // another solution would be to sort decreasingly the indices...
+ bool test = false;
+ for (size_t j = 0; j < selection.size() && !test; j++)
+ {
+ test = (selection[j] == i);
+ }
+ if (!test)
+ sequences.deleteSequence(names[i]);
+ // WARNING: what if selection contains several times the same indice? ...
+ }
+}
+
+/******************************************************************************/
+
+bool SequenceContainerTools::sequencesHaveTheSameLength(const SequenceContainer& sequences)
+{
+ vector<string> seqNames = sequences.getSequencesNames();
+ if (seqNames.size() <= 1)
+ return true;
+ size_t length = sequences.getSequence(seqNames[0]).size();
+ for (size_t i = 1; i < seqNames.size(); i++)
+ {
+ if (sequences.getSequence(seqNames[i]).size() != length)
+ return false;
+ }
+ return true;
+}
+
+/******************************************************************************/
+
+void SequenceContainerTools::getFrequencies(const SequenceContainer& sequences, std::map<int, double>& f, double pseudoCount)
+{
+ double n = 0;
+ vector<string> names = sequences.getSequencesNames();
+ for (size_t j = 0; j < names.size(); j++)
+ {
+ vector<int> seq = sequences.getContent(names[j]);
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ f[seq[i]]++;
+ }
+ n += static_cast<double>(seq.size());
+ }
+
+ if (pseudoCount != 0)
+ {
+ const Alphabet* pA = sequences.getAlphabet();
+ for (int i = 0; i < static_cast<int>(pA->getSize()); i++)
+ {
+ f[i] += pseudoCount;
+ }
+
+ n += pseudoCount * static_cast<double>(pA->getSize());
+ }
+
+ for (map<int, double>::iterator i = f.begin(); i != f.end(); i++)
+ {
+ i->second = i->second / n;
+ }
+}
+
+/******************************************************************************/
+
+void SequenceContainerTools::getCounts(const SequenceContainer& sequences, std::map<int, int>& f)
+{
+ size_t n = 0;
+ vector<string> names = sequences.getSequencesNames();
+ for (size_t j = 0; j < names.size(); j++)
+ {
+ vector<int> seq = sequences.getContent(names[j]);
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ f[seq[i]]++;
+ }
+ n += seq.size();
+ }
+}
+
+/******************************************************************************/
+
+SequenceContainer* SequenceContainerTools::getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException)
+{
+ const CodonAlphabet* calpha = dynamic_cast<const CodonAlphabet*>(sequences.getAlphabet());
+ if (!calpha)
+ throw AlphabetException("SequenceContainerTools::getCodonPosition. Input sequences should be of type codon.");
+ vector<string> names = sequences.getSequencesNames();
+ VectorSequenceContainer* newcont = new VectorSequenceContainer(calpha->getNucleicAlphabet());
+ for (size_t j = 0; j < names.size(); j++)
+ {
+ vector<int> seq = sequences.getContent(names[j]);
+ vector<int> newseq(seq.size());
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ newseq[i] = calpha->getNPosition(seq[i], pos);
+ }
+ BasicSequence s(names[j], newseq, sequences.getComments(names[j]), calpha->getNucleicAlphabet());
+ newcont->addSequence(s);
+ }
+ return newcont;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Container/SequenceContainerTools.h b/src/Bpp/Seq/Container/SequenceContainerTools.h
new file mode 100644
index 0000000..7c79514
--- /dev/null
+++ b/src/Bpp/Seq/Container/SequenceContainerTools.h
@@ -0,0 +1,299 @@
+//
+// File: SequenceContainerTools.h
+// Created by: Julien Dutheil
+// Sylvain Gaillard
+// Created on: Sat Oct 4 09:18:34 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCECONTAINERTOOLS_H_
+#define _SEQUENCECONTAINERTOOLS_H_
+
+// From the STL:
+#include <string>
+#include <vector>
+#include <map>
+#include <memory>
+
+#include "SequenceContainer.h"
+#include "OrderedSequenceContainer.h"
+
+namespace bpp
+{
+
+typedef std::vector<size_t> SequenceSelection;
+
+/**
+ * @brief Utilitary methods dealing with sequence containers.
+ */
+class SequenceContainerTools
+{
+
+ public:
+ SequenceContainerTools() {}
+ virtual ~SequenceContainerTools() {}
+
+ public:
+ /**
+ * @brief Create a container with @f$n at f$ void sequences.
+ *
+ * A new VectorSequenceContainer with the specified alphabet is created.
+ * The destruction of this new container is up to the user.
+ * Sequences have name "0", "1",... "n-1" and no content and comments.
+ *
+ * @param alphabet The alphabet to use in the container.
+ * @param size The number of sequences in the container.
+ * @return A pointer toward a newly created container.
+ */
+ static SequenceContainer* createContainerOfSpecifiedSize(const Alphabet* alphabet, size_t size);
+
+ /**
+ * @brief Create a container with specified names.
+ *
+ * A new VectorSequenceContainer with the specified alphabet is created.
+ * The destruction of this new container is up to the user.
+ * Sequences have the specified names and no content and comments.
+ *
+ * @param alphabet The alphabet to use in the container.
+ * @param seqNames The names of the sequences.
+ * @return A pointer toward a newly created container.
+ * @throw Exception If two sequence names are not unique.
+ */
+ static SequenceContainer* createContainerWithSequenceNames(
+ const Alphabet* alphabet,
+ const std::vector<std::string>& seqNames)
+ throw (Exception);
+
+ /**
+ * @brief Generic function which creates a new container from another one,
+ * by specifying the class of sequence to be stored.
+ *
+ * Compared to several copy constructors, this function allows to change the class of
+ * the inner sequence class used for storing sequences.
+ * The function used the addSequence method, so that it can also be used to
+ * concatenate containers.
+ *
+ * @param input The container to copy.
+ * @param output The container where new sequences will be appended.
+ */
+ template<class ContFrom, class ContTo, class Seq>
+ static void convertContainer(const ContFrom& input, ContTo& output) {
+ for (size_t i = 0; i < input.getNumberOfSequences(); ++i) {
+ std::auto_ptr<Seq> seq(new Seq(input.getSequence(i)));
+ output.addSequence(*seq);
+ }
+ }
+
+ /**
+ * @brief Add a specified set of sequences from a container to another.
+ *
+ * Sequences are specified by their position, beginning at 0.
+ * Name verification will be performed, only if the output container is not empty,
+ * based on the assumption that the container passed as argument is a correct one.
+ * Redundant selection is not checked, so be careful with what you're doing!
+ *
+ * @author Julien Dutheil
+ *
+ * @param sequences The container from wich sequences are to be taken.
+ * @param selection The positions of all sequences to retrieve.
+ * @param outputCont A container where the selection should be added.
+ * @throw Exception In case of bad sequence name, alphabet mismatch, etc.
+ */
+ static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
+
+ /**
+ * @brief Add a specified set of sequences from a container to another.
+ *
+ * Sequences are specified by their names.
+ * Name verification will be performed, only if the output container is not empty,
+ * based on the assumption that the container passed as argument is a correct one.
+ * Redundant selection is not checked, so be careful with what you're doing!
+ *
+ * @author Julien Dutheil
+ *
+ * @param sequences The container from wich sequences are to be taken.
+ * @param selection The names of all sequences to retrieve.
+ * @param outputCont A container where the selection should be added.
+ * @param strict If yes, trying to select a sequence that is not present
+ * will raise an exception. If no, only available sequence will be added.
+ * @throw Exception In case of bad sequence name, alphabet mismatch, etc.
+ */
+ static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
+
+ /**
+ * @brief Remove all sequences that are not in a given selection from a given container.
+ *
+ * A new VectorSequenceContainer is created with specified sequences.
+ * The destruction of the container is up to the user.
+ * Sequences are specified by their position, beginning at 0.
+ * Redundant selection is not checked, so be careful with what you're doing!
+ *
+ * @param sequences The container from wich sequences are to be taken.
+ * @param selection The positions of all sequences to retrieve.
+ * @return A new container with all selected sequences.
+ */
+ static void keepOnlySelectedSequences(OrderedSequenceContainer& sequences, const SequenceSelection& selection);
+
+ /**
+ * @brief Check if all sequences in a SequenceContainer have the same length.
+ *
+ * @param sequences The container to check.
+ * @return True is all sequence have the same length.
+ */
+ static bool sequencesHaveTheSameLength(const SequenceContainer& sequences);
+
+ /**
+ * @brief Compute base counts
+ *
+ * Example of usage: getting the GC count from a sequence container.
+ * <code>
+ * map<int, int> counts;
+ * SequenceContainerTools::getCounts(myContainer, counts); //My container is previously defined.
+ * int GCcontent = counts[1] + counts[2] ;
+ * </code>
+ *
+ * States are stored as their int code.
+ */
+
+ static void getCounts(const SequenceContainer& sequences, std::map<int, int>&);
+
+ /**
+ * @brief Compute base frequencies.
+ *
+ * Example of usage: getting the GC content from a sequence container.
+ * <code>
+ * map<int, double> freqs;
+ * SequenceContainerTools::getFrequencies(myContainer, freqs); //My container is previously defined.
+ * double GCcontent = (freqs[1] + freqs[2]) / (freqs[0] + freqs[1] + freqs[2] + freqs[3]);
+ * </code>
+ *
+ * States are stored as their int code.
+ */
+
+ static void getFrequencies(const SequenceContainer& sequences, std::map<int, double>& f, double pseudoCount = 0);
+
+ /**
+ * @brief Append all the sequences of a SequenceContainer to the end of another.
+ *
+ * @param seqCont1 The SequenceContainer in which the sequences will be added.
+ * @param seqCont2 The SequenceContainer from which the sequences are taken.
+ * @param checkNames Tell if the sequence names should be check for unicity.
+ */
+ static void append(SequenceContainer& seqCont1, const SequenceContainer& seqCont2, bool checkNames = true)
+ throw (Exception)
+ {
+ std::vector<std::string> seqNames = seqCont2.getSequencesNames();
+ for (size_t i = 0; i < seqNames.size(); i++)
+ seqCont1.addSequence(seqCont2.getSequence(seqNames[i]), checkNames);
+ }
+ /**
+ * @brief Append all the sequences of a SequenceContainer to the end of another, OrderedSequenceContainer implementation.
+ *
+ * @param seqCont1 The SequenceContainer in which the sequences will be added.
+ * @param seqCont2 The SequenceContainer from which the sequences are taken.
+ * @param checkNames Tell if the sequence names should be check for unicity.
+ */
+ static void append(SequenceContainer& seqCont1, const OrderedSequenceContainer& seqCont2, bool checkNames=true)
+ throw (Exception)
+ {
+ for (size_t i = 0; i < seqCont2.getNumberOfSequences(); i++)
+ seqCont1.addSequence(seqCont2.getSequence(i), checkNames);
+ }
+
+ /**
+ * @brief Concatenate the sequences from two containers.
+ *
+ * This method will not check the original sequence names for unicity. If sequences do not have a unique name,
+ * then the resulting merged container will contain the first sequence with the given duplicated name.
+ *
+ * @author Julien Dutheil
+ *
+ * @param seqCont1 First container.
+ * @param seqCont2 Second container. This container must contain sequences with the same names as in seqcont1.
+ * Additional sequences will be ignored.
+ * @param outputCont Output sequence container to which concatenated sequences will be added.
+ * @throw AlphabetMismatchException If the alphabet in the 3 containers do not match.
+ */
+ static void merge(const SequenceContainer& seqCont1, const SequenceContainer& seqCont2, SequenceContainer& outputCont)
+ throw (Exception)
+ {
+ if (seqCont1.getAlphabet()->getAlphabetType() != seqCont2.getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("SequenceContainerTools::merge.", seqCont1.getAlphabet(), seqCont2.getAlphabet());
+
+ std::vector<std::string> seqNames = seqCont1.getSequencesNames();
+ for (size_t i = 0; i < seqNames.size(); i++)
+ {
+ BasicSequence tmp = seqCont1.getSequence(seqNames[i]);
+ tmp.append(seqCont2.getContent(seqNames[i]));
+ outputCont.addSequence(tmp, false);
+ }
+ }
+
+ /**
+ * @brief Convert a SequenceContainer with a new alphabet.
+ *
+ * This method assume that the original container has proper sequence names.
+ * Names will be checked only if the output container is not empty.
+ * @param seqCont The container to convert.
+ * @param outputCont A container (most likely empty) with an alphabet into which the container will be converted.
+ */
+ static void convertAlphabet(const SequenceContainer& seqCont, SequenceContainer& outputCont)
+ throw (Exception)
+ {
+ std::vector<std::string> seqNames = seqCont.getSequencesNames();
+ bool checkNames = outputCont.getNumberOfSequences() > 0;
+ for (size_t i = 0; i < seqNames.size(); i++)
+ {
+ BasicSequence seq(seqNames[i], seqCont.toString(seqNames[i]), outputCont.getAlphabet());
+ outputCont.addSequence(seq, checkNames);
+ }
+ }
+
+ /**
+ * @brief Extract a certain position (1, 2 or 3) from a container of codon sequences and returns the resulting nucleotide container.
+ *
+ * @param sequences The input sequence container, with codon alphabet.
+ * @param pos The codon position to retrieve.
+ * @return A SequenceContainer with a nucleotide alphabet.
+ * @throw AlphabetException If input sequences are not registered with a codon alphabet.
+ */
+ static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
+
+};
+
+} //end of namespace bpp.
+
+#endif //_SEQUENCECONTAINERTOOLS_H_
+
diff --git a/src/Bpp/Seq/Container/SiteContainer.h b/src/Bpp/Seq/Container/SiteContainer.h
new file mode 100644
index 0000000..9da0f9c
--- /dev/null
+++ b/src/Bpp/Seq/Container/SiteContainer.h
@@ -0,0 +1,183 @@
+//
+// File SiteContainer.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _SITECONTAINER_H_
+#define _SITECONTAINER_H_
+
+#include "../Site.h"
+#include "OrderedSequenceContainer.h"
+#include "SequenceContainerExceptions.h"
+#include <Bpp/Exceptions.h>
+#include <Bpp/Numeric/VectorTools.h>
+
+// From the STL:
+#include <string>
+
+namespace bpp
+{
+/**
+ * @brief The SiteContainer interface.
+ *
+ * Container implementing the SiteContainer interface deal with <em>aligned</em> sequences.
+ * This interface provides methods to retrieve, add or set sites in the alignment.
+ * As for SequenceContainers, the maintenance of Sites is up to the container.
+ * All site objects are cloned befored being added and retrieved.
+ * All sites stored are deleted in the destructor of the container or after having called the deleteSite() method.
+ */
+class SiteContainer :
+ public virtual OrderedSequenceContainer
+{
+public:
+ SiteContainer() {}
+ virtual ~SiteContainer() {}
+
+ SiteContainer* clone() const = 0;
+
+public:
+ /**
+ * @brief Get a site from the container.
+ *
+ * @param siteIndex The position of the site in the container.
+ * @return A site objet corresponding to site i in the alignment.
+ * @throw IndexOutOfBoundsException If the specified site does not exists.
+ */
+ virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Set a site in the container.
+ *
+ * @param siteIndex The position of the site in the container.
+ * @param site The site to set.
+ * @param checkPosition Look if the position of the new site match a position attribute in the container.
+ * @throw Exception If the specified site does not exists or is not correct.
+ */
+ virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
+
+ /**
+ * @brief Add a site in the container.
+ *
+ * @param site The site to add.
+ * @param checkPosition Look if the position of the new site match a position attribute in the container.
+ * @throw Exception If the specified site does not exists or is not correct.
+ */
+ virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
+
+ /**
+ * @brief Add a site in the container.
+ *
+ * @param site The site to add.
+ * @param position The new position of the site, to superseed the one in 'site'.
+ * @param checkPosition Look if the position of the new site match a position attribute in the container.
+ * @throw Exception If the specified site does not exists or is not correct.
+ */
+ virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
+
+ /**
+ * @brief Add a site in the container.
+ *
+ * @param site The site to add.
+ * @param siteIndex The position where to insert the site.
+ * @param checkPosition Look if the position of the new site match a position attribute in the container.
+ * @throw Exception If the specified site does not exists or is not correct.
+ */
+ virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
+
+ /**
+ * @brief Add a site in the container.
+ *
+ * @param site The site to add.
+ * @param siteIndex The position where to insert the site.
+ * @param position The new position of the site, to superseed the one in 'site'.
+ * @param checkPosition Look if the position of the new site match a position attribute in the container.
+ * @throw Exception If the specified site does not exists or is not correct.
+ */
+ virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
+
+ /**
+ * @brief Remove a site from the container.
+ *
+ * The site is not deleted, a pointer toward it is returned.
+ *
+ * @param siteIndex The position of the site in the container.
+ * @return A pointer toward site i in the alignment.
+ * @throw IndexOutOfBoundsException If the specified site does not exists.
+ */
+ virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
+
+ /**
+ * @brief Delete a site in the container.
+ *
+ * @param siteIndex The position of the site in the container.
+ * @throw IndexOutOfBoundsException If the specified site does not exists.
+ */
+ virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
+
+ /**
+ * @brief Delete a continuous range of sites in the container.
+ *
+ * @param siteIndex The position of the first site in the container.
+ * @param length The length of the region to delete, starting at pposition siteIndex.
+ * @throw IndexOutOfBoundsException If the specified range is not valid.
+ */
+ virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
+
+
+ /**
+ * @brief Get the number of sites in the container.
+ *
+ * @return The number of sites in the container.
+ */
+ virtual size_t getNumberOfSites() const = 0;
+
+ /**
+ * @brief Set all positions attributes.
+ */
+ virtual void reindexSites() = 0;
+
+ /**
+ * @brief Get all position attributes of sites.
+ *
+ * @return A vector with all site positions.
+ */
+ virtual Vint getSitePositions() const = 0;
+};
+} // end of namespace bpp.
+
+#endif // _SITECONTAINER_H_
+
diff --git a/src/Bpp/Seq/Container/SiteContainerExceptions.cpp b/src/Bpp/Seq/Container/SiteContainerExceptions.cpp
new file mode 100644
index 0000000..d28f9b6
--- /dev/null
+++ b/src/Bpp/Seq/Container/SiteContainerExceptions.cpp
@@ -0,0 +1,60 @@
+//
+// File SiteContainerExceptions.cpp
+// Author: Julien Dutheil
+// Created on: mer mar 31 2004
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SiteContainerExceptions.h"
+
+using namespace bpp;
+using namespace std;
+
+/*******************************************************************************
+ * Site containers exceptions *
+ *******************************************************************************/
+
+SiteNotFoundException::SiteNotFoundException(const char * text, const char * sId) :
+ Exception("SequenceNotFoundException: " + string(text) + "(" + sId + ")"),
+ id(sId) {};
+
+SiteNotFoundException::SiteNotFoundException(const string & text, const string & sId) :
+ Exception("SequenceNotFoundException: " + text + "(" + sId + ")"),
+ id(sId) {};
+
+SiteNotFoundException::~SiteNotFoundException() throw() {};
+
+const string SiteNotFoundException::getSiteId() const { return id; }
+
diff --git a/src/Bpp/Seq/Container/SiteContainerExceptions.h b/src/Bpp/Seq/Container/SiteContainerExceptions.h
new file mode 100644
index 0000000..0d6d449
--- /dev/null
+++ b/src/Bpp/Seq/Container/SiteContainerExceptions.h
@@ -0,0 +1,100 @@
+//
+// File SiteContainerExceptions.h
+// Author: Julien Dutheil
+// Created on: mer mar 31 2004
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SITECONTAINEREXCEPTIONS_H_
+#define _SITECONTAINEREXCEPTIONS_H_
+
+// From STL
+#include <string>
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+/**
+ * @brief The site not found exception base class.
+ *
+ * @see Exception
+ */
+class SiteNotFoundException:
+ public Exception
+{
+
+ protected:
+
+ /**
+ * @brief The id of the site that was to be found.
+ */
+ const std::string id;
+
+ public: // Class constructor
+
+ /**
+ * @brief Build a new SiteNotFoundException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param sId A the id of the site that was to be found.
+ */
+ SiteNotFoundException(const char * text, const char * sId = "");
+
+ /**
+ * @brief Build a new SiteNotFoundException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param sId A the id of the site that was to be found.
+ */
+ SiteNotFoundException(const std::string & text, const std::string & sId = "");
+
+ // Class destructor
+ ~SiteNotFoundException() throw();
+
+ public:
+
+ /**
+ * @brief Get the id of the site that was to be found.
+ *
+ * @return The id of the site that was to be found.
+ */
+ virtual const std::string getSiteId() const;
+};
+
+} //end of namespace bpp.
+
+#endif // _SITECONTAINEREXCEPTIONS_H_
+
diff --git a/src/Bpp/Seq/Container/SiteContainerIterator.cpp b/src/Bpp/Seq/Container/SiteContainerIterator.cpp
new file mode 100644
index 0000000..fec06e7
--- /dev/null
+++ b/src/Bpp/Seq/Container/SiteContainerIterator.cpp
@@ -0,0 +1,144 @@
+//
+// File: SiteContainerIterator.cpp
+// Created by: Julien Dutheil
+// Created on: Sun Oct 19 12:47:16 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SiteContainerIterator.h"
+#include "../SiteTools.h"
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+
+using namespace std;
+
+/******************************************************************************/
+
+AbstractSiteContainerIterator::AbstractSiteContainerIterator(const SiteContainer& sites) :
+ sites_(&sites),
+ currentPosition_(0)
+{}
+
+/******************************************************************************/
+
+SimpleSiteContainerIterator::SimpleSiteContainerIterator(const SiteContainer& sites): AbstractSiteContainerIterator(sites) {}
+
+const Site* SimpleSiteContainerIterator::nextSite()
+{
+ const Site* s = &sites_->getSite(currentPosition_);
+ currentPosition_++;
+ return s;
+}
+
+bool SimpleSiteContainerIterator::hasMoreSites() const
+{
+ return currentPosition_ < static_cast<int>(sites_->getNumberOfSites());
+}
+
+/******************************************************************************/
+
+NoGapSiteContainerIterator::NoGapSiteContainerIterator(const SiteContainer& sites): AbstractSiteContainerIterator(sites)
+{
+ currentPosition_ = nextSiteWithoutGapPosition(-1);
+}
+
+const Site* NoGapSiteContainerIterator::nextSite()
+{
+ const Site* s = &sites_->getSite(currentPosition_);
+ currentPosition_ = nextSiteWithoutGapPosition(currentPosition_);
+ return s;
+}
+
+bool NoGapSiteContainerIterator::hasMoreSites() const
+{
+ return currentPosition_ < static_cast<int>(sites_->getNumberOfSites());
+}
+
+int NoGapSiteContainerIterator::nextSiteWithoutGapPosition(int current) const
+{
+ unsigned int position = current + 1;
+ while (position < sites_->getNumberOfSites() && SiteTools::hasGap(sites_->getSite(position)))
+ position++;
+ return position;
+}
+
+int NoGapSiteContainerIterator::previousSiteWithoutGapPosition(int current) const
+{
+ int position = current - 1;
+ while (position >= 0 && SiteTools::hasGap(sites_->getSite(position)))
+ position --;
+ return position;
+}
+
+/******************************************************************************/
+
+CompleteSiteContainerIterator::CompleteSiteContainerIterator(const SiteContainer & sites): AbstractSiteContainerIterator(sites)
+{
+ currentPosition_ = nextCompleteSitePosition(-1);
+}
+
+const Site* CompleteSiteContainerIterator::nextSite()
+{
+ const Site* s = &sites_->getSite(currentPosition_);
+ currentPosition_ = nextCompleteSitePosition(currentPosition_);
+ return s;
+}
+
+bool CompleteSiteContainerIterator::hasMoreSites() const
+{
+ return currentPosition_ < static_cast<int>(sites_->getNumberOfSites());
+}
+
+int CompleteSiteContainerIterator::nextCompleteSitePosition(int current) const
+{
+ unsigned int position = current + 1;
+ while (position < sites_->getNumberOfSites() && !SiteTools::isComplete(sites_->getSite(position)))
+ position ++;
+ return position;
+}
+
+int CompleteSiteContainerIterator::previousCompleteSitePosition(int current) const
+{
+ int position = current - 1;
+ while (position >= 0 && !SiteTools::isComplete(sites_->getSite(position)))
+ position --;
+ return position;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Container/SiteContainerIterator.h b/src/Bpp/Seq/Container/SiteContainerIterator.h
new file mode 100644
index 0000000..d2b1fa8
--- /dev/null
+++ b/src/Bpp/Seq/Container/SiteContainerIterator.h
@@ -0,0 +1,128 @@
+//
+// File: SiteContainerIterator.h
+// Created by: Julien Dutheil
+// Created on: Sun Oct 19 12:47:16 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SITECONTAINERITERATOR_H_
+#define _SITECONTAINERITERATOR_H_
+
+#include "../Site.h"
+#include "../SiteIterator.h"
+#include "SiteContainer.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Partial implementation of the SiteIterator interface, allowing to loop over a site container.
+ */
+class AbstractSiteContainerIterator :
+ public virtual ConstSiteIterator
+{
+ protected:
+ const SiteContainer* sites_;
+ int currentPosition_;
+
+ public:
+ AbstractSiteContainerIterator(const SiteContainer& sites);
+
+ AbstractSiteContainerIterator(const AbstractSiteContainerIterator& asi) :
+ sites_(asi.sites_),
+ currentPosition_(asi.currentPosition_) {}
+
+ AbstractSiteContainerIterator& operator=(const AbstractSiteContainerIterator& asi)
+ {
+ sites_ = asi.sites_;
+ currentPosition_ = asi.currentPosition_;
+ return *this;
+ }
+
+ virtual ~AbstractSiteContainerIterator() {}
+
+};
+
+/**
+ * @brief Loop over all sites in a SiteContainer.
+ */
+class SimpleSiteContainerIterator: public AbstractSiteContainerIterator
+{
+ public:
+ SimpleSiteContainerIterator(const SiteContainer& sites);
+ virtual ~SimpleSiteContainerIterator() {}
+
+ public:
+ const Site* nextSite();
+ bool hasMoreSites() const;
+};
+
+/**
+ * @brief Loop over all sites without gaps in a SiteContainer.
+ */
+class NoGapSiteContainerIterator: public AbstractSiteContainerIterator
+{
+ public:
+ NoGapSiteContainerIterator(const SiteContainer & sites);
+ virtual ~NoGapSiteContainerIterator() {}
+
+ public:
+ const Site* nextSite();
+ bool hasMoreSites() const;
+ int nextSiteWithoutGapPosition(int current) const;
+ int previousSiteWithoutGapPosition(int current) const;
+};
+
+/**
+ * @brief Loop over all complete sites in a SiteContainer
+ * (i.e. sites without gap and unresolved characters).
+ */
+class CompleteSiteContainerIterator: public AbstractSiteContainerIterator
+{
+ public:
+ CompleteSiteContainerIterator(const SiteContainer & sites);
+ virtual ~CompleteSiteContainerIterator() {}
+
+ public:
+ const Site * nextSite();
+ bool hasMoreSites() const;
+ int nextCompleteSitePosition(int current) const;
+ int previousCompleteSitePosition(int current) const;
+};
+
+} //end of namespace bpp.
+
+#endif //_SITEITERATOR_H_
+
diff --git a/src/Bpp/Seq/Container/SiteContainerTools.cpp b/src/Bpp/Seq/Container/SiteContainerTools.cpp
new file mode 100644
index 0000000..386cb3a
--- /dev/null
+++ b/src/Bpp/Seq/Container/SiteContainerTools.cpp
@@ -0,0 +1,1050 @@
+//
+// File: SiteContainerTools.cpp
+// Created by: Julien Dutheil
+// Sylvain Glémin
+// Created on: Fri Dec 12 18:55:06 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "SiteContainerTools.h"
+#include "SequenceContainerTools.h"
+#include "VectorSiteContainer.h"
+#include "SiteContainerIterator.h"
+#include "../SiteTools.h"
+#include "../Alphabet/AlphabetTools.h"
+#include "../SequenceTools.h"
+#include <Bpp/App/ApplicationTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <vector>
+#include <deque>
+#include <string>
+
+using namespace std;
+
+/******************************************************************************/
+
+SiteContainer* SiteContainerTools::getSitesWithoutGaps(const SiteContainer& sites)
+{
+ vector<string> seqNames = sites.getSequencesNames();
+ VectorSiteContainer* noGapCont = new VectorSiteContainer(seqNames.size(), sites.getAlphabet());
+ noGapCont->setSequencesNames(seqNames, false);
+ NoGapSiteContainerIterator ngsi(sites);
+ while (ngsi.hasMoreSites())
+ {
+ noGapCont->addSite(*ngsi.nextSite());
+ }
+ return noGapCont;
+}
+
+/******************************************************************************/
+
+SiteContainer* SiteContainerTools::getCompleteSites(const SiteContainer& sites)
+{
+ vector<string> seqNames = sites.getSequencesNames();
+ VectorSiteContainer* noGapCont = new VectorSiteContainer(seqNames.size(), sites.getAlphabet());
+ noGapCont->setSequencesNames(seqNames, false);
+ CompleteSiteContainerIterator csi(sites);
+ while (csi.hasMoreSites())
+ {
+ noGapCont->addSite(*csi.nextSite());
+ }
+ return noGapCont;
+}
+
+/******************************************************************************/
+
+SiteContainer* SiteContainerTools::getSelectedSites(
+ const SiteContainer& sequences,
+ const SiteSelection& selection)
+{
+ vector<string> seqNames = sequences.getSequencesNames();
+ VectorSiteContainer* sc = new VectorSiteContainer(seqNames.size(), sequences.getAlphabet());
+ sc->setSequencesNames(seqNames, false);
+ for (unsigned int i = 0; i < selection.size(); i++)
+ {
+ sc->addSite(sequences.getSite(selection[i]), false);
+ // We do not check names, we suppose that the container passed as an argument is correct.
+ // WARNING: what if selection contains many times the same indice? ...
+ }
+ sc->setGeneralComments(sequences.getGeneralComments());
+ return sc;
+}
+
+/******************************************************************************/
+
+const Sequence* SiteContainerTools::getConsensus(const SiteContainer& sc, const std::string& name, bool ignoreGap, bool resolveUnknown)
+{
+ Vint consensus;
+ SimpleSiteContainerIterator ssi(sc);
+ const Site* site;
+ while (ssi.hasMoreSites())
+ {
+ site = ssi.nextSite();
+ map<int, double> freq;
+ SiteTools::getFrequencies(*site, freq, resolveUnknown);
+ double max = 0;
+ int cons = -1; // default result
+ if (ignoreGap)
+ {
+ for (map<int, double>::iterator it = freq.begin(); it != freq.end(); it++)
+ {
+ if (it->second > max && it->first != -1)
+ {
+ max = it->second;
+ cons = it->first;
+ }
+ }
+ }
+ else
+ {
+ for (map<int, double>::iterator it = freq.begin(); it != freq.end(); it++)
+ {
+ if (it->second > max)
+ {
+ max = it->second;
+ cons = it->first;
+ }
+ }
+ }
+ consensus.push_back(cons);
+ }
+ const Sequence* seqConsensus = new BasicSequence(name, consensus, sc.getAlphabet());
+ return seqConsensus;
+}
+
+/******************************************************************************/
+
+void SiteContainerTools::changeGapsToUnknownCharacters(SiteContainer& sites)
+{
+ // NB: use iterators for a better algorithm?
+ int unknownCode = sites.getAlphabet()->getUnknownCharacterCode();
+ for (unsigned int i = 0; i < sites.getNumberOfSites(); i++)
+ {
+ for (unsigned int j = 0; j < sites.getNumberOfSequences(); j++)
+ {
+ int* element = &sites(j, i);
+ if (sites.getAlphabet()->isGap(*element))
+ *element = unknownCode;
+ }
+ }
+}
+
+/******************************************************************************/
+
+void SiteContainerTools::changeUnresolvedCharactersToGaps(SiteContainer& sites)
+{
+ // NB: use iterators for a better algorithm?
+ int gapCode = sites.getAlphabet()->getGapCharacterCode();
+ for (unsigned int i = 0; i < sites.getNumberOfSites(); i++)
+ {
+ for (unsigned int j = 0; j < sites.getNumberOfSequences(); j++)
+ {
+ int* element = &sites(j, i);
+ if (sites.getAlphabet()->isUnresolved(*element))
+ *element = gapCode;
+ }
+ }
+}
+
+/******************************************************************************/
+
+SiteContainer* SiteContainerTools::removeGapOnlySites(const SiteContainer& sites)
+{
+ vector<string> seqNames = sites.getSequencesNames();
+ VectorSiteContainer* noGapCont = new VectorSiteContainer(seqNames.size(), sites.getAlphabet());
+ noGapCont->setSequencesNames(seqNames, false);
+ for (unsigned int i = 0; i < sites.getNumberOfSites(); i++)
+ {
+ const Site* site = &sites.getSite(i);
+ if (!SiteTools::isGapOnly(*site))
+ noGapCont->addSite(*site);
+ }
+ return noGapCont;
+}
+
+/******************************************************************************/
+
+void SiteContainerTools::removeGapOnlySites(SiteContainer& sites)
+{
+ size_t n = sites.getNumberOfSites();
+ size_t i = n;
+ while (i > 1)
+ {
+ ApplicationTools::displayGauge(n - i + 1, n);
+ const Site* site = &sites.getSite(i - 1);
+ if (SiteTools::isGapOnly(*site))
+ {
+ size_t end = i;
+ while (SiteTools::isGapOnly(*site) && i > 1)
+ {
+ --i;
+ site = &sites.getSite(i - 1);
+ }
+ sites.deleteSites(i, end - i);
+ }
+ else
+ {
+ --i;
+ }
+ }
+ ApplicationTools::displayGauge(n, n);
+ const Site* site = &sites.getSite(0);
+ if (SiteTools::isGapOnly(*site))
+ sites.deleteSite(0);
+}
+
+/******************************************************************************/
+
+SiteContainer* SiteContainerTools::removeGapOrUnresolvedOnlySites(const SiteContainer& sites)
+{
+ vector<string> seqNames = sites.getSequencesNames();
+ VectorSiteContainer* noGapCont = new VectorSiteContainer(seqNames.size(), sites.getAlphabet());
+ noGapCont->setSequencesNames(seqNames, false);
+ for (unsigned int i = 0; i < sites.getNumberOfSites(); i++)
+ {
+ const Site* site = &sites.getSite(i);
+ if (!SiteTools::isGapOrUnresolvedOnly(*site))
+ noGapCont->addSite(*site, false);
+ }
+ return noGapCont;
+}
+
+/******************************************************************************/
+
+void SiteContainerTools::removeGapOrUnresolvedOnlySites(SiteContainer& sites)
+{
+ size_t n = sites.getNumberOfSites();
+ size_t i = n;
+ while (i > 1)
+ {
+ ApplicationTools::displayGauge(n - i + 1, n);
+ const Site* site = &sites.getSite(i - 1);
+ if (SiteTools::isGapOnly(*site))
+ {
+ size_t end = i;
+ while (SiteTools::isGapOrUnresolvedOnly(*site) && i > 1)
+ {
+ --i;
+ site = &sites.getSite(i - 1);
+ }
+ sites.deleteSites(i, end - i);
+ }
+ else
+ {
+ --i;
+ }
+ }
+ ApplicationTools::displayGauge(n, n);
+ const Site* site = &sites.getSite(0);
+ if (SiteTools::isGapOrUnresolvedOnly(*site))
+ sites.deleteSite(0);
+}
+
+/******************************************************************************/
+
+SiteContainer* SiteContainerTools::removeGapSites(const SiteContainer& sites, double maxFreqGaps)
+{
+ vector<string> seqNames = sites.getSequencesNames();
+ VectorSiteContainer* noGapCont = new VectorSiteContainer(seqNames.size(), sites.getAlphabet());
+ noGapCont->setSequencesNames(seqNames, false);
+ for (unsigned int i = 0; i < sites.getNumberOfSites(); ++i) {
+ map<int, double> freq;
+ SiteTools::getFrequencies(sites.getSite(i), freq);
+ if (freq[-1] <= maxFreqGaps)
+ noGapCont->addSite(sites.getSite(i), false);
+ }
+ return noGapCont;
+}
+
+/******************************************************************************/
+
+void SiteContainerTools::removeGapSites(SiteContainer& sites, double maxFreqGaps)
+{
+ for (size_t i = sites.getNumberOfSites(); i > 0; i--) {
+ map<int, double> freq;
+ SiteTools::getFrequencies(sites.getSite(i - 1), freq);
+ if (freq[-1] > maxFreqGaps)
+ sites.deleteSite(i - 1);
+ }
+}
+
+/******************************************************************************/
+
+SiteContainer* SiteContainerTools::removeStopCodonSites(const SiteContainer& sites) throw (AlphabetException)
+{
+ const CodonAlphabet* pca = dynamic_cast<const CodonAlphabet*>(sites.getAlphabet());
+ if (!pca)
+ throw AlphabetException("Not a Codon Alphabet", sites.getAlphabet());
+ vector<string> seqNames = sites.getSequencesNames();
+ VectorSiteContainer* noStopCont = new VectorSiteContainer(seqNames.size(), sites.getAlphabet());
+ noStopCont->setSequencesNames(seqNames, false);
+ for (unsigned int i = 0; i < sites.getNumberOfSites(); i++)
+ {
+ const Site* site = &sites.getSite(i);
+ if (!SiteTools::hasStopCodon(*site))
+ noStopCont->addSite(*site, false);
+ }
+ return noStopCont;
+}
+
+/******************************************************************************/
+
+SiteContainer* SiteContainerTools::resolveDottedAlignment(
+ const SiteContainer& dottedAln,
+ const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception)
+{
+ if (!AlphabetTools::isDefaultAlphabet(dottedAln.getAlphabet()))
+ throw AlphabetException("SiteContainerTools::resolveDottedAlignment. Alignment alphabet should of class 'DefaultAlphabet'.", dottedAln.getAlphabet());
+
+ // First we look for the reference sequence:
+ size_t n = dottedAln.getNumberOfSequences();
+ if (n == 0)
+ throw Exception("SiteContainerTools::resolveDottedAlignment. Input alignment contains no sequence.");
+
+ const Sequence* refSeq = 0;
+ for (size_t i = 0; i < n; ++i) // Test each sequence
+ {
+ const Sequence* seq = &dottedAln.getSequence(i);
+ bool isRef = true;
+ for (unsigned int j = 0; isRef && j < seq->size(); ++j) // For each site in the sequence
+ {
+ if (seq->getChar(j) == ".")
+ isRef = false;
+ }
+ if (isRef) // We found the reference sequence!
+ {
+ refSeq = new BasicSequence(*seq);
+ }
+ }
+ if (!refSeq)
+ throw Exception("SiteContainerTools::resolveDottedAlignment. No reference sequence was found in the input alignment.");
+
+ // Now we build a new VectorSiteContainer:
+ VectorSiteContainer* sites = new VectorSiteContainer(n, resolvedAlphabet);
+
+ // We add each site one by one:
+ size_t m = dottedAln.getNumberOfSites();
+ string state;
+ for (unsigned int i = 0; i < m; ++i)
+ {
+ string resolved = refSeq->getChar(i);
+ const Site* site = &dottedAln.getSite(i);
+ Site resolvedSite(resolvedAlphabet, site->getPosition());
+ for (unsigned int j = 0; j < n; j++)
+ {
+ state = site->getChar(j);
+ if (state == ".")
+ {
+ state = resolved;
+ }
+ resolvedSite.addElement(state);
+ }
+ // Add the new site:
+ sites->addSite(resolvedSite);
+ }
+
+ // Seq sequence names:
+ sites->setSequencesNames(dottedAln.getSequencesNames());
+
+ // Delete the copied sequence:
+ delete refSeq;
+
+ // Return result:
+ return sites;
+}
+
+/******************************************************************************/
+
+std::map<size_t, size_t> SiteContainerTools::getSequencePositions(const Sequence& seq)
+{
+ map<size_t, size_t> tln;
+ if (seq.size() == 0)
+ return tln;
+ unsigned int count = 0;
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ if (seq[i] != -1)
+ {
+ count++;
+ tln[i + 1] = count;
+ }
+ }
+ return tln;
+}
+
+/******************************************************************************/
+
+std::map<size_t, size_t> SiteContainerTools::getAlignmentPositions(const Sequence& seq)
+{
+ map<size_t, size_t> tln;
+ if (seq.size() == 0)
+ return tln;
+ unsigned int count = 0;
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ if (seq[i] != -1)
+ {
+ count++;
+ tln[count] = i + 1;
+ }
+ }
+ return tln;
+}
+
+/******************************************************************************/
+
+std::map<size_t, size_t> SiteContainerTools::translateAlignment(const Sequence& seq1, const Sequence& seq2)
+throw (AlphabetMismatchException, Exception)
+{
+ if (seq1.getAlphabet()->getAlphabetType() != seq2.getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("SiteContainerTools::translateAlignment", seq1.getAlphabet(), seq2.getAlphabet());
+ map<size_t, size_t> tln;
+ if (seq1.size() == 0)
+ return tln;
+ unsigned int count1 = 0;
+ unsigned int count2 = 0;
+ if (seq2.size() == 0)
+ throw Exception("SiteContainerTools::translateAlignment. Sequences do not match at position " + TextTools::toString(count1 + 1) + " and " + TextTools::toString(count2 + 1) + ".");
+ int state1 = seq1[count1];
+ int state2 = seq2[count2];
+ bool end = false;
+ while (!end)
+ {
+ while (state1 == -1)
+ {
+ count1++;
+ if (count1 < seq1.size())
+ state1 = seq1[count1];
+ else
+ break;
+ }
+ while (state2 == -1)
+ {
+ count2++;
+ if (count2 < seq2.size())
+ state2 = seq2[count2];
+ else
+ break;
+ }
+ if (state1 != state2)
+ throw Exception("SiteContainerTools::translateAlignment. Sequences do not match at position " + TextTools::toString(count1 + 1) + " and " + TextTools::toString(count2 + 1) + ".");
+ tln[count1 + 1] = count2 + 1; // Count start at 1
+ if (count1 == seq1.size() - 1)
+ end = true;
+ else
+ {
+ if (count2 == seq2.size() - 1)
+ {
+ state1 = seq1[++count1];
+ while (state1 == -1)
+ {
+ count1++;
+ if (count1 < seq1.size())
+ state1 = seq1[count1];
+ else
+ break;
+ }
+ if (state1 == -1)
+ end = true;
+ else
+ throw Exception("SiteContainerTools::translateAlignment. Sequences do not match at position " + TextTools::toString(count1 + 1) + " and " + TextTools::toString(count2 + 1) + ".");
+ }
+ else
+ {
+ state1 = seq1[++count1];
+ state2 = seq2[++count2];
+ }
+ }
+ }
+ return tln;
+}
+
+/******************************************************************************/
+
+std::map<size_t, size_t> SiteContainerTools::translateSequence(const SiteContainer& sequences, size_t i1, size_t i2)
+{
+ const Sequence* seq1 = &sequences.getSequence(i1);
+ const Sequence* seq2 = &sequences.getSequence(i2);
+ map<size_t, size_t> tln;
+ size_t count1 = 0; // Sequence 1 counter
+ size_t count2 = 0; // Sequence 2 counter
+ int state1;
+ int state2;
+ for (size_t i = 0; i < sequences.getNumberOfSites(); i++)
+ {
+ state1 = (*seq1)[i];
+ if (state1 != -1)
+ count1++;
+ state2 = (*seq2)[i];
+ if (state2 != -1)
+ count2++;
+ if (state1 != -1)
+ {
+ tln[count1] = (state2 == -1 ? 0 : count2);
+ }
+ }
+ return tln;
+}
+
+/******************************************************************************/
+
+AlignedSequenceContainer* SiteContainerTools::alignNW(
+ const Sequence& seq1,
+ const Sequence& seq2,
+ const AlphabetIndex2& s,
+ double gap)
+throw (AlphabetMismatchException)
+{
+ if (seq1.getAlphabet()->getAlphabetType() != seq2.getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("SiteContainerTools::alignNW", seq1.getAlphabet(), seq2.getAlphabet());
+ if (seq1.getAlphabet()->getAlphabetType() != s.getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("SiteContainerTools::alignNW", seq1.getAlphabet(), s.getAlphabet());
+ // Check that sequences have no gap!
+ auto_ptr<Sequence> s1(seq1.clone());
+ SequenceTools::removeGaps(*s1);
+ auto_ptr<Sequence> s2(seq2.clone());
+ SequenceTools::removeGaps(*s2);
+
+ // 1) Initialize matrix:
+ RowMatrix<double> m(s1->size() + 1, s2->size() + 1);
+ RowMatrix<char> p(s1->size(), s2->size());
+ double choice1, choice2, choice3, mx;
+ char px;
+ for (size_t i = 0; i <= s1->size(); i++)
+ {
+ m(i, 0) = static_cast<double>(i) * gap;
+ }
+ for (size_t j = 0; j <= s2->size(); j++)
+ {
+ m(0, j) = static_cast<double>(j) * gap;
+ }
+ for (size_t i = 1; i <= s1->size(); i++)
+ {
+ for (size_t j = 1; j <= s2->size(); j++)
+ {
+ choice1 = m(i - 1, j - 1) + static_cast<double>(s.getIndex((*s1)[i - 1], (*s2)[j - 1]));
+ choice2 = m(i - 1, j) + gap;
+ choice3 = m(i, j - 1) + gap;
+ mx = choice1; px = 'd'; // Default in case of equality of scores.
+ if (choice2 > mx)
+ {
+ mx = choice2; px = 'u';
+ }
+ if (choice3 > mx)
+ {
+ mx = choice3; px = 'l';
+ }
+ m(i, j) = mx;
+ p(i - 1, j - 1) = px;
+ }
+ }
+
+ // 2) Get alignment:
+ deque<int> a1, a2;
+ size_t i = s1->size(), j = s2->size();
+ char c;
+ while (i > 0 && j > 0)
+ {
+ c = p(i - 1, j - 1);
+ if (c == 'd')
+ {
+ a1.push_front((*s1)[i - 1]);
+ a2.push_front((*s2)[j - 1]);
+ i--;
+ j--;
+ }
+ else if (c == 'u')
+ {
+ a1.push_front((*s1)[i - 1]);
+ a2.push_front(-1);
+ i--;
+ }
+ else
+ {
+ a1.push_front(-1);
+ a2.push_front((*s2)[j - 1]);
+ j--;
+ }
+ }
+ while (i > 0)
+ {
+ a1.push_front((*s1)[i - 1]);
+ a2.push_front(-1);
+ i--;
+ }
+ while (j > 0)
+ {
+ a1.push_front(-1);
+ a2.push_front((*s2)[j - 1]);
+ j--;
+ }
+ s1->setContent(vector<int>(a1.begin(), a1.end()));
+ s2->setContent(vector<int>(a2.begin(), a2.end()));
+ AlignedSequenceContainer* asc = new AlignedSequenceContainer(s1->getAlphabet());
+ asc->addSequence(*s1, false);
+ asc->addSequence(*s2, false); // Do not check for sequence names.
+ return asc;
+}
+
+/******************************************************************************/
+
+AlignedSequenceContainer* SiteContainerTools::alignNW(
+ const Sequence& seq1,
+ const Sequence& seq2,
+ const AlphabetIndex2& s,
+ double opening,
+ double extending)
+throw (AlphabetMismatchException)
+{
+ if (seq1.getAlphabet()->getAlphabetType() != seq2.getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("SiteContainerTools::alignNW", seq1.getAlphabet(), seq2.getAlphabet());
+ if (seq1.getAlphabet()->getAlphabetType() != s.getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("SiteContainerTools::alignNW", seq1.getAlphabet(), s.getAlphabet());
+ // Check that sequences have no gap!
+ auto_ptr<Sequence> s1(seq1.clone());
+ SequenceTools::removeGaps(*s1);
+ auto_ptr<Sequence> s2(seq2.clone());
+ SequenceTools::removeGaps(*s2);
+
+ // 1) Initialize matrix:
+ RowMatrix<double> m(s1->size() + 1, s2->size() + 1);
+ RowMatrix<double> v(s1->size() + 1, s2->size() + 1);
+ RowMatrix<double> h(s1->size() + 1, s2->size() + 1);
+ RowMatrix<char> p(s1->size(), s2->size());
+
+ double choice1, choice2, choice3, mx;
+ char px;
+ m(0, 0) = 0.;
+ for (size_t i = 0; i <= s1->size(); i++)
+ {
+ v(i, 0) = log(0.);
+ }
+ for (size_t j = 0; j <= s2->size(); j++)
+ {
+ h(0, j) = log(0.);
+ }
+ for (size_t i = 1; i <= s1->size(); i++)
+ {
+ m(i, 0) = h(i, 0) = opening + static_cast<double>(i) * extending;
+ }
+ for (size_t j = 1; j <= s2->size(); j++)
+ {
+ m(0, j) = v(0, j) = opening + static_cast<double>(j) * extending;
+ }
+
+ for (size_t i = 1; i <= s1->size(); i++)
+ {
+ for (size_t j = 1; j <= s2->size(); j++)
+ {
+ choice1 = m(i - 1, j - 1) + s.getIndex((*s1)[i - 1], (*s2)[j - 1]);
+ choice2 = h(i - 1, j - 1) + opening + extending;
+ choice3 = v(i - 1, j - 1) + opening + extending;
+ mx = choice1; // Default in case of equality of scores.
+ if (choice2 > mx)
+ {
+ mx = choice2;
+ }
+ if (choice3 > mx)
+ {
+ mx = choice3;
+ }
+ m(i, j) = mx;
+
+ choice1 = m(i, j - 1) + opening + extending;
+ choice2 = h(i, j - 1) + extending;
+ mx = choice1; // Default in case of equality of scores.
+ if (choice2 > mx)
+ {
+ mx = choice2;
+ }
+ h(i, j) = mx;
+
+ choice1 = m(i - 1, j) + opening + extending;
+ choice2 = v(i - 1, j) + extending;
+ mx = choice1; // Default in case of equality of scores.
+ if (choice2 > mx)
+ {
+ mx = choice2;
+ }
+ v(i, j) = mx;
+
+ px = 'd';
+ if (v(i, j) > m(i, j))
+ px = 'u';
+ if (h(i, j) > m(i, j))
+ px = 'l';
+ p(i - 1, j - 1) = px;
+ }
+ }
+
+ // 2) Get alignment:
+ deque<int> a1, a2;
+ size_t i = s1->size(), j = s2->size();
+ char c;
+ while (i > 0 && j > 0)
+ {
+ c = p(i - 1, j - 1);
+ if (c == 'd')
+ {
+ a1.push_front((*s1)[i - 1]);
+ a2.push_front((*s2)[j - 1]);
+ i--;
+ j--;
+ }
+ else if (c == 'u')
+ {
+ a1.push_front((*s1)[i - 1]);
+ a2.push_front(-1);
+ i--;
+ }
+ else
+ {
+ a1.push_front(-1);
+ a2.push_front((*s2)[j - 1]);
+ j--;
+ }
+ }
+ while (i > 0)
+ {
+ a1.push_front((*s1)[i - 1]);
+ a2.push_front(-1);
+ i--;
+ }
+ while (j > 0)
+ {
+ a1.push_front(-1);
+ a2.push_front((*s2)[j - 1]);
+ j--;
+ }
+ s1->setContent(vector<int>(a1.begin(), a1.end()));
+ s2->setContent(vector<int>(a2.begin(), a2.end()));
+ AlignedSequenceContainer* asc = new AlignedSequenceContainer(s1->getAlphabet());
+ asc->addSequence(*s1, false);
+ asc->addSequence(*s2, false); // Do not check for sequence names.
+ return asc;
+}
+
+/******************************************************************************/
+
+VectorSiteContainer* SiteContainerTools::sampleSites(const SiteContainer& sites, size_t nbSites, vector<size_t>* index)
+{
+ VectorSiteContainer* sample = new VectorSiteContainer(sites.getSequencesNames(), sites.getAlphabet());
+ for (size_t i = 0; i < nbSites; i++)
+ {
+ size_t pos = static_cast<size_t>(RandomTools::giveIntRandomNumberBetweenZeroAndEntry(static_cast<int>(sites.getNumberOfSites())));
+ sample->addSite(sites.getSite(pos), false);
+ if (index)
+ index->push_back(pos);
+ }
+ return sample;
+}
+
+/******************************************************************************/
+
+VectorSiteContainer* SiteContainerTools::bootstrapSites(const SiteContainer& sites)
+{
+ return sampleSites(sites, sites.getNumberOfSites());
+}
+
+/******************************************************************************/
+
+const string SiteContainerTools::SIMILARITY_ALL = "all sites";
+const string SiteContainerTools::SIMILARITY_NOFULLGAP = "no full gap";
+const string SiteContainerTools::SIMILARITY_NODOUBLEGAP = "no double gap";
+const string SiteContainerTools::SIMILARITY_NOGAP = "no gap";
+
+/******************************************************************************/
+
+double SiteContainerTools::computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist, const std::string& gapOption, bool unresolvedAsGap) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception)
+{
+ if (seq1.size() != seq2.size())
+ throw SequenceNotAlignedException("SiteContainerTools::computeSimilarity.", &seq2);
+ if (seq1.getAlphabet()->getAlphabetType() != seq2.getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("SiteContainerTools::computeSimilarity.", seq1.getAlphabet(), seq2.getAlphabet());
+
+ const Alphabet* alpha = seq1.getAlphabet();
+ unsigned int s = 0;
+ unsigned int t = 0;
+ for (size_t i = 0; i < seq1.size(); i++)
+ {
+ int x = seq1[i];
+ int y = seq2[i];
+ int gapCode = alpha->getGapCharacterCode();
+ if (unresolvedAsGap)
+ {
+ if (alpha->isUnresolved(x))
+ x = gapCode;
+ if (alpha->isUnresolved(y))
+ y = gapCode;
+ }
+ if (gapOption == SIMILARITY_ALL)
+ {
+ t++;
+ if (x == y && !alpha->isGap(x) && !alpha->isGap(y))
+ s++;
+ }
+ else if (gapOption == SIMILARITY_NODOUBLEGAP)
+ {
+ if (!alpha->isGap(x) || !alpha->isGap(y))
+ {
+ t++;
+ if (x == y)
+ s++;
+ }
+ }
+ else if (gapOption == SIMILARITY_NOGAP)
+ {
+ if (!alpha->isGap(x) && !alpha->isGap(y))
+ {
+ t++;
+ if (x == y)
+ s++;
+ }
+ }
+ else
+ throw Exception("SiteContainerTools::computeSimilarity. Invalid gap option: " + gapOption);
+ }
+ double r = (t == 0 ? 0. : static_cast<double>(s) / static_cast<double>(t));
+ return dist ? 1 - r : r;
+}
+
+/******************************************************************************/
+
+DistanceMatrix* SiteContainerTools::computeSimilarityMatrix(const SiteContainer& sites, bool dist, const std::string& gapOption, bool unresolvedAsGap)
+{
+ size_t n = sites.getNumberOfSequences();
+ DistanceMatrix* mat = new DistanceMatrix(sites.getSequencesNames());
+ string pairwiseGapOption = gapOption;
+ SiteContainer* sites2;
+ if (gapOption == SIMILARITY_NOFULLGAP)
+ {
+ if (unresolvedAsGap)
+ {
+ SiteContainer* tmp = removeGapOrUnresolvedOnlySites(sites);
+ sites2 = new AlignedSequenceContainer(*tmp);
+ delete tmp;
+ }
+ else
+ {
+ SiteContainer* tmp = removeGapOnlySites(sites);
+ sites2 = new AlignedSequenceContainer(*tmp);
+ delete tmp;
+ }
+ pairwiseGapOption = SIMILARITY_ALL;
+ }
+ else
+ {
+ sites2 = new AlignedSequenceContainer(sites);
+ }
+
+ for (size_t i = 0; i < n; i++)
+ {
+ (*mat)(i, i) = dist ? 0. : 1.;
+ const Sequence* seq1 = &sites2->getSequence(i);
+ for (size_t j = i + 1; j < n; j++)
+ {
+ const Sequence* seq2 = &sites2->getSequence(j);
+ (*mat)(i, j) = (*mat)(j, i) = computeSimilarity(*seq1, *seq2, dist, pairwiseGapOption, unresolvedAsGap);
+ }
+ }
+ delete sites2;
+ return mat;
+}
+
+/******************************************************************************/
+
+void SiteContainerTools::merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs)
+throw (AlphabetMismatchException, Exception)
+{
+ if (seqCont1.getAlphabet()->getAlphabetType() != seqCont2.getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("SiteContainerTools::merge.", seqCont1.getAlphabet(), seqCont2.getAlphabet());
+
+
+ vector<string> seqNames1 = seqCont1.getSequencesNames();
+ vector<string> seqNames2 = seqCont2.getSequencesNames();
+ const SiteContainer* seqCont2bis = 0;
+ bool del = false;
+ if (seqNames1 == seqNames2)
+ {
+ seqCont2bis = &seqCont2;
+ }
+ else
+ {
+ // We shall reorder sequences first:
+ SiteContainer* seqCont2ter = new VectorSiteContainer(seqCont2.getAlphabet());
+ SequenceContainerTools::getSelectedSequences(seqCont2, seqNames1, *seqCont2ter);
+ seqCont2bis = seqCont2ter;
+ del = true;
+ }
+
+ if (leavePositionAsIs)
+ {
+ for (size_t i = 0; i < seqCont2bis->getNumberOfSites(); i++)
+ {
+ seqCont1.addSite(seqCont2bis->getSite(i), false);
+ }
+ }
+ else
+ {
+ int offset = static_cast<int>(seqCont1.getNumberOfSites());
+ for (size_t i = 0; i < seqCont2bis->getNumberOfSites(); i++)
+ {
+ seqCont1.addSite(seqCont2bis->getSite(i), offset + seqCont2bis->getSite(i).getPosition(), false);
+ }
+ }
+
+ if (del)
+ delete seqCont2bis;
+}
+
+/******************************************************************************/
+
+void SiteContainerTools::getSequencePositions(const SiteContainer& sites, Matrix<size_t>& positions)
+{
+ positions.resize(sites.getNumberOfSequences(), sites.getNumberOfSites());
+ int gap = sites.getAlphabet()->getGapCharacterCode();
+ for (size_t i = 0; i < sites.getNumberOfSequences(); ++i) {
+ const Sequence& seq = sites.getSequence(i);
+ unsigned int pos = 0;
+ for (size_t j = 0; j < sites.getNumberOfSites(); ++j) {
+ if (seq[j] != gap) {
+ ++pos;
+ positions(i, j) = pos;
+ } else {
+ positions(i, j) = 0;
+ }
+ }
+ }
+}
+
+/******************************************************************************/
+
+vector<int> SiteContainerTools::getColumnScores(const Matrix<size_t>& positions1, const Matrix<size_t>& positions2, int na)
+{
+ if (positions1.getNumberOfRows() != positions2.getNumberOfRows())
+ throw Exception("SiteContainerTools::getColumnScores. The two input alignments must have the same number of sequences!");
+ vector<int> scores(positions1.getNumberOfColumns());
+ for (size_t i = 0; i < positions1.getNumberOfColumns(); ++i) {
+ //Find an anchor point:
+ size_t whichSeq = 0;
+ size_t whichPos = 0;
+ for (size_t j = 0; j < positions1.getNumberOfRows(); ++j) {
+ if (positions1(j, i) > 0) {
+ whichSeq = j;
+ whichPos = positions1(j, i);
+ break;
+ }
+ }
+ if (whichPos == 0) {
+ //No anchor found, this alignment column is only made of gaps. We assign a score of 'na' and move to the next column.
+ scores[i] = na;
+ continue;
+ }
+ //We look for the anchor in the reference alignment:
+ size_t i2 = 0;
+ bool found = false;
+ for (size_t j = 0; !found && j < positions2.getNumberOfColumns(); ++j) {
+ if (positions2(whichSeq, j) == whichPos) {
+ i2 = j;
+ found = true;
+ }
+ }
+ if (!found) {
+ throw Exception("SiteContainerTools::getColumnScores(). Position " + TextTools::toString(whichPos) + " of sequence " + TextTools::toString(whichSeq) + " not found in reference alignment. Please make sure the two indexes are built from the same data!");
+ }
+ //Now we compare all pairs of sequences between the two positions:
+ bool test = true;
+ for (size_t j = 0; test && j < positions1.getNumberOfRows(); ++j) {
+ test = (positions1(j, i) == positions2(j, i2));
+ }
+ scores[i] = test ? 1 : 0;
+ }
+ return scores;
+}
+
+/******************************************************************************/
+
+vector<double> SiteContainerTools::getSumOfPairsScores(const Matrix<size_t>& positions1, const Matrix<size_t>& positions2, double na)
+{
+ if (positions1.getNumberOfRows() != positions2.getNumberOfRows())
+ throw Exception("SiteContainerTools::getColumnScores. The two input alignments must have the same number of sequences!");
+ vector<double> scores(positions1.getNumberOfColumns());
+ for (size_t i = 0; i < positions1.getNumberOfColumns(); ++i) {
+ //For all positions in alignment 1...
+ size_t countAlignable = 0;
+ size_t countAligned = 0;
+ for (size_t j = 0; j < positions1.getNumberOfRows(); ++j) {
+ //Get the corresponding column in alignment 2:
+ size_t whichPos = positions1(j, i);
+ if (whichPos == 0) {
+ //No position for this sequence here.
+ continue;
+ }
+ //We look for the position in the second alignment:
+ size_t i2 = 0;
+ bool found = false;
+ for (size_t k = 0; !found && k < positions2.getNumberOfColumns(); ++k) {
+ if (positions2(j, k) == whichPos) {
+ i2 = k;
+ found = true;
+ }
+ }
+ if (!found) {
+ throw Exception("SiteContainerTools::getColumnScores(). Position " + TextTools::toString(whichPos) + " of sequence " + TextTools::toString(j) + " not found in reference alignment. Please make sure the two indexes are built from the same data!");
+ }
+
+ //Now we check all other positions and see if they are aligned with this one:
+ for (size_t k = j + 1; k < positions1.getNumberOfRows(); ++k) {
+ size_t whichPos2 = positions1(k, i);
+ if (whichPos2 == 0) {
+ //Empty position
+ continue;
+ }
+ countAlignable++;
+ //check position in alignment 2:
+ if (positions2(k, i2) == whichPos2)
+ countAligned++;
+ }
+ }
+ scores[i] = countAlignable == 0 ? na : static_cast<double>(countAligned) / static_cast<double>(countAlignable);
+ }
+ return scores;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Container/SiteContainerTools.h b/src/Bpp/Seq/Container/SiteContainerTools.h
new file mode 100644
index 0000000..3f3f391
--- /dev/null
+++ b/src/Bpp/Seq/Container/SiteContainerTools.h
@@ -0,0 +1,474 @@
+//
+// File: SiteContainerTools.h
+// Created by: Julien Dutheil
+// Created on: Fri Dec 12 18:55:06 2003
+//
+
+#ifndef _SITECONTAINERTOOLS_H_
+#define _SITECONTAINERTOOLS_H_
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "SiteContainer.h"
+#include "VectorSiteContainer.h"
+#include "AlignedSequenceContainer.h"
+#include "../AlphabetIndex/AlphabetIndex2.h"
+#include "../DistanceMatrix.h"
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+//From the STL:
+#include <vector>
+#include <map>
+
+namespace bpp
+{
+
+typedef std::vector<size_t> SiteSelection;
+
+/**
+ * @brief Some utililitary methods to deal with site containers.
+ */
+class SiteContainerTools
+{
+ public:
+ SiteContainerTools() {}
+ virtual ~SiteContainerTools() {}
+
+ public:
+
+ /**
+ * @brief Retrieves sites without gaps from SiteContainer.
+ *
+ * This function build a new SiteContainer instance with only sites without gaps.
+ * The container passed as input is not modified, all sites are copied.
+ *
+ * @param sites The container to analyse.
+ * @return A pointer toward a new SiteContainer with only sites with no gaps.
+ */
+ static SiteContainer* getSitesWithoutGaps(const SiteContainer& sites);
+
+ /**
+ * @brief Retrieves complete sites from SiteContainer.
+ *
+ * This function build a new SiteContainer instance with only complete sites,
+ * i.e. site with fully resolved states (no gap, no unknown caracters).
+ * The container passed as input is not modified, all sites are copied.
+ *
+ * @param sites The container to analyse.
+ * @return A pointer toward a new SiteContainer with only complete sites.
+ */
+ static SiteContainer* getCompleteSites(const SiteContainer& sites);
+
+ /**
+ * @brief Get a site set without gap-only sites.
+ *
+ * This function build a new SiteContainer instance without sites with only gaps.
+ * The container passed as input is not modified, all sites are copied.
+ *
+ * @see removeGapOnlySites(SiteContainer& sites)
+ * @param sites The container to analyse.
+ * @return A pointer toward a new SiteContainer.
+ */
+ static SiteContainer* removeGapOnlySites(const SiteContainer& sites);
+
+ /**
+ * @brief Remove gap-only sites from a site set.
+ *
+ * @param sites The container where the sites have to be removed.
+ */
+ static void removeGapOnlySites(SiteContainer& sites);
+
+ /**
+ * @brief Get a site set without gap/unresolved-only sites.
+ *
+ * This function build a new SiteContainer instance without sites with only gaps or unresolved characters.
+ * The container passed as input is not modified, all sites are copied.
+ *
+ * @param sites The container to analyse.
+ * @return A pointer toward a new SiteContainer.
+ */
+ static SiteContainer* removeGapOrUnresolvedOnlySites(const SiteContainer& sites);
+
+ /**
+ * @brief Remove gap/unresolved-only sites from a site set.
+ *
+ * @param sites The container where the sites have to be removed.
+ */
+ static void removeGapOrUnresolvedOnlySites(SiteContainer& sites);
+
+ /**
+ * @brief Get a siteset with sites with less than a given amount of gaps.
+ *
+ * @param sites The container from which the sites have to be removed.
+ * @param maxFreqGaps The maximum frequency of gaps in each site.
+ * @return A pointer toward a new SiteContainer.
+ */
+ static SiteContainer* removeGapSites(const SiteContainer& sites, double maxFreqGaps);
+
+ /**
+ * @brief Remove sites with a given amount of gaps.
+ *
+ * @param sites The container from which the sites have to be removed.
+ * @param maxFreqGaps The maximum frequency of gaps in each site.
+ */
+ static void removeGapSites(SiteContainer& sites, double maxFreqGaps);
+
+ /**
+ * @brief Get a site set without stop codons, if the alphabet is a CodonAlphabet, otherwise throws an Exception.
+ *
+ * This function build a new SiteContainer instance without sites that have at least a stop codon.
+ * The container passed as input is not modified, all sites are copied.
+ *
+ * @param sites The container to analyse.
+ * @return A pointer toward a new SiteContainer.
+ */
+ static SiteContainer* removeStopCodonSites(const SiteContainer& sites) throw (AlphabetException);
+
+ /**
+ * @brief Create a new container with a specified set of sites.
+ *
+ * A new VectorSiteContainer is created with specified sites.
+ * The destruction of the container is up to the user.
+ * Sites are specified by their indice, beginning at 0.
+ * No position verification is performed, based on the assumption that
+ * the container passed as an argument is a correct one.
+ * Redundant selection is not checked, so be careful with what you're doing!
+ *
+ * @param sequences The container from wich sequences are to be taken.
+ * @param selection The positions of all sites to retrieve.
+ * @return A new container with all selected sites.
+ */
+ static SiteContainer* getSelectedSites(const SiteContainer& sequences, const SiteSelection& selection);
+
+ /**
+ * @brief create the consensus sequence of the alignment.
+ *
+ * In case of ambiguity (for instance a AATT site), one state will be chosen arbitrarily.
+ *
+ * @param sc a site container
+ * @param name the name of the sequence object that will be created.
+ * @param ignoreGap Tell if gap must be counted or not. If not (true option), only fully gapped sites will result in a gap in the consensus sequence.
+ * @param resolveUnknown Tell is unknnown characters must resolved. In a DNA sequence for instance, N will be counted as A=1/4, T=1/4, G=1/4 and C=1/4. Otherwise it will be counted as N=1.
+ * If this option is set to true, a consensus sequence will never contain an unknown character.
+ * @return A new Sequence object with the consensus sequence.
+ */
+ static const Sequence* getConsensus(const SiteContainer & sc, const std::string& name = "consensus", bool ignoreGap = true, bool resolveUnknown = false);
+
+ /**
+ * @brief Change all gaps to unknown state in a container, according to its alphabet.
+ *
+ * For DNA alphabets, this change all '-' to 'N'.
+ *
+ * @param sites The container to be modified.
+ */
+ static void changeGapsToUnknownCharacters(SiteContainer& sites);
+
+ /**
+ * @brief Change all unresolved characters to gaps in a container, according to its alphabet.
+ *
+ * For DNA alphabets, this change all 'N', 'M', 'R', etc. to '-'.
+ *
+ * @param sites The container to be modified.
+ */
+ static void changeUnresolvedCharactersToGaps(SiteContainer& sites);
+
+ /**
+ * @brief Resolve a container with "." notations.
+ *
+ * @code
+ * ATGCCGTTGG
+ * .C...A..C.
+ * ..A....C..
+ * @endcode
+ * will results in
+ * @code
+ * ATGCCGTTGG
+ * ACCCCATTCG
+ * ATACCGTCGG
+ * @endcode
+ * for instance.
+ * The first sequence is here called the "reference" sequence.
+ * It need not be the first in the container.
+ * The alphabet of the input alignment must be an instance of the DefaultAlphabet class, the only one which support dot characters.
+ * A new alignment is created and returned, with the specified alphabet.
+ *
+ * If several sequences that may be considered as reference are found, the first one is used.
+ *
+ * @param dottedAln The input alignment.
+ * @param resolvedAlphabet The alphabet of the output alignment.
+ * @return A pointer toward a dynamically created SiteContainer with the specified alphabet (can be a DefaultAlphabet).
+ * @throw AlphabetException If the alphabet of the input alignment is not of class DefaultAlphabet, or if one character does not match with the output alphabet.
+ * @throw Exception If no reference sequence was found, or if the input alignment contains no sequence.
+ */
+ static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
+
+ /**
+ * @name Sequences coordinates.
+ *
+ * @see SequenceWalker For an alternative approach.
+ * @{
+ */
+
+ /**
+ * @brief Get the index of each sequence position in an aligned sequence.
+ *
+ * If the sequence contains no gap, the translated and the original positions are the same.
+ * Position numbers start at 1.
+ *
+ * @param seq The sequence to translate.
+ * @return A map with original sequence positions as keys, and translated positions as values.
+ */
+ static std::map<size_t, size_t> getSequencePositions(const Sequence& seq);
+
+ /**
+ * @brief Get the index of each alignment position in an aligned sequence.
+ *
+ * If the sequence contains no gap, the translated and the original positions are the same.
+ * Position numbers start at 1.
+ *
+ * @param seq The sequence to translate.
+ * @return A map with original alignement positions as keys, and translated positions as values.
+ */
+ static std::map<size_t, size_t> getAlignmentPositions(const Sequence& seq);
+
+ /**
+ * @brief Fill a numeric matrix with the size of the alignment, containing the each sequence position.
+ *
+ * Positions start at 1, gaps have "position" 0.
+ *
+ * @param sites The input alignment.
+ * @param positions A matrix object which is going to be resized and filled with the corresponding positions.
+ * @author Julien Dutheil
+ */
+ static void getSequencePositions(const SiteContainer& sites, Matrix<size_t>& positions);
+ /** @} */
+
+ /**
+ * @brief Translate alignement positions from an aligned sequence to the same sequence in a different alignment.
+ *
+ * Takes each position (starting at 1) in sequence 1, and look for the corresponding position in sequence 2.
+ * The two sequences must be the same, excepted for the gaps.
+ * If no sequence contains gaps, or if the gaps are at the same place in both sequences, the translated postion will be the same as the original positions.
+ *
+ * @param seq1 The sequence to translate.
+ * @param seq2 The reference sequence.
+ * @return A map with original alignement positions as keys, and translated positions as values.
+ * @throw AlphabetMismatchException If the sequences do not share the same alphabet.
+ * @throw Exception If the sequence do not match.
+ */
+ static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
+
+ /**
+ * @brief Translate sequence positions from a sequence to another in the same alignment.
+ *
+ * Takes each position (starting at 1) in sequence 1, and look for the corresponding position in sequence 2 at the same site.
+ * If no corresponding position is available (i.e. if there is a gap in sequence 2 at the corresponding position), 0 is returned.
+ *
+ * @param sequences The alignment to use.
+ * @param i1 The index of the sequence to translate.
+ * @param i2 The index of the reference sequence.
+ * @return A map with original sequence positions as keys, and translated positions as values.
+ */
+ static std::map<size_t, size_t> translateSequence(const SiteContainer& sequences, size_t i1, size_t i2);
+
+ /**
+ * @brief Align two sequences using the Needleman-Wunsch dynamic algorithm.
+ *
+ * If the input sequences contain gaps, they will be ignored.
+ *
+ * @see BLOSUM50, DefaultNucleotideScore for score matrices.
+ *
+ * @param seq1 The first sequence.
+ * @param seq2 The second sequence.
+ * @param s The score matrix to use.
+ * @param gap Gap penalty.
+ * @return A new SiteContainer instance.
+ * @throw AlphabetMismatchException If the sequences and the score matrix do not share the same alphabet.
+ */
+ static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
+
+ /**
+ * @brief Align two sequences using the Needleman-Wunsch dynamic algorithm.
+ *
+ * If the input sequences contain gaps, they will be ignored.
+ *
+ * @see BLOSUM50, DefaultNucleotideScore for score matrices.
+ *
+ * @param seq1 The first sequence.
+ * @param seq2 The second sequence.
+ * @param s The score matrix to use.
+ * @param opening Gap opening penalty.
+ * @param extending Gap extending penalty.
+ * @return A new SiteContainer instance.
+ * @throw AlphabetMismatchException If the sequences and the score matrix do not share the same alphabet.
+ */
+ static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
+
+ /**
+ * @brief Sample sites in an alignment.
+ *
+ * Original site positions will be kept. The resulting container will hence probably have duplicated
+ * positions. You may wish to call the reindexSites() method on the returned container.
+ *
+ * Note: This method will be optimal with a container with vertical storage like VectorSiteContainer.
+ *
+ * @param sites An input alignment to sample.
+ * @param nbSites The size of the resulting container.
+ * @param index [out] If non-null the underlying vector will be appended with the original site indices.
+ * @return A sampled alignment with nbSites sites taken from the input one.
+ */
+ static VectorSiteContainer* sampleSites(const SiteContainer& sites, size_t nbSites, std::vector<size_t>* index = 0);
+
+ /**
+ * @brief Bootstrap sites in an alignment.
+ *
+ * Original site positions will be kept. The resulting container will hence probably have duplicated
+ * positions. You may wish to call the reindexSites() method on the returned container.
+ *
+ * Note: This method will be optimal with a container with vertical storage like VectorSiteContainer.
+ *
+ * @param sites An input alignment to sample.
+ * @return A sampled alignment with the same number of sites than the input one.
+ */
+ static VectorSiteContainer* bootstrapSites(const SiteContainer& sites);
+
+ /**
+ * @brief Compute the similarity/distance score between two aligned sequences.
+ *
+ * The similarity measures are computed as the proportion of identical match.
+ * The distance between the two sequences is defined as 1 - similarity.
+ * This function can be used with any type of alphabet.
+ *
+ * @param seq1 The first sequence.
+ * @param seq2 The second sequence.
+ * @param dist Shall we return a distance instead of similarity?
+ * @param gapOption How to deal with gaps:
+ * - SIMILARITY_ALL: all positions are used.
+ * - SIMILARITY_NODOUBLEGAP: ignore all positions with a gap in the two sequences.
+ * - SIMILARITY_NOGAP: ignore all positions with a gap in at least one of the two sequences.
+ * @param unresolvedAsGap Tell if unresolved characters must be considered as gaps when counting.
+ * If set to yes, the gap option will also apply to unresolved characters.
+ * @return The proportion of matches between the two sequences.
+ * @throw SequenceNotAlignedException If the two sequences do not have the same length.
+ * @throw AlphabetMismatchException If the two sequences do not share the same alphabet type.
+ * @throw Exception If an invalid gapOption is passed.
+ */
+ static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
+
+ /**
+ * @brief Compute the similarity matrix of an alignment.
+ *
+ * The similarity measures are computed as the proportion of identical match.
+ * The distance between the two sequences is defined as 1 - similarity.
+ * This function can be used with any type of alphabet.
+ * Several options concerning gaps and unresolved characters are proposed:
+ * - SIMILARITY_ALL: all positions are used.
+ * - SIMILARITY_NOFULLGAP: ignore positions with a gap in all the sequences in the alignment.
+ * - SIMILARITY_NODOUBLEGAP: ignore all positions with a gap in the two sequences for each pair.
+ * - SIMILARITY_NOGAP: ignore all positions with a gap in at least one of the two sequences for each pair.
+ *
+ *
+ * @see computeSimilarityMatrix
+ *
+ * @param sites The input alignment.
+ * @param dist Shall we return a distance instead of similarity?
+ * @param gapOption How to deal with gaps.
+ * @param unresolvedAsGap Tell if unresolved characters must be considered as gaps when counting.
+ * If set to yes, the gap option will also apply to unresolved characters.
+ * @return All pairwise similarity measures.
+ */
+ static DistanceMatrix* computeSimilarityMatrix(const SiteContainer& sites, bool dist = false, const std::string& gapOption = SIMILARITY_NOFULLGAP, bool unresolvedAsGap = true);
+
+ static const std::string SIMILARITY_ALL;
+ static const std::string SIMILARITY_NOFULLGAP;
+ static const std::string SIMILARITY_NODOUBLEGAP;
+ static const std::string SIMILARITY_NOGAP;
+
+ /**
+ * @brief Add the content of a site container to an exhisting one.
+ *
+ * The input containers are supposed to have unique sequence names.
+ * If it is not the case, several things can happen:
+ * - If the two containers have exactly the same names in the same order, then the content of the second one will be added as is to the first one.
+ * - If the second container does not have exactly the same sequences names or in a different order, then a reordered selection of the second contianer is created first,
+ * and in that case, only the first sequence with a given name will be used and duplicated.
+ * In any case, note that the second container should always contains all the sequence names from the first one,
+ * otherwise an exception will be thrown.
+ *
+ * @author Julien Dutheil
+ *
+ * @param seqCont1 First container.
+ * @param seqCont2 Second container. This container must contain sequences with the same names as in seqcont1.
+ * Additional sequences will be ignored.
+ * @param leavePositionAsIs Tell is site position should be unchanged. Otherwise (the default) is to add the size of container 1 to the positions in container 2.
+ * @throw AlphabetMismatchException If the alphabet in the 2 containers do not match.
+ * @throw Exception If sequence names do not match.
+ */
+ static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
+
+ /**
+ * @brief Compare an alignment to a reference alignment, and compute the column scores.
+ *
+ * Calculations are made according to formula for the "CS" score in Thompson et al 1999, Nucleic Acids Research (1999):27(13);2682–2690.
+ *
+ * @param positions1 Alignment index for the test alignment.
+ * @param positions2 Alignment index for the reference alignment.
+ * @param na The score to use if the tested column is full of gap.
+ * @return A vector of score, as 0 or 1.
+ * @see getSequencePositions for creating the alignment indexes.
+ * @warning The indexes for the two alignments must have the sequences in the exact same order!
+ * @author Julien Dutheil
+ */
+ static std::vector<int> getColumnScores(const Matrix<size_t>& positions1, const Matrix<size_t>& positions2, int na = 0);
+
+ /**
+ * @brief Compare an alignment to a reference alignment, and compute the sum-of-pairs scores.
+ *
+ * Calculations are made according to formula for the "SPS" score in Thompson et al 1999, Nucleic Acids Research (1999):27(13);2682–2690.
+ *
+ * @param positions1 Alignment index for the test alignment.
+ * @param positions2 Alignment index for the reference alignment.
+ * @param na The score to use if the tested column is not testable, that is not containing at least to residues.
+ * @return A vector of score, between 0 and 1 (+ na value).
+ * @see getSequencePositions for creating the alignment indexes.
+ * @warning The indexes for the two alignments must have the sequences in the exact same order!
+ * @author Julien Dutheil
+ */
+ static std::vector<double> getSumOfPairsScores(const Matrix<size_t>& positions1, const Matrix<size_t>& positions2, double na = 0);
+};
+
+} //end of namespace bpp.
+
+#endif //_SITECONTAINERTOOLS_H_
+
diff --git a/src/Bpp/Seq/Container/VectorSequenceContainer.cpp b/src/Bpp/Seq/Container/VectorSequenceContainer.cpp
new file mode 100644
index 0000000..61085d5
--- /dev/null
+++ b/src/Bpp/Seq/Container/VectorSequenceContainer.cpp
@@ -0,0 +1,399 @@
+//
+// File VectorSequenceContainer.cpp
+// Author : Guillaume Deuchst
+// Julien Dutheil
+// Last modification : Wednesday July 30 2003
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "VectorSequenceContainer.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+using namespace std;
+
+/** Class constructors: *******************************************************/
+
+VectorSequenceContainer::VectorSequenceContainer(
+ const std::vector<const Sequence*>& vs,
+ const Alphabet* alpha)
+throw (AlphabetMismatchException) :
+ AbstractSequenceContainer(alpha),
+ sequences_()
+{
+ for (std::vector<const Sequence*>::const_iterator i = vs.begin(); i < vs.end(); i++)
+ {
+ addSequence(**i);
+ }
+}
+
+/** Copy constructors: ********************************************************/
+
+VectorSequenceContainer::VectorSequenceContainer(
+ const VectorSequenceContainer& vsc) :
+ AbstractSequenceContainer(vsc),
+ sequences_()
+{
+ size_t max = vsc.getNumberOfSequences();
+ for (size_t i = 0; i < max; i++)
+ {
+ addSequence(vsc.getSequence(i), false);
+ }
+}
+
+VectorSequenceContainer::VectorSequenceContainer(
+ const OrderedSequenceContainer& osc) :
+ AbstractSequenceContainer(osc.getAlphabet()),
+ sequences_()
+{
+ // Sequences insertion
+ for (unsigned int i = 0; i < osc.getNumberOfSequences(); i++)
+ {
+ addSequence(osc.getSequence(i), false);
+ }
+}
+
+VectorSequenceContainer::VectorSequenceContainer(
+ const SequenceContainer& sc) :
+ AbstractSequenceContainer(sc.getAlphabet()),
+ sequences_()
+{
+ // Sequences insertion
+ std::vector<std::string> names = sc.getSequencesNames();
+ for (unsigned int i = 0; i < names.size(); i++)
+ {
+ addSequence(sc.getSequence(names[i]), false);
+ }
+
+ setGeneralComments(sc.getGeneralComments());
+}
+
+/** Assignation operator: *****************************************************/
+
+VectorSequenceContainer& VectorSequenceContainer::operator=(
+ const VectorSequenceContainer& vsc)
+{
+ clear();
+ AbstractSequenceContainer::operator=(vsc);
+
+ // Sequences insertion
+ size_t max = vsc.getNumberOfSequences();
+ for (size_t i = 0; i < max; i++)
+ {
+ addSequence(vsc.getSequence(i), false);
+ }
+
+ return *this;
+}
+
+VectorSequenceContainer& VectorSequenceContainer::operator=(
+ const OrderedSequenceContainer& osc)
+{
+ clear();
+ AbstractSequenceContainer::operator=(osc);
+
+ // Sequences insertion
+ size_t max = osc.getNumberOfSequences();
+ for (unsigned int i = 0; i < max; i++)
+ {
+ addSequence(osc.getSequence(i), false);
+ }
+
+ return *this;
+}
+
+/******************************************************************************/
+
+VectorSequenceContainer& VectorSequenceContainer::operator=(
+ const SequenceContainer& sc)
+{
+ clear();
+ AbstractSequenceContainer::operator=(sc);
+
+ // Seq names:
+ std::vector<std::string> names = sc.getSequencesNames();
+
+ for (unsigned int i = 0; i < names.size(); i++)
+ {
+ addSequence(sc.getSequence(names[i]), false);
+ }
+
+ return *this;
+}
+
+/******************************************************************************/
+
+const Sequence& VectorSequenceContainer::getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
+{
+ // Specified sequence existence verification
+ if (sequenceIndex < sequences_.size())
+ return *sequences_[sequenceIndex];
+ throw IndexOutOfBoundsException("VectorSequenceContainer::getSequence.", sequenceIndex, 0, sequences_.size() - 1);
+}
+
+/******************************************************************************/
+
+bool VectorSequenceContainer::hasSequence(const string& name) const
+{
+ // Specified sequence name research into all sequences
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ if (sequences_[i]->getName() == name)
+ return true;
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+const Sequence& VectorSequenceContainer::getSequence(const string& name) const throw (SequenceNotFoundException)
+{
+ // Specified sequence name research into all sequences
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ if (sequences_[i]->getName() == name)
+ return *sequences_[i];
+ }
+ throw SequenceNotFoundException("VectorSequenceContainer::getSequence : Specified sequence doesn't exist", name);
+}
+
+/******************************************************************************/
+
+Sequence& VectorSequenceContainer::getSequence_(size_t sequenceIndex) throw (IndexOutOfBoundsException)
+{
+ // Specified sequence existence verification
+ if (sequenceIndex < sequences_.size())
+ return *sequences_[sequenceIndex];
+ throw IndexOutOfBoundsException("VectorSequenceContainer::getSequence.", sequenceIndex, 0, sequences_.size() - 1);
+}
+
+/******************************************************************************/
+
+Sequence& VectorSequenceContainer::getSequence_(const string& name) throw (SequenceNotFoundException)
+{
+ // Specified sequence name research into all sequences
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ if (sequences_[i]->getName() == name)
+ return *sequences_[i];
+ }
+ throw SequenceNotFoundException("VectorSequenceContainer::getSequence : Specified sequence doesn't exist", name);
+}
+
+/******************************************************************************/
+
+size_t VectorSequenceContainer::getSequencePosition(const string& name) const throw (SequenceNotFoundException)
+{
+ // Specified sequence name research into all sequences
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ if (sequences_[i]->getName() == name)
+ return i;
+ }
+ throw SequenceNotFoundException("VectorSequenceContainer::getSequencePosition : Specified sequence doesn't exist", name);
+}
+
+/******************************************************************************/
+
+void VectorSequenceContainer::setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception)
+{
+ // Sequence's name existence checking
+ if (checkName)
+ {
+ // For all names in vector : throw exception if name already exists
+ for (size_t j = 0; j < sequences_.size(); j++)
+ {
+ if (sequences_[j]->getName() == sequence.getName())
+ if (j != sequenceIndex)
+ throw Exception("VectorSequenceContainer::setSequence : Sequence's name already exists in container");
+ }
+ }
+
+ // New sequence's alphabet and sequence container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() == getAlphabet()->getAlphabetType())
+ {
+ // Delete old sequence
+ delete sequences_[sequenceIndex];
+ // New sequence insertion in sequence container
+ sequences_[sequenceIndex] = dynamic_cast<Sequence*>(sequence.clone());
+ }
+ else
+ throw AlphabetMismatchException("VectorSequenceContainer::setSequence : Alphabets don't match", getAlphabet(), sequence.getAlphabet());
+}
+
+/******************************************************************************/
+
+Sequence* VectorSequenceContainer::removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException)
+{
+ // Copy sequence:
+ if (sequenceIndex >= sequences_.size())
+ throw IndexOutOfBoundsException("VectorSequenceContainer::removeSequence.", sequenceIndex, 0, sequences_.size() - 1);
+ Sequence* old = sequences_[sequenceIndex];
+ // Remove pointer toward old sequence:
+ sequences_.erase(sequences_.begin() + sequenceIndex);
+ // Send copy:
+ return old;
+}
+
+/******************************************************************************/
+
+void VectorSequenceContainer::deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException)
+{
+ // Delete sequence
+ if (sequenceIndex >= sequences_.size())
+ throw IndexOutOfBoundsException("VectorSequenceContainer::deleteSequence.", sequenceIndex, 0, sequences_.size() - 1);
+ delete sequences_[sequenceIndex];
+ // Remove pointer toward old sequence:
+ sequences_.erase(sequences_.begin() + sequenceIndex);
+}
+
+/******************************************************************************/
+
+void VectorSequenceContainer::addSequence(const Sequence& sequence, bool checkName) throw (Exception)
+{
+ // Sequence's name existence checking
+ if (checkName)
+ {
+ // For all names in vector : throw exception if name already exists
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ if (sequences_[i]->getName() == sequence.getName())
+ throw Exception("VectorSequenceContainer::addSequence : Sequence '" + sequence.getName() + "' already exists in container");
+ }
+ }
+
+ // New sequence's alphabet and sequence container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() == getAlphabet()->getAlphabetType())
+ {
+ // push_back(new Sequence(sequence.getName(), sequence.getContent(), alphabet));
+ sequences_.push_back(dynamic_cast<Sequence*>(sequence.clone()));
+ }
+ else
+ throw AlphabetMismatchException("VectorSequenceContainer::addSequence : Alphabets don't match", getAlphabet(), sequence.getAlphabet());
+}
+
+void VectorSequenceContainer::addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName) throw (Exception)
+{
+ // Sequence's name existence checking
+ if (checkName)
+ {
+ // For all names in vector : throw exception if name already exists
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ if (sequences_[i]->getName() == sequence.getName())
+ throw Exception("VectorSequenceContainer::addSequence : Sequence '" + sequence.getName() + "' already exists in container");
+ }
+ }
+
+ // New sequence's alphabet and sequence container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() == getAlphabet()->getAlphabetType())
+ {
+ // insert(begin() + pos, new Sequence(sequence.getName(), sequence.getContent(), alphabet));
+ sequences_.insert(sequences_.begin() + sequenceIndex, dynamic_cast<Sequence*>(sequence.clone()));
+ }
+ else
+ throw AlphabetMismatchException("VectorSequenceContainer::addSequence : Alphabets don't match", getAlphabet(), sequence.getAlphabet());
+}
+
+/******************************************************************************/
+
+std::vector<std::string> VectorSequenceContainer::getSequencesNames() const
+{
+ std::vector<std::string> names;
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ names.push_back(sequences_[i]->getName());
+ }
+ return names;
+}
+
+/******************************************************************************/
+
+void VectorSequenceContainer::setSequencesNames(
+ const std::vector<std::string>& names,
+ bool checkNames)
+throw (Exception)
+{
+ if (names.size() != getNumberOfSequences())
+ throw IndexOutOfBoundsException("VectorSequenceContainer::setSequenceNames : bad number of names", names.size(), getNumberOfSequences(), getNumberOfSequences());
+ if (checkNames)
+ {
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ // For all names in vector : throw exception if name already exists
+ for (size_t j = 0; j < i; j++)
+ {
+ if (names[j] == names[i])
+ throw Exception("VectorSiteContainer::setSequencesNames : Sequence's name already exists in container");
+ }
+ }
+ }
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ sequences_[i]->setName(names[i]);
+ }
+}
+
+/******************************************************************************/
+
+void VectorSequenceContainer::clear()
+{
+ // Delete sequences
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ delete sequences_[i];
+ }
+ // Delete all sequence pointers
+ sequences_.clear();
+}
+
+/******************************************************************************/
+
+void VectorSequenceContainer::setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException)
+{
+ sequences_[sequenceIndex]->setComments(comments);
+}
+
+/******************************************************************************/
+
+VectorSequenceContainer* VectorSequenceContainer::createEmptyContainer() const
+{
+ VectorSequenceContainer* vsc = new VectorSequenceContainer(getAlphabet());
+ vsc->setGeneralComments(getGeneralComments());
+ return vsc;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Container/VectorSequenceContainer.h b/src/Bpp/Seq/Container/VectorSequenceContainer.h
new file mode 100644
index 0000000..c320c98
--- /dev/null
+++ b/src/Bpp/Seq/Container/VectorSequenceContainer.h
@@ -0,0 +1,306 @@
+//
+// File VectorSequenceContainer.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _VECTORSEQUENCECONTAINER_H_
+#define _VECTORSEQUENCECONTAINER_H_
+
+#include "../Alphabet/Alphabet.h"
+#include "../Sequence.h"
+#include "AbstractSequenceContainer.h"
+#include <Bpp/Exceptions.h>
+
+// From the STL:
+#include <algorithm>
+#include <vector>
+
+namespace bpp
+{
+
+/**
+ * @brief The VectorSequenceContainer class.
+ *
+ * This is the simplest implementation of the OrderedSequenceContainer interface.
+ * Sequences are stored in a std::vector of pointers.
+ * The container is responsible for the creation and destruction of the sequence
+ * objects it contains.
+ */
+class VectorSequenceContainer:
+ public AbstractSequenceContainer
+{
+ private:
+
+ /**
+ * @brief A std::vector of pointers toward the sequences stored in the container.
+ */
+ mutable std::vector<Sequence*> sequences_;
+
+ public:
+
+ /**
+ * @brief Build a new container from a std::vector of pointers toward sequence objects.
+ *
+ * The addSequence() method is called uppon each Sequence object, hence each sequence is
+ * <i>copied</i> into the container.
+ *
+ * @param vs The std::vector of pointers toward sequence objects.
+ * @param alpha The alphabet to all sequences.
+ * @throw AlphabetMismatchException if one sequence does not match the specified alphabet.
+ */
+ VectorSequenceContainer(
+ const std::vector<const Sequence*>& vs, const Alphabet* alpha)
+ throw (AlphabetMismatchException);
+
+ /**
+ * @brief Build an empty container that will contain sequences of a particular alphabet.
+ *
+ * @param alpha The alphabet of the container.
+ */
+ VectorSequenceContainer(const Alphabet* alpha): AbstractSequenceContainer(alpha), sequences_() {}
+
+ /**
+ * @name Copy contructors:
+ *
+ * @{
+ */
+
+ /**
+ * @brief Copy from a VectorSequenceContainer.
+ *
+ * @param vsc The VectorSequenceContainer to copy into this container.
+ */
+ VectorSequenceContainer(const VectorSequenceContainer& vsc);
+
+ /**
+ * @brief Copy from an OrderedSequenceContainer.
+ *
+ * @param osc The OrderedSequenceContainer to copy into this container.
+ */
+ VectorSequenceContainer(const OrderedSequenceContainer& osc);
+
+ /**
+ * @brief Copy from a SequenceContainer.
+ *
+ * @param osc The SequenceContainer to copy into this container.
+ */
+ VectorSequenceContainer(const SequenceContainer& osc);
+
+ /** @} */
+
+ /**
+ * @brief Assign from a VectorSequenceContainer.
+ *
+ * @param vsc The VectorSequenceContainer to copy into this container.
+ */
+ VectorSequenceContainer& operator=(const VectorSequenceContainer& vsc);
+
+ /**
+ * @brief Copy from an OrderedSequenceContainer.
+ *
+ * @param osc The OrderedSequenceContainer to copy into this container.
+ */
+ VectorSequenceContainer& operator=(const OrderedSequenceContainer& osc);
+
+ /**
+ * @brief Copy from a SequenceContainer.
+ *
+ * @param osc The SequenceContainer to copy into this container.
+ */
+ VectorSequenceContainer& operator=(const SequenceContainer& osc);
+
+ /**
+ * @brief Container destructor: delete all sequences in the container.
+ */
+ virtual ~VectorSequenceContainer() { clear(); }
+
+ public:
+
+ /**
+ * @name The Clonable interface.
+ *
+ * @{
+ */
+ Clonable* clone() const { return new VectorSequenceContainer(*this); }
+ /** @} */
+
+ /**
+ * @name The SequenceContainer interface.
+ *
+ * @{
+ */
+ bool hasSequence(const std::string& name) const;
+
+ const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
+
+ void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
+ {
+ setSequence(getSequencePosition(name), sequence, checkName);
+ }
+
+ Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
+ {
+ return removeSequence(getSequencePosition(name));
+ }
+
+ void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
+ {
+ deleteSequence(getSequencePosition(name));
+ }
+
+ size_t getNumberOfSequences() const { return sequences_.size(); }
+
+ std::vector<std::string> getSequencesNames() const;
+ void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
+ void clear();
+ VectorSequenceContainer * createEmptyContainer() const;
+
+ int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
+ {
+ return getSequence_(sequenceName)[elementIndex];
+ }
+
+ const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
+ {
+ return getSequence(sequenceName)[elementIndex];
+ }
+
+ int& operator()(const std::string& sequenceName, size_t elementIndex)
+ {
+ return getSequence_(sequenceName)[elementIndex];
+ }
+
+ const int& operator()(const std::string& sequenceName, size_t elementIndex) const
+ {
+ return getSequence(sequenceName)[elementIndex];
+ }
+
+ int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
+ {
+ return getSequence_(sequenceIndex)[elementIndex];
+ }
+
+ const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
+ {
+ return getSequence(sequenceIndex)[elementIndex];
+ }
+
+ int& operator()(size_t sequenceIndex, size_t elementIndex)
+ {
+ return getSequence_(sequenceIndex)[elementIndex];
+ }
+ const int & operator()(size_t sequenceIndex, size_t elementIndex) const
+ {
+ return getSequence(sequenceIndex)[elementIndex];
+ }
+ /** @} */
+
+
+ /**
+ * @name The OrderedSequenceContainer interface.
+ *
+ * @{
+ */
+ void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
+ {
+ AbstractSequenceContainer::setComments(name, comments);
+ }
+
+ void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
+ size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
+ const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
+ void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
+ Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
+ void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
+ /** @} */
+
+ /**
+ * @name Add sequence to this container.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Add a sequence at the end of the container.
+ *
+ * The sequence is copied into the container.
+ * If checkNames is set to true, the method check if the name of the
+ * sequence is already used in the container, and sends an exception if it
+ * is the case. Otherwise, do not check the name: the method is hence faster,
+ * but use it at your own risks!
+ *
+ * @param sequence The sequence to add.
+ * @param checkName Tell if the method must check the name of the sequence
+ * before adding it.
+ * @throw Exception If the sequence couldn't be added to the container.
+ */
+ virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
+
+ /**
+ * @brief Add a sequence to the container at a particular position.
+ *
+ * The sequence is copied into the container.
+ * If checkName is set to true, the method check if the name of the
+ * sequence is already used in the container, and sends an exception if it
+ * is the case. Otherwise, do not check the name: the method is hence faster,
+ * but use it at your own risks!
+ *
+ * @param sequence The sequence to add.
+ * @param sequenceIndex The position where to insert the new sequence.
+ * All the following sequences will be pushed.
+ * @param checkName Tell if the method must check the name of the sequence
+ * before adding it.
+ * @throw Exception If the sequence couldn't be added to the container.
+ */
+ virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
+
+ protected:
+
+ /**
+ * @name AbstractSequenceContainer methods.
+ *
+ * @{
+ */
+ Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
+ Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
+ /** @} */
+};
+
+} //end of namespace bpp.
+
+#endif // _VECTORSEQUENCECONTAINER_H_
+
diff --git a/src/Bpp/Seq/Container/VectorSiteContainer.cpp b/src/Bpp/Seq/Container/VectorSiteContainer.cpp
new file mode 100644
index 0000000..e9371cd
--- /dev/null
+++ b/src/Bpp/Seq/Container/VectorSiteContainer.cpp
@@ -0,0 +1,862 @@
+//
+// File: VectorSiteContainer.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Oct 6 11:50:40 2003
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "VectorSiteContainer.h"
+
+#include <iostream>
+
+using namespace std;
+
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+/** Class constructors: *******************************************************/
+
+VectorSiteContainer::VectorSiteContainer(
+ const std::vector<const Site*>& vs,
+ const Alphabet* alpha,
+ bool checkPositions)
+throw (Exception) :
+ AbstractSequenceContainer(alpha),
+ sites_(0),
+ names_(0),
+ comments_(0),
+ sequences_(0)
+{
+ if (vs.size() == 0)
+ throw Exception("VectorSiteContainer::VectorSiteContainer. Empty site set.");
+ // Seq names and comments:
+ size_t nbSeq = vs[0]->size();
+ names_.resize(nbSeq);
+ comments_.resize(nbSeq);
+ for (size_t i = 0; i < nbSeq; i++)
+ {
+ names_[i] = "Seq_" + TextTools::toString(i);
+ comments_[i] = new Comments();
+ }
+ // Now try to add each site:
+ for (size_t i = 0; i < vs.size(); i++)
+ {
+ addSite(*vs[i], checkPositions); // This may throw an exception if position argument already exists or is size is not valid.
+ }
+
+ sequences_.resize(nbSeq);
+}
+
+/******************************************************************************/
+
+VectorSiteContainer::VectorSiteContainer(size_t size, const Alphabet* alpha) :
+ AbstractSequenceContainer(alpha),
+ sites_(0),
+ names_(size),
+ comments_(size),
+ sequences_(size)
+{
+ // Seq names and comments:
+ for (size_t i = 0; i < size; i++)
+ {
+ names_[i] = string("Seq_") + TextTools::toString(i);
+ comments_[i] = new Comments();
+ }
+}
+
+/******************************************************************************/
+
+VectorSiteContainer::VectorSiteContainer(const std::vector<std::string>& names, const Alphabet* alpha) :
+ AbstractSequenceContainer(alpha),
+ sites_(0),
+ names_(names.size()),
+ comments_(names.size()),
+ sequences_(names.size())
+{
+ // Seq names and comments:
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ names_[i] = names[i];
+ comments_[i] = new Comments();
+ }
+}
+
+/******************************************************************************/
+
+VectorSiteContainer::VectorSiteContainer(const Alphabet* alpha) :
+ AbstractSequenceContainer(alpha),
+ sites_(0),
+ names_(0),
+ comments_(0),
+ sequences_(0)
+{}
+
+/******************************************************************************/
+
+VectorSiteContainer::VectorSiteContainer(const VectorSiteContainer& vsc) :
+ AbstractSequenceContainer(vsc),
+ sites_(0),
+ names_(vsc.names_),
+ comments_(vsc.getNumberOfSequences()),
+ sequences_(vsc.getNumberOfSequences())
+{
+ // Now try to add each site:
+ for (size_t i = 0; i < vsc.getNumberOfSites(); i++)
+ {
+ addSite(vsc.getSite(i), false); // We assume that positions are correct.
+ }
+ // Seq comments:
+ for (size_t i = 0; i < vsc.getNumberOfSequences(); i++)
+ {
+ comments_[i] = new Comments(vsc.getComments(i));
+ }
+}
+
+/******************************************************************************/
+
+VectorSiteContainer::VectorSiteContainer(const SiteContainer& sc) :
+ AbstractSequenceContainer(sc),
+ sites_(0),
+ names_(sc.getSequencesNames()),
+ comments_(sc.getNumberOfSequences()),
+ sequences_(sc.getNumberOfSequences())
+{
+ // Now try to add each site:
+ for (size_t i = 0; i < sc.getNumberOfSites(); i++)
+ {
+ addSite(sc.getSite(i), false); // We assume that positions are correct.
+ }
+ // Seq comments:
+ for (size_t i = 0; i < sc.getNumberOfSequences(); i++)
+ {
+ comments_[i] = new Comments(sc.getComments(i));
+ }
+}
+
+/******************************************************************************/
+
+VectorSiteContainer::VectorSiteContainer(const OrderedSequenceContainer& osc) :
+ AbstractSequenceContainer(osc),
+ sites_(0),
+ names_(0),
+ comments_(0),
+ sequences_(0)
+{
+ for (size_t i = 0; i < osc.getNumberOfSequences(); i++)
+ {
+ addSequence(osc.getSequence(i), false);
+ }
+ reindexSites();
+}
+
+/******************************************************************************/
+
+VectorSiteContainer::VectorSiteContainer(const SequenceContainer& sc) :
+ AbstractSequenceContainer(sc),
+ sites_(0),
+ names_(0),
+ comments_(0),
+ sequences_(0)
+{
+ vector<string> names = sc.getSequencesNames();
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ addSequence(sc.getSequence(names[i]), false);
+ }
+ reindexSites();
+}
+
+/******************************************************************************/
+
+VectorSiteContainer& VectorSiteContainer::operator=(const VectorSiteContainer& vsc)
+{
+ clear();
+ AbstractSequenceContainer::operator=(vsc);
+ // Seq names:
+ names_.resize(vsc.getNumberOfSequences());
+ setSequencesNames(vsc.getSequencesNames(), true);
+ // Now try to add each site:
+ for (size_t i = 0; i < vsc.getNumberOfSites(); i++)
+ {
+ addSite(vsc.getSite(i), false); // We assume that positions are correct.
+ }
+ // Seq comments:
+ size_t nbSeq = vsc.getNumberOfSequences();
+ comments_.resize(nbSeq);
+ for (size_t i = 0; i < nbSeq; i++)
+ {
+ comments_[i] = new Comments(vsc.getComments(i));
+ }
+ sequences_.resize(nbSeq);
+
+ return *this;
+}
+
+/******************************************************************************/
+
+VectorSiteContainer& VectorSiteContainer::operator=(const SiteContainer& sc)
+{
+ clear();
+ AbstractSequenceContainer::operator=(sc);
+ // Seq names:
+ names_.resize(sc.getNumberOfSequences());
+ setSequencesNames(sc.getSequencesNames(), true);
+ // Now try to add each site:
+ for (size_t i = 0; i < sc.getNumberOfSites(); i++)
+ {
+ addSite(sc.getSite(i), false); // We assume that positions are correct.
+ }
+ // Seq comments:
+ size_t nbSeq = sc.getNumberOfSequences();
+ comments_.resize(nbSeq);
+ for (size_t i = 0; i < nbSeq; i++)
+ {
+ comments_[i] = new Comments(sc.getComments(i));
+ }
+ sequences_.resize(nbSeq);
+
+ return *this;
+}
+
+/******************************************************************************/
+
+VectorSiteContainer& VectorSiteContainer::operator=(const OrderedSequenceContainer& osc)
+{
+ clear();
+ AbstractSequenceContainer::operator=(osc);
+
+ size_t nbSeq = osc.getNumberOfSequences();
+ for (size_t i = 0; i < nbSeq; i++)
+ {
+ addSequence(osc.getSequence(i), false);
+ }
+ reindexSites();
+
+ return *this;
+}
+
+/******************************************************************************/
+
+VectorSiteContainer& VectorSiteContainer::operator=(const SequenceContainer& sc)
+{
+ clear();
+ AbstractSequenceContainer::operator=(sc);
+
+ vector<string> names = sc.getSequencesNames();
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ addSequence(sc.getSequence(names[i]), false);
+ }
+ reindexSites();
+
+ return *this;
+}
+
+/******************************************************************************/
+
+const Site& VectorSiteContainer::getSite(size_t i) const throw (IndexOutOfBoundsException)
+{
+ if (i >= getNumberOfSites())
+ throw IndexOutOfBoundsException("VectorSiteContainer::getSite.", i, 0, getNumberOfSites() - 1);
+ return *sites_[i];
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
+{
+ if (pos >= getNumberOfSites())
+ throw IndexOutOfBoundsException("VectorSiteContainer::setSite.", pos, 0, getNumberOfSites() - 1);
+
+ // Check size:
+ if (site.size() != getNumberOfSequences())
+ throw SiteException("AlignedSequenceContainer::addSite. Site does not have the appropriate length", &site);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("VectorSiteContainer::setSite", getAlphabet(), site.getAlphabet());
+
+ // Check position:
+ if (checkPositions)
+ {
+ int position = site.getPosition();
+ // For all positions in vector : throw exception if position already exists
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ if (sites_[i]->getPosition() == position)
+ throw SiteException("VectorSiteContainer::setSite: Site position already exists in container", &site);
+ }
+ }
+ delete sites_[pos];
+ sites_[pos] = dynamic_cast<Site*>(site.clone());
+}
+
+/******************************************************************************/
+
+Site* VectorSiteContainer::removeSite(size_t i) throw (IndexOutOfBoundsException)
+{
+ if (i >= getNumberOfSites())
+ throw IndexOutOfBoundsException("VectorSiteContainer::removeSite.", i, 0, getNumberOfSites() - 1);
+ Site* site = sites_[i];
+ sites_.erase(sites_.begin() + i);
+ return site;
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::deleteSite(size_t i) throw (IndexOutOfBoundsException)
+{
+ if (i >= getNumberOfSites())
+ throw IndexOutOfBoundsException("VectorSiteContainer::deleteSite.", i, 0, getNumberOfSites() - 1);
+ delete sites_[i];
+ sites_.erase(sites_.begin() + i);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException)
+{
+ if (siteIndex + length > getNumberOfSites())
+ throw IndexOutOfBoundsException("VectorSiteContainer::deleteSites.", siteIndex + length, 0, getNumberOfSites() - 1);
+ for (size_t i = siteIndex; i < siteIndex + length; ++i)
+ {
+ delete sites_[i];
+ }
+ sites_.erase(sites_.begin() + siteIndex, sites_.begin() + siteIndex + length);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
+{
+ // Check size:
+ if (site.size() != getNumberOfSequences())
+ throw SiteException("VectorSiteContainer::addSite. Site does not have the appropriate length", &site);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ {
+ throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), site.getAlphabet());
+ }
+
+ // Check position:
+ if (checkPositions)
+ {
+ int position = site.getPosition();
+ // For all positions in vector : throw exception if position already exists
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ if (sites_[i]->getPosition() == position)
+ throw SiteException("VectorSiteContainer::addSite. Site position already exists in container", &site);
+ }
+ }
+
+ sites_.push_back(dynamic_cast<Site*>(site.clone()));
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::addSite(const Site& site, int position, bool checkPositions) throw (Exception)
+{
+ // Check size:
+ if (site.size() != getNumberOfSequences())
+ throw SiteException("VectorSiteContainer::addSite. Site does not have the appropriate length", &site);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ {
+ throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), site.getAlphabet());
+ }
+
+ // Check position:
+ if (checkPositions)
+ {
+ // For all positions in vector : throw exception if position already exists
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ if (sites_[i]->getPosition() == position)
+ throw SiteException("VectorSiteContainer::addSite. Site position already exists in container", &site);
+ }
+ }
+ Site* copy = dynamic_cast<Site*>(site.clone());
+ copy->setPosition(position);
+ sites_.push_back(copy);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::addSite(const Site& site, size_t siteIndex, bool checkPositions) throw (Exception)
+{
+ if (siteIndex >= getNumberOfSites())
+ throw IndexOutOfBoundsException("VectorSiteContainer::addSite", siteIndex, 0, getNumberOfSites() - 1);
+
+ // Check size:
+ if (site.size() != getNumberOfSequences())
+ throw SiteException("VectorSiteContainer::addSite. Site does not have the appropriate length", &site);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ {
+ throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), site.getAlphabet());
+ }
+
+ // Check position:
+ if (checkPositions)
+ {
+ int position = site.getPosition();
+ // For all positions in vector : throw exception if position already exists
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ if (sites_[i]->getPosition() == position)
+ throw SiteException("VectorSiteContainer::addSite. Site position already exists in container", &site);
+ }
+ }
+
+ // insert(begin() + pos, new Site(site));
+ sites_.insert(sites_.begin() + siteIndex, dynamic_cast<Site*>(site.clone()));
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::addSite(const Site& site, size_t siteIndex, int position, bool checkPositions) throw (Exception)
+{
+ if (siteIndex >= getNumberOfSites())
+ throw IndexOutOfBoundsException("VectorSiteContainer::addSite", siteIndex, 0, getNumberOfSites() - 1);
+
+ // Check size:
+ if (site.size() != getNumberOfSequences())
+ throw SiteException("VectorSiteContainer::addSite. Site does not have the appropriate length", &site);
+
+ // New site's alphabet and site container's alphabet matching verification
+ if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ {
+ throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), site.getAlphabet());
+ }
+
+ // Check position:
+ if (checkPositions)
+ {
+ // For all positions in vector : throw exception if position already exists
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ if (sites_[i]->getPosition() == position)
+ throw SiteException("VectorSiteContainer::addSite. Site position already exists in container", &site);
+ }
+ }
+
+ Site* copy = dynamic_cast<Site*>(site.clone());
+ copy->setPosition(position);
+ sites_.insert(sites_.begin() + siteIndex, copy);
+}
+
+/******************************************************************************/
+
+size_t VectorSiteContainer::getNumberOfSites() const
+{
+ return sites_.size();
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::reindexSites()
+{
+ int pos = 1; // first position is 1.
+ for (vector<Site*>::iterator i = sites_.begin(); i < sites_.end(); i++)
+ {
+ (*i)->setPosition(pos++);
+ }
+}
+
+/******************************************************************************/
+
+Vint VectorSiteContainer::getSitePositions() const
+{
+ Vint positions(sites_.size());
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ positions[i] = sites_[i]->getPosition();
+ }
+ return positions;
+}
+
+/******************************************************************************/
+
+const Sequence& VectorSiteContainer::getSequence(size_t i) const throw (IndexOutOfBoundsException)
+{
+ if (i >= getNumberOfSequences())
+ throw IndexOutOfBoundsException("VectorSiteContainer::getSequence.", i, 0, getNumberOfSequences() - 1);
+
+ // Main loop : for all sites
+ size_t n = getNumberOfSites();
+ vector<int> sequence(n);
+ for (size_t j = 0; j < n; j++)
+ {
+ sequence[j] = sites_[j]->getContent()[i];
+ }
+ if (sequences_[i])
+ delete sequences_[i];
+ sequences_[i] = new BasicSequence(names_[i], sequence, *comments_[i], getAlphabet());
+ return *sequences_[i];
+}
+
+/******************************************************************************/
+
+const Sequence& VectorSiteContainer::getSequence(const string& name) const throw (SequenceNotFoundException)
+{
+ // Look for sequence name:
+ size_t pos = getSequencePosition(name);
+ return getSequence(pos);
+}
+
+/******************************************************************************/
+
+bool VectorSiteContainer::hasSequence(const string& name) const
+{
+ // Look for sequence name:
+ for (size_t pos = 0; pos < names_.size(); pos++)
+ {
+ if (names_[pos] == name)
+ return true;
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+size_t VectorSiteContainer::getSequencePosition(const string& name) const throw (SequenceNotFoundException)
+{
+ // Look for sequence name:
+ for (size_t pos = 0; pos < names_.size(); pos++)
+ {
+ if (names_[pos] == name)
+ return pos;
+ }
+ throw SequenceNotFoundException("VectorSiteContainer::getSequencePosition().", name);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::setSequence(const string& name, const Sequence& sequence, bool checkNames) throw (Exception)
+{
+ // Look for sequence name:
+ size_t pos = getSequencePosition(name);
+ setSequence(pos, sequence, checkNames);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::setSequence(size_t pos, const Sequence& sequence, bool checkNames)
+throw (Exception)
+{
+ if (pos >= getNumberOfSequences())
+ throw IndexOutOfBoundsException("VectorSiteContainer::setSequence", pos, 0, getNumberOfSequences() - 1);
+
+ // New sequence's alphabet and site container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), sequence.getAlphabet());
+
+ // If the container has only one sequence, we set the size to the size of this sequence:
+ if (getNumberOfSequences() == 1)
+ realloc(sequence.size());
+
+ if (sequence.size() != sites_.size())
+ throw SequenceException("VectorSiteContainer::setSequence. Sequence has not the appropriate length.", &sequence);
+
+ if (checkNames)
+ {
+ for (size_t i = 0; i < names_.size(); i++)
+ {
+ if (i != pos && sequence.getName() == names_[i])
+ throw SequenceException("VectorSiteContainer::settSequence. Name already exists in container.", &sequence);
+ }
+ }
+ // Update name:
+ names_[pos] = sequence.getName();
+ // Update elements at each site:
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ sites_[i]->setElement(pos, sequence.getValue(i));
+ }
+ // Update comments:
+ if (comments_[pos])
+ delete comments_[pos];
+ comments_[pos] = new Comments(sequence.getComments());
+ // Update sequences:
+ if (sequences_[pos])
+ delete sequences_[pos];
+ sequences_[pos] = 0;
+}
+
+/******************************************************************************/
+
+Sequence* VectorSiteContainer::removeSequence(size_t i) throw (IndexOutOfBoundsException)
+{
+ if (i >= getNumberOfSequences())
+ throw IndexOutOfBoundsException("VectorSiteContainer::removeSequence.", i, 0, getNumberOfSequences() - 1);
+
+ getSequence(i); // Actuallizes pointer.
+ Sequence* sequence = sequences_[i];
+ for (size_t j = 0; j < sites_.size(); j++)
+ {
+ // For each site:
+ sites_[j]->deleteElement(i);
+ }
+
+ // Now actualize names and comments:
+ names_.erase(names_.begin() + i);
+ if (comments_[i])
+ delete comments_[i];
+ comments_.erase(comments_.begin() + i);
+ // We remove the sequence, so the destruction of the sequence is up to the user:
+ // if (sequences_[i] != 0) delete sequences_[i];
+ sequences_.erase(sequences_.begin() + i);
+ return sequence;
+}
+
+/******************************************************************************/
+
+Sequence* VectorSiteContainer::removeSequence(const string& name) throw (SequenceNotFoundException)
+{
+ // Look for sequence name:
+ size_t pos = getSequencePosition(name);
+ return removeSequence(pos);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::deleteSequence(size_t i) throw (IndexOutOfBoundsException)
+{
+ if (i >= getNumberOfSequences())
+ throw IndexOutOfBoundsException("VectorSiteContainer::demeteSequence.", i, 0, getNumberOfSequences() - 1);
+ for (size_t j = 0; j < sites_.size(); j++)
+ {
+ sites_[j]->deleteElement(i);
+ }
+
+ // Now actualize names and comments:
+ names_.erase(names_.begin() + i);
+ if (comments_[i])
+ delete comments_[i];
+ comments_.erase(comments_.begin() + i);
+ if (sequences_[i])
+ delete sequences_[i];
+ sequences_.erase(sequences_.begin() + i);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::deleteSequence(const string& name) throw (SequenceNotFoundException)
+{
+ // Look for sequence name:
+ size_t pos = getSequencePosition(name);
+ deleteSequence(pos);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::addSequence(const Sequence& sequence, bool checkNames) throw (Exception)
+{
+ // If the container has no sequence, we set the size to the size of this sequence:
+ if (getNumberOfSequences() == 0)
+ realloc(sequence.size());
+
+ // New sequence's alphabet and site container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("VectorSiteContainer::addSequence", getAlphabet(), sequence.getAlphabet());
+
+ if (sequence.size() != sites_.size())
+ throw SequenceException("VectorSiteContainer::addSequence. Sequence has not the appropriate length: " + TextTools::toString(sequence.size()) + ", should be " + TextTools::toString(sites_.size()) + ".", &sequence);
+
+ if (checkNames)
+ {
+ for (size_t i = 0; i < names_.size(); i++)
+ {
+ if (sequence.getName() == names_[i])
+ throw SequenceException("VectorSiteContainer::addSequence. Name already exists in container.", &sequence);
+ }
+ }
+
+ // Append name:
+ names_.push_back(sequence.getName());
+
+ // Append elements at each site:
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ sites_[i]->addElement(sequence.getValue(i));
+ }
+
+ // Append comments:
+ comments_.push_back(new Comments(sequence.getComments()));
+
+ // Sequences pointers:
+ sequences_.push_back(0);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::addSequence(
+ const Sequence& sequence,
+ size_t pos,
+ bool checkNames)
+throw (Exception)
+{
+ if (pos >= getNumberOfSequences())
+ throw IndexOutOfBoundsException("VectorSiteContainer::addSequence.", pos, 0, getNumberOfSequences() - 1);
+ if (sequence.size() != sites_.size())
+ throw SequenceNotAlignedException("VectorSiteContainer::setSequence", &sequence);
+
+ // New sequence's alphabet and site container's alphabet matching verification
+ if (sequence.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
+ {
+ throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), sequence.getAlphabet());
+ }
+
+ if (checkNames)
+ {
+ for (size_t i = 0; i < names_.size(); i++)
+ {
+ if (sequence.getName() == names_[i])
+ throw SequenceException("VectorSiteContainer::addSequence. Name already exists in container.", &sequence);
+ }
+ }
+
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ // For each site:
+ sites_[i]->addElement(pos, sequence.getValue(i));
+ }
+ // Actualize names and comments:
+ names_.insert(names_.begin() + pos, sequence.getName());
+ comments_.insert(comments_.begin() + pos, new Comments(sequence.getComments()));
+ sequences_.insert(sequences_.begin() + pos, 0);
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::clear()
+{
+ // Must delete all sites in the container:
+ for (size_t i = 0; i < sites_.size(); i++)
+ {
+ delete sites_[i];
+ }
+
+ // must delete all comments too:
+ for (size_t i = 0; i < comments_.size(); i++)
+ {
+ if (comments_[i] != 0)
+ delete comments_[i];
+ }
+
+ // Delete all sequences retrieved:
+ for (size_t i = 0; i < sequences_.size(); i++)
+ {
+ if (sequences_[i] != 0)
+ delete (sequences_[i]);
+ }
+
+ // Delete all sites pointers
+ sites_.clear();
+ names_.clear();
+ comments_.clear();
+ sequences_.clear();
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::realloc(size_t n)
+{
+ clear();
+ sites_.resize(n);
+ for (size_t i = 0; i < n; i++)
+ {
+ sites_[i] = new Site(getAlphabet());
+ }
+ reindexSites();
+}
+
+/******************************************************************************/
+
+vector<string> VectorSiteContainer::getSequencesNames() const
+{
+ return names_;
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::setSequencesNames(
+ const vector<string>& names,
+ bool checkNames)
+throw (Exception)
+{
+ if (names.size() != getNumberOfSequences())
+ throw IndexOutOfBoundsException("VectorSiteContainer::setSequenceNames: bad number of names.", names.size(), getNumberOfSequences(), getNumberOfSequences());
+ if (checkNames)
+ {
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ // For all names in vector : throw exception if name already exists
+ for (size_t j = 0; j < i; j++)
+ {
+ if (names[j] == names[i])
+ throw Exception("VectorSiteContainer::setSequencesNames : Sequence's name already exists in container");
+ }
+ }
+ }
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ names_[i] = names[i];
+ }
+}
+
+/******************************************************************************/
+
+void VectorSiteContainer::setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException)
+{
+ comments_[sequenceIndex] = new Comments(comments);
+}
+
+/******************************************************************************/
+
+VectorSiteContainer* VectorSiteContainer::createEmptyContainer() const
+{
+ VectorSiteContainer* vsc = new VectorSiteContainer(getAlphabet());
+ vsc->setGeneralComments(getGeneralComments());
+ return vsc;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Container/VectorSiteContainer.h b/src/Bpp/Seq/Container/VectorSiteContainer.h
new file mode 100644
index 0000000..b66f54b
--- /dev/null
+++ b/src/Bpp/Seq/Container/VectorSiteContainer.h
@@ -0,0 +1,240 @@
+//
+// File: VectorSiteContainer.h
+// Created by: Julien Dutheil
+// Created on: Mon Oct 6 11:50:40 2003
+//
+
+/*
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _VECTORSITECONTAINER_H_
+#define _VECTORSITECONTAINER_H_
+
+#include "../Site.h"
+#include "SiteContainer.h"
+#include "AbstractSequenceContainer.h"
+#include "AlignedSequenceContainer.h"
+#include "OrderedSequenceContainer.h"
+#include <Bpp/Numeric/VectorTools.h>
+
+// From the STL library:
+#include <string>
+#include <vector>
+#include <iostream>
+
+namespace bpp
+{
+/**
+ * @brief The VectorSiteContainer class.
+ *
+ * Sites are stored in a std::vector of pointers.
+ * Site access is hence in \f$O(1)\f$, and sequence access in \f$O(l)\f$, where
+ * \f$l\f$ is the number of sites in the container.
+ *
+ * See AlignedSequenceContainer for an alternative implementation.
+ *
+ * @see Sequence, Site, AlignedSequenceContainer
+ */
+class VectorSiteContainer :
+ public AbstractSequenceContainer,
+ // This container implements the SequenceContainer interface
+ // and use the AbstractSequenceContainer adapter.
+ public virtual SiteContainer // This container is a SiteContainer.
+{
+protected:
+ std::vector<Site*> sites_;
+ std::vector<std::string> names_;
+ std::vector<Comments*> comments_; // Sequences comments.
+ mutable std::vector<Sequence*> sequences_; // To store pointer toward sequences retrieves (cf. AlignedSequenceContainer).
+
+public:
+ /**
+ * @brief Build a new container from a set of sites.
+ *
+ * @param vs A std::vector of sites.
+ * @param alpha The common alphabet for all sites.
+ * @param checkPositions Check for the redundancy of site position tag. This may turn to be very time consuming!
+ * @throw Exception If sites differ in size or in alphabet.
+ */
+ VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
+ /**
+ * @brief Build a new empty container with specified size.
+ *
+ * @param size Number of sequences in the container.
+ * @param alpha The alphabet for this container.
+ */
+ VectorSiteContainer(size_t size, const Alphabet* alpha);
+ /**
+ * @brief Build a new empty container with specified sequence names.
+ *
+ * @param names Sequence names. This will set the number of sequences in the container.
+ * @param alpha The alphabet for this container.
+ */
+ VectorSiteContainer(const std::vector<std::string>& names, const Alphabet* alpha);
+
+ /**
+ * @brief Build a new empty container.
+ *
+ * @param alpha The alphabet for this container.
+ */
+ VectorSiteContainer(const Alphabet* alpha);
+
+ VectorSiteContainer(const VectorSiteContainer& vsc);
+ VectorSiteContainer(const SiteContainer& sc);
+ VectorSiteContainer(const OrderedSequenceContainer& osc);
+ VectorSiteContainer(const SequenceContainer& sc);
+
+ VectorSiteContainer& operator=(const VectorSiteContainer& vsc);
+ VectorSiteContainer& operator=(const SiteContainer& sc);
+ VectorSiteContainer& operator=(const OrderedSequenceContainer& osc);
+ VectorSiteContainer& operator=(const SequenceContainer& sc);
+
+ virtual ~VectorSiteContainer() { clear(); }
+
+public:
+ /**
+ * @name The Clonable interface.
+ *
+ * @{
+ */
+ VectorSiteContainer* clone() const { return new VectorSiteContainer(*this); }
+ /** @} */
+
+ /**
+ * @name The SiteContainer interface implementation:
+ *
+ * @{
+ */
+ const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
+ void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
+ Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
+ void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
+ void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
+ void addSite(const Site& site, bool checkPosition = true) throw (Exception);
+ void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
+ void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
+ void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
+ size_t getNumberOfSites() const;
+ void reindexSites();
+ Vint getSitePositions() const;
+ /** @} */
+
+ // Theses methods are implemented for this class:
+
+ /**
+ * @name The SequenceContainer interface.
+ *
+ * @{
+ */
+ void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
+
+ // Method to get a sequence object from sequence container
+ const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
+ const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
+ bool hasSequence(const std::string& name) const;
+
+ // Methods to get position of a sequence in sequence container from his name
+ // This method is used by delete and remove methods
+ size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
+
+ Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
+ Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
+
+ void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
+ void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
+
+ size_t getNumberOfSequences() const { return names_.size(); }
+
+ std::vector<std::string> getSequencesNames() const;
+
+ void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
+
+ void clear();
+
+ VectorSiteContainer* createEmptyContainer() const;
+
+ int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
+ {
+ if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::valueAt(std::string, size_t).", elementIndex, 0, getNumberOfSites() - 1);
+ return (*sites_[elementIndex])[getSequencePosition(sequenceName)];
+ }
+ const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
+ {
+ if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::valueAt(std::string, size_t).", elementIndex, 0, getNumberOfSites() - 1);
+ return (*sites_[elementIndex])[getSequencePosition(sequenceName)];
+ }
+ int& operator()(const std::string& sequenceName, size_t elementIndex)
+ {
+ return (*sites_[elementIndex])[getSequencePosition(sequenceName)];
+ }
+ const int& operator()(const std::string& sequenceName, size_t elementIndex) const
+ {
+ return (*sites_[elementIndex])[getSequencePosition(sequenceName)];
+ }
+
+ int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
+ {
+ if (sequenceIndex >= getNumberOfSequences()) throw IndexOutOfBoundsException("VectorSiteContainer::valueAt(size_t, size_t).", sequenceIndex, 0, getNumberOfSequences() - 1);
+ if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::valueAt(size_t, size_t).", elementIndex, 0, getNumberOfSites() - 1);
+ return (*sites_[elementIndex])[sequenceIndex];
+ }
+ const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
+ {
+ if (sequenceIndex >= getNumberOfSequences()) throw IndexOutOfBoundsException("VectorSiteContainer::valueAt(size_t, size_t).", sequenceIndex, 0, getNumberOfSequences() - 1);
+ if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::valueAt(size_t, size_t).", elementIndex, 0, getNumberOfSites() - 1);
+ return (*sites_[elementIndex])[sequenceIndex];
+ }
+ int& operator()(size_t sequenceIndex, size_t elementIndex)
+ {
+ return (*sites_[elementIndex])[sequenceIndex];
+ }
+ const int& operator()(size_t sequenceIndex, size_t elementIndex) const
+ {
+ return (*sites_[elementIndex])[sequenceIndex];
+ }
+ /** @} */
+
+ void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
+ void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
+
+ void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
+ void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
+
+protected:
+ // Create n void sites:
+ void realloc(size_t n);
+};
+} // end of namespace bpp.
+
+#endif // _VECTORSITECONTAINER_H_
+
diff --git a/src/Bpp/Seq/DNAToRNA.cpp b/src/Bpp/Seq/DNAToRNA.cpp
new file mode 100644
index 0000000..411c883
--- /dev/null
+++ b/src/Bpp/Seq/DNAToRNA.cpp
@@ -0,0 +1,78 @@
+//
+// File: DNAToRNA.cpp
+// Created by: Julien Dutheil
+// Created on: Sun Oct 12 14:39:29 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "DNAToRNA.h"
+
+using namespace bpp;
+using namespace std;
+
+/******************************************************************************/
+
+int DNAToRNA::translate(int state) const throw (BadIntException)
+{
+ dna_->intToChar(state);
+ return state;
+}
+
+/******************************************************************************/
+
+string DNAToRNA::translate(const std::string& state) const throw (BadCharException)
+{
+ int i = dna_->charToInt(state);
+ return rna_->intToChar(i);
+}
+
+/******************************************************************************/
+
+int DNAToRNA::reverse(int state) const throw (BadIntException)
+{
+ rna_->intToChar(state);
+ return state;
+}
+
+/******************************************************************************/
+
+string DNAToRNA::reverse(const std::string& state) const throw (BadCharException)
+{
+ int i = rna_->charToInt(state);
+ return dna_->intToChar(i);
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/DNAToRNA.h b/src/Bpp/Seq/DNAToRNA.h
new file mode 100644
index 0000000..b86f2be
--- /dev/null
+++ b/src/Bpp/Seq/DNAToRNA.h
@@ -0,0 +1,100 @@
+//
+// File: DNAToRNA.h
+// Created by: Julien Dutheil
+// Created on: Sun Oct 12 14:39:29 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _DNATORNA_H_
+#define _DNATORNA_H_
+
+#include "Transliterator.h"
+#include "Alphabet/DNA.h"
+#include "Alphabet/RNA.h"
+#include "Alphabet/AlphabetTools.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Reverse iterator to convert RNA to DNA.
+ *
+ * This only changes U to T characters.
+ *
+ * @see NucleicAcidsReplication
+ */
+class DNAToRNA:
+ public AbstractReverseTransliterator
+{
+ private:
+ const Alphabet* dna_, * rna_;
+
+ public:
+ DNAToRNA(): AbstractReverseTransliterator(), dna_(&AlphabetTools::DNA_ALPHABET), rna_(&AlphabetTools::RNA_ALPHABET) {}
+
+ DNAToRNA(const DNAToRNA& d2r): AbstractReverseTransliterator(d2r), dna_(d2r.dna_), rna_(d2r.rna_) {}
+
+ DNAToRNA& operator=(const DNAToRNA& d2r)
+ {
+ AbstractReverseTransliterator::operator=(d2r);
+ dna_ = d2r.dna_;
+ rna_ = d2r.rna_;
+ return *this;
+ }
+
+ virtual ~DNAToRNA() {}
+
+ public:
+ virtual const Alphabet* getSourceAlphabet() const { return dna_; }
+ virtual const Alphabet* getTargetAlphabet() const { return rna_; }
+ int translate(int state) const throw (BadIntException);
+ std::string translate(const std::string& state) const throw (BadCharException);
+ Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
+ {
+ return AbstractReverseTransliterator::translate(sequence);
+ }
+ int reverse(int state) const throw (BadIntException);
+ std::string reverse(const std::string& state) const throw (BadCharException);
+ Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
+ {
+ return AbstractReverseTransliterator::reverse(sequence);
+ }
+
+};
+
+} //end of namespace bpp.
+
+#endif //_DNATORNA_H_
+
diff --git a/src/Bpp/Seq/DistanceMatrix.cpp b/src/Bpp/Seq/DistanceMatrix.cpp
new file mode 100644
index 0000000..c485203
--- /dev/null
+++ b/src/Bpp/Seq/DistanceMatrix.cpp
@@ -0,0 +1,53 @@
+//
+// File: DistanceMatrix.cpp
+// Created on: Sat Feb 17 15:25 2007
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for phylogenetic data analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "DistanceMatrix.h"
+
+using namespace std;
+
+using namespace bpp;
+
+size_t DistanceMatrix::getNameIndex(const std::string& name) const throw (Exception)
+{
+ for (size_t i = 0; i < names_.size(); ++i)
+ {
+ if (names_[i] == name) return i;
+ }
+ throw Exception("DistanceMatrix::getNameIndex. Name not found: '" + name + "'.");
+}
+
diff --git a/src/Bpp/Seq/DistanceMatrix.h b/src/Bpp/Seq/DistanceMatrix.h
new file mode 100644
index 0000000..fd431c4
--- /dev/null
+++ b/src/Bpp/Seq/DistanceMatrix.h
@@ -0,0 +1,237 @@
+//
+// File: DistanceMatrix.h
+// Created on: Wed jun 08 10:39 2005
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for phylogenetic data analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _DISTANCEMATRIX_H_
+#define _DISTANCEMATRIX_H_
+
+// From the STL:
+#include <vector>
+#include <string>
+#include <Bpp/Exceptions.h>
+#include <Bpp/Numeric/VectorExceptions.h> //DimensionException
+#include <Bpp/Numeric/Matrix/Matrix.h>
+
+namespace bpp
+{
+
+/**
+ * @brief A Matrix class to store phylogenetic distances.
+ */
+class DistanceMatrix:
+ public virtual RowMatrix<double>
+{
+
+ private:
+ std::vector<std::string> names_;
+
+ public:
+
+ /**
+ * @brief Build a new distance matrix with specified names.
+ *
+ * The dimension of the matrix will be equal to the number of names
+ *
+ * @param names The names to use.
+ */
+ DistanceMatrix(const std::vector<std::string>& names):
+ RowMatrix<double>(names.size(), names.size()), names_(names)
+ {
+ reset();
+ }
+
+ /**
+ * @brief Build a new distance matrix with specified size.
+ *
+ * Row names will be named 'Taxon 0', 'Taxon 1', and so on.
+ *
+ * @param n The size of the matrix.
+ */
+ DistanceMatrix(size_t n):
+ RowMatrix<double>(n, n), names_(n)
+ {
+ resize(n);
+ }
+
+ virtual ~DistanceMatrix() {}
+
+ DistanceMatrix(const DistanceMatrix& dist): RowMatrix<double>(dist), names_(dist.names_) {}
+
+ DistanceMatrix& operator=(const DistanceMatrix& dist)
+ {
+ size_t n = dist.size();
+ resize(n);
+ for(size_t i = 0; i < n; ++i)
+ {
+ for(size_t j = 0; j < n; ++j)
+ {
+ operator()(i, j) = dist(i, j);
+ }
+ }
+ names_ = dist.names_;
+ return *this;
+ }
+
+ public:
+
+ /**
+ * @brief Reset the distance matrix: all distances are set to 0.
+ */
+ void reset()
+ {
+ size_t n = size();
+ for (size_t i = 0; i < n; i++)
+ {
+ for (size_t j = 0; j < n; j++)
+ {
+ operator()(i, j) = 0;
+ }
+ }
+ }
+
+ /**
+ * @return The dimension of the matrix.
+ */
+ size_t size() const { return names_.size(); }
+
+ /**
+ * @return The names associated to the matrix.
+ */
+ const std::vector<std::string>& getNames() const { return names_; }
+
+ /**
+ * @return The ith name.
+ * @param i Name index.
+ * @throw IndexOutOfBoundsException If i is not a valid index.
+ */
+ const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
+ {
+ if (i >= size()) throw IndexOutOfBoundsException("DistanceMatrix::getName. Invalid indice.", i, 0, size());
+ return names_[i];
+ }
+
+ /**
+ * @brief Set the ith name.
+ *
+ * @param i Name index.
+ * @param name The new name.
+ * @throw IndexOutOfBoundsException If i is not a valid index.
+ */
+ void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
+ {
+ if (i >= size()) throw IndexOutOfBoundsException("DistanceMatrix::setName. Invalid indice.", i, 0, size());
+ names_[i] = name;
+ }
+
+ /**
+ * @brief Set the names associated to the matrix.
+ *
+ * @param names Matrix names.
+ * @throw DimensionException If 'names' have not the same size as the matrix.
+ */
+ void setNames(const std::vector<std::string>& names) throw (DimensionException)
+ {
+ if (names.size() != names_.size()) throw DimensionException("DistanceMatrix::setNames. Invalid number of names.", names.size(), names_.size());
+ names_ = names;
+ }
+
+ /**
+ * @brief Get the index of a given name.
+ *
+ * @param name The name to look for.
+ * @return The position of the name.
+ * @throw Exception If no names are attached to this matrix, or if the name was not found.
+ */
+ size_t getNameIndex(const std::string& name) const throw (Exception);
+
+ /**
+ * @brief Change the dimension of the matrix.
+ *
+ * @param n the new dimension of the matrix.
+ */
+ void resize(size_t n) {
+ RowMatrix<double>::resize(n, n);
+ names_.resize(n);
+ for (size_t i = 0; i < n; ++i)
+ names_[i] = "Taxon " + TextTools::toString(i);
+ reset();
+ }
+
+ /**
+ * @brief Access by name.
+ *
+ * @param iName Name 1 (row)
+ * @param jName Name 2 (column)
+ * @return A reference toward the specified distance.
+ * @throw Exception if the matrix has no name of if one of the name do not match existing names.
+ */
+ virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
+ {
+ size_t i = getNameIndex(iName);
+ size_t j = getNameIndex(jName);
+ return operator()(i,j);
+ }
+
+ /**
+ * @brief Access by name.
+ *
+ * @param iName Name 1 (row)
+ * @param jName Name 2 (column)
+ * @return A reference toward the specified distance.
+ * @throw Exception if the matrix has no name of if one of the name do not match existing names.
+ */
+ virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
+ {
+ size_t i = getNameIndex(iName);
+ size_t j = getNameIndex(jName);
+ return operator()(i,j);
+ }
+
+ virtual const double& operator()(size_t i, size_t j) const
+ {
+ return RowMatrix<double>::operator()(i, j);
+ }
+ virtual double& operator()(size_t i, size_t j)
+ {
+ return RowMatrix<double>::operator()(i, j);
+ }
+};
+
+} //end of namespace bpp.
+
+#endif //_DISTANCEMATRIX_H_
+
diff --git a/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp b/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp
new file mode 100644
index 0000000..eeab5fd
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp
@@ -0,0 +1,167 @@
+//
+// File: EchinodermMitochondrialGeneticCode.cpp
+// Created by: Eric Bazin
+// Created on: 14 11:31:27 CET 2005
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "EchinodermMitochondrialGeneticCode.h"
+#include "../Alphabet/EchinodermMitochondrialCodonAlphabet.h"
+#include "../Alphabet/ProteicAlphabet.h"
+
+using namespace bpp;
+
+#include <iostream>
+
+using namespace std;
+
+EchinodermMitochondrialGeneticCode::EchinodermMitochondrialGeneticCode(const NucleicAlphabet * alpha) : GeneticCode()
+{
+ codonAlphabet_ = new EchinodermMitochondrialCodonAlphabet(alpha);
+ proteicAlphabet_ = new ProteicAlphabet();
+}
+
+EchinodermMitochondrialGeneticCode::~EchinodermMitochondrialGeneticCode()
+{
+ delete codonAlphabet_;
+ delete proteicAlphabet_;
+}
+
+int EchinodermMitochondrialGeneticCode::translate(int state) const throw (Exception)
+{
+ if(state == codonAlphabet_->getUnknownCharacterCode()) return proteicAlphabet_->getUnknownCharacterCode();
+ vector<int> positions = codonAlphabet_->getPositions(state);
+ switch(positions[0])
+ {
+ //First position:
+ case 0 : //A
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //AA
+ switch(positions[2])
+ {
+ //Third position:
+ case 2 : return proteicAlphabet_->charToInt("K"); //Lysine
+ case 0 : case 1 : case 3 : return proteicAlphabet_->charToInt("N"); //Asparagine
+ }
+ case 1 : //AC
+ return proteicAlphabet_->charToInt("T"); //Threonine
+ case 2 : //AG
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 1 : case 2 : case 3 : return proteicAlphabet_->charToInt("S"); //Serine
+ }
+ case 3 : //AT
+ switch(positions[2])
+ {
+ //Third position:
+ case 2: return proteicAlphabet_->charToInt("M"); //Methionine
+ case 0 : case 1 : case 3 : return proteicAlphabet_->charToInt("I"); //Isoleucine
+ }
+ }
+ case 1 : //C
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //CA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("Q"); //Glutamine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("H"); //Histidine
+ }
+ case 1 : //CC
+ return proteicAlphabet_->charToInt("P"); //Proline
+ case 2 : //CG
+ return proteicAlphabet_->charToInt("R"); //Arginine
+ case 3 : //CT
+ return proteicAlphabet_->charToInt("L"); //Leucine
+ }
+ case 2 : //G
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //GA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("E"); //Glutamic acid
+ case 1 : case 3 : return proteicAlphabet_->charToInt("D"); //Aspartic acid
+ }
+ case 1 : //GC
+ return proteicAlphabet_->charToInt("A"); //Alanine
+ case 2 : //GG
+ return proteicAlphabet_->charToInt("G"); //Glycine
+ case 3 : //GT
+ return proteicAlphabet_->charToInt("V"); //Valine
+ }
+ case 3 : //T(U)
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //TA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : throw StopCodonException("", "TAA"); //Stop codon
+ case 2 : throw StopCodonException("", "TAG"); //Stop codon
+ case 1 : case 3 : return proteicAlphabet_->charToInt("Y"); //Tyrosine
+ }
+ case 1 : //TC
+ return proteicAlphabet_->charToInt("S"); //Serine
+ case 2 : //TG
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("W"); //Tryptophane
+ case 1 : case 3 : return proteicAlphabet_->charToInt("C"); //Cysteine
+ }
+ case 3 : //TT
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("L"); //Leucine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("F"); //Phenylalanine
+ }
+ }
+ }
+ throw BadIntException(state, "EchinodermMitochondrialGeneticCode::translate", codonAlphabet_);
+}
+
+string EchinodermMitochondrialGeneticCode::translate(const string & state) const throw (Exception) {
+ return proteicAlphabet_->intToChar(translate(codonAlphabet_->charToInt(state)));
+}
+
diff --git a/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h b/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h
new file mode 100644
index 0000000..bddfe20
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h
@@ -0,0 +1,74 @@
+//
+// File: EchinodermMitochondrialGeneticCode.h
+// Created by: Eric Bazin
+// Created on: 14 11:31:27 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ECHINODERMMITOCHONDRIALGENETICCODE_H_
+#define _ECHINODERMMITOCHONDRIALGENETICCODE_H_
+
+#include "GeneticCode.h"
+#include "../Alphabet/NucleicAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the Echinoderm and Faltworms
+ * Mitochondrial genetic code as describe on the NCBI website:
+ * http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG9
+ */
+
+class EchinodermMitochondrialGeneticCode:
+ public GeneticCode
+{
+ public:
+ EchinodermMitochondrialGeneticCode(const NucleicAlphabet * alpha);
+ virtual ~EchinodermMitochondrialGeneticCode();
+
+ public:
+ int translate(int state) const throw (Exception);
+ std::string translate(const std::string & state) const throw (Exception);
+ Sequence * translate(const Sequence & sequence) const throw (Exception)
+ {
+ return GeneticCode::translate(sequence);
+ }
+};
+
+} //end of namespace bpp.
+
+#endif //_ECHINODERMMITOCHONDRIALGENETICCODE_H_
+
diff --git a/src/Bpp/Seq/GeneticCode/GeneticCode.cpp b/src/Bpp/Seq/GeneticCode/GeneticCode.cpp
new file mode 100644
index 0000000..e8b780c
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/GeneticCode.cpp
@@ -0,0 +1,192 @@
+//
+// File: GeneticCode.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Oct 13 15:37:25 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "GeneticCode.h"
+#include "../SequenceTools.h"
+#include "../Alphabet/AlphabetTools.h"
+
+using namespace bpp;
+using namespace std;
+
+/**********************************************************************************************/
+
+StopCodonException::StopCodonException(const std::string& text, const std::string& codon) :
+ Exception("StopCodonException: " + text + "(" + codon + ")"),
+ codon_(codon) {}
+
+/**********************************************************************************************/
+
+vector<int> GeneticCode::getSynonymous(int aminoacid) const throw (BadIntException)
+{
+ // test:
+ proteicAlphabet_->intToChar(aminoacid);
+
+ vector<int> synonymes;
+ for (unsigned int i = 0; i < codonAlphabet_->getSize(); ++i)
+ {
+ try
+ {
+ if (translate(i) == aminoacid)
+ synonymes.push_back(i);
+ }
+ catch (StopCodonException)
+ { }
+ }
+ return synonymes;
+}
+
+/**********************************************************************************************/
+
+std::vector<std::string> GeneticCode::getSynonymous(const std::string& aminoacid) const throw (BadCharException)
+{
+ // test:
+ int aa = proteicAlphabet_->charToInt(aminoacid);
+
+ vector<string> synonymes;
+ for (unsigned int i = 0; i < codonAlphabet_->getSize(); ++i)
+ {
+ try
+ {
+ if (translate(i) == aa)
+ synonymes.push_back(codonAlphabet_->intToChar(i));
+ }
+ catch (StopCodonException)
+ { }
+ }
+ return synonymes;
+}
+
+/**********************************************************************************************/
+
+bool GeneticCode::isFourFoldDegenerated(int val) const
+{
+ if (codonAlphabet_->isStop(val))
+ return false;
+
+ vector<int> codon = codonAlphabet_->getPositions(val);
+ int acid = translate(val);
+
+ // test all the substitution on third codon position
+ for (int an = 0; an < 4; an++)
+ {
+ if (an == codon[2])
+ continue;
+ vector<int> mutcodon = codon;
+ mutcodon[2] = an;
+ int intcodon = codonAlphabet_->getCodon(mutcodon[0], mutcodon[1], mutcodon[2]);
+ if (codonAlphabet_->isStop(intcodon))
+ return false;
+ ;
+ int altacid = translate(intcodon);
+ if (altacid != acid) // if non-synonymous
+ {
+ return false;
+ }
+ }
+
+ return true;
+}
+
+/**********************************************************************************************/
+
+Sequence* GeneticCode::getCodingSequence(const Sequence& sequence, bool lookForInitCodon, bool includeInitCodon) const throw (Exception)
+{
+ size_t initPos = 0;
+ size_t stopPos = sequence.size();
+ if (AlphabetTools::isCodonAlphabet(sequence.getAlphabet()))
+ {
+ // Look for AUG(or ATG) codon:
+ if (lookForInitCodon)
+ {
+ for (unsigned int i = 0; i < sequence.size(); i++)
+ {
+ vector<int> pos = codonAlphabet_->getPositions(sequence[i]);
+ if (pos[0] == 0 && pos[1] == 3 && pos[2] == 2)
+ {
+ initPos = includeInitCodon ? i : i + 1;
+ break;
+ }
+ }
+ }
+ // Look for stop codon:
+ for (size_t i = initPos; i < sequence.size(); i++)
+ {
+ if (codonAlphabet_->isStop(sequence[i]))
+ {
+ stopPos = i;
+ break;
+ }
+ }
+ }
+ else if (AlphabetTools::isNucleicAlphabet(sequence.getAlphabet()))
+ {
+ // Look for AUG(or ATG) codon:
+ if (lookForInitCodon)
+ {
+ for (unsigned int i = 0; i < sequence.size() - 2; i++)
+ {
+ if (sequence[i] == 0 && sequence[i + 1] == 3 && sequence[i + 2] == 2)
+ {
+ initPos = includeInitCodon ? i : i + 3;
+ break;
+ }
+ }
+ }
+ // Look for stop codon:
+ const NucleicAlphabet* nucAlpha = codonAlphabet_->getNucleicAlphabet();
+ for (size_t i = initPos; i < sequence.size() - 2; i += 3)
+ {
+ string codon = nucAlpha->intToChar(sequence[i])
+ + nucAlpha->intToChar(sequence[i + 1])
+ + nucAlpha->intToChar(sequence[i + 2]);
+ if (codonAlphabet_->isStop(codon))
+ {
+ stopPos = i;
+ break;
+ }
+ }
+ }
+ else
+ throw AlphabetMismatchException("Sequence must have alphabet of type nucleic or codon in GeneticCode::getCodingSequence.", 0, sequence.getAlphabet());
+
+ return SequenceTools::subseq(sequence, initPos, stopPos - 1);
+}
+
+/**********************************************************************************************/
+
diff --git a/src/Bpp/Seq/GeneticCode/GeneticCode.h b/src/Bpp/Seq/GeneticCode/GeneticCode.h
new file mode 100644
index 0000000..294144f
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/GeneticCode.h
@@ -0,0 +1,174 @@
+//
+// File: GeneticCode.h
+// Created by: Julien Dutheil
+// Created on: Mon Oct 13 15:37:25 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _GENETICCODE_H_
+#define _GENETICCODE_H_
+
+#include "../Transliterator.h"
+#include "../Alphabet/CodonAlphabet.h"
+#include "../Alphabet/ProteicAlphabet.h"
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+ /**
+ * @brief Exception thrown when a stop codon is found.
+ */
+ class StopCodonException:
+ public Exception
+ {
+ private:
+ std::string codon_;
+
+ public:
+ // Class constructor
+ StopCodonException(const std::string& text, const std::string& codon);
+
+ // Class destructor
+ virtual ~StopCodonException() throw () {}
+
+ public:
+ virtual const std::string& getCodon() const { return codon_; }
+ };
+
+ /**
+ * @brief Partial implementation of the Transliterator interface for genetic code object.
+ *
+ * A genetic code object if a translator from a codon alphabet to a proteic alphabet.
+ * Depending on the codon alphabet used, several genetic code can be implemented.
+ *
+ * @see CodonAlphabet, ProteicAlphabet
+ */
+ class GeneticCode:
+ public AbstractTransliterator
+ {
+ protected:
+ const CodonAlphabet* codonAlphabet_;
+ const ProteicAlphabet* proteicAlphabet_;
+
+ public:
+ GeneticCode():
+ AbstractTransliterator() ,
+ codonAlphabet_(0),
+ proteicAlphabet_(0)
+ {}
+
+ GeneticCode(const GeneticCode& gc):
+ AbstractTransliterator(gc),
+ codonAlphabet_(gc.codonAlphabet_),
+ proteicAlphabet_(gc.proteicAlphabet_)
+ {}
+
+ GeneticCode& operator=(const GeneticCode& gc)
+ {
+ AbstractTransliterator::operator=(gc);
+ codonAlphabet_ = gc.codonAlphabet_;
+ proteicAlphabet_ = gc.proteicAlphabet_;
+ return *this;
+ }
+
+ virtual ~GeneticCode() {}
+
+ public:
+ /**
+ * @name Methods form the Transliterator interface.
+ *
+ * @{
+ */
+ const Alphabet* getSourceAlphabet() const { return codonAlphabet_; }
+ const Alphabet* getTargetAlphabet() const { return proteicAlphabet_; }
+ virtual int translate(int state) const throw (BadIntException, Exception) = 0;
+ virtual std::string translate(const std::string& state) const throw (BadCharException, Exception) = 0;
+ virtual Sequence* translate(const Sequence& sequence) const throw (Exception)
+ {
+ return AbstractTransliterator::translate(sequence);
+ }
+ /** @} */
+
+ public:
+ /**
+ * @name Specific methods.
+ *
+ * @{
+ */
+ bool areSynonymous(int i, int j) const throw (BadIntException)
+ {
+ return (translate(i) == translate(j));
+ }
+ bool areSynonymous(const std::string & i, const std::string & j) const throw (BadCharException)
+ {
+ return (translate(i) == translate(j));
+ }
+ std::vector<int> getSynonymous(int aminoacid) const throw (BadIntException);
+ std::vector<std::string> getSynonymous(const std::string & aminoacid) const throw (BadCharException);
+
+ /**
+ * @return True if the specified codon is fourfold degenerated
+ * (that is, if a mutation in the fourth position does not change the aminoacid).
+ * @author Benoit Nabholz, Annabelle Haudry
+ * @param codon The codon to test.
+ */
+ bool isFourFoldDegenerated(int codon) const;
+
+ /**
+ * @brief Get the subsequence corresponding to the coding part of a given sequence.
+ *
+ * If lookForInitCodon if set to 'true', the subsequence will start at the first AUG motif,
+ * otherwise the subsequence will start at the begining of the sequence.
+ * The subsequence ends at the first stop codon (excluded) found, or the end of the sequence.
+ *
+ * The sequence may have a nucleotide or codon alphabet.
+ * The subsequence has the same alphabet, name and comments of the input sequence.
+ * In case of nucleotide sequence and if the lookForInitCodon option is checked, the phase
+ * will be determined from the sequence.
+ *
+ * @param sequence The sequence to parse.
+ * @param lookForInitCodon Tell if the AUG codon must be found.
+ * @param includeInitCodon (if lookForInitCodon is true) tell if the init codon must be included in the subsequence.
+ * @return A nucleotide/codon subsequence.
+ */
+ Sequence* getCodingSequence(const Sequence& sequence, bool lookForInitCodon = false, bool includeInitCodon = false) const throw (Exception);
+ /** @} */
+ };
+
+} //end of namespace bpp.
+
+#endif //_GENETICCODE_H_
+
diff --git a/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp b/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp
new file mode 100644
index 0000000..df9c867
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp
@@ -0,0 +1,170 @@
+//
+// File: InvertebrateMitochondrialGeneticCode.cpp
+// Created by: Eric Bazin
+// Created on: wen mar 2 15:22:46 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "InvertebrateMitochondrialGeneticCode.h"
+#include "../Alphabet/InvertebrateMitochondrialCodonAlphabet.h"
+#include "../Alphabet/ProteicAlphabet.h"
+
+using namespace bpp;
+
+#include <iostream>
+
+using namespace std;
+
+InvertebrateMitochondrialGeneticCode::InvertebrateMitochondrialGeneticCode(const NucleicAlphabet * alpha) : GeneticCode()
+{
+ codonAlphabet_ = new InvertebrateMitochondrialCodonAlphabet(alpha);
+ proteicAlphabet_ = new ProteicAlphabet();
+}
+
+InvertebrateMitochondrialGeneticCode::~InvertebrateMitochondrialGeneticCode()
+{
+ delete codonAlphabet_;
+ delete proteicAlphabet_;
+}
+
+int InvertebrateMitochondrialGeneticCode::translate(int state) const throw (Exception)
+{
+ if(state == codonAlphabet_->getUnknownCharacterCode()) return proteicAlphabet_->getUnknownCharacterCode();
+ vector<int> positions = codonAlphabet_->getPositions(state);
+ switch(positions[0])
+ {
+ //First position:
+ case 0 : //A
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //AA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("K"); //Lysine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("N"); //Asparagine
+ }
+ case 1 : //AC
+ return proteicAlphabet_->charToInt("T"); //Threonine
+ case 2 : //AG
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("S"); //Serine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("S"); //Serine
+ }
+ case 3 : //AT
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2: return proteicAlphabet_->charToInt("M"); //Methionine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("I"); //Isoleucine
+ }
+ }
+ case 1 : //C
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //CA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("Q"); //Glutamine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("H"); //Histidine
+ }
+ case 1 : //CC
+ return proteicAlphabet_->charToInt("P"); //Proline
+ case 2 : //CG
+ return proteicAlphabet_->charToInt("R"); //Arginine
+ case 3 : //CT
+ return proteicAlphabet_->charToInt("L"); //Leucine
+ }
+ case 2 : //G
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //GA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("E"); //Glutamic acid
+ case 1 : case 3 : return proteicAlphabet_->charToInt("D"); //Aspartic acid
+ }
+ case 1 : //GC
+ return proteicAlphabet_->charToInt("A"); //Alanine
+ case 2 : //GG
+ return proteicAlphabet_->charToInt("G"); //Glycine
+ case 3 : //GT
+ return proteicAlphabet_->charToInt("V"); //Valine
+ }
+ case 3 : //T(U)
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //TA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : throw StopCodonException("", "TAA"); //Stop codon
+ case 2 : throw StopCodonException("", "TAG"); //Stop codon
+ case 1 : case 3 : return proteicAlphabet_->charToInt("Y"); //Tyrosine
+ }
+ case 1 : //TC
+ return proteicAlphabet_->charToInt("S"); //Serine
+ case 2 : //TG
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("W"); //Tryptophane
+ case 1 : case 3 : return proteicAlphabet_->charToInt("C"); //Cysteine
+ }
+ case 3 : //TT
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("L"); //Leucine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("F"); //Phenylalanine
+ }
+ }
+ }
+ throw BadIntException(state, "InvertebrateMitochondrialGeneticCode::translate", codonAlphabet_);
+}
+
+string InvertebrateMitochondrialGeneticCode::translate(const string & state) const throw (Exception)
+{
+ return proteicAlphabet_->intToChar(translate(codonAlphabet_->charToInt(state)));
+}
+
diff --git a/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h b/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h
new file mode 100644
index 0000000..2309852
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h
@@ -0,0 +1,75 @@
+//
+// File: InvertebrateMitochondrialGeneticCode.h
+// Created by: Eric Bazin
+// Created on: wen mar 2 15:22:46 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+
+#ifndef _INVERTEBRATEMITOCHONDRIALGENETICCODE_H_
+#define _INVERTEBRATEMITOCHONDRIALGENETICCODE_H_
+
+#include "GeneticCode.h"
+#include "../Alphabet/NucleicAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the Invertebrate
+ * Mitochondrial genetic code as describe on the NCBI website:
+ * http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG5
+ */
+
+class InvertebrateMitochondrialGeneticCode:
+ public GeneticCode
+{
+ public:
+ InvertebrateMitochondrialGeneticCode(const NucleicAlphabet * alpha);
+ virtual ~InvertebrateMitochondrialGeneticCode();
+
+ public:
+ int translate(int state) const throw (Exception);
+ std::string translate(const std::string & state) const throw (Exception);
+ Sequence * translate(const Sequence & sequence) const throw (Exception)
+ {
+ return GeneticCode::translate(sequence);
+ }
+};
+
+} //end of namespace bpp.
+
+#endif //_INVERTEBRATEMITOCHONDRIALGENETICCODE_H_
+
diff --git a/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp b/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp
new file mode 100644
index 0000000..da6fba8
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp
@@ -0,0 +1,172 @@
+//
+// File: StandardGeneticCode.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Oct 13 15:39:17 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "StandardGeneticCode.h"
+#include "../Alphabet/StandardCodonAlphabet.h"
+#include "../Alphabet/ProteicAlphabet.h"
+
+using namespace bpp;
+
+#include <iostream>
+
+using namespace std;
+
+StandardGeneticCode::StandardGeneticCode(const NucleicAlphabet* alpha) : GeneticCode()
+{
+ codonAlphabet_ = new StandardCodonAlphabet(alpha);
+ proteicAlphabet_ = new ProteicAlphabet();
+}
+
+
+StandardGeneticCode::~StandardGeneticCode()
+{
+ delete codonAlphabet_;
+ delete proteicAlphabet_;
+}
+
+int StandardGeneticCode::translate(int state) const throw (Exception)
+{
+ if (state == codonAlphabet_->getUnknownCharacterCode()) return proteicAlphabet_->getUnknownCharacterCode();
+ vector<int> positions = codonAlphabet_->getPositions(state);
+ switch (positions[0])
+ {
+ //First position:
+ case 0 : //A
+ switch (positions[1])
+ {
+ //Second position:
+ case 0 : //AA
+ switch (positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("K"); //Lysine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("N"); //Asparagine
+ }
+ case 1 : //AC
+ return proteicAlphabet_->charToInt("T"); //Threonine
+ case 2 : //AG
+ switch (positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("R"); //Arginine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("S"); //Serine
+ }
+ case 3 : //AT
+ switch (positions[2])
+ {
+ //Third position:
+ case 2: return proteicAlphabet_->charToInt("M"); //Methionine
+ case 0 : case 1 : case 3 : return proteicAlphabet_->charToInt("I"); //Isoleucine
+ }
+ }
+ case 1 : //C
+ switch (positions[1])
+ {
+ //Second position:
+ case 0 : //CA
+ switch (positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("Q"); //Glutamine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("H"); //Histidine
+ }
+ case 1 : //CC
+ return proteicAlphabet_->charToInt("P"); //Proline
+ case 2 : //CG
+ return proteicAlphabet_->charToInt("R"); //Arginine
+ case 3 : //CT
+ return proteicAlphabet_->charToInt("L"); //Leucine
+ }
+ case 2 : //G
+ switch (positions[1])
+ {
+ //Second position:
+ case 0 : //GA
+ switch (positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("E"); //Glutamic acid
+ case 1 : case 3 : return proteicAlphabet_->charToInt("D"); //Aspartic acid
+ }
+ case 1 : //GC
+ return proteicAlphabet_->charToInt("A"); //Alanine
+ case 2 : //GG
+ return proteicAlphabet_->charToInt("G"); //Glycine
+ case 3 : //GT
+ return proteicAlphabet_->charToInt("V"); //Valine
+ }
+ case 3 : //T(U)
+ switch (positions[1])
+ {
+ //Second position:
+ case 0 : //TA
+ switch (positions[2])
+ {
+ //Third position:
+ case 0 : throw StopCodonException("", "TAA"); //Stop codon
+ case 2 : throw StopCodonException("", "TAG"); //Stop codon
+ case 1 : case 3 : return proteicAlphabet_->charToInt("Y"); //Tyrosine
+ }
+ case 1 : //TC
+ return proteicAlphabet_->charToInt("S"); //Serine
+ case 2 : //TG
+ switch (positions[2])
+ {
+ //Third position:
+ case 0 : throw StopCodonException("", "TGA"); //Stop codon
+ case 2 : return proteicAlphabet_->charToInt("W"); //Tryptophane
+ case 1 : case 3 : return proteicAlphabet_->charToInt("C"); //Cysteine
+ }
+ case 3 : //TT
+ switch (positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("L"); //Leucine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("F"); //Phenylalanine
+ }
+ }
+ }
+ throw BadIntException(state, "StandardGeneticCode::translate", codonAlphabet_);
+}
+
+string StandardGeneticCode::translate(const string& state) const throw (Exception)
+{
+ return proteicAlphabet_->intToChar(translate(codonAlphabet_->charToInt(state)));
+}
+
diff --git a/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h b/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h
new file mode 100644
index 0000000..3f3eff4
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h
@@ -0,0 +1,73 @@
+//
+// File: StandardGeneticCode.h
+// Created by: Julien Dutheil
+// Created on: Mon Oct 13 15:39:17 2003
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _STANDARDGENETICCODE_H_
+#define _STANDARDGENETICCODE_H_
+
+#include "GeneticCode.h"
+#include "../Alphabet/NucleicAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the standard genetic code as describe on the NCBI
+ * web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
+ */
+
+class StandardGeneticCode:
+ public GeneticCode
+{
+ public:
+ StandardGeneticCode(const NucleicAlphabet * alpha);
+ virtual ~StandardGeneticCode();
+
+ public:
+ int translate(int state) const throw (Exception);
+ std::string translate(const std::string & state) const throw (Exception);
+ Sequence * translate(const Sequence & sequence) const throw (Exception)
+ {
+ return GeneticCode::translate(sequence);
+ }
+};
+
+} //end of namespace bpp.
+
+#endif //_STANDARDGENETICCODE_H_
+
diff --git a/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp b/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp
new file mode 100644
index 0000000..6915a18
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp
@@ -0,0 +1,172 @@
+//
+// File: VertebrateMitochondrialGeneticCode.cpp
+// Created by: Eric Bazin
+// Created on: wen mar 2 16:01:59 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "VertebrateMitochondrialGeneticCode.h"
+#include "../Alphabet/VertebrateMitochondrialCodonAlphabet.h"
+#include "../Alphabet/ProteicAlphabet.h"
+
+using namespace bpp;
+
+#include <iostream>
+
+using namespace std;
+
+VertebrateMitochondrialGeneticCode::VertebrateMitochondrialGeneticCode(const NucleicAlphabet * alpha) : GeneticCode()
+{
+ codonAlphabet_ = new VertebrateMitochondrialCodonAlphabet(alpha);
+ proteicAlphabet_ = new ProteicAlphabet();
+}
+
+
+VertebrateMitochondrialGeneticCode::~VertebrateMitochondrialGeneticCode()
+{
+ delete codonAlphabet_;
+ delete proteicAlphabet_;
+}
+
+int VertebrateMitochondrialGeneticCode::translate(int state) const throw (Exception)
+{
+ if(state == codonAlphabet_->getUnknownCharacterCode()) return proteicAlphabet_->getUnknownCharacterCode();
+ vector<int> positions = codonAlphabet_->getPositions(state);
+ switch(positions[0])
+ {
+ //First position:
+ case 0 : //A
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //AA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("K"); //Lysine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("N"); //Asparagine
+ }
+ case 1 : //AC
+ return proteicAlphabet_->charToInt("T"); //Threonine
+ case 2 : //AG
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : throw StopCodonException("", "AGA"); //Stop
+ case 2 : throw StopCodonException("", "AGG"); //Stop
+ case 1 : case 3 : return proteicAlphabet_->charToInt("S"); //Serine
+ }
+ case 3 : //AT
+ switch(positions[2])
+ {
+ //Third position:
+ case 2 : case 0 : return proteicAlphabet_->charToInt("M"); //Methionine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("I"); //Isoleucine
+ }
+ }
+ case 1 : //C
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //CA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("Q"); //Glutamine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("H"); //Histidine
+ }
+ case 1 : //CC
+ return proteicAlphabet_->charToInt("P"); //Proline
+ case 2 : //CG
+ return proteicAlphabet_->charToInt("R"); //Arginine
+ case 3 : //CT
+ return proteicAlphabet_->charToInt("L"); //Leucine
+ }
+ case 2 : //G
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //GA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("E"); //Glutamic acid
+ case 1 : case 3 : return proteicAlphabet_->charToInt("D"); //Aspartic acid
+ }
+ case 1 : //GC
+ return proteicAlphabet_->charToInt("A"); //Alanine
+ case 2 : //GG
+ return proteicAlphabet_->charToInt("G"); //Glycine
+ case 3 : //GT
+ return proteicAlphabet_->charToInt("V"); //Valine
+ }
+ case 3 : //T(U)
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //TA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : throw StopCodonException("", "TAA"); //Stop codon
+ case 2 : throw StopCodonException("", "TAG"); //Stop codon
+ case 1 : case 3 : return proteicAlphabet_->charToInt("Y"); //Tyrosine
+ }
+ case 1 : //TC
+ return proteicAlphabet_->charToInt("S"); //Serine
+ case 2 : //TG
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("W"); //Tryptophane
+ case 1 : case 3 : return proteicAlphabet_->charToInt("C"); //Cysteine
+ }
+ case 3 : //TT
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("L"); //Leucine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("F"); //Phenylalanine
+ }
+ }
+ }
+ throw BadIntException(state, "VertebrateMitochondrialGeneticCode::translate", codonAlphabet_);
+}
+
+string VertebrateMitochondrialGeneticCode::translate(const string & state) const throw (Exception)
+{
+ return proteicAlphabet_->intToChar(translate(codonAlphabet_->charToInt(state)));
+}
+
diff --git a/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h b/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h
new file mode 100644
index 0000000..a597fa0
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h
@@ -0,0 +1,73 @@
+//
+// File: VertebrateMitochondrialGeneticCode.h
+// Created by: Eric Bazin
+// Created on: wen mar 2 16:01:59 CET 2005
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _VERTEBRATEMITOCHONDRIALGENETICCODE_H_
+#define _VERTEBRATEMITOCHONDRIALGENETICCODE_H_
+
+#include "GeneticCode.h"
+#include "../Alphabet/NucleicAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the vertebrate mitochondrial genetic code as describe on the NCBI
+ * web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2
+ */
+
+class VertebrateMitochondrialGeneticCode:
+ public GeneticCode
+{
+ public:
+ VertebrateMitochondrialGeneticCode(const NucleicAlphabet* alpha);
+ virtual ~VertebrateMitochondrialGeneticCode();
+
+ public:
+ int translate(int state) const throw (Exception);
+ std::string translate(const std::string& state) const throw (Exception);
+ Sequence* translate(const Sequence& sequence) const throw (Exception)
+ {
+ return GeneticCode::translate(sequence);
+ }
+};
+
+} //end of namespace bpp.
+
+#endif //_VERTEBRATEMITOCHONDRIALGENETICCODE_H_
+
diff --git a/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp b/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp
new file mode 100644
index 0000000..d55c58a
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp
@@ -0,0 +1,170 @@
+//
+// File: YeastbrateMitochondrialGeneticCode.cpp
+// Created by: Benoit Nabholz
+// Created on: Sun Oct 10 14:33 CET 2010
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "YeastMitochondrialGeneticCode.h"
+#include "../Alphabet/YeastMitochondrialCodonAlphabet.h"
+#include "../Alphabet/ProteicAlphabet.h"
+
+using namespace bpp;
+
+#include <iostream>
+
+using namespace std;
+
+YeastMitochondrialGeneticCode::YeastMitochondrialGeneticCode(const NucleicAlphabet * alpha) : GeneticCode()
+{
+ codonAlphabet_ = new YeastMitochondrialCodonAlphabet(alpha);
+ proteicAlphabet_ = new ProteicAlphabet();
+}
+
+YeastMitochondrialGeneticCode::~YeastMitochondrialGeneticCode()
+{
+ delete codonAlphabet_;
+ delete proteicAlphabet_;
+}
+
+int YeastMitochondrialGeneticCode::translate(int state) const throw (Exception)
+{
+ if(state == codonAlphabet_->getUnknownCharacterCode()) return proteicAlphabet_->getUnknownCharacterCode();
+ vector<int> positions = codonAlphabet_->getPositions(state);
+ switch(positions[0])
+ {
+ //First position:
+ case 0 : //A
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //AA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("K"); //Lysine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("N"); //Asparagine
+ }
+ case 1 : //AC
+ return proteicAlphabet_->charToInt("T"); //Threonine
+ case 2 : //AG
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("S"); //Serine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("S"); //Serine
+ }
+ case 3 : //AT
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2: return proteicAlphabet_->charToInt("M"); //Methionine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("I"); //Isoleucine
+ }
+ }
+ case 1 : //C
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //CA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("Q"); //Glutamine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("H"); //Histidine
+ }
+ case 1 : //CC
+ return proteicAlphabet_->charToInt("P"); //Proline
+ case 2 : //CG
+ return proteicAlphabet_->charToInt("R"); //Arginine
+ case 3 : //CT
+ return proteicAlphabet_->charToInt("T"); //Threonine
+ }
+ case 2 : //G
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //GA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("E"); //Glutamic acid
+ case 1 : case 3 : return proteicAlphabet_->charToInt("D"); //Aspartic acid
+ }
+ case 1 : //GC
+ return proteicAlphabet_->charToInt("A"); //Alanine
+ case 2 : //GG
+ return proteicAlphabet_->charToInt("G"); //Glycine
+ case 3 : //GT
+ return proteicAlphabet_->charToInt("V"); //Valine
+ }
+ case 3 : //T(U)
+ switch(positions[1])
+ {
+ //Second position:
+ case 0 : //TA
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : throw StopCodonException("", "TAA"); //Stop codon
+ case 2 : throw StopCodonException("", "TAG"); //Stop codon
+ case 1 : case 3 : return proteicAlphabet_->charToInt("Y"); //Tyrosine
+ }
+ case 1 : //TC
+ return proteicAlphabet_->charToInt("S"); //Serine
+ case 2 : //TG
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("W"); //Tryptophane
+ case 1 : case 3 : return proteicAlphabet_->charToInt("C"); //Cysteine
+ }
+ case 3 : //TT
+ switch(positions[2])
+ {
+ //Third position:
+ case 0 : case 2 : return proteicAlphabet_->charToInt("L"); //Leucine
+ case 1 : case 3 : return proteicAlphabet_->charToInt("F"); //Phenylalanine
+ }
+ }
+ }
+ throw BadIntException(state, "YeastMitochondrialGeneticCode::translate", codonAlphabet_);
+}
+
+string YeastMitochondrialGeneticCode::translate(const string & state) const throw (Exception)
+{
+ return proteicAlphabet_->intToChar(translate(codonAlphabet_->charToInt(state)));
+}
+
diff --git a/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h b/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h
new file mode 100644
index 0000000..178ff19
--- /dev/null
+++ b/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h
@@ -0,0 +1,75 @@
+//
+// File: YeastbrateMitochondrialGeneticCode.h
+// Created by: Benoit Nabholz
+// Created on: Sun Oct 10 14:33 CET 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+
+#ifndef _YEASTMITOCHONDRIALGENETICCODE_H_
+#define _YEASTMITOCHONDRIALGENETICCODE_H_
+
+#include "GeneticCode.h"
+#include "../Alphabet/NucleicAlphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This class implements the Invertebrate
+ * Mitochondrial genetic code as describe on the NCBI website:
+ * http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG3
+ */
+
+class YeastMitochondrialGeneticCode:
+ public GeneticCode
+{
+ public:
+ YeastMitochondrialGeneticCode(const NucleicAlphabet * alpha);
+ virtual ~YeastMitochondrialGeneticCode();
+
+ public:
+ int translate(int state) const throw (Exception);
+ std::string translate(const std::string & state) const throw (Exception);
+ Sequence * translate(const Sequence & sequence) const throw (Exception)
+ {
+ return GeneticCode::translate(sequence);
+ }
+};
+
+} //end of namespace bpp.
+
+#endif //_YEASTMITOCHONDRIALGENETICCODE_H_
+
diff --git a/src/Bpp/Seq/Io/AbstractIAlignment.h b/src/Bpp/Seq/Io/AbstractIAlignment.h
new file mode 100644
index 0000000..a0db42e
--- /dev/null
+++ b/src/Bpp/Seq/Io/AbstractIAlignment.h
@@ -0,0 +1,185 @@
+//
+// File: AbstractIAlignment.h
+// Created by: Julien Dutheil
+// Created on: mon 27 jun 16:30 2005
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ABSTRACTIALIGNMENT_H_
+#define _ABSTRACTIALIGNMENT_H_
+
+#include "../Container/AlignedSequenceContainer.h"
+#include "../Alphabet/Alphabet.h"
+#include "ISequence.h"
+
+// From the STL:
+#include <string>
+#include <iostream>
+#include <fstream>
+
+namespace bpp
+{
+
+/**
+ * @brief Partial implementation of the IAlignment interface, dedicated to alignment readers.
+ */
+class AbstractIAlignment:
+ public virtual IAlignment
+{
+
+ public:
+ AbstractIAlignment() {}
+ virtual ~AbstractIAlignment() {}
+
+ public:
+
+ /**
+ * @name IAlignment methods:
+ *
+ * @{
+ */
+
+ /**
+ * @brief Add sequences to a container from a stream.
+ *
+ * @param input The input stream to read.
+ * @param sc The sequence container to update.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
+ {
+ appendAlignmentFromStream(input, sc);
+ }
+
+ /**
+ * @brief Add sequences to a container from a file.
+ *
+ * @param path The path to the file to read.
+ * @param sc The sequence container to update.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
+ {
+ appendAlignmentFromFile(path, sc);
+ }
+
+ virtual
+#if defined(NO_VIRTUAL_COV)
+ SiteContainer*
+#else
+ AlignedSequenceContainer*
+#endif
+ readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
+ {
+ return readAlignmentFromFile(path, alpha);
+ }
+
+ virtual
+#if defined(NO_VIRTUAL_COV)
+ SiteContainer*
+#else
+ AlignedSequenceContainer*
+#endif
+ readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
+ {
+ return readAlignmentFromStream(input, alpha);
+ }
+ /** @} */
+
+
+
+
+ protected:
+ /**
+ * @brief Append sequences to a container from a stream.
+ *
+ * This is the unique method to implement!
+ *
+ * @param input The input stream to read.
+ * @param sc The sequence container to update.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
+
+ /**
+ * @brief Append sequences to a container from a file.
+ *
+ * @param path The path to the file to read.
+ * @param sc The sequence container to update.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
+ {
+ std::ifstream input(path.c_str(), std::ios::in);
+ appendAlignmentFromStream(input, sc);
+ input.close();
+ }
+
+ /**
+ * @brief Read sequences from a stream.
+ *
+ * @param input The input stream to read.
+ * @param alpha The alphabet to use.
+ * @return A sequence container.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
+ {
+ AlignedSequenceContainer* asc = new AlignedSequenceContainer(alpha);
+ appendAlignmentFromStream(input, *asc);
+ return asc;
+ }
+
+ /**
+ * @brief Read sequences from a file.
+ *
+ * @param path The path to the file to read.
+ * @param alpha The alphabet to use.
+ * @return A sequence container.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
+ {
+ AlignedSequenceContainer* asc = new AlignedSequenceContainer(alpha);
+ appendAlignmentFromFile(path, *asc);
+ return asc;
+ }
+
+};
+
+} //end of namespace bpp.
+
+#endif // _ABSTRACTIALIGNMENT_H_
+
diff --git a/src/Bpp/Seq/Io/AbstractISequence.h b/src/Bpp/Seq/Io/AbstractISequence.h
new file mode 100644
index 0000000..c4fafb3
--- /dev/null
+++ b/src/Bpp/Seq/Io/AbstractISequence.h
@@ -0,0 +1,182 @@
+//
+// File: AbstractISequence.h
+// Created by: Julien Dutheil
+// Created on: ?
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ABSTRACTISEQUENCE_H_
+#define _ABSTRACTISEQUENCE_H_
+
+#include "ISequence.h"
+#include "../Container/VectorSequenceContainer.h"
+#include "../Alphabet/Alphabet.h"
+
+// From the STL:
+#include <string>
+#include <iostream>
+#include <fstream>
+
+namespace bpp
+{
+
+/**
+ * @brief Partial implementation of the ISequence interface.
+ */
+class AbstractISequence:
+ public virtual ISequence
+{
+
+ public:
+ AbstractISequence() {}
+ virtual ~AbstractISequence() {}
+
+ public:
+
+ /**
+ * @name ISequence methods:
+ *
+ * @{
+ */
+
+ public:
+ /**
+ * @brief Add sequences to a container from a stream.
+ *
+ * @param input The input stream to read.
+ * @param sc The sequence container to update.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
+ {
+ appendSequencesFromStream(input, sc);
+ }
+
+ /**
+ * @brief Add sequences to a container from a file.
+ *
+ * @param path The path to the file to read.
+ * @param sc The sequence container to update.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
+ {
+ appendSequencesFromFile(path, sc);
+ }
+
+ virtual
+#if defined(NO_VIRTUAL_COV)
+ SequenceContainer*
+#else
+ VectorSequenceContainer*
+#endif
+ readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
+ {
+ return readSequencesFromStream(input, alpha);
+ }
+
+ virtual
+#if defined(NO_VIRTUAL_COV)
+ SequenceContainer*
+#else
+ VectorSequenceContainer*
+#endif
+ readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
+ {
+ return readSequencesFromFile(path, alpha);
+ }
+ /** @} */
+
+
+ protected:
+ /**
+ * @brief Append sequences to a container from a stream.
+ *
+ * This is the unique method to implement!
+ *
+ * @param input The input stream to read.
+ * @param sc The sequence container to update.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
+
+ /**
+ * @brief Append sequences to a container from a file.
+ *
+ * @param path The path to the file to read.
+ * @param sc The sequence container to update.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
+ {
+ std::ifstream input(path.c_str(), std::ios::in);
+ appendSequencesFromStream(input, sc);
+ input.close();
+ }
+
+ /**
+ * @brief Read sequences from a stream.
+ *
+ * @param input The input stream to read.
+ * @param alpha The alphabet to use.
+ * @return A sequence container.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
+ {
+ VectorSequenceContainer* vsc = new VectorSequenceContainer(alpha);
+ appendSequencesFromStream(input, *vsc);
+ return vsc;
+ }
+
+ /**
+ * @brief Append sequences to a container from a file.
+ *
+ * @param path The path to the file to read.
+ * @param alpha The alphabet to use.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
+ {
+ VectorSequenceContainer* vsc = new VectorSequenceContainer(alpha);
+ appendSequencesFromFile(path, *vsc);
+ return vsc;
+ }
+};
+
+} //end of namespace bpp.
+
+#endif //_ABSTRACTISEQUENCE_H_
+
diff --git a/src/Bpp/Seq/Io/AbstractOAlignment.h b/src/Bpp/Seq/Io/AbstractOAlignment.h
new file mode 100644
index 0000000..2991063
--- /dev/null
+++ b/src/Bpp/Seq/Io/AbstractOAlignment.h
@@ -0,0 +1,86 @@
+//
+// File: AbstractOAlignment.h
+// Created by: Julien Dutheil
+// Created on: ?
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ABSTRACTOALIGNMENT_H_
+#define _ABSTRACTOALIGNMENT_H_
+
+#include "OSequence.h"
+#include "../Alphabet/Alphabet.h"
+#include "../Container/VectorSequenceContainer.h"
+
+// From the STL:
+#include <string>
+#include <fstream>
+
+namespace bpp
+{
+
+/**
+ * @brief Partial implementation of the OAlignment interface.
+ */
+class AbstractOAlignment:
+ public virtual OAlignment
+{
+
+ public:
+ AbstractOAlignment() {}
+ virtual ~AbstractOAlignment() {}
+
+ public:
+
+ /**
+ * @name OAlignment methods:
+ *
+ * @{
+ */
+ void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
+ void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
+ {
+ // Open file in specified mode
+ std::ofstream output(path.c_str(), overwrite ? (std::ios::out) : (std::ios::out | std::ios::app));
+ writeAlignment(output, sc);
+ output.close();
+ }
+ /** @} */
+};
+
+} //end of namespace bpp.
+
+#endif //_ABSTRACTOALIGNMENT_H_
+
diff --git a/src/Bpp/Seq/Io/AbstractOSequence.h b/src/Bpp/Seq/Io/AbstractOSequence.h
new file mode 100644
index 0000000..2acc7c8
--- /dev/null
+++ b/src/Bpp/Seq/Io/AbstractOSequence.h
@@ -0,0 +1,107 @@
+//
+// File: AbstractOSequence.h
+// Created by: Julien Dutheil
+// Created on: ?
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ABSTRACTOSEQUENCE_H_
+#define _ABSTRACTOSEQUENCE_H_
+
+#include "OSequence.h"
+#include "../Alphabet/Alphabet.h"
+#include "../Container/VectorSequenceContainer.h"
+
+// From the STL:
+#include <string>
+#include <fstream>
+
+namespace bpp
+{
+
+/**
+ * @brief Partial implementation of the OSequence and OAlignment interfaces.
+ */
+class AbstractOSequence:
+ public virtual OSequence,
+ public virtual OAlignment
+{
+
+ public:
+ AbstractOSequence() {}
+ virtual ~AbstractOSequence() {}
+
+ public:
+
+ /**
+ * @name OSequence methods:
+ *
+ * @{
+ */
+ void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
+ void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
+ {
+ // Open file in specified mode
+ std::ofstream output(path.c_str(), overwrite ? (std::ios::out) : (std::ios::out | std::ios::app));
+ writeSequences(output, sc);
+ output.close();
+ }
+ /** @} */
+
+ /**
+ * @name OAlignment methods:
+ *
+ * As a SiteContainer is a specialization of SequenceContainer, it is assumed that a OSequence
+ * object can write aligned sequence just like a OAlignment object.
+ * Therefore it implements the OAlignment interface by down-casting the SiteContainer
+ * to a SequenceContainer.
+ * @{
+ */
+ void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
+ {
+ writeSequences(output, dynamic_cast<const SequenceContainer&>(sc));
+ }
+ void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
+ {
+ writeSequences(path, dynamic_cast<const SequenceContainer&>(sc), overwrite);
+ }
+ /** @} */
+
+};
+
+} //end of namespace bpp.
+
+#endif //_ABSTRACTOSEQUENCE_H_
+
diff --git a/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp b/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp
new file mode 100644
index 0000000..689a9c0
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp
@@ -0,0 +1,134 @@
+//
+// File: BppOAlignmentReaderFormat.cpp
+// Created by: Julien Dutheil
+// Created on: Friday September 15th, 22:06
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "BppOAlignmentReaderFormat.h"
+#include "Mase.h"
+#include "Phylip.h"
+#include "Fasta.h"
+#include "Clustal.h"
+#include "Dcse.h"
+#include "NexusIoSequence.h"
+
+#include <Bpp/Text/KeyvalTools.h>
+
+#include <string>
+#include <memory>
+
+using namespace bpp;
+using namespace std;
+
+IAlignment* BppOAlignmentReaderFormat::read(const std::string& description) throw (Exception)
+{
+ unparsedArguments_.clear();
+ string format = "";
+ KeyvalTools::parseProcedure(description, format, unparsedArguments_);
+ auto_ptr<IAlignment> iAln;
+ if (format == "Mase")
+ {
+ iAln.reset(new Mase());
+ }
+ else if (format == "Phylip")
+ {
+ bool sequential = true, extended = true;
+ string split = " ";
+ if (unparsedArguments_.find("order") != unparsedArguments_.end())
+ {
+ if (unparsedArguments_["order"] == "sequential")
+ sequential = true;
+ else if (unparsedArguments_["order"] == "interleaved")
+ sequential = false;
+ else
+ ApplicationTools::displayWarning("Argument '" +
+ unparsedArguments_["order"] +
+ "' for argument 'Phylip#order' is unknown. " +
+ "Default used instead: sequential.");
+ }
+ else
+ ApplicationTools::displayWarning("Argument 'Phylip#order' not found. Default used instead: sequential.");
+ if (unparsedArguments_.find("type") != unparsedArguments_.end())
+ {
+ if (unparsedArguments_["type"] == "extended")
+ {
+ extended = true;
+ split = ApplicationTools::getStringParameter("split", unparsedArguments_, "spaces", "", true, false);
+ if (split == "spaces")
+ split = " ";
+ else if (split == "tab")
+ split = "\t";
+ else
+ throw Exception("Unknown option for Phylip#split: " + split);
+ }
+ else if (unparsedArguments_["type"] == "classic")
+ extended = false;
+ else
+ ApplicationTools::displayWarning("Argument '" +
+ unparsedArguments_["type"] + "' for parameter 'Phylip#type' is unknown. " +
+ "Default used instead: extended.");
+ }
+ else
+ ApplicationTools::displayWarning("Argument 'Phylip#type' not found. Default used instead: extended.");
+ iAln.reset(new Phylip(extended, sequential, 100, true, split));
+ }
+ else if (format == "Fasta")
+ {
+ bool strictNames = ApplicationTools::getBooleanParameter("strict_names", unparsedArguments_, false, "", true, false);
+ bool extended = ApplicationTools::getBooleanParameter("extended", unparsedArguments_, false, "", true, false);
+ iAln.reset(new Fasta(100, true, extended, strictNames));
+ }
+ else if (format == "Clustal")
+ {
+ unsigned int extraSpaces = ApplicationTools::getParameter<unsigned int>("extraSpaces", unparsedArguments_, 0, "", true, false);
+ iAln.reset(new Clustal(true, extraSpaces));
+ }
+ else if (format == "Dcse")
+ {
+ iAln.reset(new DCSE());
+ }
+ else if (format == "Nexus")
+ {
+ iAln.reset(new NexusIOSequence());
+ }
+ else
+ {
+ throw Exception("Sequence format '" + format + "' unknown.");
+ }
+
+ return iAln.release();
+}
+
diff --git a/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h b/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h
new file mode 100644
index 0000000..05667a5
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h
@@ -0,0 +1,95 @@
+//
+// File: BppOAlignmentReaderFormat.h
+// Created by: Julien Dutheil
+// Created on: Friday September 15th, 22:04
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _BPPOALIGNMENTREADERFORMAT_H_
+#define _BPPOALIGNMENTREADERFORMAT_H_
+
+#include "IoSequenceFactory.h"
+
+namespace bpp
+{
+
+ /**
+ * @brief Sequence I/O in BppO format.
+ *
+ * Creates a new IAlignment object according to
+ * distribution description syntax (see the Bio++ Program Suite
+ * manual for a detailed description of this syntax).
+ *
+ */
+ class BppOAlignmentReaderFormat:
+ public virtual IOFormat
+ {
+ private:
+ bool verbose_;
+ std::map<std::string, std::string> unparsedArguments_;
+
+ public:
+ BppOAlignmentReaderFormat(bool verbose = true):
+ verbose_(verbose),
+ unparsedArguments_() {}
+ virtual ~BppOAlignmentReaderFormat() {}
+
+ public:
+ const std::string getFormatName() const { return "BppO"; }
+
+ const std::string getFormatDescription() const { return "Bpp Options format."; }
+
+ const std::string getDataType() const { return "Alignment reader"; }
+
+ /**
+ * @brief Read a IAlignment object from a string.
+ *
+ * @param description A string describing the reader in the keyval syntax.
+ * @return A new IAlignment object according to options specified.
+ * @throw Exception if an error occured.
+ */
+ IAlignment* read(const std::string& description) throw (Exception);
+
+ /**
+ * @return The arguments and their unparsed values from the last call of the read function, if there are any.
+ */
+ virtual const std::map<std::string, std::string>& getUnparsedArguments() const { return unparsedArguments_; }
+
+ };
+
+} //end of namespace bpp.
+
+#endif //_BPPOALIGNMENTREADERFORMAT_H_
+
diff --git a/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp b/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp
new file mode 100644
index 0000000..035940d
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp
@@ -0,0 +1,127 @@
+//
+// File: BppOAlignmentWriterFormat.cpp
+// Created by: Julien Dutheil
+// Created on: Friday September 15th, 22:12
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "BppOAlignmentWriterFormat.h"
+#include "Fasta.h"
+#include "Mase.h"
+#include "Clustal.h"
+#include "Phylip.h"
+#include "Stockholm.h"
+
+#include <Bpp/Text/KeyvalTools.h>
+
+#include <string>
+#include <memory>
+
+using namespace bpp;
+using namespace std;
+
+OAlignment* BppOAlignmentWriterFormat::read(const std::string& description) throw (Exception)
+{
+ unparsedArguments_.clear();
+ string format = "";
+ KeyvalTools::parseProcedure(description, format, unparsedArguments_);
+ unsigned int ncol = ApplicationTools::getParameter<unsigned int>("length", unparsedArguments_, 100, "", true, false);
+ auto_ptr<OAlignment> oAln;
+ if (format == "Fasta")
+ {
+ oAln.reset(new Fasta(ncol));
+ }
+ else if (format == "Mase")
+ {
+ oAln.reset(new Mase(ncol));
+ }
+ else if (format == "Clustal")
+ {
+ oAln.reset(new Clustal(ncol));
+ }
+ else if (format == "Phylip")
+ {
+ bool sequential = true, extended = true;
+ string split = " ";
+ if (unparsedArguments_.find("order") != unparsedArguments_.end())
+ {
+ if (unparsedArguments_["order"] == "sequential")
+ sequential = true;
+ else if (unparsedArguments_["order"] == "interleaved")
+ sequential = false;
+ else
+ ApplicationTools::displayWarning("Argument '" +
+ unparsedArguments_["order"] +
+ "' for argument 'Phylip#order' is unknown. " +
+ "Default used instead: sequential.");
+ }
+ else
+ ApplicationTools::displayWarning("Argument 'Phylip#order' not found. Default used instead: sequential.");
+ if (unparsedArguments_.find("type") != unparsedArguments_.end())
+ {
+ if (unparsedArguments_["type"] == "extended")
+ {
+ extended = true;
+ split = ApplicationTools::getStringParameter("split", unparsedArguments_, "spaces", "", true, false);
+ if (split == "spaces")
+ split = " ";
+ else if (split == "tab")
+ split = "\t";
+ else
+ throw Exception("Unknown option for Phylip#split: " + split);
+ }
+ else if (unparsedArguments_["type"] == "classic")
+ extended = false;
+ else
+ ApplicationTools::displayWarning("Argument '" +
+ unparsedArguments_["type"] + "' for parameter 'Phylip#type' is unknown. " +
+ "Default used instead: extended.");
+ }
+ else
+ ApplicationTools::displayWarning("Argument 'Phylip#type' not found. Default used instead: extended.");
+ oAln.reset(new Phylip(extended, sequential, ncol, true, split));
+ }
+ else if (format == "Stockholm")
+ {
+ oAln.reset(reinterpret_cast<OAlignment*>(new Stockholm()));
+ }
+ else
+ {
+ throw Exception("Sequence format '" + format + "' unknown.");
+ }
+
+ return oAln.release();
+}
+
diff --git a/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h b/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h
new file mode 100644
index 0000000..a27451b
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h
@@ -0,0 +1,95 @@
+//
+// File: BppOAlignmentWriterFormat.h
+// Created by: Julien Dutheil
+// Created on: Saturday September 15th, 22:10
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _BPPOALIGNMENTWRITERFORMAT_H_
+#define _BPPOALIGNMENTWRITERFORMAT_H_
+
+#include "IoSequenceFactory.h"
+
+namespace bpp
+{
+
+ /**
+ * @brief Sequence I/O in BppO format.
+ *
+ * Creates a new OAlignment object according to
+ * distribution description syntax (see the Bio++ Program Suite
+ * manual for a detailed description of this syntax).
+ *
+ */
+ class BppOAlignmentWriterFormat:
+ public virtual IOFormat
+ {
+ private:
+ bool verbose_;
+ std::map<std::string, std::string> unparsedArguments_;
+
+ public:
+ BppOAlignmentWriterFormat(bool verbose = true):
+ verbose_(verbose),
+ unparsedArguments_() {}
+ virtual ~BppOAlignmentWriterFormat() {}
+
+ public:
+ const std::string getFormatName() const { return "BppO"; }
+
+ const std::string getFormatDescription() const { return "Bpp Options format."; }
+
+ const std::string getDataType() const { return "Alignment writer"; }
+
+ /**
+ * @brief Read a OAlignment object from a string.
+ *
+ * @param description A string describing the reader in the keyval syntax.
+ * @return A new OAlignment object according to options specified.
+ * @throw Exception if an error occured.
+ */
+ OAlignment* read(const std::string& description) throw (Exception);
+
+ /**
+ * @return The arguments and their unparsed values from the last call of the read function, if there are any.
+ */
+ virtual const std::map<std::string, std::string>& getUnparsedArguments() const { return unparsedArguments_; }
+
+ };
+
+} //end of namespace bpp.
+
+#endif //_BPPOALIGNMENTWRITERFORMAT_H_
+
diff --git a/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp b/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp
new file mode 100644
index 0000000..2598dd3
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp
@@ -0,0 +1,155 @@
+//
+// File: BppOAlphabetIndex1Format.cpp
+// Created by: Julien Dutheil
+// Created on: Thursday Februar 07th, 16:30
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "BppOAlphabetIndex1Format.h"
+#include "../Alphabet/AlphabetTools.h"
+#include "../AlphabetIndex/GranthamAAPolarityIndex.h"
+#include "../AlphabetIndex/GranthamAAVolumeIndex.h"
+#include "../AlphabetIndex/KleinAANetChargeIndex.h"
+#include "../AlphabetIndex/AAChouFasmanAHelixIndex.h"
+#include "../AlphabetIndex/AAChouFasmanBSheetIndex.h"
+#include "../AlphabetIndex/AAChouFasmanTurnIndex.h"
+#include "../AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h"
+#include "../AlphabetIndex/AASurfaceIndex.h"
+#include "../AlphabetIndex/AAMassIndex.h"
+#include "../AlphabetIndex/AAVolumeIndex.h"
+#include "../AlphabetIndex/AAChargeIndex.h"
+#include "../AlphabetIndex/AASEAInf10Index.h"
+#include "../AlphabetIndex/AASEA1030Index.h"
+#include "../AlphabetIndex/AASEASup30Index.h"
+#include "../AlphabetIndex/AAIndex1Entry.h"
+
+#include <Bpp/Text/KeyvalTools.h>
+#include <Bpp/App/ApplicationTools.h>
+
+#include <string>
+#include <memory>
+
+using namespace bpp;
+using namespace std;
+
+AlphabetIndex1* BppOAlphabetIndex1Format::read(const std::string& description) throw (Exception)
+{
+ if (description != "None")
+ {
+ string name;
+ map<string, string> args;
+ KeyvalTools::parseProcedure(description, name, args);
+ if (verbose_)
+ ApplicationTools::displayResult(message_, description);
+
+ //Currently, only protein indices are supported:
+ if (!AlphabetTools::isProteicAlphabet(alphabet_))
+ throw Exception("BppOAlphabetIndex1Format::read. This index is only supported with a protein alphabet.");
+ if (name == "GranthamPolarity")
+ {
+ return new GranthamAAPolarityIndex();
+ }
+ else if (name == "GranthamVolume")
+ {
+ return new GranthamAAVolumeIndex();
+ }
+ else if (name == "KleinCharge")
+ {
+ return new KleinAANetChargeIndex();
+ }
+ else if (name == "ChouFasmanAHelix")
+ {
+ return new AAChouFasmanAHelixIndex();
+ }
+ else if (name == "ChouFasmanBSheet")
+ {
+ return new AAChouFasmanBSheetIndex();
+ }
+ else if (name == "ChouFasmanTurn")
+ {
+ return new AAChouFasmanTurnIndex();
+ }
+ else if (name == "ChenGuHuangHydrophobicity")
+ {
+ return new AAChenGuHuangHydrophobicityIndex();
+ }
+ else if (name == "Surface")
+ {
+ return new AASurfaceIndex();
+ }
+ else if (name == "Mass")
+ {
+ return new AAMassIndex();
+ }
+ else if (name == "Volume")
+ {
+ return new AAVolumeIndex();
+ }
+ else if (name == "Charge")
+ {
+ return new AAChargeIndex();
+ }
+ else if (name == "SEAMedium")
+ {
+ return new AASEA1030Index();
+ }
+ else if (name == "SEAHigh")
+ {
+ return new AASEASup30Index();
+ }
+ else if (name == "SEALow")
+ {
+ return new AASEAInf10Index();
+ }
+ else if (name == "User")
+ {
+ string aax1FilePath = ApplicationTools::getAFilePath("file", args, true, true, "", false);
+ ifstream aax1File(aax1FilePath.c_str(), ios::in);
+ AAIndex1Entry* I = new AAIndex1Entry (aax1File);
+ aax1File.close();
+ return I;
+ }
+ else
+ {
+ throw Exception("Invalid index1 '" + name + "'.");
+ }
+ }
+ else
+ {
+ return 0;
+ }
+
+}
+
diff --git a/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h b/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h
new file mode 100644
index 0000000..80083ca
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h
@@ -0,0 +1,114 @@
+//
+// File: BppOAlphabetIndex1Format.h
+// Created by: Julien Dutheil
+// Created on: Thursday Februar 07th, 16:30
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _BPPOALPHABETINDEX1FORMAT_H_
+#define _BPPOALPHABETINDEX1FORMAT_H_
+
+#include <Bpp/Io/IoFormat.h>
+#include "../AlphabetIndex/AlphabetIndex1.h"
+
+// From the STL:
+#include <string>
+
+namespace bpp
+{
+
+ /**
+ * @brief AlphabetIndex1 I/O in BppO format.
+ *
+ * Enables the instanciation of AlphabetIndex1 objects according to
+ * the BppO syntax (see the Bio++ Program Suite
+ * manual for a detailed description of this syntax).
+ *
+ */
+ class BppOAlphabetIndex1Format:
+ public virtual IOFormat
+ {
+ private:
+ const Alphabet* alphabet_;
+ std::string message_;
+ bool verbose_;
+
+ public:
+ /**
+ * @param alphabet The alphabet for which indices should be built.
+ * The alphabet will be used to check that the instanciated index is compatible.
+ * @param message Some text describing what the index is intended for.
+ * @param verbose Tell if some messages should be printed while parsing.
+ */
+ BppOAlphabetIndex1Format(const Alphabet* alphabet, const std::string& message, bool verbose = true):
+ alphabet_(alphabet), message_(message), verbose_(verbose) {}
+
+ BppOAlphabetIndex1Format(const BppOAlphabetIndex1Format& format):
+ alphabet_(format.alphabet_),
+ message_(format.message_),
+ verbose_(format.verbose_) {}
+
+ BppOAlphabetIndex1Format& operator=(const BppOAlphabetIndex1Format& format)
+ {
+ alphabet_ = format.alphabet_;
+ message_ = format.message_;
+ verbose_ = format.verbose_;
+ return *this;
+ }
+
+ virtual ~BppOAlphabetIndex1Format() {}
+
+ public:
+ const std::string getFormatName() const { return "BppO"; }
+
+ const std::string getFormatDescription() const { return "Bpp Options format."; }
+
+ const std::string getDataType() const { return "AlphabetIndex1"; }
+
+ /**
+ * @brief Read a AlphabetIndex1 object from a string.
+ *
+ * @param description A string describing the index in the keyval syntax.
+ * @return A new AlphabetIndex1 object according to options specified.
+ * @throw Exception if an error occured.
+ */
+ AlphabetIndex1* read(const std::string& description) throw (Exception);
+
+ };
+
+} //end of namespace bpp.
+
+#endif //_BPPOALPHABETINDEX1FORMAT_H_
+
diff --git a/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp b/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp
new file mode 100644
index 0000000..6a17c86
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp
@@ -0,0 +1,125 @@
+//
+// File: BppOAlphabetIndex2Format.cpp
+// Created by: Julien Dutheil
+// Created on: Thursday Februar 07th, 19:26
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "BppOAlphabetIndex2Format.h"
+#include "BppOAlphabetIndex1Format.h"
+#include "../Alphabet/AlphabetTools.h"
+#include "../AlphabetIndex/BLOSUM50.h"
+#include "../AlphabetIndex/GranthamAAChemicalDistance.h"
+#include "../AlphabetIndex/MiyataAAChemicalDistance.h"
+#include "../AlphabetIndex/SimpleIndexDistance.h"
+#include "../AlphabetIndex/AAIndex2Entry.h"
+#include "../AlphabetIndex/AlphabetIndex1.h"
+
+#include <Bpp/Text/KeyvalTools.h>
+#include <Bpp/App/ApplicationTools.h>
+
+#include <string>
+#include <memory>
+
+using namespace bpp;
+using namespace std;
+
+AlphabetIndex2* BppOAlphabetIndex2Format::read(const std::string& description) throw (Exception)
+{
+ if (description != "None")
+ {
+ string name;
+ map<string, string> args;
+ KeyvalTools::parseProcedure(description, name, args);
+ if (verbose_)
+ ApplicationTools::displayResult(message_, description);
+
+ //Currently, only protein indices are supported:
+ if (!AlphabetTools::isProteicAlphabet(alphabet_))
+ throw Exception("BppOAlphabetIndex2Format::read. This index is only supported with a protein alphabet.");
+ if (name == "Blosum50")
+ {
+ return new BLOSUM50();
+ }
+ else if (name == "Grantham")
+ {
+ bool sym = ApplicationTools::getBooleanParameter("symmetrical", args, true, "", true);
+ GranthamAAChemicalDistance* M = new GranthamAAChemicalDistance();
+ M->setSymmetric(sym);
+ if (!sym) M->setPC1Sign(true);
+ return M;
+ }
+ else if (name == "Miyata")
+ {
+ bool sym = ApplicationTools::getBooleanParameter("symmetrical", args, true, "", true);
+ MiyataAAChemicalDistance* M = new MiyataAAChemicalDistance();
+ M->setSymmetric(sym);
+ return M;
+ }
+ else if (name == "Diff")
+ {
+ string index1Desc = ApplicationTools::getStringParameter("index1", args, "None", "", true);
+ bool sym = ApplicationTools::getBooleanParameter("symmetrical", args, true, "", true);
+ BppOAlphabetIndex1Format index1Reader(alphabet_, "" , false);
+ AlphabetIndex1* index1 = index1Reader.read(index1Desc);
+ if (index1) {
+ SimpleIndexDistance* M = new SimpleIndexDistance(index1);
+ M->setSymmetric(sym);
+ return M;
+ } else {
+ throw Exception("BppOAlphabetIndex2Format::read. Diff: index1 should be provided.");
+ }
+ }
+ else if (name == "User")
+ {
+ bool sym = ApplicationTools::getBooleanParameter("symmetrical", args, true, "", true);
+ string aax2FilePath = ApplicationTools::getAFilePath("file", args, true, true, "", false);
+ ifstream aax2File(aax2FilePath.c_str(), ios::in);
+ AAIndex2Entry* M = new AAIndex2Entry(aax2File, sym);
+ aax2File.close();
+ return M;
+ }
+ else
+ {
+ throw Exception("Invalid index2 '" + name + "'.");
+ }
+ }
+ else
+ {
+ return 0;
+ }
+
+}
+
diff --git a/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h b/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h
new file mode 100644
index 0000000..cbe65ff
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h
@@ -0,0 +1,114 @@
+//
+// File: BppOAlphabetIndex2Format.h
+// Created by: Julien Dutheil
+// Created on: Thursday Februar 07th, 19:26
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _BPPOALPHABETINDEX2FORMAT_H_
+#define _BPPOALPHABETINDEX2FORMAT_H_
+
+#include <Bpp/Io/IoFormat.h>
+#include "../AlphabetIndex/AlphabetIndex2.h"
+
+// From the STL:
+#include <string>
+
+namespace bpp
+{
+
+ /**
+ * @brief AlphabetIndex2 I/O in BppO format.
+ *
+ * Enables the instanciation of AlphabetIndex2 objects according to
+ * the BppO syntax (see the Bio++ Program Suite
+ * manual for a detailed description of this syntax).
+ *
+ */
+ class BppOAlphabetIndex2Format:
+ public virtual IOFormat
+ {
+ private:
+ const Alphabet* alphabet_;
+ std::string message_;
+ bool verbose_;
+
+ public:
+ /**
+ * @param alphabet The alphabet for which indices should be built.
+ * The alphabet will be used to check that the instanciated index is compatible.
+ * @param message Some text describing what the index is intended for.
+ * @param verbose Tell if some messages should be printed while parsing.
+ */
+ BppOAlphabetIndex2Format(const Alphabet* alphabet, const std::string& message, bool verbose = true):
+ alphabet_(alphabet), message_(message), verbose_(verbose) {}
+
+ BppOAlphabetIndex2Format(const BppOAlphabetIndex2Format& format):
+ alphabet_(format.alphabet_),
+ message_(format.message_),
+ verbose_(format.verbose_) {}
+
+ BppOAlphabetIndex2Format& operator=(const BppOAlphabetIndex2Format& format)
+ {
+ alphabet_ = format.alphabet_;
+ message_ = format.message_;
+ verbose_ = format.verbose_;
+ return *this;
+ }
+
+ virtual ~BppOAlphabetIndex2Format() {}
+
+ public:
+ const std::string getFormatName() const { return "BppO"; }
+
+ const std::string getFormatDescription() const { return "Bpp Options format."; }
+
+ const std::string getDataType() const { return "AlphabetIndex2"; }
+
+ /**
+ * @brief Read a AlphabetIndex1 object from a string.
+ *
+ * @param description A string describing the index in the keyval syntax.
+ * @return A new AlphabetIndex2 object according to options specified.
+ * @throw Exception if an error occured.
+ */
+ AlphabetIndex2* read(const std::string& description) throw (Exception);
+
+ };
+
+} //end of namespace bpp.
+
+#endif //_BPPOALPHABETINDEX2FORMAT_H_
+
diff --git a/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp b/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp
new file mode 100644
index 0000000..d1bc2d1
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp
@@ -0,0 +1,139 @@
+//
+// File: BppOSequenceReaderFormat.cpp
+// Created by: Julien Dutheil
+// Created on: Friday September 14th, 14:08
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "BppOSequenceReaderFormat.h"
+#include "Mase.h"
+#include "Phylip.h"
+#include "Fasta.h"
+#include "Clustal.h"
+#include "Dcse.h"
+#include "GenBank.h"
+#include "NexusIoSequence.h"
+
+#include <Bpp/Text/KeyvalTools.h>
+
+#include <string>
+#include <memory>
+
+using namespace bpp;
+using namespace std;
+
+ISequence* BppOSequenceReaderFormat::read(const std::string& description) throw (Exception)
+{
+ unparsedArguments_.clear();
+ string format = "";
+ KeyvalTools::parseProcedure(description, format, unparsedArguments_);
+ auto_ptr<ISequence> iSeq;
+ if (format == "Mase")
+ {
+ iSeq.reset(new Mase());
+ }
+ else if (format == "Phylip")
+ {
+ bool sequential = true, extended = true;
+ string split = " ";
+ if (unparsedArguments_.find("order") != unparsedArguments_.end())
+ {
+ if (unparsedArguments_["order"] == "sequential")
+ sequential = true;
+ else if (unparsedArguments_["order"] == "interleaved")
+ sequential = false;
+ else
+ ApplicationTools::displayWarning("Argument '" +
+ unparsedArguments_["order"] +
+ "' for argument 'Phylip#order' is unknown. " +
+ "Default used instead: sequential.");
+ }
+ else
+ ApplicationTools::displayWarning("Argument 'Phylip#order' not found. Default used instead: sequential.");
+ if (unparsedArguments_.find("type") != unparsedArguments_.end())
+ {
+ if (unparsedArguments_["type"] == "extended")
+ {
+ extended = true;
+ split = ApplicationTools::getStringParameter("split", unparsedArguments_, "spaces", "", true, false);
+ if (split == "spaces")
+ split = " ";
+ else if (split == "tab")
+ split = "\t";
+ else
+ throw Exception("Unknown option for Phylip#split: " + split);
+ }
+ else if (unparsedArguments_["type"] == "classic")
+ extended = false;
+ else
+ ApplicationTools::displayWarning("Argument '" +
+ unparsedArguments_["type"] + "' for parameter 'Phylip#type' is unknown. " +
+ "Default used instead: extended.");
+ }
+ else
+ ApplicationTools::displayWarning("Argument 'Phylip#type' not found. Default used instead: extended.");
+ iSeq.reset(new Phylip(extended, sequential, 100, true, split));
+ }
+ else if (format == "Fasta")
+ {
+ bool strictNames = ApplicationTools::getBooleanParameter("strict_names", unparsedArguments_, false, "", true, false);
+ bool extended = ApplicationTools::getBooleanParameter("extended", unparsedArguments_, false, "", true, false);
+ iSeq.reset(new Fasta(100, true, extended, strictNames));
+ }
+ else if (format == "Clustal")
+ {
+ unsigned int extraSpaces = ApplicationTools::getParameter<unsigned int>("extraSpaces", unparsedArguments_, 0, "", true, false);
+ iSeq.reset(new Clustal(true, extraSpaces));
+ }
+ else if (format == "Dcse")
+ {
+ iSeq.reset(new DCSE());
+ }
+ else if (format == "GenBank")
+ {
+ iSeq.reset(reinterpret_cast<ISequence*>(new GenBank())); // This is required to remove a strict-aliasing warning in gcc 4.4
+ }
+ else if (format == "Nexus")
+ {
+ iSeq.reset(new NexusIOSequence());
+ }
+ else
+ {
+ throw Exception("Sequence format '" + format + "' unknown.");
+ }
+
+ return iSeq.release();
+}
+
diff --git a/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h b/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h
new file mode 100644
index 0000000..7d11267
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h
@@ -0,0 +1,95 @@
+//
+// File: BppOSequenceReaderFormat.h
+// Created by: Julien Dutheil
+// Created on: Friday September 14th, 14:08
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _BPPOSEQUENCEREADERFORMAT_H_
+#define _BPPOSEQUENCEREADERFORMAT_H_
+
+#include "IoSequenceFactory.h"
+
+namespace bpp
+{
+
+ /**
+ * @brief Sequence I/O in BppO format.
+ *
+ * Creates a new ISequence object according to
+ * distribution description syntax (see the Bio++ Program Suite
+ * manual for a detailed description of this syntax).
+ *
+ */
+ class BppOSequenceReaderFormat:
+ public virtual IOFormat
+ {
+ private:
+ bool verbose_;
+ std::map<std::string, std::string> unparsedArguments_;
+
+ public:
+ BppOSequenceReaderFormat(bool verbose = true):
+ verbose_(verbose),
+ unparsedArguments_() {}
+ virtual ~BppOSequenceReaderFormat() {}
+
+ public:
+ const std::string getFormatName() const { return "BppO"; }
+
+ const std::string getFormatDescription() const { return "Bpp Options format."; }
+
+ const std::string getDataType() const { return "Sequence reader"; }
+
+ /**
+ * @brief Read a ISequence object from a string.
+ *
+ * @param description A string describing the reader in the keyval syntax.
+ * @return A new ISequence object according to options specified.
+ * @throw Exception if an error occured.
+ */
+ ISequence* read(const std::string& description) throw (Exception);
+
+ /**
+ * @return The arguments and their unparsed values from the last call of the read function, if there are any.
+ */
+ virtual const std::map<std::string, std::string>& getUnparsedArguments() const { return unparsedArguments_; }
+
+ };
+
+} //end of namespace bpp.
+
+#endif //_BPPOSEQUENCEREADERFORMAT_H_
+
diff --git a/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp b/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp
new file mode 100644
index 0000000..d3f8e7e
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp
@@ -0,0 +1,70 @@
+//
+// File: BppOSequenceReaderFormat.cpp
+// Created by: Julien Dutheil
+// Created on: Tuesday November 20th, 13:27
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "BppOSequenceStreamReaderFormat.h"
+#include "Fasta.h"
+
+#include <Bpp/Text/KeyvalTools.h>
+
+#include <string>
+#include <memory>
+
+using namespace bpp;
+using namespace std;
+
+ISequenceStream* BppOSequenceStreamReaderFormat::read(const std::string& description) throw (Exception)
+{
+ unparsedArguments_.clear();
+ string format = "";
+ KeyvalTools::parseProcedure(description, format, unparsedArguments_);
+ auto_ptr<ISequenceStream> iSeq;
+ if (format == "Fasta")
+ {
+ bool strictNames = ApplicationTools::getBooleanParameter("strict_names", unparsedArguments_, false, "", true, false);
+ bool extended = ApplicationTools::getBooleanParameter("extended", unparsedArguments_, false, "", true, false);
+ iSeq.reset(new Fasta(100, true, extended, strictNames));
+ }
+ else
+ {
+ throw Exception("Sequence format '" + format + "' unknown.");
+ }
+
+ return iSeq.release();
+}
+
diff --git a/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h b/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h
new file mode 100644
index 0000000..7039176
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h
@@ -0,0 +1,96 @@
+//
+// File: BppOSequenceStreamReaderFormat.h
+// Created by: Julien Dutheil
+// Created on: Tuesday November 20th, 13:27
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _BPPOSEQUENCESTREAMREADERFORMAT_H_
+#define _BPPOSEQUENCESTREAMREADERFORMAT_H_
+
+#include "IoSequenceFactory.h"
+#include "ISequenceStream.h"
+
+namespace bpp
+{
+
+ /**
+ * @brief Sequence I/O in BppO format.
+ *
+ * Creates a new ISequenceStream object according to
+ * distribution description syntax (see the Bio++ Program Suite
+ * manual for a detailed description of this syntax).
+ *
+ */
+ class BppOSequenceStreamReaderFormat:
+ public virtual IOFormat
+ {
+ private:
+ bool verbose_;
+ std::map<std::string, std::string> unparsedArguments_;
+
+ public:
+ BppOSequenceStreamReaderFormat(bool verbose = true):
+ verbose_(verbose),
+ unparsedArguments_() {}
+ virtual ~BppOSequenceStreamReaderFormat() {}
+
+ public:
+ const std::string getFormatName() const { return "BppO"; }
+
+ const std::string getFormatDescription() const { return "Bpp Options format."; }
+
+ const std::string getDataType() const { return "Sequence stream reader"; }
+
+ /**
+ * @brief Read a ISequenceStream object from a string.
+ *
+ * @param description A string describing the reader in the keyval syntax.
+ * @return A new ISequenceStream object according to options specified.
+ * @throw Exception if an error occured.
+ */
+ ISequenceStream* read(const std::string& description) throw (Exception);
+
+ /**
+ * @return The arguments and their unparsed values from the last call of the read function, if there are any.
+ */
+ virtual const std::map<std::string, std::string>& getUnparsedArguments() const { return unparsedArguments_; }
+
+ };
+
+} //end of namespace bpp.
+
+#endif //_BPPOSEQUENCESTREAMREADERFORMAT_H_
+
diff --git a/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp b/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp
new file mode 100644
index 0000000..eb1c39e
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp
@@ -0,0 +1,74 @@
+//
+// File: BppOSequenceWriterFormat.cpp
+// Created by: Julien Dutheil
+// Created on: Friday September 15th, 21:20
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "BppOSequenceWriterFormat.h"
+#include "Fasta.h"
+#include "Mase.h"
+
+#include <Bpp/Text/KeyvalTools.h>
+
+#include <string>
+#include <memory>
+
+using namespace bpp;
+using namespace std;
+
+OSequence* BppOSequenceWriterFormat::read(const std::string& description) throw (Exception)
+{
+ unparsedArguments_.clear();
+ string format = "";
+ KeyvalTools::parseProcedure(description, format, unparsedArguments_);
+ unsigned int ncol = ApplicationTools::getParameter<unsigned int>("length", unparsedArguments_, 100, "", true, false);
+ auto_ptr<OSequence> oSeq;
+ if (format == "Fasta")
+ {
+ oSeq.reset(new Fasta(ncol));
+ }
+ else if (format == "Mase")
+ {
+ oSeq.reset(new Mase(ncol));
+ }
+ else
+ {
+ throw Exception("Sequence format '" + format + "' unknown.");
+ }
+
+ return oSeq.release();
+}
+
diff --git a/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h b/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h
new file mode 100644
index 0000000..cc5f6fc
--- /dev/null
+++ b/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h
@@ -0,0 +1,95 @@
+//
+// File: BppOSequenceWriterFormat.h
+// Created by: Julien Dutheil
+// Created on: Saturday September 15th, 21:06
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _BPPOSEQUENCEWRITERFORMAT_H_
+#define _BPPOSEQUENCEWRITERFORMAT_H_
+
+#include "IoSequenceFactory.h"
+
+namespace bpp
+{
+
+ /**
+ * @brief Sequence I/O in BppO format.
+ *
+ * Creates a new OSequence object according to
+ * distribution description syntax (see the Bio++ Program Suite
+ * manual for a detailed description of this syntax).
+ *
+ */
+ class BppOSequenceWriterFormat:
+ public virtual IOFormat
+ {
+ private:
+ bool verbose_;
+ std::map<std::string, std::string> unparsedArguments_;
+
+ public:
+ BppOSequenceWriterFormat(bool verbose = true):
+ verbose_(verbose),
+ unparsedArguments_() {}
+ virtual ~BppOSequenceWriterFormat() {}
+
+ public:
+ const std::string getFormatName() const { return "BppO"; }
+
+ const std::string getFormatDescription() const { return "Bpp Options format."; }
+
+ const std::string getDataType() const { return "Sequence reader"; }
+
+ /**
+ * @brief Read a OSequence object from a string.
+ *
+ * @param description A string describing the reader in the keyval syntax.
+ * @return A new OSequence object according to options specified.
+ * @throw Exception if an error occured.
+ */
+ OSequence* read(const std::string& description) throw (Exception);
+
+ /**
+ * @return The arguments and their unparsed values from the last call of the read function, if there are any.
+ */
+ virtual const std::map<std::string, std::string>& getUnparsedArguments() const { return unparsedArguments_; }
+
+ };
+
+} //end of namespace bpp.
+
+#endif //_BPPOSEQUENCEWRITERFORMAT_H_
+
diff --git a/src/Bpp/Seq/Io/Clustal.cpp b/src/Bpp/Seq/Io/Clustal.cpp
new file mode 100644
index 0000000..568b946
--- /dev/null
+++ b/src/Bpp/Seq/Io/Clustal.cpp
@@ -0,0 +1,138 @@
+//
+// File: Clustal.cpp
+// Created by: Julien Dutheil
+// Created on: ?
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "Clustal.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+#include <Bpp/Io/FileTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+#include <iomanip>
+using namespace std;
+
+void Clustal::appendAlignmentFromStream(std::istream& input, SiteContainer & sc) const throw (Exception)
+{
+ // Checking the existence of specified file
+ if (!input) { throw IOException ("Clustal::read : fail to open file"); }
+
+ const Alphabet * alpha = sc.getAlphabet();
+ vector<BasicSequence> sequences;
+
+ string lineRead("");
+
+ Comments comments(1);
+ comments[0] = FileTools::getNextLine(input); // First line gives file generator.
+
+ lineRead = FileTools::getNextLine(input); // This is the first sequence of the first block.
+
+ string::size_type beginSeq = 0;
+ unsigned int count = 0;
+ for (size_t i = lineRead.size(); i > 0; i--) {
+ char c = lineRead[i-1];
+ if (c == ' ') {
+ count++;
+ if (count == nbSpacesBeforeSeq_) {
+ beginSeq = i - 1 + nbSpacesBeforeSeq_;
+ break;
+ }
+ }
+ else count = 0;
+ }
+ if (beginSeq == 0) throw IOException("Clustal::read. Bad intput file.");
+
+ unsigned int countSequences = 0;
+
+ //Read first sequences block:
+ bool test = true;
+ do {
+ sequences.push_back(BasicSequence(TextTools::removeSurroundingWhiteSpaces(lineRead.substr(0, beginSeq - nbSpacesBeforeSeq_)), lineRead.substr(beginSeq), alpha));
+ getline(input, lineRead, '\n');
+ countSequences++;
+ test = !TextTools::isEmpty(lineRead) && !TextTools::isEmpty(lineRead.substr(0, beginSeq - nbSpacesBeforeSeq_));
+ }
+ while (input && test);
+
+ // Read other blocks
+ lineRead = FileTools::getNextLine(input); // Read first sequence of next block.
+ while (!TextTools::isEmpty(lineRead)) {
+ // Read next block:
+ for (unsigned int i = 0; i < countSequences; ++i) {
+ // Complete sequences
+ if (TextTools::isEmpty(lineRead))
+ throw IOException("Clustal::read. Bad intput file.");
+ sequences[i].append(lineRead.substr(beginSeq));
+ getline(input, lineRead, '\n');
+ }
+ //At this point, lineRead is the first line after the current block.
+ lineRead = FileTools::getNextLine(input);
+ }
+
+ for (unsigned int i = 0; i < countSequences; ++i)
+ sc.addSequence(sequences[i], checkNames_);
+ sc.setGeneralComments(comments);
+}
+
+void Clustal::writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
+{
+ output << "CLUSTAL W (1.81) multiple sequence alignment" << endl;
+ output << endl;
+ if (sc.getNumberOfSequences() == 0)
+ return;
+
+ vector<string> text;
+ size_t length = 0;
+ for (size_t i = 0; i < sc.getNumberOfSequences(); ++i ) {
+ const Sequence& seq = sc.getSequence(i);
+ if (seq.getName().size() > length)
+ length = seq.getName().size();
+ text.push_back(sc.getSequence(i).toString());
+ }
+ length += nbSpacesBeforeSeq_;
+ for (unsigned int j = 0; j < text[0].size(); j += charsByLine_) {
+ for (unsigned int i = 0; i < sc.getNumberOfSequences(); ++i ) {
+ output << TextTools::resizeRight(sc.getSequence(i).getName(), length);
+ output << text[i].substr(j, charsByLine_) << endl;
+ }
+ output << endl;
+ }
+}
+
diff --git a/src/Bpp/Seq/Io/Clustal.h b/src/Bpp/Seq/Io/Clustal.h
new file mode 100644
index 0000000..a2cc858
--- /dev/null
+++ b/src/Bpp/Seq/Io/Clustal.h
@@ -0,0 +1,146 @@
+//
+// File: Clustal.h
+// Created by: Julien Dutheil
+// Created on: ?
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _CLUSTAL_H_
+#define _CLUSTAL_H_
+
+#include "AbstractIAlignment.h"
+#include "AbstractOAlignment.h"
+#include "../Container/SiteContainer.h"
+
+// From the STL:
+#include <iostream>
+
+namespace bpp
+{
+/**
+ * @brief The clustal sequence file format.
+ *
+ * An AlignedSequenceContainer object is used instead of a VectorSequenceContainer.
+ */
+class Clustal :
+ public AbstractIAlignment,
+ public AbstractOAlignment,
+ public virtual ISequence
+{
+private:
+ bool checkNames_;
+ unsigned int nbSpacesBeforeSeq_;
+ unsigned int charsByLine_;
+
+public:
+ /**
+ * @brief Build a new Clustal object.
+ *
+ * @param checkSequenceNames Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
+ * @param nbExtraSpacesBeforeSeq Specify the number of extra space characters separating the sequence name form content. The default is 5 (hence 6 spaces in total) for backward compatibility, using 0 will not allow for any space in the sequence names.
+ * @param charsByLine Number of character per line when writing file.
+ */
+ Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
+ checkNames_(checkSequenceNames),
+ nbSpacesBeforeSeq_(nbExtraSpacesBeforeSeq + 1),
+ charsByLine_(charsByLine)
+ {}
+
+ virtual ~Clustal() {}
+
+public:
+ /**
+ * @name The AbstractIAlignment interface.
+ *
+ * @{
+ */
+ void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
+ /** @} */
+
+ /**
+ * @name The ISequence interface.
+ *
+ * As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence
+ * interface by downcasting the interface.
+ *
+ * @{
+ */
+ virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
+ return readAlignment(input, alpha);
+ }
+ virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
+ return readAlignment(path, alpha);
+ }
+ /** @} */
+
+ /**
+ * @name The AbstractOAlignment interface.
+ *
+ * @{
+ */
+ void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
+ void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
+ {
+ AbstractOAlignment::writeAlignment(path, sc, overwrite);
+ }
+ /** @} */
+
+ /**
+ * @name The IOSequence interface.
+ *
+ * @{
+ */
+ const std::string getFormatName() const { return "Clustal"; }
+
+ const std::string getFormatDescription() const { return "The Clustal alignment tool output format."; }
+
+ /** @} */
+
+ /**
+ * @return true if the names are to be checked when reading sequences from files.
+ */
+ bool checkNames() const { return checkNames_; }
+
+ /**
+ * @brief Tell whether the sequence names should be checked when reading from files.
+ *
+ * @param yn whether the sequence names should be checked when reading from files.
+ */
+ void checkNames(bool yn) { checkNames_ = yn; }
+};
+} // end of namespace bpp.
+
+#endif // _CLUSTAL_H_
+
diff --git a/src/Bpp/Seq/Io/Dcse.cpp b/src/Bpp/Seq/Io/Dcse.cpp
new file mode 100644
index 0000000..7711850
--- /dev/null
+++ b/src/Bpp/Seq/Io/Dcse.cpp
@@ -0,0 +1,97 @@
+//
+// File: DCSE.cpp
+// Created by: Julien Dutheil
+// Created on: Wed Mar 3 2004
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "Dcse.h"
+#include "AbstractIAlignment.h"
+#include "../Sequence.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/VectorSequenceContainer.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+#include <Bpp/Io/FileTools.h>
+
+using namespace bpp;
+using namespace std;
+
+void DCSE::appendAlignmentFromStream(istream& input, SiteContainer& sc) const throw (Exception)
+{
+ // Checking the existence of specified file
+ if (!input) { throw IOException ("DCSE::read : fail to open file"); }
+
+ // Initialization
+ const Alphabet * alpha = sc.getAlphabet();
+ string line, name, sequence = "";
+
+ line = FileTools::getNextLine(input); // Copy current line in temporary string
+ //StringTokenizer st(line);
+ //st.nextToken();
+ //First line ignored for now!
+ //int n1 = TextTools::toInt(st.nextToken());
+ //int n2 = TextTools::toInt(st.nextToken());
+ //int nbSites = n2 - n1
+ //cout << nbSpecies << " species and " << nbSites << " sites." << endl;
+
+ // Main loop : for all file lines
+ while (!input.eof())
+ {
+ line = FileTools::getNextLine(input); // Copy current line in temporary string
+ if(line == "") break;
+ string::size_type endOfSeq = line.find(" ");
+ if(endOfSeq == line.npos) break;
+ sequence = string(line.begin(), line.begin() + endOfSeq);
+ sequence = TextTools::removeWhiteSpaces(sequence);
+ sequence = TextTools::removeChar(sequence, '{');
+ sequence = TextTools::removeChar(sequence, '}');
+ sequence = TextTools::removeChar(sequence, '[');
+ sequence = TextTools::removeChar(sequence, ']');
+ sequence = TextTools::removeChar(sequence, '(');
+ sequence = TextTools::removeChar(sequence, ')');
+ sequence = TextTools::removeChar(sequence, '^');
+ name = string(line.begin() + endOfSeq + 1, line.end()),
+ name = TextTools::removeFirstWhiteSpaces(name);
+ if(name.find("Helix numbering") == name.npos
+ && name.find("mask") == name.npos)
+ sc.addSequence(BasicSequence(name, sequence, alpha), true);
+ }
+}
+
+const string DCSE::getFormatName() const { return "DCSE"; }
+
+const string DCSE::getFormatDescription() const { return "RNA structure format"; }
+
diff --git a/src/Bpp/Seq/Io/Dcse.h b/src/Bpp/Seq/Io/Dcse.h
new file mode 100644
index 0000000..8ad2b2b
--- /dev/null
+++ b/src/Bpp/Seq/Io/Dcse.h
@@ -0,0 +1,109 @@
+//
+// File: DCSE.h
+// Created by: Julien Dutheil
+// Created on: Wed Mar 3 2004
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _DCSE_H_
+#define _DCSE_H_
+
+#include "AbstractIAlignment.h"
+#include "../Sequence.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/AlignedSequenceContainer.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Support for the Dedicated Comparative Sequence Editor format.
+ *
+ * Only the sequence information is retrieved.
+ * All structural information is dropped for now.
+ *
+ * A description of this format may be found here:
+ * http://www.psb.ugent.be/rRNA/help/formats/aliformat.html
+ */
+class DCSE :
+ public AbstractIAlignment,
+ public virtual ISequence
+{
+
+ public:
+ DCSE() {};
+ virtual ~DCSE() {};
+
+ public:
+
+ /**
+ * @name The AbstractIAlignment interface.
+ *
+ * @{
+ */
+ void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
+ /** @} */
+
+ /**
+ * @name The ISequence interface.
+ *
+ * As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence
+ * interface by downcasting the interface.
+ *
+ * @{
+ */
+ virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
+ return readAlignment(input, alpha);
+ }
+ virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
+ return readAlignment(path, alpha);
+ }
+ /** @} */
+
+
+ /**
+ * @name The IOSequence interface.
+ *
+ * @{
+ */
+ const std::string getFormatName() const;
+ const std::string getFormatDescription() const;
+ /** @} */
+};
+
+} //end of namespace bpp.
+
+#endif // _DCSE_H_
+
diff --git a/src/Bpp/Seq/Io/Fasta.cpp b/src/Bpp/Seq/Io/Fasta.cpp
new file mode 100644
index 0000000..ca308bb
--- /dev/null
+++ b/src/Bpp/Seq/Io/Fasta.cpp
@@ -0,0 +1,291 @@
+//
+// File: Fasta.cpp
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created: Tue Aug 21 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "Fasta.h"
+
+#include <fstream>
+
+#include "../StringSequenceTools.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+#include <Bpp/Io/FileTools.h>
+
+using namespace bpp;
+using namespace std;
+
+/******************************************************************************/
+
+bool Fasta::nextSequence(istream& input, Sequence& seq) const throw (Exception) {
+ if (!input)
+ throw IOException("Fasta::nextSequence: can't read from istream input");
+ string seqname = "";
+ string content = "";
+ Comments seqcmts;
+ short seqcpt = 0;
+ string linebuffer = "";
+ char c;
+ while (!input.eof())
+ {
+ c = static_cast<char>(input.peek());
+ if (input.eof())
+ c = '\n';
+
+ // Sequence begining detection
+ if (c == '>')
+ {
+ // Stop if find a new sequence
+ if (seqcpt++)
+ break;
+ }
+ getline(input, linebuffer);
+ if (c == '>')
+ {
+ // Get the sequence name line
+ seqname = string(linebuffer.begin() + 1, linebuffer.end());
+ }
+ if (c != '>' && !TextTools::isWhiteSpaceCharacter(c)) {
+ // Sequence content
+ content += TextTools::toUpper(TextTools::removeWhiteSpaces(linebuffer));
+ }
+ }
+
+ bool res = (!input.eof());
+ // Sequence name and comments isolation
+ if (strictNames_ || extended_) {
+ size_t pos = seqname.find_first_of(" \t\n");
+ string seqcmt;
+ if (pos != string::npos) {
+ seqcmt = seqname.substr(pos + 1);
+ seqname = seqname.substr(0, pos);
+ }
+ if (extended_) {
+ StringTokenizer st(seqcmt, " \\", true, false);
+ while (st.hasMoreToken()) {
+ seqcmts.push_back(st.nextToken());
+ }
+ } else {
+ seqcmts.push_back(seqcmt);
+ }
+ seq.setComments(seqcmts);
+ }
+ seq.setName(seqname);
+ seq.setContent(content);
+ return res;
+}
+
+/******************************************************************************/
+
+void Fasta::writeSequence(ostream& output, const Sequence& seq) const throw (Exception)
+{
+ if (!output)
+ throw IOException("Fasta::writeSequence: can't write to ostream output");
+ // Sequence name
+ output << ">" << seq.getName();
+ // Sequence comments
+ if (extended_)
+ {
+ for (unsigned int i = 0 ; i < seq.getComments().size() ; i++)
+ {
+ output << " \\" << seq.getComments()[i];
+ }
+ }
+ output << endl;
+ // Sequence content
+ string buffer; // use a buffer to format sequence with states > 1 char
+ for (unsigned int i = 0 ; i < seq.size() ; i++)
+ {
+ buffer += seq.getChar(i);
+ if (buffer.size() >= charsByLine_ || i + 1 == seq.size())
+ {
+ output << string(buffer.begin(), buffer.begin() + charsByLine_ < buffer.end() ? buffer.begin() + charsByLine_ : buffer.end()) << endl;
+ buffer.erase(0, charsByLine_);
+ }
+ }
+}
+
+/******************************************************************************/
+
+void Fasta::appendSequencesFromStream(istream& input, SequenceContainer& vsc) const throw (Exception)
+{
+ if (!input)
+ throw IOException("Fasta::appendFromStream: can't read from istream input");
+ char c = '\n';
+ char last_c;
+ bool header = false;
+ bool hasSeq = true;
+ string line = "";
+ Comments cmts;
+ while (!input.eof() && hasSeq)
+ {
+ last_c = c;
+ input.get(c);
+ // Header detection
+ if (extended_ && c == '#')
+ {
+ header = true;
+ continue;
+ }
+ // Header end detection
+ if (c == '\n')
+ {
+ if (extended_ && header)
+ {
+ if (line[0] == '\\')
+ {
+ line.erase(line.begin());
+ cmts.push_back(line);
+ }
+ line = "";
+ header = false;
+ }
+ continue;
+ }
+ // Header capture
+ if (header)
+ {
+ line.append(1, c);
+ }
+ // Sequence detection
+ if (c == '>' && last_c == '\n')
+ {
+ input.putback(c);
+ c = last_c;
+ BasicSequence tmpseq("", "", vsc.getAlphabet());
+ hasSeq = nextSequence(input, tmpseq);
+ vsc.addSequence(tmpseq, checkNames_);
+ }
+ }
+ if (extended_ && cmts.size()) {
+ vsc.setGeneralComments(cmts);
+ }
+}
+
+/******************************************************************************/
+
+void Fasta::writeSequences(ostream& output, const SequenceContainer& sc) const throw (Exception)
+{
+ if (!output)
+ throw IOException("Fasta::write: can't write to ostream output");
+
+ if (extended_)
+ {
+ // Loop for all general comments
+ for (unsigned int i = 0 ; i < sc.getGeneralComments().size() ; i++)
+ {
+ output << "#\\" << sc.getGeneralComments()[i] << endl;
+ }
+ output << endl;
+ }
+
+ // Main loop : for all sequences in vector container
+ vector<string> names = sc.getSequencesNames();
+ for (unsigned int i = 0; i < names.size(); i ++)
+ {
+ writeSequence(output, sc.getSequence(names[i]));
+ }
+}
+
+/******************************************************************************/
+
+// FileIndex class
+
+void Fasta::FileIndex::build(const std::string& path) throw (Exception) {
+ // open the file
+ std::ifstream f_in(path.c_str());
+ // get the size of the file
+ f_in.seekg(0, std::ios::end);
+ fileSize_ = f_in.tellg();
+ // feed the map
+ f_in.seekg(0, std::ios::beg);
+ streampos pos = f_in.tellg();
+ char ch;
+ std::string seq_id = "";
+ while (f_in.get(ch)) {
+ if (ch == '>') {
+ pos = static_cast<int>(f_in.tellg()) - 1;
+ std::getline(f_in, seq_id);
+ index_[seq_id] = pos;
+ }
+ }
+ f_in.close();
+}
+
+streampos Fasta::FileIndex::getSequencePosition(const std::string& id) const throw (Exception) {
+ std::map<std::string, streampos>::const_iterator it = index_.find(id);
+ if (it != index_.end()) {
+ return it->second;
+ }
+ throw Exception("Sequence not found: " + id);
+}
+
+void Fasta::FileIndex::read(const std::string& path) throw (Exception) {
+ std::ifstream f_in(path.c_str());
+ std::string line_buffer = "";
+ while (!f_in.eof()) {
+ std::getline(f_in, line_buffer);
+ if (bpp::TextTools::isEmpty(bpp::TextTools::removeSurroundingWhiteSpaces(line_buffer))) {
+ continue;
+ }
+ bpp::StringTokenizer tk(line_buffer, "\t");
+ index_[tk.getToken(0)] = bpp::TextTools::toInt(tk.getToken(1));
+ }
+ f_in.close();
+}
+
+void Fasta::FileIndex::write(const std::string& path) throw (Exception) {
+ std::ofstream f_out(path.c_str());
+ for (std::map<std::string, streampos>::const_iterator it = index_.begin() ; it != index_.end() ; ++it) {
+ f_out << it->first << "\t" << bpp::TextTools::toString(it->second) << std::endl;
+ }
+ f_out.close();
+}
+
+void Fasta::FileIndex::getSequence(const std::string& seqid, Sequence& seq, const std::string& path) const {
+ Fasta fs(60);
+ streampos seq_pos = this->getSequencePosition(seqid);
+ std::ifstream fasta(path.c_str());
+ fasta.seekg(seq_pos);
+ fs.nextSequence(fasta, seq);
+ fasta.close();
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Io/Fasta.h b/src/Bpp/Seq/Io/Fasta.h
new file mode 100644
index 0000000..aae1d65
--- /dev/null
+++ b/src/Bpp/Seq/Io/Fasta.h
@@ -0,0 +1,214 @@
+//
+// File: Fasta.h
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created: Tue Aug 21 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _BPP_SEQ_IO_FASTA_H_
+#define _BPP_SEQ_IO_FASTA_H_
+
+#include "AbstractISequence.h"
+#include "AbstractIAlignment.h"
+#include "AbstractOSequence.h"
+#include "../Sequence.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/VectorSequenceContainer.h"
+#include "ISequenceStream.h"
+#include "OSequenceStream.h"
+#include "SequenceFileIndex.h"
+
+namespace bpp
+{
+
+/**
+ * @brief The fasta sequence file format.
+ *
+ * Read and write from/to Fasta files.
+ */
+class Fasta:
+ public AbstractISequence,
+ public AbstractIAlignment,
+ public AbstractOSequence,
+ public virtual ISequenceStream,
+ public virtual OSequenceStream
+{
+ private:
+
+ /**
+ * @brief The maximum number of chars to be written on a line.
+ */
+ unsigned int charsByLine_; // Number of char by line (output only)
+ bool checkNames_; // If names must be checked in container
+ bool extended_; // If using HUPO-PSI extensions
+ bool strictNames_; // If name is between '>' and first space
+
+ public:
+
+ /**
+ * @brief Build a new Fasta object.
+ *
+ * @param charsByLine Number of character per line when writing files.
+ * @param checkSequenceNames Tells if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
+ * @param extended Tells if we should read general comments and sequence comments in HUPO-PSI format.
+ * @param strictSequenceNames Tells if the sequence names should be restricted to the characters between '>' and the first blank one.
+ */
+ Fasta(unsigned int charsByLine = 100, bool checkSequenceNames = true, bool extended = false, bool strictSequenceNames = false): charsByLine_(charsByLine), checkNames_(checkSequenceNames), extended_(extended), strictNames_(strictSequenceNames) {}
+
+ // Class destructor
+ virtual ~Fasta() {}
+
+ public:
+
+ /**
+ * @name The AbstractISequence interface.
+ *
+ * @{
+ */
+ void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
+ /** @} */
+
+ /**
+ * @name The AbstractIAlignment interface.
+ *
+ * @{
+ */
+ void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
+ appendSequencesFromStream(input, sc); //This may raise an exception if sequences are not aligned!
+ }
+ /** @} */
+
+ /**
+ * @name The OSequence interface.
+ *
+ * @{
+ */
+ void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
+
+ void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
+ {
+ AbstractOSequence::writeSequences(path, sc, overwrite);
+ }
+ /** @} */
+
+ /**
+ * @name The IOSequence interface.
+ *
+ * @{
+ */
+ const std::string getFormatName() const { return "FASTA file"; };
+ const std::string getFormatDescription() const
+ {
+ return "Sequence name (preceded by >) in one line, sequence content, no comments";
+ }
+ /** @} */
+
+ /**
+ * @name The ISequenceStream interface.
+ *
+ * @{
+ */
+ bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
+ /** @} */
+
+ /**
+ * @name The OSequenceStream interface.
+ *
+ * @{
+ */
+ void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
+ /** @} */
+
+ /**
+ * @return true if the names are to be checked when reading sequences from files.
+ */
+ bool checkNames() const { return checkNames_; }
+
+ /**
+ * @brief Tell whether the sequence names should be checked when reading from files.
+ *
+ * @param yn whether the sequence names should be checked when reading from files.
+ */
+ void checkNames(bool yn) { checkNames_ = yn; }
+
+ /**
+ * @return true if the sequence name is restricted to be between '>' and the first space character.
+ */
+ bool strictNames() const { return strictNames_; }
+
+ /**
+ * @brief Tell wethed the sequence name should be restrected to the first non blank characters.
+ *
+ * @param yn whether the sequence names should be restrected.
+ */
+ void strictNames(bool yn) { strictNames_ = yn; }
+
+ /**
+ * @brief The SequenceFileIndex class for Fasta format
+ * @author Sylvain Gaillard
+ */
+ class FileIndex: SequenceFileIndex {
+ public:
+ FileIndex(): index_(), fileSize_(0) {}
+ ~FileIndex() {}
+ void build(const std::string& path) throw (Exception);
+ std::streampos getSequencePosition(const std::string& id) const throw (Exception);
+ size_t getNumberOfSequences() const throw (Exception) {
+ return index_.size();
+ }
+ /**
+ * @brief Read the index from a file
+ */
+ void read(const std::string& path) throw (Exception);
+ /**
+ * @brief Write the index to a file
+ */
+ void write(const std::string& path) throw (Exception);
+ /**
+ * @brief Get a sequence given its ID
+ */
+ void getSequence(const std::string& seqid, Sequence& seq, const std::string& path) const;
+ private:
+ std::map<std::string, std::streampos> index_;
+ std::streampos fileSize_;
+ };
+};
+
+} //end of namespace bpp.
+
+#endif // _BPP_SEQ_IO_FASTA_H_
+
diff --git a/src/Bpp/Seq/Io/GenBank.cpp b/src/Bpp/Seq/Io/GenBank.cpp
new file mode 100644
index 0000000..b891716
--- /dev/null
+++ b/src/Bpp/Seq/Io/GenBank.cpp
@@ -0,0 +1,86 @@
+//
+// File: GenBank.cpp
+// Created by: Julien Dutheil
+// Created on: Tue Oct 2 2007
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "GenBank.h"
+
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+
+using namespace bpp;
+using namespace std;
+
+/****************************************************************************************/
+
+void GenBank::appendSequencesFromStream(std::istream& input, SequenceContainer& vsc) const throw (Exception)
+{
+ if (!input) { throw IOException ("GenBank::read: fail to open file"); }
+
+ string temp, name, sequence = ""; // Initialization
+
+ // Main loop : for all file lines
+ while (!input.eof())
+ {
+ getline(input, temp, '\n'); // Copy current line in temporary string
+
+ if(temp.size() >= 9 && temp.substr(0,9) == "ACCESSION")
+ {
+ name = TextTools::removeSurroundingWhiteSpaces(temp.substr(10));
+ StringTokenizer st(name, " ");
+ name = st.nextToken();
+ //cout << name << endl;
+ }
+ if (temp.size() >=6 && temp.substr(0,6) == "ORIGIN")
+ {
+ sequence = "";
+ getline(input, temp, '\n'); // Copy current line in temporary string
+ while (!input.eof() && temp.size() > 2 && temp.substr(0,2) != "//")
+ {
+ sequence += TextTools::removeWhiteSpaces(temp.substr(10));
+ getline(input, temp, '\n'); // Copy current line in temporary string
+ }
+ if(name == "") throw Exception("GenBank::read(). Sequence with no ACCESSION number!");
+ Sequence* seq = new BasicSequence(name, sequence, vsc.getAlphabet());
+ vsc.addSequence(*seq, true);
+ name = "";
+ }
+ }
+}
+
+/****************************************************************************************/
+
diff --git a/src/Bpp/Seq/Io/GenBank.h b/src/Bpp/Seq/Io/GenBank.h
new file mode 100644
index 0000000..f4a450f
--- /dev/null
+++ b/src/Bpp/Seq/Io/GenBank.h
@@ -0,0 +1,94 @@
+//
+// File: GenBank.h
+// Created by: Julien Dutheil
+// Created on: Tue Oct 2 2007
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _GENBANK_H_
+#define _GENBANK_H_
+
+#include "AbstractISequence.h"
+#include "../Sequence.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/VectorSequenceContainer.h"
+
+namespace bpp
+{
+
+/**
+ * @brief The GenBank sequence file format.
+ *
+ * For now, only read raw sequences. Features are not yet supported.
+ */
+class GenBank :
+ public AbstractISequence
+{
+ public:
+
+ /**
+ * @brief Build a new GenBank object.
+ */
+ GenBank() {}
+
+ virtual ~GenBank() {}
+
+ public:
+
+ /**
+ * @name The AbstractISequence interface.
+ *
+ * @{
+ */
+ void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
+ /** @} */
+
+ /**
+ * @name The IOSequence interface.
+ *
+ * @{
+ */
+ const std::string getFormatName() const { return "GenBank file"; };
+ const std::string getFormatDescription() const
+ {
+ return "Sequences following the GenBank data base format.";
+ }
+ /** @} */
+};
+
+} //end of namespace bpp.
+
+#endif // _GENBANK_H_
+
diff --git a/src/Bpp/Seq/Io/ISequence.h b/src/Bpp/Seq/Io/ISequence.h
new file mode 100644
index 0000000..01584ea
--- /dev/null
+++ b/src/Bpp/Seq/Io/ISequence.h
@@ -0,0 +1,132 @@
+//
+// File: ISequence.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: Wed Jul 30 2003
+//
+
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ISEQUENCE_H_
+#define _ISEQUENCE_H_
+
+#include "IoSequence.h"
+#include "../Sequence.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/SiteContainer.h"
+#include <Bpp/Exceptions.h>
+
+//From the STL:
+#include <iostream>
+#include <string>
+
+namespace bpp
+{
+
+/**
+ * @brief The ISequence interface.
+ *
+ * This interface defines the basic methods for reading sequences from a file.
+ * NB: This interface is effective only if the VIRTUAL_COV option is enabled (default behavior).
+ */
+class ISequence :
+ public virtual IOSequence
+{
+ public:
+ ISequence() {}
+ virtual ~ISequence() {}
+
+ public:
+
+ /**
+ * @brief Create a new container from a stream.
+ *
+ * @param input The input stream to read.
+ * @param alpha The alphabet to be associated to the container.
+ * @return A new SequenceContainer object.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
+ /**
+ * @brief Create a new container from a file.
+ *
+ * @param path The path to the file to read.
+ * @param alpha The alphabet to be associated to the container.
+ * @return A new SequenceContainer object.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
+
+};
+
+/**
+ * @brief The IAlignment interface.
+ *
+ * This interface defines the basic methods for reading aligned sequences from a file.
+ */
+class IAlignment:
+ public virtual IOSequence
+{
+ public:
+ IAlignment() {}
+ virtual ~IAlignment() {}
+
+ public:
+
+ /**
+ * @brief Create a new container from a stream.
+ *
+ * @param input The input stream to read.
+ * @param alpha The alphabet to be associated to the container.
+ * @return A new SiteContainer object.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
+ /**
+ * @brief Create a new container from a file.
+ *
+ * @param path The path to the file to read.
+ * @param alpha The alphabet to be associated to the container.
+ * @return A new SiteContainer object.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
+
+};
+
+} //end of namespace bpp.
+
+#endif // _ISEQUENCE_H_
+
diff --git a/src/Bpp/Seq/Io/ISequenceStream.h b/src/Bpp/Seq/Io/ISequenceStream.h
new file mode 100644
index 0000000..eb1cc09
--- /dev/null
+++ b/src/Bpp/Seq/Io/ISequenceStream.h
@@ -0,0 +1,82 @@
+//
+// File ISequenceStream.h
+// Author: Sylvain Gaillard
+// Created: 18/08/2009
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (August 18, 2009)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _ISEQUENCESTREAM_H_
+#define _ISEQUENCESTREAM_H_
+
+#include "IoSequenceStream.h"
+#include "../Sequence.h"
+#include "../Alphabet/Alphabet.h"
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+/**
+ * @brief The ISequenceStream interface.
+ *
+ * Interface for streaming sequences input.
+ *
+ * @author Sylvain Gaillard
+ */
+class ISequenceStream: public virtual IOSequenceStream
+{
+ public:
+ ISequenceStream() {}
+ virtual ~ISequenceStream() {}
+
+ public:
+ /**
+ * @brief Read sequence from stream.
+ *
+ * Read one sequence from a stream.
+ *
+ * @param input The stream to read.
+ * @param seq The sequence to fill.
+ * @return true if a sequence was read or false if not.
+ * @throw Exception IOExecption and Sequence related Exceptions.
+ */
+ virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
+
+};
+
+} //end of namespace bpp.
+
+#endif // _ISEQUENCESTREAM_H_
+
diff --git a/src/Bpp/Seq/Io/IoSequence.h b/src/Bpp/Seq/Io/IoSequence.h
new file mode 100644
index 0000000..131c31a
--- /dev/null
+++ b/src/Bpp/Seq/Io/IoSequence.h
@@ -0,0 +1,72 @@
+//
+// File IoSequence.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _IOSEQUENCE_H_
+#define _IOSEQUENCE_H_
+
+#include <Bpp/Exceptions.h>
+#include <Bpp/Io/IoFormat.h>
+
+// From STL:
+#include <string>
+
+namespace bpp
+{
+
+/**
+ * @brief The IOSequence interface.
+ *
+ * Interface for sequences input/ouput.
+ */
+class IOSequence: public virtual IOFormat
+{
+ public:
+ IOSequence() {}
+ virtual ~IOSequence() {}
+
+ public:
+
+ const std::string getDataType() const { return "Sequence container"; }
+
+};
+
+} //end of namespace bpp.
+
+#endif // _IOSEQUENCE_H_
+
diff --git a/src/Bpp/Seq/Io/IoSequenceFactory.cpp b/src/Bpp/Seq/Io/IoSequenceFactory.cpp
new file mode 100644
index 0000000..565cd9c
--- /dev/null
+++ b/src/Bpp/Seq/Io/IoSequenceFactory.cpp
@@ -0,0 +1,109 @@
+//
+// File IOSequenceFactory.cpp
+// Created by: Julien Dutheil
+// Created on: Tue 18/04/06 10:24
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "IoSequenceFactory.h"
+#include "Fasta.h"
+#include "Mase.h"
+#include "Clustal.h"
+#include "Dcse.h"
+#include "Phylip.h"
+#include "GenBank.h"
+#include "NexusIoSequence.h"
+
+using namespace bpp;
+using namespace std;
+
+const string IoSequenceFactory::FASTA_FORMAT = "Fasta";
+const string IoSequenceFactory::MASE_FORMAT = "Mase";
+const string IoSequenceFactory::CLUSTAL_FORMAT = "Clustal";
+const string IoSequenceFactory::DCSE_FORMAT = "DCSE";
+const string IoSequenceFactory::PHYLIP_FORMAT_INTERLEAVED = "Phylip I";
+const string IoSequenceFactory::PHYLIP_FORMAT_SEQUENTIAL = "Phylip S";
+const string IoSequenceFactory::PAML_FORMAT_INTERLEAVED = "PAML I";
+const string IoSequenceFactory::PAML_FORMAT_SEQUENTIAL = "PAML S";
+const string IoSequenceFactory::GENBANK_FORMAT = "GenBank";
+const string IoSequenceFactory::NEXUS_FORMAT = "Nexus";
+
+ISequence* IoSequenceFactory::createReader(const string& format) throw (Exception)
+{
+ if(format == FASTA_FORMAT) return new Fasta();
+ else if(format == MASE_FORMAT) return new Mase();
+ else if(format == CLUSTAL_FORMAT) return new Clustal();
+ else if(format == DCSE_FORMAT) return new DCSE();
+ else if(format == PHYLIP_FORMAT_INTERLEAVED) return new Phylip(false, false);
+ else if(format == PHYLIP_FORMAT_SEQUENTIAL) return new Phylip(false, true);
+ else if(format == PAML_FORMAT_INTERLEAVED) return new Phylip(true, false);
+ else if(format == PAML_FORMAT_SEQUENTIAL) return new Phylip(true, true);
+ else if(format == GENBANK_FORMAT) return new GenBank();
+ else if(format == NEXUS_FORMAT) return new NexusIOSequence();
+ else throw Exception("Format " + format + " is not supported for sequences input.");
+}
+
+IAlignment* IoSequenceFactory::createAlignmentReader(const string& format) throw (Exception)
+{
+ if(format == FASTA_FORMAT) return new Fasta();
+ else if(format == MASE_FORMAT) return new Mase();
+ else if(format == CLUSTAL_FORMAT) return new Clustal();
+ else if(format == DCSE_FORMAT) return new DCSE();
+ else if(format == PHYLIP_FORMAT_INTERLEAVED) return new Phylip(false, false);
+ else if(format == PHYLIP_FORMAT_SEQUENTIAL) return new Phylip(false, true);
+ else if(format == PAML_FORMAT_INTERLEAVED) return new Phylip(true, false);
+ else if(format == PAML_FORMAT_SEQUENTIAL) return new Phylip(true, true);
+ else if(format == NEXUS_FORMAT) return new NexusIOSequence();
+ else throw Exception("Format " + format + " is not supported for alignment input.");
+}
+
+OSequence* IoSequenceFactory::createWriter(const string& format) throw (Exception)
+{
+ if(format == FASTA_FORMAT) return new Fasta();
+ else if(format == MASE_FORMAT) return new Mase();
+ else throw Exception("Format " + format + " is not supported for output.");
+}
+
+OAlignment* IoSequenceFactory::createAlignmentWriter(const string& format) throw (Exception)
+{
+ if (format == FASTA_FORMAT) return new Fasta();
+ else if (format == MASE_FORMAT) return new Mase();
+ else if (format == PHYLIP_FORMAT_INTERLEAVED) return new Phylip(false, false);
+ else if (format == PHYLIP_FORMAT_SEQUENTIAL) return new Phylip(false, true);
+ else if (format == PAML_FORMAT_INTERLEAVED) return new Phylip(true, false);
+ else if (format == PAML_FORMAT_SEQUENTIAL) return new Phylip(true, true);
+ else throw Exception("Format " + format + " is not supported for output.");
+}
+
diff --git a/src/Bpp/Seq/Io/IoSequenceFactory.h b/src/Bpp/Seq/Io/IoSequenceFactory.h
new file mode 100644
index 0000000..8c0cb98
--- /dev/null
+++ b/src/Bpp/Seq/Io/IoSequenceFactory.h
@@ -0,0 +1,124 @@
+//
+// File IoSequenceFactory.h
+// Created by: Julien Dutheil
+// Created on: Tue 18/04/06 10:24
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _IOSEQUENCEFACTORY_H_
+#define _IOSEQUENCEFACTORY_H_
+
+#include "ISequence.h"
+#include "OSequence.h"
+#include "../Alphabet/Alphabet.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Utilitary class for creating sequence readers and writers.
+ */
+class IoSequenceFactory
+{
+ public:
+ static const std::string FASTA_FORMAT;
+ static const std::string MASE_FORMAT;
+ static const std::string CLUSTAL_FORMAT;
+ static const std::string DCSE_FORMAT;
+ static const std::string PHYLIP_FORMAT_INTERLEAVED;
+ static const std::string PHYLIP_FORMAT_SEQUENTIAL;
+ static const std::string PAML_FORMAT_INTERLEAVED;
+ static const std::string PAML_FORMAT_SEQUENTIAL;
+ static const std::string GENBANK_FORMAT;
+ static const std::string NEXUS_FORMAT;
+
+ public:
+
+ /**
+ * @brief Creates a new factory object.
+ *
+ * Example:
+ * @code
+ * Alphabet* alphabet = new DNA();
+ * ISequence* seqReader = IoSequenceFactory().createReader(IoSequenceFactory::FASTA_FORMAT);
+ * SequenceContainer* sequences = seqReader->read("file.fasta", alphabet);
+ * delete seqReader;
+ * @endcode
+ */
+ IoSequenceFactory() {}
+ virtual ~IoSequenceFactory() {}
+
+ /**
+ * @brief Get a new dynamically created ISequence object.
+ *
+ * @param format The input file format.
+ * @return A pointer toward a new ISequence object.
+ * @throw Exception If the format name do not match any available format.
+ */
+ virtual ISequence* createReader(const std::string& format) throw (Exception);
+
+ /**
+ * @brief Get a new dynamically created IAlignment object.
+ *
+ * @param format The input file format.
+ * @return A pointer toward a new IAlignment object.
+ * @throw Exception If the format name do not match any available format.
+ */
+ virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
+
+ /**
+ * @brief Get a new dynamically created OSequence object.
+ *
+ * @param format The output file format.
+ * @return A pointer toward a new OSequence object.
+ * @throw Exception If the format name do not match any available format.
+ */
+ virtual OSequence* createWriter(const std::string& format) throw (Exception);
+
+ /**
+ * @brief Get a new dynamically created OAlignment object.
+ *
+ * @param format The output file format.
+ * @return A pointer toward a new OAlignment object.
+ * @throw Exception If the format name do not match any available format.
+ */
+ virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
+
+};
+
+} //end of namespace bpp.
+
+#endif //_IOSEQUENCEFACTORY_H_
+
diff --git a/src/Bpp/Seq/Io/IoSequenceStream.h b/src/Bpp/Seq/Io/IoSequenceStream.h
new file mode 100644
index 0000000..94e3af4
--- /dev/null
+++ b/src/Bpp/Seq/Io/IoSequenceStream.h
@@ -0,0 +1,66 @@
+//
+// File IOSequenceStream.h
+// Author: Sylvain Gaillard
+// Created: 19/08/2009
+//
+
+/*
+Copyright or © or Copr. CNRS, (August 19, 2009)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _IOSEQUENCESTREAM_H_
+#define _IOSEQUENCESTREAM_H_
+
+#include <Bpp/Io/IoFormat.h>
+
+namespace bpp
+{
+
+/**
+ * @brief The IOSequenceStream interface.
+ *
+ * Interface for streaming sequences.
+ *
+ * @author Sylvain Gaillard
+ */
+class IOSequenceStream: public virtual IOFormat
+{
+ public:
+ IOSequenceStream() {}
+ virtual ~IOSequenceStream() {}
+
+};
+
+} //end of namespace bpp.
+
+#endif // _IOSEQUENCESTREAM_H_
+
diff --git a/src/Bpp/Seq/Io/Mase.cpp b/src/Bpp/Seq/Io/Mase.cpp
new file mode 100644
index 0000000..d09f0f7
--- /dev/null
+++ b/src/Bpp/Seq/Io/Mase.cpp
@@ -0,0 +1,313 @@
+//
+// File Mase.cpp
+// Author : Guillaume Deuchst
+// Julien Dutheil
+// Last modification: Tuesday August 21 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "Mase.h"
+#include "../StringSequenceTools.h"
+
+using namespace bpp;
+using namespace std;
+
+/****************************************************************************************/
+
+void Mase::appendSequencesFromStream(std::istream& input, SequenceContainer& vsc) const throw (Exception)
+{
+ if (!input) { throw IOException ("Mase::read : fail to open file"); }
+
+ // Initialization
+ Comments seqComments, fileComments;
+ string temp, name, sequence = "";
+ bool comments = false;
+
+ // Get current general comments is VectorSequenceContainer
+ fileComments = vsc.getGeneralComments();
+
+ // Main loop : for all file lines
+ while (!input.eof())
+ {
+ getline(input, temp, '\n'); // Copy current line in temporary string
+
+ // If first character is ;
+ if (temp[0] == ';')
+ {
+ // If second character is also ;
+ if (temp[1] == ';')
+ {
+ // File comments isolation
+ temp.erase(0,2); // Characters ;; deletion
+ if(temp != "") fileComments.push_back(temp);
+ }
+ else
+ {
+ // If a name and a sequence were founded
+ if ((name != "") && (sequence != ""))
+ {
+ // New sequence creation, and addition in existing VectorSequenceContainer
+ vsc.addSequence(BasicSequence(name, sequence, seqComments, vsc.getAlphabet()), checkNames_);
+ name = "";
+ sequence = "";
+ seqComments.clear();
+ }
+
+ // Sequence commentaries isolation
+ temp.erase(temp.begin()); // Character ; deletion
+ if (temp != "") seqComments.push_back(temp);
+ comments = true;
+ }
+ }
+ else
+ {
+ // If sequence commentaries were just isolated
+ if (comments)
+ {
+ // Sequence name isolation
+ name = temp;
+ comments = false;
+ }
+ else sequence += temp; // Sequence isolation
+ }
+ }
+
+ // Addition of the last sequence in file
+ if ((name != "") && (sequence != ""))
+ {
+ vsc.addSequence(BasicSequence(name, sequence, seqComments, vsc.getAlphabet()), checkNames_);
+ }
+
+ // Set new general comments in VectorSequenceContainer (old + new comments)
+ vsc.setGeneralComments(fileComments);
+}
+
+/****************************************************************************************/
+
+void Mase::writeSequences(ostream& output, const SequenceContainer& sc) const throw (Exception)
+{
+ // Checking the existence of specified file, and possibility to open it in write mode
+ if (!output) { throw IOException ("Mase::write : failed to open file"); }
+
+ Comments comments = sc.getGeneralComments();
+
+ // Writing all general comments in file
+ if (comments.size() == 0) {
+ output << ";;" << endl;
+ }
+ for (unsigned int i = 0 ; i < comments.size() ; i++) {
+ output << ";;" << comments[i] << endl;
+ }
+
+ string seq, temp = ""; // Initialization
+
+ // Main loop : for all sequences
+ vector<string> names = sc.getSequencesNames();
+ for (unsigned int i = 0 ; i < names.size() ; i ++)
+ {
+ comments = sc.getComments(names[i]);
+
+ // Writing all sequence comments in file
+ // If no comments are associated with current sequence, an empy commentary line will be writed
+ if (comments.size() == 0)
+ {
+ output << ";" << endl;
+ }
+ else
+ {
+ for (unsigned int j = 0 ; j < comments.size() ; j++)
+ {
+ output << ";" << comments[j] << endl;
+ }
+ }
+
+ // Sequence name writing
+ output << names[i] << endl;
+
+ // Sequence cutting to specified characters number per line
+ seq = sc.toString(names[i]);
+ while (seq != "")
+ {
+ if (seq.size() > charsByLine_)
+ {
+ temp = seq;
+ temp.erase(temp.begin() + charsByLine_ , temp.end());
+ output << temp << endl;
+ seq.erase(seq.begin(), seq.begin() + charsByLine_);
+ }
+ else
+ {
+ output << seq << endl;
+ seq = "";
+ }
+ }
+ }
+}
+
+/****************************************************************************************/
+
+void Mase::readHeader_(std::istream& input, MaseHeader& header) const throw (Exception)
+{
+ do {
+ //Check if the line is a header line:
+ if (input.peek() == ';') {
+ char c;
+ input.get(c);
+ if (input.peek() == ';') {
+ input.get(c);
+ string line = FileTools::getNextLine(input);
+
+ //Check the type of line...
+
+ //Site selection:
+ string::size_type index = line.find("# of");
+ if (index < line.npos) {
+ StringTokenizer st(string(line.begin() + index + 4, line.end()), " \t=;");
+ st.nextToken(); //skip next word: may be 'regions' or 'segments' or else ;-)
+ unsigned int numberOfSegments = TextTools::to<unsigned int>(st.nextToken());
+ string name = st.unparseRemainingTokens();
+ //Then look for the set definition:
+ MultiRange<size_t> siteSelection;
+ while (siteSelection.size() < numberOfSegments) {
+ line = FileTools::getNextLine(input);
+ if (line[0] != ';' || line[1] != ';')
+ throw Exception("Mase::readHeader_(): corrupted file, site selection " + name + " is incomplete. Aborting.");
+ line = line.substr(2);
+ StringTokenizer st2(line);
+ while (st2.hasMoreToken()) {
+ StringTokenizer st3(st2.nextToken(), ",");
+ unsigned int begin = TextTools::to<unsigned int>(st3.nextToken());
+ unsigned int end = TextTools::to<unsigned int>(st3.nextToken());
+ //WARNING!!! In the mase+ format, sites numerotation is 1-based, including, while ranges are 0-based, [a, b[:
+ siteSelection.addRange(Range<size_t>(begin - 1, end));
+ }
+ if (siteSelection.size() > numberOfSegments)
+ throw Exception("Mase::readHeader_(): incorrected file, found " + TextTools::toString(siteSelection.size()) + "segments while expected " + TextTools::toString(numberOfSegments));
+ }
+ header.setSiteSelection(name, siteSelection);
+ } else {
+ //Sequence selection:
+ index = line.find("@ of");
+ if (index < line.npos) {
+ StringTokenizer st(line.substr(index + 4), " \t=;");
+ st.nextToken(); //skip next word: may be 'sequences' or else ;-)
+ unsigned int numberOfSequences = TextTools::to<unsigned int>(st.nextToken());
+ string name = st.unparseRemainingTokens();
+ //The look for the set definition:
+ vector<size_t> sequenceSelection;
+ while (sequenceSelection.size() < numberOfSequences) {
+ line = FileTools::getNextLine(input);
+ if (line[0] != ';' || line[1] != ';')
+ throw Exception("Mase::readHeader_(): corrupted file, sequence selection " + name + " is incomplete. Aborting.");
+ line = line.substr(2);
+ StringTokenizer st2(line, ", ");
+ while (st2.hasMoreToken()) {
+ unsigned int pos = TextTools::to<unsigned int>(st2.nextToken());
+ //WARNING!!! In the mase+ format, sequence numerotation is 1-based
+ sequenceSelection.push_back(pos);
+ }
+ if (sequenceSelection.size() > numberOfSequences)
+ throw Exception("Mase::readHeader_(): incorrected file, found " + TextTools::toString(sequenceSelection.size()) + "sequences while expected " + TextTools::toString(numberOfSequences));
+ }
+ header.setSequenceSelection(name, sequenceSelection);
+ } else {
+ //Tree:
+ index = line.find("$");
+ if (index < line.npos) {
+ string name = TextTools::removeSurroundingWhiteSpaces(line.substr(index + 1));
+ //Here we stop if the line ends with a ";"
+ string tree = "";
+ do {
+ line = FileTools::getNextLine(input);
+ if (line[0] != ';' || line[1] != ';')
+ throw Exception("Mase::readHeader_(): corrupted file, tree " + name + " is incomplete. Aborting.");
+ line = TextTools::removeSurroundingWhiteSpaces(line.substr(2));
+ tree += line;
+ } while (! TextTools::endsWith(line, ";"));
+ header.setTree(name, tree);
+ }
+ }
+ }
+ } else {
+ input.putback(c);
+ break;
+ }
+ }
+ } while (true);
+}
+
+/****************************************************************************************/
+
+void Mase::writeHeader_(std::ostream& output, const MaseHeader& header) const
+{
+ //Write trees:
+ vector<string> treeNames = header.getTreeNames();
+ for (size_t i = 0; i < treeNames.size(); ++i) {
+ output << ";;$ " + treeNames[i] << endl;
+ output << ";;" + header.getTree(treeNames[i]);
+ output << endl;
+ }
+
+ //Write site selections:
+ vector<string> siteSelectionNames = header.getSiteSelectionNames();
+ for (size_t i = 0; i < siteSelectionNames.size(); ++i) {
+ MultiRange<size_t> ranges = header.getSiteSelection(siteSelectionNames[i]);
+ output << ";;# of segments=" << ranges.size() << " " << siteSelectionNames[i] << endl;
+ output << ";;";
+ for (unsigned int j = 0; j < ranges.size(); ++j) {
+ output << " " << (ranges.getRange(j).begin() + 1) << "," << ranges.getRange(j).end();
+ if ((j + 1) % 10 == 0)
+ output << endl << ";;";
+ }
+ output << endl;
+ }
+
+ //Write sequence selections:
+ vector<string> sequenceSelectionNames = header.getSequenceSelectionNames();
+ for (size_t i = 0; i < sequenceSelectionNames.size(); ++i) {
+ vector<size_t> set = header.getSequenceSelection(sequenceSelectionNames[i]);
+ output << ";;@ of species=" << set.size() << " " << sequenceSelectionNames[i] << endl;
+ output << ";;";
+ for (unsigned int j = 0; j < set.size(); ++j) {
+ output << " " << set[j];
+ if ((j + 1) % 10 == 0)
+ output << endl << ";;";
+ }
+ output << endl;
+ }
+}
+
+/****************************************************************************************/
+
diff --git a/src/Bpp/Seq/Io/Mase.h b/src/Bpp/Seq/Io/Mase.h
new file mode 100644
index 0000000..61ec8a0
--- /dev/null
+++ b/src/Bpp/Seq/Io/Mase.h
@@ -0,0 +1,256 @@
+//
+// File: Mase.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: ?
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _MASE_H_
+#define _MASE_H_
+
+#include "AbstractISequence.h"
+#include "AbstractIAlignment.h"
+#include "AbstractOSequence.h"
+#include "../Sequence.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/VectorSequenceContainer.h"
+#include <Bpp/Numeric/Range.h>
+#include <Bpp/Utils/MapTools.h>
+
+namespace bpp
+{
+
+/**
+ * @brief A class to store information from the header of Mase files.
+ *
+ * @author Julien Dutheil
+ */
+class MaseHeader
+{
+ private:
+ mutable std::map<std::string, std::string> trees_;
+ mutable std::map<std::string, MultiRange<size_t> > siteSelections_;
+ mutable std::map<std::string, std::vector<size_t> > sequenceSelections_;
+
+ public:
+ MaseHeader(): trees_(), siteSelections_(), sequenceSelections_() {}
+ virtual ~MaseHeader() {}
+
+ public:
+ size_t getNumberOfTrees() const { return trees_.size(); }
+ size_t getNumberOfSiteSelections() const { return siteSelections_.size(); }
+ size_t getNumberOfSequenceSelections() const { return sequenceSelections_.size(); }
+
+ std::vector<std::string> getTreeNames() const { return MapTools::getKeys(trees_); }
+ std::vector<std::string> getSiteSelectionNames() const { return MapTools::getKeys(siteSelections_); }
+ std::vector<std::string> getSequenceSelectionNames() const { return MapTools::getKeys(sequenceSelections_); }
+
+ const std::string& getTree(const std::string& name) const throw (Exception) {
+ if (trees_.find(name) != trees_.end()) {
+ return trees_[name];
+ } else {
+ throw Exception("MaseHeader::getTree. No tree with name " + name);
+ }
+ }
+ const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
+ if (siteSelections_.find(name) != siteSelections_.end()) {
+ return siteSelections_[name];
+ } else {
+ throw Exception("MaseHeader::getSiteSelection. No site selection with name " + name);
+ }
+ }
+ const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
+ if (sequenceSelections_.find(name) != sequenceSelections_.end()) {
+ return sequenceSelections_[name];
+ } else {
+ throw Exception("MaseHeader::getSequenceSelection. No sequence selection with name " + name);
+ }
+ }
+
+ void setTree(const std::string& name, const std::string& tree) {
+ trees_[name] = tree;
+ }
+ void setSiteSelection(const std::string& name, const MultiRange<size_t>& ranges) {
+ siteSelections_[name] = ranges;
+ }
+ void setSequenceSelection(const std::string& name, const std::vector<size_t>& set) {
+ sequenceSelections_[name] = set;
+ }
+
+};
+
+/**
+ * @brief The mase sequence file format.
+ *
+ * In addition to traditional read and write method, this class offers overloaded method
+ * with MaseHeader objects, dedicated to header information storage. If used, then the header
+ * of the mase file will be parsed accordingly. Otherwise, the header lines will be stored
+ * as general comments.
+ *
+ * @see MaseTools for alternative way of parsing headers.
+ */
+class Mase:
+ public AbstractISequence,
+ public AbstractIAlignment,
+ public AbstractOSequence
+{
+
+ private:
+
+ /**
+ * @brief The maximum number of chars to be written on a line.
+ */
+ unsigned int charsByLine_;
+ bool checkNames_;
+
+ public :
+ /**
+ * @brief Build a new Mase object.
+ *
+ * @param charsByLine Number of character per line when writing files.
+ * @param checkSequenceNames Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
+ */
+ Mase(unsigned int charsByLine = 100, bool checkSequenceNames = true): charsByLine_(charsByLine), checkNames_(checkSequenceNames) {}
+
+ // Class destructor
+ virtual ~Mase() {}
+
+ public:
+
+ /**
+ * @name Reading method including header:
+ *
+ * @{
+ */
+ VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
+ {
+ readHeader_(input, header);
+ return AbstractISequence::readSequences(input, alpha);
+ }
+ VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
+ {
+ std::ifstream input(path.c_str(), std::ios::in);
+ VectorSequenceContainer* sc = readMeta(input, alpha, header);
+ input.close();
+ return sc;
+ }
+ /** @} */
+
+ /**
+ * @name The AbstractISequence interface.
+ *
+ * @{
+ */
+ void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
+ /** @} */
+
+ /**
+ * @name The AbstractIAlignment interface.
+ *
+ * @{
+ */
+ void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
+ appendSequencesFromStream(input, sc); //This might cast an exception if sequences are not aligned!
+ }
+ /** @} */
+
+
+ /**
+ * @name The OSequence interface.
+ *
+ * @{
+ */
+ void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
+ void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
+ {
+ AbstractOSequence::writeSequences(path, sc, overwrite);
+ }
+ /** @} */
+
+ /**
+ * @name Writing methods including header:
+ *
+ * @{
+ */
+ void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
+ {
+ writeHeader_(output, header);
+ writeSequences(output, sc);
+ }
+ void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
+ {
+ // Open file in specified mode
+ std::ofstream output(path.c_str(), overwrite ? (std::ios::out) : (std::ios::out | std::ios::app));
+ writeHeader_(output, header);
+ writeSequences(output, sc);
+ output.close();
+ }
+ /** @} */
+
+ /**
+ * @name The IOSequence interface.
+ *
+ * @{
+ */
+ const std::string getFormatName() const { return "MASE file"; }
+
+ const std::string getFormatDescription() const
+ {
+ return "Optional file comments (preceeded by ;;), sequence comments (preceeded by ;), sequence name, sequence";
+ }
+ /** @} */
+
+ /**
+ * @return true if the names are to be checked when reading sequences from files.
+ */
+ bool checkNames() const { return checkNames_; }
+
+ /**
+ * @brief Tell whether the sequence names should be checked when reading from files.
+ *
+ * @param yn whether the sequence names should be checked when reading from files.
+ */
+ void checkNames(bool yn) { checkNames_ = yn; }
+
+ private:
+ void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
+ void writeHeader_(std::ostream& output, const MaseHeader& header) const;
+};
+
+} //end of namespace bpp.
+
+#endif // _MASE_H_
+
diff --git a/src/Bpp/Seq/Io/MaseTools.cpp b/src/Bpp/Seq/Io/MaseTools.cpp
new file mode 100644
index 0000000..d42c22f
--- /dev/null
+++ b/src/Bpp/Seq/Io/MaseTools.cpp
@@ -0,0 +1,306 @@
+//
+// File: MaseTools.cpp
+// Created by: Julien Dutheil
+// Created on: Tue Apr 1 09:16:59 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "MaseTools.h"
+#include "../Container/VectorSequenceContainer.h"
+#include "../Container/AlignedSequenceContainer.h"
+#include "../Container/SequenceContainerTools.h"
+#include <Bpp/Text/StringTokenizer.h>
+#include <Bpp/Text/TextTools.h>
+
+#include <iostream>
+
+using namespace std;
+using namespace bpp;
+
+SiteSelection MaseTools::getSiteSet(const Comments& maseFileHeader, const string& setName) throw (IOException)
+{
+ SiteSelection selection;
+ for (size_t i = 0; i < maseFileHeader.size(); i++)
+ {
+ string current = maseFileHeader[i];
+ string::size_type index = current.find("# of");
+ if (index < current.npos)
+ {
+ StringTokenizer st(string(current.begin() + index + 4, current.end()), " \t=;");
+ st.nextToken(); // skip next word: may be 'regions' or 'segments' or else ;-)
+ size_t numberOfSegments = TextTools::to<size_t>(st.nextToken());
+ string name = st.unparseRemainingTokens();
+ if (name == setName)
+ {
+ // cout << numberOfSegments << " segments found." << endl;
+ // Then look for the set definition:
+ i++; // next line.
+ size_t counter = 0;
+ while (i < maseFileHeader.size())
+ {
+ current = maseFileHeader[i++];
+ StringTokenizer st2(current);
+ // st.nextToken(); //Skip ';;'
+ while (st2.hasMoreToken())
+ {
+ StringTokenizer st3(st2.nextToken(), ",");
+ size_t begin = TextTools::to<size_t>(st3.nextToken());
+ size_t end = TextTools::to<size_t>(st3.nextToken());
+ // WARNING!!! In the mase+ format, sites are numbered from 1 to nbSites,
+ // Whereas in SiteContainer the index begins at 0.
+ for (size_t j = begin; j <= end; j++)
+ {
+ selection.push_back(j - 1); // bounds included.
+ }
+ counter++;
+ if (counter == numberOfSegments)
+ return selection;
+ }
+ }
+ }
+ }
+ }
+ if (selection.size() == 0)
+ {
+ throw IOException("Site set " + setName + " has not been found in the sequence file.");
+ }
+ return selection;
+}
+
+/******************************************************************************/
+
+SequenceSelection MaseTools::getSequenceSet(const Comments& maseFileHeader, const string& setName) throw (IOException)
+{
+ SequenceSelection selection;
+ for (size_t i = 0; i < maseFileHeader.size(); i++)
+ {
+ string current = maseFileHeader[i];
+
+ string::size_type index = current.find("@ of");
+ if (index < current.npos)
+ {
+ StringTokenizer st(string(current.begin() + index + 4, current.end()), " \t=;");
+ st.nextToken(); // skip next word: may be 'sequences' or else ;-)
+ size_t numberOfSequences = TextTools::to<size_t>(st.nextToken());
+ string name = st.unparseRemainingTokens();
+ size_t counter = 0;
+ if (name == setName)
+ {
+ // cout << numberOfSequences << " segments found." << endl;
+ // Then look for the set definition:
+ i++; // next line.
+ while (i < maseFileHeader.size())
+ {
+ current = maseFileHeader[i++];
+ StringTokenizer st2(current, ",");
+ while (st2.hasMoreToken())
+ {
+ int seqIndex = TextTools::toInt(st2.nextToken());
+ // WARNING!!! In the mase+ format, sequences are numbered from 1 to nbSequences,
+ // Whereas in SequenceContainer the index begins at 0.
+ selection.push_back(seqIndex - 1); // bounds included.
+ counter++;
+ if (counter == numberOfSequences)
+ return selection;
+ }
+ }
+ }
+ }
+ }
+ if (selection.size() == 0)
+ {
+ throw IOException("Sequence set " + setName + " has not been found in the sequence file.");
+ }
+ return selection;
+}
+
+/******************************************************************************/
+
+SiteContainer* MaseTools::getSelectedSites(
+ const SiteContainer& sequences,
+ const string& setName) throw (IOException)
+{
+ SiteSelection ss = getSiteSet(sequences.getGeneralComments(), setName);
+ // We need to convert positions in case of word alphabet:
+ size_t wsize = sequences.getAlphabet()->getStateCodingSize();
+ if (wsize > 1)
+ {
+ if (ss.size() % wsize != 0)
+ throw IOException("MaseTools::getSelectedSites: Site selection is not compatible with the alphabet in use in the container.");
+ SiteSelection ss2;
+ for (size_t i = 0; i < ss.size(); i += wsize)
+ {
+ if (ss[i] % wsize != 0)
+ throw IOException("MaseTools::getSelectedSites: Site selection is not compatible with the alphabet in use in the container.");
+ for (size_t j = 1; j < wsize; ++j)
+ {
+ if (ss[i + j] != (ss[i + j - 1] + 1))
+ throw IOException("MaseTools::getSelectedSites: Site selection is not compatible with the alphabet in use in the container.");
+ }
+ ss2.push_back(ss[i] / wsize);
+ }
+ return SiteContainerTools::getSelectedSites(sequences, ss2);
+ }
+ else
+ {
+ return SiteContainerTools::getSelectedSites(sequences, ss);
+ }
+}
+
+/******************************************************************************/
+
+SequenceContainer* MaseTools::getSelectedSequences(
+ const OrderedSequenceContainer& sequences,
+ const std::string& setName) throw (IOException)
+{
+ SequenceSelection ss = getSequenceSet(sequences.getGeneralComments(), setName);
+ VectorSequenceContainer* cont = new VectorSequenceContainer(sequences.getAlphabet());
+ SequenceContainerTools::getSelectedSequences(sequences, ss, *cont);
+ return cont;
+}
+
+/******************************************************************************/
+
+map<string, size_t> MaseTools::getAvailableSiteSelections(const Comments& maseHeader)
+{
+ map<string, size_t> selections;
+ for (size_t i = 0; i < maseHeader.size(); i++)
+ {
+ string current = maseHeader[i];
+
+ string::size_type index = current.find("# of");
+ if (index < current.npos)
+ {
+ StringTokenizer st(string(current.begin() + index + 4, current.end()), " \t\n\f\r=;");
+ st.nextToken(); // skip next word: may be 'sequences' or else ;-)
+ size_t numberOfSegments = TextTools::toInt(st.nextToken());
+ string name = st.nextToken();
+ while (st.hasMoreToken())
+ {
+ name += " " + st.nextToken();
+ }
+ size_t counter = 0;
+ size_t nbSites = 0;
+ while (i < maseHeader.size())
+ {
+ i++;
+ current = maseHeader[i];
+ StringTokenizer st2(current);
+ // st.nextToken(); //Skip ';;'
+ while (st2.hasMoreToken())
+ {
+ StringTokenizer st3(st2.nextToken(), ",");
+ size_t begin = TextTools::toInt(st3.nextToken());
+ size_t end = TextTools::toInt(st3.nextToken());
+ counter++;
+ nbSites += end - begin + 1;
+ }
+ if (counter == numberOfSegments)
+ {
+ selections[name] = nbSites;
+ break;
+ }
+ }
+ }
+ }
+ return selections;
+}
+
+/******************************************************************************/
+
+map<string, size_t> MaseTools::getAvailableSequenceSelections(const Comments& maseHeader)
+{
+ map<string, size_t> selections;
+ for (size_t i = 0; i < maseHeader.size(); i++)
+ {
+ string current = maseHeader[i];
+
+ string::size_type index = current.find("@ of");
+ if (index < current.npos)
+ {
+ StringTokenizer st(string(current.begin() + index + 4, current.end()), " \t\n\f\r=;");
+ st.nextToken(); // skip next word: may be 'sequences' or else ;-)
+ size_t numberOfSequences = TextTools::fromString<size_t>(st.nextToken());
+ string name = st.nextToken();
+ while (st.hasMoreToken())
+ {
+ name += st.nextToken();
+ }
+ selections[name] = numberOfSequences;
+ }
+ }
+ return selections;
+}
+
+/******************************************************************************/
+
+size_t MaseTools::getPhase(const Comments& maseFileHeader, const string& setName) throw (Exception)
+{
+ size_t phase = 0;
+ string::size_type index = 0;
+ for (size_t i = 0; i < maseFileHeader.size(); i++)
+ {
+ string current = maseFileHeader[i];
+
+ index = current.find("# of");
+ if (index < current.npos)
+ {
+ StringTokenizer st(string(current.begin() + index + 12, current.end()), " \t\n\f\r=;");
+ // size_t numberOfSegments = TextTools::toInt(st.nextToken());
+ // cout << "Number of regions: " << st.nextToken() << endl;
+ string name;
+ while (st.hasMoreToken())
+ {
+ name = st.nextToken();
+ // cout << "Name of regions: " << name << endl;
+ }
+ if (name == setName)
+ {
+ return phase;
+ }
+ }
+
+ index = current.find("/codon_start");
+ if (index < current.npos)
+ {
+ StringTokenizer st(string(current.begin() + index + 12, current.end()), " \t\n\f\r=;");
+ phase = TextTools::toInt(st.nextToken());
+ }
+ }
+ throw Exception("PolymorphismSequenceContainer::getPhase: no /codon_start found, or site selection missing.");
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Io/MaseTools.h b/src/Bpp/Seq/Io/MaseTools.h
new file mode 100644
index 0000000..2206fd4
--- /dev/null
+++ b/src/Bpp/Seq/Io/MaseTools.h
@@ -0,0 +1,146 @@
+//
+// File: MaseTools.h
+// Created by: Julien Dutheil
+// Created on: Tue Apr 1 09:16:59 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _MASETOOLS_H_
+#define _MASETOOLS_H_
+
+#include "../Container/SequenceContainer.h"
+#include "../Container/OrderedSequenceContainer.h"
+#include "../Container/SequenceContainerTools.h"
+#include "../Container/SiteContainer.h"
+#include "../Container/SiteContainerTools.h"
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+/**
+ * @brief Utilitary methods that deal with the Mase format.
+ *
+ * This class particularily covers the Mase+ format, which allows
+ * site and sequence selection.
+ * Mase+ tags are in the header of the mase file, which is stored
+ * in the 'general comment' section of sequence containers.
+ * Most of the methods here hence work on the general comments associated
+ * to a container.
+ */
+class MaseTools
+{
+ public:
+
+ /**
+ * @brief Get a site selection from a Mase+ header file.
+ *
+ * @param maseFileHeader The header of the mase+ file as comments lines.
+ * @param setName The name of the set to retrieve.
+ * @throw IOException If the specified set is not found.
+ */
+ static SiteSelection getSiteSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
+
+ /**
+ * @brief Get a sequence selection from a Mase+ header file.
+ *
+ * @param maseFileHeader The header of the mase+ file as comments lines.
+ * @param setName The name of the set to retrieve.
+ * @throw IOException If the specified set is not found.
+ */
+ static SequenceSelection getSequenceSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
+
+ /**
+ * @brief Create a new container corresponding to a site set given in the mase+ format.
+ *
+ * A new VectorSiteContainer is created, whose destruction is up to the user.
+ * The container passed as argument must have 'general comments' in the mase+ format.
+ * This function calls the getSiteSet() function on the comments and then calls for
+ * SiteContainerTools::getSelectedSites() on the selection.
+ *
+ * @param sequences The container to get the sites from.
+ * @param setName The name of the set to retrieve.
+ * @throw IOException If the specified set is not found.
+ */
+ static SiteContainer* getSelectedSites(const SiteContainer& sequences, const std::string& setName) throw (IOException);
+
+ /**
+ * @brief Create a new container corresponding to a site set given in the mase+ format.
+ *
+ * A new VectorSequenceContainer is created, whose destruction is up to the user.
+ * The container passed as argument must have 'general comments' in the mase+ format.
+ * This function calls the getSequenceSet() function on the comments and then calls for
+ * SiteContainerTools::getSelectedSequences() on the selection.
+ *
+ * @param sequences The container to get the sequence from.
+ * @param setName The name of the set to retrieve.
+ * @throw IOException If the specified set is not found.
+ */
+ static SequenceContainer* getSelectedSequences(const OrderedSequenceContainer& sequences, const std::string & setName) throw (IOException);
+
+ /**
+ * @brief Get a list of all available site selections.
+ *
+ * @param maseHeader Comments as described in the Mase+ format specification.
+ * @return A vector of selection names.
+ */
+ static std::map<std::string, size_t> getAvailableSiteSelections(const Comments & maseHeader);
+
+ /**
+ * @brief Get a list of all available sequences selections.
+ *
+ * @param maseHeader Comments as described in the Mase+ format specification.
+ * @return A vector of selection names.
+ */
+ static std::map<std::string, size_t> getAvailableSequenceSelections(const Comments & maseHeader);
+
+ /**
+ * @brief Get the phase of a given coding region from a mase+ header.
+ *
+ * Look for a /codon_start tag with a phase indice and a site selection with name setName.
+ *
+ * @param maseFileHeader Comments in Mase+ format.
+ * @param setName a cds site selection name.
+ * @return 1,2 or 3.
+ * @throw Exception If no corresponding tag found in file.
+ */
+ static size_t getPhase(const Comments & maseFileHeader, const std::string &setName) throw (Exception);
+
+};
+
+} //end of namespace bpp.
+
+#endif //_MASETOOLS_H_
+
diff --git a/src/Bpp/Seq/Io/NexusIoSequence.cpp b/src/Bpp/Seq/Io/NexusIoSequence.cpp
new file mode 100644
index 0000000..1fce73a
--- /dev/null
+++ b/src/Bpp/Seq/Io/NexusIoSequence.cpp
@@ -0,0 +1,209 @@
+//
+// File: NexusIOSequence.cpp
+// Created by: Julien Dutheil
+// Created on: Wed May 27 16:15 2009
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "NexusIoSequence.h"
+#include "NexusTools.h"
+#include "../Container/SiteContainerTools.h"
+#include "../Alphabet/AlphabetTools.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/KeyvalTools.h>
+#include <Bpp/Io/FileTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <sstream>
+
+using namespace std;
+
+/******************************************************************************/
+
+const std::vector<std::string> NexusIOSequence::splitNameAndSequence_(const std::string& s) const throw (Exception)
+{
+ vector<string> v(2);
+ string::size_type index = s.find(" ");
+ if(index == string::npos) throw Exception("NexusIOSequence::splitNameAndSequence_(). No sequence name found.");
+ v[0] = TextTools::removeSurroundingWhiteSpaces(s.substr(0, index));
+ v[1] = TextTools::removeFirstWhiteSpaces(s.substr(index + 1));
+ return v;
+}
+
+
+/******************************************************************************/
+
+void NexusIOSequence::appendAlignmentFromStream(std::istream& input, SiteContainer& vsc) const throw (Exception)
+{
+ // Checking the existence of specified file
+ if (!input) { throw IOException ("NexusIOSequence::read(). Fail to open file"); }
+
+ //Look for the DATA block:
+ string line = "";
+ while (TextTools::toUpper(line) != "BEGIN DATA;")
+ {
+ if (input.eof())
+ throw Exception("NexusIOSequence::appendFromStream(). No data block was found.");
+ line = TextTools::removeSurroundingWhiteSpaces(FileTools::getNextLine(input));
+ }
+
+ //Look for the DIMENSIONS command:
+ string cmdName = "", cmdArgs = "";
+ while (cmdName != "DIMENSIONS")
+ {
+ if (input.eof())
+ throw Exception("NexusIOSequence::appendFromStream(). No DIMENSIONS command was found.");
+ NexusTools::getNextCommand(input, cmdName, cmdArgs);
+ cmdName = TextTools::toUpper(cmdName);
+ }
+ map<string, string> args;
+ KeyvalTools::multipleKeyvals(cmdArgs, args, " ");
+ map<string, string> argsUp;
+ for (map<string, string>::iterator it = args.begin(); it != args.end(); it++)
+ argsUp[TextTools::toUpper(it->first)] = it->second;
+ if (argsUp["NTAX"] == "")
+ throw Exception("NexusIOSequence::appendFromStream(). DIMENSIONS command does not have a NTAX argument.");
+ unsigned int ntax = TextTools::to<unsigned int>(argsUp["NTAX"]);
+
+ //Look for the FORMAT command:
+ while (cmdName != "FORMAT")
+ {
+ if (input.eof())
+ throw Exception("NexusIOSequence::appendFromStream(). No FORMAT command was found.");
+ NexusTools::getNextCommand(input, cmdName, cmdArgs);
+ cmdName = TextTools::toUpper(cmdName);
+ }
+ if (TextTools::hasSubstring(cmdArgs, "TRANSPOSE"))
+ throw Exception("NexusIOSequence::appendFromStream(). TRANSPOSE option is not supported.");
+
+ //Check if the alignment is dotted or not:
+ bool matchChar = TextTools::hasSubstring(TextTools::toUpper(cmdArgs), "MATCHCHAR");
+
+ SiteContainer* alignment = 0;
+ if (matchChar)
+ alignment = new AlignedSequenceContainer(&AlphabetTools::DEFAULT_ALPHABET);
+ else
+ alignment = &vsc;
+
+ //Look for the MATRIX command:
+ line = "";
+ while (!TextTools::startsWith(TextTools::toUpper(line), "MATRIX"))
+ {
+ if (input.eof())
+ throw Exception("NexusIOSequence::appendFromStream(). No MATRIX command was found.");
+ line = TextTools::removeSurroundingWhiteSpaces(FileTools::getNextLine(input));
+ }
+ line = FileTools::getNextLine(input);
+
+ vector<string> names, seqs;
+ // Read first block:
+ bool commandFinished = false;
+ for (unsigned int i = 0; i < ntax && !input.eof(); i++)
+ {
+ if (TextTools::endsWith(line, ";"))
+ {
+ if (i < ntax - 1)
+ throw IOException("NexusIOSequence::appendFromStream. Early end of MATRIX command, some sequences are missing.");
+ else
+ {
+ commandFinished = true;
+ line = line.substr(0, line.size() - 1); //Remove trailing semi-colon.
+ }
+ }
+ vector<string> v = splitNameAndSequence_(line);
+ names.push_back(v[0]);
+ seqs.push_back(v[1]);
+ line = FileTools::getNextLine(input);
+ }
+
+ //Then read all other blocks:
+ commandFinished = TextTools::removeSurroundingWhiteSpaces(line) == ";"; //In case the end of command is on a separate line.
+ while (!commandFinished)
+ {
+ for (unsigned int i = 0; i < ntax && !input.eof(); i++)
+ {
+ if (TextTools::endsWith(line, ";"))
+ {
+ if (i < ntax - 1)
+ throw IOException("NexusIOSequence::appendFromStream. Early end of MATRIX command, some sequences are missing.");
+ else
+ {
+ commandFinished = true;
+ line = line.substr(0, line.size() - 1); //Remove trailing semi-colon.
+ }
+ }
+
+ vector<string> v = splitNameAndSequence_(line);
+ if (v[0] != names[i])
+ throw IOException("NexusIOSequence::appendFromStream. Bad file, the sequences are not in the same order in interleaved blocks, or one taxon is missing.");
+ seqs[i] += v[1];
+ line = FileTools::getNextLine(input);
+ commandFinished = TextTools::removeSurroundingWhiteSpaces(line) == ";"; //In case the end of command is on a separate line.
+ }
+ }
+ for (unsigned int i = 0; i < names.size(); i++)
+ {
+ alignment->addSequence(BasicSequence(names[i], seqs[i], vsc.getAlphabet()), checkNames_);
+ }
+
+ if (matchChar)
+ {
+ //Now we resolve the alignment:
+ SiteContainer* resolvedAlignment =
+ SiteContainerTools::resolveDottedAlignment(*alignment, vsc.getAlphabet());
+ delete alignment;
+ for (unsigned int i = 0; i < resolvedAlignment->getNumberOfSequences(); i++)
+ {
+ vsc.addSequence(resolvedAlignment->getSequence(i), false);
+ }
+ delete resolvedAlignment;
+ }
+}
+
+/******************************************************************************/
+
+const std::string NexusIOSequence::getFormatName() const { return "Nexus"; }
+
+/******************************************************************************/
+
+const std::string NexusIOSequence::getFormatDescription() const
+{
+ return "Nexus file format.";
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Io/NexusIoSequence.h b/src/Bpp/Seq/Io/NexusIoSequence.h
new file mode 100644
index 0000000..0a32843
--- /dev/null
+++ b/src/Bpp/Seq/Io/NexusIoSequence.h
@@ -0,0 +1,150 @@
+//
+// File: NexusIOSequence.h
+// Created by: Julien Dutheil
+// Created on: Wed May 27 16:15 2009
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _NEXUSIOSEQUENCE_H_
+#define _NEXUSIOSEQUENCE_H_
+
+#include "AbstractIAlignment.h"
+#include "../Sequence.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/VectorSequenceContainer.h"
+#include "../Container/AlignedSequenceContainer.h"
+
+// From the STL:
+#include <iostream>
+
+namespace bpp
+{
+
+/**
+ * @brief The Nexus format reader for sequences.
+ *
+ * An AlignedSequenceContainer is used instead of a VectorSequenceContainer.
+ *
+ * This reader is not supposed to be a full parser of the Nexus files,
+ * but only extract the sequence data. Only a basic subset of the options
+ * are and will be supported.
+ *
+ * This format is described in the following paper:
+ * Maddison D, Swofford D, and Maddison W (1997), _Syst Biol_ 46(4):590-621
+ *
+ * @author Julien Dutheil
+ */
+class NexusIOSequence:
+ public AbstractIAlignment,
+ public virtual ISequence
+{
+ protected:
+
+ /**
+ * @brief The maximum number of chars to be written on a line.
+ */
+ unsigned int charsByLine_;
+
+ bool checkNames_;
+
+ public:
+ /**
+ * @brief Build a new Phylip file reader.
+ *
+ * @param charsByLine The number of base to display in a row (ignored for now, no writing support).
+ * @param checkSequenceNames Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
+ */
+ NexusIOSequence(unsigned int charsByLine = 100, bool checkSequenceNames = true):
+ charsByLine_(charsByLine), checkNames_(checkSequenceNames) {}
+
+ virtual ~NexusIOSequence() {}
+
+ public:
+
+ /**
+ * @name The AbstractIAlignment interface.
+ *
+ * @{
+ */
+ void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
+ /** @} */
+
+ /**
+ * @name The ISequence interface.
+ *
+ * As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence
+ * interface by downcasting the interface.
+ *
+ * @{
+ */
+ virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
+ return readAlignment(input, alpha);
+ }
+ virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
+ return readAlignment(path, alpha);
+ }
+ /** @} */
+
+ /**
+ * @name The IOSequence interface.
+ *
+ * @{
+ */
+ const std::string getFormatName() const;
+ const std::string getFormatDescription() const;
+ /** @} */
+
+ /**
+ * @return true if the names are to be checked when reading sequences from files.
+ */
+ bool checkNames() const { return checkNames_; }
+
+ /**
+ * @brief Tell whether the sequence names should be checked when reading from files.
+ *
+ * @param yn whether the sequence names should be checked when reading from files.
+ */
+ void checkNames(bool yn) { checkNames_ = yn; }
+
+
+ private:
+ //Reading tools:
+ const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
+};
+
+} //end of namespace bpp.
+
+#endif //_NEXUSIOSEQUENCE_H_
+
diff --git a/src/Bpp/Seq/Io/NexusTools.cpp b/src/Bpp/Seq/Io/NexusTools.cpp
new file mode 100644
index 0000000..1914e2f
--- /dev/null
+++ b/src/Bpp/Seq/Io/NexusTools.cpp
@@ -0,0 +1,119 @@
+//
+// File: NexusTools.cpp
+// Created by: Julien Dutheil
+// Created on: Wed May 27 19:30 2009
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "NexusTools.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Io/FileTools.h>
+
+using namespace bpp;
+using namespace std;
+
+std::string NexusTools::getNextNonCommentLine(std::istream& input)
+{
+ string line = TextTools::removeSurroundingWhiteSpaces(FileTools::getNextLine(input));
+ bool test = true;
+ unsigned int countOpen = 0;
+ unsigned int countClosed = 0;
+ while(test)
+ {
+ if (line[0] == '[')
+ {
+ countOpen++;
+ }
+ if (line[line.size() - 1] == ']')
+ {
+ countClosed++;
+ }
+ if(countOpen > 0)
+ line = TextTools::removeSurroundingWhiteSpaces(FileTools::getNextLine(input));
+ if(countOpen == countClosed)
+ test = false;
+ }
+ return line;
+}
+
+
+bool NexusTools::getNextCommand(std::istream& input, std::string& name, std::string& arguments, bool lineBrk)
+ throw (IOException)
+{
+ // Checking if the stream is readable
+ if (! input) { throw IOException ("NexusTools::getNextCommand(). Failed to read from stream"); }
+
+ string line = TextTools::removeSurroundingWhiteSpaces(getNextNonCommentLine(input));
+ if (TextTools::startsWith(line, "BEGIN"))
+ {
+ return false;
+ }
+
+ // Check if the command stands on one line:
+ bool commandComplete = TextTools::endsWith(line, ";");
+ if (commandComplete)
+ line = line.substr(0, line.size() - 1);
+ // Get the command name, as the first block:
+ string::size_type limit = line.find(" ");
+ if (limit == string::npos)
+ {
+ name = line;
+ arguments = "";
+ if (commandComplete)
+ {
+ //Command with no argument:
+ return true;
+ }
+ }
+ else
+ {
+ name = line.substr(0, limit);
+ arguments = line.substr(limit + 1);
+ }
+ //Then parse the next lines:
+ while(!commandComplete)
+ {
+ if (input.eof()) { throw IOException ("NexusTools::getNextCommand(). Reached end of file before the end of the command could be found"); }
+ line = TextTools::removeSurroundingWhiteSpaces(getNextNonCommentLine(input));
+ commandComplete = TextTools::endsWith(line, ";");
+ if (commandComplete)
+ line = line.substr(0, line.size() - 1);
+ if(lineBrk)
+ arguments += "\n";
+ arguments += line;
+ }
+ return true;
+}
+
diff --git a/src/Bpp/Seq/Io/NexusTools.h b/src/Bpp/Seq/Io/NexusTools.h
new file mode 100644
index 0000000..51c8f93
--- /dev/null
+++ b/src/Bpp/Seq/Io/NexusTools.h
@@ -0,0 +1,84 @@
+//
+// File: NexusTools.h
+// Created by: Julien Dutheil
+// Created on: Wed May 27 19:30 2009
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _NEXUSTOOLS_H_
+#define _NEXUSTOOLS_H_
+
+// From the STL:
+#include <iostream>
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+/**
+ * @brief Tools for parsing Nexus files.
+ *
+ * The Nexus format is described in the following paper:
+ * Maddison D, Swofford D, and Maddison W (1997), _Syst Biol_ 46(4):590-621
+ *
+ * @author Julien Dutheil
+ */
+class NexusTools
+{
+ public:
+ /**
+ * @param input The input stream.
+ * @return A string containing the next line in the file wichi is not empty and is no a comment line.
+ */
+ static std::string getNextNonCommentLine(std::istream& input);
+
+ /**
+ * @brief parse the next command name within a block.
+ *
+ * @param input [in] The input stream.
+ * @param name [out] Will contain the name of the command.
+ * @param arguments [out] Will contain the arguments of the commans, as raw data. The arguments will not be parsed.
+ * @param lineBrk [in] Tell is the line break should be preserved in the arguments.
+ * @return Whether a command was found in the current block.
+ * @throw IOException In case of bad format.
+ */
+ static bool getNextCommand(std::istream& input, std::string& name, std::string& arguments, bool lineBrk = true) throw (IOException);
+
+};
+
+} //end of namespace bpp.
+
+#endif //_NEXUSTOOLS_H_
+
diff --git a/src/Bpp/Seq/Io/OSequence.h b/src/Bpp/Seq/Io/OSequence.h
new file mode 100644
index 0000000..bc1a01e
--- /dev/null
+++ b/src/Bpp/Seq/Io/OSequence.h
@@ -0,0 +1,128 @@
+//
+// File: OSequence.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: Tue Aug 21 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _OSEQUENCE_H_
+#define _OSEQUENCE_H_
+
+#include "../Container/SequenceContainer.h"
+#include "../Container/SiteContainer.h"
+#include "IoSequence.h"
+
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+ /**
+ * @brief The OSequence interface.
+ *
+ * This interface defines the basic methods for writing sequences to a file.
+ */
+ class OSequence:
+ public virtual IOSequence
+ {
+ public:
+ OSequence() {}
+ virtual ~OSequence() {}
+
+ public:
+
+ /**
+ * @brief Write a container to a stream.
+ *
+ * @param output The output stream where to write.
+ * @param sc The container to write.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
+
+ /**
+ * @brief Write a container to a file.
+ *
+ * @param path The path to the file to write.
+ * @param sc The container to write.
+ * @param overwrite If true the sequences are written at the beginning of the file instead of being appended.
+ * Any previous content will be lost.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
+
+ };
+
+
+ /**
+ * @brief The OAlignment interface.
+ *
+ * This interface defines the basic methods for writing alignments to a file.
+ */
+ class OAlignment:
+ public virtual IOSequence
+ {
+ public:
+ OAlignment() {}
+ virtual ~OAlignment() {}
+
+ public:
+
+ /**
+ * @brief Write a container to a stream.
+ *
+ * @param output The output stream where to write.
+ * @param sc The container to write.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
+
+ /**
+ * @brief Write a container to a file.
+ *
+ * @param path The path to the file to write.
+ * @param sc The container to write.
+ * @param overwrite If true the sequences are written at the beginning of the file instead of being appended.
+ * Any previous content will be lost.
+ * @throw Exception If the file is not in the specified format.
+ */
+ virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
+
+ };
+} //end of namespace bpp.
+
+#endif // _OSEQUENCE_H_
+
diff --git a/src/Bpp/Seq/Io/OSequenceStream.h b/src/Bpp/Seq/Io/OSequenceStream.h
new file mode 100644
index 0000000..f862a7e
--- /dev/null
+++ b/src/Bpp/Seq/Io/OSequenceStream.h
@@ -0,0 +1,81 @@
+//
+// File OSequenceStream.h
+// Author: Sylvain Gaillard
+// Created: 19/08/2009
+//
+
+/*
+Copyright or © or Copr. CNRS, (August 19, 2009)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _OSEQUENCESTREAM_H_
+#define _OSEQUENCESTREAM_H_
+
+#include "IoSequenceStream.h"
+#include "../Sequence.h"
+#include "../Alphabet/Alphabet.h"
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+/**
+ * @brief The OSequenceStream interface.
+ *
+ * Interface for streaming sequences output.
+ *
+ * @author Sylvain Gaillard
+ */
+class OSequenceStream: public virtual IOSequenceStream
+{
+ public:
+ OSequenceStream() {}
+ virtual ~OSequenceStream() {}
+
+ public:
+ /**
+ * @brief Read sequence from stream.
+ *
+ * Read one sequence from a stream.
+ *
+ * @param output The stream where write.
+ * @param seq The sequence to write.
+ * @throw Exception IOExecption.
+ */
+ virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
+
+};
+
+} //end of namespace bpp.
+
+#endif // _ISEQUENCESTREAM_H_
+
diff --git a/src/Bpp/Seq/Io/PhredPhd.cpp b/src/Bpp/Seq/Io/PhredPhd.cpp
new file mode 100644
index 0000000..84c878c
--- /dev/null
+++ b/src/Bpp/Seq/Io/PhredPhd.cpp
@@ -0,0 +1,138 @@
+//
+// File: PhredPhd.cpp
+// Created by: Sylvain Gaillard
+// Created on: Wed Nov 5 2008
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 5, 2008)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "PhredPhd.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+
+using namespace bpp;
+
+/******************************************************************************/
+
+//PhredPhd::PhredPhd() {}
+
+/******************************************************************************/
+
+bool PhredPhd::nextSequence(std::istream& input, Sequence& seq) const throw (Exception) {
+ std::vector<int> pos;
+ return nextSequence(input, seq, pos);
+}
+
+/******************************************************************************/
+
+bool PhredPhd::nextSequence(std::istream& input, Sequence& seq, std::vector<int>& pos) const throw (Exception) {
+ if (!input) {
+ throw IOException ("PhredPhd::read: fail to open stream");
+ }
+
+ bool flag = false;
+ std::string name, sequence = ""; // Initialization
+ std::vector<int> q, p;
+
+ flag = parseFile_(input, name, sequence, q, p);
+ // Sequence creation
+ if(name == "")
+ throw Exception("PhredPhd::read: sequence without name!");
+ seq.setName(name);
+ seq.setContent(sequence);
+ try {
+ SequenceWithQuality& sq = dynamic_cast<SequenceWithQuality&>(seq);
+ sq.setQualities(q);
+ } catch (...) {
+ }
+ return flag;
+}
+
+/******************************************************************************/
+
+bool PhredPhd::parseFile_(std::istream& input, std::string& name, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos) const {
+ bool readSeqFlag = false;
+ std::string temp;
+ // Read sequence info
+ // Main loop : for all lines
+ while (!input.eof()) {
+ std::getline(input, temp, '\n'); // Copy current line in temporary string
+ StringTokenizer st(temp, " ");
+ if (st.hasMoreToken()) {
+ if (st.getToken(0) == "BEGIN_SEQUENCE") {
+ name = st.getToken(1);
+ }
+ std::string flag = st.getToken(0);
+ while (flag != "END_SEQUENCE" && !input.eof()) {
+ getline(input, temp, '\n');
+ StringTokenizer st2(temp, " ");
+ if (st2.hasMoreToken()) {
+ flag = st2.getToken(0);
+ }
+ if (flag == "BEGIN_DNA") {
+ readSeqFlag = parseDNA_(input, sequence, qual, pos);
+ break; // End the whole loop after parsing DNA
+ }
+ }
+ }
+ }
+ return readSeqFlag;
+}
+
+/******************************************************************************/
+
+bool PhredPhd::parseDNA_(std::istream& input, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos) const {
+ bool readSeqFlag = false;
+ std::string line_buffer;
+ std::string flag;
+ sequence.clear();
+ qual.clear();
+ pos.clear();
+ while (flag != "END_DNA" && !input.eof()) {
+ std::getline(input, line_buffer, '\n');
+ StringTokenizer st(line_buffer, " ");
+ if (st.hasMoreToken()) {
+ flag = TextTools::toUpper(st.getToken(0));
+ if (st.numberOfRemainingTokens() == 3) {
+ sequence += flag;
+ qual.push_back(TextTools::toInt(st.getToken(1)));
+ pos.push_back(TextTools::toInt(st.getToken(2)));
+ readSeqFlag = true;
+ }
+ }
+ }
+ return readSeqFlag;
+}
+
+/******************************************************************************/
diff --git a/src/Bpp/Seq/Io/PhredPhd.h b/src/Bpp/Seq/Io/PhredPhd.h
new file mode 100644
index 0000000..6ed2d16
--- /dev/null
+++ b/src/Bpp/Seq/Io/PhredPhd.h
@@ -0,0 +1,156 @@
+//
+// File: PhredPhd.h
+// Created by: Sylvain Gaillard
+// Created on: Wed Nov 5 2008
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 5, 2008)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _PHREDPHD_H_
+#define _PHREDPHD_H_
+
+#include "ISequenceStream.h"
+#include "../Sequence.h"
+#include "../SequenceWithQuality.h"
+
+namespace bpp {
+
+ /**
+ * @brief The phd sequence file format from phred software.
+ *
+ * This class read DNA SequenceWithQuality from phd files produced by the
+ * phred program from the University of Washington.
+ *
+ * @par Usage
+ *
+ * @code
+ * // Creating a SequenceWithQuality object
+ * DNA alpha;
+ * SequenceWithQuality seq(&alpha);
+ * std::vector<int> pos;
+ *
+ * // Create a PhredPhd parser
+ * PhredPhd pp;
+ *
+ * // Opening the file
+ * std::ifstream in("my_sequence.phd");
+ *
+ * // Read the sequence
+ * pp.nextSequence(in, seq, pos);
+ *
+ * // Close the file
+ * in.close();
+ * @endcode
+ *
+ * @author Sylvain Gaillard
+ */
+ class PhredPhd: public ISequenceStream {
+ public:
+
+ /**
+ * @brief Build a new PhredPhd object.
+ */
+ PhredPhd() {}
+
+ virtual ~PhredPhd() {}
+
+ public:
+ /**
+ * @name The ISequenceStream interface.
+ *
+ * @{
+ */
+ bool nextSequence(
+ std::istream& input,
+ Sequence& seq
+ ) const throw (Exception);
+ /** @} */
+
+ /**
+ * @brief Read a SequenceWithQuality from stream and store chromatographic positions
+ *
+ * A more complete parser that read a SequenceWithQuality and store
+ * the position of each base call on the chromatogram in a vector of
+ * int.
+ *
+ * @param input The stram to read.
+ * @param seq The sequence to fill.
+ * @param pos The vector of positions to fill.
+ * @throw Exception IOException and Sequence related exceptions.
+ */
+ bool nextSequence(
+ std::istream& input,
+ Sequence& seq,
+ std::vector<int>& pos
+ ) const throw (Exception);
+
+ /**
+ * @name The IOFormat interface.
+ *
+ * @{
+ */
+ const std::string getDataType() const { return "SequenceWithQuality"; };
+ const std::string getFormatName() const { return "phd file"; };
+ const std::string getFormatDescription() const {
+ return "Sequences following the phd format as describe in the phred documentation.";
+ }
+ /** @} */
+
+ private:
+ /**
+ * @brief Global file parser
+ *
+ * @param input The stream to read
+ * @param name The string to store the sequence name
+ * @param sequence The string to store the sequence
+ * @param qual The vector to store qualities
+ * @param pos The vector to store positions
+ */
+ bool parseFile_(std::istream& input, std::string& name, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos) const;
+
+ /**
+ * @brief Parse the DNA part of the file
+ *
+ * Read the DNA part until `END_DNA' or EOF.
+ *
+ * @param input The stream to read
+ * @param sequence The string to store the sequence
+ * @param qual The vector to store qualities
+ * @param pos The vector to store positions
+ */
+ bool parseDNA_(std::istream& input, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos) const;
+ };
+} //end of namespace bpp
+
+#endif // _PHREDPHD_H_
diff --git a/src/Bpp/Seq/Io/PhredPoly.cpp b/src/Bpp/Seq/Io/PhredPoly.cpp
new file mode 100644
index 0000000..967024b
--- /dev/null
+++ b/src/Bpp/Seq/Io/PhredPoly.cpp
@@ -0,0 +1,97 @@
+//
+// File: PhredPoly.cpp
+// Created by: Sylvain Gaillard
+// Created on: Fri Oct 31 2008
+//
+
+/*
+Copyright or © or Copr. CNRS, (October 31, 2008)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "PhredPoly.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+#include <Bpp/Numeric/NumTools.h>
+
+using namespace bpp;
+using namespace std;
+
+/******************************************************************************/
+
+PhredPoly::PhredPoly(double ratio) : ratio_(ratio) {}
+
+/******************************************************************************/
+
+bool PhredPoly::nextSequence(istream& input, Sequence& seq) const throw (Exception) {
+ if (!input) { throw IOException ("PhredPoly::read: fail to open stream"); }
+
+ string temp, name, sequence = ""; // Initialization
+ bool flag = false;
+
+ // Read first line
+ if (!input.eof()) {
+ getline(input, temp, '\n'); // Copy current line in temporary string
+ StringTokenizer st(temp, " ");
+ name = st.getToken(0);
+ }
+
+ const Alphabet* alpha = seq.getAlphabet();
+
+ // Main loop : for all other lines
+ while (!input.eof()) {
+ getline(input, temp, '\n'); // Copy current line in temporary string
+ StringTokenizer st(temp, " ");
+ if (st.numberOfRemainingTokens() == 12) {
+ double a = TextTools::toDouble(st.getToken(3));
+ double b = TextTools::toDouble(st.getToken(7));
+ if (a < b) {
+ NumTools::swap(a, b);
+ }
+ vector<string> v;
+ v.push_back(st.getToken(0)); // Get the called base
+ if (b / a > this->ratio_) {
+ v.push_back(st.getToken(4)); // Get the uncalled base if relative picks areas are similar
+ }
+ sequence += alpha->getGeneric(v);
+ }
+ }
+ if(name == "") {
+ throw Exception("PhredPoly::read: sequence without name!");
+ } else {
+ seq.setName(name);
+ seq.setContent(sequence);
+ flag = true;
+ }
+ return flag;
+}
+
+/******************************************************************************/
diff --git a/src/Bpp/Seq/Io/PhredPoly.h b/src/Bpp/Seq/Io/PhredPoly.h
new file mode 100644
index 0000000..8aeb4ff
--- /dev/null
+++ b/src/Bpp/Seq/Io/PhredPoly.h
@@ -0,0 +1,91 @@
+//
+// File: PhredPoly.h
+// Created by: Sylvain Gaillard
+// Created on: Fri Oct 31 2008
+//
+
+/*
+Copyright or © or Copr. CNRS, (October 31, 2008)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _PHREDPOLY_H_
+#define _PHREDPOLY_H_
+
+#include "ISequenceStream.h"
+#include "../Sequence.h"
+
+namespace bpp {
+
+ /**
+ * @brief The poly sequence file format from phred software.
+ *
+ * This class read DNA sequence from poly files produced by the phred program
+ * from the University of Washington.
+ * For now, only read raw sequences and do a basic filter on heterozygous site.
+ */
+ class PhredPoly: public ISequenceStream {
+ protected:
+ double ratio_;
+
+ public:
+
+ /**
+ * @brief Build a new PhredPoly object.
+ */
+ PhredPoly(double ratio = 0.8);
+
+ virtual ~PhredPoly() {}
+
+ public:
+ /**
+ * @name The AbstractISequence interface.
+ *
+ * @{
+ */
+ bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
+ /** @} */
+
+ /**
+ * @name The IOSequence interface.
+ *
+ * @{
+ */
+ const std::string getDataType() const { return "Sequence"; };
+ const std::string getFormatName() const { return "poly file"; };
+ const std::string getFormatDescription() const {
+ return "Sequences following the poly format as describe in the phred documentation.";
+ }
+ /** @} */
+ };
+} //end of namespace bpp
+
+#endif // _PHREDPOLY_H_
diff --git a/src/Bpp/Seq/Io/Phylip.cpp b/src/Bpp/Seq/Io/Phylip.cpp
new file mode 100644
index 0000000..378335f
--- /dev/null
+++ b/src/Bpp/Seq/Io/Phylip.cpp
@@ -0,0 +1,304 @@
+//
+// File: Phylip.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Oct 27 12:22:56 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "Phylip.h"
+#include "../Container/SequenceContainerTools.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+#include <Bpp/Io/FileTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <sstream>
+
+using namespace std;
+
+/******************************************************************************/
+
+const std::vector<std::string> Phylip::splitNameAndSequence(const std::string& s) const throw (Exception)
+{
+ vector<string> v(2);
+ if (extended_)
+ {
+ string::size_type index = s.find(namesSplit_);
+ if(index == string::npos) throw Exception("No sequence name found.");
+ v[0] = TextTools::removeSurroundingWhiteSpaces(s.substr(0, index));
+ v[1] = TextTools::removeFirstWhiteSpaces (s.substr(index + namesSplit_.size())); //There may be more than 2 white spaces.
+ }
+ else
+ {
+ v[0] = TextTools::removeSurroundingWhiteSpaces(s.substr(0, 10));
+ v[1] = s.substr(10);
+ }
+ return v;
+}
+
+/******************************************************************************/
+
+void Phylip::readSequential(std::istream& in, SiteContainer& asc) const throw (Exception)
+{
+ string temp;
+
+ //Ignore first line:
+ getline(in, temp, '\n'); // Copy current line in temporary string
+ temp = TextTools::removeSurroundingWhiteSpaces(FileTools::getNextLine(in));
+ string name = "";
+ string seq = "";
+
+ while (!in.eof())
+ {
+ // Read each sequence:
+ vector<string> v;
+ bool hasName = true;
+ try
+ {
+ v = splitNameAndSequence(temp);
+ }
+ catch (Exception & e)
+ {
+ hasName = false;
+ }
+ if (hasName)
+ {
+ // a new sequence is found:
+ if (!TextTools::isEmpty(name)) //If this is not the first sequence!
+ {
+ // Add the previous sequence to the container:
+ asc.addSequence(BasicSequence(name, seq, asc.getAlphabet()), checkNames_);
+ }
+ name = v[0];
+ seq = v[1];
+ }
+ else
+ {
+ //No sequence name found.
+ if (TextTools::isEmpty(name))
+ throw Exception("First sequence in file has no name!");
+ seq += TextTools::removeWhiteSpaces(temp);
+ }
+ //while(!TextTools::isEmpty(temp))
+ //{
+ // //Sequences are separated by at least one blank line:
+ // getline(in, temp, '\n'); // read next line in file.
+ // seq += TextTools::removeWhiteSpaces(temp);
+ //}
+ //end of this sequence:
+ temp = TextTools::removeSurroundingWhiteSpaces(FileTools::getNextLine(in));
+
+ }
+ // Add last sequence:
+ asc.addSequence(BasicSequence(name, seq, asc.getAlphabet()), checkNames_);
+}
+
+/******************************************************************************/
+
+void Phylip::readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception)
+{
+ string temp;
+
+ //Read first line:
+ getline(in, temp, '\n'); // Copy current line in temporary string
+ StringTokenizer st(temp);
+ unsigned int nbSequences = TextTools::to<unsigned int>(st.nextToken());
+ //int nbSites = TextTools::toInt(st.nextToken());
+ temp = FileTools::getNextLine(in);
+
+ vector<string> names, seqs;
+ // Read first block:
+ for (unsigned int i = 0; i < nbSequences && !in.eof() && !TextTools::isEmpty(temp); i++)
+ {
+ vector<string> v = splitNameAndSequence(temp);
+ names.push_back(v[0]);
+ seqs.push_back(v[1]);
+ getline(in, temp, '\n'); // read next line in file.
+ }
+
+ //Then read all other blocks:
+ temp = FileTools::getNextLine(in);
+ while (!in.eof())
+ {
+ for (unsigned int i = 0; i < names.size(); i++)
+ {
+ if (TextTools::isEmpty(temp))
+ throw IOException("Phylip::readInterleaved. Bad file,there are not the same number of sequence in each block.");
+ seqs[i] += TextTools::removeWhiteSpaces(temp);
+ getline(in, temp, '\n'); // read next line in file.
+ }
+ temp = FileTools::getNextLine(in);
+ }
+ for (unsigned int i = 0; i < names.size(); i++)
+ {
+ asc.addSequence(BasicSequence(names[i], seqs[i], asc.getAlphabet()), checkNames_);
+ }
+}
+
+/******************************************************************************/
+
+void Phylip::appendAlignmentFromStream(std::istream& input, SiteContainer& vsc) const throw (Exception)
+{
+ // Checking the existence of specified file
+ if (!input) { throw IOException ("Phylip::read: fail to open file"); }
+
+ if(sequential_) readSequential (input, vsc);
+ else readInterleaved(input, vsc);
+}
+
+/******************************************************************************/
+
+unsigned int Phylip::getNumberOfSequences(const std::string& path) const throw (IOException)
+{
+ // Checking the existence of specified file
+ ifstream file (path.c_str(), ios::in);
+ if (! file) { throw IOException ("Phylip::getNumberOfSequences: failed to open file"); }
+ string firstLine = FileTools::getNextLine(file);
+ StringTokenizer st(firstLine, " \t");
+ istringstream iss(st.nextToken());
+ int nb;
+ iss >> nb;
+ file.close();
+ return nb;
+}
+
+/******************************************************************************/
+
+std::vector<std::string> Phylip::getSizedNames(const std::vector<std::string>& names) const
+{
+ vector<string> sizedNames(names.size());
+ if (extended_)
+ {
+ //Add 6 white spaces to the larger name and align other names.
+ //First, determine the size of the wider name:
+ size_t sizeMax = 0;
+ for (size_t i = 0; i < names.size(); i++)
+ if (names[i].size() > sizeMax) sizeMax = names[i].size();
+ //Quite easy ;-) Now update all lengths:
+ for (size_t i = 0; i < names.size(); i++)
+ sizedNames[i] = TextTools::resizeRight(names[i], sizeMax) + namesSplit_;
+ }
+ else
+ {
+ //We trunc all names to ten characters:
+ for(unsigned int i = 0; i < names.size(); i++) sizedNames[i] = TextTools::resizeRight(names[i], 10);
+ cout << "Warning: names have been truncated to 10 characters. They may be ambiguous sequence names then." << endl;
+ }
+ return sizedNames;
+}
+
+/******************************************************************************/
+
+void Phylip::writeSequential(std::ostream& out, const SequenceContainer& sc, int charsByLine) const
+{
+ //cout << "Write sequential" << endl;
+ size_t numberOfSites = sc.getSequence(sc.getSequencesNames()[0]).size() * sc.getAlphabet()->getStateCodingSize();
+ out << sc.getNumberOfSequences() << " " << numberOfSites << endl;
+
+ vector<string> seqNames = sc.getSequencesNames();
+ vector<string> names = getSizedNames(seqNames);
+ for (size_t i = 0; i < seqNames.size(); i++)
+ {
+ vector<string> seq = TextTools::split(sc.toString(seqNames[i]), charsByLine);
+ out << names[i] << seq[0] << endl;
+ for (unsigned int j = 1; j < seq.size(); j++)
+ {
+ out << string(names[i].size(), ' ') << seq[j] << endl;
+ }
+ out << endl;
+ }
+}
+
+void Phylip::writeInterleaved(std::ostream& out, const SequenceContainer& sc, int charsByLine) const
+{
+ //cout << "Write interleaved;" << endl;
+ size_t numberOfSites = sc.getSequence(sc.getSequencesNames()[0]).size() * sc.getAlphabet()->getStateCodingSize();
+ out << sc.getNumberOfSequences() << " " << numberOfSites << endl;
+
+ vector<string> seqNames = sc.getSequencesNames();
+ vector<string> names = getSizedNames(seqNames);
+ //Split sequences:
+ vector< vector<string> > seqs(sc.getNumberOfSequences());
+ for (size_t i = 0; i < seqNames.size(); i++)
+ {
+ seqs[i] = TextTools::split(sc.toString(seqNames[i]), charsByLine);
+ }
+ //Write first block:
+ for (size_t i = 0; i < names.size(); i++)
+ {
+ out << names[i] << seqs[i][0] << endl;
+ }
+ out << endl;
+ //Write other blocks:
+ for (size_t j = 1; j < seqs[0].size(); j++)
+ {
+ for (unsigned int i = 0; i < sc.getNumberOfSequences(); i++)
+ {
+ out << seqs[i][j] << endl;
+ }
+ out << endl;
+ }
+}
+
+/******************************************************************************/
+
+void Phylip::writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
+{
+ //First must check if all sequences are aligned:
+ if (sc.getNumberOfSequences() == 0)
+ throw Exception("Phylip::write. SequenceContainer appear to contain no sequence.");
+
+ // Checking the existence of specified file, and possibility to open it in write mode
+ if (!output) { throw IOException ("Phylip::write : failed to open file"); }
+
+ if (sequential_) writeSequential (output, sc, charsByLine_);
+ else writeInterleaved(output, sc, charsByLine_);
+}
+
+/******************************************************************************/
+
+const std::string Phylip::getFormatName() const { return "Phylip file, " + string(extended_ ? "extended," : "") + string(sequential_ ? "sequential" : "interleaved"); }
+
+/******************************************************************************/
+
+const std::string Phylip::getFormatDescription() const
+{
+ return "Phylip file format, sequential and interleaved. PAML extension also supported.";
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Io/Phylip.h b/src/Bpp/Seq/Io/Phylip.h
new file mode 100644
index 0000000..a7604e0
--- /dev/null
+++ b/src/Bpp/Seq/Io/Phylip.h
@@ -0,0 +1,196 @@
+//
+// File: Phylip.h
+// Created by: Julien Dutheil
+// Created on: Mon Oct 27 12:22:56 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _PHYLIP_H_
+#define _PHYLIP_H_
+
+#include "AbstractIAlignment.h"
+#include "AbstractOAlignment.h"
+#include "../Sequence.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/VectorSequenceContainer.h"
+#include "../Container/AlignedSequenceContainer.h"
+
+// From the STL:
+#include <iostream>
+
+namespace bpp
+{
+
+/**
+ * @brief The Phylip & co format.
+ *
+ * An AlignedSequenceContainer is used instead of a VectorSequenceContainer.
+ *
+ * This format is described on the Phylip package documentation website:
+ * http://evolution.genetics.washington.edu/phylip/doc/sequence.html
+ */
+class Phylip :
+ public AbstractIAlignment,
+ public AbstractOAlignment,
+ public virtual ISequence
+{
+ private:
+
+ /* this class allows two kinds of Phylip format:
+ * traditional, with names limited to 10 chars,
+ * and 'extended', defined by PAML, with names separated from sequences by at least 6 white spaces.
+ */
+ bool extended_;
+ /* tells if sequences are in the seuqential or the interleave format/
+ */
+ bool sequential_;
+
+ /**
+ * @brief The maximum number of chars to be written on a line.
+ */
+ unsigned int charsByLine_;
+
+ bool checkNames_;
+
+ std::string namesSplit_;
+
+ public:
+ /**
+ * @brief Build a new Phylip file reader.
+ *
+ * @param extended If true, sequences with names longer than 10 characters are allowed.
+ * @param sequential If false, sequences are supposed to be interlaved.
+ * @param charsByLine The number of base to display in a row.
+ * @param checkSequenceNames Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
+ * @param split The string to use to split sequence name from content (only for 'extended' format). This will typically be " " (two spaces) or "\t" (a tabulation).
+ */
+ Phylip(bool extended = true, bool sequential = true, unsigned int charsByLine = 100, bool checkSequenceNames = true, const std::string& split = " "):
+ extended_(extended), sequential_(sequential), charsByLine_(charsByLine), checkNames_(checkSequenceNames), namesSplit_(split) {}
+
+ virtual ~Phylip() {}
+
+ public:
+
+ /**
+ * @name The AbstractIAlignment interface.
+ *
+ * @{
+ */
+ void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
+ /** @} */
+
+ /**
+ * @name The ISequence interface.
+ *
+ * As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence
+ * interface by downcasting the interface.
+ *
+ * @{
+ */
+ virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
+ return readAlignment(input, alpha);
+ }
+ virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
+ return readAlignment(path, alpha);
+ }
+ /** @} */
+
+ /**
+ * @return The number of sequences contained in the specified file.
+ *
+ * This methods parses the firt line of the phylip file.
+ * @param path The path of the file to parse.
+ */
+ unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
+
+ /**
+ * @name The OSequence interface.
+ *
+ * @{
+ */
+ void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
+ void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
+ {
+ AbstractOAlignment::writeAlignment(path, sc, overwrite);
+ }
+ /** @} */
+
+
+ /**
+ * @name The IOSequence interface.
+ *
+ * @{
+ */
+ const std::string getFormatName() const;
+ const std::string getFormatDescription() const;
+ /** @} */
+
+ /**
+ * @return true if the names are to be checked when reading sequences from files.
+ */
+ bool checkNames() const { return checkNames_; }
+
+ /**
+ * @brief Tell whether the sequence names should be checked when reading from files.
+ *
+ * @param yn whether the sequence names should be checked when reading from files.
+ */
+ void checkNames(bool yn) { checkNames_ = yn; }
+
+ /**
+ * @return The string used to split sequence name from content.
+ */
+ const std::string& getSplit() const { return namesSplit_; }
+
+ /**
+ * @param split The string to be used to split sequence name from content.
+ */
+ void setSplit(const std::string& split) { namesSplit_ = split; }
+
+ protected:
+ //Reading tools:
+ const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
+ void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
+ void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
+ //Writing tools:
+ std::vector<std::string> getSizedNames(const std::vector<std::string>& names) const;
+ void writeSequential (std::ostream& out, const SequenceContainer& sc, int charsByLine) const;
+ void writeInterleaved(std::ostream& out, const SequenceContainer& sc, int charsByLine) const;
+};
+
+} //end of namespace bpp.
+
+#endif //_PHYLIP_H_
+
diff --git a/src/Bpp/Seq/Io/SequenceFileIndex.h b/src/Bpp/Seq/Io/SequenceFileIndex.h
new file mode 100644
index 0000000..98e34d2
--- /dev/null
+++ b/src/Bpp/Seq/Io/SequenceFileIndex.h
@@ -0,0 +1,75 @@
+//
+// File: SequenceFileIndex.h
+// Author: Sylvain Gaillard
+// Created: 19/04/2010 10:16:13
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCEFILEINDEX_H_
+#define _SEQUENCEFILEINDEX_H_
+
+#include <string>
+#include <Bpp/Exceptions.h>
+
+namespace bpp {
+ /**
+ * @brief Index to retrieve Sequence in a file
+ *
+ * This class is designed to build an in-memory index of a Sequence file in
+ * order to retrieve Sequence given its ID.
+ *
+ * @author Sylvain Gaillard
+ */
+ class SequenceFileIndex {
+ public:
+ virtual ~SequenceFileIndex() {}
+ /**
+ * @brief Build the index given a path to the file.
+ */
+ virtual void build(const std::string& path) throw (Exception) = 0;
+
+ /**
+ * @brief Get the position of a Sequence given its ID.
+ */
+ virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
+
+ /**
+ * @brief Get the number of sequences
+ */
+ virtual size_t getNumberOfSequences() const throw (Exception) = 0;
+ };
+}
+
+#endif // _SEQUENCEFILEINDEX_H_
diff --git a/src/Bpp/Seq/Io/Stockholm.cpp b/src/Bpp/Seq/Io/Stockholm.cpp
new file mode 100644
index 0000000..485f332
--- /dev/null
+++ b/src/Bpp/Seq/Io/Stockholm.cpp
@@ -0,0 +1,83 @@
+//
+// File: Stockholm.cpp
+// Authors: Julien Dutheil
+// Created: Thu Apr 15 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team (2010)
+
+Julien.Dutheil at univ-montp2.fr
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "Stockholm.h"
+
+#include "../StringSequenceTools.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/StringTokenizer.h>
+#include <Bpp/Io/FileTools.h>
+
+using namespace bpp;
+using namespace std;
+
+/******************************************************************************/
+
+void Stockholm::writeAlignment(ostream& output, const SiteContainer& sc) const throw (Exception)
+{
+ if (!output)
+ throw IOException("Stockholm::writeAlignment: can't write to ostream output");
+
+ output << "# STOCKHOLM 1.0" << endl;
+ // Loop for all general comments
+ for (size_t i = 0; i < sc.getGeneralComments().size(); ++i)
+ {
+ output << "#=GF CC " << sc.getGeneralComments()[i] << endl;
+ }
+
+ // Main loop : for all sequences in vector container
+ vector<string> names = sc.getSequencesNames();
+ size_t maxSize = 0;
+ for(unsigned int i = 0; i < names.size(); ++i)
+ {
+ names[i] = TextTools::removeWhiteSpaces(names[i]);
+ if (names[i].size() > maxSize) maxSize = names[i].size();
+ }
+ if (maxSize > 255) maxSize = 255;
+ for (size_t i = 0; i < sc.getNumberOfSequences(); ++i)
+ {
+ output << TextTools::resizeRight(names[i], maxSize) << " " << sc.getSequence(i).toString() << endl;
+ }
+ output << "//" << endl;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Io/Stockholm.h b/src/Bpp/Seq/Io/Stockholm.h
new file mode 100644
index 0000000..ec9278d
--- /dev/null
+++ b/src/Bpp/Seq/Io/Stockholm.h
@@ -0,0 +1,120 @@
+//
+// File: Stockholm.h
+// Authors: Julien Dutheil
+// Created: Thu Apr 15 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team (2010)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _STOCKHOLM_H_
+#define _STOCKHOLM_H_
+
+#include "AbstractOAlignment.h"
+#include "../Sequence.h"
+#include "../Container/SequenceContainer.h"
+#include "../Container/AlignedSequenceContainer.h"
+
+namespace bpp
+{
+
+/**
+ * @brief The Stockholm alignment file format.
+ *
+ * Write to Stockholm files.
+ * Only sequence data is read/written, annotation and secondary structures are ignored.
+ */
+class Stockholm:
+ public AbstractOAlignment
+{
+ private:
+
+ bool checkNames_;
+
+ public:
+
+ /**
+ * @brief Build a new Stockholm object.
+ *
+ * @param checkSequenceNames Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
+ */
+ Stockholm(bool checkSequenceNames = true) : checkNames_(checkSequenceNames) {}
+
+ // Class destructor
+ virtual ~Stockholm() {}
+
+ public:
+
+ /**
+ * @name The OAlignment interface.
+ *
+ * @{
+ */
+ void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
+ void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
+ {
+ AbstractOAlignment::writeAlignment(path, sc, overwrite);
+ }
+ /** @} */
+
+ /**
+ * @name The IOSequence interface.
+ *
+ * @{
+ */
+ const std::string getFormatName() const { return "Stockholm file"; };
+ const std::string getFormatDescription() const
+ {
+ return "See http://en.wikipedia.org/wiki/Stockholm_format";
+ }
+ /** @} */
+
+ /**
+ * @warning This is not used for now, will be when reading is implemented.
+ * @return true if the names are to be checked when reading sequences from files.
+ */
+ bool checkNames() const { return checkNames_; }
+
+ /**
+ * @brief Tell whether the sequence names should be checked when reading from files.
+ *
+ * @warning This is not used for now, will be when reading is implemented.
+ * @param yn whether the sequence names should be checked when reading from files.
+ */
+ void checkNames(bool yn) { checkNames_ = yn; }
+};
+
+} //end of namespace bpp.
+
+#endif // _FASTA_H_
+
diff --git a/src/Bpp/Seq/Io/StreamSequenceIterator.cpp b/src/Bpp/Seq/Io/StreamSequenceIterator.cpp
new file mode 100644
index 0000000..aecacee
--- /dev/null
+++ b/src/Bpp/Seq/Io/StreamSequenceIterator.cpp
@@ -0,0 +1,97 @@
+//
+// File: StreamSequenceIterator.cpp
+// Created by: Julien Dutheil
+// Created on: Tue Feb 26 14:27 2013
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "StreamSequenceIterator.h"
+
+using namespace bpp;
+
+StreamSequenceIterator::StreamSequenceIterator(ISequenceStream& seqStream, std::istream& stream, const Alphabet* alphabet):
+ alphabet_(alphabet),
+ seqStream_(&seqStream),
+ stream_(&stream),
+ nextSeq_(new BasicSequence(alphabet_))
+{
+ bool test = seqStream_->nextSequence(*stream_, *nextSeq_);
+ if (!test) {
+ delete nextSeq_;
+ nextSeq_ = 0; //No more sequence available
+ }
+}
+
+Sequence* StreamSequenceIterator::nextSequence()
+{
+ BasicSequence* seq = nextSeq_;
+ if (nextSeq_) {
+ nextSeq_ = new BasicSequence(alphabet_);
+ bool test = seqStream_->nextSequence(*stream_, *nextSeq_);
+ if (!test) {
+ delete nextSeq_;
+ nextSeq_ = 0; //No more sequence available
+ }
+ }
+ return seq;
+}
+
+StreamSequenceWithQualityIterator::StreamSequenceWithQualityIterator(ISequenceStream& seqStream, std::istream& stream, const Alphabet* alphabet):
+ alphabet_(alphabet),
+ seqStream_(&seqStream),
+ stream_(&stream),
+ nextSeq_(new SequenceWithQuality(alphabet_))
+{
+ bool test = seqStream_->nextSequence(*stream_, *nextSeq_);
+ if (!test) {
+ delete nextSeq_;
+ nextSeq_ = 0; //No more sequence available
+ }
+}
+
+SequenceWithQuality* StreamSequenceWithQualityIterator::nextSequence()
+{
+ SequenceWithQuality* seq = nextSeq_;
+ if (nextSeq_) {
+ nextSeq_ = new SequenceWithQuality(alphabet_);
+ bool test = seqStream_->nextSequence(*stream_, *nextSeq_);
+ if (!test) {
+ delete nextSeq_;
+ nextSeq_ = 0; //No more sequence available
+ }
+ }
+ return seq;
+}
+
diff --git a/src/Bpp/Seq/Io/StreamSequenceIterator.h b/src/Bpp/Seq/Io/StreamSequenceIterator.h
new file mode 100644
index 0000000..67dc2bc
--- /dev/null
+++ b/src/Bpp/Seq/Io/StreamSequenceIterator.h
@@ -0,0 +1,138 @@
+//
+// File: StreamSequenceIterator.h
+// Created by: Julien Dutheil
+// Created on: Tue Feb 26 14:27 2013
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _STREAMSEQUENCEITERATOR_H_
+#define _STREAMSEQUENCEITERATOR_H_
+
+#include "../SequenceIterator.h"
+#include "ISequenceStream.h"
+
+// From the STL:
+#include <istream>
+
+namespace bpp
+{
+
+/**
+ * @brief A sequence iterator based on a sequence stream.
+ *
+ * This iterator uses a bpp::BasicSequence object for storing sequences.
+ */
+class StreamSequenceIterator:
+ public virtual SequenceIterator
+{
+ private:
+ const Alphabet* alphabet_;
+ const ISequenceStream* seqStream_;
+ std::istream* stream_;
+ BasicSequence* nextSeq_;
+
+ public:
+ StreamSequenceIterator(ISequenceStream& seqStream, std::istream& stream, const Alphabet* alphabet);
+
+ virtual ~StreamSequenceIterator() {}
+
+ private: //Recopy is forbidden
+ StreamSequenceIterator(const StreamSequenceIterator& ssi):
+ alphabet_(ssi.alphabet_),
+ seqStream_(ssi.seqStream_),
+ stream_(ssi.stream_),
+ nextSeq_(0) {}
+
+ StreamSequenceIterator& operator=(const StreamSequenceIterator& ssi)
+ {
+ alphabet_ = ssi.alphabet_;
+ seqStream_ = ssi.seqStream_;
+ stream_ = ssi.stream_;
+ nextSeq_ = 0;
+ return *this;
+ }
+
+ public:
+ virtual Sequence* nextSequence();
+
+ virtual bool hasMoreSequences() const { return nextSeq_ != 0; }
+};
+
+/**
+ * @brief A sequence iterator based on a sequence stream.
+ *
+ * This iterator uses a bpp::SequenceWithQuality object for storing sequences.
+ */
+class StreamSequenceWithQualityIterator:
+ public virtual SequenceWithQualityIterator
+{
+ private:
+ const Alphabet* alphabet_;
+ const ISequenceStream* seqStream_;
+ std::istream* stream_;
+ SequenceWithQuality* nextSeq_;
+
+ public:
+ StreamSequenceWithQualityIterator(ISequenceStream& seqStream, std::istream& stream, const Alphabet* alphabet);
+
+ virtual ~StreamSequenceWithQualityIterator() {}
+
+ private: //Recopy is forbidden
+ StreamSequenceWithQualityIterator(const StreamSequenceWithQualityIterator& ssi):
+ alphabet_(ssi.alphabet_),
+ seqStream_(ssi.seqStream_),
+ stream_(ssi.stream_),
+ nextSeq_(0) {}
+
+ StreamSequenceWithQualityIterator& operator=(const StreamSequenceWithQualityIterator& ssi)
+ {
+ alphabet_ = ssi.alphabet_;
+ seqStream_ = ssi.seqStream_;
+ stream_ = ssi.stream_;
+ nextSeq_ = 0;
+ return *this;
+ }
+
+ public:
+ virtual SequenceWithQuality* nextSequence();
+
+ virtual bool hasMoreSequences() const { return nextSeq_ != 0; }
+};
+
+
+} //end of namespace bpp.
+
+#endif //_SEQUENCEITERATOR_H_
+
diff --git a/src/Bpp/Seq/NucleicAcidsReplication.cpp b/src/Bpp/Seq/NucleicAcidsReplication.cpp
new file mode 100644
index 0000000..3c1f4f9
--- /dev/null
+++ b/src/Bpp/Seq/NucleicAcidsReplication.cpp
@@ -0,0 +1,120 @@
+//
+// File: NucleicAcidsReplication.cpp
+// Created by: Julien Dutheil
+// Created on: Fri May 20 14:40 2005
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "NucleicAcidsReplication.h"
+
+using namespace bpp;
+
+using namespace std;
+
+NucleicAcidsReplication::NucleicAcidsReplication(const NucleicAlphabet* nuc1, const NucleicAlphabet* nuc2) :
+ nuc1_(nuc1), nuc2_(nuc2), trans_()
+{
+ trans_[-1] = -1;
+ trans_[0] = 3;
+ trans_[1] = 2;
+ trans_[2] = 1;
+ trans_[3] = 0;
+
+ trans_[4] = 9;
+ trans_[5] = 8;
+ trans_[6] = 6;
+ trans_[7] = 7;
+ trans_[8] = 5;
+ trans_[9] = 4;
+
+ trans_[10] = 13;
+ trans_[11] = 12;
+ trans_[12] = 11;
+ trans_[13] = 10;
+
+ trans_[14] = 14;
+}
+
+int NucleicAcidsReplication::translate(int state) const throw (BadIntException)
+{
+ nuc1_->intToChar(state);
+ return trans_[state];
+}
+
+std::string NucleicAcidsReplication::translate(const std::string& state) const throw (BadCharException)
+{
+ int i = nuc1_->charToInt(state);
+ return nuc2_->intToChar(trans_[i]);
+}
+
+Sequence* NucleicAcidsReplication::translate(const Sequence& sequence) const throw (AlphabetMismatchException)
+{
+ if (sequence.getAlphabet()->getAlphabetType() != getSourceAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("NucleicAcidsReplication::translate", getSourceAlphabet(), getTargetAlphabet());
+ BasicSequence* tSeq = new BasicSequence(sequence.getName(), "", sequence.getComments(), getTargetAlphabet());
+ for (unsigned int i = 0; i < sequence.size(); i++)
+ {
+ tSeq->addElement(translate(sequence.getValue(i)));
+ }
+ //tSeq->setSense(!tSeq->getSense());
+ return tSeq;
+}
+
+
+int NucleicAcidsReplication::reverse(int state) const throw (BadIntException)
+{
+ nuc2_->intToChar(state);
+ return trans_[state];
+}
+
+std::string NucleicAcidsReplication::reverse(const std::string& state) const throw (BadCharException)
+{
+ int i = nuc2_->charToInt(state);
+ return nuc1_->intToChar(trans_[i]);
+}
+
+Sequence* NucleicAcidsReplication::reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
+{
+ if (sequence.getAlphabet()->getAlphabetType() != getTargetAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("NucleicAcidsReplication::reverse", getSourceAlphabet(), getTargetAlphabet());
+ BasicSequence* rSeq = new BasicSequence(sequence.getName(), "", sequence.getComments(), getSourceAlphabet());
+ for (unsigned int i = 0; i < sequence.size(); i++)
+ {
+ rSeq->addElement(reverse(sequence.getValue(i)));
+ }
+ //rSeq->setSense(! rSeq->getSense());
+ return rSeq;
+}
+
diff --git a/src/Bpp/Seq/NucleicAcidsReplication.h b/src/Bpp/Seq/NucleicAcidsReplication.h
new file mode 100644
index 0000000..7e42167
--- /dev/null
+++ b/src/Bpp/Seq/NucleicAcidsReplication.h
@@ -0,0 +1,105 @@
+//
+// File: NucleicAcidsReplication.h
+// Created by: Julien Dutheil
+// Created on: Fri May 20 14:20 2005
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _NUCLEICACIDSREPLICATION_H_
+#define _NUCLEICACIDSREPLICATION_H_
+
+#include "Transliterator.h"
+#include "Alphabet/NucleicAlphabet.h"
+
+// From the STL:
+#include <map>
+
+namespace bpp
+{
+
+/**
+ * @brief Replication between to nucleic acids.
+ *
+ * Example of use:
+ * - DNA -> DNA: DNA Replication
+ * - RNA -> RNA: RNA Replication
+ * - DNA -> RNA: Transcription
+ * - RNA -> DNA: Reverse transcription
+ *
+ * Since this is an instance of the ReverseIterator interface, transcription and
+ * reverse transcription may be achieved from the same instance of the object by
+ * using the translate and reverse methods.
+ */
+class NucleicAcidsReplication :
+ public ReverseTransliterator
+{
+ private:
+ const NucleicAlphabet* nuc1_, * nuc2_;
+ mutable std::map<int, int> trans_;
+
+ public:
+ NucleicAcidsReplication(const NucleicAlphabet* nuc1, const NucleicAlphabet* nuc2);
+ NucleicAcidsReplication(const NucleicAcidsReplication& nar):
+ ReverseTransliterator(nar),
+ nuc1_(nar.nuc1_), nuc2_(nar.nuc2_), trans_(nar.trans_)
+ {}
+ NucleicAcidsReplication& operator=(const NucleicAcidsReplication& nar)
+ {
+ ReverseTransliterator::operator=(nar);
+ nuc1_ = nar.nuc1_;
+ nuc2_ = nar.nuc2_;
+ trans_ = nar.trans_;
+ return *this;
+ }
+
+ virtual ~NucleicAcidsReplication() {}
+
+ public:
+ const Alphabet* getSourceAlphabet() const { return nuc1_; }
+ const Alphabet* getTargetAlphabet() const { return nuc2_; }
+
+ int translate(int state) const throw (BadIntException);
+ std::string translate(const std::string& state) const throw (BadCharException);
+ Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
+ int reverse(int state) const throw (BadIntException);
+ std::string reverse(const std::string& state) const throw (BadCharException);
+ Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
+
+};
+
+} //end of namespace bpp.
+
+#endif //_NUCLEICACIDSREPLICATION_H_
+
diff --git a/src/Bpp/Seq/Sequence.cpp b/src/Bpp/Seq/Sequence.cpp
new file mode 100644
index 0000000..ac05354
--- /dev/null
+++ b/src/Bpp/Seq/Sequence.cpp
@@ -0,0 +1,222 @@
+//
+// File: Sequence.cpp
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: Tue Aug 21 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "Sequence.h" // class's header file
+
+#include "Alphabet/AlphabetTools.h"
+#include "StringSequenceTools.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+
+using namespace std;
+
+/* Constructors: **************************************************************/
+
+BasicSequence::BasicSequence(const Alphabet* alpha):
+ BasicSymbolList(alpha),
+ name_(),
+ comments_()
+{}
+
+BasicSequence::BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha)
+throw (BadCharException) :
+ BasicSymbolList(alpha),
+ name_(name),
+ comments_()
+{
+ if (sequence!="")
+ setContent(sequence);
+}
+
+BasicSequence::BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha)
+ throw (BadCharException) :
+ BasicSymbolList(alpha),
+ name_(name),
+ comments_(comments)
+{
+ if (sequence!="")
+ setContent(sequence);
+}
+
+BasicSequence::BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha)
+throw (BadCharException) :
+ BasicSymbolList(sequence, alpha),
+ name_(name),
+ comments_()
+{}
+
+BasicSequence::BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha)
+ throw (BadCharException) :
+ BasicSymbolList(sequence, alpha),
+ name_(name),
+ comments_(comments)
+{}
+
+BasicSequence::BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha)
+ throw (BadIntException) :
+ BasicSymbolList(sequence, alpha),
+ name_(name),
+ comments_()
+{}
+
+BasicSequence::BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha)
+ throw (BadIntException) :
+ BasicSymbolList(sequence, alpha),
+ name_(name),
+ comments_(comments)
+{}
+
+/* Copy constructors: *********************************************************/
+
+BasicSequence::BasicSequence(const Sequence& s) :
+ BasicSymbolList(s),
+ name_(s.getName()),
+ comments_(s.getComments())
+{}
+
+BasicSequence::BasicSequence(const BasicSequence& s) :
+ BasicSymbolList(s),
+ name_(s.getName()),
+ comments_(s.getComments())
+{}
+
+/* Assignation operator: ******************************************************/
+
+BasicSequence& BasicSequence::operator=(const Sequence& s)
+{
+ BasicSymbolList::operator=(s);
+ name_ = s.getName();
+ comments_ = s.getComments();
+ return *this;
+}
+
+BasicSequence& BasicSequence::operator=(const BasicSequence& s)
+{
+ BasicSymbolList::operator=(s);
+ name_ = s.getName();
+ comments_ = s.getComments();
+ return *this;
+}
+
+/******************************************************************************/
+
+void BasicSequence::setContent(const std::string& sequence) throw (BadCharException)
+{
+ // Remove blanks in sequence
+ content_ = StringSequenceTools::codeSequence(TextTools::removeWhiteSpaces(sequence), getAlphabet());
+ //Warning, an exception may be thrown here!
+}
+
+/******************************************************************************/
+
+void BasicSequence::setToSizeR(size_t newSize)
+{
+ // Size verification
+ size_t seqSize = content_.size();
+ if (newSize == seqSize) return;
+
+ if (newSize < seqSize)
+ {
+ content_.resize(newSize);
+ return;
+ }
+
+ // Add gaps up to specified size
+ int gap = getAlphabet()->getGapCharacterCode();
+ while (content_.size() < newSize) content_.push_back(gap);
+}
+
+/******************************************************************************/
+
+void BasicSequence::setToSizeL(size_t newSize)
+{
+ // Size verification
+ size_t seqSize = content_.size();
+ if (newSize == seqSize) return;
+
+ if (newSize < seqSize)
+ {
+ //We must truncate sequence from the left.
+ //This is a very unefficient method!
+ content_.erase(content_.begin(), content_.begin() + (seqSize - newSize));
+ return;
+ }
+
+ // Add gaps up to specified size
+ int gap = getAlphabet()->getGapCharacterCode();
+ content_.insert(content_.begin(), newSize - seqSize, gap);
+}
+
+/******************************************************************************/
+
+void BasicSequence::append(const std::vector<int>& content) throw (BadIntException)
+{
+ // Check list for incorrect characters
+ for (size_t i = 0; i < content.size(); i++)
+ if(!getAlphabet()->isIntInAlphabet(content[i]))
+ throw BadIntException(content[i], "BasicSequence::append", getAlphabet());
+ //BasicSequence is valid:
+ for (size_t i = 0; i < content.size(); i++)
+ content_.push_back(content[i]);
+}
+
+void BasicSequence::append(const std::vector<std::string>& content) throw (BadCharException)
+{
+ // Check list for incorrect characters
+ for (size_t i = 0; i < content.size(); i++)
+ if(!getAlphabet()->isCharInAlphabet(content[i]))
+ throw BadCharException(content[i], "BasicSequence::append", getAlphabet());
+
+ //BasicSequence is valid:
+ for (size_t i = 0; i < content.size(); i++)
+ content_.push_back(getAlphabet()->charToInt(content[i]));
+}
+
+void BasicSequence::append(const std::string& content) throw (BadCharException)
+{
+ append(StringSequenceTools::codeSequence(content, getAlphabet()));
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/Sequence.h b/src/Bpp/Seq/Sequence.h
new file mode 100644
index 0000000..3ea81a3
--- /dev/null
+++ b/src/Bpp/Seq/Sequence.h
@@ -0,0 +1,465 @@
+//
+// File: Sequence.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+// Created on: Tue Aug 21 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCE_H_
+#define _SEQUENCE_H_
+
+#include "SymbolList.h"
+#include "SequenceExceptions.h"
+
+// From the STL:
+#include <string>
+#include <vector>
+
+namespace bpp
+{
+
+/**
+ * @brief Declaration of Comments type.
+ *
+ * Comments are defined as a std::vector of std::strings to allow the later creation of a
+ * full Comments class.
+ */
+typedef std::vector<std::string> Comments;
+
+/**
+ * @brief The sequence interface.
+ *
+ * This is a general purpose container, containing an ordered list of states.
+ * The states that allowed to be present in the sequence are defined
+ * by an alphabet object.
+ *
+ * Sequence objets also contain a name attribute and potentially several comment lines.
+ * A sequence object is also event-driven, allowing easy extension.
+ *
+ * @see Alphabet
+ */
+class Sequence:
+ public virtual SymbolList
+{
+ public:
+ virtual ~Sequence() {}
+
+ public:
+
+#ifndef NO_VIRTUAL_COV
+ Sequence* clone() const = 0;
+#endif
+
+ /**
+ * @name Setting/getting the name of the sequence.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the name of this sequence.
+ *
+ * @return This sequence name.
+ */
+ virtual const std::string& getName() const = 0;
+
+ /**
+ * @brief Set the name of this sequence.
+ *
+ * @param name The new name of the sequence.
+ */
+ virtual void setName(const std::string& name) = 0;
+ /** @} */
+
+ /**
+ * @name Setting/getting the comments associated to the sequence.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the comments associated to this sequence.
+ *
+ * @return The comments of the sequence.
+ */
+ virtual const Comments& getComments() const = 0;
+
+ /**
+ * @brief Set the comments associated to this sequence.
+ *
+ * @param comments The new comments of the sequence.
+ */
+ virtual void setComments(const Comments& comments) = 0;
+
+ /** @} */
+
+ /**
+ * @name Adjusting the size of the sequence.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Set the whole content of the sequence.
+ *
+ * @param sequence The new content of the sequence.
+ * @see The Sequence constructor for information about the way sequences are internaly stored.
+ */
+ virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
+ virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
+ virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
+
+ /**
+ * @brief Set up the size of a sequence from the right side.
+ *
+ * All new characters are filled with gaps.
+ * If the specified size is < to the sequence size, the sequence will be truncated.
+ *
+ * @param newSize The new size of the sequence.
+ */
+ virtual void setToSizeR(size_t newSize) = 0;
+
+ /**
+ * @brief Set up the size of a sequence from the left side.
+ *
+ * All new characters are filled with gaps.
+ * If the specified size is < to the sequence size, the sequence will be truncated.
+ *
+ * @param newSize The new size of the sequence.
+ */
+ virtual void setToSizeL(size_t newSize) = 0;
+
+ /**
+ * @brief Append the specified content to the sequence.
+ *
+ * @param content The content to append to the sequence.
+ * @throw BadIntException If the content does not match the current alphabet.
+ */
+ virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
+
+ /**
+ * @brief Append the specified content to the sequence.
+ *
+ * @param content The content to append to the sequence.
+ * @throw BadCharException If the content does not match the current alphabet.
+ */
+ virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
+
+ /**
+ * @brief Append the specified content to the sequence.
+ *
+ * @param content The content to append to the sequence.
+ * @throw BadCharException If the content does not match the current alphabet.
+ */
+ virtual void append(const std::string& content) throw (BadCharException) = 0;
+ /** @} */
+
+};
+
+
+/**
+ * @brief A basic implementation of the Sequence interface.
+ *
+ * This is a general purpose container, containing an ordered list of states.
+ * The states that allowed to be present in the sequence are defined
+ * by an alphabet object, which is passed to the sequence constructor by a pointer.
+ *
+ * For programming convenience, the states are stored as integers, but the translation toward
+ * and from a char description is easily performed with the Alphabet classes.
+ *
+ * Sequence objets also contain a name attribute and potentially several comment lines.
+ *
+ * @see Alphabet
+ */
+class BasicSequence :
+ public Sequence,
+ public BasicSymbolList
+{
+ private:
+
+ /**
+ * @brief The sequence name.
+ */
+ std::string name_;
+
+ /**
+ * @brief The sequence comments.
+ */
+ Comments comments_;
+
+ public:
+
+ /**
+ * @brief Empty constructor: build a void Sequence with just an Alphabet
+ *
+ * You can use it safely for all type of Alphabet in order to build an
+ * empty Sequence i.e. without name nor sequence data.
+ *
+ * @param alpha A pointer toward the Alphabet to be used with this Sequence.
+ */
+ BasicSequence(const Alphabet* alpha);
+
+ /**
+ * @brief Direct constructor: build a Sequence object from a std::string
+ * You can use it safely for RNA, DNA and protein sequences.
+ *
+ * It can be used with codon sequences too, the std::string will be cut into
+ * parts of size 3. But for more complicated alphabets, you should use one
+ * complete constructors.
+ *
+ * @param name The sequence name.
+ * @param sequence The whole sequence to be parsed as a std::string.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief Direct constructor: build a Sequence object from a std::string.
+ *
+ * You can use it safely for RNA, DNA and protein sequences.
+ *
+ * It can be used with codon sequences too, the std::string will be cut into
+ * tokens of size 3. But for more complicated alphabets, you should use one
+ * complete constructors.
+ *
+ * @param name The sequence name.
+ * @param sequence The whole sequence to be parsed as a std::string.
+ * @param comments Comments to add to the sequence.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief General purpose constructor, can be used with any alphabet.
+ *
+ * You should note that the sequence is stored as a std::vector of int.
+ * Hence each std::string in the std::vector will be translated using the alphabet object.
+ *
+ * @param name The sequence name.
+ * @param sequence The sequence content.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief General purpose constructor, can be used with any alphabet.
+ *
+ * You should note that the sequence is stored as a std::vector of int.
+ * Hence each std::string in the std::vector will be translated using the alphabet object.
+ *
+ * @param name The sequence name.
+ * @param sequence The sequence content.
+ * @param comments Comments to add to the sequence.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief General purpose constructor, can be used with any alphabet.
+ *
+ * @param name The sequence name.
+ * @param sequence The sequence content.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
+
+ /**
+ * @brief General purpose constructor, can be used with any alphabet.
+ *
+ * @param name The sequence name.
+ * @param sequence The sequence content.
+ * @param comments Comments to add to the sequence.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
+
+ /**
+ * @brief The Sequence generic copy constructor. This does not perform a hard copy of the alphabet object.
+ */
+ BasicSequence(const Sequence& s);
+
+ /**
+ * @brief The Sequence copy constructor. This does not perform a hard copy of the alphabet object.
+ */
+ BasicSequence(const BasicSequence& s);
+
+ /**
+ * @brief The Sequence generic assignment operator. This does not perform a hard copy of the alphabet object.
+ *
+ * @return A ref toward the assigned Sequence.
+ */
+ BasicSequence& operator=(const Sequence& s);
+
+ /**
+ * @brief The Sequence assignment operator. This does not perform a hard copy of the alphabet object.
+ *
+ * @return A ref toward the assigned Sequence.
+ */
+ BasicSequence& operator=(const BasicSequence& s);
+
+ virtual ~BasicSequence() {}
+
+ public:
+
+ /**
+ * @name The Clonable interface
+ *
+ * @{
+ */
+ BasicSequence* clone() const { return new BasicSequence(*this); }
+ /** @} */
+
+
+ /**
+ * @name Setting/getting the name of the sequence.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the name of this sequence.
+ *
+ * @return This sequence name.
+ */
+ const std::string& getName() const { return name_; }
+
+ /**
+ * @brief Set the name of this sequence.
+ *
+ * @param name The new name of the sequence.
+ */
+ void setName(const std::string& name) { name_ = name; }
+
+ /** @} */
+
+ /**
+ * @name Setting/getting the comments associated to the sequence.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the comments associated to this sequence.
+ *
+ * @return The comments of the sequence.
+ */
+ const Comments& getComments() const { return comments_; }
+
+ /**
+ * @brief Set the comments associated to this sequence.
+ *
+ * @param comments The new comments of the sequence.
+ */
+ void setComments(const Comments& comments) { comments_ = comments; }
+
+ /** @} */
+
+
+ /**
+ * @name Adjusting the size of the sequence.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Set the whole content of the sequence.
+ *
+ * @param sequence The new content of the sequence.
+ * @see The Sequence constructor for information about the way sequences are internaly stored.
+ */
+ virtual void setContent(const std::string& sequence) throw (BadCharException);
+ void setContent(const std::vector<int>& list) throw (BadIntException)
+ {
+ BasicSymbolList::setContent(list);
+ }
+ void setContent(const std::vector<std::string>& list) throw (BadCharException)
+ {
+ BasicSymbolList::setContent(list);
+ }
+
+
+ /**
+ * @brief Set up the size of a sequence from the right side.
+ *
+ * All new characters are filled with gaps.
+ * If the specified size is < to the sequence size, the sequence will be truncated.
+ *
+ * @param newSize The new size of the sequence.
+ */
+ virtual void setToSizeR(size_t newSize);
+
+ /**
+ * @brief Set up the size of a sequence from the left side.
+ *
+ * All new characters are filled with gaps.
+ * If the specified size is < to the sequence size, the sequence will be truncated.
+ *
+ * @param newSize The new size of the sequence.
+ */
+ virtual void setToSizeL(size_t newSize);
+
+ /**
+ * @brief Append the specified content to the sequence.
+ *
+ * @param content The content to append to the sequence.
+ * @throw BadIntException If the content does not match the current alphabet.
+ */
+ virtual void append(const std::vector<int>& content) throw (BadIntException);
+
+ /**
+ * @brief Append the specified content to the sequence.
+ *
+ * @param content The content to append to the sequence.
+ * @throw BadCharException If the content does not match the current alphabet.
+ */
+ virtual void append(const std::vector<std::string>& content) throw (BadCharException);
+
+ /**
+ * @brief Append the specified content to the sequence.
+ *
+ * @param content The content to append to the sequence.
+ * @throw BadCharException If the content does not match the current alphabet.
+ */
+ virtual void append(const std::string& content) throw (BadCharException);
+
+ /** @} */
+
+};
+
+} //end of namespace bpp.
+
+#endif // _SEQUENCE_H_
+
diff --git a/src/Bpp/Seq/SequenceExceptions.cpp b/src/Bpp/Seq/SequenceExceptions.cpp
new file mode 100644
index 0000000..a85679c
--- /dev/null
+++ b/src/Bpp/Seq/SequenceExceptions.cpp
@@ -0,0 +1,68 @@
+//
+// File: SequenceExceptions.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Nov 3 16:35:30 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SequenceExceptions.h"
+#include "Sequence.h"
+
+using namespace bpp;
+using namespace std;
+
+/******************************************************************************/
+
+SequenceException::SequenceException(const std::string& text, const Sequence* seq) :
+ Exception("SequenceException: " + text + (seq != 0 ? "(" + seq->getName() + ")" : string(""))),
+ sequence_(seq) {};
+
+/******************************************************************************/
+
+EmptySequenceException::EmptySequenceException(const std::string& text, const Sequence* seq) :
+ SequenceException("EmptySequenceException: " + text, seq) {};
+
+/******************************************************************************/
+
+SequenceWithGapException::SequenceWithGapException(const std::string& text, const Sequence* seq) :
+ SequenceException("SequenceWithGapException: " + text, seq) {};
+
+/******************************************************************************/
+
+SequenceNotAlignedException::SequenceNotAlignedException(const std::string& text, const Sequence* seq) :
+ SequenceException("SequenceNotAlignedException: " + text, seq) {};
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/SequenceExceptions.h b/src/Bpp/Seq/SequenceExceptions.h
new file mode 100644
index 0000000..f1a4acf
--- /dev/null
+++ b/src/Bpp/Seq/SequenceExceptions.h
@@ -0,0 +1,161 @@
+//
+// File: SequenceExceptions.h
+// Created by: Julien Dutheil
+// Created on: Mon Nov 3 16:35:30 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCEEXCEPTIONS_H_
+#define _SEQUENCEEXCEPTIONS_H_
+
+#include "Alphabet/Alphabet.h"
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+class Sequence;
+
+/**
+ * @brief The sequence exception base class.
+ *
+ * @see Exception
+ */
+class SequenceException :
+ public Exception
+{
+ private:
+
+ /**
+ * @brief A pointer toward a sequence object.
+ */
+ const Sequence* sequence_;
+
+ public:
+
+ /**
+ * @brief Build a new SequenceException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param seq A const pointer toward the sequence that threw the exception.
+ */
+ SequenceException(const std::string& text, const Sequence * seq = 0);
+
+ SequenceException(const SequenceException& se): Exception(se), sequence_(se.sequence_) {}
+ SequenceException& operator=(const SequenceException& se)
+ {
+ Exception::operator=(se);
+ sequence_ = se.sequence_;
+ return *this;
+ }
+
+ virtual ~SequenceException() throw() {}
+
+ public:
+
+ /**
+ * @brief Get the sequence that threw the exception.
+ *
+ * @return A const pointer toward the sequence.
+ */
+ virtual const Sequence* getSequence() const { return sequence_; }
+};
+
+/**
+ * @brief Exception thrown when a sequence is found to be empty and it should not.
+ */
+class EmptySequenceException :
+ public SequenceException
+{
+
+ public:
+
+ /**
+ * @brief Build a new EmptySequenceException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param seq A const pointer toward the sequence that threw the exception.
+ */
+ EmptySequenceException(const std::string& text, const Sequence* seq = 0);
+
+ virtual ~EmptySequenceException() throw() {}
+};
+
+/**
+ * @brief Exception thrown when a sequence is found to have gap and it should not.
+ */
+class SequenceWithGapException :
+ public SequenceException
+{
+
+ public:
+
+ /**
+ * @brief Build a new SequenceWithGapException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param seq A const pointer toward the sequence that threw the exception.
+ */
+ SequenceWithGapException(const std::string& text, const Sequence* seq = 0);
+
+ virtual ~SequenceWithGapException() throw() {}
+};
+
+/**
+ * @brief Exception thrown when a sequence is not align with others.
+ *
+ * Typically, this may occur when you try to add a bad sequence to a site container.
+ */
+class SequenceNotAlignedException :
+ public SequenceException
+{
+
+ public:
+
+ /**
+ * @brief Build a new SequenceNotAlignedException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param seq A const pointer toward the sequence that threw the exception.
+ */
+ SequenceNotAlignedException(const std::string& text, const Sequence* seq);
+
+ virtual ~SequenceNotAlignedException() throw() {}
+};
+
+} //end of namespace bpp.
+
+#endif //_SEQUENCEEXCEPTIONS_H_
+
diff --git a/src/Bpp/Seq/SequenceIterator.h b/src/Bpp/Seq/SequenceIterator.h
new file mode 100644
index 0000000..2e6d1f4
--- /dev/null
+++ b/src/Bpp/Seq/SequenceIterator.h
@@ -0,0 +1,108 @@
+//
+// File: SequenceIterator.h
+// Created by: Julien Dutheil
+// Created on: Tue Feb 26 14:27 2013
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCEITERATOR_H_
+#define _SEQUENCEITERATOR_H_
+
+#include "Sequence.h"
+#include "SequenceWithQuality.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Generic sequence iterator interface, allowing to loop over sequences.
+ */
+class SequenceIterator
+{
+ public:
+ SequenceIterator() {}
+ virtual ~SequenceIterator() {}
+
+ public:
+ virtual Sequence* nextSequence() = 0;
+ virtual bool hasMoreSequences() const = 0;
+};
+
+/**
+ * @brief Generic const sequence iterator interface, allowing to loop over const sequences.
+ */
+class ConstSequenceIterator
+{
+ public:
+ ConstSequenceIterator() {}
+ virtual ~ConstSequenceIterator() {}
+
+ public:
+ virtual const Sequence* nextSequence() = 0;
+ virtual bool hasMoreSequences() const = 0;
+};
+
+/**
+ * @brief Generic sequence iterator interface, allowing to loop over sequences with quality scores.
+ */
+class SequenceWithQualityIterator:
+ public virtual SequenceIterator
+{
+ public:
+ SequenceWithQualityIterator() {}
+ virtual ~SequenceWithQualityIterator() {}
+
+ public:
+ virtual SequenceWithQuality* nextSequence() = 0;
+};
+
+/**
+ * @brief Generic const sequence iterator interface, allowing to loop over const sequences with quality scores.
+ */
+class ConstSequenceWithQualityIterator:
+ public virtual ConstSequenceIterator
+{
+ public:
+ ConstSequenceWithQualityIterator() {}
+ virtual ~ConstSequenceWithQualityIterator() {}
+
+ public:
+ virtual const SequenceWithQuality* nextSequence() = 0;
+};
+
+} //end of namespace bpp.
+
+#endif //_SEQUENCEITERATOR_H_
+
diff --git a/src/Bpp/Seq/SequencePositionIterators.cpp b/src/Bpp/Seq/SequencePositionIterators.cpp
new file mode 100644
index 0000000..4c20ebe
--- /dev/null
+++ b/src/Bpp/Seq/SequencePositionIterators.cpp
@@ -0,0 +1,146 @@
+//
+// File: SequencePositionIterators.cpp
+// Author: Sylvain Gaillard
+// Created: 23/06/2009 11:38:27
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (June 23, 2009)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SequencePositionIterators.h"
+
+using namespace bpp;
+using namespace std; // for the STL
+
+//=================================
+// AbstractSequencePositionIterator
+//=================================
+/******************************************************************************/
+
+bool AbstractSequencePositionIterator::operator==(const SequencePositionIterator & it) const {
+ return this->getPosition() == it.getPosition();
+}
+
+/******************************************************************************/
+
+bool AbstractSequencePositionIterator::operator!=(const SequencePositionIterator & it) const {
+ return this->getPosition() != it.getPosition();
+}
+
+/******************************************************************************/
+
+void AbstractSequencePositionIterator::setPosition(unsigned int pos) {
+ this->currentPosition_ = pos;
+}
+
+/******************************************************************************/
+
+const Sequence & AbstractSequencePositionIterator::getSequence() const {
+ return * (this->sequence_);
+}
+
+/******************************************************************************/
+
+unsigned int AbstractSequencePositionIterator::getPosition() const {
+ return this->currentPosition_;
+}
+
+/******************************************************************************/
+
+int AbstractSequencePositionIterator::getValue() const {
+ return this->sequence_->getValue(this->currentPosition_);
+}
+
+/******************************************************************************/
+
+string AbstractSequencePositionIterator::getChar() const {
+ return this->sequence_->getChar(this->currentPosition_);
+}
+
+
+//===============================
+// SimpleSequencePositionIterator
+//===============================
+/******************************************************************************/
+
+SimpleSequencePositionIterator::SimpleSequencePositionIterator(const SequencePositionIterator& it):
+ AbstractSequencePositionIterator(it.getSequence(), it.getPosition()) {};
+
+/******************************************************************************/
+
+SimpleSequencePositionIterator & SimpleSequencePositionIterator::operator++() {
+ this->setPosition(this->getPosition() + 1);
+ return *this;
+}
+
+/******************************************************************************/
+
+SimpleSequencePositionIterator SimpleSequencePositionIterator::operator++(int i) {
+ SimpleSequencePositionIterator ans = * this;
+ ++(* this);
+ return ans;
+}
+
+/******************************************************************************/
+
+SimpleSequencePositionIterator & SimpleSequencePositionIterator::operator+=(int i) {
+ this->setPosition(this->getPosition() + i);
+ return * this;
+}
+
+/******************************************************************************/
+
+SimpleSequencePositionIterator & SimpleSequencePositionIterator::operator-=(int i) {
+ return (* this) += -i;
+}
+
+/******************************************************************************/
+
+SimpleSequencePositionIterator SimpleSequencePositionIterator::operator+(int i) const {
+ SimpleSequencePositionIterator res(* this);
+ res += i;
+ return res;
+}
+
+/******************************************************************************/
+
+SimpleSequencePositionIterator SimpleSequencePositionIterator::operator-(int i) const {
+ return (* this) + (- i);
+}
+
+/******************************************************************************/
+
+bool SimpleSequencePositionIterator::hasMorePositions() const {
+ return (this->getPosition() < this->getSequence().size());
+}
+/******************************************************************************/
diff --git a/src/Bpp/Seq/SequencePositionIterators.h b/src/Bpp/Seq/SequencePositionIterators.h
new file mode 100644
index 0000000..5dd2ed6
--- /dev/null
+++ b/src/Bpp/Seq/SequencePositionIterators.h
@@ -0,0 +1,210 @@
+//
+// File: SequencePositionIterators.h
+// Author: Sylvain Gaillard
+// Created: 23/06/2009 10:35:28
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (June 23, 2009)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCEPOSITIONITERATORS_H_
+#define _SEQUENCEPOSITIONITERATORS_H_
+
+// from STL
+#include <string>
+
+#include "Sequence.h"
+
+namespace bpp
+{
+
+ /**
+ * @brief Loop over a Sequence.
+ *
+ * This is the SequencePositionIterator interface.
+ *
+ * @author Sylvain Gaillard
+ */
+ class SequencePositionIterator
+ {
+ public:
+ SequencePositionIterator() {}
+ virtual ~SequencePositionIterator() {}
+
+ public:
+ /**
+ * @brief Get the actual position of the iterator in the Sequence.
+ */
+ virtual unsigned int getPosition() const = 0;
+ /**
+ * @brief Set the position of the iterator.
+ * @param pos The position on the Sequence
+ */
+ virtual void setPosition(unsigned int pos) = 0;
+ /**
+ * @brief Get the numerical value of the Sequence at current position.
+ */
+ virtual int getValue() const = 0;
+ /**
+ * @brief Get the textual value of the Sequence at current position.
+ */
+ virtual std::string getChar() const = 0;
+
+ virtual bool operator==(const SequencePositionIterator & it) const = 0;
+ virtual bool operator!=(const SequencePositionIterator & it) const = 0;
+ virtual SequencePositionIterator & operator+=(int i) = 0;
+ virtual SequencePositionIterator & operator-=(int i) = 0;
+ virtual SequencePositionIterator& operator++() = 0;
+
+ /**
+ * @brief Tells if there is more positions in the Sequence.
+ * @return true if there is more positions in the Sequence
+ */
+ virtual bool hasMorePositions() const = 0;
+ /**
+ * @brief Get the Sequence on which the iterator loops.
+ * @return A reference toward the Sequence object.
+ */
+ virtual const Sequence & getSequence() const = 0;
+ };
+
+ /**
+ * @brief Partial implementation of the SequencePositionIterator interface.
+ *
+ * @author Sylvain Gaillard
+ */
+ class AbstractSequencePositionIterator :
+ public virtual SequencePositionIterator
+ {
+ private:
+ const Sequence* sequence_;
+ unsigned int currentPosition_;
+
+
+ public:
+ AbstractSequencePositionIterator(const Sequence& seq, unsigned int pos = 0) :
+ sequence_(&seq), currentPosition_(pos) {}
+
+ AbstractSequencePositionIterator(const AbstractSequencePositionIterator& aspi) :
+ sequence_(aspi.sequence_), currentPosition_(aspi.currentPosition_) {}
+
+ AbstractSequencePositionIterator& operator=(const AbstractSequencePositionIterator& aspi)
+ {
+ sequence_ = aspi.sequence_;
+ currentPosition_ = aspi.currentPosition_;
+ return *this;
+ }
+
+ virtual ~AbstractSequencePositionIterator() {}
+
+ public:
+
+ /**
+ * @name Comparison operators
+ *
+ * @{
+ */
+ bool operator==(const SequencePositionIterator& it) const;
+ bool operator!=(const SequencePositionIterator& it) const;
+ /** @} */
+
+ unsigned int getPosition() const;
+ void setPosition(unsigned int pos);
+ int getValue() const;
+ std::string getChar() const;
+ const Sequence& getSequence() const;
+ };
+
+ /**
+ * @brief Loop over all positions in a Sequence
+ *
+ * This is the simplest implementation of SequencePositionIterator.
+ * It just loops over all positions of a Sequence.
+ *
+ * @code
+ * Sequence seq = Sequence("seq1", "ATTCGATCCG-G", &AlphabetTools::DNA_ALPHABET);
+ * for (SimpleSequencePositionIterator it(seq) ; it.hasMorePositions() ; ++it) {
+ * cout << it.getPosition() << " : " << it.getValue() << " (" << it.getChar() << ")" << endl;
+ * }
+ * @endcode
+ *
+ * @author Sylvain Gaillard
+ */
+ class SimpleSequencePositionIterator:
+ public AbstractSequencePositionIterator
+ {
+ public:
+ /**
+ * @name Constructors and destructor
+ *
+ * @{
+ */
+
+ /**
+ * @brief General constructor
+ *
+ * @param seq A reference toward the Sequence object we want to loop over
+ * @param pos Optional integer where to start on the Sequence object
+ *
+ */
+ SimpleSequencePositionIterator(const Sequence& seq, unsigned int pos = 0):
+ AbstractSequencePositionIterator(seq, pos) {}
+ /**
+ * @brief Copie constructor.
+ *
+ * @param it A reference toward a SequencePositionIterator
+ */
+ SimpleSequencePositionIterator(const SequencePositionIterator& it);
+ virtual ~SimpleSequencePositionIterator() {}
+ /** @} */
+
+ public:
+ /**
+ * @name Operators
+ *
+ * @{
+ */
+ SimpleSequencePositionIterator & operator++();
+ virtual SimpleSequencePositionIterator operator++(int i);
+ SimpleSequencePositionIterator & operator+=(int i);
+ SimpleSequencePositionIterator & operator-=(int i);
+ virtual SimpleSequencePositionIterator operator+(int i) const;
+ virtual SimpleSequencePositionIterator operator-(int i) const;
+ /** @} */
+
+ bool hasMorePositions() const;
+ };
+
+}
+
+#endif //_SEQUENCEPOSITIONITERATORS_H_
diff --git a/src/Bpp/Seq/SequenceTools.cpp b/src/Bpp/Seq/SequenceTools.cpp
new file mode 100644
index 0000000..f4d5ce7
--- /dev/null
+++ b/src/Bpp/Seq/SequenceTools.cpp
@@ -0,0 +1,699 @@
+//
+// File: SequenceTools.cpp
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created on: Tue Aug 21 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "SequenceTools.h"
+
+#include "Alphabet/AlphabetTools.h"
+#include "StringSequenceTools.h"
+#include <Bpp/Numeric/Matrix/Matrix.h>
+#include <Bpp/Numeric/VectorTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <ctype.h>
+#include <cmath>
+#include <list>
+#include <iostream>
+
+using namespace std;
+
+DNA SequenceTools::_DNA;
+RNA SequenceTools::_RNA;
+RNY SequenceTools::_RNY(_DNA);
+NucleicAcidsReplication SequenceTools::_DNARep(&_DNA, &_DNA);
+NucleicAcidsReplication SequenceTools::_RNARep(&_RNA, &_RNA);
+NucleicAcidsReplication SequenceTools::_transc(&_DNA, &_RNA);
+
+/******************************************************************************/
+
+Sequence* SequenceTools::subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception)
+{
+ // Checking interval
+ if (end >= sequence.size())
+ throw IndexOutOfBoundsException ("SequenceTools::subseq : Invalid upper bound", end, 0, sequence.size());
+ if (end < begin)
+ throw Exception ("SequenceTools::subseq : Invalid interval");
+
+ // Copy sequence
+ vector<int> temp(sequence.getContent());
+
+ // Truncate sequence
+ temp.erase(temp.begin() + end + 1, temp.end());
+ temp.erase(temp.begin(), temp.begin() + begin);
+
+ // New sequence creation
+ return new BasicSequence(sequence.getName(), temp, sequence.getComments(), sequence.getAlphabet());
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::concatenate(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception)
+{
+ // Sequence's alphabets matching verification
+ if ((seq1.getAlphabet()->getAlphabetType()) != (seq2.getAlphabet()->getAlphabetType()))
+ throw AlphabetMismatchException("SequenceTools::concatenate : Sequence's alphabets don't match ", seq1.getAlphabet(), seq2.getAlphabet());
+
+ // Sequence's names matching verification
+ if (seq1.getName() != seq2.getName())
+ throw Exception ("SequenceTools::concatenate : Sequence's names don't match");
+
+ // Concatenate sequences and send result
+ vector<int> sequence = seq1.getContent();
+ vector<int> sequence2 = seq2.getContent();
+ sequence.insert(sequence.end(), sequence2.begin(), sequence2.end());
+ return new BasicSequence(seq1.getName(), sequence, seq1.getComments(), seq1.getAlphabet());
+}
+
+/******************************************************************************/
+
+Sequence& SequenceTools::complement(Sequence& seq) throw (AlphabetException)
+{
+ // Alphabet type checking
+ NucleicAcidsReplication* NAR;
+ if (seq.getAlphabet()->getAlphabetType() == "DNA alphabet")
+ {
+ NAR = &_DNARep;
+ }
+ else if (seq.getAlphabet()->getAlphabetType() == "RNA alphabet")
+ {
+ NAR = &_RNARep;
+ }
+ else
+ {
+ throw AlphabetException("SequenceTools::complement: Sequence must be nucleic.", seq.getAlphabet());
+ }
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ seq.setElement(i, NAR->translate(seq.getValue(i)));
+ }
+ return seq;
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::getComplement(const Sequence& sequence) throw (AlphabetException)
+{
+ // Alphabet type checking
+ NucleicAcidsReplication* NAR;
+ if (sequence.getAlphabet()->getAlphabetType() == "DNA alphabet")
+ {
+ NAR = &_DNARep;
+ }
+ else if (sequence.getAlphabet()->getAlphabetType() == "RNA alphabet")
+ {
+ NAR = &_RNARep;
+ }
+ else
+ {
+ throw AlphabetException ("SequenceTools::getComplement: Sequence must be nucleic.", sequence.getAlphabet());
+ }
+
+ return NAR->translate(sequence);
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::transcript(const Sequence& sequence) throw (AlphabetException)
+{
+ // Alphabet type checking
+ if (sequence.getAlphabet()->getAlphabetType() != "DNA alphabet")
+ {
+ throw AlphabetException ("SequenceTools::transcript : Sequence must be DNA", sequence.getAlphabet());
+ }
+
+ return _transc.translate(sequence);
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::reverseTranscript(const Sequence& sequence) throw (AlphabetException)
+{
+ // Alphabet type checking
+ if (sequence.getAlphabet()->getAlphabetType() != "RNA alphabet")
+ {
+ throw AlphabetException ("SequenceTools::reverseTranscript : Sequence must be RNA", sequence.getAlphabet());
+ }
+
+ return _transc.reverse(sequence);
+}
+
+/******************************************************************************/
+
+Sequence& SequenceTools::invert(Sequence& seq)
+{
+ size_t seq_size = seq.size(); // store seq size for efficiency
+ unsigned int tmp_state = 0; // to store one state when swapping positions
+ size_t j = seq_size; // symetric position iterator from sequence end
+ for (size_t i = 0; i < seq_size / 2; i++)
+ {
+ j = seq_size - 1 - i;
+ tmp_state = seq.getValue(i);
+ seq.setElement(i, seq.getValue(j));
+ seq.setElement(j, tmp_state);
+ }
+ return seq;
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::getInvert(const Sequence& sequence)
+{
+ Sequence* iSeq = sequence.clone();
+ invert(*iSeq);
+ return iSeq;
+}
+
+/******************************************************************************/
+
+Sequence& SequenceTools::invertComplement(Sequence& seq)
+{
+ // Alphabet type checking
+ NucleicAcidsReplication* NAR;
+ if (seq.getAlphabet()->getAlphabetType() == "DNA alphabet")
+ {
+ NAR = &_DNARep;
+ }
+ else if (seq.getAlphabet()->getAlphabetType() == "RNA alphabet")
+ {
+ NAR = &_RNARep;
+ }
+ else
+ {
+ throw AlphabetException("SequenceTools::complement: Sequence must be nucleic.", seq.getAlphabet());
+ }
+ // for (size_t i = 0 ; i < seq.size() ; i++) {
+ // seq.setElement(i, NAR->translate(seq.getValue(i)));
+ // }
+ size_t seq_size = seq.size(); // store seq size for efficiency
+ int tmp_state = 0; // to store one state when swapping positions
+ size_t j = seq_size; // symetric position iterator from sequence end
+ for (size_t i = 0; i < seq_size / 2; i++)
+ {
+ j = seq_size - 1 - i;
+ tmp_state = seq.getValue(i);
+ seq.setElement(i, NAR->translate(seq.getValue(j)));
+ seq.setElement(j, NAR->translate(tmp_state));
+ }
+ if (seq_size % 2) // treate the state in the middle of odd sequences
+ {
+ seq.setElement(seq_size / 2, NAR->translate(seq.getValue(seq_size / 2)));
+ }
+ return seq;
+}
+
+/******************************************************************************/
+
+double SequenceTools::getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps) throw (AlphabetMismatchException, SequenceNotAlignedException)
+{
+ if (seq1.getAlphabet()->getAlphabetType() != seq2.getAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("SequenceTools::getPercentIdentity", seq1.getAlphabet(), seq2.getAlphabet());
+ if (seq1.size() != seq2.size())
+ throw SequenceNotAlignedException("SequenceTools::getPercentIdentity", &seq2);
+ int gap = seq1.getAlphabet()->getGapCharacterCode();
+ size_t id = 0;
+ size_t tot = 0;
+ for (size_t i = 0; i < seq1.size(); i++)
+ {
+ int x = seq1.getValue(i);
+ int y = seq2.getValue(i);
+ if (ignoreGaps)
+ {
+ if (x != gap && y != gap)
+ {
+ tot++;
+ if (x == y)
+ id++;
+ }
+ }
+ else
+ {
+ tot++;
+ if (x == y)
+ id++;
+ }
+ }
+ return static_cast<double>(id) / static_cast<double>(tot) * 100.;
+}
+
+/******************************************************************************/
+
+size_t SequenceTools::getNumberOfSites(const Sequence& seq)
+{
+ size_t count = 0;
+ const Alphabet* alpha = seq.getAlphabet();
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ if (!alpha->isGap(seq[i]))
+ count++;
+ }
+ return count;
+}
+
+/******************************************************************************/
+
+size_t SequenceTools::getNumberOfCompleteSites(const Sequence& seq)
+{
+ size_t count = 0;
+ const Alphabet* alpha = seq.getAlphabet();
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ if (!alpha->isGap(seq[i]) && !alpha->isUnresolved(seq[i]))
+ count++;
+ }
+ return count;
+}
+
+/******************************************************************************/
+
+size_t SequenceTools::getNumberOfUnresolvedSites(const Sequence& seq)
+{
+ size_t count = 0;
+ const Alphabet* alpha = seq.getAlphabet();
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ if (alpha->isUnresolved(seq[i]))
+ count++;
+ }
+ return count;
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::getSequenceWithoutGaps(const Sequence& seq)
+{
+ const Alphabet* alpha = seq.getAlphabet();
+ vector<int> content;
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ if (!alpha->isGap(seq[i]))
+ content.push_back(seq[i]);
+ }
+ Sequence* newSeq = dynamic_cast<Sequence*>(seq.clone());
+ newSeq->setContent(content);
+ return newSeq;
+}
+
+/******************************************************************************/
+
+void SequenceTools::removeGaps(Sequence& seq)
+{
+ const Alphabet* alpha = seq.getAlphabet();
+ for (size_t i = seq.size(); i > 0; --i)
+ {
+ if (alpha->isGap(seq[i - 1]))
+ seq.deleteElement(i - 1);
+ }
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::getSequenceWithoutStops(const Sequence& seq) throw (Exception)
+{
+ const CodonAlphabet* calpha = dynamic_cast<const CodonAlphabet*>(seq.getAlphabet());
+ if (!calpha)
+ throw Exception("SequenceTools::getSequenceWithoutStops. Input sequence should have a codon alphabet.");
+ vector<int> content;
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ if (!calpha->isStop(seq[i]))
+ content.push_back(seq[i]);
+ }
+ Sequence* newSeq = dynamic_cast<Sequence*>(seq.clone());
+ newSeq->setContent(content);
+ return newSeq;
+}
+
+/******************************************************************************/
+
+void SequenceTools::removeStops(Sequence& seq) throw (Exception)
+{
+ const CodonAlphabet* calpha = dynamic_cast<const CodonAlphabet*>(seq.getAlphabet());
+ if (!calpha)
+ throw Exception("SequenceTools::removeStops. Input sequence should have a codon alphabet.");
+ for (size_t i = seq.size(); i > 0; --i)
+ {
+ if (calpha->isStop(seq[i - 1]))
+ seq.deleteElement(i - 1);
+ }
+}
+
+/******************************************************************************/
+
+void SequenceTools::replaceStopsWithGaps(Sequence& seq) throw (Exception)
+{
+ const CodonAlphabet* calpha = dynamic_cast<const CodonAlphabet*>(seq.getAlphabet());
+ if (!calpha)
+ throw Exception("SequenceTools::replaceStopsWithGaps. Input sequence should have a codon alphabet.");
+ int gap = calpha->getGapCharacterCode();
+ for (size_t i = 0; i < seq.size(); ++i)
+ {
+ if (calpha->isStop(seq[i]))
+ seq.setElement(i, gap);
+ }
+}
+
+/******************************************************************************/
+
+BowkerTest* SequenceTools::bowkerTest(const Sequence& seq1, const Sequence& seq2)
+throw (SequenceNotAlignedException)
+{
+ if (seq1.size() != seq2.size())
+ throw SequenceNotAlignedException("SequenceTools::bowkerTest.", &seq2);
+ size_t n = seq1.size();
+ const Alphabet* alpha = seq1.getAlphabet();
+ unsigned int r = alpha->getSize();
+
+ // Compute contingency table:
+ RowMatrix<double> array(r, r);
+ int x, y;
+ for (size_t i = 0; i < n; i++)
+ {
+ x = seq1[i];
+ y = seq2[i];
+ if (!alpha->isGap(x) && !alpha->isUnresolved(x)
+ && !alpha->isGap(y) && !alpha->isUnresolved(y))
+ {
+ array(static_cast<size_t>(x), static_cast<size_t>(y))++;
+ }
+ }
+
+ // Compute Bowker's statistic:
+ double sb2 = 0, nij, nji;
+ for (unsigned int i = 1; i < r; ++i)
+ {
+ for (unsigned int j = 0; j < i; ++j)
+ {
+ nij = array(i, j);
+ nji = array(j, i);
+ if (nij != 0 || nji != 0)
+ {
+ sb2 += pow(nij - nji, 2) / (nij + nji);
+ }
+ // Else: we should display a warning there.
+ }
+ }
+
+ // Compute p-value:
+ double pvalue = 1. - RandomTools::pChisq(sb2, (r - 1) * r / 2);
+
+ // Return results:
+ BowkerTest* test = new BowkerTest();
+ test->setStatistic(sb2);
+ test->setPValue(pvalue);
+ return test;
+}
+
+/******************************************************************************/
+
+void SequenceTools::getPutativeHaplotypes(const Sequence& seq, std::vector<Sequence*>& hap, unsigned int level)
+{
+ vector< vector< int > > states(seq.size());
+ list<Sequence*> t_hap;
+ const Alphabet* alpha = seq.getAlphabet();
+ unsigned int hap_count = 1;
+ // Vector of available states at each position
+ for (size_t i = 0; i < seq.size(); i++)
+ {
+ vector<int> st = alpha->getAlias(seq[i]);
+ if (!st.size())
+ {
+ st.push_back(alpha->getGapCharacterCode());
+ }
+ if (st.size() <= level)
+ {
+ states[i] = st;
+ }
+ else
+ {
+ states[i] = vector<int>(1, seq[i]);
+ }
+ }
+ // Combinatorial haplotypes building (the use of tree may be more accurate)
+ t_hap.push_back(new BasicSequence(seq.getName() + "_hap" + TextTools::toString(hap_count++), "", alpha));
+ for (size_t i = 0; i < states.size(); i++)
+ {
+ for (list<Sequence*>::iterator it = t_hap.begin(); it != t_hap.end(); it++)
+ {
+ for (unsigned int j = 0; j < states[i].size(); j++)
+ {
+ Sequence* tmp_seq = new BasicSequence(seq.getName() + "_hap", (**it).getContent(), alpha);
+ if (j < states[i].size() - 1)
+ {
+ tmp_seq->setName(tmp_seq->getName() + TextTools::toString(hap_count++));
+ tmp_seq->addElement(states[i][j]);
+ t_hap.insert(it, tmp_seq);
+ }
+ else
+ {
+ (**it).addElement(states[i][j]);
+ }
+ }
+ }
+ }
+ for (list<Sequence*>::reverse_iterator it = t_hap.rbegin(); it != t_hap.rend(); it++)
+ {
+ hap.push_back(*it);
+ }
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException)
+{
+ if (s1.getAlphabet()->getAlphabetType() != s2.getAlphabet()->getAlphabetType())
+ {
+ throw AlphabetMismatchException("SequenceTools::combineSequences(const Sequence& s1, const Sequence& s2): s1 and s2 don't have same Alphabet.", s1.getAlphabet(), s2.getAlphabet());
+ }
+ const Alphabet* alpha = s1.getAlphabet();
+ vector<int> st;
+ vector<int> seq;
+ size_t length = NumTools::max(s1.size(), s2.size());
+ for (size_t i = 0; i < length; i++)
+ {
+ if (i < s1.size())
+ st.push_back(s1.getValue(i));
+ if (i < s2.size())
+ st.push_back(s2.getValue(i));
+ seq.push_back(alpha->getGeneric(st));
+ st.clear();
+ }
+ Sequence* s = new BasicSequence(s1.getName() + "+" + s2.getName(), seq, alpha);
+ return s;
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::subtractHaplotype(const Sequence& s, const Sequence& h, string name, unsigned int level) throw (SequenceNotAlignedException)
+{
+ const Alphabet* alpha = s.getAlphabet();
+ if (name.size() == 0)
+ name = s.getName() + "_haplotype";
+ string seq;
+ if (s.size() != h.size())
+ throw SequenceNotAlignedException("SequenceTools::subtractHaplotype: haplotype must be aligned with the sequence.", &h);
+ for (unsigned int i = 0; i < s.size(); ++i)
+ {
+ string c;
+ vector<int> nucs = alpha->getAlias(s.getValue(i));
+ if (nucs.size() > 1)
+ {
+ remove(nucs.begin(), nucs.end(), h.getValue(i));
+ nucs = vector<int>(nucs.begin(), nucs.end() - 1);
+ }
+ else
+ {
+ nucs = vector<int>(nucs.begin(), nucs.end());
+ }
+ c = alpha->intToChar(alpha->getGeneric(nucs));
+ if (level <= nucs.size() && (alpha->isUnresolved(s.getValue(i)) || alpha->isUnresolved(h.getValue(i))))
+ {
+ c = alpha->intToChar(alpha->getUnknownCharacterCode());
+ }
+ seq += c;
+ }
+ Sequence* hap = new BasicSequence(name, seq, alpha);
+ return hap;
+}
+
+/******************************************************************************/
+
+Sequence* SequenceTools::RNYslice(const Sequence& seq, int ph) throw (AlphabetException)
+{
+ // Alphabet type checking
+ if (seq.getAlphabet()->getAlphabetType() != "DNA alphabet")
+ {
+ throw AlphabetException ("SequenceTools::transcript : Sequence must be DNA", seq.getAlphabet());
+ }
+
+ if ((ph < 1) || (ph > 3))
+ throw Exception("Bad phase for RNYSlice: " + TextTools::toString(ph) + ". Should be between 1 and 3.");
+
+ size_t s = seq.size();
+ size_t n = (s - ph + 3) / 3;
+
+ vector<int> content(n);
+
+ int tir = seq.getAlphabet()->getGapCharacterCode();
+ size_t j;
+
+ for (size_t i = 0; i < n; i++)
+ {
+ j = i * 3 + ph - 1;
+
+ if (j == 0)
+ content[i] = _RNY.getRNY(tir, seq[0], seq[1], *seq.getAlphabet());
+ else
+ {
+ if (j == s - 1)
+ content[i] = _RNY.getRNY(seq[j - 1], seq[j], tir, *seq.getAlphabet());
+ else
+ content[i] = _RNY.getRNY(seq[j - 1], seq[j], seq[j + 1], *seq.getAlphabet());
+ }
+ }
+
+ // New sequence creating, and sense reversing
+ Sequence* sq = new BasicSequence(seq.getName(), content,
+ seq.getComments(), &_RNY);
+
+ // Send result
+ return sq;
+}
+
+Sequence* SequenceTools::RNYslice(const Sequence& seq) throw (AlphabetException)
+{
+ // Alphabet type checking
+ if (seq.getAlphabet()->getAlphabetType() != "DNA alphabet")
+ {
+ throw AlphabetException ("SequenceTools::transcript : Sequence must be DNA", seq.getAlphabet());
+ }
+
+ size_t n = seq.size();
+
+ vector<int> content(n);
+
+ int tir = seq.getAlphabet()->getGapCharacterCode();
+
+ if (seq.size() >= 2)
+ {
+ content[0] = _RNY.getRNY(tir, seq[0], seq[1], *seq.getAlphabet());
+
+ for (unsigned int i = 1; i < n - 1; i++)
+ {
+ content[i] = _RNY.getRNY(seq[i - 1], seq[i], seq[i + 1],
+ *seq.getAlphabet());
+ }
+
+ content[n - 1] = _RNY.getRNY(seq[n - 2], seq[n - 1], tir, *seq.getAlphabet());
+ }
+
+ // New sequence creating, and sense reversing
+ Sequence* s = new BasicSequence(seq.getName(), content,
+ seq.getComments(), &_RNY);
+
+ // Send result
+ return s;
+}
+
+/******************************************************************************/
+
+
+void SequenceTools::getCDS(Sequence& sequence, bool checkInit, bool checkStop, bool includeInit, bool includeStop)
+{
+ const CodonAlphabet* alphabet = dynamic_cast<const CodonAlphabet*>(sequence.getAlphabet());
+ if (!alphabet)
+ throw AlphabetException("SequenceTools::getCDS. Sequence is not a codon sequence.");
+ if (checkInit)
+ {
+ unsigned int i;
+ for (i = 0; i < sequence.size() && !alphabet->isInit(sequence[i]); ++i)
+ {}
+ for (unsigned int j = 0; includeInit ? j < i : j <= i; ++j)
+ {
+ sequence.deleteElement(j);
+ }
+ }
+ if (checkStop)
+ {
+ unsigned int i;
+ for (i = 0; i < sequence.size() && !alphabet->isStop(sequence[i]); ++i)
+ {}
+ for (unsigned int j = includeStop ? i + 1 : i; j < sequence.size(); ++j)
+ {
+ sequence.deleteElement(j);
+ }
+ }
+}
+
+/******************************************************************************/
+
+size_t SequenceTools::findFirstOf(const Sequence& seq, const Sequence& motif, bool strict)
+{
+ if (motif.size() > seq.size())
+ return seq.size();
+ for (size_t seqi = 0; seqi < seq.size() - motif.size() + 1; seqi++)
+ {
+ bool match = false;
+ for (size_t moti = 0; moti < motif.size(); moti++)
+ {
+ if (strict)
+ {
+ match = seq.getValue(seqi + moti) == motif.getValue(moti);
+ }
+ else
+ {
+ match = AlphabetTools::match(seq.getAlphabet(), seq.getValue(seqi + moti), motif.getValue(moti));
+ }
+ if (!match)
+ {
+ break;
+ }
+ }
+ if (match)
+ {
+ return seqi;
+ }
+ }
+ return seq.size();
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/SequenceTools.h b/src/Bpp/Seq/SequenceTools.h
new file mode 100644
index 0000000..ee85eb4
--- /dev/null
+++ b/src/Bpp/Seq/SequenceTools.h
@@ -0,0 +1,410 @@
+//
+// File: SequenceTools.h
+// Authors: Guillaume Deuchst
+// Julien Dutheil
+// Sylvain Gaillard
+// Created on: Tue Aug 21 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _SEQUENCETOOLS_H_
+#define _SEQUENCETOOLS_H_
+
+#include "Alphabet/Alphabet.h"
+#include "Alphabet/DNA.h"
+#include "Alphabet/RNA.h"
+#include "Alphabet/RNY.h"
+#include "Sequence.h"
+#include "SymbolListTools.h"
+#include "NucleicAcidsReplication.h"
+#include <Bpp/Exceptions.h>
+#include <Bpp/Numeric/Random/RandomTools.h>
+#include <Bpp/Numeric/Stat/StatTest.h>
+
+// From the STL:
+#include <string>
+#include <map>
+#include <vector>
+#include <algorithm>
+
+namespace bpp
+{
+/**
+ * @brief Bowker's homogeneity test results class.
+ */
+class BowkerTest :
+ public StatTest
+{
+private:
+ double pvalue_;
+ double stat_;
+
+public:
+ BowkerTest() : pvalue_(1.),
+ stat_(0.) {}
+
+ virtual ~BowkerTest() {}
+
+ BowkerTest* clone() const { return new BowkerTest(*this); }
+
+public:
+ std::string getName() const { return "Bowker's test for homogeneity."; }
+ double getStatistic() const { return stat_; }
+ double getPValue() const { return pvalue_; }
+
+ void setStatistic(double stat) { stat_ = stat; }
+ void setPValue(double pvalue) { pvalue_ = pvalue; }
+};
+
+/**
+ * @brief SequenceTools static class
+ *
+ * Implement methods to manipulate sequences
+ */
+class SequenceTools :
+ public SymbolListTools
+{
+private:
+ static DNA _DNA;
+ static RNA _RNA;
+ static RNY _RNY;
+ static NucleicAcidsReplication _DNARep;
+ static NucleicAcidsReplication _RNARep;
+ static NucleicAcidsReplication _transc;
+
+public:
+ SequenceTools() {}
+ virtual ~SequenceTools() {}
+
+public:
+ /**
+ * @brief Get a sub-sequence.
+ *
+ * @param sequence The sequence to trunc.
+ * @param begin The first position of the subsequence.
+ * @param end The last position of the subsequence.
+ * @return A new sequence object with the given subsequence.
+ * @throw IndexOutOfBoundsException, Exception In case of bad indices.
+ */
+ static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception);
+
+ /**
+ * @brief Concatenate two sequences.
+ *
+ * Sequences must have the same name and alphabets.
+ * Only first sequence's commentaries are kept.
+ *
+ * @param seq1 The first sequence.
+ * @param seq2 The second sequence.
+ * @return A new sequence object with the concatenation of the two sequences.
+ * @throw AlphabetMismatchException If the two alphabets do not match.
+ * @throw Exception If the sequence names do not match.
+ */
+ static Sequence* concatenate(const Sequence& seq1, const Sequence& seq2)
+ throw (AlphabetMismatchException, Exception);
+
+ /**
+ * @brief Complement the nucleotide sequence itself
+ *
+ * @param seq The sequence to be complemented.
+ * @return A ref toward the complemented sequence.
+ * @throw AlphabetException if the sequence is not a nucleotide sequence.
+ * @author Sylvain Gaillard
+ */
+ static Sequence& complement(Sequence& seq) throw (AlphabetException);
+
+ /**
+ * @brief Get the complementary sequence of a nucleotide sequence.
+ *
+ * @see DNAReplication
+ * @return A new sequence object with the complementary sequence.
+ * @param sequence The sequence to complement.
+ * @throw AlphabetException If the sequence is not a nucleotide sequence.
+ */
+ static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
+
+ /**
+ * @brief Get the transcription sequence of a DNA sequence.
+ *
+ * Translate DNA sequence into RNA sequence.
+ *
+ * @see DNAReplication
+ * @return sequence A new sequence object with the transcription sequence.
+ * @param sequence The sequence to transcript.
+ * @throw AlphabetException If the sequence is not a DNA sequence.
+ */
+ static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
+
+ /**
+ * @brief Get the reverse-transcription sequence of a RNA sequence.
+ *
+ * Translate RNA sequence into DNA sequence.
+ *
+ * @see DNAReplication
+ * @return sequence A new sequence object with the reverse-transcription sequence.
+ * @param sequence The sequence to reverse-transcript.
+ * @throw AlphabetException If the sequence is not a RNA sequence.
+ */
+ static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
+
+ /**
+ * @brief Inverse a sequence from 5'->3' to 3'->5' and vice-versa.
+ *
+ * ABCDEF becomes FEDCBA, and the sense attribute is changed (may be
+ * inhibited).
+ *
+ * @param seq The sequence to inverse.
+ * @return A ref toward the sequence.
+ * @author Sylvain Gaillard
+ */
+ static Sequence& invert(Sequence& seq);
+
+ /**
+ * @brief Inverse a sequence from 5'->3' to 3'->5' and vice-versa.
+ *
+ * ABCDEF becomes FEDCBA, and the sense attribute is changed (may be
+ * inhibited).
+ *
+ * @param sequence The sequence to inverse.
+ * @return A new sequence object containing the inverted sequence.
+ * @author Sylvain Gaillard
+ */
+ static Sequence* getInvert(const Sequence& sequence);
+
+ /**
+ * @brief Inverse and complement a sequence.
+ *
+ * This methode is more accurate than calling invert and complement
+ * separatly.
+ *
+ * @param seq The sequence to inverse and complement.
+ * @return A ref toward the sequence.
+ * @author Sylvain Gaillard
+ */
+ static Sequence& invertComplement(Sequence& seq);
+
+ /**
+ * @return The identity percent of 2 sequence.
+ * One match is counted if the two sequences have identical states.
+ * @param seq1 The first sequence.
+ * @param seq2 The second sequence.
+ * @param ignoreGaps If true, only positions without gaps will be used for the counting.
+ * @throw AlphabetMismatchException If the two sequences do not have the same alphabet.
+ * @throw SequenceNotAlignedException If the two sequences do not have the same length.
+ */
+ static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
+
+ /**
+ * @return The number of sites in the sequences, <i>i.e.</i> all positions without gaps.
+ *
+ * @param seq The sequence to analyse.
+ */
+ static size_t getNumberOfSites(const Sequence& seq);
+
+ /**
+ * @return The number of complete sites in the sequences, <i>i.e.</i> all positions without gaps and unresolved states (generic characters).
+ *
+ * @param seq The sequence to analyse.
+ */
+ static size_t getNumberOfCompleteSites(const Sequence& seq);
+
+ /**
+ * @return The number of unresolved sites in the sequence.
+ *
+ * @param seq The sequence to analyse.
+ *
+ * @author Sylvain Gaillard
+ */
+ static size_t getNumberOfUnresolvedSites(const Sequence& seq);
+
+ /**
+ * @brief Remove gaps from a sequence.
+ *
+ * The deleteElement method of the Sequence object will be used where appropriate.
+ * @param seq The sequence to analyse.
+ */
+ static void removeGaps(Sequence& seq);
+
+ /**
+ * @brief Get a copy of the sequence without gaps.
+ *
+ * A whole new sequence will be created by adding all non-gap positions.
+ * The original sequence will be cloned to serve as a template.
+ *
+ * @param seq The sequence to analyse.
+ * @return A new sequence object without gaps.
+ */
+ static Sequence* getSequenceWithoutGaps(const Sequence& seq);
+
+ /**
+ * @brief Remove stops from a codon sequence.
+ *
+ * The deleteElement method of the Sequence object will be used where appropriate.
+ * @param seq The sequence to analyse.
+ * @throw Exception if the input sequence does not have a codon alphabet.
+ */
+ static void removeStops(Sequence& seq) throw (Exception);
+
+ /**
+ * @brief Get a copy of the codon sequence without stops.
+ *
+ * A whole new sequence will be created by adding all non-stop positions.
+ * The original sequence will be cloned to serve as a template.
+ *
+ * @param seq The sequence to analyse.
+ * @return A new sequence object without stops.
+ * @throw Exception if the input sequence does not have a codon alphabet.
+ */
+ static Sequence* getSequenceWithoutStops(const Sequence& seq) throw (Exception);
+
+ /**
+ * @brief Replace stop codons by gaps.
+ *
+ * The setElement method of the Sequence object will be used where appropriate.
+ * @param seq The sequence to analyse.
+ * @throw Exception if the input sequence does not have a codon alphabet.
+ */
+ static void replaceStopsWithGaps(Sequence& seq) throw (Exception);
+
+ /**
+ * @brief Bowker's test for homogeneity.
+ *
+ * Computes the contingency table of occurrence of all pairs of states and test its symmetry using Bowker's (1948) test.
+ *
+ * Reference:<br>
+ * @code
+ * Ababneh F. Bioinformatics 2006 22(10) 1225-1231
+ * @endcode
+ *
+ * @param seq1 The first sequence.
+ * @param seq2 The second sequence.
+ * @return A BowkerTest object with the computed statistic and p-value (computed from a chi square distribution).
+ * @throw SequenceNotAlignedException If the two sequences do not have the same length.
+ */
+ static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
+
+ /**
+ * @brief Get all putatives haplotypes from an heterozygous sequence.
+ *
+ * @param seq The sequence to resolve
+ * @param hap The vector to fill with the new sequences
+ * @param level The maximum number of states that a generic char must code
+ * (if this number is higher than level, the state will not be resolved).
+ * For instance if level = 3 and Alphabet is DNA, all generic char will be
+ * resolved but N.
+ *
+ * @author Sylvain Gaillard
+ */
+ static void getPutativeHaplotypes(const Sequence& seq, std::vector<Sequence*>& hap, unsigned int level = 2);
+
+ /**
+ * @brief Combine two sequences.
+ *
+ * @author Sylvain Gaillard
+ */
+
+ static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
+
+ /**
+ * @brief Subtract haplotype from an heterozygous sequence.
+ *
+ * Subtract an haplotype (i.e. a fully resolved sequence) from an heterozygous
+ * sequence to get the other haplotype. The new haplotype could be an unresolved
+ * sequence if unresolved characters in the sequence code for more than 2 states.
+ *
+ * For example:<br>
+ * @code
+ * >heterozygous sequence
+ * ATTCGGGKWTATRYRM
+ * >haplotype
+ * ATTCGGGTATATGCAA
+ * >subtracted haplotype
+ * ATTCGGGGTTATATGC
+ * @endcode
+ *
+ * @param s The heterozygous sequence.
+ * @param h The haplotype to subtract.
+ * @param name The name of the new computed haplotype.
+ * @param level The number of states from which the site is set to fully unresolved.
+ * @throw SequenceNotAlignedException if s and h don't have the same size.
+ *
+ * @author Sylvain Gaillard
+ */
+ static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
+
+ /**
+ * @brief Get the RNY decomposition of a DNA sequence; with a given
+ * phase between 1 and 3, it gives the decomposition in this phase;
+ * in phase 1, the first triplet is centered on the first character.
+ * Without a phase the function gives the alternative succession in
+ * phases 1, 2 and 3.
+ *
+ * @return sequence A new sequence object with the transcription sequence.
+ * @param sequence The sequence to transcript.
+ * @param ph The phase to use (1,2 or 3).
+ * @throw AlphabetException If the sequence is not a DNA sequence.
+ *
+ * @author Laurent Guéguen
+ */
+ static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
+ static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
+
+ /**
+ * @brief Extract CDS part from a codon sequence. Optionally check for intiator and stop codons, or both.
+ *
+ * @param sequence The sequence to be reduced to CDS part.
+ * @param checkInit If true, then everything before the initiator codon will be removed, together with the initiator codon if includeInit is false.
+ * @param checkStop If true, then everything after the first stop codon will be removed, together with the stop codon if includeStop is false.
+ * @param includeInit Tell if initiator codon should be kept or removed. No effect if checkInit is false.
+ * @param includeStop Tell if stop codon should be kept or removed. No effect if checkStop is false.
+ */
+ static void getCDS(Sequence& sequence, bool checkInit, bool checkStop, bool includeInit = true, bool includeStop = true);
+
+ /**
+ * @brief Find the position of a motif in a sequence
+ *
+ * @param seq The reference sequence
+ * @param motif The motif to find
+ * @param strict If true (default) find exactly the motif
+ * If false find compatible match
+ * @return The position of the first occurence of the motif or the seq
+ * length.
+ */
+ static size_t findFirstOf(const Sequence& seq, const Sequence& motif, bool strict = true);
+};
+} // end of namespace bpp.
+
+#endif // _SEQUENCETOOLS_H_
+
diff --git a/src/Bpp/Seq/SequenceWalker.cpp b/src/Bpp/Seq/SequenceWalker.cpp
new file mode 100644
index 0000000..a74dbb9
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWalker.cpp
@@ -0,0 +1,107 @@
+//
+// File: SequenceWalker.cpp
+// Created by: Julien Dutheil
+// Created on: Thu Nov 24 2011
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2011)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include <iostream>
+using namespace std;
+
+#include "SequenceWalker.h"
+
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+size_t SequenceWalker::getAlignmentPosition(size_t seqPos) throw (Exception)
+{
+ if (seqPos == seqPos_) return alnPos_;
+ if (seqPos > seqPos_) {
+ //Move forward
+ while (alnPos_ < seq_->size() && seqPos_ < seqPos) {
+ if (alnPos_ == seq_->size() - 1)
+ throw Exception("SequenceWalker::getAlignmentPosition(). Forward1. Position out of bound.");
+ ++alnPos_;
+
+ if ((*seq_)[alnPos_] != gap_) {
+ ++seqPos_;
+ }
+ }
+ if (seqPos_ != seqPos)
+ throw Exception("SequenceWalker::getAlignmentPosition(). Forward2. Position out of bound (" + TextTools::toString(alnPos_) + ")");
+ } else {
+ //Move backward
+ if (alnPos_ == 0)
+ throw Exception("SequenceWalker::getAlignmentPosition(). Backward. Position out of bound.");
+ while (alnPos_ > 0 && seqPos_ > seqPos) {
+ --alnPos_;
+ if ((*seq_)[alnPos_] != gap_) {
+ --seqPos_;
+ }
+ }
+ if (seqPos_ != seqPos)
+ throw Exception("SequenceWalker::getAlignmentPosition(). Position out of bound.");
+ }
+ return alnPos_;
+}
+
+size_t SequenceWalker::getSequencePosition(size_t alnPos) throw (Exception)
+{
+ if (alnPos == alnPos_) return seqPos_;
+ if (alnPos >= seq_->size())
+ throw Exception("SequenceWalker::getSequencePosition(). Position out of bound.");
+ if (alnPos > alnPos_) {
+ //Move forward
+ while (alnPos_ < alnPos) {
+ ++alnPos_;
+ if ((*seq_)[alnPos_] != gap_) {
+ ++seqPos_;
+ }
+ }
+ } else {
+ //Move backward
+ while (alnPos_ > alnPos) {
+ if (seqPos_ == 0)
+ return 0;
+ --alnPos_;
+ if ((*seq_)[alnPos_ + 1] != gap_) {
+ --seqPos_;
+ }
+ }
+ }
+ return seqPos_;
+}
+
diff --git a/src/Bpp/Seq/SequenceWalker.h b/src/Bpp/Seq/SequenceWalker.h
new file mode 100644
index 0000000..d98cad4
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWalker.h
@@ -0,0 +1,88 @@
+//
+// File: SequenceWalker.h
+// Created by: Julien Dutheil
+// Created on: Thu Nov 24 2011
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2011)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCEWALKER_H_
+#define _SEQUENCEWALKER_H_
+
+#include "Sequence.h"
+
+namespace bpp
+{
+
+/**
+ * @brief A helper class to easily convert coordinates between sequence and alignments.
+ *
+ * Coordinates are 0-based.
+ * The walker will be more efficient if coordinates are called in pre-ordered way.
+ */
+class SequenceWalker
+{
+ private:
+ const Sequence* seq_;
+ size_t seqPos_, alnPos_;
+ int gap_;
+
+ public:
+ SequenceWalker(const Sequence& seq):
+ seq_(&seq), seqPos_(0), alnPos_(0), gap_(seq.getAlphabet()->getGapCharacterCode()) {
+ if (seq_->size() > 0) {
+ while ((*seq_)[alnPos_] == gap_)
+ ++alnPos_;
+ }
+ }
+ SequenceWalker(const SequenceWalker& walker):
+ seq_(walker.seq_), seqPos_(walker.seqPos_), alnPos_(walker.alnPos_), gap_(walker.gap_) {}
+ SequenceWalker& operator=(const SequenceWalker& walker) {
+ seq_ = walker.seq_;
+ seqPos_ = walker.seqPos_;
+ alnPos_ = walker.alnPos_;
+ gap_ = walker.gap_;
+ return *this;
+ }
+ virtual ~SequenceWalker() {}
+
+ public:
+ size_t getAlignmentPosition(size_t seqPos) throw (Exception);
+ size_t getSequencePosition(size_t alnPos) throw (Exception);
+};
+
+} //end of namespace bpp.
+
+#endif //_SEQUENCEWALKER_H_
+
diff --git a/src/Bpp/Seq/SequenceWithAnnotation.cpp b/src/Bpp/Seq/SequenceWithAnnotation.cpp
new file mode 100644
index 0000000..d1caeca
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWithAnnotation.cpp
@@ -0,0 +1,303 @@
+//
+// File: SequenceWithAnnotation.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Jul 19 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SequenceWithAnnotation.h" // class's header file
+
+#include "Alphabet/AlphabetTools.h"
+#include "StringSequenceTools.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+
+using namespace std;
+
+/* Constructors: **************************************************************/
+
+SequenceWithAnnotation::SequenceWithAnnotation(const Alphabet* alpha):
+ EdSymbolList(alpha),
+ name_(),
+ comments_()
+{}
+
+SequenceWithAnnotation::SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha)
+throw (BadCharException) :
+ EdSymbolList(alpha),
+ name_(name),
+ comments_()
+{
+ if (sequence!="")
+ setContent(sequence);
+}
+
+SequenceWithAnnotation::SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha)
+ throw (BadCharException) :
+ EdSymbolList(alpha),
+ name_(name),
+ comments_(comments)
+{
+ if (sequence != "")
+ setContent(sequence);
+}
+
+SequenceWithAnnotation::SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha)
+throw (BadCharException) :
+ EdSymbolList(sequence, alpha),
+ name_(name),
+ comments_()
+{}
+
+SequenceWithAnnotation::SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha)
+ throw (BadCharException) :
+ EdSymbolList(sequence, alpha),
+ name_(name),
+ comments_(comments)
+{}
+
+SequenceWithAnnotation::SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha)
+ throw (BadIntException) :
+ EdSymbolList(sequence, alpha),
+ name_(name),
+ comments_()
+{}
+
+SequenceWithAnnotation::SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha)
+ throw (BadIntException) :
+ EdSymbolList(sequence, alpha),
+ name_(name),
+ comments_(comments)
+{}
+
+/* Copy constructors: *********************************************************/
+
+SequenceWithAnnotation::SequenceWithAnnotation(const Sequence& s) :
+ EdSymbolList(s),
+ name_(s.getName()),
+ comments_(s.getComments())
+{}
+
+SequenceWithAnnotation::SequenceWithAnnotation(const SequenceWithAnnotation& s) :
+ EdSymbolList(s),
+ name_(s.getName()),
+ comments_(s.getComments())
+{}
+
+/* Assignation operator: ******************************************************/
+
+SequenceWithAnnotation& SequenceWithAnnotation::operator=(const Sequence& s)
+{
+ EdSymbolList::operator=(s);
+ name_ = s.getName();
+ comments_ = s.getComments();
+ return *this;
+}
+
+SequenceWithAnnotation& SequenceWithAnnotation::operator=(const SequenceWithAnnotation& s)
+{
+ EdSymbolList::operator=(s);
+ name_ = s.getName();
+ comments_ = s.getComments();
+ return *this;
+}
+
+/******************************************************************************/
+
+void SequenceWithAnnotation::setContent(const std::string& sequence) throw (BadCharException)
+{
+ SymbolListEditionEvent event(this);
+ fireBeforeSequenceChanged(event);
+ // Remove blanks in sequence
+ content_ = StringSequenceTools::codeSequence(TextTools::removeWhiteSpaces(sequence), getAlphabet());
+ //Warning, an exception may be thrown here!
+ fireAfterSequenceChanged(event);
+}
+
+/******************************************************************************/
+
+void SequenceWithAnnotation::setToSizeR(size_t newSize)
+{
+ // Size verification
+ size_t seqSize = content_.size();
+ if (newSize == seqSize) return;
+
+ if (newSize < seqSize)
+ {
+ SymbolListDeletionEvent event(this, newSize, seqSize - newSize);
+ fireBeforeSequenceDeleted(event);
+ content_.resize(newSize);
+ fireAfterSequenceDeleted(event);
+ return;
+ }
+
+ // Add gaps up to specified size
+ SymbolListInsertionEvent event(this, seqSize, newSize - seqSize);
+ fireBeforeSequenceInserted(event);
+ int gap = getAlphabet()->getGapCharacterCode();
+ while (content_.size() < newSize) content_.push_back(gap);
+ fireAfterSequenceInserted(event);
+}
+
+/******************************************************************************/
+
+void SequenceWithAnnotation::setToSizeL(size_t newSize)
+{
+ // Size verification
+ size_t seqSize = content_.size();
+ if (newSize == seqSize) return;
+
+ if (newSize < seqSize)
+ {
+ //We must truncate sequence from the left.
+ SymbolListDeletionEvent event(this, 0, seqSize - newSize);
+ fireBeforeSequenceDeleted(event);
+ content_.erase(content_.begin(), content_.begin() + (seqSize - newSize));
+ fireAfterSequenceDeleted(event);
+ return;
+ }
+
+ // Add gaps up to specified size
+ SymbolListInsertionEvent event(this, 0, newSize - seqSize);
+ fireBeforeSequenceInserted(event);
+ int gap = getAlphabet()->getGapCharacterCode();
+ content_.insert(content_.begin(), newSize - seqSize, gap);
+ fireAfterSequenceInserted(event);
+}
+
+/******************************************************************************/
+
+void SequenceWithAnnotation::append(const std::vector<int>& content) throw (BadIntException)
+{
+ SymbolListInsertionEvent event(this, content_.size(), content.size());
+ fireBeforeSequenceInserted(event);
+ // Check list for incorrect characters
+ for (unsigned int i = 0; i < content.size(); i++)
+ if(!getAlphabet()->isIntInAlphabet(content[i]))
+ throw BadIntException(content[i], "SequenceWithAnnotation::append", getAlphabet());
+ //SequenceWithAnnotation is valid:
+ for (unsigned int i = 0; i < content.size(); i++)
+ content_.push_back(content[i]);
+
+ fireAfterSequenceInserted(event);
+}
+
+void SequenceWithAnnotation::append(const std::vector<std::string>& content) throw (BadCharException)
+{
+ SymbolListInsertionEvent event(this, content_.size(), content.size());
+ fireBeforeSequenceInserted(event);
+ // Check list for incorrect characters
+ for (unsigned int i = 0; i < content.size(); i++)
+ if(!getAlphabet()->isCharInAlphabet(content[i]))
+ throw BadCharException(content[i], "SequenceWithAnnotation::append", getAlphabet());
+
+ //SequenceWithAnnotation is valid:
+ for (unsigned int i = 0; i < content.size(); i++)
+ content_.push_back(getAlphabet()->charToInt(content[i]));
+
+ fireAfterSequenceInserted(event);
+}
+
+void SequenceWithAnnotation::append(const std::string& content) throw (BadCharException)
+{
+ append(StringSequenceTools::codeSequence(content, getAlphabet()));
+}
+
+/******************************************************************************/
+
+vector<string> SequenceWithAnnotation::getAnnotationTypes() const
+{
+ vector<string> types;
+ for (unsigned int i = 0; i < getNumberOfListeners(); ++i) {
+ const SequenceAnnotation* anno = dynamic_cast<const SequenceAnnotation*>(&getListener(i));
+ if (anno)
+ types.push_back(anno->getType());
+ }
+ return types;
+}
+
+/******************************************************************************/
+
+void SequenceWithAnnotation::merge(const SequenceWithAnnotation& swa)
+ throw (AlphabetMismatchException, Exception)
+{
+ // Sequence's alphabets matching verification
+ if ((swa.getAlphabet()->getAlphabetType()) != (getAlphabet()->getAlphabetType()))
+ throw AlphabetMismatchException("SequenceWithAnnotation::merge: Sequence's alphabets don't match ", swa.getAlphabet(), getAlphabet());
+
+ // Sequence's names matching verification
+ if (swa.getName() != getName())
+ throw Exception ("SequenceWithAnnotation::merge: Sequence's names don't match");
+
+ // Concatenate sequences and send result
+ propagateEvents(false);
+ append(swa.getContent());
+ propagateEvents(true);
+
+ // Try to merge annotations.
+ //First start with annotations in this sequence:
+ vector<string> types = getAnnotationTypes();
+ vector<string> newTypes = swa.getAnnotationTypes();
+ for (unsigned int i = 0; i < types.size(); ++i) {
+ vector<string>::iterator it = find(newTypes.begin(), newTypes.end(), types[i]);
+ if (it != newTypes.end()) {
+ //Merge annotations:
+ getAnnotation(types[i]).merge(swa.getAnnotation(types[i]));
+ //Remove annotation from the list:
+ newTypes.erase(it);
+ } else {
+ //Extend annotation to the right:
+ auto_ptr<SequenceAnnotation> anno(getAnnotation(types[i]).clone());
+ anno->init(swa);
+ getAnnotation(types[i]).merge(*anno);
+ }
+ }
+ //Now look for annotations in the input sequence:
+ for (unsigned int i = 0; i < newTypes.size(); ++i) {
+ //Extend annotation from the left:
+ SequenceAnnotation* anno = swa.getAnnotation(newTypes[i]).clone();
+ anno->init(*this);
+ anno->merge(swa.getAnnotation(newTypes[i]));
+ addAnnotation(anno);
+ }
+}
+
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/SequenceWithAnnotation.h b/src/Bpp/Seq/SequenceWithAnnotation.h
new file mode 100644
index 0000000..158f849
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWithAnnotation.h
@@ -0,0 +1,443 @@
+//
+// File: SequenceWithAnnotation.h
+// Created by: Julien Dutheil
+// Created on: Mon Jul 19 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCEWITHANNOTATION_H_
+#define _SEQUENCEWITHANNOTATION_H_
+
+#include "Sequence.h"
+
+// From the STL:
+#include <string>
+#include <vector>
+
+namespace bpp
+{
+
+class SequenceWithAnnotation;
+
+/**
+ * @brief Interface for sequence annotations.
+ */
+class SequenceAnnotation :
+ public virtual SymbolListListener
+{
+ public:
+ virtual SequenceAnnotation* clone() const = 0;
+
+ /**
+ * Creates a default annotation according to a given sequence.
+ *
+ * @param seq The template sequence (typically the one with which the annotation will be attached).
+ */
+ virtual void init(const Sequence& seq) = 0;
+
+ /**
+ * @return The type of the annotation. This is used for querying annotations.
+ */
+ virtual const std::string& getType() const = 0;
+
+ /**
+ * @brief Test is the annotation is valid for a given sequence.
+ *
+ * @param sequence The sequence to be validated against.
+ * @param throwException If set to yes, throw an exception if the sequence is not valid.
+ * @return true if this annotation is complient with the given sequence.
+ */
+ virtual bool isValidWith(const SequenceWithAnnotation& sequence, bool throwException = true) const = 0;
+
+ /**
+ * @brief Merge the input annotation with the current one.
+ *
+ * @param anno The annotation to fuse.
+ * @return true if the fusion was possible and succesful.
+ */
+ virtual bool merge(const SequenceAnnotation& anno) = 0;
+
+ /**
+ * @return A new annotation corresponding to a part of the sequence.
+ * The implementation of this highly depends on the annotation type, and might not be supported.
+ * @param pos Starting point of the region.
+ * @param len The length of the region, in number of positions.
+ */
+ virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
+};
+
+/**
+ * @brief An implementation of the Sequence interface that supports annotation.
+ *
+ * This is a general purpose container, containing an ordered list of states.
+ * The states that allowed to be present in the sequence are defined
+ * by an alphabet object, which is passed to the sequence constructor by a pointer.
+ *
+ * For programming convenience, the states are stored as integers, but the translation toward
+ * and from a char description is easily performed with the Alphabet classes.
+ *
+ * Sequence objets also contain a name attribute and potentially several comment lines.
+ *
+ * The gestion of sequence content is identical to the BasicSequence object, but edition events are
+ * properly fired. Listener are therefore properly handled.
+ *
+ * @see BasicSequence
+ */
+class SequenceWithAnnotation :
+ public Sequence,
+ public EdSymbolList
+{
+ private:
+
+ /**
+ * @brief The sequence name.
+ */
+ std::string name_;
+
+ /**
+ * @brief The sequence comments.
+ */
+ Comments comments_;
+
+ public:
+
+ /**
+ * @brief Empty constructor: build a void Sequence with just an Alphabet
+ *
+ * You can use it safely for all type of Alphabet in order to build an
+ * empty Sequence i.e. without name nor sequence data.
+ *
+ * @param alpha A pointer toward the Alphabet to be used with this Sequence.
+ */
+ SequenceWithAnnotation(const Alphabet* alpha);
+
+ /**
+ * @brief Direct constructor: build a Sequence object from a std::string
+ * You can use it safely for RNA, DNA and protein sequences.
+ *
+ * It can be used with codon sequences too, the std::string will be cut into
+ * parts of size 3. But for more complicated alphabets, you should use one
+ * complete constructors.
+ *
+ * @param name The sequence name.
+ * @param sequence The whole sequence to be parsed as a std::string.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief Direct constructor: build a Sequence object from a std::string.
+ *
+ * You can use it safely for RNA, DNA and protein sequences.
+ *
+ * It can be used with codon sequences too, the std::string will be cut into
+ * tokens of size 3. But for more complicated alphabets, you should use one
+ * complete constructors.
+ *
+ * @param name The sequence name.
+ * @param sequence The whole sequence to be parsed as a std::string.
+ * @param comments Comments to add to the sequence.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief General purpose constructor, can be used with any alphabet.
+ *
+ * You should note that the sequence is stored as a std::vector of int.
+ * Hence each std::string in the std::vector will be translated using the alphabet object.
+ *
+ * @param name The sequence name.
+ * @param sequence The sequence content.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief General purpose constructor, can be used with any alphabet.
+ *
+ * You should note that the sequence is stored as a std::vector of int.
+ * Hence each std::string in the std::vector will be translated using the alphabet object.
+ *
+ * @param name The sequence name.
+ * @param sequence The sequence content.
+ * @param comments Comments to add to the sequence.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief General purpose constructor, can be used with any alphabet.
+ *
+ * @param name The sequence name.
+ * @param sequence The sequence content.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
+
+ /**
+ * @brief General purpose constructor, can be used with any alphabet.
+ *
+ * @param name The sequence name.
+ * @param sequence The sequence content.
+ * @param comments Comments to add to the sequence.
+ * @param alpha A pointer toward the alphabet to be used with this sequence.
+ */
+ SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
+
+ /**
+ * @brief The Sequence generic copy constructor. This does not perform a hard copy of the alphabet object.
+ */
+ SequenceWithAnnotation(const Sequence& s);
+
+ /**
+ * @brief The Sequence copy constructor. This does not perform a hard copy of the alphabet object.
+ */
+ SequenceWithAnnotation(const SequenceWithAnnotation& s);
+
+ /**
+ * @brief The Sequence generic assignment operator. This does not perform a hard copy of the alphabet object.
+ *
+ * @return A ref toward the assigned Sequence.
+ */
+ SequenceWithAnnotation& operator=(const Sequence& s);
+
+ /**
+ * @brief The Sequence assignment operator. This does not perform a hard copy of the alphabet object.
+ *
+ * @return A ref toward the assigned Sequence.
+ */
+ SequenceWithAnnotation& operator=(const SequenceWithAnnotation& s);
+
+ virtual ~SequenceWithAnnotation() {}
+
+ public:
+
+ /**
+ * @name The Clonable interface
+ *
+ * @{
+ */
+ SequenceWithAnnotation* clone() const { return new SequenceWithAnnotation(*this); }
+ /** @} */
+
+
+ /**
+ * @name Setting/getting the name of the sequence.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the name of this sequence.
+ *
+ * @return This sequence name.
+ */
+ const std::string& getName() const { return name_; }
+
+ /**
+ * @brief Set the name of this sequence.
+ *
+ * @param name The new name of the sequence.
+ */
+ void setName(const std::string& name) { name_ = name; }
+
+ /** @} */
+
+ /**
+ * @name Setting/getting the comments associated to the sequence.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the comments associated to this sequence.
+ *
+ * @return The comments of the sequence.
+ */
+ const Comments& getComments() const { return comments_; }
+
+ /**
+ * @brief Set the comments associated to this sequence.
+ *
+ * @param comments The new comments of the sequence.
+ */
+ void setComments(const Comments& comments) { comments_ = comments; }
+
+ /** @} */
+
+
+ /**
+ * @name Adjusting the size of the sequence.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Set the whole content of the sequence.
+ *
+ * @param sequence The new content of the sequence.
+ * @see The Sequence constructor for information about the way sequences are internaly stored.
+ */
+ virtual void setContent(const std::string& sequence) throw (BadCharException);
+ void setContent(const std::vector<int>& list) throw (BadIntException)
+ {
+ EdSymbolList::setContent(list);
+ }
+ void setContent(const std::vector<std::string>& list) throw (BadCharException)
+ {
+ EdSymbolList::setContent(list);
+ }
+
+
+ /**
+ * @brief Set up the size of a sequence from the right side.
+ *
+ * All new characters are filled with gaps.
+ * If the specified size is < to the sequence size, the sequence will be truncated.
+ *
+ * @param newSize The new size of the sequence.
+ */
+ virtual void setToSizeR(size_t newSize);
+
+ /**
+ * @brief Set up the size of a sequence from the left side.
+ *
+ * All new characters are filled with gaps.
+ * If the specified size is < to the sequence size, the sequence will be truncated.
+ *
+ * @param newSize The new size of the sequence.
+ */
+ virtual void setToSizeL(size_t newSize);
+
+ /**
+ * @brief Append the specified content to the sequence.
+ *
+ * @param content The content to append to the sequence.
+ * @throw BadIntException If the content does not match the current alphabet.
+ */
+ void append(const std::vector<int>& content) throw (BadIntException);
+
+ /**
+ * @brief Append the specified content to the sequence.
+ *
+ * @param content The content to append to the sequence.
+ * @throw BadCharException If the content does not match the current alphabet.
+ */
+ void append(const std::vector<std::string>& content) throw (BadCharException);
+
+ /**
+ * @brief Append the specified content to the sequence.
+ *
+ * @param content The content to append to the sequence.
+ * @throw BadCharException If the content does not match the current alphabet.
+ */
+ void append(const std::string& content) throw (BadCharException);
+
+ /** @} */
+
+ /**
+ * @brief Add a new annotation to the sequence.
+ *
+ * @param anno The annotation object to be added. Unless the annotation is shared,
+ * the annotation object will be owned by the sequence object, and will be copied
+ * and deleted when needed.
+ * @throw Exception If the annotation is not valid for this sequence.
+ * @see SequenceWithAnnotation::isValidWith
+ */
+ virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
+ {
+ anno->isValidWith(*this);
+ addSymbolListListener(anno);
+ }
+
+ virtual bool hasAnnotation(const std::string& type) const
+ {
+ for (size_t i = 0; i < getNumberOfListeners(); ++i) {
+ const SymbolListListener* listener = &getListener(i);
+ const SequenceAnnotation* anno = dynamic_cast<const SequenceAnnotation*>(listener);
+ if (anno && anno->getType() == type) return true;
+ }
+ return false;
+ }
+
+
+ virtual const SequenceAnnotation& getAnnotation(const std::string& type) const
+ {
+ for (size_t i = 0; i < getNumberOfListeners(); ++i) {
+ const SymbolListListener* listener = &getListener(i);
+ const SequenceAnnotation* anno = dynamic_cast<const SequenceAnnotation*>(listener);
+ if (anno && anno->getType() == type) return *anno;
+ }
+ throw Exception("SequenceWithAnnotation::getAnnotation. No annotation found with type '" + type + "'.");
+ }
+
+ virtual SequenceAnnotation& getAnnotation(const std::string& type)
+ {
+ for (size_t i = 0; i < getNumberOfListeners(); ++i) {
+ SymbolListListener* listener = &getListener(i);
+ SequenceAnnotation* anno = dynamic_cast<SequenceAnnotation*>(listener);
+ if (anno && anno->getType() == type) return *anno;
+ }
+ throw Exception("SequenceWithAnnotation::getAnnotation. No annotation found with type '" + type + "'.");
+ }
+
+ /**
+ * @return The list of annotation types contained in this sequence.
+ */
+ virtual std::vector<std::string> getAnnotationTypes() const;
+
+ /**
+ * @brief Merge a sequence with the current one.
+ *
+ * Sequences must have the same name and alphabets.
+ * Only first sequence's commentaries are kept.
+ * Annotations that could not be merged will not be added in the concatenated sequence.
+ * See the documentation of each annotation class for more details.
+ *
+ * @param swa The sequence to merge with.
+ * @throw AlphabetMismatchException If the two alphabets do not match.
+ * @throw Exception If the sequence names do not match.
+ */
+ virtual void merge(const SequenceWithAnnotation& swa)
+ throw (AlphabetMismatchException, Exception);
+
+
+};
+
+} //end of namespace bpp.
+
+#endif // _SEQUENCEWITHANNOTATION_H_
+
diff --git a/src/Bpp/Seq/SequenceWithAnnotationTools.cpp b/src/Bpp/Seq/SequenceWithAnnotationTools.cpp
new file mode 100644
index 0000000..8db345b
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWithAnnotationTools.cpp
@@ -0,0 +1,89 @@
+//
+// File: SequenceWithAnnotationTools.cpp
+// Authors: Julien Dutheil
+// Created on: 06 Sep 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (Sep 06, 2010)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SequenceWithAnnotationTools.h"
+#include "Alphabet/CaseMaskedAlphabet.h"
+
+using namespace bpp;
+using namespace std;
+
+const string SequenceMask::MASK = "Boolean mask";
+
+/******************************************************************************/
+
+void SequenceMask::afterSequenceChanged(const SymbolListEditionEvent& event)
+{
+ mask_.clear();
+ mask_.insert(mask_.begin(), event.getSymbolList()->size(), false);
+}
+
+/******************************************************************************/
+
+void SequenceMask::afterSequenceInserted(const SymbolListInsertionEvent& event)
+{
+ mask_.insert(mask_.begin() + event.getPosition(), event.getLength(), false);
+}
+
+/******************************************************************************/
+
+void SequenceMask::afterSequenceDeleted(const SymbolListDeletionEvent& event)
+{
+ mask_.erase(mask_.begin() + event.getPosition(), mask_.begin() + event.getPosition() + event.getLength());
+}
+
+/******************************************************************************/
+
+SequenceWithAnnotation* SequenceWithAnnotationTools::createMaskAnnotation(const Sequence& seq) throw (AlphabetException)
+{
+ const CaseMaskedAlphabet* cma = dynamic_cast<const CaseMaskedAlphabet*>(seq.getAlphabet());
+ if (cma) {
+ SequenceWithAnnotation* seqa = new SequenceWithAnnotation(seq.getName(), seq.toString(), seq.getComments(), seq.getAlphabet());
+ vector<bool> mask(seq.size());
+ for (unsigned int i = 0; i < seq.size(); ++i) {
+ mask[i] = cma->isMasked(seq[i]);
+ }
+ seqa->addAnnotation(new SequenceMask(mask));
+ return seqa;
+ } else {
+ throw AlphabetException("SequenceWithAnnotationTools::createMaskAnnotation. Alphabet should be a CaseMaskedAlphabet.", seq.getAlphabet());
+ }
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/SequenceWithAnnotationTools.h b/src/Bpp/Seq/SequenceWithAnnotationTools.h
new file mode 100644
index 0000000..c482f07
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWithAnnotationTools.h
@@ -0,0 +1,205 @@
+//
+// File: SequenceWithAnnotationTools.h
+// Authors: Julien Dutheil
+// Created on: 06 Sep 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (Sep 06, 2010)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCEWITHANNOTATIONTOOLS_H_
+#define _SEQUENCEWITHANNOTATIONTOOLS_H_
+
+#include "SequenceTools.h"
+#include "SequenceWithAnnotation.h"
+#include <Bpp/Numeric/VectorTools.h>
+
+namespace bpp {
+
+ class SequenceMask :
+ public virtual SequenceAnnotation
+ {
+ private:
+ bool removable_;
+ std::vector<bool> mask_;
+
+ public:
+ static const std::string MASK;
+
+ public:
+
+ /**
+ * @name Constructors
+ * @{
+ */
+
+ /**
+ * @brief Build a new SequenceMask object
+ *
+ * Build a new SequenceMask object and set the mask to false.
+ *
+ * @param size The size of the sequence.
+ * @param removable Tell if this listener can be removed by the user.
+ */
+ SequenceMask(size_t size = 0, bool removable = true) :
+ removable_(removable),
+ mask_(size, false)
+ {}
+
+
+ /**
+ * @brief Build a new SequenceMask object
+ *
+ * Build a new SequenceMask object and set the mask as a vector of bool.
+ *
+ * @param mask The boolean mask
+ * @param removable Tell if this listener can be removed by the user.
+ */
+ SequenceMask(const std::vector<bool>& mask, bool removable = true) :
+ removable_(removable),
+ mask_(mask)
+ {}
+
+ /** @} */
+
+ /**
+ * @name Destructor
+ * @{
+ */
+ virtual ~SequenceMask() {}
+ /** @} */
+
+ /**
+ * @name The Clonable interface
+ * @{
+ */
+#ifdef NO_VIRTUAL_COV
+ Clonable*
+#else
+ SequenceMask*
+#endif
+ clone() const { return new SequenceMask(*this); }
+ /** @} */
+
+ public:
+ void init(const Sequence& seq)
+ {
+ mask_.resize(seq.size());
+ std::fill(mask_.begin(), mask_.end(), false);
+ }
+
+ const std::string& getType() const { return MASK; }
+
+ bool isValidWith(const SequenceWithAnnotation& sequence, bool throwException = true) const
+ {
+ if (throwException && mask_.size() != sequence.size()) throw Exception("SequenceMask. The mask size must match the sequence size.");
+ return (mask_.size() == sequence.size());
+ }
+
+ bool isRemovable() const { return removable_; }
+ bool isShared() const { return false; }
+ void beforeSequenceChanged(const SymbolListEditionEvent& event) {}
+ void afterSequenceChanged(const SymbolListEditionEvent& event);
+ void beforeSequenceInserted(const SymbolListInsertionEvent& event) {}
+ void afterSequenceInserted(const SymbolListInsertionEvent& event);
+ void beforeSequenceDeleted(const SymbolListDeletionEvent& event) {}
+ void afterSequenceDeleted(const SymbolListDeletionEvent& event);
+ void beforeSequenceSubstituted(const SymbolListSubstitutionEvent& event) {}
+ void afterSequenceSubstituted(const SymbolListSubstitutionEvent& event) {}
+
+ size_t getSize() const { return mask_.size(); }
+
+ const bool operator[](size_t i) const { return mask_[i]; }
+
+ void setMask(const std::vector<bool>& mask) {
+ if (mask.size() != mask_.size())
+ throw DimensionException("SequenceMask::setMask. Trying to replace mask by a vector with different length.", mask.size(), mask_.size());
+ mask_ = mask;
+ }
+
+ /**
+ * @return The mask as a vector.
+ */
+ const std::vector<bool>& getMask() const { return mask_; }
+
+ void setMask(size_t pos, bool mask) {
+ if (pos >= mask_.size())
+ throw Exception("SequenceMask::setMask. Vector overflow. Scores number: " + TextTools::toString(mask_.size()) + ", but trying to insert mask at position " + TextTools::toString(pos) + ".");
+ mask_[pos] = mask;
+ }
+
+ void setMask(size_t pos, const std::vector<bool>& mask) {
+ if (pos + mask.size() > mask_.size())
+ throw Exception("SequenceMask::setMask. Vector overflow. Scores number: " + TextTools::toString(mask_.size()) + ", but trying to insert " + TextTools::toString(mask.size()) + " scores at position " + TextTools::toString(pos) + ".");
+ std::copy(mask.begin(), mask.end(), mask_.begin() + pos);
+ }
+
+ bool merge(const SequenceAnnotation& anno) {
+ try {
+ const SequenceMask* mask = & dynamic_cast<const SequenceMask&>(anno);
+ VectorTools::append(mask_, mask->getMask());
+ return true;
+ } catch (std::exception& e) {
+ return false;
+ }
+ }
+
+ SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
+ return new SequenceMask(std::vector<bool>(mask_.begin() + pos, mask_.begin() + pos + len), removable_);
+ }
+ };
+
+ /**
+ * @brief The SequenceWithAnnotationTools static class
+ *
+ * Implement methods to manipulate SequencesWithAnnotation
+ *
+ * @author Julien Dutheil
+ */
+
+ class SequenceWithAnnotationTools {
+
+ public:
+ /**
+ * @brief Parse a sequence with a CaseMaskedAlphabet and creates a new SequenceWithAnnotation object with original alphabet and a mask annotation.
+ *
+ * @param seq The sequence to parse.
+ * @return A new SequenceWithAnnotation object.
+ * @throw AlphabetException if the input sequence does not have a CaseMaskedAlphabet.
+ */
+ SequenceWithAnnotation* createMaskAnnotation(const Sequence& seq) throw (AlphabetException);
+
+ };
+}
+
+#endif // _SEQUENCEWITHANNOTATIONTOOLS_H_
diff --git a/src/Bpp/Seq/SequenceWithQuality.cpp b/src/Bpp/Seq/SequenceWithQuality.cpp
new file mode 100644
index 0000000..8613310
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWithQuality.cpp
@@ -0,0 +1,76 @@
+//
+// File: SequenceWithQuality.cpp
+// Author: Sylvain Gaillard
+// Created: 19/01/2010 16:09:02
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (January 19, 2010)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SequenceWithQuality.h"
+#include <Bpp/Numeric/VectorTools.h>
+
+using namespace bpp;
+
+#include <string>
+#include <iostream>
+
+using namespace std;
+
+const string SequenceQuality::QUALITY_SCORE = "Quality score";
+const int SequenceQuality::DEFAULT_QUALITY_VALUE = 20;
+
+/******************************************************************************/
+
+void SequenceQuality::afterSequenceChanged(const SymbolListEditionEvent& event)
+{
+ qualScores_.clear();
+ qualScores_.insert(qualScores_.begin(), event.getSymbolList()->size(), DEFAULT_QUALITY_VALUE);
+}
+
+/******************************************************************************/
+
+void SequenceQuality::afterSequenceInserted(const SymbolListInsertionEvent& event)
+{
+ qualScores_.insert(qualScores_.begin() + event.getPosition(), event.getLength(), DEFAULT_QUALITY_VALUE);
+}
+
+/******************************************************************************/
+
+void SequenceQuality::afterSequenceDeleted(const SymbolListDeletionEvent& event)
+{
+ qualScores_.erase(qualScores_.begin() + event.getPosition(), qualScores_.begin() + event.getPosition() + event.getLength());
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/SequenceWithQuality.h b/src/Bpp/Seq/SequenceWithQuality.h
new file mode 100644
index 0000000..f0aebe4
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWithQuality.h
@@ -0,0 +1,781 @@
+//
+// File: SequenceWithQuality.h
+// Authors: Sylvain Gaillard
+// Vincent Cahais
+// Julien Dutheil
+// Created: 19/01/2010 16:01:20
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (January 19, 2010)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SEQUENCEQUALITY_H_
+#define _SEQUENCEQUALITY_H_
+
+#include "SequenceWithAnnotation.h"
+#include <Bpp/Numeric/VectorTools.h>
+#include <Bpp/Numeric/VectorExceptions.h>
+
+// From the STL
+
+#include <string>
+#include <vector>
+
+namespace bpp {
+ /**
+ * @brief The SequenceQuality class
+ *
+ * This is a sequence with quality score associated to each element.
+ * The score is a signed int value that can represent the phred or the
+ * Solexa quality score for nucleic sequence.
+ *
+ * @author Sylvain Gaillard, Vincent Cahais, Julien Dutheil
+ */
+ class SequenceQuality :
+ public virtual SequenceAnnotation
+ {
+ private:
+ bool removable_;
+ std::vector<int> qualScores_;
+
+ public:
+ static const std::string QUALITY_SCORE;
+ static const int DEFAULT_QUALITY_VALUE;
+
+ public:
+
+ /**
+ * @name Constructors
+ * @{
+ */
+
+ /**
+ * @brief Build a new SequenceQuality object
+ *
+ * Build a new SequenceQuality object and set the quality scores to
+ * the default value DEFAULT_QUALITY_VALUE.
+ *
+ * @param size The size of the sequence.
+ * @param removable Tell if this listener can be removed by the user.
+ */
+ SequenceQuality(size_t size = 0, bool removable = true) :
+ removable_(removable),
+ qualScores_(size, DEFAULT_QUALITY_VALUE) {}
+
+
+ /**
+ * @brief Build a new SequenceQuality object
+ *
+ * Build a new SequenceQuality and assign quality scores from
+ * a vector of int.
+ *
+ * @param quality The quality scores
+ * @param removable Tell if this listener can be removed by the user.
+ */
+ SequenceQuality(const std::vector<int>& quality, bool removable = true) :
+ removable_(removable),
+ qualScores_(quality)
+ {
+ // if (size() != qualScores_.size())
+ // throw DimensionException("SequenceWithQuality constructor: sequence and quality must have the same length", qualScores_.size(), size());
+ }
+
+ /** @} */
+
+ /**
+ * @name Destructor
+ * @{
+ */
+ virtual ~SequenceQuality() {}
+ /** @} */
+
+ /**
+ * @name The Clonable interface
+ * @{
+ */
+#ifdef NO_VIRTUAL_COV
+ Clonable*
+#else
+ SequenceQuality*
+#endif
+ clone() const { return new SequenceQuality(*this); }
+ /** @} */
+
+ public:
+ void init(const Sequence& seq)
+ {
+ qualScores_.resize(seq.size());
+ std::fill(qualScores_.begin(), qualScores_.end(), DEFAULT_QUALITY_VALUE);
+ }
+
+ const std::string& getType() const { return QUALITY_SCORE; }
+
+ bool isValidWith(const SequenceWithAnnotation& sequence, bool throwException = true) const
+ {
+ if (throwException && qualScores_.size() != sequence.size()) throw Exception("SequenceQuality. Quality scores must match the sequence size.");
+ return (qualScores_.size() == sequence.size());
+ }
+
+ bool isRemovable() const { return removable_; }
+ bool isShared() const { return false; }
+ void beforeSequenceChanged(const SymbolListEditionEvent& event) {}
+ void afterSequenceChanged(const SymbolListEditionEvent& event);
+ void beforeSequenceInserted(const SymbolListInsertionEvent& event) {}
+ void afterSequenceInserted(const SymbolListInsertionEvent& event);
+ void beforeSequenceDeleted(const SymbolListDeletionEvent& event) {}
+ void afterSequenceDeleted(const SymbolListDeletionEvent& event);
+ void beforeSequenceSubstituted(const SymbolListSubstitutionEvent& event) {}
+ void afterSequenceSubstituted(const SymbolListSubstitutionEvent& event) {}
+
+ size_t getSize() const { return qualScores_.size(); }
+
+ const int& operator[](size_t i) const { return qualScores_[i]; }
+ int& operator[](size_t i) { return qualScores_[i]; }
+
+ void setScores(const std::vector<int>& scores) {
+ if (scores.size() != qualScores_.size())
+ throw DimensionException("SequenceQuality::setScores. Trying to replace score by a vector with different length.", scores.size(), qualScores_.size());
+ qualScores_ = scores;
+ }
+
+ /**
+ * @return All scores as a vector.
+ */
+ const std::vector<int>& getScores() const { return qualScores_; }
+
+ void setScore(size_t pos, int score) {
+ if (pos >= qualScores_.size())
+ throw Exception("SequenceQuality::setScore. Vector overflow. Scores number: " + TextTools::toString(qualScores_.size()) + ", but trying to insert score at position " + TextTools::toString(pos) + ".");
+ qualScores_[pos] = score;
+ }
+
+ void setScores(size_t pos, const std::vector<int>& scores) {
+ if (pos + scores.size() > qualScores_.size())
+ throw Exception("SequenceQuality::setScores. Vector overflow. Scores number: " + TextTools::toString(qualScores_.size()) + ", but trying to insert " + TextTools::toString(scores.size()) + " scores at position " + TextTools::toString(pos) + ".");
+ std::copy(scores.begin(), scores.end(), qualScores_.begin() + pos);
+ }
+
+ bool merge(const SequenceAnnotation& anno) {
+ try {
+ const SequenceQuality* qual = & dynamic_cast<const SequenceQuality&>(anno);
+ VectorTools::append(qualScores_, qual->getScores());
+ return true;
+ } catch (std::exception& e) {
+ return false;
+ }
+ }
+
+ SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
+ return new SequenceQuality(std::vector<int>(qualScores_.begin() + pos, qualScores_.begin() + pos + len), removable_);
+ }
+ };
+
+
+
+ /**
+ * @brief A SequenceWithAnnotation class with quality scores attached.
+ *
+ * This classes adds some usefull functions to handle quality scores.
+ *
+ * @see SequenceQuality
+ * @author Sylvain Gaillard, Vincent Cahais, Julien Dutheil
+ */
+ class SequenceWithQuality :
+ public SequenceWithAnnotation
+ {
+ private:
+ SequenceQuality* qualScores_;
+
+ public:
+
+ /**
+ * @name Constructors
+ * @{
+ */
+
+ /**
+ * @brief Build a new empty SequenceWithQuality
+ *
+ * @param alpha A pointer to an Alphabet
+ *
+ * @throw BadCharException if a state is not alowed by the Alphabet
+ */
+ SequenceWithQuality(
+ const Alphabet* alpha
+ ):
+ SequenceWithAnnotation(alpha),
+ qualScores_(new SequenceQuality(0, false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality from a std::string
+ *
+ * Build a new SequenceWithQuality and set the quality scores to
+ * the default value DEFAULT_QUALITY_VALUE.
+ *
+ * @param name The name of the sequence
+ * @param sequence The string representing the sequence
+ * @param alpha A pointer to an Alphabet
+ *
+ * @throw BadCharException if a state is not alowed by the Alphabet
+ */
+ SequenceWithQuality(
+ const std::string& name,
+ const std::string& sequence,
+ const Alphabet* alpha
+ ) throw (BadCharException):
+ SequenceWithAnnotation(name, sequence, alpha),
+ qualScores_(new SequenceQuality(sequence.size(), false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality from a std::string
+ *
+ * Build a new SequenceWithQuality and set the quality scores to
+ * the default value DEFAULT_QUALITY_VALUE.
+ *
+ * @param name The name of the sequence
+ * @param sequence The string representing the sequence
+ * @param comments Comments to add to the sequence
+ * @param alpha A pointer to an Alphabet
+ *
+ * @throw BadCharException if a state is not alowed by the Alphabet
+ *
+ * @author Vincent Cahais
+ */
+ SequenceWithQuality(
+ const std::string& name,
+ const std::string& sequence,
+ const Comments& comments,
+ const Alphabet* alpha
+ ) throw (BadCharException):
+ SequenceWithAnnotation(name, sequence, comments, alpha),
+ qualScores_(new SequenceQuality(sequence.size(), false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality from a std::string
+ *
+ * Build a new SequenceWithQuality and assign quality scores from
+ * a vector of int.
+ *
+ * @param name The name of the sequence
+ * @param sequence The string representing the sequence
+ * @param quality The quality scores
+ * @param alpha A pointer to an alphabet
+ *
+ * @throw BadCharException if a state is not alowed by the Alphabet
+ * @throw DimensionException if the number of quality values is not equal
+ * to the number of sequence states
+ */
+ SequenceWithQuality(
+ const std::string& name,
+ const std::string& sequence,
+ const std::vector<int>& quality,
+ const Alphabet* alpha)
+ throw (BadCharException, DimensionException):
+ SequenceWithAnnotation(name, sequence, alpha),
+ qualScores_(new SequenceQuality(quality, false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality from a std::string
+ *
+ * Build a new SequenceWithQuality and assign quality scores from
+ * a vector of int.
+ *
+ * @param name The name of the sequence
+ * @param sequence The string representing the sequence
+ * @param quality The quality scores
+ * @param comments Comments to add to the sequence
+ * @param alpha A pointer to an alphabet
+ *
+ * @throw BadCharException if a state is not alowed by the Alphabet
+ * @throw DimensionException if the number of quality values is not equal
+ * to the number of sequence states
+ *
+ * @author Vincent Cahais
+ */
+ SequenceWithQuality(
+ const std::string& name,
+ const std::string& sequence,
+ const std::vector<int>& quality,
+ const Comments& comments,
+ const Alphabet* alpha)
+ throw (BadCharException, DimensionException):
+ SequenceWithAnnotation(name, sequence, comments, alpha),
+ qualScores_(new SequenceQuality(quality, false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality from a std::vector<int>
+ *
+ * Build a new SequenceWithQuality and set the quality scores to
+ * the default value DEFAULT_QUALITY_VALUE.
+ *
+ * @param name The name of the sequence
+ * @param sequence The sequence in int
+ * @param alpha A pointer to an Alphabet
+ *
+ * @throw BadIntException if a state is not alowed by the Alphabet
+ */
+ SequenceWithQuality(
+ const std::string& name,
+ const std::vector<int>& sequence,
+ const Alphabet* alpha)
+ throw (BadIntException):
+ SequenceWithAnnotation(name, sequence, alpha),
+ qualScores_(new SequenceQuality(sequence.size(), false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality from a std::vector<int>
+ *
+ * Build a new SequenceWithQuality and set the quality scores to
+ * the default value DEFAULT_QUALITY_VALUE.
+ *
+ * @param name The name of the sequence
+ * @param sequence The sequence in int
+ * @param comments Comments to add to the sequence
+ * @param alpha A pointer to an Alphabet
+ *
+ * @throw BadIntException if a state is not alowed by the Alphabet
+ *
+ * @author Vincent Cahais
+ */
+ SequenceWithQuality(
+ const std::string& name,
+ const std::vector<int>& sequence,
+ const Comments& comments,
+ const Alphabet* alpha)
+ throw (BadIntException):
+ SequenceWithAnnotation(name, sequence, comments, alpha),
+ qualScores_(new SequenceQuality(sequence.size(), false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality from a std::vector<int>
+ *
+ * Build a new SequenceWithQuality and assign quality scores from
+ * a vector of int.
+ *
+ * @param name The name of the sequence
+ * @param sequence The sequence in int
+ * @param quality The quality scores
+ * @param alpha A pointer to an Alphabet
+ *
+ * @throw BadIntException if a state is not alowed by the Alphabet
+ * @throw DimensionException if the number of quality values is not equal
+ * to the number of sequence states
+ */
+ SequenceWithQuality(
+ const std::string& name,
+ const std::vector<int>& sequence,
+ const std::vector<int>& quality,
+ const Alphabet* alpha)
+ throw (BadIntException, DimensionException):
+ SequenceWithAnnotation(name, sequence, alpha),
+ qualScores_(new SequenceQuality(quality, false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality from a std::vector<int>
+ *
+ * Build a new SequenceWithQuality and assign quality scores from
+ * a vector of int.
+ *
+ * @param name The name of the sequence
+ * @param sequence The sequence in int
+ * @param quality The quality scores
+ * @param comments Comments to add to the sequence
+ * @param alpha A pointer to an Alphabet
+ *
+ * @throw BadIntException if a state is not alowed by the Alphabet
+ * @throw DimensionException if the number of quality values is not equal
+ * to the number of sequence states
+ *
+ * @author Vincent Cahais
+ */
+ SequenceWithQuality(
+ const std::string& name,
+ const std::vector<int>& sequence,
+ const std::vector<int>& quality,
+ const Comments& comments,
+ const Alphabet* alpha)
+ throw (BadIntException, DimensionException):
+ SequenceWithAnnotation(name, sequence, comments, alpha),
+ qualScores_(new SequenceQuality(quality, false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality
+ *
+ * Build a new SequenceWithQuality from a Sequence object and set the
+ * quality scores to the default value DEFAULT_QUALITY_VALUE.
+ *
+ * @param s The Sequence object
+ */
+ SequenceWithQuality(const Sequence& s) :
+ SequenceWithAnnotation(s), qualScores_(new SequenceQuality(s.size(), false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /**
+ * @brief Build a new SequenceWithQuality
+ *
+ * Build a new SequenceWithQuality from a Sequence object and set the
+ * quality scores from a vector of int.
+ *
+ * @param s The Sequence object
+ * @param sc The quality scores
+ *
+ * @throw DimensionException if the number of quality values is not equal
+ * to the number of sequence states
+ */
+ SequenceWithQuality(
+ const Sequence& s,
+ const std::vector<int>& sc)
+ throw (DimensionException):
+ SequenceWithAnnotation(s),
+ qualScores_(new SequenceQuality(sc, false))
+ {
+ addAnnotation(qualScores_);
+ }
+
+ /** @} */
+
+ /**
+ * @name Destructor
+ * @{
+ */
+ virtual ~SequenceWithQuality() {}
+ /** @} */
+
+ SequenceWithQuality(const SequenceWithQuality& sequence) :
+ SequenceWithAnnotation(sequence), qualScores_(0)
+ {
+ qualScores_ = dynamic_cast<SequenceQuality*>(&getAnnotation(SequenceQuality::QUALITY_SCORE));
+ }
+
+ SequenceWithQuality& operator=(const SequenceWithQuality& sequence)
+ {
+ SequenceWithAnnotation::operator=(sequence);
+ qualScores_ = dynamic_cast<SequenceQuality*>(&getAnnotation(SequenceQuality::QUALITY_SCORE));
+ return *this;
+ }
+
+ /**
+ * @name The Clonable interface
+ * @{
+ */
+#ifdef NO_VIRTUAL_COV
+ Clonable*
+#else
+ SequenceWithQuality*
+#endif
+ clone() const { return new SequenceWithQuality(*this); }
+ /** @} */
+
+ /**
+ * @name Dealing with quality
+ * @{
+ */
+
+ /**
+ * @brief Set the quality score
+ *
+ * @param pos The position where the quality must be set
+ * @param quality The quality value
+ *
+ * @throw IndexOutOfBoundsException if pos is greater than the
+ * sequence size
+ */
+ void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
+ //if (pos >= qualScores_->getSize())
+ // throw IndexOutOfBoundsException("SequenceWithQuality::setQuality: pos out of bounds", pos, 0, qualScores_->getSize() - 1);
+ //qualScores_[pos] = quality;
+ qualScores_->setScore(pos, quality);
+ }
+
+ /**
+ * @brief Get the quality score
+ *
+ * @param pos The position where the quality is read
+ *
+ * @return The quality score
+ *
+ * @throw IndexOutOfBoundsException if pos is greater than the
+ * sequence size
+ */
+ int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
+ if (pos >= qualScores_->getSize())
+ throw IndexOutOfBoundsException("SequenceWithQuality::getQuality: pos out of bounds", pos, 0, qualScores_->getSize() - 1);
+ return (*qualScores_)[pos];
+ }
+
+ /**
+ * @brief Set the whole quality scores
+ *
+ * @param quality The vector of quality scores
+ *
+ * @throw DimensionException if the quality vector does not feet the
+ * sequence size
+ */
+ void setQualities(const std::vector<int>& quality) throw (DimensionException) {
+ if (quality.size() != qualScores_->getSize())
+ throw DimensionException("SequenceWithQuality::setQualities: quality must fit sequence size", quality.size(), qualScores_->getSize());
+ qualScores_->setScores(quality);
+ }
+
+ /**
+ * @brief Get the whole quality scores
+ *
+ * @return A reference to the quality vector
+ */
+ const std::vector<int>& getQualities() const {
+ return qualScores_->getScores();
+ }
+
+ void append(const std::vector<int>& content)
+ throw (BadIntException)
+ {
+ SequenceWithAnnotation::append(content);
+ }
+
+ /**
+ * @brief Append content with quality
+ *
+ * @param content A vector of int to append to the sequence
+ * @param qualities A vector of int to append to the qualities
+ *
+ * @throw BadIntException if one of the content int is not in the
+ * Alphabet
+ * @throw DimensionException if qualities does not have the same size as
+ * content
+ */
+ void append(
+ const std::vector<int>& content,
+ const std::vector<int>& qualities)
+ throw (BadIntException, DimensionException)
+ {
+ if (content.size() != qualities.size())
+ throw DimensionException("SequenceWithQuality::append: qualities must fit content size", qualities.size(), content.size());
+ size_t pos = qualScores_->getSize();
+ append(content); //This automatically extend scores array with default values through the listener
+ //Update scores:
+ qualScores_->setScores(pos, qualities);
+ }
+
+ void append(const std::vector<std::string>& content)
+ throw (BadCharException)
+ {
+ SequenceWithAnnotation::append(content);
+ }
+
+ /**
+ * @brief Append content with quality
+ *
+ * @param content A vector of string to append to the sequence
+ * @param qualities A vector of int to append to the qualities
+ *
+ * @throw BadCharException if one of the content string is not in the
+ * Alphabet
+ * @throw DimensionException if qualities does not have the same size as
+ * content
+ */
+ void append(
+ const std::vector<std::string>& content,
+ const std::vector<int>& qualities)
+ throw (BadCharException, DimensionException)
+ {
+ if (content.size() != qualities.size())
+ throw DimensionException("SequenceWithQuality::append: qualities must fit content size", qualities.size(), content.size());
+ size_t pos = qualScores_->getSize();
+ SequenceWithAnnotation::append(content); //This automatically extend scores array with default values through the listener
+ //Update scores:
+ qualScores_->setScores(pos, qualities);
+ }
+
+ void append(const std::string& content)
+ throw (BadCharException)
+ {
+ SequenceWithAnnotation::append(content);
+ }
+
+ /**
+ * @brief Append content with quality
+ *
+ * @param content A string to append to the sequence
+ * @param qualities A vector of int to append to the qualities
+ *
+ * @throw BadCharException if one of the character of the string is not in
+ * the Alphabet
+ * @throw DimensionException if qualities does not have the same size as
+ * content
+ */
+ void append(
+ const std::string& content,
+ const std::vector<int>& qualities)
+ throw (BadCharException, DimensionException)
+ {
+ if (content.size() / this->getAlphabet()->getStateCodingSize()
+ != qualities.size())
+ throw DimensionException("SequenceWithQuality::append: qualities must fit content size", qualities.size(), content.size() / this->getAlphabet()->getStateCodingSize());
+ size_t pos = qualScores_->getSize();
+ SequenceWithAnnotation::append(content); //This automatically extend scores array with default values through the listener
+ //Update scores:
+ qualScores_->setScores(pos, qualities);
+ }
+
+ void addElement(
+ const std::string& c)
+ throw (BadCharException)
+ {
+ SequenceWithAnnotation::addElement(c);
+ }
+
+ /**
+ * @brief Add a character to the end of the list with quality
+ *
+ * @param c The element to add to the sequence
+ * @param q The quality of this element
+ *
+ * @throw BadCharException if one of the character of the string is not in
+ * the Alphabet
+ */
+ void addElement(
+ const std::string& c, int q)
+ throw (BadCharException)
+ {
+ SequenceWithAnnotation::addElement(c);
+ qualScores_->setScore(size() - 1, q);
+ }
+
+ void addElement(size_t pos, const std::string& c)
+ throw (BadCharException, IndexOutOfBoundsException)
+ {
+ SequenceWithAnnotation::addElement(pos, c);
+ }
+
+ /**
+ * @brief Add a character to a certain position in the list with quality
+ *
+ * @param pos The position where the element will be inserted
+ * @param c The element to add to the sequence
+ * @param q The quality of this element
+ *
+ * @throw BadCharException if one of the character of the string is not in
+ * the Alphabet
+ * @throw IndexOutOfBoundsException if pos is greater than the sequence
+ * size
+ */
+ void addElement(
+ size_t pos, const std::string& c, int q)
+ throw (BadCharException, IndexOutOfBoundsException)
+ {
+ SequenceWithAnnotation::addElement(pos, c);
+ qualScores_->setScore(pos, q);
+ }
+
+ void addElement(int v)
+ throw (BadIntException)
+ {
+ SequenceWithAnnotation::addElement(v);
+ }
+
+ /**
+ * @brief Add a character to the end of the list with quality
+ *
+ * @param v The element to add to the sequence
+ * @param q The quality of this element
+ *
+ * @throw BadIntException if the value does not match the current Alphabet
+ */
+ void addElement(int v, int q)
+ throw (BadIntException)
+ {
+ SequenceWithAnnotation::addElement(v);
+ qualScores_->setScore(size() - 1, q);
+ }
+
+ void addElement(size_t pos, int v)
+ throw (BadIntException, IndexOutOfBoundsException)
+ {
+ SequenceWithAnnotation::addElement(pos, v);
+ }
+
+ /**
+ * @brief Add a character to a certain position in the list with quality
+ *
+ * @param pos The position where the element will be inserted
+ * @param v The element to add to the sequence
+ * @param q The quality of this element
+ *
+ * @throw BadIntException if the value does not match the current Alphabet
+ * @throw IndexOutOfBoundsException if pos is greater than the sequence
+ * size
+ */
+ void addElement(size_t pos, int v, int q)
+ throw (BadCharException, IndexOutOfBoundsException)
+ {
+ SequenceWithAnnotation::addElement(pos, v);
+ qualScores_->setScore(pos, q);
+ }
+
+ /** @} */
+
+ };
+
+} // end of namespace bpp.
+
+#endif // _SEQUENCEWITHQUALITY_H_
+
diff --git a/src/Bpp/Seq/SequenceWithQualityTools.cpp b/src/Bpp/Seq/SequenceWithQualityTools.cpp
new file mode 100644
index 0000000..8a104d3
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWithQualityTools.cpp
@@ -0,0 +1,194 @@
+//
+// File: SequenceWithQualityTools.h
+// Authors: Vincent Cahais
+// Sylvain Gaillard
+// Created on: 16 Apr 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (Apr 16, 2010)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SequenceWithQualityTools.h"
+
+using namespace bpp;
+using namespace std;
+
+DNA SequenceWithQualityTools::_DNA;
+RNA SequenceWithQualityTools::_RNA;
+NucleicAcidsReplication SequenceWithQualityTools::_DNARep(& _DNA, & _DNA);
+NucleicAcidsReplication SequenceWithQualityTools::_RNARep(& _RNA, & _RNA);
+NucleicAcidsReplication SequenceWithQualityTools::_transc(& _DNA, & _RNA);
+
+/******************************************************************************/
+
+SequenceWithQuality * SequenceWithQualityTools::subseq(const SequenceWithQuality & sequence, unsigned int begin, unsigned int end) throw (IndexOutOfBoundsException, Exception)
+{
+ // Checking interval
+ if (end >= sequence.size()) throw IndexOutOfBoundsException ("SequenceTools::subseq : Invalid upper bound", end, 0, sequence.size());
+ if (end < begin) throw Exception ("SequenceTools::subseq : Invalid interval");
+
+ // Copy sequence
+ vector<int> temp(sequence.getContent());
+ vector<int> qualtemp(sequence.getQualities());
+
+ // Truncate sequence
+ temp.erase(temp.begin() + end + 1, temp.end());
+ temp.erase(temp.begin(), temp.begin() + begin);
+ qualtemp.erase(qualtemp.begin() + end + 1, qualtemp.end());
+ qualtemp.erase(qualtemp.begin(), qualtemp.begin() + begin);
+
+ // New sequence creation
+ return new SequenceWithQuality(sequence.getName(), temp, qualtemp, sequence.getComments(), sequence.getAlphabet());
+
+}
+
+/******************************************************************************/
+
+SequenceWithQuality* SequenceWithQualityTools::concatenate(const SequenceWithQuality& seqwq1, const SequenceWithQuality& seqwq2) throw (AlphabetMismatchException, Exception)
+{
+ // Sequence's alphabets matching verification
+ if ((seqwq1.getAlphabet()->getAlphabetType()) != (seqwq2.getAlphabet()->getAlphabetType()))
+ throw AlphabetMismatchException("SequenceTools::concatenate : Sequence's alphabets don't match ", seqwq1.getAlphabet(), seqwq2.getAlphabet());
+
+ // Sequence's names matching verification
+ if (seqwq1.getName() != seqwq2.getName())
+ throw Exception ("SequenceTools::concatenate : Sequence's names don't match");
+
+ // Concatenate sequences and send result
+ vector<int> sequence = seqwq1.getContent();
+ vector<int> sequence2 = seqwq2.getContent();
+ vector<int> qualities = seqwq1.getQualities();
+ vector<int> qualities2 = seqwq2.getQualities();
+
+ sequence.insert(sequence.end(), sequence2.begin(), sequence2.end());
+ qualities.insert(qualities.end(), qualities2.begin(), qualities2.end());
+ return new SequenceWithQuality(seqwq1.getName(), sequence, qualities, seqwq1.getComments(), seqwq1.getAlphabet());
+}
+
+/******************************************************************************/
+
+SequenceWithQuality* SequenceWithQualityTools::complement(const SequenceWithQuality& sequence) throw (AlphabetException)
+{
+ // Alphabet type checking
+ NucleicAcidsReplication * NAR;
+ if (sequence.getAlphabet()->getAlphabetType() == "DNA alphabet")
+ {
+ NAR = &_DNARep;
+ }
+ else if(sequence.getAlphabet()->getAlphabetType() == "RNA alphabet")
+ {
+ NAR = &_RNARep;
+ }
+ else
+ {
+ throw AlphabetException ("SequenceTools::complement : Sequence must be nucleic.", sequence.getAlphabet());
+ }
+ Sequence * seq = NAR->translate(sequence);
+ SequenceWithQuality * seqwq = new SequenceWithQuality(sequence.getName(), seq->getContent(), sequence.getQualities(), sequence.getComments(), sequence.getAlphabet());
+ delete seq;
+ return seqwq;
+}
+
+/******************************************************************************/
+
+SequenceWithQuality* SequenceWithQualityTools::transcript(const SequenceWithQuality& sequence) throw (AlphabetException)
+{
+ // Alphabet type checking
+ if (sequence.getAlphabet()->getAlphabetType() != "DNA alphabet")
+ {
+ throw AlphabetException ("SequenceTools::transcript : Sequence must be DNA", sequence.getAlphabet());
+ }
+ Sequence * seq = _transc.translate(sequence);
+ SequenceWithQuality * seqwq = new SequenceWithQuality(sequence.getName(), seq->getContent(), sequence.getQualities(), sequence.getComments(), sequence.getAlphabet());
+ delete seq;
+ return seqwq;
+}
+
+/******************************************************************************/
+
+SequenceWithQuality* SequenceWithQualityTools::reverseTranscript(const SequenceWithQuality& sequence) throw (AlphabetException)
+{
+ // Alphabet type checking
+ if (sequence.getAlphabet()->getAlphabetType() != "RNA alphabet")
+ {
+ throw AlphabetException ("SequenceTools::reverseTranscript : Sequence must be RNA", sequence.getAlphabet());
+ }
+
+ Sequence * seq = _transc.reverse(sequence);
+ SequenceWithQuality * seqwq = new SequenceWithQuality(sequence.getName(), seq->getContent(), sequence.getQualities(), sequence.getComments(), sequence.getAlphabet());
+ delete seq;
+ return seqwq;
+}
+
+/******************************************************************************/
+
+SequenceWithQuality* SequenceWithQualityTools::invert(const SequenceWithQuality& sequence)
+{
+ vector<int> iContent(sequence.getContent().rbegin(),sequence.getContent().rend());
+ vector<int> iQualities(sequence.getQualities().rbegin(),sequence.getQualities().rend());
+ SequenceWithQuality* iSeq = sequence.clone();
+ iSeq->setContent(iContent);
+ iSeq->setQualities(iQualities);
+
+ return iSeq;
+}
+
+/******************************************************************************/
+
+SequenceWithQuality* SequenceWithQualityTools::removeGaps(const SequenceWithQuality& seq)
+{
+ vector<int> content;
+ vector<int> qualities;
+ const Alphabet * alpha = seq.getAlphabet();
+ for(unsigned int i = 0; i < seq.size(); i++)
+ {
+ if(! alpha->isGap(seq[i]))
+ {
+ content.push_back(seq[i]);
+ qualities.push_back(seq.getQualities()[i]);
+ }
+ }
+ SequenceWithQuality * newSeq = dynamic_cast<SequenceWithQuality *>(seq.clone());
+ newSeq->setContent(content);
+ newSeq->setQualities(qualities);
+ return newSeq;
+}
+
+/******************************************************************************/
+
+SequenceWithQuality& SequenceWithQualityTools::trimLeft(SequenceWithQuality& seq) {
+ bool badqual = false;
+ while (badqual) {
+ }
+ return seq;
+}
diff --git a/src/Bpp/Seq/SequenceWithQualityTools.h b/src/Bpp/Seq/SequenceWithQualityTools.h
new file mode 100644
index 0000000..41035d0
--- /dev/null
+++ b/src/Bpp/Seq/SequenceWithQualityTools.h
@@ -0,0 +1,175 @@
+//
+// File: SequenceWithQualityTools.h
+// Authors: Vincent Cahais
+// Sylvain Gaillard
+// Created on: 16 Apr 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (Apr 16, 2010)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef SEQUENCEWITHQUALITYTOOLS_H_
+#define SEQUENCEWITHQUALITYTOOLS_H_
+
+#include "SequenceTools.h"
+#include "SequenceWithQuality.h"
+
+namespace bpp {
+ /**
+ * @brief The SequenceWithQualityTools static class
+ *
+ * Implement methods to manipulate SequencesWithQuality
+ *
+ * @todo
+ * - does complement, transcript and reverseTranscript have a meaning on
+ * SequenceWithQuality as the quality is not transferable
+ *
+ * @author Cahais Vincent
+ */
+
+ class SequenceWithQualityTools {
+ private:
+ static DNA _DNA;
+ static RNA _RNA;
+ static NucleicAcidsReplication _DNARep;
+ static NucleicAcidsReplication _RNARep;
+ static NucleicAcidsReplication _transc;
+
+ public:
+
+ /**
+ * @brief Get a sub-sequence.
+ *
+ * @param sequence The sequence to trunc.
+ * @param begin The first position of the subsequence.
+ * @param end The last position of the subsequence.
+ * @return A new SequenceWithQuality object with the given subsequence.
+ * @throw IndexOutOfBoundsException, Exception In case of bad indices.
+ */
+ static SequenceWithQuality* subseq(
+ const SequenceWithQuality& sequence,
+ unsigned int begin,
+ unsigned int end
+ ) throw (IndexOutOfBoundsException, Exception) ;
+
+ /**
+ * @brief Concatenate two sequences.
+ *
+ * Sequences must have the same name and alphabets.
+ * Only first sequence's commentaries are kept.
+ *
+ * @param seqwq1 The first SequenceWithQuality.
+ * @param seqwq2 The second SequenceWithQuality.
+ * @return A new SequenceWithQuality object with the concatenation of the
+ * two sequences.
+ * @throw AlphabetMismatchException If the two alphabets do not match.
+ * @throw Exception If the sequence names do not match.
+ */
+ static SequenceWithQuality* concatenate(
+ const SequenceWithQuality& seqwq1,
+ const SequenceWithQuality& seqwq2
+ ) throw (AlphabetMismatchException, Exception) ;
+
+ /**
+ * @brief Get the complementary sequence of a nucleotide sequence.
+ *
+ * @see DNAReplication
+ * @return sequence A new SequenceWithQuality object with the
+ * complementary sequence.
+ * @param sequence The sequence to complement.
+ * @throw AlphabetException If the sequence is not a nucleotide sequence.
+ */
+ static SequenceWithQuality* complement(
+ const SequenceWithQuality& sequence
+ ) throw (AlphabetException);
+
+ /**
+ * @brief Get the transcription sequence of a DNA sequence.
+ *
+ * @see DNAReplication
+ * @return sequence A new SequenceWithQuality object with the
+ * transcription sequence.
+ * @param sequence The sequence to transcript.
+ * @throw AlphabetException If the sequence is not a DNA sequence.
+ */
+ static SequenceWithQuality* transcript(
+ const SequenceWithQuality& sequence
+ ) throw (AlphabetException);
+
+ /**
+ * @brief Get the reverse-transcription sequence of a RNA sequence.
+ *
+ * @see DNAReplication
+ * @return sequence A new SequenceWithQuality object with the reverse-
+ * transcription sequence.
+ * @param sequence The SequenceWithQuality to reverse-transcript.
+ * @throw AlphabetException If the sequence is not a RNA sequence.
+ */
+
+ static SequenceWithQuality* reverseTranscript(
+ const SequenceWithQuality& sequence
+ ) throw (AlphabetException);
+ /**
+ * @brief Inverse a sequence from 5'->3' to 3'->5' and vice-versa.
+ *
+ * ABCDEF becomes FEDCBA, and the sense attribute is changed (may be
+ * inhibited).
+ *
+ * @return A new SequenceWithQuality object containing the inverted
+ * sequence.
+ * @param sequence The SequenceWithQuality to inverse.
+ */
+ static SequenceWithQuality* invert(
+ const SequenceWithQuality& sequence
+ );
+
+ /**
+ * @brief Remove gaps from a SequenceWithQuality.
+ *
+ * @param seq The sequence to analyse.
+ * @return A new SequenceWithQuality object without gaps.
+ */
+ static SequenceWithQuality* removeGaps(const SequenceWithQuality& seq);
+
+ /**
+ * @brief Trim the left part of the sequence according to quality
+ *
+ * @param seq The sequence to analyse.
+ * @return The modified sequence.
+ */
+ static SequenceWithQuality& trimLeft(SequenceWithQuality& seq);
+
+ };
+}
+
+#endif /* SEQUENCEWITHQUALITYTOOLS_H_ */
diff --git a/src/Bpp/Seq/Site.cpp b/src/Bpp/Seq/Site.cpp
new file mode 100644
index 0000000..c1f8bf4
--- /dev/null
+++ b/src/Bpp/Seq/Site.cpp
@@ -0,0 +1,101 @@
+//
+// File Site.cpp
+// Author: Julien Dutheil
+// Guillaume Deuchst
+// Created on: Tuesday August 7 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "Site.h"
+
+#include "StringSequenceTools.h"
+
+using namespace bpp;
+
+// From the STL:
+#include <iostream>
+
+using namespace std;
+
+/****************************************************************************************/
+
+Site::Site(const Alphabet* alpha) : BasicSymbolList(alpha), position_(0) {}
+
+Site::Site(const Alphabet* alpha, int position) : BasicSymbolList(alpha), position_(position) {}
+
+Site::Site(const vector<string>& site, const Alphabet* alpha) throw (BadCharException) : BasicSymbolList(site, alpha), position_(0) {}
+
+Site::Site(const vector<string>& site, const Alphabet* alpha, int position) throw (BadCharException) : BasicSymbolList(site, alpha), position_(position) {}
+
+Site::Site(const vector<int>& site, const Alphabet* alpha) throw (BadIntException) : BasicSymbolList(site, alpha), position_(0) {}
+
+Site::Site(const vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException) : BasicSymbolList(site, alpha), position_(position) {}
+
+/****************************************************************************************/
+
+Site::Site(const Site& site): BasicSymbolList(site), position_(site.getPosition()) {}
+
+Site& Site::operator=(const Site& s)
+{
+ SymbolList::operator=(s);
+ content_ = s.getContent();
+ position_ = s.getPosition();
+ return *this;
+}
+
+/****************************************************************************************/
+
+bool operator==(const Site& site1, const Site& site2)
+{
+ // Verify that site's size, position and content are equals
+ if(site1.size() != site2.size()) return false;
+ if(site1.getPosition() != site2.getPosition()) return false;
+ else {
+ for(unsigned int i = 0; i < site1.size(); i++) {
+ if(site1[i] != site2[i]) return false;
+ }
+ return true;
+ }
+}
+
+/****************************************************************************************/
+
+bool operator<(const Site& site1, const Site& site2)
+{
+ return site1.getPosition() < site2.getPosition();
+}
+
+/****************************************************************************************/
+
diff --git a/src/Bpp/Seq/Site.h b/src/Bpp/Seq/Site.h
new file mode 100644
index 0000000..397c57f
--- /dev/null
+++ b/src/Bpp/Seq/Site.h
@@ -0,0 +1,179 @@
+//
+// File Site.h
+// Created by: Guillaume Deuchst
+// Julien Dutheil
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SITE_H_
+#define _SITE_H_
+
+#include "SymbolList.h"
+#include "SiteExceptions.h"
+
+namespace bpp
+{
+
+/**
+ * @brief The Site class.
+ *
+ * Define specific attributes and methods for sites manipulation.
+ * It is very similar to the Sequence object (a site is a vertical sequence!),
+ * and characters at each position are coded as integers.
+ * Sites have a 'position' attribute.
+ * This attribute stands for an indice in a an alignment, and may be used as a unique identifier,
+ * in the same manner that names identify sequence objects.
+ * But for now, we do not allow to construct a Site directly from a string.
+ * This should not be a constraint, since you never read sites directly from a file.
+ */
+class Site:
+ public BasicSymbolList
+{
+ private:
+ /**
+ * @brief The position associated to this site.
+ */
+ int position_;
+
+ public:
+
+ /**
+ * @brief Build a new void Site object with the specified alphabet.
+ *
+ * @param alpha The alphabet to use.
+ */
+ Site(const Alphabet* alpha);
+
+ /**
+ * @brief Build a new void Site object with the specified alphabet and position.
+ *
+ * @param alpha The alphabet to use.
+ * @param position The position attribute for this site.
+ */
+ Site(const Alphabet* alpha, int position);
+
+ /**
+ * @brief Build a new Site object with the specified alphabet.
+ * The content of the site is initialized from a vector of characters.
+ *
+ * @param site The content of the site.
+ * @param alpha The alphabet to use.
+ * @throw BadCharException If the content does not match the specified alphabet.
+ */
+ Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief Build a new Site object with the specified alphabet and position.
+ * The content of the site is initialized from a vector of characters.
+ *
+ * @param site The content of the site.
+ * @param alpha The alphabet to use.
+ * @param position The position attribute for this site.
+ * @throw BadCharException If the content does not match the specified alphabet.
+ */
+ Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
+
+ /**
+ * @brief Build a new Site object with the specified alphabet.
+ * The content of the site is initialized from a vector of integers.
+ *
+ * @param site The content of the site.
+ * @param alpha The alphabet to use.
+ * @throw BadIntException If the content does not match the specified alphabet.
+ */
+ Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
+
+ /**
+ * @brief Build a new Site object with the specified alphabet and position.
+ * The content of the site is initialized from a vector of integers.
+ *
+ * @param site The content of the site.
+ * @param alpha The alphabet to use.
+ * @param position The position attribute for this site.
+ * @throw BadIntException If the content does not match the specified alphabet.
+ */
+ Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
+
+ /**
+ * @brief The copy constructor.
+ */
+ Site(const Site& site);
+
+ /**
+ * @brief The assignment operator.
+ */
+ Site& operator=(const Site& s);
+
+ virtual ~Site() {}
+
+ public:
+
+ /**
+ * @name The Clonable interface
+ *
+ * @{
+ */
+ Site* clone() const { return new Site(*this); }
+ /** @} */
+
+ /**
+ * @name Setting/getting the position of the site.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the position of this site.
+ *
+ * @return This site position.
+ */
+ virtual int getPosition() const { return position_; }
+
+ /**
+ * @brief Set the position of this site.
+ *
+ * @param position The new position of the site.
+ */
+ virtual void setPosition(int position) { position_ = position; }
+};
+
+// Sites comparison operators overload
+bool operator == (const Site& site1, const Site& site2);
+bool operator < (const Site& site1, const Site& site2);
+
+} //end of namespace bpp.
+
+#endif //_SITE_H_
+
diff --git a/src/Bpp/Seq/SiteExceptions.cpp b/src/Bpp/Seq/SiteExceptions.cpp
new file mode 100644
index 0000000..4acf100
--- /dev/null
+++ b/src/Bpp/Seq/SiteExceptions.cpp
@@ -0,0 +1,52 @@
+// File: SiteExceptions.cpp
+// Author: Julien Dutheil
+// Created On: dim mar 7 2004
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SiteExceptions.h"
+#include "Site.h"
+#include <Bpp/Text/TextTools.h>
+
+using namespace bpp;
+using namespace std;
+
+/***************************************************************************/
+
+SiteException::SiteException(const std::string& text, const Site* s) :
+ Exception(text + (s != 0 ? "(" + TextTools::toString(s->getPosition()) + ")" : string(""))),
+ site_(s) {};
+
+/***************************************************************************/
+
diff --git a/src/Bpp/Seq/SiteExceptions.h b/src/Bpp/Seq/SiteExceptions.h
new file mode 100644
index 0000000..8a35e22
--- /dev/null
+++ b/src/Bpp/Seq/SiteExceptions.h
@@ -0,0 +1,124 @@
+//
+// File: SiteExceptions.h
+// Author : Julien Dutheil
+// Created on: dim mar 7 2004
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SITEEXCEPTIONS_H_
+#define _SITEEXCEPTIONS_H_
+
+#include <Bpp/Exceptions.h>
+
+namespace bpp
+{
+
+class Site;
+
+/**
+ * @brief The site exception base class.
+ *
+ * @see Exception
+ */
+class SiteException:
+ public Exception
+{
+ private:
+
+ /**
+ * @brief A pointer toward a site object.
+ */
+ const Site* site_;
+
+ public: // Class constructor
+
+ /**
+ * @brief Build a new SiteException object.
+ *
+ * @param text A message to be passed to the exception hierarchy.
+ * @param s A const pointer toward the site that threw the exception.
+ */
+ SiteException(const std::string& text, const Site* s = 0);
+
+ SiteException(const SiteException& se): Exception(se), site_(se.site_) {}
+
+ SiteException& operator=(const SiteException& se)
+ {
+ Exception::operator=(se);
+ site_ = se.site_;
+ return *this;
+ }
+
+ // Class destructor
+ virtual ~SiteException() throw() {}
+
+ public:
+
+ /**
+ * @brief Get the site that threw the exception.
+ *
+ * @return A const pointer toward the site.
+ */
+ virtual const Site* getSite() const { return site_; };
+};
+
+/**
+ * @brief Exception sent when a empty site is found.
+ */
+class EmptySiteException:
+ public SiteException
+{
+ public:
+ EmptySiteException(const std::string& text, const Site* s = 0): SiteException(text, s) {}
+
+ virtual ~EmptySiteException() throw() {}
+};
+
+/**
+ * @brief Exception sent when a site containing gap is found.
+ */
+class SiteWithGapException:
+ public SiteException
+{
+ public:
+ SiteWithGapException(const std::string& text, const Site* s = 0): SiteException(text, s) {}
+
+ virtual ~SiteWithGapException() throw() {}
+};
+
+} //end of namespace bpp.
+
+#endif // _SITEEXCEPTIONS_H_
+
diff --git a/src/Bpp/Seq/SiteIterator.h b/src/Bpp/Seq/SiteIterator.h
new file mode 100644
index 0000000..efb427a
--- /dev/null
+++ b/src/Bpp/Seq/SiteIterator.h
@@ -0,0 +1,80 @@
+//
+// File: SiteIterator.h
+// Created by: Julien Dutheil
+// Created on: Sun Oct 19 12:47:16 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SITEITERATOR_H_
+#define _SITEITERATOR_H_
+
+#include "Site.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Generic site iterator interface, allowing to loop over sites.
+ */
+class SiteIterator
+{
+ public:
+ SiteIterator() {}
+ virtual ~SiteIterator() {}
+
+ public:
+ virtual Site* nextSite() = 0;
+ virtual bool hasMoreSites() const = 0;
+};
+
+/**
+ * @brief Generic const site iterator interface, allowing to loop over const sites.
+ */
+class ConstSiteIterator
+{
+ public:
+ ConstSiteIterator() {}
+ virtual ~ConstSiteIterator() {}
+
+ public:
+ virtual const Site* nextSite() = 0;
+ virtual bool hasMoreSites() const = 0;
+};
+
+
+} //end of namespace bpp.
+
+#endif //_SITEITERATOR_H_
+
diff --git a/src/Bpp/Seq/SiteTools.cpp b/src/Bpp/Seq/SiteTools.cpp
new file mode 100644
index 0000000..f731b41
--- /dev/null
+++ b/src/Bpp/Seq/SiteTools.cpp
@@ -0,0 +1,426 @@
+//
+// File SiteTools.cpp
+// Author : Julien Dutheil
+// Guillaume Deuchst
+// Created on: Friday August 8 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "SiteTools.h"
+#include "Alphabet/CodonAlphabet.h"
+#include <Bpp/Utils/MapTools.h>
+#include <Bpp/Numeric/NumTools.h>
+#include <Bpp/Numeric/VectorTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <cmath>
+
+using namespace std;
+
+/******************************************************************************/
+
+bool SiteTools::hasGap(const Site& site)
+{
+ // Main loop : for all characters in site
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (site.getAlphabet()->isGap(site[i]))
+ return true;
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+bool SiteTools::isGapOnly(const Site& site)
+{
+ // Main loop : for all characters in site
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (!site.getAlphabet()->isGap(site[i]))
+ return false;
+ }
+ return true;
+}
+
+/******************************************************************************/
+
+bool SiteTools::isGapOrUnresolvedOnly(const Site& site)
+{
+ // Main loop : for all characters in site
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (!site.getAlphabet()->isGap(site[i]) && !site.getAlphabet()->isUnresolved(site[i]))
+ return false;
+ }
+ return true;
+}
+
+/******************************************************************************/
+
+bool SiteTools::hasUnknown(const Site& site)
+{
+ // Main loop : for all characters in site
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (site[i] == site.getAlphabet()->getUnknownCharacterCode())
+ return true;
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+bool SiteTools::hasStopCodon(const Site& site)
+{
+ // Main loop : for all characters in site
+ const CodonAlphabet* pca = dynamic_cast<const CodonAlphabet*>(site.getAlphabet());
+ if (pca == 0)
+ return false;
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (pca->isStop(site[i]))
+ return true;
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+bool SiteTools::isComplete(const Site& site)
+{
+ // Main loop : for all characters in site
+ for (size_t i = 0; i < site.size(); i++)
+ {
+ if (site.getAlphabet()->isGap(site[i]) || site.getAlphabet()->isUnresolved(site[i]))
+ return false;
+ }
+ return true;
+}
+
+/******************************************************************************/
+
+bool SiteTools::areSitesIdentical(const Site& site1, const Site& site2)
+{
+ // Site's size and content checking
+ if (site1.getAlphabet()->getAlphabetType() != site2.getAlphabet()->getAlphabetType())
+ return false;
+ if (site1.size() != site2.size())
+ return false;
+ else
+ {
+ for (size_t i = 0; i < site1.size(); i++)
+ {
+ if (site1[i] != site2[i])
+ return false;
+ }
+ return true;
+ }
+}
+
+/******************************************************************************/
+
+bool SiteTools::isConstant(const Site& site, bool ignoreUnknown, bool unresolvedRaisesException) throw (EmptySiteException)
+{
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("SiteTools::isConstant: Incorrect specified site, size must be > 0", &site);
+
+ // For all site's characters
+ int gap = site.getAlphabet()->getGapCharacterCode();
+ if (ignoreUnknown)
+ {
+ int s = site[0];
+ int unknown = site.getAlphabet()->getUnknownCharacterCode();
+ size_t i = 0;
+ while (i < site.size() && (s == gap || s == unknown))
+ {
+ s = site[i];
+ i++;
+ }
+ if (s == unknown || s == gap)
+ {
+ if (unresolvedRaisesException)
+ throw EmptySiteException("SiteTools::isConstant: Site is only made of gaps or generic characters.");
+ else
+ return false;
+ }
+ while (i < site.size())
+ {
+ if (site[i] != s && site[i] != gap && site[i] != unknown)
+ return false;
+ i++;
+ }
+ }
+ else
+ {
+ int s = site[0];
+ size_t i = 0;
+ while (i < site.size() && s == gap)
+ {
+ s = site[i];
+ i++;
+ }
+ if (s == gap)
+ {
+ if (unresolvedRaisesException)
+ throw EmptySiteException("SiteTools::isConstant: Site is only made of gaps.");
+ else
+ return false;
+ }
+ while (i < site.size())
+ {
+ if (site[i] != s && site[i] != gap)
+ return false;
+ i++;
+ }
+ }
+
+ return true;
+}
+
+/******************************************************************************/
+
+double SiteTools::variabilityShannon(const Site& site, bool resolveUnknown) throw (EmptySiteException)
+{
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("SiteTools::variabilityShannon: Incorrect specified site, size must be > 0", &site);
+ map<int, double> p;
+ getFrequencies(site, p, resolveUnknown);
+ // We need to correct frequencies for gaps:
+ double s = 0.;
+ for (int i = 0; i < static_cast<int>(site.getAlphabet()->getSize()); i++)
+ {
+ double f = p[i];
+ if (f > 0)
+ s += f * log(f);
+ }
+ return -s;
+}
+
+/******************************************************************************/
+
+double SiteTools::mutualInformation(const Site& site1, const Site& site2, bool resolveUnknown) throw (DimensionException, EmptySiteException)
+{
+ // Empty site checking
+ if (site1.size() == 0)
+ throw EmptySiteException("SiteTools::mutualInformation: Incorrect specified site, size must be > 0", &site1);
+ if (site2.size() == 0)
+ throw EmptySiteException("SiteTools::mutualInformation: Incorrect specified site, size must be > 0", &site2);
+ if (site1.size() != site2.size())
+ throw DimensionException("SiteTools::mutualInformation: sites must have the same size!", site1.size(), site2.size());
+ vector<double> p1(site1.getAlphabet()->getSize());
+ vector<double> p2(site2.getAlphabet()->getSize());
+ map<int, map<int, double> > p12;
+ getCounts(site1, site2, p12, resolveUnknown);
+ double mi = 0, tot = 0, pxy;
+ // We need to correct frequencies for gaps:
+ for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
+ {
+ for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
+ {
+ pxy = p12[static_cast<int>(i)][static_cast<int>(j)];
+ tot += pxy;
+ p1[i] += pxy;
+ p2[j] += pxy;
+ }
+ }
+ for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
+ {
+ p1[i] /= tot;
+ }
+ for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
+ {
+ p2[j] /= tot;
+ }
+ for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
+ {
+ for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
+ {
+ pxy = p12[static_cast<int>(i)][static_cast<int>(j)] / tot;
+ if (pxy > 0)
+ mi += pxy * log(pxy / (p1[i] * p2[j]));
+ }
+ }
+ return mi;
+}
+
+/******************************************************************************/
+
+double SiteTools::jointEntropy(const Site& site1, const Site& site2, bool resolveUnknown) throw (DimensionException, EmptySiteException)
+{
+ // Empty site checking
+ if (site1.size() == 0)
+ throw EmptySiteException("SiteTools::jointEntropy: Incorrect specified site, size must be > 0", &site1);
+ if (site2.size() == 0)
+ throw EmptySiteException("SiteTools::jointEntropy: Incorrect specified site, size must be > 0", &site2);
+ if (site1.size() != site2.size())
+ throw DimensionException("SiteTools::jointEntropy: sites must have the same size!", site1.size(), site2.size());
+ map<int, map<int, double> > p12;
+ getCounts(site1, site2, p12, resolveUnknown);
+ double tot = 0, pxy, h = 0;
+ // We need to correct frequencies for gaps:
+ for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
+ {
+ for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
+ {
+ pxy = p12[static_cast<int>(i)][static_cast<int>(j)];
+ tot += pxy;
+ }
+ }
+ for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
+ {
+ for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
+ {
+ pxy = p12[static_cast<int>(i)][static_cast<int>(j)] / tot;
+ if (pxy > 0)
+ h += pxy * log(pxy);
+ }
+ }
+ return -h;
+}
+
+/******************************************************************************/
+
+double SiteTools::variabilityFactorial(const Site& site) throw (EmptySiteException)
+{
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("SiteTools::variabilityFactorial: Incorrect specified site, size must be > 0", &site);
+ map<int, size_t> p;
+ getCounts(site, p);
+ vector<size_t> c = MapTools::getValues(p);
+ size_t s = VectorTools::sum(c);
+ long double l = static_cast<long double>(NumTools::fact(s)) / static_cast<long double>(VectorTools::sum(VectorTools::fact(c)));
+ return (static_cast<double>(std::log(l)));
+}
+
+/******************************************************************************/
+
+double SiteTools::heterozygosity(const Site& site) throw (EmptySiteException)
+{
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("SiteTools::heterozygosity: Incorrect specified site, size must be > 0", &site);
+ map<int, double> p;
+ getFrequencies(site, p);
+ vector<double> c = MapTools::getValues(p);
+ double n = VectorTools::norm<double, double>(MapTools::getValues(p));
+ return 1. - n * n;
+}
+
+/******************************************************************************/
+
+size_t SiteTools::getNumberOfDistinctCharacters(const Site& site) throw (EmptySiteException)
+{
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("SiteTools::getNumberOfDistinctCharacters(): Incorrect specified site, size must be > 0", &site);
+ // For all site's characters
+ if (SiteTools::isConstant(site))
+ return 1;
+ map<int, size_t> counts;
+ SymbolListTools::getCounts(site, counts);
+ int s = 0;
+ for (map<int, size_t>::iterator it = counts.begin(); it != counts.end(); it++)
+ {
+ if (it->second != 0)
+ s++;
+ }
+ return s;
+}
+
+/******************************************************************************/
+
+bool SiteTools::hasSingleton(const Site& site) throw (EmptySiteException)
+{
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("SiteTools::hasSingleton: Incorrect specified site, size must be > 0", &site);
+ // For all site's characters
+ if (SiteTools::isConstant(site))
+ return false;
+ map<int, size_t> counts;
+ getCounts(site, counts);
+ for (map<int, size_t>::iterator it = counts.begin(); it != counts.end(); it++)
+ {
+ if (it->second == 1)
+ return true;
+ }
+ return false;
+}
+
+/******************************************************************************/
+
+bool SiteTools::isParsimonyInformativeSite(const Site& site) throw (EmptySiteException)
+{
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("SiteTools::isParsimonyInformativeSite: Incorrect specified site, size must be > 0", &site);
+ // For all site's characters
+ if (SiteTools::isConstant(site, false, false))
+ return false;
+ map<int, size_t> counts;
+ SymbolListTools::getCounts(site, counts);
+ size_t npars = 0;
+ for (map<int, size_t>::iterator it = counts.begin(); it != counts.end(); it++)
+ {
+ if (it->second > 1)
+ npars++;
+ }
+ if (npars > 1)
+ return true;
+ return false;
+}
+
+/******************************************************************************/
+
+bool SiteTools::isTriplet(const Site& site) throw (EmptySiteException)
+{
+ // Empty site checking
+ if (site.size() == 0)
+ throw EmptySiteException("SiteTools::isTriplet: Incorrect specified site, size must be > 0", &site);
+ // For all site's characters
+ if (SiteTools::getNumberOfDistinctCharacters(site) >= 3)
+ return true;
+ else
+ return false;
+}
+
+/******************************************************************************/
+
diff --git a/src/Bpp/Seq/SiteTools.h b/src/Bpp/Seq/SiteTools.h
new file mode 100644
index 0000000..b8fac4f
--- /dev/null
+++ b/src/Bpp/Seq/SiteTools.h
@@ -0,0 +1,259 @@
+//
+// File SiteTools.h
+// Author: Julien Dutheil
+// Guillaume Deuchst
+// Last modification : Friday August 8 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#ifndef _SITETOOLS_H_
+#define _SITETOOLS_H_
+
+#include "SymbolListTools.h"
+#include "Site.h"
+#include <Bpp/Exceptions.h>
+
+// From the STL:
+#include <map>
+
+namespace bpp
+{
+/**
+ * @brief Utilitary methods dealing with sites.
+ */
+
+class SiteTools :
+ public SymbolListTools
+{
+public:
+ SiteTools() {}
+ virtual ~SiteTools() {}
+
+public:
+ /**
+ * @param site A site.
+ * @return True if the site contains one or several gap(s).
+ */
+ static bool hasGap(const Site& site);
+
+ /**
+ * @param site A site.
+ * @return True if the site contains only gaps.
+ */
+ static bool isGapOnly(const Site& site);
+
+ /**
+ * @param site A site.
+ * @return True if the site contains only gaps.
+ */
+ static bool isGapOrUnresolvedOnly(const Site& site);
+
+ /**
+ * @param site A site.
+ * @return True if the site contains one or several unknwn characters.
+ */
+ static bool hasUnknown(const Site& site);
+
+ /**
+ * @param site A site.
+ * @return True if the site contains a Stop Codon, when the alphabet is a CodonAlphabet.
+ */
+ static bool hasStopCodon(const Site& site);
+ /**
+ * @param site A site.
+ * @return True if the site contains no gap and no unknown characters.
+ */
+ static bool isComplete(const Site& site);
+
+ /**
+ * @brief Tell if a site is constant, that is displaying the same state in all sequences that do not present a gap.
+ *
+ * @param site A site.
+ * @param ignoreUnknown If true, positions with unknown positions will be ignored.
+ * Otherwise, a site with one single state + any uncertain state will not be considered as constant.
+ * @param unresolvedRaisesException In case of ambiguous case (gap only site for instance), throw an exception. Otherwise returns false.
+ * @return True if the site is made of only one state.
+ * @throw EmptySiteException If the site has size 0 or if the site cannot be resolved (for instance is made of gaps only) and unresolvedRaisesException is set to true.
+ */
+ static bool isConstant(const Site& site, bool ignoreUnknown = false, bool unresolvedRaisesException = true) throw (EmptySiteException);
+
+ /**
+ * @param site1 The first site.
+ * @param site2 The second site.
+ * @return True if the two states have the same content (and, of course, alphabet).
+ */
+ static bool areSitesIdentical(const Site& site1, const Site& site2);
+
+ /**
+ * @brief Compute the Shannon entropy index of a site.
+ *
+ * \f[
+ * I = - \sum_x f_x\cdot \ln(f_x)
+ * \f]
+ * where \f$f_x\f$ is the frequency of state \f$x\f$.
+ *
+ * @author J. Dutheil
+ * @param site A site.
+ * @param resolveUnknowns Tell is unknown characters must be resolved.
+ * @return The Shannon entropy index of this site.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static double variabilityShannon(const Site& site, bool resolveUnknowns) throw (EmptySiteException);
+
+ /**
+ * @brief Compute the factorial diversity index of a site.
+ *
+ * \f[
+ * F = \frac{log\left(\left(\sum_x p_x\right)!\right)}{\sum_x \log(p_x)!}
+ * \f]
+ * where \f$p_x\f$ is the number of times state \f$x\f$ is observed in the site.
+ *
+ * @author J. Dutheil
+ * @param site A site.
+ * @return The factorial diversity index of this site.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static double variabilityFactorial(const Site& site) throw (EmptySiteException);
+
+ /**
+ * @brief Compute the mutual information between two sites.
+ *
+ * \f[
+ * MI = \sum_x \sum_y p_{x,y}\ln\left(\frac{p_{x,y}}{p_x \cdot p_y}\right)
+ * \f]
+ * where \f$p_x\f$ and \f$p_y\f$ are the frequencies of states \f$x\f$ and \f$y\f$, and
+ * \f$p_{x,y}\f$ is the frequency of the pair \f$(x,y)\f$.
+ *
+ * @author J. Dutheil
+ * @param site1 First site
+ * @param site2 Second site
+ * @param resolveUnknowns Tell is unknown characters must be resolved.
+ * @return The mutual information for the pair of sites.
+ * @throw DimensionException If the sites do not have the same length.
+ * @throw EmptySiteException If the sites have size 0.
+ */
+ static double mutualInformation(const Site& site1, const Site& site2, bool resolveUnknowns) throw (DimensionException,EmptySiteException);
+
+ /**
+ * @brief Compute the entropy of a site. This is an alias of method variabilityShannon.
+ *
+ * \f[
+ * I = - \sum_x f_x\cdot \ln(f_x)
+ * \f]
+ * where \f$f_x\f$ is the frequency of state \f$x\f$.
+ *
+ * @author J. Dutheil
+ * @param site A site.
+ * @param resolveUnknowns Tell is unknown characters must be resolved.
+ * @return The Shannon entropy index of this site.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static double entropy(const Site& site, bool resolveUnknowns) throw (EmptySiteException) {
+ return variabilityShannon(site, resolveUnknowns);
+ }
+
+
+ /**
+ * @brief Compute the joint entropy between two sites.
+ *
+ * \f[
+ * H_{i,j} = - \sum_x \sum_y p_{x,y}\ln\left(p_{x,y}\right)
+ * \f]
+ * where \f$p_{x,y}\f$ is the frequency of the pair \f$(x,y)\f$.
+ *
+ * @author J. Dutheil
+ * @param site1 First site
+ * @param site2 Second site
+ * @param resolveUnknowns Tell is unknown characters must be resolved.
+ * @return The mutual information for the pair of sites.
+ * @throw DimensionException If the sites do not have the same length.
+ * @throw EmptySiteException If the sites have size 0.
+ */
+ static double jointEntropy(const Site& site1, const Site& site2, bool resolveUnknowns) throw (DimensionException,EmptySiteException);
+
+ /**
+ * @brief Compute the heterozygosity index of a site.
+ *
+ * \f[
+ * H = 1 - \sum_x f_x^2
+ * \f]
+ * where \f$f_x\f$ is the frequency of state \f$x\f$.
+ *
+ * @param site A site.
+ * @return The heterozygosity index of this site.
+ * @throw EmptySiteException If the site has size 0.
+ */
+ static double heterozygosity(const Site& site) throw (EmptySiteException);
+
+ /**
+ * @brief Give the number of distinct characters at a site.
+ *
+ * @param site a Site
+ * @return The number of distinct characters in the given site.
+ */
+ static size_t getNumberOfDistinctCharacters(const Site& site) throw (EmptySiteException);
+
+ /**
+ * @brief Tell if a site has singletons
+ *
+ *
+ * @param site a Site.
+ * @return True if the site has singletons.
+ */
+ static bool hasSingleton(const Site& site) throw (EmptySiteException);
+
+ /**
+ * @brief Tell if a site is a parsimony informative site.
+ *
+ * At least two distinct characters must be present.
+ *
+ * @param site a Site.
+ * @return True if the site is parsimony informative.
+ */
+ static bool isParsimonyInformativeSite(const Site& site) throw (EmptySiteException);
+
+
+ /**
+ * @brief Tell if a site has more than 2 distinct characters
+ *
+ * @param site a Site.
+ * @return True if the site has more than 2 distinct characters
+ */
+ static bool isTriplet(const Site& site) throw (EmptySiteException);
+};
+} // end of namespace bpp.
+
+#endif // _SITETOOLS_H_
+
diff --git a/src/Bpp/Seq/StringSequenceTools.cpp b/src/Bpp/Seq/StringSequenceTools.cpp
new file mode 100644
index 0000000..36cbf47
--- /dev/null
+++ b/src/Bpp/Seq/StringSequenceTools.cpp
@@ -0,0 +1,344 @@
+//
+// File: StringSequenceTools.cpp
+// Created by: Julien Dutheil
+// Created on: Sun Nov 30 11:29:07 2003
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include "StringSequenceTools.h"
+
+#include "Alphabet/AlphabetTools.h"
+#include "Alphabet/DNA.h"
+#include "Alphabet/RNA.h"
+#include "Alphabet/ProteicAlphabet.h"
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Numeric/Random/RandomTools.h>
+
+using namespace bpp;
+
+// From the STL:
+#include <map>
+#include <ctype.h>
+#include <algorithm>
+#include <iostream>
+
+using namespace std;
+
+/****************************************************************************************/
+
+string StringSequenceTools::subseq(const string& sequence, int begin, int end) throw (Exception)
+{
+ // Checking interval
+ if (end < begin)
+ throw Exception ("StringSequenceTools::subseq: Invalid interval");
+
+ // Copy sequence
+ string temp(sequence);
+
+ // Truncate sequence
+ temp.erase(temp.begin() + end + 1, temp.end());
+ temp.erase(temp.begin(), temp.begin() + begin);
+
+ // Send result
+ return temp;
+}
+
+/****************************************************************************************/
+
+string StringSequenceTools::setToSizeR(const string& sequence, int size)
+{
+ return TextTools::resizeRight(sequence, size, '-');
+}
+
+string StringSequenceTools::setToSizeL(const string& sequence, int size)
+{
+ return TextTools::resizeLeft(sequence, size, '-');
+}
+
+/****************************************************************************************/
+
+string StringSequenceTools::deleteChar(const string& sequence, char chars)
+{
+ // Copy sequence
+ string result(sequence);
+
+ // Search and delete specified char
+ for (unsigned int i = 0; i < result.size(); i++)
+ {
+ if (result[i] == chars)
+ result.erase(result.begin() + i);
+ }
+
+ return result;
+}
+
+/****************************************************************************************/
+
+string StringSequenceTools::deleteChar(const string& sequence, string chars)
+{
+ // Copy sequence
+ string result(sequence);
+
+ // For all characters to delete
+ for (unsigned int i = 0; i < chars.size(); i++)
+ {
+ // Search and delete char
+ for (unsigned int j = 0; j < result.size(); j++)
+ {
+ if (result[j] == chars[i])
+ result.erase(result.begin() + j);
+ }
+ }
+
+ return result;
+}
+
+/****************************************************************************************/
+
+string* StringSequenceTools::reverse(const string& sequence)
+{
+ // Initializing
+ string* result = new string;
+
+ // Main loop : reverse all characters of sequence
+ size_t size = sequence.size();
+ for (size_t i = 0; i < size; i++)
+ {
+ *result += sequence[size - i - 1];
+ }
+
+ // Send result
+ return result;
+}
+
+/****************************************************************************************/
+
+string* StringSequenceTools::complement(const string& sequence)
+{
+ // Initializing
+ string* result = new string;
+
+ // Main loop : completement all characters
+ size_t size = sequence.size();
+ for (unsigned int i = 0; i < size; i++)
+ {
+ switch (sequence[i])
+ {
+ case 'A': *result += 'T';
+ break;
+ case 'C': *result += 'G';
+ break;
+ case 'G': *result += 'C';
+ break;
+ case 'T': *result += 'A';
+ break;
+ case 'M': *result += 'K';
+ break;
+ case 'R': *result += 'Y';
+ break;
+ case 'Y': *result += 'R';
+ break;
+ case 'K': *result += 'M';
+ break;
+ case 'V': *result += 'B';
+ break;
+ case 'H': *result += 'D';
+ break;
+ case 'D': *result += 'H';
+ break;
+ case 'B': *result += 'V';
+ break;
+ default: *result += sequence[i];
+ break;
+ }
+ }
+
+ // Send new sequence
+ return result;
+}
+
+/****************************************************************************************/
+
+double StringSequenceTools::getGCcontent(const string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception)
+{
+ // Frequency counts for nucleotids A, C, G, T
+ map<char, double> counts;
+
+ // Window size checking
+ if (window < sequence.size())
+ throw BadIntegerException("StringSequenceTools::getGCContent : specified window too high", static_cast<int>(window));
+
+ // For last nucleotides
+ if (pos + window > sequence.size())
+ {
+ pos = sequence.size() - window;
+ }
+
+ // Main loop
+ for (size_t i = pos; i < pos + window; i++)
+ {
+ switch (toupper(sequence[i]))
+ {
+ case 'A': counts['A'] += 1;
+ break;
+ case 'C': counts['C'] += 1;
+ break;
+ case 'G': counts['G'] += 1;
+ break;
+ case 'T': counts['T'] += 1;
+ break;
+ case 'M': counts['A'] += 0.5;
+ counts['C'] += 0.5;
+ break;
+ case 'R': counts['A'] += 0.5;
+ counts['G'] += 0.5;
+ break;
+ case 'W': counts['A'] += 0.5;
+ counts['T'] += 0.5;
+ break;
+ case 'S': counts['C'] += 0.5;
+ counts['G'] += 0.5;
+ break;
+ case 'Y': counts['C'] += 0.5;
+ counts['T'] += 0.5;
+ break;
+ case 'K': counts['G'] += 0.5;
+ counts['T'] += 0.5;
+ break;
+ case 'V': counts['A'] += 0.34;
+ counts['C'] += 0.34;
+ counts['G'] += 0.34;
+ break;
+ case 'H': counts['A'] += 0.34;
+ counts['C'] += 0.34;
+ counts['T'] += 0.34;
+ break;
+ case 'D': counts['A'] += 0.34;
+ counts['G'] += 0.34;
+ counts['T'] += 0.34;
+ break;
+ case 'B': counts['C'] += 0.34;
+ counts['G'] += 0.34;
+ counts['T'] += 0.34;
+ break;
+ case '-': throw Exception("StringSequenceTools::getGCContent : Gap found in sequence");
+ break;
+ // Unresolved bases
+ default: counts['A'] += 0.25;
+ counts['C'] += 0.25;
+ counts['G'] += 0.25;
+ counts['T'] += 0.25;
+ }
+ }
+
+ // Calculate and send GC rate
+ return (counts['G'] + counts['C']) / static_cast<double>(window);
+}
+
+/****************************************************************************************/
+
+vector<int> StringSequenceTools::codeSequence(const string& sequence, const Alphabet* alphabet)
+throw (BadCharException)
+{
+ unsigned int size = AlphabetTools::getAlphabetCodingSize(alphabet); // Warning, an exception may be casted here!
+ vector<int> code((int)floor((double)sequence.size() / (double)size));
+ unsigned int pos = 0;
+ unsigned int count = 0;
+ while (pos + size <= sequence.size())
+ {
+ code[count] = alphabet->charToInt(sequence.substr(pos, size));
+ count++;
+ pos += size;
+ }
+ return code;
+}
+
+/****************************************************************************************/
+
+string StringSequenceTools::decodeSequence(const vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException)
+{
+ string result = "";
+ for (unsigned int i = 0; i < sequence.size(); i++)
+ {
+ result += alphabet->intToChar(sequence[i]);
+ }
+ return result;
+}
+
+/****************************************************************************************/
+
+Alphabet* StringSequenceTools::getAlphabetFromSequence(const std::string& sequence)
+throw (EmptySequenceException, SequenceException, AlphabetException)
+{
+ // empty sequence test
+ if (sequence.size() == 0)
+ {
+ throw EmptySequenceException("Sequence::getAlphabetFromSequence : Empty sequence string");
+ }
+
+ // initialisation
+ bool p = false; // indicates that a protein specific character is found
+ bool r = false; // indicates that a RNA specific character is found
+ bool u = false; // indicates that an unknown character is found
+ bool pd = false; // Protein or DNA (T)
+
+ // Main loop : for all character in sequence
+ for (unsigned int i = 0; i < sequence.size(); i++)
+ {
+ // Character analyse
+ switch (AlphabetTools::getType(sequence[i]))
+ {
+ case 0: u = true; break;
+ case 3: p = true; break;
+ case 2: r = true; break;
+ case 5: pd = true; break;
+ }
+ }
+
+ if (u)
+ throw AlphabetException ("Sequence::getAlphabetFromSequence : Unknow character detected in specified sequence");
+ if (r && pd)
+ throw SequenceException ("Sequence::getAlphabetFromSequence : Both 'T' and 'U' in the same sequence!");
+ if (r && p)
+ throw SequenceException ("Sequence::getAlphabetFromSequence : Protein character and 'U' in the same sequence!");
+ if (p)
+ return new ProteicAlphabet();
+ if (r)
+ return new RNA();
+ return new DNA();
+}
+
+/****************************************************************************************/
+
diff --git a/src/Bpp/Seq/StringSequenceTools.h b/src/Bpp/Seq/StringSequenceTools.h
new file mode 100644
index 0000000..45ee54c
--- /dev/null
+++ b/src/Bpp/Seq/StringSequenceTools.h
@@ -0,0 +1,204 @@
+//
+// File: StringSequenceTools.h
+// Created by: Julien Dutheil
+// Created on: Sun Nov 30 11:29:07 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _STRINGSEQUENCETOOLS_H_
+#define _STRINGSEQUENCETOOLS_H_
+
+#include "Alphabet/Alphabet.h"
+#include "Alphabet/AlphabetExceptions.h"
+#include "SequenceExceptions.h"
+#include <Bpp/Exceptions.h>
+
+// From the STL:
+#include <string>
+#include <vector>
+
+namespace bpp
+{
+
+/**
+ * @brief Utilitary methods working on raw string objects.
+ *
+ * Sequences may be stored as strings, but this approach is not as
+ * powerful as using true sequence objects.
+ * Consider using the Sequence and SequenceTools classes for more methods.
+ *
+ * Some of the methods implemented here are internally used by the Sequence object.
+ *
+ * @see Sequence, Site, SequenceTools, SiteTools
+ */
+class StringSequenceTools
+{
+ public:
+ StringSequenceTools() {};
+ ~StringSequenceTools() {};
+
+ public:
+
+ /**
+ * @brief Get a subsequence.
+ *
+ * @param sequence The input sequence.
+ * @param begin The begining position (included).
+ * @param end The ending position (included).
+ * @return A string with the subsequence.
+ * @throw Exception If position does not not match the interval [0, length].
+ */
+ static std::string subseq(const std::string& sequence, int begin, int end) throw (Exception);
+
+ /**
+ * @brief Set up the size of a sequence from the right side.
+ *
+ * All new characters are filled with gaps.
+ * If the specified size is < to the sequence size, the sequence will be truncated.
+ *
+ * @param sequence The input sequence.
+ * @param size The new size of the sequence.
+ */
+ static std::string setToSizeR(const std::string& sequence, int size);
+
+ /**
+ * @brief Set up the size of a sequence from the left side.
+ *
+ * All new characters are filled with gaps.
+ * If the specified size is < to the sequence size, the sequence will be truncated.
+ *
+ * @param sequence The input sequence.
+ * @param size The new size of the sequence.
+ */
+ static std::string setToSizeL(const std::string& sequence, int size);
+
+ /**
+ * @brief Delete all occurence of a character in the sequence.
+ *
+ * @param sequence The sequence to parse.
+ * @param chars The character to remove.
+ * @return The sequence with all specified characters removed.
+ */
+ static std::string deleteChar(const std::string& sequence, char chars);
+
+ /**
+ * @brief Delete all occurence of several characters in the sequence.
+ *
+ * @param sequence The sequence to parse.
+ * @param chars The characters to remove.
+ * @return The sequence with all specified characters removed.
+ */
+ static std::string deleteChar(const std::string& sequence, std::string chars);
+
+ /**
+ * @brief Reverse the sequence.
+ *
+ * @param sequence The sequence to reverse.
+ * @return The reversed sequence.
+ */
+ static std::string* reverse(const std::string& sequence);
+
+ /**
+ * @brief Get the complement of a sequence.
+ * @deprecated Consider working with sequence objects and translators.
+ *
+ * For this method, sequence is supposed to be of type DNA.
+ *
+ * @param sequence The sequence to complement.
+ * @return The complementary sequence.
+ * @see Sequence
+ * @see NucleicAcidsReplication
+ */
+ static std::string* complement(const std::string& sequence);
+
+ /**
+ * @brief Calculate the local GC content of a sequence.
+ *
+ * GC contents are calculated using a window of specified size around the given position.
+ * Note : Calculus for last nucleotides (sequence's size - window size) will return
+ * the last possible rate calculated.
+ *
+ * @param sequence The sequence to analyse.
+ * @param pos The position where to compute the GC content.
+ * @param window The size of the window to use.
+ * @return The GC content as a ratio (# of GC / window).
+ * @throw BadIntException If the sequence is not of type DNA or RNA.
+ * @throw Exception Error in calculus (if the sequence contain gaps for instance).
+ */
+ static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
+
+ /**
+ * @brief Convert a string sequence to a vector of int.
+ *
+ * This method is used in the sequence constructor.
+ * This deals with the most simple cases: the sequence (string) contains
+ * a succession of all characters. This is indeed the case for simple
+ * alphabets, but may be more complicated if the alphabet is coded with
+ * variable code length.
+ *
+ * @param sequence The sequence to parse.
+ * @param alphabet The alphabet to use to code the sequence.
+ * @return A vector of int codes.
+ * @throw BarCharException If some character does not match the specified alphabet.
+ */
+ static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
+
+ /**
+ * @brief Convert a sequence to its string representation.
+ *
+ * @param sequence The sequence object to convert.
+ * @param alphabet The alphabet to use to decode the sequence.
+ * @return A string representation of the sequence.
+ * @throw BarIntException If some value does not match the specified alphabet.
+ */
+ static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
+
+ /**
+ * @brief Parse a sequence and try to guess the correct alphabet to use.
+ *
+ * @param sequence The sequence to parse.
+ * @return A pointer toward a new Alphabet object.
+ * @throw EmptySequenceException if the sequence is empty.
+ * @throw SequenceException if their is an ambiguity between several alphabet.
+ * @throw AlphabetException if the sequence does not match any alphabet.
+ */
+ static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
+
+};
+
+} //end of namespace bpp.
+
+#endif //_STRINGSEQUENCETOOLS_H
+
diff --git a/src/Bpp/Seq/SymbolList.cpp b/src/Bpp/Seq/SymbolList.cpp
new file mode 100644
index 0000000..fcf595f
--- /dev/null
+++ b/src/Bpp/Seq/SymbolList.cpp
@@ -0,0 +1,442 @@
+//
+// File: SymbolList.cpp
+// Created by: Julien Dutheil
+// Created on: Fri Apr 9 2005
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SymbolList.h"
+#include "StringSequenceTools.h"
+
+using namespace bpp;
+
+using namespace std;
+
+/****************************************************************************************/
+
+BasicSymbolList::BasicSymbolList(const std::vector<string>& list, const Alphabet* alpha) throw (BadCharException) :
+ alphabet_(alpha), content_()
+{
+ setContent(list);
+}
+
+BasicSymbolList::BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException) :
+ alphabet_(alpha), content_()
+{
+ setContent(list);
+}
+
+/****************************************************************************************/
+
+BasicSymbolList::BasicSymbolList(const SymbolList& list):
+ alphabet_(list.getAlphabet()), content_(list.getContent()) {}
+
+BasicSymbolList::BasicSymbolList(const BasicSymbolList& list):
+ alphabet_(list.getAlphabet()), content_(list.getContent()) {}
+
+BasicSymbolList& BasicSymbolList::operator=(const SymbolList& list)
+{
+ content_ = list.getContent();
+ alphabet_ = list.getAlphabet();
+ return *this;
+}
+
+BasicSymbolList& BasicSymbolList::operator=(const BasicSymbolList& list)
+{
+ content_ = list.getContent();
+ alphabet_ = list.getAlphabet();
+ return *this;
+}
+
+/****************************************************************************************/
+
+void BasicSymbolList::setContent(const vector<string>& list) throw (BadCharException)
+{
+ // Check list for incorrect characters
+ vector<int> coded(list.size());
+ for (size_t i = 0; i < list.size(); i++)
+ if(!alphabet_->isCharInAlphabet(list[i])) throw BadCharException(list[i], "BasicSymbolList::setContent", alphabet_);
+
+ for (size_t i = 0; i < list.size(); i++)
+ coded[i] = alphabet_->charToInt(list[i]);
+
+ //BasicSymbolList is valid:
+ content_ = coded;
+};
+
+/****************************************************************************************/
+
+void BasicSymbolList::setContent(const vector<int>& list) throw (BadIntException)
+{
+ // Check list for incorrect characters
+ for (size_t i = 0; i < list.size(); i++)
+ if(!alphabet_->isIntInAlphabet(list[i]))
+ throw BadIntException(list[i], "BasicSymbolList::setContent", alphabet_);
+
+ //Sequence is valid:
+ content_ = list;
+};
+
+/****************************************************************************************/
+
+string BasicSymbolList::toString() const
+{
+ return StringSequenceTools::decodeSequence(content_, alphabet_);
+};
+
+/****************************************************************************************/
+
+void BasicSymbolList::addElement(const string& c) throw (BadCharException)
+{
+ content_.push_back(alphabet_->charToInt(c));
+}
+
+/****************************************************************************************/
+
+void BasicSymbolList::addElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
+{
+ if(pos >= content_.size()) throw IndexOutOfBoundsException("BasicSymbolList::addElement. Invalid position.", pos, 0, size() - 1);
+ content_.insert(content_.begin() + pos, alphabet_->charToInt(c));
+}
+
+/****************************************************************************************/
+
+void BasicSymbolList::setElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
+{
+ if(pos >= content_.size())
+ throw IndexOutOfBoundsException("BasicSymbolList::setElement. Invalid position.", pos, 0, size() - 1);
+ content_[pos] = alphabet_->charToInt(c);
+}
+
+/****************************************************************************************/
+
+string BasicSymbolList::getChar(size_t pos) const throw (IndexOutOfBoundsException)
+{
+ if(pos >= content_.size())
+ throw IndexOutOfBoundsException("BasicSymbolList::getChar. Invalid position.", pos, 0, size() - 1);
+ string c = "";
+ try
+ {
+ c = alphabet_->intToChar(content_[pos]);
+ }
+ catch(BadIntException bie)
+ {
+ //This should never happen!
+ }
+ return c;
+}
+
+/****************************************************************************************/
+
+void BasicSymbolList::deleteElement(size_t pos) throw (IndexOutOfBoundsException)
+{
+ if(pos >= content_.size())
+ throw IndexOutOfBoundsException("BasicSymbolList::deleteElement. Invalid position.", pos, 0, size() - 1);
+ content_.erase(content_.begin() + pos);
+}
+
+/****************************************************************************************/
+
+void BasicSymbolList::deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException)
+{
+ if (pos + len > content_.size())
+ throw IndexOutOfBoundsException("BasicSymbolList::deleteElements. Invalid position.", pos + len, 0, size() - 1);
+ content_.erase(content_.begin() + pos, content_.begin() + pos + len);
+}
+
+/****************************************************************************************/
+
+void BasicSymbolList::addElement(int v) throw (BadIntException)
+{
+ //test:
+ alphabet_->intToChar(v);
+ content_.push_back(v);
+}
+
+/****************************************************************************************/
+
+void BasicSymbolList::addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
+{
+ //test:
+ if(pos >= content_.size())
+ throw IndexOutOfBoundsException("BasicSymbolList::addElement. Invalid position.", pos, 0, size() - 1);
+ alphabet_->intToChar(v);
+ content_.insert(content_.begin() + pos, v);
+}
+
+/****************************************************************************************/
+
+void BasicSymbolList::setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
+{
+ //test:
+ if(pos >= content_.size())
+ throw IndexOutOfBoundsException("BasicSymbolList::setElement. Invalid position.", pos, 0, size() - 1);
+ alphabet_->intToChar(v);
+ content_[pos] = v;
+}
+
+/****************************************************************************************/
+
+int BasicSymbolList::getValue(size_t pos) const throw (IndexOutOfBoundsException)
+{
+ if(pos >= content_.size())
+ throw IndexOutOfBoundsException("BasicSymbolList::getValue. Invalid position.", pos, 0, size() - 1);
+ return content_[pos];
+}
+
+/****************************************************************************************/
+
+
+/****************************************************************************************/
+
+EdSymbolList::EdSymbolList(const std::vector<string>& list, const Alphabet* alpha) throw (BadCharException) :
+ alphabet_(alpha), propagateEvents_(true), content_(), listeners_()
+{
+ setContent(list);
+}
+
+EdSymbolList::EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException) :
+ alphabet_(alpha), propagateEvents_(true), content_(), listeners_()
+{
+ setContent(list);
+}
+
+/****************************************************************************************/
+
+EdSymbolList::EdSymbolList(const SymbolList& list):
+ alphabet_(list.getAlphabet()), propagateEvents_(true), content_(list.getContent()), listeners_() {}
+
+EdSymbolList::EdSymbolList(const EdSymbolList& list):
+ alphabet_(list.getAlphabet()), propagateEvents_(list.propagateEvents_), content_(list.getContent()), listeners_(list.listeners_)
+{
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ if (!list.listeners_[i]->isShared())
+ listeners_[i] = dynamic_cast<SymbolListListener*>(list.listeners_[i]->clone());
+}
+
+EdSymbolList& EdSymbolList::operator=(const SymbolList& list)
+{
+ content_ = list.getContent();
+ alphabet_ = list.getAlphabet();
+ propagateEvents_ = true;
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ if (!listeners_[i]->isShared())
+ delete listeners_[i];
+ listeners_.clear();
+ return *this;
+}
+
+EdSymbolList& EdSymbolList::operator=(const EdSymbolList& list)
+{
+ content_ = list.getContent();
+ alphabet_ = list.getAlphabet();
+ propagateEvents_ = list.propagateEvents_;
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ delete listeners_[i];
+ listeners_ = list.listeners_;
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ if (!list.listeners_[i]->isShared())
+ listeners_[i] = dynamic_cast<SymbolListListener*>(list.listeners_[i]->clone());
+ return *this;
+}
+
+/****************************************************************************************/
+
+void EdSymbolList::setContent(const vector<string>& list) throw (BadCharException)
+{
+ SymbolListEditionEvent event(this);
+ fireBeforeSequenceChanged(event);
+
+ // Check list for incorrect characters
+ vector<int> coded(list.size());
+ for (size_t i = 0; i < list.size(); i++)
+ if (!alphabet_->isCharInAlphabet(list[i])) throw BadCharException(list[i], "EdSymbolList::setContent", alphabet_);
+
+ for (size_t i = 0; i < list.size(); i++)
+ coded[i] = alphabet_->charToInt(list[i]);
+
+ //SymbolList is valid:
+ content_ = coded;
+ fireAfterSequenceChanged(event);
+};
+
+/****************************************************************************************/
+
+void EdSymbolList::setContent(const vector<int>& list) throw (BadIntException)
+{
+ SymbolListEditionEvent event(this);
+ fireBeforeSequenceChanged(event);
+
+ // Check list for incorrect characters
+ for (size_t i = 0; i < list.size(); i++)
+ if(!alphabet_->isIntInAlphabet(list[i]))
+ throw BadIntException(list[i], "EdSymbolList::setContent", alphabet_);
+
+ //Sequence is valid:
+ content_ = list;
+ fireAfterSequenceChanged(event);
+};
+
+/****************************************************************************************/
+
+string EdSymbolList::toString() const
+{
+ return StringSequenceTools::decodeSequence(content_, alphabet_);
+};
+
+/****************************************************************************************/
+
+void EdSymbolList::addElement(const string& c) throw (BadCharException)
+{
+ SymbolListInsertionEvent event(this, size(), 1);
+ fireBeforeSequenceInserted(event);
+ content_.push_back(alphabet_->charToInt(c));
+ fireAfterSequenceInserted(event);
+}
+
+/****************************************************************************************/
+
+void EdSymbolList::addElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
+{
+ if (pos >= content_.size()) throw IndexOutOfBoundsException("EdSymbolList::addElement. Invalid position.", pos, 0, size() - 1);
+ SymbolListInsertionEvent event(this, pos, 1);
+ fireBeforeSequenceInserted(event);
+ content_.insert(content_.begin() + pos, alphabet_->charToInt(c));
+ fireAfterSequenceInserted(event);
+}
+
+/****************************************************************************************/
+
+void EdSymbolList::setElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
+{
+ if (pos >= content_.size())
+ throw IndexOutOfBoundsException("EdSymbolList::setElement. Invalid position.", pos, 0, size() - 1);
+ SymbolListSubstitutionEvent event(this, pos, pos);
+ fireBeforeSequenceSubstituted(event);
+ content_[pos] = alphabet_->charToInt(c);
+ fireAfterSequenceSubstituted(event);
+}
+
+/****************************************************************************************/
+
+string EdSymbolList::getChar(size_t pos) const throw (IndexOutOfBoundsException)
+{
+ if (pos >= content_.size())
+ throw IndexOutOfBoundsException("EdSymbolList::getChar. Invalid position.", pos, 0, size() - 1);
+ string c = "";
+ try {
+ c = alphabet_->intToChar(content_[pos]);
+ } catch(BadIntException bie) {
+ //This should never happen!
+ }
+ return c;
+}
+
+/****************************************************************************************/
+
+void EdSymbolList::deleteElement(size_t pos) throw (IndexOutOfBoundsException)
+{
+ if (pos >= content_.size())
+ throw IndexOutOfBoundsException("EdSymbolList::deleteElement. Invalid position.", pos, 0, size() - 1);
+ SymbolListDeletionEvent event(this, pos, 1);
+ fireBeforeSequenceDeleted(event);
+ content_.erase(content_.begin() + pos);
+ fireAfterSequenceDeleted(event);
+}
+
+/****************************************************************************************/
+
+void EdSymbolList::deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException)
+{
+ if(pos + len > content_.size())
+ throw IndexOutOfBoundsException("EdSymbolList::deleteElements. Invalid position.", pos + len, 0, size() - 1);
+ SymbolListDeletionEvent event(this, pos, len);
+ fireBeforeSequenceDeleted(event);
+ content_.erase(content_.begin() + pos, content_.begin() + pos + len);
+ fireAfterSequenceDeleted(event);
+}
+
+
+/****************************************************************************************/
+
+void EdSymbolList::addElement(int v) throw (BadIntException)
+{
+ SymbolListInsertionEvent event(this, size(), 1);
+ fireBeforeSequenceInserted(event);
+ //test:
+ alphabet_->intToChar(v);
+ content_.push_back(v);
+ fireAfterSequenceInserted(event);
+}
+
+/****************************************************************************************/
+
+void EdSymbolList::addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
+{
+ //test:
+ if (pos >= content_.size())
+ throw IndexOutOfBoundsException("EdSymbolList::addElement. Invalid position.", pos, 0, size() - 1);
+ SymbolListInsertionEvent event(this, pos, 1);
+ fireBeforeSequenceInserted(event);
+ alphabet_->intToChar(v);
+ content_.insert(content_.begin() + pos, v);
+ fireAfterSequenceInserted(event);
+}
+
+/****************************************************************************************/
+
+void EdSymbolList::setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
+{
+ //test:
+ if (pos >= content_.size())
+ throw IndexOutOfBoundsException("EdSymbolList::setElement. Invalid position.", pos, 0, size() - 1);
+ SymbolListSubstitutionEvent event(this, pos, pos);
+ fireBeforeSequenceSubstituted(event);
+ alphabet_->intToChar(v);
+ content_[pos] = v;
+ fireAfterSequenceSubstituted(event);
+}
+
+/****************************************************************************************/
+
+int EdSymbolList::getValue(size_t pos) const throw (IndexOutOfBoundsException)
+{
+ if (pos >= content_.size())
+ throw IndexOutOfBoundsException("EdSymbolList::getValue. Invalid position.", pos, 0, size() - 1);
+ return content_[pos];
+}
+
+/****************************************************************************************/
+
diff --git a/src/Bpp/Seq/SymbolList.h b/src/Bpp/Seq/SymbolList.h
new file mode 100644
index 0000000..6b18dad
--- /dev/null
+++ b/src/Bpp/Seq/SymbolList.h
@@ -0,0 +1,745 @@
+//
+// File: SymbolList.h
+// Created by: Julien Dutheil
+// Created on: Fri Apr 9 2005
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SYMBOLLIST_H_
+#define _SYMBOLLIST_H_
+
+#include "Alphabet/Alphabet.h"
+#include <Bpp/Clonable.h>
+
+// From the STL:
+#include <string>
+#include <vector>
+#include <algorithm>
+#include <iostream>
+
+namespace bpp
+{
+
+ /**
+ * @brief The SymbolList interface.
+ *
+ * @see Alphabet
+ */
+ class SymbolList:
+ public virtual Clonable
+ {
+
+ public:
+ /**
+ * @name The Clonable interface
+ *
+ * @{
+ */
+#ifndef NO_VIRTUAL_COV
+ SymbolList* clone() const = 0;
+#endif
+ /** @} */
+
+ // Class destructor
+ virtual ~SymbolList() {}
+
+ public:
+
+ /**
+ * @brief Get the alphabet associated to the list.
+ *
+ * @return A const pointer to the alphabet.
+ * @see Alphabet class.
+ */
+ virtual const Alphabet* getAlphabet() const = 0;
+
+ /**
+ * @brief Get the number of elements in the list.
+ *
+ * @return The number of sites in the list.
+ */
+ virtual size_t size() const = 0;
+
+ /**
+ * @name Acting on the content of the list.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the whole content of the list as a vector of int.
+ *
+ * @return A reference to the content of the list.
+ */
+ virtual const std::vector<int>& getContent() const = 0;
+
+ /**
+ * @brief Set the whole content of the list.
+ *
+ * @param list The new content of the list.
+ * @see The list constructor for information about the way lists are internaly stored.
+ */
+ virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
+
+ /**
+ * @brief Set the whole content of the list.
+ *
+ * @param list The new content of the list.
+ * @see The list constructor for information about the way lists are internaly stored.
+ */
+ virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
+
+ /** @} */
+
+ /**
+ * @brief Convert the list as a string.
+ *
+ * This method is useful for dumping a list to a file or to the screen for display.
+ *
+ * @return The whole list as a string.
+ */
+ virtual std::string toString() const = 0;
+
+ /**
+ * @name Edition methods.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Add a character to the end of the list.
+ *
+ * @param c The character to add, given as a string.
+ */
+ virtual void addElement(const std::string& c) throw (BadCharException) = 0;
+
+ /**
+ * @brief Add a character at a certain position in the list.
+ *
+ * @param pos The postion where to insert the element.
+ * @param c The character to add, given as a string.
+ */
+ virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Set the element at position 'pos' to character 'c'.
+ *
+ * @param pos The position of the character to set.
+ * @param c The value of the element, given as a string.
+ */
+ virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Delete the element at position 'pos'.
+ *
+ * @param pos The position of the element to delete.
+ */
+ virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Delete the elements at position 'pos'.
+ *
+ * @param pos The position of the first element to delete.
+ * @param len The length of the region to delete.
+ */
+ virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
+
+
+ /**
+ * @brief Get the element at position 'pos' as a character.
+ *
+ * @param pos The position of the character to retrieve.
+ */
+ virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Add a character to the end of the list.
+ *
+ * @param v The character to add, given as an int.
+ */
+ virtual void addElement(int v) throw (BadIntException) = 0;
+
+ /**
+ * @brief Add a character at a certain position in the list.
+ *
+ * @param pos The postion where to insert the element.
+ * @param v The character to add, given as an int.
+ */
+ virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Set the element at position 'pos' to character 'v'.
+ *
+ * @param pos The position of the character to set.
+ * @param v The value of the element, given as an int.
+ */
+ virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
+
+ /**
+ * @brief Get the element at position 'pos' as an int.
+ *
+ * @param pos The position of the character to retrieve.
+ */
+ virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
+
+ /** @} */
+
+ /**
+ * @name Provide direct access to the list content.
+ *
+ * @warning These operators allow you to modifiy the list content.
+ * No alphabet checking is performed for your modifications, so use with care, or
+ * consider using the setContent() method.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Operator [] overloaded for quick access to a character in list.
+ *
+ * @param i The position to retrieve.
+ * @return The integer value of character at position i.
+ */
+ virtual const int& operator[](size_t i) const = 0;
+ /**
+ * @brief Operator [] overloaded for quick access to a character in list.
+ *
+ * @param i The position to retrieve.
+ * @return The integer value of character at position i.
+ */
+ virtual int& operator[](size_t i) = 0;
+
+ /**
+ * @brief Randomly shuffle the content of the list, with linear complexity.
+ */
+ virtual void shuffle() = 0;
+ /** @} */
+ };
+
+
+ /**
+ * @brief A basic SymbolList object.
+ *
+ * This is a general purpose container, containing an ordered list of states(= letters).
+ * The states that allowed to be present in the list are defined by an alphabet object,
+ * which is passed to the list constructor by a pointer.
+ *
+ * For programming convenience, the states are stored as integers, but the translation toward
+ * and from a char description is easily performed with the Alphabet classes.
+ *
+ * @see Alphabet
+ */
+ class BasicSymbolList:
+ public virtual SymbolList
+ {
+
+ private:
+ /**
+ * @brief The Alphabet attribute must be initialized in constructor and then can never be changed.
+ *
+ * To apply another alphabet to a list you'll have to create a new list.
+ */
+ const Alphabet* alphabet_;
+
+ protected:
+ /**
+ * @brief The list content.
+ */
+ std::vector<int> content_;
+
+ public:
+ /**
+ * @brief Build a new void BasicSymbolList object with the specified alphabet.
+ *
+ * @param alpha The alphabet to use.
+ */
+ BasicSymbolList(const Alphabet* alpha) : alphabet_(alpha), content_() {}
+
+ /**
+ * @brief Build a new BasicSymbolList object with the specified alphabet.
+ * The content of the site is initialized from a vector of characters.
+ *
+ * @param list The content of the site.
+ * @param alpha The alphabet to use.
+ * @throw BadCharException If the content does not match the specified alphabet.
+ */
+ BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief Build a new BasicSymbolList object with the specified alphabet.
+ * The content of the site is initialized from a vector of integers.
+ *
+ * @param list The content of the site.
+ * @param alpha The alphabet to use.
+ * @throw BadIntException If the content does not match the specified alphabet.
+ */
+ BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
+
+ /**
+ * @brief The generic copy constructor.
+ */
+ BasicSymbolList(const SymbolList& list);
+
+ /**
+ * @brief The copy constructor.
+ */
+ BasicSymbolList(const BasicSymbolList& list);
+
+ /**
+ * @brief The generic assignment operator.
+ */
+ BasicSymbolList& operator=(const SymbolList& list);
+
+ /**
+ * @brief The assignment operator.
+ */
+ BasicSymbolList& operator=(const BasicSymbolList& list);
+
+ /**
+ * @name The Clonable interface
+ *
+ * @{
+ */
+#ifdef NO_VIRTUAL_COV
+ Clonable*
+#else
+ BasicSymbolList*
+#endif
+ clone() const { return new BasicSymbolList(* this); }
+ /** @} */
+
+ // Class destructor
+ virtual ~BasicSymbolList() {}
+
+ public:
+
+ virtual const Alphabet* getAlphabet() const { return alphabet_; }
+
+ virtual size_t size() const { return static_cast<size_t>(content_.size()); }
+
+ virtual const std::vector<int>& getContent() const { return content_; }
+
+ virtual void setContent(const std::vector<int>& list) throw (BadIntException);
+
+ virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
+
+ virtual std::string toString() const;
+
+ virtual void addElement(const std::string& c) throw (BadCharException);
+
+ virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
+
+ virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
+
+ virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
+
+ virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
+
+ virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
+
+ virtual void addElement(int v) throw (BadIntException);
+
+ virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
+
+ virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
+
+ virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
+
+ virtual const int& operator[](size_t i) const { return content_[i]; }
+
+ virtual int& operator[](size_t i) { return content_[i]; }
+
+ virtual void shuffle()
+ {
+ random_shuffle(content_.begin(), content_.end());
+ }
+ };
+
+ class SymbolListEditionEvent
+ {
+ private:
+ SymbolList* list_;
+
+ public:
+ SymbolListEditionEvent(SymbolList* list):
+ list_(list) {}
+
+ SymbolListEditionEvent(const SymbolListEditionEvent& slee): list_(slee.list_) {}
+
+ SymbolListEditionEvent& operator=(const SymbolListEditionEvent& slee) {
+ list_ = slee.list_;
+ return *this;
+ }
+
+ virtual ~SymbolListEditionEvent() {}
+
+ public:
+ virtual SymbolList* getSymbolList() { return list_; }
+ virtual const SymbolList* getSymbolList() const { return list_; }
+ };
+
+
+ class SymbolListInsertionEvent:
+ public SymbolListEditionEvent
+ {
+ private:
+ size_t pos_;
+ size_t len_;
+
+ public:
+ SymbolListInsertionEvent(SymbolList* list, size_t pos, size_t len):
+ SymbolListEditionEvent(list), pos_(pos), len_(len) {}
+
+ public:
+ virtual size_t getPosition() const { return pos_; }
+ virtual size_t getLength() const { return len_; }
+ };
+
+
+ class SymbolListDeletionEvent:
+ public SymbolListEditionEvent
+ {
+ private:
+ size_t pos_;
+ size_t len_;
+
+ public:
+ SymbolListDeletionEvent(SymbolList* list, size_t pos, size_t len):
+ SymbolListEditionEvent(list), pos_(pos), len_(len) {}
+
+ public:
+ virtual size_t getPosition() const { return pos_; }
+ virtual size_t getLength() const { return len_; }
+ };
+
+
+ class SymbolListSubstitutionEvent:
+ public SymbolListEditionEvent
+ {
+ private:
+ size_t begin_;
+ size_t end_;
+
+ public:
+ SymbolListSubstitutionEvent(SymbolList* list, size_t begin, size_t end) :
+ SymbolListEditionEvent(list), begin_(begin), end_(end) {}
+
+ public:
+ virtual size_t getBegin() const { return begin_; }
+ virtual size_t getEnd() const { return end_; }
+ };
+
+ class SymbolListListener :
+ public virtual Clonable
+ {
+ public:
+ virtual ~SymbolListListener() {}
+
+#ifndef NO_VIRTUAL_COV
+ virtual SymbolListListener* clone() const = 0;
+#endif
+
+ public:
+ virtual bool isRemovable() const = 0;
+ virtual bool isShared() const = 0;
+ virtual void beforeSequenceChanged(const SymbolListEditionEvent& event) = 0;
+ virtual void afterSequenceChanged(const SymbolListEditionEvent& event) = 0;
+ virtual void beforeSequenceInserted(const SymbolListInsertionEvent& event) = 0;
+ virtual void afterSequenceInserted(const SymbolListInsertionEvent& event) = 0;
+ virtual void beforeSequenceDeleted(const SymbolListDeletionEvent& event) = 0;
+ virtual void afterSequenceDeleted(const SymbolListDeletionEvent& event) = 0;
+ virtual void beforeSequenceSubstituted(const SymbolListSubstitutionEvent& event) = 0;
+ virtual void afterSequenceSubstituted(const SymbolListSubstitutionEvent& event) = 0;
+ };
+
+
+ /**
+ * @brief A event-driven SymbolList object.
+ *
+ * This is a general purpose container, containing an ordered list of states(= letters).
+ * The states that allowed to be present in the list are defined by an alphabet object,
+ * which is passed to the list constructor by a pointer.
+ *
+ * For programming convenience, the states are stored as integers, but the translation toward
+ * and from a char description is easily performed with the Alphabet classes.
+ *
+ * @see Alphabet
+ */
+ class EdSymbolList:
+ public virtual SymbolList
+ {
+
+ private:
+ /**
+ * @brief The Alphabet attribute must be initialized in constructor and then can never be changed.
+ *
+ * To apply another alphabet to a list you'll have to create a new list.
+ */
+ const Alphabet* alphabet_;
+
+ bool propagateEvents_;
+
+ protected:
+ /**
+ * @brief The list content.
+ */
+ std::vector<int> content_;
+
+ /**
+ * @brief Contains the listeners.
+ */
+ std::vector<SymbolListListener*> listeners_;
+
+
+ public:
+ /**
+ * @brief Build a new void BasicSymbolList object with the specified alphabet.
+ *
+ * @param alpha The alphabet to use.
+ */
+ EdSymbolList(const Alphabet* alpha) : alphabet_(alpha), propagateEvents_(true), content_(), listeners_() {}
+
+ /**
+ * @brief Build a new BasicSymbolList object with the specified alphabet.
+ * The content of the site is initialized from a vector of characters.
+ *
+ * @param list The content of the site.
+ * @param alpha The alphabet to use.
+ * @throw BadCharException If the content does not match the specified alphabet.
+ */
+ EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
+
+ /**
+ * @brief Build a new BasicSymbolList object with the specified alphabet.
+ * The content of the site is initialized from a vector of integers.
+ *
+ * @param list The content of the site.
+ * @param alpha The alphabet to use.
+ * @throw BadIntException If the content does not match the specified alphabet.
+ */
+ EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
+
+ /**
+ * @brief The generic copy constructor.
+ */
+ EdSymbolList(const SymbolList& list);
+
+ /**
+ * @brief The copy constructor.
+ */
+ EdSymbolList(const EdSymbolList& list);
+
+ /**
+ * @brief The generic assignment operator.
+ */
+ EdSymbolList& operator=(const SymbolList& list);
+
+ /**
+ * @brief The assignment operator.
+ */
+ EdSymbolList& operator=(const EdSymbolList& list);
+
+ /**
+ * @name The Clonable interface
+ *
+ * @{
+ */
+#ifdef NO_VIRTUAL_COV
+ Clonable*
+#else
+ EdSymbolList*
+#endif
+ clone() const { return new EdSymbolList(* this); }
+ /** @} */
+
+ // Class destructor
+ virtual ~EdSymbolList()
+ {
+ for (size_t i = 0; i < listeners_.size(); ++i) {
+ if (listeners_[i] && !listeners_[i]->isShared()) {
+ delete listeners_[i];
+ }
+ }
+ }
+
+ public:
+
+ virtual const Alphabet* getAlphabet() const { return alphabet_; }
+
+ virtual size_t size() const { return static_cast<size_t>(content_.size()); }
+
+ virtual const std::vector<int>& getContent() const { return content_; }
+
+ virtual void setContent(const std::vector<int>& list) throw (BadIntException);
+
+ virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
+
+ virtual std::string toString() const;
+
+ virtual void addElement(const std::string& c) throw (BadCharException);
+
+ virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
+
+ virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
+
+ virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
+
+ virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
+
+ virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
+
+ virtual void addElement(int v) throw (BadIntException);
+
+ virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
+
+ virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
+
+ virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
+
+ virtual const int& operator[](size_t i) const { return content_[i]; }
+
+ virtual int& operator[](size_t i) { return content_[i]; }
+
+ virtual void shuffle()
+ {
+ random_shuffle(content_.begin(), content_.end());
+ }
+
+ /**
+ * @name Events handling
+ *
+ * @{
+ */
+ virtual size_t getNumberOfListeners() const { return listeners_.size(); }
+
+ virtual const SymbolListListener& getListener(size_t i) const {
+ if (listeners_[i] == 0) std::cout << "aie!!!" << std::endl;
+ return *listeners_[i];
+ }
+
+ virtual SymbolListListener& getListener(size_t i) {
+ if (listeners_[i] == 0) std::cout << "aie!!!" << std::endl;
+ return *listeners_[i];
+ }
+
+ virtual void addSymbolListListener(SymbolListListener* listener) {
+ listeners_.push_back(listener);
+ }
+
+ virtual void removeSymbolListListener(SymbolListListener* listener) {
+ if (listener->isRemovable())
+ listeners_.erase(remove(listeners_.begin(), listeners_.end(), listener), listeners_.end());
+ else
+ throw Exception("EdSymbolList::removeSymbolListListener. Listener is not removable.");
+ }
+
+ protected:
+ virtual void beforeSequenceChanged(const SymbolListEditionEvent& event) {};
+ virtual void afterSequenceChanged(const SymbolListEditionEvent& event) {};
+ virtual void beforeSequenceInserted(const SymbolListInsertionEvent& event) {};
+ virtual void afterSequenceInserted(const SymbolListInsertionEvent& event) {};
+ virtual void beforeSequenceDeleted(const SymbolListDeletionEvent& event) {};
+ virtual void afterSequenceDeleted(const SymbolListDeletionEvent& event) {};
+ virtual void beforeSequenceSubstituted(const SymbolListSubstitutionEvent& event) {};
+ virtual void afterSequenceSubstituted(const SymbolListSubstitutionEvent& event) {};
+
+ void fireBeforeSequenceChanged(const SymbolListEditionEvent& event) {
+ beforeSequenceChanged(event);
+ if (propagateEvents_)
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ listeners_[i]->beforeSequenceChanged(event);
+ }
+
+ void fireAfterSequenceChanged(const SymbolListEditionEvent& event) {
+ afterSequenceChanged(event);
+ if (propagateEvents_)
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ listeners_[i]->afterSequenceChanged(event);
+ }
+
+ void fireBeforeSequenceInserted(const SymbolListInsertionEvent& event) {
+ beforeSequenceInserted(event);
+ if (propagateEvents_)
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ listeners_[i]->beforeSequenceInserted(event);
+ }
+
+ void fireAfterSequenceInserted(const SymbolListInsertionEvent& event) {
+ afterSequenceInserted(event);
+ if (propagateEvents_)
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ listeners_[i]->afterSequenceInserted(event);
+ }
+
+ void fireBeforeSequenceDeleted(const SymbolListDeletionEvent& event) {
+ beforeSequenceDeleted(event);
+ if (propagateEvents_)
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ listeners_[i]->beforeSequenceDeleted(event);
+ }
+
+ void fireAfterSequenceDeleted(const SymbolListDeletionEvent& event) {
+ afterSequenceDeleted(event);
+ if (propagateEvents_)
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ listeners_[i]->afterSequenceDeleted(event);
+ }
+
+ void fireBeforeSequenceSubstituted(const SymbolListSubstitutionEvent& event) {
+ beforeSequenceSubstituted(event);
+ if (propagateEvents_)
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ listeners_[i]->beforeSequenceSubstituted(event);
+ }
+
+ void fireAfterSequenceSubstituted(const SymbolListSubstitutionEvent& event) {
+ afterSequenceSubstituted(event);
+ if (propagateEvents_)
+ for (size_t i = 0; i < listeners_.size(); ++i)
+ listeners_[i]->afterSequenceSubstituted(event);
+ }
+ /** @} */
+
+ protected:
+ void propagateEvents(bool yn) { propagateEvents_ = yn; }
+ bool propagateEvents() const { return propagateEvents_; }
+
+ };
+
+
+} //end of namespace bpp.
+
+#endif // _SYMBOLLIST_H_
+
diff --git a/src/Bpp/Seq/SymbolListTools.cpp b/src/Bpp/Seq/SymbolListTools.cpp
new file mode 100644
index 0000000..e43bcbb
--- /dev/null
+++ b/src/Bpp/Seq/SymbolListTools.cpp
@@ -0,0 +1,197 @@
+//
+// File: SymbolListTools.cpp
+// Created by: Julien Dutheil
+// Created on: Wed Apr 9 2004
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SymbolListTools.h"
+#include "Alphabet/AlphabetTools.h"
+#include <Bpp/Numeric/Random/RandomTools.h>
+
+//From the STL:
+#include <algorithm>
+
+using namespace std;
+
+using namespace bpp;
+
+void SymbolListTools::getCounts(const SymbolList& list, map<int, double>& counts, bool resolveUnknowns)
+{
+ if (!resolveUnknowns)
+ {
+ for (vector<int>::const_iterator seqit = list.getContent().begin();
+ seqit != list.getContent().end();
+ seqit++)
+ counts[*seqit]++;
+ }
+ else
+ {
+ for (vector<int>::const_iterator seqit = list.getContent().begin();
+ seqit != list.getContent().end();
+ seqit++)
+ {
+ vector<int> alias = list.getAlphabet()->getAlias(*seqit);
+ double n = (double)alias.size();
+ for (size_t j = 0; j < alias.size(); j++) counts[alias[j]] += 1./n ;
+ }
+ }
+}
+
+void SymbolListTools::getCounts(const SymbolList& list1, const SymbolList& list2, map< int, map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException)
+{
+ if (list1.size() != list2.size()) throw DimensionException("SymbolListTools::getCounts: the two sites must have the same size.", list1.size(), list2.size());
+ if (!resolveUnknowns)
+ {
+ for (size_t i = 0; i < list1.size(); i++)
+ counts[list1[i]][list2[i]]++;
+ }
+ else
+ {
+ for (size_t i = 0; i < list1.size(); i++)
+ {
+ vector<int> alias1 = list1.getAlphabet()->getAlias(list1[i]);
+ vector<int> alias2 = list2.getAlphabet()->getAlias(list2[i]);
+ double n1 = (double)alias1.size();
+ double n2 = (double)alias2.size();
+ for (size_t j = 0; j < alias1.size(); j++)
+ for (size_t k = 0; k < alias2.size(); k++)
+ counts[alias1[j]][alias2[k]] += 1./(n1*n2) ;
+ }
+ }
+}
+
+void SymbolListTools::getFrequencies(const SymbolList& list, map<int, double>& frequencies, bool resolveUnknowns)
+{
+ double n = (double)list.size();
+ map<int, double> counts;
+ getCounts(list, counts, resolveUnknowns);
+ for (map<int, double>::iterator i = counts.begin(); i != counts.end(); i++)
+ {
+ frequencies[i->first] = i->second / n;
+ }
+}
+
+void SymbolListTools::getFrequencies(const SymbolList& list1, const SymbolList& list2, map<int, map<int, double> >& frequencies, bool resolveUnknowns) throw (DimensionException)
+{
+ double n2 = (double)list1.size() * (double)list1.size();
+ map<int, map<int, double> > counts;
+ getCounts(list1, list2, counts, resolveUnknowns);
+ for (map<int, map<int, double> >::iterator i = counts.begin(); i != counts.end(); i++)
+ for (map<int, double>::iterator j = i->second.begin(); j != i->second.end(); j++)
+ {
+ frequencies[i->first][j->first] = j->second / n2;
+ }
+}
+
+double SymbolListTools::getGCContent(const SymbolList& list, bool ignoreUnresolved, bool ignoreGap) throw (AlphabetException)
+{
+ const Alphabet * alphabet = list.getAlphabet();
+ if (!AlphabetTools::isNucleicAlphabet(alphabet))
+ throw AlphabetException("SymbolListTools::getGCContent. Method only works on nucleotides.", alphabet);
+ double gc = 0;
+ double total = 0;
+ for (size_t i = 0; i < list.size(); i++) {
+ int state = list.getValue(i);
+ if (state > -1) { // not a gap
+ if (state == 1 || state == 2) { // G or C
+ gc++;
+ total++;
+ } else if (state == 0 || state == 3) { // A, T or U
+ total++;
+ } else { // Unresolved character
+ if (!ignoreUnresolved) {
+ total++;
+ switch(state) {
+ case(7): gc++; break;// G or C
+ case(4): gc+=0.5; break;// A or C
+ case(5): gc+=0.5; break;// A or G
+ case(6): gc+=0.5; break;// C or T
+ case(9): gc+=0.5; break;// G or T
+ case(10): gc+=2./3.; break;// A or C or G
+ case(11): gc+=1./3.; break;// A or C or T
+ case(12): gc+=1./3.; break;// A or G or T
+ case(13): gc+=2./3.; break;// C or G or T
+ case(14): gc+=0.5; break;// A or C or G or T
+ }
+ }
+ }
+ } else {
+ if (!ignoreGap) total++;
+ }
+ }
+ return total != 0 ? gc/total : 0;
+}
+
+size_t SymbolListTools::getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException)
+{
+ if (l1.getAlphabet()->getAlphabetType() != l2.getAlphabet()->getAlphabetType()) throw AlphabetMismatchException("SymbolListTools::getNumberOfDistinctPositions.", l1.getAlphabet(), l2.getAlphabet());
+ size_t n = min(l1.size(), l2.size());
+ size_t count = 0;
+ for (size_t i = 0; i < n; i++) {
+ if (l1[i] != l2[i]) count++;
+ }
+ return count;
+}
+
+size_t SymbolListTools::getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException)
+{
+ if (l1.getAlphabet() -> getAlphabetType() != l2.getAlphabet() -> getAlphabetType()) throw AlphabetMismatchException("SymbolListTools::getNumberOfDistinctPositions.", l1.getAlphabet(), l2.getAlphabet());
+ size_t n = min(l1.size(), l2.size());
+ size_t count = 0;
+ for (size_t i = 0; i < n; i++) {
+ if (l1[i] != -1 && l2[i] != -1) count++;
+ }
+ return count;
+}
+
+void SymbolListTools::changeGapsToUnknownCharacters(SymbolList& l)
+{
+ int unknownCode = l.getAlphabet()->getUnknownCharacterCode();
+ for (size_t i = 0; i < l.size(); i++)
+ {
+ if (l.getAlphabet()->isGap(l[i])) l[i] = unknownCode;
+ }
+}
+
+void SymbolListTools::changeUnresolvedCharactersToGaps(SymbolList& l)
+{
+ int gapCode = l.getAlphabet()->getGapCharacterCode();
+ for (size_t i = 0; i < l.size(); i++)
+ {
+ if (l.getAlphabet()->isUnresolved(l[i])) l[i] = gapCode;
+ }
+}
+
diff --git a/src/Bpp/Seq/SymbolListTools.h b/src/Bpp/Seq/SymbolListTools.h
new file mode 100644
index 0000000..9e8ef9e
--- /dev/null
+++ b/src/Bpp/Seq/SymbolListTools.h
@@ -0,0 +1,207 @@
+//
+// File: SymbolListTools.h
+// Created by: Julien Dutheil
+// Created on: Wed Apr 9 2004
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SYMBOLLISTTOOLS_H_
+#define _SYMBOLLISTTOOLS_H_
+
+#include "SymbolList.h"
+#include "Alphabet/AlphabetExceptions.h"
+#include <Bpp/Numeric/VectorExceptions.h>
+
+// From the STL:
+#include <map>
+
+namespace bpp
+{
+
+/**
+ * @brief Utilitary functions dealing with both sites and sequences.
+ */
+class SymbolListTools
+{
+ public:
+ SymbolListTools() {}
+ virtual ~SymbolListTools() {}
+
+ public:
+ /**
+ * @brief Count all states in the list.
+ *
+ * @author J. Dutheil
+ * @param list The list.
+ * @param counts The output map to store the counts (existing counts will be incremented).
+ */
+ static void getCounts(const SymbolList& list, std::map<int, size_t>& counts)
+ {
+ for(std::vector<int>::const_iterator seqit = list.getContent().begin();
+ seqit != list.getContent().end();
+ seqit++)
+ counts[*seqit]++;
+ }
+
+ /**
+ * @brief Count all pair of states for two lists of the same size.
+ *
+ * NB: The two lists do node need to share the same alphabet!
+ * The states of the first list will be used as the first index in the output,
+ * and the ones from the second list as the second index.
+ *
+ * @author J. Dutheil
+ * @param list1 The first list.
+ * @param list2 The second list.
+ * @param counts The output map to store the counts (existing counts will be incremented).
+ */
+ static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
+ {
+ if(list1.size() != list2.size()) throw DimensionException("SymbolListTools::getCounts: the two sites must have the same size.", list1.size(), list2.size());
+ for(size_t i = 0; i < list1.size(); i++)
+ counts[list1[i]][list2[i]]++;
+ }
+
+ /**
+ * @brief Count all states in the list, optionaly resolving unknown characters.
+ *
+ * For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.
+ *
+ * @author J. Dutheil
+ * @param list The list.
+ * @param counts The output map to store the counts (existing ocunts will be incremented).
+ * @param resolveUnknowns Tell is unknown characters must be resolved.
+ * For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.
+ * @return A map with all states and corresponding counts.
+ */
+ static void getCounts(const SymbolList& list, std::map<int, double>& counts, bool resolveUnknowns);
+
+ /**
+ * @brief Count all pair of states for two lists of the same size, optionaly resolving unknown characters.
+ *
+ * For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.
+ *
+ * NB: The two lists do node need to share the same alphabet!
+ * The states of the first list will be used as the first index in the output,
+ * and the ones from the second list as the second index.
+ *
+ * @author J. Dutheil
+ * @param list1 The first list.
+ * @param list2 The second list.
+ * @param counts The output map to store the counts (existing ocunts will be incremented).
+ * @param resolveUnknowns Tell is unknown characters must be resolved.
+ * For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.
+ * @return A map with all states and corresponding counts.
+ */
+ static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
+
+ /**
+ * @brief Get all states frequencies in the list.
+ *
+ * @author J. Dutheil
+ * @param list The list.
+ * @param resolveUnknowns Tell is unknown characters must be resolved.
+ * For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.
+ * @param frequencies The output map with all states and corresponding frequencies. Existing frequencies will be erased if any.
+ */
+ static void getFrequencies(const SymbolList& list, std::map<int, double>& frequencies, bool resolveUnknowns = false);
+
+ /**
+ * @brief Get all state pairs frequencies for two lists of the same size..
+ *
+ * @author J. Dutheil
+ * @param list1 The first list.
+ * @param list2 The second list.
+ * @param resolveUnknowns Tell is unknown characters must be resolved.
+ * For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.
+ * @param frequencies The output map with all state pairs and corresponding frequencies. Existing frequencies will be erased if any.
+ */
+ static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
+
+ /**
+ * @brief Get the GC content of a symbol list.
+ *
+ * @param list The list.
+ * @return The proportion of G and C states in the list.
+ * @param ignoreUnresolved Do not count unresolved states. Otherwise, weight by each state probability in case of ambiguity (e.g. the R state counts for 0.5).
+ * @param ignoreGap Do not count gaps in total.
+ * @throw AlphabetException If the list is not made of nucleotide states.
+ */
+ static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
+
+ /**
+ * @brief Get the number of distinct positions.
+ *
+ * The comparison in achieved from position 0 to the minimum size of the two vectors.
+ *
+ * @param l1 SymbolList 1.
+ * @param l2 SymbolList 2.
+ * @return The number of distinct positions.
+ * @throw AlphabetMismatchException if the two lists have not the same alphabet type.
+ */
+ static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
+
+ /**
+ * @brief Get the number of positions without gap.
+ *
+ * The comparison in achieved from position 0 to the minimum size of the two vectors.
+ *
+ * @param l1 SymbolList 1.
+ * @param l2 SymbolList 2.
+ * @return The number of positions without gap.
+ * @throw AlphabetMismatchException if the two lists have not the same alphabet type.
+ */
+ static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
+
+ /**
+ * @brief Change all gap elements to unknown characters.
+ *
+ * @param l The input list of characters.
+ */
+ static void changeGapsToUnknownCharacters(SymbolList& l);
+
+ /**
+ * @brief Change all unknown characters to gap elements.
+ *
+ * @param l The input list of characters.
+ */
+ static void changeUnresolvedCharactersToGaps(SymbolList& l);
+
+};
+
+} //end of namespace bpp.
+
+#endif // _SYMBOLLISTTOOLS_H_
+
diff --git a/src/Bpp/Seq/Transliterator.cpp b/src/Bpp/Seq/Transliterator.cpp
new file mode 100644
index 0000000..990632c
--- /dev/null
+++ b/src/Bpp/Seq/Transliterator.cpp
@@ -0,0 +1,72 @@
+//
+// File: Transliterator.cpp
+// Created by: Julien Dutheil
+// Created on: Sun Oct 12 14:25:25 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "Transliterator.h"
+
+using namespace bpp;
+
+Sequence* AbstractTransliterator::translate(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
+{
+ if (sequence.getAlphabet()->getAlphabetType() != getSourceAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("AbstractTransliterator::translate", getSourceAlphabet(), getTargetAlphabet());
+ Sequence* tSeq = new BasicSequence(sequence.getName(), "", sequence.getComments(), getTargetAlphabet());
+ int gap = sequence.getAlphabet()->getGapCharacterCode();
+ for (unsigned int i = 0; i < sequence.size(); ++i)
+ {
+ int state = sequence.getValue(i);
+ if (state == gap)
+ tSeq->addElement(gap);
+ else
+ tSeq->addElement(translate(state));
+ }
+ return tSeq;
+}
+
+Sequence* AbstractReverseTransliterator::reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
+{
+ if (sequence.getAlphabet()->getAlphabetType() != getTargetAlphabet()->getAlphabetType())
+ throw AlphabetMismatchException("AbstractReverseTransliterator::reverse", getSourceAlphabet(), getTargetAlphabet());
+ Sequence* rSeq = new BasicSequence(sequence.getName(), "", sequence.getComments(), getSourceAlphabet());
+ for (unsigned int i = 0; i < sequence.size(); ++i)
+ {
+ rSeq->addElement(reverse(sequence.getValue(i)));
+ }
+ return rSeq;
+}
+
diff --git a/src/Bpp/Seq/Transliterator.h b/src/Bpp/Seq/Transliterator.h
new file mode 100644
index 0000000..b7e971f
--- /dev/null
+++ b/src/Bpp/Seq/Transliterator.h
@@ -0,0 +1,187 @@
+//
+// File: Transliterator.h
+// Created by: Julien Dutheil
+// Created on: Sun Oct 12 14:25:25 2003
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _TRANSLITERATOR_H_
+#define _TRANSLITERATOR_H_
+
+#include "Alphabet/Alphabet.h"
+#include "Sequence.h"
+
+namespace bpp
+{
+
+/**
+ * @brief This interface is used when translating a sequence from an alphabet to another: it gives the translation rules, eg: RNA -> DNA.
+ */
+class Transliterator
+{
+ public:
+ Transliterator() {}
+ virtual ~Transliterator() {}
+
+ public:
+
+ /**
+ * @brief Get the source alphabet.
+ *
+ * @return The source alphabet.
+ */
+ virtual const Alphabet * getSourceAlphabet() const = 0;
+
+ /**
+ * @brief Get the target alphabet.
+ *
+ * @return The target alphabet.
+ */
+ virtual const Alphabet * getTargetAlphabet() const = 0;
+
+ /**
+ * @brief Translate a given state coded as a int from source alphabet to target alphabet.
+ *
+ * @param state A state in source alphabet.
+ * @return The corresponding state in target alphabet.
+ * @throw BadIntException If the state is not a proper state for source alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+ virtual int translate(int state) const throw (BadIntException, Exception) = 0;
+
+ /**
+ * @brief Translate a given state coded as a string from source alphabet to target alphabet.
+ *
+ * @param state A state in source alphabet.
+ * @return The corresponding state in target alphabet.
+ * @throw BadCharException If the state is not a proper state for source alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+ virtual std::string translate(const std::string & state) const throw (BadCharException, Exception) = 0;
+
+ /**
+ * @brief Translate a whole sequence from source alphabet to target alphabet.
+ *
+ * @param sequence A sequence in source alphabet.
+ * @return The corresponding sequence in target alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the source alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+ virtual Sequence * translate(const Sequence & sequence) const throw (AlphabetMismatchException, Exception) = 0;
+};
+
+/**
+ * @brief The same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA;
+ */
+class ReverseTransliterator:
+ public virtual Transliterator
+{
+ public:
+ ReverseTransliterator() {}
+ virtual ~ReverseTransliterator() {}
+
+ public:
+
+ /**
+ * @brief Translate a given state coded as a int from target alphabet to source alphabet.
+ *
+ * @param state A state in target alphabet.
+ * @return The corresponding state in source alphabet.
+ * @throw BadIntException If the state is not a proper state for target alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+ virtual int reverse(int state) const throw (BadIntException, Exception) = 0;
+
+ /**
+ * @brief Translate a given state coded as a string from target alphabet to source alphabet.
+ *
+ * @param state A state in target alphabet.
+ * @return The corresponding state in source alphabet.
+ * @throw BadCharException If the state is not a proper state for target alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+ virtual std::string reverse(const std::string & state) const throw (BadCharException, Exception) = 0;
+
+ /**
+ * @brief Translate a whole sequence from target alphabet to source alphabet.
+ *
+ * @param sequence A sequence in target alphabet.
+ * @return The corresponding sequence in source alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the target alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+ virtual Sequence * reverse(const Sequence & sequence) const throw (AlphabetMismatchException, Exception) = 0;
+};
+
+/**
+ * @brief Partial implementation of the Transliterator interface.
+ */
+class AbstractTransliterator:
+ public virtual Transliterator
+{
+ public:
+ AbstractTransliterator() {}
+ virtual ~AbstractTransliterator() {}
+
+ public:
+ virtual int translate(int state) const throw (BadIntException, Exception) = 0;
+ virtual std::string translate(const std::string & state) const throw (BadCharException, Exception) = 0;
+ virtual Sequence * translate(const Sequence & sequence) const throw (AlphabetMismatchException, Exception);
+};
+
+/**
+ * @brief Partial implementation of the ReverseTransliterator interface.
+ */
+class AbstractReverseTransliterator:
+ public ReverseTransliterator,
+ public AbstractTransliterator
+{
+ public:
+ AbstractReverseTransliterator() {}
+ virtual ~AbstractReverseTransliterator() {}
+
+ public:
+ //These two redeclarations must be here because of the multiple inheritance.
+ virtual const Alphabet * getSourceAlphabet() const = 0;
+ virtual const Alphabet * getTargetAlphabet() const = 0;
+ virtual int reverse(int state) const throw (BadIntException, Exception) = 0;
+ virtual std::string reverse(const std::string & state) const throw (BadCharException, Exception) = 0;
+ virtual Sequence * reverse(const Sequence & sequence) const throw (AlphabetMismatchException, Exception);
+};
+
+} //end of namespace bpp.
+
+#endif //_TRANSLITERATOR_H_
+
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 0000000..2478551
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,246 @@
+# CMake script for Bio++ Sequence Library
+# Author: Sylvain Gaillard and Julien Dutheil
+# Created: 20/08/2009
+
+# File list
+SET(CPP_FILES
+ Bpp/Seq/DNAToRNA.cpp
+ Bpp/Seq/NucleicAcidsReplication.cpp
+ Bpp/Seq/Sequence.cpp
+ Bpp/Seq/SequenceWithAnnotation.cpp
+ Bpp/Seq/SequenceWithAnnotationTools.cpp
+ Bpp/Seq/SequenceWithQuality.cpp
+ Bpp/Seq/SequenceExceptions.cpp
+ Bpp/Seq/SequencePositionIterators.cpp
+ Bpp/Seq/SequenceTools.cpp
+ Bpp/Seq/SequenceWithQualityTools.cpp
+ Bpp/Seq/SequenceWalker.cpp
+ Bpp/Seq/Site.cpp
+ Bpp/Seq/SiteExceptions.cpp
+ Bpp/Seq/SiteTools.cpp
+ Bpp/Seq/StringSequenceTools.cpp
+ Bpp/Seq/SymbolList.cpp
+ Bpp/Seq/SymbolListTools.cpp
+ Bpp/Seq/Transliterator.cpp
+ Bpp/Seq/DistanceMatrix.cpp
+ Bpp/Seq/CodonSiteTools.cpp
+ Bpp/Seq/Alphabet/AbstractAlphabet.cpp
+ Bpp/Seq/Alphabet/AlphabetExceptions.cpp
+ Bpp/Seq/Alphabet/AlphabetTools.cpp
+ Bpp/Seq/Alphabet/CodonAlphabet.cpp
+ Bpp/Seq/Alphabet/DefaultAlphabet.cpp
+ Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp
+ Bpp/Seq/Alphabet/DNA.cpp
+ Bpp/Seq/Alphabet/ProteicAlphabet.cpp
+ Bpp/Seq/Alphabet/RNA.cpp
+ Bpp/Seq/Alphabet/StandardCodonAlphabet.cpp
+ Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.cpp
+ Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.cpp
+ Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.cpp
+ Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.cpp
+ Bpp/Seq/Alphabet/WordAlphabet.cpp
+ Bpp/Seq/Alphabet/RNY.cpp
+ Bpp/Seq/Alphabet/BinaryAlphabet.cpp
+ Bpp/Seq/GeneticCode/GeneticCode.cpp
+ Bpp/Seq/GeneticCode/StandardGeneticCode.cpp
+ Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp
+ Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp
+ Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp
+ Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp
+ Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp
+ Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp
+ Bpp/Seq/AlphabetIndex/BLOSUM50.cpp
+ Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp
+ Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp
+ Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp
+ Bpp/Seq/AlphabetIndex/SimpleScore.cpp
+ Bpp/Seq/AlphabetIndex/__GranthamMatrixCode
+ Bpp/Seq/AlphabetIndex/__MiyataMatrixCode
+ Bpp/Seq/AlphabetIndex/__BLOSUM50MatrixCode
+ Bpp/Seq/Container/AbstractSequenceContainer.cpp
+ Bpp/Seq/Container/AlignedSequenceContainer.cpp
+ Bpp/Seq/Container/MapSequenceContainer.cpp
+ Bpp/Seq/Container/SequenceContainerTools.cpp
+ Bpp/Seq/Container/SiteContainerExceptions.cpp
+ Bpp/Seq/Container/SiteContainerTools.cpp
+ Bpp/Seq/Container/VectorSequenceContainer.cpp
+ Bpp/Seq/Container/VectorSiteContainer.cpp
+ Bpp/Seq/Container/CompressedVectorSiteContainer.cpp
+ Bpp/Seq/Container/SiteContainerIterator.cpp
+ Bpp/Seq/Container/SequenceContainerIterator.cpp
+ Bpp/Seq/Io/Clustal.cpp
+ Bpp/Seq/Io/Dcse.cpp
+ Bpp/Seq/Io/Fasta.cpp
+ Bpp/Seq/Io/Mase.cpp
+ Bpp/Seq/Io/MaseTools.cpp
+ Bpp/Seq/Io/Phylip.cpp
+ Bpp/Seq/Io/IoSequenceFactory.cpp
+ Bpp/Seq/Io/GenBank.cpp
+ Bpp/Seq/Io/PhredPhd.cpp
+ Bpp/Seq/Io/PhredPoly.cpp
+ Bpp/Seq/Io/NexusIoSequence.cpp
+ Bpp/Seq/Io/NexusTools.cpp
+ Bpp/Seq/Io/Stockholm.cpp
+ Bpp/Seq/Io/StreamSequenceIterator.cpp
+ Bpp/Seq/Io/BppOSequenceReaderFormat.cpp
+ Bpp/Seq/Io/BppOSequenceWriterFormat.cpp
+ Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp
+ Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp
+ Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp
+ Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp
+ Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp
+ Bpp/Seq/App/SequenceApplicationTools.cpp
+ )
+
+SET(H_FILES
+ Bpp/Seq/CodonSiteTools.h
+ Bpp/Seq/DNAToRNA.h
+ Bpp/Seq/NucleicAcidsReplication.h
+ Bpp/Seq/SequenceExceptions.h
+ Bpp/Seq/SequencePositionIterators.h
+ Bpp/Seq/Sequence.h
+ Bpp/Seq/SequenceIterator.h
+ Bpp/Seq/SequenceWithAnnotation.h
+ Bpp/Seq/SequenceWithAnnotationTools.h
+ Bpp/Seq/SequenceWithQuality.h
+ Bpp/Seq/SequenceTools.h
+ Bpp/Seq/SequenceWithQualityTools.h
+ Bpp/Seq/SequenceWalker.h
+ Bpp/Seq/SiteExceptions.h
+ Bpp/Seq/Site.h
+ Bpp/Seq/SiteIterator.h
+ Bpp/Seq/SiteTools.h
+ Bpp/Seq/StringSequenceTools.h
+ Bpp/Seq/SymbolList.h
+ Bpp/Seq/SymbolListTools.h
+ Bpp/Seq/Transliterator.h
+ Bpp/Seq/DistanceMatrix.h
+ Bpp/Seq/Alphabet/AbstractAlphabet.h
+ Bpp/Seq/Alphabet/AlphabetExceptions.h
+ Bpp/Seq/Alphabet/Alphabet.h
+ Bpp/Seq/Alphabet/AlphabetState.h
+ Bpp/Seq/Alphabet/AlphabetTools.h
+ Bpp/Seq/Alphabet/CodonAlphabet.h
+ Bpp/Seq/Alphabet/CaseMaskedAlphabet.h
+ Bpp/Seq/Alphabet/DefaultAlphabet.h
+ Bpp/Seq/Alphabet/DNA.h
+ Bpp/Seq/Alphabet/LetterAlphabet.h
+ Bpp/Seq/Alphabet/NucleicAlphabet.h
+ Bpp/Seq/Alphabet/NucleicAlphabetState.h
+ Bpp/Seq/Alphabet/ProteicAlphabet.h
+ Bpp/Seq/Alphabet/ProteicAlphabetState.h
+ Bpp/Seq/Alphabet/RNA.h
+ Bpp/Seq/Alphabet/StandardCodonAlphabet.h
+ Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.h
+ Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.h
+ Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.h
+ Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.h
+ Bpp/Seq/Alphabet/WordAlphabet.h
+ Bpp/Seq/Alphabet/RNY.h
+ Bpp/Seq/Alphabet/BinaryAlphabet.h
+ Bpp/Seq/GeneticCode/GeneticCode.h
+ Bpp/Seq/GeneticCode/StandardGeneticCode.h
+ Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h
+ Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h
+ Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h
+ Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h
+ Bpp/Seq/Io/AbstractISequence.h
+ Bpp/Seq/Io/AbstractIAlignment.h
+ Bpp/Seq/Io/AbstractOSequence.h
+ Bpp/Seq/Io/AbstractOAlignment.h
+ Bpp/Seq/Io/Clustal.h
+ Bpp/Seq/Io/Dcse.h
+ Bpp/Seq/Io/Fasta.h
+ Bpp/Seq/Io/IOSequence.h
+ Bpp/Seq/Io/ISequence.h
+ Bpp/Seq/Io/ISequenceStream.h
+ Bpp/Seq/Io/IoSequenceStream.h
+ Bpp/Seq/Io/Mase.h
+ Bpp/Seq/Io/MaseTools.h
+ Bpp/Seq/Io/OSequence.h
+ Bpp/Seq/Io/OSequenceStream.h
+ Bpp/Seq/Io/Phylip.h
+ Bpp/Seq/Io/GenBank.h
+ Bpp/Seq/Io/PhredPhd.h
+ Bpp/Seq/Io/PhredPoly.h
+ Bpp/Seq/Io/NexusIOSequence.h
+ Bpp/Seq/Io/NexusTools.h
+ Bpp/Seq/Io/Stockholm.h
+ Bpp/Seq/Io/IoSequenceFactory.h
+ Bpp/Seq/Io/SequenceFileIndex.h
+ Bpp/Seq/Io/StreamSequenceIterator.h
+ Bpp/Seq/Io/BppOSequenceReaderFormat.h
+ Bpp/Seq/Io/BppOSequenceWriterFormat.h
+ Bpp/Seq/Io/BppOAlignmentReaderFormat.h
+ Bpp/Seq/Io/BppOAlignmentWriterFormat.h
+ Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h
+ Bpp/Seq/Io/BppOAlphabetIndex1Format.h
+ Bpp/Seq/Io/BppOAlphabetIndex2Format.h
+ Bpp/Seq/Container/VectorSequenceContainer.h
+ Bpp/Seq/Container/VectorSiteContainer.h
+ Bpp/Seq/Container/CompressedVectorSiteContainer.h
+ Bpp/Seq/Container/MapSequenceContainer.h
+ Bpp/Seq/Container/OrderedSequenceContainer.h
+ Bpp/Seq/Container/AbstractSequenceContainer.h
+ Bpp/Seq/Container/AlignedSequenceContainer.h
+ Bpp/Seq/Container/SequenceContainerExceptions.h
+ Bpp/Seq/Container/SequenceContainer.h
+ Bpp/Seq/Container/SequenceContainerTools.h
+ Bpp/Seq/Container/SiteContainerExceptions.h
+ Bpp/Seq/Container/SiteContainer.h
+ Bpp/Seq/Container/SiteContainerTools.h
+ Bpp/Seq/Container/SiteContainerIterator.h
+ Bpp/Seq/AlphabetIndex/AlphabetIndex1.h
+ Bpp/Seq/AlphabetIndex/AlphabetIndex2.h
+ Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h
+ Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h
+ Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h
+ Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h
+ Bpp/Seq/AlphabetIndex/BLOSUM50.h
+ Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h
+ Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h
+ Bpp/Seq/AlphabetIndex/AAIndex1Entry.h
+ Bpp/Seq/AlphabetIndex/AAIndex2Entry.h
+ Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h
+ Bpp/Seq/AlphabetIndex/AAChargeIndex.h
+ Bpp/Seq/AlphabetIndex/SimpleScore.h
+ Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h
+ Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h
+ Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h
+ Bpp/Seq/AlphabetIndex/AAVolumeIndex.h
+ Bpp/Seq/AlphabetIndex/AASurfaceIndex.h
+ Bpp/Seq/AlphabetIndex/AAMassIndex.h
+ Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h
+ Bpp/Seq/AlphabetIndex/AASEASup30Index.h
+ Bpp/Seq/AlphabetIndex/AASEAInf10Index.h
+ Bpp/Seq/AlphabetIndex/AASEA1030Index.h
+ Bpp/Seq/App/SequenceApplicationTools.h
+ )
+
+# Build the static lib
+ADD_LIBRARY(bppseq-static STATIC ${CPP_FILES})
+SET_TARGET_PROPERTIES(bppseq-static
+ PROPERTIES OUTPUT_NAME bpp-seq
+ CLEAN_DIRECT_OUTPUT 1
+ )
+TARGET_LINK_LIBRARIES(bppseq-static ${LIBS})
+
+# Build the shared lib
+ADD_LIBRARY(bppseq-shared SHARED ${CPP_FILES})
+SET_TARGET_PROPERTIES(bppseq-shared
+ PROPERTIES OUTPUT_NAME bpp-seq
+ CLEAN_DIRECT_OUTPUT 1
+ VERSION ${BPPSEQ_VERSION}
+ SOVERSION ${BPPSEQ_VERSION_MAJOR}
+ )
+TARGET_LINK_LIBRARIES(bppseq-shared ${LIBS})
+
+# Install libs
+INSTALL(TARGETS bppseq-static bppseq-shared DESTINATION lib${LIB_SUFFIX})
+
+# Install headers
+INSTALL(DIRECTORY Bpp/ DESTINATION include/Bpp FILES_MATCHING PATTERN "*.h")
+
+# Generate generic include files (.all)
+INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_SOURCE_DIR}/genIncludes.sh ${CMAKE_PREFIX_PATH}/include/Bpp)")
+
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
new file mode 100644
index 0000000..57a9c55
--- /dev/null
+++ b/test/CMakeLists.txt
@@ -0,0 +1,66 @@
+# CMake script for bpp-seq unit tests
+# Author: Julien Dutheil
+# Created: 30/10/2010
+
+MACRO(TEST_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
+ #start:
+ FIND_PATH(${lib_name}_INCLUDE_DIR ${include_to_find})
+
+ SET(${lib_name}_NAMES ${lib_name} ${lib_name}.lib ${lib_name}.dll)
+ FIND_LIBRARY(${lib_name}_LIBRARY NAMES ${${lib_name}_NAMES})
+ IF(${lib_name}_LIBRARY)
+ MESSAGE("-- Library ${lib_name} found here:")
+ MESSAGE(" includes: ${${lib_name}_INCLUDE_DIR}")
+ MESSAGE(" dynamic libraries: ${${lib_name}_LIBRARY}")
+ MESSAGE(WARNING "Library ${lib_name} is already installed in the system tree. Test will be built against it. This may lead to unexpected results. You may want to do 'make install' before 'make test', or remove the installed version.")
+ ELSE()
+ SET(${lib_name}_LIBRARY "-L../src -lbpp-seq")
+ SET(${lib_name}_INCLUDE_DIR "../src/")
+ ENDIF()
+ INCLUDE_DIRECTORIES(${${lib_name}_INCLUDE_DIR})
+ SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_LIBRARY})
+ENDMACRO(TEST_FIND_LIBRARY)
+
+#Find the bpp-seq library library:
+TEST_FIND_LIBRARY(LIBS bpp-seq Bpp/Seq/Alphabet/Alphabet.h)
+
+ADD_EXECUTABLE(test_alphabets test_alphabets.cpp)
+TARGET_LINK_LIBRARIES(test_alphabets ${LIBS})
+ADD_TEST(test_alphabets "test_alphabets")
+
+ADD_EXECUTABLE(test_sequences test_sequences.cpp)
+TARGET_LINK_LIBRARIES(test_sequences ${LIBS})
+ADD_TEST(test_sequences "test_sequences")
+
+ADD_EXECUTABLE(test_io test_io.cpp)
+TARGET_LINK_LIBRARIES(test_io ${LIBS})
+ADD_TEST(test_io "test_io")
+
+ADD_EXECUTABLE(test_containers test_containers.cpp)
+TARGET_LINK_LIBRARIES(test_containers ${LIBS})
+ADD_TEST(test_containers "test_containers")
+
+ADD_EXECUTABLE(test_alignment_scores test_alignment_scores.cpp)
+TARGET_LINK_LIBRARIES(test_alignment_scores ${LIBS})
+ADD_TEST(test_alignment_scores "test_alignment_scores")
+
+ADD_EXECUTABLE(test_walker test_walker.cpp)
+TARGET_LINK_LIBRARIES(test_walker ${LIBS})
+ADD_TEST(test_walker "test_walker")
+
+ADD_EXECUTABLE(test_bowker test_bowker.cpp)
+TARGET_LINK_LIBRARIES(test_bowker ${LIBS})
+ADD_TEST(test_bowker "test_bowker")
+
+IF(UNIX)
+ SET_PROPERTY(TEST test_alphabets test_sequences test_io test_containers test_alignment_scores test_walker test_bowker PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:../src")
+ENDIF()
+
+IF(APPLE)
+ SET_PROPERTY(TEST test_alphabets test_sequences test_io test_containers test_alignment_scores test_walker test_bowker PROPERTY ENVIRONMENT "DYLD_LIBRARY_PATH=$ENV{DYLD_LIBRARY_PATH}:../src")
+ENDIF()
+
+IF(WIN32)
+ SET(ENV{PATH} "$ENV{PATH};..\\src")
+ENDIF()
+
diff --git a/test/example.aln b/test/example.aln
new file mode 100644
index 0000000..577476e
--- /dev/null
+++ b/test/example.aln
@@ -0,0 +1,2143 @@
+CLUSTAL W (1.8) multiple sequence alignment
+
+
+t73 LIVSQIRVMVRDG--IHKAMDEE-V------------LIARRVKPYSGNGTQVRNDVEDA
+t66 LIVSQIRVMVRDG--IHKAMDEE-V------------LIARRVKPCSGNGTQVRNDVEDA
+t32 LIVSQIRVMVRDG--IHKAMDEE-V------------LIARRVKPYSGNGTQVRNDVEDA
+t75 LIVSEIRVMVRDE--VHKAMDEE-C------------LIARRVKPYSGNGNQIRNDIEDA
+t79 LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTFSGSQNQVRNAVEDA
+t27 LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTMSGSQNQVRNAVEDA
+t93 LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTMSGSQNQVRNAVEDA
+t59 LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTFSGSQNQVRNAVEDA
+t7 LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKKFSGSQGQVRNAIEDA
+t78 LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTFSGSQGQVRNAIEDA
+t12 LIVSEVRVMVRDG--INIAIDEL-C------------LIANRVKAFSGHQNQVRNAMEDA
+t81 LIVSEVRHMVRDG--ANVAIDEL-C------------LIACRVKAFSGHGHQVRNAVEDA
+t21 LIVSEVRHMVRDG--ANIAIDEL-C------------LIACRVKAFSGHGNQVRNAVEDA
+t80 LIVSEVRHMVRDG--VNIAVDEI-C------------LIANRVKSMSGQGNQVRNAMEMA
+t14 LIVSEVRHMVRDG--VNIAVDEI-C------------LIANRVKSMSGQGNQVRNAMEMA
+t85 LIVSEVRHVVRDG--VNIAVDEI-C------------LIANRVKSMSGQGNQVRNAMEMA
+t62 LIVSEVRVMVRDG--IHIAVDEI-C------------LIANRVKCMSGQGNQARNAMEMA
+t19 LIVSEVRHMVRDG--INIAVDEI-C------------LIANRVKCVSGQGNQARNAMEMA
+t77 LIVSEVRHMVRDG--INIAVDEI-C------------LIANRVKSMSGQGNQARNAMEMA
+t88 LIVSECRLIIRDG--NHDAIDEM-CCVANDLNNEIERLVASMVKSFRGHDSQARNNSECM
+t37 LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECI
+t35 LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECI
+t48 LIVSDMRLIIREG--SDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECI
+t55 LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECI
+t46 LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECI
+t67 LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECI
+t57 LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECI
+t56 LIVSEWRLFIRDG--HDDAIDEM-CCEANELNNDIEKLVASMVKGFRGHDSQARNNAECI
+t13 GIVSECRMIIRDE--HDDAIDEM-C------------LVASMVKKLSGCENQARNNHECA
+t5 GIVSECRMIIRDE--HDDAIDEM-C------------LVASMVKKLSGCENQARNNHECA
+t38 GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECA
+t33 GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECA
+t100 GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECA
+t34 GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECA
+t84 GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCDDQARNNHECA
+t92 GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECA
+t3 GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEQQARNNRECA
+t22 GIVSECRVIIRDQ--SDDAIDER-Y------------LVASVVKRLSGCENQARNNRECA
+t64 GIVSECRMIIRDE--TDDAIDEV-C------------LVASMVKKLSGCENQTRNNRECA
+t18 GIVSECRMIIRDE--TDDAIDEV-C------------LVASMVKKLSGCENQTRNNRECA
+t68 GIVSECRMIIRDE--TDDAIDEV-C------------LVASMVKKLSGCENQTRNNRECA
+t28 GIVSECRMIIRDE--ADDAIDEM-C------------LVASMVKKLSGCENQARNNRECA
+t82 GIVSECRMIIRDE--ADDAIDEM-C------------LVASMVKKLSGCENQARNNRECA
+t41 GIVSECRMIIRDE--ADDAIDEM-C------------LVASMVKKLSGCENQARNNRECA
+t71 GIVSECRMIIRDQ--SDDAIDEMVV------------LVASMVKEMSGCENQARNNSECA
+t94 GIVSECRMIIRDQ--SDDAIDEMVC------------LVASMVKELSGCENQARNNRECA
+t99 GIVSEVRMIIRDE--SDDAIDEM-C------------LVASMVKALSGCENQARNNRECA
+t40 GIVSECRMIIRDE--SDDAIDEV-C------------LVASMVKALSGCENQARNNRECA
+t90 GIVSECRMIIRDE--SDDAIDEV-C------------LVASMVKALSGCENQARNNRECA
+t4 GIVSECRMIIRDE--PDDAIDEV-C------------LVASMVKELSGCENQARNNRECA
+t36 MIWSEVRKMVRER--REQAIDNK-C------------LIAARVKMMSGYVLQVRNALEDA
+t87 MIWSEVRKMVRER--REQAIDNK-C------------LIAARVKMMSGYMLQVRNALEDA
+t89 MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDA
+t39 MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDA
+t8 MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDA
+t6 MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDA
+t58 MIWSEYRHMVREG--RDQAIDNK-C------------LIAARVKVMSGYVLQVRNAPEDA
+t54 MIWSEYRHMVREG--RDQAIDNK-C------------LIAARVKVMSGYVLQVRNAPEDA
+t65 MIWSEYRQMVREG--NDQSIDNK-C------------LIADRVKMMSGVVRQVRNAPEDA
+t29 MIWSEYRQMVREG--NDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t98 MIWSEHRQMVREG--NDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t83 MIWSEYRQMVREG--NDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t95 MIWSEYRQMVREG--TDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t20 MIWSEYRQMVREG--TDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t69 MIWSDYRQMVREG--GDDSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t2 MIWSDYRQMVREG--GDDSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t10 MIWSDYRQMVREG--GDDSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t31 MIWSEYRSMVREG--ADQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t15 MIWSEYRSMVREG--SDQSIDNH-C------------LIAARVKMMSGVVRQVRNAPEDA
+t63 MIWSEYRSMVREG--SDQSIDNK-C------------LTAARVKLMSGVVRQVRNAPEDA
+t50 MIWSEYRSMVREG--SDQSIDNK-C------------LTAARVKLMSGVVRQVRNAPEDA
+t25 MIWSEYRSMVREG--SDQSIDNK-C------------LTAARVKMMSGVVRQVRNAPEDA
+t51 MIWSEYRSMVREG--SDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDA
+t9 MIWSECRQMVREK--TDNAIDNQ-C------------LIAARVKENSGHVKQVRNDSEDI
+t47 MIWSECRQMVREK--SDNAIDNQ-C------------QIAARVKRNSGHVKQVRNDSEDI
+t60 MIWSECRQMVREK--TDNAIDNQ-C------------QIAARVKENSGHVKQVRNDSEDI
+t30 MIWSECRQMVREK--TDNAIDNQ-C------------QIAARVKENSGHVKQVRNDSEDI
+t70 MIWSECRQMVREK--NDNAIDNQ-C------------LIAARVKEDSGHVKQVRNASEDI
+t91 MIWSECRQMVREK--NDNAIDNQ-C------------LIAARVKEDSGHVKQVRNASEDI
+t49 MIWSECRQMVREK--NDNAIDNQ-C------------LIAARVKENSGHVKQVRNASEDI
+t52 MIWSEERQMVREK--VDNAVDNQ-C------------LIAARVKENCGHVKQVRNASEDI
+t43 MIWSEVRQMVREG--SDNAIDNR-C------------LIAARVKHVQGHVKQVRNANEDA
+t1 MIWSEVRQMMREG--TDNAIDNQ-C------------LIAARVKHMQGHVKQVRNANEDA
+t86 MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKPVQGHVKQVRNANEDA
+t72 MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHVQGHVKQVRNANEDA
+t96 MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHVQGHVKQVRNANEDA
+t44 MIWSEVRQMVREG--TDNAIDTR-C------------LIAARVKHMQGHVKQVRNANEDA
+t45 MIWSEVRQMVREG--TDNAIDNC-C------------LIAARVKHMQGHVKQVRNANEDA
+t74 MIWSEVRQMVREG--TDNAIDNC-C------------LIAARVKHMQGHVKQVRNANEDA
+t26 MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHMSGHVKQVRNANEDA
+t61 MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHMSGHVKQVRNANEDA
+t97 MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHMSGHMKQVRNANEDA
+t17 MIWSEVRQMVREG--ADNAIDNR-C------------LIAARVKHFSGHTKQVRNANEDA
+t11 MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHFSGHTKQVRNANEDA
+t23 MIWSECQRMLREH--EDQAIANE-C------------LIAFKVKLVNGHVKQVRNASEDA
+t76 LSSSHEVRVVNHKSKPDEHIADK-D------------MCADAMCNGSGHTGRIHNAVEGG
+t53 LSSSHEVRVVNHKSKPDEHIADK-D------------MCADAMCNGSGHTGRIHNAVEGG
+t16 LSSSHEVRVVNHKSKPDEHIADK-D------------MCADAMCNGSGHTGRIHNAVEGG
+t42 LSSSHEMRVVHHKSKPDEEIADQ-D------------LCAEEMCKGSGHTGRIHSAVEGG
+t24 QSSSHEMRVVHHKSKPDEEITDQ-D------------LCAEEMCKGSGHTGRIHSAVEGG
+
+
+t73 N--CQEFVGI---RELGKH-YK-CMDGFHTVNNGAGEN-SESAMWIFDLWMCKLNHGMQR
+t66 N--CQEFVGI---RELGKH-YK-CMDGFHTVNNGAGEN-SESAMWIFDLWMCKLNHGMQR
+t32 N--CQEFVGI---RELGKH-YK-CMDGFHTVNNGAGEN-SESAMWIFDLWMCKLNHGMQR
+t75 N--GQEFVGI---RELGKH-YD-CMDGYHTVNNGAGEN-SESAMWIFDLWMCKLNHGMQR
+t79 A--RPDFVGT---RELGKQ-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW
+t27 A--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW
+t93 A--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW
+t59 A--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-SESAVVIFDVWMCQLPHGMQW
+t7 A--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW
+t78 A--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW
+t12 Q--RPDFVGI---RELGKQ-YQ-CMDGHGAVDTGAGRN-SESAVWIFDIWMCKLAHGMQW
+t81 A--RPDFIGI---RELGKP-Y--CMDGHGAVNTGAGHN-SESAVWIFDIWMYKLSHGMQW
+t21 P--RPDFIGV---RELGKP-Y--CMDGHGAVNTGAGVN-SESAVWIFDIWMYKLSHGMQW
+t80 A--RQNFVGM---RELEKV-YE-CMDGQGAVNTEAGNN-SESAVWIFDIWMCKLTHGMQD
+t14 A--RQNFVGM---RELEKV-YQ-CMDGQGAVNTEAGNN-SESAVWIFDIWMCKLTHGMQD
+t85 A--RQNFVGM---RELDKA-YQ-CMDGQKAVNTEAGNN-SESAVWIFDICMCKLTHGMQD
+t62 A--RQNFVGM---RELGKQ-YQ-CMDGQGAVNTEAGNN-SESAVWIFDIWMCRLTHGMQD
+t19 A--RQNFVGM---RELGKQ-YQ-CMDGQGAVNTEAGNN-SESAVWIFDIWMCRLTHGMQD
+t77 A--RQNFVGM---RELGKQ-YH-CMDGQGTVNTEAGNN-SESAVWIFDIWLCRLTHGMQD
+t88 R--SAPFIGV---RELFKR-YHKCVEGAGCVHTVAGTP-SDSPVWMFDQFMCQLTHSMVD
+t37 T--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN
+t35 T--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN
+t48 T--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN
+t55 T--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN
+t46 T--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN
+t67 T--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN
+t57 T--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN
+t56 I--AAPFIGV---RELFKR-YIKCVEGAGCVYTVA-AP-SESPVWMFDKFMCHLTHSMVV
+t13 I--PPPFHGV---REMFKRVYE-CMEGIGCVNTVAGNP-SESSAWMFDKVMYQLTHSMVW
+t5 I--PPPFHGV---REMFKRVYE-CMEGIGCVNTVAGNP-SESSAWMFDKVMYQLTHSMVW
+t38 I--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW
+t33 I--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW
+t100 I--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW
+t34 I--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW
+t84 I--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW
+t92 I--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW
+t3 T--SIPFLGV---RELWKR-YE-CMEGIGCVNTVAGKP-SQSSVWMFDRFMYKLTHSMVW
+t22 I--SIPFLGV---RELWKR-YE-CMEGIGCVNTVAGTP-SESSVWMFDRFMYKLTHSMVW
+t64 IT-SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW
+t18 IT-SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW
+t68 I--SPPFIGV---RELFKR-YG-CVEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW
+t28 I--SPPFIGV---RELFKR-YH-CMEGIGCVNTVAGMP-SESSVWMFDQFMYKLTHSMIW
+t82 I--SPPFIGL---RELFKR-YV-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW
+t41 I--SPPFIGL---RELFKR-YV-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW
+t71 I--SPQFIGV---RELFKR-YR-CMEGIGCVNTVAGAP-SESSVWMFDRFMYKLTHSMVW
+t94 I--SPPFTGV---RELFKR-YR-CMEGIGCVNTVAGIP-SESSVWMFDRFMYRLTHSMVW
+t99 I--SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGIP-SESSIWMFDRFMYKLTHSMVW
+t40 I--SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGIP-SESSVWMFDRFMYKLTHSMVW
+t90 I--SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGIP-SESSVWMFDRFMYKLTHSMVW
+t4 I--SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW
+t36 L--YVFFTGTKGTRELVKY-YM-CMEGHGCVNTMAKKS-SQSGIWKFNAFMC-LMHLMEG
+t87 L--YVFFTGNKGTRELVKY-YM-CMEGHGCVNTMAKKS-SQSGIWKFNAFMC-LMHLMEG
+t89 L--YNFFTGHKGTRELVKY-YM-CMEGEGVVNTMAKKS-SQSGIWKFNAFMC-LMRLMQG
+t39 L--YNFFTGHKGTRELVKY-YM-CMEGEGVVNTMAKKS-SQSGIWKFNAFMC-LMRLMQG
+t8 L--YNFFTGHKGTRELVKY-YM-CMEGEGVVNTMAKKS-SQSGIWKFNAFMC-LMRLMQG
+t6 L--YNFFTGHKGTRELVKY-YM-CMEGEGVVNTMAKKS-SQSGIWKFNAFMC-LMRLMQG
+t58 L--YNFFTGHKGTRELVKY-YM-CMEGEGCVNTMAKKS-SQSGIWKFNAFMC-LMHLMQG
+t54 L--YNFFTGHKGTRELVKY-YM-CMEGEGCVHTMAKKS-SQSGIWKFNAFMC-LMHLMQG
+t65 L--YNFFTGQKGTRELIKF-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQS
+t29 L--YNFFTGQKGTRELIKF-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQS
+t98 L--YNFFTGQKGTKELVKF-YF-CMEGCGCVNTMAKKS-SQSAPWKFNRFMC-LMHLMQS
+t83 L--YNFFTGQKGTKELIKF-YF-CMEGCGTVNTMAKDS-SQSAPWKFNRFMC-LMHLMQS
+t95 L--YNFFTGQKGTRELIKF-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQL
+t20 L--YNFFTGQKGTRELIKF-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQL
+t69 L--YNFFTGHKGTRELVKY-YH-CMEGCGCVNTMAKSS-SQSAPWKFNRFMC-LMHLMQE
+t2 L--YNFFTGQKGTRELVKY-YH-CMEGCGCVNTMAKSS-SQSAPWKFNRFMC-LMYLMQD
+t10 L--YNFFTGQKGTRELVKY-YH-CMEGCGCVNTMAKSS-SQSAPWKFNRFMC-LMYLMQD
+t31 L--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKQS-SQSAPWKFNRFMC-LMHLMQN
+t15 L--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQN
+t63 L--YTFFTGQKGKRELIKY-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQD
+t50 L--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKNS-SQSAPWKFNHFMC-LMHLMQN
+t25 L--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQN
+t51 L--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQN
+t9 L--YNHFTGKKGARELIKR-YV-CMEGHDCVNTVANVS-SQSAIWKFDRFMCDLMHLMQN
+t47 L-CYHHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-SQSAVWNFDRFMCDLMHLMQN
+t60 L-CYHHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-SQSAVWNFDRFMCDLMHLMQN
+t30 L-CYHHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-SQSAVWNFDRFMCDLMHLMQN
+t70 M--YNHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-SQSAVWKFDRFMCDLMHLMQD
+t91 M--YNHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-SQSAVWKFDRFMCDLMHLMQD
+t49 M--YNHFTGNKGACELIKG-YV-CMEGHDCVNTMANIS-SQSAVWKFDRFMCDLMHLMQD
+t52 L--YNHFTGKKGARELIKR-YI-CMEGHDCVNTMAHDS-SQSATWKFDRFMCDLMHLMQG
+t43 L--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCALMHLMQK
+t1 L--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCCLMHLMQN
+t86 L--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCALMHLMQN
+t72 L--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKVS-SQSAVWKFDRFMCALMHLMQN
+t96 L--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCALMHLMQV
+t44 L--YQNFSGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCDLMHLMQN
+t45 L--YQNFTGQKGAREKIKR-YK-CMEGHDCVNTMAKSS-SQSAVWKFDRFMCDLMHLMQN
+t74 L--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCDLMHLMQN
+t26 L--YQNFTGKKGAREKIKR-YL-CMEGHECVVTMAKNS-SISAMWKFDRFMCDLMHLMQN
+t61 L--YQNFTGQKGAREKIKR-YL-CMEGHECVNTMAKNS-SVSAVWKFDQFMCDLMHLMQN
+t97 L--YQNFTGQKGAREKIKR-YL-CMEGHECVNTMAKNS-SVSAVWKFDRFMCDLMHLMQN
+t17 L--YQNFTGQKGAREKIKR-YL-CMEGQDCVNTMAKSS-SQSAVWKFDRFMCDLVHLMQN
+t11 L--YQNFTGQKGAREKIKR-YL-CMEGQDCVNTMAKSS-SQSAVWKFDRFMCDLVHLMQN
+t23 H--YTFFAGEKGARELIKR-YS-CMEGDGCVNTMAEGR-SESAVWKFDPFMCQLTHSMQS
+t76 I--VTNFHGF---AEMPKN-HD-VMEEQGGPGTCLAPQQSADTSWPFVMFTVDLAHRCRG
+t53 I--VTNFHGF---AEMPKN-YD-VMEEQGGPGTCLAPQQSADTSWPFVMFTVDLAHRCRG
+t16 I--VTNFHGF---AEMPKN-YD-VMEEQGGPGTCLAPQQSADTSWPFVMFTVDLAHRCRG
+t42 I--WTNFHGF---AEMPKN-YD-VMEEQGGPGTCIAPRQSADTSWPFMVFTVDLAHRCRG
+t24 I--WTNFHGF---AEMPKN-YD-VMEEQGGPGTCVAPRQSADTNWPFMVFPVELAHRCRG
+
+
+t73 --------GDIGRVKRDVQKFPKLKEGAPNCSSFVKPYFMGCDMFHKQVEYRGTHGLVLD
+t66 --------GDIGRVKRDVQKFPKLKEGAPNCSSFVKPYFMGCDMFHKQVEYRGTHGLVLD
+t32 --------GDIGRVKQDVQKFPKLKEGAPNCSSFVKPYFMGCDMFHKQVEYRGTHGLVLD
+t75 --------GDIGRVQQDVHKFPKLKEGAPNCSSFVKPVFMGCDMFHRQVQNRGNHGLVLD
+t79 --------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGVDMFHREVILKGAKGLVLP
+t27 --------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGCDMFHREVILKGAKGLVLP
+t93 --------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGCDMFHREVILKGAKGLVLP
+t59 --------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGCDMFHREVILKGAKGLVLP
+t7 --------GDIGRVVVDHPKFLKLEEGAPNCSSMPMPYFLGCDMFHREVILKGAKGLVLP
+t78 --------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGCDMFHREVILKGAKGLVLP
+t12 --------GDIGRVSVDHPKFLKLEEGAPRCSSCPMPYFLGCEMFHRQVILKGAKGLVLP
+t81 --------GDIGRVGVDHPKFLKLEEGAPNCSSLPMPYFLGVDMFHRQVTIKGAKGLVLP
+t21 --------GDIGRVDVDHPKFLKLEEGAPNCSSLPMPYFLGVDMFHKQVTLKGAKGLVLP
+t80 FGD-----GDIGRVVVDHPKFEKLEEGAPNCSSHPVPYFLGIDMFHKQVMAKGSKGLILP
+t14 FGD-----GDIGRVVCDHPKFEKLEEGAPNCSSHPMPYFLGVDMFHEQVMAKGSKGLILP
+t85 --------GDIGRVVCDHPKFEKLEEGAPNCSSIPMPYFLGIDMFHKQVMAKGSKGLILP
+t62 --------GDIGRVECDHPKFAKLEEGAPNCSSLPMPYFLGIDMFHNQVMAKGSKGLILP
+t19 --------GDIGRVECDHPKFAKLEEGAPNCSSLPMPYFLGIDMFHKQVMGKGSKGLILP
+t77 --------GDIGRVECDHPKFAKLEEGAPNCSSLPMPYFLGIDMFHRQVMAKGSKGLILP
+t88 --------GDLGRVVQDNVIFAKLKEGAPHCISL--PHFLGIDMFHTQVFVGGH--LILP
+t37 --------GDLGRVVHDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFVGGN--LILP
+t35 --------GDLGRVVHDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFVGGN--LILP
+t48 --------GDLGRVVHDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFVGGN--LILP
+t55 --------GDLGRVVHDNWTFTKLKEGAPHCIAI--PYFMGIDMFHIQVFVGGN--LILP
+t46 --------GDLGRVVHDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFVGGN--LILP
+t67 --------GDLGRVVMDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFLGGD--LILP
+t57 --------GDLGRVVMDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFIGGD--LILP
+t56 --------GDLGRVLRDNTTFAKLKEGAPVCISL--PYFLGMDMFHQQVFMGGN--LILP
+t13 --------GDLRRVVHDNVTFSKLKEGAPHCISH--PYFLGIDMFHIQVYSKGF--LTLP
+t5 --------GDLRRVVHDNVTFSKLKEGAPHCISH--PYFLGIDMFHIQVYSKGF--LTLP
+t38 --------GDLGRVYYDNITFSKLKEGAPHCISQ--PFFLGIDMFHIQVYFKGS--LTLP
+t33 --------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLP
+t100 --------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLP
+t34 --------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLP
+t84 --------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLP
+t92 --------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLP
+t3 --------GDLGRVYWDNLTFQKLKEGAPHCIAV--PNYLNIDMFHIQVFYKGP--LTLP
+t22 --------GDLGRVYVDNQTFSKLKEGAPHCISA--PYYLNIDMFHIQVFYKGS--LTLP
+t64 --------GDLRRVFPDNATFSKLKEGAPHVISH--PYFLGIDMFHDQVVYRGP--LTLP
+t18 --------GDLRRVFPDNATFSKLKEGAPHVISH--PYFLGIDMFHEQVVYRGP--LTLP
+t68 --------GDLRRVFPDNAHFSKLKEGAPHVISH--PYFLGIDMFHDQVVYRGP--LTLP
+t28 --------GDLGRVFPDNATFSKLKEGAPHVISH--PYFLGIDMFHAQVFYRGS--LTLP
+t82 --------GDLGRVFPDNCTFSKLKEGAPHVISH--PYFLGIDMFHGQVVYRGS--LTLP
+t41 --------GDLGRVFPDNCTFSKLKEGAPHVISH--PYFLGIDMFHGQVVYRGS--LTLP
+t71 --------GDLARVFHDNGTFAKLKEGAPHVISV--PYFLGIDMFHGQVFLRGS--LTLP
+t94 --------GDLGRVFQDNATFSKLKEGAPHVISH--PYFLGIDMFHGQVFYRGS--LTLP
+t99 --------GDLGQVFPDVSTFSKLKEGAPHVISQ--PYFLGIDMFHDQVFYRGS--LTLP
+t40 --------GDLGRVYPDNPTFSKLKEGAPHVISH--PYFLGIDMFHDQVFYRGS--LTLP
+t90 --------GDLGRVYPDNPTFSKLKEGAPHVISH--PYFLGIDMFHDQVFYRGS--LTLP
+t4 --------GDLGRVFPDNATFSKLKEGAPHVISV--PYFLGIDMFHDQVFYRGS--LTLP
+t36 --------GDL--------------------CSY--PSFLGMCMFHAMVQSKGD--LVLP
+t87 --------GDL--------------------CSY--PSFLGMCMFHAMVQSKGD--LVLP
+t89 --------GDL--------------------CSY--PSFLGMCMFYAMVQSKGD--LVLP
+t39 --------GDL--------------------CSY--PSFLGMCMFYAMVQSKGD--LVLP
+t8 --------GDL--------------------CSY--PSFLGMCMFYAMVQSKGD--LVLP
+t6 --------GDL--------------------CSH--PSFLGMCMFYAMVQSKGD--LVLP
+t58 --------GDL--------------------CSH--PSFLGMCMFHAMVKSKGN--LVLP
+t54 --------GDL--------------------CSH--PSFLGMCMFHAMVQSKGN--LVLP
+t65 --------GDL--------------------CNS--PSFLGMCMFHPQVQAKGE--LVLP
+t29 --------GDL--------------------CNC--PSFLGMCMFHPQVQAKGE--LVLP
+t98 --------GDL--------------------CNS--PPFLGMCMFHPQVQMKGE--LVLP
+t83 --------GDL--------------------CNS--PSFLGMCMFHPQVQAKGE--LVLP
+t95 --------GDL--------------------CNP--PSFLGMCMFHPQVRSKGE--LVLP
+t20 --------GDL--------------------CNP--PSFLGMCMFHPQVRSKGE--LVLP
+t69 --------GDL--------------------CNS--PGFLGMCMFHPQVQRKGE--LVLP
+t2 --------GDL--------------------CNS--PGFLGMCMFHPQVQAKGE--LVLP
+t10 --------GDL--------------------CNS--PGFLGMCMFHPQVQAKGE--LVLP
+t31 --------GDL--------------------CNL--PSFLGMCMFHNQVQCKGE--LVLP
+t15 --------GDL--------------------CNS--PSFLGMCMFHNQVPNKGA--LVLP
+t63 --------GDL--------------------CNS--PSFLGMCMFHNQVSFKGE--LVLP
+t50 --------GDL--------------------CNS--PSFLGMCMFHNQVSVKGE--LVLP
+t25 --------GDL--------------------CNS--PSFLGMCMFVNQVSFKGE--LVLP
+t51 --------GDL--------------------CNS--PSFLGMCMFHVQVQFKGE--LVLP
+t9 --------GDL--------------------CSY--PSFLPMCMFVPQVLSKGE--LVLP
+t47 --------GDL--------------------CSY--PSFLPMCMFVSQVLSKGE--LVLP
+t60 --------GDL--------------------CSV--PSFLPMCMFVSQVLHKGE--LVLP
+t30 --------GDL--------------------CSV--PSFLPMCMFVSQVLHKGE--LVLP
+t70 --------GDL--------------------CSY--PSFLPMCMFVAQVIAKGE--LVLP
+t91 --------GDL--------------------CSY--PSFLPMCMFVAQVIAKGE--LVLP
+t49 --------GDL--------------------CSY--PSFLPMCMFVAQVIAKGE--LVLP
+t52 --------GDL--------------------CSY--PSFLPVCMFVAQVINKGE--LVLP
+t43 --------GDL--------------------CSH--PSFLGMCMFHEQVRCKGE--LVLP
+t1 --------GDL--------------------CSH--PSFLGMCMFVEQVRCKGE--LVLP
+t86 --------GDL--------------------CSH--PSFLGMCMFHEQVRRKGE--LVLP
+t72 --------GDL--------------------CSH--PSFLGMCMFHEQVRRKGE--LVLP
+t96 --------GDL--------------------CSH--PSFLGMCMFHEQVRRKGE--LVLP
+t44 --------GDL--------------------CSH--PSFLGMCMFHEQVRCKGE--LVLP
+t45 --------GDL--------------------CSV--PSFLGMCMFHEQVRCKGE--LVLP
+t74 --------GDL--------------------CSV--PSFLGMCMFHEQVRCKGE--LVLP
+t26 --------GDL--------------------CSF--PSFLGMCMFHDQVRCKGE--LVLP
+t61 --------GDL--------------------CSF--PSFLGMCMFHEQVRCKGE--LVLS
+t97 --------GDL--------------------CSF--PSFLGMCMFHQQVRCKGE--LVLP
+t17 ---GARGSGDL--------------------CSF--PSFLGMCMFHEQVRCKGE--LVLP
+t11 ---GARGSGDL--------------------CSF--PSFLGMCMFHEQVRCKGE--LVLP
+t23 --------GDL--------------------CSV--PSFLGVCMFQRQVVMKGE--LVLP
+t76 --------GDMPQNTGDSMTCPHLAEGLAAVNS---RAFIGVSIYDLKVSHKMI--QACN
+t53 --------GDIPQNTGDSMTCPHLAEGLAAVNS---RAFIGVSTYDLKVSHKMI--QACN
+t16 --------GDIPQNTGDSMTCPHLAEGLAAVNS---RAFIGVSTYDLKVSHKMI--QACN
+t42 --------GDTPTQAGDSMTFPHLAEGLPAVNS---RAFVGVSSYDLRVSHKMI--QACT
+t24 --------GDTP--------FPHLAEGLPAVNS---RAFIGVSSYDLKVSHKMI--QACN
+
+
+t73 DTWNEESATFPYPQVHSRSDKRCLNGLHQGDHEESVH---HAPRI----MR---LIGH-H
+t66 DTWNEESATFPYPQVHSRSDKRCLNGLHQGDHEESVH---HAPRI----MR---LIGH-H
+t32 DTWNEESATFPYPQVHSRSDKRCLNGLHQGDHEESVH---HAPRI----MR---LIGH-H
+t75 DTWNEESGTFPYPQVHSRNEKRCINKLHQGDHNESCH---HNPRI----VR---RIGH-H
+t79 D--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIGL-N
+t27 D--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIGM-N
+t93 D--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIGM-N
+t59 D--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIGM-N
+t7 D--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIGM-N
+t78 D--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIGM-N
+t12 D--NEDSMAFPYVQVHSRSVKRCLNVLVQGDHDESRH---HNARI----VA---RIGM-N
+t81 DIWNESPMAFPYAQVHSKSHKRCLNVLVQGDHEESEH---HNARI----MS---KIGT-H
+t21 DIWNESPMAFPYAQVHSKSHKRCLNVLVQGDHEESEH---HNARI----MS---RIGT-H
+t80 DTWNEASMAFPYPQVHSKSHRRVLNVLHQGDVEES-H---HSARC----VR---RIGF-H
+t14 DTWNEASMAFPYPQVHSKSHRRVLNVLHQGDVEES-H---HSARC----VR---RIGF-H
+t85 DTWNEASMAFPYPQVHSKSHRRVLNVLHQGDHEES-H---VSARC----MR---RIGF-H
+t62 DTWNEASMAFPYPQVHSKSHRRVLNVLHQGDHEES-H---HSARC----MR---RIGY-H
+t19 DTWNEASMAFPYPQVHSKSHRRVLNVLHQGDHEES-H---HSARC----MR---RIGYGH
+t77 DTWNEASMAFPYPQVHSKSHRRVLNVLHQGDHEES-H---HSARC----MR---RIGY-V
+t88 DPCYELSISVMYAGHASYNQKRCINNLDQGDQEDSNHRKEHKIRASVLLYR---QIGI-L
+t37 DPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L
+t35 DPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L
+t48 DPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L
+t55 DPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L
+t46 DPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L
+t67 DPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L
+t57 DPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPQKEHKIRNSVLLYR---QIGL-L
+t56 DPCYELSISVMYAGHASYNQKRCLNNLDQGDREDSSHRKEHKIRRSVLLYQ---QIGC-L
+t13 DPRYEISMSVMYSQHHSFSMKRCLNGLDHGDREESPHQIEHKMRKSVLIYN---PIGY-L
+t5 DPRYEISMSVMYSQHHSFSMKRCLNGLDHGDREESPHQIEHKMRKSVLIYS---PIGY-L
+t38 DPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHHIDHKMRKSVLIYN---PIGY-L
+t33 DPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L
+t100 DPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L
+t34 DPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L
+t84 DPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L
+t92 DPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L
+t3 DPHYELSMSVMYAQHHSFSQKRCLNALDHGDREESPHQIEHKMRKSVLLYN---PIGY-L
+t22 DPRYELSMSVMYAQHHSFSQKRCLNALDYGDREESPHQIEHKMRKSVLLYY---TIGW-L
+t64 DPRYELSMSVMYAQHHSFSQKRCLNALDHGDTQESPHGIEHNMRNSVLLYN---PIGF-L
+t18 DPRYELSMSVMYAQHHSFSQKRCLNALDHGDTQESPHGIEHNMRNSVLLYN---PIGF-L
+t68 DPRYELSMSVMYAQHHSFSQKRCLNALDHGDTQESPHGIEHNMRNSVLLYN---PIGF-L
+t28 DPRYELSMSVMYSQHHSFSQKRCLNPLDHGDRQESSHGIEHNMRSSVLLYN---PIGF-L
+t82 DPRYELSMSVMYSQHHSFSQKRCLNPLDHGDRQESPHGIEHNMRSSVLLYN---PIGF-L
+t41 DPRYELSMSVMYSQHHSFSQKRCLNPLDHGDRQESPHGIEHNMRSSVLLYN---PIGF-L
+t71 DPRYELSMSVMYAQHHSFSQKRCLNHLDHGDRQESPHGIEHNMRKSVLLYN---PQGY-L
+t94 DPRYELSMSVMYAQHHSMSQKRCLNTLDHGDRQESPHGIEHNMRKSVLLYD---PIGY-L
+t99 DPRYELSMSVMYAQHHSFSQKRCLNALDHGDRQESPHGIEHNMRKSVLLDS---PIGY-L
+t40 DPRYELSMSVMYAQHHSFSQKRCLNALDHGDRQESPHGIEHNMRKSVLLDS---SIGY-I
+t90 DPRYELSMSVMYAQHHSFSQKRCLNALDHGDRQESPHGIEHNMRKSVLLDS---PIGY-I
+t4 DPRYEMSMSVMYAQHHSFSQKRCLNALDYGDRQESPHGIEHNMRKNVLLDN---PIGH-L
+t36 DSPNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSEHIKEKHMRI----YA---NIGG-H
+t87 DSPNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHVKEKHMRI----YA---NIGG-H
+t89 DSCNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHTKEKHMRI----YA---NIGG-H
+t39 DSCNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHTKEKHMRI----YA---NIGG-H
+t8 DSCNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHTKEKHMRI----YA---NIGG-H
+t6 DSCNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHTKEKHMRI----YA---NIGG-H
+t58 DSCNEDSVSFMYIQHHSFHEKRCLNHLNVGDREDSEHIKEKHMRV----YA---SIGG-H
+t54 DSCNEDSVSFMYIQHHSFHEKRCLNHLNVGDREDSEHIKEKHMRI----YA---SIGG-H
+t65 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDSQDSQHLREKQLRI----YG---RIGK-V
+t29 DNPNENSVEFMYRRHHSLSDKRCLNLLFVGDSQDSQHQREKQLRI----YG---RIGK-V
+t98 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDSQDSQHLREKQLRI----YG---RIGK-V
+t83 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDSQDSQHLREKQLRI----YG---RIGK-V
+t95 DNPNENSVEFMYRRHHSLSDKRCLNLLYTGDSQDSQHLREKQLRI----YG---RIGR-V
+t20 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDSQDSQHLREKQLRI----YG---RIGR-V
+t69 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRM----YG---EIGK-V
+t2 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRM----YG---EIGK-V
+t10 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRM----YG---EIGK-V
+t31 DNVNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRI----YQ---NIGK-V
+t15 DNVNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRI----YP---SIGK-V
+t63 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDEQDSSHLREKQLRL----YA---RIGK-V
+t50 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSSHLREKQLRL----YA---RIGK-V
+t25 DNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSSHLREKQLRL----YA---RIGK-V
+t51 DHPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRI----YA---RIGK-V
+t9 DSSNEESISFVYLQHHSFSVKRCLNYLNVGDSADSKHLKEKHLRA----EGMPGNIGK-H
+t47 DSSNEESISFVYLQHHSFSDKRCLNYLNVGDNSDSKHLKEKHLRA----QGMPGNIGK-H
+t60 DSSNEESISFVYLQHHSFSDKRCLNYLNVGDNADSKHLKEKHLRA----QGMPGNIGK-H
+t30 DSSNEESISFVYLQHHSFSEKRCLNYLNVGDNADSRHLKEKHLRA----QGMPGNIGK-H
+t70 DSSTEESISFMYLQHHSFSDKRCLNYLNVGDNEDSKHAKEKFLRG----DG---GIGQ-H
+t91 DSSTEESISFMYLQHHSFSDKRCLNYLNVGDNEDSKHAKEKFLRG----DG---GIGQ-H
+t49 DSSNEESISFMYLQHHSFSDKRCLNCLNVGDNEDSKHLKEKFLRA----DG---GIGQ-H
+t52 DSSNEESISFMYLQHHSFSEKRCLNYLNVGDNEDSKHLKEKFLRA----DG---NIGQ-H
+t43 DSPNEESVSFVYIQHHSFSDKRCLNCLNVGDNDDSEHLKEKHLRI----YG---QIGH-H
+t1 DSPNEESLSFVYIQHHSFSDKRCLNCLNVGDNDDSEHLKEKHLRI----YG---QIGR-H
+t86 DSPNEESVSFVYIQHHSFSDKRCLNCLNVGDNDDSEHLKEKHLRI----YG---QIGR-H
+t72 DSPNEESVSFVYIQHHSFSDKRCLNCLNAGDNDDSEHLKEKHLRT----YG---QIGR-H
+t96 DSPNEESVSFVYIQHHSFSDKRCLNCLNVGDNDDSEHLKEKHLRV----YG---QIGR-H
+t44 DSPNEESVSFVYIQHHSFSDKRCLNYLNVGDNDDSEHLKEKHLRI----YG---VIGK-H
+t45 DSPNEESVSFVYIQHHSFSDKRCLNYLNVGDNDDSEHLKEKHLRI----YG---EIGK-H
+t74 DSPNEESVSFVYIQHHSFSDKRCLNYLNVGDNDDSEHIKEKHLRI----YG---EIGK-H
+t26 DSKNEESVSFVYIQHHSFSDKRCLNYLNVGDNEDSEHLKEKHLRV----YG---NIGK-H
+t61 DSKNEESVSFVYIQHPSFSDKRCLNYLNVGDNEDSEHLKEKVLRV----YG---DIGK-H
+t97 DSKNEESVSFVYIQHHSFNDKRCLNYLNVGDNEDSEHLEEKHLRV----YG---NIGK-H
+t17 DSKNEESVSFVYIQHHSFSDKRCLNELNVGDNEDSIHLKEKHLRI----YG---NIGK-V
+t11 DSKNEESVSFVYIQHHSFSDKRCLNSLNVGDNEDSIHLKEKHLRI----YG---DIGK-H
+t23 DSADEGSVSFMYIQHHSFAAKRCLNVLNVGDNEDSVHLRHKQLRV----YG---KIGK-H
+t76 PIQN---------DNHAFSDQRCLNDLSQGVVGASFPKMQHGVRH----YK---K-----
+t53 PIQN---------DNHAFSDQRCLNDLAQGVVGASHPKMQHGVRH----YK---K-----
+t16 PIQN---------DNHAFSDQRCLNDLAQGVVGASHPKMQHGVRH----YK---K-----
+t42 LIQN---------DNVAFSDQRPLNDLNQGCVGTSHPKMPHGVRH----YK---K-----
+t24 PIQN---------DNVAFSDQRVLNDLSQGCVGTSHPKMPHGVRH----YK---K-----
+
+
+t73 LVIIVLMNHDMGRLNHLEPDAVIPSPLRIGGDGWVPKPI------------------EDG
+t66 LVIIVLMNHDMGRLNHLEPDAVIPSPLRIGGDGWVPKPI------------------EDG
+t32 LVIIVLMNHDMGRLNHLEPDAVIPSPLRIGGDGWVPKPI------------------EDG
+t75 LVIIVLVNRDMGRLNYIEPDALVPSPLRFGGDEWVPKPI------------------EDG
+t79 LVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------GDG
+t27 LVIISYANVDMGRLNHCEDQAIVYSPLRYGGAGFVSKPI------------------ADG
+t93 LVIISYANVDMGRLNHCEDQAIVYSPLRYGGAGFVSKPI------------------ADG
+t59 LVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------ADG
+t7 LVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------ADG
+t78 LVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------ADG
+t12 MVIIRYLNVEMGRLNHCEDDAMVYSPLRIGGAGTHSKPI------------------ADG
+t81 LVIINIINVEMQRLNHCEDKAIVYSPDRIGGAGFHSKPI------------------ADG
+t21 LVIVNVINVEMQRLNHCEDKAIVYSPDRIGGAGFHSKPI------------------ADG
+t80 LVIIVFWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPV------------------DDG
+t14 LVIIVYWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPV------------------DDG
+t85 LVIINFWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPI------------------NDG
+t62 RVIINYWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPI------------------ADG
+t19 LVIINFWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPI------------------ADG
+t77 LVIINFWNVEMGRLIHCEDEAIIYSPLRIGGAGFHSKPI------------------ADG
+t88 -VIIKEANELMNRLNHKEPENGIIFPLR---DAQDPKQI------------------LNG
+t37 -VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+t35 -VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+t48 -VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+t55 -VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+t46 -VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+t67 -VIIKEANELMGRLNHKERKNGVIFPLR---GAQGPKQI------------------SNG
+t57 -VIIKEANEIMGRLNHKERKNGVIFPLR---GAQGPKQI------------------SNG
+t56 -VITRERNELMGRLNHKEPRDGVIFPHR---GAQGPKQL------------------ANG
+t13 -VIIKDANSMMGRLNHHESRAVVAFPLR---GAEGPKQV------------------MEG
+t5 -VIIKDANSMMGRLNHHESRAIVAFPLR---GAEGPKQV------------------MEG
+t38 -VIIKNANSLMGRLNHHESRLIVTFPLR---GAEGPKQV------------------MEG
+t33 -VIIKNANSLMGRLNHYESRAIVTFPLR---GAEGPKQV------------------MEG
+t100 -VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEG
+t34 -VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEG
+t84 -VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEG
+t92 -VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEG
+t3 -VIIKNANSMMGRLNHHESCAIVMFPLR---GAEGPKQI------------------IEG
+t22 -VIIKNADSMMGRLNHHESCAMVMFPLR---GAEGPKQI------------------MEG
+t64 -VIIKNINSMMGRLNHHESRAVVGFPLR---GAENPKQI------------------MEG
+t18 -VIIKNINSMMGRLNHHESRAVVGFPLR---GAENPKQI------------------MEG
+t68 -VIIKNINSMMGRLNHYESRAVVGFPLR---GAENPKQI------------------MEG
+t28 -VIIDNINPMMGRLNHHESRAIVTFPLR---GAEHPKQI------------------VEG
+t82 -VIIDNINPMMGRLNHHESRAIVTFPLR---GAEHPKQI------------------MEG
+t41 -VIIDNINPMMGRLNHHESRAIVTFPLR---GAEHPKQI------------------MEG
+t71 -VIIKNVNSMMGRLNHHESRAVVTFPLR---GADNPRQI------------------MEG
+t94 -VIIKNVNSMMGRLNHHESRAKVTFPLR---GADNPRQI------------------MEG
+t99 -VIIKNINSMMGRLNHHESRAVFAFPLR---GAENPKQI------------------MEG
+t40 -VIIKNLNSMMGRLNHHESRAVVTFPLR---GAEDPKQI------------------MEG
+t90 -VIIKNVNSMMGRLNHHESRAVVTFPLR---GAEDPKQI------------------MEG
+t4 -VIIKNENSMMGRLNHHESRAVVTFPLR---GAEDPKQK------------------MEG
+t36 -IIIREWNDVMGRLNHIEPGAEVIFPLRK--RGQHSKPV------------------IDG
+t87 -IIIREWNDVMGRLNHIEPGAEVIFPLRK--RGQHSKPV------------------IDG
+t89 -IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDG
+t39 -IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDG
+t8 -IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDG
+t6 -IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDG
+t58 -IIIREWNDVMGRLNHIEPGAEVTFPLRR--RGQASKPV------------------IDG
+t54 -IIIREWNEVMGRLNHIEVGAEVTFPLRR--RGQASKPV------------------IDG
+t65 -VIIKVWNAVMGRLNHHEPPAEVMFPLRK--GGQDSKPF------------------IDG
+t29 -VIIKVWNAAMGRLNHVEPPAEVMFPLRR--GGSDSKPF------------------LDG
+t98 -VIIKVWNAVMGRLNHHEPPAEVMFPLRR--GGSDSKPF------------------IDG
+t83 -VIIKVWNAVMGRLNHHEPPAEVMFPLRR--GGSCSKPF------------------VDG
+t95 -VILQVWNAVMGRLNHHEPPAEVMFPLRK--GGSNSKPV------------------YDG
+t20 -VILQVWNAVMGRLNHHEPPAEVMFPLRK--GGSNSKAV------------------YDG
+t69 -VIIKVVNAVMGRLNHVEPSAEVMFPLRK--GGSDSKPF------------------IDG
+t2 -VIIKVVNAVMGRLNHHEPSAEVMFPLRK--GGSDSKPF------------------IDG
+t10 -VIIKVVNAVMGRLNHHEPSAEVMFPLRK--GGSDSKPF------------------IDG
+t31 -VIIKVWNANMGRLNHHEPPAEVMFPLRK--GGSDSKPF------------------IDG
+t15 -VIIKVWNAAMGRLNHHEPPAEVMFPLRK--GGSDSKPF------------------IDG
+t63 -VIIKVWNAVMGRLNHHEPPAAVMFPLRK--GGSDSKPF------------------IDG
+t50 -VIIKVWNAVMGRLNHHEPPAEVMFPLRK--CGSDSKPF------------------IDG
+t25 -VIIKVWNAVMGRLNHHEPPAEVVFPLRK--GGSDSKPF------------------IDG
+t51 -VIIKVWNAVMGRLNHHEPPAEVVFPLRK--GGSDSKPF------------------IDG
+t9 -VIINVWNAVMGRLNHHEPPAEVVFPLRQ--GGPDSKPM------------------IDG
+t47 -VIINVWNAVMGRLNHHESPAEVVFPLRQ--GGPDSKPM------------------IDG
+t60 -VIINVWNAVMGRLNHHEPPAEVVFPLRQ--GGPDSKPM------------------IDG
+t30 -VIISVWNAVMGRLNHHEPPAEVVFPLRQ--GGPDSKPM------------------MDG
+t70 -VIINVWNAVMGRLNHHEPPPEVVFPLRQ--GGPDSKPM------------------VDG
+t91 -VIINVWNAVMGRLNHHEPPPEVVFPLRQ--GGPDSKPM------------------VDG
+t49 -VIINMWNAVMGRLNHHEPPPEVVYPLRQ--GGPNSKPM------------------VDG
+t52 -VIINMWNAVMGRLNHHEPPAEVNFPLRQ--GGPDSKPM------------------VDG
+t43 -VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSK-M------------------VDG
+t1 -VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSKPV------------------VDG
+t86 -VIINVWNAFMGRLNHHEPPAEAVYPLRK--GGPDSKPM------------------VDG
+t72 -VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSKPM------------------VDG
+t96 -VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSKLM------------------VDG
+t44 -VIINVWNAFMGRLNHHEPPADVEYPLRK--GGPDSKPM------------------VDG
+t45 -VIINVWNAFMGRLNHHEPPAEVMYPLRK--GGPESKPM------------------VDG
+t74 -VIINVWNAFMGRLNHHEPPAEVMYPLRK--GGPESKPM------------------VDG
+t26 -VIINSWNAMMGRLNHHEPAAEVVYPLRK--GGPESKPM------------------VDG
+t61 -VIINVWNAMMGRLNHHEPAAEVVCPLRK--GGPDSKPM------------------VDG
+t97 -VIINVWNAMMGRLNHHEPAAEVVCPLRK--GGPDSKPM------------------VDG
+t17 -VIINVWNAMMGRLNHHEPAAEVVYPLRK--GGPDSKPM------------------VDG
+t11 -VIINVWNAMMGRLNHHEPAAEVVYPLRK--GGPDSKPM------------------VDG
+t23 -VIISVPNAIMGRLNHHEPSAIVVFPLRQ--RGADSKSV------------------GDG
+t76 ---RVYENEVGGRLDDAEAIDDMGVWIRW--EGVKHAWCHPIGSCPDHLVCSLLVLQPAR
+t53 ---RVYENEVGGRLDDAEAIDDMGVWIRW--EGVKHAWCHPIGSCPDHLVCSLLVLQPAR
+t16 ---RVYENEVGGRLDDAEAIDDMGVWIRW--EGVKHAWCHPIGSCPDHLVCSLLVLQPAR
+t42 ---KVYENEVGDRLDDAEGIDDVGVWMRW--NGVKHAWCHIIGSCPDHLVCSLLVLQPGR
+t24 ---RVYENEVGDRLDDAEAVDDVGVWMRW--AGVKVAVCHVIGSCPDHLVVSLLVLQPAR
+
+
+t73 FFDK-D-Q------SRPDVANASIVPDK----DQWVGAHNQWGSSLRKVGLAVHDLR-NI
+t66 FFDK-D-Q------SRPDVANASIVPDK----DQWVGAHNQWGSSLRKVGLAVHDLR-NI
+t32 FFDK-D-Q------ARPDVANASIVPDK----DQWVGAHNQWGSSLRKVGLAVHDLR-NI
+t75 FFDK-D-Q------ARPDVANA-IVPDR----DQWVGAHKEWGSSLCKVGLAVHDLR-NV
+t79 FFDK-D-Q------ARPLMANAVCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NI
+t27 FFDK-D-Q------ARPLMANAVCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NI
+t93 FFDK-D-Q------ARPLMANAVCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NI
+t59 FFDK-D-Q------ARPLMANAHCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NI
+t7 FFDK-D-Q------ARPLMANAHCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NI
+t78 FFDK-D-Q------ARPLMANAHCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NI
+t12 FFDK-D-Q------ARPLIANAHIVPEN----DQWTGAVAQWCSSVIKCGLANHDLE-NI
+t81 FFDK-D-Q------ARPIIANAHIVPVN----DQWTGPMAQWCSSVIKCGLANHELE-DV
+t21 FFDK-D-Q------ARPIIANAHIVPIY----DQWTGPMAQWCSSVIKCGLANHELK-VV
+t80 FFDK-D-Q------ARPVIASAHIVPEH----DQWSGAMAQWCSSVIKCGLANHDLE-NV
+t14 FFDK-D-Q------ARPVIASAHIVPEH----DQWSGAMAQWCSSVIKCGLANHDLE-NV
+t85 FFDK-D-Q------ARPVIANAHIVPEH----DQWSGAMAQWCSSVIKCGLANHDLE-NV
+t62 FFDK-D-Q------ARPVIANAHIVPEY----DQWSGAMAQWCSSVIKCGLANHDLE-NV
+t19 FFDK-D-Q------ARPVIANAHIVPEY----DQWSGAMAQWCSSVIKCGLANHDLE-NV
+t77 FFDK-D-Q------ARPVIANAHIVPEY----DQWSGAMPQWVSSVIKCGLANHDLE-NV
+t88 LFDK-E-E------NRPMVQDADSVVGS----AQWAGQHRSWCSSDDKA-----------
+t37 LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------
+t35 LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------
+t48 LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------
+t55 LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------
+t46 LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------
+t67 LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------
+t57 LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------
+t56 LFEK-E-E------NRPMVQDAGSVPER----AQWPGQQRAWCSSDDKA-----------
+t13 LFDK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t5 LFDK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t38 LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t33 LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t100 LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t34 LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t84 LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t92 LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t3 LFDK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t22 LFDK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------
+t64 HFDK-E-E------ARPIVQDAASVPGK----AQWVGRVRAWCSSDVKA-----------
+t18 HFDK-E-E------ARPIVQDAASVPGK----AQWVGRVRAWCSSDVKA-----------
+t68 HFDK-E-E------ARPIVQDAASVPEK----AQWVGRVRAWCSSDVKA-----------
+t28 HFDK-E-E------ARPIVKDAASVPGK----AQWVGRIRAWCSSDVKA-----------
+t82 HFDK-E-E------ARPIVQDAASVPGE----AQWVGHIRAWCSSDIKA-----------
+t41 HFDK-E-E------ARPIVQDAASVPGE----AQWVGHIRAWCSSDIKA-----------
+t71 HFDK-E-E------ARPVVQDAPGVPGK----AQWVGKVRAWCSSDVKA-----------
+t94 HFDK-E-E------ARPVVQDAPGVPEQ----AQWVGKMRAWCSSDVKA-----------
+t99 HFDK-EKE------ARPVVQDAPGVPGK----AQWVGRIRAWCSSDVKA-----------
+t40 HFDK-E-E------ARPVVQDAPGVPGK----AQWVGRVRAWCSSEIKT-----------
+t90 HFDK-E-E------ARPVVQDAPGVPGK----AQWVGRVRAWCSSEIKT-----------
+t4 SFDK-E-E------ARPVVQDAPGVPGR----AQWVGRVRPWCSSDVKA-----------
+t36 FFAK-D-E------DRPGIQNAVSVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEP
+t87 FFAK-D-E------DRPGIQNAMSVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEP
+t89 FFAK-D-E------ERPGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEP
+t39 FFAK-D-E------ERPGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEP
+t8 FFAK-D-E------ERPGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEP
+t6 FFAK-D-E------ERPGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEP
+t58 FFAK-D-E------DRPGIQNAMSVPCG----DQWVGSVRGWCSSQHRYGLAIHILVHQQ
+t54 FFAK-D-E------DRPGIQNAMSVPCG----EQWVGSVRGWCSSQHRYGLAIHILVHQQ
+t65 FF------------DRPGIANAMSVKCG----DQWVGSIRGWCSSQHQYGLANHILVHGP
+t29 FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILIHGP
+t98 FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHNP
+t83 FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILIHNP
+t95 FF------------DRPAIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHGP
+t20 FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHGP
+t69 FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHGP
+t2 FF------------DRPGIANAMSVPCG----DQWMGSIKGWCSSQHQYGLANHILVHGP
+t10 FF------------DRPGIANAMSVPCG----DQWMGSIKGWCSSQHQYGLANHILVHGP
+t31 FF------------DRPGIANAMNVPCG----DQWVGCIRGWCSSQHQYGLANHILVHGP
+t15 FF------------DRPGIANAMSVPCG----DQWVGCIRGWCSSQHQYGLANHILVHGP
+t63 FF------------DRPGIANAMSVPCG----DQWMGIIRGWCSSQHQYGLANHILVHGP
+t50 FF------------DRPGIANAMSVPCG----DQWMGVIRGWCSSQHQYGLANHVLVHGP
+t25 FF------------DRPGIANAMSVPCG----DQWMGVIRGWCSSQHQYGLANHILVHGP
+t51 FF------------DRPGIANAMSVPCG----DQWVGVIRGWCSSQHQYGLANHILVHGP
+t9 FFDK-D-D------DRPGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHDP
+t47 FFDK-D-D------DRPGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHDP
+t60 FFDK-D-D------DRPGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHNP
+t30 FFDK-D-D------DRPGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHTP
+t70 FFDK-D-D------DRPGIANAMNVPCG----DQWGGPIRGWCSSQHKFGLAFHTLSHDP
+t91 FFDK-D-D------DRPGIANAMNVPCG----DQWGGPIRGWCSSQHKFGLAFHTLSHDP
+t49 FFDK-D-D------DRPGIANAMNVPCG----DQWGGPIRGWCSSQHRFGLAFHTLKHDP
+t52 FFDK-D-D------DSPGIANAMNVPCG----DQWGGPIRGWCSSQHKFGLASHTLSHDP
+t43 FFDK-E-D------DRPGIANAVSVPCA----DQVGGPIRGWCSSQVNFGLANHTLVQ-P
+t1 FFDK-E-D------DRPGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVQ-P
+t86 FFDK-E-D------DRPGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVQ-P
+t72 FFDK-E-D------HRPGIANAVSVPCA----DQVGGPLRGWCSSQVKFGLANHTLVQ-P
+t96 FFDK-E-D------ERPGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVQ-P
+t44 FFDK-E-D------DRPGIANAVSVPCG----DQVGGPIRGWCSSQVKFGLANHTLAQNP
+t45 FFDK-E-D------DRPGIANAVSVPCT----DQVGGPIRGWCSSQVKFGLANHTLVHNP
+t74 FFDK-E-D------DRPGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVHNP
+t26 FFDK-E-D------DRPGIANAVSVPCD----DQWGGPVRGWCSSQHKFGLADHTLIHIP
+t61 FFDK-E-D------DRPGVANAVSVPCD----DQWGGPVRGWCSSQHKFGLADHTLVHIP
+t97 FFDK-E-D------DRPGVANAMSVPCD----DQWGGPVRGWCSSQHKFGLADHTLVHVP
+t17 FFDK-E-D------DRPGIANAVAVPCS----DQWGGPVRGWCSSQHKFGLADHTLVHVP
+t11 FFDK-E-D------DRPGIANAVAVPCS----DQWGGPVRGWCSSQHKFGLADHTLVHVP
+t23 FYDK-D-E------DRPGIANAVSVPVA----EQWVGSVRGWYSSEHKYGLANHILI-GP
+t76 NFIQLS-MVRDTPHRLPKMASAAPVYKQTCHLEQVQGTARMWGKSGPRVVLNGHMLK-TQ
+t53 NFIQLS-MVRDTPHGLPKMASAAPVYKQTCHLEQVQGTARMWGKSGPRVVLNGHMLK-TQ
+t16 NFIQLS-MVRDTPHGLPKMASAAPVYKQTCHLEQVQGTARMWGKSGPRVVLNGHMLK-TQ
+t42 NFIQLS-VVHDTPHRLPKMASAAAVFKQTCHLEQVPGTARMWGKSGPRVRLNGHVLK-NQ
+t24 NFIQLS-VVHDTPHRLPKMASAAAVFKQTCHLEQVAGTARVWGKSGPRVKLNGHVLK-NQ
+
+
+t73 SDLYRCVWMDCHLGANHYRQISRMKMITPTYTHMTEYANGL----WHPFYKASDHKNEAQ
+t66 SDLYRCVWMDCHLGANHYRQISRMKMITPTYTHMTEYANGL----WHPFYKASDHKNEAQ
+t32 SDLYRCVWMDCHLGANHYRQISRMKMITPTYTHMTEYANGL----WHPFYKASDHKNEAQ
+t75 SDLYRCVWMECVLGANHYQQVSRMKMVTPAYTHMTEYANGL----WHPFYKNPDHKNEAQ
+t79 SRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHGL----WKPFYQASDHKNEAQ
+t27 SRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHGL----WKPFYQASDHKNEAQ
+t93 SRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHGL----WKPFYQASDHKNEAQ
+t59 SRLLRCVVMECILGANVYHQISRMKMHGPTYSHVMEYAHGM----WKPFYQASDHKNEAQ
+t7 SRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHGM----WKPFYQASDHKNEAQ
+t78 SRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHGM----WKPFYQASDHKNEAQ
+t12 SRLLRCVVMECVLGANVYHQASRMKMHGPYYAHVTEYAHGL----WKPFYQTSDHKNEAQ
+t81 SRLLRCVGMECNLGANHYHQVSRMKMHGPIYSHMTEYAVGL----WKPFYQASEHKNEAQ
+t21 SRLLRCVGMECNLGANHYHQVSRMKMHGPIYSHMTEYAHGL----WKPFYQASEHKNEAQ
+t80 SRLLRCVMIDCNQGANHYIQISRMKVHGPTYSHMTEYAHGL----WKPFYQASDHKNDAQ
+t14 SRLLRCVMIDCNQGANHYIQISRMKVHGPTYSHMTEYAHGL----WKPFYQASDHKSDAQ
+t85 SRLLRCVEIDCNQGANHYVQISRMKMYGPTYSHMTEYAHGL----WKPFYQASDHKNDAQ
+t62 SRLLRCVVIDCNHGANHYVQISRMKMHGPTYSHMTEYAHGL----WKPFYQASDHKNDAQ
+t19 SRLLRCVVIDCNHGANHYVQISRMKMHGPTYSHMTEYAHGL----WKPFYQASDHKNDAQ
+t77 SRLLRCVVIDVNQGANHYVQISRMKMHGPTYSHMTEYAHGL----WKPFYQASDHKNDAQ
+t88 SQLPRNTHIVVEIGANVYEQFSRMKTNIPIYAHVTEYAVGV----ERPFYE-SEFKNEAQ
+t37 SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVGV----ARPFYD-AEFKNEAQ
+t35 SQLPRNTRIVAEIGANVYEQYSRMKTVIPIYARVTEYAVGV----PRPFYD-AEFKNEAQ
+t48 SQLPRNTRIVAEVGANVYEQYSRMKTVIPIYARVTEYAVGV----PRPFYD-AEFKNEAQ
+t55 SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVGV----ARPFYD-AEFKNEAQ
+t46 SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVGV----ARPFYD-AEFKNEAQ
+t67 SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVGV----ARPFYD-AEFKNEAQ
+t57 SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVGV----ARPFYD-AEFKNEAQ
+t56 SKLPRNTKMVAEIGANVYEQASRMKTNIPIYAHVTEYALGV----DRPFYD-SEFKNEAQ
+t13 SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVGI----VKPFYD-NEWKQEAQ
+t5 SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVGI----VKPFYD-NEWKQEAQ
+t38 SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVGI----VKPFYD-SEWKQEAQ
+t33 SHLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVGI----VKPFYD-SEWKQEAQ
+t100 SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVGI----VKPFYD-SEWKQEAQ
+t34 SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVGI----VKPFYD-SEWKQEAQ
+t84 SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVGI----VKPFYD-SEWKQEAQ
+t92 SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVGI----VKPFYD-SEWKQEAQ
+t3 SRLPRNDPVVHEVGANVYQQISRMKTSIPIYAHVTEYAVGI----IKPFYD-NEWKQEAQ
+t22 SQLPTNDPIVPEVGANVYQQVSRMKTSIPIYAHVTEYAVGI----VKPFYD-NEWKQEAQ
+t64 SKLPRNDPIVPEVGANVYQQLSRMKTNIPIYAHVTEYAVGI----VKPFYD-NEWKQEAQ
+t18 SKLPRNDPIVPEVGANVYQQLSRMKTNIPIYAHVTEYAVGI----VKPFYD-NEWKQEAQ
+t68 SKLPRNDPIVPEVGANVYQQISRMKTNIPIYAHVTEYAVGI----VKPFYD-NEWKQEAQ
+t28 SQLPRNDPIVPEVGANVYQQDSRMKTNIPIYAHVTEYACGI----VKPFYE-NEWKQEAQ
+t82 SQLPRNDPIVPEVGANVYQQVSRMKTNIPIYAHTTEYACGI----VKPFYE-NEWKQEAQ
+t41 SQLPRNDPIVPEVGANVYQQVSRMKTNIPIYAHTTEYACGI----VKPFYE-NEWKQEAQ
+t71 SQLPRNDTIVPEVGANVYQQVSRVKTHIPIYAHVTEYAVGI----VKPFYN-NEWKQEAQ
+t94 SQLPRNDTIVPEVGANVYQQVSRVKTNIPIYAHVTEYAVGI----VKPFYN-NEWKQEAQ
+t99 SELPRNDAIVPEVGANVYQQVSRMKTNIPIYAHATEYAVGI----VKPFYD-NEWKQEAQ
+t40 SELPRNDAIVVEVGANVYQQISRMKTDIPIYAHATEYAVGI----VKPVYD-NEWKQEAQ
+t90 SELPRNDAIVPEVGANVYQQISRMKTDIPIYAHATEYAVGI----VKPVYD-NEWKQEAQ
+t4 SELPRNDAIWPEVGANVYQQISRMKTNIPIYPHVTEYAVGI----VKPFYL-NEWKQEAQ
+t36 SKLHKTYRINRKVGANAYDQDSRMKAAAPVYPHIMEYAHGM----FNPFYGLSEPKNNAQ
+t87 SKLHKTYRINRKVGANAYDQDSRMKAAAPVYPHIMEYAHGM----FNPFYGLSEPKNNAQ
+t89 SKLHKTYKINRKVGANAYDQVSRMKAAAPVYPHIMEYAHGM----FNPFYGLSEPKNNAQ
+t39 SKLHKTYKINRKVGANAYDQVSRMKAAAPVYPHIMEYAHGM----FNPFYGLSEPKNNAQ
+t8 SKLHKTYKINRKVGANAYDQVSRMKAAAPVYPHIMEYAHGM----FNPFYGLSEPKNNAQ
+t6 SKLHKTYKVVRKVGANAYDQVSRMKAAAPVYPHIMEYAHGM----FNPFYGLSEPKNNAQ
+t58 SRLHKTYNIDRKNGANAYEQDSRMKAGAPVYPHIMEYAHGM----FNPFYGMSEPKNNAQ
+t54 SRLHKTYNIDRKNGANAYDQDSRMKAGAPVYPHIMEYAHGM----FVPFYGMSEPKNNAQ
+t65 SKLHRTYAINKKMGANVYQQTSRMKAAAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t29 SKLHRTYAINKKMGANVYQQTSRMKAAAPLYPHIMEYAHGM----VKPFYGQSEPKNEAQ
+t98 SRLHRTYAINKKMGANVYQQSSRMKAAAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t83 SRLHRTYAINKKMGANVYQQTSRMKAAAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t95 SKLHRTYAINRKVGANVYQQTSRMKAAAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t20 SKLHRTYAINRKVGANVYQQMSRMKAAAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t69 SKLHRTYAINKKMGANVYQQISRMKALAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t2 SKLHRTYAINKKMGANVYQQISRMKALAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t10 SKLHRTYAINKKMGANVYQQISRMKALAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t31 SKLHRTYAINKKMGANVYQQTSRMKAAAPIYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t15 SKLHRTYAINRKMGANVYQQTSRMKAAAPLYPHIMEYAHGM----VEPFYGISEPKNEAQ
+t63 SKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t50 SKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t25 SKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t51 SKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIMEYAHGM----VKPFYGISEPKNEAQ
+t9 SSLHRTFAINRKMGANVYQQTSRMKASAPFYPHCMEYAHGV----CKPFYEHSEPKNEAQ
+t47 SNLHRTFAINRKMGANVYQQASRMKASAPFYHHCMEYAHGV----CKPFYEHSEPKNEAQ
+t60 SNLHRTFAINRKMGANVYQQTSRMKASAPFYHHCMEYAHGV----CKPFYEHSEPKNEAQ
+t30 SNLHRTFAINRKMGANVYQQTSRMKASAPFYHHCMEYAHGV----CKPFYEHSEPKNEAQ
+t70 SKLHRTFAINQKMGANVYQQMSRMKTPAPFYPHVMEYAHGV----CKPFYEHSEPKNEAQ
+t91 SKLHRTFAINQKMGANVYQQMSRMKTPAPFYPHVMEYAHGV----CKPFYEHSEPKNEAQ
+t49 SKLHRTFAINEKMGANVYQQNSRMKASAPFYPHVMEYAHGV----CKPFYEHSEPKNDAQ
+t52 SKLHRTFGINKNMGANVYQQTSRMKANAPFYPHVMEYAHGV----CKPFYEHSEPKNEAQ
+t43 SKLHRTFKINKKMGANVYQQTSRMKAEAPVYPHIMEYAHGV----CKPFYERSEPKNEAQ
+t1 SKLHRTFKINKKMGANVYQQTSRMKAEAPVYPHIMEYAHGV----CKPFYERSEPKNEAQ
+t86 SKLHRTFKINKKMGANVYHQTSRMKAEAPVYPHIMEYAHGV----CKPFYERSEPKNEAQ
+t72 SKLHRTFKINKKIGANVYQQTSRMKADAPVYPHIMEYAHGV----YKPFYERSEPKNEAQ
+t96 SKLHRTFKINKKIGANVYQQTSRMKAEAPVYPHIMEYAHGV----CKPFYERSEPKNEAQ
+t44 SKLHRTFKINKKMGANVYQQTSRMKAEAPVYPHIMEYAHGV----CKPFYDRSEPKNEAQ
+t45 SKLHRTFAINKKMGANVYQQTSRMKAEAPVYPHIMEYAHGV----CKPFYERSEPKNEAQ
+t74 SKLHRTFAINKKMGANVYQQTSRMKAEAPVYPHIMEYAHGV----CKPFYERSEPKNEAQ
+t26 SKLHRTFAINKKMGANVYQQTSRMKAAAPVYSHVMEYAHKV----VKPFYARSEPKNEAQ
+t61 SKLHRTFAITKKMGANVYQQTSRMKATAPVYPHVMEYAHGV----VKPFYDRSEPKNEAQ
+t97 SKLHRTFPINKKMGANVYQQTSRMKATAPVYPHVMEYAHGV----IKPFYDRSEPKNEAQ
+t17 SLLHRTFAINRKMGANVYQQTSRMKAAAPVYPHMMEYAHGV----VKPFYERSEPKNEAQ
+t11 SLLHRTFAINKKMGANVYQQTSRMKAAAPVYPHMMEYAHGV----VKPFYERSEPKNEAQ
+t23 SKLHRTYQTTAKMGANVVKATNRMKRPQPVYPHVMEYANGV----VKPFYEVAESKNEAQ
+t76 NTLHRQYLVDVELQATMVFVAARMKTDSSMYMSVREILHG------------CGIKDEAQ
+t53 NTLHRQYLVDVELGATMVFVAARMKTDLSMYMSVREILHG------------CGIKDEAQ
+t16 NTLHRQYLVDVELGATMVFVAARMKTDLSMYMSVREILHG------------CGIKDEAQ
+t42 NILHRQYLVDVNLGATMVFVLARMKTDASMYMSHREILHGGTFDAAKPFRQICGTKDEAQ
+t24 NVLHRQYLVDVDLGATMVFVAARMKTDASMYMSHREILHGGTFDAAKPFRQICGVKDEAQ
+
+
+t73 GVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVVKPLLGDWEGCKCRS-
+t66 GVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVVKPLLGDWEGCKCRS-
+t32 GVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVVKPLLGDWEGCKCRS-
+t75 GVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVAKPVLGDWEGCKCRSD
+t79 GVGER-THQLPCVESHTCQYEVKHAKVCKLVHH-ALYLLGLRTVMKPHLGDVDGCRCRSD
+t27 GVGER-THQLPCVESHTCQYEVKHAKVCKLVHH-ALYLLGIHTVMKPHLGNVDGCRCRSD
+t93 GVGER-THQLPCVESHTCQYEVKHAKVCKLVHH-ALYLLGIHTVMKPHLGNVDGCRCRSD
+t59 GVGER-THQLPCVDSHTCQYEVKHAQVCKLVHH-ALYLLGLRTVMKPHLGDVDGCRCRSD
+t7 GVGER-THQLPCVDSHTCQYEVKHAQVCKLVHH-ALYLLGLRTVMKPHLGDVDGCRCRSD
+t78 GVGER-THQLPCVDSHTCQYEVKHAQVCKLVHH-ALYLLGLRTVMKPHLGDVDGCRCRSD
+t12 GVGES-THQLPCVESQTCQYEVKHAKVCKLVHH-ALYLLALHTMMKPRLGDIDGCRCRSE
+t81 GLGER-PHQLPCVESQTCQYEIKVAKVCKLVHV-ALYLVGLKTVVKPKLGDWDGIRCRSE
+t21 GVGER-PHQLPCVESQKCQYEVKVAKVCKLVHV-ALYLVGLKTVVKPKLGDWDGVRCRSD
+t80 GVGER-PHQLPCVESQTCQYEMKHAKVCKLVHG-ALYLIALKTVVKPKLGVWQGCRCRSQ
+t14 GVGER-PHQLPCVESQTCQYEMKHAKVCKLVHG-ALYLIALKTVVKPKLGVWQGCRCRSQ
+t85 GVGER-PHQLPCVESQTCQYEVKHANVCKLVHA-ALYLIGLKTVVKPELGVWEGCRCRSQ
+t62 GVGER-PHQLPCVEPQTCQYEVKHAKVCKLVHG-ALYLIGLQTVVKPKLGVWEGVQCRSQ
+t19 GVGER-THQLPCVEPQTCQYEVKHAKVCKLVHG-ALYLIGLQNVVKPKLGVWEGVQCRSQ
+t77 GVGER-VHQLPCVEPQTCQYEVKHAKVCKHVHG-ALYLIGLQTVVKPKLGVWEGCQCRSQ
+t88 GWGES-GTSIPCVDSPDVQYEMKVAWVDKLMHT-ALYLMPLATVHKPEMGTVRGERCRAI
+t37 GQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTI
+t35 GQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPQMGTVKGERCRTI
+t48 GQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTI
+t55 GQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLSTVHKPEMGTVKGERCRTI
+t46 GQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTI
+t67 RQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTI
+t57 GQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTI
+t56 GQGES-GTSIPCVDSPDVQYELKHAWVDKLMHT-ALYLMPLPTVHKPKMGTVKGERCRAM
+t13 GQGEA-GACIPCVDSKDVQYELKHAYVKKLMHT-SLYLMHIETCHKPVMGTVKGNRCRAI
+t5 GQGEA-GACIPCVDSKDVQYELKHAYVKKLMHT-SLYLMHIETCHKPVMGTVKGNRCRAI
+t38 GQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTIKGNRCRAI
+t33 GQGEA-GACIPCVDSPDVQYELKHAYVKKLVHN-SLYLMHIDTCHKPAMGTVKGNRCRAI
+t100 GQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKGNRCRAI
+t34 GQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKGNRCRAI
+t84 GQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKGNRCRAI
+t92 GQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKGNRCRAI
+t3 GQGEA-GASIPCVNSPDVQYELKHAHIKKLMHT-SLYLMHLGTCHKPVMGTVKGDRCRAI
+t22 GQGEA-GASIPCVNSPDVQYELKHAHIKKLMHT-SLYLMHLKTCHKPVMGTVKGDRCRAI
+t64 GVGEA-GASIPCVDSPDVQYELKHAEVRKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAI
+t18 GVGEA-GASIPCVDSPDVQYELKHAEVRKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAI
+t68 GVGEA-GASIPCVDSPDVQYELKHAEVRKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAI
+t28 GQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAI
+t82 GQGEA-GASIPCVDSPDVQYELKHANVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAI
+t41 GQGEA-GASIPCVDSPDVQYELKHANVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAI
+t71 GQGEA-GASIPCVDSPDDQYELKHAEVKKLMHD-SLYLPHLETCHKPIMGTVKGGRCRAS
+t94 GQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLPHLETCHKPIMGTVKGGRCRAS
+t99 GQGET-GASIPCVDSPDVQYEMKHAEVKKLMHD-SLYLMHIETCHKPIMGTVKGDRCRAT
+t40 GQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAT
+t90 GQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAT
+t4 GQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLWHLETCVKPIMGTVKGDRCRAT
+t36 GNGEN-PMNKPCVESEDCQYEKKHASMDKLMHQ-SLYLMHINIMSKPAMGEWVGNRCRNE
+t87 GNGEN-PMNKPCVESEDCQYEKKHASMDKLMHQ-SLYLMHINVMSKPAMGEWVGNRCRND
+t89 GNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHINIMSKPAMGEWVGVRCRNE
+t39 GNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHINIMSKPAMGEWVGVRCRNE
+t8 GNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHVNIMSKPAMGEWVGVRCRNE
+t6 GNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHINIMSKPAMGEWVGVRCRNE
+t58 GNGEN-PMNVPCVESDDCQYEKKHASMDKQMHQ-SLYLMHMNIMSKPAMGEWVGNRCRNE
+t54 GNGEN-PMNVPCVESDDCQYEKKHASMDKQMHQ-SLYLMHMNIMSKPAMGEWVGNRCRNE
+t65 GNGEN-PMNVPSVESGECQYEHKHAAMEKLMHH-SLYLMRVNTMSKPVMGDWVGNRCRAE
+t29 GNGEN-PMNVPSVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMPKPVMGDWDGNRCRAE
+t98 GNGEN-PMNVPSVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAE
+t83 GNGEN-PMNVPSVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAE
+t95 GNGEN-PMNVPSVESGECVYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGHRCRAE
+t20 GNGEN-PMNVPSVESGECVYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGHRCRAE
+t69 GNGEN-PMNVPCVESGECQYENKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAE
+t2 GNGEN-PMNVPCVESGECQYENKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAE
+t10 GNGEN-PMNVPCVESGECQYENKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAE
+t31 KNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAE
+t15 KNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVLGDWVGNRCRAE
+t63 KNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRANTMSKPVMGDWVGSRCRAE
+t50 KNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRANTMSKPVMGDWVGSRCRAE
+t25 KNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRANTMSKPVMGDWVGSRCRAE
+t51 KNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPIMGDWVGNRCRAD
+t9 GNGEK-PMNVPCVESIDCQYENKHATMTKLMHH-SLYLMRMHTMSKPIMGDVNGNRCRAD
+t47 GNGEK-PMNVPCVESRDCQYENKHATMTKLMHQ-SLYLMRMHTMSKPIMGHVNGNRCRAD
+t60 GNGEK-PMNVPCVESIDCQYESKHAAMTKLMHQ-SLYLMRIHTMSKPIMGDVNGNRCRAD
+t30 GNGEK-PMNVPCVESIDCQYENKHATMTKLMHQ-SLYLMRMHTMSKPIMGDVNGNRCRAD
+t70 GNGEKVPMNVPCVESMDCQYENKHAPMAKLMHQDSLYLMRMHTMSKPLMGDVNGNRCRAD
+t91 GNGEKVPMNVPCVESMDCQYENKHAPMAKLMHQ-SLYLMRMHTMSKPLMGDVNGNRCRAD
+t49 GNGDKVPMNVPCVESMDCQYENKHAPMAKLMHQ-SLYLMRMYTMSKPIMGDVNGNRCRAE
+t52 GNGEK-PMNVPCVESIECQYENKHATMAKLMHD-SLYLMRMHTMSKPVMGDVNGHRCRAD
+t43 GNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAG
+t1 GNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAK
+t86 GNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAG
+t72 GNGEK-QGNVPCVESVECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAG
+t96 GNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAG
+t44 GNGEK-QGNVPCVESMDCQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGYVDGHRCRAG
+t45 GNGEK-QGNVPCVESMDCQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAG
+t74 GNGEK-QGNVPCVESMDCQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAG
+t26 GNGEK-QWNVPCVESMDCQYENKHATMAKLMHP-PLYLMRMQTMAKPPMGDVDGHRCRAG
+t61 GNGEK-QWNVPCVESMDCQYENKHATMAKLMHP-PLYLVKMQTMSKPPMGDVDGHRCRAG
+t97 GNGEK-QWNVPCVESMDCQYENKHATMAKLMHP-PLYLVKMQTMSKPPMGDVDGHRCRAG
+t17 GNGEK-QWNVPCVQSVDCQYENKHATMAKLMHP-PLYLMRMETMSKPPMGDVDGVRCRAG
+t11 GNGEK-QWNVPCVQSVDCQYENKHATMAKLMHP-PLYLMRMETMSKPPMGDVDGVRCRAG
+t23 GNGEK-PVNVPCVESPDCQYESKHARVNKLMHP-SLYLMCMEAMNKPIMGDWDGNRCRSP
+t76 ADGQR-PATLIVVLSKDNKGITEHGAVLKKIHP----------LCKRCMENGRCLRYKND
+t53 ADGQR-PATLIVVLSKDNKGITEHGAVLKKIHP----------LCKRCMENGRCLRYKND
+t16 ADGQR-PATLIVVLSKDNKGITEHGAVLKKIHP----------LCKRCMENGRCLRYKND
+t42 PDGRR-PATLLVVLSKDNQGITEHGAVLKHVHP----------LCKKDCNNNRCLRCKNV
+t24 PDGQR-PATLLVVLSKDNVGITEHGAVLKHVHP----------LCKKDCNNNRCLRCKNV
+
+
+t73 --KLYVSQLDH----KTLSK-NLGLY--MQKRTWLATAPLQ------IGCMFMLVGRKKN
+t66 --KLYVSQLDH----KTLSK-NLGLY--MQKRTWLATAPLQ------IGCMFMLVGRKKN
+t32 --KLYVSQLDH----KTLSK-NLGLY--MQKRTWLATAPLQ------IGCMFMLVGRKKN
+t75 LIKLYVSQLDH----KTLSK-NMGLY--MRNRTWLATSPLQ------IGCIFMLVGRKKN
+t79 LNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQ
+t27 LNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQ
+t93 LNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQ
+t59 LNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQ
+t7 LNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQ
+t78 LNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQ
+t12 LNKLALSQLDD----KTLSK-NCFQY--LGNMTWLATSPLH------VGCMIIF------
+t81 LNKLYLSQLDD----KTLSK-NCFIY--LGNMTWLATSPLQ------IGWLVLFDGRKRQ
+t21 LNKLYLSQLDD----KTLSK-NCFRY--LGNMTWLATSPLQ------NGCVVIFAGRKRQ
+t80 LSKLVLSQLDE----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCVILFGGRKRQ
+t14 LSKLVLSQLDE----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCVILFGGRKRQ
+t85 LSKLALSQLDE----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCIILFGGRKRQ
+t62 LSKLILSQLDD----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCIIMFDGRKRQ
+t19 LSKLILSQLDD----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCIILFDGRKRQ
+t77 LSKLILSQLDD----KTLSK-NCNIY--LGNMTWLATFPLQ------IGCIILFDGRKRQ
+t88 L-KLLMMQLD------TLSR-NQLPK--LCQGTWLDASPLQ------IGVQVMLVGKKGG
+t37 L-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRG
+t35 L-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRG
+t48 L-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRG
+t55 L-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRG
+t46 L-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVKVVLVGKKRG
+t67 L-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRG
+t57 L-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRG
+t56 L-KLNMMQLDE----KTLSQ-NQIIK--LCQRTWLDASPLQ------IGVNCVLPGKKGG
+t13 L-KLSMIQLDQ----KTLSQ-NQRAK--LCQRTWLDTSPLQ------MGMTLVLVGKKVG
+t5 L-KLSMIQLDQ----KTLSQ-NQRAK--LCQRTWLDTSPLQ------MGMTLVLVGKKVG
+t38 L-KLTMIQLDQ----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLVGKKVG
+t33 L-KLTMIQLDQ----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLVGKKVG
+t100 L-KLTMIQLDQ----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLVGKKVG
+t34 L-KLTMIQLDV----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLMGKKVG
+t84 L-KLTMIQLDV----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLMGKKVG
+t92 L-KLTMIQLDV----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLMGKKVG
+t3 L-KLSMIQLDQ----KTLSQ-NVRAR--LCQRTWLDTSPLQ------MGMVAVLLGKKLG
+t22 L-KLKMIQLDQ----KTLSQ-NQAAR--LCKRTWLDTSPLQ------MGMNVVLIGQKLG
+t64 L-KLPMIQLDQ----KTLSH-NQPRR--LCQRTWLDASPLQ------VGMNIMLMGKKAP
+t18 L-KLPMIQLDQ----KTLSH-NQPRR--LCQRTWLDASPLQ------VGMNIMLKGKKAP
+t68 L-KLPMIQLDQ----KTLSH-NQPRR--LCQRTWLDASPLQ------VGMNIMLMGKKAP
+t28 L-KLSMIQLDE----KTLSQ-NQRPG--LCQRTWLDANPLQ------MGMNTMLVGKKTP
+t82 L-KLNMIQLDQ----KTLSQ-NQRPG--LCQRTWLDASPLQ------MGMHIMLVGKKTP
+t41 L-KLNMIQLDQ----KTLSQ-NQRPG--LCQRTWLDASPLQ------MGMHIMLVGKKTP
+t71 L-KLKMIQLDQ----KTLSQ-NQQRR--LCQRTWLDSSPLQ------MGMKIMLQGKKTP
+t94 L-KLNMIQLDQ----KTLSQ-NQQRR--LCQRTWLDASPLQ------MGMKIMLQGKKIP
+t99 L-KLKMIQLDQ----KTLSQ-NQKRR--LCQRTWLDASPLQ------MGMKMMLQGKKTP
+t40 L-KLKMIQLDQ----KTLSQ-NQKKR--LCQCTWLDACPLQ------MGMKIMLQGKKTP
+t90 L-KLKMIQLDQ----KTLSQ-NQKKR--LCQCTWLDACPLQ------LGMKIMLQGKKTP
+t4 L-KLKMIVLDP----KTLSQ-NQKRR--LCQRTWLDASPLQ------VGMKIMLQGKKTP
+t36 LTALRIIQLDVGVSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVMSVEKKEA
+t87 LTALRIIQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCLVMSVEKKEA
+t89 LTALRIVQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEA
+t39 LTALRIVQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEA
+t8 LTALRIVQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEA
+t6 LTALRIVQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEA
+t58 LTALHVVQLDVGFSGKTLGQ-NIGISELLNDRTWLATSPLE------IGCGVMAVEKKEA
+t54 LTALHIVQLDVGFSGKTLGQ-NIGISELLNDRTWLATSPLE------IGCGVMAVEKKEA
+t65 LTALQTVQLDVGSSGKTLGQ-NIVTSKKLGDRTWLAASPLQ------IGCGVMVQEKKIA
+t29 LTALQTVQLDVGSSGKTLGQ-NIVTSKKLGDRTWLAASPLQ------IGCGVMVQEKKIA
+t98 LTALQTVQLDVGSSEKTLGQ-NIVTSKRLGDRTWLAASPLQ------IGCGVMVQEKKIA
+t83 LTALQTVQLDLGSSGKTLGQ-NIVTSKKLGDRTWLAASPLQ------IGCGIMVQEKKIA
+t95 LTELQTVQLDVGSSGKTLGQ-NIVTSKKLGDRTWLAASPLQ------IGCGVMVQEKKIA
+t20 LTELQTVQLDVGSSGKTLGQ-NIVTSKKLGDRTWLAAPPLQ------IGCDVMVQEKKIA
+t69 LTALKTGQLDVGSSGKTLGQ-NIMTSKKLGDRTWLAANPLQ------IGRGVMVWEKKVA
+t2 LTALKTGQLDVGSSGKTLGQ-NIMVSKKLGDRTWLAASPLQ------IGCGVMVWEKKVP
+t10 LTALKTGQLDVGSSGKTLGQ-NIMVSKKLGDRTWLAASPLQ------IGCGVMVWEKKVP
+t31 LTALKTVQLDVGSNGKTLGK-NIMTPKKLGDRTWLAASPLQ------IGCGVMVQEKKVA
+t15 LTALKTVQLDIGNSGKTLGQ-NIMTPKRLGERTWLAASPLQ------IGCGVVVQEKKVA
+t63 LTALKTVQLDVGSSGKTLGQ-NIMTPKKLGDRTWLAASPLQ------IGCDVMVQEKKVA
+t50 LTALKTVQLDVGSSGKTLGQ-NIMTPKKLGDRTWLAASPLQ------IGCDVMVQEKKVA
+t25 LTALKIVQLDVGSSGKTLGQ-NIMTPKKLGDRTWLAASPLQ------IGCDVMVQEKKVA
+t51 LTALKTVQLDVGSSGKTLGQ-NIMTPKNLGDKTWLAASPLQ------IGCGIMVQEKKVA
+t9 LTALKMLQLDIGFSAKTLGQ-NVVVPHLLGHRTWLATSPLQ------IGCGVMIFGNKIG
+t47 LTALKMLQLDIGFSAKTLCQ-NIVVAHLLGHRTWLATSPLQ------IGCMVMIFGNKIG
+t60 LTALKMLQLDIGFSAKTLGQ-NIVVPHCLGHRTWLATSPLQ------IGCMVMIFGNKIG
+t30 LTALKMLQLDIGFSAKTLGQ-NIIVPHCLGHRTWLATSPLQ------IGCMVMIVGNKIG
+t70 LTSLKMLQLDIGFCAKTLGQ-NIVVPKLLGHRTWLATAPLQ------IGCGMMIFGNKIG
+t91 LTSLKMLQLDIGFCAKTLGQ-NIVVPKLLGHRTWLATAPLQ------IGCGMMIFGNKIG
+t49 LTSLKMLQLDIGFSAKTLGQ-NIVPPKLLGHRTWLATSPLQ------IGCGVMIFGNKIG
+t52 LTALKMLQLDIGFSAKTLGQ-NIVAPKLLGVRTWLATSPLQ------IGCGVMIFGNKIG
+t43 LTALKVVQLDIGFSSKTLGQLNIIDCKLLGHRTWLATSPLQ------IGVDVMVMGNKIG
+t1 LTALKIVQLDIGFSAKTLGQLNIIDCKLLGRHTWLATSPLQ------IGCDMMVMGNKIG
+t86 LTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVMGNKIG
+t72 LTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVMGNKIG
+t96 LTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVIGNKIG
+t44 LTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDIMVMGNKIG
+t45 LTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVMGNKIG
+t74 LTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVVGNKIG
+t26 LTALKIVQLDIGFSQKTLGQ-NIIDSKHLGHRTWLATSPLQ------IGCSAMVMGNKIG
+t61 LTALKIVQLDIGFSSKTLGQ-NIIHSKLLGHRTWLATSPLQ------IGCDVMVMGNKIG
+t97 LTALQIVQLDIGFSAKTLGQ-NIIHSKLLGHRTWLATSPLQ------IGCDVVVMGNKIG
+t17 LTALKIVQLDIGFSAKTLGQ-NIIDSKLLGHRTWLATSPLQ------IGCDVMVVGNKIG
+t11 LTALKIVQLDIGFSAKTLGQ-NIIDSKLLGHRTWLATSPLQ------IGCDVMVVGNKIG
+t23 LCLLKVIQLDMGVSGKTLGQ-NIVMAKLLGERTWLATSPLQ------IGCDVVAVGKKPE
+t76 LTGDQLVQLAD----NTCAW-NLFEC--LRDSKSLFGSPLFIKVDEDRGFTAP-------
+t53 LAGDQLVQLAD----NTCAW-NLFEC--LRDSKSLFGSPLFIKVDEDRGFTAP-------
+t16 LAGDQLVQLAD----NTCLW-NLFEC--LRDSKSLFGSPLFIKVDEDRGFTAP-------
+t42 LAGNQLIQLSD----VTCAW-NLFEC--LGDSESLFGSPLAIKVDEDRGFTAP-------
+t24 LAGNQLVQLAD----ITCAW-NLFEC--LGDSESLFGSPLAIKVDEDRGFTAP-------
+
+
+t73 SEE-NYNKAADPTVIWFYTQPIVYV-ADVFGCTKGKNPQEMRG------NNVMSESLGDD
+t66 SEE-NYNKAADPTVIWFYTQPIVYV-ADVFGCTKRKNPQEMRG------NNVMSESLGDD
+t32 SEE-NYNKAADPTVIWFYTQPIVYV-ADVFGCTKGKNPQEMRG------NNVMSESLGDD
+t75 SEE-NYNKAADPTVIWFYTQPIVYV-ADVFGCTKGKNPQEMRK------NNVISESLGDD
+t79 SAN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+t27 SAN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+t93 SAN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+t59 SGN-NYNQAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+t7 SGN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+t78 SGN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+t12 ------------------------------------------V------NNVLSQSLGDD
+t81 SAE-DYNRAADPTTISFCRKPIVQH-ADVFGCDRDKDPQEMRT------NNVISESLGDD
+t21 SAE-DYNRAADPTTIAFCRKPIVQH-ADVFGCDKDKDPQEMRM------NNVISESLGDD
+t80 SHGLNYNRAADPTTICFYKKPIVVQGADVFGCARGKDPQEMKA------NNVISGSLGDD
+t14 SHGLNYNRAADPTTICFYKKPIVVQGADVFGCARGKDPQEMKA------NNVISGSLGDD
+t85 SHGLNYNRAADPTMICFYKKPIVVQGADIFGCARGKDPQEMKS------NNVISGSLGDD
+t62 SHGLQYNRAADPTTICFYKKPIVVQGADIFGCARGKDPQEMKA------NNVTSGSLGDD
+t19 SHGLQYNRAADPTTICFYKKPIVVQGADIFGCARGKDPQEMKA------NNVTSGSLGDD
+t77 SYGLQYNRAADPTTICFYKKPIVVQGADIFGCARGKDPQEMKA------NNVTSGSLGDD
+t88 SKK-EYELAADQVIIYFYQAPIIYVKADVFSGTVAKKAQAMR-------KSTGSQSIGDD
+t37 SKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+t35 SKK-DYELAADPVIIYFYQAPIIYHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+t48 SKK-DYELAADPVIIYFYQAPIIYHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+t55 SKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+t46 SKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+t67 SKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKAQAMRS------RSIGSPSVGDD
+t57 SKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKAQAMRS------RSIGSPSVGDD
+t56 SNK-DYELAADPVIIYFYQAPIIHHKADVFSGTVAKKAQAMRQ------QSTGSQSVGDD
+t13 SKK-DYEVAADPVIMYFYDAPMIMRPTDVFEGTNNKKAQAMRS------RSTASQSIGDD
+t5 SKK-DYEVAADPVIMYFYDAPMIMRPTDVFEGTNNKKAQAMRS------RSTASQSIGDD
+t38 SKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+t33 SKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+t100 SKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+t34 SKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+t84 SKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+t92 SKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+t3 SKK-DYEIAADPVIKYFYQAPIIMRRTDVFEGTDDQKAQAMRV------RSTASQSIGDD
+t22 SKH-DYEIAADPVIMYFYQAPIIMRRTDVFEGTDDQKAQAMRL------RSTASRSIGDD
+t64 SKK-DYEIAADPVIMYFYQAPIIMRRTDVFEGTHNKKAQAMRV------RSTASQSIGDD
+t18 SKK-DYEIAADPVIMYFYQAPIIMRRTDVFEGTHNKKAQAMRV------RSTASQSIGDD
+t68 SKK-NYEIAADPVIMYFYQAPIIMRRTDVFEGTHNKKAQAMRV------RSTASQSIGDD
+t28 SKK-DYEIAADPVIMYFYQAPIIMRRTDVFEGTNNKKSQAMRV------QSTSSQSIGDD
+t82 SKK-DYEIAADPVIMYFYQAPIIMQRTDVFEGTNNKKSQAMRV------HSTSSQSIGDD
+t41 SKK-DYEIAADPVIMYFYQAPIIMQRTDVFEGTNNKKSQAMRV------HSTSSQSIGDD
+t71 SKK-DYEIAADPAIMHFYRAPIIMRRTDVFEGTNNKKAQAMRI------RSTASQSIGDD
+t94 SKK-DYEIAADPAIMYFYQATIIMRRTDVFEGTNNKKAQAMRM------RSTASQSIGDD
+t99 SKK-DYEIAADPVIMYFYQSPIIMRRTDVFEGTNNKKAQAMRV------RSTASQSIGDD
+t40 SKK-DYEIAADPVIMYFYQSPIIMRRTDVFEGTNNKKAQAMRI------RSTASQSIGDD
+t90 SKK-DYEIAADPVIMYFYQSPIIMRRTDVFEGTNNKKAQAMRV------RSTASQSIGDD
+t4 SKK-DYEIAADPVIMYFYQSPIIMRHTDVFEGTNNKKAQAMRL------RSTASQSIGDD
+t36 SPK-EFEVAADPTVIYFYRNLIIQKITDVLSAVRMESPQEMRT------QDVNSSSLGDN
+t87 SGK-EFEVAADPTVIYFYRNLIIAKITDVLSAVRMESPQEMRE------QDVNSSSLGDN
+t89 SPK-EFEVAADPTVIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDN
+t39 SPK-EFEVAADPTVIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDN
+t8 SPK-EFEVAADPTVIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDN
+t6 SPK-EFEVAADPTVIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDN
+t58 SPK-EFEVAADPTVIYFYRNLIIQHITDVLSAVRMDSPQEMRV------QDVNSPSLGDN
+t54 SPK-EFEVAADPTVIYFYRNLIIQHITDVLSAVRMDSPQEMRV------QDVNSPSLGDN
+t65 SPQ-EVEVAAD---IYFYRNMVVQRLTDVVAAVRMQSPQEMRTPVLVCIQKVDSVSLGDD
+t29 SPQ-EVEVAAD---IYFYRNMVVQRLTDVVAAVRMQSPQEMRTPVLVCIQKVDSVSLGDD
+t98 SPQ-EVEVAAD---IYFYRNMVVQRHTDVVAAVRMQSPQEMRNPVLVCIQKVDSASLGDD
+t83 SPQ-EVEVAAD---IYFYRNMVVQRHTDVVAAVRMQSPQEMRNPVLVCIQKVDSISLGDD
+t95 SPQ-QVEVAAD---IYFYRNMVVQRLTDVVAAVRMQSPQEMRCRKLVCIQKVDSPSLGDD
+t20 SPQ-QVEVAAD---IYFYRNMVVQRLTDVVAAVRMQSPQEMRTPKLVCIQKVDSPSLGDD
+t69 SPQ-EVEVAAD---IYFYRNMVIECLTDVVRAVRMQSPQEMRAPVLVCIQKVDSPSLGDD
+t2 SPQ-EVEVAAD---IYFYRNMVIECLTDVVRAVRMQSPQEMRAPVLVCIQKVDSPSLGDD
+t10 SPQ-EVEVAAD---IYFYRNMVIECLTDVVRAVRMQSPQEMRAPVLVCIQKVDSPSLGDD
+t31 SPQ-EVE-AAD---IFFYRNMVIQRLTDVVAAVRMQSPQEMRPPVLVCIQYVDSPSLGDD
+t15 SPQ-EVEVAAD---IYFYRNMVIQTLTDVVAAVRMQSPQEMRPPVLVCIQDVDSVSLGDD
+t63 SPQ-EVEVAAD---IYFYRNMVIQRLTDVVAAVRMQSPQEMRLPVLVCIQDVDSPSLGDD
+t50 SPQ-EVEVAAD---IYFYRNMVIQRLTDVVAAVRMQSPQEMRLPVLVCIQDVDSPSLGDD
+t25 SPQ-EVEVAAD---IYFYRNMVIQRLTDVVAAVRMQSPQEMRLPVLVCIQDVDSPSLGDD
+t51 SPQ-EVEVAAD---IYFYRNMVIQRLTDVVAAVRMQSPQEMRPPVLVCIQDVDSPSLGDD
+t9 SAN-EFEAAADPTVIYFYRNRIVRRLADVISTVRMNSPQEMRN------QDVDSHSLGDD
+t47 SAN-EFEAAADPTVIYFYRNRIVRRLADVISTVRMNSPQEMRE------QDVDSHSLGDD
+t60 SEN-EFEAAADPTVIYFYRNRIVRRLADVISTVRMNSPQEMRN------QDVDSHSLGDD
+t30 SEN-EFEAAADPTVIYFYRNRIVRRLADVISTVRMNSPQEMRN------QDVDSHSLGDD
+t70 STQ-EFEAAADPTVIYFYRNRIVRRMADVISTVRMKSPQEMRG------QDVDSHSLGDD
+t91 STQ-EFEAAADPTVIYFYRNRIVRRMADVISTVRMKSPQEMRG------QDVDSHSLGDD
+t49 STQ-EFESAADPTVIYFYRNRIVKRMADVISTVRMKSPQEMRG------QDVDSHSLGDD
+t52 STQ-EFEAAADPTVIYFYRNRIIRRVADVISTVRMKSPQEMRE------QDVDSHSLGDD
+t43 SPS-EFEVAADPTIIWFYRNCIVHKLADTVSTAKMKSPQEMRH------QDVDSPSLGDD
+t1 SPS-EFEVAADPTIIWFYRDCIVHKLADTVSTAKMKAPQEMRV------QDVDSPSLGDD
+t86 SPS-EFEVAADPTIIWFYRNCIVHKLADTVSTAKMKAPQEMRV------QDVDSPSLGDD
+t72 SPS-EFEVAADPTIIWFYRNCIVHKLADTVSTAKMKAPQEMRH------QDVDSPSLGDD
+t96 SPS-EFEIAADPTIIWFYRNCIVHKLADTVSTAKMKAPQEMRV------QDVDSPSLGDD
+t44 SPS-EFEVAADPTIIWFYRNCIVHKLADVVSTAKMKSPQEMRV------QDVDSPSLGDD
+t45 SPA-EFEVAADPTIIWFYRNCIVHKLADLVSTAKMKSPQEMRV------QDVDSPSLGDD
+t74 SPA-GFEVAADPTIIWFYRNCIVHKLADLVSTAKMKSPQEMRV------QDVDSPSLGDD
+t26 SPQ-EVELAADPTVIYFYRNCIVQKMADVVSTVKMKSPQEMRV------QDVDSASLGDD
+t61 SPQ-EVELAADPSVIYFYQNCIVQKMADVVSTVKMKSPQEMRV------QDVDSASLGDD
+t97 SPQ-EVELAADPSVIYFYQNCIVQKMADVVSTVKMKSPQEMRV------QDVDSASLGDD
+t17 SPQ-EFELAADPTVIYFYRNCIVQKLADVVSTVKMKSPQEMRV------QDVDSPSLGDD
+t11 SPQ-EFELAADPTVIYFYRNCIVQKLADVVSTVKMKSPQEMRV------QDVDSPSLGDD
+t23 SPQ-EFECAADPTVIYFYKNLIIQQAADYVSAVQVKSPQEMRY------QDVNSPSDGDE
+t76 SK-------VEPKCAQFYSKSCTHC----------------TM------CSVGSHASEED
+t53 SK-------VEPKCAQFYSKSCTHC----------------TM------CSVGSHASEED
+t16 SK-------VEPKCAQFYSKSCTHC----------------TM------CSVGSHASEED
+t42 SK-------VEPKCAQFYSKSCTHH----------------MM------CSVGSNASEED
+t24 SK-------VEPKCQQFYSKSCTHC----------------VM------CSVGSNASEED
+
+
+t73 NLQD--MSGVPVTVCTSSVMVRKDMQD-SVDKRGCTWNAKE-DHLCPSSFCKGER---ED
+t66 NLQD--MSGVPVTVCTSSVMVRKDMQD-SVDKRGCTWNAKE-DHLCPSSFCKGER---ED
+t32 NLQD--MSGVPVTVCTSSVMVRKDMQD-SVDKRGCTWNAKE-DHLCPSSFCKGER---ED
+t75 NLQD--MPGMPVTVCTSSVMVRKDMHQ-SVDKRGYTWHAKE-DHLCPDSFCKGEK---EE
+t79 SLQQ--MPAVPVDVCVMSVMVNKSMPQ-SHDKRGYTWQAKQ-DHLFPVNVVKGEQ---EE
+t27 SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNCVKGEQ---EE
+t93 SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNCVKGEQ---EE
+t59 SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNFVKGEQ---EE
+t7 SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNFVKGEQ---EE
+t78 SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNFVKGEQ---EE
+t12 SLQQ--MHAMPVTVVVVSHMVKKSMPQ-SHDKRGYTWQAKDFDQLIPVSFVKGEQ---EE
+t81 FLQQ--MPAVPVSVCVYSHMVKKFVPQ-SHEKRGYTWKAKE-DHLVPISYCKGEH---EE
+t21 FLQQ--MPAVPVSVCVHSHMVKKFVPQ-SHEKRGVTWKAKE-DHLVPISLCKGEH---EE
+t80 RLQQ--MPAMPVTICVSSYMVKKSVIQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---DE
+t14 RLQQ--MPAMPVTICVSSYMVKKSVPQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---DE
+t85 RLQH--MPAMPVTICVFSYMVKKAVPQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---DE
+t62 RLQQ--MPAMPVTICVFSYMVKKSVPQ-SHVKRGYTWRAKE-DHLIPVSFCKGEL---EE
+t19 RLQQ--MPAMPVTICVFSYMVKKLVPQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---EE
+t77 RLQQ--MPAMPVTICVFSYMVKKSVPQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---EE
+t88 GMQS--MPLMQNAVCVWSKMVRKVQPD-GQDKREQTWMAKD-DTLCPPSMKRGEK---TA
+t37 GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DTLCPPCEEQGEK---AA
+t35 GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DTLCPPCEEQGEK---AA
+t48 GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DTLCPPCEEQGEK---AA
+t55 GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DTLCPPCEEQGEK---AA
+t46 GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DALCPPCKEQGEK---AA
+t67 GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWVAKD-DTLCPPCKEQGEK---AA
+t57 GMQK--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWVAKD-DTLCPPCKDQGEK---AA
+t56 GTQV--MPLMQNLVCVWSKMVRKCMID-GQEKREQTWMAKD-DKLCPPSQEQGEK---AA
+t13 DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKD-DTLCPQSRDQGEK---HH
+t5 DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKD-DTLCPQSRDQGEK---HH
+t38 DMLN--MPLTQNAMCVESEMVRKSQPD-GQDKRGYTWVAKE-DDLCPQSGDQGEK---YA
+t33 DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSGDQGEK---YA
+t100 DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSEDQGEK---YA
+t34 DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSGDQGEK---YA
+t84 DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSGDQGEK---YA
+t92 DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSGDQGEK---YA
+t3 DMLI--MPLVQNAMCVKSEMVRKCQPD-GPDKRGYTWMAKD-DTLCPVSAGQGEK---YA
+t22 DMLI--MPLVQNAMCVNPEMVRKCQPD-GQDKRGYTWMAKN-DTLCPVSAGQGEC---YA
+t64 DMLK--MPLVQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANQGEK---YA
+t18 DMLK--MPLVQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANQGEK---YA
+t68 DMLK--MPLRQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANQGEK---YA
+t28 DMLN--MPLVQNAMCVSSEMVRKCQPD-GQNKRGCTWMAKN-DTLCPQSGNQGEK---FA
+t82 DMLN--MPLVQNAMCVSSEMVRKCQPD-GQNKRGYTWMAKH-DTLCPQSGNQGEK---YA
+t41 DMLN--MPLVQNAMCVSSEMVRKCQPD-GQNKRGYTWMAKH-DTLCPQSGNQGEK---YA
+t71 DMLN--MPLHQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSPNQGEK---YA
+t94 DMLN--MPLHQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLYPQSANQGEK---YA
+t99 EMLN--MPLVQNAMCVPSEMVRKCQPD-GQDKRGYTWMAKD-DPLCPQSANVGEK---YA
+t40 EMLN--MPQVQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANVGEK---YA
+t90 EMLN--MPLVQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANQGEK---YA
+t4 EMLN--MPLIQNAMCVQSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQLHNQAEK---YA
+t36 NGQA--MNIVPYWVCVASGVVRKTHKD-SVDKRGQTWTAKS-DFLCPLAVDQGEP---GA
+t87 NGQA--MNIVPYWVCVGSGVVRKTHKD-SVDKRGQTWTAKS-DFLCPLAMDQGEI---GA
+t89 NGQA--MNIVPYWVCVASGVVRKMHKD-SVEKRGQTWEAKS-DFLCPLAVDQGEP---AA
+t39 NGQA--MNIVPYWVCVASGVVRKMHKD-SVEKRGQTWEAKS-DFLCPLAVDQGEP---AA
+t8 NGQA--MNIVPYWVCVASGVVRKMHKD-SVEKRGQTWEAKS-DFLCPLAVDQGEP---AA
+t6 NGQA--MNIVPYWVCVASGVVRKMHKD-SVEKRGQTWEAKS-DFLCPLAVDQGEP---AA
+t58 NGQA--MNIVPYWVCVVSGVVRKTHKD-SVEKRGQTWTAKS-DFLCPIAVNQGEP---GA
+t54 NGQA--MNIVPYWVCVVSGVVRKTHKD-SVEKRGQTWTAKS-DFLCPIAVNQGEP---GA
+t65 DPQM--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPAAVNEGEH---GA
+t29 DPQM--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GA
+t98 DPQM--MKIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GA
+t83 DPQM--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GA
+t95 DPQM--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GA
+t20 DPQC--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GA
+t69 VPQM--MNIVPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAMNEGEH---GA
+t2 VPQM--MNIVPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAMNEGEH---GA
+t10 VPQM--MNIVPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAMNEGEH---GA
+t31 TPQM--MNIAPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKA-DFLCPPAVSEGEH---GA
+t15 TPQM--MNIAPYWVCVCSGVVKKTQPD-SVDKRGKTWVAKS-DFLCPPAVSEGEH---GA
+t63 TPQK--MNIAPYWVCVCSGVVKKAQLD-SVEKRGKTWVAKS-DFLCPPAVSEGEH---GP
+t50 TPQK--MNIAPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAVSEGEH---GP
+t25 TPQK--MNIAPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAVSEGEH---GP
+t51 TPQM--MNIAPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAISEGEH---GA
+t9 DNQA--MVILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKV-DFLCPPAFNQGEH---RA
+t47 DNQA--MNILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKM-DFLCPPAFNQGEH---RA
+t60 DNQA--MNILPYVVCVCSGVVRKDHPDTSIHKRGRTWLAKV-DFLCPPAFNQGEH---RA
+t30 DNQA--MNILPYVVCVCSGVVRKEHPDTSISKRGRTWLAKI-DFLCPPAFNQGEH---RA
+t70 DNQA--MNILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKI-DFLFPPAFNQGEH---HA
+t91 DNQA--MNILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKI-DFLFPPAFNQGEH---HA
+t49 DNQA--MNILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKI-DFLFPPAFNQGEH---HA
+t52 DNQA--MTILPHWVCVVSGVVRKEHPDTSINKRGSTWLAKV-DFLCPPAFNQGEH---HA
+t43 DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFNQGEH---ER
+t1 DQQE--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFNQGEH---EA
+t86 DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFNQGEH---GA
+t72 DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFKQGEH---EA
+t96 DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFNQGEH---EA
+t44 DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFEQGEH---EA
+t45 DQEA--MDILPYWVCVMSGVVRKEQPD-SVNKRGRTWLAKK-DFLVPPAFNQGEH---EA
+t74 DQEA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKK-DFLVPPAFNQGEH---EA
+t26 DQQP--MNIIPYWVCVTSGVVHKEQPD-SVNKRGRTWTAKN-DFLCPDAFNQGEH---GA
+t61 DQQP--MNIIPYWVCVTSGVVRKEQPD-SVNKRGHTWTAKN-DFLCPPAYNQGEH---GA
+t97 DQQP--MNIIPYWVCVTSGVVRKEQPD-SVNKRGRTWSAKN-DFLCPPAFNQGEH---GA
+t17 NQQS--MNIIPYWVCVHSGVVQKEQPD-SVHKRGRTWTAKN-DFLCPPAFDQGEH---GA
+t11 NQQS--MNIIPYWVCVHSGVVQKEQPD-SVHKRGRTWTAKN-DFLCPPAFDQGEH---GA
+t23 NGQS--MHIGPYWVCVSSEVVKKSQPD-SVDKRGRTWVAKN-EFLCPPDHMQGEHSIEGA
+t76 ALDLYTHKPVPDAQCFVSRVARNIPEH-SPCK----------------------------
+t53 ALDLYTHRPVPDAQCFVSRVARNIPEH-SPCK----------------------------
+t16 ALDLYTHKPVPDAQCFVSRVARNIPEH-SPCK----------------------------
+t42 ALELYTHKPVPDPQCFVSIVVRNIPEH-SPCK----------------------------
+t24 ALELYTHKPVPDPQCFVSIVVRNIPEH-SPCK----------------------------
+
+
+t73 EPGGVTQ-----------------RCIENIAKLLYIKDV-LCNEVLNGLQWQLCWSV-GD
+t66 EPGGVTQ-----------------RCIENIAKLLYIKDV-LCNEVLNGLQWQLCWSV-GD
+t32 EPGGVTQ-----------------RCIENIAKLLYIKDV-LCNDVLNLLVWQLCWSV-GD
+t75 EPGGVRR-----------------RIVENIVKLLYIKDV-LCNQVLNLLQWQLCWSV-GD
+t79 EPEGADQ-----------------RTVHDMVRLLYSKDV-DCNMVLSLLVWQLC--H-GD
+t27 EPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIVLSLLVWQLC--H-GD
+t93 EPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIVLSLLVWQLC--H-GD
+t59 EPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIDLSLLVWQLC--H-GD
+t7 EPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIVLSLLVWQLC--H-GD
+t78 EPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIVLSLLVWQLC--H-GD
+t12 EPEGPNN-----------------RVVHNIVKLLYTKDV-DCNTVLSLLIWQLC--H-GD
+t81 EPEGAQY-----------------RVVQNIVKLLYTKDV-DCNVVLSLLVWQLC--H-GD
+t21 EPEGAQY-----------------RCVQNIVKLLYTKDV-DCNVVLSLLVWQLC--H-GD
+t80 EPDAAQQ-----------------RIVQNIVKLLYTKDV-SCNVVLSMLIWQIC--H-GD
+t14 EPDAAQQ-----------------RIVQNIVKLLYTKDV-SCNVVLSMLIWQIC--H-GD
+t85 EPDGAQQ-----------------RVVQNIVKLLYTKDV-SCNKVLSMLIWQIC--H-GD
+t62 EPEGAQH-----------------RMVQNIVKLLYTKDV-SCNVVLSMLIWQIC--H-GD
+t19 EPEGAKQ-----------------RMVQNIVKLLYTKDV-SCNVVLSMLIWQIC--H-GD
+t77 EPEGAQQ-----------------RIVQNIVKLLYTKDI-SCNVVLSMLIWQIC--H-GD
+t88 EPTQWMG-----------------TVTVNKIKLLYCKDC-SCNEVMKILSWWLCNSV-GD
+t37 EPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAWWLCDSV-GD
+t35 EPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAWWLCDSV-GD
+t48 EPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAWWLCDSV-GD
+t55 EPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAWWLCDSV-GD
+t46 EPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAWWLCDSV-GD
+t67 EPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAWWLCDSV-GD
+t57 EPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAWWLCDSV-GD
+t56 EPTQWED-----------------ICTANVIKLLYCKDC-SCNEVLRVLSWWLCDSV-GD
+t13 EPHHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t5 EPHHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t38 EPQHIRN-----------------QFSENVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t33 EPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t100 EPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t34 EPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t84 EPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t92 EPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t3 EPHQIKN-----------------KFSVNVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t22 EPHQTCN-----------------KFRVNVIKLLYCKDC-SCNKVLKILKWQLCESV-DD
+t64 EPHVIGD-----------------KVSVNVIKLLYCKDC-SCNQVLKILVWQLCESV-DD
+t18 EPHVIGD-----------------KVSVNVIKLLYCKDC-SCNQVLKILIWQLCESV-DD
+t68 EPVVIGD-----------------KVSVNVIKLLYCKDC-SCNQVLKILVWQLCESV-DD
+t28 EPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKMLKILVWQLCESV-DD
+t82 EPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t41 EPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t71 EPHQIRN-----------------KISVNVIKLLYCKDC-SCNQVLKILVWQLCESV-DD
+t94 EPHQIRN-----------------KISVNVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t99 EPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKVLKILVWQLCDSVQDD
+t40 EPHQIRN-----------------KVSTNVIKLLYCKDC-SCNKVLKILVWQLCDSV-DD
+t90 EPHQIRN-----------------KVSTNVIKLLYCKDC-SCNKVLKILVWQLCDSV-DD
+t4 EPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKVLKILVWQLCESV-DD
+t36 EQKPAVGEENPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKWQLCDSH-GD
+t87 EQKPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKWQLCDSH-GD
+t89 EQRPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKWQLCDSH-GD
+t39 EQRPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKWQLCDSH-GD
+t8 EQKPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKWQLCDSH-GD
+t6 EQKPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKWQLCDSH-GD
+t58 EQKPAVGA-NPIVKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKWQLCDSH-GD
+t54 EQKPAVGA-DPIVKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKWQLCDSH-GD
+t65 EQRP-FGTQNPVCKPWRFVIMNTQTFAKNIIRLLYIKDI-SCNQVLQLLDWQLCDSH-GD
+t29 EQRPVFGTHNPVCKPWRFVIMHTQTFSKNIIRLLYIKDI-SCNQVLQLLDWQLCDSH-GD
+t98 EQRPVFGTQNPVCKPWRFVIMNTQTFSKNIIRLLYIKDI-SCNQVLQLLDWQLCDSH-GD
+t83 EQRPVFGTQNPVCRPWRFVIMNMQTFSKNIIRLLYIKDI-SCNQVLQLLDWQLCDSH-GD
+t95 EQRPVFGGQNPACKPWHFVIMNRQTFAKNMIRLLYIKDI-SCNEVLQLLDWQLCDSH-GD
+t20 EQRPVFGGQNPACQPWHFVIMNTQTFAKNMIRLLYIKDI-SCNQVLQLLDWQLCDSH-GD
+t69 EQRPVFGTQNPVCKPWRFVIMNTETFAKNIIRLLYVKDV-SCNQVLQLLDWQLCDSH-GD
+t2 EQRPVFGTQNPVCKPWRFVIMNVETFAKNIIRLLYVKDV-SCNQVLQLLDWQLCDSH-GD
+t10 EQRPVFGTQNPVCKPWRFVIMNVETFAKNIIRLLYVKDV-SCNQVLQLLDWQLCDSH-GD
+t31 EQRPVFGMQNPACKPWRFVIMNTQTFAKNIIRLLYIKDV-SCNAVLQLLDWQLCYSH-GD
+t15 EQRPVFGMRNPICKPWRFVIMNTQTFAKNIIRLLYVKDV-SCNAVLQLLDWQLCYSH-GD
+t63 EQRPVFGVQNPVCKPWRFVIMNTQTFAANIIRLLYVKDV-SCNAVLQLLDWQLCYSH-ED
+t50 EQRPVFGVQNPVCKPWRFVIMNTQT-AKNIIRLLYVKDV-SCNAVLQLLDWQLCYSH-GD
+t25 EQRPVFGMQNPVCKPWRFVIMNTQTFAKNIIRLLYVKDV-SCNAVLQLLDWQLCYSH-GD
+t51 EQRPVFGMQNPVCRPWRFVIMNTQTFAKNVIRLLYVKDV-SCNKVLQLLDWQLCYSH-GD
+t9 EQKPASKFEHPVCGPWEFVIVNYQTSAKDIILLLYIKDV-GCNCVLELLNWQLCTSH-GD
+t47 EQKPALKFKHPVCGPWEFVIVNYQTSAKDIILLLYIKDV-GCNCVLELLKWQLCTSH-GD
+t60 EQKPAFKFKHPVCGPWEFVIVNYQTEAKDIILLLYIKDV-GCNCVLELLEWQLCTSH-GD
+t30 EQKPAFKFKHPCCGPWEFVIVNYQTSAKDIILLLYIKDV-GCNCVLELLKWQLCTSH-GD
+t70 EQKPVFGFKHPHCGPWEFVICNYQTVAKDIILLLYIKDV-GCNCVLELLAWQLCTSH-GD
+t91 EQKPVFGFKHPHCGPWEFVICNYQTVAKDIILLLYIKDV-GCNCVLELLAWQLCTSH-GD
+t49 EQKPVFGFKHPHCGPWEFVICNYQTMAKDIILLLYIKDV-GCNCVLELLAWQLCTSH-GD
+t52 EQKPVFGFKHPHVGPWEFVICNYQTSAHDIILLLYIKDV-GCNCVLELLVWQLCTSH-GD
+t43 EQRPVYGFKHPGCRPWQFVIANYQTSAKNIIMLLYVKDV-SCNGVLQLLNWHLCDSH-GD
+t1 EQRPVYGFVHPRCRPWQFVIANYQTSAKNIIMLLYVKDV-SCNGVLQLLNWQLCDSH-GD
+t86 EQRPVYGFQHPRCRPWQFVIANYQTFAKNIIMLLYVKDV-SCNRVLQLLNWQLCDSH-GD
+t72 EQRPVYGFQHPRCRPWQFVIANYQSSAKNIIMLLYVKDV-SCNGVLQLLNWQLCDSH-GD
+t96 EQRPVYGFQHPRCRPWQFVIGNYQTSAKNIIMLLYVKDV-SCNGVLQLLNWQLCDSH-GD
+t44 EQCPVHGFKHPRCRPWQFVIADYQTSAKNIIMLLYVKDV-SCNGVLQLLNWQLCDSH-GD
+t45 EQKPVYGFDHPRCRPWQFVIANYQTSAKNIIMLLYVKDV-SCNGVLQLLNWQLCDSH-GD
+t74 EQKPVYGFDHPRCRPWQFVIANYQTSAKNIIMLLYVKDV-SCNGVLQLLNWQLCDSH-GD
+t26 EQKPTHGFEHPRCRPWQFVIPVYQTGAKNIILLLYIKDV-SVNGVLQLLIWQLCDSH-GD
+t61 EQKPVHGFEHPRCRPWQFVISVYRTGAKNINLLLYIKDV-SCNGVLQLLNWQLCDSH-GD
+t97 EQKPVHEFQHPRCRPWQFVISVYRTGAKNINLLLYIKDV-SCNGVLQLLNWQLCDSH-GD
+t17 EQKPVHGFEHPRCRPWQFVIANYQTGAKNIILLLYVKDV-SCNGVLQLLNWQLCDSH-GD
+t11 EQKPVHGFEHPRCRPWQFVIANYQTGAKNIILLLYVKDV-SCNGVLQLLNWQLCDSH-GD
+t23 EQKPFFGFAGPFPQPWQFVIVNPQTWAHNIIRLLYCKDV-SCNCVLTCLNWVLCDSH-GD
+t76 -P---CS-----------------VEEVCYCKVCDSKDVRAVKNAYQDLQVPLSKLK-AP
+t53 -P---CS-----------------VEEVCYCKVCDSKDVRAVKNAYQDLQVPLSKLK-AP
+t16 -P---CS-----------------VEEVCYCKVCDSKDVRAVKNAYQDLQVPLSKLK-AP
+t42 -P---CS-----------------VEEVAYCKNCDSKDVRAVQNAYQDLAVPLSKLK-AP
+t24 -P---CS-----------------VEEVCYCKNCDSKDVRATQNAYQELAIPLSKLK-AP
+
+
+t73 WESLIPQACWDAKKDLAVCAWKMELVPGL---NRNNENLAKVIYFGPDGH-------DEG
+t66 WESLIPQACWDAKKDLAVCAWKMELVPGL---NRNNENLAKVIYFGPDGH-------DEG
+t32 WESLIPQACWDAKKDLAVCAWKMELVPGL---NRNNENLAKVIYFGPDGH-------DEG
+t75 WESLVPQACWGAKKDLAVCAWKMELVPGL---NRNNENLAKIIYFGPDGH-------DEG
+t79 WEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEG
+t27 WEPLLPQACEGARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEG
+t93 WEPLLPQACEGARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEG
+t59 WEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEG
+t7 WEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEG
+t78 WEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEG
+t12 WEQLVPQACAGARSDLAVCAWKRELVPGL---NHNNENLAKVIYFGPDGH-------DEG
+t81 WEPLIPQACQTAKKDLAVCAWKRELVPGL---NCNNEYLAKIIYFGPDGH-------DEG
+t21 WEPLVPQACQTAKKDLAVCAWKRELVPGL---NCNNEYLAKIIYFGPDGH-------DEG
+t80 WEPQIPKACSNARKDLAVCAWKRELVPGL---NHNNENLAKIMYFGHDGH-------DEG
+t14 WEPQIPKACSNARKDLAVCAWKRELVPGL---NHNNENLAKIMYFGHDGH-------DEG
+t85 WEPQIPKACNAARKDLAVCAWKRELVPGL---NHNNEDLAKIMYFGPDGH-------DEG
+t62 WEPQIPKACDAARKDLAVCAWKRELVPGL---NHNDENLAKIMYFGPDGH-------DEG
+t19 WEPQIPKACDAARKDLAVCAWKRELVPGL---NHNDENLAKIMYFGPDGH-------DEG
+t77 WEPQLPKACDAARKDLAVCAWKRELVPGL---NHNDENLAKIMYFGPDGH-------DEG
+t88 WQTLMSQACITADPNPPVCVWKRELVPGL---NRSVENLAKIIYFCPDEH-------DER
+t37 WQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DER
+t35 WQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DER
+t48 WQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DER
+t55 WQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DER
+t46 WQSLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DER
+t67 WQTLMNDACSSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DER
+t57 WQTLMNDACSSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DER
+t56 WRTLMSDACALANPNPPVCVWKRELVPGL---NRNVENLAKIIYFCPDEH-------DER
+t13 WQTLSSDACMHAEQNPPVCVWQRELVPQL---NRNIEDLARIIYFGPDEH-------DEG
+t5 WQTLSSDACMHAEQNPPVCVWQRELVPQL---NRNIEDLARIIYFGPDEH-------DEG
+t38 WQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEG
+t33 WQTLASDACVSAEPNTPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEG
+t100 WQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEG
+t34 WQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEG
+t84 WQTLASDACVSAEHNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEG
+t92 WQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEG
+t3 WVTLASDACLSAEPQPPVCVWQRELVPQL---NRNVEDLARVIYFGPDEH-------DEG
+t22 WQTLASDACILAKPQPPVCVWQRELVPQL---NRNVEDLARVIYFGPDEH-------DEG
+t64 WQTLTSDPCMSAQVNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEG
+t18 WQTLTSDPCMSAQVNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEG
+t68 WQTLTSDPCMSAQVNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEG
+t28 WQTLASDPCVSAEPNSPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEG
+t82 WQTLASDPCMSAEPNPPVCVWQRELVPQL---NRNVEDLARTIYFGPDEH-------DEG
+t41 WQTLASDPCMSAEPNPPVCVWQRELVPQL---NRNVEDLARTIYFGPDEH-------DEG
+t71 WQTLTSDPCVPAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEG
+t94 WQTLTSDPCVPAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEG
+t99 WQPLTSDPCVNAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEG
+t40 WQTLTSDPCVSAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEG
+t90 WQTLTSDPCVSAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEG
+t4 WQTLTSDPCISAEPNPPVCVWQRELVPQL---NRNIEDLARIIYFGPDEH-------DEG
+t36 WQSLYADSCPIA-VNAAVCGWKRELVPGL---NHSCEHLAKSVYFEPDGE-------GEG
+t87 WQSLYADSCPIA-INAAVCGWKRELVPGL---NHSCEHLAKSVYFEPDGE-------GEG
+t89 WQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEG
+t39 WQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEG
+t8 WQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEG
+t6 WQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEG
+t58 WQSLFADSCPTA-VNAAVCAWKRELVPGL---NHSCEHLAKSVYFEPDGE-------DEG
+t54 WQSLFADSCPIA-VNAAVCAWKRELVPGL---NHSCEHLAKSVYFEPDGE-------DEG
+t65 WQSLMADSCPNA-VNIAVCCWKRELMPGL---NHSCEHLAKSVYFKPDGE-------DEG
+t29 WQSLMADSCPNA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEG
+t98 WQSLMADSCPPA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEG
+t83 WQSLMADSCPPA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEG
+t95 WQSLIADSCPNA-SNIAVCCWKRELMPGL---NFSCEHLAKTVYFKPDGE-------DEG
+t20 WQSLIADSCPNA-VNIAVCCWKRELMPGL---NFSCEHLAKTVYFKPDGE-------DEG
+t69 WQSLVADSCPNA-VNIAVCCWKRELMPGL---NHSCQHLAKTVYFKPDGE-------DEG
+t2 WQSMVADSCHNA-VNIAVCCWKRELMPGL---NHSCQHLAKTVYFKPDGE-------DEG
+t10 WQSMVADSCHNA-VNIAVCCWKRELMPGL---NHSCQHLAKTVYFKPDGE-------DEG
+t31 WQSLIADSCPTA-ANIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEG
+t15 WQSLIADSCSTA-ANIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEG
+t63 WQSLIADACPTA-VNIAVCCWKRELMPGL---NHSCEHLAKSVYFKPDGE-------DEG
+t50 WQSLIADACSTA-VNIAVCCWKRELMPGL---NHSVEHLAKSVYFKPDGE-------DEG
+t25 WQSLIADACPTA-VNIAVCCWKRELMPGL---NHSCEHLAKSVYFKPDGE-------DEG
+t51 WQSLIADACPAA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEG
+t9 WQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEG
+t47 WQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCDRLAKHIYFQPDGE-------DEG
+t60 WQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEG
+t30 WQSLVADSCVWA-HNVAVCEWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEG
+t70 WQSLVADSCIWA-HNVAVCAWKRELVPGL---NHSCEHLAKHIYFQPDGE-------DEG
+t91 WQSLVADSCIWA-HNVAVCAWKRELVPGL---NHSCEHLAKHIYFQPDGE-------DEG
+t49 WQSLVADSCIWA-HNVAVCAWKRELVPGL---NHSCEHLAKHIYFQPDGE-------DEG
+t52 WQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEG
+t43 WQSLVADSCCWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEG
+t1 WQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEG
+t86 WQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEG
+t72 WQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEG
+t96 WQSLVADSCMWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEG
+t44 WQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEG
+t45 WQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEG
+t74 WQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEG
+t26 WQSLVADSCAWA-VNVAVCGWKRELVPGL---NHACEMLAKTVYFEPDGE-------DEG
+t61 WQSLVADSCAWA-VNVAVCGWKRELVPGL---NHACEMLAKSVYFEPDGE-------DEG
+t97 WQSLVADSCAWA-VNLAVCGWKRELVPGL---NHACEMLAKSVYFEPDGE-------DEG
+t17 WQSLSADSCAWA-HNVAVCGWKRELVPGL---NHACEMLAKTVYFEPDGE-------DEG
+t11 WQSLSADSCAWA-HNVAVCGWKRELVPGL---NHACEMLAKTVYFEPDGE-------DEG
+t23 WHSLIADACPCA-HNVAVCGWKRELVPGL---NHSNEHMAKTIYFEPDGH-------DEG
+t76 WLSMGHCECWEEDINNILSVVKHELVDDVDRMNRLTEVAAKMAYFGPDGFHWDVELWEEN
+t53 WLSMGHCECWEEDINNILSVVKHELVDDVDRMNRLTEVAAKMAYFGPDGFHWDVELWEEN
+t16 WLSMGHCECWEEDINNILSVVKHELVDDVDRMNRLTEVAAKMAYFGPDGFHWDVELWEEN
+t42 WLSMGHCECWEEDINNILSMVKHELVVDQDMVNRSPEVAAKMAYFGPDGFHWDVELCEES
+t24 WLSMGHCECWEEGINNILSMVKHELVVDQDMVNRSPEVAAKMAYFGPDGFHWDIELCEEN
+
+
+t73 PMQAKIVTLHW-EMDVSHRG-SSVDDNVV-VVMLAFAVSFCHPWGHYIQGLGD-QHKLAR
+t66 PMQAKIVTLHW-EMDVSHRG-SSVDDNVV-VVMLAFAVSFCHPWGHYIQGLGD-QHKLAR
+t32 PMQAKIVTLHW-EMDVSHRG-SSVDDNVV-VVMLAFAVSFCHPWGHYIQGLGD-QHKLAR
+t75 NMQAKIVTLHW-EMDVSHRG-SSVDDNVV-VVMLAFQASFCDPWGHYIQGLGD-QYKLAR
+t79 PMGQKIVDLHW-EMEASHRE-SSVRDNMI-VIMLPFNINSIDPWRHYILGLND-QIQLTR
+t27 PMGQKIVDLHW-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTR
+t93 PMGQKIVDLHW-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTR
+t59 PMGQKIVDLHW-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTR
+t7 PMGQKIVDLHW-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTR
+t78 PMGQKIVDLHW-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTR
+t12 PMGRKIVDLHW-EMEASHRD-SSVRDNML-VIMLPFLVNNLDPWRHYILGLND-QIQLTR
+t81 PMGRKIVDLHW-EMEASHRD-SSVRDNYI-VIMLPFKINSRDPWRHYILGIND-QVCLNR
+t21 PMGRKIIQLHW-EMEASHRD-SSVRDNII-VIMLPFKINSRDPWRHYILGLND-QVCLTR
+t80 PMGRKIVTLHV-EMEVSHRE-SSVKDNMIRVIMLPFSNSSVDPWRHVILGLND-QIKLTR
+t14 PMGRKIVTLHV-EMEVSHRE-SSVKDNMIRVIMLPFPSSSVDPWRHVILGLND-QIKLTR
+t85 PMGRKIVNLHV-EMEVSHRE-SSVKDNMIRVVMLPFDNNSWDPWRHVILGLND-QIKLTR
+t62 PMGEKIVNLHV-EMEASHRE-SSVKDNMIRVIMLPFSNNSWDPWRHVILGLND-KIKLTR
+t19 PMGEKIVNLHV-EMEASHRE-SSVKDNMIRVIMLPFSNNSWDPWRHVILGLND-QIKLTR
+t77 PMGEKIVNLHV-EMEASHRE-SSVKDNMIRVIMLPFGENSWDPWRHVILGLND-QIKLTR
+t88 KMWGKIFALEW-EMDISHRH-SSVDDNHC-VEMLPFMCQRVDPWGHYVQILAD-RQDLAR
+t37 RMWGKIFALEW-EMDISHRH-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLDLTR
+t35 RMWGKIFALEW-EMDISHRH-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLDLTR
+t48 RMWGKIFALEW-EMDISHRH-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLDLTR
+t55 RMWGKIFALEW-EMDISHRH-SSVDDNQC-VELLPYNCQRMDPWGHYVQILAD-RLDLTR
+t46 RMWGKIFALEW-EMDISHRH-SSVDDNQC-VELLPYVCQRMDPWGHYVQVLAD-RLDLTR
+t67 RMWGKIFALEW-EMDISHRM-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLVLTR
+t57 RMWGKIFALEW-EMDISHRV-SSVDDNQC-VELLPYLCQRMDPWGHYVQILAD-RLNLTR
+t56 KMWGKIFCLEW-EMDISHRH-SSVDDNVC-VEMLPFVCQKMDPWGHYVQILAD-RLDLTR
+t13 KMMNKIFALEW-EMDMSHRV-SSVDDNYI-IEMLPFVCDRVGPWGHYAQVLAD-QLHLTR
+t5 KMMNKIFALEW-EMDMSHRV-SSVDDNYI-IEMLPFVCDRVGPWGHYAQVLAD-QLHLTR
+t38 KMMCKIFALEW-EMDMSHRM-SSVDDNYI-IEMLPFVCDRVGPWGHYAQILAD-QLNLTR
+t33 KMMCKIFALEW-EMDMSHRM-SSVDDNYI-IEMLPFVCDRVGPWGHYAQILAD-QLNLTR
+t100 KMMCKIFALEW-EMDMSHRM-SSVDDNYI-IEMLPFVCDRVGPWGHYAQILAD-QLNLTR
+t34 KMMCKIFALEW-EMDMSHRM-SSVDDNYI-IEMLPFVCDRIGPWGHYAQILAD-QLNLTR
+t84 KMMCKIFALEW-EMDMSHRM-SSVDDNYI-IEMLPFVCDRIGPWGHYAQILAD-QLNLTR
+t92 KMMCKIFALEW-EMDMSHRM-SSVDDNYI-IEMLPFVCDRIGPWGHYAQILAD-QLNLTR
+t3 KMMPKIFKLAW-EMDMSHRA-SSVDDNYV-IEMLPFVCHRVGPWGHYAQVQAD-QQNLTR
+t22 KMMSKIFNLEW-EMDMSHRT-SSVDDNYV-IDMLPFICHRVGPWGHYAQVLAD-QINLTR
+t64 KMMSKIFALEW-EMDMSHRV-SSVDDNFV-IEMLPFVCHRIGPWGHYAQMLAD-QIVLTR
+t18 KMMFKIFALEW-EMDMSHRV-SSVDDNFV-IEMLPFVCHRIGPWGHYAQMLAD-QIVLTR
+t68 KMMSKIFALEW-EMDMSHRV-SSVDDNFV-IEMLPFVCHRIGPWGHYAQMLAD-QIVLTR
+t28 KMMSKIFALEW-EMDMSHRI-SSVDYNYV-IEMLPFVYHRVGPWGHYAQMLSD-QIVLTR
+t82 KMMSKIYALEW-EMDMSHRV-SSVDYNYV-IEMLPFVYHRVGPWGHYAQMLAD-QIVLTR
+t41 KMMSKIYALEW-EMDMSHRV-SSVDYNYV-IEMLPFVYHRVGPWGHYAQMLAD-QIVLTR
+t71 KMMRKIFALEW-EMDMSHRD-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTR
+t94 KMMRKIFALEW-EMDMSHRD-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-KLVLTR
+t99 KMMNKIFALEW-EMDMSHRDSSSVDDNYI-IEMLPFVCHRVGPWGHYAQQLAD-RLVLTR
+t40 KMMRKIFALEW-EMDMSHRN-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTR
+t90 KMMRKIFALEW-EMDMSHRN-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTR
+t4 KMMGKIFALEW-EHDMSHRD-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTR
+t36 KVMLKIFGLDWCEVERSHEH-SSVDDNYN-VNMLPFQNSRKDPVGHYVQDLED-ARRLIR
+t87 KVMLKIFGLDWCEVERSHEH-SSVDDNYN-VNMLPFQNSRKDPVGHYVQDLED-ARRLIR
+t89 KMMLKIFGLEWCEVERSHEH-SSIDDNYT-VNMLEFPNSRKDPVGHYVQNLED-AIRLIR
+t39 KMMLKIFGLEWCEVERSHEH-SSIDDNYT-VNMLEFPNSRKDPVGHYVQNLED-AIRLIR
+t8 KMMLKIFGLEWCEVERSHEH-SSIDDNYT-VNMLPFPNSRKDPVGHYVQDLED-AIRLIR
+t6 KMMLKIFGLEWCEVERSHER-SSIDDNYT-VNMLPFPNSRKDPVGHYVQDLED-AIRLIR
+t58 KMMLKIFGLDWCEVERSHEH-SSVDDNYN-VNMLPFPNSRQDPVGHYVQDLED-LLRLIR
+t54 KMMLKIFGLDWCEVERSHEH-SSVDDNYN-VNMLPFPNSRKDPVGHYVQDLED-LLRLIR
+t65 QMTMKIFNLDWCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELED-ALRLIR
+t29 QMSQKIFNLDWCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELEDSALRLIR
+t98 QMTMKIFNLDWCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELED-ALRLIR
+t83 QMTMKIFNLDWCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELED-ALRLIR
+t95 QMIMKIFNLDWCEVEKSHEK-SSVDDNYD-VNMLPFMQSHGDPVGHYVQGLED-ALRLIR
+t20 QMIMKIFNLDWCEVEKSHEK-SSVDDNYD-VNMLPFMQSHGDPVGHYVQGLED-ALRLIR
+t69 QMIVKIFNLDWCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQGLED-ALRLIR
+t2 QMMVKIFNLDWCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQGLED-ALRLIR
+t10 QMMVKIFNLDWCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQGLED-ALRLIR
+t31 QMIMKIFNLDWCEVEKSHEK-SSVDDNYH-VNMLPFAQSNRDPVGHYVQGLED-ALRLIR
+t15 QMIVKIFHLDWCEVEKSHEK-SSVDDNYH-VNMLPFAQSNGDPVGHYVQGLED-ALRLIR
+t63 QMFMKIFNLDWCEVEKSHEK-SSVDDNYN-VNMLPFVQSNGDPVGHYVQGLED-ALLLIR
+t50 QMIMKIFNLDWCEVEKSHEK-SSVDDNYN-VNMLPFVQSNGDPVGHYVQGLED-ALLLIR
+t25 QMIMKIFNLDWCEVEKSHEK-SSVDDNYD-VNMLPFVQSNGDPVGHYVQGLED-ALLLIR
+t51 QMIMKIFGLDWCEVEKSHEE-SSVDDNYN-VNMLPFVSSNGDPVGHYVQGLED-ALRLIR
+t9 KMVLKIFGLDWCEMEKSHQR-SGVDDNYQ-VNMLPFNHSKNNPVGHYVQGLED-ALNLIR
+t47 KMILKIFGLDWCEMEKSHQR-SGVDDNVQ-VNMLPFNHSKHNPVGHYVQGLED-ELNLIR
+t60 KMILKIFGLDWCEMEKSHQR-SGVDDNYQ-VNMLPFNHSKHNPVGHYVQGLED-ALNLIR
+t30 KMILKIFGLDWCEMEKSHQR-SGVDDNYQ-VNMLPFKHSKHNPVGHYVQGLED-ALNLIR
+t70 KMILKIFGLDWCEVERSHQR-SGVDDNYK-VNMLPFSHSKHNPVGHYVQGLGD-ALRLIR
+t91 KMILKIFGLDWCEVERSHQR-SGVDDNYK-VNMLPFSHSKHNPVGHYVQGLGD-ALRLIR
+t49 KMIIKIFGLDWCEVEKSHQR-SGVDDNYK-VNMLPFSHSNHNPVGHYVQGLGD-ALRLIR
+t52 KMILKIFELNWCEVEKSHQH-SGVDDNYQ-VNMLPFDHCKHNPVGHYVQGLED-ALGLIR
+t43 KMVLKIFELDWVEMEKSHQQ-SSVDDNYL-VNMLPFLHSRQNPVGHYVQGLED-PMHLIR
+t1 KMVLKIFELDWVEMEKSHQQ-SSVDDNYL-VNMLPFMQSRENPVGHYVQGLED-PMHLIR
+t86 KMVLKIFELDWVEMEKSHQQ-SSVDDNYL-VNMLPFIHSRDNPVGHYVQGLED-PMHLIR
+t72 QMVLKIFELDWVEMEKSHQQ-SSVDDNYL-VNMLPFIHSRENPVGHYVQGLED-PMHLIR
+t96 KMVLKIFELDWVEMEKSHQQ-SSVDDNYL-VNMLPFIRSRENPVGHYVQGLED-PMHLIR
+t44 KMVLKIFELDWVEMEKSHQQ-SSVDDNYL-VNMLPFMHSRENPVGHYVQGLED-PMHLIR
+t45 KMVHKIFELDWVEMEKSHQQ-SSVDDNYL-VNMLPFFHSRENPVGHYVQGLED-PMHLIR
+t74 KMVHKIFELDWVEMEKSHQQ-SSVDDNYL-VNMLPFFHSRENPVGHYVQGLED-PMHLIR
+t26 KMVIKIFGLDWCEIEKSHQQ-SSVDDNYL-VNMLPFTHSRETPVGHYVQGLED-PMHLMR
+t61 KMVLKIFGLDWCEIEKSHQQ-SSVDDNYL-VNMLPFAHSRQTPVGHYVQGLED-PMHLMR
+t97 KMNLKIFGLDWCEIEKSHQQ-SSVDDNYL-VNMLPFTHSRETPVGHYVQDLED-PMHLMR
+t17 KMVIKIFGLDWCEMEKAHQQ-SSVDDNYL-VNMLPFTHSRENPVGHYVQGLED-PMHLIR
+t11 KMVIKIFGLDWCEMEKAHQQ-SSVDDNYL-VNMLPFTHSRENPVGHYVQGLED-PMHLIR
+t23 KMILNIFGLDWCEVETSHQE-SSSDDNHL-VNMLPFGVSRDDPVGHYMLGLED-AIRLYR
+t76 DLNCDDFELGW-NLKH-------EDDHPL-LCIGSFSVHKYVSVMVYPLPMND-CVRMSQ
+t53 DLNCDDFELGW-NLKP-------EDDHPL-LCIGSFSVHKYVSVMVYPLPMND-CVRMSQ
+t16 DLNCDDFELGW-NLKP-------EDDHPL-LCIGSFSVHKYVSVMVYPLPMND-CVRMSQ
+t42 DLTVDDFELGW-VLKP-------EDDHPL-ICIGSFSVHKQFSVMVYPLPMND-AIRMSQ
+t24 DLTCDDFELGW-VLKP-------EDDHPL-ICIGSFSVHKQFSVMVYPLPMND-AIRMSQ
+
+
+t73 PNT---AQKLSILT---VFHFSGGFRDKPM-ERSQLHS-TYSED----KKDQKVLIHAMK
+t66 PNT---AQKLSILT---VFHFSGGFRDKPM-ERSQLHS-TYSED----KKDQKVLIHAMK
+t32 PNT---AQKLSILT---VFHFSGGFRDKPM-ERSQLHS-TYSED----KKDQKVLIHAMK
+t75 PNT---ARQLSILV---VMHFSGGFRDKPI-ERSQLHC-TYSEN----KKDQKVVIRAMK
+t79 PNT---ARRLSILH---VMHYSGEFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+t27 PNT---ARRLSILH---VMHYSGAFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+t93 PNT---ARRLSILH---VMHYSGAFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+t59 PNT---ACRLSILH---VMHYSGEFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+t7 PNT---ACRLSILH---VMHYSGEFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+t78 PNT---ACRLSILH---VMHYSGEFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+t12 PNT---ARRLSILM---VMHYSGEFHDKSP-ERSQLHFDSYSEH----KNDHKCVILASK
+t81 PET---ARRLSILA---VMHYSGEFHDKSP-ERSHLHF-RYSEM----KNDVKCVI---K
+t21 PET---ARRLSILV---VMHYSGEFHDKSP-ERSHLHY-RYSEV----KNDVKCVILASK
+t80 PNT---AHRLSILV---VTHYSGGFHDKSA-ERSQHHF-IYNEV----KDDHKCVILASK
+t14 PNT---AHRLSILV---VTHYSGGFHDKSA-ERSQHHF-IYNEV----KDDHKCVILASK
+t85 PNT---AHRLSILV---VMHYSGGFHDKSS-ERSQHHF-IYNEV----KNDHKCVILASK
+t62 PNT---AHRLSILV---VMHYSGGFHDKSA-ERSQHHF-IYNEI----KNDHKCVILASK
+t19 PNT---AHRLSILV---VMHYSGGFHDKSA-ERSQHHF-IYNEI----KNDHKCVILASK
+t77 PNT---AHRLSILV---VMHYSGGFHDNSA-ERSQHHF-IYNEV----KNDHKCVILASK
+t88 PVT---LQALSILP---CPHASGKEQDGAV-ERSQHYV-VYAEL----QVDHKCTIAAHK
+t37 PVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+t35 PVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+t48 PVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+t55 PVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+t46 PVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+t67 PVT---LHGLSILP---CPHASGKEQDGAE-ERSQHYG-VYQEL----QNDAKSTIDANK
+t57 PVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDAKSTIDANK
+t56 PVT---LQGLGILV---CPHASGKEQDGAM-ERSQHYV-VYAEL----QNDHKNTINANK
+t13 PHT---LRDLYILAC--CPVASGKEQDGNK-ERSQHYT-IYAEI----QNDHKNPISANN
+t5 PHT---LRDLYILAC--CPVASGKEQDGNK-ERSQHYT-IYAEI----QNDHKNPISANN
+t38 PHT---LRELYILA---CPVASGKEQDGAQ-ERSQCYT-IYAEL----QNDHKSLISANH
+t33 PHT---LRELYILA---CPVASGKEQDGAK-ERSQCYT-IYAEL----QNDHKSLISANH
+t100 PHT---LRELYILA---CPVASGKEQDGAQ-ERSQCYT-IYAEL----QNDHKSLISANH
+t34 PHT---LRELYILA---CPVASGKEQDGAQ-ERSQCYT-IYAEL----QNDHKSLISANH
+t84 PHT---LRELYILA---CPVASGKEQDGAK-ERSQCYT-IYAEL----QNDHKSLIAANH
+t92 PHT---LRELYILA---CPVASGKEQDGAQ-ERSQCYT-IYAEL----QNDHKSLISANH
+t3 PHT---LADLFILS---CPVASGKEQDGAT-ERSQYYV-VYAEL----QNDHKSPISANK
+t22 PHT---LRDLFILA---CPVASGKEQDGAT-ERSQHYV-VYAEL----QNDHKSPISANK
+t64 PHT---LRDLFILS---CPVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+t18 PHT---LRDLFILS---CPVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+t68 PHT---LRDLFILS---CPVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+t28 PHT---LRDLFILA---CRVASGGEVDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+t82 PHT---LRDLFILA---CPVASGGEQDGNA-ERSQHYI-VYAEL----VNDHKSPISANK
+t41 PHT---LRDLFILA---CPVASGGEQDGNA-ERSQHYI-VYAEL----VNDHKSPISANK
+t71 PHT---LRDLFILA---CPVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+t94 PHT---LRDLFILA---CYVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPILANK
+t99 PHT---LRDIFILA---CPVASGGEQDGNT-ERSQHYI-VYAEL----QDDHKSPISANK
+t40 PHT---LRNIFILA---CPVASGGEQDENT-ERSQHYI-VYAEL----QNDHKSPIHANK
+t90 PHT---LRNIFILA---CPVASGGEQDENT-ERSQHYI-VYAEL----QNDHKSPINANK
+t4 PHT---LRDIFILA---CPVASGGEQDAVT-ERSQHYI-VYAEL----QNDHKSPISASK
+t36 PGT---ARSLTILF-YGCQYYSGEFQDCEI-ERSQLYN-VYCEH----KQDHKSAIIANK
+t87 PGT---ARSLTILF-YGCQYYSGEFQDCEI-ERSQLYN-VYCEH----KQDHKSAIIANK
+t89 PGT---ARSLTILL-YGCQYYSGEFQDCEV-ERSQCYN-VYCEL----KQDHKSAIIANK
+t39 PGT---ARSLTILL-YGCQYYSGEFQDCEV-ERSQCYN-VYCEL----KQDHKSAIIANK
+t8 PGT---ARSLTILL-YGCQYYSGEFQDCEV-ERSQCYN-VYCEL----KQDHKSAIIANK
+t6 PGT---ARSLTILL-YGCQYYSGEFQDCEV-ERSQCYN-IYCEL----KQDHKSAIIANK
+t58 PGT---ARSLTVLF-YGCQYYSGQFQDCEI-ERSQLYN-VYCEL----KQDHKSAIMANK
+t54 PGT---ARSLTVLF-YGCQYYSGEFQDCEI-ERSQLYN-VYCEL----KQDHKSAIMANK
+t65 PGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDYKSAIIANQ
+t29 PGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDYKSAIIANQ
+t98 PGT---ARALVILF-YGCQYYSGKFQDSEMFERSQLYR-VYCEI----KKDYKSAIIANQ
+t83 PGT---ARALVILF-YGCQYYSGKFQDSDMFERSQLYR-VYCEI----KKDYKSAIIANQ
+t95 PGT---ARALIILF-YGCQYYSGKFQDSELFERSQLYR-MYCEI----KKDHKSAIIANQ
+t20 PGT---ARALIILF-YGCQYYSGKFQDSELFERSQLYR-MYCEI----KKDHKSAIIANQ
+t69 PGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHNSAIIANQ
+t2 PGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHNSAIIANQ
+t10 PGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHNSAIIANQ
+t31 PGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIIANQ
+t15 PGT---ARALVILS-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIVANQ
+t63 PGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIIANQ
+t50 PGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIMANQ
+t25 PGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSTIIANQ
+t51 PGT---ARALVILF-YGCQFYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIIANQ
+t9 PGT---ARALNILF-YGCEVYSGEFQDSES-ERSWIYN-VYCEI----KKDHKSAIIAHK
+t47 PGT---ARALNILF-YGCEYYSGEFQDSES-ERSWIYN-VYCEI----KKDHKSAIMACK
+t60 PGT---ARALNILF-YGCEYYSGEFQDSES-ERSWIYN-VYCEI----KKDHKSAIMAYK
+t30 PGT---ARALNILF-YGCEYYSGEFQDSES-ERSWIYN-VYCEI----KKDHKSAIMAYK
+t70 PGT---ARALNILF-YGCQYCSGEFQDSEE-ERSWIYN-VYCEI----KKDHKSAILAHK
+t91 PGT---ARALNILF-YGCQYCSGEFQDSEE-ERSWIYN-VYCEI----KKDHKSAILAHK
+t49 PGT---ARALNILF-YGCEYYSGEFQDSEE-ERSWIYN-VYCEI----KKDHKSAIMAHK
+t52 PGT---ARALNILF-YGCQYYSGEFQDSEA-ERSWIYN-VYCEI----KKDHKSGIMAHK
+t43 PGT---ARKLNILF-YGCEYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVIAHK
+t1 PGT---ARKLNILF-YGCEYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+t86 PGT---ARKLNILF-YGCEYYSGQFPDGEA-ERSWIYP-VYCEM----KKDHKSAVVAHK
+t72 PGT---ARKLNILF-YGCEYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+t96 PGT---ARKLNILF-YGCEYYSGQFPDAEA-ERSWIYD-VYCEM----KKDHKSAVYAHK
+t44 PGT---ARKLNILF-YGCEYYSGQFPDCEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+t45 PGT---ARKLNILF-YGCQYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+t74 PGT---ARKLNILF-YGCQYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+t26 PGT---ARALNILF-YGCEYYSGQFPDGEP-ERSWIYD-VYCEL----KKDHKNAIVAVK
+t61 PGT---ARALNILF-YGCEYYSGHFPDGEA-ERSWIYD-MYCEL----KKDHKSAIVAVK
+t97 PGT---ARALNILF-YGCEYYSGHFPDGEP-ERSWIYD-MYCEL----KKDHKSAIVAVK
+t17 PGT---ARALNILF-YGCEYYSGQFPDGEP-ERSWIYD-VYCEL----KKDHKSAIVAVK
+t11 PGT---ARALNILF-YGCEYYSGQFPDGEP-ERSWIYD-VYCEL----KKDHKSAIVAVK
+t23 PGT---ARALNILF---VNYYSGDFQDPEL-ERSQLYN-VYCEQ----KQDHRNAIRASK
+t76 PCHAAHAQDIPTEQ---TRYQIHTFLDDSI-RRDLCNQ-GCHEENMVWRDDLKDPISTEV
+t53 PCHAAHAQDIPTEQ---TRYQIHTFLDDSI-RRDLCNQ-GCHEENMVWRDDLKDPISTEV
+t16 PCHAAHAQDIPTEQ---TRYQIHTFLDDSI-RRDLCNQ-GCHEENMVWRDDLKDPISTEV
+t42 PCHAAHAQDIHTDQ---DRYDVRTFLGHSI-KCHMCNQ-ACHEENIVWRDDLKDPITTEV
+t24 PCYAAHAQDIHTDQ---DRYDIRTFLEHSI-RCHLCNQ-ACHEENIVWRDDLKDPITTEV
+
+
+t73 -RNKGLDWHAGND-MKGGPK-IIYLGMLFY-------AENNVAKQKAHFVVFL-ISDATR
+t66 -RNKGLDWHAGND-MKGGPK-IIYLGMLFY-------AENNVAKQKAHFVVFL-ISDATR
+t32 -RNKGLDWHAGND-MKGGPK-IIYLGMLFY-------AENNVAKQKAHFVVFL-LSDATR
+t75 -RNKGCDWHAGKD-MAGGPK-IIYVGMLFY-------AESNWAKQKAHFVVFL-ISDATR
+t79 -HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVR
+t27 -VNKDHDWITGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVR
+t93 -VNKDHDWITGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVR
+t59 -HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVR
+t7 -HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVR
+t78 -HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVR
+t12 -HNKGLDWATGKDDMKGGAK-IMMSGALFY-------AEQNWIRARNHFVIFL-ICDAVR
+t81 -SNKGLDWTAGKDGMKGEAK-AMMNGALFY-------AEQNWFRKKNHFVIFV-FCDAVR
+t21 -SNKGLDWTAGKDGMKGENK-AMMNGTLFY-------AEQNWFRQKNHFVIFV-ICDAVR
+t80 -CNKGLDWAAGKD-MKGGAK-VMMNGALFY-------AERNWIRQKHHFVIFV-VCDAVR
+t14 -CNKGLDWAAGKD-MKGGAK-IMMNGALFY-------AERNWIRQKHHFVIFV-VCDAVR
+t85 -SNKGLDWAAGKD-MKGGAK-MMANGALFY-------EERNWIRQKNHFVIFV-VCDAVR
+t62 -ANKPLDWAAGKD-MKGGAK-MMANGALFY-------AERNWIRQKNHFVIFI-ICDAVR
+t19 -ANKGLDWAAGKD-MKGGAK-MMVNGALFY-------AERNWIRQKNHFVIFV-ICDAVR
+t77 -ANKGLDWAAGKD-MKGGAK-MMVNGALFY-------AERNWIRQKNHFVIFV-ICDAVR
+t88 YQDKMKDWDTGKN-MDEGAK-MYVEIHLFY-------AENNIRRQNDHSVIFW-ISDAKK
+t37 NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLRKQNEHSVTFV-ISDAQK
+t35 NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLRKQNEHSVTFV-ISDAQK
+t48 NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLIKQNEHSVTFV-ISDAQK
+t55 NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLRKQNEHSVTFV-ISDAQK
+t46 NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNIRKQNEHSVTFV-ISDAQK
+t67 NPNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNIRKLNEHSVTFV-ISDAQK
+t57 NPNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNIRKQNEHSVTFV-ISDAQK
+t56 VPRKMLDWDTGKN-MDKGAKGMYHEIVLFF-------AENNVKKQVEHSVIFI-IADAQK
+t13 QPNKMLDWDTGKT-MDRGAA-MCGEIKLFY-------AEPNVWNQNDHSVMFI-ISDAQN
+t5 QPNKMLDWDTGKT-MDRGAA-MCGEIKLFY-------AEPNVWNQNDHSVMFI-ISDAQN
+t38 VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQN
+t33 VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQN
+t100 VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQN
+t34 VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQN
+t84 VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQN
+t92 VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQN
+t3 HPDKMLDWDTGKS-MDRGAA-MCREIKLFY-------AEPNVWKQNDHSVVFI-ISDAVN
+t22 HPNKLLDWDTGKT-MDRGAA-MCHEIKLFH-------AEPNVWRQNDHSVMFI-ISDASN
+t64 HLNKMLDWDTGKT-MDREAT-MCREMKLFY-------AETNLWKQNDHSVMFI-ISDAQN
+t18 HLNKMLDWDTGKT-MDREAT-MCREMKLFY-------AETNLWKQNDHSVMFI-ISDAQN
+t68 HLNKMLDWDTGKT-MDREAT-MCREMKLFY-------AETNLWKQNDHSVMFI-ISDAQN
+t28 VLNKMLDWDTGKT-MDREAA-MCREIKLFY-------AETNVWKQNDHSVMFI-ISDAQN
+t82 VLNKMLDWDTGKT-MDREAA-MCRDIKLFY-------AETNVWKQNDHSVMFI-ISDAQN
+t41 VLNKMLDWDTGKT-MDREAA-MCRDIKLFY-------AETNVWKQNDHSVMFI-ISDAQN
+t71 HMNKMLDWDTGKT-MDFEAA-MCREIKLFY-------AETNVWKINDHSVMFI-VSDAQN
+t94 VVNKMLDWDMGKT-MDFEAA-MCREIKLFY-------AETNVWKQNNHSVMFI-VSDAHN
+t99 HMRKMLDWDTGKT-MDREAA-VCREIKLFY-------AETNCWKQNDHSVMFI-VSDAQN
+t40 VMNKMLDWDTGKT-MDREAA-MCREIKLFV-------AETNVWKQNDHSVMFIVISDAQN
+t90 VMNKMLDWDTGKT-MDREAA-MCREIKLFV-------AETNVWKQNDHSVMFIVISDAQN
+t4 HMNKMLDWDTGKT-MDREAA-MCREIKLFY-------AETNVWKQNDHSVMFI-ISDAQN
+t36 QEQKGMDWNTGKE-MEQGPK-IILHGSLFF-------AEPNIVRQPGVSHIFI-GNDARR
+t87 QEQKGMDWNTGKE-MEQGPK-VILHGTLFF-------AESNIVRQPGVSHIFI-GNDARR
+t89 QEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGVSHIFT-ENDARR
+t39 QEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGVSHIFT-ENDARR
+t8 QEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGVSHIFT-ENDARR
+t6 QEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGVSHIFI-ENDARR
+t58 QEQKGMDWNTGKE-MEQGPK-IILHGVLFF-------AEPNVVRQPGVSHIFV-GNDARR
+t54 QEQKGMDWNTGKE-MEQGPK-IILHGVLFF-------AEPNVVRQPGVSHIFV-GNDARR
+t65 QEHKGMEWDTGKE-MQQGPK-VVVHLALFYAPSNVLAAEPNIIGQPQVSHVFV-GNDARR
+t29 QDHKGMEWDTGKE-MQQGPK-VVVHLALFYMPSNVLAAEPNIIGQPQVSHWFV-GNDARR
+t98 QEHKGMEWDTGKE-MQQGPK-IVVHLGLFYMPSNVLAAEPNIIGQPQVSHVFV-ANDARR
+t83 QEHKGMEWDTGKE-MQQGPQ-IEVHLALFYMPSNVLPAEPNIIGQPQVSHVFV-GNDARR
+t95 QEHKGMEWDTGKE-MQQGPK-VVLHHALFYAPSNVLAAEPNIIGQPQVSHVFV-GNDARR
+t20 QEHKGMEWDTGKE-MQQGPK-VVLHHALFYAPSNVLAAEPNIIGQPQVSHVFV-GDDARR
+t69 QEHKGMDWDTGKE-MQQGPK-IVVVLALFYQPSNVLAAEPNIMGQPQVSVVFV-GNDGRR
+t2 QEHKGMDWDTGKE-MQQGPK-IVVVLALFYQPSNVLAAEPNIMGQPQVSVVFV-GNDARR
+t10 QEHKGMDWDTGKE-MQQGPK-IVVVLALFYQPSNVLAAEPNIMGQPQVSVVFV-GNDARR
+t31 HEVKGMDWNTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIVGQPQVSHVFV-GNDARR
+t15 QEVKGMDWDTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIVGQPQVSHVFV-GNDARR
+t63 QGVKGMDWDTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIIGQPQVSHVFV-DNDARR
+t50 QGVKGMDWDTGKE-MQQGPK-IVMHLALFYAPSNVLAAEPNIIGQPQVSHVFV-DNDARR
+t25 QGVKGMDWDTGKE-MQQGPK-IVVHLTLFYAPSNVLAAEPNIFGQPQVSHVFV-DNDARR
+t51 QGVKGMDWDTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIIGQPQVSHVFV-DNDIRR
+t9 YEHKGMDWDTGKE-AQQGPE-VVHHNLLFF-------AEPNIHGQPGVGHIFV-GNDARR
+t47 YRHKGMDWDTGKE-AEQGPE-VVHHNLLFF-------AEPNIQGQPGVGHIFV-GNDARR
+t60 FEHKGMDWDTGKE-AEQGPE-VVHHNLLFF-------AEPNIQGQPGVGHIFV-GNDARR
+t30 YEHKGMDWDTGKE-AEQGPE-VVHHNLLFF-------AEPNIHGQPGVGHIFV-GNDARR
+t70 YKHKGMDWDTGKE-MEQGPK-VVNYNLLFY-------AEPNIHGQPRVGHIFV-GNDAHR
+t91 YKHKGMDWDTGKE-MEQGPK-VVNYNLLFY-------AEPNIHGQPRVGHIFV-GNDAHR
+t49 YEHKGMDWDTGKE-MEQGPK-VVHHNILFY-------AEPNIHGQPRVGHIFV-GNDAVR
+t52 YDHKGVDWDTGKE-MEQGPK-VLHHNLLFY-------AEPNIHGQPTVGHIFV-GNDARR
+t43 HEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATR
+t1 VEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATR
+t86 AEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATR
+t72 VEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATR
+t96 VEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATR
+t44 HEHKGMDWDTGKE-MNQGPK-VVMHGVLFN-------AEPNIHGQPGVSHVFM-GNDATR
+t45 HQHKGMDWDTGKE-MNQGPK-VVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATR
+t74 HQHKGMDWDTGKE-MNQGPK-VVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATR
+t26 HEHKGMDWDTGKE-MNHGPK-VIVHGVLFH-------AEPNIGGQPGVSHVFV-GNDATR
+t61 HCHKGMDWDTGKE-MNHGPK-VIIHGLLFH-------AEPNIGGQPGVSHVFV-GNDATR
+t97 HCHKGMDWDTGKE-MNHGPK-VIIHGVLFH-------AEPNIGGQPGVSHVFV-GNDATR
+t17 HEHKGMDWDTGKE-MNQGPK-VIIHGVLFH-------AEVNIHGQPGVSHVFV-GNDATR
+t11 HEHKGMDWDTGKE-MNQGPK-VIIHGILFH-------AEVNIHGQPGVSHVFV-GNDATR
+t23 NDHKGMAWDTAKD-MEQGPK-MVEHQVLFY-------AEPNMHGQPEVIHIFI-GNDAMC
+t76 IADKLHEWPTNVN-KENSAD----HRQLFH-------ANSSALDKHQHNVVMN-GSPCIR
+t53 IADKLHEWPTNQN-KENSAD----HRQLFH-------ANSSALDKHQHNVVMN-GSPCIR
+t16 IADKLHEWPTNQN-KENSAD----HRQLFH-------ANSSALDKHQHNVVMN-GSPCIR
+t42 IAEKLQEWPTNQN-KENVAD----HRQLFH-------ANSSALDKHRHNVMMN-GSACIR
+t24 IADKLQEWPTNQN-AENVAD----HRQLFH-------ANSSCLDRHRHNVMMN-GSSCIR
+
+
+t73 LLIVHEGCMIDYTFMEFACHPFFAELFMEHMVARYQYYSNVDIKIFDTCFRSAVYAVDNS
+t66 LLIVHEGCMIDYTFMEFACHPFFAELFMEHMVARYQYYSNVDIKIFDTCFRSAVYAVDNS
+t32 LLIVHEGCMIDYTFMEFACHPFFAELFMEHMVARYQYYSNVDIKIFDTCFRSAVYAVDNS
+t75 LLIHHVGCMIEYTFMEFACHPFFAELFMEHMVIRYQYYNNVDIKIFDTCFRGAVYAEDNS
+t79 ILILHHGCMTDHTFMEFACNPFFSELFMEHVYIRYQYINNHDIKIKDTVFRLAVYAWDNF
+t27 ILILHHGCMTDHTFMEFACNPFFSELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENF
+t93 ILILHHGCMTDHTFMEFACNPFFSELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENF
+t59 ILILHHGCMTDHTFMEFACNPFFAELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENF
+t7 ILILHHGCMTDRTFMEFACNPFFAELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENF
+t78 ILILHHGCMTDRTFMEFACNPFFAELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENF
+t12 ILIVLHGCMTAWTFMEFACNPFFAELFMEHVYIRYQYVNNHDIKIKDTEFRLAVYAWENS
+t81 ILIMHSGVMIGYTFMEFACNPFFAELFMEHVMVRYQYESNHDIKIKDTCFRLAVYAWENS
+t21 ILIVHSGVMTGFTFMEFACNPFFAELFMEHVYIRYQYQANHDIKIKDTCFRLAVYAWENS
+t80 ILIVHYGCMIGYTFMDFACNPFFAELFMDHVFIRYVYMNNHDIKIMDTCFRVAVYTWENS
+t14 ILIVHYRCMIGYTFMDFACNPFFAELFMDHVFIRYQYMNNHDIKIMDTCFRVAVYTWENS
+t85 ILIVHYGCMVPYTFMAFACNPFFAELFMEHVFIRYQYVNNHDIKIMDTCFRVAVYTWENS
+t62 ILIVHYGCMVGDTFMDFACNPFFAELFMEHVFIRYQYIPNHDIKIMDTCFRVAVYTWENS
+t19 ILIVHYGCMVGDTFMDFACNPFFAELFMEHVFIRYQYIPNHDIKIMDTCFRVAVYTWENS
+t77 ILIVHYGCMVGDTFMDFACNPFFAELFMEHVVIRYQYIPNHDIKIMDTCFRVAVYTWENS
+t88 RLICGMSSMCLVTFMTLACNPLFAKLFMEVVPMRYDYLTNHDIKI------MEVYAPENS
+t37 RLICGVSSMVMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENS
+t35 RLICGVSSMAMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENS
+t48 RLICGVSSMVMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENS
+t55 RLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENS
+t46 RLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPDNS
+t67 RLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENS
+t57 RLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENS
+t56 RLICGVSSMCLQTFMNLACNPFFAKLFMEVIPMRYDYQTNHDIKI------KEVYAPENS
+t13 RLIVANSIMVGQTFMAMACNPHFSKLFMEVVCMRYNYTSNHSIKI------FEVYADENS
+t5 RLIVANSIMVGQTFMAMACNPHFSKLFMEVVCMRYNYTSNHSIKI------FEVYADENS
+t38 KLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------FEVYADENS
+t33 RLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------FEVYADENS
+t100 RLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------FEVYADENS
+t34 RLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------LEVYADENS
+t84 RLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------LEVYADENS
+t92 RLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------LEVYADENS
+t3 RLICANSIMCGLTFMAMACNPHFAKLFMEVVCMRYDYFSNHSIKI------FEVYAEDDS
+t22 RLICANSIMCGLTFMAMACNPHFAKLFMEVVCMRYEYFSNHSIKI------FEVYAEENS
+t64 RLICGNSIMCGLTFMAMACNPHFAKLFMEVVCVHYDYGANHDIKI------FEVYAAENS
+t18 RLICGNSIMCGLTFMAMACNPHFAKLFMEVVCVHYDYGANHDIKI------FEVYAAENS
+t68 RLICGNSIMCGLTFMAMACNPHFAKLFMEVVCVHYDYGANHDIKI------FEVYAVENS
+t28 RLICGNSIMCGITFMAMACNPHFAKLFMEVACMRYDYFANPDIKI------FEVYAAENS
+t82 RLICGNSIMCGLTFMAMACNPHFAKLFMEVACMRYDYFANPDIKI------FEVYADENS
+t41 RLICGNSIMCGLTFMAMACNPHFAKLFMEVACMRYDYFANPDIKI------FEVYADENS
+t71 RLICGNSIMCGLTFMAMACNPHFAKLFMEGVCMRYDYSANHDIKI------FEVYADENS
+t94 RLICGNSIMCALTFMAMACNPHFAKLFMEAVCMRYDYSANHDIKI------VEVYADENS
+t99 RLICGSSIMCRLTFMAMAVNPHFAKLFMEDVCMRYDYSPNHDIKI------FEVYADENS
+t40 RLICGSSIMCRLTFMAMAVNPHFAKLFMEESCVRYDYSANHDIKI------FEVYANENS
+t90 RLICGSSIMCGLTFMAMAVNPHFAKLFMEESCVRYDYSRNHDIKI------FEVYANENS
+t4 RLICGSSIMCGLTFMATACNPHFAKLFMEEVCMRYDYAANHDIKI------SEVYAEENS
+t36 VLICGKSMMPGHRFMREACVPFFHKLFMAVNQMRYDYMMNYDIKIYETHWRMGVYALDNS
+t87 VLICGLSMMPGHRFMREACVPFFHKLFMAVNQMRYDYMVNYDIKIYETHWRMGVYALDNS
+t89 MLICGNSMMPRHRFMREACVPFFHKLFMAVNQMRYDYVTNYDIKIYETHWRVGVYAIDNS
+t39 MLICGNSMMPRHRFMREACVPFFHKLFMAVNQMRYDYVTNYDIKIYETHWRVGVYAIDNS
+t8 MLICGNSMMPRHRFMREACVPFFHKLFMAANQMRYDYVTNYDIKIYETHWRVGVYAIDNS
+t6 MLICGNSMMPRHRFMREACVPFFHKLFMAVNQMRYDYMTNYDIKIYETHWRVGVYAIDNS
+t58 MLICGLSMMPGHRFMKEACVPFFHKLFMAVRRMRYDYMSNYDIKIYETHWRPGVYALDNS
+t54 MLICGLSMMPGHRFMKEACVPFFHKLFMAVRRMRYDYMTNYDIKIYETHWRPGVYALDNS
+t65 MLIVGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYMWNYDIKIYETHFRMGVYAVDNS
+t29 MLIVGVSMMPAYKFMREACVPFFRKLFMADNQVRYDYMWNYDIKIYETHFRMGVYAVDNS
+t98 MLIVGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYVWNYDIKIYETHFRMGVYAVDNS
+t83 MLIVGVSLMPAYKFMREACVPFFRKLFMAENQVRYDYMWNYDIKIYETHFRMGVYAVDNS
+t95 MLITGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYVWNYDIKIYETHYRMGVYAVDNS
+t20 MLITGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYVWNYDIKIYETHYRMGVYAVDNS
+t69 MLIVGCSMMPDYKFMREACVPFFRKLFMAEVQDRYDYAWNYNIKIYETHFRDGVYAVDNS
+t2 MLIVGCSMMPDYKFMREACVPFFRKLFMAEVQDRYDYNWNYNIKIYETHFRVGVYAVDNS
+t10 MLIVGCSMMPDYKFMREACVPFFRKLFMAEVQDRYDYNWNYNIKIYETHFRVGVYAVDNS
+t31 MLIVGVSVMPSYKFMREACVPFFHKLFMADNQVRHEYMWNYDIKIYETHFRMGVYAVDNS
+t15 MLIVGVSVMPAYKFMREACVPFFHKLFMAENQVRHDYMWNYDIKIYETHFRMGVYAVDNS
+t63 MLIVGQSVMPPYKFMREACVPFFHKLFMAENQVRHDYVWNYDIKIYETHFRMGVYAIDNS
+t50 MLIVGQSVMPAYKFMREACVPFFHKLFMAENQVRHDYVWNYDIKIYETHFRMGVYAVDNS
+t25 MLIVGQSVMPAYKFMREACVPFFHKLFMAENQVRHDYVWNYDIKIYETHFRMGVYAVDNS
+t51 MLIVGVSVMPAYKFMREACVPFFHKLFMAENQVRHDYVWNYDIKIYETHFRMGVYAVDNS
+t9 KLIAGVSFMSMVKFMCEACVPFFRKLFMAVGQMRYDYVNNYDIKIWETVFRGGVYAIENS
+t47 KLIAGLSFMAMMKFMCEACVPFFRKLFMAVGHMRYDYVSNYDIKIWETVFRGGVYAIENS
+t60 KLIAGVSFMAVMKFMCEACVPFFRKLFMAVGQMRYDYMNNYDIKIWETFFRGGVYAIENS
+t30 HLIAGVSFMAVVKFMCEACVPFFRKLFMAVGQMRYDYVNNYDIKIWETVFRGGVYAIENS
+t70 KLIAGVSFMSIMKFMCEACVPFFRKLFMAVRQMRYMYMNNYDIKIWETAFRGGVYAIENS
+t91 KLIAGVSFMSIMKFMCEACVPFFRKLFMAVRQMRYMYMNNYDIKIWETAFRGGVYAIENS
+t49 NLIAGVSFMSIMKFMCEACVPFFRKLFMAVRQMRYMYMNNYDIKIWETAFRGGVYAMENS
+t52 KLIAGVSFMSVVKFMCEACVPFFRKLFMAFRQMRYDYVNNYDIKIWETVFRGGVYAIENS
+t43 KLITGVSVMPTYKFMCGACVPFFHKLFMAVRNMRYDYNVNYDIKIWETHIRHGVYAVENS
+t1 KLITGVSVMPTYKFMCGACVQFFHKLFMAVRNMRYDYTVNYDIKIWETHIRQGVYAVENS
+t86 KLITGVSVMPTYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHIRHGVYAVENS
+t72 KLITGFSIMPTYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHIRHGVYAVENS
+t96 KLISGVSVMPTYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDVKIWETHIRHGVYAVENS
+t44 KLITGVSVMPTYKFMCNACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHMRHGVYAVENS
+t45 KLIPGVSVMHDYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHLRHGVYAVENS
+t74 KLIPGVSVMHDYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHLRHGVYAVENS
+t26 KLIAGVSVMPIVKFMCGACVPFFRKLFMALRNMRYDYASNYDIKIVETHLREGVYAVENS
+t61 KLIAGASVMFIVKFMCGACVPFFRKLFMALRNMRYDYSQNYDIKIVETHLREGVYAIENS
+t97 KLIAGVSVMPIVKFMCGACVPFFRKLFMALRNMRYDYSQNYDIKIVETHLREGVYAVENS
+t17 KLIAGVSVMPFVKFMCGACVPFFRKLFMALRNMRYDYTSNYDIKIIETHLRNGVYAVENS
+t11 KLIAGVSVMPFVKFMCGACVPFFRKLFMALRNMRYDYTSNYDIKIMETHLRNGVYAVENS
+t23 MLIPGMSVMVHHKFMRAACMPFFNKLFMAVRYMRYDYVDNYDIKIDETRYRDGVYARRNS
+t76 ALIIGGSSVGVNHFMMGPCQEFFTDLFMMYEGLQYACVCAMNITIQCLHTGEGVMCNVKC
+t53 ALIIGGSSVGVNHFMMGPCQEFFTDLFMMYEGLQYACVCAMNITIQCLHTGEGVVCNVKC
+t16 ALIIGGSSVGVNHFMMGPCQEFFTDLFMMYEGLQYACVCAMNITIQCLHTGEGVVCNVKC
+t42 TLIIGGSIVGVNVFMMEPCQEFFTDLFMVYEGLQYAVVCAVNIIIQCLHTNEGVVCNVKC
+t24 TLIIGGSIVGVNVFMMGPCQEFFTDLFMVYEGLQYAVVCAINIIIQVLHTNEGVVCNVKC
+
+
+t73 WETLCDY-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMR
+t66 WETLCDY-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMR
+t32 WETLCDY-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMR
+t75 WETLCGY-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMR
+t79 WETLCKC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPL
+t27 WETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPL
+t93 WETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPL
+t59 WETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPL
+t7 WETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPL
+t78 WETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPL
+t12 WETLCNC-EMLSGHIGAKINHNPRLFEQVC-PPCELTVSGLKGKH-VGWPYLTDITRTPL
+t81 WETLCNV-EMLSGHFGAKINHVPRLPEQVC-PPCDLTVSGLKGKQ-NGLPYLTDITRTPL
+t21 WETLCNV-EMLSGHFGAKINHVPRLPEQVC-PPCDLTVSGLKGKQ-NGWPYLTDITRTPL
+t80 WETCFNR-EMLSGTFGAKISHNPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPL
+t14 WETCCNR-EMLSGTFGAKISHNPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTEITRTPL
+t85 WETCCNR-EMLSGTFGAKISHNPRLPEQVI-PPCDLTVSGLKGKH-NGWPYLTDITRTPL
+t62 WETCCNR-EMLSGTFGARISHVPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPL
+t19 WETCCNR-EMLSGTFGARISHVPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPL
+t77 WETCCNR-EMLSGTFGARISHVPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPL
+t88 WETIKNV-EMVSGKEGAEINHTPQLPEQVI-PPCNLTVSNLKGMI-PPCPALTEITRTV-
+t37 WETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPVPALTEITRTP-
+t35 WETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP-
+t48 WETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP-
+t55 WETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP-
+t46 WETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP-
+t67 WETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPVPALTEITRTP-
+t57 WETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPVPALTEITRTP-
+t56 WETIKNV-EMVSGKAGKQINHEPQLPEQVI-PPCSLTVSNLKGMM-PPCPAMTEITRTV-
+t13 WENVRNF-EMVSGRAGAHINHIPQLPEQAY-PPCKLTVSNLKGVA-ASCPAITEITRTA-
+t5 WENVRNF-EMVSGRAGAHINHIPQLPEQAY-PPCVLTVSNLKGVA-ASCPAITEITRTA-
+t38 WENIRNF-EMVSGRAGAYINHIPQLPEQAV-PPCHLTVSNLKGVA-ASCPAITEITRTA-
+t33 WENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAITEITRTA-
+t100 WENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAITEITRTA-
+t34 WENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAMTEITRTA-
+t84 WENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAMTEITRTA-
+t92 WENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAMTEITRTA-
+t3 WENICNF-EMMSGRTGAQINHIPQLPEQVC-PPCHLTVSNLKGCC-ASVPAITEITRTV-
+t22 WENVCNF-EMMSGRAGAQINHIPQLPEQVC-PPCVLTVSNLKGCC-ASCPANTEITRTV-
+t64 WENARNF-EMMSGRAGAEINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV-
+t18 WENARNF-EMMSGRAGAEINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV-
+t68 WENARNF-EMMSGRAGAEINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV-
+t28 WENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPDITEITRTV-
+t82 WENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPDITEITRTV-
+t41 WENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPDITEITRTV-
+t71 WENVRNF-EMMSGRAGAQINH-PQLPEQVCNPPCHLTVSNLKGVC-ASCPAITEITRTV-
+t94 WENVRNF-EMMSGRAGAQINH-PQLPEQVCNPPCHLTVSNLKGVC-ASCPAITEITRTV-
+t99 WENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV-
+t40 WENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASVPAITEITRTV-
+t90 WENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASVPAITEITRTV-
+t4 WENVRNF-EMMSGRAGAQINH-PQLPEQVV-PPCHLTVSNLKGVC-ASCPAITEITRTV-
+t36 WETLNVS-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPD
+t87 WETLNVS-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPD
+t89 WETLNVS-EMTSGRMGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPD
+t39 WETLNVS-EMTSGRMGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPD
+t8 WETLNVS-EMTSGRMGAKINHLPRLPEHVI-PPCMLTVSGLKDTM-AGMKQETEITKTPD
+t6 WETLNVS-EMTSGRMGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPD
+t58 WETLNVS-EMTSGRIGAKINHLPRLPETVI-PPCVLTVSGLKDTM-AGMKHGTEITKTPD
+t54 WETLNVS-EMTSGRIGAKINHLPRLPETVI-PPCVLTVSGLKDTM-AGMKHGTEITKTPD
+t65 WETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPCILTVSGLKRTV-AGAPDETEITKSPV
+t29 WETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPCILTVSGLKRTV-AGAPDETEITKSPV
+t98 WETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPCDLTVSGLKRTV-AGPPDETEITKSPV
+t83 WETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPCILTVSGLKRTI-AGAPDETEITKSPV
+t95 WETLVYC-EMTSGRIGAKVNHLPRLPEQVT-PPWVLTVSGLKRTV-AGAPDETEITKSPI
+t20 WETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPWVLTVSGLKRTV-AGAPDETEITKSPI
+t69 WETLVYV-EMASGRIGAKINHQPRLPEQVI-PPCILTVSGLKRTI-ADEPDETEITKTPI
+t2 WETLVYV-EMASGRIGAKINHMPRLPEQVI-PPCILTVSGLKRTI-ADEPDETEITKTPI
+t10 WETLVYV-EMASGRIGAKINHMPRLPEQVI-PPCILTVSGLKRTI-ADEPDETEITKTPI
+t31 WETLVYC-EMTSGRIGANINHLPRLPEQVV-PPCILTVSGLKRTI-AGSPDETEITKTLI
+t15 WETLVYC-EMTSGRIGAKINHLPRLPEQVV-PPCILTVSGLKRTI-AGAPDETEITKTLI
+t63 WETLVYC-EMTSGRIGAKINHQPRLPEQVV-PPCVLTVSGLKRTI-AGAPDETEITKTLI
+t50 WETLVYC-EMTSGRIGAKINHQPRLPEQVV-PPCILTVSGLKRTI-AGAPDETEITKTLI
+t25 WEALVYC-EMTSGRTGAKINHQPRLPEQVV-PPCILTVSGLKRTI-AGAPDETEITKTLI
+t51 WETLVYC-EMTSGRIGAKINHLPRLPEQVF-PPCILTVSGLKRTI-AGAPDETEITKTLI
+t9 WETLVLC-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETK-AGLIDGTEITKTPD
+t47 WETLVLC-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETK-AGIIDGTEITKTPE
+t60 WETLVLC-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETR-AGIIEGTEITKTPD
+t30 WETLVLC-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETR-AGIIDGTEITKTPD
+t70 WETLVLC-EMTSGRSGAKMNHLPRLFEQVC-PPCLLTVSGLKETV-AGIIDGTEITKTPE
+t91 WETLVLC-EMTSGRSGAKMNHLPRLFEQVC-PPCLLTVSGLKETV-AGIIDGTEITKTPE
+t49 WETLVLC-EMTSGRVGARMNHLPRLFEQVC-PPCILTVSGLKETV-AGVIDGTEITKTPE
+t52 WETLILC-EMTSGRCGAKMNHMPRLFEQVC-PPCILTVSGLKETM-AGVIDGTEITKTPD
+t43 WETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCVLTVSGLKQPM-AGYNDQTEITKTPD
+t1 WETLITC-EMTSGRIGAKINHLPRLPEQVV-PPCILTVSGLKQPM-AGYNDETQITKTPD
+t86 WETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGYNDETQITKTPD
+t72 WETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPV-AGYNDETQITKTPD
+t96 WETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGYNMETQITKTPD
+t44 WETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGYNDETEITKTPD
+t45 WETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGFVDETEITKTPD
+t74 WETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGFVDETEITKTPD
+t26 WETLVVC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQSV-SGYNDETEITKTPD
+t61 WETLVVC-EMTSGRMGAKINHLPRLPEQVI-PPCILTVSGLKRAV-NGYNDETEITKTPD
+t97 WETLVVC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQAV-NDCNDETEITKTPD
+t17 WETLVVC-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKQAM-AGVNDETEITKTPD
+t11 WETLVVC-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKQAM-AGVNDETEITKTPD
+t23 WETANVC-EMSSGRSGAKINHNPRLPEQVT-PPRSLTVSGLKDTM-PGHPDVTEITKTPV
+t76 KEFLQREDEMKAGLIGIICNHLSRMIMVIL-VHCLLTHAGLKSME-IGFDR-TGVVRMPL
+t53 KEFLQREDEMKAGLIGIICNHLSRMIMVIL-VHCLLTHAGLKSME-IGFDR-TGVVRMPL
+t16 KEFLQREDEMKAGLIGIICNHLSRMIMVIL-VHCLLTHAGLKSME-IGFDR-TGVVRMPL
+t42 KEFLQREEDMKSGLIGIICNHISRMCMHIL-VVCLLTHCGLKAME-IPFDI-TGVVRGPL
+t24 KEFLQREDDMKSGLIGIICNHISRMCMHIL-VHCLLTHCGLKAME-IPFDR-TGVVRGPL
+
+
+t73 IQIAIRVSGSE-SENVVLQYCLYYEENKSIR-----------QNNTGSADLPK-------
+t66 IQIAIRVSGSE-SENVVLQYCLYYEENKSIR-----------QNNTGSADLPK-------
+t32 IQIAIRVSGSE-SENVVLQYCLYYEENKSIR-----------QNNTGSADLPK-------
+t75 IQIPIRISGSE-SENVVLQYCLYYEENKSIR-----------QNNTGSAVLPK-------
+t79 IRIKIREPGSE-SENTVVMYVIYYKERKSIR-----------QNNTGCAKLPQ-------
+t27 IRIKIREPGSE-SENTVVMYVIYYKERKSIR-----------QNNTGCAKLPQ-------
+t93 IRIKIREPGSE-SENTVVMYVIYYKERKSIR-----------QNNTGCAKLPQ-------
+t59 IGIKIREPGSQ-SENTVVMYVIYYKERKSIR-----------QNNTGCAKLPQ-------
+t7 IGIKIREPGSQ-SENTVVMYVIYYKERKSIR-----------QNNTGCAKLPQ-------
+t78 IGIKIREPGSQ-SENTVVMYVIYYKERKSIR-----------QNNTGCAKLPQ-------
+t12 IRIQIREPGSE-CENSVVMYVIYYKERKSIR-----------QNNTGCAKLPQ-------
+t81 IRIQIRVPGSE-SENVVVMYMVYYKERKSIR-----------QNNTGCANLPQ-------
+t21 IRIQIRVPGSE-SENITVMYMVYYKERKSIR-----------QNNTGCANLPQ-------
+t80 IKIHIRVPGSQ-SENHVVMYCVYYKEHKSIR-----------QNNTGCANLPQ-------
+t14 IKIHIRVPGSQ-SENHVVMYCVYYKEHKSIR-----------QNNTGCANLPQ-------
+t85 IKIHIRIPGSQ-SENHVVMYCVYYKEHKSIR-----------QNNTGCANLPQ-------
+t62 IRIHIRVPGSE-SENHVVMYCVYYKEHKSIR-----------QNNTGCANLPQ-------
+t19 IRIHIRVPGSE-SENHVVMYCVYYKEHKSIR-----------QNNTGCANLPQ-------
+t77 IRIHIRVPGSE-SENHVVMYCVYYKEHKSIR-----------QNNTGCANLPQ-------
+t88 -FIV--MYYAI-LRNKIMQYCFYYKENRSVR-----------LNNTGRAELPK-------
+t37 -FIV--MYVAI-LRNDIMQYCFYYKENRSVR-----------LNNTGRAELPK-------
+t35 -FIV--MYVAI-LRNDIMQYCFYYKENRSVR-----------LNNTGRAELPK-------
+t48 -FIV--MYVAI-LRNDIMQYCFYYKENRSVR-----------LNNTGRAELPK-------
+t55 -FIV--MYVAI-LRNDIMQYCFYYKENRSVR-----------LNNTGRAELPK-------
+t46 -FIM--MYVAM-LRNDIMQYCFYYKENRSVR-----------LNNTGRAELPK-------
+t67 -FIV--MYVAI-LRNDIMQYCFYYKENRSVR-----------LNNTGRAELPK-------
+t57 -FIV--MYVAI-LRNDIMQYCFYYKENRSVR-----------LNNTGRAELPK-------
+t56 -III--MYYAI-LRNEIMQYCFYYKENRSVR-----------INNTGQAELPK-------
+t13 -VIV--MYGSI-LRNDVMQYVFYYRENRSVR-----------QNNTGNAELPK-------
+t5 -VIV--MYGSI-LRNDVMQYVFYYRENRSVR-----------QNNTGNAELPK-------
+t38 -VIV--MYVSI-LRNDVMQYVFYYRENRIVR-----------QNNTGVAELPK-------
+t33 -VIV--MYVSI-LRNDVMQYVFYYRENRIVR-----------QNNTGVAELPK-------
+t100 -VIV--MYVSI-LRNDVMQYVFYYRENRIVR-----------QNNTGVAELPK-------
+t34 -VIV--MYVSI-LRNDVMRYVFYYRENRIAR-----------QNNTGVAELPK-------
+t84 -VIV--MYVSI-LRNDVMRYVFYYRENRIAR-----------QNNTGVAELPK-------
+t92 -VIV--MYVSI-LRNDVMRYVFYYRENRIAR-----------QNNTGVAELPK-------
+t3 -VIC--MYVSI-LCNVVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t22 -VIC--MYVSI-LRNVVMQYVFYYKENRSVR-----------QNNTGAAELPK-------
+t64 -VIC--MYVSI-LRNDVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t18 -VIC--MYVSI-LRNDVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t68 -VIC--MYVSI-LRNDVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t28 -VIC--MYVSI-LRNDVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t82 -VIC--MYISI-LRNDVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t41 -VIC--MYISI-LRNDVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t71 -VIV--MWISI-LRNDVMQYVVYYKENRSVR-----------QNNTGKAELPR-------
+t94 -VIV--MWISI-LRNDVMQYVFYYKENRSVR-----------QNNTGKAELPR-------
+t99 -VIC--MYVSI-LRNDVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t40 -VIC--MYISI-LRNNVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t90 -VIC--MYISI-LRNNVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t4 -VIC--MYVSI-LRNVVMQYVFYYKENRSVR-----------QNNTGKAELPK-------
+t36 IKIY--MWGTINFKNRVMQYCNYYKENRSVR-----------INNTGLAELPK-------
+t87 IKIY--MWGTICFKNRVMQYCNYYKENRSVR-----------INNTGLAELPK-------
+t89 IEIY--MWGTINFKNQVMQYCNYYKENRSVR-----------INNTGGAELPK-------
+t39 IEIY--MWGTINFKNQVMQYCNYYKENRSVR-----------INNTGGAELPK-------
+t8 IEIY--MWGTINFKNQVMQYCNYYKENRSVR-----------INNTGGAELPK-------
+t6 IEIY--MWGTINFKNQVMQYCNYYKENRSVR-----------INNTGGAELPK-------
+t58 IKIH--MWGTINFKNKVMQYCTYYKENRSVR-----------INNTGGAELPK-------
+t54 IKIH--MWGTINFKNKVMQYCTYYKENRSVR-----------INNTGGAELPK-------
+t65 IHIV--MWADIMFKNCVMQYCTYYKENRSVR-----------ANNTGGAELPK-------
+t29 IHIV--MWADIMFKNCVMQYCTYYKENRSVR-----------ANNTGGAELPK-------
+t98 IHIV--MWADIVFKNCVMQYCTYYKENRSVR-----------ANNTGGAELPK-------
+t83 IHIV--MWADIMFKNCVMQYCTYYKENRSVR-----------ANNTGGAELPK-------
+t95 IHII--MWEEIMFKNCVMQYCTYYKENRSVR-----------ANNTGGAELPK-------
+t20 IHII--MWEDIMFKNCVMQYCTYYKENRSVR-----------ANNTGGAELPK-------
+t69 IHIV--MWADIMFKNCVMQYCNYYKENRSVR-----------VNNTGGAELPK-------
+t2 IHIV--MWADIMFKNCVMQYCNYYKENRSVR-----------VNNTGGAELPK-------
+t10 IHIV--MWADIMFKNCVMQYCNYYKENRSVR-----------VNNTGGAELPK-------
+t31 YHIV--MWADIMFKNCVMQYSTYYKENRSVR-----------ANNTGGAELPK-------
+t15 YHIV--MWADIMFKNCVMQYSTYYKENRSVR-----------GNNTGGAELPK-------
+t63 YHIV--MWADIMFKNCVMQYSTYYKENRSVR-----------VNNTGGAELPK-------
+t50 YHIV--MWADIMFKNCVMQYSTYYKENRSVR-----------VNNTGGAELPK-------
+t25 YHIV--MWADIMFKNCVMQYSTYYKENRSVR-----------VNNTGGAELPK-------
+t51 YHIV--MWADIMFKNCVMQYATYYKENRSVR-----------VNNTGGAELPK-------
+t9 IGIC--MWETIHFKNPVMQYCCYYKENRSVR-----------VNNTGGAALPK-------
+t47 IGIC--MWDTIEFKNPVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t60 IGIC--MWDTIHFKNPVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t30 IGIC--MWDTIHFKNPVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t70 IGIC--MWDTIHFKNPVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t91 IGIC--MWDTIHFKNPVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t49 IGIC--MWDTIHFKNPVMQYCCYYKEPRSVR-----------VNNTGGAELPK-------
+t52 IGIG--MWDSIHFKNPVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t43 ICIC--TWGTIHFKNFVMQYCVYYKENRSVR-----------VNNTGGAELPQ-------
+t1 ICIC--TWGTIHFKNSVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t86 ICIC--GVGTIHFKNLVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t72 ICIC--TWGTIHFKNSVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t96 ICIC--TWGTIHFKNSVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t44 ICIC--TWGTIHFKNSVMQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t45 ICIC--TWGTIHFKNSVVQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t74 ICIC--TWGTIHFKNSVVQYCCYYKENRSVR-----------VNNTGGAELPK-------
+t26 IKIC--TWGTIHFKNSVMQYCCYYKENRSVR-----------LNNTGGAELPK-------
+t61 IKIC--TWGTIHFKNSVMQYCCYYKENRSVR-----------FNNTGGAELPK-------
+t97 IKIC--TWPTIHFKNGMMQYCCYYKENRSVR-----------FNNTGGAELPK-------
+t17 IKIC--TWGTIHFKNFVMQYCVYYKENRSVR-----------FNNTGGAELPK-------
+t11 IKIC--TWGTIHFKNFVMQYCVYYKENRSVR-----------FNNTGGAELPK-------
+t23 IAIV--MWGTINLKNHVMQYCCYYKETRSVR-----------VNNTGGAELPK-------
+t76 IAEP--LYLVI-YVNAVEPYTDAYKKPKSMHQFQFDDCQIRYRTNTGFEETPVGATHLTH
+t53 IAEP--LYLVI-YVNAVEPYTDAYKKPKSMHQFQFDDCQIRYRTNTGFEETPMGATHLTH
+t16 IAEP--LYLVI-YVNAVEPYTDAYKKPKSMHQFQFDDCQIRYRTNTGFEETPMGATHLTH
+t42 ITEP--LYLII-YVNAVEPYTDAYKKPKSMHQFQFDDVQIRYRTNTGFEENPKLATHLVH
+t24 IAEP--LYLII-YVNAVEPYTDAYKKPKSMHQFQFDDVQIRYRTNTGFEENPKLATHLVH
+
+
+t73 --------------DRLVNSFVD-ELYNSI---YTAAPKKK--RHL-GIGDNGGMELVRE
+t66 --------------DRLVNSFVD-ELYNSI---YTAAPKKK--RHL-GIGDNGGMELVRE
+t32 --------------DRLVNSFVD-ELYNSI---YTAAPKKK--RHL-GIGDNGGMELVRE
+t75 --------------DRLVNNFVD-ELYNSV---YTAAPKKK--RHL-GIGDNGGMELVRE
+t79 --------------ARLVNKVVD-ELYNNV---YHAIPKKE--MNQ-GVGDSGGVEMVQE
+t27 --------------ARLVNKVVD-ELYNNV---YHAIPKKD--MNQ-GVGDSGGVEMVQE
+t93 --------------ARLVNKVVD-ELYNNV---YHAIPKKD--MNQ-GVGDSGGVEMVQE
+t59 --------------HRLVNKVVD-ELYNNV---YHAIPKKD--MNQ-GVGDSGGVEMVQE
+t7 --------------HRLVNKVVD-ELYNNP---YHAIPKKD--MNQ-GVGDSGGIEMVQE
+t78 --------------HRLVNKVVD-ELYNNP---YHAIPKKD--MNQ-GVGDSGGIEMVQE
+t12 --------------HRLVNKVVD-ELYNNV---YHAIPKKD--INV-GVGDSGGMEVVQE
+t81 --------------HRLVVKVAD-ELYNNI---YHAIPKKD--GVLLGIGDSGGMEMVQE
+t21 --------------HRLVVKVAD-ELYNNI---YHAIPKKD--GVLLGIGDSGGMEMAQE
+t80 --------------HRLVDQVVD-ELYSKF---YHAIPKKP--GNM-GVGDSGGMEMVQE
+t14 --------------HRLVDQVVD-ELYSKF---YHAIPKKP--GNM-GVGDSGGMEMVQE
+t85 --------------HRLVDKVVD-ELYSKF---YHAIPKKP--GNM-GIGDSGGMEMVQE
+t62 --------------HRLVDRVVD-ELYSKF---YHAIPKKP--GNM-DVGDSGGMEMVME
+t19 --------------HRLVDKVVD-ELYSKF---YHAIPKKP--GNM-DVGDSGGMEMVME
+t77 --------------HRLVDKVVD-ELYSKF---YHAIPKKP--GNM-DVGDSGGMEMVME
+t88 --------------HHMQNIFID-ELYPGG---YHAAPKKE--EMV-GPGDNGGVEDIKE
+t37 --------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-SPGDNGGVEAIRE
+t35 --------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-SPGDNGGVEAIRE
+t48 --------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-SPGDNGGVEAIRE
+t55 --------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-SPGDNGGVEAIRE
+t46 --------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-APGDNGGVEAIRE
+t67 --------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-APGDNGGVEAIRE
+t57 --------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-APGDNGGVEAIRE
+t56 --------------HHVQNVFID-ELYPGH---YHAAPKKN--ENV-GPGDNGGVEGIKE
+t13 --------------HHMQDVFID-ELYLGP---YHASPKKD--RFC-NPGDNGGMETYQE
+t5 --------------HHMQDVFID-ELYLGP---YHASPKKD--RFC-NPGDNGGMDTYQE
+t38 --------------HHMQDVFID-ELYLGP---YHASPKKE--RFC-NVGDNGGMETIQE
+t33 --------------HHMQDVFID-ELYLGP---YHASPKKE--RFC-NPGDNGGMETIQE
+t100 --------------HHMQDVFID-ELYLGP---YHASPKKE--RFC-NPGDNGGMETIQE
+t34 --------------HHMQDIFID-ELYLGP---YHASPKKQ--RFC-NPGENGGMETIRE
+t84 --------------HHMQDIFID-ELYLGP---YHASPKKE--RFC-NPGENGGMETIRE
+t92 --------------HHMQDIFID-ELYLGP---YHASPKKE--RFC-NPGENGGMETIRE
+t3 --------------HHMQDIFID-ELYPGQ---YHASPKKK--KIC-GPGDNGGMETIEE
+t22 --------------HHMQDIFID-ELYPGL---YHASPKKK--KVC-GPGDNGGMETIQE
+t64 --------------HHMQDIVID-ELYPGP---YHATPKKH--RFC-GTGDNGGMQAIQE
+t18 --------------HHMQDIFID-ELYPGP---YHATPKKH--RFC-GTGDNGGMQAIQE
+t68 --------------HHMQDIFID-ELYPGP---DHATPKKH--RFC-GTGDNGGMQTIQE
+t28 --------------HHMQDIFID-ELYPGH---YHATPKKN--RYC-GPGDNGGMQVIEE
+t82 --------------HHMQDIFID-ELYPGH---YHATPKKN--RFC-GPGDNGGMQVIEE
+t41 --------------HHMQDIFID-ELYPGH---YHATPKKN--RFC-GPGDNGGMQVIEE
+t71 --------------HPMQEIFID-ELYPGH---YHATPKKN--RFC-GPGDNGGMQSMQE
+t94 --------------HPVQDIFID-ELYPGH---YHATPKKV--RFC-GPGDNGGMQAIQE
+t99 --------------HHMQDIFID-ELYPGR---YHATPKKN--RYC-GPGDNGGMQPIQE
+t40 --------------HHMQDIFID-ELYPGH---YQATPKKD--KFC-GPGDNGGMQTIQE
+t90 --------------HHMQDIFID-ELYPGH---YHATPKKD--KFC-GPGDNGGMQTIQE
+t4 --------------HHMQDIFID-ELYPGH---YHATPKKN--RCC-GPGDNGGMQTVQE
+t36 --------------YHHQNILID-ELYSNV---YPAAPKKH--QYM-GVGDVGGYEVICE
+t87 --------------YHHQNILID-ELYSNV---YPAAPKKH--QYM-GVGDVGGYEMICE
+t89 --------------YHHQNILID-ELYNNI---YPAAPKKH--KFL-GVGDVGGYEIICE
+t39 --------------YHHQNILID-ELYNNI---YPAAPKKH--KFL-GVGDVGGYEIICE
+t8 --------------YHHQNILID-ELYNDI---YPAAPKKH--KFL-GVGDVGGYEIICE
+t6 --------------YHHQNILID-ELYNNI---YPAAPKKH--KFL-GVGDVGGYEIICE
+t58 --------------YHHQNILID-ELYSNI---YPATPKKH--QYM-GVGDVGGYEVICE
+t54 --------------YHHQNILID-ELYSNI---YPATPKKH--QYM-GVGDVGGYEVICE
+t65 --------------YHQQNILTD-ELYSDV---YPAAQKKY--QVM-GVGDIGGYELICE
+t29 --------------YHQQNILTD-ELYSDL---YPAAPKKY--QEM-GVGDIGGYELIVE
+t98 --------------YHQQNLLTD-ELYSDI---YPAAPKKY--QVM-GVGDIGGYELIVE
+t83 --------------YHQQNLLTD-ELYSDI---YPAAPKKY--QVM-GVGDIGGYELIVE
+t95 --------------YHQQNILTD-ELYSDI---YPAAPKKY--QVM-GVGDIGGYELICE
+t20 --------------YHQQNILTD-ELYSDI---YPAAPKKY--QVM-GVGDIGGYELICE
+t69 --------------YHQQNILTD-ELYSDI---YPAAPKKY--QIM-GVGDIGGYELICE
+t2 --------------YHQQNILTD-ELYSDI---YPAAPKKY--QIM-GVGDIGGYELICE
+t10 --------------YHQQNILTD-ELYSDI---YPAAPKKY--QIM-GVGDIGGYELICE
+t31 --------------YHQQNILTD-ELYSDM---YPAAPKKYVIRVM-GVGDIGGYEMICE
+t15 --------------YHQQNILTD-ELYSDV---YPTAPKKYVIRVM-GVGDIGGYELICE
+t63 --------------YHQQNILTD-ELYSDM---YPAAPKKYVIRQM-GMGDIGGYELICE
+t50 --------------YHQQNILTD-ELYSDM---YPAAPKKYVIRQM-GMGDIGGYELICE
+t25 --------------YHQQNILTD-ELYSDM---YPAAPKKYVIRQM-GMGDIGGYELICE
+t51 --------------YHQQNILTD-ELYSDM---YPAAPKKYVIREM-GVGDIGGYELICE
+t9 --------------YHHQNTLVD-ELYSDV---YPAAPKKK--VCM-GVGDVGGYEVMGE
+t47 --------------YHHQNTLVD-ELYSDI---YPAAPKKK--VCM-GVGDVGGYEVMGE
+t60 --------------YHHQNTLVD-ELYSDI---YPAAPKKK--VCM-GVGEVGGYEVMGE
+t30 --------------YHDQNTLVD-ELYSDV---YPAAPKKK--VCM-GVGDVGGYEVMGE
+t70 --------------YHNQNTLVD-ELYSDV---YPAAPKKQ--HYM-GVGDVGGYEVMGE
+t91 --------------YHNQNTLVD-ELYSDV---YPAAPKKQ--HYM-GVGDVGGYEVMGE
+t49 --------------YHNFNALVD-ELYSDV---YPAAPKKK--HYM-GVGDVGGYEVMGE
+t52 --------------YHHQNSLVD-ELYSDV---YPAAPKKK--HYM-GVGDVGGYEVMGE
+t43 --------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+t1 --------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+t86 --------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+t72 --------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+t96 --------------YHHQNILVD-ELYSDV---YPAAPKKK--HYV-GAGDVGGYEVMSE
+t44 --------------YHHQNMLVD-ELYSDM---YPAAPKKK--VYV-GAGDVGGYEVMSE
+t45 --------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+t74 --------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+t26 --------------YHHQNVLVD-ELYGEA---YPAAPKKK--HYM-GAGDVGGYEVMSE
+t61 --------------YHHQNVLVD-ELYSEL---YPAAPKKA--HYM-GAGDIGGYEVMSE
+t97 --------------YHHQNVLVD-ELYSEV---YPAAPKKA--FYM-GAGDIGGYEVMSE
+t17 --------------YHHQNALVD-ELYSDV---YPAAPKKK--HYM-GEGDVGGYEVMSE
+t11 --------------YHHQNVLVD-ELYSDG---YPAAPKKK--HYM-GEGDVGGYEVMSE
+t23 --------------YHYQNILVD-ELYSND---YPAAPKKA--QFM-GVGDVGGYEIVCE
+t76 VCVCVPHPWTKGKSEILQNMGSA-VLYNDVIRDHNASEQKE--AHV-PMGDEGRISRAKD
+t53 VCVCVPHPWTKGKSEILQNMGSA-VLYNDVIRDHNASEQKE--AHV-PMGDQGRISRAKD
+t16 VCVCVPHPWTKGKSEILQNMGSA-VLYNDVIRDYNASEQKE--AHV-PMGDQGRISRAKD
+t42 VCVVVPHPWTKGKSEILQNMESA-HLYNAVIRDNNASEQKE--AHV-PVGDEGRISRAKN
+t24 VCVVVPHPWTKGKSEILQNMESARHLYNAVIRDNNASHQKE--AHV-PAGDQGRISRAKN
+
+
+t73 DIFQILVCV
+t66 DIFQILVCV
+t32 DIFQILVCV
+t75 DIFQILVCV
+t79 DVFQILVCI
+t27 DVFQILVCI
+t93 DVFQILVCI
+t59 DVFQILVCI
+t7 DVFQILVCI
+t78 DVFQILVCI
+t12 DVFQILVCI
+t81 DLFQILVCA
+t21 DLFQILVCV
+t80 DVFQILVCL
+t14 DVFQILVCL
+t85 DLFQILVCI
+t62 DVFQILVCV
+t19 DVFQILVCV
+t77 DVFQILVCA
+t88 DMFQVLVCR
+t37 DMFQVLVCK
+t35 DMFQVLVCK
+t48 DMFQVLVCK
+t55 DMFQVLVCK
+t46 DMFQVLVCK
+t67 DMFQVLVCK
+t57 DMFQVLVCK
+t56 DMFQVLVCQ
+t13 DMFQVLVCV
+t5 DMFQVLVCV
+t38 DMFQVLVCI
+t33 DMFQVLVCV
+t100 DMFQVLVCV
+t34 DMFQVLVCV
+t84 DMFQVLVCV
+t92 DMFQVLVCV
+t3 DMFQVLVCV
+t22 DMFQVLVCV
+t64 DMFQVLVCV
+t18 DMFQVLVCV
+t68 DMFQVLVCV
+t28 DMFQVLVYV
+t82 DMFQVLVYV
+t41 DMFQVLVYV
+t71 DVFQVLVCV
+t94 DVFQVLVCV
+t99 DMFQVLVCV
+t40 DMFQVLVCV
+t90 DMFQVLVCV
+t4 DMFQVLVCV
+t36 NLFQILVVE
+t87 NLFQILVVE
+t89 NLFQILVVE
+t39 NLFQILVVE
+t8 NLFQILVVE
+t6 NLFQILVVE
+t58 NLFQILVVE
+t54 NLFQILVVE
+t65 DLFQILVCQ
+t29 DLFQILVCE
+t98 DLFQILVCE
+t83 DLFQILVCE
+t95 DLFQILVCE
+t20 DLFQILVCE
+t69 DLFQILVCE
+t2 DLFQILVCE
+t10 DLFQILVCE
+t31 DLFQILVCE
+t15 DLFQILVCQ
+t63 DLFQILVCE
+t50 DLFQILVCE
+t25 DLFQILVCE
+t51 DLFQILVCE
+t9 DLFQILVCE
+t47 DLFQILVCE
+t60 DLFQILVCE
+t30 DLFQILVCE
+t70 DLFQILVCE
+t91 DLFQILVCE
+t49 DLFQILVCE
+t52 DLFQILVCE
+t43 DLFQILVHE
+t1 DLFQILVHE
+t86 DLFQILVHE
+t72 DLFQILVHE
+t96 DLFQILVHG
+t44 DLFQILVHA
+t45 DLFQILVHE
+t74 DLFQILVHE
+t26 DLFQILVHE
+t61 DLFQILVHE
+t97 DLFQILVHK
+t17 DLFQILVHA
+t11 DLFQILVHA
+t23 DIFQILVCD
+t76 EIMYIRDLE
+t53 EIMYIRDLE
+t16 EIMYIRDLE
+t42 EILYIRDLE
+t24 EILYIRDLE
diff --git a/test/example.fasta b/test/example.fasta
new file mode 100644
index 0000000..68bb46e
--- /dev/null
+++ b/test/example.fasta
@@ -0,0 +1,1702 @@
+>t73
+LIVSQIRVMVRDG--IHKAMDEE-V------------LIARRVKPYSGNGTQVRNDVEDAN--CQEFVGI---RELGKH
+-YK-CMDGFHTVNNGAGEN-SESAMWIFDLWMCKLNHGMQR--------GDIGRVKRDVQKFPKLKEGAPNCSSFVKPY
+FMGCDMFHKQVEYRGTHGLVLDDTWNEESATFPYPQVHSRSDKRCLNGLHQGDHEESVH---HAPRI----MR---LIG
+H-HLVIIVLMNHDMGRLNHLEPDAVIPSPLRIGGDGWVPKPI------------------EDGFFDK-D-Q------SR
+PDVANASIVPDK----DQWVGAHNQWGSSLRKVGLAVHDLR-NISDLYRCVWMDCHLGANHYRQISRMKMITPTYTHMT
+EYANGL----WHPFYKASDHKNEAQGVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVVKPLLGDWEG
+CKCRS---KLYVSQLDH----KTLSK-NLGLY--MQKRTWLATAPLQ------IGCMFMLVGRKKNSEE-NYNKAADPT
+VIWFYTQPIVYV-ADVFGCTKGKNPQEMRG------NNVMSESLGDDNLQD--MSGVPVTVCTSSVMVRKDMQD-SVDK
+RGCTWNAKE-DHLCPSSFCKGER---EDEPGGVTQ-----------------RCIENIAKLLYIKDV-LCNEVLNGLQW
+QLCWSV-GDWESLIPQACWDAKKDLAVCAWKMELVPGL---NRNNENLAKVIYFGPDGH-------DEGPMQAKIVTLH
+W-EMDVSHRG-SSVDDNVV-VVMLAFAVSFCHPWGHYIQGLGD-QHKLARPNT---AQKLSILT---VFHFSGGFRDKP
+M-ERSQLHS-TYSED----KKDQKVLIHAMK-RNKGLDWHAGND-MKGGPK-IIYLGMLFY-------AENNVAKQKAH
+FVVFL-ISDATRLLIVHEGCMIDYTFMEFACHPFFAELFMEHMVARYQYYSNVDIKIFDTCFRSAVYAVDNSWETLCDY
+-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMRIQIAIRVSGSE-SENVVLQYCLYYEE
+NKSIR-----------QNNTGSADLPK---------------------DRLVNSFVD-ELYNSI---YTAAPKKK--RH
+L-GIGDNGGMELVREDIFQILVCV
+>t66
+LIVSQIRVMVRDG--IHKAMDEE-V------------LIARRVKPCSGNGTQVRNDVEDAN--CQEFVGI---RELGKH
+-YK-CMDGFHTVNNGAGEN-SESAMWIFDLWMCKLNHGMQR--------GDIGRVKRDVQKFPKLKEGAPNCSSFVKPY
+FMGCDMFHKQVEYRGTHGLVLDDTWNEESATFPYPQVHSRSDKRCLNGLHQGDHEESVH---HAPRI----MR---LIG
+H-HLVIIVLMNHDMGRLNHLEPDAVIPSPLRIGGDGWVPKPI------------------EDGFFDK-D-Q------SR
+PDVANASIVPDK----DQWVGAHNQWGSSLRKVGLAVHDLR-NISDLYRCVWMDCHLGANHYRQISRMKMITPTYTHMT
+EYANGL----WHPFYKASDHKNEAQGVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVVKPLLGDWEG
+CKCRS---KLYVSQLDH----KTLSK-NLGLY--MQKRTWLATAPLQ------IGCMFMLVGRKKNSEE-NYNKAADPT
+VIWFYTQPIVYV-ADVFGCTKRKNPQEMRG------NNVMSESLGDDNLQD--MSGVPVTVCTSSVMVRKDMQD-SVDK
+RGCTWNAKE-DHLCPSSFCKGER---EDEPGGVTQ-----------------RCIENIAKLLYIKDV-LCNEVLNGLQW
+QLCWSV-GDWESLIPQACWDAKKDLAVCAWKMELVPGL---NRNNENLAKVIYFGPDGH-------DEGPMQAKIVTLH
+W-EMDVSHRG-SSVDDNVV-VVMLAFAVSFCHPWGHYIQGLGD-QHKLARPNT---AQKLSILT---VFHFSGGFRDKP
+M-ERSQLHS-TYSED----KKDQKVLIHAMK-RNKGLDWHAGND-MKGGPK-IIYLGMLFY-------AENNVAKQKAH
+FVVFL-ISDATRLLIVHEGCMIDYTFMEFACHPFFAELFMEHMVARYQYYSNVDIKIFDTCFRSAVYAVDNSWETLCDY
+-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMRIQIAIRVSGSE-SENVVLQYCLYYEE
+NKSIR-----------QNNTGSADLPK---------------------DRLVNSFVD-ELYNSI---YTAAPKKK--RH
+L-GIGDNGGMELVREDIFQILVCV
+>t32
+LIVSQIRVMVRDG--IHKAMDEE-V------------LIARRVKPYSGNGTQVRNDVEDAN--CQEFVGI---RELGKH
+-YK-CMDGFHTVNNGAGEN-SESAMWIFDLWMCKLNHGMQR--------GDIGRVKQDVQKFPKLKEGAPNCSSFVKPY
+FMGCDMFHKQVEYRGTHGLVLDDTWNEESATFPYPQVHSRSDKRCLNGLHQGDHEESVH---HAPRI----MR---LIG
+H-HLVIIVLMNHDMGRLNHLEPDAVIPSPLRIGGDGWVPKPI------------------EDGFFDK-D-Q------AR
+PDVANASIVPDK----DQWVGAHNQWGSSLRKVGLAVHDLR-NISDLYRCVWMDCHLGANHYRQISRMKMITPTYTHMT
+EYANGL----WHPFYKASDHKNEAQGVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVVKPLLGDWEG
+CKCRS---KLYVSQLDH----KTLSK-NLGLY--MQKRTWLATAPLQ------IGCMFMLVGRKKNSEE-NYNKAADPT
+VIWFYTQPIVYV-ADVFGCTKGKNPQEMRG------NNVMSESLGDDNLQD--MSGVPVTVCTSSVMVRKDMQD-SVDK
+RGCTWNAKE-DHLCPSSFCKGER---EDEPGGVTQ-----------------RCIENIAKLLYIKDV-LCNDVLNLLVW
+QLCWSV-GDWESLIPQACWDAKKDLAVCAWKMELVPGL---NRNNENLAKVIYFGPDGH-------DEGPMQAKIVTLH
+W-EMDVSHRG-SSVDDNVV-VVMLAFAVSFCHPWGHYIQGLGD-QHKLARPNT---AQKLSILT---VFHFSGGFRDKP
+M-ERSQLHS-TYSED----KKDQKVLIHAMK-RNKGLDWHAGND-MKGGPK-IIYLGMLFY-------AENNVAKQKAH
+FVVFL-LSDATRLLIVHEGCMIDYTFMEFACHPFFAELFMEHMVARYQYYSNVDIKIFDTCFRSAVYAVDNSWETLCDY
+-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMRIQIAIRVSGSE-SENVVLQYCLYYEE
+NKSIR-----------QNNTGSADLPK---------------------DRLVNSFVD-ELYNSI---YTAAPKKK--RH
+L-GIGDNGGMELVREDIFQILVCV
+>t75
+LIVSEIRVMVRDE--VHKAMDEE-C------------LIARRVKPYSGNGNQIRNDIEDAN--GQEFVGI---RELGKH
+-YD-CMDGYHTVNNGAGEN-SESAMWIFDLWMCKLNHGMQR--------GDIGRVQQDVHKFPKLKEGAPNCSSFVKPV
+FMGCDMFHRQVQNRGNHGLVLDDTWNEESGTFPYPQVHSRNEKRCINKLHQGDHNESCH---HNPRI----VR---RIG
+H-HLVIIVLVNRDMGRLNYIEPDALVPSPLRFGGDEWVPKPI------------------EDGFFDK-D-Q------AR
+PDVANA-IVPDR----DQWVGAHKEWGSSLCKVGLAVHDLR-NVSDLYRCVWMECVLGANHYQQVSRMKMVTPAYTHMT
+EYANGL----WHPFYKNPDHKNEAQGVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVAKPVLGDWEG
+CKCRSDLIKLYVSQLDH----KTLSK-NMGLY--MRNRTWLATSPLQ------IGCIFMLVGRKKNSEE-NYNKAADPT
+VIWFYTQPIVYV-ADVFGCTKGKNPQEMRK------NNVISESLGDDNLQD--MPGMPVTVCTSSVMVRKDMHQ-SVDK
+RGYTWHAKE-DHLCPDSFCKGEK---EEEPGGVRR-----------------RIVENIVKLLYIKDV-LCNQVLNLLQW
+QLCWSV-GDWESLVPQACWGAKKDLAVCAWKMELVPGL---NRNNENLAKIIYFGPDGH-------DEGNMQAKIVTLH
+W-EMDVSHRG-SSVDDNVV-VVMLAFQASFCDPWGHYIQGLGD-QYKLARPNT---ARQLSILV---VMHFSGGFRDKP
+I-ERSQLHC-TYSEN----KKDQKVVIRAMK-RNKGCDWHAGKD-MAGGPK-IIYVGMLFY-------AESNWAKQKAH
+FVVFL-ISDATRLLIHHVGCMIEYTFMEFACHPFFAELFMEHMVIRYQYYNNVDIKIFDTCFRGAVYAEDNSWETLCGY
+-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMRIQIPIRISGSE-SENVVLQYCLYYEE
+NKSIR-----------QNNTGSAVLPK---------------------DRLVNNFVD-ELYNSV---YTAAPKKK--RH
+L-GIGDNGGMELVREDIFQILVCV
+>t79
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTFSGSQNQVRNAVEDAA--RPDFVGT---RELGKQ
+-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPY
+FLGVDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIG
+L-NLVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------GDGFFDK-D-Q------AR
+PLMANAVCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVM
+EYAHGL----WKPFYQASDHKNEAQGVGER-THQLPCVESHTCQYEVKHAKVCKLVHH-ALYLLGLRTVMKPHLGDVDG
+CRCRSDLNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSAN-NYNRAGDPT
+TICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDDSLQQ--MPAVPVDVCVMSVMVNKSMPQ-SHDK
+RGYTWQAKQ-DHLFPVNVVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-DCNMVLSLLVW
+QLC--H-GDWEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLH
+W-EMEASHRE-SSVRDNMI-VIMLPFNINSIDPWRHYILGLND-QIQLTRPNT---ARRLSILH---VMHYSGEFHDKS
+A-ERSQLHS-RYSEH----KNDHKCVILASK-HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNH
+FVIFL-ICDAVRILILHHGCMTDHTFMEFACNPFFSELFMEHVYIRYQYINNHDIKIKDTVFRLAVYAWDNFWETLCKC
+-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIRIKIREPGSE-SENTVVMYVIYYKE
+RKSIR-----------QNNTGCAKLPQ---------------------ARLVNKVVD-ELYNNV---YHAIPKKE--MN
+Q-GVGDSGGVEMVQEDVFQILVCI
+>t27
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTMSGSQNQVRNAVEDAA--RPDFVGI---RELGKQ
+-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPY
+FLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIG
+M-NLVIISYANVDMGRLNHCEDQAIVYSPLRYGGAGFVSKPI------------------ADGFFDK-D-Q------AR
+PLMANAVCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVM
+EYAHGL----WKPFYQASDHKNEAQGVGER-THQLPCVESHTCQYEVKHAKVCKLVHH-ALYLLGIHTVMKPHLGNVDG
+CRCRSDLNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSAN-NYNRAGDPT
+TICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDDSLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDK
+RGYTWQAKQ-DHLFPVNCVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIVLSLLVW
+QLC--H-GDWEPLLPQACEGARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLH
+W-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ARRLSILH---VMHYSGAFHDKS
+A-ERSQLHS-RYSEH----KNDHKCVILASK-VNKDHDWITGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNH
+FVIFL-ICDAVRILILHHGCMTDHTFMEFACNPFFSELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENFWETLCNC
+-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIRIKIREPGSE-SENTVVMYVIYYKE
+RKSIR-----------QNNTGCAKLPQ---------------------ARLVNKVVD-ELYNNV---YHAIPKKD--MN
+Q-GVGDSGGVEMVQEDVFQILVCI
+>t93
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTMSGSQNQVRNAVEDAA--RPDFVGI---RELGKQ
+-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPY
+FLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIG
+M-NLVIISYANVDMGRLNHCEDQAIVYSPLRYGGAGFVSKPI------------------ADGFFDK-D-Q------AR
+PLMANAVCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVM
+EYAHGL----WKPFYQASDHKNEAQGVGER-THQLPCVESHTCQYEVKHAKVCKLVHH-ALYLLGIHTVMKPHLGNVDG
+CRCRSDLNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSAN-NYNRAGDPT
+TICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDDSLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDK
+RGYTWQAKQ-DHLFPVNCVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIVLSLLVW
+QLC--H-GDWEPLLPQACEGARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLH
+W-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ARRLSILH---VMHYSGAFHDKS
+A-ERSQLHS-RYSEH----KNDHKCVILASK-VNKDHDWITGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNH
+FVIFL-ICDAVRILILHHGCMTDHTFMEFACNPFFSELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENFWETLCNC
+-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIRIKIREPGSE-SENTVVMYVIYYKE
+RKSIR-----------QNNTGCAKLPQ---------------------ARLVNKVVD-ELYNNV---YHAIPKKD--MN
+Q-GVGDSGGVEMVQEDVFQILVCI
+>t59
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTFSGSQNQVRNAVEDAA--RPDFVGI---RELGKQ
+-YE-CMDGVGAVDTGAGDN-SESAVVIFDVWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPY
+FLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIG
+M-NLVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------ADGFFDK-D-Q------AR
+PLMANAHCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECILGANVYHQISRMKMHGPTYSHVM
+EYAHGM----WKPFYQASDHKNEAQGVGER-THQLPCVDSHTCQYEVKHAQVCKLVHH-ALYLLGLRTVMKPHLGDVDG
+CRCRSDLNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSGN-NYNQAGDPT
+TICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDDSLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDK
+RGYTWQAKQ-DHLFPVNFVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIDLSLLVW
+QLC--H-GDWEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLH
+W-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ACRLSILH---VMHYSGEFHDKS
+A-ERSQLHS-RYSEH----KNDHKCVILASK-HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNH
+FVIFL-ICDAVRILILHHGCMTDHTFMEFACNPFFAELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENFWETLCNC
+-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIGIKIREPGSQ-SENTVVMYVIYYKE
+RKSIR-----------QNNTGCAKLPQ---------------------HRLVNKVVD-ELYNNV---YHAIPKKD--MN
+Q-GVGDSGGVEMVQEDVFQILVCI
+>t7
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKKFSGSQGQVRNAIEDAA--RPDFVGI---RELGKQ
+-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSMPMPY
+FLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIG
+M-NLVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------ADGFFDK-D-Q------AR
+PLMANAHCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVM
+EYAHGM----WKPFYQASDHKNEAQGVGER-THQLPCVDSHTCQYEVKHAQVCKLVHH-ALYLLGLRTVMKPHLGDVDG
+CRCRSDLNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSGN-NYNRAGDPT
+TICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDDSLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDK
+RGYTWQAKQ-DHLFPVNFVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIVLSLLVW
+QLC--H-GDWEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLH
+W-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ACRLSILH---VMHYSGEFHDKS
+A-ERSQLHS-RYSEH----KNDHKCVILASK-HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNH
+FVIFL-ICDAVRILILHHGCMTDRTFMEFACNPFFAELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENFWETLCNC
+-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIGIKIREPGSQ-SENTVVMYVIYYKE
+RKSIR-----------QNNTGCAKLPQ---------------------HRLVNKVVD-ELYNNP---YHAIPKKD--MN
+Q-GVGDSGGIEMVQEDVFQILVCI
+>t78
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTFSGSQGQVRNAIEDAA--RPDFVGI---RELGKQ
+-YE-CMDGVGAVDTGAGDN-SESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPY
+FLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSVKRCLNVLHQGDHEESRH---HNARI----VR---RIG
+M-NLVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------ADGFFDK-D-Q------AR
+PLMANAHCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVM
+EYAHGM----WKPFYQASDHKNEAQGVGER-THQLPCVDSHTCQYEVKHAQVCKLVHH-ALYLLGLRTVMKPHLGDVDG
+CRCRSDLNNLILSQLDD----KTLSK-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSGN-NYNRAGDPT
+TICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDDSLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDK
+RGYTWQAKQ-DHLFPVNFVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-DCNIVLSLLVW
+QLC--H-GDWEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLH
+W-EMEASHRE-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ACRLSILH---VMHYSGEFHDKS
+A-ERSQLHS-RYSEH----KNDHKCVILASK-HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNH
+FVIFL-ICDAVRILILHHGCMTDRTFMEFACNPFFAELFMEHVYIRYQYVNNHDIKIKDTVFRLAVYAWENFWETLCNC
+-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIGIKIREPGSQ-SENTVVMYVIYYKE
+RKSIR-----------QNNTGCAKLPQ---------------------HRLVNKVVD-ELYNNP---YHAIPKKD--MN
+Q-GVGDSGGIEMVQEDVFQILVCI
+>t12
+LIVSEVRVMVRDG--INIAIDEL-C------------LIANRVKAFSGHQNQVRNAMEDAQ--RPDFVGI---RELGKQ
+-YQ-CMDGHGAVDTGAGRN-SESAVWIFDIWMCKLAHGMQW--------GDIGRVSVDHPKFLKLEEGAPRCSSCPMPY
+FLGCEMFHRQVILKGAKGLVLPD--NEDSMAFPYVQVHSRSVKRCLNVLVQGDHDESRH---HNARI----VA---RIG
+M-NMVIIRYLNVEMGRLNHCEDDAMVYSPLRIGGAGTHSKPI------------------ADGFFDK-D-Q------AR
+PLIANAHIVPEN----DQWTGAVAQWCSSVIKCGLANHDLE-NISRLLRCVVMECVLGANVYHQASRMKMHGPYYAHVT
+EYAHGL----WKPFYQTSDHKNEAQGVGES-THQLPCVESQTCQYEVKHAKVCKLVHH-ALYLLALHTMMKPRLGDIDG
+CRCRSELNKLALSQLDD----KTLSK-NCFQY--LGNMTWLATSPLH------VGCMIIF-------------------
+-----------------------------V------NNVLSQSLGDDSLQQ--MHAMPVTVVVVSHMVKKSMPQ-SHDK
+RGYTWQAKDFDQLIPVSFVKGEQ---EEEPEGPNN-----------------RVVHNIVKLLYTKDV-DCNTVLSLLIW
+QLC--H-GDWEQLVPQACAGARSDLAVCAWKRELVPGL---NHNNENLAKVIYFGPDGH-------DEGPMGRKIVDLH
+W-EMEASHRD-SSVRDNML-VIMLPFLVNNLDPWRHYILGLND-QIQLTRPNT---ARRLSILM---VMHYSGEFHDKS
+P-ERSQLHFDSYSEH----KNDHKCVILASK-HNKGLDWATGKDDMKGGAK-IMMSGALFY-------AEQNWIRARNH
+FVIFL-ICDAVRILIVLHGCMTAWTFMEFACNPFFAELFMEHVYIRYQYVNNHDIKIKDTEFRLAVYAWENSWETLCNC
+-EMLSGHIGAKINHNPRLFEQVC-PPCELTVSGLKGKH-VGWPYLTDITRTPLIRIQIREPGSE-CENSVVMYVIYYKE
+RKSIR-----------QNNTGCAKLPQ---------------------HRLVNKVVD-ELYNNV---YHAIPKKD--IN
+V-GVGDSGGMEVVQEDVFQILVCI
+>t81
+LIVSEVRHMVRDG--ANVAIDEL-C------------LIACRVKAFSGHGHQVRNAVEDAA--RPDFIGI---RELGKP
+-Y--CMDGHGAVNTGAGHN-SESAVWIFDIWMYKLSHGMQW--------GDIGRVGVDHPKFLKLEEGAPNCSSLPMPY
+FLGVDMFHRQVTIKGAKGLVLPDIWNESPMAFPYAQVHSKSHKRCLNVLVQGDHEESEH---HNARI----MS---KIG
+T-HLVIINIINVEMQRLNHCEDKAIVYSPDRIGGAGFHSKPI------------------ADGFFDK-D-Q------AR
+PIIANAHIVPVN----DQWTGPMAQWCSSVIKCGLANHELE-DVSRLLRCVGMECNLGANHYHQVSRMKMHGPIYSHMT
+EYAVGL----WKPFYQASEHKNEAQGLGER-PHQLPCVESQTCQYEIKVAKVCKLVHV-ALYLVGLKTVVKPKLGDWDG
+IRCRSELNKLYLSQLDD----KTLSK-NCFIY--LGNMTWLATSPLQ------IGWLVLFDGRKRQSAE-DYNRAADPT
+TISFCRKPIVQH-ADVFGCDRDKDPQEMRT------NNVISESLGDDFLQQ--MPAVPVSVCVYSHMVKKFVPQ-SHEK
+RGYTWKAKE-DHLVPISYCKGEH---EEEPEGAQY-----------------RVVQNIVKLLYTKDV-DCNVVLSLLVW
+QLC--H-GDWEPLIPQACQTAKKDLAVCAWKRELVPGL---NCNNEYLAKIIYFGPDGH-------DEGPMGRKIVDLH
+W-EMEASHRD-SSVRDNYI-VIMLPFKINSRDPWRHYILGIND-QVCLNRPET---ARRLSILA---VMHYSGEFHDKS
+P-ERSHLHF-RYSEM----KNDVKCVI---K-SNKGLDWTAGKDGMKGEAK-AMMNGALFY-------AEQNWFRKKNH
+FVIFV-FCDAVRILIMHSGVMIGYTFMEFACNPFFAELFMEHVMVRYQYESNHDIKIKDTCFRLAVYAWENSWETLCNV
+-EMLSGHFGAKINHVPRLPEQVC-PPCDLTVSGLKGKQ-NGLPYLTDITRTPLIRIQIRVPGSE-SENVVVMYMVYYKE
+RKSIR-----------QNNTGCANLPQ---------------------HRLVVKVAD-ELYNNI---YHAIPKKD--GV
+LLGIGDSGGMEMVQEDLFQILVCA
+>t21
+LIVSEVRHMVRDG--ANIAIDEL-C------------LIACRVKAFSGHGNQVRNAVEDAP--RPDFIGV---RELGKP
+-Y--CMDGHGAVNTGAGVN-SESAVWIFDIWMYKLSHGMQW--------GDIGRVDVDHPKFLKLEEGAPNCSSLPMPY
+FLGVDMFHKQVTLKGAKGLVLPDIWNESPMAFPYAQVHSKSHKRCLNVLVQGDHEESEH---HNARI----MS---RIG
+T-HLVIVNVINVEMQRLNHCEDKAIVYSPDRIGGAGFHSKPI------------------ADGFFDK-D-Q------AR
+PIIANAHIVPIY----DQWTGPMAQWCSSVIKCGLANHELK-VVSRLLRCVGMECNLGANHYHQVSRMKMHGPIYSHMT
+EYAHGL----WKPFYQASEHKNEAQGVGER-PHQLPCVESQKCQYEVKVAKVCKLVHV-ALYLVGLKTVVKPKLGDWDG
+VRCRSDLNKLYLSQLDD----KTLSK-NCFRY--LGNMTWLATSPLQ------NGCVVIFAGRKRQSAE-DYNRAADPT
+TIAFCRKPIVQH-ADVFGCDKDKDPQEMRM------NNVISESLGDDFLQQ--MPAVPVSVCVHSHMVKKFVPQ-SHEK
+RGVTWKAKE-DHLVPISLCKGEH---EEEPEGAQY-----------------RCVQNIVKLLYTKDV-DCNVVLSLLVW
+QLC--H-GDWEPLVPQACQTAKKDLAVCAWKRELVPGL---NCNNEYLAKIIYFGPDGH-------DEGPMGRKIIQLH
+W-EMEASHRD-SSVRDNII-VIMLPFKINSRDPWRHYILGLND-QVCLTRPET---ARRLSILV---VMHYSGEFHDKS
+P-ERSHLHY-RYSEV----KNDVKCVILASK-SNKGLDWTAGKDGMKGENK-AMMNGTLFY-------AEQNWFRQKNH
+FVIFV-ICDAVRILIVHSGVMTGFTFMEFACNPFFAELFMEHVYIRYQYQANHDIKIKDTCFRLAVYAWENSWETLCNV
+-EMLSGHFGAKINHVPRLPEQVC-PPCDLTVSGLKGKQ-NGWPYLTDITRTPLIRIQIRVPGSE-SENITVMYMVYYKE
+RKSIR-----------QNNTGCANLPQ---------------------HRLVVKVAD-ELYNNI---YHAIPKKD--GV
+LLGIGDSGGMEMAQEDLFQILVCV
+>t80
+LIVSEVRHMVRDG--VNIAVDEI-C------------LIANRVKSMSGQGNQVRNAMEMAA--RQNFVGM---RELEKV
+-YE-CMDGQGAVNTEAGNN-SESAVWIFDIWMCKLTHGMQDFGD-----GDIGRVVVDHPKFEKLEEGAPNCSSHPVPY
+FLGIDMFHKQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSHRRVLNVLHQGDVEES-H---HSARC----VR---RIG
+F-HLVIIVFWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPV------------------DDGFFDK-D-Q------AR
+PVIASAHIVPEH----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVMIDCNQGANHYIQISRMKVHGPTYSHMT
+EYAHGL----WKPFYQASDHKNDAQGVGER-PHQLPCVESQTCQYEMKHAKVCKLVHG-ALYLIALKTVVKPKLGVWQG
+CRCRSQLSKLVLSQLDE----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCVILFGGRKRQSHGLNYNRAADPT
+TICFYKKPIVVQGADVFGCARGKDPQEMKA------NNVISGSLGDDRLQQ--MPAMPVTICVSSYMVKKSVIQ-SHQK
+RGYTWRAKE-DHLIPVSFCKGEL---DEEPDAAQQ-----------------RIVQNIVKLLYTKDV-SCNVVLSMLIW
+QIC--H-GDWEPQIPKACSNARKDLAVCAWKRELVPGL---NHNNENLAKIMYFGHDGH-------DEGPMGRKIVTLH
+V-EMEVSHRE-SSVKDNMIRVIMLPFSNSSVDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VTHYSGGFHDKS
+A-ERSQHHF-IYNEV----KDDHKCVILASK-CNKGLDWAAGKD-MKGGAK-VMMNGALFY-------AERNWIRQKHH
+FVIFV-VCDAVRILIVHYGCMIGYTFMDFACNPFFAELFMDHVFIRYVYMNNHDIKIMDTCFRVAVYTWENSWETCFNR
+-EMLSGTFGAKISHNPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPLIKIHIRVPGSQ-SENHVVMYCVYYKE
+HKSIR-----------QNNTGCANLPQ---------------------HRLVDQVVD-ELYSKF---YHAIPKKP--GN
+M-GVGDSGGMEMVQEDVFQILVCL
+>t14
+LIVSEVRHMVRDG--VNIAVDEI-C------------LIANRVKSMSGQGNQVRNAMEMAA--RQNFVGM---RELEKV
+-YQ-CMDGQGAVNTEAGNN-SESAVWIFDIWMCKLTHGMQDFGD-----GDIGRVVCDHPKFEKLEEGAPNCSSHPMPY
+FLGVDMFHEQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSHRRVLNVLHQGDVEES-H---HSARC----VR---RIG
+F-HLVIIVYWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPV------------------DDGFFDK-D-Q------AR
+PVIASAHIVPEH----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVMIDCNQGANHYIQISRMKVHGPTYSHMT
+EYAHGL----WKPFYQASDHKSDAQGVGER-PHQLPCVESQTCQYEMKHAKVCKLVHG-ALYLIALKTVVKPKLGVWQG
+CRCRSQLSKLVLSQLDE----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCVILFGGRKRQSHGLNYNRAADPT
+TICFYKKPIVVQGADVFGCARGKDPQEMKA------NNVISGSLGDDRLQQ--MPAMPVTICVSSYMVKKSVPQ-SHQK
+RGYTWRAKE-DHLIPVSFCKGEL---DEEPDAAQQ-----------------RIVQNIVKLLYTKDV-SCNVVLSMLIW
+QIC--H-GDWEPQIPKACSNARKDLAVCAWKRELVPGL---NHNNENLAKIMYFGHDGH-------DEGPMGRKIVTLH
+V-EMEVSHRE-SSVKDNMIRVIMLPFPSSSVDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VTHYSGGFHDKS
+A-ERSQHHF-IYNEV----KDDHKCVILASK-CNKGLDWAAGKD-MKGGAK-IMMNGALFY-------AERNWIRQKHH
+FVIFV-VCDAVRILIVHYRCMIGYTFMDFACNPFFAELFMDHVFIRYQYMNNHDIKIMDTCFRVAVYTWENSWETCCNR
+-EMLSGTFGAKISHNPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTEITRTPLIKIHIRVPGSQ-SENHVVMYCVYYKE
+HKSIR-----------QNNTGCANLPQ---------------------HRLVDQVVD-ELYSKF---YHAIPKKP--GN
+M-GVGDSGGMEMVQEDVFQILVCL
+>t85
+LIVSEVRHVVRDG--VNIAVDEI-C------------LIANRVKSMSGQGNQVRNAMEMAA--RQNFVGM---RELDKA
+-YQ-CMDGQKAVNTEAGNN-SESAVWIFDICMCKLTHGMQD--------GDIGRVVCDHPKFEKLEEGAPNCSSIPMPY
+FLGIDMFHKQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSHRRVLNVLHQGDHEES-H---VSARC----MR---RIG
+F-HLVIINFWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPI------------------NDGFFDK-D-Q------AR
+PVIANAHIVPEH----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVEIDCNQGANHYVQISRMKMYGPTYSHMT
+EYAHGL----WKPFYQASDHKNDAQGVGER-PHQLPCVESQTCQYEVKHANVCKLVHA-ALYLIGLKTVVKPELGVWEG
+CRCRSQLSKLALSQLDE----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCIILFGGRKRQSHGLNYNRAADPT
+MICFYKKPIVVQGADIFGCARGKDPQEMKS------NNVISGSLGDDRLQH--MPAMPVTICVFSYMVKKAVPQ-SHQK
+RGYTWRAKE-DHLIPVSFCKGEL---DEEPDGAQQ-----------------RVVQNIVKLLYTKDV-SCNKVLSMLIW
+QIC--H-GDWEPQIPKACNAARKDLAVCAWKRELVPGL---NHNNEDLAKIMYFGPDGH-------DEGPMGRKIVNLH
+V-EMEVSHRE-SSVKDNMIRVVMLPFDNNSWDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VMHYSGGFHDKS
+S-ERSQHHF-IYNEV----KNDHKCVILASK-SNKGLDWAAGKD-MKGGAK-MMANGALFY-------EERNWIRQKNH
+FVIFV-VCDAVRILIVHYGCMVPYTFMAFACNPFFAELFMEHVFIRYQYVNNHDIKIMDTCFRVAVYTWENSWETCCNR
+-EMLSGTFGAKISHNPRLPEQVI-PPCDLTVSGLKGKH-NGWPYLTDITRTPLIKIHIRIPGSQ-SENHVVMYCVYYKE
+HKSIR-----------QNNTGCANLPQ---------------------HRLVDKVVD-ELYSKF---YHAIPKKP--GN
+M-GIGDSGGMEMVQEDLFQILVCI
+>t62
+LIVSEVRVMVRDG--IHIAVDEI-C------------LIANRVKCMSGQGNQARNAMEMAA--RQNFVGM---RELGKQ
+-YQ-CMDGQGAVNTEAGNN-SESAVWIFDIWMCRLTHGMQD--------GDIGRVECDHPKFAKLEEGAPNCSSLPMPY
+FLGIDMFHNQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSHRRVLNVLHQGDHEES-H---HSARC----MR---RIG
+Y-HRVIINYWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPI------------------ADGFFDK-D-Q------AR
+PVIANAHIVPEY----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVVIDCNHGANHYVQISRMKMHGPTYSHMT
+EYAHGL----WKPFYQASDHKNDAQGVGER-PHQLPCVEPQTCQYEVKHAKVCKLVHG-ALYLIGLQTVVKPKLGVWEG
+VQCRSQLSKLILSQLDD----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCIIMFDGRKRQSHGLQYNRAADPT
+TICFYKKPIVVQGADIFGCARGKDPQEMKA------NNVTSGSLGDDRLQQ--MPAMPVTICVFSYMVKKSVPQ-SHVK
+RGYTWRAKE-DHLIPVSFCKGEL---EEEPEGAQH-----------------RMVQNIVKLLYTKDV-SCNVVLSMLIW
+QIC--H-GDWEPQIPKACDAARKDLAVCAWKRELVPGL---NHNDENLAKIMYFGPDGH-------DEGPMGEKIVNLH
+V-EMEASHRE-SSVKDNMIRVIMLPFSNNSWDPWRHVILGLND-KIKLTRPNT---AHRLSILV---VMHYSGGFHDKS
+A-ERSQHHF-IYNEI----KNDHKCVILASK-ANKPLDWAAGKD-MKGGAK-MMANGALFY-------AERNWIRQKNH
+FVIFI-ICDAVRILIVHYGCMVGDTFMDFACNPFFAELFMEHVFIRYQYIPNHDIKIMDTCFRVAVYTWENSWETCCNR
+-EMLSGTFGARISHVPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPLIRIHIRVPGSE-SENHVVMYCVYYKE
+HKSIR-----------QNNTGCANLPQ---------------------HRLVDRVVD-ELYSKF---YHAIPKKP--GN
+M-DVGDSGGMEMVMEDVFQILVCV
+>t19
+LIVSEVRHMVRDG--INIAVDEI-C------------LIANRVKCVSGQGNQARNAMEMAA--RQNFVGM---RELGKQ
+-YQ-CMDGQGAVNTEAGNN-SESAVWIFDIWMCRLTHGMQD--------GDIGRVECDHPKFAKLEEGAPNCSSLPMPY
+FLGIDMFHKQVMGKGSKGLILPDTWNEASMAFPYPQVHSKSHRRVLNVLHQGDHEES-H---HSARC----MR---RIG
+YGHLVIINFWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPI------------------ADGFFDK-D-Q------AR
+PVIANAHIVPEY----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVVIDCNHGANHYVQISRMKMHGPTYSHMT
+EYAHGL----WKPFYQASDHKNDAQGVGER-THQLPCVEPQTCQYEVKHAKVCKLVHG-ALYLIGLQNVVKPKLGVWEG
+VQCRSQLSKLILSQLDD----KTLSK-NCSIY--LGNMTWLATSPLQ------IGCIILFDGRKRQSHGLQYNRAADPT
+TICFYKKPIVVQGADIFGCARGKDPQEMKA------NNVTSGSLGDDRLQQ--MPAMPVTICVFSYMVKKLVPQ-SHQK
+RGYTWRAKE-DHLIPVSFCKGEL---EEEPEGAKQ-----------------RMVQNIVKLLYTKDV-SCNVVLSMLIW
+QIC--H-GDWEPQIPKACDAARKDLAVCAWKRELVPGL---NHNDENLAKIMYFGPDGH-------DEGPMGEKIVNLH
+V-EMEASHRE-SSVKDNMIRVIMLPFSNNSWDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VMHYSGGFHDKS
+A-ERSQHHF-IYNEI----KNDHKCVILASK-ANKGLDWAAGKD-MKGGAK-MMVNGALFY-------AERNWIRQKNH
+FVIFV-ICDAVRILIVHYGCMVGDTFMDFACNPFFAELFMEHVFIRYQYIPNHDIKIMDTCFRVAVYTWENSWETCCNR
+-EMLSGTFGARISHVPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPLIRIHIRVPGSE-SENHVVMYCVYYKE
+HKSIR-----------QNNTGCANLPQ---------------------HRLVDKVVD-ELYSKF---YHAIPKKP--GN
+M-DVGDSGGMEMVMEDVFQILVCV
+>t77
+LIVSEVRHMVRDG--INIAVDEI-C------------LIANRVKSMSGQGNQARNAMEMAA--RQNFVGM---RELGKQ
+-YH-CMDGQGTVNTEAGNN-SESAVWIFDIWLCRLTHGMQD--------GDIGRVECDHPKFAKLEEGAPNCSSLPMPY
+FLGIDMFHRQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSHRRVLNVLHQGDHEES-H---HSARC----MR---RIG
+Y-VLVIINFWNVEMGRLIHCEDEAIIYSPLRIGGAGFHSKPI------------------ADGFFDK-D-Q------AR
+PVIANAHIVPEY----DQWSGAMPQWVSSVIKCGLANHDLE-NVSRLLRCVVIDVNQGANHYVQISRMKMHGPTYSHMT
+EYAHGL----WKPFYQASDHKNDAQGVGER-VHQLPCVEPQTCQYEVKHAKVCKHVHG-ALYLIGLQTVVKPKLGVWEG
+CQCRSQLSKLILSQLDD----KTLSK-NCNIY--LGNMTWLATFPLQ------IGCIILFDGRKRQSYGLQYNRAADPT
+TICFYKKPIVVQGADIFGCARGKDPQEMKA------NNVTSGSLGDDRLQQ--MPAMPVTICVFSYMVKKSVPQ-SHQK
+RGYTWRAKE-DHLIPVSFCKGEL---EEEPEGAQQ-----------------RIVQNIVKLLYTKDI-SCNVVLSMLIW
+QIC--H-GDWEPQLPKACDAARKDLAVCAWKRELVPGL---NHNDENLAKIMYFGPDGH-------DEGPMGEKIVNLH
+V-EMEASHRE-SSVKDNMIRVIMLPFGENSWDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VMHYSGGFHDNS
+A-ERSQHHF-IYNEV----KNDHKCVILASK-ANKGLDWAAGKD-MKGGAK-MMVNGALFY-------AERNWIRQKNH
+FVIFV-ICDAVRILIVHYGCMVGDTFMDFACNPFFAELFMEHVVIRYQYIPNHDIKIMDTCFRVAVYTWENSWETCCNR
+-EMLSGTFGARISHVPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPLIRIHIRVPGSE-SENHVVMYCVYYKE
+HKSIR-----------QNNTGCANLPQ---------------------HRLVDKVVD-ELYSKF---YHAIPKKP--GN
+M-DVGDSGGMEMVMEDVFQILVCA
+>t88
+LIVSECRLIIRDG--NHDAIDEM-CCVANDLNNEIERLVASMVKSFRGHDSQARNNSECMR--SAPFIGV---RELFKR
+-YHKCVEGAGCVHTVAGTP-SDSPVWMFDQFMCQLTHSMVD--------GDLGRVVQDNVIFAKLKEGAPHCISL--PH
+FLGIDMFHTQVFVGGH--LILPDPCYELSISVMYAGHASYNQKRCINNLDQGDQEDSNHRKEHKIRASVLLYR---QIG
+I-L-VIIKEANELMNRLNHKEPENGIIFPLR---DAQDPKQI------------------LNGLFDK-E-E------NR
+PMVQDADSVVGS----AQWAGQHRSWCSSDDKA-----------SQLPRNTHIVVEIGANVYEQFSRMKTNIPIYAHVT
+EYAVGV----ERPFYE-SEFKNEAQGWGES-GTSIPCVDSPDVQYEMKVAWVDKLMHT-ALYLMPLATVHKPEMGTVRG
+ERCRAIL-KLLMMQLD------TLSR-NQLPK--LCQGTWLDASPLQ------IGVQVMLVGKKGGSKK-EYELAADQV
+IIYFYQAPIIYVKADVFSGTVAKKAQAMR-------KSTGSQSIGDDGMQS--MPLMQNAVCVWSKMVRKVQPD-GQDK
+REQTWMAKD-DTLCPPSMKRGEK---TAEPTQWMG-----------------TVTVNKIKLLYCKDC-SCNEVMKILSW
+WLCNSV-GDWQTLMSQACITADPNPPVCVWKRELVPGL---NRSVENLAKIIYFCPDEH-------DERKMWGKIFALE
+W-EMDISHRH-SSVDDNHC-VEMLPFMCQRVDPWGHYVQILAD-RQDLARPVT---LQALSILP---CPHASGKEQDGA
+V-ERSQHYV-VYAEL----QVDHKCTIAAHKYQDKMKDWDTGKN-MDEGAK-MYVEIHLFY-------AENNIRRQNDH
+SVIFW-ISDAKKRLICGMSSMCLVTFMTLACNPLFAKLFMEVVPMRYDYLTNHDIKI------MEVYAPENSWETIKNV
+-EMVSGKEGAEINHTPQLPEQVI-PPCNLTVSNLKGMI-PPCPALTEITRTV--FIV--MYYAI-LRNKIMQYCFYYKE
+NRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGG---YHAAPKKE--EM
+V-GPGDNGGVEDIKEDMFQVLVCR
+>t37
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR
+-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAL--PY
+FMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIG
+L-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNGLFEK-E-E------NR
+PMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVT
+EYAVGV----ARPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKG
+ERCRTIL-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPV
+IIYFYQAPIIHHKADVFAGTVAKKSQAMRS------RSIGSQSVGDDGMQN--MPLMQNAVCVWSQMVRKVQPD-GQDK
+REQTWMAKD-DTLCPPCEEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAW
+WLCDSV-GDWQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALE
+W-EMDISHRH-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGA
+V-ERSQHYG-VYQEL----QNDHKSTIDANKNDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLRKQNEH
+SVTFV-ISDAQKRLICGVSSMVMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENSWETTKVV
+-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPVPALTEITRTP--FIV--MYVAI-LRNDIMQYCFYYKE
+NRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--EL
+M-SPGDNGGVEAIREDMFQVLVCK
+>t35
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR
+-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAL--PY
+FMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIG
+L-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNGLFEK-E-E------NR
+PMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTVIPIYARVT
+EYAVGV----PRPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPQMGTVKG
+ERCRTIL-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPV
+IIYFYQAPIIYHKADVFAGTVAKKSQAMRS------RSIGSQSVGDDGMQN--MPLMQNAVCVWSQMVRKVQPD-GQDK
+REQTWMAKD-DTLCPPCEEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAW
+WLCDSV-GDWQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALE
+W-EMDISHRH-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGA
+V-ERSQHYG-VYQEL----QNDHKSTIDANKNDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLRKQNEH
+SVTFV-ISDAQKRLICGVSSMAMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENSWETTKVV
+-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP--FIV--MYVAI-LRNDIMQYCFYYKE
+NRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--EL
+M-SPGDNGGVEAIREDMFQVLVCK
+>t48
+LIVSDMRLIIREG--SDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR
+-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAL--PY
+FMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIG
+L-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNGLFEK-E-E------NR
+PMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEVGANVYEQYSRMKTVIPIYARVT
+EYAVGV----PRPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKG
+ERCRTIL-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPV
+IIYFYQAPIIYHKADVFAGTVAKKSQAMRS------RSIGSQSVGDDGMQN--MPLMQNAVCVWSQMVRKVQPD-GQDK
+REQTWMAKD-DTLCPPCEEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAW
+WLCDSV-GDWQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALE
+W-EMDISHRH-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGA
+V-ERSQHYG-VYQEL----QNDHKSTIDANKNDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLIKQNEH
+SVTFV-ISDAQKRLICGVSSMVMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENSWETTKVV
+-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP--FIV--MYVAI-LRNDIMQYCFYYKE
+NRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--EL
+M-SPGDNGGVEAIREDMFQVLVCK
+>t55
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR
+-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAI--PY
+FMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIG
+L-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNGLFEK-E-E------NR
+PMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVT
+EYAVGV----ARPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLSTVHKPEMGTVKG
+ERCRTIL-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPV
+IIYFYQAPIIHHKADVFAGTVAKKSQAMRS------RSIGSQSVGDDGMQN--MPLMQNAVCVWSQMVRKVQPD-GQDK
+REQTWMAKD-DTLCPPCEEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAW
+WLCDSV-GDWQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALE
+W-EMDISHRH-SSVDDNQC-VELLPYNCQRMDPWGHYVQILAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGA
+V-ERSQHYG-VYQEL----QNDHKSTIDANKNDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLRKQNEH
+SVTFV-ISDAQKRLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENSWETTKVV
+-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP--FIV--MYVAI-LRNDIMQYCFYYKE
+NRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--EL
+M-SPGDNGGVEAIREDMFQVLVCK
+>t46
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR
+-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAL--PY
+FMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIG
+L-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNGLFEK-E-E------NR
+PMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVT
+EYAVGV----ARPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKG
+ERCRTIL-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVKVVLVGKKRGSKK-DYELAADPV
+IIYFYQAPIIHHKADVFAGTVAKKSQAMRS------RSIGSQSVGDDGMQN--MPLMQNAVCVWSQMVRKVQPD-GQDK
+REQTWMAKD-DALCPPCKEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAW
+WLCDSV-GDWQSLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALE
+W-EMDISHRH-SSVDDNQC-VELLPYVCQRMDPWGHYVQVLAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGA
+V-ERSQHYG-VYQEL----QNDHKSTIDANKNDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNIRKQNEH
+SVTFV-ISDAQKRLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPDNSWETTKVV
+-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP--FIM--MYVAM-LRNDIMQYCFYYKE
+NRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--EL
+M-APGDNGGVEAIREDMFQVLVCK
+>t67
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR
+-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN--------GDLGRVVMDNWTFTKLKEGAPHCIAL--PY
+FMGIDMFHIQVFLGGD--LILPDPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIG
+L-L-VIIKEANELMGRLNHKERKNGVIFPLR---GAQGPKQI------------------SNGLFEK-E-E------NR
+PMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVT
+EYAVGV----ARPFYD-AEFKNEAQRQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKG
+ERCRTIL-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPV
+IIYFYQAPIIHHKADVFAGTVAKKAQAMRS------RSIGSPSVGDDGMQN--MPLMQNAVCVWSQMVRKVQPD-GQDK
+REQTWVAKD-DTLCPPCKEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAW
+WLCDSV-GDWQTLMNDACSSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALE
+W-EMDISHRM-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLVLTRPVT---LHGLSILP---CPHASGKEQDGA
+E-ERSQHYG-VYQEL----QNDAKSTIDANKNPNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNIRKLNEH
+SVTFV-ISDAQKRLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENSWETTKVV
+-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPVPALTEITRTP--FIV--MYVAI-LRNDIMQYCFYYKE
+NRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--EL
+M-APGDNGGVEAIREDMFQVLVCK
+>t57
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR
+-YPKCMEGARCVHTVAGPP-SESPVWMFDKFMCQLTHSMVN--------GDLGRVVMDNWTFTKLKEGAPHCIAL--PY
+FMGIDMFHIQVFIGGD--LILPDPCYELSISVMYAGHASYNQKRCINGLDNGDRQDSDPQKEHKIRNSVLLYR---QIG
+L-L-VIIKEANEIMGRLNHKERKNGVIFPLR---GAQGPKQI------------------SNGLFEK-E-E------NR
+PMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVT
+EYAVGV----ARPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKG
+ERCRTIL-KLLMVQLDE----KTLSQ-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPV
+IIYFYQAPIIHHKADVFAGTVAKKAQAMRS------RSIGSPSVGDDGMQK--MPLMQNAVCVWSQMVRKVQPD-GQDK
+REQTWVAKD-DTLCPPCKDQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-SCNEVLKILAW
+WLCDSV-GDWQTLMNDACSSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALE
+W-EMDISHRV-SSVDDNQC-VELLPYLCQRMDPWGHYVQILAD-RLNLTRPVT---LQGLSILP---CPHASGKEQDGA
+V-ERSQHYG-VYQEL----QNDAKSTIDANKNPNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNIRKQNEH
+SVTFV-ISDAQKRLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPNHDIKI------IEVYAPENSWETTKVV
+-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPVPALTEITRTP--FIV--MYVAI-LRNDIMQYCFYYKE
+NRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--EL
+M-APGDNGGVEAIREDMFQVLVCK
+>t56
+LIVSEWRLFIRDG--HDDAIDEM-CCEANELNNDIEKLVASMVKGFRGHDSQARNNAECII--AAPFIGV---RELFKR
+-YIKCVEGAGCVYTVA-AP-SESPVWMFDKFMCHLTHSMVV--------GDLGRVLRDNTTFAKLKEGAPVCISL--PY
+FLGMDMFHQQVFMGGN--LILPDPCYELSISVMYAGHASYNQKRCLNNLDQGDREDSSHRKEHKIRRSVLLYQ---QIG
+C-L-VITRERNELMGRLNHKEPRDGVIFPHR---GAQGPKQL------------------ANGLFEK-E-E------NR
+PMVQDAGSVPER----AQWPGQQRAWCSSDDKA-----------SKLPRNTKMVAEIGANVYEQASRMKTNIPIYAHVT
+EYALGV----DRPFYD-SEFKNEAQGQGES-GTSIPCVDSPDVQYELKHAWVDKLMHT-ALYLMPLPTVHKPKMGTVKG
+ERCRAML-KLNMMQLDE----KTLSQ-NQIIK--LCQRTWLDASPLQ------IGVNCVLPGKKGGSNK-DYELAADPV
+IIYFYQAPIIHHKADVFSGTVAKKAQAMRQ------QSTGSQSVGDDGTQV--MPLMQNLVCVWSKMVRKCMID-GQEK
+REQTWMAKD-DKLCPPSQEQGEK---AAEPTQWED-----------------ICTANVIKLLYCKDC-SCNEVLRVLSW
+WLCDSV-GDWRTLMSDACALANPNPPVCVWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERKMWGKIFCLE
+W-EMDISHRH-SSVDDNVC-VEMLPFVCQKMDPWGHYVQILAD-RLDLTRPVT---LQGLGILV---CPHASGKEQDGA
+M-ERSQHYV-VYAEL----QNDHKNTINANKVPRKMLDWDTGKN-MDKGAKGMYHEIVLFF-------AENNVKKQVEH
+SVIFI-IADAQKRLICGVSSMCLQTFMNLACNPFFAKLFMEVIPMRYDYQTNHDIKI------KEVYAPENSWETIKNV
+-EMVSGKAGKQINHEPQLPEQVI-PPCSLTVSNLKGMM-PPCPAMTEITRTV--III--MYYAI-LRNEIMQYCFYYKE
+NRSVR-----------INNTGQAELPK---------------------HHVQNVFID-ELYPGH---YHAAPKKN--EN
+V-GPGDNGGVEGIKEDMFQVLVCQ
+>t13
+GIVSECRMIIRDE--HDDAIDEM-C------------LVASMVKKLSGCENQARNNHECAI--PPPFHGV---REMFKR
+VYE-CMEGIGCVNTVAGNP-SESSAWMFDKVMYQLTHSMVW--------GDLRRVVHDNVTFSKLKEGAPHCISH--PY
+FLGIDMFHIQVYSKGF--LTLPDPRYEISMSVMYSQHHSFSMKRCLNGLDHGDREESPHQIEHKMRKSVLIYN---PIG
+Y-L-VIIKDANSMMGRLNHHESRAVVAFPLR---GAEGPKQV------------------MEGLFDK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVT
+EYAVGI----VKPFYD-NEWKQEAQGQGEA-GACIPCVDSKDVQYELKHAYVKKLMHT-SLYLMHIETCHKPVMGTVKG
+NRCRAIL-KLSMIQLDQ----KTLSQ-NQRAK--LCQRTWLDTSPLQ------MGMTLVLVGKKVGSKK-DYEVAADPV
+IMYFYDAPMIMRPTDVFEGTNNKKAQAMRS------RSTASQSIGDDDMLN--MPLTQNAMCVESEMVRKCQPD-GQDK
+RGYTWVAKD-DTLCPQSRDQGEK---HHEPHHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLSSDACMHAEQNPPVCVWQRELVPQL---NRNIEDLARIIYFGPDEH-------DEGKMMNKIFALE
+W-EMDMSHRV-SSVDDNYI-IEMLPFVCDRVGPWGHYAQVLAD-QLHLTRPHT---LRDLYILAC--CPVASGKEQDGN
+K-ERSQHYT-IYAEI----QNDHKNPISANNQPNKMLDWDTGKT-MDRGAA-MCGEIKLFY-------AEPNVWNQNDH
+SVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFSKLFMEVVCMRYNYTSNHSIKI------FEVYADENSWENVRNF
+-EMVSGRAGAHINHIPQLPEQAY-PPCKLTVSNLKGVA-ASCPAITEITRTA--VIV--MYGSI-LRNDVMQYVFYYRE
+NRSVR-----------QNNTGNAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKD--RF
+C-NPGDNGGMETYQEDMFQVLVCV
+>t5
+GIVSECRMIIRDE--HDDAIDEM-C------------LVASMVKKLSGCENQARNNHECAI--PPPFHGV---REMFKR
+VYE-CMEGIGCVNTVAGNP-SESSAWMFDKVMYQLTHSMVW--------GDLRRVVHDNVTFSKLKEGAPHCISH--PY
+FLGIDMFHIQVYSKGF--LTLPDPRYEISMSVMYSQHHSFSMKRCLNGLDHGDREESPHQIEHKMRKSVLIYS---PIG
+Y-L-VIIKDANSMMGRLNHHESRAIVAFPLR---GAEGPKQV------------------MEGLFDK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVT
+EYAVGI----VKPFYD-NEWKQEAQGQGEA-GACIPCVDSKDVQYELKHAYVKKLMHT-SLYLMHIETCHKPVMGTVKG
+NRCRAIL-KLSMIQLDQ----KTLSQ-NQRAK--LCQRTWLDTSPLQ------MGMTLVLVGKKVGSKK-DYEVAADPV
+IMYFYDAPMIMRPTDVFEGTNNKKAQAMRS------RSTASQSIGDDDMLN--MPLTQNAMCVESEMVRKCQPD-GQDK
+RGYTWVAKD-DTLCPQSRDQGEK---HHEPHHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLSSDACMHAEQNPPVCVWQRELVPQL---NRNIEDLARIIYFGPDEH-------DEGKMMNKIFALE
+W-EMDMSHRV-SSVDDNYI-IEMLPFVCDRVGPWGHYAQVLAD-QLHLTRPHT---LRDLYILAC--CPVASGKEQDGN
+K-ERSQHYT-IYAEI----QNDHKNPISANNQPNKMLDWDTGKT-MDRGAA-MCGEIKLFY-------AEPNVWNQNDH
+SVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFSKLFMEVVCMRYNYTSNHSIKI------FEVYADENSWENVRNF
+-EMVSGRAGAHINHIPQLPEQAY-PPCVLTVSNLKGVA-ASCPAITEITRTA--VIV--MYGSI-LRNDVMQYVFYYRE
+NRSVR-----------QNNTGNAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKD--RF
+C-NPGDNGGMDTYQEDMFQVLVCV
+>t38
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR
+-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISQ--PF
+FLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHHIDHKMRKSVLIYN---PIG
+Y-L-VIIKNANSLMGRLNHHESRLIVTFPLR---GAEGPKQV------------------MEGLFLK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVT
+EYAVGI----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTIKG
+NRCRAIL-KLTMIQLDQ----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLVGKKVGSKK-DYEIAADPV
+IMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDDDMLN--MPLTQNAMCVESEMVRKSQPD-GQDK
+RGYTWVAKE-DDLCPQSGDQGEK---YAEPQHIRN-----------------QFSENVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALE
+W-EMDMSHRM-SSVDDNYI-IEMLPFVCDRVGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGA
+Q-ERSQCYT-IYAEL----QNDHKSLISANHVPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDH
+SVMFI-ISDAQNKLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------FEVYADENSWENIRNF
+-EMVSGRAGAYINHIPQLPEQAV-PPCHLTVSNLKGVA-ASCPAITEITRTA--VIV--MYVSI-LRNDVMQYVFYYRE
+NRIVR-----------QNNTGVAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKE--RF
+C-NVGDNGGMETIQEDMFQVLVCI
+>t33
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR
+-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PF
+FLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIG
+Y-L-VIIKNANSLMGRLNHYESRAIVTFPLR---GAEGPKQV------------------MEGLFLK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SHLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVT
+EYAVGI----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHN-SLYLMHIDTCHKPAMGTVKG
+NRCRAIL-KLTMIQLDQ----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLVGKKVGSKK-DYEIAADPV
+IMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDDDMLN--MPLTQNAMCVESEMVRKCQPD-GQDK
+RGYTWVAKE-DTLCPQSGDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLASDACVSAEPNTPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALE
+W-EMDMSHRM-SSVDDNYI-IEMLPFVCDRVGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGA
+K-ERSQCYT-IYAEL----QNDHKSLISANHVPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDH
+SVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------FEVYADENSWENIRNF
+-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAITEITRTA--VIV--MYVSI-LRNDVMQYVFYYRE
+NRIVR-----------QNNTGVAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKE--RF
+C-NPGDNGGMETIQEDMFQVLVCV
+>t100
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR
+-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PF
+FLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIG
+Y-L-VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEGLFLK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVT
+EYAVGI----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKG
+NRCRAIL-KLTMIQLDQ----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLVGKKVGSKK-DYEIAADPV
+IMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDDDMLN--MPLTQNAMCVESEMVRKCQPD-GQDK
+RGYTWVAKE-DTLCPQSEDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALE
+W-EMDMSHRM-SSVDDNYI-IEMLPFVCDRVGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGA
+Q-ERSQCYT-IYAEL----QNDHKSLISANHVPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDH
+SVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------FEVYADENSWENIRNF
+-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAITEITRTA--VIV--MYVSI-LRNDVMQYVFYYRE
+NRIVR-----------QNNTGVAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKE--RF
+C-NPGDNGGMETIQEDMFQVLVCV
+>t34
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR
+-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PF
+FLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIG
+Y-L-VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEGLFLK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVT
+EYAVGI----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKG
+NRCRAIL-KLTMIQLDV----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLMGKKVGSKK-DYEIAADPV
+IMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDDDMLN--MPLTQNAMCVESEMVRKCQPD-GQDK
+RGYTWVAKE-DTLCPQSGDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALE
+W-EMDMSHRM-SSVDDNYI-IEMLPFVCDRIGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGA
+Q-ERSQCYT-IYAEL----QNDHKSLISANHVPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDH
+SVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------LEVYADENSWENIRNF
+-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAMTEITRTA--VIV--MYVSI-LRNDVMRYVFYYRE
+NRIAR-----------QNNTGVAELPK---------------------HHMQDIFID-ELYLGP---YHASPKKQ--RF
+C-NPGENGGMETIREDMFQVLVCV
+>t84
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCDDQARNNHECAI--SHPFHGV---REMFKR
+-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PF
+FLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIG
+Y-L-VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEGLFLK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVT
+EYAVGI----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKG
+NRCRAIL-KLTMIQLDV----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLMGKKVGSKK-DYEIAADPV
+IMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDDDMLN--MPLTQNAMCVESEMVRKCQPD-GQDK
+RGYTWVAKE-DTLCPQSGDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLASDACVSAEHNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALE
+W-EMDMSHRM-SSVDDNYI-IEMLPFVCDRIGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGA
+K-ERSQCYT-IYAEL----QNDHKSLIAANHVPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDH
+SVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------LEVYADENSWENIRNF
+-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAMTEITRTA--VIV--MYVSI-LRNDVMRYVFYYRE
+NRIAR-----------QNNTGVAELPK---------------------HHMQDIFID-ELYLGP---YHASPKKE--RF
+C-NPGENGGMETIREDMFQVLVCV
+>t92
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR
+-YE-CMEGIGCVNTVAGNP-SESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PF
+FLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQKRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIG
+Y-L-VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEGLFLK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVT
+EYAVGI----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKG
+NRCRAIL-KLTMIQLDV----KTLSQ-NQRAR--LCQRTWLDTSPLQ------MGMTIVLMGKKVGSKK-DYEIAADPV
+IMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDDDMLN--MPLTQNAMCVESEMVRKCQPD-GQDK
+RGYTWVAKE-DTLCPQSGDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALE
+W-EMDMSHRM-SSVDDNYI-IEMLPFVCDRIGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGA
+Q-ERSQCYT-IYAEL----QNDHKSLISANHVPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDH
+SVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSNHSIKI------LEVYADENSWENIRNF
+-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAMTEITRTA--VIV--MYVSI-LRNDVMRYVFYYRE
+NRIAR-----------QNNTGVAELPK---------------------HHMQDIFID-ELYLGP---YHASPKKE--RF
+C-NPGENGGMETIREDMFQVLVCV
+>t3
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEQQARNNRECAT--SIPFLGV---RELWKR
+-YE-CMEGIGCVNTVAGKP-SQSSVWMFDRFMYKLTHSMVW--------GDLGRVYWDNLTFQKLKEGAPHCIAV--PN
+YLNIDMFHIQVFYKGP--LTLPDPHYELSMSVMYAQHHSFSQKRCLNALDHGDREESPHQIEHKMRKSVLLYN---PIG
+Y-L-VIIKNANSMMGRLNHHESCAIVMFPLR---GAEGPKQI------------------IEGLFDK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SRLPRNDPVVHEVGANVYQQISRMKTSIPIYAHVT
+EYAVGI----IKPFYD-NEWKQEAQGQGEA-GASIPCVNSPDVQYELKHAHIKKLMHT-SLYLMHLGTCHKPVMGTVKG
+DRCRAIL-KLSMIQLDQ----KTLSQ-NVRAR--LCQRTWLDTSPLQ------MGMVAVLLGKKLGSKK-DYEIAADPV
+IKYFYQAPIIMRRTDVFEGTDDQKAQAMRV------RSTASQSIGDDDMLI--MPLVQNAMCVKSEMVRKCQPD-GPDK
+RGYTWMAKD-DTLCPVSAGQGEK---YAEPHQIKN-----------------KFSVNVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWVTLASDACLSAEPQPPVCVWQRELVPQL---NRNVEDLARVIYFGPDEH-------DEGKMMPKIFKLA
+W-EMDMSHRA-SSVDDNYV-IEMLPFVCHRVGPWGHYAQVQAD-QQNLTRPHT---LADLFILS---CPVASGKEQDGA
+T-ERSQYYV-VYAEL----QNDHKSPISANKHPDKMLDWDTGKS-MDRGAA-MCREIKLFY-------AEPNVWKQNDH
+SVVFI-ISDAVNRLICANSIMCGLTFMAMACNPHFAKLFMEVVCMRYDYFSNHSIKI------FEVYAEDDSWENICNF
+-EMMSGRTGAQINHIPQLPEQVC-PPCHLTVSNLKGCC-ASVPAITEITRTV--VIC--MYVSI-LCNVVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGQ---YHASPKKK--KI
+C-GPGDNGGMETIEEDMFQVLVCV
+>t22
+GIVSECRVIIRDQ--SDDAIDER-Y------------LVASVVKRLSGCENQARNNRECAI--SIPFLGV---RELWKR
+-YE-CMEGIGCVNTVAGTP-SESSVWMFDRFMYKLTHSMVW--------GDLGRVYVDNQTFSKLKEGAPHCISA--PY
+YLNIDMFHIQVFYKGS--LTLPDPRYELSMSVMYAQHHSFSQKRCLNALDYGDREESPHQIEHKMRKSVLLYY---TIG
+W-L-VIIKNADSMMGRLNHHESCAMVMFPLR---GAEGPKQI------------------MEGLFDK-E-E------AR
+PMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPTNDPIVPEVGANVYQQVSRMKTSIPIYAHVT
+EYAVGI----VKPFYD-NEWKQEAQGQGEA-GASIPCVNSPDVQYELKHAHIKKLMHT-SLYLMHLKTCHKPVMGTVKG
+DRCRAIL-KLKMIQLDQ----KTLSQ-NQAAR--LCKRTWLDTSPLQ------MGMNVVLIGQKLGSKH-DYEIAADPV
+IMYFYQAPIIMRRTDVFEGTDDQKAQAMRL------RSTASRSIGDDDMLI--MPLVQNAMCVNPEMVRKCQPD-GQDK
+RGYTWMAKN-DTLCPVSAGQGEC---YAEPHQTCN-----------------KFRVNVIKLLYCKDC-SCNKVLKILKW
+QLCESV-DDWQTLASDACILAKPQPPVCVWQRELVPQL---NRNVEDLARVIYFGPDEH-------DEGKMMSKIFNLE
+W-EMDMSHRT-SSVDDNYV-IDMLPFICHRVGPWGHYAQVLAD-QINLTRPHT---LRDLFILA---CPVASGKEQDGA
+T-ERSQHYV-VYAEL----QNDHKSPISANKHPNKLLDWDTGKT-MDRGAA-MCHEIKLFH-------AEPNVWRQNDH
+SVMFI-ISDASNRLICANSIMCGLTFMAMACNPHFAKLFMEVVCMRYEYFSNHSIKI------FEVYAEENSWENVCNF
+-EMMSGRAGAQINHIPQLPEQVC-PPCVLTVSNLKGCC-ASCPANTEITRTV--VIC--MYVSI-LRNVVMQYVFYYKE
+NRSVR-----------QNNTGAAELPK---------------------HHMQDIFID-ELYPGL---YHASPKKK--KV
+C-GPGDNGGMETIQEDMFQVLVCV
+>t64
+GIVSECRMIIRDE--TDDAIDEV-C------------LVASMVKKLSGCENQTRNNRECAIT-SPPFIGV---RELFKR
+-YG-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW--------GDLRRVFPDNATFSKLKEGAPHVISH--PY
+FLGIDMFHDQVVYRGP--LTLPDPRYELSMSVMYAQHHSFSQKRCLNALDHGDTQESPHGIEHNMRNSVLLYN---PIG
+F-L-VIIKNINSMMGRLNHHESRAVVGFPLR---GAENPKQI------------------MEGHFDK-E-E------AR
+PIVQDAASVPGK----AQWVGRVRAWCSSDVKA-----------SKLPRNDPIVPEVGANVYQQLSRMKTNIPIYAHVT
+EYAVGI----VKPFYD-NEWKQEAQGVGEA-GASIPCVDSPDVQYELKHAEVRKLMHD-SLYLMHLETCHKPIMGTVKG
+DRCRAIL-KLPMIQLDQ----KTLSH-NQPRR--LCQRTWLDASPLQ------VGMNIMLMGKKAPSKK-DYEIAADPV
+IMYFYQAPIIMRRTDVFEGTHNKKAQAMRV------RSTASQSIGDDDMLK--MPLVQNAMCVSSEMVRKCQPD-GQDK
+RGYTWMAKD-DTLCPQSANQGEK---YAEPHVIGD-----------------KVSVNVIKLLYCKDC-SCNQVLKILVW
+QLCESV-DDWQTLTSDPCMSAQVNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMSKIFALE
+W-EMDMSHRV-SSVDDNFV-IEMLPFVCHRIGPWGHYAQMLAD-QIVLTRPHT---LRDLFILS---CPVASGGEQDGN
+T-ERSQHYI-VYAEL----QNDHKSPISANKHLNKMLDWDTGKT-MDREAT-MCREMKLFY-------AETNLWKQNDH
+SVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVVCVHYDYGANHDIKI------FEVYAAENSWENARNF
+-EMMSGRAGAEINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNDVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIVID-ELYPGP---YHATPKKH--RF
+C-GTGDNGGMQAIQEDMFQVLVCV
+>t18
+GIVSECRMIIRDE--TDDAIDEV-C------------LVASMVKKLSGCENQTRNNRECAIT-SPPFIGV---RELFKR
+-YG-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW--------GDLRRVFPDNATFSKLKEGAPHVISH--PY
+FLGIDMFHEQVVYRGP--LTLPDPRYELSMSVMYAQHHSFSQKRCLNALDHGDTQESPHGIEHNMRNSVLLYN---PIG
+F-L-VIIKNINSMMGRLNHHESRAVVGFPLR---GAENPKQI------------------MEGHFDK-E-E------AR
+PIVQDAASVPGK----AQWVGRVRAWCSSDVKA-----------SKLPRNDPIVPEVGANVYQQLSRMKTNIPIYAHVT
+EYAVGI----VKPFYD-NEWKQEAQGVGEA-GASIPCVDSPDVQYELKHAEVRKLMHD-SLYLMHLETCHKPIMGTVKG
+DRCRAIL-KLPMIQLDQ----KTLSH-NQPRR--LCQRTWLDASPLQ------VGMNIMLKGKKAPSKK-DYEIAADPV
+IMYFYQAPIIMRRTDVFEGTHNKKAQAMRV------RSTASQSIGDDDMLK--MPLVQNAMCVSSEMVRKCQPD-GQDK
+RGYTWMAKD-DTLCPQSANQGEK---YAEPHVIGD-----------------KVSVNVIKLLYCKDC-SCNQVLKILIW
+QLCESV-DDWQTLTSDPCMSAQVNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMFKIFALE
+W-EMDMSHRV-SSVDDNFV-IEMLPFVCHRIGPWGHYAQMLAD-QIVLTRPHT---LRDLFILS---CPVASGGEQDGN
+T-ERSQHYI-VYAEL----QNDHKSPISANKHLNKMLDWDTGKT-MDREAT-MCREMKLFY-------AETNLWKQNDH
+SVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVVCVHYDYGANHDIKI------FEVYAAENSWENARNF
+-EMMSGRAGAEINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNDVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGP---YHATPKKH--RF
+C-GTGDNGGMQAIQEDMFQVLVCV
+>t68
+GIVSECRMIIRDE--TDDAIDEV-C------------LVASMVKKLSGCENQTRNNRECAI--SPPFIGV---RELFKR
+-YG-CVEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW--------GDLRRVFPDNAHFSKLKEGAPHVISH--PY
+FLGIDMFHDQVVYRGP--LTLPDPRYELSMSVMYAQHHSFSQKRCLNALDHGDTQESPHGIEHNMRNSVLLYN---PIG
+F-L-VIIKNINSMMGRLNHYESRAVVGFPLR---GAENPKQI------------------MEGHFDK-E-E------AR
+PIVQDAASVPEK----AQWVGRVRAWCSSDVKA-----------SKLPRNDPIVPEVGANVYQQISRMKTNIPIYAHVT
+EYAVGI----VKPFYD-NEWKQEAQGVGEA-GASIPCVDSPDVQYELKHAEVRKLMHD-SLYLMHLETCHKPIMGTVKG
+DRCRAIL-KLPMIQLDQ----KTLSH-NQPRR--LCQRTWLDASPLQ------VGMNIMLMGKKAPSKK-NYEIAADPV
+IMYFYQAPIIMRRTDVFEGTHNKKAQAMRV------RSTASQSIGDDDMLK--MPLRQNAMCVSSEMVRKCQPD-GQDK
+RGYTWMAKD-DTLCPQSANQGEK---YAEPVVIGD-----------------KVSVNVIKLLYCKDC-SCNQVLKILVW
+QLCESV-DDWQTLTSDPCMSAQVNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMSKIFALE
+W-EMDMSHRV-SSVDDNFV-IEMLPFVCHRIGPWGHYAQMLAD-QIVLTRPHT---LRDLFILS---CPVASGGEQDGN
+T-ERSQHYI-VYAEL----QNDHKSPISANKHLNKMLDWDTGKT-MDREAT-MCREMKLFY-------AETNLWKQNDH
+SVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVVCVHYDYGANHDIKI------FEVYAVENSWENARNF
+-EMMSGRAGAEINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNDVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGP---DHATPKKH--RF
+C-GTGDNGGMQTIQEDMFQVLVCV
+>t28
+GIVSECRMIIRDE--ADDAIDEM-C------------LVASMVKKLSGCENQARNNRECAI--SPPFIGV---RELFKR
+-YH-CMEGIGCVNTVAGMP-SESSVWMFDQFMYKLTHSMIW--------GDLGRVFPDNATFSKLKEGAPHVISH--PY
+FLGIDMFHAQVFYRGS--LTLPDPRYELSMSVMYSQHHSFSQKRCLNPLDHGDRQESSHGIEHNMRSSVLLYN---PIG
+F-L-VIIDNINPMMGRLNHHESRAIVTFPLR---GAEHPKQI------------------VEGHFDK-E-E------AR
+PIVKDAASVPGK----AQWVGRIRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQDSRMKTNIPIYAHVT
+EYACGI----VKPFYE-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLMHLETCHKPIMGTVKG
+DRCRAIL-KLSMIQLDE----KTLSQ-NQRPG--LCQRTWLDANPLQ------MGMNTMLVGKKTPSKK-DYEIAADPV
+IMYFYQAPIIMRRTDVFEGTNNKKSQAMRV------QSTSSQSIGDDDMLN--MPLVQNAMCVSSEMVRKCQPD-GQNK
+RGCTWMAKN-DTLCPQSGNQGEK---FAEPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKMLKILVW
+QLCESV-DDWQTLASDPCVSAEPNSPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMSKIFALE
+W-EMDMSHRI-SSVDYNYV-IEMLPFVYHRVGPWGHYAQMLSD-QIVLTRPHT---LRDLFILA---CRVASGGEVDGN
+T-ERSQHYI-VYAEL----QNDHKSPISANKVLNKMLDWDTGKT-MDREAA-MCREIKLFY-------AETNVWKQNDH
+SVMFI-ISDAQNRLICGNSIMCGITFMAMACNPHFAKLFMEVACMRYDYFANPDIKI------FEVYAAENSWENVRNF
+-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPDITEITRTV--VIC--MYVSI-LRNDVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKN--RY
+C-GPGDNGGMQVIEEDMFQVLVYV
+>t82
+GIVSECRMIIRDE--ADDAIDEM-C------------LVASMVKKLSGCENQARNNRECAI--SPPFIGL---RELFKR
+-YV-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW--------GDLGRVFPDNCTFSKLKEGAPHVISH--PY
+FLGIDMFHGQVVYRGS--LTLPDPRYELSMSVMYSQHHSFSQKRCLNPLDHGDRQESPHGIEHNMRSSVLLYN---PIG
+F-L-VIIDNINPMMGRLNHHESRAIVTFPLR---GAEHPKQI------------------MEGHFDK-E-E------AR
+PIVQDAASVPGE----AQWVGHIRAWCSSDIKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIYAHTT
+EYACGI----VKPFYE-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHANVKKLMHD-SLYLMHLETCHKPIMGTVKG
+DRCRAIL-KLNMIQLDQ----KTLSQ-NQRPG--LCQRTWLDASPLQ------MGMHIMLVGKKTPSKK-DYEIAADPV
+IMYFYQAPIIMQRTDVFEGTNNKKSQAMRV------HSTSSQSIGDDDMLN--MPLVQNAMCVSSEMVRKCQPD-GQNK
+RGYTWMAKH-DTLCPQSGNQGEK---YAEPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLASDPCMSAEPNPPVCVWQRELVPQL---NRNVEDLARTIYFGPDEH-------DEGKMMSKIYALE
+W-EMDMSHRV-SSVDYNYV-IEMLPFVYHRVGPWGHYAQMLAD-QIVLTRPHT---LRDLFILA---CPVASGGEQDGN
+A-ERSQHYI-VYAEL----VNDHKSPISANKVLNKMLDWDTGKT-MDREAA-MCRDIKLFY-------AETNVWKQNDH
+SVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVACMRYDYFANPDIKI------FEVYADENSWENVRNF
+-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPDITEITRTV--VIC--MYISI-LRNDVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKN--RF
+C-GPGDNGGMQVIEEDMFQVLVYV
+>t41
+GIVSECRMIIRDE--ADDAIDEM-C------------LVASMVKKLSGCENQARNNRECAI--SPPFIGL---RELFKR
+-YV-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW--------GDLGRVFPDNCTFSKLKEGAPHVISH--PY
+FLGIDMFHGQVVYRGS--LTLPDPRYELSMSVMYSQHHSFSQKRCLNPLDHGDRQESPHGIEHNMRSSVLLYN---PIG
+F-L-VIIDNINPMMGRLNHHESRAIVTFPLR---GAEHPKQI------------------MEGHFDK-E-E------AR
+PIVQDAASVPGE----AQWVGHIRAWCSSDIKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIYAHTT
+EYACGI----VKPFYE-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHANVKKLMHD-SLYLMHLETCHKPIMGTVKG
+DRCRAIL-KLNMIQLDQ----KTLSQ-NQRPG--LCQRTWLDASPLQ------MGMHIMLVGKKTPSKK-DYEIAADPV
+IMYFYQAPIIMQRTDVFEGTNNKKSQAMRV------HSTSSQSIGDDDMLN--MPLVQNAMCVSSEMVRKCQPD-GQNK
+RGYTWMAKH-DTLCPQSGNQGEK---YAEPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLASDPCMSAEPNPPVCVWQRELVPQL---NRNVEDLARTIYFGPDEH-------DEGKMMSKIYALE
+W-EMDMSHRV-SSVDYNYV-IEMLPFVYHRVGPWGHYAQMLAD-QIVLTRPHT---LRDLFILA---CPVASGGEQDGN
+A-ERSQHYI-VYAEL----VNDHKSPISANKVLNKMLDWDTGKT-MDREAA-MCRDIKLFY-------AETNVWKQNDH
+SVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVACMRYDYFANPDIKI------FEVYADENSWENVRNF
+-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPDITEITRTV--VIC--MYISI-LRNDVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKN--RF
+C-GPGDNGGMQVIEEDMFQVLVYV
+>t71
+GIVSECRMIIRDQ--SDDAIDEMVV------------LVASMVKEMSGCENQARNNSECAI--SPQFIGV---RELFKR
+-YR-CMEGIGCVNTVAGAP-SESSVWMFDRFMYKLTHSMVW--------GDLARVFHDNGTFAKLKEGAPHVISV--PY
+FLGIDMFHGQVFLRGS--LTLPDPRYELSMSVMYAQHHSFSQKRCLNHLDHGDRQESPHGIEHNMRKSVLLYN---PQG
+Y-L-VIIKNVNSMMGRLNHHESRAVVTFPLR---GADNPRQI------------------MEGHFDK-E-E------AR
+PVVQDAPGVPGK----AQWVGKVRAWCSSDVKA-----------SQLPRNDTIVPEVGANVYQQVSRVKTHIPIYAHVT
+EYAVGI----VKPFYN-NEWKQEAQGQGEA-GASIPCVDSPDDQYELKHAEVKKLMHD-SLYLPHLETCHKPIMGTVKG
+GRCRASL-KLKMIQLDQ----KTLSQ-NQQRR--LCQRTWLDSSPLQ------MGMKIMLQGKKTPSKK-DYEIAADPA
+IMHFYRAPIIMRRTDVFEGTNNKKAQAMRI------RSTASQSIGDDDMLN--MPLHQNAMCVSSEMVRKCQPD-GQDK
+RGYTWMAKD-DTLCPQSPNQGEK---YAEPHQIRN-----------------KISVNVIKLLYCKDC-SCNQVLKILVW
+QLCESV-DDWQTLTSDPCVPAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMRKIFALE
+W-EMDMSHRD-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTRPHT---LRDLFILA---CPVASGGEQDGN
+T-ERSQHYI-VYAEL----QNDHKSPISANKHMNKMLDWDTGKT-MDFEAA-MCREIKLFY-------AETNVWKINDH
+SVMFI-VSDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEGVCMRYDYSANHDIKI------FEVYADENSWENVRNF
+-EMMSGRAGAQINH-PQLPEQVCNPPCHLTVSNLKGVC-ASCPAITEITRTV--VIV--MWISI-LRNDVMQYVVYYKE
+NRSVR-----------QNNTGKAELPR---------------------HPMQEIFID-ELYPGH---YHATPKKN--RF
+C-GPGDNGGMQSMQEDVFQVLVCV
+>t94
+GIVSECRMIIRDQ--SDDAIDEMVC------------LVASMVKELSGCENQARNNRECAI--SPPFTGV---RELFKR
+-YR-CMEGIGCVNTVAGIP-SESSVWMFDRFMYRLTHSMVW--------GDLGRVFQDNATFSKLKEGAPHVISH--PY
+FLGIDMFHGQVFYRGS--LTLPDPRYELSMSVMYAQHHSMSQKRCLNTLDHGDRQESPHGIEHNMRKSVLLYD---PIG
+Y-L-VIIKNVNSMMGRLNHHESRAKVTFPLR---GADNPRQI------------------MEGHFDK-E-E------AR
+PVVQDAPGVPEQ----AQWVGKMRAWCSSDVKA-----------SQLPRNDTIVPEVGANVYQQVSRVKTNIPIYAHVT
+EYAVGI----VKPFYN-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLPHLETCHKPIMGTVKG
+GRCRASL-KLNMIQLDQ----KTLSQ-NQQRR--LCQRTWLDASPLQ------MGMKIMLQGKKIPSKK-DYEIAADPA
+IMYFYQATIIMRRTDVFEGTNNKKAQAMRM------RSTASQSIGDDDMLN--MPLHQNAMCVSSEMVRKCQPD-GQDK
+RGYTWMAKD-DTLYPQSANQGEK---YAEPHQIRN-----------------KISVNVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLTSDPCVPAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMRKIFALE
+W-EMDMSHRD-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-KLVLTRPHT---LRDLFILA---CYVASGGEQDGN
+T-ERSQHYI-VYAEL----QNDHKSPILANKVVNKMLDWDMGKT-MDFEAA-MCREIKLFY-------AETNVWKQNNH
+SVMFI-VSDAHNRLICGNSIMCALTFMAMACNPHFAKLFMEAVCMRYDYSANHDIKI------VEVYADENSWENVRNF
+-EMMSGRAGAQINH-PQLPEQVCNPPCHLTVSNLKGVC-ASCPAITEITRTV--VIV--MWISI-LRNDVMQYVFYYKE
+NRSVR-----------QNNTGKAELPR---------------------HPVQDIFID-ELYPGH---YHATPKKV--RF
+C-GPGDNGGMQAIQEDVFQVLVCV
+>t99
+GIVSEVRMIIRDE--SDDAIDEM-C------------LVASMVKALSGCENQARNNRECAI--SPPFIGV---RELFKR
+-YG-CMEGIGCVNTVAGIP-SESSIWMFDRFMYKLTHSMVW--------GDLGQVFPDVSTFSKLKEGAPHVISQ--PY
+FLGIDMFHDQVFYRGS--LTLPDPRYELSMSVMYAQHHSFSQKRCLNALDHGDRQESPHGIEHNMRKSVLLDS---PIG
+Y-L-VIIKNINSMMGRLNHHESRAVFAFPLR---GAENPKQI------------------MEGHFDK-EKE------AR
+PVVQDAPGVPGK----AQWVGRIRAWCSSDVKA-----------SELPRNDAIVPEVGANVYQQVSRMKTNIPIYAHAT
+EYAVGI----VKPFYD-NEWKQEAQGQGET-GASIPCVDSPDVQYEMKHAEVKKLMHD-SLYLMHIETCHKPIMGTVKG
+DRCRATL-KLKMIQLDQ----KTLSQ-NQKRR--LCQRTWLDASPLQ------MGMKMMLQGKKTPSKK-DYEIAADPV
+IMYFYQSPIIMRRTDVFEGTNNKKAQAMRV------RSTASQSIGDDEMLN--MPLVQNAMCVPSEMVRKCQPD-GQDK
+RGYTWMAKD-DPLCPQSANVGEK---YAEPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKVLKILVW
+QLCDSVQDDWQPLTSDPCVNAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMNKIFALE
+W-EMDMSHRDSSSVDDNYI-IEMLPFVCHRVGPWGHYAQQLAD-RLVLTRPHT---LRDIFILA---CPVASGGEQDGN
+T-ERSQHYI-VYAEL----QDDHKSPISANKHMRKMLDWDTGKT-MDREAA-VCREIKLFY-------AETNCWKQNDH
+SVMFI-VSDAQNRLICGSSIMCRLTFMAMAVNPHFAKLFMEDVCMRYDYSPNHDIKI------FEVYADENSWENVRNF
+-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNDVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGR---YHATPKKN--RY
+C-GPGDNGGMQPIQEDMFQVLVCV
+>t40
+GIVSECRMIIRDE--SDDAIDEV-C------------LVASMVKALSGCENQARNNRECAI--SPPFIGV---RELFKR
+-YG-CMEGIGCVNTVAGIP-SESSVWMFDRFMYKLTHSMVW--------GDLGRVYPDNPTFSKLKEGAPHVISH--PY
+FLGIDMFHDQVFYRGS--LTLPDPRYELSMSVMYAQHHSFSQKRCLNALDHGDRQESPHGIEHNMRKSVLLDS---SIG
+Y-I-VIIKNLNSMMGRLNHHESRAVVTFPLR---GAEDPKQI------------------MEGHFDK-E-E------AR
+PVVQDAPGVPGK----AQWVGRVRAWCSSEIKT-----------SELPRNDAIVVEVGANVYQQISRMKTDIPIYAHAT
+EYAVGI----VKPVYD-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLMHLETCHKPIMGTVKG
+DRCRATL-KLKMIQLDQ----KTLSQ-NQKKR--LCQCTWLDACPLQ------MGMKIMLQGKKTPSKK-DYEIAADPV
+IMYFYQSPIIMRRTDVFEGTNNKKAQAMRI------RSTASQSIGDDEMLN--MPQVQNAMCVSSEMVRKCQPD-GQDK
+RGYTWMAKD-DTLCPQSANVGEK---YAEPHQIRN-----------------KVSTNVIKLLYCKDC-SCNKVLKILVW
+QLCDSV-DDWQTLTSDPCVSAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMRKIFALE
+W-EMDMSHRN-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTRPHT---LRNIFILA---CPVASGGEQDEN
+T-ERSQHYI-VYAEL----QNDHKSPIHANKVMNKMLDWDTGKT-MDREAA-MCREIKLFV-------AETNVWKQNDH
+SVMFIVISDAQNRLICGSSIMCRLTFMAMAVNPHFAKLFMEESCVRYDYSANHDIKI------FEVYANENSWENVRNF
+-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASVPAITEITRTV--VIC--MYISI-LRNNVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YQATPKKD--KF
+C-GPGDNGGMQTIQEDMFQVLVCV
+>t90
+GIVSECRMIIRDE--SDDAIDEV-C------------LVASMVKALSGCENQARNNRECAI--SPPFIGV---RELFKR
+-YG-CMEGIGCVNTVAGIP-SESSVWMFDRFMYKLTHSMVW--------GDLGRVYPDNPTFSKLKEGAPHVISH--PY
+FLGIDMFHDQVFYRGS--LTLPDPRYELSMSVMYAQHHSFSQKRCLNALDHGDRQESPHGIEHNMRKSVLLDS---PIG
+Y-I-VIIKNVNSMMGRLNHHESRAVVTFPLR---GAEDPKQI------------------MEGHFDK-E-E------AR
+PVVQDAPGVPGK----AQWVGRVRAWCSSEIKT-----------SELPRNDAIVPEVGANVYQQISRMKTDIPIYAHAT
+EYAVGI----VKPVYD-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLMHLETCHKPIMGTVKG
+DRCRATL-KLKMIQLDQ----KTLSQ-NQKKR--LCQCTWLDACPLQ------LGMKIMLQGKKTPSKK-DYEIAADPV
+IMYFYQSPIIMRRTDVFEGTNNKKAQAMRV------RSTASQSIGDDEMLN--MPLVQNAMCVSSEMVRKCQPD-GQDK
+RGYTWMAKD-DTLCPQSANQGEK---YAEPHQIRN-----------------KVSTNVIKLLYCKDC-SCNKVLKILVW
+QLCDSV-DDWQTLTSDPCVSAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMRKIFALE
+W-EMDMSHRN-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTRPHT---LRNIFILA---CPVASGGEQDEN
+T-ERSQHYI-VYAEL----QNDHKSPINANKVMNKMLDWDTGKT-MDREAA-MCREIKLFV-------AETNVWKQNDH
+SVMFIVISDAQNRLICGSSIMCGLTFMAMAVNPHFAKLFMEESCVRYDYSRNHDIKI------FEVYANENSWENVRNF
+-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASVPAITEITRTV--VIC--MYISI-LRNNVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKD--KF
+C-GPGDNGGMQTIQEDMFQVLVCV
+>t4
+GIVSECRMIIRDE--PDDAIDEV-C------------LVASMVKELSGCENQARNNRECAI--SPPFIGV---RELFKR
+-YG-CMEGIGCVNTVAGMP-SESSVWMFDRFMYKLTHSMVW--------GDLGRVFPDNATFSKLKEGAPHVISV--PY
+FLGIDMFHDQVFYRGS--LTLPDPRYEMSMSVMYAQHHSFSQKRCLNALDYGDRQESPHGIEHNMRKNVLLDN---PIG
+H-L-VIIKNENSMMGRLNHHESRAVVTFPLR---GAEDPKQK------------------MEGSFDK-E-E------AR
+PVVQDAPGVPGR----AQWVGRVRPWCSSDVKA-----------SELPRNDAIWPEVGANVYQQISRMKTNIPIYPHVT
+EYAVGI----VKPFYL-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLWHLETCVKPIMGTVKG
+DRCRATL-KLKMIVLDP----KTLSQ-NQKRR--LCQRTWLDASPLQ------VGMKIMLQGKKTPSKK-DYEIAADPV
+IMYFYQSPIIMRHTDVFEGTNNKKAQAMRL------RSTASQSIGDDEMLN--MPLIQNAMCVQSEMVRKCQPD-GQDK
+RGYTWMAKD-DTLCPQLHNQAEK---YAEPHQIRN-----------------KVSVNVIKLLYCKDC-SCNKVLKILVW
+QLCESV-DDWQTLTSDPCISAEPNPPVCVWQRELVPQL---NRNIEDLARIIYFGPDEH-------DEGKMMGKIFALE
+W-EHDMSHRD-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTRPHT---LRDIFILA---CPVASGGEQDAV
+T-ERSQHYI-VYAEL----QNDHKSPISASKHMNKMLDWDTGKT-MDREAA-MCREIKLFY-------AETNVWKQNDH
+SVMFI-ISDAQNRLICGSSIMCGLTFMATACNPHFAKLFMEEVCMRYDYAANHDIKI------SEVYAEENSWENVRNF
+-EMMSGRAGAQINH-PQLPEQVV-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNVVMQYVFYYKE
+NRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKN--RC
+C-GPGDNGGMQTVQEDMFQVLVCV
+>t36
+MIWSEVRKMVRER--REQAIDNK-C------------LIAARVKMMSGYVLQVRNALEDAL--YVFFTGTKGTRELVKY
+-YM-CMEGHGCVNTMAKKS-SQSGIWKFNAFMC-LMHLMEG--------GDL--------------------CSY--PS
+FLGMCMFHAMVQSKGD--LVLPDSPNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSEHIKEKHMRI----YA---NIG
+G-H-IIIREWNDVMGRLNHIEPGAEVIFPLRK--RGQHSKPV------------------IDGFFAK-D-E------DR
+PGIQNAVSVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYRINRKVGANAYDQDSRMKAAAPVYPHIM
+EYAHGM----FNPFYGLSEPKNNAQGNGEN-PMNKPCVESEDCQYEKKHASMDKLMHQ-SLYLMHINIMSKPAMGEWVG
+NRCRNELTALRIIQLDVGVSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVMSVEKKEASPK-EFEVAADPT
+VIYFYRNLIIQKITDVLSAVRMESPQEMRT------QDVNSSSLGDNNGQA--MNIVPYWVCVASGVVRKTHKD-SVDK
+RGQTWTAKS-DFLCPLAVDQGEP---GAEQKPAVGEENPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKW
+QLCDSH-GDWQSLYADSCPIA-VNAAVCGWKRELVPGL---NHSCEHLAKSVYFEPDGE-------GEGKVMLKIFGLD
+WCEVERSHEH-SSVDDNYN-VNMLPFQNSRKDPVGHYVQDLED-ARRLIRPGT---ARSLTILF-YGCQYYSGEFQDCE
+I-ERSQLYN-VYCEH----KQDHKSAIIANKQEQKGMDWNTGKE-MEQGPK-IILHGSLFF-------AEPNIVRQPGV
+SHIFI-GNDARRVLICGKSMMPGHRFMREACVPFFHKLFMAVNQMRYDYMMNYDIKIYETHWRMGVYALDNSWETLNVS
+-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIKIY--MWGTINFKNRVMQYCNYYKE
+NRSVR-----------INNTGLAELPK---------------------YHHQNILID-ELYSNV---YPAAPKKH--QY
+M-GVGDVGGYEVICENLFQILVVE
+>t87
+MIWSEVRKMVRER--REQAIDNK-C------------LIAARVKMMSGYMLQVRNALEDAL--YVFFTGNKGTRELVKY
+-YM-CMEGHGCVNTMAKKS-SQSGIWKFNAFMC-LMHLMEG--------GDL--------------------CSY--PS
+FLGMCMFHAMVQSKGD--LVLPDSPNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHVKEKHMRI----YA---NIG
+G-H-IIIREWNDVMGRLNHIEPGAEVIFPLRK--RGQHSKPV------------------IDGFFAK-D-E------DR
+PGIQNAMSVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYRINRKVGANAYDQDSRMKAAAPVYPHIM
+EYAHGM----FNPFYGLSEPKNNAQGNGEN-PMNKPCVESEDCQYEKKHASMDKLMHQ-SLYLMHINVMSKPAMGEWVG
+NRCRNDLTALRIIQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCLVMSVEKKEASGK-EFEVAADPT
+VIYFYRNLIIAKITDVLSAVRMESPQEMRE------QDVNSSSLGDNNGQA--MNIVPYWVCVGSGVVRKTHKD-SVDK
+RGQTWTAKS-DFLCPLAMDQGEI---GAEQKPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKW
+QLCDSH-GDWQSLYADSCPIA-INAAVCGWKRELVPGL---NHSCEHLAKSVYFEPDGE-------GEGKVMLKIFGLD
+WCEVERSHEH-SSVDDNYN-VNMLPFQNSRKDPVGHYVQDLED-ARRLIRPGT---ARSLTILF-YGCQYYSGEFQDCE
+I-ERSQLYN-VYCEH----KQDHKSAIIANKQEQKGMDWNTGKE-MEQGPK-VILHGTLFF-------AESNIVRQPGV
+SHIFI-GNDARRVLICGLSMMPGHRFMREACVPFFHKLFMAVNQMRYDYMVNYDIKIYETHWRMGVYALDNSWETLNVS
+-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIKIY--MWGTICFKNRVMQYCNYYKE
+NRSVR-----------INNTGLAELPK---------------------YHHQNILID-ELYSNV---YPAAPKKH--QY
+M-GVGDVGGYEMICENLFQILVVE
+>t89
+MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDAL--YNFFTGHKGTRELVKY
+-YM-CMEGEGVVNTMAKKS-SQSGIWKFNAFMC-LMRLMQG--------GDL--------------------CSY--PS
+FLGMCMFYAMVQSKGD--LVLPDSCNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHTKEKHMRI----YA---NIG
+G-H-IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDGFFAK-D-E------ER
+PGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYKINRKVGANAYDQVSRMKAAAPVYPHIM
+EYAHGM----FNPFYGLSEPKNNAQGNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHINIMSKPAMGEWVG
+VRCRNELTALRIVQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEASPK-EFEVAADPT
+VIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDNNGQA--MNIVPYWVCVASGVVRKMHKD-SVEK
+RGQTWEAKS-DFLCPLAVDQGEP---AAEQRPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKW
+QLCDSH-GDWQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEGKMMLKIFGLE
+WCEVERSHEH-SSIDDNYT-VNMLEFPNSRKDPVGHYVQNLED-AIRLIRPGT---ARSLTILL-YGCQYYSGEFQDCE
+V-ERSQCYN-VYCEL----KQDHKSAIIANKQEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGV
+SHIFT-ENDARRMLICGNSMMPRHRFMREACVPFFHKLFMAVNQMRYDYVTNYDIKIYETHWRVGVYAIDNSWETLNVS
+-EMTSGRMGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIEIY--MWGTINFKNQVMQYCNYYKE
+NRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYNNI---YPAAPKKH--KF
+L-GVGDVGGYEIICENLFQILVVE
+>t39
+MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDAL--YNFFTGHKGTRELVKY
+-YM-CMEGEGVVNTMAKKS-SQSGIWKFNAFMC-LMRLMQG--------GDL--------------------CSY--PS
+FLGMCMFYAMVQSKGD--LVLPDSCNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHTKEKHMRI----YA---NIG
+G-H-IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDGFFAK-D-E------ER
+PGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYKINRKVGANAYDQVSRMKAAAPVYPHIM
+EYAHGM----FNPFYGLSEPKNNAQGNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHINIMSKPAMGEWVG
+VRCRNELTALRIVQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEASPK-EFEVAADPT
+VIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDNNGQA--MNIVPYWVCVASGVVRKMHKD-SVEK
+RGQTWEAKS-DFLCPLAVDQGEP---AAEQRPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKW
+QLCDSH-GDWQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEGKMMLKIFGLE
+WCEVERSHEH-SSIDDNYT-VNMLEFPNSRKDPVGHYVQNLED-AIRLIRPGT---ARSLTILL-YGCQYYSGEFQDCE
+V-ERSQCYN-VYCEL----KQDHKSAIIANKQEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGV
+SHIFT-ENDARRMLICGNSMMPRHRFMREACVPFFHKLFMAVNQMRYDYVTNYDIKIYETHWRVGVYAIDNSWETLNVS
+-EMTSGRMGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIEIY--MWGTINFKNQVMQYCNYYKE
+NRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYNNI---YPAAPKKH--KF
+L-GVGDVGGYEIICENLFQILVVE
+>t8
+MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDAL--YNFFTGHKGTRELVKY
+-YM-CMEGEGVVNTMAKKS-SQSGIWKFNAFMC-LMRLMQG--------GDL--------------------CSY--PS
+FLGMCMFYAMVQSKGD--LVLPDSCNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHTKEKHMRI----YA---NIG
+G-H-IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDGFFAK-D-E------ER
+PGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYKINRKVGANAYDQVSRMKAAAPVYPHIM
+EYAHGM----FNPFYGLSEPKNNAQGNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHVNIMSKPAMGEWVG
+VRCRNELTALRIVQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEASPK-EFEVAADPT
+VIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDNNGQA--MNIVPYWVCVASGVVRKMHKD-SVEK
+RGQTWEAKS-DFLCPLAVDQGEP---AAEQKPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKW
+QLCDSH-GDWQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEGKMMLKIFGLE
+WCEVERSHEH-SSIDDNYT-VNMLPFPNSRKDPVGHYVQDLED-AIRLIRPGT---ARSLTILL-YGCQYYSGEFQDCE
+V-ERSQCYN-VYCEL----KQDHKSAIIANKQEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGV
+SHIFT-ENDARRMLICGNSMMPRHRFMREACVPFFHKLFMAANQMRYDYVTNYDIKIYETHWRVGVYAIDNSWETLNVS
+-EMTSGRMGAKINHLPRLPEHVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIEIY--MWGTINFKNQVMQYCNYYKE
+NRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYNDI---YPAAPKKH--KF
+L-GVGDVGGYEIICENLFQILVVE
+>t6
+MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDAL--YNFFTGHKGTRELVKY
+-YM-CMEGEGVVNTMAKKS-SQSGIWKFNAFMC-LMRLMQG--------GDL--------------------CSH--PS
+FLGMCMFYAMVQSKGD--LVLPDSCNEDSVSFMYIQHHSFHEKRCLNPLNVGDREDSDHTKEKHMRI----YA---NIG
+G-H-IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDGFFAK-D-E------ER
+PGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYKVVRKVGANAYDQVSRMKAAAPVYPHIM
+EYAHGM----FNPFYGLSEPKNNAQGNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHINIMSKPAMGEWVG
+VRCRNELTALRIVQLDVGHSGKTLGQ-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEASPK-EFEVAADPT
+VIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDNNGQA--MNIVPYWVCVASGVVRKMHKD-SVEK
+RGQTWEAKS-DFLCPLAVDQGEP---AAEQKPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKW
+QLCDSH-GDWQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEGKMMLKIFGLE
+WCEVERSHER-SSIDDNYT-VNMLPFPNSRKDPVGHYVQDLED-AIRLIRPGT---ARSLTILL-YGCQYYSGEFQDCE
+V-ERSQCYN-IYCEL----KQDHKSAIIANKQEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGV
+SHIFI-ENDARRMLICGNSMMPRHRFMREACVPFFHKLFMAVNQMRYDYMTNYDIKIYETHWRVGVYAIDNSWETLNVS
+-EMTSGRMGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIEIY--MWGTINFKNQVMQYCNYYKE
+NRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYNNI---YPAAPKKH--KF
+L-GVGDVGGYEIICENLFQILVVE
+>t58
+MIWSEYRHMVREG--RDQAIDNK-C------------LIAARVKVMSGYVLQVRNAPEDAL--YNFFTGHKGTRELVKY
+-YM-CMEGEGCVNTMAKKS-SQSGIWKFNAFMC-LMHLMQG--------GDL--------------------CSH--PS
+FLGMCMFHAMVKSKGN--LVLPDSCNEDSVSFMYIQHHSFHEKRCLNHLNVGDREDSEHIKEKHMRV----YA---SIG
+G-H-IIIREWNDVMGRLNHIEPGAEVTFPLRR--RGQASKPV------------------IDGFFAK-D-E------DR
+PGIQNAMSVPCG----DQWVGSVRGWCSSQHRYGLAIHILVHQQSRLHKTYNIDRKNGANAYEQDSRMKAGAPVYPHIM
+EYAHGM----FNPFYGMSEPKNNAQGNGEN-PMNVPCVESDDCQYEKKHASMDKQMHQ-SLYLMHMNIMSKPAMGEWVG
+NRCRNELTALHVVQLDVGFSGKTLGQ-NIGISELLNDRTWLATSPLE------IGCGVMAVEKKEASPK-EFEVAADPT
+VIYFYRNLIIQHITDVLSAVRMDSPQEMRV------QDVNSPSLGDNNGQA--MNIVPYWVCVVSGVVRKTHKD-SVEK
+RGQTWTAKS-DFLCPIAVNQGEP---GAEQKPAVGA-NPIVKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKW
+QLCDSH-GDWQSLFADSCPTA-VNAAVCAWKRELVPGL---NHSCEHLAKSVYFEPDGE-------DEGKMMLKIFGLD
+WCEVERSHEH-SSVDDNYN-VNMLPFPNSRQDPVGHYVQDLED-LLRLIRPGT---ARSLTVLF-YGCQYYSGQFQDCE
+I-ERSQLYN-VYCEL----KQDHKSAIMANKQEQKGMDWNTGKE-MEQGPK-IILHGVLFF-------AEPNVVRQPGV
+SHIFV-GNDARRMLICGLSMMPGHRFMKEACVPFFHKLFMAVRRMRYDYMSNYDIKIYETHWRPGVYALDNSWETLNVS
+-EMTSGRIGAKINHLPRLPETVI-PPCVLTVSGLKDTM-AGMKHGTEITKTPDIKIH--MWGTINFKNKVMQYCTYYKE
+NRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYSNI---YPATPKKH--QY
+M-GVGDVGGYEVICENLFQILVVE
+>t54
+MIWSEYRHMVREG--RDQAIDNK-C------------LIAARVKVMSGYVLQVRNAPEDAL--YNFFTGHKGTRELVKY
+-YM-CMEGEGCVHTMAKKS-SQSGIWKFNAFMC-LMHLMQG--------GDL--------------------CSH--PS
+FLGMCMFHAMVQSKGN--LVLPDSCNEDSVSFMYIQHHSFHEKRCLNHLNVGDREDSEHIKEKHMRI----YA---SIG
+G-H-IIIREWNEVMGRLNHIEVGAEVTFPLRR--RGQASKPV------------------IDGFFAK-D-E------DR
+PGIQNAMSVPCG----EQWVGSVRGWCSSQHRYGLAIHILVHQQSRLHKTYNIDRKNGANAYDQDSRMKAGAPVYPHIM
+EYAHGM----FVPFYGMSEPKNNAQGNGEN-PMNVPCVESDDCQYEKKHASMDKQMHQ-SLYLMHMNIMSKPAMGEWVG
+NRCRNELTALHIVQLDVGFSGKTLGQ-NIGISELLNDRTWLATSPLE------IGCGVMAVEKKEASPK-EFEVAADPT
+VIYFYRNLIIQHITDVLSAVRMDSPQEMRV------QDVNSPSLGDNNGQA--MNIVPYWVCVVSGVVRKTHKD-SVEK
+RGQTWTAKS-DFLCPIAVNQGEP---GAEQKPAVGA-DPIVKPWQFVIMNTTTFAKNIFRLLYVKDV-SCNGVLPLLKW
+QLCDSH-GDWQSLFADSCPIA-VNAAVCAWKRELVPGL---NHSCEHLAKSVYFEPDGE-------DEGKMMLKIFGLD
+WCEVERSHEH-SSVDDNYN-VNMLPFPNSRKDPVGHYVQDLED-LLRLIRPGT---ARSLTVLF-YGCQYYSGEFQDCE
+I-ERSQLYN-VYCEL----KQDHKSAIMANKQEQKGMDWNTGKE-MEQGPK-IILHGVLFF-------AEPNVVRQPGV
+SHIFV-GNDARRMLICGLSMMPGHRFMKEACVPFFHKLFMAVRRMRYDYMTNYDIKIYETHWRPGVYALDNSWETLNVS
+-EMTSGRIGAKINHLPRLPETVI-PPCVLTVSGLKDTM-AGMKHGTEITKTPDIKIH--MWGTINFKNKVMQYCTYYKE
+NRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYSNI---YPATPKKH--QY
+M-GVGDVGGYEVICENLFQILVVE
+>t65
+MIWSEYRQMVREG--NDQSIDNK-C------------LIADRVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELIKF
+-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQS--------GDL--------------------CNS--PS
+FLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDSQDSQHLREKQLRI----YG---RIG
+K-V-VIIKVWNAVMGRLNHHEPPAEVMFPLRK--GGQDSKPF------------------IDGFF------------DR
+PGIANAMSVKCG----DQWVGSIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQTSRMKAAAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECQYEHKHAAMEKLMHH-SLYLMRVNTMSKPVMGDWVG
+NRCRAELTALQTVQLDVGSSGKTLGQ-NIVTSKKLGDRTWLAASPLQ------IGCGVMVQEKKIASPQ-EVEVAAD--
+-IYFYRNMVVQRLTDVVAAVRMQSPQEMRTPVLVCIQKVDSVSLGDDDPQM--MNIVPYWVCVCSGVVKKAEPD-SVDK
+RGKTWVAKS-DFLCPAAVNEGEH---GAEQRP-FGTQNPVCKPWRFVIMNTQTFAKNIIRLLYIKDI-SCNQVLQLLDW
+QLCDSH-GDWQSLMADSCPNA-VNIAVCCWKRELMPGL---NHSCEHLAKSVYFKPDGE-------DEGQMTMKIFNLD
+WCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDYKSAIIANQQEHKGMEWDTGKE-MQQGPK-VVVHLALFYAPSNVLAAEPNIIGQPQV
+SHVFV-GNDARRMLIVGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYMWNYDIKIYETHFRMGVYAVDNSWETLVYC
+-EMTSGRIGAKINHLPRLPEQVT-PPCILTVSGLKRTV-AGAPDETEITKSPVIHIV--MWADIMFKNCVMQYCTYYKE
+NRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDV---YPAAQKKY--QV
+M-GVGDIGGYELICEDLFQILVCQ
+>t29
+MIWSEYRQMVREG--NDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELIKF
+-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQS--------GDL--------------------CNC--PS
+FLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLFVGDSQDSQHQREKQLRI----YG---RIG
+K-V-VIIKVWNAAMGRLNHVEPPAEVMFPLRR--GGSDSKPF------------------LDGFF------------DR
+PGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILIHGPSKLHRTYAINKKMGANVYQQTSRMKAAAPLYPHIM
+EYAHGM----VKPFYGQSEPKNEAQGNGEN-PMNVPSVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMPKPVMGDWDG
+NRCRAELTALQTVQLDVGSSGKTLGQ-NIVTSKKLGDRTWLAASPLQ------IGCGVMVQEKKIASPQ-EVEVAAD--
+-IYFYRNMVVQRLTDVVAAVRMQSPQEMRTPVLVCIQKVDSVSLGDDDPQM--MNIVPYWVCVCSGVVKKAEPD-SVDK
+RGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGTHNPVCKPWRFVIMHTQTFSKNIIRLLYIKDI-SCNQVLQLLDW
+QLCDSH-GDWQSLMADSCPNA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMSQKIFNLD
+WCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELEDSALRLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDYKSAIIANQQDHKGMEWDTGKE-MQQGPK-VVVHLALFYMPSNVLAAEPNIIGQPQV
+SHWFV-GNDARRMLIVGVSMMPAYKFMREACVPFFRKLFMADNQVRYDYMWNYDIKIYETHFRMGVYAVDNSWETLVYC
+-EMTSGRIGAKINHLPRLPEQVT-PPCILTVSGLKRTV-AGAPDETEITKSPVIHIV--MWADIMFKNCVMQYCTYYKE
+NRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDL---YPAAPKKY--QE
+M-GVGDIGGYELIVEDLFQILVCE
+>t98
+MIWSEHRQMVREG--NDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTKELVKF
+-YF-CMEGCGCVNTMAKKS-SQSAPWKFNRFMC-LMHLMQS--------GDL--------------------CNS--PP
+FLGMCMFHPQVQMKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDSQDSQHLREKQLRI----YG---RIG
+K-V-VIIKVWNAVMGRLNHHEPPAEVMFPLRR--GGSDSKPF------------------IDGFF------------DR
+PGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHNPSRLHRTYAINKKMGANVYQQSSRMKAAAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVG
+NRCRAELTALQTVQLDVGSSEKTLGQ-NIVTSKRLGDRTWLAASPLQ------IGCGVMVQEKKIASPQ-EVEVAAD--
+-IYFYRNMVVQRHTDVVAAVRMQSPQEMRNPVLVCIQKVDSASLGDDDPQM--MKIVPYWVCVCSGVVKKAEPD-SVDK
+RGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGTQNPVCKPWRFVIMNTQTFSKNIIRLLYIKDI-SCNQVLQLLDW
+QLCDSH-GDWQSLMADSCPPA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMTMKIFNLD
+WCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+MFERSQLYR-VYCEI----KKDYKSAIIANQQEHKGMEWDTGKE-MQQGPK-IVVHLGLFYMPSNVLAAEPNIIGQPQV
+SHVFV-ANDARRMLIVGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYVWNYDIKIYETHFRMGVYAVDNSWETLVYC
+-EMTSGRIGAKINHLPRLPEQVT-PPCDLTVSGLKRTV-AGPPDETEITKSPVIHIV--MWADIVFKNCVMQYCTYYKE
+NRSVR-----------ANNTGGAELPK---------------------YHQQNLLTD-ELYSDI---YPAAPKKY--QV
+M-GVGDIGGYELIVEDLFQILVCE
+>t83
+MIWSEYRQMVREG--NDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTKELIKF
+-YF-CMEGCGTVNTMAKDS-SQSAPWKFNRFMC-LMHLMQS--------GDL--------------------CNS--PS
+FLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDSQDSQHLREKQLRI----YG---RIG
+K-V-VIIKVWNAVMGRLNHHEPPAEVMFPLRR--GGSCSKPF------------------VDGFF------------DR
+PGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILIHNPSRLHRTYAINKKMGANVYQQTSRMKAAAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVG
+NRCRAELTALQTVQLDLGSSGKTLGQ-NIVTSKKLGDRTWLAASPLQ------IGCGIMVQEKKIASPQ-EVEVAAD--
+-IYFYRNMVVQRHTDVVAAVRMQSPQEMRNPVLVCIQKVDSISLGDDDPQM--MNIVPYWVCVCSGVVKKAEPD-SVDK
+RGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGTQNPVCRPWRFVIMNMQTFSKNIIRLLYIKDI-SCNQVLQLLDW
+QLCDSH-GDWQSLMADSCPPA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMTMKIFNLD
+WCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSD
+MFERSQLYR-VYCEI----KKDYKSAIIANQQEHKGMEWDTGKE-MQQGPQ-IEVHLALFYMPSNVLPAEPNIIGQPQV
+SHVFV-GNDARRMLIVGVSLMPAYKFMREACVPFFRKLFMAENQVRYDYMWNYDIKIYETHFRMGVYAVDNSWETLVYC
+-EMTSGRIGAKINHLPRLPEQVT-PPCILTVSGLKRTI-AGAPDETEITKSPVIHIV--MWADIMFKNCVMQYCTYYKE
+NRSVR-----------ANNTGGAELPK---------------------YHQQNLLTD-ELYSDI---YPAAPKKY--QV
+M-GVGDIGGYELIVEDLFQILVCE
+>t95
+MIWSEYRQMVREG--TDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELIKF
+-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQL--------GDL--------------------CNP--PS
+FLGMCMFHPQVRSKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYTGDSQDSQHLREKQLRI----YG---RIG
+R-V-VILQVWNAVMGRLNHHEPPAEVMFPLRK--GGSNSKPV------------------YDGFF------------DR
+PAIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHGPSKLHRTYAINRKVGANVYQQTSRMKAAAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECVYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVG
+HRCRAELTELQTVQLDVGSSGKTLGQ-NIVTSKKLGDRTWLAASPLQ------IGCGVMVQEKKIASPQ-QVEVAAD--
+-IYFYRNMVVQRLTDVVAAVRMQSPQEMRCRKLVCIQKVDSPSLGDDDPQM--MNIVPYWVCVCSGVVKKAEPD-SVDK
+RGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGGQNPACKPWHFVIMNRQTFAKNMIRLLYIKDI-SCNEVLQLLDW
+QLCDSH-GDWQSLIADSCPNA-SNIAVCCWKRELMPGL---NFSCEHLAKTVYFKPDGE-------DEGQMIMKIFNLD
+WCEVEKSHEK-SSVDDNYD-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALIILF-YGCQYYSGKFQDSE
+LFERSQLYR-MYCEI----KKDHKSAIIANQQEHKGMEWDTGKE-MQQGPK-VVLHHALFYAPSNVLAAEPNIIGQPQV
+SHVFV-GNDARRMLITGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYVWNYDIKIYETHYRMGVYAVDNSWETLVYC
+-EMTSGRIGAKVNHLPRLPEQVT-PPWVLTVSGLKRTV-AGAPDETEITKSPIIHII--MWEEIMFKNCVMQYCTYYKE
+NRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QV
+M-GVGDIGGYELICEDLFQILVCE
+>t20
+MIWSEYRQMVREG--TDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELIKF
+-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQL--------GDL--------------------CNP--PS
+FLGMCMFHPQVRSKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDSQDSQHLREKQLRI----YG---RIG
+R-V-VILQVWNAVMGRLNHHEPPAEVMFPLRK--GGSNSKAV------------------YDGFF------------DR
+PGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHGPSKLHRTYAINRKVGANVYQQMSRMKAAAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECVYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVG
+HRCRAELTELQTVQLDVGSSGKTLGQ-NIVTSKKLGDRTWLAAPPLQ------IGCDVMVQEKKIASPQ-QVEVAAD--
+-IYFYRNMVVQRLTDVVAAVRMQSPQEMRTPKLVCIQKVDSPSLGDDDPQC--MNIVPYWVCVCSGVVKKAEPD-SVDK
+RGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGGQNPACQPWHFVIMNTQTFAKNMIRLLYIKDI-SCNQVLQLLDW
+QLCDSH-GDWQSLIADSCPNA-VNIAVCCWKRELMPGL---NFSCEHLAKTVYFKPDGE-------DEGQMIMKIFNLD
+WCEVEKSHEK-SSVDDNYD-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALIILF-YGCQYYSGKFQDSE
+LFERSQLYR-MYCEI----KKDHKSAIIANQQEHKGMEWDTGKE-MQQGPK-VVLHHALFYAPSNVLAAEPNIIGQPQV
+SHVFV-GDDARRMLITGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYVWNYDIKIYETHYRMGVYAVDNSWETLVYC
+-EMTSGRIGAKINHLPRLPEQVT-PPWVLTVSGLKRTV-AGAPDETEITKSPIIHII--MWEDIMFKNCVMQYCTYYKE
+NRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QV
+M-GVGDIGGYELICEDLFQILVCE
+>t69
+MIWSDYRQMVREG--GDDSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGHKGTRELVKY
+-YH-CMEGCGCVNTMAKSS-SQSAPWKFNRFMC-LMHLMQE--------GDL--------------------CNS--PG
+FLGMCMFHPQVQRKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRM----YG---EIG
+K-V-VIIKVVNAVMGRLNHVEPSAEVMFPLRK--GGSDSKPF------------------IDGFF------------DR
+PGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQISRMKALAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQGNGEN-PMNVPCVESGECQYENKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVG
+NRCRAELTALKTGQLDVGSSGKTLGQ-NIMTSKKLGDRTWLAANPLQ------IGRGVMVWEKKVASPQ-EVEVAAD--
+-IYFYRNMVIECLTDVVRAVRMQSPQEMRAPVLVCIQKVDSPSLGDDVPQM--MNIVPYWVCVCSGVVKKAQPD-SVDK
+RGKTWVAKS-DFLCPPAMNEGEH---GAEQRPVFGTQNPVCKPWRFVIMNTETFAKNIIRLLYVKDV-SCNQVLQLLDW
+QLCDSH-GDWQSLVADSCPNA-VNIAVCCWKRELMPGL---NHSCQHLAKTVYFKPDGE-------DEGQMIVKIFNLD
+WCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDHNSAIIANQQEHKGMDWDTGKE-MQQGPK-IVVVLALFYQPSNVLAAEPNIMGQPQV
+SVVFV-GNDGRRMLIVGCSMMPDYKFMREACVPFFRKLFMAEVQDRYDYAWNYNIKIYETHFRDGVYAVDNSWETLVYV
+-EMASGRIGAKINHQPRLPEQVI-PPCILTVSGLKRTI-ADEPDETEITKTPIIHIV--MWADIMFKNCVMQYCNYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QI
+M-GVGDIGGYELICEDLFQILVCE
+>t2
+MIWSDYRQMVREG--GDDSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELVKY
+-YH-CMEGCGCVNTMAKSS-SQSAPWKFNRFMC-LMYLMQD--------GDL--------------------CNS--PG
+FLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRM----YG---EIG
+K-V-VIIKVVNAVMGRLNHHEPSAEVMFPLRK--GGSDSKPF------------------IDGFF------------DR
+PGIANAMSVPCG----DQWMGSIKGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQISRMKALAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQGNGEN-PMNVPCVESGECQYENKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVG
+NRCRAELTALKTGQLDVGSSGKTLGQ-NIMVSKKLGDRTWLAASPLQ------IGCGVMVWEKKVPSPQ-EVEVAAD--
+-IYFYRNMVIECLTDVVRAVRMQSPQEMRAPVLVCIQKVDSPSLGDDVPQM--MNIVPYWVCVCSGVVKKAQPD-SVDK
+RGKTWVAKS-DFLCPPAMNEGEH---GAEQRPVFGTQNPVCKPWRFVIMNVETFAKNIIRLLYVKDV-SCNQVLQLLDW
+QLCDSH-GDWQSMVADSCHNA-VNIAVCCWKRELMPGL---NHSCQHLAKTVYFKPDGE-------DEGQMMVKIFNLD
+WCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDHNSAIIANQQEHKGMDWDTGKE-MQQGPK-IVVVLALFYQPSNVLAAEPNIMGQPQV
+SVVFV-GNDARRMLIVGCSMMPDYKFMREACVPFFRKLFMAEVQDRYDYNWNYNIKIYETHFRVGVYAVDNSWETLVYV
+-EMASGRIGAKINHMPRLPEQVI-PPCILTVSGLKRTI-ADEPDETEITKTPIIHIV--MWADIMFKNCVMQYCNYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QI
+M-GVGDIGGYELICEDLFQILVCE
+>t10
+MIWSDYRQMVREG--GDDSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELVKY
+-YH-CMEGCGCVNTMAKSS-SQSAPWKFNRFMC-LMYLMQD--------GDL--------------------CNS--PG
+FLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRM----YG---EIG
+K-V-VIIKVVNAVMGRLNHHEPSAEVMFPLRK--GGSDSKPF------------------IDGFF------------DR
+PGIANAMSVPCG----DQWMGSIKGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQISRMKALAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQGNGEN-PMNVPCVESGECQYENKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVG
+NRCRAELTALKTGQLDVGSSGKTLGQ-NIMVSKKLGDRTWLAASPLQ------IGCGVMVWEKKVPSPQ-EVEVAAD--
+-IYFYRNMVIECLTDVVRAVRMQSPQEMRAPVLVCIQKVDSPSLGDDVPQM--MNIVPYWVCVCSGVVKKAQPD-SVDK
+RGKTWVAKS-DFLCPPAMNEGEH---GAEQRPVFGTQNPVCKPWRFVIMNVETFAKNIIRLLYVKDV-SCNQVLQLLDW
+QLCDSH-GDWQSMVADSCHNA-VNIAVCCWKRELMPGL---NHSCQHLAKTVYFKPDGE-------DEGQMMVKIFNLD
+WCEVEKSHEK-SSVDDNYN-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDHNSAIIANQQEHKGMDWDTGKE-MQQGPK-IVVVLALFYQPSNVLAAEPNIMGQPQV
+SVVFV-GNDARRMLIVGCSMMPDYKFMREACVPFFRKLFMAEVQDRYDYNWNYNIKIYETHFRVGVYAVDNSWETLVYV
+-EMASGRIGAKINHMPRLPEQVI-PPCILTVSGLKRTI-ADEPDETEITKTPIIHIV--MWADIMFKNCVMQYCNYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QI
+M-GVGDIGGYELICEDLFQILVCE
+>t31
+MIWSEYRSMVREG--ADQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY
+-YF-CMEGCGCVNTMAKQS-SQSAPWKFNRFMC-LMHLMQN--------GDL--------------------CNL--PS
+FLGMCMFHNQVQCKGE--LVLPDNVNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRI----YQ---NIG
+K-V-VIIKVWNANMGRLNHHEPPAEVMFPLRK--GGSDSKPF------------------IDGFF------------DR
+PGIANAMNVPCG----DQWVGCIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQTSRMKAAAPIYPHIM
+EYAHGM----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVG
+NRCRAELTALKTVQLDVGSNGKTLGK-NIMTPKKLGDRTWLAASPLQ------IGCGVMVQEKKVASPQ-EVE-AAD--
+-IFFYRNMVIQRLTDVVAAVRMQSPQEMRPPVLVCIQYVDSPSLGDDTPQM--MNIAPYWVCVCSGVVKKAQPD-SVDK
+RGKTWVAKA-DFLCPPAVSEGEH---GAEQRPVFGMQNPACKPWRFVIMNTQTFAKNIIRLLYIKDV-SCNAVLQLLDW
+QLCYSH-GDWQSLIADSCPTA-ANIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMIMKIFNLD
+WCEVEKSHEK-SSVDDNYH-VNMLPFAQSNRDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDHKSAIIANQHEVKGMDWNTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIVGQPQV
+SHVFV-GNDARRMLIVGVSVMPSYKFMREACVPFFHKLFMADNQVRHEYMWNYDIKIYETHFRMGVYAVDNSWETLVYC
+-EMTSGRIGANINHLPRLPEQVV-PPCILTVSGLKRTI-AGSPDETEITKTLIYHIV--MWADIMFKNCVMQYSTYYKE
+NRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIRV
+M-GVGDIGGYEMICEDLFQILVCE
+>t15
+MIWSEYRSMVREG--SDQSIDNH-C------------LIAARVKMMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY
+-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQN--------GDL--------------------CNS--PS
+FLGMCMFHNQVPNKGA--LVLPDNVNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRI----YP---SIG
+K-V-VIIKVWNAAMGRLNHHEPPAEVMFPLRK--GGSDSKPF------------------IDGFF------------DR
+PGIANAMSVPCG----DQWVGCIRGWCSSQHQYGLANHILVHGPSKLHRTYAINRKMGANVYQQTSRMKAAAPLYPHIM
+EYAHGM----VEPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVLGDWVG
+NRCRAELTALKTVQLDIGNSGKTLGQ-NIMTPKRLGERTWLAASPLQ------IGCGVVVQEKKVASPQ-EVEVAAD--
+-IYFYRNMVIQTLTDVVAAVRMQSPQEMRPPVLVCIQDVDSVSLGDDTPQM--MNIAPYWVCVCSGVVKKTQPD-SVDK
+RGKTWVAKS-DFLCPPAVSEGEH---GAEQRPVFGMRNPICKPWRFVIMNTQTFAKNIIRLLYVKDV-SCNAVLQLLDW
+QLCYSH-GDWQSLIADSCSTA-ANIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMIVKIFHLD
+WCEVEKSHEK-SSVDDNYH-VNMLPFAQSNGDPVGHYVQGLED-ALRLIRPGT---ARALVILS-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDHKSAIVANQQEVKGMDWDTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIVGQPQV
+SHVFV-GNDARRMLIVGVSVMPAYKFMREACVPFFHKLFMAENQVRHDYMWNYDIKIYETHFRMGVYAVDNSWETLVYC
+-EMTSGRIGAKINHLPRLPEQVV-PPCILTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQYSTYYKE
+NRSVR-----------GNNTGGAELPK---------------------YHQQNILTD-ELYSDV---YPTAPKKYVIRV
+M-GVGDIGGYELICEDLFQILVCQ
+>t63
+MIWSEYRSMVREG--SDQSIDNK-C------------LTAARVKLMSGVVRQVRNAPEDAL--YTFFTGQKGKRELIKY
+-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQD--------GDL--------------------CNS--PS
+FLGMCMFHNQVSFKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDEQDSSHLREKQLRL----YA---RIG
+K-V-VIIKVWNAVMGRLNHHEPPAAVMFPLRK--GGSDSKPF------------------IDGFF------------DR
+PGIANAMSVPCG----DQWMGIIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRANTMSKPVMGDWVG
+SRCRAELTALKTVQLDVGSSGKTLGQ-NIMTPKKLGDRTWLAASPLQ------IGCDVMVQEKKVASPQ-EVEVAAD--
+-IYFYRNMVIQRLTDVVAAVRMQSPQEMRLPVLVCIQDVDSPSLGDDTPQK--MNIAPYWVCVCSGVVKKAQLD-SVEK
+RGKTWVAKS-DFLCPPAVSEGEH---GPEQRPVFGVQNPVCKPWRFVIMNTQTFAANIIRLLYVKDV-SCNAVLQLLDW
+QLCYSH-EDWQSLIADACPTA-VNIAVCCWKRELMPGL---NHSCEHLAKSVYFKPDGE-------DEGQMFMKIFNLD
+WCEVEKSHEK-SSVDDNYN-VNMLPFVQSNGDPVGHYVQGLED-ALLLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDHKSAIIANQQGVKGMDWDTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIIGQPQV
+SHVFV-DNDARRMLIVGQSVMPPYKFMREACVPFFHKLFMAENQVRHDYVWNYDIKIYETHFRMGVYAIDNSWETLVYC
+-EMTSGRIGAKINHQPRLPEQVV-PPCVLTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQYSTYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIRQ
+M-GMGDIGGYELICEDLFQILVCE
+>t50
+MIWSEYRSMVREG--SDQSIDNK-C------------LTAARVKLMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY
+-YF-CMEGCGCVNTMAKNS-SQSAPWKFNHFMC-LMHLMQN--------GDL--------------------CNS--PS
+FLGMCMFHNQVSVKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSSHLREKQLRL----YA---RIG
+K-V-VIIKVWNAVMGRLNHHEPPAEVMFPLRK--CGSDSKPF------------------IDGFF------------DR
+PGIANAMSVPCG----DQWMGVIRGWCSSQHQYGLANHVLVHGPSKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRANTMSKPVMGDWVG
+SRCRAELTALKTVQLDVGSSGKTLGQ-NIMTPKKLGDRTWLAASPLQ------IGCDVMVQEKKVASPQ-EVEVAAD--
+-IYFYRNMVIQRLTDVVAAVRMQSPQEMRLPVLVCIQDVDSPSLGDDTPQK--MNIAPYWVCVCSGVVKKAQPD-SVDK
+RGKTWVAKS-DFLCPPAVSEGEH---GPEQRPVFGVQNPVCKPWRFVIMNTQT-AKNIIRLLYVKDV-SCNAVLQLLDW
+QLCYSH-GDWQSLIADACSTA-VNIAVCCWKRELMPGL---NHSVEHLAKSVYFKPDGE-------DEGQMIMKIFNLD
+WCEVEKSHEK-SSVDDNYN-VNMLPFVQSNGDPVGHYVQGLED-ALLLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDHKSAIMANQQGVKGMDWDTGKE-MQQGPK-IVMHLALFYAPSNVLAAEPNIIGQPQV
+SHVFV-DNDARRMLIVGQSVMPAYKFMREACVPFFHKLFMAENQVRHDYVWNYDIKIYETHFRMGVYAVDNSWETLVYC
+-EMTSGRIGAKINHQPRLPEQVV-PPCILTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQYSTYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIRQ
+M-GMGDIGGYELICEDLFQILVCE
+>t25
+MIWSEYRSMVREG--SDQSIDNK-C------------LTAARVKMMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY
+-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQN--------GDL--------------------CNS--PS
+FLGMCMFVNQVSFKGE--LVLPDNPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSSHLREKQLRL----YA---RIG
+K-V-VIIKVWNAVMGRLNHHEPPAEVVFPLRK--GGSDSKPF------------------IDGFF------------DR
+PGIANAMSVPCG----DQWMGVIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRANTMSKPVMGDWVG
+SRCRAELTALKIVQLDVGSSGKTLGQ-NIMTPKKLGDRTWLAASPLQ------IGCDVMVQEKKVASPQ-EVEVAAD--
+-IYFYRNMVIQRLTDVVAAVRMQSPQEMRLPVLVCIQDVDSPSLGDDTPQK--MNIAPYWVCVCSGVVKKAQPD-SVDK
+RGKTWVAKS-DFLCPPAVSEGEH---GPEQRPVFGMQNPVCKPWRFVIMNTQTFAKNIIRLLYVKDV-SCNAVLQLLDW
+QLCYSH-GDWQSLIADACPTA-VNIAVCCWKRELMPGL---NHSCEHLAKSVYFKPDGE-------DEGQMIMKIFNLD
+WCEVEKSHEK-SSVDDNYD-VNMLPFVQSNGDPVGHYVQGLED-ALLLIRPGT---ARALVILF-YGCQYYSGKFQDSE
+LFERSQLYR-VYCEI----KKDHKSTIIANQQGVKGMDWDTGKE-MQQGPK-IVVHLTLFYAPSNVLAAEPNIFGQPQV
+SHVFV-DNDARRMLIVGQSVMPAYKFMREACVPFFHKLFMAENQVRHDYVWNYDIKIYETHFRMGVYAVDNSWEALVYC
+-EMTSGRTGAKINHQPRLPEQVV-PPCILTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQYSTYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIRQ
+M-GMGDIGGYELICEDLFQILVCE
+>t51
+MIWSEYRSMVREG--SDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY
+-YF-CMEGCGCVNTMAKNS-SQSAPWKFNRFMC-LMHLMQN--------GDL--------------------CNS--PS
+FLGMCMFHVQVQFKGE--LVLPDHPNENSVEFMYRRHHSLSDKRCLNLLYVGDNQDSQHLREKQLRI----YA---RIG
+K-V-VIIKVWNAVMGRLNHHEPPAEVVFPLRK--GGSDSKPF------------------IDGFF------------DR
+PGIANAMSVPCG----DQWVGVIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIM
+EYAHGM----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPIMGDWVG
+NRCRADLTALKTVQLDVGSSGKTLGQ-NIMTPKNLGDKTWLAASPLQ------IGCGIMVQEKKVASPQ-EVEVAAD--
+-IYFYRNMVIQRLTDVVAAVRMQSPQEMRPPVLVCIQDVDSPSLGDDTPQM--MNIAPYWVCVCSGVVKKAQPD-SVDK
+RGKTWVAKS-DFLCPPAISEGEH---GAEQRPVFGMQNPVCRPWRFVIMNTQTFAKNVIRLLYVKDV-SCNKVLQLLDW
+QLCYSH-GDWQSLIADACPAA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMIMKIFGLD
+WCEVEKSHEE-SSVDDNYN-VNMLPFVSSNGDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQFYSGKFQDSE
+LFERSQLYR-VYCEI----KKDHKSAIIANQQGVKGMDWDTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIIGQPQV
+SHVFV-DNDIRRMLIVGVSVMPAYKFMREACVPFFHKLFMAENQVRHDYVWNYDIKIYETHFRMGVYAVDNSWETLVYC
+-EMTSGRIGAKINHLPRLPEQVF-PPCILTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQYATYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIRE
+M-GVGDIGGYELICEDLFQILVCE
+>t9
+MIWSECRQMVREK--TDNAIDNQ-C------------LIAARVKENSGHVKQVRNDSEDIL--YNHFTGKKGARELIKR
+-YV-CMEGHDCVNTVANVS-SQSAIWKFDRFMCDLMHLMQN--------GDL--------------------CSY--PS
+FLPMCMFVPQVLSKGE--LVLPDSSNEESISFVYLQHHSFSVKRCLNYLNVGDSADSKHLKEKHLRA----EGMPGNIG
+K-H-VIINVWNAVMGRLNHHEPPAEVVFPLRQ--GGPDSKPM------------------IDGFFDK-D-D------DR
+PGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHDPSSLHRTFAINRKMGANVYQQTSRMKASAPFYPHCM
+EYAHGV----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESIDCQYENKHATMTKLMHH-SLYLMRMHTMSKPIMGDVNG
+NRCRADLTALKMLQLDIGFSAKTLGQ-NVVVPHLLGHRTWLATSPLQ------IGCGVMIFGNKIGSAN-EFEAAADPT
+VIYFYRNRIVRRLADVISTVRMNSPQEMRN------QDVDSHSLGDDDNQA--MVILPYWVCVCSGVVRKEHPDTSINK
+RGRTWLAKV-DFLCPPAFNQGEH---RAEQKPASKFEHPVCGPWEFVIVNYQTSAKDIILLLYIKDV-GCNCVLELLNW
+QLCTSH-GDWQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEGKMVLKIFGLD
+WCEMEKSHQR-SGVDDNYQ-VNMLPFNHSKNNPVGHYVQGLED-ALNLIRPGT---ARALNILF-YGCEVYSGEFQDSE
+S-ERSWIYN-VYCEI----KKDHKSAIIAHKYEHKGMDWDTGKE-AQQGPE-VVHHNLLFF-------AEPNIHGQPGV
+GHIFV-GNDARRKLIAGVSFMSMVKFMCEACVPFFRKLFMAVGQMRYDYVNNYDIKIWETVFRGGVYAIENSWETLVLC
+-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETK-AGLIDGTEITKTPDIGIC--MWETIHFKNPVMQYCCYYKE
+NRSVR-----------VNNTGGAALPK---------------------YHHQNTLVD-ELYSDV---YPAAPKKK--VC
+M-GVGDVGGYEVMGEDLFQILVCE
+>t47
+MIWSECRQMVREK--SDNAIDNQ-C------------QIAARVKRNSGHVKQVRNDSEDIL-CYHHFTGKKGARELIKR
+-YI-CMEGHDCVNTMANVS-SQSAVWNFDRFMCDLMHLMQN--------GDL--------------------CSY--PS
+FLPMCMFVSQVLSKGE--LVLPDSSNEESISFVYLQHHSFSDKRCLNYLNVGDNSDSKHLKEKHLRA----QGMPGNIG
+K-H-VIINVWNAVMGRLNHHESPAEVVFPLRQ--GGPDSKPM------------------IDGFFDK-D-D------DR
+PGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHDPSNLHRTFAINRKMGANVYQQASRMKASAPFYHHCM
+EYAHGV----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESRDCQYENKHATMTKLMHQ-SLYLMRMHTMSKPIMGHVNG
+NRCRADLTALKMLQLDIGFSAKTLCQ-NIVVAHLLGHRTWLATSPLQ------IGCMVMIFGNKIGSAN-EFEAAADPT
+VIYFYRNRIVRRLADVISTVRMNSPQEMRE------QDVDSHSLGDDDNQA--MNILPYWVCVCSGVVRKEHPDTSINK
+RGRTWLAKM-DFLCPPAFNQGEH---RAEQKPALKFKHPVCGPWEFVIVNYQTSAKDIILLLYIKDV-GCNCVLELLKW
+QLCTSH-GDWQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCDRLAKHIYFQPDGE-------DEGKMILKIFGLD
+WCEMEKSHQR-SGVDDNVQ-VNMLPFNHSKHNPVGHYVQGLED-ELNLIRPGT---ARALNILF-YGCEYYSGEFQDSE
+S-ERSWIYN-VYCEI----KKDHKSAIMACKYRHKGMDWDTGKE-AEQGPE-VVHHNLLFF-------AEPNIQGQPGV
+GHIFV-GNDARRKLIAGLSFMAMMKFMCEACVPFFRKLFMAVGHMRYDYVSNYDIKIWETVFRGGVYAIENSWETLVLC
+-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETK-AGIIDGTEITKTPEIGIC--MWDTIEFKNPVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNTLVD-ELYSDI---YPAAPKKK--VC
+M-GVGDVGGYEVMGEDLFQILVCE
+>t60
+MIWSECRQMVREK--TDNAIDNQ-C------------QIAARVKENSGHVKQVRNDSEDIL-CYHHFTGKKGARELIKR
+-YI-CMEGHDCVNTMANVS-SQSAVWNFDRFMCDLMHLMQN--------GDL--------------------CSV--PS
+FLPMCMFVSQVLHKGE--LVLPDSSNEESISFVYLQHHSFSDKRCLNYLNVGDNADSKHLKEKHLRA----QGMPGNIG
+K-H-VIINVWNAVMGRLNHHEPPAEVVFPLRQ--GGPDSKPM------------------IDGFFDK-D-D------DR
+PGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHNPSNLHRTFAINRKMGANVYQQTSRMKASAPFYHHCM
+EYAHGV----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESIDCQYESKHAAMTKLMHQ-SLYLMRIHTMSKPIMGDVNG
+NRCRADLTALKMLQLDIGFSAKTLGQ-NIVVPHCLGHRTWLATSPLQ------IGCMVMIFGNKIGSEN-EFEAAADPT
+VIYFYRNRIVRRLADVISTVRMNSPQEMRN------QDVDSHSLGDDDNQA--MNILPYVVCVCSGVVRKDHPDTSIHK
+RGRTWLAKV-DFLCPPAFNQGEH---RAEQKPAFKFKHPVCGPWEFVIVNYQTEAKDIILLLYIKDV-GCNCVLELLEW
+QLCTSH-GDWQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEGKMILKIFGLD
+WCEMEKSHQR-SGVDDNYQ-VNMLPFNHSKHNPVGHYVQGLED-ALNLIRPGT---ARALNILF-YGCEYYSGEFQDSE
+S-ERSWIYN-VYCEI----KKDHKSAIMAYKFEHKGMDWDTGKE-AEQGPE-VVHHNLLFF-------AEPNIQGQPGV
+GHIFV-GNDARRKLIAGVSFMAVMKFMCEACVPFFRKLFMAVGQMRYDYMNNYDIKIWETFFRGGVYAIENSWETLVLC
+-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETR-AGIIEGTEITKTPDIGIC--MWDTIHFKNPVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNTLVD-ELYSDI---YPAAPKKK--VC
+M-GVGEVGGYEVMGEDLFQILVCE
+>t30
+MIWSECRQMVREK--TDNAIDNQ-C------------QIAARVKENSGHVKQVRNDSEDIL-CYHHFTGKKGARELIKR
+-YI-CMEGHDCVNTMANVS-SQSAVWNFDRFMCDLMHLMQN--------GDL--------------------CSV--PS
+FLPMCMFVSQVLHKGE--LVLPDSSNEESISFVYLQHHSFSEKRCLNYLNVGDNADSRHLKEKHLRA----QGMPGNIG
+K-H-VIISVWNAVMGRLNHHEPPAEVVFPLRQ--GGPDSKPM------------------MDGFFDK-D-D------DR
+PGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHTPSNLHRTFAINRKMGANVYQQTSRMKASAPFYHHCM
+EYAHGV----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESIDCQYENKHATMTKLMHQ-SLYLMRMHTMSKPIMGDVNG
+NRCRADLTALKMLQLDIGFSAKTLGQ-NIIVPHCLGHRTWLATSPLQ------IGCMVMIVGNKIGSEN-EFEAAADPT
+VIYFYRNRIVRRLADVISTVRMNSPQEMRN------QDVDSHSLGDDDNQA--MNILPYVVCVCSGVVRKEHPDTSISK
+RGRTWLAKI-DFLCPPAFNQGEH---RAEQKPAFKFKHPCCGPWEFVIVNYQTSAKDIILLLYIKDV-GCNCVLELLKW
+QLCTSH-GDWQSLVADSCVWA-HNVAVCEWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEGKMILKIFGLD
+WCEMEKSHQR-SGVDDNYQ-VNMLPFKHSKHNPVGHYVQGLED-ALNLIRPGT---ARALNILF-YGCEYYSGEFQDSE
+S-ERSWIYN-VYCEI----KKDHKSAIMAYKYEHKGMDWDTGKE-AEQGPE-VVHHNLLFF-------AEPNIHGQPGV
+GHIFV-GNDARRHLIAGVSFMAVVKFMCEACVPFFRKLFMAVGQMRYDYVNNYDIKIWETVFRGGVYAIENSWETLVLC
+-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETR-AGIIDGTEITKTPDIGIC--MWDTIHFKNPVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHDQNTLVD-ELYSDV---YPAAPKKK--VC
+M-GVGDVGGYEVMGEDLFQILVCE
+>t70
+MIWSECRQMVREK--NDNAIDNQ-C------------LIAARVKEDSGHVKQVRNASEDIM--YNHFTGKKGARELIKR
+-YI-CMEGHDCVNTMANVS-SQSAVWKFDRFMCDLMHLMQD--------GDL--------------------CSY--PS
+FLPMCMFVAQVIAKGE--LVLPDSSTEESISFMYLQHHSFSDKRCLNYLNVGDNEDSKHAKEKFLRG----DG---GIG
+Q-H-VIINVWNAVMGRLNHHEPPPEVVFPLRQ--GGPDSKPM------------------VDGFFDK-D-D------DR
+PGIANAMNVPCG----DQWGGPIRGWCSSQHKFGLAFHTLSHDPSKLHRTFAINQKMGANVYQQMSRMKTPAPFYPHVM
+EYAHGV----CKPFYEHSEPKNEAQGNGEKVPMNVPCVESMDCQYENKHAPMAKLMHQDSLYLMRMHTMSKPLMGDVNG
+NRCRADLTSLKMLQLDIGFCAKTLGQ-NIVVPKLLGHRTWLATAPLQ------IGCGMMIFGNKIGSTQ-EFEAAADPT
+VIYFYRNRIVRRMADVISTVRMKSPQEMRG------QDVDSHSLGDDDNQA--MNILPYWVCVCSGVVRKEHPDTSINK
+RGRTWLAKI-DFLFPPAFNQGEH---HAEQKPVFGFKHPHCGPWEFVICNYQTVAKDIILLLYIKDV-GCNCVLELLAW
+QLCTSH-GDWQSLVADSCIWA-HNVAVCAWKRELVPGL---NHSCEHLAKHIYFQPDGE-------DEGKMILKIFGLD
+WCEVERSHQR-SGVDDNYK-VNMLPFSHSKHNPVGHYVQGLGD-ALRLIRPGT---ARALNILF-YGCQYCSGEFQDSE
+E-ERSWIYN-VYCEI----KKDHKSAILAHKYKHKGMDWDTGKE-MEQGPK-VVNYNLLFY-------AEPNIHGQPRV
+GHIFV-GNDAHRKLIAGVSFMSIMKFMCEACVPFFRKLFMAVRQMRYMYMNNYDIKIWETAFRGGVYAIENSWETLVLC
+-EMTSGRSGAKMNHLPRLFEQVC-PPCLLTVSGLKETV-AGIIDGTEITKTPEIGIC--MWDTIHFKNPVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHNQNTLVD-ELYSDV---YPAAPKKQ--HY
+M-GVGDVGGYEVMGEDLFQILVCE
+>t91
+MIWSECRQMVREK--NDNAIDNQ-C------------LIAARVKEDSGHVKQVRNASEDIM--YNHFTGKKGARELIKR
+-YI-CMEGHDCVNTMANVS-SQSAVWKFDRFMCDLMHLMQD--------GDL--------------------CSY--PS
+FLPMCMFVAQVIAKGE--LVLPDSSTEESISFMYLQHHSFSDKRCLNYLNVGDNEDSKHAKEKFLRG----DG---GIG
+Q-H-VIINVWNAVMGRLNHHEPPPEVVFPLRQ--GGPDSKPM------------------VDGFFDK-D-D------DR
+PGIANAMNVPCG----DQWGGPIRGWCSSQHKFGLAFHTLSHDPSKLHRTFAINQKMGANVYQQMSRMKTPAPFYPHVM
+EYAHGV----CKPFYEHSEPKNEAQGNGEKVPMNVPCVESMDCQYENKHAPMAKLMHQ-SLYLMRMHTMSKPLMGDVNG
+NRCRADLTSLKMLQLDIGFCAKTLGQ-NIVVPKLLGHRTWLATAPLQ------IGCGMMIFGNKIGSTQ-EFEAAADPT
+VIYFYRNRIVRRMADVISTVRMKSPQEMRG------QDVDSHSLGDDDNQA--MNILPYWVCVCSGVVRKEHPDTSINK
+RGRTWLAKI-DFLFPPAFNQGEH---HAEQKPVFGFKHPHCGPWEFVICNYQTVAKDIILLLYIKDV-GCNCVLELLAW
+QLCTSH-GDWQSLVADSCIWA-HNVAVCAWKRELVPGL---NHSCEHLAKHIYFQPDGE-------DEGKMILKIFGLD
+WCEVERSHQR-SGVDDNYK-VNMLPFSHSKHNPVGHYVQGLGD-ALRLIRPGT---ARALNILF-YGCQYCSGEFQDSE
+E-ERSWIYN-VYCEI----KKDHKSAILAHKYKHKGMDWDTGKE-MEQGPK-VVNYNLLFY-------AEPNIHGQPRV
+GHIFV-GNDAHRKLIAGVSFMSIMKFMCEACVPFFRKLFMAVRQMRYMYMNNYDIKIWETAFRGGVYAIENSWETLVLC
+-EMTSGRSGAKMNHLPRLFEQVC-PPCLLTVSGLKETV-AGIIDGTEITKTPEIGIC--MWDTIHFKNPVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHNQNTLVD-ELYSDV---YPAAPKKQ--HY
+M-GVGDVGGYEVMGEDLFQILVCE
+>t49
+MIWSECRQMVREK--NDNAIDNQ-C------------LIAARVKENSGHVKQVRNASEDIM--YNHFTGNKGACELIKG
+-YV-CMEGHDCVNTMANIS-SQSAVWKFDRFMCDLMHLMQD--------GDL--------------------CSY--PS
+FLPMCMFVAQVIAKGE--LVLPDSSNEESISFMYLQHHSFSDKRCLNCLNVGDNEDSKHLKEKFLRA----DG---GIG
+Q-H-VIINMWNAVMGRLNHHEPPPEVVYPLRQ--GGPNSKPM------------------VDGFFDK-D-D------DR
+PGIANAMNVPCG----DQWGGPIRGWCSSQHRFGLAFHTLKHDPSKLHRTFAINEKMGANVYQQNSRMKASAPFYPHVM
+EYAHGV----CKPFYEHSEPKNDAQGNGDKVPMNVPCVESMDCQYENKHAPMAKLMHQ-SLYLMRMYTMSKPIMGDVNG
+NRCRAELTSLKMLQLDIGFSAKTLGQ-NIVPPKLLGHRTWLATSPLQ------IGCGVMIFGNKIGSTQ-EFESAADPT
+VIYFYRNRIVKRMADVISTVRMKSPQEMRG------QDVDSHSLGDDDNQA--MNILPYWVCVCSGVVRKEHPDTSINK
+RGRTWLAKI-DFLFPPAFNQGEH---HAEQKPVFGFKHPHCGPWEFVICNYQTMAKDIILLLYIKDV-GCNCVLELLAW
+QLCTSH-GDWQSLVADSCIWA-HNVAVCAWKRELVPGL---NHSCEHLAKHIYFQPDGE-------DEGKMIIKIFGLD
+WCEVEKSHQR-SGVDDNYK-VNMLPFSHSNHNPVGHYVQGLGD-ALRLIRPGT---ARALNILF-YGCEYYSGEFQDSE
+E-ERSWIYN-VYCEI----KKDHKSAIMAHKYEHKGMDWDTGKE-MEQGPK-VVHHNILFY-------AEPNIHGQPRV
+GHIFV-GNDAVRNLIAGVSFMSIMKFMCEACVPFFRKLFMAVRQMRYMYMNNYDIKIWETAFRGGVYAMENSWETLVLC
+-EMTSGRVGARMNHLPRLFEQVC-PPCILTVSGLKETV-AGVIDGTEITKTPEIGIC--MWDTIHFKNPVMQYCCYYKE
+PRSVR-----------VNNTGGAELPK---------------------YHNFNALVD-ELYSDV---YPAAPKKK--HY
+M-GVGDVGGYEVMGEDLFQILVCE
+>t52
+MIWSEERQMVREK--VDNAVDNQ-C------------LIAARVKENCGHVKQVRNASEDIL--YNHFTGKKGARELIKR
+-YI-CMEGHDCVNTMAHDS-SQSATWKFDRFMCDLMHLMQG--------GDL--------------------CSY--PS
+FLPVCMFVAQVINKGE--LVLPDSSNEESISFMYLQHHSFSEKRCLNYLNVGDNEDSKHLKEKFLRA----DG---NIG
+Q-H-VIINMWNAVMGRLNHHEPPAEVNFPLRQ--GGPDSKPM------------------VDGFFDK-D-D------DS
+PGIANAMNVPCG----DQWGGPIRGWCSSQHKFGLASHTLSHDPSKLHRTFGINKNMGANVYQQTSRMKANAPFYPHVM
+EYAHGV----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESIECQYENKHATMAKLMHD-SLYLMRMHTMSKPVMGDVNG
+HRCRADLTALKMLQLDIGFSAKTLGQ-NIVAPKLLGVRTWLATSPLQ------IGCGVMIFGNKIGSTQ-EFEAAADPT
+VIYFYRNRIIRRVADVISTVRMKSPQEMRE------QDVDSHSLGDDDNQA--MTILPHWVCVVSGVVRKEHPDTSINK
+RGSTWLAKV-DFLCPPAFNQGEH---HAEQKPVFGFKHPHVGPWEFVICNYQTSAHDIILLLYIKDV-GCNCVLELLVW
+QLCTSH-GDWQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEGKMILKIFELN
+WCEVEKSHQH-SGVDDNYQ-VNMLPFDHCKHNPVGHYVQGLED-ALGLIRPGT---ARALNILF-YGCQYYSGEFQDSE
+A-ERSWIYN-VYCEI----KKDHKSGIMAHKYDHKGVDWDTGKE-MEQGPK-VLHHNLLFY-------AEPNIHGQPTV
+GHIFV-GNDARRKLIAGVSFMSVVKFMCEACVPFFRKLFMAFRQMRYDYVNNYDIKIWETVFRGGVYAIENSWETLILC
+-EMTSGRCGAKMNHMPRLFEQVC-PPCILTVSGLKETM-AGVIDGTEITKTPDIGIG--MWDSIHFKNPVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNSLVD-ELYSDV---YPAAPKKK--HY
+M-GVGDVGGYEVMGEDLFQILVCE
+>t43
+MIWSEVRQMVREG--SDNAIDNR-C------------LIAARVKHVQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCALMHLMQK--------GDL--------------------CSH--PS
+FLGMCMFHEQVRCKGE--LVLPDSPNEESVSFVYIQHHSFSDKRCLNCLNVGDNDDSEHLKEKHLRI----YG---QIG
+H-H-VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSK-M------------------VDGFFDK-E-D------DR
+PGIANAVSVPCA----DQVGGPIRGWCSSQVNFGLANHTLVQ-PSKLHRTFKINKKMGANVYQQTSRMKAEAPVYPHIM
+EYAHGV----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDG
+HRCRAGLTALKVVQLDIGFSSKTLGQLNIIDCKLLGHRTWLATSPLQ------IGVDVMVMGNKIGSPS-EFEVAADPT
+IIWFYRNCIVHKLADTVSTAKMKSPQEMRH------QDVDSPSLGDDDQQA--MDILPYWVCVTSGVVRKEQPD-SVNK
+RGRTWLAKN-DFLCPPAFNQGEH---EREQRPVYGFKHPGCRPWQFVIANYQTSAKNIIMLLYVKDV-SCNGVLQLLNW
+HLCDSH-GDWQSLVADSCCWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELD
+WVEMEKSHQQ-SSVDDNYL-VNMLPFLHSRQNPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDGE
+A-ERSWIYD-VYCEM----KKDHKSAVIAHKHEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGV
+SHVFM-GNDATRKLITGVSVMPTYKFMCGACVPFFHKLFMAVRNMRYDYNVNYDIKIWETHIRHGVYAVENSWETLVTC
+-EMTSGRIGAKINHLPRLPEQVI-PPCVLTVSGLKQPM-AGYNDQTEITKTPDICIC--TWGTIHFKNFVMQYCVYYKE
+NRSVR-----------VNNTGGAELPQ---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HY
+V-GAGDVGGYEVMSEDLFQILVHE
+>t1
+MIWSEVRQMMREG--TDNAIDNQ-C------------LIAARVKHMQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCCLMHLMQN--------GDL--------------------CSH--PS
+FLGMCMFVEQVRCKGE--LVLPDSPNEESLSFVYIQHHSFSDKRCLNCLNVGDNDDSEHLKEKHLRI----YG---QIG
+R-H-VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSKPV------------------VDGFFDK-E-D------DR
+PGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVQ-PSKLHRTFKINKKMGANVYQQTSRMKAEAPVYPHIM
+EYAHGV----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDG
+HRCRAKLTALKIVQLDIGFSAKTLGQLNIIDCKLLGRHTWLATSPLQ------IGCDMMVMGNKIGSPS-EFEVAADPT
+IIWFYRDCIVHKLADTVSTAKMKAPQEMRV------QDVDSPSLGDDDQQE--MDILPYWVCVTSGVVRKEQPD-SVNK
+RGRTWLAKN-DFLCPPAFNQGEH---EAEQRPVYGFVHPRCRPWQFVIANYQTSAKNIIMLLYVKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELD
+WVEMEKSHQQ-SSVDDNYL-VNMLPFMQSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDGE
+A-ERSWIYD-VYCEM----KKDHKSAVVAHKVEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGV
+SHVFM-GNDATRKLITGVSVMPTYKFMCGACVQFFHKLFMAVRNMRYDYTVNYDIKIWETHIRQGVYAVENSWETLITC
+-EMTSGRIGAKINHLPRLPEQVV-PPCILTVSGLKQPM-AGYNDETQITKTPDICIC--TWGTIHFKNSVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HY
+V-GAGDVGGYEVMSEDLFQILVHE
+>t86
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKPVQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCALMHLMQN--------GDL--------------------CSH--PS
+FLGMCMFHEQVRRKGE--LVLPDSPNEESVSFVYIQHHSFSDKRCLNCLNVGDNDDSEHLKEKHLRI----YG---QIG
+R-H-VIINVWNAFMGRLNHHEPPAEAVYPLRK--GGPDSKPM------------------VDGFFDK-E-D------DR
+PGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVQ-PSKLHRTFKINKKMGANVYHQTSRMKAEAPVYPHIM
+EYAHGV----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDG
+HRCRAGLTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVMGNKIGSPS-EFEVAADPT
+IIWFYRNCIVHKLADTVSTAKMKAPQEMRV------QDVDSPSLGDDDQQA--MDILPYWVCVTSGVVRKEQPD-SVNK
+RGRTWLAKN-DFLCPPAFNQGEH---GAEQRPVYGFQHPRCRPWQFVIANYQTFAKNIIMLLYVKDV-SCNRVLQLLNW
+QLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELD
+WVEMEKSHQQ-SSVDDNYL-VNMLPFIHSRDNPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDGE
+A-ERSWIYP-VYCEM----KKDHKSAVVAHKAEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGV
+SHVFM-GNDATRKLITGVSVMPTYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHIRHGVYAVENSWETLVTC
+-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGYNDETQITKTPDICIC--GVGTIHFKNLVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HY
+V-GAGDVGGYEVMSEDLFQILVHE
+>t72
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHVQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGHDCVNTMAKVS-SQSAVWKFDRFMCALMHLMQN--------GDL--------------------CSH--PS
+FLGMCMFHEQVRRKGE--LVLPDSPNEESVSFVYIQHHSFSDKRCLNCLNAGDNDDSEHLKEKHLRT----YG---QIG
+R-H-VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSKPM------------------VDGFFDK-E-D------HR
+PGIANAVSVPCA----DQVGGPLRGWCSSQVKFGLANHTLVQ-PSKLHRTFKINKKIGANVYQQTSRMKADAPVYPHIM
+EYAHGV----YKPFYERSEPKNEAQGNGEK-QGNVPCVESVECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDG
+HRCRAGLTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVMGNKIGSPS-EFEVAADPT
+IIWFYRNCIVHKLADTVSTAKMKAPQEMRH------QDVDSPSLGDDDQQA--MDILPYWVCVTSGVVRKEQPD-SVNK
+RGRTWLAKN-DFLCPPAFKQGEH---EAEQRPVYGFQHPRCRPWQFVIANYQSSAKNIIMLLYVKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGQMVLKIFELD
+WVEMEKSHQQ-SSVDDNYL-VNMLPFIHSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDGE
+A-ERSWIYD-VYCEM----KKDHKSAVVAHKVEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGV
+SHVFM-GNDATRKLITGFSIMPTYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHIRHGVYAVENSWETLVTC
+-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPV-AGYNDETQITKTPDICIC--TWGTIHFKNSVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HY
+V-GAGDVGGYEVMSEDLFQILVHE
+>t96
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHVQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCALMHLMQV--------GDL--------------------CSH--PS
+FLGMCMFHEQVRRKGE--LVLPDSPNEESVSFVYIQHHSFSDKRCLNCLNVGDNDDSEHLKEKHLRV----YG---QIG
+R-H-VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSKLM------------------VDGFFDK-E-D------ER
+PGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVQ-PSKLHRTFKINKKIGANVYQQTSRMKAEAPVYPHIM
+EYAHGV----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDG
+HRCRAGLTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVIGNKIGSPS-EFEIAADPT
+IIWFYRNCIVHKLADTVSTAKMKAPQEMRV------QDVDSPSLGDDDQQA--MDILPYWVCVTSGVVRKEQPD-SVNK
+RGRTWLAKN-DFLCPPAFNQGEH---EAEQRPVYGFQHPRCRPWQFVIGNYQTSAKNIIMLLYVKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLVADSCMWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELD
+WVEMEKSHQQ-SSVDDNYL-VNMLPFIRSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDAE
+A-ERSWIYD-VYCEM----KKDHKSAVYAHKVEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGV
+SHVFM-GNDATRKLISGVSVMPTYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDVKIWETHIRHGVYAVENSWETLVTC
+-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGYNMETQITKTPDICIC--TWGTIHFKNSVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDV---YPAAPKKK--HY
+V-GAGDVGGYEVMSEDLFQILVHG
+>t44
+MIWSEVRQMVREG--TDNAIDTR-C------------LIAARVKHMQGHVKQVRNANEDAL--YQNFSGQKGAREKIKR
+-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCDLMHLMQN--------GDL--------------------CSH--PS
+FLGMCMFHEQVRCKGE--LVLPDSPNEESVSFVYIQHHSFSDKRCLNYLNVGDNDDSEHLKEKHLRI----YG---VIG
+K-H-VIINVWNAFMGRLNHHEPPADVEYPLRK--GGPDSKPM------------------VDGFFDK-E-D------DR
+PGIANAVSVPCG----DQVGGPIRGWCSSQVKFGLANHTLAQNPSKLHRTFKINKKMGANVYQQTSRMKAEAPVYPHIM
+EYAHGV----CKPFYDRSEPKNEAQGNGEK-QGNVPCVESMDCQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGYVDG
+HRCRAGLTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDIMVMGNKIGSPS-EFEVAADPT
+IIWFYRNCIVHKLADVVSTAKMKSPQEMRV------QDVDSPSLGDDDQQA--MDILPYWVCVTSGVVRKEQPD-SVNK
+RGRTWLAKN-DFLCPPAFEQGEH---EAEQCPVHGFKHPRCRPWQFVIADYQTSAKNIIMLLYVKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELD
+WVEMEKSHQQ-SSVDDNYL-VNMLPFMHSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDCE
+A-ERSWIYD-VYCEM----KKDHKSAVVAHKHEHKGMDWDTGKE-MNQGPK-VVMHGVLFN-------AEPNIHGQPGV
+SHVFM-GNDATRKLITGVSVMPTYKFMCNACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHMRHGVYAVENSWETLVTC
+-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGYNDETEITKTPDICIC--TWGTIHFKNSVMQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNMLVD-ELYSDM---YPAAPKKK--VY
+V-GAGDVGGYEVMSEDLFQILVHA
+>t45
+MIWSEVRQMVREG--TDNAIDNC-C------------LIAARVKHMQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YK-CMEGHDCVNTMAKSS-SQSAVWKFDRFMCDLMHLMQN--------GDL--------------------CSV--PS
+FLGMCMFHEQVRCKGE--LVLPDSPNEESVSFVYIQHHSFSDKRCLNYLNVGDNDDSEHLKEKHLRI----YG---EIG
+K-H-VIINVWNAFMGRLNHHEPPAEVMYPLRK--GGPESKPM------------------VDGFFDK-E-D------DR
+PGIANAVSVPCT----DQVGGPIRGWCSSQVKFGLANHTLVHNPSKLHRTFAINKKMGANVYQQTSRMKAEAPVYPHIM
+EYAHGV----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMDCQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDG
+HRCRAGLTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVMGNKIGSPA-EFEVAADPT
+IIWFYRNCIVHKLADLVSTAKMKSPQEMRV------QDVDSPSLGDDDQEA--MDILPYWVCVMSGVVRKEQPD-SVNK
+RGRTWLAKK-DFLVPPAFNQGEH---EAEQKPVYGFDHPRCRPWQFVIANYQTSAKNIIMLLYVKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVHKIFELD
+WVEMEKSHQQ-SSVDDNYL-VNMLPFFHSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCQYYSGQFPDGE
+A-ERSWIYD-VYCEM----KKDHKSAVVAHKHQHKGMDWDTGKE-MNQGPK-VVLHGVLFN-------AEPNIHGQPGV
+SHVFM-GNDATRKLIPGVSVMHDYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHLRHGVYAVENSWETLVTC
+-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGFVDETEITKTPDICIC--TWGTIHFKNSVVQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HY
+V-GAGDVGGYEVMSEDLFQILVHE
+>t74
+MIWSEVRQMVREG--TDNAIDNC-C------------LIAARVKHMQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGHDCVNTMAKPS-SQSAVWKFDRFMCDLMHLMQN--------GDL--------------------CSV--PS
+FLGMCMFHEQVRCKGE--LVLPDSPNEESVSFVYIQHHSFSDKRCLNYLNVGDNDDSEHIKEKHLRI----YG---EIG
+K-H-VIINVWNAFMGRLNHHEPPAEVMYPLRK--GGPESKPM------------------VDGFFDK-E-D------DR
+PGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVHNPSKLHRTFAINKKMGANVYQQTSRMKAEAPVYPHIM
+EYAHGV----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMDCQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDG
+HRCRAGLTALKIVQLDIGFSAKTLGQLNIIDCKLLGHRTWLATSPLQ------IGCDVMVVGNKIGSPA-GFEVAADPT
+IIWFYRNCIVHKLADLVSTAKMKSPQEMRV------QDVDSPSLGDDDQEA--MDILPYWVCVTSGVVRKEQPD-SVNK
+RGRTWLAKK-DFLVPPAFNQGEH---EAEQKPVYGFDHPRCRPWQFVIANYQTSAKNIIMLLYVKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVHKIFELD
+WVEMEKSHQQ-SSVDDNYL-VNMLPFFHSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCQYYSGQFPDGE
+A-ERSWIYD-VYCEM----KKDHKSAVVAHKHQHKGMDWDTGKE-MNQGPK-VVLHGVLFN-------AEPNIHGQPGV
+SHVFM-GNDATRKLIPGVSVMHDYKFMCGACVPFFHKLFMAVRNMRYDYTVNYDIKIWETHLRHGVYAVENSWETLVTC
+-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGFVDETEITKTPDICIC--TWGTIHFKNSVVQYCCYYKE
+NRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HY
+V-GAGDVGGYEVMSEDLFQILVHE
+>t26
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHMSGHVKQVRNANEDAL--YQNFTGKKGAREKIKR
+-YL-CMEGHECVVTMAKNS-SISAMWKFDRFMCDLMHLMQN--------GDL--------------------CSF--PS
+FLGMCMFHDQVRCKGE--LVLPDSKNEESVSFVYIQHHSFSDKRCLNYLNVGDNEDSEHLKEKHLRV----YG---NIG
+K-H-VIINSWNAMMGRLNHHEPAAEVVYPLRK--GGPESKPM------------------VDGFFDK-E-D------DR
+PGIANAVSVPCD----DQWGGPVRGWCSSQHKFGLADHTLIHIPSKLHRTFAINKKMGANVYQQTSRMKAAAPVYSHVM
+EYAHKV----VKPFYARSEPKNEAQGNGEK-QWNVPCVESMDCQYENKHATMAKLMHP-PLYLMRMQTMAKPPMGDVDG
+HRCRAGLTALKIVQLDIGFSQKTLGQ-NIIDSKHLGHRTWLATSPLQ------IGCSAMVMGNKIGSPQ-EVELAADPT
+VIYFYRNCIVQKMADVVSTVKMKSPQEMRV------QDVDSASLGDDDQQP--MNIIPYWVCVTSGVVHKEQPD-SVNK
+RGRTWTAKN-DFLCPDAFNQGEH---GAEQKPTHGFEHPRCRPWQFVIPVYQTGAKNIILLLYIKDV-SVNGVLQLLIW
+QLCDSH-GDWQSLVADSCAWA-VNVAVCGWKRELVPGL---NHACEMLAKTVYFEPDGE-------DEGKMVIKIFGLD
+WCEIEKSHQQ-SSVDDNYL-VNMLPFTHSRETPVGHYVQGLED-PMHLMRPGT---ARALNILF-YGCEYYSGQFPDGE
+P-ERSWIYD-VYCEL----KKDHKNAIVAVKHEHKGMDWDTGKE-MNHGPK-VIVHGVLFH-------AEPNIGGQPGV
+SHVFV-GNDATRKLIAGVSVMPIVKFMCGACVPFFRKLFMALRNMRYDYASNYDIKIVETHLREGVYAVENSWETLVVC
+-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQSV-SGYNDETEITKTPDIKIC--TWGTIHFKNSVMQYCCYYKE
+NRSVR-----------LNNTGGAELPK---------------------YHHQNVLVD-ELYGEA---YPAAPKKK--HY
+M-GAGDVGGYEVMSEDLFQILVHE
+>t61
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHMSGHVKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGHECVNTMAKNS-SVSAVWKFDQFMCDLMHLMQN--------GDL--------------------CSF--PS
+FLGMCMFHEQVRCKGE--LVLSDSKNEESVSFVYIQHPSFSDKRCLNYLNVGDNEDSEHLKEKVLRV----YG---DIG
+K-H-VIINVWNAMMGRLNHHEPAAEVVCPLRK--GGPDSKPM------------------VDGFFDK-E-D------DR
+PGVANAVSVPCD----DQWGGPVRGWCSSQHKFGLADHTLVHIPSKLHRTFAITKKMGANVYQQTSRMKATAPVYPHVM
+EYAHGV----VKPFYDRSEPKNEAQGNGEK-QWNVPCVESMDCQYENKHATMAKLMHP-PLYLVKMQTMSKPPMGDVDG
+HRCRAGLTALKIVQLDIGFSSKTLGQ-NIIHSKLLGHRTWLATSPLQ------IGCDVMVMGNKIGSPQ-EVELAADPS
+VIYFYQNCIVQKMADVVSTVKMKSPQEMRV------QDVDSASLGDDDQQP--MNIIPYWVCVTSGVVRKEQPD-SVNK
+RGHTWTAKN-DFLCPPAYNQGEH---GAEQKPVHGFEHPRCRPWQFVISVYRTGAKNINLLLYIKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLVADSCAWA-VNVAVCGWKRELVPGL---NHACEMLAKSVYFEPDGE-------DEGKMVLKIFGLD
+WCEIEKSHQQ-SSVDDNYL-VNMLPFAHSRQTPVGHYVQGLED-PMHLMRPGT---ARALNILF-YGCEYYSGHFPDGE
+A-ERSWIYD-MYCEL----KKDHKSAIVAVKHCHKGMDWDTGKE-MNHGPK-VIIHGLLFH-------AEPNIGGQPGV
+SHVFV-GNDATRKLIAGASVMFIVKFMCGACVPFFRKLFMALRNMRYDYSQNYDIKIVETHLREGVYAIENSWETLVVC
+-EMTSGRMGAKINHLPRLPEQVI-PPCILTVSGLKRAV-NGYNDETEITKTPDIKIC--TWGTIHFKNSVMQYCCYYKE
+NRSVR-----------FNNTGGAELPK---------------------YHHQNVLVD-ELYSEL---YPAAPKKA--HY
+M-GAGDIGGYEVMSEDLFQILVHE
+>t97
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHMSGHMKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGHECVNTMAKNS-SVSAVWKFDRFMCDLMHLMQN--------GDL--------------------CSF--PS
+FLGMCMFHQQVRCKGE--LVLPDSKNEESVSFVYIQHHSFNDKRCLNYLNVGDNEDSEHLEEKHLRV----YG---NIG
+K-H-VIINVWNAMMGRLNHHEPAAEVVCPLRK--GGPDSKPM------------------VDGFFDK-E-D------DR
+PGVANAMSVPCD----DQWGGPVRGWCSSQHKFGLADHTLVHVPSKLHRTFPINKKMGANVYQQTSRMKATAPVYPHVM
+EYAHGV----IKPFYDRSEPKNEAQGNGEK-QWNVPCVESMDCQYENKHATMAKLMHP-PLYLVKMQTMSKPPMGDVDG
+HRCRAGLTALQIVQLDIGFSAKTLGQ-NIIHSKLLGHRTWLATSPLQ------IGCDVVVMGNKIGSPQ-EVELAADPS
+VIYFYQNCIVQKMADVVSTVKMKSPQEMRV------QDVDSASLGDDDQQP--MNIIPYWVCVTSGVVRKEQPD-SVNK
+RGRTWSAKN-DFLCPPAFNQGEH---GAEQKPVHEFQHPRCRPWQFVISVYRTGAKNINLLLYIKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLVADSCAWA-VNLAVCGWKRELVPGL---NHACEMLAKSVYFEPDGE-------DEGKMNLKIFGLD
+WCEIEKSHQQ-SSVDDNYL-VNMLPFTHSRETPVGHYVQDLED-PMHLMRPGT---ARALNILF-YGCEYYSGHFPDGE
+P-ERSWIYD-MYCEL----KKDHKSAIVAVKHCHKGMDWDTGKE-MNHGPK-VIIHGVLFH-------AEPNIGGQPGV
+SHVFV-GNDATRKLIAGVSVMPIVKFMCGACVPFFRKLFMALRNMRYDYSQNYDIKIVETHLREGVYAVENSWETLVVC
+-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQAV-NDCNDETEITKTPDIKIC--TWPTIHFKNGMMQYCCYYKE
+NRSVR-----------FNNTGGAELPK---------------------YHHQNVLVD-ELYSEV---YPAAPKKA--FY
+M-GAGDIGGYEVMSEDLFQILVHK
+>t17
+MIWSEVRQMVREG--ADNAIDNR-C------------LIAARVKHFSGHTKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGQDCVNTMAKSS-SQSAVWKFDRFMCDLVHLMQN---GARGSGDL--------------------CSF--PS
+FLGMCMFHEQVRCKGE--LVLPDSKNEESVSFVYIQHHSFSDKRCLNELNVGDNEDSIHLKEKHLRI----YG---NIG
+K-V-VIINVWNAMMGRLNHHEPAAEVVYPLRK--GGPDSKPM------------------VDGFFDK-E-D------DR
+PGIANAVAVPCS----DQWGGPVRGWCSSQHKFGLADHTLVHVPSLLHRTFAINRKMGANVYQQTSRMKAAAPVYPHMM
+EYAHGV----VKPFYERSEPKNEAQGNGEK-QWNVPCVQSVDCQYENKHATMAKLMHP-PLYLMRMETMSKPPMGDVDG
+VRCRAGLTALKIVQLDIGFSAKTLGQ-NIIDSKLLGHRTWLATSPLQ------IGCDVMVVGNKIGSPQ-EFELAADPT
+VIYFYRNCIVQKLADVVSTVKMKSPQEMRV------QDVDSPSLGDDNQQS--MNIIPYWVCVHSGVVQKEQPD-SVHK
+RGRTWTAKN-DFLCPPAFDQGEH---GAEQKPVHGFEHPRCRPWQFVIANYQTGAKNIILLLYVKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLSADSCAWA-HNVAVCGWKRELVPGL---NHACEMLAKTVYFEPDGE-------DEGKMVIKIFGLD
+WCEMEKAHQQ-SSVDDNYL-VNMLPFTHSRENPVGHYVQGLED-PMHLIRPGT---ARALNILF-YGCEYYSGQFPDGE
+P-ERSWIYD-VYCEL----KKDHKSAIVAVKHEHKGMDWDTGKE-MNQGPK-VIIHGVLFH-------AEVNIHGQPGV
+SHVFV-GNDATRKLIAGVSVMPFVKFMCGACVPFFRKLFMALRNMRYDYTSNYDIKIIETHLRNGVYAVENSWETLVVC
+-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKQAM-AGVNDETEITKTPDIKIC--TWGTIHFKNFVMQYCVYYKE
+NRSVR-----------FNNTGGAELPK---------------------YHHQNALVD-ELYSDV---YPAAPKKK--HY
+M-GEGDVGGYEVMSEDLFQILVHA
+>t11
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHFSGHTKQVRNANEDAL--YQNFTGQKGAREKIKR
+-YL-CMEGQDCVNTMAKSS-SQSAVWKFDRFMCDLVHLMQN---GARGSGDL--------------------CSF--PS
+FLGMCMFHEQVRCKGE--LVLPDSKNEESVSFVYIQHHSFSDKRCLNSLNVGDNEDSIHLKEKHLRI----YG---DIG
+K-H-VIINVWNAMMGRLNHHEPAAEVVYPLRK--GGPDSKPM------------------VDGFFDK-E-D------DR
+PGIANAVAVPCS----DQWGGPVRGWCSSQHKFGLADHTLVHVPSLLHRTFAINKKMGANVYQQTSRMKAAAPVYPHMM
+EYAHGV----VKPFYERSEPKNEAQGNGEK-QWNVPCVQSVDCQYENKHATMAKLMHP-PLYLMRMETMSKPPMGDVDG
+VRCRAGLTALKIVQLDIGFSAKTLGQ-NIIDSKLLGHRTWLATSPLQ------IGCDVMVVGNKIGSPQ-EFELAADPT
+VIYFYRNCIVQKLADVVSTVKMKSPQEMRV------QDVDSPSLGDDNQQS--MNIIPYWVCVHSGVVQKEQPD-SVHK
+RGRTWTAKN-DFLCPPAFDQGEH---GAEQKPVHGFEHPRCRPWQFVIANYQTGAKNIILLLYVKDV-SCNGVLQLLNW
+QLCDSH-GDWQSLSADSCAWA-HNVAVCGWKRELVPGL---NHACEMLAKTVYFEPDGE-------DEGKMVIKIFGLD
+WCEMEKAHQQ-SSVDDNYL-VNMLPFTHSRENPVGHYVQGLED-PMHLIRPGT---ARALNILF-YGCEYYSGQFPDGE
+P-ERSWIYD-VYCEL----KKDHKSAIVAVKHEHKGMDWDTGKE-MNQGPK-VIIHGILFH-------AEVNIHGQPGV
+SHVFV-GNDATRKLIAGVSVMPFVKFMCGACVPFFRKLFMALRNMRYDYTSNYDIKIMETHLRNGVYAVENSWETLVVC
+-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKQAM-AGVNDETEITKTPDIKIC--TWGTIHFKNFVMQYCVYYKE
+NRSVR-----------FNNTGGAELPK---------------------YHHQNVLVD-ELYSDG---YPAAPKKK--HY
+M-GEGDVGGYEVMSEDLFQILVHA
+>t23
+MIWSECQRMLREH--EDQAIANE-C------------LIAFKVKLVNGHVKQVRNASEDAH--YTFFAGEKGARELIKR
+-YS-CMEGDGCVNTMAEGR-SESAVWKFDPFMCQLTHSMQS--------GDL--------------------CSV--PS
+FLGVCMFQRQVVMKGE--LVLPDSADEGSVSFMYIQHHSFAAKRCLNVLNVGDNEDSVHLRHKQLRV----YG---KIG
+K-H-VIISVPNAIMGRLNHHEPSAIVVFPLRQ--RGADSKSV------------------GDGFYDK-D-E------DR
+PGIANAVSVPVA----EQWVGSVRGWYSSEHKYGLANHILI-GPSKLHRTYQTTAKMGANVVKATNRMKRPQPVYPHVM
+EYANGV----VKPFYEVAESKNEAQGNGEK-PVNVPCVESPDCQYESKHARVNKLMHP-SLYLMCMEAMNKPIMGDWDG
+NRCRSPLCLLKVIQLDMGVSGKTLGQ-NIVMAKLLGERTWLATSPLQ------IGCDVVAVGKKPESPQ-EFECAADPT
+VIYFYKNLIIQQAADYVSAVQVKSPQEMRY------QDVNSPSDGDENGQS--MHIGPYWVCVSSEVVKKSQPD-SVDK
+RGRTWVAKN-EFLCPPDHMQGEHSIEGAEQKPFFGFAGPFPQPWQFVIVNPQTWAHNIIRLLYCKDV-SCNCVLTCLNW
+VLCDSH-GDWHSLIADACPCA-HNVAVCGWKRELVPGL---NHSNEHMAKTIYFEPDGH-------DEGKMILNIFGLD
+WCEVETSHQE-SSSDDNHL-VNMLPFGVSRDDPVGHYMLGLED-AIRLYRPGT---ARALNILF---VNYYSGDFQDPE
+L-ERSQLYN-VYCEQ----KQDHRNAIRASKNDHKGMAWDTAKD-MEQGPK-MVEHQVLFY-------AEPNMHGQPEV
+IHIFI-GNDAMCMLIPGMSVMVHHKFMRAACMPFFNKLFMAVRYMRYDYVDNYDIKIDETRYRDGVYARRNSWETANVC
+-EMSSGRSGAKINHNPRLPEQVT-PPRSLTVSGLKDTM-PGHPDVTEITKTPVIAIV--MWGTINLKNHVMQYCCYYKE
+TRSVR-----------VNNTGGAELPK---------------------YHYQNILVD-ELYSND---YPAAPKKA--QF
+M-GVGDVGGYEIVCEDIFQILVCD
+>t76
+LSSSHEVRVVNHKSKPDEHIADK-D------------MCADAMCNGSGHTGRIHNAVEGGI--VTNFHGF---AEMPKN
+-HD-VMEEQGGPGTCLAPQQSADTSWPFVMFTVDLAHRCRG--------GDMPQNTGDSMTCPHLAEGLAAVNS---RA
+FIGVSIYDLKVSHKMI--QACNPIQN---------DNHAFSDQRCLNDLSQGVVGASFPKMQHGVRH----YK---K--
+------RVYENEVGGRLDDAEAIDDMGVWIRW--EGVKHAWCHPIGSCPDHLVCSLLVLQPARNFIQLS-MVRDTPHRL
+PKMASAAPVYKQTCHLEQVQGTARMWGKSGPRVVLNGHMLK-TQNTLHRQYLVDVELQATMVFVAARMKTDSSMYMSVR
+EILHG------------CGIKDEAQADGQR-PATLIVVLSKDNKGITEHGAVLKKIHP----------LCKRCMENGRC
+LRYKNDLTGDQLVQLAD----NTCAW-NLFEC--LRDSKSLFGSPLFIKVDEDRGFTAP-------SK-------VEPK
+CAQFYSKSCTHC----------------TM------CSVGSHASEEDALDLYTHKPVPDAQCFVSRVARNIPEH-SPCK
+-----------------------------P---CS-----------------VEEVCYCKVCDSKDVRAVKNAYQDLQV
+PLSKLK-APWLSMGHCECWEEDINNILSVVKHELVDDVDRMNRLTEVAAKMAYFGPDGFHWDVELWEENDLNCDDFELG
+W-NLKH-------EDDHPL-LCIGSFSVHKYVSVMVYPLPMND-CVRMSQPCHAAHAQDIPTEQ---TRYQIHTFLDDS
+I-RRDLCNQ-GCHEENMVWRDDLKDPISTEVIADKLHEWPTNVN-KENSAD----HRQLFH-------ANSSALDKHQH
+NVVMN-GSPCIRALIIGGSSVGVNHFMMGPCQEFFTDLFMMYEGLQYACVCAMNITIQCLHTGEGVMCNVKCKEFLQRE
+DEMKAGLIGIICNHLSRMIMVIL-VHCLLTHAGLKSME-IGFDR-TGVVRMPLIAEP--LYLVI-YVNAVEPYTDAYKK
+PKSMHQFQFDDCQIRYRTNTGFEETPVGATHLTHVCVCVPHPWTKGKSEILQNMGSA-VLYNDVIRDHNASEQKE--AH
+V-PMGDEGRISRAKDEIMYIRDLE
+>t53
+LSSSHEVRVVNHKSKPDEHIADK-D------------MCADAMCNGSGHTGRIHNAVEGGI--VTNFHGF---AEMPKN
+-YD-VMEEQGGPGTCLAPQQSADTSWPFVMFTVDLAHRCRG--------GDIPQNTGDSMTCPHLAEGLAAVNS---RA
+FIGVSTYDLKVSHKMI--QACNPIQN---------DNHAFSDQRCLNDLAQGVVGASHPKMQHGVRH----YK---K--
+------RVYENEVGGRLDDAEAIDDMGVWIRW--EGVKHAWCHPIGSCPDHLVCSLLVLQPARNFIQLS-MVRDTPHGL
+PKMASAAPVYKQTCHLEQVQGTARMWGKSGPRVVLNGHMLK-TQNTLHRQYLVDVELGATMVFVAARMKTDLSMYMSVR
+EILHG------------CGIKDEAQADGQR-PATLIVVLSKDNKGITEHGAVLKKIHP----------LCKRCMENGRC
+LRYKNDLAGDQLVQLAD----NTCAW-NLFEC--LRDSKSLFGSPLFIKVDEDRGFTAP-------SK-------VEPK
+CAQFYSKSCTHC----------------TM------CSVGSHASEEDALDLYTHRPVPDAQCFVSRVARNIPEH-SPCK
+-----------------------------P---CS-----------------VEEVCYCKVCDSKDVRAVKNAYQDLQV
+PLSKLK-APWLSMGHCECWEEDINNILSVVKHELVDDVDRMNRLTEVAAKMAYFGPDGFHWDVELWEENDLNCDDFELG
+W-NLKP-------EDDHPL-LCIGSFSVHKYVSVMVYPLPMND-CVRMSQPCHAAHAQDIPTEQ---TRYQIHTFLDDS
+I-RRDLCNQ-GCHEENMVWRDDLKDPISTEVIADKLHEWPTNQN-KENSAD----HRQLFH-------ANSSALDKHQH
+NVVMN-GSPCIRALIIGGSSVGVNHFMMGPCQEFFTDLFMMYEGLQYACVCAMNITIQCLHTGEGVVCNVKCKEFLQRE
+DEMKAGLIGIICNHLSRMIMVIL-VHCLLTHAGLKSME-IGFDR-TGVVRMPLIAEP--LYLVI-YVNAVEPYTDAYKK
+PKSMHQFQFDDCQIRYRTNTGFEETPMGATHLTHVCVCVPHPWTKGKSEILQNMGSA-VLYNDVIRDHNASEQKE--AH
+V-PMGDQGRISRAKDEIMYIRDLE
+>t16
+LSSSHEVRVVNHKSKPDEHIADK-D------------MCADAMCNGSGHTGRIHNAVEGGI--VTNFHGF---AEMPKN
+-YD-VMEEQGGPGTCLAPQQSADTSWPFVMFTVDLAHRCRG--------GDIPQNTGDSMTCPHLAEGLAAVNS---RA
+FIGVSTYDLKVSHKMI--QACNPIQN---------DNHAFSDQRCLNDLAQGVVGASHPKMQHGVRH----YK---K--
+------RVYENEVGGRLDDAEAIDDMGVWIRW--EGVKHAWCHPIGSCPDHLVCSLLVLQPARNFIQLS-MVRDTPHGL
+PKMASAAPVYKQTCHLEQVQGTARMWGKSGPRVVLNGHMLK-TQNTLHRQYLVDVELGATMVFVAARMKTDLSMYMSVR
+EILHG------------CGIKDEAQADGQR-PATLIVVLSKDNKGITEHGAVLKKIHP----------LCKRCMENGRC
+LRYKNDLAGDQLVQLAD----NTCLW-NLFEC--LRDSKSLFGSPLFIKVDEDRGFTAP-------SK-------VEPK
+CAQFYSKSCTHC----------------TM------CSVGSHASEEDALDLYTHKPVPDAQCFVSRVARNIPEH-SPCK
+-----------------------------P---CS-----------------VEEVCYCKVCDSKDVRAVKNAYQDLQV
+PLSKLK-APWLSMGHCECWEEDINNILSVVKHELVDDVDRMNRLTEVAAKMAYFGPDGFHWDVELWEENDLNCDDFELG
+W-NLKP-------EDDHPL-LCIGSFSVHKYVSVMVYPLPMND-CVRMSQPCHAAHAQDIPTEQ---TRYQIHTFLDDS
+I-RRDLCNQ-GCHEENMVWRDDLKDPISTEVIADKLHEWPTNQN-KENSAD----HRQLFH-------ANSSALDKHQH
+NVVMN-GSPCIRALIIGGSSVGVNHFMMGPCQEFFTDLFMMYEGLQYACVCAMNITIQCLHTGEGVVCNVKCKEFLQRE
+DEMKAGLIGIICNHLSRMIMVIL-VHCLLTHAGLKSME-IGFDR-TGVVRMPLIAEP--LYLVI-YVNAVEPYTDAYKK
+PKSMHQFQFDDCQIRYRTNTGFEETPMGATHLTHVCVCVPHPWTKGKSEILQNMGSA-VLYNDVIRDYNASEQKE--AH
+V-PMGDQGRISRAKDEIMYIRDLE
+>t42
+LSSSHEMRVVHHKSKPDEEIADQ-D------------LCAEEMCKGSGHTGRIHSAVEGGI--WTNFHGF---AEMPKN
+-YD-VMEEQGGPGTCIAPRQSADTSWPFMVFTVDLAHRCRG--------GDTPTQAGDSMTFPHLAEGLPAVNS---RA
+FVGVSSYDLRVSHKMI--QACTLIQN---------DNVAFSDQRPLNDLNQGCVGTSHPKMPHGVRH----YK---K--
+------KVYENEVGDRLDDAEGIDDVGVWMRW--NGVKHAWCHIIGSCPDHLVCSLLVLQPGRNFIQLS-VVHDTPHRL
+PKMASAAAVFKQTCHLEQVPGTARMWGKSGPRVRLNGHVLK-NQNILHRQYLVDVNLGATMVFVLARMKTDASMYMSHR
+EILHGGTFDAAKPFRQICGTKDEAQPDGRR-PATLLVVLSKDNQGITEHGAVLKHVHP----------LCKKDCNNNRC
+LRCKNVLAGNQLIQLSD----VTCAW-NLFEC--LGDSESLFGSPLAIKVDEDRGFTAP-------SK-------VEPK
+CAQFYSKSCTHH----------------MM------CSVGSNASEEDALELYTHKPVPDPQCFVSIVVRNIPEH-SPCK
+-----------------------------P---CS-----------------VEEVAYCKNCDSKDVRAVQNAYQDLAV
+PLSKLK-APWLSMGHCECWEEDINNILSMVKHELVVDQDMVNRSPEVAAKMAYFGPDGFHWDVELCEESDLTVDDFELG
+W-VLKP-------EDDHPL-ICIGSFSVHKQFSVMVYPLPMND-AIRMSQPCHAAHAQDIHTDQ---DRYDVRTFLGHS
+I-KCHMCNQ-ACHEENIVWRDDLKDPITTEVIAEKLQEWPTNQN-KENVAD----HRQLFH-------ANSSALDKHRH
+NVMMN-GSACIRTLIIGGSIVGVNVFMMEPCQEFFTDLFMVYEGLQYAVVCAVNIIIQCLHTNEGVVCNVKCKEFLQRE
+EDMKSGLIGIICNHISRMCMHIL-VVCLLTHCGLKAME-IPFDI-TGVVRGPLITEP--LYLII-YVNAVEPYTDAYKK
+PKSMHQFQFDDVQIRYRTNTGFEENPKLATHLVHVCVVVPHPWTKGKSEILQNMESA-HLYNAVIRDNNASEQKE--AH
+V-PVGDEGRISRAKNEILYIRDLE
+>t24
+QSSSHEMRVVHHKSKPDEEITDQ-D------------LCAEEMCKGSGHTGRIHSAVEGGI--WTNFHGF---AEMPKN
+-YD-VMEEQGGPGTCVAPRQSADTNWPFMVFPVELAHRCRG--------GDTP--------FPHLAEGLPAVNS---RA
+FIGVSSYDLKVSHKMI--QACNPIQN---------DNVAFSDQRVLNDLSQGCVGTSHPKMPHGVRH----YK---K--
+------RVYENEVGDRLDDAEAVDDVGVWMRW--AGVKVAVCHVIGSCPDHLVVSLLVLQPARNFIQLS-VVHDTPHRL
+PKMASAAAVFKQTCHLEQVAGTARVWGKSGPRVKLNGHVLK-NQNVLHRQYLVDVDLGATMVFVAARMKTDASMYMSHR
+EILHGGTFDAAKPFRQICGVKDEAQPDGQR-PATLLVVLSKDNVGITEHGAVLKHVHP----------LCKKDCNNNRC
+LRCKNVLAGNQLVQLAD----ITCAW-NLFEC--LGDSESLFGSPLAIKVDEDRGFTAP-------SK-------VEPK
+CQQFYSKSCTHC----------------VM------CSVGSNASEEDALELYTHKPVPDPQCFVSIVVRNIPEH-SPCK
+-----------------------------P---CS-----------------VEEVCYCKNCDSKDVRATQNAYQELAI
+PLSKLK-APWLSMGHCECWEEGINNILSMVKHELVVDQDMVNRSPEVAAKMAYFGPDGFHWDIELCEENDLTCDDFELG
+W-VLKP-------EDDHPL-ICIGSFSVHKQFSVMVYPLPMND-AIRMSQPCYAAHAQDIHTDQ---DRYDIRTFLEHS
+I-RCHLCNQ-ACHEENIVWRDDLKDPITTEVIADKLQEWPTNQN-AENVAD----HRQLFH-------ANSSCLDRHRH
+NVMMN-GSSCIRTLIIGGSIVGVNVFMMGPCQEFFTDLFMVYEGLQYAVVCAINIIIQVLHTNEGVVCNVKCKEFLQRE
+DDMKSGLIGIICNHISRMCMHIL-VHCLLTHCGLKAME-IPFDR-TGVVRGPLIAEP--LYLII-YVNAVEPYTDAYKK
+PKSMHQFQFDDVQIRYRTNTGFEENPKLATHLVHVCVVVPHPWTKGKSEILQNMESARHLYNAVIRDNNASHQKE--AH
+V-PAGDQGRISRAKNEILYIRDLE
+
+
diff --git a/test/example.fastq b/test/example.fastq
new file mode 100644
index 0000000..0f67574
--- /dev/null
+++ b/test/example.fastq
@@ -0,0 +1,12 @@
+ at EAS54_6_R1_2_1_413_324
+CCCTTCTTGTCTTCAGCGTTTCTCC
++
+;;3;;;;;;;;;;;;7;;;;;;;88
+ at EAS54_6_R1_2_1_540_792
+TTGGCAGGCCAAGGCCGATGGATCA
++
+;;;;;;;;;;;7;;;;;-;;;3;83
+ at EAS54_6_R1_2_1_443_348
+GTTGCTTCTGGCGTGGGTGGGGGGG
++EAS54_6_R1_2_1_443_348
+;;;;;;;;;;;9;7;;.7;393333
diff --git a/test/example.gff b/test/example.gff
new file mode 100644
index 0000000..0f129a4
--- /dev/null
+++ b/test/example.gff
@@ -0,0 +1,25 @@
+##gff-version 3
+##sequence-region ctg123 1 1497228
+ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN
+ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001
+ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1
+ctg123 . mRNA 1050 9000 . + . ID=mRNA00002;Parent=gene00001;Name=EDEN.2
+ctg123 . mRNA 1300 9000 . + . ID=mRNA00003;Parent=gene00001;Name=EDEN.3
+ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mRNA00003
+ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mRNA00001,mRNA00002
+ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mRNA00001,mRNA00003
+ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA00003
+ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA00003
+ctg123 . CDS 1201 1500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
+ctg123 . CDS 3000 3902 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
+ctg123 . CDS 5000 5500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
+ctg123 . CDS 7000 7600 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
+ctg123 . CDS 1201 1500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
+ctg123 . CDS 5000 5500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
+ctg123 . CDS 7000 7600 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
+ctg123 . CDS 3301 3902 . + 0 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
+ctg123 . CDS 5000 5500 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
+ctg123 . CDS 7000 7600 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
+ctg123 . CDS 3391 3902 . + 0 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
+ctg123 . CDS 5000 5500 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
+ctg123 . CDS 7000 7600 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
diff --git a/test/example.mase b/test/example.mase
new file mode 100644
index 0000000..7e5891d
--- /dev/null
+++ b/test/example.mase
@@ -0,0 +1,1500 @@
+;
+t73
+LIVSQIRVMVRDG--IHKAMDEE-V------------LIARRVKPYSGNGTQVRNDVEDAN--CQEFVGI---RELGKH-YK-CMDGFHTVNNGAGEN-S
+ESAMWIFDLWMCKLNHGMQR--------GDIGRVKRDVQKFPKLKEGAPNCSSFVKPYFMGCDMFHKQVEYRGTHGLVLDDTWNEESATFPYPQVHSRSD
+KRCLNGLHQGDHEESVH---HAPRI----MR---LIGH-HLVIIVLMNHDMGRLNHLEPDAVIPSPLRIGGDGWVPKPI------------------EDG
+FFDK-D-Q------SRPDVANASIVPDK----DQWVGAHNQWGSSLRKVGLAVHDLR-NISDLYRCVWMDCHLGANHYRQISRMKMITPTYTHMTEYANG
+L----WHPFYKASDHKNEAQGVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVVKPLLGDWEGCKCRS---KLYVSQLDH----KTLSK
+-NLGLY--MQKRTWLATAPLQ------IGCMFMLVGRKKNSEE-NYNKAADPTVIWFYTQPIVYV-ADVFGCTKGKNPQEMRG------NNVMSESLGDD
+NLQD--MSGVPVTVCTSSVMVRKDMQD-SVDKRGCTWNAKE-DHLCPSSFCKGER---EDEPGGVTQ-----------------RCIENIAKLLYIKDV-
+LCNEVLNGLQWQLCWSV-GDWESLIPQACWDAKKDLAVCAWKMELVPGL---NRNNENLAKVIYFGPDGH-------DEGPMQAKIVTLHW-EMDVSHRG
+-SSVDDNVV-VVMLAFAVSFCHPWGHYIQGLGD-QHKLARPNT---AQKLSILT---VFHFSGGFRDKPM-ERSQLHS-TYSED----KKDQKVLIHAMK
+-RNKGLDWHAGND-MKGGPK-IIYLGMLFY-------AENNVAKQKAHFVVFL-ISDATRLLIVHEGCMIDYTFMEFACHPFFAELFMEHMVARYQYYSN
+VDIKIFDTCFRSAVYAVDNSWETLCDY-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMRIQIAIRVSGSE-SENVVLQY
+CLYYEENKSIR-----------QNNTGSADLPK---------------------DRLVNSFVD-ELYNSI---YTAAPKKK--RHL-GIGDNGGMELVRE
+DIFQILVCV
+;
+t66
+LIVSQIRVMVRDG--IHKAMDEE-V------------LIARRVKPCSGNGTQVRNDVEDAN--CQEFVGI---RELGKH-YK-CMDGFHTVNNGAGEN-S
+ESAMWIFDLWMCKLNHGMQR--------GDIGRVKRDVQKFPKLKEGAPNCSSFVKPYFMGCDMFHKQVEYRGTHGLVLDDTWNEESATFPYPQVHSRSD
+KRCLNGLHQGDHEESVH---HAPRI----MR---LIGH-HLVIIVLMNHDMGRLNHLEPDAVIPSPLRIGGDGWVPKPI------------------EDG
+FFDK-D-Q------SRPDVANASIVPDK----DQWVGAHNQWGSSLRKVGLAVHDLR-NISDLYRCVWMDCHLGANHYRQISRMKMITPTYTHMTEYANG
+L----WHPFYKASDHKNEAQGVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVVKPLLGDWEGCKCRS---KLYVSQLDH----KTLSK
+-NLGLY--MQKRTWLATAPLQ------IGCMFMLVGRKKNSEE-NYNKAADPTVIWFYTQPIVYV-ADVFGCTKRKNPQEMRG------NNVMSESLGDD
+NLQD--MSGVPVTVCTSSVMVRKDMQD-SVDKRGCTWNAKE-DHLCPSSFCKGER---EDEPGGVTQ-----------------RCIENIAKLLYIKDV-
+LCNEVLNGLQWQLCWSV-GDWESLIPQACWDAKKDLAVCAWKMELVPGL---NRNNENLAKVIYFGPDGH-------DEGPMQAKIVTLHW-EMDVSHRG
+-SSVDDNVV-VVMLAFAVSFCHPWGHYIQGLGD-QHKLARPNT---AQKLSILT---VFHFSGGFRDKPM-ERSQLHS-TYSED----KKDQKVLIHAMK
+-RNKGLDWHAGND-MKGGPK-IIYLGMLFY-------AENNVAKQKAHFVVFL-ISDATRLLIVHEGCMIDYTFMEFACHPFFAELFMEHMVARYQYYSN
+VDIKIFDTCFRSAVYAVDNSWETLCDY-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMRIQIAIRVSGSE-SENVVLQY
+CLYYEENKSIR-----------QNNTGSADLPK---------------------DRLVNSFVD-ELYNSI---YTAAPKKK--RHL-GIGDNGGMELVRE
+DIFQILVCV
+;
+t32
+LIVSQIRVMVRDG--IHKAMDEE-V------------LIARRVKPYSGNGTQVRNDVEDAN--CQEFVGI---RELGKH-YK-CMDGFHTVNNGAGEN-S
+ESAMWIFDLWMCKLNHGMQR--------GDIGRVKQDVQKFPKLKEGAPNCSSFVKPYFMGCDMFHKQVEYRGTHGLVLDDTWNEESATFPYPQVHSRSD
+KRCLNGLHQGDHEESVH---HAPRI----MR---LIGH-HLVIIVLMNHDMGRLNHLEPDAVIPSPLRIGGDGWVPKPI------------------EDG
+FFDK-D-Q------ARPDVANASIVPDK----DQWVGAHNQWGSSLRKVGLAVHDLR-NISDLYRCVWMDCHLGANHYRQISRMKMITPTYTHMTEYANG
+L----WHPFYKASDHKNEAQGVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVVKPLLGDWEGCKCRS---KLYVSQLDH----KTLSK
+-NLGLY--MQKRTWLATAPLQ------IGCMFMLVGRKKNSEE-NYNKAADPTVIWFYTQPIVYV-ADVFGCTKGKNPQEMRG------NNVMSESLGDD
+NLQD--MSGVPVTVCTSSVMVRKDMQD-SVDKRGCTWNAKE-DHLCPSSFCKGER---EDEPGGVTQ-----------------RCIENIAKLLYIKDV-
+LCNDVLNLLVWQLCWSV-GDWESLIPQACWDAKKDLAVCAWKMELVPGL---NRNNENLAKVIYFGPDGH-------DEGPMQAKIVTLHW-EMDVSHRG
+-SSVDDNVV-VVMLAFAVSFCHPWGHYIQGLGD-QHKLARPNT---AQKLSILT---VFHFSGGFRDKPM-ERSQLHS-TYSED----KKDQKVLIHAMK
+-RNKGLDWHAGND-MKGGPK-IIYLGMLFY-------AENNVAKQKAHFVVFL-LSDATRLLIVHEGCMIDYTFMEFACHPFFAELFMEHMVARYQYYSN
+VDIKIFDTCFRSAVYAVDNSWETLCDY-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMRIQIAIRVSGSE-SENVVLQY
+CLYYEENKSIR-----------QNNTGSADLPK---------------------DRLVNSFVD-ELYNSI---YTAAPKKK--RHL-GIGDNGGMELVRE
+DIFQILVCV
+;
+t75
+LIVSEIRVMVRDE--VHKAMDEE-C------------LIARRVKPYSGNGNQIRNDIEDAN--GQEFVGI---RELGKH-YD-CMDGYHTVNNGAGEN-S
+ESAMWIFDLWMCKLNHGMQR--------GDIGRVQQDVHKFPKLKEGAPNCSSFVKPVFMGCDMFHRQVQNRGNHGLVLDDTWNEESGTFPYPQVHSRNE
+KRCINKLHQGDHNESCH---HNPRI----VR---RIGH-HLVIIVLVNRDMGRLNYIEPDALVPSPLRFGGDEWVPKPI------------------EDG
+FFDK-D-Q------ARPDVANA-IVPDR----DQWVGAHKEWGSSLCKVGLAVHDLR-NVSDLYRCVWMECVLGANHYQQVSRMKMVTPAYTHMTEYANG
+L----WHPFYKNPDHKNEAQGVGEK-PHQLPCVESETCQYETKHAKVCKQVHG-ALYLIGMKTVAKPVLGDWEGCKCRSDLIKLYVSQLDH----KTLSK
+-NMGLY--MRNRTWLATSPLQ------IGCIFMLVGRKKNSEE-NYNKAADPTVIWFYTQPIVYV-ADVFGCTKGKNPQEMRK------NNVISESLGDD
+NLQD--MPGMPVTVCTSSVMVRKDMHQ-SVDKRGYTWHAKE-DHLCPDSFCKGEK---EEEPGGVRR-----------------RIVENIVKLLYIKDV-
+LCNQVLNLLQWQLCWSV-GDWESLVPQACWGAKKDLAVCAWKMELVPGL---NRNNENLAKIIYFGPDGH-------DEGNMQAKIVTLHW-EMDVSHRG
+-SSVDDNVV-VVMLAFQASFCDPWGHYIQGLGD-QYKLARPNT---ARQLSILV---VMHFSGGFRDKPI-ERSQLHC-TYSEN----KKDQKVVIRAMK
+-RNKGCDWHAGKD-MAGGPK-IIYVGMLFY-------AESNWAKQKAHFVVFL-ISDATRLLIHHVGCMIEYTFMEFACHPFFAELFMEHMVIRYQYYNN
+VDIKIFDTCFRGAVYAEDNSWETLCGY-EMLSGYFGAEINHNPRLPEQVC-PPCTITVSGLKGKLHNRWPVLTQITRTMRIQIPIRISGSE-SENVVLQY
+CLYYEENKSIR-----------QNNTGSAVLPK---------------------DRLVNNFVD-ELYNSV---YTAAPKKK--RHL-GIGDNGGMELVRE
+DIFQILVCV
+;
+t79
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTFSGSQNQVRNAVEDAA--RPDFVGT---RELGKQ-YE-CMDGVGAVDTGAGDN-S
+ESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGVDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSV
+KRCLNVLHQGDHEESRH---HNARI----VR---RIGL-NLVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------GDG
+FFDK-D-Q------ARPLMANAVCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHG
+L----WKPFYQASDHKNEAQGVGER-THQLPCVESHTCQYEVKHAKVCKLVHH-ALYLLGLRTVMKPHLGDVDGCRCRSDLNNLILSQLDD----KTLSK
+-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSAN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+SLQQ--MPAVPVDVCVMSVMVNKSMPQ-SHDKRGYTWQAKQ-DHLFPVNVVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-
+DCNMVLSLLVWQLC--H-GDWEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLHW-EMEASHRE
+-SSVRDNMI-VIMLPFNINSIDPWRHYILGLND-QIQLTRPNT---ARRLSILH---VMHYSGEFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+-HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVRILILHHGCMTDHTFMEFACNPFFSELFMEHVYIRYQYINN
+HDIKIKDTVFRLAVYAWDNFWETLCKC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIRIKIREPGSE-SENTVVMY
+VIYYKERKSIR-----------QNNTGCAKLPQ---------------------ARLVNKVVD-ELYNNV---YHAIPKKE--MNQ-GVGDSGGVEMVQE
+DVFQILVCI
+;
+t27
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTMSGSQNQVRNAVEDAA--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-S
+ESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSV
+KRCLNVLHQGDHEESRH---HNARI----VR---RIGM-NLVIISYANVDMGRLNHCEDQAIVYSPLRYGGAGFVSKPI------------------ADG
+FFDK-D-Q------ARPLMANAVCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHG
+L----WKPFYQASDHKNEAQGVGER-THQLPCVESHTCQYEVKHAKVCKLVHH-ALYLLGIHTVMKPHLGNVDGCRCRSDLNNLILSQLDD----KTLSK
+-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSAN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNCVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-
+DCNIVLSLLVWQLC--H-GDWEPLLPQACEGARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLHW-EMEASHRE
+-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ARRLSILH---VMHYSGAFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+-VNKDHDWITGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVRILILHHGCMTDHTFMEFACNPFFSELFMEHVYIRYQYVNN
+HDIKIKDTVFRLAVYAWENFWETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIRIKIREPGSE-SENTVVMY
+VIYYKERKSIR-----------QNNTGCAKLPQ---------------------ARLVNKVVD-ELYNNV---YHAIPKKD--MNQ-GVGDSGGVEMVQE
+DVFQILVCI
+;
+t93
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTMSGSQNQVRNAVEDAA--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-S
+ESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSV
+KRCLNVLHQGDHEESRH---HNARI----VR---RIGM-NLVIISYANVDMGRLNHCEDQAIVYSPLRYGGAGFVSKPI------------------ADG
+FFDK-D-Q------ARPLMANAVCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHG
+L----WKPFYQASDHKNEAQGVGER-THQLPCVESHTCQYEVKHAKVCKLVHH-ALYLLGIHTVMKPHLGNVDGCRCRSDLNNLILSQLDD----KTLSK
+-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSAN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNCVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-
+DCNIVLSLLVWQLC--H-GDWEPLLPQACEGARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLHW-EMEASHRE
+-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ARRLSILH---VMHYSGAFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+-VNKDHDWITGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVRILILHHGCMTDHTFMEFACNPFFSELFMEHVYIRYQYVNN
+HDIKIKDTVFRLAVYAWENFWETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIRIKIREPGSE-SENTVVMY
+VIYYKERKSIR-----------QNNTGCAKLPQ---------------------ARLVNKVVD-ELYNNV---YHAIPKKD--MNQ-GVGDSGGVEMVQE
+DVFQILVCI
+;
+t59
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTFSGSQNQVRNAVEDAA--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-S
+ESAVVIFDVWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSV
+KRCLNVLHQGDHEESRH---HNARI----VR---RIGM-NLVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------ADG
+FFDK-D-Q------ARPLMANAHCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECILGANVYHQISRMKMHGPTYSHVMEYAHG
+M----WKPFYQASDHKNEAQGVGER-THQLPCVDSHTCQYEVKHAQVCKLVHH-ALYLLGLRTVMKPHLGDVDGCRCRSDLNNLILSQLDD----KTLSK
+-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSGN-NYNQAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNFVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-
+DCNIDLSLLVWQLC--H-GDWEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLHW-EMEASHRE
+-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ACRLSILH---VMHYSGEFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+-HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVRILILHHGCMTDHTFMEFACNPFFAELFMEHVYIRYQYVNN
+HDIKIKDTVFRLAVYAWENFWETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIGIKIREPGSQ-SENTVVMY
+VIYYKERKSIR-----------QNNTGCAKLPQ---------------------HRLVNKVVD-ELYNNV---YHAIPKKD--MNQ-GVGDSGGVEMVQE
+DVFQILVCI
+;
+t7
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKKFSGSQGQVRNAIEDAA--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-S
+ESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSMPMPYFLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSV
+KRCLNVLHQGDHEESRH---HNARI----VR---RIGM-NLVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------ADG
+FFDK-D-Q------ARPLMANAHCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHG
+M----WKPFYQASDHKNEAQGVGER-THQLPCVDSHTCQYEVKHAQVCKLVHH-ALYLLGLRTVMKPHLGDVDGCRCRSDLNNLILSQLDD----KTLSK
+-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSGN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNFVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-
+DCNIVLSLLVWQLC--H-GDWEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLHW-EMEASHRE
+-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ACRLSILH---VMHYSGEFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+-HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVRILILHHGCMTDRTFMEFACNPFFAELFMEHVYIRYQYVNN
+HDIKIKDTVFRLAVYAWENFWETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIGIKIREPGSQ-SENTVVMY
+VIYYKERKSIR-----------QNNTGCAKLPQ---------------------HRLVNKVVD-ELYNNP---YHAIPKKD--MNQ-GVGDSGGIEMVQE
+DVFQILVCI
+;
+t78
+LIVSEVRVMVRDG--LNIAIDEL-C------------LIANRVKTFSGSQGQVRNAIEDAA--RPDFVGI---RELGKQ-YE-CMDGVGAVDTGAGDN-S
+ESAVVIFDIWMCQLPHGMQW--------GDIGRVVVDHPKFLKLEEGAPNCSSIPMPYFLGCDMFHREVILKGAKGLVLPD--NEDSMAFPYVQVHSRSV
+KRCLNVLHQGDHEESRH---HNARI----VR---RIGM-NLVIISYANVDMGRLNHCEDEAIVFSPLRYGGAGFVSKPI------------------ADG
+FFDK-D-Q------ARPLMANAHCVPEN----DQWTGAVGQWCSSVVKCGLADHPLE-NISRLLRCVVMECVLGANVYHQISRMKMHGPTYSHVMEYAHG
+M----WKPFYQASDHKNEAQGVGER-THQLPCVDSHTCQYEVKHAQVCKLVHH-ALYLLGLRTVMKPHLGDVDGCRCRSDLNNLILSQLDD----KTLSK
+-NCFTY--LGNMTWLATSPLH------IGCMIIFVGRKQQSGN-NYNRAGDPTTICFCRKPIVMH-ADVFGCARAKDPQEMRM------NNVISESLGDD
+SLQQ--MPAVPVTVCVMSHMVKKSMPQ-SHDKRGYTWQAKQ-DHLFPVNFVKGEQ---EEEPEGADQ-----------------RTVHDMVRLLYSKDV-
+DCNIVLSLLVWQLC--H-GDWEPLLPQACESARRDLAVCAWKRELVPGL---NHNNEFLAKIIYFGPDGH-------DEGPMGQKIVDLHW-EMEASHRE
+-SSVRDNMI-VIMLPFSINSIDPWRHYILGLND-QIQLTRPNT---ACRLSILH---VMHYSGEFHDKSA-ERSQLHS-RYSEH----KNDHKCVILASK
+-HNKDHDWATGKDEMKGGAK-IMNPGALFY-------AEQNWVRPKNHFVIFL-ICDAVRILILHHGCMTDRTFMEFACNPFFAELFMEHVYIRYQYVNN
+HDIKIKDTVFRLAVYAWENFWETLCNC-EMLSGHVGAKINHNPRLFEQVC-PPVELTVSGLKGKV-NGWPYLTDITRTPLIGIKIREPGSQ-SENTVVMY
+VIYYKERKSIR-----------QNNTGCAKLPQ---------------------HRLVNKVVD-ELYNNP---YHAIPKKD--MNQ-GVGDSGGIEMVQE
+DVFQILVCI
+;
+t12
+LIVSEVRVMVRDG--INIAIDEL-C------------LIANRVKAFSGHQNQVRNAMEDAQ--RPDFVGI---RELGKQ-YQ-CMDGHGAVDTGAGRN-S
+ESAVWIFDIWMCKLAHGMQW--------GDIGRVSVDHPKFLKLEEGAPRCSSCPMPYFLGCEMFHRQVILKGAKGLVLPD--NEDSMAFPYVQVHSRSV
+KRCLNVLVQGDHDESRH---HNARI----VA---RIGM-NMVIIRYLNVEMGRLNHCEDDAMVYSPLRIGGAGTHSKPI------------------ADG
+FFDK-D-Q------ARPLIANAHIVPEN----DQWTGAVAQWCSSVIKCGLANHDLE-NISRLLRCVVMECVLGANVYHQASRMKMHGPYYAHVTEYAHG
+L----WKPFYQTSDHKNEAQGVGES-THQLPCVESQTCQYEVKHAKVCKLVHH-ALYLLALHTMMKPRLGDIDGCRCRSELNKLALSQLDD----KTLSK
+-NCFQY--LGNMTWLATSPLH------VGCMIIF------------------------------------------------V------NNVLSQSLGDD
+SLQQ--MHAMPVTVVVVSHMVKKSMPQ-SHDKRGYTWQAKDFDQLIPVSFVKGEQ---EEEPEGPNN-----------------RVVHNIVKLLYTKDV-
+DCNTVLSLLIWQLC--H-GDWEQLVPQACAGARSDLAVCAWKRELVPGL---NHNNENLAKVIYFGPDGH-------DEGPMGRKIVDLHW-EMEASHRD
+-SSVRDNML-VIMLPFLVNNLDPWRHYILGLND-QIQLTRPNT---ARRLSILM---VMHYSGEFHDKSP-ERSQLHFDSYSEH----KNDHKCVILASK
+-HNKGLDWATGKDDMKGGAK-IMMSGALFY-------AEQNWIRARNHFVIFL-ICDAVRILIVLHGCMTAWTFMEFACNPFFAELFMEHVYIRYQYVNN
+HDIKIKDTEFRLAVYAWENSWETLCNC-EMLSGHIGAKINHNPRLFEQVC-PPCELTVSGLKGKH-VGWPYLTDITRTPLIRIQIREPGSE-CENSVVMY
+VIYYKERKSIR-----------QNNTGCAKLPQ---------------------HRLVNKVVD-ELYNNV---YHAIPKKD--INV-GVGDSGGMEVVQE
+DVFQILVCI
+;
+t81
+LIVSEVRHMVRDG--ANVAIDEL-C------------LIACRVKAFSGHGHQVRNAVEDAA--RPDFIGI---RELGKP-Y--CMDGHGAVNTGAGHN-S
+ESAVWIFDIWMYKLSHGMQW--------GDIGRVGVDHPKFLKLEEGAPNCSSLPMPYFLGVDMFHRQVTIKGAKGLVLPDIWNESPMAFPYAQVHSKSH
+KRCLNVLVQGDHEESEH---HNARI----MS---KIGT-HLVIINIINVEMQRLNHCEDKAIVYSPDRIGGAGFHSKPI------------------ADG
+FFDK-D-Q------ARPIIANAHIVPVN----DQWTGPMAQWCSSVIKCGLANHELE-DVSRLLRCVGMECNLGANHYHQVSRMKMHGPIYSHMTEYAVG
+L----WKPFYQASEHKNEAQGLGER-PHQLPCVESQTCQYEIKVAKVCKLVHV-ALYLVGLKTVVKPKLGDWDGIRCRSELNKLYLSQLDD----KTLSK
+-NCFIY--LGNMTWLATSPLQ------IGWLVLFDGRKRQSAE-DYNRAADPTTISFCRKPIVQH-ADVFGCDRDKDPQEMRT------NNVISESLGDD
+FLQQ--MPAVPVSVCVYSHMVKKFVPQ-SHEKRGYTWKAKE-DHLVPISYCKGEH---EEEPEGAQY-----------------RVVQNIVKLLYTKDV-
+DCNVVLSLLVWQLC--H-GDWEPLIPQACQTAKKDLAVCAWKRELVPGL---NCNNEYLAKIIYFGPDGH-------DEGPMGRKIVDLHW-EMEASHRD
+-SSVRDNYI-VIMLPFKINSRDPWRHYILGIND-QVCLNRPET---ARRLSILA---VMHYSGEFHDKSP-ERSHLHF-RYSEM----KNDVKCVI---K
+-SNKGLDWTAGKDGMKGEAK-AMMNGALFY-------AEQNWFRKKNHFVIFV-FCDAVRILIMHSGVMIGYTFMEFACNPFFAELFMEHVMVRYQYESN
+HDIKIKDTCFRLAVYAWENSWETLCNV-EMLSGHFGAKINHVPRLPEQVC-PPCDLTVSGLKGKQ-NGLPYLTDITRTPLIRIQIRVPGSE-SENVVVMY
+MVYYKERKSIR-----------QNNTGCANLPQ---------------------HRLVVKVAD-ELYNNI---YHAIPKKD--GVLLGIGDSGGMEMVQE
+DLFQILVCA
+;
+t21
+LIVSEVRHMVRDG--ANIAIDEL-C------------LIACRVKAFSGHGNQVRNAVEDAP--RPDFIGV---RELGKP-Y--CMDGHGAVNTGAGVN-S
+ESAVWIFDIWMYKLSHGMQW--------GDIGRVDVDHPKFLKLEEGAPNCSSLPMPYFLGVDMFHKQVTLKGAKGLVLPDIWNESPMAFPYAQVHSKSH
+KRCLNVLVQGDHEESEH---HNARI----MS---RIGT-HLVIVNVINVEMQRLNHCEDKAIVYSPDRIGGAGFHSKPI------------------ADG
+FFDK-D-Q------ARPIIANAHIVPIY----DQWTGPMAQWCSSVIKCGLANHELK-VVSRLLRCVGMECNLGANHYHQVSRMKMHGPIYSHMTEYAHG
+L----WKPFYQASEHKNEAQGVGER-PHQLPCVESQKCQYEVKVAKVCKLVHV-ALYLVGLKTVVKPKLGDWDGVRCRSDLNKLYLSQLDD----KTLSK
+-NCFRY--LGNMTWLATSPLQ------NGCVVIFAGRKRQSAE-DYNRAADPTTIAFCRKPIVQH-ADVFGCDKDKDPQEMRM------NNVISESLGDD
+FLQQ--MPAVPVSVCVHSHMVKKFVPQ-SHEKRGVTWKAKE-DHLVPISLCKGEH---EEEPEGAQY-----------------RCVQNIVKLLYTKDV-
+DCNVVLSLLVWQLC--H-GDWEPLVPQACQTAKKDLAVCAWKRELVPGL---NCNNEYLAKIIYFGPDGH-------DEGPMGRKIIQLHW-EMEASHRD
+-SSVRDNII-VIMLPFKINSRDPWRHYILGLND-QVCLTRPET---ARRLSILV---VMHYSGEFHDKSP-ERSHLHY-RYSEV----KNDVKCVILASK
+-SNKGLDWTAGKDGMKGENK-AMMNGTLFY-------AEQNWFRQKNHFVIFV-ICDAVRILIVHSGVMTGFTFMEFACNPFFAELFMEHVYIRYQYQAN
+HDIKIKDTCFRLAVYAWENSWETLCNV-EMLSGHFGAKINHVPRLPEQVC-PPCDLTVSGLKGKQ-NGWPYLTDITRTPLIRIQIRVPGSE-SENITVMY
+MVYYKERKSIR-----------QNNTGCANLPQ---------------------HRLVVKVAD-ELYNNI---YHAIPKKD--GVLLGIGDSGGMEMAQE
+DLFQILVCV
+;
+t80
+LIVSEVRHMVRDG--VNIAVDEI-C------------LIANRVKSMSGQGNQVRNAMEMAA--RQNFVGM---RELEKV-YE-CMDGQGAVNTEAGNN-S
+ESAVWIFDIWMCKLTHGMQDFGD-----GDIGRVVVDHPKFEKLEEGAPNCSSHPVPYFLGIDMFHKQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSH
+RRVLNVLHQGDVEES-H---HSARC----VR---RIGF-HLVIIVFWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPV------------------DDG
+FFDK-D-Q------ARPVIASAHIVPEH----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVMIDCNQGANHYIQISRMKVHGPTYSHMTEYAHG
+L----WKPFYQASDHKNDAQGVGER-PHQLPCVESQTCQYEMKHAKVCKLVHG-ALYLIALKTVVKPKLGVWQGCRCRSQLSKLVLSQLDE----KTLSK
+-NCSIY--LGNMTWLATSPLQ------IGCVILFGGRKRQSHGLNYNRAADPTTICFYKKPIVVQGADVFGCARGKDPQEMKA------NNVISGSLGDD
+RLQQ--MPAMPVTICVSSYMVKKSVIQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---DEEPDAAQQ-----------------RIVQNIVKLLYTKDV-
+SCNVVLSMLIWQIC--H-GDWEPQIPKACSNARKDLAVCAWKRELVPGL---NHNNENLAKIMYFGHDGH-------DEGPMGRKIVTLHV-EMEVSHRE
+-SSVKDNMIRVIMLPFSNSSVDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VTHYSGGFHDKSA-ERSQHHF-IYNEV----KDDHKCVILASK
+-CNKGLDWAAGKD-MKGGAK-VMMNGALFY-------AERNWIRQKHHFVIFV-VCDAVRILIVHYGCMIGYTFMDFACNPFFAELFMDHVFIRYVYMNN
+HDIKIMDTCFRVAVYTWENSWETCFNR-EMLSGTFGAKISHNPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPLIKIHIRVPGSQ-SENHVVMY
+CVYYKEHKSIR-----------QNNTGCANLPQ---------------------HRLVDQVVD-ELYSKF---YHAIPKKP--GNM-GVGDSGGMEMVQE
+DVFQILVCL
+;
+t14
+LIVSEVRHMVRDG--VNIAVDEI-C------------LIANRVKSMSGQGNQVRNAMEMAA--RQNFVGM---RELEKV-YQ-CMDGQGAVNTEAGNN-S
+ESAVWIFDIWMCKLTHGMQDFGD-----GDIGRVVCDHPKFEKLEEGAPNCSSHPMPYFLGVDMFHEQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSH
+RRVLNVLHQGDVEES-H---HSARC----VR---RIGF-HLVIIVYWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPV------------------DDG
+FFDK-D-Q------ARPVIASAHIVPEH----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVMIDCNQGANHYIQISRMKVHGPTYSHMTEYAHG
+L----WKPFYQASDHKSDAQGVGER-PHQLPCVESQTCQYEMKHAKVCKLVHG-ALYLIALKTVVKPKLGVWQGCRCRSQLSKLVLSQLDE----KTLSK
+-NCSIY--LGNMTWLATSPLQ------IGCVILFGGRKRQSHGLNYNRAADPTTICFYKKPIVVQGADVFGCARGKDPQEMKA------NNVISGSLGDD
+RLQQ--MPAMPVTICVSSYMVKKSVPQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---DEEPDAAQQ-----------------RIVQNIVKLLYTKDV-
+SCNVVLSMLIWQIC--H-GDWEPQIPKACSNARKDLAVCAWKRELVPGL---NHNNENLAKIMYFGHDGH-------DEGPMGRKIVTLHV-EMEVSHRE
+-SSVKDNMIRVIMLPFPSSSVDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VTHYSGGFHDKSA-ERSQHHF-IYNEV----KDDHKCVILASK
+-CNKGLDWAAGKD-MKGGAK-IMMNGALFY-------AERNWIRQKHHFVIFV-VCDAVRILIVHYRCMIGYTFMDFACNPFFAELFMDHVFIRYQYMNN
+HDIKIMDTCFRVAVYTWENSWETCCNR-EMLSGTFGAKISHNPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTEITRTPLIKIHIRVPGSQ-SENHVVMY
+CVYYKEHKSIR-----------QNNTGCANLPQ---------------------HRLVDQVVD-ELYSKF---YHAIPKKP--GNM-GVGDSGGMEMVQE
+DVFQILVCL
+;
+t85
+LIVSEVRHVVRDG--VNIAVDEI-C------------LIANRVKSMSGQGNQVRNAMEMAA--RQNFVGM---RELDKA-YQ-CMDGQKAVNTEAGNN-S
+ESAVWIFDICMCKLTHGMQD--------GDIGRVVCDHPKFEKLEEGAPNCSSIPMPYFLGIDMFHKQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSH
+RRVLNVLHQGDHEES-H---VSARC----MR---RIGF-HLVIINFWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPI------------------NDG
+FFDK-D-Q------ARPVIANAHIVPEH----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVEIDCNQGANHYVQISRMKMYGPTYSHMTEYAHG
+L----WKPFYQASDHKNDAQGVGER-PHQLPCVESQTCQYEVKHANVCKLVHA-ALYLIGLKTVVKPELGVWEGCRCRSQLSKLALSQLDE----KTLSK
+-NCSIY--LGNMTWLATSPLQ------IGCIILFGGRKRQSHGLNYNRAADPTMICFYKKPIVVQGADIFGCARGKDPQEMKS------NNVISGSLGDD
+RLQH--MPAMPVTICVFSYMVKKAVPQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---DEEPDGAQQ-----------------RVVQNIVKLLYTKDV-
+SCNKVLSMLIWQIC--H-GDWEPQIPKACNAARKDLAVCAWKRELVPGL---NHNNEDLAKIMYFGPDGH-------DEGPMGRKIVNLHV-EMEVSHRE
+-SSVKDNMIRVVMLPFDNNSWDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VMHYSGGFHDKSS-ERSQHHF-IYNEV----KNDHKCVILASK
+-SNKGLDWAAGKD-MKGGAK-MMANGALFY-------EERNWIRQKNHFVIFV-VCDAVRILIVHYGCMVPYTFMAFACNPFFAELFMEHVFIRYQYVNN
+HDIKIMDTCFRVAVYTWENSWETCCNR-EMLSGTFGAKISHNPRLPEQVI-PPCDLTVSGLKGKH-NGWPYLTDITRTPLIKIHIRIPGSQ-SENHVVMY
+CVYYKEHKSIR-----------QNNTGCANLPQ---------------------HRLVDKVVD-ELYSKF---YHAIPKKP--GNM-GIGDSGGMEMVQE
+DLFQILVCI
+;
+t62
+LIVSEVRVMVRDG--IHIAVDEI-C------------LIANRVKCMSGQGNQARNAMEMAA--RQNFVGM---RELGKQ-YQ-CMDGQGAVNTEAGNN-S
+ESAVWIFDIWMCRLTHGMQD--------GDIGRVECDHPKFAKLEEGAPNCSSLPMPYFLGIDMFHNQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSH
+RRVLNVLHQGDHEES-H---HSARC----MR---RIGY-HRVIINYWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPI------------------ADG
+FFDK-D-Q------ARPVIANAHIVPEY----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVVIDCNHGANHYVQISRMKMHGPTYSHMTEYAHG
+L----WKPFYQASDHKNDAQGVGER-PHQLPCVEPQTCQYEVKHAKVCKLVHG-ALYLIGLQTVVKPKLGVWEGVQCRSQLSKLILSQLDD----KTLSK
+-NCSIY--LGNMTWLATSPLQ------IGCIIMFDGRKRQSHGLQYNRAADPTTICFYKKPIVVQGADIFGCARGKDPQEMKA------NNVTSGSLGDD
+RLQQ--MPAMPVTICVFSYMVKKSVPQ-SHVKRGYTWRAKE-DHLIPVSFCKGEL---EEEPEGAQH-----------------RMVQNIVKLLYTKDV-
+SCNVVLSMLIWQIC--H-GDWEPQIPKACDAARKDLAVCAWKRELVPGL---NHNDENLAKIMYFGPDGH-------DEGPMGEKIVNLHV-EMEASHRE
+-SSVKDNMIRVIMLPFSNNSWDPWRHVILGLND-KIKLTRPNT---AHRLSILV---VMHYSGGFHDKSA-ERSQHHF-IYNEI----KNDHKCVILASK
+-ANKPLDWAAGKD-MKGGAK-MMANGALFY-------AERNWIRQKNHFVIFI-ICDAVRILIVHYGCMVGDTFMDFACNPFFAELFMEHVFIRYQYIPN
+HDIKIMDTCFRVAVYTWENSWETCCNR-EMLSGTFGARISHVPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPLIRIHIRVPGSE-SENHVVMY
+CVYYKEHKSIR-----------QNNTGCANLPQ---------------------HRLVDRVVD-ELYSKF---YHAIPKKP--GNM-DVGDSGGMEMVME
+DVFQILVCV
+;
+t19
+LIVSEVRHMVRDG--INIAVDEI-C------------LIANRVKCVSGQGNQARNAMEMAA--RQNFVGM---RELGKQ-YQ-CMDGQGAVNTEAGNN-S
+ESAVWIFDIWMCRLTHGMQD--------GDIGRVECDHPKFAKLEEGAPNCSSLPMPYFLGIDMFHKQVMGKGSKGLILPDTWNEASMAFPYPQVHSKSH
+RRVLNVLHQGDHEES-H---HSARC----MR---RIGYGHLVIINFWNVEMGRLNHCEDEAIIYSPLRIGGAGFHSKPI------------------ADG
+FFDK-D-Q------ARPVIANAHIVPEY----DQWSGAMAQWCSSVIKCGLANHDLE-NVSRLLRCVVIDCNHGANHYVQISRMKMHGPTYSHMTEYAHG
+L----WKPFYQASDHKNDAQGVGER-THQLPCVEPQTCQYEVKHAKVCKLVHG-ALYLIGLQNVVKPKLGVWEGVQCRSQLSKLILSQLDD----KTLSK
+-NCSIY--LGNMTWLATSPLQ------IGCIILFDGRKRQSHGLQYNRAADPTTICFYKKPIVVQGADIFGCARGKDPQEMKA------NNVTSGSLGDD
+RLQQ--MPAMPVTICVFSYMVKKLVPQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---EEEPEGAKQ-----------------RMVQNIVKLLYTKDV-
+SCNVVLSMLIWQIC--H-GDWEPQIPKACDAARKDLAVCAWKRELVPGL---NHNDENLAKIMYFGPDGH-------DEGPMGEKIVNLHV-EMEASHRE
+-SSVKDNMIRVIMLPFSNNSWDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VMHYSGGFHDKSA-ERSQHHF-IYNEI----KNDHKCVILASK
+-ANKGLDWAAGKD-MKGGAK-MMVNGALFY-------AERNWIRQKNHFVIFV-ICDAVRILIVHYGCMVGDTFMDFACNPFFAELFMEHVFIRYQYIPN
+HDIKIMDTCFRVAVYTWENSWETCCNR-EMLSGTFGARISHVPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPLIRIHIRVPGSE-SENHVVMY
+CVYYKEHKSIR-----------QNNTGCANLPQ---------------------HRLVDKVVD-ELYSKF---YHAIPKKP--GNM-DVGDSGGMEMVME
+DVFQILVCV
+;
+t77
+LIVSEVRHMVRDG--INIAVDEI-C------------LIANRVKSMSGQGNQARNAMEMAA--RQNFVGM---RELGKQ-YH-CMDGQGTVNTEAGNN-S
+ESAVWIFDIWLCRLTHGMQD--------GDIGRVECDHPKFAKLEEGAPNCSSLPMPYFLGIDMFHRQVMAKGSKGLILPDTWNEASMAFPYPQVHSKSH
+RRVLNVLHQGDHEES-H---HSARC----MR---RIGY-VLVIINFWNVEMGRLIHCEDEAIIYSPLRIGGAGFHSKPI------------------ADG
+FFDK-D-Q------ARPVIANAHIVPEY----DQWSGAMPQWVSSVIKCGLANHDLE-NVSRLLRCVVIDVNQGANHYVQISRMKMHGPTYSHMTEYAHG
+L----WKPFYQASDHKNDAQGVGER-VHQLPCVEPQTCQYEVKHAKVCKHVHG-ALYLIGLQTVVKPKLGVWEGCQCRSQLSKLILSQLDD----KTLSK
+-NCNIY--LGNMTWLATFPLQ------IGCIILFDGRKRQSYGLQYNRAADPTTICFYKKPIVVQGADIFGCARGKDPQEMKA------NNVTSGSLGDD
+RLQQ--MPAMPVTICVFSYMVKKSVPQ-SHQKRGYTWRAKE-DHLIPVSFCKGEL---EEEPEGAQQ-----------------RIVQNIVKLLYTKDI-
+SCNVVLSMLIWQIC--H-GDWEPQLPKACDAARKDLAVCAWKRELVPGL---NHNDENLAKIMYFGPDGH-------DEGPMGEKIVNLHV-EMEASHRE
+-SSVKDNMIRVIMLPFGENSWDPWRHVILGLND-QIKLTRPNT---AHRLSILV---VMHYSGGFHDNSA-ERSQHHF-IYNEV----KNDHKCVILASK
+-ANKGLDWAAGKD-MKGGAK-MMVNGALFY-------AERNWIRQKNHFVIFV-ICDAVRILIVHYGCMVGDTFMDFACNPFFAELFMEHVVIRYQYIPN
+HDIKIMDTCFRVAVYTWENSWETCCNR-EMLSGTFGARISHVPRLPEQVI-PPCELTVSGLKGKH-NGWPYLTDITRTPLIRIHIRVPGSE-SENHVVMY
+CVYYKEHKSIR-----------QNNTGCANLPQ---------------------HRLVDKVVD-ELYSKF---YHAIPKKP--GNM-DVGDSGGMEMVME
+DVFQILVCA
+;
+t88
+LIVSECRLIIRDG--NHDAIDEM-CCVANDLNNEIERLVASMVKSFRGHDSQARNNSECMR--SAPFIGV---RELFKR-YHKCVEGAGCVHTVAGTP-S
+DSPVWMFDQFMCQLTHSMVD--------GDLGRVVQDNVIFAKLKEGAPHCISL--PHFLGIDMFHTQVFVGGH--LILPDPCYELSISVMYAGHASYNQ
+KRCINNLDQGDQEDSNHRKEHKIRASVLLYR---QIGI-L-VIIKEANELMNRLNHKEPENGIIFPLR---DAQDPKQI------------------LNG
+LFDK-E-E------NRPMVQDADSVVGS----AQWAGQHRSWCSSDDKA-----------SQLPRNTHIVVEIGANVYEQFSRMKTNIPIYAHVTEYAVG
+V----ERPFYE-SEFKNEAQGWGES-GTSIPCVDSPDVQYEMKVAWVDKLMHT-ALYLMPLATVHKPEMGTVRGERCRAIL-KLLMMQLD------TLSR
+-NQLPK--LCQGTWLDASPLQ------IGVQVMLVGKKGGSKK-EYELAADQVIIYFYQAPIIYVKADVFSGTVAKKAQAMR-------KSTGSQSIGDD
+GMQS--MPLMQNAVCVWSKMVRKVQPD-GQDKREQTWMAKD-DTLCPPSMKRGEK---TAEPTQWMG-----------------TVTVNKIKLLYCKDC-
+SCNEVMKILSWWLCNSV-GDWQTLMSQACITADPNPPVCVWKRELVPGL---NRSVENLAKIIYFCPDEH-------DERKMWGKIFALEW-EMDISHRH
+-SSVDDNHC-VEMLPFMCQRVDPWGHYVQILAD-RQDLARPVT---LQALSILP---CPHASGKEQDGAV-ERSQHYV-VYAEL----QVDHKCTIAAHK
+YQDKMKDWDTGKN-MDEGAK-MYVEIHLFY-------AENNIRRQNDHSVIFW-ISDAKKRLICGMSSMCLVTFMTLACNPLFAKLFMEVVPMRYDYLTN
+HDIKI------MEVYAPENSWETIKNV-EMVSGKEGAEINHTPQLPEQVI-PPCNLTVSNLKGMI-PPCPALTEITRTV--FIV--MYYAI-LRNKIMQY
+CFYYKENRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGG---YHAAPKKE--EMV-GPGDNGGVEDIKE
+DMFQVLVCR
+;
+t37
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-S
+ESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQ
+KRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVG
+V----ARPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTIL-KLLMVQLDE----KTLSQ
+-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DTLCPPCEEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-
+SCNEVLKILAWWLCDSV-GDWQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALEW-EMDISHRH
+-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLRKQNEHSVTFV-ISDAQKRLICGVSSMVMRTFMTLACNPFFAKLFMEVVPMSYDYVPN
+HDIKI------IEVYAPENSWETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPVPALTEITRTP--FIV--MYVAI-LRNDIMQY
+CFYYKENRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-SPGDNGGVEAIRE
+DMFQVLVCK
+;
+t35
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-S
+ESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQ
+KRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTVIPIYARVTEYAVG
+V----PRPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPQMGTVKGERCRTIL-KLLMVQLDE----KTLSQ
+-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPVIIYFYQAPIIYHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DTLCPPCEEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-
+SCNEVLKILAWWLCDSV-GDWQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALEW-EMDISHRH
+-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLRKQNEHSVTFV-ISDAQKRLICGVSSMAMRTFMTLACNPFFAKLFMEVVPMSYDYVPN
+HDIKI------IEVYAPENSWETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP--FIV--MYVAI-LRNDIMQY
+CFYYKENRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-SPGDNGGVEAIRE
+DMFQVLVCK
+;
+t48
+LIVSDMRLIIREG--SDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-S
+ESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQ
+KRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEVGANVYEQYSRMKTVIPIYARVTEYAVG
+V----PRPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTIL-KLLMVQLDE----KTLSQ
+-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPVIIYFYQAPIIYHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DTLCPPCEEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-
+SCNEVLKILAWWLCDSV-GDWQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALEW-EMDISHRH
+-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLIKQNEHSVTFV-ISDAQKRLICGVSSMVMRTFMTLACNPFFAKLFMEVVPMSYDYVPN
+HDIKI------IEVYAPENSWETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP--FIV--MYVAI-LRNDIMQY
+CFYYKENRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-SPGDNGGVEAIRE
+DMFQVLVCK
+;
+t55
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-S
+ESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAI--PYFMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQ
+KRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVG
+V----ARPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLSTVHKPEMGTVKGERCRTIL-KLLMVQLDE----KTLSQ
+-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DTLCPPCEEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-
+SCNEVLKILAWWLCDSV-GDWQTLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALEW-EMDISHRH
+-SSVDDNQC-VELLPYNCQRMDPWGHYVQILAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNLRKQNEHSVTFV-ISDAQKRLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPN
+HDIKI------IEVYAPENSWETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP--FIV--MYVAI-LRNDIMQY
+CFYYKENRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-SPGDNGGVEAIRE
+DMFQVLVCK
+;
+t46
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-S
+ESPVWMFDKFMCQLTHSMVN--------GDLGRVVHDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFVGGN--LILPDPCYELSISVMYAGHASYNQ
+KRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L-VIIKEANELMGRLNHKEPKNGVIFPLR---GAQGPKQI------------------SNG
+LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVG
+V----ARPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTIL-KLLMVQLDE----KTLSQ
+-NQIPD--LCQRTWLDASPLQ------IGVKVVLVGKKRGSKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKSQAMRS------RSIGSQSVGDD
+GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWMAKD-DALCPPCKEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-
+SCNEVLKILAWWLCDSV-GDWQSLMNDACRSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALEW-EMDISHRH
+-SSVDDNQC-VELLPYVCQRMDPWGHYVQVLAD-RLDLTRPVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDHKSTIDANK
+NDNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNIRKQNEHSVTFV-ISDAQKRLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPN
+HDIKI------IEVYAPDNSWETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPCPALTEITRTP--FIM--MYVAM-LRNDIMQY
+CFYYKENRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-APGDNGGVEAIRE
+DMFQVLVCK
+;
+t67
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-S
+ESPVWMFDKFMCQLTHSMVN--------GDLGRVVMDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFLGGD--LILPDPCYELSISVMYAGHASYNQ
+KRCINGLDNGDRQDSDPRKEHKIRNSVLLYR---QIGL-L-VIIKEANELMGRLNHKERKNGVIFPLR---GAQGPKQI------------------SNG
+LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVG
+V----ARPFYD-AEFKNEAQRQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTIL-KLLMVQLDE----KTLSQ
+-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKAQAMRS------RSIGSPSVGDD
+GMQN--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWVAKD-DTLCPPCKEQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-
+SCNEVLKILAWWLCDSV-GDWQTLMNDACSSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALEW-EMDISHRM
+-SSVDDNQC-VELLPYVCQRMDPWGHYVQILAD-RLVLTRPVT---LHGLSILP---CPHASGKEQDGAE-ERSQHYG-VYQEL----QNDAKSTIDANK
+NPNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNIRKLNEHSVTFV-ISDAQKRLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPN
+HDIKI------IEVYAPENSWETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPVPALTEITRTP--FIV--MYVAI-LRNDIMQY
+CFYYKENRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-APGDNGGVEAIRE
+DMFQVLVCK
+;
+t57
+LIVSDMRLIIREG--NDDAIDEM-CCVANELNNVIERLVASMVKEFRGHDCQARNNSECIT--AAAFIGT---RELFKR-YPKCMEGARCVHTVAGPP-S
+ESPVWMFDKFMCQLTHSMVN--------GDLGRVVMDNWTFTKLKEGAPHCIAL--PYFMGIDMFHIQVFIGGD--LILPDPCYELSISVMYAGHASYNQ
+KRCINGLDNGDRQDSDPQKEHKIRNSVLLYR---QIGL-L-VIIKEANEIMGRLNHKERKNGVIFPLR---GAQGPKQI------------------SNG
+LFEK-E-E------NRPMVQDAGSVPGR----KQWAGQHRAWCSSDDKA-----------SQLPRNTRIVAEIGANVYEQYSRMKTNIPIYARVTEYAVG
+V----ARPFYD-AEFKNEAQGQGES-GTSIPCVDSPDIQYEMKHAWVEKLMHS-ALYLMPLATVHKPEMGTVKGERCRTIL-KLLMVQLDE----KTLSQ
+-NQIPD--LCQRTWLDASPLQ------IGVQVVLVGKKRGSKK-DYELAADPVIIYFYQAPIIHHKADVFAGTVAKKAQAMRS------RSIGSPSVGDD
+GMQK--MPLMQNAVCVWSQMVRKVQPD-GQDKREQTWVAKD-DTLCPPCKDQGEK---AAEPTQWVG-----------------TCTSNVIKLLYCKDC-
+SCNEVLKILAWWLCDSV-GDWQTLMNDACSSANPNYPVCIWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERRMWGKIFALEW-EMDISHRV
+-SSVDDNQC-VELLPYLCQRMDPWGHYVQILAD-RLNLTRPVT---LQGLSILP---CPHASGKEQDGAV-ERSQHYG-VYQEL----QNDAKSTIDANK
+NPNKMLDWDTGKN-MDKGAK-MFYKIVLFY-------AENNIRKQNEHSVTFV-ISDAQKRLICGVSSMCMRTFMTLACNPFFAKLFMEVVPMSYDYVPN
+HDIKI------IEVYAPENSWETTKVV-EMVSGKSGAQINHTPQLPEQVI-PPCCLTVSNLKGMI-PPVPALTEITRTP--FIV--MYVAI-LRNDIMQY
+CFYYKENRSVR-----------LNNTGRAELPK---------------------HHMQNIFID-ELYPGP---YHAAPKKE--ELM-APGDNGGVEAIRE
+DMFQVLVCK
+;
+t56
+LIVSEWRLFIRDG--HDDAIDEM-CCEANELNNDIEKLVASMVKGFRGHDSQARNNAECII--AAPFIGV---RELFKR-YIKCVEGAGCVYTVA-AP-S
+ESPVWMFDKFMCHLTHSMVV--------GDLGRVLRDNTTFAKLKEGAPVCISL--PYFLGMDMFHQQVFMGGN--LILPDPCYELSISVMYAGHASYNQ
+KRCLNNLDQGDREDSSHRKEHKIRRSVLLYQ---QIGC-L-VITRERNELMGRLNHKEPRDGVIFPHR---GAQGPKQL------------------ANG
+LFEK-E-E------NRPMVQDAGSVPER----AQWPGQQRAWCSSDDKA-----------SKLPRNTKMVAEIGANVYEQASRMKTNIPIYAHVTEYALG
+V----DRPFYD-SEFKNEAQGQGES-GTSIPCVDSPDVQYELKHAWVDKLMHT-ALYLMPLPTVHKPKMGTVKGERCRAML-KLNMMQLDE----KTLSQ
+-NQIIK--LCQRTWLDASPLQ------IGVNCVLPGKKGGSNK-DYELAADPVIIYFYQAPIIHHKADVFSGTVAKKAQAMRQ------QSTGSQSVGDD
+GTQV--MPLMQNLVCVWSKMVRKCMID-GQEKREQTWMAKD-DKLCPPSQEQGEK---AAEPTQWED-----------------ICTANVIKLLYCKDC-
+SCNEVLRVLSWWLCDSV-GDWRTLMSDACALANPNPPVCVWKRELVPGL---NRNVENLAKIIYFCPDEH-------DERKMWGKIFCLEW-EMDISHRH
+-SSVDDNVC-VEMLPFVCQKMDPWGHYVQILAD-RLDLTRPVT---LQGLGILV---CPHASGKEQDGAM-ERSQHYV-VYAEL----QNDHKNTINANK
+VPRKMLDWDTGKN-MDKGAKGMYHEIVLFF-------AENNVKKQVEHSVIFI-IADAQKRLICGVSSMCLQTFMNLACNPFFAKLFMEVIPMRYDYQTN
+HDIKI------KEVYAPENSWETIKNV-EMVSGKAGKQINHEPQLPEQVI-PPCSLTVSNLKGMM-PPCPAMTEITRTV--III--MYYAI-LRNEIMQY
+CFYYKENRSVR-----------INNTGQAELPK---------------------HHVQNVFID-ELYPGH---YHAAPKKN--ENV-GPGDNGGVEGIKE
+DMFQVLVCQ
+;
+t13
+GIVSECRMIIRDE--HDDAIDEM-C------------LVASMVKKLSGCENQARNNHECAI--PPPFHGV---REMFKRVYE-CMEGIGCVNTVAGNP-S
+ESSAWMFDKVMYQLTHSMVW--------GDLRRVVHDNVTFSKLKEGAPHCISH--PYFLGIDMFHIQVYSKGF--LTLPDPRYEISMSVMYSQHHSFSM
+KRCLNGLDHGDREESPHQIEHKMRKSVLIYN---PIGY-L-VIIKDANSMMGRLNHHESRAVVAFPLR---GAEGPKQV------------------MEG
+LFDK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVG
+I----VKPFYD-NEWKQEAQGQGEA-GACIPCVDSKDVQYELKHAYVKKLMHT-SLYLMHIETCHKPVMGTVKGNRCRAIL-KLSMIQLDQ----KTLSQ
+-NQRAK--LCQRTWLDTSPLQ------MGMTLVLVGKKVGSKK-DYEVAADPVIMYFYDAPMIMRPTDVFEGTNNKKAQAMRS------RSTASQSIGDD
+DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKD-DTLCPQSRDQGEK---HHEPHHIRN-----------------KFSENVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLSSDACMHAEQNPPVCVWQRELVPQL---NRNIEDLARIIYFGPDEH-------DEGKMMNKIFALEW-EMDMSHRV
+-SSVDDNYI-IEMLPFVCDRVGPWGHYAQVLAD-QLHLTRPHT---LRDLYILAC--CPVASGKEQDGNK-ERSQHYT-IYAEI----QNDHKNPISANN
+QPNKMLDWDTGKT-MDRGAA-MCGEIKLFY-------AEPNVWNQNDHSVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFSKLFMEVVCMRYNYTSN
+HSIKI------FEVYADENSWENVRNF-EMVSGRAGAHINHIPQLPEQAY-PPCKLTVSNLKGVA-ASCPAITEITRTA--VIV--MYGSI-LRNDVMQY
+VFYYRENRSVR-----------QNNTGNAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKD--RFC-NPGDNGGMETYQE
+DMFQVLVCV
+;
+t5
+GIVSECRMIIRDE--HDDAIDEM-C------------LVASMVKKLSGCENQARNNHECAI--PPPFHGV---REMFKRVYE-CMEGIGCVNTVAGNP-S
+ESSAWMFDKVMYQLTHSMVW--------GDLRRVVHDNVTFSKLKEGAPHCISH--PYFLGIDMFHIQVYSKGF--LTLPDPRYEISMSVMYSQHHSFSM
+KRCLNGLDHGDREESPHQIEHKMRKSVLIYS---PIGY-L-VIIKDANSMMGRLNHHESRAIVAFPLR---GAEGPKQV------------------MEG
+LFDK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVG
+I----VKPFYD-NEWKQEAQGQGEA-GACIPCVDSKDVQYELKHAYVKKLMHT-SLYLMHIETCHKPVMGTVKGNRCRAIL-KLSMIQLDQ----KTLSQ
+-NQRAK--LCQRTWLDTSPLQ------MGMTLVLVGKKVGSKK-DYEVAADPVIMYFYDAPMIMRPTDVFEGTNNKKAQAMRS------RSTASQSIGDD
+DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKD-DTLCPQSRDQGEK---HHEPHHIRN-----------------KFSENVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLSSDACMHAEQNPPVCVWQRELVPQL---NRNIEDLARIIYFGPDEH-------DEGKMMNKIFALEW-EMDMSHRV
+-SSVDDNYI-IEMLPFVCDRVGPWGHYAQVLAD-QLHLTRPHT---LRDLYILAC--CPVASGKEQDGNK-ERSQHYT-IYAEI----QNDHKNPISANN
+QPNKMLDWDTGKT-MDRGAA-MCGEIKLFY-------AEPNVWNQNDHSVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFSKLFMEVVCMRYNYTSN
+HSIKI------FEVYADENSWENVRNF-EMVSGRAGAHINHIPQLPEQAY-PPCVLTVSNLKGVA-ASCPAITEITRTA--VIV--MYGSI-LRNDVMQY
+VFYYRENRSVR-----------QNNTGNAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKD--RFC-NPGDNGGMDTYQE
+DMFQVLVCV
+;
+t38
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-S
+ESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISQ--PFFLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQ
+KRCLNGLDVGDREESPHHIDHKMRKSVLIYN---PIGY-L-VIIKNANSLMGRLNHHESRLIVTFPLR---GAEGPKQV------------------MEG
+LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVG
+I----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTIKGNRCRAIL-KLTMIQLDQ----KTLSQ
+-NQRAR--LCQRTWLDTSPLQ------MGMTIVLVGKKVGSKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+DMLN--MPLTQNAMCVESEMVRKSQPD-GQDKRGYTWVAKE-DDLCPQSGDQGEK---YAEPQHIRN-----------------QFSENVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALEW-EMDMSHRM
+-SSVDDNYI-IEMLPFVCDRVGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGAQ-ERSQCYT-IYAEL----QNDHKSLISANH
+VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQNKLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSN
+HSIKI------FEVYADENSWENIRNF-EMVSGRAGAYINHIPQLPEQAV-PPCHLTVSNLKGVA-ASCPAITEITRTA--VIV--MYVSI-LRNDVMQY
+VFYYRENRIVR-----------QNNTGVAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKE--RFC-NVGDNGGMETIQE
+DMFQVLVCI
+;
+t33
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-S
+ESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQ
+KRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L-VIIKNANSLMGRLNHYESRAIVTFPLR---GAEGPKQV------------------MEG
+LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SHLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVG
+I----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHN-SLYLMHIDTCHKPAMGTVKGNRCRAIL-KLTMIQLDQ----KTLSQ
+-NQRAR--LCQRTWLDTSPLQ------MGMTIVLVGKKVGSKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSGDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLASDACVSAEPNTPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALEW-EMDMSHRM
+-SSVDDNYI-IEMLPFVCDRVGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGAK-ERSQCYT-IYAEL----QNDHKSLISANH
+VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSN
+HSIKI------FEVYADENSWENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAITEITRTA--VIV--MYVSI-LRNDVMQY
+VFYYRENRIVR-----------QNNTGVAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKE--RFC-NPGDNGGMETIQE
+DMFQVLVCV
+;
+t100
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-S
+ESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQ
+KRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L-VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEG
+LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVG
+I----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKGNRCRAIL-KLTMIQLDQ----KTLSQ
+-NQRAR--LCQRTWLDTSPLQ------MGMTIVLVGKKVGSKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSEDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALEW-EMDMSHRM
+-SSVDDNYI-IEMLPFVCDRVGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGAQ-ERSQCYT-IYAEL----QNDHKSLISANH
+VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSN
+HSIKI------FEVYADENSWENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAITEITRTA--VIV--MYVSI-LRNDVMQY
+VFYYRENRIVR-----------QNNTGVAELPK---------------------HHMQDVFID-ELYLGP---YHASPKKE--RFC-NPGDNGGMETIQE
+DMFQVLVCV
+;
+t34
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-S
+ESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQ
+KRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L-VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEG
+LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVG
+I----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKGNRCRAIL-KLTMIQLDV----KTLSQ
+-NQRAR--LCQRTWLDTSPLQ------MGMTIVLMGKKVGSKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSGDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALEW-EMDMSHRM
+-SSVDDNYI-IEMLPFVCDRIGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGAQ-ERSQCYT-IYAEL----QNDHKSLISANH
+VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSN
+HSIKI------LEVYADENSWENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAMTEITRTA--VIV--MYVSI-LRNDVMRY
+VFYYRENRIAR-----------QNNTGVAELPK---------------------HHMQDIFID-ELYLGP---YHASPKKQ--RFC-NPGENGGMETIRE
+DMFQVLVCV
+;
+t84
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCDDQARNNHECAI--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-S
+ESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQ
+KRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L-VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEG
+LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVG
+I----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKGNRCRAIL-KLTMIQLDV----KTLSQ
+-NQRAR--LCQRTWLDTSPLQ------MGMTIVLMGKKVGSKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSGDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLASDACVSAEHNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALEW-EMDMSHRM
+-SSVDDNYI-IEMLPFVCDRIGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGAK-ERSQCYT-IYAEL----QNDHKSLIAANH
+VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSN
+HSIKI------LEVYADENSWENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAMTEITRTA--VIV--MYVSI-LRNDVMRY
+VFYYRENRIAR-----------QNNTGVAELPK---------------------HHMQDIFID-ELYLGP---YHASPKKE--RFC-NPGENGGMETIRE
+DMFQVLVCV
+;
+t92
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEDQARNNHECAI--SHPFHGV---REMFKR-YE-CMEGIGCVNTVAGNP-S
+ESSAWMFDKFMYQLTHSMVW--------GDLGRVYYDNITFSKLKEGAPHCISH--PFFLGIDMFHIQVYFKGS--LTLPDPRYELSMSVMYSQHHSFSQ
+KRCLNGLDVGDREESPHQIEHKMRKSVLIYN---PIGY-L-VIIKNANSLMGRLNHHESRAIVTFPLR---GAEGPKQV------------------MEG
+LFLK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIFAHVTEYAVG
+I----VKPFYD-SEWKQEAQGQGEA-GACIPCVDSPDVQYELKHAYVKKLVHT-SLYLMHIDTCHKPVMGTVKGNRCRAIL-KLTMIQLDV----KTLSQ
+-NQRAR--LCQRTWLDTSPLQ------MGMTIVLMGKKVGSKK-DYEIAADPVIMYFYQAPMIMRPTDVFEGTNNRKAQAMRS------RSTASQSIGDD
+DMLN--MPLTQNAMCVESEMVRKCQPD-GQDKRGYTWVAKE-DTLCPQSGDQGEK---YAEPQHIRN-----------------KFSENVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLASDACVSAEPNPPVCVWQRELVPQL---NRNAEDLARIIYFGPDEH-------DEGKMMCKIFALEW-EMDMSHRM
+-SSVDDNYI-IEMLPFVCDRIGPWGHYAQILAD-QLNLTRPHT---LRELYILA---CPVASGKEQDGAQ-ERSQCYT-IYAEL----QNDHKSLISANH
+VPNKMLDWDTGKT-MDRGAA-MCAEIKLFY-------AEPNVWKQNDHSVMFI-ISDAQNRLIVANSIMVGQTFMAMACNPHFAKLFMEVVVMRYDYCSN
+HSIKI------LEVYADENSWENIRNF-EMVSGRAGAHINHIPQLPEQAC-PPCVLTVSNLKGVA-ASCPAMTEITRTA--VIV--MYVSI-LRNDVMRY
+VFYYRENRIAR-----------QNNTGVAELPK---------------------HHMQDIFID-ELYLGP---YHASPKKE--RFC-NPGENGGMETIRE
+DMFQVLVCV
+;
+t3
+GIVSECRMIIRDE--SDDAIDEM-C------------LVASMVKKLSGCEQQARNNRECAT--SIPFLGV---RELWKR-YE-CMEGIGCVNTVAGKP-S
+QSSVWMFDRFMYKLTHSMVW--------GDLGRVYWDNLTFQKLKEGAPHCIAV--PNYLNIDMFHIQVFYKGP--LTLPDPHYELSMSVMYAQHHSFSQ
+KRCLNALDHGDREESPHQIEHKMRKSVLLYN---PIGY-L-VIIKNANSMMGRLNHHESCAIVMFPLR---GAEGPKQI------------------IEG
+LFDK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SRLPRNDPVVHEVGANVYQQISRMKTSIPIYAHVTEYAVG
+I----IKPFYD-NEWKQEAQGQGEA-GASIPCVNSPDVQYELKHAHIKKLMHT-SLYLMHLGTCHKPVMGTVKGDRCRAIL-KLSMIQLDQ----KTLSQ
+-NVRAR--LCQRTWLDTSPLQ------MGMVAVLLGKKLGSKK-DYEIAADPVIKYFYQAPIIMRRTDVFEGTDDQKAQAMRV------RSTASQSIGDD
+DMLI--MPLVQNAMCVKSEMVRKCQPD-GPDKRGYTWMAKD-DTLCPVSAGQGEK---YAEPHQIKN-----------------KFSVNVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWVTLASDACLSAEPQPPVCVWQRELVPQL---NRNVEDLARVIYFGPDEH-------DEGKMMPKIFKLAW-EMDMSHRA
+-SSVDDNYV-IEMLPFVCHRVGPWGHYAQVQAD-QQNLTRPHT---LADLFILS---CPVASGKEQDGAT-ERSQYYV-VYAEL----QNDHKSPISANK
+HPDKMLDWDTGKS-MDRGAA-MCREIKLFY-------AEPNVWKQNDHSVVFI-ISDAVNRLICANSIMCGLTFMAMACNPHFAKLFMEVVCMRYDYFSN
+HSIKI------FEVYAEDDSWENICNF-EMMSGRTGAQINHIPQLPEQVC-PPCHLTVSNLKGCC-ASVPAITEITRTV--VIC--MYVSI-LCNVVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGQ---YHASPKKK--KIC-GPGDNGGMETIEE
+DMFQVLVCV
+;
+t22
+GIVSECRVIIRDQ--SDDAIDER-Y------------LVASVVKRLSGCENQARNNRECAI--SIPFLGV---RELWKR-YE-CMEGIGCVNTVAGTP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLGRVYVDNQTFSKLKEGAPHCISA--PYYLNIDMFHIQVFYKGS--LTLPDPRYELSMSVMYAQHHSFSQ
+KRCLNALDYGDREESPHQIEHKMRKSVLLYY---TIGW-L-VIIKNADSMMGRLNHHESCAMVMFPLR---GAEGPKQI------------------MEG
+LFDK-E-E------ARPMVQDAASVPGR----AQWVGRVRAWCSSDVKA-----------SQLPTNDPIVPEVGANVYQQVSRMKTSIPIYAHVTEYAVG
+I----VKPFYD-NEWKQEAQGQGEA-GASIPCVNSPDVQYELKHAHIKKLMHT-SLYLMHLKTCHKPVMGTVKGDRCRAIL-KLKMIQLDQ----KTLSQ
+-NQAAR--LCKRTWLDTSPLQ------MGMNVVLIGQKLGSKH-DYEIAADPVIMYFYQAPIIMRRTDVFEGTDDQKAQAMRL------RSTASRSIGDD
+DMLI--MPLVQNAMCVNPEMVRKCQPD-GQDKRGYTWMAKN-DTLCPVSAGQGEC---YAEPHQTCN-----------------KFRVNVIKLLYCKDC-
+SCNKVLKILKWQLCESV-DDWQTLASDACILAKPQPPVCVWQRELVPQL---NRNVEDLARVIYFGPDEH-------DEGKMMSKIFNLEW-EMDMSHRT
+-SSVDDNYV-IDMLPFICHRVGPWGHYAQVLAD-QINLTRPHT---LRDLFILA---CPVASGKEQDGAT-ERSQHYV-VYAEL----QNDHKSPISANK
+HPNKLLDWDTGKT-MDRGAA-MCHEIKLFH-------AEPNVWRQNDHSVMFI-ISDASNRLICANSIMCGLTFMAMACNPHFAKLFMEVVCMRYEYFSN
+HSIKI------FEVYAEENSWENVCNF-EMMSGRAGAQINHIPQLPEQVC-PPCVLTVSNLKGCC-ASCPANTEITRTV--VIC--MYVSI-LRNVVMQY
+VFYYKENRSVR-----------QNNTGAAELPK---------------------HHMQDIFID-ELYPGL---YHASPKKK--KVC-GPGDNGGMETIQE
+DMFQVLVCV
+;
+t64
+GIVSECRMIIRDE--TDDAIDEV-C------------LVASMVKKLSGCENQTRNNRECAIT-SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGMP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLRRVFPDNATFSKLKEGAPHVISH--PYFLGIDMFHDQVVYRGP--LTLPDPRYELSMSVMYAQHHSFSQ
+KRCLNALDHGDTQESPHGIEHNMRNSVLLYN---PIGF-L-VIIKNINSMMGRLNHHESRAVVGFPLR---GAENPKQI------------------MEG
+HFDK-E-E------ARPIVQDAASVPGK----AQWVGRVRAWCSSDVKA-----------SKLPRNDPIVPEVGANVYQQLSRMKTNIPIYAHVTEYAVG
+I----VKPFYD-NEWKQEAQGVGEA-GASIPCVDSPDVQYELKHAEVRKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAIL-KLPMIQLDQ----KTLSH
+-NQPRR--LCQRTWLDASPLQ------VGMNIMLMGKKAPSKK-DYEIAADPVIMYFYQAPIIMRRTDVFEGTHNKKAQAMRV------RSTASQSIGDD
+DMLK--MPLVQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANQGEK---YAEPHVIGD-----------------KVSVNVIKLLYCKDC-
+SCNQVLKILVWQLCESV-DDWQTLTSDPCMSAQVNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMSKIFALEW-EMDMSHRV
+-SSVDDNFV-IEMLPFVCHRIGPWGHYAQMLAD-QIVLTRPHT---LRDLFILS---CPVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+HLNKMLDWDTGKT-MDREAT-MCREMKLFY-------AETNLWKQNDHSVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVVCVHYDYGAN
+HDIKI------FEVYAAENSWENARNF-EMMSGRAGAEINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNDVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIVID-ELYPGP---YHATPKKH--RFC-GTGDNGGMQAIQE
+DMFQVLVCV
+;
+t18
+GIVSECRMIIRDE--TDDAIDEV-C------------LVASMVKKLSGCENQTRNNRECAIT-SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGMP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLRRVFPDNATFSKLKEGAPHVISH--PYFLGIDMFHEQVVYRGP--LTLPDPRYELSMSVMYAQHHSFSQ
+KRCLNALDHGDTQESPHGIEHNMRNSVLLYN---PIGF-L-VIIKNINSMMGRLNHHESRAVVGFPLR---GAENPKQI------------------MEG
+HFDK-E-E------ARPIVQDAASVPGK----AQWVGRVRAWCSSDVKA-----------SKLPRNDPIVPEVGANVYQQLSRMKTNIPIYAHVTEYAVG
+I----VKPFYD-NEWKQEAQGVGEA-GASIPCVDSPDVQYELKHAEVRKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAIL-KLPMIQLDQ----KTLSH
+-NQPRR--LCQRTWLDASPLQ------VGMNIMLKGKKAPSKK-DYEIAADPVIMYFYQAPIIMRRTDVFEGTHNKKAQAMRV------RSTASQSIGDD
+DMLK--MPLVQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANQGEK---YAEPHVIGD-----------------KVSVNVIKLLYCKDC-
+SCNQVLKILIWQLCESV-DDWQTLTSDPCMSAQVNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMFKIFALEW-EMDMSHRV
+-SSVDDNFV-IEMLPFVCHRIGPWGHYAQMLAD-QIVLTRPHT---LRDLFILS---CPVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+HLNKMLDWDTGKT-MDREAT-MCREMKLFY-------AETNLWKQNDHSVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVVCVHYDYGAN
+HDIKI------FEVYAAENSWENARNF-EMMSGRAGAEINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNDVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGP---YHATPKKH--RFC-GTGDNGGMQAIQE
+DMFQVLVCV
+;
+t68
+GIVSECRMIIRDE--TDDAIDEV-C------------LVASMVKKLSGCENQTRNNRECAI--SPPFIGV---RELFKR-YG-CVEGIGCVNTVAGMP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLRRVFPDNAHFSKLKEGAPHVISH--PYFLGIDMFHDQVVYRGP--LTLPDPRYELSMSVMYAQHHSFSQ
+KRCLNALDHGDTQESPHGIEHNMRNSVLLYN---PIGF-L-VIIKNINSMMGRLNHYESRAVVGFPLR---GAENPKQI------------------MEG
+HFDK-E-E------ARPIVQDAASVPEK----AQWVGRVRAWCSSDVKA-----------SKLPRNDPIVPEVGANVYQQISRMKTNIPIYAHVTEYAVG
+I----VKPFYD-NEWKQEAQGVGEA-GASIPCVDSPDVQYELKHAEVRKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAIL-KLPMIQLDQ----KTLSH
+-NQPRR--LCQRTWLDASPLQ------VGMNIMLMGKKAPSKK-NYEIAADPVIMYFYQAPIIMRRTDVFEGTHNKKAQAMRV------RSTASQSIGDD
+DMLK--MPLRQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANQGEK---YAEPVVIGD-----------------KVSVNVIKLLYCKDC-
+SCNQVLKILVWQLCESV-DDWQTLTSDPCMSAQVNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMSKIFALEW-EMDMSHRV
+-SSVDDNFV-IEMLPFVCHRIGPWGHYAQMLAD-QIVLTRPHT---LRDLFILS---CPVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+HLNKMLDWDTGKT-MDREAT-MCREMKLFY-------AETNLWKQNDHSVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVVCVHYDYGAN
+HDIKI------FEVYAVENSWENARNF-EMMSGRAGAEINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNDVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGP---DHATPKKH--RFC-GTGDNGGMQTIQE
+DMFQVLVCV
+;
+t28
+GIVSECRMIIRDE--ADDAIDEM-C------------LVASMVKKLSGCENQARNNRECAI--SPPFIGV---RELFKR-YH-CMEGIGCVNTVAGMP-S
+ESSVWMFDQFMYKLTHSMIW--------GDLGRVFPDNATFSKLKEGAPHVISH--PYFLGIDMFHAQVFYRGS--LTLPDPRYELSMSVMYSQHHSFSQ
+KRCLNPLDHGDRQESSHGIEHNMRSSVLLYN---PIGF-L-VIIDNINPMMGRLNHHESRAIVTFPLR---GAEHPKQI------------------VEG
+HFDK-E-E------ARPIVKDAASVPGK----AQWVGRIRAWCSSDVKA-----------SQLPRNDPIVPEVGANVYQQDSRMKTNIPIYAHVTEYACG
+I----VKPFYE-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAIL-KLSMIQLDE----KTLSQ
+-NQRPG--LCQRTWLDANPLQ------MGMNTMLVGKKTPSKK-DYEIAADPVIMYFYQAPIIMRRTDVFEGTNNKKSQAMRV------QSTSSQSIGDD
+DMLN--MPLVQNAMCVSSEMVRKCQPD-GQNKRGCTWMAKN-DTLCPQSGNQGEK---FAEPHQIRN-----------------KVSVNVIKLLYCKDC-
+SCNKMLKILVWQLCESV-DDWQTLASDPCVSAEPNSPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMSKIFALEW-EMDMSHRI
+-SSVDYNYV-IEMLPFVYHRVGPWGHYAQMLSD-QIVLTRPHT---LRDLFILA---CRVASGGEVDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+VLNKMLDWDTGKT-MDREAA-MCREIKLFY-------AETNVWKQNDHSVMFI-ISDAQNRLICGNSIMCGITFMAMACNPHFAKLFMEVACMRYDYFAN
+PDIKI------FEVYAAENSWENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPDITEITRTV--VIC--MYVSI-LRNDVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKN--RYC-GPGDNGGMQVIEE
+DMFQVLVYV
+;
+t82
+GIVSECRMIIRDE--ADDAIDEM-C------------LVASMVKKLSGCENQARNNRECAI--SPPFIGL---RELFKR-YV-CMEGIGCVNTVAGMP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLGRVFPDNCTFSKLKEGAPHVISH--PYFLGIDMFHGQVVYRGS--LTLPDPRYELSMSVMYSQHHSFSQ
+KRCLNPLDHGDRQESPHGIEHNMRSSVLLYN---PIGF-L-VIIDNINPMMGRLNHHESRAIVTFPLR---GAEHPKQI------------------MEG
+HFDK-E-E------ARPIVQDAASVPGE----AQWVGHIRAWCSSDIKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIYAHTTEYACG
+I----VKPFYE-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHANVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAIL-KLNMIQLDQ----KTLSQ
+-NQRPG--LCQRTWLDASPLQ------MGMHIMLVGKKTPSKK-DYEIAADPVIMYFYQAPIIMQRTDVFEGTNNKKSQAMRV------HSTSSQSIGDD
+DMLN--MPLVQNAMCVSSEMVRKCQPD-GQNKRGYTWMAKH-DTLCPQSGNQGEK---YAEPHQIRN-----------------KVSVNVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLASDPCMSAEPNPPVCVWQRELVPQL---NRNVEDLARTIYFGPDEH-------DEGKMMSKIYALEW-EMDMSHRV
+-SSVDYNYV-IEMLPFVYHRVGPWGHYAQMLAD-QIVLTRPHT---LRDLFILA---CPVASGGEQDGNA-ERSQHYI-VYAEL----VNDHKSPISANK
+VLNKMLDWDTGKT-MDREAA-MCRDIKLFY-------AETNVWKQNDHSVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVACMRYDYFAN
+PDIKI------FEVYADENSWENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPDITEITRTV--VIC--MYISI-LRNDVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKN--RFC-GPGDNGGMQVIEE
+DMFQVLVYV
+;
+t41
+GIVSECRMIIRDE--ADDAIDEM-C------------LVASMVKKLSGCENQARNNRECAI--SPPFIGL---RELFKR-YV-CMEGIGCVNTVAGMP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLGRVFPDNCTFSKLKEGAPHVISH--PYFLGIDMFHGQVVYRGS--LTLPDPRYELSMSVMYSQHHSFSQ
+KRCLNPLDHGDRQESPHGIEHNMRSSVLLYN---PIGF-L-VIIDNINPMMGRLNHHESRAIVTFPLR---GAEHPKQI------------------MEG
+HFDK-E-E------ARPIVQDAASVPGE----AQWVGHIRAWCSSDIKA-----------SQLPRNDPIVPEVGANVYQQVSRMKTNIPIYAHTTEYACG
+I----VKPFYE-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHANVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRAIL-KLNMIQLDQ----KTLSQ
+-NQRPG--LCQRTWLDASPLQ------MGMHIMLVGKKTPSKK-DYEIAADPVIMYFYQAPIIMQRTDVFEGTNNKKSQAMRV------HSTSSQSIGDD
+DMLN--MPLVQNAMCVSSEMVRKCQPD-GQNKRGYTWMAKH-DTLCPQSGNQGEK---YAEPHQIRN-----------------KVSVNVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLASDPCMSAEPNPPVCVWQRELVPQL---NRNVEDLARTIYFGPDEH-------DEGKMMSKIYALEW-EMDMSHRV
+-SSVDYNYV-IEMLPFVYHRVGPWGHYAQMLAD-QIVLTRPHT---LRDLFILA---CPVASGGEQDGNA-ERSQHYI-VYAEL----VNDHKSPISANK
+VLNKMLDWDTGKT-MDREAA-MCRDIKLFY-------AETNVWKQNDHSVMFI-ISDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEVACMRYDYFAN
+PDIKI------FEVYADENSWENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPDITEITRTV--VIC--MYISI-LRNDVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKN--RFC-GPGDNGGMQVIEE
+DMFQVLVYV
+;
+t71
+GIVSECRMIIRDQ--SDDAIDEMVV------------LVASMVKEMSGCENQARNNSECAI--SPQFIGV---RELFKR-YR-CMEGIGCVNTVAGAP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLARVFHDNGTFAKLKEGAPHVISV--PYFLGIDMFHGQVFLRGS--LTLPDPRYELSMSVMYAQHHSFSQ
+KRCLNHLDHGDRQESPHGIEHNMRKSVLLYN---PQGY-L-VIIKNVNSMMGRLNHHESRAVVTFPLR---GADNPRQI------------------MEG
+HFDK-E-E------ARPVVQDAPGVPGK----AQWVGKVRAWCSSDVKA-----------SQLPRNDTIVPEVGANVYQQVSRVKTHIPIYAHVTEYAVG
+I----VKPFYN-NEWKQEAQGQGEA-GASIPCVDSPDDQYELKHAEVKKLMHD-SLYLPHLETCHKPIMGTVKGGRCRASL-KLKMIQLDQ----KTLSQ
+-NQQRR--LCQRTWLDSSPLQ------MGMKIMLQGKKTPSKK-DYEIAADPAIMHFYRAPIIMRRTDVFEGTNNKKAQAMRI------RSTASQSIGDD
+DMLN--MPLHQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSPNQGEK---YAEPHQIRN-----------------KISVNVIKLLYCKDC-
+SCNQVLKILVWQLCESV-DDWQTLTSDPCVPAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMRKIFALEW-EMDMSHRD
+-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTRPHT---LRDLFILA---CPVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPISANK
+HMNKMLDWDTGKT-MDFEAA-MCREIKLFY-------AETNVWKINDHSVMFI-VSDAQNRLICGNSIMCGLTFMAMACNPHFAKLFMEGVCMRYDYSAN
+HDIKI------FEVYADENSWENVRNF-EMMSGRAGAQINH-PQLPEQVCNPPCHLTVSNLKGVC-ASCPAITEITRTV--VIV--MWISI-LRNDVMQY
+VVYYKENRSVR-----------QNNTGKAELPR---------------------HPMQEIFID-ELYPGH---YHATPKKN--RFC-GPGDNGGMQSMQE
+DVFQVLVCV
+;
+t94
+GIVSECRMIIRDQ--SDDAIDEMVC------------LVASMVKELSGCENQARNNRECAI--SPPFTGV---RELFKR-YR-CMEGIGCVNTVAGIP-S
+ESSVWMFDRFMYRLTHSMVW--------GDLGRVFQDNATFSKLKEGAPHVISH--PYFLGIDMFHGQVFYRGS--LTLPDPRYELSMSVMYAQHHSMSQ
+KRCLNTLDHGDRQESPHGIEHNMRKSVLLYD---PIGY-L-VIIKNVNSMMGRLNHHESRAKVTFPLR---GADNPRQI------------------MEG
+HFDK-E-E------ARPVVQDAPGVPEQ----AQWVGKMRAWCSSDVKA-----------SQLPRNDTIVPEVGANVYQQVSRVKTNIPIYAHVTEYAVG
+I----VKPFYN-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLPHLETCHKPIMGTVKGGRCRASL-KLNMIQLDQ----KTLSQ
+-NQQRR--LCQRTWLDASPLQ------MGMKIMLQGKKIPSKK-DYEIAADPAIMYFYQATIIMRRTDVFEGTNNKKAQAMRM------RSTASQSIGDD
+DMLN--MPLHQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLYPQSANQGEK---YAEPHQIRN-----------------KISVNVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLTSDPCVPAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMRKIFALEW-EMDMSHRD
+-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-KLVLTRPHT---LRDLFILA---CYVASGGEQDGNT-ERSQHYI-VYAEL----QNDHKSPILANK
+VVNKMLDWDMGKT-MDFEAA-MCREIKLFY-------AETNVWKQNNHSVMFI-VSDAHNRLICGNSIMCALTFMAMACNPHFAKLFMEAVCMRYDYSAN
+HDIKI------VEVYADENSWENVRNF-EMMSGRAGAQINH-PQLPEQVCNPPCHLTVSNLKGVC-ASCPAITEITRTV--VIV--MWISI-LRNDVMQY
+VFYYKENRSVR-----------QNNTGKAELPR---------------------HPVQDIFID-ELYPGH---YHATPKKV--RFC-GPGDNGGMQAIQE
+DVFQVLVCV
+;
+t99
+GIVSEVRMIIRDE--SDDAIDEM-C------------LVASMVKALSGCENQARNNRECAI--SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGIP-S
+ESSIWMFDRFMYKLTHSMVW--------GDLGQVFPDVSTFSKLKEGAPHVISQ--PYFLGIDMFHDQVFYRGS--LTLPDPRYELSMSVMYAQHHSFSQ
+KRCLNALDHGDRQESPHGIEHNMRKSVLLDS---PIGY-L-VIIKNINSMMGRLNHHESRAVFAFPLR---GAENPKQI------------------MEG
+HFDK-EKE------ARPVVQDAPGVPGK----AQWVGRIRAWCSSDVKA-----------SELPRNDAIVPEVGANVYQQVSRMKTNIPIYAHATEYAVG
+I----VKPFYD-NEWKQEAQGQGET-GASIPCVDSPDVQYEMKHAEVKKLMHD-SLYLMHIETCHKPIMGTVKGDRCRATL-KLKMIQLDQ----KTLSQ
+-NQKRR--LCQRTWLDASPLQ------MGMKMMLQGKKTPSKK-DYEIAADPVIMYFYQSPIIMRRTDVFEGTNNKKAQAMRV------RSTASQSIGDD
+EMLN--MPLVQNAMCVPSEMVRKCQPD-GQDKRGYTWMAKD-DPLCPQSANVGEK---YAEPHQIRN-----------------KVSVNVIKLLYCKDC-
+SCNKVLKILVWQLCDSVQDDWQPLTSDPCVNAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMNKIFALEW-EMDMSHRD
+SSSVDDNYI-IEMLPFVCHRVGPWGHYAQQLAD-RLVLTRPHT---LRDIFILA---CPVASGGEQDGNT-ERSQHYI-VYAEL----QDDHKSPISANK
+HMRKMLDWDTGKT-MDREAA-VCREIKLFY-------AETNCWKQNDHSVMFI-VSDAQNRLICGSSIMCRLTFMAMAVNPHFAKLFMEDVCMRYDYSPN
+HDIKI------FEVYADENSWENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNDVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGR---YHATPKKN--RYC-GPGDNGGMQPIQE
+DMFQVLVCV
+;
+t40
+GIVSECRMIIRDE--SDDAIDEV-C------------LVASMVKALSGCENQARNNRECAI--SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGIP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLGRVYPDNPTFSKLKEGAPHVISH--PYFLGIDMFHDQVFYRGS--LTLPDPRYELSMSVMYAQHHSFSQ
+KRCLNALDHGDRQESPHGIEHNMRKSVLLDS---SIGY-I-VIIKNLNSMMGRLNHHESRAVVTFPLR---GAEDPKQI------------------MEG
+HFDK-E-E------ARPVVQDAPGVPGK----AQWVGRVRAWCSSEIKT-----------SELPRNDAIVVEVGANVYQQISRMKTDIPIYAHATEYAVG
+I----VKPVYD-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRATL-KLKMIQLDQ----KTLSQ
+-NQKKR--LCQCTWLDACPLQ------MGMKIMLQGKKTPSKK-DYEIAADPVIMYFYQSPIIMRRTDVFEGTNNKKAQAMRI------RSTASQSIGDD
+EMLN--MPQVQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANVGEK---YAEPHQIRN-----------------KVSTNVIKLLYCKDC-
+SCNKVLKILVWQLCDSV-DDWQTLTSDPCVSAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMRKIFALEW-EMDMSHRN
+-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTRPHT---LRNIFILA---CPVASGGEQDENT-ERSQHYI-VYAEL----QNDHKSPIHANK
+VMNKMLDWDTGKT-MDREAA-MCREIKLFV-------AETNVWKQNDHSVMFIVISDAQNRLICGSSIMCRLTFMAMAVNPHFAKLFMEESCVRYDYSAN
+HDIKI------FEVYANENSWENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASVPAITEITRTV--VIC--MYISI-LRNNVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YQATPKKD--KFC-GPGDNGGMQTIQE
+DMFQVLVCV
+;
+t90
+GIVSECRMIIRDE--SDDAIDEV-C------------LVASMVKALSGCENQARNNRECAI--SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGIP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLGRVYPDNPTFSKLKEGAPHVISH--PYFLGIDMFHDQVFYRGS--LTLPDPRYELSMSVMYAQHHSFSQ
+KRCLNALDHGDRQESPHGIEHNMRKSVLLDS---PIGY-I-VIIKNVNSMMGRLNHHESRAVVTFPLR---GAEDPKQI------------------MEG
+HFDK-E-E------ARPVVQDAPGVPGK----AQWVGRVRAWCSSEIKT-----------SELPRNDAIVPEVGANVYQQISRMKTDIPIYAHATEYAVG
+I----VKPVYD-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLMHLETCHKPIMGTVKGDRCRATL-KLKMIQLDQ----KTLSQ
+-NQKKR--LCQCTWLDACPLQ------LGMKIMLQGKKTPSKK-DYEIAADPVIMYFYQSPIIMRRTDVFEGTNNKKAQAMRV------RSTASQSIGDD
+EMLN--MPLVQNAMCVSSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQSANQGEK---YAEPHQIRN-----------------KVSTNVIKLLYCKDC-
+SCNKVLKILVWQLCDSV-DDWQTLTSDPCVSAEPNPPVCVWQRELVPQL---NRNVEDLARIIYFGPDEH-------DEGKMMRKIFALEW-EMDMSHRN
+-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTRPHT---LRNIFILA---CPVASGGEQDENT-ERSQHYI-VYAEL----QNDHKSPINANK
+VMNKMLDWDTGKT-MDREAA-MCREIKLFV-------AETNVWKQNDHSVMFIVISDAQNRLICGSSIMCGLTFMAMAVNPHFAKLFMEESCVRYDYSRN
+HDIKI------FEVYANENSWENVRNF-EMMSGRAGAQINH-PQLPEQVC-PPCHLTVSNLKGVC-ASVPAITEITRTV--VIC--MYISI-LRNNVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKD--KFC-GPGDNGGMQTIQE
+DMFQVLVCV
+;
+t4
+GIVSECRMIIRDE--PDDAIDEV-C------------LVASMVKELSGCENQARNNRECAI--SPPFIGV---RELFKR-YG-CMEGIGCVNTVAGMP-S
+ESSVWMFDRFMYKLTHSMVW--------GDLGRVFPDNATFSKLKEGAPHVISV--PYFLGIDMFHDQVFYRGS--LTLPDPRYEMSMSVMYAQHHSFSQ
+KRCLNALDYGDRQESPHGIEHNMRKNVLLDN---PIGH-L-VIIKNENSMMGRLNHHESRAVVTFPLR---GAEDPKQK------------------MEG
+SFDK-E-E------ARPVVQDAPGVPGR----AQWVGRVRPWCSSDVKA-----------SELPRNDAIWPEVGANVYQQISRMKTNIPIYPHVTEYAVG
+I----VKPFYL-NEWKQEAQGQGEA-GASIPCVDSPDVQYELKHAEVKKLMHD-SLYLWHLETCVKPIMGTVKGDRCRATL-KLKMIVLDP----KTLSQ
+-NQKRR--LCQRTWLDASPLQ------VGMKIMLQGKKTPSKK-DYEIAADPVIMYFYQSPIIMRHTDVFEGTNNKKAQAMRL------RSTASQSIGDD
+EMLN--MPLIQNAMCVQSEMVRKCQPD-GQDKRGYTWMAKD-DTLCPQLHNQAEK---YAEPHQIRN-----------------KVSVNVIKLLYCKDC-
+SCNKVLKILVWQLCESV-DDWQTLTSDPCISAEPNPPVCVWQRELVPQL---NRNIEDLARIIYFGPDEH-------DEGKMMGKIFALEW-EHDMSHRD
+-SSVDDNYV-IEMLPFMCHRVGPWGHYAQQLAD-RLVLTRPHT---LRDIFILA---CPVASGGEQDAVT-ERSQHYI-VYAEL----QNDHKSPISASK
+HMNKMLDWDTGKT-MDREAA-MCREIKLFY-------AETNVWKQNDHSVMFI-ISDAQNRLICGSSIMCGLTFMATACNPHFAKLFMEEVCMRYDYAAN
+HDIKI------SEVYAEENSWENVRNF-EMMSGRAGAQINH-PQLPEQVV-PPCHLTVSNLKGVC-ASCPAITEITRTV--VIC--MYVSI-LRNVVMQY
+VFYYKENRSVR-----------QNNTGKAELPK---------------------HHMQDIFID-ELYPGH---YHATPKKN--RCC-GPGDNGGMQTVQE
+DMFQVLVCV
+;
+t36
+MIWSEVRKMVRER--REQAIDNK-C------------LIAARVKMMSGYVLQVRNALEDAL--YVFFTGTKGTRELVKY-YM-CMEGHGCVNTMAKKS-S
+QSGIWKFNAFMC-LMHLMEG--------GDL--------------------CSY--PSFLGMCMFHAMVQSKGD--LVLPDSPNEDSVSFMYIQHHSFHE
+KRCLNPLNVGDREDSEHIKEKHMRI----YA---NIGG-H-IIIREWNDVMGRLNHIEPGAEVIFPLRK--RGQHSKPV------------------IDG
+FFAK-D-E------DRPGIQNAVSVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYRINRKVGANAYDQDSRMKAAAPVYPHIMEYAHG
+M----FNPFYGLSEPKNNAQGNGEN-PMNKPCVESEDCQYEKKHASMDKLMHQ-SLYLMHINIMSKPAMGEWVGNRCRNELTALRIIQLDVGVSGKTLGQ
+-NIGVSKLLNDRTWLATSPLE------IGCGVMSVEKKEASPK-EFEVAADPTVIYFYRNLIIQKITDVLSAVRMESPQEMRT------QDVNSSSLGDN
+NGQA--MNIVPYWVCVASGVVRKTHKD-SVDKRGQTWTAKS-DFLCPLAVDQGEP---GAEQKPAVGEENPICKPWQFVIMNTTTFAKNIFRLLYVKDV-
+SCNGVLPLLKWQLCDSH-GDWQSLYADSCPIA-VNAAVCGWKRELVPGL---NHSCEHLAKSVYFEPDGE-------GEGKVMLKIFGLDWCEVERSHEH
+-SSVDDNYN-VNMLPFQNSRKDPVGHYVQDLED-ARRLIRPGT---ARSLTILF-YGCQYYSGEFQDCEI-ERSQLYN-VYCEH----KQDHKSAIIANK
+QEQKGMDWNTGKE-MEQGPK-IILHGSLFF-------AEPNIVRQPGVSHIFI-GNDARRVLICGKSMMPGHRFMREACVPFFHKLFMAVNQMRYDYMMN
+YDIKIYETHWRMGVYALDNSWETLNVS-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIKIY--MWGTINFKNRVMQY
+CNYYKENRSVR-----------INNTGLAELPK---------------------YHHQNILID-ELYSNV---YPAAPKKH--QYM-GVGDVGGYEVICE
+NLFQILVVE
+;
+t87
+MIWSEVRKMVRER--REQAIDNK-C------------LIAARVKMMSGYMLQVRNALEDAL--YVFFTGNKGTRELVKY-YM-CMEGHGCVNTMAKKS-S
+QSGIWKFNAFMC-LMHLMEG--------GDL--------------------CSY--PSFLGMCMFHAMVQSKGD--LVLPDSPNEDSVSFMYIQHHSFHE
+KRCLNPLNVGDREDSDHVKEKHMRI----YA---NIGG-H-IIIREWNDVMGRLNHIEPGAEVIFPLRK--RGQHSKPV------------------IDG
+FFAK-D-E------DRPGIQNAMSVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYRINRKVGANAYDQDSRMKAAAPVYPHIMEYAHG
+M----FNPFYGLSEPKNNAQGNGEN-PMNKPCVESEDCQYEKKHASMDKLMHQ-SLYLMHINVMSKPAMGEWVGNRCRNDLTALRIIQLDVGHSGKTLGQ
+-NIGVSKLLNDRTWLATSPLE------IGCLVMSVEKKEASGK-EFEVAADPTVIYFYRNLIIAKITDVLSAVRMESPQEMRE------QDVNSSSLGDN
+NGQA--MNIVPYWVCVGSGVVRKTHKD-SVDKRGQTWTAKS-DFLCPLAMDQGEI---GAEQKPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-
+SCNGVLPLLKWQLCDSH-GDWQSLYADSCPIA-INAAVCGWKRELVPGL---NHSCEHLAKSVYFEPDGE-------GEGKVMLKIFGLDWCEVERSHEH
+-SSVDDNYN-VNMLPFQNSRKDPVGHYVQDLED-ARRLIRPGT---ARSLTILF-YGCQYYSGEFQDCEI-ERSQLYN-VYCEH----KQDHKSAIIANK
+QEQKGMDWNTGKE-MEQGPK-VILHGTLFF-------AESNIVRQPGVSHIFI-GNDARRVLICGLSMMPGHRFMREACVPFFHKLFMAVNQMRYDYMVN
+YDIKIYETHWRMGVYALDNSWETLNVS-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIKIY--MWGTICFKNRVMQY
+CNYYKENRSVR-----------INNTGLAELPK---------------------YHHQNILID-ELYSNV---YPAAPKKH--QYM-GVGDVGGYEMICE
+NLFQILVVE
+;
+t89
+MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDAL--YNFFTGHKGTRELVKY-YM-CMEGEGVVNTMAKKS-S
+QSGIWKFNAFMC-LMRLMQG--------GDL--------------------CSY--PSFLGMCMFYAMVQSKGD--LVLPDSCNEDSVSFMYIQHHSFHE
+KRCLNPLNVGDREDSDHTKEKHMRI----YA---NIGG-H-IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDG
+FFAK-D-E------ERPGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYKINRKVGANAYDQVSRMKAAAPVYPHIMEYAHG
+M----FNPFYGLSEPKNNAQGNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHINIMSKPAMGEWVGVRCRNELTALRIVQLDVGHSGKTLGQ
+-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEASPK-EFEVAADPTVIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDN
+NGQA--MNIVPYWVCVASGVVRKMHKD-SVEKRGQTWEAKS-DFLCPLAVDQGEP---AAEQRPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-
+SCNGVLPLLKWQLCDSH-GDWQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEGKMMLKIFGLEWCEVERSHEH
+-SSIDDNYT-VNMLEFPNSRKDPVGHYVQNLED-AIRLIRPGT---ARSLTILL-YGCQYYSGEFQDCEV-ERSQCYN-VYCEL----KQDHKSAIIANK
+QEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGVSHIFT-ENDARRMLICGNSMMPRHRFMREACVPFFHKLFMAVNQMRYDYVTN
+YDIKIYETHWRVGVYAIDNSWETLNVS-EMTSGRMGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIEIY--MWGTINFKNQVMQY
+CNYYKENRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYNNI---YPAAPKKH--KFL-GVGDVGGYEIICE
+NLFQILVVE
+;
+t39
+MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDAL--YNFFTGHKGTRELVKY-YM-CMEGEGVVNTMAKKS-S
+QSGIWKFNAFMC-LMRLMQG--------GDL--------------------CSY--PSFLGMCMFYAMVQSKGD--LVLPDSCNEDSVSFMYIQHHSFHE
+KRCLNPLNVGDREDSDHTKEKHMRI----YA---NIGG-H-IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDG
+FFAK-D-E------ERPGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYKINRKVGANAYDQVSRMKAAAPVYPHIMEYAHG
+M----FNPFYGLSEPKNNAQGNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHINIMSKPAMGEWVGVRCRNELTALRIVQLDVGHSGKTLGQ
+-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEASPK-EFEVAADPTVIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDN
+NGQA--MNIVPYWVCVASGVVRKMHKD-SVEKRGQTWEAKS-DFLCPLAVDQGEP---AAEQRPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-
+SCNGVLPLLKWQLCDSH-GDWQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEGKMMLKIFGLEWCEVERSHEH
+-SSIDDNYT-VNMLEFPNSRKDPVGHYVQNLED-AIRLIRPGT---ARSLTILL-YGCQYYSGEFQDCEV-ERSQCYN-VYCEL----KQDHKSAIIANK
+QEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGVSHIFT-ENDARRMLICGNSMMPRHRFMREACVPFFHKLFMAVNQMRYDYVTN
+YDIKIYETHWRVGVYAIDNSWETLNVS-EMTSGRMGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIEIY--MWGTINFKNQVMQY
+CNYYKENRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYNNI---YPAAPKKH--KFL-GVGDVGGYEIICE
+NLFQILVVE
+;
+t8
+MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDAL--YNFFTGHKGTRELVKY-YM-CMEGEGVVNTMAKKS-S
+QSGIWKFNAFMC-LMRLMQG--------GDL--------------------CSY--PSFLGMCMFYAMVQSKGD--LVLPDSCNEDSVSFMYIQHHSFHE
+KRCLNPLNVGDREDSDHTKEKHMRI----YA---NIGG-H-IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDG
+FFAK-D-E------ERPGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYKINRKVGANAYDQVSRMKAAAPVYPHIMEYAHG
+M----FNPFYGLSEPKNNAQGNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHVNIMSKPAMGEWVGVRCRNELTALRIVQLDVGHSGKTLGQ
+-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEASPK-EFEVAADPTVIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDN
+NGQA--MNIVPYWVCVASGVVRKMHKD-SVEKRGQTWEAKS-DFLCPLAVDQGEP---AAEQKPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-
+SCNGVLPLLKWQLCDSH-GDWQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEGKMMLKIFGLEWCEVERSHEH
+-SSIDDNYT-VNMLPFPNSRKDPVGHYVQDLED-AIRLIRPGT---ARSLTILL-YGCQYYSGEFQDCEV-ERSQCYN-VYCEL----KQDHKSAIIANK
+QEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGVSHIFT-ENDARRMLICGNSMMPRHRFMREACVPFFHKLFMAANQMRYDYVTN
+YDIKIYETHWRVGVYAIDNSWETLNVS-EMTSGRMGAKINHLPRLPEHVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIEIY--MWGTINFKNQVMQY
+CNYYKENRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYNDI---YPAAPKKH--KFL-GVGDVGGYEIICE
+NLFQILVVE
+;
+t6
+MIWSEHRKMVREG--REQAIDNK-C------------LIAKRVKVMSGYILQVRNAPEDAL--YNFFTGHKGTRELVKY-YM-CMEGEGVVNTMAKKS-S
+QSGIWKFNAFMC-LMRLMQG--------GDL--------------------CSH--PSFLGMCMFYAMVQSKGD--LVLPDSCNEDSVSFMYIQHHSFHE
+KRCLNPLNVGDREDSDHTKEKHMRI----YA---NIGG-H-IIIREWNDVMGRLNVIEPEAEVIFPLRK--RGQHSKPV------------------IDG
+FFAK-D-E------ERPGIQNAMNVPCG----DQWVGSIRGWCSSQHRYGLANHILVHEPSKLHKTYKVVRKVGANAYDQVSRMKAAAPVYPHIMEYAHG
+M----FNPFYGLSEPKNNAQGNGEN-PMNVPCVESEDCQYEKKHASMTKLMHQ-SLYLMHINIMSKPAMGEWVGVRCRNELTALRIVQLDVGHSGKTLGQ
+-NIGVSKLLNDRTWLATSPLE------IGCGVISVEKKEASPK-EFEVAADPTVIYFYRSLIIVHITDVLSAVRMDSPQEMRN------QDVNSPSLGDN
+NGQA--MNIVPYWVCVASGVVRKMHKD-SVEKRGQTWEAKS-DFLCPLAVDQGEP---AAEQKPAVGEKNPICKPWQFVIMNTTTFAKNIFRLLYVKDV-
+SCNGVLPLLKWQLCDSH-GDWQSLFPDSCPFA-LNAAVCGWKRELVPGL---NHSCEHLAKGVYFEPDGE-------DEGKMMLKIFGLEWCEVERSHER
+-SSIDDNYT-VNMLPFPNSRKDPVGHYVQDLED-AIRLIRPGT---ARSLTILL-YGCQYYSGEFQDCEV-ERSQCYN-IYCEL----KQDHKSAIIANK
+QEQKGMDWNTGKE-MEQGPK-IILHGCLFF-------AEPNIVRQPGVSHIFI-ENDARRMLICGNSMMPRHRFMREACVPFFHKLFMAVNQMRYDYMTN
+YDIKIYETHWRVGVYAIDNSWETLNVS-EMTSGRMGAKINHLPRLPEQVI-PPCMLTVSGLKDTM-AGMKQETEITKTPDIEIY--MWGTINFKNQVMQY
+CNYYKENRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYNNI---YPAAPKKH--KFL-GVGDVGGYEIICE
+NLFQILVVE
+;
+t58
+MIWSEYRHMVREG--RDQAIDNK-C------------LIAARVKVMSGYVLQVRNAPEDAL--YNFFTGHKGTRELVKY-YM-CMEGEGCVNTMAKKS-S
+QSGIWKFNAFMC-LMHLMQG--------GDL--------------------CSH--PSFLGMCMFHAMVKSKGN--LVLPDSCNEDSVSFMYIQHHSFHE
+KRCLNHLNVGDREDSEHIKEKHMRV----YA---SIGG-H-IIIREWNDVMGRLNHIEPGAEVTFPLRR--RGQASKPV------------------IDG
+FFAK-D-E------DRPGIQNAMSVPCG----DQWVGSVRGWCSSQHRYGLAIHILVHQQSRLHKTYNIDRKNGANAYEQDSRMKAGAPVYPHIMEYAHG
+M----FNPFYGMSEPKNNAQGNGEN-PMNVPCVESDDCQYEKKHASMDKQMHQ-SLYLMHMNIMSKPAMGEWVGNRCRNELTALHVVQLDVGFSGKTLGQ
+-NIGISELLNDRTWLATSPLE------IGCGVMAVEKKEASPK-EFEVAADPTVIYFYRNLIIQHITDVLSAVRMDSPQEMRV------QDVNSPSLGDN
+NGQA--MNIVPYWVCVVSGVVRKTHKD-SVEKRGQTWTAKS-DFLCPIAVNQGEP---GAEQKPAVGA-NPIVKPWQFVIMNTTTFAKNIFRLLYVKDV-
+SCNGVLPLLKWQLCDSH-GDWQSLFADSCPTA-VNAAVCAWKRELVPGL---NHSCEHLAKSVYFEPDGE-------DEGKMMLKIFGLDWCEVERSHEH
+-SSVDDNYN-VNMLPFPNSRQDPVGHYVQDLED-LLRLIRPGT---ARSLTVLF-YGCQYYSGQFQDCEI-ERSQLYN-VYCEL----KQDHKSAIMANK
+QEQKGMDWNTGKE-MEQGPK-IILHGVLFF-------AEPNVVRQPGVSHIFV-GNDARRMLICGLSMMPGHRFMKEACVPFFHKLFMAVRRMRYDYMSN
+YDIKIYETHWRPGVYALDNSWETLNVS-EMTSGRIGAKINHLPRLPETVI-PPCVLTVSGLKDTM-AGMKHGTEITKTPDIKIH--MWGTINFKNKVMQY
+CTYYKENRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYSNI---YPATPKKH--QYM-GVGDVGGYEVICE
+NLFQILVVE
+;
+t54
+MIWSEYRHMVREG--RDQAIDNK-C------------LIAARVKVMSGYVLQVRNAPEDAL--YNFFTGHKGTRELVKY-YM-CMEGEGCVHTMAKKS-S
+QSGIWKFNAFMC-LMHLMQG--------GDL--------------------CSH--PSFLGMCMFHAMVQSKGN--LVLPDSCNEDSVSFMYIQHHSFHE
+KRCLNHLNVGDREDSEHIKEKHMRI----YA---SIGG-H-IIIREWNEVMGRLNHIEVGAEVTFPLRR--RGQASKPV------------------IDG
+FFAK-D-E------DRPGIQNAMSVPCG----EQWVGSVRGWCSSQHRYGLAIHILVHQQSRLHKTYNIDRKNGANAYDQDSRMKAGAPVYPHIMEYAHG
+M----FVPFYGMSEPKNNAQGNGEN-PMNVPCVESDDCQYEKKHASMDKQMHQ-SLYLMHMNIMSKPAMGEWVGNRCRNELTALHIVQLDVGFSGKTLGQ
+-NIGISELLNDRTWLATSPLE------IGCGVMAVEKKEASPK-EFEVAADPTVIYFYRNLIIQHITDVLSAVRMDSPQEMRV------QDVNSPSLGDN
+NGQA--MNIVPYWVCVVSGVVRKTHKD-SVEKRGQTWTAKS-DFLCPIAVNQGEP---GAEQKPAVGA-DPIVKPWQFVIMNTTTFAKNIFRLLYVKDV-
+SCNGVLPLLKWQLCDSH-GDWQSLFADSCPIA-VNAAVCAWKRELVPGL---NHSCEHLAKSVYFEPDGE-------DEGKMMLKIFGLDWCEVERSHEH
+-SSVDDNYN-VNMLPFPNSRKDPVGHYVQDLED-LLRLIRPGT---ARSLTVLF-YGCQYYSGEFQDCEI-ERSQLYN-VYCEL----KQDHKSAIMANK
+QEQKGMDWNTGKE-MEQGPK-IILHGVLFF-------AEPNVVRQPGVSHIFV-GNDARRMLICGLSMMPGHRFMKEACVPFFHKLFMAVRRMRYDYMTN
+YDIKIYETHWRPGVYALDNSWETLNVS-EMTSGRIGAKINHLPRLPETVI-PPCVLTVSGLKDTM-AGMKHGTEITKTPDIKIH--MWGTINFKNKVMQY
+CTYYKENRSVR-----------INNTGGAELPK---------------------YHHQNILID-ELYSNI---YPATPKKH--QYM-GVGDVGGYEVICE
+NLFQILVVE
+;
+t65
+MIWSEYRQMVREG--NDQSIDNK-C------------LIADRVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELIKF-YF-CMEGCGCVNTMAKNS-S
+QSAPWKFNRFMC-LMHLMQS--------GDL--------------------CNS--PSFLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDSQDSQHLREKQLRI----YG---RIGK-V-VIIKVWNAVMGRLNHHEPPAEVMFPLRK--GGQDSKPF------------------IDG
+FF------------DRPGIANAMSVKCG----DQWVGSIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQTSRMKAAAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECQYEHKHAAMEKLMHH-SLYLMRVNTMSKPVMGDWVGNRCRAELTALQTVQLDVGSSGKTLGQ
+-NIVTSKKLGDRTWLAASPLQ------IGCGVMVQEKKIASPQ-EVEVAAD---IYFYRNMVVQRLTDVVAAVRMQSPQEMRTPVLVCIQKVDSVSLGDD
+DPQM--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPAAVNEGEH---GAEQRP-FGTQNPVCKPWRFVIMNTQTFAKNIIRLLYIKDI-
+SCNQVLQLLDWQLCDSH-GDWQSLMADSCPNA-VNIAVCCWKRELMPGL---NHSCEHLAKSVYFKPDGE-------DEGQMTMKIFNLDWCEVEKSHEK
+-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDYKSAIIANQ
+QEHKGMEWDTGKE-MQQGPK-VVVHLALFYAPSNVLAAEPNIIGQPQVSHVFV-GNDARRMLIVGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYMWN
+YDIKIYETHFRMGVYAVDNSWETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPCILTVSGLKRTV-AGAPDETEITKSPVIHIV--MWADIMFKNCVMQY
+CTYYKENRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDV---YPAAQKKY--QVM-GVGDIGGYELICE
+DLFQILVCQ
+;
+t29
+MIWSEYRQMVREG--NDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELIKF-YF-CMEGCGCVNTMAKNS-S
+QSAPWKFNRFMC-LMHLMQS--------GDL--------------------CNC--PSFLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLFVGDSQDSQHQREKQLRI----YG---RIGK-V-VIIKVWNAAMGRLNHVEPPAEVMFPLRR--GGSDSKPF------------------LDG
+FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILIHGPSKLHRTYAINKKMGANVYQQTSRMKAAAPLYPHIMEYAHG
+M----VKPFYGQSEPKNEAQGNGEN-PMNVPSVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMPKPVMGDWDGNRCRAELTALQTVQLDVGSSGKTLGQ
+-NIVTSKKLGDRTWLAASPLQ------IGCGVMVQEKKIASPQ-EVEVAAD---IYFYRNMVVQRLTDVVAAVRMQSPQEMRTPVLVCIQKVDSVSLGDD
+DPQM--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGTHNPVCKPWRFVIMHTQTFSKNIIRLLYIKDI-
+SCNQVLQLLDWQLCDSH-GDWQSLMADSCPNA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMSQKIFNLDWCEVEKSHEK
+-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELEDSALRLIRPGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDYKSAIIANQ
+QDHKGMEWDTGKE-MQQGPK-VVVHLALFYMPSNVLAAEPNIIGQPQVSHWFV-GNDARRMLIVGVSMMPAYKFMREACVPFFRKLFMADNQVRYDYMWN
+YDIKIYETHFRMGVYAVDNSWETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPCILTVSGLKRTV-AGAPDETEITKSPVIHIV--MWADIMFKNCVMQY
+CTYYKENRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDL---YPAAPKKY--QEM-GVGDIGGYELIVE
+DLFQILVCE
+;
+t98
+MIWSEHRQMVREG--NDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTKELVKF-YF-CMEGCGCVNTMAKKS-S
+QSAPWKFNRFMC-LMHLMQS--------GDL--------------------CNS--PPFLGMCMFHPQVQMKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDSQDSQHLREKQLRI----YG---RIGK-V-VIIKVWNAVMGRLNHHEPPAEVMFPLRR--GGSDSKPF------------------IDG
+FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHNPSRLHRTYAINKKMGANVYQQSSRMKAAAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAELTALQTVQLDVGSSEKTLGQ
+-NIVTSKRLGDRTWLAASPLQ------IGCGVMVQEKKIASPQ-EVEVAAD---IYFYRNMVVQRHTDVVAAVRMQSPQEMRNPVLVCIQKVDSASLGDD
+DPQM--MKIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGTQNPVCKPWRFVIMNTQTFSKNIIRLLYIKDI-
+SCNQVLQLLDWQLCDSH-GDWQSLMADSCPPA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMTMKIFNLDWCEVEKSHEK
+-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSEMFERSQLYR-VYCEI----KKDYKSAIIANQ
+QEHKGMEWDTGKE-MQQGPK-IVVHLGLFYMPSNVLAAEPNIIGQPQVSHVFV-ANDARRMLIVGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYVWN
+YDIKIYETHFRMGVYAVDNSWETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPCDLTVSGLKRTV-AGPPDETEITKSPVIHIV--MWADIVFKNCVMQY
+CTYYKENRSVR-----------ANNTGGAELPK---------------------YHQQNLLTD-ELYSDI---YPAAPKKY--QVM-GVGDIGGYELIVE
+DLFQILVCE
+;
+t83
+MIWSEYRQMVREG--NDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTKELIKF-YF-CMEGCGTVNTMAKDS-S
+QSAPWKFNRFMC-LMHLMQS--------GDL--------------------CNS--PSFLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDSQDSQHLREKQLRI----YG---RIGK-V-VIIKVWNAVMGRLNHHEPPAEVMFPLRR--GGSCSKPF------------------VDG
+FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILIHNPSRLHRTYAINKKMGANVYQQTSRMKAAAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAELTALQTVQLDLGSSGKTLGQ
+-NIVTSKKLGDRTWLAASPLQ------IGCGIMVQEKKIASPQ-EVEVAAD---IYFYRNMVVQRHTDVVAAVRMQSPQEMRNPVLVCIQKVDSISLGDD
+DPQM--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGTQNPVCRPWRFVIMNMQTFSKNIIRLLYIKDI-
+SCNQVLQLLDWQLCDSH-GDWQSLMADSCPPA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMTMKIFNLDWCEVEKSHEK
+-SSVDDNYN-VNMLPFMQSHGDPVGHYVQELED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSDMFERSQLYR-VYCEI----KKDYKSAIIANQ
+QEHKGMEWDTGKE-MQQGPQ-IEVHLALFYMPSNVLPAEPNIIGQPQVSHVFV-GNDARRMLIVGVSLMPAYKFMREACVPFFRKLFMAENQVRYDYMWN
+YDIKIYETHFRMGVYAVDNSWETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPCILTVSGLKRTI-AGAPDETEITKSPVIHIV--MWADIMFKNCVMQY
+CTYYKENRSVR-----------ANNTGGAELPK---------------------YHQQNLLTD-ELYSDI---YPAAPKKY--QVM-GVGDIGGYELIVE
+DLFQILVCE
+;
+t95
+MIWSEYRQMVREG--TDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELIKF-YF-CMEGCGCVNTMAKNS-S
+QSAPWKFNRFMC-LMHLMQL--------GDL--------------------CNP--PSFLGMCMFHPQVRSKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYTGDSQDSQHLREKQLRI----YG---RIGR-V-VILQVWNAVMGRLNHHEPPAEVMFPLRK--GGSNSKPV------------------YDG
+FF------------DRPAIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHGPSKLHRTYAINRKVGANVYQQTSRMKAAAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECVYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGHRCRAELTELQTVQLDVGSSGKTLGQ
+-NIVTSKKLGDRTWLAASPLQ------IGCGVMVQEKKIASPQ-QVEVAAD---IYFYRNMVVQRLTDVVAAVRMQSPQEMRCRKLVCIQKVDSPSLGDD
+DPQM--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGGQNPACKPWHFVIMNRQTFAKNMIRLLYIKDI-
+SCNEVLQLLDWQLCDSH-GDWQSLIADSCPNA-SNIAVCCWKRELMPGL---NFSCEHLAKTVYFKPDGE-------DEGQMIMKIFNLDWCEVEKSHEK
+-SSVDDNYD-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALIILF-YGCQYYSGKFQDSELFERSQLYR-MYCEI----KKDHKSAIIANQ
+QEHKGMEWDTGKE-MQQGPK-VVLHHALFYAPSNVLAAEPNIIGQPQVSHVFV-GNDARRMLITGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYVWN
+YDIKIYETHYRMGVYAVDNSWETLVYC-EMTSGRIGAKVNHLPRLPEQVT-PPWVLTVSGLKRTV-AGAPDETEITKSPIIHII--MWEEIMFKNCVMQY
+CTYYKENRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QVM-GVGDIGGYELICE
+DLFQILVCE
+;
+t20
+MIWSEYRQMVREG--TDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELIKF-YF-CMEGCGCVNTMAKNS-S
+QSAPWKFNRFMC-LMHLMQL--------GDL--------------------CNP--PSFLGMCMFHPQVRSKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDSQDSQHLREKQLRI----YG---RIGR-V-VILQVWNAVMGRLNHHEPPAEVMFPLRK--GGSNSKAV------------------YDG
+FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHGPSKLHRTYAINRKVGANVYQQMSRMKAAAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQGNGEN-PMNVPSVESGECVYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGHRCRAELTELQTVQLDVGSSGKTLGQ
+-NIVTSKKLGDRTWLAAPPLQ------IGCDVMVQEKKIASPQ-QVEVAAD---IYFYRNMVVQRLTDVVAAVRMQSPQEMRTPKLVCIQKVDSPSLGDD
+DPQC--MNIVPYWVCVCSGVVKKAEPD-SVDKRGKTWVAKS-DFLCPPAVNEGEH---GAEQRPVFGGQNPACQPWHFVIMNTQTFAKNMIRLLYIKDI-
+SCNQVLQLLDWQLCDSH-GDWQSLIADSCPNA-VNIAVCCWKRELMPGL---NFSCEHLAKTVYFKPDGE-------DEGQMIMKIFNLDWCEVEKSHEK
+-SSVDDNYD-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALIILF-YGCQYYSGKFQDSELFERSQLYR-MYCEI----KKDHKSAIIANQ
+QEHKGMEWDTGKE-MQQGPK-VVLHHALFYAPSNVLAAEPNIIGQPQVSHVFV-GDDARRMLITGVSMMPAYKFMREACVPFFRKLFMAENQVRYDYVWN
+YDIKIYETHYRMGVYAVDNSWETLVYC-EMTSGRIGAKINHLPRLPEQVT-PPWVLTVSGLKRTV-AGAPDETEITKSPIIHII--MWEDIMFKNCVMQY
+CTYYKENRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QVM-GVGDIGGYELICE
+DLFQILVCE
+;
+t69
+MIWSDYRQMVREG--GDDSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGHKGTRELVKY-YH-CMEGCGCVNTMAKSS-S
+QSAPWKFNRFMC-LMHLMQE--------GDL--------------------CNS--PGFLGMCMFHPQVQRKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDNQDSQHLREKQLRM----YG---EIGK-V-VIIKVVNAVMGRLNHVEPSAEVMFPLRK--GGSDSKPF------------------IDG
+FF------------DRPGIANAMSVPCG----DQWVGSIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQISRMKALAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQGNGEN-PMNVPCVESGECQYENKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAELTALKTGQLDVGSSGKTLGQ
+-NIMTSKKLGDRTWLAANPLQ------IGRGVMVWEKKVASPQ-EVEVAAD---IYFYRNMVIECLTDVVRAVRMQSPQEMRAPVLVCIQKVDSPSLGDD
+VPQM--MNIVPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAMNEGEH---GAEQRPVFGTQNPVCKPWRFVIMNTETFAKNIIRLLYVKDV-
+SCNQVLQLLDWQLCDSH-GDWQSLVADSCPNA-VNIAVCCWKRELMPGL---NHSCQHLAKTVYFKPDGE-------DEGQMIVKIFNLDWCEVEKSHEK
+-SSVDDNYN-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHNSAIIANQ
+QEHKGMDWDTGKE-MQQGPK-IVVVLALFYQPSNVLAAEPNIMGQPQVSVVFV-GNDGRRMLIVGCSMMPDYKFMREACVPFFRKLFMAEVQDRYDYAWN
+YNIKIYETHFRDGVYAVDNSWETLVYV-EMASGRIGAKINHQPRLPEQVI-PPCILTVSGLKRTI-ADEPDETEITKTPIIHIV--MWADIMFKNCVMQY
+CNYYKENRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QIM-GVGDIGGYELICE
+DLFQILVCE
+;
+t2
+MIWSDYRQMVREG--GDDSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELVKY-YH-CMEGCGCVNTMAKSS-S
+QSAPWKFNRFMC-LMYLMQD--------GDL--------------------CNS--PGFLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDNQDSQHLREKQLRM----YG---EIGK-V-VIIKVVNAVMGRLNHHEPSAEVMFPLRK--GGSDSKPF------------------IDG
+FF------------DRPGIANAMSVPCG----DQWMGSIKGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQISRMKALAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQGNGEN-PMNVPCVESGECQYENKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAELTALKTGQLDVGSSGKTLGQ
+-NIMVSKKLGDRTWLAASPLQ------IGCGVMVWEKKVPSPQ-EVEVAAD---IYFYRNMVIECLTDVVRAVRMQSPQEMRAPVLVCIQKVDSPSLGDD
+VPQM--MNIVPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAMNEGEH---GAEQRPVFGTQNPVCKPWRFVIMNVETFAKNIIRLLYVKDV-
+SCNQVLQLLDWQLCDSH-GDWQSMVADSCHNA-VNIAVCCWKRELMPGL---NHSCQHLAKTVYFKPDGE-------DEGQMMVKIFNLDWCEVEKSHEK
+-SSVDDNYN-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHNSAIIANQ
+QEHKGMDWDTGKE-MQQGPK-IVVVLALFYQPSNVLAAEPNIMGQPQVSVVFV-GNDARRMLIVGCSMMPDYKFMREACVPFFRKLFMAEVQDRYDYNWN
+YNIKIYETHFRVGVYAVDNSWETLVYV-EMASGRIGAKINHMPRLPEQVI-PPCILTVSGLKRTI-ADEPDETEITKTPIIHIV--MWADIMFKNCVMQY
+CNYYKENRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QIM-GVGDIGGYELICE
+DLFQILVCE
+;
+t10
+MIWSDYRQMVREG--GDDSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YNFFTGQKGTRELVKY-YH-CMEGCGCVNTMAKSS-S
+QSAPWKFNRFMC-LMYLMQD--------GDL--------------------CNS--PGFLGMCMFHPQVQAKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDNQDSQHLREKQLRM----YG---EIGK-V-VIIKVVNAVMGRLNHHEPSAEVMFPLRK--GGSDSKPF------------------IDG
+FF------------DRPGIANAMSVPCG----DQWMGSIKGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQISRMKALAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQGNGEN-PMNVPCVESGECQYENKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAELTALKTGQLDVGSSGKTLGQ
+-NIMVSKKLGDRTWLAASPLQ------IGCGVMVWEKKVPSPQ-EVEVAAD---IYFYRNMVIECLTDVVRAVRMQSPQEMRAPVLVCIQKVDSPSLGDD
+VPQM--MNIVPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAMNEGEH---GAEQRPVFGTQNPVCKPWRFVIMNVETFAKNIIRLLYVKDV-
+SCNQVLQLLDWQLCDSH-GDWQSMVADSCHNA-VNIAVCCWKRELMPGL---NHSCQHLAKTVYFKPDGE-------DEGQMMVKIFNLDWCEVEKSHEK
+-SSVDDNYN-VNMLPFMQSHGDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHNSAIIANQ
+QEHKGMDWDTGKE-MQQGPK-IVVVLALFYQPSNVLAAEPNIMGQPQVSVVFV-GNDARRMLIVGCSMMPDYKFMREACVPFFRKLFMAEVQDRYDYNWN
+YNIKIYETHFRVGVYAVDNSWETLVYV-EMASGRIGAKINHMPRLPEQVI-PPCILTVSGLKRTI-ADEPDETEITKTPIIHIV--MWADIMFKNCVMQY
+CNYYKENRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDI---YPAAPKKY--QIM-GVGDIGGYELICE
+DLFQILVCE
+;
+t31
+MIWSEYRSMVREG--ADQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKQS-S
+QSAPWKFNRFMC-LMHLMQN--------GDL--------------------CNL--PSFLGMCMFHNQVQCKGE--LVLPDNVNENSVEFMYRRHHSLSD
+KRCLNLLYVGDNQDSQHLREKQLRI----YQ---NIGK-V-VIIKVWNANMGRLNHHEPPAEVMFPLRK--GGSDSKPF------------------IDG
+FF------------DRPGIANAMNVPCG----DQWVGCIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQTSRMKAAAPIYPHIMEYAHG
+M----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVMGDWVGNRCRAELTALKTVQLDVGSNGKTLGK
+-NIMTPKKLGDRTWLAASPLQ------IGCGVMVQEKKVASPQ-EVE-AAD---IFFYRNMVIQRLTDVVAAVRMQSPQEMRPPVLVCIQYVDSPSLGDD
+TPQM--MNIAPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKA-DFLCPPAVSEGEH---GAEQRPVFGMQNPACKPWRFVIMNTQTFAKNIIRLLYIKDV-
+SCNAVLQLLDWQLCYSH-GDWQSLIADSCPTA-ANIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMIMKIFNLDWCEVEKSHEK
+-SSVDDNYH-VNMLPFAQSNRDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIIANQ
+HEVKGMDWNTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIVGQPQVSHVFV-GNDARRMLIVGVSVMPSYKFMREACVPFFHKLFMADNQVRHEYMWN
+YDIKIYETHFRMGVYAVDNSWETLVYC-EMTSGRIGANINHLPRLPEQVV-PPCILTVSGLKRTI-AGSPDETEITKTLIYHIV--MWADIMFKNCVMQY
+STYYKENRSVR-----------ANNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIRVM-GVGDIGGYEMICE
+DLFQILVCE
+;
+t15
+MIWSEYRSMVREG--SDQSIDNH-C------------LIAARVKMMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKNS-S
+QSAPWKFNRFMC-LMHLMQN--------GDL--------------------CNS--PSFLGMCMFHNQVPNKGA--LVLPDNVNENSVEFMYRRHHSLSD
+KRCLNLLYVGDNQDSQHLREKQLRI----YP---SIGK-V-VIIKVWNAAMGRLNHHEPPAEVMFPLRK--GGSDSKPF------------------IDG
+FF------------DRPGIANAMSVPCG----DQWVGCIRGWCSSQHQYGLANHILVHGPSKLHRTYAINRKMGANVYQQTSRMKAAAPLYPHIMEYAHG
+M----VEPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPVLGDWVGNRCRAELTALKTVQLDIGNSGKTLGQ
+-NIMTPKRLGERTWLAASPLQ------IGCGVVVQEKKVASPQ-EVEVAAD---IYFYRNMVIQTLTDVVAAVRMQSPQEMRPPVLVCIQDVDSVSLGDD
+TPQM--MNIAPYWVCVCSGVVKKTQPD-SVDKRGKTWVAKS-DFLCPPAVSEGEH---GAEQRPVFGMRNPICKPWRFVIMNTQTFAKNIIRLLYVKDV-
+SCNAVLQLLDWQLCYSH-GDWQSLIADSCSTA-ANIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMIVKIFHLDWCEVEKSHEK
+-SSVDDNYH-VNMLPFAQSNGDPVGHYVQGLED-ALRLIRPGT---ARALVILS-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIVANQ
+QEVKGMDWDTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIVGQPQVSHVFV-GNDARRMLIVGVSVMPAYKFMREACVPFFHKLFMAENQVRHDYMWN
+YDIKIYETHFRMGVYAVDNSWETLVYC-EMTSGRIGAKINHLPRLPEQVV-PPCILTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQY
+STYYKENRSVR-----------GNNTGGAELPK---------------------YHQQNILTD-ELYSDV---YPTAPKKYVIRVM-GVGDIGGYELICE
+DLFQILVCQ
+;
+t63
+MIWSEYRSMVREG--SDQSIDNK-C------------LTAARVKLMSGVVRQVRNAPEDAL--YTFFTGQKGKRELIKY-YF-CMEGCGCVNTMAKNS-S
+QSAPWKFNRFMC-LMHLMQD--------GDL--------------------CNS--PSFLGMCMFHNQVSFKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDEQDSSHLREKQLRL----YA---RIGK-V-VIIKVWNAVMGRLNHHEPPAAVMFPLRK--GGSDSKPF------------------IDG
+FF------------DRPGIANAMSVPCG----DQWMGIIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRANTMSKPVMGDWVGSRCRAELTALKTVQLDVGSSGKTLGQ
+-NIMTPKKLGDRTWLAASPLQ------IGCDVMVQEKKVASPQ-EVEVAAD---IYFYRNMVIQRLTDVVAAVRMQSPQEMRLPVLVCIQDVDSPSLGDD
+TPQK--MNIAPYWVCVCSGVVKKAQLD-SVEKRGKTWVAKS-DFLCPPAVSEGEH---GPEQRPVFGVQNPVCKPWRFVIMNTQTFAANIIRLLYVKDV-
+SCNAVLQLLDWQLCYSH-EDWQSLIADACPTA-VNIAVCCWKRELMPGL---NHSCEHLAKSVYFKPDGE-------DEGQMFMKIFNLDWCEVEKSHEK
+-SSVDDNYN-VNMLPFVQSNGDPVGHYVQGLED-ALLLIRPGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIIANQ
+QGVKGMDWDTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIIGQPQVSHVFV-DNDARRMLIVGQSVMPPYKFMREACVPFFHKLFMAENQVRHDYVWN
+YDIKIYETHFRMGVYAIDNSWETLVYC-EMTSGRIGAKINHQPRLPEQVV-PPCVLTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQY
+STYYKENRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIRQM-GMGDIGGYELICE
+DLFQILVCE
+;
+t50
+MIWSEYRSMVREG--SDQSIDNK-C------------LTAARVKLMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKNS-S
+QSAPWKFNHFMC-LMHLMQN--------GDL--------------------CNS--PSFLGMCMFHNQVSVKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDNQDSSHLREKQLRL----YA---RIGK-V-VIIKVWNAVMGRLNHHEPPAEVMFPLRK--CGSDSKPF------------------IDG
+FF------------DRPGIANAMSVPCG----DQWMGVIRGWCSSQHQYGLANHVLVHGPSKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRANTMSKPVMGDWVGSRCRAELTALKTVQLDVGSSGKTLGQ
+-NIMTPKKLGDRTWLAASPLQ------IGCDVMVQEKKVASPQ-EVEVAAD---IYFYRNMVIQRLTDVVAAVRMQSPQEMRLPVLVCIQDVDSPSLGDD
+TPQK--MNIAPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAVSEGEH---GPEQRPVFGVQNPVCKPWRFVIMNTQT-AKNIIRLLYVKDV-
+SCNAVLQLLDWQLCYSH-GDWQSLIADACSTA-VNIAVCCWKRELMPGL---NHSVEHLAKSVYFKPDGE-------DEGQMIMKIFNLDWCEVEKSHEK
+-SSVDDNYN-VNMLPFVQSNGDPVGHYVQGLED-ALLLIRPGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIMANQ
+QGVKGMDWDTGKE-MQQGPK-IVMHLALFYAPSNVLAAEPNIIGQPQVSHVFV-DNDARRMLIVGQSVMPAYKFMREACVPFFHKLFMAENQVRHDYVWN
+YDIKIYETHFRMGVYAVDNSWETLVYC-EMTSGRIGAKINHQPRLPEQVV-PPCILTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQY
+STYYKENRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIRQM-GMGDIGGYELICE
+DLFQILVCE
+;
+t25
+MIWSEYRSMVREG--SDQSIDNK-C------------LTAARVKMMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKNS-S
+QSAPWKFNRFMC-LMHLMQN--------GDL--------------------CNS--PSFLGMCMFVNQVSFKGE--LVLPDNPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDNQDSSHLREKQLRL----YA---RIGK-V-VIIKVWNAVMGRLNHHEPPAEVVFPLRK--GGSDSKPF------------------IDG
+FF------------DRPGIANAMSVPCG----DQWMGVIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRANTMSKPVMGDWVGSRCRAELTALKIVQLDVGSSGKTLGQ
+-NIMTPKKLGDRTWLAASPLQ------IGCDVMVQEKKVASPQ-EVEVAAD---IYFYRNMVIQRLTDVVAAVRMQSPQEMRLPVLVCIQDVDSPSLGDD
+TPQK--MNIAPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAVSEGEH---GPEQRPVFGMQNPVCKPWRFVIMNTQTFAKNIIRLLYVKDV-
+SCNAVLQLLDWQLCYSH-GDWQSLIADACPTA-VNIAVCCWKRELMPGL---NHSCEHLAKSVYFKPDGE-------DEGQMIMKIFNLDWCEVEKSHEK
+-SSVDDNYD-VNMLPFVQSNGDPVGHYVQGLED-ALLLIRPGT---ARALVILF-YGCQYYSGKFQDSELFERSQLYR-VYCEI----KKDHKSTIIANQ
+QGVKGMDWDTGKE-MQQGPK-IVVHLTLFYAPSNVLAAEPNIFGQPQVSHVFV-DNDARRMLIVGQSVMPAYKFMREACVPFFHKLFMAENQVRHDYVWN
+YDIKIYETHFRMGVYAVDNSWEALVYC-EMTSGRTGAKINHQPRLPEQVV-PPCILTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQY
+STYYKENRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIRQM-GMGDIGGYELICE
+DLFQILVCE
+;
+t51
+MIWSEYRSMVREG--SDQSIDNK-C------------LIAARVKMMSGVVRQVRNAPEDAL--YTFFTGQKGTRELIKY-YF-CMEGCGCVNTMAKNS-S
+QSAPWKFNRFMC-LMHLMQN--------GDL--------------------CNS--PSFLGMCMFHVQVQFKGE--LVLPDHPNENSVEFMYRRHHSLSD
+KRCLNLLYVGDNQDSQHLREKQLRI----YA---RIGK-V-VIIKVWNAVMGRLNHHEPPAEVVFPLRK--GGSDSKPF------------------IDG
+FF------------DRPGIANAMSVPCG----DQWVGVIRGWCSSQHQYGLANHILVHGPSKLHRTYAINKKMGANVYQQDSRMKAAAPLYPHIMEYAHG
+M----VKPFYGISEPKNEAQKNGEN-PMNVPCVESGECQYESKHAAMEKLMHQ-SLYLMRVNTMSKPIMGDWVGNRCRADLTALKTVQLDVGSSGKTLGQ
+-NIMTPKNLGDKTWLAASPLQ------IGCGIMVQEKKVASPQ-EVEVAAD---IYFYRNMVIQRLTDVVAAVRMQSPQEMRPPVLVCIQDVDSPSLGDD
+TPQM--MNIAPYWVCVCSGVVKKAQPD-SVDKRGKTWVAKS-DFLCPPAISEGEH---GAEQRPVFGMQNPVCRPWRFVIMNTQTFAKNVIRLLYVKDV-
+SCNKVLQLLDWQLCYSH-GDWQSLIADACPAA-VNIAVCCWKRELMPGL---NHSCEHLAKTVYFKPDGE-------DEGQMIMKIFGLDWCEVEKSHEE
+-SSVDDNYN-VNMLPFVSSNGDPVGHYVQGLED-ALRLIRPGT---ARALVILF-YGCQFYSGKFQDSELFERSQLYR-VYCEI----KKDHKSAIIANQ
+QGVKGMDWDTGKE-MQQGPK-IVVHLALFYAPSNVLAAEPNIIGQPQVSHVFV-DNDIRRMLIVGVSVMPAYKFMREACVPFFHKLFMAENQVRHDYVWN
+YDIKIYETHFRMGVYAVDNSWETLVYC-EMTSGRIGAKINHLPRLPEQVF-PPCILTVSGLKRTI-AGAPDETEITKTLIYHIV--MWADIMFKNCVMQY
+ATYYKENRSVR-----------VNNTGGAELPK---------------------YHQQNILTD-ELYSDM---YPAAPKKYVIREM-GVGDIGGYELICE
+DLFQILVCE
+;
+t9
+MIWSECRQMVREK--TDNAIDNQ-C------------LIAARVKENSGHVKQVRNDSEDIL--YNHFTGKKGARELIKR-YV-CMEGHDCVNTVANVS-S
+QSAIWKFDRFMCDLMHLMQN--------GDL--------------------CSY--PSFLPMCMFVPQVLSKGE--LVLPDSSNEESISFVYLQHHSFSV
+KRCLNYLNVGDSADSKHLKEKHLRA----EGMPGNIGK-H-VIINVWNAVMGRLNHHEPPAEVVFPLRQ--GGPDSKPM------------------IDG
+FFDK-D-D------DRPGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHDPSSLHRTFAINRKMGANVYQQTSRMKASAPFYPHCMEYAHG
+V----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESIDCQYENKHATMTKLMHH-SLYLMRMHTMSKPIMGDVNGNRCRADLTALKMLQLDIGFSAKTLGQ
+-NVVVPHLLGHRTWLATSPLQ------IGCGVMIFGNKIGSAN-EFEAAADPTVIYFYRNRIVRRLADVISTVRMNSPQEMRN------QDVDSHSLGDD
+DNQA--MVILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKV-DFLCPPAFNQGEH---RAEQKPASKFEHPVCGPWEFVIVNYQTSAKDIILLLYIKDV-
+GCNCVLELLNWQLCTSH-GDWQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEGKMVLKIFGLDWCEMEKSHQR
+-SGVDDNYQ-VNMLPFNHSKNNPVGHYVQGLED-ALNLIRPGT---ARALNILF-YGCEVYSGEFQDSES-ERSWIYN-VYCEI----KKDHKSAIIAHK
+YEHKGMDWDTGKE-AQQGPE-VVHHNLLFF-------AEPNIHGQPGVGHIFV-GNDARRKLIAGVSFMSMVKFMCEACVPFFRKLFMAVGQMRYDYVNN
+YDIKIWETVFRGGVYAIENSWETLVLC-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETK-AGLIDGTEITKTPDIGIC--MWETIHFKNPVMQY
+CCYYKENRSVR-----------VNNTGGAALPK---------------------YHHQNTLVD-ELYSDV---YPAAPKKK--VCM-GVGDVGGYEVMGE
+DLFQILVCE
+;
+t47
+MIWSECRQMVREK--SDNAIDNQ-C------------QIAARVKRNSGHVKQVRNDSEDIL-CYHHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-S
+QSAVWNFDRFMCDLMHLMQN--------GDL--------------------CSY--PSFLPMCMFVSQVLSKGE--LVLPDSSNEESISFVYLQHHSFSD
+KRCLNYLNVGDNSDSKHLKEKHLRA----QGMPGNIGK-H-VIINVWNAVMGRLNHHESPAEVVFPLRQ--GGPDSKPM------------------IDG
+FFDK-D-D------DRPGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHDPSNLHRTFAINRKMGANVYQQASRMKASAPFYHHCMEYAHG
+V----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESRDCQYENKHATMTKLMHQ-SLYLMRMHTMSKPIMGHVNGNRCRADLTALKMLQLDIGFSAKTLCQ
+-NIVVAHLLGHRTWLATSPLQ------IGCMVMIFGNKIGSAN-EFEAAADPTVIYFYRNRIVRRLADVISTVRMNSPQEMRE------QDVDSHSLGDD
+DNQA--MNILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKM-DFLCPPAFNQGEH---RAEQKPALKFKHPVCGPWEFVIVNYQTSAKDIILLLYIKDV-
+GCNCVLELLKWQLCTSH-GDWQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCDRLAKHIYFQPDGE-------DEGKMILKIFGLDWCEMEKSHQR
+-SGVDDNVQ-VNMLPFNHSKHNPVGHYVQGLED-ELNLIRPGT---ARALNILF-YGCEYYSGEFQDSES-ERSWIYN-VYCEI----KKDHKSAIMACK
+YRHKGMDWDTGKE-AEQGPE-VVHHNLLFF-------AEPNIQGQPGVGHIFV-GNDARRKLIAGLSFMAMMKFMCEACVPFFRKLFMAVGHMRYDYVSN
+YDIKIWETVFRGGVYAIENSWETLVLC-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETK-AGIIDGTEITKTPEIGIC--MWDTIEFKNPVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNTLVD-ELYSDI---YPAAPKKK--VCM-GVGDVGGYEVMGE
+DLFQILVCE
+;
+t60
+MIWSECRQMVREK--TDNAIDNQ-C------------QIAARVKENSGHVKQVRNDSEDIL-CYHHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-S
+QSAVWNFDRFMCDLMHLMQN--------GDL--------------------CSV--PSFLPMCMFVSQVLHKGE--LVLPDSSNEESISFVYLQHHSFSD
+KRCLNYLNVGDNADSKHLKEKHLRA----QGMPGNIGK-H-VIINVWNAVMGRLNHHEPPAEVVFPLRQ--GGPDSKPM------------------IDG
+FFDK-D-D------DRPGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHNPSNLHRTFAINRKMGANVYQQTSRMKASAPFYHHCMEYAHG
+V----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESIDCQYESKHAAMTKLMHQ-SLYLMRIHTMSKPIMGDVNGNRCRADLTALKMLQLDIGFSAKTLGQ
+-NIVVPHCLGHRTWLATSPLQ------IGCMVMIFGNKIGSEN-EFEAAADPTVIYFYRNRIVRRLADVISTVRMNSPQEMRN------QDVDSHSLGDD
+DNQA--MNILPYVVCVCSGVVRKDHPDTSIHKRGRTWLAKV-DFLCPPAFNQGEH---RAEQKPAFKFKHPVCGPWEFVIVNYQTEAKDIILLLYIKDV-
+GCNCVLELLEWQLCTSH-GDWQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEGKMILKIFGLDWCEMEKSHQR
+-SGVDDNYQ-VNMLPFNHSKHNPVGHYVQGLED-ALNLIRPGT---ARALNILF-YGCEYYSGEFQDSES-ERSWIYN-VYCEI----KKDHKSAIMAYK
+FEHKGMDWDTGKE-AEQGPE-VVHHNLLFF-------AEPNIQGQPGVGHIFV-GNDARRKLIAGVSFMAVMKFMCEACVPFFRKLFMAVGQMRYDYMNN
+YDIKIWETFFRGGVYAIENSWETLVLC-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETR-AGIIEGTEITKTPDIGIC--MWDTIHFKNPVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNTLVD-ELYSDI---YPAAPKKK--VCM-GVGEVGGYEVMGE
+DLFQILVCE
+;
+t30
+MIWSECRQMVREK--TDNAIDNQ-C------------QIAARVKENSGHVKQVRNDSEDIL-CYHHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-S
+QSAVWNFDRFMCDLMHLMQN--------GDL--------------------CSV--PSFLPMCMFVSQVLHKGE--LVLPDSSNEESISFVYLQHHSFSE
+KRCLNYLNVGDNADSRHLKEKHLRA----QGMPGNIGK-H-VIISVWNAVMGRLNHHEPPAEVVFPLRQ--GGPDSKPM------------------MDG
+FFDK-D-D------DRPGIANAMSVPCG----EQWGGPTRGWCSSQQKFGLASHTLSHTPSNLHRTFAINRKMGANVYQQTSRMKASAPFYHHCMEYAHG
+V----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESIDCQYENKHATMTKLMHQ-SLYLMRMHTMSKPIMGDVNGNRCRADLTALKMLQLDIGFSAKTLGQ
+-NIIVPHCLGHRTWLATSPLQ------IGCMVMIVGNKIGSEN-EFEAAADPTVIYFYRNRIVRRLADVISTVRMNSPQEMRN------QDVDSHSLGDD
+DNQA--MNILPYVVCVCSGVVRKEHPDTSISKRGRTWLAKI-DFLCPPAFNQGEH---RAEQKPAFKFKHPCCGPWEFVIVNYQTSAKDIILLLYIKDV-
+GCNCVLELLKWQLCTSH-GDWQSLVADSCVWA-HNVAVCEWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEGKMILKIFGLDWCEMEKSHQR
+-SGVDDNYQ-VNMLPFKHSKHNPVGHYVQGLED-ALNLIRPGT---ARALNILF-YGCEYYSGEFQDSES-ERSWIYN-VYCEI----KKDHKSAIMAYK
+YEHKGMDWDTGKE-AEQGPE-VVHHNLLFF-------AEPNIHGQPGVGHIFV-GNDARRHLIAGVSFMAVVKFMCEACVPFFRKLFMAVGQMRYDYVNN
+YDIKIWETVFRGGVYAIENSWETLVLC-EMTSGRCGAKMNHLPRLFEQVC-PPCILTVSGLKETR-AGIIDGTEITKTPDIGIC--MWDTIHFKNPVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHDQNTLVD-ELYSDV---YPAAPKKK--VCM-GVGDVGGYEVMGE
+DLFQILVCE
+;
+t70
+MIWSECRQMVREK--NDNAIDNQ-C------------LIAARVKEDSGHVKQVRNASEDIM--YNHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-S
+QSAVWKFDRFMCDLMHLMQD--------GDL--------------------CSY--PSFLPMCMFVAQVIAKGE--LVLPDSSTEESISFMYLQHHSFSD
+KRCLNYLNVGDNEDSKHAKEKFLRG----DG---GIGQ-H-VIINVWNAVMGRLNHHEPPPEVVFPLRQ--GGPDSKPM------------------VDG
+FFDK-D-D------DRPGIANAMNVPCG----DQWGGPIRGWCSSQHKFGLAFHTLSHDPSKLHRTFAINQKMGANVYQQMSRMKTPAPFYPHVMEYAHG
+V----CKPFYEHSEPKNEAQGNGEKVPMNVPCVESMDCQYENKHAPMAKLMHQDSLYLMRMHTMSKPLMGDVNGNRCRADLTSLKMLQLDIGFCAKTLGQ
+-NIVVPKLLGHRTWLATAPLQ------IGCGMMIFGNKIGSTQ-EFEAAADPTVIYFYRNRIVRRMADVISTVRMKSPQEMRG------QDVDSHSLGDD
+DNQA--MNILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKI-DFLFPPAFNQGEH---HAEQKPVFGFKHPHCGPWEFVICNYQTVAKDIILLLYIKDV-
+GCNCVLELLAWQLCTSH-GDWQSLVADSCIWA-HNVAVCAWKRELVPGL---NHSCEHLAKHIYFQPDGE-------DEGKMILKIFGLDWCEVERSHQR
+-SGVDDNYK-VNMLPFSHSKHNPVGHYVQGLGD-ALRLIRPGT---ARALNILF-YGCQYCSGEFQDSEE-ERSWIYN-VYCEI----KKDHKSAILAHK
+YKHKGMDWDTGKE-MEQGPK-VVNYNLLFY-------AEPNIHGQPRVGHIFV-GNDAHRKLIAGVSFMSIMKFMCEACVPFFRKLFMAVRQMRYMYMNN
+YDIKIWETAFRGGVYAIENSWETLVLC-EMTSGRSGAKMNHLPRLFEQVC-PPCLLTVSGLKETV-AGIIDGTEITKTPEIGIC--MWDTIHFKNPVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHNQNTLVD-ELYSDV---YPAAPKKQ--HYM-GVGDVGGYEVMGE
+DLFQILVCE
+;
+t91
+MIWSECRQMVREK--NDNAIDNQ-C------------LIAARVKEDSGHVKQVRNASEDIM--YNHFTGKKGARELIKR-YI-CMEGHDCVNTMANVS-S
+QSAVWKFDRFMCDLMHLMQD--------GDL--------------------CSY--PSFLPMCMFVAQVIAKGE--LVLPDSSTEESISFMYLQHHSFSD
+KRCLNYLNVGDNEDSKHAKEKFLRG----DG---GIGQ-H-VIINVWNAVMGRLNHHEPPPEVVFPLRQ--GGPDSKPM------------------VDG
+FFDK-D-D------DRPGIANAMNVPCG----DQWGGPIRGWCSSQHKFGLAFHTLSHDPSKLHRTFAINQKMGANVYQQMSRMKTPAPFYPHVMEYAHG
+V----CKPFYEHSEPKNEAQGNGEKVPMNVPCVESMDCQYENKHAPMAKLMHQ-SLYLMRMHTMSKPLMGDVNGNRCRADLTSLKMLQLDIGFCAKTLGQ
+-NIVVPKLLGHRTWLATAPLQ------IGCGMMIFGNKIGSTQ-EFEAAADPTVIYFYRNRIVRRMADVISTVRMKSPQEMRG------QDVDSHSLGDD
+DNQA--MNILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKI-DFLFPPAFNQGEH---HAEQKPVFGFKHPHCGPWEFVICNYQTVAKDIILLLYIKDV-
+GCNCVLELLAWQLCTSH-GDWQSLVADSCIWA-HNVAVCAWKRELVPGL---NHSCEHLAKHIYFQPDGE-------DEGKMILKIFGLDWCEVERSHQR
+-SGVDDNYK-VNMLPFSHSKHNPVGHYVQGLGD-ALRLIRPGT---ARALNILF-YGCQYCSGEFQDSEE-ERSWIYN-VYCEI----KKDHKSAILAHK
+YKHKGMDWDTGKE-MEQGPK-VVNYNLLFY-------AEPNIHGQPRVGHIFV-GNDAHRKLIAGVSFMSIMKFMCEACVPFFRKLFMAVRQMRYMYMNN
+YDIKIWETAFRGGVYAIENSWETLVLC-EMTSGRSGAKMNHLPRLFEQVC-PPCLLTVSGLKETV-AGIIDGTEITKTPEIGIC--MWDTIHFKNPVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHNQNTLVD-ELYSDV---YPAAPKKQ--HYM-GVGDVGGYEVMGE
+DLFQILVCE
+;
+t49
+MIWSECRQMVREK--NDNAIDNQ-C------------LIAARVKENSGHVKQVRNASEDIM--YNHFTGNKGACELIKG-YV-CMEGHDCVNTMANIS-S
+QSAVWKFDRFMCDLMHLMQD--------GDL--------------------CSY--PSFLPMCMFVAQVIAKGE--LVLPDSSNEESISFMYLQHHSFSD
+KRCLNCLNVGDNEDSKHLKEKFLRA----DG---GIGQ-H-VIINMWNAVMGRLNHHEPPPEVVYPLRQ--GGPNSKPM------------------VDG
+FFDK-D-D------DRPGIANAMNVPCG----DQWGGPIRGWCSSQHRFGLAFHTLKHDPSKLHRTFAINEKMGANVYQQNSRMKASAPFYPHVMEYAHG
+V----CKPFYEHSEPKNDAQGNGDKVPMNVPCVESMDCQYENKHAPMAKLMHQ-SLYLMRMYTMSKPIMGDVNGNRCRAELTSLKMLQLDIGFSAKTLGQ
+-NIVPPKLLGHRTWLATSPLQ------IGCGVMIFGNKIGSTQ-EFESAADPTVIYFYRNRIVKRMADVISTVRMKSPQEMRG------QDVDSHSLGDD
+DNQA--MNILPYWVCVCSGVVRKEHPDTSINKRGRTWLAKI-DFLFPPAFNQGEH---HAEQKPVFGFKHPHCGPWEFVICNYQTMAKDIILLLYIKDV-
+GCNCVLELLAWQLCTSH-GDWQSLVADSCIWA-HNVAVCAWKRELVPGL---NHSCEHLAKHIYFQPDGE-------DEGKMIIKIFGLDWCEVEKSHQR
+-SGVDDNYK-VNMLPFSHSNHNPVGHYVQGLGD-ALRLIRPGT---ARALNILF-YGCEYYSGEFQDSEE-ERSWIYN-VYCEI----KKDHKSAIMAHK
+YEHKGMDWDTGKE-MEQGPK-VVHHNILFY-------AEPNIHGQPRVGHIFV-GNDAVRNLIAGVSFMSIMKFMCEACVPFFRKLFMAVRQMRYMYMNN
+YDIKIWETAFRGGVYAMENSWETLVLC-EMTSGRVGARMNHLPRLFEQVC-PPCILTVSGLKETV-AGVIDGTEITKTPEIGIC--MWDTIHFKNPVMQY
+CCYYKEPRSVR-----------VNNTGGAELPK---------------------YHNFNALVD-ELYSDV---YPAAPKKK--HYM-GVGDVGGYEVMGE
+DLFQILVCE
+;
+t52
+MIWSEERQMVREK--VDNAVDNQ-C------------LIAARVKENCGHVKQVRNASEDIL--YNHFTGKKGARELIKR-YI-CMEGHDCVNTMAHDS-S
+QSATWKFDRFMCDLMHLMQG--------GDL--------------------CSY--PSFLPVCMFVAQVINKGE--LVLPDSSNEESISFMYLQHHSFSE
+KRCLNYLNVGDNEDSKHLKEKFLRA----DG---NIGQ-H-VIINMWNAVMGRLNHHEPPAEVNFPLRQ--GGPDSKPM------------------VDG
+FFDK-D-D------DSPGIANAMNVPCG----DQWGGPIRGWCSSQHKFGLASHTLSHDPSKLHRTFGINKNMGANVYQQTSRMKANAPFYPHVMEYAHG
+V----CKPFYEHSEPKNEAQGNGEK-PMNVPCVESIECQYENKHATMAKLMHD-SLYLMRMHTMSKPVMGDVNGHRCRADLTALKMLQLDIGFSAKTLGQ
+-NIVAPKLLGVRTWLATSPLQ------IGCGVMIFGNKIGSTQ-EFEAAADPTVIYFYRNRIIRRVADVISTVRMKSPQEMRE------QDVDSHSLGDD
+DNQA--MTILPHWVCVVSGVVRKEHPDTSINKRGSTWLAKV-DFLCPPAFNQGEH---HAEQKPVFGFKHPHVGPWEFVICNYQTSAHDIILLLYIKDV-
+GCNCVLELLVWQLCTSH-GDWQSLVADSCVWA-HNVAVCAWKRELVPGL---NHSCERLAKHIYFQPDGE-------DEGKMILKIFELNWCEVEKSHQH
+-SGVDDNYQ-VNMLPFDHCKHNPVGHYVQGLED-ALGLIRPGT---ARALNILF-YGCQYYSGEFQDSEA-ERSWIYN-VYCEI----KKDHKSGIMAHK
+YDHKGVDWDTGKE-MEQGPK-VLHHNLLFY-------AEPNIHGQPTVGHIFV-GNDARRKLIAGVSFMSVVKFMCEACVPFFRKLFMAFRQMRYDYVNN
+YDIKIWETVFRGGVYAIENSWETLILC-EMTSGRCGAKMNHMPRLFEQVC-PPCILTVSGLKETM-AGVIDGTEITKTPDIGIG--MWDSIHFKNPVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNSLVD-ELYSDV---YPAAPKKK--HYM-GVGDVGGYEVMGE
+DLFQILVCE
+;
+t43
+MIWSEVRQMVREG--SDNAIDNR-C------------LIAARVKHVQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-S
+QSAVWKFDRFMCALMHLMQK--------GDL--------------------CSH--PSFLGMCMFHEQVRCKGE--LVLPDSPNEESVSFVYIQHHSFSD
+KRCLNCLNVGDNDDSEHLKEKHLRI----YG---QIGH-H-VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSK-M------------------VDG
+FFDK-E-D------DRPGIANAVSVPCA----DQVGGPIRGWCSSQVNFGLANHTLVQ-PSKLHRTFKINKKMGANVYQQTSRMKAEAPVYPHIMEYAHG
+V----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAGLTALKVVQLDIGFSSKTLGQ
+LNIIDCKLLGHRTWLATSPLQ------IGVDVMVMGNKIGSPS-EFEVAADPTIIWFYRNCIVHKLADTVSTAKMKSPQEMRH------QDVDSPSLGDD
+DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFNQGEH---EREQRPVYGFKHPGCRPWQFVIANYQTSAKNIIMLLYVKDV-
+SCNGVLQLLNWHLCDSH-GDWQSLVADSCCWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELDWVEMEKSHQQ
+-SSVDDNYL-VNMLPFLHSRQNPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVIAHK
+HEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATRKLITGVSVMPTYKFMCGACVPFFHKLFMAVRNMRYDYNVN
+YDIKIWETHIRHGVYAVENSWETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCVLTVSGLKQPM-AGYNDQTEITKTPDICIC--TWGTIHFKNFVMQY
+CVYYKENRSVR-----------VNNTGGAELPQ---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+DLFQILVHE
+;
+t1
+MIWSEVRQMMREG--TDNAIDNQ-C------------LIAARVKHMQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-S
+QSAVWKFDRFMCCLMHLMQN--------GDL--------------------CSH--PSFLGMCMFVEQVRCKGE--LVLPDSPNEESLSFVYIQHHSFSD
+KRCLNCLNVGDNDDSEHLKEKHLRI----YG---QIGR-H-VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSKPV------------------VDG
+FFDK-E-D------DRPGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVQ-PSKLHRTFKINKKMGANVYQQTSRMKAEAPVYPHIMEYAHG
+V----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAKLTALKIVQLDIGFSAKTLGQ
+LNIIDCKLLGRHTWLATSPLQ------IGCDMMVMGNKIGSPS-EFEVAADPTIIWFYRDCIVHKLADTVSTAKMKAPQEMRV------QDVDSPSLGDD
+DQQE--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFNQGEH---EAEQRPVYGFVHPRCRPWQFVIANYQTSAKNIIMLLYVKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELDWVEMEKSHQQ
+-SSVDDNYL-VNMLPFMQSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+VEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATRKLITGVSVMPTYKFMCGACVQFFHKLFMAVRNMRYDYTVN
+YDIKIWETHIRQGVYAVENSWETLITC-EMTSGRIGAKINHLPRLPEQVV-PPCILTVSGLKQPM-AGYNDETQITKTPDICIC--TWGTIHFKNSVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+DLFQILVHE
+;
+t86
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKPVQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-S
+QSAVWKFDRFMCALMHLMQN--------GDL--------------------CSH--PSFLGMCMFHEQVRRKGE--LVLPDSPNEESVSFVYIQHHSFSD
+KRCLNCLNVGDNDDSEHLKEKHLRI----YG---QIGR-H-VIINVWNAFMGRLNHHEPPAEAVYPLRK--GGPDSKPM------------------VDG
+FFDK-E-D------DRPGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVQ-PSKLHRTFKINKKMGANVYHQTSRMKAEAPVYPHIMEYAHG
+V----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAGLTALKIVQLDIGFSAKTLGQ
+LNIIDCKLLGHRTWLATSPLQ------IGCDVMVMGNKIGSPS-EFEVAADPTIIWFYRNCIVHKLADTVSTAKMKAPQEMRV------QDVDSPSLGDD
+DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFNQGEH---GAEQRPVYGFQHPRCRPWQFVIANYQTFAKNIIMLLYVKDV-
+SCNRVLQLLNWQLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELDWVEMEKSHQQ
+-SSVDDNYL-VNMLPFIHSRDNPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDGEA-ERSWIYP-VYCEM----KKDHKSAVVAHK
+AEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATRKLITGVSVMPTYKFMCGACVPFFHKLFMAVRNMRYDYTVN
+YDIKIWETHIRHGVYAVENSWETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGYNDETQITKTPDICIC--GVGTIHFKNLVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+DLFQILVHE
+;
+t72
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHVQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKVS-S
+QSAVWKFDRFMCALMHLMQN--------GDL--------------------CSH--PSFLGMCMFHEQVRRKGE--LVLPDSPNEESVSFVYIQHHSFSD
+KRCLNCLNAGDNDDSEHLKEKHLRT----YG---QIGR-H-VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSKPM------------------VDG
+FFDK-E-D------HRPGIANAVSVPCA----DQVGGPLRGWCSSQVKFGLANHTLVQ-PSKLHRTFKINKKIGANVYQQTSRMKADAPVYPHIMEYAHG
+V----YKPFYERSEPKNEAQGNGEK-QGNVPCVESVECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAGLTALKIVQLDIGFSAKTLGQ
+LNIIDCKLLGHRTWLATSPLQ------IGCDVMVMGNKIGSPS-EFEVAADPTIIWFYRNCIVHKLADTVSTAKMKAPQEMRH------QDVDSPSLGDD
+DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFKQGEH---EAEQRPVYGFQHPRCRPWQFVIANYQSSAKNIIMLLYVKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGQMVLKIFELDWVEMEKSHQQ
+-SSVDDNYL-VNMLPFIHSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+VEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATRKLITGFSIMPTYKFMCGACVPFFHKLFMAVRNMRYDYTVN
+YDIKIWETHIRHGVYAVENSWETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPV-AGYNDETQITKTPDICIC--TWGTIHFKNSVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+DLFQILVHE
+;
+t96
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHVQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-S
+QSAVWKFDRFMCALMHLMQV--------GDL--------------------CSH--PSFLGMCMFHEQVRRKGE--LVLPDSPNEESVSFVYIQHHSFSD
+KRCLNCLNVGDNDDSEHLKEKHLRV----YG---QIGR-H-VIINVWNAFMGRLNHHEPPAEVVYPLRK--GGPDSKLM------------------VDG
+FFDK-E-D------ERPGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVQ-PSKLHRTFKINKKIGANVYQQTSRMKAEAPVYPHIMEYAHG
+V----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMECQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAGLTALKIVQLDIGFSAKTLGQ
+LNIIDCKLLGHRTWLATSPLQ------IGCDVMVIGNKIGSPS-EFEIAADPTIIWFYRNCIVHKLADTVSTAKMKAPQEMRV------QDVDSPSLGDD
+DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFNQGEH---EAEQRPVYGFQHPRCRPWQFVIGNYQTSAKNIIMLLYVKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLVADSCMWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELDWVEMEKSHQQ
+-SSVDDNYL-VNMLPFIRSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDAEA-ERSWIYD-VYCEM----KKDHKSAVYAHK
+VEHKGMDWDTGKE-MNQGPK-IVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATRKLISGVSVMPTYKFMCGACVPFFHKLFMAVRNMRYDYTVN
+YDVKIWETHIRHGVYAVENSWETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGYNMETQITKTPDICIC--TWGTIHFKNSVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDV---YPAAPKKK--HYV-GAGDVGGYEVMSE
+DLFQILVHG
+;
+t44
+MIWSEVRQMVREG--TDNAIDTR-C------------LIAARVKHMQGHVKQVRNANEDAL--YQNFSGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-S
+QSAVWKFDRFMCDLMHLMQN--------GDL--------------------CSH--PSFLGMCMFHEQVRCKGE--LVLPDSPNEESVSFVYIQHHSFSD
+KRCLNYLNVGDNDDSEHLKEKHLRI----YG---VIGK-H-VIINVWNAFMGRLNHHEPPADVEYPLRK--GGPDSKPM------------------VDG
+FFDK-E-D------DRPGIANAVSVPCG----DQVGGPIRGWCSSQVKFGLANHTLAQNPSKLHRTFKINKKMGANVYQQTSRMKAEAPVYPHIMEYAHG
+V----CKPFYDRSEPKNEAQGNGEK-QGNVPCVESMDCQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGYVDGHRCRAGLTALKIVQLDIGFSAKTLGQ
+LNIIDCKLLGHRTWLATSPLQ------IGCDIMVMGNKIGSPS-EFEVAADPTIIWFYRNCIVHKLADVVSTAKMKSPQEMRV------QDVDSPSLGDD
+DQQA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKN-DFLCPPAFEQGEH---EAEQCPVHGFKHPRCRPWQFVIADYQTSAKNIIMLLYVKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVLKIFELDWVEMEKSHQQ
+-SSVDDNYL-VNMLPFMHSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCEYYSGQFPDCEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+HEHKGMDWDTGKE-MNQGPK-VVMHGVLFN-------AEPNIHGQPGVSHVFM-GNDATRKLITGVSVMPTYKFMCNACVPFFHKLFMAVRNMRYDYTVN
+YDIKIWETHMRHGVYAVENSWETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGYNDETEITKTPDICIC--TWGTIHFKNSVMQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNMLVD-ELYSDM---YPAAPKKK--VYV-GAGDVGGYEVMSE
+DLFQILVHA
+;
+t45
+MIWSEVRQMVREG--TDNAIDNC-C------------LIAARVKHMQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR-YK-CMEGHDCVNTMAKSS-S
+QSAVWKFDRFMCDLMHLMQN--------GDL--------------------CSV--PSFLGMCMFHEQVRCKGE--LVLPDSPNEESVSFVYIQHHSFSD
+KRCLNYLNVGDNDDSEHLKEKHLRI----YG---EIGK-H-VIINVWNAFMGRLNHHEPPAEVMYPLRK--GGPESKPM------------------VDG
+FFDK-E-D------DRPGIANAVSVPCT----DQVGGPIRGWCSSQVKFGLANHTLVHNPSKLHRTFAINKKMGANVYQQTSRMKAEAPVYPHIMEYAHG
+V----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMDCQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAGLTALKIVQLDIGFSAKTLGQ
+LNIIDCKLLGHRTWLATSPLQ------IGCDVMVMGNKIGSPA-EFEVAADPTIIWFYRNCIVHKLADLVSTAKMKSPQEMRV------QDVDSPSLGDD
+DQEA--MDILPYWVCVMSGVVRKEQPD-SVNKRGRTWLAKK-DFLVPPAFNQGEH---EAEQKPVYGFDHPRCRPWQFVIANYQTSAKNIIMLLYVKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVHKIFELDWVEMEKSHQQ
+-SSVDDNYL-VNMLPFFHSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCQYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+HQHKGMDWDTGKE-MNQGPK-VVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATRKLIPGVSVMHDYKFMCGACVPFFHKLFMAVRNMRYDYTVN
+YDIKIWETHLRHGVYAVENSWETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGFVDETEITKTPDICIC--TWGTIHFKNSVVQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+DLFQILVHE
+;
+t74
+MIWSEVRQMVREG--TDNAIDNC-C------------LIAARVKHMQGHVKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGHDCVNTMAKPS-S
+QSAVWKFDRFMCDLMHLMQN--------GDL--------------------CSV--PSFLGMCMFHEQVRCKGE--LVLPDSPNEESVSFVYIQHHSFSD
+KRCLNYLNVGDNDDSEHIKEKHLRI----YG---EIGK-H-VIINVWNAFMGRLNHHEPPAEVMYPLRK--GGPESKPM------------------VDG
+FFDK-E-D------DRPGIANAVSVPCA----DQVGGPIRGWCSSQVKFGLANHTLVHNPSKLHRTFAINKKMGANVYQQTSRMKAEAPVYPHIMEYAHG
+V----CKPFYERSEPKNEAQGNGEK-QGNVPCVESMDCQYENKHAIMAKLMHP-PLYLMRMETMSKPPMGDVDGHRCRAGLTALKIVQLDIGFSAKTLGQ
+LNIIDCKLLGHRTWLATSPLQ------IGCDVMVVGNKIGSPA-GFEVAADPTIIWFYRNCIVHKLADLVSTAKMKSPQEMRV------QDVDSPSLGDD
+DQEA--MDILPYWVCVTSGVVRKEQPD-SVNKRGRTWLAKK-DFLVPPAFNQGEH---EAEQKPVYGFDHPRCRPWQFVIANYQTSAKNIIMLLYVKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLVADSCVWA-HNVAVCGWKRELVPGL---NHSCEMLAKTVYFEPDGE-------DEGKMVHKIFELDWVEMEKSHQQ
+-SSVDDNYL-VNMLPFFHSRENPVGHYVQGLED-PMHLIRPGT---ARKLNILF-YGCQYYSGQFPDGEA-ERSWIYD-VYCEM----KKDHKSAVVAHK
+HQHKGMDWDTGKE-MNQGPK-VVLHGVLFN-------AEPNIHGQPGVSHVFM-GNDATRKLIPGVSVMHDYKFMCGACVPFFHKLFMAVRNMRYDYTVN
+YDIKIWETHLRHGVYAVENSWETLVTC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQPM-AGFVDETEITKTPDICIC--TWGTIHFKNSVVQY
+CCYYKENRSVR-----------VNNTGGAELPK---------------------YHHQNILVD-ELYSDM---YPAAPKKK--HYV-GAGDVGGYEVMSE
+DLFQILVHE
+;
+t26
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHMSGHVKQVRNANEDAL--YQNFTGKKGAREKIKR-YL-CMEGHECVVTMAKNS-S
+ISAMWKFDRFMCDLMHLMQN--------GDL--------------------CSF--PSFLGMCMFHDQVRCKGE--LVLPDSKNEESVSFVYIQHHSFSD
+KRCLNYLNVGDNEDSEHLKEKHLRV----YG---NIGK-H-VIINSWNAMMGRLNHHEPAAEVVYPLRK--GGPESKPM------------------VDG
+FFDK-E-D------DRPGIANAVSVPCD----DQWGGPVRGWCSSQHKFGLADHTLIHIPSKLHRTFAINKKMGANVYQQTSRMKAAAPVYSHVMEYAHK
+V----VKPFYARSEPKNEAQGNGEK-QWNVPCVESMDCQYENKHATMAKLMHP-PLYLMRMQTMAKPPMGDVDGHRCRAGLTALKIVQLDIGFSQKTLGQ
+-NIIDSKHLGHRTWLATSPLQ------IGCSAMVMGNKIGSPQ-EVELAADPTVIYFYRNCIVQKMADVVSTVKMKSPQEMRV------QDVDSASLGDD
+DQQP--MNIIPYWVCVTSGVVHKEQPD-SVNKRGRTWTAKN-DFLCPDAFNQGEH---GAEQKPTHGFEHPRCRPWQFVIPVYQTGAKNIILLLYIKDV-
+SVNGVLQLLIWQLCDSH-GDWQSLVADSCAWA-VNVAVCGWKRELVPGL---NHACEMLAKTVYFEPDGE-------DEGKMVIKIFGLDWCEIEKSHQQ
+-SSVDDNYL-VNMLPFTHSRETPVGHYVQGLED-PMHLMRPGT---ARALNILF-YGCEYYSGQFPDGEP-ERSWIYD-VYCEL----KKDHKNAIVAVK
+HEHKGMDWDTGKE-MNHGPK-VIVHGVLFH-------AEPNIGGQPGVSHVFV-GNDATRKLIAGVSVMPIVKFMCGACVPFFRKLFMALRNMRYDYASN
+YDIKIVETHLREGVYAVENSWETLVVC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQSV-SGYNDETEITKTPDIKIC--TWGTIHFKNSVMQY
+CCYYKENRSVR-----------LNNTGGAELPK---------------------YHHQNVLVD-ELYGEA---YPAAPKKK--HYM-GAGDVGGYEVMSE
+DLFQILVHE
+;
+t61
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHMSGHVKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGHECVNTMAKNS-S
+VSAVWKFDQFMCDLMHLMQN--------GDL--------------------CSF--PSFLGMCMFHEQVRCKGE--LVLSDSKNEESVSFVYIQHPSFSD
+KRCLNYLNVGDNEDSEHLKEKVLRV----YG---DIGK-H-VIINVWNAMMGRLNHHEPAAEVVCPLRK--GGPDSKPM------------------VDG
+FFDK-E-D------DRPGVANAVSVPCD----DQWGGPVRGWCSSQHKFGLADHTLVHIPSKLHRTFAITKKMGANVYQQTSRMKATAPVYPHVMEYAHG
+V----VKPFYDRSEPKNEAQGNGEK-QWNVPCVESMDCQYENKHATMAKLMHP-PLYLVKMQTMSKPPMGDVDGHRCRAGLTALKIVQLDIGFSSKTLGQ
+-NIIHSKLLGHRTWLATSPLQ------IGCDVMVMGNKIGSPQ-EVELAADPSVIYFYQNCIVQKMADVVSTVKMKSPQEMRV------QDVDSASLGDD
+DQQP--MNIIPYWVCVTSGVVRKEQPD-SVNKRGHTWTAKN-DFLCPPAYNQGEH---GAEQKPVHGFEHPRCRPWQFVISVYRTGAKNINLLLYIKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLVADSCAWA-VNVAVCGWKRELVPGL---NHACEMLAKSVYFEPDGE-------DEGKMVLKIFGLDWCEIEKSHQQ
+-SSVDDNYL-VNMLPFAHSRQTPVGHYVQGLED-PMHLMRPGT---ARALNILF-YGCEYYSGHFPDGEA-ERSWIYD-MYCEL----KKDHKSAIVAVK
+HCHKGMDWDTGKE-MNHGPK-VIIHGLLFH-------AEPNIGGQPGVSHVFV-GNDATRKLIAGASVMFIVKFMCGACVPFFRKLFMALRNMRYDYSQN
+YDIKIVETHLREGVYAIENSWETLVVC-EMTSGRMGAKINHLPRLPEQVI-PPCILTVSGLKRAV-NGYNDETEITKTPDIKIC--TWGTIHFKNSVMQY
+CCYYKENRSVR-----------FNNTGGAELPK---------------------YHHQNVLVD-ELYSEL---YPAAPKKA--HYM-GAGDIGGYEVMSE
+DLFQILVHE
+;
+t97
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHMSGHMKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGHECVNTMAKNS-S
+VSAVWKFDRFMCDLMHLMQN--------GDL--------------------CSF--PSFLGMCMFHQQVRCKGE--LVLPDSKNEESVSFVYIQHHSFND
+KRCLNYLNVGDNEDSEHLEEKHLRV----YG---NIGK-H-VIINVWNAMMGRLNHHEPAAEVVCPLRK--GGPDSKPM------------------VDG
+FFDK-E-D------DRPGVANAMSVPCD----DQWGGPVRGWCSSQHKFGLADHTLVHVPSKLHRTFPINKKMGANVYQQTSRMKATAPVYPHVMEYAHG
+V----IKPFYDRSEPKNEAQGNGEK-QWNVPCVESMDCQYENKHATMAKLMHP-PLYLVKMQTMSKPPMGDVDGHRCRAGLTALQIVQLDIGFSAKTLGQ
+-NIIHSKLLGHRTWLATSPLQ------IGCDVVVMGNKIGSPQ-EVELAADPSVIYFYQNCIVQKMADVVSTVKMKSPQEMRV------QDVDSASLGDD
+DQQP--MNIIPYWVCVTSGVVRKEQPD-SVNKRGRTWSAKN-DFLCPPAFNQGEH---GAEQKPVHEFQHPRCRPWQFVISVYRTGAKNINLLLYIKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLVADSCAWA-VNLAVCGWKRELVPGL---NHACEMLAKSVYFEPDGE-------DEGKMNLKIFGLDWCEIEKSHQQ
+-SSVDDNYL-VNMLPFTHSRETPVGHYVQDLED-PMHLMRPGT---ARALNILF-YGCEYYSGHFPDGEP-ERSWIYD-MYCEL----KKDHKSAIVAVK
+HCHKGMDWDTGKE-MNHGPK-VIIHGVLFH-------AEPNIGGQPGVSHVFV-GNDATRKLIAGVSVMPIVKFMCGACVPFFRKLFMALRNMRYDYSQN
+YDIKIVETHLREGVYAVENSWETLVVC-EMTSGRIGAKINHLPRLPEQVI-PPCILTVSGLKQAV-NDCNDETEITKTPDIKIC--TWPTIHFKNGMMQY
+CCYYKENRSVR-----------FNNTGGAELPK---------------------YHHQNVLVD-ELYSEV---YPAAPKKA--FYM-GAGDIGGYEVMSE
+DLFQILVHK
+;
+t17
+MIWSEVRQMVREG--ADNAIDNR-C------------LIAARVKHFSGHTKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGQDCVNTMAKSS-S
+QSAVWKFDRFMCDLVHLMQN---GARGSGDL--------------------CSF--PSFLGMCMFHEQVRCKGE--LVLPDSKNEESVSFVYIQHHSFSD
+KRCLNELNVGDNEDSIHLKEKHLRI----YG---NIGK-V-VIINVWNAMMGRLNHHEPAAEVVYPLRK--GGPDSKPM------------------VDG
+FFDK-E-D------DRPGIANAVAVPCS----DQWGGPVRGWCSSQHKFGLADHTLVHVPSLLHRTFAINRKMGANVYQQTSRMKAAAPVYPHMMEYAHG
+V----VKPFYERSEPKNEAQGNGEK-QWNVPCVQSVDCQYENKHATMAKLMHP-PLYLMRMETMSKPPMGDVDGVRCRAGLTALKIVQLDIGFSAKTLGQ
+-NIIDSKLLGHRTWLATSPLQ------IGCDVMVVGNKIGSPQ-EFELAADPTVIYFYRNCIVQKLADVVSTVKMKSPQEMRV------QDVDSPSLGDD
+NQQS--MNIIPYWVCVHSGVVQKEQPD-SVHKRGRTWTAKN-DFLCPPAFDQGEH---GAEQKPVHGFEHPRCRPWQFVIANYQTGAKNIILLLYVKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLSADSCAWA-HNVAVCGWKRELVPGL---NHACEMLAKTVYFEPDGE-------DEGKMVIKIFGLDWCEMEKAHQQ
+-SSVDDNYL-VNMLPFTHSRENPVGHYVQGLED-PMHLIRPGT---ARALNILF-YGCEYYSGQFPDGEP-ERSWIYD-VYCEL----KKDHKSAIVAVK
+HEHKGMDWDTGKE-MNQGPK-VIIHGVLFH-------AEVNIHGQPGVSHVFV-GNDATRKLIAGVSVMPFVKFMCGACVPFFRKLFMALRNMRYDYTSN
+YDIKIIETHLRNGVYAVENSWETLVVC-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKQAM-AGVNDETEITKTPDIKIC--TWGTIHFKNFVMQY
+CVYYKENRSVR-----------FNNTGGAELPK---------------------YHHQNALVD-ELYSDV---YPAAPKKK--HYM-GEGDVGGYEVMSE
+DLFQILVHA
+;
+t11
+MIWSEVRQMVREG--TDNAIDNR-C------------LIAARVKHFSGHTKQVRNANEDAL--YQNFTGQKGAREKIKR-YL-CMEGQDCVNTMAKSS-S
+QSAVWKFDRFMCDLVHLMQN---GARGSGDL--------------------CSF--PSFLGMCMFHEQVRCKGE--LVLPDSKNEESVSFVYIQHHSFSD
+KRCLNSLNVGDNEDSIHLKEKHLRI----YG---DIGK-H-VIINVWNAMMGRLNHHEPAAEVVYPLRK--GGPDSKPM------------------VDG
+FFDK-E-D------DRPGIANAVAVPCS----DQWGGPVRGWCSSQHKFGLADHTLVHVPSLLHRTFAINKKMGANVYQQTSRMKAAAPVYPHMMEYAHG
+V----VKPFYERSEPKNEAQGNGEK-QWNVPCVQSVDCQYENKHATMAKLMHP-PLYLMRMETMSKPPMGDVDGVRCRAGLTALKIVQLDIGFSAKTLGQ
+-NIIDSKLLGHRTWLATSPLQ------IGCDVMVVGNKIGSPQ-EFELAADPTVIYFYRNCIVQKLADVVSTVKMKSPQEMRV------QDVDSPSLGDD
+NQQS--MNIIPYWVCVHSGVVQKEQPD-SVHKRGRTWTAKN-DFLCPPAFDQGEH---GAEQKPVHGFEHPRCRPWQFVIANYQTGAKNIILLLYVKDV-
+SCNGVLQLLNWQLCDSH-GDWQSLSADSCAWA-HNVAVCGWKRELVPGL---NHACEMLAKTVYFEPDGE-------DEGKMVIKIFGLDWCEMEKAHQQ
+-SSVDDNYL-VNMLPFTHSRENPVGHYVQGLED-PMHLIRPGT---ARALNILF-YGCEYYSGQFPDGEP-ERSWIYD-VYCEL----KKDHKSAIVAVK
+HEHKGMDWDTGKE-MNQGPK-VIIHGILFH-------AEVNIHGQPGVSHVFV-GNDATRKLIAGVSVMPFVKFMCGACVPFFRKLFMALRNMRYDYTSN
+YDIKIMETHLRNGVYAVENSWETLVVC-EMTSGRIGAKINHLPRLPEQVI-PPCMLTVSGLKQAM-AGVNDETEITKTPDIKIC--TWGTIHFKNFVMQY
+CVYYKENRSVR-----------FNNTGGAELPK---------------------YHHQNVLVD-ELYSDG---YPAAPKKK--HYM-GEGDVGGYEVMSE
+DLFQILVHA
+;
+t23
+MIWSECQRMLREH--EDQAIANE-C------------LIAFKVKLVNGHVKQVRNASEDAH--YTFFAGEKGARELIKR-YS-CMEGDGCVNTMAEGR-S
+ESAVWKFDPFMCQLTHSMQS--------GDL--------------------CSV--PSFLGVCMFQRQVVMKGE--LVLPDSADEGSVSFMYIQHHSFAA
+KRCLNVLNVGDNEDSVHLRHKQLRV----YG---KIGK-H-VIISVPNAIMGRLNHHEPSAIVVFPLRQ--RGADSKSV------------------GDG
+FYDK-D-E------DRPGIANAVSVPVA----EQWVGSVRGWYSSEHKYGLANHILI-GPSKLHRTYQTTAKMGANVVKATNRMKRPQPVYPHVMEYANG
+V----VKPFYEVAESKNEAQGNGEK-PVNVPCVESPDCQYESKHARVNKLMHP-SLYLMCMEAMNKPIMGDWDGNRCRSPLCLLKVIQLDMGVSGKTLGQ
+-NIVMAKLLGERTWLATSPLQ------IGCDVVAVGKKPESPQ-EFECAADPTVIYFYKNLIIQQAADYVSAVQVKSPQEMRY------QDVNSPSDGDE
+NGQS--MHIGPYWVCVSSEVVKKSQPD-SVDKRGRTWVAKN-EFLCPPDHMQGEHSIEGAEQKPFFGFAGPFPQPWQFVIVNPQTWAHNIIRLLYCKDV-
+SCNCVLTCLNWVLCDSH-GDWHSLIADACPCA-HNVAVCGWKRELVPGL---NHSNEHMAKTIYFEPDGH-------DEGKMILNIFGLDWCEVETSHQE
+-SSSDDNHL-VNMLPFGVSRDDPVGHYMLGLED-AIRLYRPGT---ARALNILF---VNYYSGDFQDPEL-ERSQLYN-VYCEQ----KQDHRNAIRASK
+NDHKGMAWDTAKD-MEQGPK-MVEHQVLFY-------AEPNMHGQPEVIHIFI-GNDAMCMLIPGMSVMVHHKFMRAACMPFFNKLFMAVRYMRYDYVDN
+YDIKIDETRYRDGVYARRNSWETANVC-EMSSGRSGAKINHNPRLPEQVT-PPRSLTVSGLKDTM-PGHPDVTEITKTPVIAIV--MWGTINLKNHVMQY
+CCYYKETRSVR-----------VNNTGGAELPK---------------------YHYQNILVD-ELYSND---YPAAPKKA--QFM-GVGDVGGYEIVCE
+DIFQILVCD
+;
+t76
+LSSSHEVRVVNHKSKPDEHIADK-D------------MCADAMCNGSGHTGRIHNAVEGGI--VTNFHGF---AEMPKN-HD-VMEEQGGPGTCLAPQQS
+ADTSWPFVMFTVDLAHRCRG--------GDMPQNTGDSMTCPHLAEGLAAVNS---RAFIGVSIYDLKVSHKMI--QACNPIQN---------DNHAFSD
+QRCLNDLSQGVVGASFPKMQHGVRH----YK---K--------RVYENEVGGRLDDAEAIDDMGVWIRW--EGVKHAWCHPIGSCPDHLVCSLLVLQPAR
+NFIQLS-MVRDTPHRLPKMASAAPVYKQTCHLEQVQGTARMWGKSGPRVVLNGHMLK-TQNTLHRQYLVDVELQATMVFVAARMKTDSSMYMSVREILHG
+------------CGIKDEAQADGQR-PATLIVVLSKDNKGITEHGAVLKKIHP----------LCKRCMENGRCLRYKNDLTGDQLVQLAD----NTCAW
+-NLFEC--LRDSKSLFGSPLFIKVDEDRGFTAP-------SK-------VEPKCAQFYSKSCTHC----------------TM------CSVGSHASEED
+ALDLYTHKPVPDAQCFVSRVARNIPEH-SPCK-----------------------------P---CS-----------------VEEVCYCKVCDSKDVR
+AVKNAYQDLQVPLSKLK-APWLSMGHCECWEEDINNILSVVKHELVDDVDRMNRLTEVAAKMAYFGPDGFHWDVELWEENDLNCDDFELGW-NLKH----
+---EDDHPL-LCIGSFSVHKYVSVMVYPLPMND-CVRMSQPCHAAHAQDIPTEQ---TRYQIHTFLDDSI-RRDLCNQ-GCHEENMVWRDDLKDPISTEV
+IADKLHEWPTNVN-KENSAD----HRQLFH-------ANSSALDKHQHNVVMN-GSPCIRALIIGGSSVGVNHFMMGPCQEFFTDLFMMYEGLQYACVCA
+MNITIQCLHTGEGVMCNVKCKEFLQREDEMKAGLIGIICNHLSRMIMVIL-VHCLLTHAGLKSME-IGFDR-TGVVRMPLIAEP--LYLVI-YVNAVEPY
+TDAYKKPKSMHQFQFDDCQIRYRTNTGFEETPVGATHLTHVCVCVPHPWTKGKSEILQNMGSA-VLYNDVIRDHNASEQKE--AHV-PMGDEGRISRAKD
+EIMYIRDLE
+;
+t53
+LSSSHEVRVVNHKSKPDEHIADK-D------------MCADAMCNGSGHTGRIHNAVEGGI--VTNFHGF---AEMPKN-YD-VMEEQGGPGTCLAPQQS
+ADTSWPFVMFTVDLAHRCRG--------GDIPQNTGDSMTCPHLAEGLAAVNS---RAFIGVSTYDLKVSHKMI--QACNPIQN---------DNHAFSD
+QRCLNDLAQGVVGASHPKMQHGVRH----YK---K--------RVYENEVGGRLDDAEAIDDMGVWIRW--EGVKHAWCHPIGSCPDHLVCSLLVLQPAR
+NFIQLS-MVRDTPHGLPKMASAAPVYKQTCHLEQVQGTARMWGKSGPRVVLNGHMLK-TQNTLHRQYLVDVELGATMVFVAARMKTDLSMYMSVREILHG
+------------CGIKDEAQADGQR-PATLIVVLSKDNKGITEHGAVLKKIHP----------LCKRCMENGRCLRYKNDLAGDQLVQLAD----NTCAW
+-NLFEC--LRDSKSLFGSPLFIKVDEDRGFTAP-------SK-------VEPKCAQFYSKSCTHC----------------TM------CSVGSHASEED
+ALDLYTHRPVPDAQCFVSRVARNIPEH-SPCK-----------------------------P---CS-----------------VEEVCYCKVCDSKDVR
+AVKNAYQDLQVPLSKLK-APWLSMGHCECWEEDINNILSVVKHELVDDVDRMNRLTEVAAKMAYFGPDGFHWDVELWEENDLNCDDFELGW-NLKP----
+---EDDHPL-LCIGSFSVHKYVSVMVYPLPMND-CVRMSQPCHAAHAQDIPTEQ---TRYQIHTFLDDSI-RRDLCNQ-GCHEENMVWRDDLKDPISTEV
+IADKLHEWPTNQN-KENSAD----HRQLFH-------ANSSALDKHQHNVVMN-GSPCIRALIIGGSSVGVNHFMMGPCQEFFTDLFMMYEGLQYACVCA
+MNITIQCLHTGEGVVCNVKCKEFLQREDEMKAGLIGIICNHLSRMIMVIL-VHCLLTHAGLKSME-IGFDR-TGVVRMPLIAEP--LYLVI-YVNAVEPY
+TDAYKKPKSMHQFQFDDCQIRYRTNTGFEETPMGATHLTHVCVCVPHPWTKGKSEILQNMGSA-VLYNDVIRDHNASEQKE--AHV-PMGDQGRISRAKD
+EIMYIRDLE
+;
+t16
+LSSSHEVRVVNHKSKPDEHIADK-D------------MCADAMCNGSGHTGRIHNAVEGGI--VTNFHGF---AEMPKN-YD-VMEEQGGPGTCLAPQQS
+ADTSWPFVMFTVDLAHRCRG--------GDIPQNTGDSMTCPHLAEGLAAVNS---RAFIGVSTYDLKVSHKMI--QACNPIQN---------DNHAFSD
+QRCLNDLAQGVVGASHPKMQHGVRH----YK---K--------RVYENEVGGRLDDAEAIDDMGVWIRW--EGVKHAWCHPIGSCPDHLVCSLLVLQPAR
+NFIQLS-MVRDTPHGLPKMASAAPVYKQTCHLEQVQGTARMWGKSGPRVVLNGHMLK-TQNTLHRQYLVDVELGATMVFVAARMKTDLSMYMSVREILHG
+------------CGIKDEAQADGQR-PATLIVVLSKDNKGITEHGAVLKKIHP----------LCKRCMENGRCLRYKNDLAGDQLVQLAD----NTCLW
+-NLFEC--LRDSKSLFGSPLFIKVDEDRGFTAP-------SK-------VEPKCAQFYSKSCTHC----------------TM------CSVGSHASEED
+ALDLYTHKPVPDAQCFVSRVARNIPEH-SPCK-----------------------------P---CS-----------------VEEVCYCKVCDSKDVR
+AVKNAYQDLQVPLSKLK-APWLSMGHCECWEEDINNILSVVKHELVDDVDRMNRLTEVAAKMAYFGPDGFHWDVELWEENDLNCDDFELGW-NLKP----
+---EDDHPL-LCIGSFSVHKYVSVMVYPLPMND-CVRMSQPCHAAHAQDIPTEQ---TRYQIHTFLDDSI-RRDLCNQ-GCHEENMVWRDDLKDPISTEV
+IADKLHEWPTNQN-KENSAD----HRQLFH-------ANSSALDKHQHNVVMN-GSPCIRALIIGGSSVGVNHFMMGPCQEFFTDLFMMYEGLQYACVCA
+MNITIQCLHTGEGVVCNVKCKEFLQREDEMKAGLIGIICNHLSRMIMVIL-VHCLLTHAGLKSME-IGFDR-TGVVRMPLIAEP--LYLVI-YVNAVEPY
+TDAYKKPKSMHQFQFDDCQIRYRTNTGFEETPMGATHLTHVCVCVPHPWTKGKSEILQNMGSA-VLYNDVIRDYNASEQKE--AHV-PMGDQGRISRAKD
+EIMYIRDLE
+;
+t42
+LSSSHEMRVVHHKSKPDEEIADQ-D------------LCAEEMCKGSGHTGRIHSAVEGGI--WTNFHGF---AEMPKN-YD-VMEEQGGPGTCIAPRQS
+ADTSWPFMVFTVDLAHRCRG--------GDTPTQAGDSMTFPHLAEGLPAVNS---RAFVGVSSYDLRVSHKMI--QACTLIQN---------DNVAFSD
+QRPLNDLNQGCVGTSHPKMPHGVRH----YK---K--------KVYENEVGDRLDDAEGIDDVGVWMRW--NGVKHAWCHIIGSCPDHLVCSLLVLQPGR
+NFIQLS-VVHDTPHRLPKMASAAAVFKQTCHLEQVPGTARMWGKSGPRVRLNGHVLK-NQNILHRQYLVDVNLGATMVFVLARMKTDASMYMSHREILHG
+GTFDAAKPFRQICGTKDEAQPDGRR-PATLLVVLSKDNQGITEHGAVLKHVHP----------LCKKDCNNNRCLRCKNVLAGNQLIQLSD----VTCAW
+-NLFEC--LGDSESLFGSPLAIKVDEDRGFTAP-------SK-------VEPKCAQFYSKSCTHH----------------MM------CSVGSNASEED
+ALELYTHKPVPDPQCFVSIVVRNIPEH-SPCK-----------------------------P---CS-----------------VEEVAYCKNCDSKDVR
+AVQNAYQDLAVPLSKLK-APWLSMGHCECWEEDINNILSMVKHELVVDQDMVNRSPEVAAKMAYFGPDGFHWDVELCEESDLTVDDFELGW-VLKP----
+---EDDHPL-ICIGSFSVHKQFSVMVYPLPMND-AIRMSQPCHAAHAQDIHTDQ---DRYDVRTFLGHSI-KCHMCNQ-ACHEENIVWRDDLKDPITTEV
+IAEKLQEWPTNQN-KENVAD----HRQLFH-------ANSSALDKHRHNVMMN-GSACIRTLIIGGSIVGVNVFMMEPCQEFFTDLFMVYEGLQYAVVCA
+VNIIIQCLHTNEGVVCNVKCKEFLQREEDMKSGLIGIICNHISRMCMHIL-VVCLLTHCGLKAME-IPFDI-TGVVRGPLITEP--LYLII-YVNAVEPY
+TDAYKKPKSMHQFQFDDVQIRYRTNTGFEENPKLATHLVHVCVVVPHPWTKGKSEILQNMESA-HLYNAVIRDNNASEQKE--AHV-PVGDEGRISRAKN
+EILYIRDLE
+;
+t24
+QSSSHEMRVVHHKSKPDEEITDQ-D------------LCAEEMCKGSGHTGRIHSAVEGGI--WTNFHGF---AEMPKN-YD-VMEEQGGPGTCVAPRQS
+ADTNWPFMVFPVELAHRCRG--------GDTP--------FPHLAEGLPAVNS---RAFIGVSSYDLKVSHKMI--QACNPIQN---------DNVAFSD
+QRVLNDLSQGCVGTSHPKMPHGVRH----YK---K--------RVYENEVGDRLDDAEAVDDVGVWMRW--AGVKVAVCHVIGSCPDHLVVSLLVLQPAR
+NFIQLS-VVHDTPHRLPKMASAAAVFKQTCHLEQVAGTARVWGKSGPRVKLNGHVLK-NQNVLHRQYLVDVDLGATMVFVAARMKTDASMYMSHREILHG
+GTFDAAKPFRQICGVKDEAQPDGQR-PATLLVVLSKDNVGITEHGAVLKHVHP----------LCKKDCNNNRCLRCKNVLAGNQLVQLAD----ITCAW
+-NLFEC--LGDSESLFGSPLAIKVDEDRGFTAP-------SK-------VEPKCQQFYSKSCTHC----------------VM------CSVGSNASEED
+ALELYTHKPVPDPQCFVSIVVRNIPEH-SPCK-----------------------------P---CS-----------------VEEVCYCKNCDSKDVR
+ATQNAYQELAIPLSKLK-APWLSMGHCECWEEGINNILSMVKHELVVDQDMVNRSPEVAAKMAYFGPDGFHWDIELCEENDLTCDDFELGW-VLKP----
+---EDDHPL-ICIGSFSVHKQFSVMVYPLPMND-AIRMSQPCYAAHAQDIHTDQ---DRYDIRTFLEHSI-RCHLCNQ-ACHEENIVWRDDLKDPITTEV
+IADKLQEWPTNQN-AENVAD----HRQLFH-------ANSSCLDRHRHNVMMN-GSSCIRTLIIGGSIVGVNVFMMGPCQEFFTDLFMVYEGLQYAVVCA
+INIIIQVLHTNEGVVCNVKCKEFLQREDDMKSGLIGIICNHISRMCMHIL-VHCLLTHCGLKAME-IPFDR-TGVVRGPLIAEP--LYLII-YVNAVEPY
+TDAYKKPKSMHQFQFDDVQIRYRTNTGFEENPKLATHLVHVCVVVPHPWTKGKSEILQNMESARHLYNAVIRDNNASHQKE--AHV-PAGDQGRISRAKN
+EILYIRDLE
diff --git a/test/example.ph b/test/example.ph
new file mode 100644
index 0000000..5f84796
--- /dev/null
+++ b/test/example.ph
@@ -0,0 +1,2526 @@
+ 100 1209
+t73 LIVSQIRVMV RDG--IHKAM DEE-V----- -------LIA RRVKPYSGNG
+t66 LIVSQIRVMV RDG--IHKAM DEE-V----- -------LIA RRVKPCSGNG
+t32 LIVSQIRVMV RDG--IHKAM DEE-V----- -------LIA RRVKPYSGNG
+t75 LIVSEIRVMV RDE--VHKAM DEE-C----- -------LIA RRVKPYSGNG
+t79 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTFSGSQ
+t27 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTMSGSQ
+t93 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTMSGSQ
+t59 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTFSGSQ
+t7 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKKFSGSQ
+t78 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTFSGSQ
+t12 LIVSEVRVMV RDG--INIAI DEL-C----- -------LIA NRVKAFSGHQ
+t81 LIVSEVRHMV RDG--ANVAI DEL-C----- -------LIA CRVKAFSGHG
+t21 LIVSEVRHMV RDG--ANIAI DEL-C----- -------LIA CRVKAFSGHG
+t80 LIVSEVRHMV RDG--VNIAV DEI-C----- -------LIA NRVKSMSGQG
+t14 LIVSEVRHMV RDG--VNIAV DEI-C----- -------LIA NRVKSMSGQG
+t85 LIVSEVRHVV RDG--VNIAV DEI-C----- -------LIA NRVKSMSGQG
+t62 LIVSEVRVMV RDG--IHIAV DEI-C----- -------LIA NRVKCMSGQG
+t19 LIVSEVRHMV RDG--INIAV DEI-C----- -------LIA NRVKCVSGQG
+t77 LIVSEVRHMV RDG--INIAV DEI-C----- -------LIA NRVKSMSGQG
+t88 LIVSECRLII RDG--NHDAI DEM-CCVAND LNNEIERLVA SMVKSFRGHD
+t37 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+t35 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+t48 LIVSDMRLII REG--SDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+t55 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+t46 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+t67 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+t57 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+t56 LIVSEWRLFI RDG--HDDAI DEM-CCEANE LNNDIEKLVA SMVKGFRGHD
+t13 GIVSECRMII RDE--HDDAI DEM-C----- -------LVA SMVKKLSGCE
+t5 GIVSECRMII RDE--HDDAI DEM-C----- -------LVA SMVKKLSGCE
+t38 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+t33 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+t100 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+t34 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+t84 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCD
+t92 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+t3 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+t22 GIVSECRVII RDQ--SDDAI DER-Y----- -------LVA SVVKRLSGCE
+t64 GIVSECRMII RDE--TDDAI DEV-C----- -------LVA SMVKKLSGCE
+t18 GIVSECRMII RDE--TDDAI DEV-C----- -------LVA SMVKKLSGCE
+t68 GIVSECRMII RDE--TDDAI DEV-C----- -------LVA SMVKKLSGCE
+t28 GIVSECRMII RDE--ADDAI DEM-C----- -------LVA SMVKKLSGCE
+t82 GIVSECRMII RDE--ADDAI DEM-C----- -------LVA SMVKKLSGCE
+t41 GIVSECRMII RDE--ADDAI DEM-C----- -------LVA SMVKKLSGCE
+t71 GIVSECRMII RDQ--SDDAI DEMVV----- -------LVA SMVKEMSGCE
+t94 GIVSECRMII RDQ--SDDAI DEMVC----- -------LVA SMVKELSGCE
+t99 GIVSEVRMII RDE--SDDAI DEM-C----- -------LVA SMVKALSGCE
+t40 GIVSECRMII RDE--SDDAI DEV-C----- -------LVA SMVKALSGCE
+t90 GIVSECRMII RDE--SDDAI DEV-C----- -------LVA SMVKALSGCE
+t4 GIVSECRMII RDE--PDDAI DEV-C----- -------LVA SMVKELSGCE
+t36 MIWSEVRKMV RER--REQAI DNK-C----- -------LIA ARVKMMSGYV
+t87 MIWSEVRKMV RER--REQAI DNK-C----- -------LIA ARVKMMSGYM
+t89 MIWSEHRKMV REG--REQAI DNK-C----- -------LIA KRVKVMSGYI
+t39 MIWSEHRKMV REG--REQAI DNK-C----- -------LIA KRVKVMSGYI
+t8 MIWSEHRKMV REG--REQAI DNK-C----- -------LIA KRVKVMSGYI
+t6 MIWSEHRKMV REG--REQAI DNK-C----- -------LIA KRVKVMSGYI
+t58 MIWSEYRHMV REG--RDQAI DNK-C----- -------LIA ARVKVMSGYV
+t54 MIWSEYRHMV REG--RDQAI DNK-C----- -------LIA ARVKVMSGYV
+t65 MIWSEYRQMV REG--NDQSI DNK-C----- -------LIA DRVKMMSGVV
+t29 MIWSEYRQMV REG--NDQSI DNK-C----- -------LIA ARVKMMSGVV
+t98 MIWSEHRQMV REG--NDQSI DNK-C----- -------LIA ARVKMMSGVV
+t83 MIWSEYRQMV REG--NDQSI DNK-C----- -------LIA ARVKMMSGVV
+t95 MIWSEYRQMV REG--TDQSI DNK-C----- -------LIA ARVKMMSGVV
+t20 MIWSEYRQMV REG--TDQSI DNK-C----- -------LIA ARVKMMSGVV
+t69 MIWSDYRQMV REG--GDDSI DNK-C----- -------LIA ARVKMMSGVV
+t2 MIWSDYRQMV REG--GDDSI DNK-C----- -------LIA ARVKMMSGVV
+t10 MIWSDYRQMV REG--GDDSI DNK-C----- -------LIA ARVKMMSGVV
+t31 MIWSEYRSMV REG--ADQSI DNK-C----- -------LIA ARVKMMSGVV
+t15 MIWSEYRSMV REG--SDQSI DNH-C----- -------LIA ARVKMMSGVV
+t63 MIWSEYRSMV REG--SDQSI DNK-C----- -------LTA ARVKLMSGVV
+t50 MIWSEYRSMV REG--SDQSI DNK-C----- -------LTA ARVKLMSGVV
+t25 MIWSEYRSMV REG--SDQSI DNK-C----- -------LTA ARVKMMSGVV
+t51 MIWSEYRSMV REG--SDQSI DNK-C----- -------LIA ARVKMMSGVV
+t9 MIWSECRQMV REK--TDNAI DNQ-C----- -------LIA ARVKENSGHV
+t47 MIWSECRQMV REK--SDNAI DNQ-C----- -------QIA ARVKRNSGHV
+t60 MIWSECRQMV REK--TDNAI DNQ-C----- -------QIA ARVKENSGHV
+t30 MIWSECRQMV REK--TDNAI DNQ-C----- -------QIA ARVKENSGHV
+t70 MIWSECRQMV REK--NDNAI DNQ-C----- -------LIA ARVKEDSGHV
+t91 MIWSECRQMV REK--NDNAI DNQ-C----- -------LIA ARVKEDSGHV
+t49 MIWSECRQMV REK--NDNAI DNQ-C----- -------LIA ARVKENSGHV
+t52 MIWSEERQMV REK--VDNAV DNQ-C----- -------LIA ARVKENCGHV
+t43 MIWSEVRQMV REG--SDNAI DNR-C----- -------LIA ARVKHVQGHV
+t1 MIWSEVRQMM REG--TDNAI DNQ-C----- -------LIA ARVKHMQGHV
+t86 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKPVQGHV
+t72 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHVQGHV
+t96 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHVQGHV
+t44 MIWSEVRQMV REG--TDNAI DTR-C----- -------LIA ARVKHMQGHV
+t45 MIWSEVRQMV REG--TDNAI DNC-C----- -------LIA ARVKHMQGHV
+t74 MIWSEVRQMV REG--TDNAI DNC-C----- -------LIA ARVKHMQGHV
+t26 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHMSGHV
+t61 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHMSGHV
+t97 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHMSGHM
+t17 MIWSEVRQMV REG--ADNAI DNR-C----- -------LIA ARVKHFSGHT
+t11 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHFSGHT
+t23 MIWSECQRML REH--EDQAI ANE-C----- -------LIA FKVKLVNGHV
+t76 LSSSHEVRVV NHKSKPDEHI ADK-D----- -------MCA DAMCNGSGHT
+t53 LSSSHEVRVV NHKSKPDEHI ADK-D----- -------MCA DAMCNGSGHT
+t16 LSSSHEVRVV NHKSKPDEHI ADK-D----- -------MCA DAMCNGSGHT
+t42 LSSSHEMRVV HHKSKPDEEI ADQ-D----- -------LCA EEMCKGSGHT
+t24 QSSSHEMRVV HHKSKPDEEI TDQ-D----- -------LCA EEMCKGSGHT
+
+ TQVRNDVEDA N--CQEFVGI ---RELGKH- YK-CMDGFHT VNNGAGEN-S
+ TQVRNDVEDA N--CQEFVGI ---RELGKH- YK-CMDGFHT VNNGAGEN-S
+ TQVRNDVEDA N--CQEFVGI ---RELGKH- YK-CMDGFHT VNNGAGEN-S
+ NQIRNDIEDA N--GQEFVGI ---RELGKH- YD-CMDGYHT VNNGAGEN-S
+ NQVRNAVEDA A--RPDFVGT ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ NQVRNAVEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ NQVRNAVEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ NQVRNAVEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ GQVRNAIEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ GQVRNAIEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ NQVRNAMEDA Q--RPDFVGI ---RELGKQ- YQ-CMDGHGA VDTGAGRN-S
+ HQVRNAVEDA A--RPDFIGI ---RELGKP- Y--CMDGHGA VNTGAGHN-S
+ NQVRNAVEDA P--RPDFIGV ---RELGKP- Y--CMDGHGA VNTGAGVN-S
+ NQVRNAMEMA A--RQNFVGM ---RELEKV- YE-CMDGQGA VNTEAGNN-S
+ NQVRNAMEMA A--RQNFVGM ---RELEKV- YQ-CMDGQGA VNTEAGNN-S
+ NQVRNAMEMA A--RQNFVGM ---RELDKA- YQ-CMDGQKA VNTEAGNN-S
+ NQARNAMEMA A--RQNFVGM ---RELGKQ- YQ-CMDGQGA VNTEAGNN-S
+ NQARNAMEMA A--RQNFVGM ---RELGKQ- YQ-CMDGQGA VNTEAGNN-S
+ NQARNAMEMA A--RQNFVGM ---RELGKQ- YH-CMDGQGT VNTEAGNN-S
+ SQARNNSECM R--SAPFIGV ---RELFKR- YHKCVEGAGC VHTVAGTP-S
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ SQARNNAECI I--AAPFIGV ---RELFKR- YIKCVEGAGC VYTVA-AP-S
+ NQARNNHECA I--PPPFHGV ---REMFKRV YE-CMEGIGC VNTVAGNP-S
+ NQARNNHECA I--PPPFHGV ---REMFKRV YE-CMEGIGC VNTVAGNP-S
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ QQARNNRECA T--SIPFLGV ---RELWKR- YE-CMEGIGC VNTVAGKP-S
+ NQARNNRECA I--SIPFLGV ---RELWKR- YE-CMEGIGC VNTVAGTP-S
+ NQTRNNRECA IT-SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGMP-S
+ NQTRNNRECA IT-SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGMP-S
+ NQTRNNRECA I--SPPFIGV ---RELFKR- YG-CVEGIGC VNTVAGMP-S
+ NQARNNRECA I--SPPFIGV ---RELFKR- YH-CMEGIGC VNTVAGMP-S
+ NQARNNRECA I--SPPFIGL ---RELFKR- YV-CMEGIGC VNTVAGMP-S
+ NQARNNRECA I--SPPFIGL ---RELFKR- YV-CMEGIGC VNTVAGMP-S
+ NQARNNSECA I--SPQFIGV ---RELFKR- YR-CMEGIGC VNTVAGAP-S
+ NQARNNRECA I--SPPFTGV ---RELFKR- YR-CMEGIGC VNTVAGIP-S
+ NQARNNRECA I--SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGIP-S
+ NQARNNRECA I--SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGIP-S
+ NQARNNRECA I--SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGIP-S
+ NQARNNRECA I--SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGMP-S
+ LQVRNALEDA L--YVFFTGT KGTRELVKY- YM-CMEGHGC VNTMAKKS-S
+ LQVRNALEDA L--YVFFTGN KGTRELVKY- YM-CMEGHGC VNTMAKKS-S
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGV VNTMAKKS-S
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGV VNTMAKKS-S
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGV VNTMAKKS-S
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGV VNTMAKKS-S
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGC VNTMAKKS-S
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGC VHTMAKKS-S
+ RQVRNAPEDA L--YNFFTGQ KGTRELIKF- YF-CMEGCGC VNTMAKNS-S
+ RQVRNAPEDA L--YNFFTGQ KGTRELIKF- YF-CMEGCGC VNTMAKNS-S
+ RQVRNAPEDA L--YNFFTGQ KGTKELVKF- YF-CMEGCGC VNTMAKKS-S
+ RQVRNAPEDA L--YNFFTGQ KGTKELIKF- YF-CMEGCGT VNTMAKDS-S
+ RQVRNAPEDA L--YNFFTGQ KGTRELIKF- YF-CMEGCGC VNTMAKNS-S
+ RQVRNAPEDA L--YNFFTGQ KGTRELIKF- YF-CMEGCGC VNTMAKNS-S
+ RQVRNAPEDA L--YNFFTGH KGTRELVKY- YH-CMEGCGC VNTMAKSS-S
+ RQVRNAPEDA L--YNFFTGQ KGTRELVKY- YH-CMEGCGC VNTMAKSS-S
+ RQVRNAPEDA L--YNFFTGQ KGTRELVKY- YH-CMEGCGC VNTMAKSS-S
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKQS-S
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKNS-S
+ RQVRNAPEDA L--YTFFTGQ KGKRELIKY- YF-CMEGCGC VNTMAKNS-S
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKNS-S
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKNS-S
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKNS-S
+ KQVRNDSEDI L--YNHFTGK KGARELIKR- YV-CMEGHDC VNTVANVS-S
+ KQVRNDSEDI L-CYHHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ KQVRNDSEDI L-CYHHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ KQVRNDSEDI L-CYHHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ KQVRNASEDI M--YNHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ KQVRNASEDI M--YNHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ KQVRNASEDI M--YNHFTGN KGACELIKG- YV-CMEGHDC VNTMANIS-S
+ KQVRNASEDI L--YNHFTGK KGARELIKR- YI-CMEGHDC VNTMAHDS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKVS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ KQVRNANEDA L--YQNFSGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YK-CMEGHDC VNTMAKSS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ KQVRNANEDA L--YQNFTGK KGAREKIKR- YL-CMEGHEC VVTMAKNS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHEC VNTMAKNS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHEC VNTMAKNS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGQDC VNTMAKSS-S
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGQDC VNTMAKSS-S
+ KQVRNASEDA H--YTFFAGE KGARELIKR- YS-CMEGDGC VNTMAEGR-S
+ GRIHNAVEGG I--VTNFHGF ---AEMPKN- HD-VMEEQGG PGTCLAPQQS
+ GRIHNAVEGG I--VTNFHGF ---AEMPKN- YD-VMEEQGG PGTCLAPQQS
+ GRIHNAVEGG I--VTNFHGF ---AEMPKN- YD-VMEEQGG PGTCLAPQQS
+ GRIHSAVEGG I--WTNFHGF ---AEMPKN- YD-VMEEQGG PGTCIAPRQS
+ GRIHSAVEGG I--WTNFHGF ---AEMPKN- YD-VMEEQGG PGTCVAPRQS
+
+ ESAMWIFDLW MCKLNHGMQR --------GD IGRVKRDVQK FPKLKEGAPN
+ ESAMWIFDLW MCKLNHGMQR --------GD IGRVKRDVQK FPKLKEGAPN
+ ESAMWIFDLW MCKLNHGMQR --------GD IGRVKQDVQK FPKLKEGAPN
+ ESAMWIFDLW MCKLNHGMQR --------GD IGRVQQDVHK FPKLKEGAPN
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ ESAVVIFDVW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ ESAVWIFDIW MCKLAHGMQW --------GD IGRVSVDHPK FLKLEEGAPR
+ ESAVWIFDIW MYKLSHGMQW --------GD IGRVGVDHPK FLKLEEGAPN
+ ESAVWIFDIW MYKLSHGMQW --------GD IGRVDVDHPK FLKLEEGAPN
+ ESAVWIFDIW MCKLTHGMQD FGD-----GD IGRVVVDHPK FEKLEEGAPN
+ ESAVWIFDIW MCKLTHGMQD FGD-----GD IGRVVCDHPK FEKLEEGAPN
+ ESAVWIFDIC MCKLTHGMQD --------GD IGRVVCDHPK FEKLEEGAPN
+ ESAVWIFDIW MCRLTHGMQD --------GD IGRVECDHPK FAKLEEGAPN
+ ESAVWIFDIW MCRLTHGMQD --------GD IGRVECDHPK FAKLEEGAPN
+ ESAVWIFDIW LCRLTHGMQD --------GD IGRVECDHPK FAKLEEGAPN
+ DSPVWMFDQF MCQLTHSMVD --------GD LGRVVQDNVI FAKLKEGAPH
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVMDNWT FTKLKEGAPH
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVMDNWT FTKLKEGAPH
+ ESPVWMFDKF MCHLTHSMVV --------GD LGRVLRDNTT FAKLKEGAPV
+ ESSAWMFDKV MYQLTHSMVW --------GD LRRVVHDNVT FSKLKEGAPH
+ ESSAWMFDKV MYQLTHSMVW --------GD LRRVVHDNVT FSKLKEGAPH
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ QSSVWMFDRF MYKLTHSMVW --------GD LGRVYWDNLT FQKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVYVDNQT FSKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LRRVFPDNAT FSKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LRRVFPDNAT FSKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LRRVFPDNAH FSKLKEGAPH
+ ESSVWMFDQF MYKLTHSMIW --------GD LGRVFPDNAT FSKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVFPDNCT FSKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVFPDNCT FSKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LARVFHDNGT FAKLKEGAPH
+ ESSVWMFDRF MYRLTHSMVW --------GD LGRVFQDNAT FSKLKEGAPH
+ ESSIWMFDRF MYKLTHSMVW --------GD LGQVFPDVST FSKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVYPDNPT FSKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVYPDNPT FSKLKEGAPH
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVFPDNAT FSKLKEGAPH
+ QSGIWKFNAF MC-LMHLMEG --------GD L--------- ----------
+ QSGIWKFNAF MC-LMHLMEG --------GD L--------- ----------
+ QSGIWKFNAF MC-LMRLMQG --------GD L--------- ----------
+ QSGIWKFNAF MC-LMRLMQG --------GD L--------- ----------
+ QSGIWKFNAF MC-LMRLMQG --------GD L--------- ----------
+ QSGIWKFNAF MC-LMRLMQG --------GD L--------- ----------
+ QSGIWKFNAF MC-LMHLMQG --------GD L--------- ----------
+ QSGIWKFNAF MC-LMHLMQG --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQS --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQS --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQS --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQS --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQL --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQL --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQE --------GD L--------- ----------
+ QSAPWKFNRF MC-LMYLMQD --------GD L--------- ----------
+ QSAPWKFNRF MC-LMYLMQD --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQN --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQN --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQD --------GD L--------- ----------
+ QSAPWKFNHF MC-LMHLMQN --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQN --------GD L--------- ----------
+ QSAPWKFNRF MC-LMHLMQN --------GD L--------- ----------
+ QSAIWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ QSAVWNFDRF MCDLMHLMQN --------GD L--------- ----------
+ QSAVWNFDRF MCDLMHLMQN --------GD L--------- ----------
+ QSAVWNFDRF MCDLMHLMQN --------GD L--------- ----------
+ QSAVWKFDRF MCDLMHLMQD --------GD L--------- ----------
+ QSAVWKFDRF MCDLMHLMQD --------GD L--------- ----------
+ QSAVWKFDRF MCDLMHLMQD --------GD L--------- ----------
+ QSATWKFDRF MCDLMHLMQG --------GD L--------- ----------
+ QSAVWKFDRF MCALMHLMQK --------GD L--------- ----------
+ QSAVWKFDRF MCCLMHLMQN --------GD L--------- ----------
+ QSAVWKFDRF MCALMHLMQN --------GD L--------- ----------
+ QSAVWKFDRF MCALMHLMQN --------GD L--------- ----------
+ QSAVWKFDRF MCALMHLMQV --------GD L--------- ----------
+ QSAVWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ QSAVWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ QSAVWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ ISAMWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ VSAVWKFDQF MCDLMHLMQN --------GD L--------- ----------
+ VSAVWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ QSAVWKFDRF MCDLVHLMQN ---GARGSGD L--------- ----------
+ QSAVWKFDRF MCDLVHLMQN ---GARGSGD L--------- ----------
+ ESAVWKFDPF MCQLTHSMQS --------GD L--------- ----------
+ ADTSWPFVMF TVDLAHRCRG --------GD MPQNTGDSMT CPHLAEGLAA
+ ADTSWPFVMF TVDLAHRCRG --------GD IPQNTGDSMT CPHLAEGLAA
+ ADTSWPFVMF TVDLAHRCRG --------GD IPQNTGDSMT CPHLAEGLAA
+ ADTSWPFMVF TVDLAHRCRG --------GD TPTQAGDSMT FPHLAEGLPA
+ ADTNWPFMVF PVELAHRCRG --------GD TP-------- FPHLAEGLPA
+
+ CSSFVKPYFM GCDMFHKQVE YRGTHGLVLD DTWNEESATF PYPQVHSRSD
+ CSSFVKPYFM GCDMFHKQVE YRGTHGLVLD DTWNEESATF PYPQVHSRSD
+ CSSFVKPYFM GCDMFHKQVE YRGTHGLVLD DTWNEESATF PYPQVHSRSD
+ CSSFVKPVFM GCDMFHRQVQ NRGNHGLVLD DTWNEESGTF PYPQVHSRNE
+ CSSIPMPYFL GVDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ CSSIPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ CSSIPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ CSSIPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ CSSMPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ CSSIPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ CSSCPMPYFL GCEMFHRQVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ CSSLPMPYFL GVDMFHRQVT IKGAKGLVLP DIWNESPMAF PYAQVHSKSH
+ CSSLPMPYFL GVDMFHKQVT LKGAKGLVLP DIWNESPMAF PYAQVHSKSH
+ CSSHPVPYFL GIDMFHKQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ CSSHPMPYFL GVDMFHEQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ CSSIPMPYFL GIDMFHKQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ CSSLPMPYFL GIDMFHNQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ CSSLPMPYFL GIDMFHKQVM GKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ CSSLPMPYFL GIDMFHRQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ CISL--PHFL GIDMFHTQVF VGGH--LILP DPCYELSISV MYAGHASYNQ
+ CIAL--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ CIAL--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ CIAL--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ CIAI--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ CIAL--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ CIAL--PYFM GIDMFHIQVF LGGD--LILP DPCYELSISV MYAGHASYNQ
+ CIAL--PYFM GIDMFHIQVF IGGD--LILP DPCYELSISV MYAGHASYNQ
+ CISL--PYFL GMDMFHQQVF MGGN--LILP DPCYELSISV MYAGHASYNQ
+ CISH--PYFL GIDMFHIQVY SKGF--LTLP DPRYEISMSV MYSQHHSFSM
+ CISH--PYFL GIDMFHIQVY SKGF--LTLP DPRYEISMSV MYSQHHSFSM
+ CISQ--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ CIAV--PNYL NIDMFHIQVF YKGP--LTLP DPHYELSMSV MYAQHHSFSQ
+ CISA--PYYL NIDMFHIQVF YKGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ VISH--PYFL GIDMFHDQVV YRGP--LTLP DPRYELSMSV MYAQHHSFSQ
+ VISH--PYFL GIDMFHEQVV YRGP--LTLP DPRYELSMSV MYAQHHSFSQ
+ VISH--PYFL GIDMFHDQVV YRGP--LTLP DPRYELSMSV MYAQHHSFSQ
+ VISH--PYFL GIDMFHAQVF YRGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ VISH--PYFL GIDMFHGQVV YRGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ VISH--PYFL GIDMFHGQVV YRGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ VISV--PYFL GIDMFHGQVF LRGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ VISH--PYFL GIDMFHGQVF YRGS--LTLP DPRYELSMSV MYAQHHSMSQ
+ VISQ--PYFL GIDMFHDQVF YRGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ VISH--PYFL GIDMFHDQVF YRGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ VISH--PYFL GIDMFHDQVF YRGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ VISV--PYFL GIDMFHDQVF YRGS--LTLP DPRYEMSMSV MYAQHHSFSQ
+ -CSY--PSFL GMCMFHAMVQ SKGD--LVLP DSPNEDSVSF MYIQHHSFHE
+ -CSY--PSFL GMCMFHAMVQ SKGD--LVLP DSPNEDSVSF MYIQHHSFHE
+ -CSY--PSFL GMCMFYAMVQ SKGD--LVLP DSCNEDSVSF MYIQHHSFHE
+ -CSY--PSFL GMCMFYAMVQ SKGD--LVLP DSCNEDSVSF MYIQHHSFHE
+ -CSY--PSFL GMCMFYAMVQ SKGD--LVLP DSCNEDSVSF MYIQHHSFHE
+ -CSH--PSFL GMCMFYAMVQ SKGD--LVLP DSCNEDSVSF MYIQHHSFHE
+ -CSH--PSFL GMCMFHAMVK SKGN--LVLP DSCNEDSVSF MYIQHHSFHE
+ -CSH--PSFL GMCMFHAMVQ SKGN--LVLP DSCNEDSVSF MYIQHHSFHE
+ -CNS--PSFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNC--PSFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNS--PPFL GMCMFHPQVQ MKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNS--PSFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNP--PSFL GMCMFHPQVR SKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNP--PSFL GMCMFHPQVR SKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNS--PGFL GMCMFHPQVQ RKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNS--PGFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNS--PGFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNL--PSFL GMCMFHNQVQ CKGE--LVLP DNVNENSVEF MYRRHHSLSD
+ -CNS--PSFL GMCMFHNQVP NKGA--LVLP DNVNENSVEF MYRRHHSLSD
+ -CNS--PSFL GMCMFHNQVS FKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNS--PSFL GMCMFHNQVS VKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNS--PSFL GMCMFVNQVS FKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ -CNS--PSFL GMCMFHVQVQ FKGE--LVLP DHPNENSVEF MYRRHHSLSD
+ -CSY--PSFL PMCMFVPQVL SKGE--LVLP DSSNEESISF VYLQHHSFSV
+ -CSY--PSFL PMCMFVSQVL SKGE--LVLP DSSNEESISF VYLQHHSFSD
+ -CSV--PSFL PMCMFVSQVL HKGE--LVLP DSSNEESISF VYLQHHSFSD
+ -CSV--PSFL PMCMFVSQVL HKGE--LVLP DSSNEESISF VYLQHHSFSE
+ -CSY--PSFL PMCMFVAQVI AKGE--LVLP DSSTEESISF MYLQHHSFSD
+ -CSY--PSFL PMCMFVAQVI AKGE--LVLP DSSTEESISF MYLQHHSFSD
+ -CSY--PSFL PMCMFVAQVI AKGE--LVLP DSSNEESISF MYLQHHSFSD
+ -CSY--PSFL PVCMFVAQVI NKGE--LVLP DSSNEESISF MYLQHHSFSE
+ -CSH--PSFL GMCMFHEQVR CKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ -CSH--PSFL GMCMFVEQVR CKGE--LVLP DSPNEESLSF VYIQHHSFSD
+ -CSH--PSFL GMCMFHEQVR RKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ -CSH--PSFL GMCMFHEQVR RKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ -CSH--PSFL GMCMFHEQVR RKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ -CSH--PSFL GMCMFHEQVR CKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ -CSV--PSFL GMCMFHEQVR CKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ -CSV--PSFL GMCMFHEQVR CKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ -CSF--PSFL GMCMFHDQVR CKGE--LVLP DSKNEESVSF VYIQHHSFSD
+ -CSF--PSFL GMCMFHEQVR CKGE--LVLS DSKNEESVSF VYIQHPSFSD
+ -CSF--PSFL GMCMFHQQVR CKGE--LVLP DSKNEESVSF VYIQHHSFND
+ -CSF--PSFL GMCMFHEQVR CKGE--LVLP DSKNEESVSF VYIQHHSFSD
+ -CSF--PSFL GMCMFHEQVR CKGE--LVLP DSKNEESVSF VYIQHHSFSD
+ -CSV--PSFL GVCMFQRQVV MKGE--LVLP DSADEGSVSF MYIQHHSFAA
+ VNS---RAFI GVSIYDLKVS HKMI--QACN PIQN------ ---DNHAFSD
+ VNS---RAFI GVSTYDLKVS HKMI--QACN PIQN------ ---DNHAFSD
+ VNS---RAFI GVSTYDLKVS HKMI--QACN PIQN------ ---DNHAFSD
+ VNS---RAFV GVSSYDLRVS HKMI--QACT LIQN------ ---DNVAFSD
+ VNS---RAFI GVSSYDLKVS HKMI--QACN PIQN------ ---DNVAFSD
+
+ KRCLNGLHQG DHEESVH--- HAPRI----M R---LIGH-H LVIIVLMNHD
+ KRCLNGLHQG DHEESVH--- HAPRI----M R---LIGH-H LVIIVLMNHD
+ KRCLNGLHQG DHEESVH--- HAPRI----M R---LIGH-H LVIIVLMNHD
+ KRCINKLHQG DHNESCH--- HNPRI----V R---RIGH-H LVIIVLVNRD
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGL-N LVIISYANVD
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ KRCLNVLVQG DHDESRH--- HNARI----V A---RIGM-N MVIIRYLNVE
+ KRCLNVLVQG DHEESEH--- HNARI----M S---KIGT-H LVIINIINVE
+ KRCLNVLVQG DHEESEH--- HNARI----M S---RIGT-H LVIVNVINVE
+ RRVLNVLHQG DVEES-H--- HSARC----V R---RIGF-H LVIIVFWNVE
+ RRVLNVLHQG DVEES-H--- HSARC----V R---RIGF-H LVIIVYWNVE
+ RRVLNVLHQG DHEES-H--- VSARC----M R---RIGF-H LVIINFWNVE
+ RRVLNVLHQG DHEES-H--- HSARC----M R---RIGY-H RVIINYWNVE
+ RRVLNVLHQG DHEES-H--- HSARC----M R---RIGYGH LVIINFWNVE
+ RRVLNVLHQG DHEES-H--- HSARC----M R---RIGY-V LVIINFWNVE
+ KRCINNLDQG DQEDSNHRKE HKIRASVLLY R---QIGI-L -VIIKEANEL
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ KRCINGLDNG DRQDSDPQKE HKIRNSVLLY R---QIGL-L -VIIKEANEI
+ KRCLNNLDQG DREDSSHRKE HKIRRSVLLY Q---QIGC-L -VITRERNEL
+ KRCLNGLDHG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKDANSM
+ KRCLNGLDHG DREESPHQIE HKMRKSVLIY S---PIGY-L -VIIKDANSM
+ KRCLNGLDVG DREESPHHID HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ KRCLNALDHG DREESPHQIE HKMRKSVLLY N---PIGY-L -VIIKNANSM
+ KRCLNALDYG DREESPHQIE HKMRKSVLLY Y---TIGW-L -VIIKNADSM
+ KRCLNALDHG DTQESPHGIE HNMRNSVLLY N---PIGF-L -VIIKNINSM
+ KRCLNALDHG DTQESPHGIE HNMRNSVLLY N---PIGF-L -VIIKNINSM
+ KRCLNALDHG DTQESPHGIE HNMRNSVLLY N---PIGF-L -VIIKNINSM
+ KRCLNPLDHG DRQESSHGIE HNMRSSVLLY N---PIGF-L -VIIDNINPM
+ KRCLNPLDHG DRQESPHGIE HNMRSSVLLY N---PIGF-L -VIIDNINPM
+ KRCLNPLDHG DRQESPHGIE HNMRSSVLLY N---PIGF-L -VIIDNINPM
+ KRCLNHLDHG DRQESPHGIE HNMRKSVLLY N---PQGY-L -VIIKNVNSM
+ KRCLNTLDHG DRQESPHGIE HNMRKSVLLY D---PIGY-L -VIIKNVNSM
+ KRCLNALDHG DRQESPHGIE HNMRKSVLLD S---PIGY-L -VIIKNINSM
+ KRCLNALDHG DRQESPHGIE HNMRKSVLLD S---SIGY-I -VIIKNLNSM
+ KRCLNALDHG DRQESPHGIE HNMRKSVLLD S---PIGY-I -VIIKNVNSM
+ KRCLNALDYG DRQESPHGIE HNMRKNVLLD N---PIGH-L -VIIKNENSM
+ KRCLNPLNVG DREDSEHIKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ KRCLNPLNVG DREDSDHVKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ KRCLNPLNVG DREDSDHTKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ KRCLNPLNVG DREDSDHTKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ KRCLNPLNVG DREDSDHTKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ KRCLNPLNVG DREDSDHTKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ KRCLNHLNVG DREDSEHIKE KHMRV----Y A---SIGG-H -IIIREWNDV
+ KRCLNHLNVG DREDSEHIKE KHMRI----Y A---SIGG-H -IIIREWNEV
+ KRCLNLLYVG DSQDSQHLRE KQLRI----Y G---RIGK-V -VIIKVWNAV
+ KRCLNLLFVG DSQDSQHQRE KQLRI----Y G---RIGK-V -VIIKVWNAA
+ KRCLNLLYVG DSQDSQHLRE KQLRI----Y G---RIGK-V -VIIKVWNAV
+ KRCLNLLYVG DSQDSQHLRE KQLRI----Y G---RIGK-V -VIIKVWNAV
+ KRCLNLLYTG DSQDSQHLRE KQLRI----Y G---RIGR-V -VILQVWNAV
+ KRCLNLLYVG DSQDSQHLRE KQLRI----Y G---RIGR-V -VILQVWNAV
+ KRCLNLLYVG DNQDSQHLRE KQLRM----Y G---EIGK-V -VIIKVVNAV
+ KRCLNLLYVG DNQDSQHLRE KQLRM----Y G---EIGK-V -VIIKVVNAV
+ KRCLNLLYVG DNQDSQHLRE KQLRM----Y G---EIGK-V -VIIKVVNAV
+ KRCLNLLYVG DNQDSQHLRE KQLRI----Y Q---NIGK-V -VIIKVWNAN
+ KRCLNLLYVG DNQDSQHLRE KQLRI----Y P---SIGK-V -VIIKVWNAA
+ KRCLNLLYVG DEQDSSHLRE KQLRL----Y A---RIGK-V -VIIKVWNAV
+ KRCLNLLYVG DNQDSSHLRE KQLRL----Y A---RIGK-V -VIIKVWNAV
+ KRCLNLLYVG DNQDSSHLRE KQLRL----Y A---RIGK-V -VIIKVWNAV
+ KRCLNLLYVG DNQDSQHLRE KQLRI----Y A---RIGK-V -VIIKVWNAV
+ KRCLNYLNVG DSADSKHLKE KHLRA----E GMPGNIGK-H -VIINVWNAV
+ KRCLNYLNVG DNSDSKHLKE KHLRA----Q GMPGNIGK-H -VIINVWNAV
+ KRCLNYLNVG DNADSKHLKE KHLRA----Q GMPGNIGK-H -VIINVWNAV
+ KRCLNYLNVG DNADSRHLKE KHLRA----Q GMPGNIGK-H -VIISVWNAV
+ KRCLNYLNVG DNEDSKHAKE KFLRG----D G---GIGQ-H -VIINVWNAV
+ KRCLNYLNVG DNEDSKHAKE KFLRG----D G---GIGQ-H -VIINVWNAV
+ KRCLNCLNVG DNEDSKHLKE KFLRA----D G---GIGQ-H -VIINMWNAV
+ KRCLNYLNVG DNEDSKHLKE KFLRA----D G---NIGQ-H -VIINMWNAV
+ KRCLNCLNVG DNDDSEHLKE KHLRI----Y G---QIGH-H -VIINVWNAF
+ KRCLNCLNVG DNDDSEHLKE KHLRI----Y G---QIGR-H -VIINVWNAF
+ KRCLNCLNVG DNDDSEHLKE KHLRI----Y G---QIGR-H -VIINVWNAF
+ KRCLNCLNAG DNDDSEHLKE KHLRT----Y G---QIGR-H -VIINVWNAF
+ KRCLNCLNVG DNDDSEHLKE KHLRV----Y G---QIGR-H -VIINVWNAF
+ KRCLNYLNVG DNDDSEHLKE KHLRI----Y G---VIGK-H -VIINVWNAF
+ KRCLNYLNVG DNDDSEHLKE KHLRI----Y G---EIGK-H -VIINVWNAF
+ KRCLNYLNVG DNDDSEHIKE KHLRI----Y G---EIGK-H -VIINVWNAF
+ KRCLNYLNVG DNEDSEHLKE KHLRV----Y G---NIGK-H -VIINSWNAM
+ KRCLNYLNVG DNEDSEHLKE KVLRV----Y G---DIGK-H -VIINVWNAM
+ KRCLNYLNVG DNEDSEHLEE KHLRV----Y G---NIGK-H -VIINVWNAM
+ KRCLNELNVG DNEDSIHLKE KHLRI----Y G---NIGK-V -VIINVWNAM
+ KRCLNSLNVG DNEDSIHLKE KHLRI----Y G---DIGK-H -VIINVWNAM
+ KRCLNVLNVG DNEDSVHLRH KQLRV----Y G---KIGK-H -VIISVPNAI
+ QRCLNDLSQG VVGASFPKMQ HGVRH----Y K---K----- ---RVYENEV
+ QRCLNDLAQG VVGASHPKMQ HGVRH----Y K---K----- ---RVYENEV
+ QRCLNDLAQG VVGASHPKMQ HGVRH----Y K---K----- ---RVYENEV
+ QRPLNDLNQG CVGTSHPKMP HGVRH----Y K---K----- ---KVYENEV
+ QRVLNDLSQG CVGTSHPKMP HGVRH----Y K---K----- ---RVYENEV
+
+ MGRLNHLEPD AVIPSPLRIG GDGWVPKPI- ---------- -------EDG
+ MGRLNHLEPD AVIPSPLRIG GDGWVPKPI- ---------- -------EDG
+ MGRLNHLEPD AVIPSPLRIG GDGWVPKPI- ---------- -------EDG
+ MGRLNYIEPD ALVPSPLRFG GDEWVPKPI- ---------- -------EDG
+ MGRLNHCEDE AIVFSPLRYG GAGFVSKPI- ---------- -------GDG
+ MGRLNHCEDQ AIVYSPLRYG GAGFVSKPI- ---------- -------ADG
+ MGRLNHCEDQ AIVYSPLRYG GAGFVSKPI- ---------- -------ADG
+ MGRLNHCEDE AIVFSPLRYG GAGFVSKPI- ---------- -------ADG
+ MGRLNHCEDE AIVFSPLRYG GAGFVSKPI- ---------- -------ADG
+ MGRLNHCEDE AIVFSPLRYG GAGFVSKPI- ---------- -------ADG
+ MGRLNHCEDD AMVYSPLRIG GAGTHSKPI- ---------- -------ADG
+ MQRLNHCEDK AIVYSPDRIG GAGFHSKPI- ---------- -------ADG
+ MQRLNHCEDK AIVYSPDRIG GAGFHSKPI- ---------- -------ADG
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPV- ---------- -------DDG
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPV- ---------- -------DDG
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPI- ---------- -------NDG
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPI- ---------- -------ADG
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPI- ---------- -------ADG
+ MGRLIHCEDE AIIYSPLRIG GAGFHSKPI- ---------- -------ADG
+ MNRLNHKEPE NGIIFPLR-- -DAQDPKQI- ---------- -------LNG
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ MGRLNHKERK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ MGRLNHKERK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ MGRLNHKEPR DGVIFPHR-- -GAQGPKQL- ---------- -------ANG
+ MGRLNHHESR AVVAFPLR-- -GAEGPKQV- ---------- -------MEG
+ MGRLNHHESR AIVAFPLR-- -GAEGPKQV- ---------- -------MEG
+ MGRLNHHESR LIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ MGRLNHYESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ MGRLNHHESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ MGRLNHHESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ MGRLNHHESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ MGRLNHHESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ MGRLNHHESC AIVMFPLR-- -GAEGPKQI- ---------- -------IEG
+ MGRLNHHESC AMVMFPLR-- -GAEGPKQI- ---------- -------MEG
+ MGRLNHHESR AVVGFPLR-- -GAENPKQI- ---------- -------MEG
+ MGRLNHHESR AVVGFPLR-- -GAENPKQI- ---------- -------MEG
+ MGRLNHYESR AVVGFPLR-- -GAENPKQI- ---------- -------MEG
+ MGRLNHHESR AIVTFPLR-- -GAEHPKQI- ---------- -------VEG
+ MGRLNHHESR AIVTFPLR-- -GAEHPKQI- ---------- -------MEG
+ MGRLNHHESR AIVTFPLR-- -GAEHPKQI- ---------- -------MEG
+ MGRLNHHESR AVVTFPLR-- -GADNPRQI- ---------- -------MEG
+ MGRLNHHESR AKVTFPLR-- -GADNPRQI- ---------- -------MEG
+ MGRLNHHESR AVFAFPLR-- -GAENPKQI- ---------- -------MEG
+ MGRLNHHESR AVVTFPLR-- -GAEDPKQI- ---------- -------MEG
+ MGRLNHHESR AVVTFPLR-- -GAEDPKQI- ---------- -------MEG
+ MGRLNHHESR AVVTFPLR-- -GAEDPKQK- ---------- -------MEG
+ MGRLNHIEPG AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ MGRLNHIEPG AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ MGRLNVIEPE AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ MGRLNVIEPE AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ MGRLNVIEPE AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ MGRLNVIEPE AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ MGRLNHIEPG AEVTFPLRR- -RGQASKPV- ---------- -------IDG
+ MGRLNHIEVG AEVTFPLRR- -RGQASKPV- ---------- -------IDG
+ MGRLNHHEPP AEVMFPLRK- -GGQDSKPF- ---------- -------IDG
+ MGRLNHVEPP AEVMFPLRR- -GGSDSKPF- ---------- -------LDG
+ MGRLNHHEPP AEVMFPLRR- -GGSDSKPF- ---------- -------IDG
+ MGRLNHHEPP AEVMFPLRR- -GGSCSKPF- ---------- -------VDG
+ MGRLNHHEPP AEVMFPLRK- -GGSNSKPV- ---------- -------YDG
+ MGRLNHHEPP AEVMFPLRK- -GGSNSKAV- ---------- -------YDG
+ MGRLNHVEPS AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ MGRLNHHEPS AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ MGRLNHHEPS AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ MGRLNHHEPP AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ MGRLNHHEPP AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ MGRLNHHEPP AAVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ MGRLNHHEPP AEVMFPLRK- -CGSDSKPF- ---------- -------IDG
+ MGRLNHHEPP AEVVFPLRK- -GGSDSKPF- ---------- -------IDG
+ MGRLNHHEPP AEVVFPLRK- -GGSDSKPF- ---------- -------IDG
+ MGRLNHHEPP AEVVFPLRQ- -GGPDSKPM- ---------- -------IDG
+ MGRLNHHESP AEVVFPLRQ- -GGPDSKPM- ---------- -------IDG
+ MGRLNHHEPP AEVVFPLRQ- -GGPDSKPM- ---------- -------IDG
+ MGRLNHHEPP AEVVFPLRQ- -GGPDSKPM- ---------- -------MDG
+ MGRLNHHEPP PEVVFPLRQ- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPP PEVVFPLRQ- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPP PEVVYPLRQ- -GGPNSKPM- ---------- -------VDG
+ MGRLNHHEPP AEVNFPLRQ- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPP AEVVYPLRK- -GGPDSK-M- ---------- -------VDG
+ MGRLNHHEPP AEVVYPLRK- -GGPDSKPV- ---------- -------VDG
+ MGRLNHHEPP AEAVYPLRK- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPP AEVVYPLRK- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPP AEVVYPLRK- -GGPDSKLM- ---------- -------VDG
+ MGRLNHHEPP ADVEYPLRK- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPP AEVMYPLRK- -GGPESKPM- ---------- -------VDG
+ MGRLNHHEPP AEVMYPLRK- -GGPESKPM- ---------- -------VDG
+ MGRLNHHEPA AEVVYPLRK- -GGPESKPM- ---------- -------VDG
+ MGRLNHHEPA AEVVCPLRK- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPA AEVVCPLRK- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPA AEVVYPLRK- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPA AEVVYPLRK- -GGPDSKPM- ---------- -------VDG
+ MGRLNHHEPS AIVVFPLRQ- -RGADSKSV- ---------- -------GDG
+ GGRLDDAEAI DDMGVWIRW- -EGVKHAWCH PIGSCPDHLV CSLLVLQPAR
+ GGRLDDAEAI DDMGVWIRW- -EGVKHAWCH PIGSCPDHLV CSLLVLQPAR
+ GGRLDDAEAI DDMGVWIRW- -EGVKHAWCH PIGSCPDHLV CSLLVLQPAR
+ GDRLDDAEGI DDVGVWMRW- -NGVKHAWCH IIGSCPDHLV CSLLVLQPGR
+ GDRLDDAEAV DDVGVWMRW- -AGVKVAVCH VIGSCPDHLV VSLLVLQPAR
+
+ FFDK-D-Q-- ----SRPDVA NASIVPDK-- --DQWVGAHN QWGSSLRKVG
+ FFDK-D-Q-- ----SRPDVA NASIVPDK-- --DQWVGAHN QWGSSLRKVG
+ FFDK-D-Q-- ----ARPDVA NASIVPDK-- --DQWVGAHN QWGSSLRKVG
+ FFDK-D-Q-- ----ARPDVA NA-IVPDR-- --DQWVGAHK EWGSSLCKVG
+ FFDK-D-Q-- ----ARPLMA NAVCVPEN-- --DQWTGAVG QWCSSVVKCG
+ FFDK-D-Q-- ----ARPLMA NAVCVPEN-- --DQWTGAVG QWCSSVVKCG
+ FFDK-D-Q-- ----ARPLMA NAVCVPEN-- --DQWTGAVG QWCSSVVKCG
+ FFDK-D-Q-- ----ARPLMA NAHCVPEN-- --DQWTGAVG QWCSSVVKCG
+ FFDK-D-Q-- ----ARPLMA NAHCVPEN-- --DQWTGAVG QWCSSVVKCG
+ FFDK-D-Q-- ----ARPLMA NAHCVPEN-- --DQWTGAVG QWCSSVVKCG
+ FFDK-D-Q-- ----ARPLIA NAHIVPEN-- --DQWTGAVA QWCSSVIKCG
+ FFDK-D-Q-- ----ARPIIA NAHIVPVN-- --DQWTGPMA QWCSSVIKCG
+ FFDK-D-Q-- ----ARPIIA NAHIVPIY-- --DQWTGPMA QWCSSVIKCG
+ FFDK-D-Q-- ----ARPVIA SAHIVPEH-- --DQWSGAMA QWCSSVIKCG
+ FFDK-D-Q-- ----ARPVIA SAHIVPEH-- --DQWSGAMA QWCSSVIKCG
+ FFDK-D-Q-- ----ARPVIA NAHIVPEH-- --DQWSGAMA QWCSSVIKCG
+ FFDK-D-Q-- ----ARPVIA NAHIVPEY-- --DQWSGAMA QWCSSVIKCG
+ FFDK-D-Q-- ----ARPVIA NAHIVPEY-- --DQWSGAMA QWCSSVIKCG
+ FFDK-D-Q-- ----ARPVIA NAHIVPEY-- --DQWSGAMP QWVSSVIKCG
+ LFDK-E-E-- ----NRPMVQ DADSVVGS-- --AQWAGQHR SWCSSDDKA-
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ LFEK-E-E-- ----NRPMVQ DAGSVPER-- --AQWPGQQR AWCSSDDKA-
+ LFDK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ LFDK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ LFDK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ LFDK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ HFDK-E-E-- ----ARPIVQ DAASVPGK-- --AQWVGRVR AWCSSDVKA-
+ HFDK-E-E-- ----ARPIVQ DAASVPGK-- --AQWVGRVR AWCSSDVKA-
+ HFDK-E-E-- ----ARPIVQ DAASVPEK-- --AQWVGRVR AWCSSDVKA-
+ HFDK-E-E-- ----ARPIVK DAASVPGK-- --AQWVGRIR AWCSSDVKA-
+ HFDK-E-E-- ----ARPIVQ DAASVPGE-- --AQWVGHIR AWCSSDIKA-
+ HFDK-E-E-- ----ARPIVQ DAASVPGE-- --AQWVGHIR AWCSSDIKA-
+ HFDK-E-E-- ----ARPVVQ DAPGVPGK-- --AQWVGKVR AWCSSDVKA-
+ HFDK-E-E-- ----ARPVVQ DAPGVPEQ-- --AQWVGKMR AWCSSDVKA-
+ HFDK-EKE-- ----ARPVVQ DAPGVPGK-- --AQWVGRIR AWCSSDVKA-
+ HFDK-E-E-- ----ARPVVQ DAPGVPGK-- --AQWVGRVR AWCSSEIKT-
+ HFDK-E-E-- ----ARPVVQ DAPGVPGK-- --AQWVGRVR AWCSSEIKT-
+ SFDK-E-E-- ----ARPVVQ DAPGVPGR-- --AQWVGRVR PWCSSDVKA-
+ FFAK-D-E-- ----DRPGIQ NAVSVPCG-- --DQWVGSIR GWCSSQHRYG
+ FFAK-D-E-- ----DRPGIQ NAMSVPCG-- --DQWVGSIR GWCSSQHRYG
+ FFAK-D-E-- ----ERPGIQ NAMNVPCG-- --DQWVGSIR GWCSSQHRYG
+ FFAK-D-E-- ----ERPGIQ NAMNVPCG-- --DQWVGSIR GWCSSQHRYG
+ FFAK-D-E-- ----ERPGIQ NAMNVPCG-- --DQWVGSIR GWCSSQHRYG
+ FFAK-D-E-- ----ERPGIQ NAMNVPCG-- --DQWVGSIR GWCSSQHRYG
+ FFAK-D-E-- ----DRPGIQ NAMSVPCG-- --DQWVGSVR GWCSSQHRYG
+ FFAK-D-E-- ----DRPGIQ NAMSVPCG-- --EQWVGSVR GWCSSQHRYG
+ FF-------- ----DRPGIA NAMSVKCG-- --DQWVGSIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ FF-------- ----DRPAIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGSIK GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGSIK GWCSSQHQYG
+ FF-------- ----DRPGIA NAMNVPCG-- --DQWVGCIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGCIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGIIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGVIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGVIR GWCSSQHQYG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGVIR GWCSSQHQYG
+ FFDK-D-D-- ----DRPGIA NAMSVPCG-- --EQWGGPTR GWCSSQQKFG
+ FFDK-D-D-- ----DRPGIA NAMSVPCG-- --EQWGGPTR GWCSSQQKFG
+ FFDK-D-D-- ----DRPGIA NAMSVPCG-- --EQWGGPTR GWCSSQQKFG
+ FFDK-D-D-- ----DRPGIA NAMSVPCG-- --EQWGGPTR GWCSSQQKFG
+ FFDK-D-D-- ----DRPGIA NAMNVPCG-- --DQWGGPIR GWCSSQHKFG
+ FFDK-D-D-- ----DRPGIA NAMNVPCG-- --DQWGGPIR GWCSSQHKFG
+ FFDK-D-D-- ----DRPGIA NAMNVPCG-- --DQWGGPIR GWCSSQHRFG
+ FFDK-D-D-- ----DSPGIA NAMNVPCG-- --DQWGGPIR GWCSSQHKFG
+ FFDK-E-D-- ----DRPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVNFG
+ FFDK-E-D-- ----DRPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVKFG
+ FFDK-E-D-- ----DRPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVKFG
+ FFDK-E-D-- ----HRPGIA NAVSVPCA-- --DQVGGPLR GWCSSQVKFG
+ FFDK-E-D-- ----ERPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVKFG
+ FFDK-E-D-- ----DRPGIA NAVSVPCG-- --DQVGGPIR GWCSSQVKFG
+ FFDK-E-D-- ----DRPGIA NAVSVPCT-- --DQVGGPIR GWCSSQVKFG
+ FFDK-E-D-- ----DRPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVKFG
+ FFDK-E-D-- ----DRPGIA NAVSVPCD-- --DQWGGPVR GWCSSQHKFG
+ FFDK-E-D-- ----DRPGVA NAVSVPCD-- --DQWGGPVR GWCSSQHKFG
+ FFDK-E-D-- ----DRPGVA NAMSVPCD-- --DQWGGPVR GWCSSQHKFG
+ FFDK-E-D-- ----DRPGIA NAVAVPCS-- --DQWGGPVR GWCSSQHKFG
+ FFDK-E-D-- ----DRPGIA NAVAVPCS-- --DQWGGPVR GWCSSQHKFG
+ FYDK-D-E-- ----DRPGIA NAVSVPVA-- --EQWVGSVR GWYSSEHKYG
+ NFIQLS-MVR DTPHRLPKMA SAAPVYKQTC HLEQVQGTAR MWGKSGPRVV
+ NFIQLS-MVR DTPHGLPKMA SAAPVYKQTC HLEQVQGTAR MWGKSGPRVV
+ NFIQLS-MVR DTPHGLPKMA SAAPVYKQTC HLEQVQGTAR MWGKSGPRVV
+ NFIQLS-VVH DTPHRLPKMA SAAAVFKQTC HLEQVPGTAR MWGKSGPRVR
+ NFIQLS-VVH DTPHRLPKMA SAAAVFKQTC HLEQVAGTAR VWGKSGPRVK
+
+ LAVHDLR-NI SDLYRCVWMD CHLGANHYRQ ISRMKMITPT YTHMTEYANG
+ LAVHDLR-NI SDLYRCVWMD CHLGANHYRQ ISRMKMITPT YTHMTEYANG
+ LAVHDLR-NI SDLYRCVWMD CHLGANHYRQ ISRMKMITPT YTHMTEYANG
+ LAVHDLR-NV SDLYRCVWME CVLGANHYQQ VSRMKMVTPA YTHMTEYANG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ LADHPLE-NI SRLLRCVVME CILGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ LANHDLE-NI SRLLRCVVME CVLGANVYHQ ASRMKMHGPY YAHVTEYAHG
+ LANHELE-DV SRLLRCVGME CNLGANHYHQ VSRMKMHGPI YSHMTEYAVG
+ LANHELK-VV SRLLRCVGME CNLGANHYHQ VSRMKMHGPI YSHMTEYAHG
+ LANHDLE-NV SRLLRCVMID CNQGANHYIQ ISRMKVHGPT YSHMTEYAHG
+ LANHDLE-NV SRLLRCVMID CNQGANHYIQ ISRMKVHGPT YSHMTEYAHG
+ LANHDLE-NV SRLLRCVEID CNQGANHYVQ ISRMKMYGPT YSHMTEYAHG
+ LANHDLE-NV SRLLRCVVID CNHGANHYVQ ISRMKMHGPT YSHMTEYAHG
+ LANHDLE-NV SRLLRCVVID CNHGANHYVQ ISRMKMHGPT YSHMTEYAHG
+ LANHDLE-NV SRLLRCVVID VNQGANHYVQ ISRMKMHGPT YSHMTEYAHG
+ ---------- SQLPRNTHIV VEIGANVYEQ FSRMKTNIPI YAHVTEYAVG
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTVIPI YARVTEYAVG
+ ---------- SQLPRNTRIV AEVGANVYEQ YSRMKTVIPI YARVTEYAVG
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ ---------- SKLPRNTKMV AEIGANVYEQ ASRMKTNIPI YAHVTEYALG
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ ---------- SHLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ ---------- SRLPRNDPVV HEVGANVYQQ ISRMKTSIPI YAHVTEYAVG
+ ---------- SQLPTNDPIV PEVGANVYQQ VSRMKTSIPI YAHVTEYAVG
+ ---------- SKLPRNDPIV PEVGANVYQQ LSRMKTNIPI YAHVTEYAVG
+ ---------- SKLPRNDPIV PEVGANVYQQ LSRMKTNIPI YAHVTEYAVG
+ ---------- SKLPRNDPIV PEVGANVYQQ ISRMKTNIPI YAHVTEYAVG
+ ---------- SQLPRNDPIV PEVGANVYQQ DSRMKTNIPI YAHVTEYACG
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI YAHTTEYACG
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI YAHTTEYACG
+ ---------- SQLPRNDTIV PEVGANVYQQ VSRVKTHIPI YAHVTEYAVG
+ ---------- SQLPRNDTIV PEVGANVYQQ VSRVKTNIPI YAHVTEYAVG
+ ---------- SELPRNDAIV PEVGANVYQQ VSRMKTNIPI YAHATEYAVG
+ ---------- SELPRNDAIV VEVGANVYQQ ISRMKTDIPI YAHATEYAVG
+ ---------- SELPRNDAIV PEVGANVYQQ ISRMKTDIPI YAHATEYAVG
+ ---------- SELPRNDAIW PEVGANVYQQ ISRMKTNIPI YPHVTEYAVG
+ LANHILVHEP SKLHKTYRIN RKVGANAYDQ DSRMKAAAPV YPHIMEYAHG
+ LANHILVHEP SKLHKTYRIN RKVGANAYDQ DSRMKAAAPV YPHIMEYAHG
+ LANHILVHEP SKLHKTYKIN RKVGANAYDQ VSRMKAAAPV YPHIMEYAHG
+ LANHILVHEP SKLHKTYKIN RKVGANAYDQ VSRMKAAAPV YPHIMEYAHG
+ LANHILVHEP SKLHKTYKIN RKVGANAYDQ VSRMKAAAPV YPHIMEYAHG
+ LANHILVHEP SKLHKTYKVV RKVGANAYDQ VSRMKAAAPV YPHIMEYAHG
+ LAIHILVHQQ SRLHKTYNID RKNGANAYEQ DSRMKAGAPV YPHIMEYAHG
+ LAIHILVHQQ SRLHKTYNID RKNGANAYDQ DSRMKAGAPV YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ LANHILIHGP SKLHRTYAIN KKMGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ LANHILVHNP SRLHRTYAIN KKMGANVYQQ SSRMKAAAPL YPHIMEYAHG
+ LANHILIHNP SRLHRTYAIN KKMGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN RKVGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN RKVGANVYQQ MSRMKAAAPL YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ ISRMKALAPL YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ ISRMKALAPL YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ ISRMKALAPL YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ TSRMKAAAPI YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN RKMGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ DSRMKAAAPL YPHIMEYAHG
+ LANHVLVHGP SKLHRTYAIN KKMGANVYQQ DSRMKAAAPL YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ DSRMKAAAPL YPHIMEYAHG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ DSRMKAAAPL YPHIMEYAHG
+ LASHTLSHDP SSLHRTFAIN RKMGANVYQQ TSRMKASAPF YPHCMEYAHG
+ LASHTLSHDP SNLHRTFAIN RKMGANVYQQ ASRMKASAPF YHHCMEYAHG
+ LASHTLSHNP SNLHRTFAIN RKMGANVYQQ TSRMKASAPF YHHCMEYAHG
+ LASHTLSHTP SNLHRTFAIN RKMGANVYQQ TSRMKASAPF YHHCMEYAHG
+ LAFHTLSHDP SKLHRTFAIN QKMGANVYQQ MSRMKTPAPF YPHVMEYAHG
+ LAFHTLSHDP SKLHRTFAIN QKMGANVYQQ MSRMKTPAPF YPHVMEYAHG
+ LAFHTLKHDP SKLHRTFAIN EKMGANVYQQ NSRMKASAPF YPHVMEYAHG
+ LASHTLSHDP SKLHRTFGIN KNMGANVYQQ TSRMKANAPF YPHVMEYAHG
+ LANHTLVQ-P SKLHRTFKIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ LANHTLVQ-P SKLHRTFKIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ LANHTLVQ-P SKLHRTFKIN KKMGANVYHQ TSRMKAEAPV YPHIMEYAHG
+ LANHTLVQ-P SKLHRTFKIN KKIGANVYQQ TSRMKADAPV YPHIMEYAHG
+ LANHTLVQ-P SKLHRTFKIN KKIGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ LANHTLAQNP SKLHRTFKIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ LANHTLVHNP SKLHRTFAIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ LANHTLVHNP SKLHRTFAIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ LADHTLIHIP SKLHRTFAIN KKMGANVYQQ TSRMKAAAPV YSHVMEYAHK
+ LADHTLVHIP SKLHRTFAIT KKMGANVYQQ TSRMKATAPV YPHVMEYAHG
+ LADHTLVHVP SKLHRTFPIN KKMGANVYQQ TSRMKATAPV YPHVMEYAHG
+ LADHTLVHVP SLLHRTFAIN RKMGANVYQQ TSRMKAAAPV YPHMMEYAHG
+ LADHTLVHVP SLLHRTFAIN KKMGANVYQQ TSRMKAAAPV YPHMMEYAHG
+ LANHILI-GP SKLHRTYQTT AKMGANVVKA TNRMKRPQPV YPHVMEYANG
+ LNGHMLK-TQ NTLHRQYLVD VELQATMVFV AARMKTDSSM YMSVREILHG
+ LNGHMLK-TQ NTLHRQYLVD VELGATMVFV AARMKTDLSM YMSVREILHG
+ LNGHMLK-TQ NTLHRQYLVD VELGATMVFV AARMKTDLSM YMSVREILHG
+ LNGHVLK-NQ NILHRQYLVD VNLGATMVFV LARMKTDASM YMSHREILHG
+ LNGHVLK-NQ NVLHRQYLVD VDLGATMVFV AARMKTDASM YMSHREILHG
+
+ L----WHPFY KASDHKNEAQ GVGEK-PHQL PCVESETCQY ETKHAKVCKQ
+ L----WHPFY KASDHKNEAQ GVGEK-PHQL PCVESETCQY ETKHAKVCKQ
+ L----WHPFY KASDHKNEAQ GVGEK-PHQL PCVESETCQY ETKHAKVCKQ
+ L----WHPFY KNPDHKNEAQ GVGEK-PHQL PCVESETCQY ETKHAKVCKQ
+ L----WKPFY QASDHKNEAQ GVGER-THQL PCVESHTCQY EVKHAKVCKL
+ L----WKPFY QASDHKNEAQ GVGER-THQL PCVESHTCQY EVKHAKVCKL
+ L----WKPFY QASDHKNEAQ GVGER-THQL PCVESHTCQY EVKHAKVCKL
+ M----WKPFY QASDHKNEAQ GVGER-THQL PCVDSHTCQY EVKHAQVCKL
+ M----WKPFY QASDHKNEAQ GVGER-THQL PCVDSHTCQY EVKHAQVCKL
+ M----WKPFY QASDHKNEAQ GVGER-THQL PCVDSHTCQY EVKHAQVCKL
+ L----WKPFY QTSDHKNEAQ GVGES-THQL PCVESQTCQY EVKHAKVCKL
+ L----WKPFY QASEHKNEAQ GLGER-PHQL PCVESQTCQY EIKVAKVCKL
+ L----WKPFY QASEHKNEAQ GVGER-PHQL PCVESQKCQY EVKVAKVCKL
+ L----WKPFY QASDHKNDAQ GVGER-PHQL PCVESQTCQY EMKHAKVCKL
+ L----WKPFY QASDHKSDAQ GVGER-PHQL PCVESQTCQY EMKHAKVCKL
+ L----WKPFY QASDHKNDAQ GVGER-PHQL PCVESQTCQY EVKHANVCKL
+ L----WKPFY QASDHKNDAQ GVGER-PHQL PCVEPQTCQY EVKHAKVCKL
+ L----WKPFY QASDHKNDAQ GVGER-THQL PCVEPQTCQY EVKHAKVCKL
+ L----WKPFY QASDHKNDAQ GVGER-VHQL PCVEPQTCQY EVKHAKVCKH
+ V----ERPFY E-SEFKNEAQ GWGES-GTSI PCVDSPDVQY EMKVAWVDKL
+ V----ARPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ V----PRPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ V----PRPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ V----ARPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ V----ARPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ V----ARPFY D-AEFKNEAQ RQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ V----ARPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ V----DRPFY D-SEFKNEAQ GQGES-GTSI PCVDSPDVQY ELKHAWVDKL
+ I----VKPFY D-NEWKQEAQ GQGEA-GACI PCVDSKDVQY ELKHAYVKKL
+ I----VKPFY D-NEWKQEAQ GQGEA-GACI PCVDSKDVQY ELKHAYVKKL
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ I----IKPFY D-NEWKQEAQ GQGEA-GASI PCVNSPDVQY ELKHAHIKKL
+ I----VKPFY D-NEWKQEAQ GQGEA-GASI PCVNSPDVQY ELKHAHIKKL
+ I----VKPFY D-NEWKQEAQ GVGEA-GASI PCVDSPDVQY ELKHAEVRKL
+ I----VKPFY D-NEWKQEAQ GVGEA-GASI PCVDSPDVQY ELKHAEVRKL
+ I----VKPFY D-NEWKQEAQ GVGEA-GASI PCVDSPDVQY ELKHAEVRKL
+ I----VKPFY E-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ I----VKPFY E-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHANVKKL
+ I----VKPFY E-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHANVKKL
+ I----VKPFY N-NEWKQEAQ GQGEA-GASI PCVDSPDDQY ELKHAEVKKL
+ I----VKPFY N-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ I----VKPFY D-NEWKQEAQ GQGET-GASI PCVDSPDVQY EMKHAEVKKL
+ I----VKPVY D-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ I----VKPVY D-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ I----VKPFY L-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNK PCVESEDCQY EKKHASMDKL
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNK PCVESEDCQY EKKHASMDKL
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNV PCVESEDCQY EKKHASMTKL
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNV PCVESEDCQY EKKHASMTKL
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNV PCVESEDCQY EKKHASMTKL
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNV PCVESEDCQY EKKHASMTKL
+ M----FNPFY GMSEPKNNAQ GNGEN-PMNV PCVESDDCQY EKKHASMDKQ
+ M----FVPFY GMSEPKNNAQ GNGEN-PMNV PCVESDDCQY EKKHASMDKQ
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECQY EHKHAAMEKL
+ M----VKPFY GQSEPKNEAQ GNGEN-PMNV PSVESGECQY ESKHAAMEKL
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECQY ESKHAAMEKL
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECQY ESKHAAMEKL
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECVY ESKHAAMEKL
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECVY ESKHAAMEKL
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PCVESGECQY ENKHAAMEKL
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PCVESGECQY ENKHAAMEKL
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PCVESGECQY ENKHAAMEKL
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ M----VEPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESIDCQY ENKHATMTKL
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESRDCQY ENKHATMTKL
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESIDCQY ESKHAAMTKL
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESIDCQY ENKHATMTKL
+ V----CKPFY EHSEPKNEAQ GNGEKVPMNV PCVESMDCQY ENKHAPMAKL
+ V----CKPFY EHSEPKNEAQ GNGEKVPMNV PCVESMDCQY ENKHAPMAKL
+ V----CKPFY EHSEPKNDAQ GNGDKVPMNV PCVESMDCQY ENKHAPMAKL
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESIECQY ENKHATMAKL
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMECQY ENKHAIMAKL
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMECQY ENKHAIMAKL
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMECQY ENKHAIMAKL
+ V----YKPFY ERSEPKNEAQ GNGEK-QGNV PCVESVECQY ENKHAIMAKL
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMECQY ENKHAIMAKL
+ V----CKPFY DRSEPKNEAQ GNGEK-QGNV PCVESMDCQY ENKHAIMAKL
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMDCQY ENKHAIMAKL
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMDCQY ENKHAIMAKL
+ V----VKPFY ARSEPKNEAQ GNGEK-QWNV PCVESMDCQY ENKHATMAKL
+ V----VKPFY DRSEPKNEAQ GNGEK-QWNV PCVESMDCQY ENKHATMAKL
+ V----IKPFY DRSEPKNEAQ GNGEK-QWNV PCVESMDCQY ENKHATMAKL
+ V----VKPFY ERSEPKNEAQ GNGEK-QWNV PCVQSVDCQY ENKHATMAKL
+ V----VKPFY ERSEPKNEAQ GNGEK-QWNV PCVQSVDCQY ENKHATMAKL
+ V----VKPFY EVAESKNEAQ GNGEK-PVNV PCVESPDCQY ESKHARVNKL
+ ---------- --CGIKDEAQ ADGQR-PATL IVVLSKDNKG ITEHGAVLKK
+ ---------- --CGIKDEAQ ADGQR-PATL IVVLSKDNKG ITEHGAVLKK
+ ---------- --CGIKDEAQ ADGQR-PATL IVVLSKDNKG ITEHGAVLKK
+ GTFDAAKPFR QICGTKDEAQ PDGRR-PATL LVVLSKDNQG ITEHGAVLKH
+ GTFDAAKPFR QICGVKDEAQ PDGQR-PATL LVVLSKDNVG ITEHGAVLKH
+
+ VHG-ALYLIG MKTVVKPLLG DWEGCKCRS- --KLYVSQLD H----KTLSK
+ VHG-ALYLIG MKTVVKPLLG DWEGCKCRS- --KLYVSQLD H----KTLSK
+ VHG-ALYLIG MKTVVKPLLG DWEGCKCRS- --KLYVSQLD H----KTLSK
+ VHG-ALYLIG MKTVAKPVLG DWEGCKCRSD LIKLYVSQLD H----KTLSK
+ VHH-ALYLLG LRTVMKPHLG DVDGCRCRSD LNNLILSQLD D----KTLSK
+ VHH-ALYLLG IHTVMKPHLG NVDGCRCRSD LNNLILSQLD D----KTLSK
+ VHH-ALYLLG IHTVMKPHLG NVDGCRCRSD LNNLILSQLD D----KTLSK
+ VHH-ALYLLG LRTVMKPHLG DVDGCRCRSD LNNLILSQLD D----KTLSK
+ VHH-ALYLLG LRTVMKPHLG DVDGCRCRSD LNNLILSQLD D----KTLSK
+ VHH-ALYLLG LRTVMKPHLG DVDGCRCRSD LNNLILSQLD D----KTLSK
+ VHH-ALYLLA LHTMMKPRLG DIDGCRCRSE LNKLALSQLD D----KTLSK
+ VHV-ALYLVG LKTVVKPKLG DWDGIRCRSE LNKLYLSQLD D----KTLSK
+ VHV-ALYLVG LKTVVKPKLG DWDGVRCRSD LNKLYLSQLD D----KTLSK
+ VHG-ALYLIA LKTVVKPKLG VWQGCRCRSQ LSKLVLSQLD E----KTLSK
+ VHG-ALYLIA LKTVVKPKLG VWQGCRCRSQ LSKLVLSQLD E----KTLSK
+ VHA-ALYLIG LKTVVKPELG VWEGCRCRSQ LSKLALSQLD E----KTLSK
+ VHG-ALYLIG LQTVVKPKLG VWEGVQCRSQ LSKLILSQLD D----KTLSK
+ VHG-ALYLIG LQNVVKPKLG VWEGVQCRSQ LSKLILSQLD D----KTLSK
+ VHG-ALYLIG LQTVVKPKLG VWEGCQCRSQ LSKLILSQLD D----KTLSK
+ MHT-ALYLMP LATVHKPEMG TVRGERCRAI L-KLLMMQLD ------TLSR
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ MHS-ALYLMP LATVHKPQMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ MHS-ALYLMP LSTVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ MHT-ALYLMP LPTVHKPKMG TVKGERCRAM L-KLNMMQLD E----KTLSQ
+ MHT-SLYLMH IETCHKPVMG TVKGNRCRAI L-KLSMIQLD Q----KTLSQ
+ MHT-SLYLMH IETCHKPVMG TVKGNRCRAI L-KLSMIQLD Q----KTLSQ
+ VHT-SLYLMH IDTCHKPVMG TIKGNRCRAI L-KLTMIQLD Q----KTLSQ
+ VHN-SLYLMH IDTCHKPAMG TVKGNRCRAI L-KLTMIQLD Q----KTLSQ
+ VHT-SLYLMH IDTCHKPVMG TVKGNRCRAI L-KLTMIQLD Q----KTLSQ
+ VHT-SLYLMH IDTCHKPVMG TVKGNRCRAI L-KLTMIQLD V----KTLSQ
+ VHT-SLYLMH IDTCHKPVMG TVKGNRCRAI L-KLTMIQLD V----KTLSQ
+ VHT-SLYLMH IDTCHKPVMG TVKGNRCRAI L-KLTMIQLD V----KTLSQ
+ MHT-SLYLMH LGTCHKPVMG TVKGDRCRAI L-KLSMIQLD Q----KTLSQ
+ MHT-SLYLMH LKTCHKPVMG TVKGDRCRAI L-KLKMIQLD Q----KTLSQ
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLPMIQLD Q----KTLSH
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLPMIQLD Q----KTLSH
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLPMIQLD Q----KTLSH
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLSMIQLD E----KTLSQ
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLNMIQLD Q----KTLSQ
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLNMIQLD Q----KTLSQ
+ MHD-SLYLPH LETCHKPIMG TVKGGRCRAS L-KLKMIQLD Q----KTLSQ
+ MHD-SLYLPH LETCHKPIMG TVKGGRCRAS L-KLNMIQLD Q----KTLSQ
+ MHD-SLYLMH IETCHKPIMG TVKGDRCRAT L-KLKMIQLD Q----KTLSQ
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAT L-KLKMIQLD Q----KTLSQ
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAT L-KLKMIQLD Q----KTLSQ
+ MHD-SLYLWH LETCVKPIMG TVKGDRCRAT L-KLKMIVLD P----KTLSQ
+ MHQ-SLYLMH INIMSKPAMG EWVGNRCRNE LTALRIIQLD VGVSGKTLGQ
+ MHQ-SLYLMH INVMSKPAMG EWVGNRCRND LTALRIIQLD VGHSGKTLGQ
+ MHQ-SLYLMH INIMSKPAMG EWVGVRCRNE LTALRIVQLD VGHSGKTLGQ
+ MHQ-SLYLMH INIMSKPAMG EWVGVRCRNE LTALRIVQLD VGHSGKTLGQ
+ MHQ-SLYLMH VNIMSKPAMG EWVGVRCRNE LTALRIVQLD VGHSGKTLGQ
+ MHQ-SLYLMH INIMSKPAMG EWVGVRCRNE LTALRIVQLD VGHSGKTLGQ
+ MHQ-SLYLMH MNIMSKPAMG EWVGNRCRNE LTALHVVQLD VGFSGKTLGQ
+ MHQ-SLYLMH MNIMSKPAMG EWVGNRCRNE LTALHIVQLD VGFSGKTLGQ
+ MHH-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALQTVQLD VGSSGKTLGQ
+ MHQ-SLYLMR VNTMPKPVMG DWDGNRCRAE LTALQTVQLD VGSSGKTLGQ
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALQTVQLD VGSSEKTLGQ
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALQTVQLD LGSSGKTLGQ
+ MHQ-SLYLMR VNTMSKPVMG DWVGHRCRAE LTELQTVQLD VGSSGKTLGQ
+ MHQ-SLYLMR VNTMSKPVMG DWVGHRCRAE LTELQTVQLD VGSSGKTLGQ
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALKTGQLD VGSSGKTLGQ
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALKTGQLD VGSSGKTLGQ
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALKTGQLD VGSSGKTLGQ
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALKTVQLD VGSNGKTLGK
+ MHQ-SLYLMR VNTMSKPVLG DWVGNRCRAE LTALKTVQLD IGNSGKTLGQ
+ MHQ-SLYLMR ANTMSKPVMG DWVGSRCRAE LTALKTVQLD VGSSGKTLGQ
+ MHQ-SLYLMR ANTMSKPVMG DWVGSRCRAE LTALKTVQLD VGSSGKTLGQ
+ MHQ-SLYLMR ANTMSKPVMG DWVGSRCRAE LTALKIVQLD VGSSGKTLGQ
+ MHQ-SLYLMR VNTMSKPIMG DWVGNRCRAD LTALKTVQLD VGSSGKTLGQ
+ MHH-SLYLMR MHTMSKPIMG DVNGNRCRAD LTALKMLQLD IGFSAKTLGQ
+ MHQ-SLYLMR MHTMSKPIMG HVNGNRCRAD LTALKMLQLD IGFSAKTLCQ
+ MHQ-SLYLMR IHTMSKPIMG DVNGNRCRAD LTALKMLQLD IGFSAKTLGQ
+ MHQ-SLYLMR MHTMSKPIMG DVNGNRCRAD LTALKMLQLD IGFSAKTLGQ
+ MHQDSLYLMR MHTMSKPLMG DVNGNRCRAD LTSLKMLQLD IGFCAKTLGQ
+ MHQ-SLYLMR MHTMSKPLMG DVNGNRCRAD LTSLKMLQLD IGFCAKTLGQ
+ MHQ-SLYLMR MYTMSKPIMG DVNGNRCRAE LTSLKMLQLD IGFSAKTLGQ
+ MHD-SLYLMR MHTMSKPVMG DVNGHRCRAD LTALKMLQLD IGFSAKTLGQ
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKVVQLD IGFSSKTLGQ
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAK LTALKIVQLD IGFSAKTLGQ
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ MHP-PLYLMR METMSKPPMG YVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ MHP-PLYLMR MQTMAKPPMG DVDGHRCRAG LTALKIVQLD IGFSQKTLGQ
+ MHP-PLYLVK MQTMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSSKTLGQ
+ MHP-PLYLVK MQTMSKPPMG DVDGHRCRAG LTALQIVQLD IGFSAKTLGQ
+ MHP-PLYLMR METMSKPPMG DVDGVRCRAG LTALKIVQLD IGFSAKTLGQ
+ MHP-PLYLMR METMSKPPMG DVDGVRCRAG LTALKIVQLD IGFSAKTLGQ
+ MHP-SLYLMC MEAMNKPIMG DWDGNRCRSP LCLLKVIQLD MGVSGKTLGQ
+ IHP------- ---LCKRCME NGRCLRYKND LTGDQLVQLA D----NTCAW
+ IHP------- ---LCKRCME NGRCLRYKND LAGDQLVQLA D----NTCAW
+ IHP------- ---LCKRCME NGRCLRYKND LAGDQLVQLA D----NTCLW
+ VHP------- ---LCKKDCN NNRCLRCKNV LAGNQLIQLS D----VTCAW
+ VHP------- ---LCKKDCN NNRCLRCKNV LAGNQLVQLA D----ITCAW
+
+ -NLGLY--MQ KRTWLATAPL Q------IGC MFMLVGRKKN SEE-NYNKAA
+ -NLGLY--MQ KRTWLATAPL Q------IGC MFMLVGRKKN SEE-NYNKAA
+ -NLGLY--MQ KRTWLATAPL Q------IGC MFMLVGRKKN SEE-NYNKAA
+ -NMGLY--MR NRTWLATSPL Q------IGC IFMLVGRKKN SEE-NYNKAA
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SAN-NYNRAG
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SAN-NYNRAG
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SAN-NYNRAG
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SGN-NYNQAG
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SGN-NYNRAG
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SGN-NYNRAG
+ -NCFQY--LG NMTWLATSPL H------VGC MIIF------ ----------
+ -NCFIY--LG NMTWLATSPL Q------IGW LVLFDGRKRQ SAE-DYNRAA
+ -NCFRY--LG NMTWLATSPL Q------NGC VVIFAGRKRQ SAE-DYNRAA
+ -NCSIY--LG NMTWLATSPL Q------IGC VILFGGRKRQ SHGLNYNRAA
+ -NCSIY--LG NMTWLATSPL Q------IGC VILFGGRKRQ SHGLNYNRAA
+ -NCSIY--LG NMTWLATSPL Q------IGC IILFGGRKRQ SHGLNYNRAA
+ -NCSIY--LG NMTWLATSPL Q------IGC IIMFDGRKRQ SHGLQYNRAA
+ -NCSIY--LG NMTWLATSPL Q------IGC IILFDGRKRQ SHGLQYNRAA
+ -NCNIY--LG NMTWLATFPL Q------IGC IILFDGRKRQ SYGLQYNRAA
+ -NQLPK--LC QGTWLDASPL Q------IGV QVMLVGKKGG SKK-EYELAA
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ -NQIPD--LC QRTWLDASPL Q------IGV KVVLVGKKRG SKK-DYELAA
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ -NQIIK--LC QRTWLDASPL Q------IGV NCVLPGKKGG SNK-DYELAA
+ -NQRAK--LC QRTWLDTSPL Q------MGM TLVLVGKKVG SKK-DYEVAA
+ -NQRAK--LC QRTWLDTSPL Q------MGM TLVLVGKKVG SKK-DYEVAA
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLVGKKVG SKK-DYEIAA
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLVGKKVG SKK-DYEIAA
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLVGKKVG SKK-DYEIAA
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLMGKKVG SKK-DYEIAA
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLMGKKVG SKK-DYEIAA
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLMGKKVG SKK-DYEIAA
+ -NVRAR--LC QRTWLDTSPL Q------MGM VAVLLGKKLG SKK-DYEIAA
+ -NQAAR--LC KRTWLDTSPL Q------MGM NVVLIGQKLG SKH-DYEIAA
+ -NQPRR--LC QRTWLDASPL Q------VGM NIMLMGKKAP SKK-DYEIAA
+ -NQPRR--LC QRTWLDASPL Q------VGM NIMLKGKKAP SKK-DYEIAA
+ -NQPRR--LC QRTWLDASPL Q------VGM NIMLMGKKAP SKK-NYEIAA
+ -NQRPG--LC QRTWLDANPL Q------MGM NTMLVGKKTP SKK-DYEIAA
+ -NQRPG--LC QRTWLDASPL Q------MGM HIMLVGKKTP SKK-DYEIAA
+ -NQRPG--LC QRTWLDASPL Q------MGM HIMLVGKKTP SKK-DYEIAA
+ -NQQRR--LC QRTWLDSSPL Q------MGM KIMLQGKKTP SKK-DYEIAA
+ -NQQRR--LC QRTWLDASPL Q------MGM KIMLQGKKIP SKK-DYEIAA
+ -NQKRR--LC QRTWLDASPL Q------MGM KMMLQGKKTP SKK-DYEIAA
+ -NQKKR--LC QCTWLDACPL Q------MGM KIMLQGKKTP SKK-DYEIAA
+ -NQKKR--LC QCTWLDACPL Q------LGM KIMLQGKKTP SKK-DYEIAA
+ -NQKRR--LC QRTWLDASPL Q------VGM KIMLQGKKTP SKK-DYEIAA
+ -NIGVSKLLN DRTWLATSPL E------IGC GVMSVEKKEA SPK-EFEVAA
+ -NIGVSKLLN DRTWLATSPL E------IGC LVMSVEKKEA SGK-EFEVAA
+ -NIGVSKLLN DRTWLATSPL E------IGC GVISVEKKEA SPK-EFEVAA
+ -NIGVSKLLN DRTWLATSPL E------IGC GVISVEKKEA SPK-EFEVAA
+ -NIGVSKLLN DRTWLATSPL E------IGC GVISVEKKEA SPK-EFEVAA
+ -NIGVSKLLN DRTWLATSPL E------IGC GVISVEKKEA SPK-EFEVAA
+ -NIGISELLN DRTWLATSPL E------IGC GVMAVEKKEA SPK-EFEVAA
+ -NIGISELLN DRTWLATSPL E------IGC GVMAVEKKEA SPK-EFEVAA
+ -NIVTSKKLG DRTWLAASPL Q------IGC GVMVQEKKIA SPQ-EVEVAA
+ -NIVTSKKLG DRTWLAASPL Q------IGC GVMVQEKKIA SPQ-EVEVAA
+ -NIVTSKRLG DRTWLAASPL Q------IGC GVMVQEKKIA SPQ-EVEVAA
+ -NIVTSKKLG DRTWLAASPL Q------IGC GIMVQEKKIA SPQ-EVEVAA
+ -NIVTSKKLG DRTWLAASPL Q------IGC GVMVQEKKIA SPQ-QVEVAA
+ -NIVTSKKLG DRTWLAAPPL Q------IGC DVMVQEKKIA SPQ-QVEVAA
+ -NIMTSKKLG DRTWLAANPL Q------IGR GVMVWEKKVA SPQ-EVEVAA
+ -NIMVSKKLG DRTWLAASPL Q------IGC GVMVWEKKVP SPQ-EVEVAA
+ -NIMVSKKLG DRTWLAASPL Q------IGC GVMVWEKKVP SPQ-EVEVAA
+ -NIMTPKKLG DRTWLAASPL Q------IGC GVMVQEKKVA SPQ-EVE-AA
+ -NIMTPKRLG ERTWLAASPL Q------IGC GVVVQEKKVA SPQ-EVEVAA
+ -NIMTPKKLG DRTWLAASPL Q------IGC DVMVQEKKVA SPQ-EVEVAA
+ -NIMTPKKLG DRTWLAASPL Q------IGC DVMVQEKKVA SPQ-EVEVAA
+ -NIMTPKKLG DRTWLAASPL Q------IGC DVMVQEKKVA SPQ-EVEVAA
+ -NIMTPKNLG DKTWLAASPL Q------IGC GIMVQEKKVA SPQ-EVEVAA
+ -NVVVPHLLG HRTWLATSPL Q------IGC GVMIFGNKIG SAN-EFEAAA
+ -NIVVAHLLG HRTWLATSPL Q------IGC MVMIFGNKIG SAN-EFEAAA
+ -NIVVPHCLG HRTWLATSPL Q------IGC MVMIFGNKIG SEN-EFEAAA
+ -NIIVPHCLG HRTWLATSPL Q------IGC MVMIVGNKIG SEN-EFEAAA
+ -NIVVPKLLG HRTWLATAPL Q------IGC GMMIFGNKIG STQ-EFEAAA
+ -NIVVPKLLG HRTWLATAPL Q------IGC GMMIFGNKIG STQ-EFEAAA
+ -NIVPPKLLG HRTWLATSPL Q------IGC GVMIFGNKIG STQ-EFESAA
+ -NIVAPKLLG VRTWLATSPL Q------IGC GVMIFGNKIG STQ-EFEAAA
+ LNIIDCKLLG HRTWLATSPL Q------IGV DVMVMGNKIG SPS-EFEVAA
+ LNIIDCKLLG RHTWLATSPL Q------IGC DMMVMGNKIG SPS-EFEVAA
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVMGNKIG SPS-EFEVAA
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVMGNKIG SPS-EFEVAA
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVIGNKIG SPS-EFEIAA
+ LNIIDCKLLG HRTWLATSPL Q------IGC DIMVMGNKIG SPS-EFEVAA
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVMGNKIG SPA-EFEVAA
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVVGNKIG SPA-GFEVAA
+ -NIIDSKHLG HRTWLATSPL Q------IGC SAMVMGNKIG SPQ-EVELAA
+ -NIIHSKLLG HRTWLATSPL Q------IGC DVMVMGNKIG SPQ-EVELAA
+ -NIIHSKLLG HRTWLATSPL Q------IGC DVVVMGNKIG SPQ-EVELAA
+ -NIIDSKLLG HRTWLATSPL Q------IGC DVMVVGNKIG SPQ-EFELAA
+ -NIIDSKLLG HRTWLATSPL Q------IGC DVMVVGNKIG SPQ-EFELAA
+ -NIVMAKLLG ERTWLATSPL Q------IGC DVVAVGKKPE SPQ-EFECAA
+ -NLFEC--LR DSKSLFGSPL FIKVDEDRGF TAP------- SK-------V
+ -NLFEC--LR DSKSLFGSPL FIKVDEDRGF TAP------- SK-------V
+ -NLFEC--LR DSKSLFGSPL FIKVDEDRGF TAP------- SK-------V
+ -NLFEC--LG DSESLFGSPL AIKVDEDRGF TAP------- SK-------V
+ -NLFEC--LG DSESLFGSPL AIKVDEDRGF TAP------- SK-------V
+
+ DPTVIWFYTQ PIVYV-ADVF GCTKGKNPQE MRG------N NVMSESLGDD
+ DPTVIWFYTQ PIVYV-ADVF GCTKRKNPQE MRG------N NVMSESLGDD
+ DPTVIWFYTQ PIVYV-ADVF GCTKGKNPQE MRG------N NVMSESLGDD
+ DPTVIWFYTQ PIVYV-ADVF GCTKGKNPQE MRK------N NVISESLGDD
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ ---------- ---------- ---------- --V------N NVLSQSLGDD
+ DPTTISFCRK PIVQH-ADVF GCDRDKDPQE MRT------N NVISESLGDD
+ DPTTIAFCRK PIVQH-ADVF GCDKDKDPQE MRM------N NVISESLGDD
+ DPTTICFYKK PIVVQGADVF GCARGKDPQE MKA------N NVISGSLGDD
+ DPTTICFYKK PIVVQGADVF GCARGKDPQE MKA------N NVISGSLGDD
+ DPTMICFYKK PIVVQGADIF GCARGKDPQE MKS------N NVISGSLGDD
+ DPTTICFYKK PIVVQGADIF GCARGKDPQE MKA------N NVTSGSLGDD
+ DPTTICFYKK PIVVQGADIF GCARGKDPQE MKA------N NVTSGSLGDD
+ DPTTICFYKK PIVVQGADIF GCARGKDPQE MKA------N NVTSGSLGDD
+ DQVIIYFYQA PIIYVKADVF SGTVAKKAQA MR-------K STGSQSIGDD
+ DPVIIYFYQA PIIHHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ DPVIIYFYQA PIIYHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ DPVIIYFYQA PIIYHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ DPVIIYFYQA PIIHHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ DPVIIYFYQA PIIHHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ DPVIIYFYQA PIIHHKADVF AGTVAKKAQA MRS------R SIGSPSVGDD
+ DPVIIYFYQA PIIHHKADVF AGTVAKKAQA MRS------R SIGSPSVGDD
+ DPVIIYFYQA PIIHHKADVF SGTVAKKAQA MRQ------Q STGSQSVGDD
+ DPVIMYFYDA PMIMRPTDVF EGTNNKKAQA MRS------R STASQSIGDD
+ DPVIMYFYDA PMIMRPTDVF EGTNNKKAQA MRS------R STASQSIGDD
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DPVIKYFYQA PIIMRRTDVF EGTDDQKAQA MRV------R STASQSIGDD
+ DPVIMYFYQA PIIMRRTDVF EGTDDQKAQA MRL------R STASRSIGDD
+ DPVIMYFYQA PIIMRRTDVF EGTHNKKAQA MRV------R STASQSIGDD
+ DPVIMYFYQA PIIMRRTDVF EGTHNKKAQA MRV------R STASQSIGDD
+ DPVIMYFYQA PIIMRRTDVF EGTHNKKAQA MRV------R STASQSIGDD
+ DPVIMYFYQA PIIMRRTDVF EGTNNKKSQA MRV------Q STSSQSIGDD
+ DPVIMYFYQA PIIMQRTDVF EGTNNKKSQA MRV------H STSSQSIGDD
+ DPVIMYFYQA PIIMQRTDVF EGTNNKKSQA MRV------H STSSQSIGDD
+ DPAIMHFYRA PIIMRRTDVF EGTNNKKAQA MRI------R STASQSIGDD
+ DPAIMYFYQA TIIMRRTDVF EGTNNKKAQA MRM------R STASQSIGDD
+ DPVIMYFYQS PIIMRRTDVF EGTNNKKAQA MRV------R STASQSIGDD
+ DPVIMYFYQS PIIMRRTDVF EGTNNKKAQA MRI------R STASQSIGDD
+ DPVIMYFYQS PIIMRRTDVF EGTNNKKAQA MRV------R STASQSIGDD
+ DPVIMYFYQS PIIMRHTDVF EGTNNKKAQA MRL------R STASQSIGDD
+ DPTVIYFYRN LIIQKITDVL SAVRMESPQE MRT------Q DVNSSSLGDN
+ DPTVIYFYRN LIIAKITDVL SAVRMESPQE MRE------Q DVNSSSLGDN
+ DPTVIYFYRS LIIVHITDVL SAVRMDSPQE MRN------Q DVNSPSLGDN
+ DPTVIYFYRS LIIVHITDVL SAVRMDSPQE MRN------Q DVNSPSLGDN
+ DPTVIYFYRS LIIVHITDVL SAVRMDSPQE MRN------Q DVNSPSLGDN
+ DPTVIYFYRS LIIVHITDVL SAVRMDSPQE MRN------Q DVNSPSLGDN
+ DPTVIYFYRN LIIQHITDVL SAVRMDSPQE MRV------Q DVNSPSLGDN
+ DPTVIYFYRN LIIQHITDVL SAVRMDSPQE MRV------Q DVNSPSLGDN
+ D---IYFYRN MVVQRLTDVV AAVRMQSPQE MRTPVLVCIQ KVDSVSLGDD
+ D---IYFYRN MVVQRLTDVV AAVRMQSPQE MRTPVLVCIQ KVDSVSLGDD
+ D---IYFYRN MVVQRHTDVV AAVRMQSPQE MRNPVLVCIQ KVDSASLGDD
+ D---IYFYRN MVVQRHTDVV AAVRMQSPQE MRNPVLVCIQ KVDSISLGDD
+ D---IYFYRN MVVQRLTDVV AAVRMQSPQE MRCRKLVCIQ KVDSPSLGDD
+ D---IYFYRN MVVQRLTDVV AAVRMQSPQE MRTPKLVCIQ KVDSPSLGDD
+ D---IYFYRN MVIECLTDVV RAVRMQSPQE MRAPVLVCIQ KVDSPSLGDD
+ D---IYFYRN MVIECLTDVV RAVRMQSPQE MRAPVLVCIQ KVDSPSLGDD
+ D---IYFYRN MVIECLTDVV RAVRMQSPQE MRAPVLVCIQ KVDSPSLGDD
+ D---IFFYRN MVIQRLTDVV AAVRMQSPQE MRPPVLVCIQ YVDSPSLGDD
+ D---IYFYRN MVIQTLTDVV AAVRMQSPQE MRPPVLVCIQ DVDSVSLGDD
+ D---IYFYRN MVIQRLTDVV AAVRMQSPQE MRLPVLVCIQ DVDSPSLGDD
+ D---IYFYRN MVIQRLTDVV AAVRMQSPQE MRLPVLVCIQ DVDSPSLGDD
+ D---IYFYRN MVIQRLTDVV AAVRMQSPQE MRLPVLVCIQ DVDSPSLGDD
+ D---IYFYRN MVIQRLTDVV AAVRMQSPQE MRPPVLVCIQ DVDSPSLGDD
+ DPTVIYFYRN RIVRRLADVI STVRMNSPQE MRN------Q DVDSHSLGDD
+ DPTVIYFYRN RIVRRLADVI STVRMNSPQE MRE------Q DVDSHSLGDD
+ DPTVIYFYRN RIVRRLADVI STVRMNSPQE MRN------Q DVDSHSLGDD
+ DPTVIYFYRN RIVRRLADVI STVRMNSPQE MRN------Q DVDSHSLGDD
+ DPTVIYFYRN RIVRRMADVI STVRMKSPQE MRG------Q DVDSHSLGDD
+ DPTVIYFYRN RIVRRMADVI STVRMKSPQE MRG------Q DVDSHSLGDD
+ DPTVIYFYRN RIVKRMADVI STVRMKSPQE MRG------Q DVDSHSLGDD
+ DPTVIYFYRN RIIRRVADVI STVRMKSPQE MRE------Q DVDSHSLGDD
+ DPTIIWFYRN CIVHKLADTV STAKMKSPQE MRH------Q DVDSPSLGDD
+ DPTIIWFYRD CIVHKLADTV STAKMKAPQE MRV------Q DVDSPSLGDD
+ DPTIIWFYRN CIVHKLADTV STAKMKAPQE MRV------Q DVDSPSLGDD
+ DPTIIWFYRN CIVHKLADTV STAKMKAPQE MRH------Q DVDSPSLGDD
+ DPTIIWFYRN CIVHKLADTV STAKMKAPQE MRV------Q DVDSPSLGDD
+ DPTIIWFYRN CIVHKLADVV STAKMKSPQE MRV------Q DVDSPSLGDD
+ DPTIIWFYRN CIVHKLADLV STAKMKSPQE MRV------Q DVDSPSLGDD
+ DPTIIWFYRN CIVHKLADLV STAKMKSPQE MRV------Q DVDSPSLGDD
+ DPTVIYFYRN CIVQKMADVV STVKMKSPQE MRV------Q DVDSASLGDD
+ DPSVIYFYQN CIVQKMADVV STVKMKSPQE MRV------Q DVDSASLGDD
+ DPSVIYFYQN CIVQKMADVV STVKMKSPQE MRV------Q DVDSASLGDD
+ DPTVIYFYRN CIVQKLADVV STVKMKSPQE MRV------Q DVDSPSLGDD
+ DPTVIYFYRN CIVQKLADVV STVKMKSPQE MRV------Q DVDSPSLGDD
+ DPTVIYFYKN LIIQQAADYV SAVQVKSPQE MRY------Q DVNSPSDGDE
+ EPKCAQFYSK SCTHC----- ---------- -TM------C SVGSHASEED
+ EPKCAQFYSK SCTHC----- ---------- -TM------C SVGSHASEED
+ EPKCAQFYSK SCTHC----- ---------- -TM------C SVGSHASEED
+ EPKCAQFYSK SCTHH----- ---------- -MM------C SVGSNASEED
+ EPKCQQFYSK SCTHC----- ---------- -VM------C SVGSNASEED
+
+ NLQD--MSGV PVTVCTSSVM VRKDMQD-SV DKRGCTWNAK E-DHLCPSSF
+ NLQD--MSGV PVTVCTSSVM VRKDMQD-SV DKRGCTWNAK E-DHLCPSSF
+ NLQD--MSGV PVTVCTSSVM VRKDMQD-SV DKRGCTWNAK E-DHLCPSSF
+ NLQD--MPGM PVTVCTSSVM VRKDMHQ-SV DKRGYTWHAK E-DHLCPDSF
+ SLQQ--MPAV PVDVCVMSVM VNKSMPQ-SH DKRGYTWQAK Q-DHLFPVNV
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNC
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNC
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNF
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNF
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNF
+ SLQQ--MHAM PVTVVVVSHM VKKSMPQ-SH DKRGYTWQAK DFDQLIPVSF
+ FLQQ--MPAV PVSVCVYSHM VKKFVPQ-SH EKRGYTWKAK E-DHLVPISY
+ FLQQ--MPAV PVSVCVHSHM VKKFVPQ-SH EKRGVTWKAK E-DHLVPISL
+ RLQQ--MPAM PVTICVSSYM VKKSVIQ-SH QKRGYTWRAK E-DHLIPVSF
+ RLQQ--MPAM PVTICVSSYM VKKSVPQ-SH QKRGYTWRAK E-DHLIPVSF
+ RLQH--MPAM PVTICVFSYM VKKAVPQ-SH QKRGYTWRAK E-DHLIPVSF
+ RLQQ--MPAM PVTICVFSYM VKKSVPQ-SH VKRGYTWRAK E-DHLIPVSF
+ RLQQ--MPAM PVTICVFSYM VKKLVPQ-SH QKRGYTWRAK E-DHLIPVSF
+ RLQQ--MPAM PVTICVFSYM VKKSVPQ-SH QKRGYTWRAK E-DHLIPVSF
+ GMQS--MPLM QNAVCVWSKM VRKVQPD-GQ DKREQTWMAK D-DTLCPPSM
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DTLCPPCE
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DTLCPPCE
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DTLCPPCE
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DTLCPPCE
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DALCPPCK
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWVAK D-DTLCPPCK
+ GMQK--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWVAK D-DTLCPPCK
+ GTQV--MPLM QNLVCVWSKM VRKCMID-GQ EKREQTWMAK D-DKLCPPSQ
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK D-DTLCPQSR
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK D-DTLCPQSR
+ DMLN--MPLT QNAMCVESEM VRKSQPD-GQ DKRGYTWVAK E-DDLCPQSG
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSG
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSE
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSG
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSG
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSG
+ DMLI--MPLV QNAMCVKSEM VRKCQPD-GP DKRGYTWMAK D-DTLCPVSA
+ DMLI--MPLV QNAMCVNPEM VRKCQPD-GQ DKRGYTWMAK N-DTLCPVSA
+ DMLK--MPLV QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ DMLK--MPLV QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ DMLK--MPLR QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ DMLN--MPLV QNAMCVSSEM VRKCQPD-GQ NKRGCTWMAK N-DTLCPQSG
+ DMLN--MPLV QNAMCVSSEM VRKCQPD-GQ NKRGYTWMAK H-DTLCPQSG
+ DMLN--MPLV QNAMCVSSEM VRKCQPD-GQ NKRGYTWMAK H-DTLCPQSG
+ DMLN--MPLH QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSP
+ DMLN--MPLH QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLYPQSA
+ EMLN--MPLV QNAMCVPSEM VRKCQPD-GQ DKRGYTWMAK D-DPLCPQSA
+ EMLN--MPQV QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ EMLN--MPLV QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ EMLN--MPLI QNAMCVQSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQLH
+ NGQA--MNIV PYWVCVASGV VRKTHKD-SV DKRGQTWTAK S-DFLCPLAV
+ NGQA--MNIV PYWVCVGSGV VRKTHKD-SV DKRGQTWTAK S-DFLCPLAM
+ NGQA--MNIV PYWVCVASGV VRKMHKD-SV EKRGQTWEAK S-DFLCPLAV
+ NGQA--MNIV PYWVCVASGV VRKMHKD-SV EKRGQTWEAK S-DFLCPLAV
+ NGQA--MNIV PYWVCVASGV VRKMHKD-SV EKRGQTWEAK S-DFLCPLAV
+ NGQA--MNIV PYWVCVASGV VRKMHKD-SV EKRGQTWEAK S-DFLCPLAV
+ NGQA--MNIV PYWVCVVSGV VRKTHKD-SV EKRGQTWTAK S-DFLCPIAV
+ NGQA--MNIV PYWVCVVSGV VRKTHKD-SV EKRGQTWTAK S-DFLCPIAV
+ DPQM--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPAAV
+ DPQM--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ DPQM--MKIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ DPQM--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ DPQM--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ DPQC--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ VPQM--MNIV PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAM
+ VPQM--MNIV PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAM
+ VPQM--MNIV PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAM
+ TPQM--MNIA PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK A-DFLCPPAV
+ TPQM--MNIA PYWVCVCSGV VKKTQPD-SV DKRGKTWVAK S-DFLCPPAV
+ TPQK--MNIA PYWVCVCSGV VKKAQLD-SV EKRGKTWVAK S-DFLCPPAV
+ TPQK--MNIA PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAV
+ TPQK--MNIA PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAV
+ TPQM--MNIA PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAI
+ DNQA--MVIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK V-DFLCPPAF
+ DNQA--MNIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK M-DFLCPPAF
+ DNQA--MNIL PYVVCVCSGV VRKDHPDTSI HKRGRTWLAK V-DFLCPPAF
+ DNQA--MNIL PYVVCVCSGV VRKEHPDTSI SKRGRTWLAK I-DFLCPPAF
+ DNQA--MNIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK I-DFLFPPAF
+ DNQA--MNIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK I-DFLFPPAF
+ DNQA--MNIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK I-DFLFPPAF
+ DNQA--MTIL PHWVCVVSGV VRKEHPDTSI NKRGSTWLAK V-DFLCPPAF
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ DQQE--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ DQEA--MDIL PYWVCVMSGV VRKEQPD-SV NKRGRTWLAK K-DFLVPPAF
+ DQEA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK K-DFLVPPAF
+ DQQP--MNII PYWVCVTSGV VHKEQPD-SV NKRGRTWTAK N-DFLCPDAF
+ DQQP--MNII PYWVCVTSGV VRKEQPD-SV NKRGHTWTAK N-DFLCPPAY
+ DQQP--MNII PYWVCVTSGV VRKEQPD-SV NKRGRTWSAK N-DFLCPPAF
+ NQQS--MNII PYWVCVHSGV VQKEQPD-SV HKRGRTWTAK N-DFLCPPAF
+ NQQS--MNII PYWVCVHSGV VQKEQPD-SV HKRGRTWTAK N-DFLCPPAF
+ NGQS--MHIG PYWVCVSSEV VKKSQPD-SV DKRGRTWVAK N-EFLCPPDH
+ ALDLYTHKPV PDAQCFVSRV ARNIPEH-SP CK-------- ----------
+ ALDLYTHRPV PDAQCFVSRV ARNIPEH-SP CK-------- ----------
+ ALDLYTHKPV PDAQCFVSRV ARNIPEH-SP CK-------- ----------
+ ALELYTHKPV PDPQCFVSIV VRNIPEH-SP CK-------- ----------
+ ALELYTHKPV PDPQCFVSIV VRNIPEH-SP CK-------- ----------
+
+ CKGER---ED EPGGVTQ--- ---------- ----RCIENI AKLLYIKDV-
+ CKGER---ED EPGGVTQ--- ---------- ----RCIENI AKLLYIKDV-
+ CKGER---ED EPGGVTQ--- ---------- ----RCIENI AKLLYIKDV-
+ CKGEK---EE EPGGVRR--- ---------- ----RIVENI VKLLYIKDV-
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ VKGEQ---EE EPEGPNN--- ---------- ----RVVHNI VKLLYTKDV-
+ CKGEH---EE EPEGAQY--- ---------- ----RVVQNI VKLLYTKDV-
+ CKGEH---EE EPEGAQY--- ---------- ----RCVQNI VKLLYTKDV-
+ CKGEL---DE EPDAAQQ--- ---------- ----RIVQNI VKLLYTKDV-
+ CKGEL---DE EPDAAQQ--- ---------- ----RIVQNI VKLLYTKDV-
+ CKGEL---DE EPDGAQQ--- ---------- ----RVVQNI VKLLYTKDV-
+ CKGEL---EE EPEGAQH--- ---------- ----RMVQNI VKLLYTKDV-
+ CKGEL---EE EPEGAKQ--- ---------- ----RMVQNI VKLLYTKDV-
+ CKGEL---EE EPEGAQQ--- ---------- ----RIVQNI VKLLYTKDI-
+ KRGEK---TA EPTQWMG--- ---------- ----TVTVNK IKLLYCKDC-
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ DQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ EQGEK---AA EPTQWED--- ---------- ----ICTANV IKLLYCKDC-
+ DQGEK---HH EPHHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ DQGEK---HH EPHHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ DQGEK---YA EPQHIRN--- ---------- ----QFSENV IKLLYCKDC-
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ GQGEK---YA EPHQIKN--- ---------- ----KFSVNV IKLLYCKDC-
+ GQGEC---YA EPHQTCN--- ---------- ----KFRVNV IKLLYCKDC-
+ NQGEK---YA EPHVIGD--- ---------- ----KVSVNV IKLLYCKDC-
+ NQGEK---YA EPHVIGD--- ---------- ----KVSVNV IKLLYCKDC-
+ NQGEK---YA EPVVIGD--- ---------- ----KVSVNV IKLLYCKDC-
+ NQGEK---FA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ NQGEK---YA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ NQGEK---YA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ NQGEK---YA EPHQIRN--- ---------- ----KISVNV IKLLYCKDC-
+ NQGEK---YA EPHQIRN--- ---------- ----KISVNV IKLLYCKDC-
+ NVGEK---YA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ NVGEK---YA EPHQIRN--- ---------- ----KVSTNV IKLLYCKDC-
+ NQGEK---YA EPHQIRN--- ---------- ----KVSTNV IKLLYCKDC-
+ NQAEK---YA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ DQGEP---GA EQKPAVGEEN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ DQGEI---GA EQKPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ DQGEP---AA EQRPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ DQGEP---AA EQRPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ DQGEP---AA EQKPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ DQGEP---AA EQKPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ NQGEP---GA EQKPAVGA-N PIVKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ NQGEP---GA EQKPAVGA-D PIVKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ NEGEH---GA EQRP-FGTQN PVCKPWRFVI MNTQTFAKNI IRLLYIKDI-
+ NEGEH---GA EQRPVFGTHN PVCKPWRFVI MHTQTFSKNI IRLLYIKDI-
+ NEGEH---GA EQRPVFGTQN PVCKPWRFVI MNTQTFSKNI IRLLYIKDI-
+ NEGEH---GA EQRPVFGTQN PVCRPWRFVI MNMQTFSKNI IRLLYIKDI-
+ NEGEH---GA EQRPVFGGQN PACKPWHFVI MNRQTFAKNM IRLLYIKDI-
+ NEGEH---GA EQRPVFGGQN PACQPWHFVI MNTQTFAKNM IRLLYIKDI-
+ NEGEH---GA EQRPVFGTQN PVCKPWRFVI MNTETFAKNI IRLLYVKDV-
+ NEGEH---GA EQRPVFGTQN PVCKPWRFVI MNVETFAKNI IRLLYVKDV-
+ NEGEH---GA EQRPVFGTQN PVCKPWRFVI MNVETFAKNI IRLLYVKDV-
+ SEGEH---GA EQRPVFGMQN PACKPWRFVI MNTQTFAKNI IRLLYIKDV-
+ SEGEH---GA EQRPVFGMRN PICKPWRFVI MNTQTFAKNI IRLLYVKDV-
+ SEGEH---GP EQRPVFGVQN PVCKPWRFVI MNTQTFAANI IRLLYVKDV-
+ SEGEH---GP EQRPVFGVQN PVCKPWRFVI MNTQT-AKNI IRLLYVKDV-
+ SEGEH---GP EQRPVFGMQN PVCKPWRFVI MNTQTFAKNI IRLLYVKDV-
+ SEGEH---GA EQRPVFGMQN PVCRPWRFVI MNTQTFAKNV IRLLYVKDV-
+ NQGEH---RA EQKPASKFEH PVCGPWEFVI VNYQTSAKDI ILLLYIKDV-
+ NQGEH---RA EQKPALKFKH PVCGPWEFVI VNYQTSAKDI ILLLYIKDV-
+ NQGEH---RA EQKPAFKFKH PVCGPWEFVI VNYQTEAKDI ILLLYIKDV-
+ NQGEH---RA EQKPAFKFKH PCCGPWEFVI VNYQTSAKDI ILLLYIKDV-
+ NQGEH---HA EQKPVFGFKH PHCGPWEFVI CNYQTVAKDI ILLLYIKDV-
+ NQGEH---HA EQKPVFGFKH PHCGPWEFVI CNYQTVAKDI ILLLYIKDV-
+ NQGEH---HA EQKPVFGFKH PHCGPWEFVI CNYQTMAKDI ILLLYIKDV-
+ NQGEH---HA EQKPVFGFKH PHVGPWEFVI CNYQTSAHDI ILLLYIKDV-
+ NQGEH---ER EQRPVYGFKH PGCRPWQFVI ANYQTSAKNI IMLLYVKDV-
+ NQGEH---EA EQRPVYGFVH PRCRPWQFVI ANYQTSAKNI IMLLYVKDV-
+ NQGEH---GA EQRPVYGFQH PRCRPWQFVI ANYQTFAKNI IMLLYVKDV-
+ KQGEH---EA EQRPVYGFQH PRCRPWQFVI ANYQSSAKNI IMLLYVKDV-
+ NQGEH---EA EQRPVYGFQH PRCRPWQFVI GNYQTSAKNI IMLLYVKDV-
+ EQGEH---EA EQCPVHGFKH PRCRPWQFVI ADYQTSAKNI IMLLYVKDV-
+ NQGEH---EA EQKPVYGFDH PRCRPWQFVI ANYQTSAKNI IMLLYVKDV-
+ NQGEH---EA EQKPVYGFDH PRCRPWQFVI ANYQTSAKNI IMLLYVKDV-
+ NQGEH---GA EQKPTHGFEH PRCRPWQFVI PVYQTGAKNI ILLLYIKDV-
+ NQGEH---GA EQKPVHGFEH PRCRPWQFVI SVYRTGAKNI NLLLYIKDV-
+ NQGEH---GA EQKPVHEFQH PRCRPWQFVI SVYRTGAKNI NLLLYIKDV-
+ DQGEH---GA EQKPVHGFEH PRCRPWQFVI ANYQTGAKNI ILLLYVKDV-
+ DQGEH---GA EQKPVHGFEH PRCRPWQFVI ANYQTGAKNI ILLLYVKDV-
+ MQGEHSIEGA EQKPFFGFAG PFPQPWQFVI VNPQTWAHNI IRLLYCKDV-
+ ---------- -P---CS--- ---------- ----VEEVCY CKVCDSKDVR
+ ---------- -P---CS--- ---------- ----VEEVCY CKVCDSKDVR
+ ---------- -P---CS--- ---------- ----VEEVCY CKVCDSKDVR
+ ---------- -P---CS--- ---------- ----VEEVAY CKNCDSKDVR
+ ---------- -P---CS--- ---------- ----VEEVCY CKNCDSKDVR
+
+ LCNEVLNGLQ WQLCWSV-GD WESLIPQACW DAKKDLAVCA WKMELVPGL-
+ LCNEVLNGLQ WQLCWSV-GD WESLIPQACW DAKKDLAVCA WKMELVPGL-
+ LCNDVLNLLV WQLCWSV-GD WESLIPQACW DAKKDLAVCA WKMELVPGL-
+ LCNQVLNLLQ WQLCWSV-GD WESLVPQACW GAKKDLAVCA WKMELVPGL-
+ DCNMVLSLLV WQLC--H-GD WEPLLPQACE SARRDLAVCA WKRELVPGL-
+ DCNIVLSLLV WQLC--H-GD WEPLLPQACE GARRDLAVCA WKRELVPGL-
+ DCNIVLSLLV WQLC--H-GD WEPLLPQACE GARRDLAVCA WKRELVPGL-
+ DCNIDLSLLV WQLC--H-GD WEPLLPQACE SARRDLAVCA WKRELVPGL-
+ DCNIVLSLLV WQLC--H-GD WEPLLPQACE SARRDLAVCA WKRELVPGL-
+ DCNIVLSLLV WQLC--H-GD WEPLLPQACE SARRDLAVCA WKRELVPGL-
+ DCNTVLSLLI WQLC--H-GD WEQLVPQACA GARSDLAVCA WKRELVPGL-
+ DCNVVLSLLV WQLC--H-GD WEPLIPQACQ TAKKDLAVCA WKRELVPGL-
+ DCNVVLSLLV WQLC--H-GD WEPLVPQACQ TAKKDLAVCA WKRELVPGL-
+ SCNVVLSMLI WQIC--H-GD WEPQIPKACS NARKDLAVCA WKRELVPGL-
+ SCNVVLSMLI WQIC--H-GD WEPQIPKACS NARKDLAVCA WKRELVPGL-
+ SCNKVLSMLI WQIC--H-GD WEPQIPKACN AARKDLAVCA WKRELVPGL-
+ SCNVVLSMLI WQIC--H-GD WEPQIPKACD AARKDLAVCA WKRELVPGL-
+ SCNVVLSMLI WQIC--H-GD WEPQIPKACD AARKDLAVCA WKRELVPGL-
+ SCNVVLSMLI WQIC--H-GD WEPQLPKACD AARKDLAVCA WKRELVPGL-
+ SCNEVMKILS WWLCNSV-GD WQTLMSQACI TADPNPPVCV WKRELVPGL-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACR SANPNYPVCI WKRELVPGL-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACR SANPNYPVCI WKRELVPGL-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACR SANPNYPVCI WKRELVPGL-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACR SANPNYPVCI WKRELVPGL-
+ SCNEVLKILA WWLCDSV-GD WQSLMNDACR SANPNYPVCI WKRELVPGL-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACS SANPNYPVCI WKRELVPGL-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACS SANPNYPVCI WKRELVPGL-
+ SCNEVLRVLS WWLCDSV-GD WRTLMSDACA LANPNPPVCV WKRELVPGL-
+ SCNKVLKILV WQLCESV-DD WQTLSSDACM HAEQNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLSSDACM HAEQNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNTPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEHNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WVTLASDACL SAEPQPPVCV WQRELVPQL-
+ SCNKVLKILK WQLCESV-DD WQTLASDACI LAKPQPPVCV WQRELVPQL-
+ SCNQVLKILV WQLCESV-DD WQTLTSDPCM SAQVNPPVCV WQRELVPQL-
+ SCNQVLKILI WQLCESV-DD WQTLTSDPCM SAQVNPPVCV WQRELVPQL-
+ SCNQVLKILV WQLCESV-DD WQTLTSDPCM SAQVNPPVCV WQRELVPQL-
+ SCNKMLKILV WQLCESV-DD WQTLASDPCV SAEPNSPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLASDPCM SAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLASDPCM SAEPNPPVCV WQRELVPQL-
+ SCNQVLKILV WQLCESV-DD WQTLTSDPCV PAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLTSDPCV PAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCDSVQDD WQPLTSDPCV NAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCDSV-DD WQTLTSDPCV SAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCDSV-DD WQTLTSDPCV SAEPNPPVCV WQRELVPQL-
+ SCNKVLKILV WQLCESV-DD WQTLTSDPCI SAEPNPPVCV WQRELVPQL-
+ SCNGVLPLLK WQLCDSH-GD WQSLYADSCP IA-VNAAVCG WKRELVPGL-
+ SCNGVLPLLK WQLCDSH-GD WQSLYADSCP IA-INAAVCG WKRELVPGL-
+ SCNGVLPLLK WQLCDSH-GD WQSLFPDSCP FA-LNAAVCG WKRELVPGL-
+ SCNGVLPLLK WQLCDSH-GD WQSLFPDSCP FA-LNAAVCG WKRELVPGL-
+ SCNGVLPLLK WQLCDSH-GD WQSLFPDSCP FA-LNAAVCG WKRELVPGL-
+ SCNGVLPLLK WQLCDSH-GD WQSLFPDSCP FA-LNAAVCG WKRELVPGL-
+ SCNGVLPLLK WQLCDSH-GD WQSLFADSCP TA-VNAAVCA WKRELVPGL-
+ SCNGVLPLLK WQLCDSH-GD WQSLFADSCP IA-VNAAVCA WKRELVPGL-
+ SCNQVLQLLD WQLCDSH-GD WQSLMADSCP NA-VNIAVCC WKRELMPGL-
+ SCNQVLQLLD WQLCDSH-GD WQSLMADSCP NA-VNIAVCC WKRELMPGL-
+ SCNQVLQLLD WQLCDSH-GD WQSLMADSCP PA-VNIAVCC WKRELMPGL-
+ SCNQVLQLLD WQLCDSH-GD WQSLMADSCP PA-VNIAVCC WKRELMPGL-
+ SCNEVLQLLD WQLCDSH-GD WQSLIADSCP NA-SNIAVCC WKRELMPGL-
+ SCNQVLQLLD WQLCDSH-GD WQSLIADSCP NA-VNIAVCC WKRELMPGL-
+ SCNQVLQLLD WQLCDSH-GD WQSLVADSCP NA-VNIAVCC WKRELMPGL-
+ SCNQVLQLLD WQLCDSH-GD WQSMVADSCH NA-VNIAVCC WKRELMPGL-
+ SCNQVLQLLD WQLCDSH-GD WQSMVADSCH NA-VNIAVCC WKRELMPGL-
+ SCNAVLQLLD WQLCYSH-GD WQSLIADSCP TA-ANIAVCC WKRELMPGL-
+ SCNAVLQLLD WQLCYSH-GD WQSLIADSCS TA-ANIAVCC WKRELMPGL-
+ SCNAVLQLLD WQLCYSH-ED WQSLIADACP TA-VNIAVCC WKRELMPGL-
+ SCNAVLQLLD WQLCYSH-GD WQSLIADACS TA-VNIAVCC WKRELMPGL-
+ SCNAVLQLLD WQLCYSH-GD WQSLIADACP TA-VNIAVCC WKRELMPGL-
+ SCNKVLQLLD WQLCYSH-GD WQSLIADACP AA-VNIAVCC WKRELMPGL-
+ GCNCVLELLN WQLCTSH-GD WQSLVADSCV WA-HNVAVCA WKRELVPGL-
+ GCNCVLELLK WQLCTSH-GD WQSLVADSCV WA-HNVAVCA WKRELVPGL-
+ GCNCVLELLE WQLCTSH-GD WQSLVADSCV WA-HNVAVCA WKRELVPGL-
+ GCNCVLELLK WQLCTSH-GD WQSLVADSCV WA-HNVAVCE WKRELVPGL-
+ GCNCVLELLA WQLCTSH-GD WQSLVADSCI WA-HNVAVCA WKRELVPGL-
+ GCNCVLELLA WQLCTSH-GD WQSLVADSCI WA-HNVAVCA WKRELVPGL-
+ GCNCVLELLA WQLCTSH-GD WQSLVADSCI WA-HNVAVCA WKRELVPGL-
+ GCNCVLELLV WQLCTSH-GD WQSLVADSCV WA-HNVAVCA WKRELVPGL-
+ SCNGVLQLLN WHLCDSH-GD WQSLVADSCC WA-HNVAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ SCNRVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCM WA-HNVAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ SVNGVLQLLI WQLCDSH-GD WQSLVADSCA WA-VNVAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCA WA-VNVAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCA WA-VNLAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLSADSCA WA-HNVAVCG WKRELVPGL-
+ SCNGVLQLLN WQLCDSH-GD WQSLSADSCA WA-HNVAVCG WKRELVPGL-
+ SCNCVLTCLN WVLCDSH-GD WHSLIADACP CA-HNVAVCG WKRELVPGL-
+ AVKNAYQDLQ VPLSKLK-AP WLSMGHCECW EEDINNILSV VKHELVDDVD
+ AVKNAYQDLQ VPLSKLK-AP WLSMGHCECW EEDINNILSV VKHELVDDVD
+ AVKNAYQDLQ VPLSKLK-AP WLSMGHCECW EEDINNILSV VKHELVDDVD
+ AVQNAYQDLA VPLSKLK-AP WLSMGHCECW EEDINNILSM VKHELVVDQD
+ ATQNAYQELA IPLSKLK-AP WLSMGHCECW EEGINNILSM VKHELVVDQD
+
+ --NRNNENLA KVIYFGPDGH -------DEG PMQAKIVTLH W-EMDVSHRG
+ --NRNNENLA KVIYFGPDGH -------DEG PMQAKIVTLH W-EMDVSHRG
+ --NRNNENLA KVIYFGPDGH -------DEG PMQAKIVTLH W-EMDVSHRG
+ --NRNNENLA KIIYFGPDGH -------DEG NMQAKIVTLH W-EMDVSHRG
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ --NHNNENLA KVIYFGPDGH -------DEG PMGRKIVDLH W-EMEASHRD
+ --NCNNEYLA KIIYFGPDGH -------DEG PMGRKIVDLH W-EMEASHRD
+ --NCNNEYLA KIIYFGPDGH -------DEG PMGRKIIQLH W-EMEASHRD
+ --NHNNENLA KIMYFGHDGH -------DEG PMGRKIVTLH V-EMEVSHRE
+ --NHNNENLA KIMYFGHDGH -------DEG PMGRKIVTLH V-EMEVSHRE
+ --NHNNEDLA KIMYFGPDGH -------DEG PMGRKIVNLH V-EMEVSHRE
+ --NHNDENLA KIMYFGPDGH -------DEG PMGEKIVNLH V-EMEASHRE
+ --NHNDENLA KIMYFGPDGH -------DEG PMGEKIVNLH V-EMEASHRE
+ --NHNDENLA KIMYFGPDGH -------DEG PMGEKIVNLH V-EMEASHRE
+ --NRSVENLA KIIYFCPDEH -------DER KMWGKIFALE W-EMDISHRH
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRM
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRV
+ --NRNVENLA KIIYFCPDEH -------DER KMWGKIFCLE W-EMDISHRH
+ --NRNIEDLA RIIYFGPDEH -------DEG KMMNKIFALE W-EMDMSHRV
+ --NRNIEDLA RIIYFGPDEH -------DEG KMMNKIFALE W-EMDMSHRV
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ --NRNVEDLA RVIYFGPDEH -------DEG KMMPKIFKLA W-EMDMSHRA
+ --NRNVEDLA RVIYFGPDEH -------DEG KMMSKIFNLE W-EMDMSHRT
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMSKIFALE W-EMDMSHRV
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMFKIFALE W-EMDMSHRV
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMSKIFALE W-EMDMSHRV
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMSKIFALE W-EMDMSHRI
+ --NRNVEDLA RTIYFGPDEH -------DEG KMMSKIYALE W-EMDMSHRV
+ --NRNVEDLA RTIYFGPDEH -------DEG KMMSKIYALE W-EMDMSHRV
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMRKIFALE W-EMDMSHRD
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMRKIFALE W-EMDMSHRD
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMNKIFALE W-EMDMSHRD
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMRKIFALE W-EMDMSHRN
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMRKIFALE W-EMDMSHRN
+ --NRNIEDLA RIIYFGPDEH -------DEG KMMGKIFALE W-EHDMSHRD
+ --NHSCEHLA KSVYFEPDGE -------GEG KVMLKIFGLD WCEVERSHEH
+ --NHSCEHLA KSVYFEPDGE -------GEG KVMLKIFGLD WCEVERSHEH
+ --NHSCEHLA KGVYFEPDGE -------DEG KMMLKIFGLE WCEVERSHEH
+ --NHSCEHLA KGVYFEPDGE -------DEG KMMLKIFGLE WCEVERSHEH
+ --NHSCEHLA KGVYFEPDGE -------DEG KMMLKIFGLE WCEVERSHEH
+ --NHSCEHLA KGVYFEPDGE -------DEG KMMLKIFGLE WCEVERSHER
+ --NHSCEHLA KSVYFEPDGE -------DEG KMMLKIFGLD WCEVERSHEH
+ --NHSCEHLA KSVYFEPDGE -------DEG KMMLKIFGLD WCEVERSHEH
+ --NHSCEHLA KSVYFKPDGE -------DEG QMTMKIFNLD WCEVEKSHEK
+ --NHSCEHLA KTVYFKPDGE -------DEG QMSQKIFNLD WCEVEKSHEK
+ --NHSCEHLA KTVYFKPDGE -------DEG QMTMKIFNLD WCEVEKSHEK
+ --NHSCEHLA KTVYFKPDGE -------DEG QMTMKIFNLD WCEVEKSHEK
+ --NFSCEHLA KTVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ --NFSCEHLA KTVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ --NHSCQHLA KTVYFKPDGE -------DEG QMIVKIFNLD WCEVEKSHEK
+ --NHSCQHLA KTVYFKPDGE -------DEG QMMVKIFNLD WCEVEKSHEK
+ --NHSCQHLA KTVYFKPDGE -------DEG QMMVKIFNLD WCEVEKSHEK
+ --NHSCEHLA KTVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ --NHSCEHLA KTVYFKPDGE -------DEG QMIVKIFHLD WCEVEKSHEK
+ --NHSCEHLA KSVYFKPDGE -------DEG QMFMKIFNLD WCEVEKSHEK
+ --NHSVEHLA KSVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ --NHSCEHLA KSVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ --NHSCEHLA KTVYFKPDGE -------DEG QMIMKIFGLD WCEVEKSHEE
+ --NHSCERLA KHIYFQPDGE -------DEG KMVLKIFGLD WCEMEKSHQR
+ --NHSCDRLA KHIYFQPDGE -------DEG KMILKIFGLD WCEMEKSHQR
+ --NHSCERLA KHIYFQPDGE -------DEG KMILKIFGLD WCEMEKSHQR
+ --NHSCERLA KHIYFQPDGE -------DEG KMILKIFGLD WCEMEKSHQR
+ --NHSCEHLA KHIYFQPDGE -------DEG KMILKIFGLD WCEVERSHQR
+ --NHSCEHLA KHIYFQPDGE -------DEG KMILKIFGLD WCEVERSHQR
+ --NHSCEHLA KHIYFQPDGE -------DEG KMIIKIFGLD WCEVEKSHQR
+ --NHSCERLA KHIYFQPDGE -------DEG KMILKIFELN WCEVEKSHQH
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ --NHSCEMLA KTVYFEPDGE -------DEG QMVLKIFELD WVEMEKSHQQ
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVHKIFELD WVEMEKSHQQ
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVHKIFELD WVEMEKSHQQ
+ --NHACEMLA KTVYFEPDGE -------DEG KMVIKIFGLD WCEIEKSHQQ
+ --NHACEMLA KSVYFEPDGE -------DEG KMVLKIFGLD WCEIEKSHQQ
+ --NHACEMLA KSVYFEPDGE -------DEG KMNLKIFGLD WCEIEKSHQQ
+ --NHACEMLA KTVYFEPDGE -------DEG KMVIKIFGLD WCEMEKAHQQ
+ --NHACEMLA KTVYFEPDGE -------DEG KMVIKIFGLD WCEMEKAHQQ
+ --NHSNEHMA KTIYFEPDGH -------DEG KMILNIFGLD WCEVETSHQE
+ RMNRLTEVAA KMAYFGPDGF HWDVELWEEN DLNCDDFELG W-NLKH----
+ RMNRLTEVAA KMAYFGPDGF HWDVELWEEN DLNCDDFELG W-NLKP----
+ RMNRLTEVAA KMAYFGPDGF HWDVELWEEN DLNCDDFELG W-NLKP----
+ MVNRSPEVAA KMAYFGPDGF HWDVELCEES DLTVDDFELG W-VLKP----
+ MVNRSPEVAA KMAYFGPDGF HWDIELCEEN DLTCDDFELG W-VLKP----
+
+ -SSVDDNVV- VVMLAFAVSF CHPWGHYIQG LGD-QHKLAR PNT---AQKL
+ -SSVDDNVV- VVMLAFAVSF CHPWGHYIQG LGD-QHKLAR PNT---AQKL
+ -SSVDDNVV- VVMLAFAVSF CHPWGHYIQG LGD-QHKLAR PNT---AQKL
+ -SSVDDNVV- VVMLAFQASF CDPWGHYIQG LGD-QYKLAR PNT---ARQL
+ -SSVRDNMI- VIMLPFNINS IDPWRHYILG LND-QIQLTR PNT---ARRL
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ARRL
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ARRL
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ACRL
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ACRL
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ACRL
+ -SSVRDNML- VIMLPFLVNN LDPWRHYILG LND-QIQLTR PNT---ARRL
+ -SSVRDNYI- VIMLPFKINS RDPWRHYILG IND-QVCLNR PET---ARRL
+ -SSVRDNII- VIMLPFKINS RDPWRHYILG LND-QVCLTR PET---ARRL
+ -SSVKDNMIR VIMLPFSNSS VDPWRHVILG LND-QIKLTR PNT---AHRL
+ -SSVKDNMIR VIMLPFPSSS VDPWRHVILG LND-QIKLTR PNT---AHRL
+ -SSVKDNMIR VVMLPFDNNS WDPWRHVILG LND-QIKLTR PNT---AHRL
+ -SSVKDNMIR VIMLPFSNNS WDPWRHVILG LND-KIKLTR PNT---AHRL
+ -SSVKDNMIR VIMLPFSNNS WDPWRHVILG LND-QIKLTR PNT---AHRL
+ -SSVKDNMIR VIMLPFGENS WDPWRHVILG LND-QIKLTR PNT---AHRL
+ -SSVDDNHC- VEMLPFMCQR VDPWGHYVQI LAD-RQDLAR PVT---LQAL
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ -SSVDDNQC- VELLPYNCQR MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQV LAD-RLDLTR PVT---LQGL
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQI LAD-RLVLTR PVT---LHGL
+ -SSVDDNQC- VELLPYLCQR MDPWGHYVQI LAD-RLNLTR PVT---LQGL
+ -SSVDDNVC- VEMLPFVCQK MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQV LAD-QLHLTR PHT---LRDL
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQV LAD-QLHLTR PHT---LRDL
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQI LAD-QLNLTR PHT---LREL
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQI LAD-QLNLTR PHT---LREL
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQI LAD-QLNLTR PHT---LREL
+ -SSVDDNYI- IEMLPFVCDR IGPWGHYAQI LAD-QLNLTR PHT---LREL
+ -SSVDDNYI- IEMLPFVCDR IGPWGHYAQI LAD-QLNLTR PHT---LREL
+ -SSVDDNYI- IEMLPFVCDR IGPWGHYAQI LAD-QLNLTR PHT---LREL
+ -SSVDDNYV- IEMLPFVCHR VGPWGHYAQV QAD-QQNLTR PHT---LADL
+ -SSVDDNYV- IDMLPFICHR VGPWGHYAQV LAD-QINLTR PHT---LRDL
+ -SSVDDNFV- IEMLPFVCHR IGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ -SSVDDNFV- IEMLPFVCHR IGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ -SSVDDNFV- IEMLPFVCHR IGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ -SSVDYNYV- IEMLPFVYHR VGPWGHYAQM LSD-QIVLTR PHT---LRDL
+ -SSVDYNYV- IEMLPFVYHR VGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ -SSVDYNYV- IEMLPFVYHR VGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRDL
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-KLVLTR PHT---LRDL
+ SSSVDDNYI- IEMLPFVCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRDI
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRNI
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRNI
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRDI
+ -SSVDDNYN- VNMLPFQNSR KDPVGHYVQD LED-ARRLIR PGT---ARSL
+ -SSVDDNYN- VNMLPFQNSR KDPVGHYVQD LED-ARRLIR PGT---ARSL
+ -SSIDDNYT- VNMLEFPNSR KDPVGHYVQN LED-AIRLIR PGT---ARSL
+ -SSIDDNYT- VNMLEFPNSR KDPVGHYVQN LED-AIRLIR PGT---ARSL
+ -SSIDDNYT- VNMLPFPNSR KDPVGHYVQD LED-AIRLIR PGT---ARSL
+ -SSIDDNYT- VNMLPFPNSR KDPVGHYVQD LED-AIRLIR PGT---ARSL
+ -SSVDDNYN- VNMLPFPNSR QDPVGHYVQD LED-LLRLIR PGT---ARSL
+ -SSVDDNYN- VNMLPFPNSR KDPVGHYVQD LED-LLRLIR PGT---ARSL
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQE LED-ALRLIR PGT---ARAL
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQE LEDSALRLIR PGT---ARAL
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQE LED-ALRLIR PGT---ARAL
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQE LED-ALRLIR PGT---ARAL
+ -SSVDDNYD- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ -SSVDDNYD- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ -SSVDDNYH- VNMLPFAQSN RDPVGHYVQG LED-ALRLIR PGT---ARAL
+ -SSVDDNYH- VNMLPFAQSN GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ -SSVDDNYN- VNMLPFVQSN GDPVGHYVQG LED-ALLLIR PGT---ARAL
+ -SSVDDNYN- VNMLPFVQSN GDPVGHYVQG LED-ALLLIR PGT---ARAL
+ -SSVDDNYD- VNMLPFVQSN GDPVGHYVQG LED-ALLLIR PGT---ARAL
+ -SSVDDNYN- VNMLPFVSSN GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ -SGVDDNYQ- VNMLPFNHSK NNPVGHYVQG LED-ALNLIR PGT---ARAL
+ -SGVDDNVQ- VNMLPFNHSK HNPVGHYVQG LED-ELNLIR PGT---ARAL
+ -SGVDDNYQ- VNMLPFNHSK HNPVGHYVQG LED-ALNLIR PGT---ARAL
+ -SGVDDNYQ- VNMLPFKHSK HNPVGHYVQG LED-ALNLIR PGT---ARAL
+ -SGVDDNYK- VNMLPFSHSK HNPVGHYVQG LGD-ALRLIR PGT---ARAL
+ -SGVDDNYK- VNMLPFSHSK HNPVGHYVQG LGD-ALRLIR PGT---ARAL
+ -SGVDDNYK- VNMLPFSHSN HNPVGHYVQG LGD-ALRLIR PGT---ARAL
+ -SGVDDNYQ- VNMLPFDHCK HNPVGHYVQG LED-ALGLIR PGT---ARAL
+ -SSVDDNYL- VNMLPFLHSR QNPVGHYVQG LED-PMHLIR PGT---ARKL
+ -SSVDDNYL- VNMLPFMQSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ -SSVDDNYL- VNMLPFIHSR DNPVGHYVQG LED-PMHLIR PGT---ARKL
+ -SSVDDNYL- VNMLPFIHSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ -SSVDDNYL- VNMLPFIRSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ -SSVDDNYL- VNMLPFMHSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ -SSVDDNYL- VNMLPFFHSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ -SSVDDNYL- VNMLPFFHSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ -SSVDDNYL- VNMLPFTHSR ETPVGHYVQG LED-PMHLMR PGT---ARAL
+ -SSVDDNYL- VNMLPFAHSR QTPVGHYVQG LED-PMHLMR PGT---ARAL
+ -SSVDDNYL- VNMLPFTHSR ETPVGHYVQD LED-PMHLMR PGT---ARAL
+ -SSVDDNYL- VNMLPFTHSR ENPVGHYVQG LED-PMHLIR PGT---ARAL
+ -SSVDDNYL- VNMLPFTHSR ENPVGHYVQG LED-PMHLIR PGT---ARAL
+ -SSSDDNHL- VNMLPFGVSR DDPVGHYMLG LED-AIRLYR PGT---ARAL
+ ---EDDHPL- LCIGSFSVHK YVSVMVYPLP MND-CVRMSQ PCHAAHAQDI
+ ---EDDHPL- LCIGSFSVHK YVSVMVYPLP MND-CVRMSQ PCHAAHAQDI
+ ---EDDHPL- LCIGSFSVHK YVSVMVYPLP MND-CVRMSQ PCHAAHAQDI
+ ---EDDHPL- ICIGSFSVHK QFSVMVYPLP MND-AIRMSQ PCHAAHAQDI
+ ---EDDHPL- ICIGSFSVHK QFSVMVYPLP MND-AIRMSQ PCYAAHAQDI
+
+ SILT---VFH FSGGFRDKPM -ERSQLHS-T YSED----KK DQKVLIHAMK
+ SILT---VFH FSGGFRDKPM -ERSQLHS-T YSED----KK DQKVLIHAMK
+ SILT---VFH FSGGFRDKPM -ERSQLHS-T YSED----KK DQKVLIHAMK
+ SILV---VMH FSGGFRDKPI -ERSQLHC-T YSEN----KK DQKVVIRAMK
+ SILH---VMH YSGEFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ SILH---VMH YSGAFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ SILH---VMH YSGAFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ SILH---VMH YSGEFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ SILH---VMH YSGEFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ SILH---VMH YSGEFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ SILM---VMH YSGEFHDKSP -ERSQLHFDS YSEH----KN DHKCVILASK
+ SILA---VMH YSGEFHDKSP -ERSHLHF-R YSEM----KN DVKCVI---K
+ SILV---VMH YSGEFHDKSP -ERSHLHY-R YSEV----KN DVKCVILASK
+ SILV---VTH YSGGFHDKSA -ERSQHHF-I YNEV----KD DHKCVILASK
+ SILV---VTH YSGGFHDKSA -ERSQHHF-I YNEV----KD DHKCVILASK
+ SILV---VMH YSGGFHDKSS -ERSQHHF-I YNEV----KN DHKCVILASK
+ SILV---VMH YSGGFHDKSA -ERSQHHF-I YNEI----KN DHKCVILASK
+ SILV---VMH YSGGFHDKSA -ERSQHHF-I YNEI----KN DHKCVILASK
+ SILV---VMH YSGGFHDNSA -ERSQHHF-I YNEV----KN DHKCVILASK
+ SILP---CPH ASGKEQDGAV -ERSQHYV-V YAEL----QV DHKCTIAAHK
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ SILP---CPH ASGKEQDGAE -ERSQHYG-V YQEL----QN DAKSTIDANK
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DAKSTIDANK
+ GILV---CPH ASGKEQDGAM -ERSQHYV-V YAEL----QN DHKNTINANK
+ YILAC--CPV ASGKEQDGNK -ERSQHYT-I YAEI----QN DHKNPISANN
+ YILAC--CPV ASGKEQDGNK -ERSQHYT-I YAEI----QN DHKNPISANN
+ YILA---CPV ASGKEQDGAQ -ERSQCYT-I YAEL----QN DHKSLISANH
+ YILA---CPV ASGKEQDGAK -ERSQCYT-I YAEL----QN DHKSLISANH
+ YILA---CPV ASGKEQDGAQ -ERSQCYT-I YAEL----QN DHKSLISANH
+ YILA---CPV ASGKEQDGAQ -ERSQCYT-I YAEL----QN DHKSLISANH
+ YILA---CPV ASGKEQDGAK -ERSQCYT-I YAEL----QN DHKSLIAANH
+ YILA---CPV ASGKEQDGAQ -ERSQCYT-I YAEL----QN DHKSLISANH
+ FILS---CPV ASGKEQDGAT -ERSQYYV-V YAEL----QN DHKSPISANK
+ FILA---CPV ASGKEQDGAT -ERSQHYV-V YAEL----QN DHKSPISANK
+ FILS---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ FILS---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ FILS---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ FILA---CRV ASGGEVDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ FILA---CPV ASGGEQDGNA -ERSQHYI-V YAEL----VN DHKSPISANK
+ FILA---CPV ASGGEQDGNA -ERSQHYI-V YAEL----VN DHKSPISANK
+ FILA---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ FILA---CYV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPILANK
+ FILA---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QD DHKSPISANK
+ FILA---CPV ASGGEQDENT -ERSQHYI-V YAEL----QN DHKSPIHANK
+ FILA---CPV ASGGEQDENT -ERSQHYI-V YAEL----QN DHKSPINANK
+ FILA---CPV ASGGEQDAVT -ERSQHYI-V YAEL----QN DHKSPISASK
+ TILF-YGCQY YSGEFQDCEI -ERSQLYN-V YCEH----KQ DHKSAIIANK
+ TILF-YGCQY YSGEFQDCEI -ERSQLYN-V YCEH----KQ DHKSAIIANK
+ TILL-YGCQY YSGEFQDCEV -ERSQCYN-V YCEL----KQ DHKSAIIANK
+ TILL-YGCQY YSGEFQDCEV -ERSQCYN-V YCEL----KQ DHKSAIIANK
+ TILL-YGCQY YSGEFQDCEV -ERSQCYN-V YCEL----KQ DHKSAIIANK
+ TILL-YGCQY YSGEFQDCEV -ERSQCYN-I YCEL----KQ DHKSAIIANK
+ TVLF-YGCQY YSGQFQDCEI -ERSQLYN-V YCEL----KQ DHKSAIMANK
+ TVLF-YGCQY YSGEFQDCEI -ERSQLYN-V YCEL----KQ DHKSAIMANK
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DYKSAIIANQ
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DYKSAIIANQ
+ VILF-YGCQY YSGKFQDSEM FERSQLYR-V YCEI----KK DYKSAIIANQ
+ VILF-YGCQY YSGKFQDSDM FERSQLYR-V YCEI----KK DYKSAIIANQ
+ IILF-YGCQY YSGKFQDSEL FERSQLYR-M YCEI----KK DHKSAIIANQ
+ IILF-YGCQY YSGKFQDSEL FERSQLYR-M YCEI----KK DHKSAIIANQ
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHNSAIIANQ
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHNSAIIANQ
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHNSAIIANQ
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIIANQ
+ VILS-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIVANQ
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIIANQ
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIMANQ
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSTIIANQ
+ VILF-YGCQF YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIIANQ
+ NILF-YGCEV YSGEFQDSES -ERSWIYN-V YCEI----KK DHKSAIIAHK
+ NILF-YGCEY YSGEFQDSES -ERSWIYN-V YCEI----KK DHKSAIMACK
+ NILF-YGCEY YSGEFQDSES -ERSWIYN-V YCEI----KK DHKSAIMAYK
+ NILF-YGCEY YSGEFQDSES -ERSWIYN-V YCEI----KK DHKSAIMAYK
+ NILF-YGCQY CSGEFQDSEE -ERSWIYN-V YCEI----KK DHKSAILAHK
+ NILF-YGCQY CSGEFQDSEE -ERSWIYN-V YCEI----KK DHKSAILAHK
+ NILF-YGCEY YSGEFQDSEE -ERSWIYN-V YCEI----KK DHKSAIMAHK
+ NILF-YGCQY YSGEFQDSEA -ERSWIYN-V YCEI----KK DHKSGIMAHK
+ NILF-YGCEY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVIAHK
+ NILF-YGCEY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ NILF-YGCEY YSGQFPDGEA -ERSWIYP-V YCEM----KK DHKSAVVAHK
+ NILF-YGCEY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ NILF-YGCEY YSGQFPDAEA -ERSWIYD-V YCEM----KK DHKSAVYAHK
+ NILF-YGCEY YSGQFPDCEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ NILF-YGCQY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ NILF-YGCQY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ NILF-YGCEY YSGQFPDGEP -ERSWIYD-V YCEL----KK DHKNAIVAVK
+ NILF-YGCEY YSGHFPDGEA -ERSWIYD-M YCEL----KK DHKSAIVAVK
+ NILF-YGCEY YSGHFPDGEP -ERSWIYD-M YCEL----KK DHKSAIVAVK
+ NILF-YGCEY YSGQFPDGEP -ERSWIYD-V YCEL----KK DHKSAIVAVK
+ NILF-YGCEY YSGQFPDGEP -ERSWIYD-V YCEL----KK DHKSAIVAVK
+ NILF---VNY YSGDFQDPEL -ERSQLYN-V YCEQ----KQ DHRNAIRASK
+ PTEQ---TRY QIHTFLDDSI -RRDLCNQ-G CHEENMVWRD DLKDPISTEV
+ PTEQ---TRY QIHTFLDDSI -RRDLCNQ-G CHEENMVWRD DLKDPISTEV
+ PTEQ---TRY QIHTFLDDSI -RRDLCNQ-G CHEENMVWRD DLKDPISTEV
+ HTDQ---DRY DVRTFLGHSI -KCHMCNQ-A CHEENIVWRD DLKDPITTEV
+ HTDQ---DRY DIRTFLEHSI -RCHLCNQ-A CHEENIVWRD DLKDPITTEV
+
+ -RNKGLDWHA GND-MKGGPK -IIYLGMLFY -------AEN NVAKQKAHFV
+ -RNKGLDWHA GND-MKGGPK -IIYLGMLFY -------AEN NVAKQKAHFV
+ -RNKGLDWHA GND-MKGGPK -IIYLGMLFY -------AEN NVAKQKAHFV
+ -RNKGCDWHA GKD-MAGGPK -IIYVGMLFY -------AES NWAKQKAHFV
+ -HNKDHDWAT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ -VNKDHDWIT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ -VNKDHDWIT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ -HNKDHDWAT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ -HNKDHDWAT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ -HNKDHDWAT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ -HNKGLDWAT GKDDMKGGAK -IMMSGALFY -------AEQ NWIRARNHFV
+ -SNKGLDWTA GKDGMKGEAK -AMMNGALFY -------AEQ NWFRKKNHFV
+ -SNKGLDWTA GKDGMKGENK -AMMNGTLFY -------AEQ NWFRQKNHFV
+ -CNKGLDWAA GKD-MKGGAK -VMMNGALFY -------AER NWIRQKHHFV
+ -CNKGLDWAA GKD-MKGGAK -IMMNGALFY -------AER NWIRQKHHFV
+ -SNKGLDWAA GKD-MKGGAK -MMANGALFY -------EER NWIRQKNHFV
+ -ANKPLDWAA GKD-MKGGAK -MMANGALFY -------AER NWIRQKNHFV
+ -ANKGLDWAA GKD-MKGGAK -MMVNGALFY -------AER NWIRQKNHFV
+ -ANKGLDWAA GKD-MKGGAK -MMVNGALFY -------AER NWIRQKNHFV
+ YQDKMKDWDT GKN-MDEGAK -MYVEIHLFY -------AEN NIRRQNDHSV
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NLRKQNEHSV
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NLRKQNEHSV
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NLIKQNEHSV
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NLRKQNEHSV
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NIRKQNEHSV
+ NPNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NIRKLNEHSV
+ NPNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NIRKQNEHSV
+ VPRKMLDWDT GKN-MDKGAK GMYHEIVLFF -------AEN NVKKQVEHSV
+ QPNKMLDWDT GKT-MDRGAA -MCGEIKLFY -------AEP NVWNQNDHSV
+ QPNKMLDWDT GKT-MDRGAA -MCGEIKLFY -------AEP NVWNQNDHSV
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ HPDKMLDWDT GKS-MDRGAA -MCREIKLFY -------AEP NVWKQNDHSV
+ HPNKLLDWDT GKT-MDRGAA -MCHEIKLFH -------AEP NVWRQNDHSV
+ HLNKMLDWDT GKT-MDREAT -MCREMKLFY -------AET NLWKQNDHSV
+ HLNKMLDWDT GKT-MDREAT -MCREMKLFY -------AET NLWKQNDHSV
+ HLNKMLDWDT GKT-MDREAT -MCREMKLFY -------AET NLWKQNDHSV
+ VLNKMLDWDT GKT-MDREAA -MCREIKLFY -------AET NVWKQNDHSV
+ VLNKMLDWDT GKT-MDREAA -MCRDIKLFY -------AET NVWKQNDHSV
+ VLNKMLDWDT GKT-MDREAA -MCRDIKLFY -------AET NVWKQNDHSV
+ HMNKMLDWDT GKT-MDFEAA -MCREIKLFY -------AET NVWKINDHSV
+ VVNKMLDWDM GKT-MDFEAA -MCREIKLFY -------AET NVWKQNNHSV
+ HMRKMLDWDT GKT-MDREAA -VCREIKLFY -------AET NCWKQNDHSV
+ VMNKMLDWDT GKT-MDREAA -MCREIKLFV -------AET NVWKQNDHSV
+ VMNKMLDWDT GKT-MDREAA -MCREIKLFV -------AET NVWKQNDHSV
+ HMNKMLDWDT GKT-MDREAA -MCREIKLFY -------AET NVWKQNDHSV
+ QEQKGMDWNT GKE-MEQGPK -IILHGSLFF -------AEP NIVRQPGVSH
+ QEQKGMDWNT GKE-MEQGPK -VILHGTLFF -------AES NIVRQPGVSH
+ QEQKGMDWNT GKE-MEQGPK -IILHGCLFF -------AEP NIVRQPGVSH
+ QEQKGMDWNT GKE-MEQGPK -IILHGCLFF -------AEP NIVRQPGVSH
+ QEQKGMDWNT GKE-MEQGPK -IILHGCLFF -------AEP NIVRQPGVSH
+ QEQKGMDWNT GKE-MEQGPK -IILHGCLFF -------AEP NIVRQPGVSH
+ QEQKGMDWNT GKE-MEQGPK -IILHGVLFF -------AEP NVVRQPGVSH
+ QEQKGMDWNT GKE-MEQGPK -IILHGVLFF -------AEP NVVRQPGVSH
+ QEHKGMEWDT GKE-MQQGPK -VVVHLALFY APSNVLAAEP NIIGQPQVSH
+ QDHKGMEWDT GKE-MQQGPK -VVVHLALFY MPSNVLAAEP NIIGQPQVSH
+ QEHKGMEWDT GKE-MQQGPK -IVVHLGLFY MPSNVLAAEP NIIGQPQVSH
+ QEHKGMEWDT GKE-MQQGPQ -IEVHLALFY MPSNVLPAEP NIIGQPQVSH
+ QEHKGMEWDT GKE-MQQGPK -VVLHHALFY APSNVLAAEP NIIGQPQVSH
+ QEHKGMEWDT GKE-MQQGPK -VVLHHALFY APSNVLAAEP NIIGQPQVSH
+ QEHKGMDWDT GKE-MQQGPK -IVVVLALFY QPSNVLAAEP NIMGQPQVSV
+ QEHKGMDWDT GKE-MQQGPK -IVVVLALFY QPSNVLAAEP NIMGQPQVSV
+ QEHKGMDWDT GKE-MQQGPK -IVVVLALFY QPSNVLAAEP NIMGQPQVSV
+ HEVKGMDWNT GKE-MQQGPK -IVVHLALFY APSNVLAAEP NIVGQPQVSH
+ QEVKGMDWDT GKE-MQQGPK -IVVHLALFY APSNVLAAEP NIVGQPQVSH
+ QGVKGMDWDT GKE-MQQGPK -IVVHLALFY APSNVLAAEP NIIGQPQVSH
+ QGVKGMDWDT GKE-MQQGPK -IVMHLALFY APSNVLAAEP NIIGQPQVSH
+ QGVKGMDWDT GKE-MQQGPK -IVVHLTLFY APSNVLAAEP NIFGQPQVSH
+ QGVKGMDWDT GKE-MQQGPK -IVVHLALFY APSNVLAAEP NIIGQPQVSH
+ YEHKGMDWDT GKE-AQQGPE -VVHHNLLFF -------AEP NIHGQPGVGH
+ YRHKGMDWDT GKE-AEQGPE -VVHHNLLFF -------AEP NIQGQPGVGH
+ FEHKGMDWDT GKE-AEQGPE -VVHHNLLFF -------AEP NIQGQPGVGH
+ YEHKGMDWDT GKE-AEQGPE -VVHHNLLFF -------AEP NIHGQPGVGH
+ YKHKGMDWDT GKE-MEQGPK -VVNYNLLFY -------AEP NIHGQPRVGH
+ YKHKGMDWDT GKE-MEQGPK -VVNYNLLFY -------AEP NIHGQPRVGH
+ YEHKGMDWDT GKE-MEQGPK -VVHHNILFY -------AEP NIHGQPRVGH
+ YDHKGVDWDT GKE-MEQGPK -VLHHNLLFY -------AEP NIHGQPTVGH
+ HEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ VEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ AEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ VEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ VEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ HEHKGMDWDT GKE-MNQGPK -VVMHGVLFN -------AEP NIHGQPGVSH
+ HQHKGMDWDT GKE-MNQGPK -VVLHGVLFN -------AEP NIHGQPGVSH
+ HQHKGMDWDT GKE-MNQGPK -VVLHGVLFN -------AEP NIHGQPGVSH
+ HEHKGMDWDT GKE-MNHGPK -VIVHGVLFH -------AEP NIGGQPGVSH
+ HCHKGMDWDT GKE-MNHGPK -VIIHGLLFH -------AEP NIGGQPGVSH
+ HCHKGMDWDT GKE-MNHGPK -VIIHGVLFH -------AEP NIGGQPGVSH
+ HEHKGMDWDT GKE-MNQGPK -VIIHGVLFH -------AEV NIHGQPGVSH
+ HEHKGMDWDT GKE-MNQGPK -VIIHGILFH -------AEV NIHGQPGVSH
+ NDHKGMAWDT AKD-MEQGPK -MVEHQVLFY -------AEP NMHGQPEVIH
+ IADKLHEWPT NVN-KENSAD ----HRQLFH -------ANS SALDKHQHNV
+ IADKLHEWPT NQN-KENSAD ----HRQLFH -------ANS SALDKHQHNV
+ IADKLHEWPT NQN-KENSAD ----HRQLFH -------ANS SALDKHQHNV
+ IAEKLQEWPT NQN-KENVAD ----HRQLFH -------ANS SALDKHRHNV
+ IADKLQEWPT NQN-AENVAD ----HRQLFH -------ANS SCLDRHRHNV
+
+ VFL-ISDATR LLIVHEGCMI DYTFMEFACH PFFAELFMEH MVARYQYYSN
+ VFL-ISDATR LLIVHEGCMI DYTFMEFACH PFFAELFMEH MVARYQYYSN
+ VFL-LSDATR LLIVHEGCMI DYTFMEFACH PFFAELFMEH MVARYQYYSN
+ VFL-ISDATR LLIHHVGCMI EYTFMEFACH PFFAELFMEH MVIRYQYYNN
+ IFL-ICDAVR ILILHHGCMT DHTFMEFACN PFFSELFMEH VYIRYQYINN
+ IFL-ICDAVR ILILHHGCMT DHTFMEFACN PFFSELFMEH VYIRYQYVNN
+ IFL-ICDAVR ILILHHGCMT DHTFMEFACN PFFSELFMEH VYIRYQYVNN
+ IFL-ICDAVR ILILHHGCMT DHTFMEFACN PFFAELFMEH VYIRYQYVNN
+ IFL-ICDAVR ILILHHGCMT DRTFMEFACN PFFAELFMEH VYIRYQYVNN
+ IFL-ICDAVR ILILHHGCMT DRTFMEFACN PFFAELFMEH VYIRYQYVNN
+ IFL-ICDAVR ILIVLHGCMT AWTFMEFACN PFFAELFMEH VYIRYQYVNN
+ IFV-FCDAVR ILIMHSGVMI GYTFMEFACN PFFAELFMEH VMVRYQYESN
+ IFV-ICDAVR ILIVHSGVMT GFTFMEFACN PFFAELFMEH VYIRYQYQAN
+ IFV-VCDAVR ILIVHYGCMI GYTFMDFACN PFFAELFMDH VFIRYVYMNN
+ IFV-VCDAVR ILIVHYRCMI GYTFMDFACN PFFAELFMDH VFIRYQYMNN
+ IFV-VCDAVR ILIVHYGCMV PYTFMAFACN PFFAELFMEH VFIRYQYVNN
+ IFI-ICDAVR ILIVHYGCMV GDTFMDFACN PFFAELFMEH VFIRYQYIPN
+ IFV-ICDAVR ILIVHYGCMV GDTFMDFACN PFFAELFMEH VFIRYQYIPN
+ IFV-ICDAVR ILIVHYGCMV GDTFMDFACN PFFAELFMEH VVIRYQYIPN
+ IFW-ISDAKK RLICGMSSMC LVTFMTLACN PLFAKLFMEV VPMRYDYLTN
+ TFV-ISDAQK RLICGVSSMV MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ TFV-ISDAQK RLICGVSSMA MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ TFV-ISDAQK RLICGVSSMV MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ TFV-ISDAQK RLICGVSSMC MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ TFV-ISDAQK RLICGVSSMC MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ TFV-ISDAQK RLICGVSSMC MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ TFV-ISDAQK RLICGVSSMC MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ IFI-IADAQK RLICGVSSMC LQTFMNLACN PFFAKLFMEV IPMRYDYQTN
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFSKLFMEV VCMRYNYTSN
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFSKLFMEV VCMRYNYTSN
+ MFI-ISDAQN KLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ VFI-ISDAVN RLICANSIMC GLTFMAMACN PHFAKLFMEV VCMRYDYFSN
+ MFI-ISDASN RLICANSIMC GLTFMAMACN PHFAKLFMEV VCMRYEYFSN
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV VCVHYDYGAN
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV VCVHYDYGAN
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV VCVHYDYGAN
+ MFI-ISDAQN RLICGNSIMC GITFMAMACN PHFAKLFMEV ACMRYDYFAN
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV ACMRYDYFAN
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV ACMRYDYFAN
+ MFI-VSDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEG VCMRYDYSAN
+ MFI-VSDAHN RLICGNSIMC ALTFMAMACN PHFAKLFMEA VCMRYDYSAN
+ MFI-VSDAQN RLICGSSIMC RLTFMAMAVN PHFAKLFMED VCMRYDYSPN
+ MFIVISDAQN RLICGSSIMC RLTFMAMAVN PHFAKLFMEE SCVRYDYSAN
+ MFIVISDAQN RLICGSSIMC GLTFMAMAVN PHFAKLFMEE SCVRYDYSRN
+ MFI-ISDAQN RLICGSSIMC GLTFMATACN PHFAKLFMEE VCMRYDYAAN
+ IFI-GNDARR VLICGKSMMP GHRFMREACV PFFHKLFMAV NQMRYDYMMN
+ IFI-GNDARR VLICGLSMMP GHRFMREACV PFFHKLFMAV NQMRYDYMVN
+ IFT-ENDARR MLICGNSMMP RHRFMREACV PFFHKLFMAV NQMRYDYVTN
+ IFT-ENDARR MLICGNSMMP RHRFMREACV PFFHKLFMAV NQMRYDYVTN
+ IFT-ENDARR MLICGNSMMP RHRFMREACV PFFHKLFMAA NQMRYDYVTN
+ IFI-ENDARR MLICGNSMMP RHRFMREACV PFFHKLFMAV NQMRYDYMTN
+ IFV-GNDARR MLICGLSMMP GHRFMKEACV PFFHKLFMAV RRMRYDYMSN
+ IFV-GNDARR MLICGLSMMP GHRFMKEACV PFFHKLFMAV RRMRYDYMTN
+ VFV-GNDARR MLIVGVSMMP AYKFMREACV PFFRKLFMAE NQVRYDYMWN
+ WFV-GNDARR MLIVGVSMMP AYKFMREACV PFFRKLFMAD NQVRYDYMWN
+ VFV-ANDARR MLIVGVSMMP AYKFMREACV PFFRKLFMAE NQVRYDYVWN
+ VFV-GNDARR MLIVGVSLMP AYKFMREACV PFFRKLFMAE NQVRYDYMWN
+ VFV-GNDARR MLITGVSMMP AYKFMREACV PFFRKLFMAE NQVRYDYVWN
+ VFV-GDDARR MLITGVSMMP AYKFMREACV PFFRKLFMAE NQVRYDYVWN
+ VFV-GNDGRR MLIVGCSMMP DYKFMREACV PFFRKLFMAE VQDRYDYAWN
+ VFV-GNDARR MLIVGCSMMP DYKFMREACV PFFRKLFMAE VQDRYDYNWN
+ VFV-GNDARR MLIVGCSMMP DYKFMREACV PFFRKLFMAE VQDRYDYNWN
+ VFV-GNDARR MLIVGVSVMP SYKFMREACV PFFHKLFMAD NQVRHEYMWN
+ VFV-GNDARR MLIVGVSVMP AYKFMREACV PFFHKLFMAE NQVRHDYMWN
+ VFV-DNDARR MLIVGQSVMP PYKFMREACV PFFHKLFMAE NQVRHDYVWN
+ VFV-DNDARR MLIVGQSVMP AYKFMREACV PFFHKLFMAE NQVRHDYVWN
+ VFV-DNDARR MLIVGQSVMP AYKFMREACV PFFHKLFMAE NQVRHDYVWN
+ VFV-DNDIRR MLIVGVSVMP AYKFMREACV PFFHKLFMAE NQVRHDYVWN
+ IFV-GNDARR KLIAGVSFMS MVKFMCEACV PFFRKLFMAV GQMRYDYVNN
+ IFV-GNDARR KLIAGLSFMA MMKFMCEACV PFFRKLFMAV GHMRYDYVSN
+ IFV-GNDARR KLIAGVSFMA VMKFMCEACV PFFRKLFMAV GQMRYDYMNN
+ IFV-GNDARR HLIAGVSFMA VVKFMCEACV PFFRKLFMAV GQMRYDYVNN
+ IFV-GNDAHR KLIAGVSFMS IMKFMCEACV PFFRKLFMAV RQMRYMYMNN
+ IFV-GNDAHR KLIAGVSFMS IMKFMCEACV PFFRKLFMAV RQMRYMYMNN
+ IFV-GNDAVR NLIAGVSFMS IMKFMCEACV PFFRKLFMAV RQMRYMYMNN
+ IFV-GNDARR KLIAGVSFMS VVKFMCEACV PFFRKLFMAF RQMRYDYVNN
+ VFM-GNDATR KLITGVSVMP TYKFMCGACV PFFHKLFMAV RNMRYDYNVN
+ VFM-GNDATR KLITGVSVMP TYKFMCGACV QFFHKLFMAV RNMRYDYTVN
+ VFM-GNDATR KLITGVSVMP TYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ VFM-GNDATR KLITGFSIMP TYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ VFM-GNDATR KLISGVSVMP TYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ VFM-GNDATR KLITGVSVMP TYKFMCNACV PFFHKLFMAV RNMRYDYTVN
+ VFM-GNDATR KLIPGVSVMH DYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ VFM-GNDATR KLIPGVSVMH DYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ VFV-GNDATR KLIAGVSVMP IVKFMCGACV PFFRKLFMAL RNMRYDYASN
+ VFV-GNDATR KLIAGASVMF IVKFMCGACV PFFRKLFMAL RNMRYDYSQN
+ VFV-GNDATR KLIAGVSVMP IVKFMCGACV PFFRKLFMAL RNMRYDYSQN
+ VFV-GNDATR KLIAGVSVMP FVKFMCGACV PFFRKLFMAL RNMRYDYTSN
+ VFV-GNDATR KLIAGVSVMP FVKFMCGACV PFFRKLFMAL RNMRYDYTSN
+ IFI-GNDAMC MLIPGMSVMV HHKFMRAACM PFFNKLFMAV RYMRYDYVDN
+ VMN-GSPCIR ALIIGGSSVG VNHFMMGPCQ EFFTDLFMMY EGLQYACVCA
+ VMN-GSPCIR ALIIGGSSVG VNHFMMGPCQ EFFTDLFMMY EGLQYACVCA
+ VMN-GSPCIR ALIIGGSSVG VNHFMMGPCQ EFFTDLFMMY EGLQYACVCA
+ MMN-GSACIR TLIIGGSIVG VNVFMMEPCQ EFFTDLFMVY EGLQYAVVCA
+ MMN-GSSCIR TLIIGGSIVG VNVFMMGPCQ EFFTDLFMVY EGLQYAVVCA
+
+ VDIKIFDTCF RSAVYAVDNS WETLCDY-EM LSGYFGAEIN HNPRLPEQVC
+ VDIKIFDTCF RSAVYAVDNS WETLCDY-EM LSGYFGAEIN HNPRLPEQVC
+ VDIKIFDTCF RSAVYAVDNS WETLCDY-EM LSGYFGAEIN HNPRLPEQVC
+ VDIKIFDTCF RGAVYAEDNS WETLCGY-EM LSGYFGAEIN HNPRLPEQVC
+ HDIKIKDTVF RLAVYAWDNF WETLCKC-EM LSGHVGAKIN HNPRLFEQVC
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ HDIKIKDTEF RLAVYAWENS WETLCNC-EM LSGHIGAKIN HNPRLFEQVC
+ HDIKIKDTCF RLAVYAWENS WETLCNV-EM LSGHFGAKIN HVPRLPEQVC
+ HDIKIKDTCF RLAVYAWENS WETLCNV-EM LSGHFGAKIN HVPRLPEQVC
+ HDIKIMDTCF RVAVYTWENS WETCFNR-EM LSGTFGAKIS HNPRLPEQVI
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGAKIS HNPRLPEQVI
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGAKIS HNPRLPEQVI
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGARIS HVPRLPEQVI
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGARIS HVPRLPEQVI
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGARIS HVPRLPEQVI
+ HDIKI----- -MEVYAPENS WETIKNV-EM VSGKEGAEIN HTPQLPEQVI
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ HDIKI----- -IEVYAPDNS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ HDIKI----- -KEVYAPENS WETIKNV-EM VSGKAGKQIN HEPQLPEQVI
+ HSIKI----- -FEVYADENS WENVRNF-EM VSGRAGAHIN HIPQLPEQAY
+ HSIKI----- -FEVYADENS WENVRNF-EM VSGRAGAHIN HIPQLPEQAY
+ HSIKI----- -FEVYADENS WENIRNF-EM VSGRAGAYIN HIPQLPEQAV
+ HSIKI----- -FEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ HSIKI----- -FEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ HSIKI----- -LEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ HSIKI----- -LEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ HSIKI----- -LEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ HSIKI----- -FEVYAEDDS WENICNF-EM MSGRTGAQIN HIPQLPEQVC
+ HSIKI----- -FEVYAEENS WENVCNF-EM MSGRAGAQIN HIPQLPEQVC
+ HDIKI----- -FEVYAAENS WENARNF-EM MSGRAGAEIN H-PQLPEQVC
+ HDIKI----- -FEVYAAENS WENARNF-EM MSGRAGAEIN H-PQLPEQVC
+ HDIKI----- -FEVYAVENS WENARNF-EM MSGRAGAEIN H-PQLPEQVC
+ PDIKI----- -FEVYAAENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ PDIKI----- -FEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ PDIKI----- -FEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ HDIKI----- -FEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ HDIKI----- -VEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ HDIKI----- -FEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ HDIKI----- -FEVYANENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ HDIKI----- -FEVYANENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ HDIKI----- -SEVYAEENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVV
+ YDIKIYETHW RMGVYALDNS WETLNVS-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIYETHW RMGVYALDNS WETLNVS-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIYETHW RVGVYAIDNS WETLNVS-EM TSGRMGAKIN HLPRLPEQVI
+ YDIKIYETHW RVGVYAIDNS WETLNVS-EM TSGRMGAKIN HLPRLPEQVI
+ YDIKIYETHW RVGVYAIDNS WETLNVS-EM TSGRMGAKIN HLPRLPEHVI
+ YDIKIYETHW RVGVYAIDNS WETLNVS-EM TSGRMGAKIN HLPRLPEQVI
+ YDIKIYETHW RPGVYALDNS WETLNVS-EM TSGRIGAKIN HLPRLPETVI
+ YDIKIYETHW RPGVYALDNS WETLNVS-EM TSGRIGAKIN HLPRLPETVI
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ YDIKIYETHY RMGVYAVDNS WETLVYC-EM TSGRIGAKVN HLPRLPEQVT
+ YDIKIYETHY RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ YNIKIYETHF RDGVYAVDNS WETLVYV-EM ASGRIGAKIN HQPRLPEQVI
+ YNIKIYETHF RVGVYAVDNS WETLVYV-EM ASGRIGAKIN HMPRLPEQVI
+ YNIKIYETHF RVGVYAVDNS WETLVYV-EM ASGRIGAKIN HMPRLPEQVI
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGANIN HLPRLPEQVV
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVV
+ YDIKIYETHF RMGVYAIDNS WETLVYC-EM TSGRIGAKIN HQPRLPEQVV
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HQPRLPEQVV
+ YDIKIYETHF RMGVYAVDNS WEALVYC-EM TSGRTGAKIN HQPRLPEQVV
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVF
+ YDIKIWETVF RGGVYAIENS WETLVLC-EM TSGRCGAKMN HLPRLFEQVC
+ YDIKIWETVF RGGVYAIENS WETLVLC-EM TSGRCGAKMN HLPRLFEQVC
+ YDIKIWETFF RGGVYAIENS WETLVLC-EM TSGRCGAKMN HLPRLFEQVC
+ YDIKIWETVF RGGVYAIENS WETLVLC-EM TSGRCGAKMN HLPRLFEQVC
+ YDIKIWETAF RGGVYAIENS WETLVLC-EM TSGRSGAKMN HLPRLFEQVC
+ YDIKIWETAF RGGVYAIENS WETLVLC-EM TSGRSGAKMN HLPRLFEQVC
+ YDIKIWETAF RGGVYAMENS WETLVLC-EM TSGRVGARMN HLPRLFEQVC
+ YDIKIWETVF RGGVYAIENS WETLILC-EM TSGRCGAKMN HMPRLFEQVC
+ YDIKIWETHI RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIWETHI RQGVYAVENS WETLITC-EM TSGRIGAKIN HLPRLPEQVV
+ YDIKIWETHI RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIWETHI RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ YDVKIWETHI RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIWETHM RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIWETHL RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIWETHL RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIVETHL REGVYAVENS WETLVVC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIVETHL REGVYAIENS WETLVVC-EM TSGRMGAKIN HLPRLPEQVI
+ YDIKIVETHL REGVYAVENS WETLVVC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIIETHL RNGVYAVENS WETLVVC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIMETHL RNGVYAVENS WETLVVC-EM TSGRIGAKIN HLPRLPEQVI
+ YDIKIDETRY RDGVYARRNS WETANVC-EM SSGRSGAKIN HNPRLPEQVT
+ MNITIQCLHT GEGVMCNVKC KEFLQREDEM KAGLIGIICN HLSRMIMVIL
+ MNITIQCLHT GEGVVCNVKC KEFLQREDEM KAGLIGIICN HLSRMIMVIL
+ MNITIQCLHT GEGVVCNVKC KEFLQREDEM KAGLIGIICN HLSRMIMVIL
+ VNIIIQCLHT NEGVVCNVKC KEFLQREEDM KSGLIGIICN HISRMCMHIL
+ INIIIQVLHT NEGVVCNVKC KEFLQREDDM KSGLIGIICN HISRMCMHIL
+
+ -PPCTITVSG LKGKLHNRWP VLTQITRTMR IQIAIRVSGS E-SENVVLQY
+ -PPCTITVSG LKGKLHNRWP VLTQITRTMR IQIAIRVSGS E-SENVVLQY
+ -PPCTITVSG LKGKLHNRWP VLTQITRTMR IQIAIRVSGS E-SENVVLQY
+ -PPCTITVSG LKGKLHNRWP VLTQITRTMR IQIPIRISGS E-SENVVLQY
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IRIKIREPGS E-SENTVVMY
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IRIKIREPGS E-SENTVVMY
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IRIKIREPGS E-SENTVVMY
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IGIKIREPGS Q-SENTVVMY
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IGIKIREPGS Q-SENTVVMY
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IGIKIREPGS Q-SENTVVMY
+ -PPCELTVSG LKGKH-VGWP YLTDITRTPL IRIQIREPGS E-CENSVVMY
+ -PPCDLTVSG LKGKQ-NGLP YLTDITRTPL IRIQIRVPGS E-SENVVVMY
+ -PPCDLTVSG LKGKQ-NGWP YLTDITRTPL IRIQIRVPGS E-SENITVMY
+ -PPCELTVSG LKGKH-NGWP YLTDITRTPL IKIHIRVPGS Q-SENHVVMY
+ -PPCELTVSG LKGKH-NGWP YLTEITRTPL IKIHIRVPGS Q-SENHVVMY
+ -PPCDLTVSG LKGKH-NGWP YLTDITRTPL IKIHIRIPGS Q-SENHVVMY
+ -PPCELTVSG LKGKH-NGWP YLTDITRTPL IRIHIRVPGS E-SENHVVMY
+ -PPCELTVSG LKGKH-NGWP YLTDITRTPL IRIHIRVPGS E-SENHVVMY
+ -PPCELTVSG LKGKH-NGWP YLTDITRTPL IRIHIRVPGS E-SENHVVMY
+ -PPCNLTVSN LKGMI-PPCP ALTEITRTV- -FIV--MYYA I-LRNKIMQY
+ -PPCCLTVSN LKGMI-PPVP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ -PPCCLTVSN LKGMI-PPCP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ -PPCCLTVSN LKGMI-PPCP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ -PPCCLTVSN LKGMI-PPCP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ -PPCCLTVSN LKGMI-PPCP ALTEITRTP- -FIM--MYVA M-LRNDIMQY
+ -PPCCLTVSN LKGMI-PPVP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ -PPCCLTVSN LKGMI-PPVP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ -PPCSLTVSN LKGMM-PPCP AMTEITRTV- -III--MYYA I-LRNEIMQY
+ -PPCKLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYGS I-LRNDVMQY
+ -PPCVLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYGS I-LRNDVMQY
+ -PPCHLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYVS I-LRNDVMQY
+ -PPCVLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYVS I-LRNDVMQY
+ -PPCVLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYVS I-LRNDVMQY
+ -PPCVLTVSN LKGVA-ASCP AMTEITRTA- -VIV--MYVS I-LRNDVMRY
+ -PPCVLTVSN LKGVA-ASCP AMTEITRTA- -VIV--MYVS I-LRNDVMRY
+ -PPCVLTVSN LKGVA-ASCP AMTEITRTA- -VIV--MYVS I-LRNDVMRY
+ -PPCHLTVSN LKGCC-ASVP AITEITRTV- -VIC--MYVS I-LCNVVMQY
+ -PPCVLTVSN LKGCC-ASCP ANTEITRTV- -VIC--MYVS I-LRNVVMQY
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNDVMQY
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNDVMQY
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNDVMQY
+ -PPCHLTVSN LKGVC-ASCP DITEITRTV- -VIC--MYVS I-LRNDVMQY
+ -PPCHLTVSN LKGVC-ASCP DITEITRTV- -VIC--MYIS I-LRNDVMQY
+ -PPCHLTVSN LKGVC-ASCP DITEITRTV- -VIC--MYIS I-LRNDVMQY
+ NPPCHLTVSN LKGVC-ASCP AITEITRTV- -VIV--MWIS I-LRNDVMQY
+ NPPCHLTVSN LKGVC-ASCP AITEITRTV- -VIV--MWIS I-LRNDVMQY
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNDVMQY
+ -PPCHLTVSN LKGVC-ASVP AITEITRTV- -VIC--MYIS I-LRNNVMQY
+ -PPCHLTVSN LKGVC-ASVP AITEITRTV- -VIC--MYIS I-LRNNVMQY
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNVVMQY
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IKIY--MWGT INFKNRVMQY
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IKIY--MWGT ICFKNRVMQY
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IEIY--MWGT INFKNQVMQY
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IEIY--MWGT INFKNQVMQY
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IEIY--MWGT INFKNQVMQY
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IEIY--MWGT INFKNQVMQY
+ -PPCVLTVSG LKDTM-AGMK HGTEITKTPD IKIH--MWGT INFKNKVMQY
+ -PPCVLTVSG LKDTM-AGMK HGTEITKTPD IKIH--MWGT INFKNKVMQY
+ -PPCILTVSG LKRTV-AGAP DETEITKSPV IHIV--MWAD IMFKNCVMQY
+ -PPCILTVSG LKRTV-AGAP DETEITKSPV IHIV--MWAD IMFKNCVMQY
+ -PPCDLTVSG LKRTV-AGPP DETEITKSPV IHIV--MWAD IVFKNCVMQY
+ -PPCILTVSG LKRTI-AGAP DETEITKSPV IHIV--MWAD IMFKNCVMQY
+ -PPWVLTVSG LKRTV-AGAP DETEITKSPI IHII--MWEE IMFKNCVMQY
+ -PPWVLTVSG LKRTV-AGAP DETEITKSPI IHII--MWED IMFKNCVMQY
+ -PPCILTVSG LKRTI-ADEP DETEITKTPI IHIV--MWAD IMFKNCVMQY
+ -PPCILTVSG LKRTI-ADEP DETEITKTPI IHIV--MWAD IMFKNCVMQY
+ -PPCILTVSG LKRTI-ADEP DETEITKTPI IHIV--MWAD IMFKNCVMQY
+ -PPCILTVSG LKRTI-AGSP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ -PPCILTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ -PPCVLTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ -PPCILTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ -PPCILTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ -PPCILTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ -PPCILTVSG LKETK-AGLI DGTEITKTPD IGIC--MWET IHFKNPVMQY
+ -PPCILTVSG LKETK-AGII DGTEITKTPE IGIC--MWDT IEFKNPVMQY
+ -PPCILTVSG LKETR-AGII EGTEITKTPD IGIC--MWDT IHFKNPVMQY
+ -PPCILTVSG LKETR-AGII DGTEITKTPD IGIC--MWDT IHFKNPVMQY
+ -PPCLLTVSG LKETV-AGII DGTEITKTPE IGIC--MWDT IHFKNPVMQY
+ -PPCLLTVSG LKETV-AGII DGTEITKTPE IGIC--MWDT IHFKNPVMQY
+ -PPCILTVSG LKETV-AGVI DGTEITKTPE IGIC--MWDT IHFKNPVMQY
+ -PPCILTVSG LKETM-AGVI DGTEITKTPD IGIG--MWDS IHFKNPVMQY
+ -PPCVLTVSG LKQPM-AGYN DQTEITKTPD ICIC--TWGT IHFKNFVMQY
+ -PPCILTVSG LKQPM-AGYN DETQITKTPD ICIC--TWGT IHFKNSVMQY
+ -PPCILTVSG LKQPM-AGYN DETQITKTPD ICIC--GVGT IHFKNLVMQY
+ -PPCILTVSG LKQPV-AGYN DETQITKTPD ICIC--TWGT IHFKNSVMQY
+ -PPCILTVSG LKQPM-AGYN METQITKTPD ICIC--TWGT IHFKNSVMQY
+ -PPCILTVSG LKQPM-AGYN DETEITKTPD ICIC--TWGT IHFKNSVMQY
+ -PPCILTVSG LKQPM-AGFV DETEITKTPD ICIC--TWGT IHFKNSVVQY
+ -PPCILTVSG LKQPM-AGFV DETEITKTPD ICIC--TWGT IHFKNSVVQY
+ -PPCILTVSG LKQSV-SGYN DETEITKTPD IKIC--TWGT IHFKNSVMQY
+ -PPCILTVSG LKRAV-NGYN DETEITKTPD IKIC--TWGT IHFKNSVMQY
+ -PPCILTVSG LKQAV-NDCN DETEITKTPD IKIC--TWPT IHFKNGMMQY
+ -PPCMLTVSG LKQAM-AGVN DETEITKTPD IKIC--TWGT IHFKNFVMQY
+ -PPCMLTVSG LKQAM-AGVN DETEITKTPD IKIC--TWGT IHFKNFVMQY
+ -PPRSLTVSG LKDTM-PGHP DVTEITKTPV IAIV--MWGT INLKNHVMQY
+ -VHCLLTHAG LKSME-IGFD R-TGVVRMPL IAEP--LYLV I-YVNAVEPY
+ -VHCLLTHAG LKSME-IGFD R-TGVVRMPL IAEP--LYLV I-YVNAVEPY
+ -VHCLLTHAG LKSME-IGFD R-TGVVRMPL IAEP--LYLV I-YVNAVEPY
+ -VVCLLTHCG LKAME-IPFD I-TGVVRGPL ITEP--LYLI I-YVNAVEPY
+ -VHCLLTHCG LKAME-IPFD R-TGVVRGPL IAEP--LYLI I-YVNAVEPY
+
+ CLYYEENKSI R--------- --QNNTGSAD LPK------- ----------
+ CLYYEENKSI R--------- --QNNTGSAD LPK------- ----------
+ CLYYEENKSI R--------- --QNNTGSAD LPK------- ----------
+ CLYYEENKSI R--------- --QNNTGSAV LPK------- ----------
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ MVYYKERKSI R--------- --QNNTGCAN LPQ------- ----------
+ MVYYKERKSI R--------- --QNNTGCAN LPQ------- ----------
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ CFYYKENRSV R--------- --INNTGQAE LPK------- ----------
+ VFYYRENRSV R--------- --QNNTGNAE LPK------- ----------
+ VFYYRENRSV R--------- --QNNTGNAE LPK------- ----------
+ VFYYRENRIV R--------- --QNNTGVAE LPK------- ----------
+ VFYYRENRIV R--------- --QNNTGVAE LPK------- ----------
+ VFYYRENRIV R--------- --QNNTGVAE LPK------- ----------
+ VFYYRENRIA R--------- --QNNTGVAE LPK------- ----------
+ VFYYRENRIA R--------- --QNNTGVAE LPK------- ----------
+ VFYYRENRIA R--------- --QNNTGVAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGAAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VVYYKENRSV R--------- --QNNTGKAE LPR------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPR------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ CNYYKENRSV R--------- --INNTGLAE LPK------- ----------
+ CNYYKENRSV R--------- --INNTGLAE LPK------- ----------
+ CNYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ CNYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ CNYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ CNYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ CTYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ CTYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ CNYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CNYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CNYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ STYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ STYYKENRSV R--------- --GNNTGGAE LPK------- ----------
+ STYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ STYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ STYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ATYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAA LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKEPRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CVYYKENRSV R--------- --VNNTGGAE LPQ------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --LNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --FNNTGGAE LPK------- ----------
+ CCYYKENRSV R--------- --FNNTGGAE LPK------- ----------
+ CVYYKENRSV R--------- --FNNTGGAE LPK------- ----------
+ CVYYKENRSV R--------- --FNNTGGAE LPK------- ----------
+ CCYYKETRSV R--------- --VNNTGGAE LPK------- ----------
+ TDAYKKPKSM HQFQFDDCQI RYRTNTGFEE TPVGATHLTH VCVCVPHPWT
+ TDAYKKPKSM HQFQFDDCQI RYRTNTGFEE TPMGATHLTH VCVCVPHPWT
+ TDAYKKPKSM HQFQFDDCQI RYRTNTGFEE TPMGATHLTH VCVCVPHPWT
+ TDAYKKPKSM HQFQFDDVQI RYRTNTGFEE NPKLATHLVH VCVVVPHPWT
+ TDAYKKPKSM HQFQFDDVQI RYRTNTGFEE NPKLATHLVH VCVVVPHPWT
+
+ ----DRLVNS FVD-ELYNSI ---YTAAPKK K--RHL-GIG DNGGMELVRE
+ ----DRLVNS FVD-ELYNSI ---YTAAPKK K--RHL-GIG DNGGMELVRE
+ ----DRLVNS FVD-ELYNSI ---YTAAPKK K--RHL-GIG DNGGMELVRE
+ ----DRLVNN FVD-ELYNSV ---YTAAPKK K--RHL-GIG DNGGMELVRE
+ ----ARLVNK VVD-ELYNNV ---YHAIPKK E--MNQ-GVG DSGGVEMVQE
+ ----ARLVNK VVD-ELYNNV ---YHAIPKK D--MNQ-GVG DSGGVEMVQE
+ ----ARLVNK VVD-ELYNNV ---YHAIPKK D--MNQ-GVG DSGGVEMVQE
+ ----HRLVNK VVD-ELYNNV ---YHAIPKK D--MNQ-GVG DSGGVEMVQE
+ ----HRLVNK VVD-ELYNNP ---YHAIPKK D--MNQ-GVG DSGGIEMVQE
+ ----HRLVNK VVD-ELYNNP ---YHAIPKK D--MNQ-GVG DSGGIEMVQE
+ ----HRLVNK VVD-ELYNNV ---YHAIPKK D--INV-GVG DSGGMEVVQE
+ ----HRLVVK VAD-ELYNNI ---YHAIPKK D--GVLLGIG DSGGMEMVQE
+ ----HRLVVK VAD-ELYNNI ---YHAIPKK D--GVLLGIG DSGGMEMAQE
+ ----HRLVDQ VVD-ELYSKF ---YHAIPKK P--GNM-GVG DSGGMEMVQE
+ ----HRLVDQ VVD-ELYSKF ---YHAIPKK P--GNM-GVG DSGGMEMVQE
+ ----HRLVDK VVD-ELYSKF ---YHAIPKK P--GNM-GIG DSGGMEMVQE
+ ----HRLVDR VVD-ELYSKF ---YHAIPKK P--GNM-DVG DSGGMEMVME
+ ----HRLVDK VVD-ELYSKF ---YHAIPKK P--GNM-DVG DSGGMEMVME
+ ----HRLVDK VVD-ELYSKF ---YHAIPKK P--GNM-DVG DSGGMEMVME
+ ----HHMQNI FID-ELYPGG ---YHAAPKK E--EMV-GPG DNGGVEDIKE
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-SPG DNGGVEAIRE
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-SPG DNGGVEAIRE
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-SPG DNGGVEAIRE
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-SPG DNGGVEAIRE
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-APG DNGGVEAIRE
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-APG DNGGVEAIRE
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-APG DNGGVEAIRE
+ ----HHVQNV FID-ELYPGH ---YHAAPKK N--ENV-GPG DNGGVEGIKE
+ ----HHMQDV FID-ELYLGP ---YHASPKK D--RFC-NPG DNGGMETYQE
+ ----HHMQDV FID-ELYLGP ---YHASPKK D--RFC-NPG DNGGMDTYQE
+ ----HHMQDV FID-ELYLGP ---YHASPKK E--RFC-NVG DNGGMETIQE
+ ----HHMQDV FID-ELYLGP ---YHASPKK E--RFC-NPG DNGGMETIQE
+ ----HHMQDV FID-ELYLGP ---YHASPKK E--RFC-NPG DNGGMETIQE
+ ----HHMQDI FID-ELYLGP ---YHASPKK Q--RFC-NPG ENGGMETIRE
+ ----HHMQDI FID-ELYLGP ---YHASPKK E--RFC-NPG ENGGMETIRE
+ ----HHMQDI FID-ELYLGP ---YHASPKK E--RFC-NPG ENGGMETIRE
+ ----HHMQDI FID-ELYPGQ ---YHASPKK K--KIC-GPG DNGGMETIEE
+ ----HHMQDI FID-ELYPGL ---YHASPKK K--KVC-GPG DNGGMETIQE
+ ----HHMQDI VID-ELYPGP ---YHATPKK H--RFC-GTG DNGGMQAIQE
+ ----HHMQDI FID-ELYPGP ---YHATPKK H--RFC-GTG DNGGMQAIQE
+ ----HHMQDI FID-ELYPGP ---DHATPKK H--RFC-GTG DNGGMQTIQE
+ ----HHMQDI FID-ELYPGH ---YHATPKK N--RYC-GPG DNGGMQVIEE
+ ----HHMQDI FID-ELYPGH ---YHATPKK N--RFC-GPG DNGGMQVIEE
+ ----HHMQDI FID-ELYPGH ---YHATPKK N--RFC-GPG DNGGMQVIEE
+ ----HPMQEI FID-ELYPGH ---YHATPKK N--RFC-GPG DNGGMQSMQE
+ ----HPVQDI FID-ELYPGH ---YHATPKK V--RFC-GPG DNGGMQAIQE
+ ----HHMQDI FID-ELYPGR ---YHATPKK N--RYC-GPG DNGGMQPIQE
+ ----HHMQDI FID-ELYPGH ---YQATPKK D--KFC-GPG DNGGMQTIQE
+ ----HHMQDI FID-ELYPGH ---YHATPKK D--KFC-GPG DNGGMQTIQE
+ ----HHMQDI FID-ELYPGH ---YHATPKK N--RCC-GPG DNGGMQTVQE
+ ----YHHQNI LID-ELYSNV ---YPAAPKK H--QYM-GVG DVGGYEVICE
+ ----YHHQNI LID-ELYSNV ---YPAAPKK H--QYM-GVG DVGGYEMICE
+ ----YHHQNI LID-ELYNNI ---YPAAPKK H--KFL-GVG DVGGYEIICE
+ ----YHHQNI LID-ELYNNI ---YPAAPKK H--KFL-GVG DVGGYEIICE
+ ----YHHQNI LID-ELYNDI ---YPAAPKK H--KFL-GVG DVGGYEIICE
+ ----YHHQNI LID-ELYNNI ---YPAAPKK H--KFL-GVG DVGGYEIICE
+ ----YHHQNI LID-ELYSNI ---YPATPKK H--QYM-GVG DVGGYEVICE
+ ----YHHQNI LID-ELYSNI ---YPATPKK H--QYM-GVG DVGGYEVICE
+ ----YHQQNI LTD-ELYSDV ---YPAAQKK Y--QVM-GVG DIGGYELICE
+ ----YHQQNI LTD-ELYSDL ---YPAAPKK Y--QEM-GVG DIGGYELIVE
+ ----YHQQNL LTD-ELYSDI ---YPAAPKK Y--QVM-GVG DIGGYELIVE
+ ----YHQQNL LTD-ELYSDI ---YPAAPKK Y--QVM-GVG DIGGYELIVE
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QVM-GVG DIGGYELICE
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QVM-GVG DIGGYELICE
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QIM-GVG DIGGYELICE
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QIM-GVG DIGGYELICE
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QIM-GVG DIGGYELICE
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIRVM-GVG DIGGYEMICE
+ ----YHQQNI LTD-ELYSDV ---YPTAPKK YVIRVM-GVG DIGGYELICE
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIRQM-GMG DIGGYELICE
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIRQM-GMG DIGGYELICE
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIRQM-GMG DIGGYELICE
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIREM-GVG DIGGYELICE
+ ----YHHQNT LVD-ELYSDV ---YPAAPKK K--VCM-GVG DVGGYEVMGE
+ ----YHHQNT LVD-ELYSDI ---YPAAPKK K--VCM-GVG DVGGYEVMGE
+ ----YHHQNT LVD-ELYSDI ---YPAAPKK K--VCM-GVG EVGGYEVMGE
+ ----YHDQNT LVD-ELYSDV ---YPAAPKK K--VCM-GVG DVGGYEVMGE
+ ----YHNQNT LVD-ELYSDV ---YPAAPKK Q--HYM-GVG DVGGYEVMGE
+ ----YHNQNT LVD-ELYSDV ---YPAAPKK Q--HYM-GVG DVGGYEVMGE
+ ----YHNFNA LVD-ELYSDV ---YPAAPKK K--HYM-GVG DVGGYEVMGE
+ ----YHHQNS LVD-ELYSDV ---YPAAPKK K--HYM-GVG DVGGYEVMGE
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ ----YHHQNI LVD-ELYSDV ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ ----YHHQNM LVD-ELYSDM ---YPAAPKK K--VYV-GAG DVGGYEVMSE
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ ----YHHQNV LVD-ELYGEA ---YPAAPKK K--HYM-GAG DVGGYEVMSE
+ ----YHHQNV LVD-ELYSEL ---YPAAPKK A--HYM-GAG DIGGYEVMSE
+ ----YHHQNV LVD-ELYSEV ---YPAAPKK A--FYM-GAG DIGGYEVMSE
+ ----YHHQNA LVD-ELYSDV ---YPAAPKK K--HYM-GEG DVGGYEVMSE
+ ----YHHQNV LVD-ELYSDG ---YPAAPKK K--HYM-GEG DVGGYEVMSE
+ ----YHYQNI LVD-ELYSND ---YPAAPKK A--QFM-GVG DVGGYEIVCE
+ KGKSEILQNM GSA-VLYNDV IRDHNASEQK E--AHV-PMG DEGRISRAKD
+ KGKSEILQNM GSA-VLYNDV IRDHNASEQK E--AHV-PMG DQGRISRAKD
+ KGKSEILQNM GSA-VLYNDV IRDYNASEQK E--AHV-PMG DQGRISRAKD
+ KGKSEILQNM ESA-HLYNAV IRDNNASEQK E--AHV-PVG DEGRISRAKN
+ KGKSEILQNM ESARHLYNAV IRDNNASHQK E--AHV-PAG DQGRISRAKN
+
+ DIFQILVCV
+ DIFQILVCV
+ DIFQILVCV
+ DIFQILVCV
+ DVFQILVCI
+ DVFQILVCI
+ DVFQILVCI
+ DVFQILVCI
+ DVFQILVCI
+ DVFQILVCI
+ DVFQILVCI
+ DLFQILVCA
+ DLFQILVCV
+ DVFQILVCL
+ DVFQILVCL
+ DLFQILVCI
+ DVFQILVCV
+ DVFQILVCV
+ DVFQILVCA
+ DMFQVLVCR
+ DMFQVLVCK
+ DMFQVLVCK
+ DMFQVLVCK
+ DMFQVLVCK
+ DMFQVLVCK
+ DMFQVLVCK
+ DMFQVLVCK
+ DMFQVLVCQ
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCI
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVYV
+ DMFQVLVYV
+ DMFQVLVYV
+ DVFQVLVCV
+ DVFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ DMFQVLVCV
+ NLFQILVVE
+ NLFQILVVE
+ NLFQILVVE
+ NLFQILVVE
+ NLFQILVVE
+ NLFQILVVE
+ NLFQILVVE
+ NLFQILVVE
+ DLFQILVCQ
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCQ
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVCE
+ DLFQILVHE
+ DLFQILVHE
+ DLFQILVHE
+ DLFQILVHE
+ DLFQILVHG
+ DLFQILVHA
+ DLFQILVHE
+ DLFQILVHE
+ DLFQILVHE
+ DLFQILVHE
+ DLFQILVHK
+ DLFQILVHA
+ DLFQILVHA
+ DIFQILVCD
+ EIMYIRDLE
+ EIMYIRDLE
+ EIMYIRDLE
+ EILYIRDLE
+ EILYIRDLE
+
diff --git a/test/example.ph3 b/test/example.ph3
new file mode 100644
index 0000000..bc08705
--- /dev/null
+++ b/test/example.ph3
@@ -0,0 +1,2601 @@
+ 100 1209 I
+t73 LIVSQIRVMV RDG--IHKAM DEE-V----- -------LIA RRVKPYSGNG
+ TQVRNDVEDA N--CQEFVGI ---RELGKH- YK-CMDGFHT VNNGAGEN-S
+ ESAMWIFDLW MCKLNHGMQR --------GD IGRVKRDVQK FPKLKEGAPN
+ CSSFVKPYFM GCDMFHKQVE YRGTHGLVLD DTWNEESATF PYPQVHSRSD
+ KRCLNGLHQG DHEESVH--- HAPRI----M R---LIGH-H LVIIVLMNHD
+ MGRLNHLEPD AVIPSPLRIG GDGWVPKPI- ---------- -------EDG
+ FFDK-D-Q-- ----SRPDVA NASIVPDK-- --DQWVGAHN QWGSSLRKVG
+ LAVHDLR-NI SDLYRCVWMD CHLGANHYRQ ISRMKMITPT YTHMTEYANG
+ L----WHPFY KASDHKNEAQ GVGEK-PHQL PCVESETCQY ETKHAKVCKQ
+ VHG-ALYLIG MKTVVKPLLG DWEGCKCRS- --KLYVSQLD H----KTLSK
+ -NLGLY--MQ KRTWLATAPL Q------IGC MFMLVGRKKN SEE-NYNKAA
+ DPTVIWFYTQ PIVYV-ADVF GCTKGKNPQE MRG------N NVMSESLGDD
+ NLQD--MSGV PVTVCTSSVM VRKDMQD-SV DKRGCTWNAK E-DHLCPSSF
+ CKGER---ED EPGGVTQ--- ---------- ----RCIENI AKLLYIKDV-
+ LCNEVLNGLQ WQLCWSV-GD WESLIPQACW DAKKDLAVCA WKMELVPGL-
+ --NRNNENLA KVIYFGPDGH -------DEG PMQAKIVTLH W-EMDVSHRG
+ -SSVDDNVV- VVMLAFAVSF CHPWGHYIQG LGD-QHKLAR PNT---AQKL
+ SILT---VFH FSGGFRDKPM -ERSQLHS-T YSED----KK DQKVLIHAMK
+ -RNKGLDWHA GND-MKGGPK -IIYLGMLFY -------AEN NVAKQKAHFV
+ VFL-ISDATR LLIVHEGCMI DYTFMEFACH PFFAELFMEH MVARYQYYSN
+ VDIKIFDTCF RSAVYAVDNS WETLCDY-EM LSGYFGAEIN HNPRLPEQVC
+ -PPCTITVSG LKGKLHNRWP VLTQITRTMR IQIAIRVSGS E-SENVVLQY
+ CLYYEENKSI R--------- --QNNTGSAD LPK------- ----------
+ ----DRLVNS FVD-ELYNSI ---YTAAPKK K--RHL-GIG DNGGMELVRE
+ DIFQILVCV
+
+t66 LIVSQIRVMV RDG--IHKAM DEE-V----- -------LIA RRVKPCSGNG
+ TQVRNDVEDA N--CQEFVGI ---RELGKH- YK-CMDGFHT VNNGAGEN-S
+ ESAMWIFDLW MCKLNHGMQR --------GD IGRVKRDVQK FPKLKEGAPN
+ CSSFVKPYFM GCDMFHKQVE YRGTHGLVLD DTWNEESATF PYPQVHSRSD
+ KRCLNGLHQG DHEESVH--- HAPRI----M R---LIGH-H LVIIVLMNHD
+ MGRLNHLEPD AVIPSPLRIG GDGWVPKPI- ---------- -------EDG
+ FFDK-D-Q-- ----SRPDVA NASIVPDK-- --DQWVGAHN QWGSSLRKVG
+ LAVHDLR-NI SDLYRCVWMD CHLGANHYRQ ISRMKMITPT YTHMTEYANG
+ L----WHPFY KASDHKNEAQ GVGEK-PHQL PCVESETCQY ETKHAKVCKQ
+ VHG-ALYLIG MKTVVKPLLG DWEGCKCRS- --KLYVSQLD H----KTLSK
+ -NLGLY--MQ KRTWLATAPL Q------IGC MFMLVGRKKN SEE-NYNKAA
+ DPTVIWFYTQ PIVYV-ADVF GCTKRKNPQE MRG------N NVMSESLGDD
+ NLQD--MSGV PVTVCTSSVM VRKDMQD-SV DKRGCTWNAK E-DHLCPSSF
+ CKGER---ED EPGGVTQ--- ---------- ----RCIENI AKLLYIKDV-
+ LCNEVLNGLQ WQLCWSV-GD WESLIPQACW DAKKDLAVCA WKMELVPGL-
+ --NRNNENLA KVIYFGPDGH -------DEG PMQAKIVTLH W-EMDVSHRG
+ -SSVDDNVV- VVMLAFAVSF CHPWGHYIQG LGD-QHKLAR PNT---AQKL
+ SILT---VFH FSGGFRDKPM -ERSQLHS-T YSED----KK DQKVLIHAMK
+ -RNKGLDWHA GND-MKGGPK -IIYLGMLFY -------AEN NVAKQKAHFV
+ VFL-ISDATR LLIVHEGCMI DYTFMEFACH PFFAELFMEH MVARYQYYSN
+ VDIKIFDTCF RSAVYAVDNS WETLCDY-EM LSGYFGAEIN HNPRLPEQVC
+ -PPCTITVSG LKGKLHNRWP VLTQITRTMR IQIAIRVSGS E-SENVVLQY
+ CLYYEENKSI R--------- --QNNTGSAD LPK------- ----------
+ ----DRLVNS FVD-ELYNSI ---YTAAPKK K--RHL-GIG DNGGMELVRE
+ DIFQILVCV
+
+t32 LIVSQIRVMV RDG--IHKAM DEE-V----- -------LIA RRVKPYSGNG
+ TQVRNDVEDA N--CQEFVGI ---RELGKH- YK-CMDGFHT VNNGAGEN-S
+ ESAMWIFDLW MCKLNHGMQR --------GD IGRVKQDVQK FPKLKEGAPN
+ CSSFVKPYFM GCDMFHKQVE YRGTHGLVLD DTWNEESATF PYPQVHSRSD
+ KRCLNGLHQG DHEESVH--- HAPRI----M R---LIGH-H LVIIVLMNHD
+ MGRLNHLEPD AVIPSPLRIG GDGWVPKPI- ---------- -------EDG
+ FFDK-D-Q-- ----ARPDVA NASIVPDK-- --DQWVGAHN QWGSSLRKVG
+ LAVHDLR-NI SDLYRCVWMD CHLGANHYRQ ISRMKMITPT YTHMTEYANG
+ L----WHPFY KASDHKNEAQ GVGEK-PHQL PCVESETCQY ETKHAKVCKQ
+ VHG-ALYLIG MKTVVKPLLG DWEGCKCRS- --KLYVSQLD H----KTLSK
+ -NLGLY--MQ KRTWLATAPL Q------IGC MFMLVGRKKN SEE-NYNKAA
+ DPTVIWFYTQ PIVYV-ADVF GCTKGKNPQE MRG------N NVMSESLGDD
+ NLQD--MSGV PVTVCTSSVM VRKDMQD-SV DKRGCTWNAK E-DHLCPSSF
+ CKGER---ED EPGGVTQ--- ---------- ----RCIENI AKLLYIKDV-
+ LCNDVLNLLV WQLCWSV-GD WESLIPQACW DAKKDLAVCA WKMELVPGL-
+ --NRNNENLA KVIYFGPDGH -------DEG PMQAKIVTLH W-EMDVSHRG
+ -SSVDDNVV- VVMLAFAVSF CHPWGHYIQG LGD-QHKLAR PNT---AQKL
+ SILT---VFH FSGGFRDKPM -ERSQLHS-T YSED----KK DQKVLIHAMK
+ -RNKGLDWHA GND-MKGGPK -IIYLGMLFY -------AEN NVAKQKAHFV
+ VFL-LSDATR LLIVHEGCMI DYTFMEFACH PFFAELFMEH MVARYQYYSN
+ VDIKIFDTCF RSAVYAVDNS WETLCDY-EM LSGYFGAEIN HNPRLPEQVC
+ -PPCTITVSG LKGKLHNRWP VLTQITRTMR IQIAIRVSGS E-SENVVLQY
+ CLYYEENKSI R--------- --QNNTGSAD LPK------- ----------
+ ----DRLVNS FVD-ELYNSI ---YTAAPKK K--RHL-GIG DNGGMELVRE
+ DIFQILVCV
+
+t75 LIVSEIRVMV RDE--VHKAM DEE-C----- -------LIA RRVKPYSGNG
+ NQIRNDIEDA N--GQEFVGI ---RELGKH- YD-CMDGYHT VNNGAGEN-S
+ ESAMWIFDLW MCKLNHGMQR --------GD IGRVQQDVHK FPKLKEGAPN
+ CSSFVKPVFM GCDMFHRQVQ NRGNHGLVLD DTWNEESGTF PYPQVHSRNE
+ KRCINKLHQG DHNESCH--- HNPRI----V R---RIGH-H LVIIVLVNRD
+ MGRLNYIEPD ALVPSPLRFG GDEWVPKPI- ---------- -------EDG
+ FFDK-D-Q-- ----ARPDVA NA-IVPDR-- --DQWVGAHK EWGSSLCKVG
+ LAVHDLR-NV SDLYRCVWME CVLGANHYQQ VSRMKMVTPA YTHMTEYANG
+ L----WHPFY KNPDHKNEAQ GVGEK-PHQL PCVESETCQY ETKHAKVCKQ
+ VHG-ALYLIG MKTVAKPVLG DWEGCKCRSD LIKLYVSQLD H----KTLSK
+ -NMGLY--MR NRTWLATSPL Q------IGC IFMLVGRKKN SEE-NYNKAA
+ DPTVIWFYTQ PIVYV-ADVF GCTKGKNPQE MRK------N NVISESLGDD
+ NLQD--MPGM PVTVCTSSVM VRKDMHQ-SV DKRGYTWHAK E-DHLCPDSF
+ CKGEK---EE EPGGVRR--- ---------- ----RIVENI VKLLYIKDV-
+ LCNQVLNLLQ WQLCWSV-GD WESLVPQACW GAKKDLAVCA WKMELVPGL-
+ --NRNNENLA KIIYFGPDGH -------DEG NMQAKIVTLH W-EMDVSHRG
+ -SSVDDNVV- VVMLAFQASF CDPWGHYIQG LGD-QYKLAR PNT---ARQL
+ SILV---VMH FSGGFRDKPI -ERSQLHC-T YSEN----KK DQKVVIRAMK
+ -RNKGCDWHA GKD-MAGGPK -IIYVGMLFY -------AES NWAKQKAHFV
+ VFL-ISDATR LLIHHVGCMI EYTFMEFACH PFFAELFMEH MVIRYQYYNN
+ VDIKIFDTCF RGAVYAEDNS WETLCGY-EM LSGYFGAEIN HNPRLPEQVC
+ -PPCTITVSG LKGKLHNRWP VLTQITRTMR IQIPIRISGS E-SENVVLQY
+ CLYYEENKSI R--------- --QNNTGSAV LPK------- ----------
+ ----DRLVNN FVD-ELYNSV ---YTAAPKK K--RHL-GIG DNGGMELVRE
+ DIFQILVCV
+
+t79 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTFSGSQ
+ NQVRNAVEDA A--RPDFVGT ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ CSSIPMPYFL GVDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGL-N LVIISYANVD
+ MGRLNHCEDE AIVFSPLRYG GAGFVSKPI- ---------- -------GDG
+ FFDK-D-Q-- ----ARPLMA NAVCVPEN-- --DQWTGAVG QWCSSVVKCG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ L----WKPFY QASDHKNEAQ GVGER-THQL PCVESHTCQY EVKHAKVCKL
+ VHH-ALYLLG LRTVMKPHLG DVDGCRCRSD LNNLILSQLD D----KTLSK
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SAN-NYNRAG
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ SLQQ--MPAV PVDVCVMSVM VNKSMPQ-SH DKRGYTWQAK Q-DHLFPVNV
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ DCNMVLSLLV WQLC--H-GD WEPLLPQACE SARRDLAVCA WKRELVPGL-
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ -SSVRDNMI- VIMLPFNINS IDPWRHYILG LND-QIQLTR PNT---ARRL
+ SILH---VMH YSGEFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ -HNKDHDWAT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ IFL-ICDAVR ILILHHGCMT DHTFMEFACN PFFSELFMEH VYIRYQYINN
+ HDIKIKDTVF RLAVYAWDNF WETLCKC-EM LSGHVGAKIN HNPRLFEQVC
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IRIKIREPGS E-SENTVVMY
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ ----ARLVNK VVD-ELYNNV ---YHAIPKK E--MNQ-GVG DSGGVEMVQE
+ DVFQILVCI
+
+t27 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTMSGSQ
+ NQVRNAVEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ CSSIPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ MGRLNHCEDQ AIVYSPLRYG GAGFVSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPLMA NAVCVPEN-- --DQWTGAVG QWCSSVVKCG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ L----WKPFY QASDHKNEAQ GVGER-THQL PCVESHTCQY EVKHAKVCKL
+ VHH-ALYLLG IHTVMKPHLG NVDGCRCRSD LNNLILSQLD D----KTLSK
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SAN-NYNRAG
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNC
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ DCNIVLSLLV WQLC--H-GD WEPLLPQACE GARRDLAVCA WKRELVPGL-
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ARRL
+ SILH---VMH YSGAFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ -VNKDHDWIT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ IFL-ICDAVR ILILHHGCMT DHTFMEFACN PFFSELFMEH VYIRYQYVNN
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IRIKIREPGS E-SENTVVMY
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ ----ARLVNK VVD-ELYNNV ---YHAIPKK D--MNQ-GVG DSGGVEMVQE
+ DVFQILVCI
+
+t93 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTMSGSQ
+ NQVRNAVEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ CSSIPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ MGRLNHCEDQ AIVYSPLRYG GAGFVSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPLMA NAVCVPEN-- --DQWTGAVG QWCSSVVKCG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ L----WKPFY QASDHKNEAQ GVGER-THQL PCVESHTCQY EVKHAKVCKL
+ VHH-ALYLLG IHTVMKPHLG NVDGCRCRSD LNNLILSQLD D----KTLSK
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SAN-NYNRAG
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNC
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ DCNIVLSLLV WQLC--H-GD WEPLLPQACE GARRDLAVCA WKRELVPGL-
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ARRL
+ SILH---VMH YSGAFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ -VNKDHDWIT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ IFL-ICDAVR ILILHHGCMT DHTFMEFACN PFFSELFMEH VYIRYQYVNN
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IRIKIREPGS E-SENTVVMY
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ ----ARLVNK VVD-ELYNNV ---YHAIPKK D--MNQ-GVG DSGGVEMVQE
+ DVFQILVCI
+
+t59 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTFSGSQ
+ NQVRNAVEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ ESAVVIFDVW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ CSSIPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ MGRLNHCEDE AIVFSPLRYG GAGFVSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPLMA NAHCVPEN-- --DQWTGAVG QWCSSVVKCG
+ LADHPLE-NI SRLLRCVVME CILGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ M----WKPFY QASDHKNEAQ GVGER-THQL PCVDSHTCQY EVKHAQVCKL
+ VHH-ALYLLG LRTVMKPHLG DVDGCRCRSD LNNLILSQLD D----KTLSK
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SGN-NYNQAG
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNF
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ DCNIDLSLLV WQLC--H-GD WEPLLPQACE SARRDLAVCA WKRELVPGL-
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ACRL
+ SILH---VMH YSGEFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ -HNKDHDWAT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ IFL-ICDAVR ILILHHGCMT DHTFMEFACN PFFAELFMEH VYIRYQYVNN
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IGIKIREPGS Q-SENTVVMY
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ ----HRLVNK VVD-ELYNNV ---YHAIPKK D--MNQ-GVG DSGGVEMVQE
+ DVFQILVCI
+
+t7 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKKFSGSQ
+ GQVRNAIEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ CSSMPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ MGRLNHCEDE AIVFSPLRYG GAGFVSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPLMA NAHCVPEN-- --DQWTGAVG QWCSSVVKCG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ M----WKPFY QASDHKNEAQ GVGER-THQL PCVDSHTCQY EVKHAQVCKL
+ VHH-ALYLLG LRTVMKPHLG DVDGCRCRSD LNNLILSQLD D----KTLSK
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SGN-NYNRAG
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNF
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ DCNIVLSLLV WQLC--H-GD WEPLLPQACE SARRDLAVCA WKRELVPGL-
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ACRL
+ SILH---VMH YSGEFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ -HNKDHDWAT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ IFL-ICDAVR ILILHHGCMT DRTFMEFACN PFFAELFMEH VYIRYQYVNN
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IGIKIREPGS Q-SENTVVMY
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ ----HRLVNK VVD-ELYNNP ---YHAIPKK D--MNQ-GVG DSGGIEMVQE
+ DVFQILVCI
+
+t78 LIVSEVRVMV RDG--LNIAI DEL-C----- -------LIA NRVKTFSGSQ
+ GQVRNAIEDA A--RPDFVGI ---RELGKQ- YE-CMDGVGA VDTGAGDN-S
+ ESAVVIFDIW MCQLPHGMQW --------GD IGRVVVDHPK FLKLEEGAPN
+ CSSIPMPYFL GCDMFHREVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ KRCLNVLHQG DHEESRH--- HNARI----V R---RIGM-N LVIISYANVD
+ MGRLNHCEDE AIVFSPLRYG GAGFVSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPLMA NAHCVPEN-- --DQWTGAVG QWCSSVVKCG
+ LADHPLE-NI SRLLRCVVME CVLGANVYHQ ISRMKMHGPT YSHVMEYAHG
+ M----WKPFY QASDHKNEAQ GVGER-THQL PCVDSHTCQY EVKHAQVCKL
+ VHH-ALYLLG LRTVMKPHLG DVDGCRCRSD LNNLILSQLD D----KTLSK
+ -NCFTY--LG NMTWLATSPL H------IGC MIIFVGRKQQ SGN-NYNRAG
+ DPTTICFCRK PIVMH-ADVF GCARAKDPQE MRM------N NVISESLGDD
+ SLQQ--MPAV PVTVCVMSHM VKKSMPQ-SH DKRGYTWQAK Q-DHLFPVNF
+ VKGEQ---EE EPEGADQ--- ---------- ----RTVHDM VRLLYSKDV-
+ DCNIVLSLLV WQLC--H-GD WEPLLPQACE SARRDLAVCA WKRELVPGL-
+ --NHNNEFLA KIIYFGPDGH -------DEG PMGQKIVDLH W-EMEASHRE
+ -SSVRDNMI- VIMLPFSINS IDPWRHYILG LND-QIQLTR PNT---ACRL
+ SILH---VMH YSGEFHDKSA -ERSQLHS-R YSEH----KN DHKCVILASK
+ -HNKDHDWAT GKDEMKGGAK -IMNPGALFY -------AEQ NWVRPKNHFV
+ IFL-ICDAVR ILILHHGCMT DRTFMEFACN PFFAELFMEH VYIRYQYVNN
+ HDIKIKDTVF RLAVYAWENF WETLCNC-EM LSGHVGAKIN HNPRLFEQVC
+ -PPVELTVSG LKGKV-NGWP YLTDITRTPL IGIKIREPGS Q-SENTVVMY
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ ----HRLVNK VVD-ELYNNP ---YHAIPKK D--MNQ-GVG DSGGIEMVQE
+ DVFQILVCI
+
+t12 LIVSEVRVMV RDG--INIAI DEL-C----- -------LIA NRVKAFSGHQ
+ NQVRNAMEDA Q--RPDFVGI ---RELGKQ- YQ-CMDGHGA VDTGAGRN-S
+ ESAVWIFDIW MCKLAHGMQW --------GD IGRVSVDHPK FLKLEEGAPR
+ CSSCPMPYFL GCEMFHRQVI LKGAKGLVLP D--NEDSMAF PYVQVHSRSV
+ KRCLNVLVQG DHDESRH--- HNARI----V A---RIGM-N MVIIRYLNVE
+ MGRLNHCEDD AMVYSPLRIG GAGTHSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPLIA NAHIVPEN-- --DQWTGAVA QWCSSVIKCG
+ LANHDLE-NI SRLLRCVVME CVLGANVYHQ ASRMKMHGPY YAHVTEYAHG
+ L----WKPFY QTSDHKNEAQ GVGES-THQL PCVESQTCQY EVKHAKVCKL
+ VHH-ALYLLA LHTMMKPRLG DIDGCRCRSE LNKLALSQLD D----KTLSK
+ -NCFQY--LG NMTWLATSPL H------VGC MIIF------ ----------
+ ---------- ---------- ---------- --V------N NVLSQSLGDD
+ SLQQ--MHAM PVTVVVVSHM VKKSMPQ-SH DKRGYTWQAK DFDQLIPVSF
+ VKGEQ---EE EPEGPNN--- ---------- ----RVVHNI VKLLYTKDV-
+ DCNTVLSLLI WQLC--H-GD WEQLVPQACA GARSDLAVCA WKRELVPGL-
+ --NHNNENLA KVIYFGPDGH -------DEG PMGRKIVDLH W-EMEASHRD
+ -SSVRDNML- VIMLPFLVNN LDPWRHYILG LND-QIQLTR PNT---ARRL
+ SILM---VMH YSGEFHDKSP -ERSQLHFDS YSEH----KN DHKCVILASK
+ -HNKGLDWAT GKDDMKGGAK -IMMSGALFY -------AEQ NWIRARNHFV
+ IFL-ICDAVR ILIVLHGCMT AWTFMEFACN PFFAELFMEH VYIRYQYVNN
+ HDIKIKDTEF RLAVYAWENS WETLCNC-EM LSGHIGAKIN HNPRLFEQVC
+ -PPCELTVSG LKGKH-VGWP YLTDITRTPL IRIQIREPGS E-CENSVVMY
+ VIYYKERKSI R--------- --QNNTGCAK LPQ------- ----------
+ ----HRLVNK VVD-ELYNNV ---YHAIPKK D--INV-GVG DSGGMEVVQE
+ DVFQILVCI
+
+t81 LIVSEVRHMV RDG--ANVAI DEL-C----- -------LIA CRVKAFSGHG
+ HQVRNAVEDA A--RPDFIGI ---RELGKP- Y--CMDGHGA VNTGAGHN-S
+ ESAVWIFDIW MYKLSHGMQW --------GD IGRVGVDHPK FLKLEEGAPN
+ CSSLPMPYFL GVDMFHRQVT IKGAKGLVLP DIWNESPMAF PYAQVHSKSH
+ KRCLNVLVQG DHEESEH--- HNARI----M S---KIGT-H LVIINIINVE
+ MQRLNHCEDK AIVYSPDRIG GAGFHSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPIIA NAHIVPVN-- --DQWTGPMA QWCSSVIKCG
+ LANHELE-DV SRLLRCVGME CNLGANHYHQ VSRMKMHGPI YSHMTEYAVG
+ L----WKPFY QASEHKNEAQ GLGER-PHQL PCVESQTCQY EIKVAKVCKL
+ VHV-ALYLVG LKTVVKPKLG DWDGIRCRSE LNKLYLSQLD D----KTLSK
+ -NCFIY--LG NMTWLATSPL Q------IGW LVLFDGRKRQ SAE-DYNRAA
+ DPTTISFCRK PIVQH-ADVF GCDRDKDPQE MRT------N NVISESLGDD
+ FLQQ--MPAV PVSVCVYSHM VKKFVPQ-SH EKRGYTWKAK E-DHLVPISY
+ CKGEH---EE EPEGAQY--- ---------- ----RVVQNI VKLLYTKDV-
+ DCNVVLSLLV WQLC--H-GD WEPLIPQACQ TAKKDLAVCA WKRELVPGL-
+ --NCNNEYLA KIIYFGPDGH -------DEG PMGRKIVDLH W-EMEASHRD
+ -SSVRDNYI- VIMLPFKINS RDPWRHYILG IND-QVCLNR PET---ARRL
+ SILA---VMH YSGEFHDKSP -ERSHLHF-R YSEM----KN DVKCVI---K
+ -SNKGLDWTA GKDGMKGEAK -AMMNGALFY -------AEQ NWFRKKNHFV
+ IFV-FCDAVR ILIMHSGVMI GYTFMEFACN PFFAELFMEH VMVRYQYESN
+ HDIKIKDTCF RLAVYAWENS WETLCNV-EM LSGHFGAKIN HVPRLPEQVC
+ -PPCDLTVSG LKGKQ-NGLP YLTDITRTPL IRIQIRVPGS E-SENVVVMY
+ MVYYKERKSI R--------- --QNNTGCAN LPQ------- ----------
+ ----HRLVVK VAD-ELYNNI ---YHAIPKK D--GVLLGIG DSGGMEMVQE
+ DLFQILVCA
+
+t21 LIVSEVRHMV RDG--ANIAI DEL-C----- -------LIA CRVKAFSGHG
+ NQVRNAVEDA P--RPDFIGV ---RELGKP- Y--CMDGHGA VNTGAGVN-S
+ ESAVWIFDIW MYKLSHGMQW --------GD IGRVDVDHPK FLKLEEGAPN
+ CSSLPMPYFL GVDMFHKQVT LKGAKGLVLP DIWNESPMAF PYAQVHSKSH
+ KRCLNVLVQG DHEESEH--- HNARI----M S---RIGT-H LVIVNVINVE
+ MQRLNHCEDK AIVYSPDRIG GAGFHSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPIIA NAHIVPIY-- --DQWTGPMA QWCSSVIKCG
+ LANHELK-VV SRLLRCVGME CNLGANHYHQ VSRMKMHGPI YSHMTEYAHG
+ L----WKPFY QASEHKNEAQ GVGER-PHQL PCVESQKCQY EVKVAKVCKL
+ VHV-ALYLVG LKTVVKPKLG DWDGVRCRSD LNKLYLSQLD D----KTLSK
+ -NCFRY--LG NMTWLATSPL Q------NGC VVIFAGRKRQ SAE-DYNRAA
+ DPTTIAFCRK PIVQH-ADVF GCDKDKDPQE MRM------N NVISESLGDD
+ FLQQ--MPAV PVSVCVHSHM VKKFVPQ-SH EKRGVTWKAK E-DHLVPISL
+ CKGEH---EE EPEGAQY--- ---------- ----RCVQNI VKLLYTKDV-
+ DCNVVLSLLV WQLC--H-GD WEPLVPQACQ TAKKDLAVCA WKRELVPGL-
+ --NCNNEYLA KIIYFGPDGH -------DEG PMGRKIIQLH W-EMEASHRD
+ -SSVRDNII- VIMLPFKINS RDPWRHYILG LND-QVCLTR PET---ARRL
+ SILV---VMH YSGEFHDKSP -ERSHLHY-R YSEV----KN DVKCVILASK
+ -SNKGLDWTA GKDGMKGENK -AMMNGTLFY -------AEQ NWFRQKNHFV
+ IFV-ICDAVR ILIVHSGVMT GFTFMEFACN PFFAELFMEH VYIRYQYQAN
+ HDIKIKDTCF RLAVYAWENS WETLCNV-EM LSGHFGAKIN HVPRLPEQVC
+ -PPCDLTVSG LKGKQ-NGWP YLTDITRTPL IRIQIRVPGS E-SENITVMY
+ MVYYKERKSI R--------- --QNNTGCAN LPQ------- ----------
+ ----HRLVVK VAD-ELYNNI ---YHAIPKK D--GVLLGIG DSGGMEMAQE
+ DLFQILVCV
+
+t80 LIVSEVRHMV RDG--VNIAV DEI-C----- -------LIA NRVKSMSGQG
+ NQVRNAMEMA A--RQNFVGM ---RELEKV- YE-CMDGQGA VNTEAGNN-S
+ ESAVWIFDIW MCKLTHGMQD FGD-----GD IGRVVVDHPK FEKLEEGAPN
+ CSSHPVPYFL GIDMFHKQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ RRVLNVLHQG DVEES-H--- HSARC----V R---RIGF-H LVIIVFWNVE
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPV- ---------- -------DDG
+ FFDK-D-Q-- ----ARPVIA SAHIVPEH-- --DQWSGAMA QWCSSVIKCG
+ LANHDLE-NV SRLLRCVMID CNQGANHYIQ ISRMKVHGPT YSHMTEYAHG
+ L----WKPFY QASDHKNDAQ GVGER-PHQL PCVESQTCQY EMKHAKVCKL
+ VHG-ALYLIA LKTVVKPKLG VWQGCRCRSQ LSKLVLSQLD E----KTLSK
+ -NCSIY--LG NMTWLATSPL Q------IGC VILFGGRKRQ SHGLNYNRAA
+ DPTTICFYKK PIVVQGADVF GCARGKDPQE MKA------N NVISGSLGDD
+ RLQQ--MPAM PVTICVSSYM VKKSVIQ-SH QKRGYTWRAK E-DHLIPVSF
+ CKGEL---DE EPDAAQQ--- ---------- ----RIVQNI VKLLYTKDV-
+ SCNVVLSMLI WQIC--H-GD WEPQIPKACS NARKDLAVCA WKRELVPGL-
+ --NHNNENLA KIMYFGHDGH -------DEG PMGRKIVTLH V-EMEVSHRE
+ -SSVKDNMIR VIMLPFSNSS VDPWRHVILG LND-QIKLTR PNT---AHRL
+ SILV---VTH YSGGFHDKSA -ERSQHHF-I YNEV----KD DHKCVILASK
+ -CNKGLDWAA GKD-MKGGAK -VMMNGALFY -------AER NWIRQKHHFV
+ IFV-VCDAVR ILIVHYGCMI GYTFMDFACN PFFAELFMDH VFIRYVYMNN
+ HDIKIMDTCF RVAVYTWENS WETCFNR-EM LSGTFGAKIS HNPRLPEQVI
+ -PPCELTVSG LKGKH-NGWP YLTDITRTPL IKIHIRVPGS Q-SENHVVMY
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ ----HRLVDQ VVD-ELYSKF ---YHAIPKK P--GNM-GVG DSGGMEMVQE
+ DVFQILVCL
+
+t14 LIVSEVRHMV RDG--VNIAV DEI-C----- -------LIA NRVKSMSGQG
+ NQVRNAMEMA A--RQNFVGM ---RELEKV- YQ-CMDGQGA VNTEAGNN-S
+ ESAVWIFDIW MCKLTHGMQD FGD-----GD IGRVVCDHPK FEKLEEGAPN
+ CSSHPMPYFL GVDMFHEQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ RRVLNVLHQG DVEES-H--- HSARC----V R---RIGF-H LVIIVYWNVE
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPV- ---------- -------DDG
+ FFDK-D-Q-- ----ARPVIA SAHIVPEH-- --DQWSGAMA QWCSSVIKCG
+ LANHDLE-NV SRLLRCVMID CNQGANHYIQ ISRMKVHGPT YSHMTEYAHG
+ L----WKPFY QASDHKSDAQ GVGER-PHQL PCVESQTCQY EMKHAKVCKL
+ VHG-ALYLIA LKTVVKPKLG VWQGCRCRSQ LSKLVLSQLD E----KTLSK
+ -NCSIY--LG NMTWLATSPL Q------IGC VILFGGRKRQ SHGLNYNRAA
+ DPTTICFYKK PIVVQGADVF GCARGKDPQE MKA------N NVISGSLGDD
+ RLQQ--MPAM PVTICVSSYM VKKSVPQ-SH QKRGYTWRAK E-DHLIPVSF
+ CKGEL---DE EPDAAQQ--- ---------- ----RIVQNI VKLLYTKDV-
+ SCNVVLSMLI WQIC--H-GD WEPQIPKACS NARKDLAVCA WKRELVPGL-
+ --NHNNENLA KIMYFGHDGH -------DEG PMGRKIVTLH V-EMEVSHRE
+ -SSVKDNMIR VIMLPFPSSS VDPWRHVILG LND-QIKLTR PNT---AHRL
+ SILV---VTH YSGGFHDKSA -ERSQHHF-I YNEV----KD DHKCVILASK
+ -CNKGLDWAA GKD-MKGGAK -IMMNGALFY -------AER NWIRQKHHFV
+ IFV-VCDAVR ILIVHYRCMI GYTFMDFACN PFFAELFMDH VFIRYQYMNN
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGAKIS HNPRLPEQVI
+ -PPCELTVSG LKGKH-NGWP YLTEITRTPL IKIHIRVPGS Q-SENHVVMY
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ ----HRLVDQ VVD-ELYSKF ---YHAIPKK P--GNM-GVG DSGGMEMVQE
+ DVFQILVCL
+
+t85 LIVSEVRHVV RDG--VNIAV DEI-C----- -------LIA NRVKSMSGQG
+ NQVRNAMEMA A--RQNFVGM ---RELDKA- YQ-CMDGQKA VNTEAGNN-S
+ ESAVWIFDIC MCKLTHGMQD --------GD IGRVVCDHPK FEKLEEGAPN
+ CSSIPMPYFL GIDMFHKQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ RRVLNVLHQG DHEES-H--- VSARC----M R---RIGF-H LVIINFWNVE
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPI- ---------- -------NDG
+ FFDK-D-Q-- ----ARPVIA NAHIVPEH-- --DQWSGAMA QWCSSVIKCG
+ LANHDLE-NV SRLLRCVEID CNQGANHYVQ ISRMKMYGPT YSHMTEYAHG
+ L----WKPFY QASDHKNDAQ GVGER-PHQL PCVESQTCQY EVKHANVCKL
+ VHA-ALYLIG LKTVVKPELG VWEGCRCRSQ LSKLALSQLD E----KTLSK
+ -NCSIY--LG NMTWLATSPL Q------IGC IILFGGRKRQ SHGLNYNRAA
+ DPTMICFYKK PIVVQGADIF GCARGKDPQE MKS------N NVISGSLGDD
+ RLQH--MPAM PVTICVFSYM VKKAVPQ-SH QKRGYTWRAK E-DHLIPVSF
+ CKGEL---DE EPDGAQQ--- ---------- ----RVVQNI VKLLYTKDV-
+ SCNKVLSMLI WQIC--H-GD WEPQIPKACN AARKDLAVCA WKRELVPGL-
+ --NHNNEDLA KIMYFGPDGH -------DEG PMGRKIVNLH V-EMEVSHRE
+ -SSVKDNMIR VVMLPFDNNS WDPWRHVILG LND-QIKLTR PNT---AHRL
+ SILV---VMH YSGGFHDKSS -ERSQHHF-I YNEV----KN DHKCVILASK
+ -SNKGLDWAA GKD-MKGGAK -MMANGALFY -------EER NWIRQKNHFV
+ IFV-VCDAVR ILIVHYGCMV PYTFMAFACN PFFAELFMEH VFIRYQYVNN
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGAKIS HNPRLPEQVI
+ -PPCDLTVSG LKGKH-NGWP YLTDITRTPL IKIHIRIPGS Q-SENHVVMY
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ ----HRLVDK VVD-ELYSKF ---YHAIPKK P--GNM-GIG DSGGMEMVQE
+ DLFQILVCI
+
+t62 LIVSEVRVMV RDG--IHIAV DEI-C----- -------LIA NRVKCMSGQG
+ NQARNAMEMA A--RQNFVGM ---RELGKQ- YQ-CMDGQGA VNTEAGNN-S
+ ESAVWIFDIW MCRLTHGMQD --------GD IGRVECDHPK FAKLEEGAPN
+ CSSLPMPYFL GIDMFHNQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ RRVLNVLHQG DHEES-H--- HSARC----M R---RIGY-H RVIINYWNVE
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPVIA NAHIVPEY-- --DQWSGAMA QWCSSVIKCG
+ LANHDLE-NV SRLLRCVVID CNHGANHYVQ ISRMKMHGPT YSHMTEYAHG
+ L----WKPFY QASDHKNDAQ GVGER-PHQL PCVEPQTCQY EVKHAKVCKL
+ VHG-ALYLIG LQTVVKPKLG VWEGVQCRSQ LSKLILSQLD D----KTLSK
+ -NCSIY--LG NMTWLATSPL Q------IGC IIMFDGRKRQ SHGLQYNRAA
+ DPTTICFYKK PIVVQGADIF GCARGKDPQE MKA------N NVTSGSLGDD
+ RLQQ--MPAM PVTICVFSYM VKKSVPQ-SH VKRGYTWRAK E-DHLIPVSF
+ CKGEL---EE EPEGAQH--- ---------- ----RMVQNI VKLLYTKDV-
+ SCNVVLSMLI WQIC--H-GD WEPQIPKACD AARKDLAVCA WKRELVPGL-
+ --NHNDENLA KIMYFGPDGH -------DEG PMGEKIVNLH V-EMEASHRE
+ -SSVKDNMIR VIMLPFSNNS WDPWRHVILG LND-KIKLTR PNT---AHRL
+ SILV---VMH YSGGFHDKSA -ERSQHHF-I YNEI----KN DHKCVILASK
+ -ANKPLDWAA GKD-MKGGAK -MMANGALFY -------AER NWIRQKNHFV
+ IFI-ICDAVR ILIVHYGCMV GDTFMDFACN PFFAELFMEH VFIRYQYIPN
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGARIS HVPRLPEQVI
+ -PPCELTVSG LKGKH-NGWP YLTDITRTPL IRIHIRVPGS E-SENHVVMY
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ ----HRLVDR VVD-ELYSKF ---YHAIPKK P--GNM-DVG DSGGMEMVME
+ DVFQILVCV
+
+t19 LIVSEVRHMV RDG--INIAV DEI-C----- -------LIA NRVKCVSGQG
+ NQARNAMEMA A--RQNFVGM ---RELGKQ- YQ-CMDGQGA VNTEAGNN-S
+ ESAVWIFDIW MCRLTHGMQD --------GD IGRVECDHPK FAKLEEGAPN
+ CSSLPMPYFL GIDMFHKQVM GKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ RRVLNVLHQG DHEES-H--- HSARC----M R---RIGYGH LVIINFWNVE
+ MGRLNHCEDE AIIYSPLRIG GAGFHSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPVIA NAHIVPEY-- --DQWSGAMA QWCSSVIKCG
+ LANHDLE-NV SRLLRCVVID CNHGANHYVQ ISRMKMHGPT YSHMTEYAHG
+ L----WKPFY QASDHKNDAQ GVGER-THQL PCVEPQTCQY EVKHAKVCKL
+ VHG-ALYLIG LQNVVKPKLG VWEGVQCRSQ LSKLILSQLD D----KTLSK
+ -NCSIY--LG NMTWLATSPL Q------IGC IILFDGRKRQ SHGLQYNRAA
+ DPTTICFYKK PIVVQGADIF GCARGKDPQE MKA------N NVTSGSLGDD
+ RLQQ--MPAM PVTICVFSYM VKKLVPQ-SH QKRGYTWRAK E-DHLIPVSF
+ CKGEL---EE EPEGAKQ--- ---------- ----RMVQNI VKLLYTKDV-
+ SCNVVLSMLI WQIC--H-GD WEPQIPKACD AARKDLAVCA WKRELVPGL-
+ --NHNDENLA KIMYFGPDGH -------DEG PMGEKIVNLH V-EMEASHRE
+ -SSVKDNMIR VIMLPFSNNS WDPWRHVILG LND-QIKLTR PNT---AHRL
+ SILV---VMH YSGGFHDKSA -ERSQHHF-I YNEI----KN DHKCVILASK
+ -ANKGLDWAA GKD-MKGGAK -MMVNGALFY -------AER NWIRQKNHFV
+ IFV-ICDAVR ILIVHYGCMV GDTFMDFACN PFFAELFMEH VFIRYQYIPN
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGARIS HVPRLPEQVI
+ -PPCELTVSG LKGKH-NGWP YLTDITRTPL IRIHIRVPGS E-SENHVVMY
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ ----HRLVDK VVD-ELYSKF ---YHAIPKK P--GNM-DVG DSGGMEMVME
+ DVFQILVCV
+
+t77 LIVSEVRHMV RDG--INIAV DEI-C----- -------LIA NRVKSMSGQG
+ NQARNAMEMA A--RQNFVGM ---RELGKQ- YH-CMDGQGT VNTEAGNN-S
+ ESAVWIFDIW LCRLTHGMQD --------GD IGRVECDHPK FAKLEEGAPN
+ CSSLPMPYFL GIDMFHRQVM AKGSKGLILP DTWNEASMAF PYPQVHSKSH
+ RRVLNVLHQG DHEES-H--- HSARC----M R---RIGY-V LVIINFWNVE
+ MGRLIHCEDE AIIYSPLRIG GAGFHSKPI- ---------- -------ADG
+ FFDK-D-Q-- ----ARPVIA NAHIVPEY-- --DQWSGAMP QWVSSVIKCG
+ LANHDLE-NV SRLLRCVVID VNQGANHYVQ ISRMKMHGPT YSHMTEYAHG
+ L----WKPFY QASDHKNDAQ GVGER-VHQL PCVEPQTCQY EVKHAKVCKH
+ VHG-ALYLIG LQTVVKPKLG VWEGCQCRSQ LSKLILSQLD D----KTLSK
+ -NCNIY--LG NMTWLATFPL Q------IGC IILFDGRKRQ SYGLQYNRAA
+ DPTTICFYKK PIVVQGADIF GCARGKDPQE MKA------N NVTSGSLGDD
+ RLQQ--MPAM PVTICVFSYM VKKSVPQ-SH QKRGYTWRAK E-DHLIPVSF
+ CKGEL---EE EPEGAQQ--- ---------- ----RIVQNI VKLLYTKDI-
+ SCNVVLSMLI WQIC--H-GD WEPQLPKACD AARKDLAVCA WKRELVPGL-
+ --NHNDENLA KIMYFGPDGH -------DEG PMGEKIVNLH V-EMEASHRE
+ -SSVKDNMIR VIMLPFGENS WDPWRHVILG LND-QIKLTR PNT---AHRL
+ SILV---VMH YSGGFHDNSA -ERSQHHF-I YNEV----KN DHKCVILASK
+ -ANKGLDWAA GKD-MKGGAK -MMVNGALFY -------AER NWIRQKNHFV
+ IFV-ICDAVR ILIVHYGCMV GDTFMDFACN PFFAELFMEH VVIRYQYIPN
+ HDIKIMDTCF RVAVYTWENS WETCCNR-EM LSGTFGARIS HVPRLPEQVI
+ -PPCELTVSG LKGKH-NGWP YLTDITRTPL IRIHIRVPGS E-SENHVVMY
+ CVYYKEHKSI R--------- --QNNTGCAN LPQ------- ----------
+ ----HRLVDK VVD-ELYSKF ---YHAIPKK P--GNM-DVG DSGGMEMVME
+ DVFQILVCA
+
+t88 LIVSECRLII RDG--NHDAI DEM-CCVAND LNNEIERLVA SMVKSFRGHD
+ SQARNNSECM R--SAPFIGV ---RELFKR- YHKCVEGAGC VHTVAGTP-S
+ DSPVWMFDQF MCQLTHSMVD --------GD LGRVVQDNVI FAKLKEGAPH
+ CISL--PHFL GIDMFHTQVF VGGH--LILP DPCYELSISV MYAGHASYNQ
+ KRCINNLDQG DQEDSNHRKE HKIRASVLLY R---QIGI-L -VIIKEANEL
+ MNRLNHKEPE NGIIFPLR-- -DAQDPKQI- ---------- -------LNG
+ LFDK-E-E-- ----NRPMVQ DADSVVGS-- --AQWAGQHR SWCSSDDKA-
+ ---------- SQLPRNTHIV VEIGANVYEQ FSRMKTNIPI YAHVTEYAVG
+ V----ERPFY E-SEFKNEAQ GWGES-GTSI PCVDSPDVQY EMKVAWVDKL
+ MHT-ALYLMP LATVHKPEMG TVRGERCRAI L-KLLMMQLD ------TLSR
+ -NQLPK--LC QGTWLDASPL Q------IGV QVMLVGKKGG SKK-EYELAA
+ DQVIIYFYQA PIIYVKADVF SGTVAKKAQA MR-------K STGSQSIGDD
+ GMQS--MPLM QNAVCVWSKM VRKVQPD-GQ DKREQTWMAK D-DTLCPPSM
+ KRGEK---TA EPTQWMG--- ---------- ----TVTVNK IKLLYCKDC-
+ SCNEVMKILS WWLCNSV-GD WQTLMSQACI TADPNPPVCV WKRELVPGL-
+ --NRSVENLA KIIYFCPDEH -------DER KMWGKIFALE W-EMDISHRH
+ -SSVDDNHC- VEMLPFMCQR VDPWGHYVQI LAD-RQDLAR PVT---LQAL
+ SILP---CPH ASGKEQDGAV -ERSQHYV-V YAEL----QV DHKCTIAAHK
+ YQDKMKDWDT GKN-MDEGAK -MYVEIHLFY -------AEN NIRRQNDHSV
+ IFW-ISDAKK RLICGMSSMC LVTFMTLACN PLFAKLFMEV VPMRYDYLTN
+ HDIKI----- -MEVYAPENS WETIKNV-EM VSGKEGAEIN HTPQLPEQVI
+ -PPCNLTVSN LKGMI-PPCP ALTEITRTV- -FIV--MYYA I-LRNKIMQY
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ ----HHMQNI FID-ELYPGG ---YHAAPKK E--EMV-GPG DNGGVEDIKE
+ DMFQVLVCR
+
+t37 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ CIAL--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ V----ARPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ DPVIIYFYQA PIIHHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DTLCPPCE
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACR SANPNYPVCI WKRELVPGL-
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NLRKQNEHSV
+ TFV-ISDAQK RLICGVSSMV MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ -PPCCLTVSN LKGMI-PPVP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-SPG DNGGVEAIRE
+ DMFQVLVCK
+
+t35 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ CIAL--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTVIPI YARVTEYAVG
+ V----PRPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ MHS-ALYLMP LATVHKPQMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ DPVIIYFYQA PIIYHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DTLCPPCE
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACR SANPNYPVCI WKRELVPGL-
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NLRKQNEHSV
+ TFV-ISDAQK RLICGVSSMA MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ -PPCCLTVSN LKGMI-PPCP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-SPG DNGGVEAIRE
+ DMFQVLVCK
+
+t48 LIVSDMRLII REG--SDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ CIAL--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ ---------- SQLPRNTRIV AEVGANVYEQ YSRMKTVIPI YARVTEYAVG
+ V----PRPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ DPVIIYFYQA PIIYHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DTLCPPCE
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACR SANPNYPVCI WKRELVPGL-
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NLIKQNEHSV
+ TFV-ISDAQK RLICGVSSMV MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ -PPCCLTVSN LKGMI-PPCP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-SPG DNGGVEAIRE
+ DMFQVLVCK
+
+t55 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ CIAI--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ V----ARPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ MHS-ALYLMP LSTVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ DPVIIYFYQA PIIHHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DTLCPPCE
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACR SANPNYPVCI WKRELVPGL-
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ -SSVDDNQC- VELLPYNCQR MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NLRKQNEHSV
+ TFV-ISDAQK RLICGVSSMC MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ -PPCCLTVSN LKGMI-PPCP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-SPG DNGGVEAIRE
+ DMFQVLVCK
+
+t46 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVHDNWT FTKLKEGAPH
+ CIAL--PYFM GIDMFHIQVF VGGN--LILP DPCYELSISV MYAGHASYNQ
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ MGRLNHKEPK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ V----ARPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ -NQIPD--LC QRTWLDASPL Q------IGV KVVLVGKKRG SKK-DYELAA
+ DPVIIYFYQA PIIHHKADVF AGTVAKKSQA MRS------R SIGSQSVGDD
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWMAK D-DALCPPCK
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ SCNEVLKILA WWLCDSV-GD WQSLMNDACR SANPNYPVCI WKRELVPGL-
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRH
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQV LAD-RLDLTR PVT---LQGL
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DHKSTIDANK
+ NDNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NIRKQNEHSV
+ TFV-ISDAQK RLICGVSSMC MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ HDIKI----- -IEVYAPDNS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ -PPCCLTVSN LKGMI-PPCP ALTEITRTP- -FIM--MYVA M-LRNDIMQY
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-APG DNGGVEAIRE
+ DMFQVLVCK
+
+t67 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVMDNWT FTKLKEGAPH
+ CIAL--PYFM GIDMFHIQVF LGGD--LILP DPCYELSISV MYAGHASYNQ
+ KRCINGLDNG DRQDSDPRKE HKIRNSVLLY R---QIGL-L -VIIKEANEL
+ MGRLNHKERK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ V----ARPFY D-AEFKNEAQ RQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ DPVIIYFYQA PIIHHKADVF AGTVAKKAQA MRS------R SIGSPSVGDD
+ GMQN--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWVAK D-DTLCPPCK
+ EQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACS SANPNYPVCI WKRELVPGL-
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRM
+ -SSVDDNQC- VELLPYVCQR MDPWGHYVQI LAD-RLVLTR PVT---LHGL
+ SILP---CPH ASGKEQDGAE -ERSQHYG-V YQEL----QN DAKSTIDANK
+ NPNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NIRKLNEHSV
+ TFV-ISDAQK RLICGVSSMC MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ -PPCCLTVSN LKGMI-PPVP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-APG DNGGVEAIRE
+ DMFQVLVCK
+
+t57 LIVSDMRLII REG--NDDAI DEM-CCVANE LNNVIERLVA SMVKEFRGHD
+ CQARNNSECI T--AAAFIGT ---RELFKR- YPKCMEGARC VHTVAGPP-S
+ ESPVWMFDKF MCQLTHSMVN --------GD LGRVVMDNWT FTKLKEGAPH
+ CIAL--PYFM GIDMFHIQVF IGGD--LILP DPCYELSISV MYAGHASYNQ
+ KRCINGLDNG DRQDSDPQKE HKIRNSVLLY R---QIGL-L -VIIKEANEI
+ MGRLNHKERK NGVIFPLR-- -GAQGPKQI- ---------- -------SNG
+ LFEK-E-E-- ----NRPMVQ DAGSVPGR-- --KQWAGQHR AWCSSDDKA-
+ ---------- SQLPRNTRIV AEIGANVYEQ YSRMKTNIPI YARVTEYAVG
+ V----ARPFY D-AEFKNEAQ GQGES-GTSI PCVDSPDIQY EMKHAWVEKL
+ MHS-ALYLMP LATVHKPEMG TVKGERCRTI L-KLLMVQLD E----KTLSQ
+ -NQIPD--LC QRTWLDASPL Q------IGV QVVLVGKKRG SKK-DYELAA
+ DPVIIYFYQA PIIHHKADVF AGTVAKKAQA MRS------R SIGSPSVGDD
+ GMQK--MPLM QNAVCVWSQM VRKVQPD-GQ DKREQTWVAK D-DTLCPPCK
+ DQGEK---AA EPTQWVG--- ---------- ----TCTSNV IKLLYCKDC-
+ SCNEVLKILA WWLCDSV-GD WQTLMNDACS SANPNYPVCI WKRELVPGL-
+ --NRNVENLA KIIYFCPDEH -------DER RMWGKIFALE W-EMDISHRV
+ -SSVDDNQC- VELLPYLCQR MDPWGHYVQI LAD-RLNLTR PVT---LQGL
+ SILP---CPH ASGKEQDGAV -ERSQHYG-V YQEL----QN DAKSTIDANK
+ NPNKMLDWDT GKN-MDKGAK -MFYKIVLFY -------AEN NIRKQNEHSV
+ TFV-ISDAQK RLICGVSSMC MRTFMTLACN PFFAKLFMEV VPMSYDYVPN
+ HDIKI----- -IEVYAPENS WETTKVV-EM VSGKSGAQIN HTPQLPEQVI
+ -PPCCLTVSN LKGMI-PPVP ALTEITRTP- -FIV--MYVA I-LRNDIMQY
+ CFYYKENRSV R--------- --LNNTGRAE LPK------- ----------
+ ----HHMQNI FID-ELYPGP ---YHAAPKK E--ELM-APG DNGGVEAIRE
+ DMFQVLVCK
+
+t56 LIVSEWRLFI RDG--HDDAI DEM-CCEANE LNNDIEKLVA SMVKGFRGHD
+ SQARNNAECI I--AAPFIGV ---RELFKR- YIKCVEGAGC VYTVA-AP-S
+ ESPVWMFDKF MCHLTHSMVV --------GD LGRVLRDNTT FAKLKEGAPV
+ CISL--PYFL GMDMFHQQVF MGGN--LILP DPCYELSISV MYAGHASYNQ
+ KRCLNNLDQG DREDSSHRKE HKIRRSVLLY Q---QIGC-L -VITRERNEL
+ MGRLNHKEPR DGVIFPHR-- -GAQGPKQL- ---------- -------ANG
+ LFEK-E-E-- ----NRPMVQ DAGSVPER-- --AQWPGQQR AWCSSDDKA-
+ ---------- SKLPRNTKMV AEIGANVYEQ ASRMKTNIPI YAHVTEYALG
+ V----DRPFY D-SEFKNEAQ GQGES-GTSI PCVDSPDVQY ELKHAWVDKL
+ MHT-ALYLMP LPTVHKPKMG TVKGERCRAM L-KLNMMQLD E----KTLSQ
+ -NQIIK--LC QRTWLDASPL Q------IGV NCVLPGKKGG SNK-DYELAA
+ DPVIIYFYQA PIIHHKADVF SGTVAKKAQA MRQ------Q STGSQSVGDD
+ GTQV--MPLM QNLVCVWSKM VRKCMID-GQ EKREQTWMAK D-DKLCPPSQ
+ EQGEK---AA EPTQWED--- ---------- ----ICTANV IKLLYCKDC-
+ SCNEVLRVLS WWLCDSV-GD WRTLMSDACA LANPNPPVCV WKRELVPGL-
+ --NRNVENLA KIIYFCPDEH -------DER KMWGKIFCLE W-EMDISHRH
+ -SSVDDNVC- VEMLPFVCQK MDPWGHYVQI LAD-RLDLTR PVT---LQGL
+ GILV---CPH ASGKEQDGAM -ERSQHYV-V YAEL----QN DHKNTINANK
+ VPRKMLDWDT GKN-MDKGAK GMYHEIVLFF -------AEN NVKKQVEHSV
+ IFI-IADAQK RLICGVSSMC LQTFMNLACN PFFAKLFMEV IPMRYDYQTN
+ HDIKI----- -KEVYAPENS WETIKNV-EM VSGKAGKQIN HEPQLPEQVI
+ -PPCSLTVSN LKGMM-PPCP AMTEITRTV- -III--MYYA I-LRNEIMQY
+ CFYYKENRSV R--------- --INNTGQAE LPK------- ----------
+ ----HHVQNV FID-ELYPGH ---YHAAPKK N--ENV-GPG DNGGVEGIKE
+ DMFQVLVCQ
+
+t13 GIVSECRMII RDE--HDDAI DEM-C----- -------LVA SMVKKLSGCE
+ NQARNNHECA I--PPPFHGV ---REMFKRV YE-CMEGIGC VNTVAGNP-S
+ ESSAWMFDKV MYQLTHSMVW --------GD LRRVVHDNVT FSKLKEGAPH
+ CISH--PYFL GIDMFHIQVY SKGF--LTLP DPRYEISMSV MYSQHHSFSM
+ KRCLNGLDHG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKDANSM
+ MGRLNHHESR AVVAFPLR-- -GAEGPKQV- ---------- -------MEG
+ LFDK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ I----VKPFY D-NEWKQEAQ GQGEA-GACI PCVDSKDVQY ELKHAYVKKL
+ MHT-SLYLMH IETCHKPVMG TVKGNRCRAI L-KLSMIQLD Q----KTLSQ
+ -NQRAK--LC QRTWLDTSPL Q------MGM TLVLVGKKVG SKK-DYEVAA
+ DPVIMYFYDA PMIMRPTDVF EGTNNKKAQA MRS------R STASQSIGDD
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK D-DTLCPQSR
+ DQGEK---HH EPHHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLSSDACM HAEQNPPVCV WQRELVPQL-
+ --NRNIEDLA RIIYFGPDEH -------DEG KMMNKIFALE W-EMDMSHRV
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQV LAD-QLHLTR PHT---LRDL
+ YILAC--CPV ASGKEQDGNK -ERSQHYT-I YAEI----QN DHKNPISANN
+ QPNKMLDWDT GKT-MDRGAA -MCGEIKLFY -------AEP NVWNQNDHSV
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFSKLFMEV VCMRYNYTSN
+ HSIKI----- -FEVYADENS WENVRNF-EM VSGRAGAHIN HIPQLPEQAY
+ -PPCKLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYGS I-LRNDVMQY
+ VFYYRENRSV R--------- --QNNTGNAE LPK------- ----------
+ ----HHMQDV FID-ELYLGP ---YHASPKK D--RFC-NPG DNGGMETYQE
+ DMFQVLVCV
+
+t5 GIVSECRMII RDE--HDDAI DEM-C----- -------LVA SMVKKLSGCE
+ NQARNNHECA I--PPPFHGV ---REMFKRV YE-CMEGIGC VNTVAGNP-S
+ ESSAWMFDKV MYQLTHSMVW --------GD LRRVVHDNVT FSKLKEGAPH
+ CISH--PYFL GIDMFHIQVY SKGF--LTLP DPRYEISMSV MYSQHHSFSM
+ KRCLNGLDHG DREESPHQIE HKMRKSVLIY S---PIGY-L -VIIKDANSM
+ MGRLNHHESR AIVAFPLR-- -GAEGPKQV- ---------- -------MEG
+ LFDK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ I----VKPFY D-NEWKQEAQ GQGEA-GACI PCVDSKDVQY ELKHAYVKKL
+ MHT-SLYLMH IETCHKPVMG TVKGNRCRAI L-KLSMIQLD Q----KTLSQ
+ -NQRAK--LC QRTWLDTSPL Q------MGM TLVLVGKKVG SKK-DYEVAA
+ DPVIMYFYDA PMIMRPTDVF EGTNNKKAQA MRS------R STASQSIGDD
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK D-DTLCPQSR
+ DQGEK---HH EPHHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLSSDACM HAEQNPPVCV WQRELVPQL-
+ --NRNIEDLA RIIYFGPDEH -------DEG KMMNKIFALE W-EMDMSHRV
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQV LAD-QLHLTR PHT---LRDL
+ YILAC--CPV ASGKEQDGNK -ERSQHYT-I YAEI----QN DHKNPISANN
+ QPNKMLDWDT GKT-MDRGAA -MCGEIKLFY -------AEP NVWNQNDHSV
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFSKLFMEV VCMRYNYTSN
+ HSIKI----- -FEVYADENS WENVRNF-EM VSGRAGAHIN HIPQLPEQAY
+ -PPCVLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYGS I-LRNDVMQY
+ VFYYRENRSV R--------- --QNNTGNAE LPK------- ----------
+ ----HHMQDV FID-ELYLGP ---YHASPKK D--RFC-NPG DNGGMDTYQE
+ DMFQVLVCV
+
+t38 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ CISQ--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ KRCLNGLDVG DREESPHHID HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ MGRLNHHESR LIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ VHT-SLYLMH IDTCHKPVMG TIKGNRCRAI L-KLTMIQLD Q----KTLSQ
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLVGKKVG SKK-DYEIAA
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DMLN--MPLT QNAMCVESEM VRKSQPD-GQ DKRGYTWVAK E-DDLCPQSG
+ DQGEK---YA EPQHIRN--- ---------- ----QFSENV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNPPVCV WQRELVPQL-
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQI LAD-QLNLTR PHT---LREL
+ YILA---CPV ASGKEQDGAQ -ERSQCYT-I YAEL----QN DHKSLISANH
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ MFI-ISDAQN KLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ HSIKI----- -FEVYADENS WENIRNF-EM VSGRAGAYIN HIPQLPEQAV
+ -PPCHLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYVS I-LRNDVMQY
+ VFYYRENRIV R--------- --QNNTGVAE LPK------- ----------
+ ----HHMQDV FID-ELYLGP ---YHASPKK E--RFC-NVG DNGGMETIQE
+ DMFQVLVCI
+
+t33 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ MGRLNHYESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SHLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ VHN-SLYLMH IDTCHKPAMG TVKGNRCRAI L-KLTMIQLD Q----KTLSQ
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLVGKKVG SKK-DYEIAA
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSG
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNTPVCV WQRELVPQL-
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQI LAD-QLNLTR PHT---LREL
+ YILA---CPV ASGKEQDGAK -ERSQCYT-I YAEL----QN DHKSLISANH
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ HSIKI----- -FEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ -PPCVLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYVS I-LRNDVMQY
+ VFYYRENRIV R--------- --QNNTGVAE LPK------- ----------
+ ----HHMQDV FID-ELYLGP ---YHASPKK E--RFC-NPG DNGGMETIQE
+ DMFQVLVCV
+
+t100 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ MGRLNHHESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ VHT-SLYLMH IDTCHKPVMG TVKGNRCRAI L-KLTMIQLD Q----KTLSQ
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLVGKKVG SKK-DYEIAA
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSE
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNPPVCV WQRELVPQL-
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ -SSVDDNYI- IEMLPFVCDR VGPWGHYAQI LAD-QLNLTR PHT---LREL
+ YILA---CPV ASGKEQDGAQ -ERSQCYT-I YAEL----QN DHKSLISANH
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ HSIKI----- -FEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ -PPCVLTVSN LKGVA-ASCP AITEITRTA- -VIV--MYVS I-LRNDVMQY
+ VFYYRENRIV R--------- --QNNTGVAE LPK------- ----------
+ ----HHMQDV FID-ELYLGP ---YHASPKK E--RFC-NPG DNGGMETIQE
+ DMFQVLVCV
+
+t34 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ MGRLNHHESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ VHT-SLYLMH IDTCHKPVMG TVKGNRCRAI L-KLTMIQLD V----KTLSQ
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLMGKKVG SKK-DYEIAA
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSG
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNPPVCV WQRELVPQL-
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ -SSVDDNYI- IEMLPFVCDR IGPWGHYAQI LAD-QLNLTR PHT---LREL
+ YILA---CPV ASGKEQDGAQ -ERSQCYT-I YAEL----QN DHKSLISANH
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ HSIKI----- -LEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ -PPCVLTVSN LKGVA-ASCP AMTEITRTA- -VIV--MYVS I-LRNDVMRY
+ VFYYRENRIA R--------- --QNNTGVAE LPK------- ----------
+ ----HHMQDI FID-ELYLGP ---YHASPKK Q--RFC-NPG ENGGMETIRE
+ DMFQVLVCV
+
+t84 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCD
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ MGRLNHHESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ VHT-SLYLMH IDTCHKPVMG TVKGNRCRAI L-KLTMIQLD V----KTLSQ
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLMGKKVG SKK-DYEIAA
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSG
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEHNPPVCV WQRELVPQL-
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ -SSVDDNYI- IEMLPFVCDR IGPWGHYAQI LAD-QLNLTR PHT---LREL
+ YILA---CPV ASGKEQDGAK -ERSQCYT-I YAEL----QN DHKSLIAANH
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ HSIKI----- -LEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ -PPCVLTVSN LKGVA-ASCP AMTEITRTA- -VIV--MYVS I-LRNDVMRY
+ VFYYRENRIA R--------- --QNNTGVAE LPK------- ----------
+ ----HHMQDI FID-ELYLGP ---YHASPKK E--RFC-NPG ENGGMETIRE
+ DMFQVLVCV
+
+t92 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+ DQARNNHECA I--SHPFHGV ---REMFKR- YE-CMEGIGC VNTVAGNP-S
+ ESSAWMFDKF MYQLTHSMVW --------GD LGRVYYDNIT FSKLKEGAPH
+ CISH--PFFL GIDMFHIQVY FKGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ KRCLNGLDVG DREESPHQIE HKMRKSVLIY N---PIGY-L -VIIKNANSL
+ MGRLNHHESR AIVTFPLR-- -GAEGPKQV- ---------- -------MEG
+ LFLK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI FAHVTEYAVG
+ I----VKPFY D-SEWKQEAQ GQGEA-GACI PCVDSPDVQY ELKHAYVKKL
+ VHT-SLYLMH IDTCHKPVMG TVKGNRCRAI L-KLTMIQLD V----KTLSQ
+ -NQRAR--LC QRTWLDTSPL Q------MGM TIVLMGKKVG SKK-DYEIAA
+ DPVIMYFYQA PMIMRPTDVF EGTNNRKAQA MRS------R STASQSIGDD
+ DMLN--MPLT QNAMCVESEM VRKCQPD-GQ DKRGYTWVAK E-DTLCPQSG
+ DQGEK---YA EPQHIRN--- ---------- ----KFSENV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLASDACV SAEPNPPVCV WQRELVPQL-
+ --NRNAEDLA RIIYFGPDEH -------DEG KMMCKIFALE W-EMDMSHRM
+ -SSVDDNYI- IEMLPFVCDR IGPWGHYAQI LAD-QLNLTR PHT---LREL
+ YILA---CPV ASGKEQDGAQ -ERSQCYT-I YAEL----QN DHKSLISANH
+ VPNKMLDWDT GKT-MDRGAA -MCAEIKLFY -------AEP NVWKQNDHSV
+ MFI-ISDAQN RLIVANSIMV GQTFMAMACN PHFAKLFMEV VVMRYDYCSN
+ HSIKI----- -LEVYADENS WENIRNF-EM VSGRAGAHIN HIPQLPEQAC
+ -PPCVLTVSN LKGVA-ASCP AMTEITRTA- -VIV--MYVS I-LRNDVMRY
+ VFYYRENRIA R--------- --QNNTGVAE LPK------- ----------
+ ----HHMQDI FID-ELYLGP ---YHASPKK E--RFC-NPG ENGGMETIRE
+ DMFQVLVCV
+
+t3 GIVSECRMII RDE--SDDAI DEM-C----- -------LVA SMVKKLSGCE
+ QQARNNRECA T--SIPFLGV ---RELWKR- YE-CMEGIGC VNTVAGKP-S
+ QSSVWMFDRF MYKLTHSMVW --------GD LGRVYWDNLT FQKLKEGAPH
+ CIAV--PNYL NIDMFHIQVF YKGP--LTLP DPHYELSMSV MYAQHHSFSQ
+ KRCLNALDHG DREESPHQIE HKMRKSVLLY N---PIGY-L -VIIKNANSM
+ MGRLNHHESC AIVMFPLR-- -GAEGPKQI- ---------- -------IEG
+ LFDK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SRLPRNDPVV HEVGANVYQQ ISRMKTSIPI YAHVTEYAVG
+ I----IKPFY D-NEWKQEAQ GQGEA-GASI PCVNSPDVQY ELKHAHIKKL
+ MHT-SLYLMH LGTCHKPVMG TVKGDRCRAI L-KLSMIQLD Q----KTLSQ
+ -NVRAR--LC QRTWLDTSPL Q------MGM VAVLLGKKLG SKK-DYEIAA
+ DPVIKYFYQA PIIMRRTDVF EGTDDQKAQA MRV------R STASQSIGDD
+ DMLI--MPLV QNAMCVKSEM VRKCQPD-GP DKRGYTWMAK D-DTLCPVSA
+ GQGEK---YA EPHQIKN--- ---------- ----KFSVNV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WVTLASDACL SAEPQPPVCV WQRELVPQL-
+ --NRNVEDLA RVIYFGPDEH -------DEG KMMPKIFKLA W-EMDMSHRA
+ -SSVDDNYV- IEMLPFVCHR VGPWGHYAQV QAD-QQNLTR PHT---LADL
+ FILS---CPV ASGKEQDGAT -ERSQYYV-V YAEL----QN DHKSPISANK
+ HPDKMLDWDT GKS-MDRGAA -MCREIKLFY -------AEP NVWKQNDHSV
+ VFI-ISDAVN RLICANSIMC GLTFMAMACN PHFAKLFMEV VCMRYDYFSN
+ HSIKI----- -FEVYAEDDS WENICNF-EM MSGRTGAQIN HIPQLPEQVC
+ -PPCHLTVSN LKGCC-ASVP AITEITRTV- -VIC--MYVS I-LCNVVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGQ ---YHASPKK K--KIC-GPG DNGGMETIEE
+ DMFQVLVCV
+
+t22 GIVSECRVII RDQ--SDDAI DER-Y----- -------LVA SVVKRLSGCE
+ NQARNNRECA I--SIPFLGV ---RELWKR- YE-CMEGIGC VNTVAGTP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVYVDNQT FSKLKEGAPH
+ CISA--PYYL NIDMFHIQVF YKGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ KRCLNALDYG DREESPHQIE HKMRKSVLLY Y---TIGW-L -VIIKNADSM
+ MGRLNHHESC AMVMFPLR-- -GAEGPKQI- ---------- -------MEG
+ LFDK-E-E-- ----ARPMVQ DAASVPGR-- --AQWVGRVR AWCSSDVKA-
+ ---------- SQLPTNDPIV PEVGANVYQQ VSRMKTSIPI YAHVTEYAVG
+ I----VKPFY D-NEWKQEAQ GQGEA-GASI PCVNSPDVQY ELKHAHIKKL
+ MHT-SLYLMH LKTCHKPVMG TVKGDRCRAI L-KLKMIQLD Q----KTLSQ
+ -NQAAR--LC KRTWLDTSPL Q------MGM NVVLIGQKLG SKH-DYEIAA
+ DPVIMYFYQA PIIMRRTDVF EGTDDQKAQA MRL------R STASRSIGDD
+ DMLI--MPLV QNAMCVNPEM VRKCQPD-GQ DKRGYTWMAK N-DTLCPVSA
+ GQGEC---YA EPHQTCN--- ---------- ----KFRVNV IKLLYCKDC-
+ SCNKVLKILK WQLCESV-DD WQTLASDACI LAKPQPPVCV WQRELVPQL-
+ --NRNVEDLA RVIYFGPDEH -------DEG KMMSKIFNLE W-EMDMSHRT
+ -SSVDDNYV- IDMLPFICHR VGPWGHYAQV LAD-QINLTR PHT---LRDL
+ FILA---CPV ASGKEQDGAT -ERSQHYV-V YAEL----QN DHKSPISANK
+ HPNKLLDWDT GKT-MDRGAA -MCHEIKLFH -------AEP NVWRQNDHSV
+ MFI-ISDASN RLICANSIMC GLTFMAMACN PHFAKLFMEV VCMRYEYFSN
+ HSIKI----- -FEVYAEENS WENVCNF-EM MSGRAGAQIN HIPQLPEQVC
+ -PPCVLTVSN LKGCC-ASCP ANTEITRTV- -VIC--MYVS I-LRNVVMQY
+ VFYYKENRSV R--------- --QNNTGAAE LPK------- ----------
+ ----HHMQDI FID-ELYPGL ---YHASPKK K--KVC-GPG DNGGMETIQE
+ DMFQVLVCV
+
+t64 GIVSECRMII RDE--TDDAI DEV-C----- -------LVA SMVKKLSGCE
+ NQTRNNRECA IT-SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGMP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LRRVFPDNAT FSKLKEGAPH
+ VISH--PYFL GIDMFHDQVV YRGP--LTLP DPRYELSMSV MYAQHHSFSQ
+ KRCLNALDHG DTQESPHGIE HNMRNSVLLY N---PIGF-L -VIIKNINSM
+ MGRLNHHESR AVVGFPLR-- -GAENPKQI- ---------- -------MEG
+ HFDK-E-E-- ----ARPIVQ DAASVPGK-- --AQWVGRVR AWCSSDVKA-
+ ---------- SKLPRNDPIV PEVGANVYQQ LSRMKTNIPI YAHVTEYAVG
+ I----VKPFY D-NEWKQEAQ GVGEA-GASI PCVDSPDVQY ELKHAEVRKL
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLPMIQLD Q----KTLSH
+ -NQPRR--LC QRTWLDASPL Q------VGM NIMLMGKKAP SKK-DYEIAA
+ DPVIMYFYQA PIIMRRTDVF EGTHNKKAQA MRV------R STASQSIGDD
+ DMLK--MPLV QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ NQGEK---YA EPHVIGD--- ---------- ----KVSVNV IKLLYCKDC-
+ SCNQVLKILV WQLCESV-DD WQTLTSDPCM SAQVNPPVCV WQRELVPQL-
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMSKIFALE W-EMDMSHRV
+ -SSVDDNFV- IEMLPFVCHR IGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ FILS---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ HLNKMLDWDT GKT-MDREAT -MCREMKLFY -------AET NLWKQNDHSV
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV VCVHYDYGAN
+ HDIKI----- -FEVYAAENS WENARNF-EM MSGRAGAEIN H-PQLPEQVC
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNDVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI VID-ELYPGP ---YHATPKK H--RFC-GTG DNGGMQAIQE
+ DMFQVLVCV
+
+t18 GIVSECRMII RDE--TDDAI DEV-C----- -------LVA SMVKKLSGCE
+ NQTRNNRECA IT-SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGMP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LRRVFPDNAT FSKLKEGAPH
+ VISH--PYFL GIDMFHEQVV YRGP--LTLP DPRYELSMSV MYAQHHSFSQ
+ KRCLNALDHG DTQESPHGIE HNMRNSVLLY N---PIGF-L -VIIKNINSM
+ MGRLNHHESR AVVGFPLR-- -GAENPKQI- ---------- -------MEG
+ HFDK-E-E-- ----ARPIVQ DAASVPGK-- --AQWVGRVR AWCSSDVKA-
+ ---------- SKLPRNDPIV PEVGANVYQQ LSRMKTNIPI YAHVTEYAVG
+ I----VKPFY D-NEWKQEAQ GVGEA-GASI PCVDSPDVQY ELKHAEVRKL
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLPMIQLD Q----KTLSH
+ -NQPRR--LC QRTWLDASPL Q------VGM NIMLKGKKAP SKK-DYEIAA
+ DPVIMYFYQA PIIMRRTDVF EGTHNKKAQA MRV------R STASQSIGDD
+ DMLK--MPLV QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ NQGEK---YA EPHVIGD--- ---------- ----KVSVNV IKLLYCKDC-
+ SCNQVLKILI WQLCESV-DD WQTLTSDPCM SAQVNPPVCV WQRELVPQL-
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMFKIFALE W-EMDMSHRV
+ -SSVDDNFV- IEMLPFVCHR IGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ FILS---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ HLNKMLDWDT GKT-MDREAT -MCREMKLFY -------AET NLWKQNDHSV
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV VCVHYDYGAN
+ HDIKI----- -FEVYAAENS WENARNF-EM MSGRAGAEIN H-PQLPEQVC
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNDVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGP ---YHATPKK H--RFC-GTG DNGGMQAIQE
+ DMFQVLVCV
+
+t68 GIVSECRMII RDE--TDDAI DEV-C----- -------LVA SMVKKLSGCE
+ NQTRNNRECA I--SPPFIGV ---RELFKR- YG-CVEGIGC VNTVAGMP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LRRVFPDNAH FSKLKEGAPH
+ VISH--PYFL GIDMFHDQVV YRGP--LTLP DPRYELSMSV MYAQHHSFSQ
+ KRCLNALDHG DTQESPHGIE HNMRNSVLLY N---PIGF-L -VIIKNINSM
+ MGRLNHYESR AVVGFPLR-- -GAENPKQI- ---------- -------MEG
+ HFDK-E-E-- ----ARPIVQ DAASVPEK-- --AQWVGRVR AWCSSDVKA-
+ ---------- SKLPRNDPIV PEVGANVYQQ ISRMKTNIPI YAHVTEYAVG
+ I----VKPFY D-NEWKQEAQ GVGEA-GASI PCVDSPDVQY ELKHAEVRKL
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLPMIQLD Q----KTLSH
+ -NQPRR--LC QRTWLDASPL Q------VGM NIMLMGKKAP SKK-NYEIAA
+ DPVIMYFYQA PIIMRRTDVF EGTHNKKAQA MRV------R STASQSIGDD
+ DMLK--MPLR QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ NQGEK---YA EPVVIGD--- ---------- ----KVSVNV IKLLYCKDC-
+ SCNQVLKILV WQLCESV-DD WQTLTSDPCM SAQVNPPVCV WQRELVPQL-
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMSKIFALE W-EMDMSHRV
+ -SSVDDNFV- IEMLPFVCHR IGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ FILS---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ HLNKMLDWDT GKT-MDREAT -MCREMKLFY -------AET NLWKQNDHSV
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV VCVHYDYGAN
+ HDIKI----- -FEVYAVENS WENARNF-EM MSGRAGAEIN H-PQLPEQVC
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNDVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGP ---DHATPKK H--RFC-GTG DNGGMQTIQE
+ DMFQVLVCV
+
+t28 GIVSECRMII RDE--ADDAI DEM-C----- -------LVA SMVKKLSGCE
+ NQARNNRECA I--SPPFIGV ---RELFKR- YH-CMEGIGC VNTVAGMP-S
+ ESSVWMFDQF MYKLTHSMIW --------GD LGRVFPDNAT FSKLKEGAPH
+ VISH--PYFL GIDMFHAQVF YRGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ KRCLNPLDHG DRQESSHGIE HNMRSSVLLY N---PIGF-L -VIIDNINPM
+ MGRLNHHESR AIVTFPLR-- -GAEHPKQI- ---------- -------VEG
+ HFDK-E-E-- ----ARPIVK DAASVPGK-- --AQWVGRIR AWCSSDVKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ DSRMKTNIPI YAHVTEYACG
+ I----VKPFY E-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLSMIQLD E----KTLSQ
+ -NQRPG--LC QRTWLDANPL Q------MGM NTMLVGKKTP SKK-DYEIAA
+ DPVIMYFYQA PIIMRRTDVF EGTNNKKSQA MRV------Q STSSQSIGDD
+ DMLN--MPLV QNAMCVSSEM VRKCQPD-GQ NKRGCTWMAK N-DTLCPQSG
+ NQGEK---FA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ SCNKMLKILV WQLCESV-DD WQTLASDPCV SAEPNSPVCV WQRELVPQL-
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMSKIFALE W-EMDMSHRI
+ -SSVDYNYV- IEMLPFVYHR VGPWGHYAQM LSD-QIVLTR PHT---LRDL
+ FILA---CRV ASGGEVDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ VLNKMLDWDT GKT-MDREAA -MCREIKLFY -------AET NVWKQNDHSV
+ MFI-ISDAQN RLICGNSIMC GITFMAMACN PHFAKLFMEV ACMRYDYFAN
+ PDIKI----- -FEVYAAENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ -PPCHLTVSN LKGVC-ASCP DITEITRTV- -VIC--MYVS I-LRNDVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGH ---YHATPKK N--RYC-GPG DNGGMQVIEE
+ DMFQVLVYV
+
+t82 GIVSECRMII RDE--ADDAI DEM-C----- -------LVA SMVKKLSGCE
+ NQARNNRECA I--SPPFIGL ---RELFKR- YV-CMEGIGC VNTVAGMP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVFPDNCT FSKLKEGAPH
+ VISH--PYFL GIDMFHGQVV YRGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ KRCLNPLDHG DRQESPHGIE HNMRSSVLLY N---PIGF-L -VIIDNINPM
+ MGRLNHHESR AIVTFPLR-- -GAEHPKQI- ---------- -------MEG
+ HFDK-E-E-- ----ARPIVQ DAASVPGE-- --AQWVGHIR AWCSSDIKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI YAHTTEYACG
+ I----VKPFY E-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHANVKKL
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLNMIQLD Q----KTLSQ
+ -NQRPG--LC QRTWLDASPL Q------MGM HIMLVGKKTP SKK-DYEIAA
+ DPVIMYFYQA PIIMQRTDVF EGTNNKKSQA MRV------H STSSQSIGDD
+ DMLN--MPLV QNAMCVSSEM VRKCQPD-GQ NKRGYTWMAK H-DTLCPQSG
+ NQGEK---YA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLASDPCM SAEPNPPVCV WQRELVPQL-
+ --NRNVEDLA RTIYFGPDEH -------DEG KMMSKIYALE W-EMDMSHRV
+ -SSVDYNYV- IEMLPFVYHR VGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ FILA---CPV ASGGEQDGNA -ERSQHYI-V YAEL----VN DHKSPISANK
+ VLNKMLDWDT GKT-MDREAA -MCRDIKLFY -------AET NVWKQNDHSV
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV ACMRYDYFAN
+ PDIKI----- -FEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ -PPCHLTVSN LKGVC-ASCP DITEITRTV- -VIC--MYIS I-LRNDVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGH ---YHATPKK N--RFC-GPG DNGGMQVIEE
+ DMFQVLVYV
+
+t41 GIVSECRMII RDE--ADDAI DEM-C----- -------LVA SMVKKLSGCE
+ NQARNNRECA I--SPPFIGL ---RELFKR- YV-CMEGIGC VNTVAGMP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVFPDNCT FSKLKEGAPH
+ VISH--PYFL GIDMFHGQVV YRGS--LTLP DPRYELSMSV MYSQHHSFSQ
+ KRCLNPLDHG DRQESPHGIE HNMRSSVLLY N---PIGF-L -VIIDNINPM
+ MGRLNHHESR AIVTFPLR-- -GAEHPKQI- ---------- -------MEG
+ HFDK-E-E-- ----ARPIVQ DAASVPGE-- --AQWVGHIR AWCSSDIKA-
+ ---------- SQLPRNDPIV PEVGANVYQQ VSRMKTNIPI YAHTTEYACG
+ I----VKPFY E-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHANVKKL
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAI L-KLNMIQLD Q----KTLSQ
+ -NQRPG--LC QRTWLDASPL Q------MGM HIMLVGKKTP SKK-DYEIAA
+ DPVIMYFYQA PIIMQRTDVF EGTNNKKSQA MRV------H STSSQSIGDD
+ DMLN--MPLV QNAMCVSSEM VRKCQPD-GQ NKRGYTWMAK H-DTLCPQSG
+ NQGEK---YA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLASDPCM SAEPNPPVCV WQRELVPQL-
+ --NRNVEDLA RTIYFGPDEH -------DEG KMMSKIYALE W-EMDMSHRV
+ -SSVDYNYV- IEMLPFVYHR VGPWGHYAQM LAD-QIVLTR PHT---LRDL
+ FILA---CPV ASGGEQDGNA -ERSQHYI-V YAEL----VN DHKSPISANK
+ VLNKMLDWDT GKT-MDREAA -MCRDIKLFY -------AET NVWKQNDHSV
+ MFI-ISDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEV ACMRYDYFAN
+ PDIKI----- -FEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ -PPCHLTVSN LKGVC-ASCP DITEITRTV- -VIC--MYIS I-LRNDVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGH ---YHATPKK N--RFC-GPG DNGGMQVIEE
+ DMFQVLVYV
+
+t71 GIVSECRMII RDQ--SDDAI DEMVV----- -------LVA SMVKEMSGCE
+ NQARNNSECA I--SPQFIGV ---RELFKR- YR-CMEGIGC VNTVAGAP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LARVFHDNGT FAKLKEGAPH
+ VISV--PYFL GIDMFHGQVF LRGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ KRCLNHLDHG DRQESPHGIE HNMRKSVLLY N---PQGY-L -VIIKNVNSM
+ MGRLNHHESR AVVTFPLR-- -GADNPRQI- ---------- -------MEG
+ HFDK-E-E-- ----ARPVVQ DAPGVPGK-- --AQWVGKVR AWCSSDVKA-
+ ---------- SQLPRNDTIV PEVGANVYQQ VSRVKTHIPI YAHVTEYAVG
+ I----VKPFY N-NEWKQEAQ GQGEA-GASI PCVDSPDDQY ELKHAEVKKL
+ MHD-SLYLPH LETCHKPIMG TVKGGRCRAS L-KLKMIQLD Q----KTLSQ
+ -NQQRR--LC QRTWLDSSPL Q------MGM KIMLQGKKTP SKK-DYEIAA
+ DPAIMHFYRA PIIMRRTDVF EGTNNKKAQA MRI------R STASQSIGDD
+ DMLN--MPLH QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSP
+ NQGEK---YA EPHQIRN--- ---------- ----KISVNV IKLLYCKDC-
+ SCNQVLKILV WQLCESV-DD WQTLTSDPCV PAEPNPPVCV WQRELVPQL-
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMRKIFALE W-EMDMSHRD
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRDL
+ FILA---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPISANK
+ HMNKMLDWDT GKT-MDFEAA -MCREIKLFY -------AET NVWKINDHSV
+ MFI-VSDAQN RLICGNSIMC GLTFMAMACN PHFAKLFMEG VCMRYDYSAN
+ HDIKI----- -FEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ NPPCHLTVSN LKGVC-ASCP AITEITRTV- -VIV--MWIS I-LRNDVMQY
+ VVYYKENRSV R--------- --QNNTGKAE LPR------- ----------
+ ----HPMQEI FID-ELYPGH ---YHATPKK N--RFC-GPG DNGGMQSMQE
+ DVFQVLVCV
+
+t94 GIVSECRMII RDQ--SDDAI DEMVC----- -------LVA SMVKELSGCE
+ NQARNNRECA I--SPPFTGV ---RELFKR- YR-CMEGIGC VNTVAGIP-S
+ ESSVWMFDRF MYRLTHSMVW --------GD LGRVFQDNAT FSKLKEGAPH
+ VISH--PYFL GIDMFHGQVF YRGS--LTLP DPRYELSMSV MYAQHHSMSQ
+ KRCLNTLDHG DRQESPHGIE HNMRKSVLLY D---PIGY-L -VIIKNVNSM
+ MGRLNHHESR AKVTFPLR-- -GADNPRQI- ---------- -------MEG
+ HFDK-E-E-- ----ARPVVQ DAPGVPEQ-- --AQWVGKMR AWCSSDVKA-
+ ---------- SQLPRNDTIV PEVGANVYQQ VSRVKTNIPI YAHVTEYAVG
+ I----VKPFY N-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ MHD-SLYLPH LETCHKPIMG TVKGGRCRAS L-KLNMIQLD Q----KTLSQ
+ -NQQRR--LC QRTWLDASPL Q------MGM KIMLQGKKIP SKK-DYEIAA
+ DPAIMYFYQA TIIMRRTDVF EGTNNKKAQA MRM------R STASQSIGDD
+ DMLN--MPLH QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLYPQSA
+ NQGEK---YA EPHQIRN--- ---------- ----KISVNV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLTSDPCV PAEPNPPVCV WQRELVPQL-
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMRKIFALE W-EMDMSHRD
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-KLVLTR PHT---LRDL
+ FILA---CYV ASGGEQDGNT -ERSQHYI-V YAEL----QN DHKSPILANK
+ VVNKMLDWDM GKT-MDFEAA -MCREIKLFY -------AET NVWKQNNHSV
+ MFI-VSDAHN RLICGNSIMC ALTFMAMACN PHFAKLFMEA VCMRYDYSAN
+ HDIKI----- -VEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ NPPCHLTVSN LKGVC-ASCP AITEITRTV- -VIV--MWIS I-LRNDVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPR------- ----------
+ ----HPVQDI FID-ELYPGH ---YHATPKK V--RFC-GPG DNGGMQAIQE
+ DVFQVLVCV
+
+t99 GIVSEVRMII RDE--SDDAI DEM-C----- -------LVA SMVKALSGCE
+ NQARNNRECA I--SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGIP-S
+ ESSIWMFDRF MYKLTHSMVW --------GD LGQVFPDVST FSKLKEGAPH
+ VISQ--PYFL GIDMFHDQVF YRGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ KRCLNALDHG DRQESPHGIE HNMRKSVLLD S---PIGY-L -VIIKNINSM
+ MGRLNHHESR AVFAFPLR-- -GAENPKQI- ---------- -------MEG
+ HFDK-EKE-- ----ARPVVQ DAPGVPGK-- --AQWVGRIR AWCSSDVKA-
+ ---------- SELPRNDAIV PEVGANVYQQ VSRMKTNIPI YAHATEYAVG
+ I----VKPFY D-NEWKQEAQ GQGET-GASI PCVDSPDVQY EMKHAEVKKL
+ MHD-SLYLMH IETCHKPIMG TVKGDRCRAT L-KLKMIQLD Q----KTLSQ
+ -NQKRR--LC QRTWLDASPL Q------MGM KMMLQGKKTP SKK-DYEIAA
+ DPVIMYFYQS PIIMRRTDVF EGTNNKKAQA MRV------R STASQSIGDD
+ EMLN--MPLV QNAMCVPSEM VRKCQPD-GQ DKRGYTWMAK D-DPLCPQSA
+ NVGEK---YA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ SCNKVLKILV WQLCDSVQDD WQPLTSDPCV NAEPNPPVCV WQRELVPQL-
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMNKIFALE W-EMDMSHRD
+ SSSVDDNYI- IEMLPFVCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRDI
+ FILA---CPV ASGGEQDGNT -ERSQHYI-V YAEL----QD DHKSPISANK
+ HMRKMLDWDT GKT-MDREAA -VCREIKLFY -------AET NCWKQNDHSV
+ MFI-VSDAQN RLICGSSIMC RLTFMAMAVN PHFAKLFMED VCMRYDYSPN
+ HDIKI----- -FEVYADENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNDVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGR ---YHATPKK N--RYC-GPG DNGGMQPIQE
+ DMFQVLVCV
+
+t40 GIVSECRMII RDE--SDDAI DEV-C----- -------LVA SMVKALSGCE
+ NQARNNRECA I--SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGIP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVYPDNPT FSKLKEGAPH
+ VISH--PYFL GIDMFHDQVF YRGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ KRCLNALDHG DRQESPHGIE HNMRKSVLLD S---SIGY-I -VIIKNLNSM
+ MGRLNHHESR AVVTFPLR-- -GAEDPKQI- ---------- -------MEG
+ HFDK-E-E-- ----ARPVVQ DAPGVPGK-- --AQWVGRVR AWCSSEIKT-
+ ---------- SELPRNDAIV VEVGANVYQQ ISRMKTDIPI YAHATEYAVG
+ I----VKPVY D-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAT L-KLKMIQLD Q----KTLSQ
+ -NQKKR--LC QCTWLDACPL Q------MGM KIMLQGKKTP SKK-DYEIAA
+ DPVIMYFYQS PIIMRRTDVF EGTNNKKAQA MRI------R STASQSIGDD
+ EMLN--MPQV QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ NVGEK---YA EPHQIRN--- ---------- ----KVSTNV IKLLYCKDC-
+ SCNKVLKILV WQLCDSV-DD WQTLTSDPCV SAEPNPPVCV WQRELVPQL-
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMRKIFALE W-EMDMSHRN
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRNI
+ FILA---CPV ASGGEQDENT -ERSQHYI-V YAEL----QN DHKSPIHANK
+ VMNKMLDWDT GKT-MDREAA -MCREIKLFV -------AET NVWKQNDHSV
+ MFIVISDAQN RLICGSSIMC RLTFMAMAVN PHFAKLFMEE SCVRYDYSAN
+ HDIKI----- -FEVYANENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ -PPCHLTVSN LKGVC-ASVP AITEITRTV- -VIC--MYIS I-LRNNVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGH ---YQATPKK D--KFC-GPG DNGGMQTIQE
+ DMFQVLVCV
+
+t90 GIVSECRMII RDE--SDDAI DEV-C----- -------LVA SMVKALSGCE
+ NQARNNRECA I--SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGIP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVYPDNPT FSKLKEGAPH
+ VISH--PYFL GIDMFHDQVF YRGS--LTLP DPRYELSMSV MYAQHHSFSQ
+ KRCLNALDHG DRQESPHGIE HNMRKSVLLD S---PIGY-I -VIIKNVNSM
+ MGRLNHHESR AVVTFPLR-- -GAEDPKQI- ---------- -------MEG
+ HFDK-E-E-- ----ARPVVQ DAPGVPGK-- --AQWVGRVR AWCSSEIKT-
+ ---------- SELPRNDAIV PEVGANVYQQ ISRMKTDIPI YAHATEYAVG
+ I----VKPVY D-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ MHD-SLYLMH LETCHKPIMG TVKGDRCRAT L-KLKMIQLD Q----KTLSQ
+ -NQKKR--LC QCTWLDACPL Q------LGM KIMLQGKKTP SKK-DYEIAA
+ DPVIMYFYQS PIIMRRTDVF EGTNNKKAQA MRV------R STASQSIGDD
+ EMLN--MPLV QNAMCVSSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQSA
+ NQGEK---YA EPHQIRN--- ---------- ----KVSTNV IKLLYCKDC-
+ SCNKVLKILV WQLCDSV-DD WQTLTSDPCV SAEPNPPVCV WQRELVPQL-
+ --NRNVEDLA RIIYFGPDEH -------DEG KMMRKIFALE W-EMDMSHRN
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRNI
+ FILA---CPV ASGGEQDENT -ERSQHYI-V YAEL----QN DHKSPINANK
+ VMNKMLDWDT GKT-MDREAA -MCREIKLFV -------AET NVWKQNDHSV
+ MFIVISDAQN RLICGSSIMC GLTFMAMAVN PHFAKLFMEE SCVRYDYSRN
+ HDIKI----- -FEVYANENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVC
+ -PPCHLTVSN LKGVC-ASVP AITEITRTV- -VIC--MYIS I-LRNNVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGH ---YHATPKK D--KFC-GPG DNGGMQTIQE
+ DMFQVLVCV
+
+t4 GIVSECRMII RDE--PDDAI DEV-C----- -------LVA SMVKELSGCE
+ NQARNNRECA I--SPPFIGV ---RELFKR- YG-CMEGIGC VNTVAGMP-S
+ ESSVWMFDRF MYKLTHSMVW --------GD LGRVFPDNAT FSKLKEGAPH
+ VISV--PYFL GIDMFHDQVF YRGS--LTLP DPRYEMSMSV MYAQHHSFSQ
+ KRCLNALDYG DRQESPHGIE HNMRKNVLLD N---PIGH-L -VIIKNENSM
+ MGRLNHHESR AVVTFPLR-- -GAEDPKQK- ---------- -------MEG
+ SFDK-E-E-- ----ARPVVQ DAPGVPGR-- --AQWVGRVR PWCSSDVKA-
+ ---------- SELPRNDAIW PEVGANVYQQ ISRMKTNIPI YPHVTEYAVG
+ I----VKPFY L-NEWKQEAQ GQGEA-GASI PCVDSPDVQY ELKHAEVKKL
+ MHD-SLYLWH LETCVKPIMG TVKGDRCRAT L-KLKMIVLD P----KTLSQ
+ -NQKRR--LC QRTWLDASPL Q------VGM KIMLQGKKTP SKK-DYEIAA
+ DPVIMYFYQS PIIMRHTDVF EGTNNKKAQA MRL------R STASQSIGDD
+ EMLN--MPLI QNAMCVQSEM VRKCQPD-GQ DKRGYTWMAK D-DTLCPQLH
+ NQAEK---YA EPHQIRN--- ---------- ----KVSVNV IKLLYCKDC-
+ SCNKVLKILV WQLCESV-DD WQTLTSDPCI SAEPNPPVCV WQRELVPQL-
+ --NRNIEDLA RIIYFGPDEH -------DEG KMMGKIFALE W-EHDMSHRD
+ -SSVDDNYV- IEMLPFMCHR VGPWGHYAQQ LAD-RLVLTR PHT---LRDI
+ FILA---CPV ASGGEQDAVT -ERSQHYI-V YAEL----QN DHKSPISASK
+ HMNKMLDWDT GKT-MDREAA -MCREIKLFY -------AET NVWKQNDHSV
+ MFI-ISDAQN RLICGSSIMC GLTFMATACN PHFAKLFMEE VCMRYDYAAN
+ HDIKI----- -SEVYAEENS WENVRNF-EM MSGRAGAQIN H-PQLPEQVV
+ -PPCHLTVSN LKGVC-ASCP AITEITRTV- -VIC--MYVS I-LRNVVMQY
+ VFYYKENRSV R--------- --QNNTGKAE LPK------- ----------
+ ----HHMQDI FID-ELYPGH ---YHATPKK N--RCC-GPG DNGGMQTVQE
+ DMFQVLVCV
+
+t36 MIWSEVRKMV RER--REQAI DNK-C----- -------LIA ARVKMMSGYV
+ LQVRNALEDA L--YVFFTGT KGTRELVKY- YM-CMEGHGC VNTMAKKS-S
+ QSGIWKFNAF MC-LMHLMEG --------GD L--------- ----------
+ -CSY--PSFL GMCMFHAMVQ SKGD--LVLP DSPNEDSVSF MYIQHHSFHE
+ KRCLNPLNVG DREDSEHIKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ MGRLNHIEPG AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ FFAK-D-E-- ----DRPGIQ NAVSVPCG-- --DQWVGSIR GWCSSQHRYG
+ LANHILVHEP SKLHKTYRIN RKVGANAYDQ DSRMKAAAPV YPHIMEYAHG
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNK PCVESEDCQY EKKHASMDKL
+ MHQ-SLYLMH INIMSKPAMG EWVGNRCRNE LTALRIIQLD VGVSGKTLGQ
+ -NIGVSKLLN DRTWLATSPL E------IGC GVMSVEKKEA SPK-EFEVAA
+ DPTVIYFYRN LIIQKITDVL SAVRMESPQE MRT------Q DVNSSSLGDN
+ NGQA--MNIV PYWVCVASGV VRKTHKD-SV DKRGQTWTAK S-DFLCPLAV
+ DQGEP---GA EQKPAVGEEN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ SCNGVLPLLK WQLCDSH-GD WQSLYADSCP IA-VNAAVCG WKRELVPGL-
+ --NHSCEHLA KSVYFEPDGE -------GEG KVMLKIFGLD WCEVERSHEH
+ -SSVDDNYN- VNMLPFQNSR KDPVGHYVQD LED-ARRLIR PGT---ARSL
+ TILF-YGCQY YSGEFQDCEI -ERSQLYN-V YCEH----KQ DHKSAIIANK
+ QEQKGMDWNT GKE-MEQGPK -IILHGSLFF -------AEP NIVRQPGVSH
+ IFI-GNDARR VLICGKSMMP GHRFMREACV PFFHKLFMAV NQMRYDYMMN
+ YDIKIYETHW RMGVYALDNS WETLNVS-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IKIY--MWGT INFKNRVMQY
+ CNYYKENRSV R--------- --INNTGLAE LPK------- ----------
+ ----YHHQNI LID-ELYSNV ---YPAAPKK H--QYM-GVG DVGGYEVICE
+ NLFQILVVE
+
+t87 MIWSEVRKMV RER--REQAI DNK-C----- -------LIA ARVKMMSGYM
+ LQVRNALEDA L--YVFFTGN KGTRELVKY- YM-CMEGHGC VNTMAKKS-S
+ QSGIWKFNAF MC-LMHLMEG --------GD L--------- ----------
+ -CSY--PSFL GMCMFHAMVQ SKGD--LVLP DSPNEDSVSF MYIQHHSFHE
+ KRCLNPLNVG DREDSDHVKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ MGRLNHIEPG AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ FFAK-D-E-- ----DRPGIQ NAMSVPCG-- --DQWVGSIR GWCSSQHRYG
+ LANHILVHEP SKLHKTYRIN RKVGANAYDQ DSRMKAAAPV YPHIMEYAHG
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNK PCVESEDCQY EKKHASMDKL
+ MHQ-SLYLMH INVMSKPAMG EWVGNRCRND LTALRIIQLD VGHSGKTLGQ
+ -NIGVSKLLN DRTWLATSPL E------IGC LVMSVEKKEA SGK-EFEVAA
+ DPTVIYFYRN LIIAKITDVL SAVRMESPQE MRE------Q DVNSSSLGDN
+ NGQA--MNIV PYWVCVGSGV VRKTHKD-SV DKRGQTWTAK S-DFLCPLAM
+ DQGEI---GA EQKPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ SCNGVLPLLK WQLCDSH-GD WQSLYADSCP IA-INAAVCG WKRELVPGL-
+ --NHSCEHLA KSVYFEPDGE -------GEG KVMLKIFGLD WCEVERSHEH
+ -SSVDDNYN- VNMLPFQNSR KDPVGHYVQD LED-ARRLIR PGT---ARSL
+ TILF-YGCQY YSGEFQDCEI -ERSQLYN-V YCEH----KQ DHKSAIIANK
+ QEQKGMDWNT GKE-MEQGPK -VILHGTLFF -------AES NIVRQPGVSH
+ IFI-GNDARR VLICGLSMMP GHRFMREACV PFFHKLFMAV NQMRYDYMVN
+ YDIKIYETHW RMGVYALDNS WETLNVS-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IKIY--MWGT ICFKNRVMQY
+ CNYYKENRSV R--------- --INNTGLAE LPK------- ----------
+ ----YHHQNI LID-ELYSNV ---YPAAPKK H--QYM-GVG DVGGYEMICE
+ NLFQILVVE
+
+t89 MIWSEHRKMV REG--REQAI DNK-C----- -------LIA KRVKVMSGYI
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGV VNTMAKKS-S
+ QSGIWKFNAF MC-LMRLMQG --------GD L--------- ----------
+ -CSY--PSFL GMCMFYAMVQ SKGD--LVLP DSCNEDSVSF MYIQHHSFHE
+ KRCLNPLNVG DREDSDHTKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ MGRLNVIEPE AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ FFAK-D-E-- ----ERPGIQ NAMNVPCG-- --DQWVGSIR GWCSSQHRYG
+ LANHILVHEP SKLHKTYKIN RKVGANAYDQ VSRMKAAAPV YPHIMEYAHG
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNV PCVESEDCQY EKKHASMTKL
+ MHQ-SLYLMH INIMSKPAMG EWVGVRCRNE LTALRIVQLD VGHSGKTLGQ
+ -NIGVSKLLN DRTWLATSPL E------IGC GVISVEKKEA SPK-EFEVAA
+ DPTVIYFYRS LIIVHITDVL SAVRMDSPQE MRN------Q DVNSPSLGDN
+ NGQA--MNIV PYWVCVASGV VRKMHKD-SV EKRGQTWEAK S-DFLCPLAV
+ DQGEP---AA EQRPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ SCNGVLPLLK WQLCDSH-GD WQSLFPDSCP FA-LNAAVCG WKRELVPGL-
+ --NHSCEHLA KGVYFEPDGE -------DEG KMMLKIFGLE WCEVERSHEH
+ -SSIDDNYT- VNMLEFPNSR KDPVGHYVQN LED-AIRLIR PGT---ARSL
+ TILL-YGCQY YSGEFQDCEV -ERSQCYN-V YCEL----KQ DHKSAIIANK
+ QEQKGMDWNT GKE-MEQGPK -IILHGCLFF -------AEP NIVRQPGVSH
+ IFT-ENDARR MLICGNSMMP RHRFMREACV PFFHKLFMAV NQMRYDYVTN
+ YDIKIYETHW RVGVYAIDNS WETLNVS-EM TSGRMGAKIN HLPRLPEQVI
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IEIY--MWGT INFKNQVMQY
+ CNYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ ----YHHQNI LID-ELYNNI ---YPAAPKK H--KFL-GVG DVGGYEIICE
+ NLFQILVVE
+
+t39 MIWSEHRKMV REG--REQAI DNK-C----- -------LIA KRVKVMSGYI
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGV VNTMAKKS-S
+ QSGIWKFNAF MC-LMRLMQG --------GD L--------- ----------
+ -CSY--PSFL GMCMFYAMVQ SKGD--LVLP DSCNEDSVSF MYIQHHSFHE
+ KRCLNPLNVG DREDSDHTKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ MGRLNVIEPE AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ FFAK-D-E-- ----ERPGIQ NAMNVPCG-- --DQWVGSIR GWCSSQHRYG
+ LANHILVHEP SKLHKTYKIN RKVGANAYDQ VSRMKAAAPV YPHIMEYAHG
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNV PCVESEDCQY EKKHASMTKL
+ MHQ-SLYLMH INIMSKPAMG EWVGVRCRNE LTALRIVQLD VGHSGKTLGQ
+ -NIGVSKLLN DRTWLATSPL E------IGC GVISVEKKEA SPK-EFEVAA
+ DPTVIYFYRS LIIVHITDVL SAVRMDSPQE MRN------Q DVNSPSLGDN
+ NGQA--MNIV PYWVCVASGV VRKMHKD-SV EKRGQTWEAK S-DFLCPLAV
+ DQGEP---AA EQRPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ SCNGVLPLLK WQLCDSH-GD WQSLFPDSCP FA-LNAAVCG WKRELVPGL-
+ --NHSCEHLA KGVYFEPDGE -------DEG KMMLKIFGLE WCEVERSHEH
+ -SSIDDNYT- VNMLEFPNSR KDPVGHYVQN LED-AIRLIR PGT---ARSL
+ TILL-YGCQY YSGEFQDCEV -ERSQCYN-V YCEL----KQ DHKSAIIANK
+ QEQKGMDWNT GKE-MEQGPK -IILHGCLFF -------AEP NIVRQPGVSH
+ IFT-ENDARR MLICGNSMMP RHRFMREACV PFFHKLFMAV NQMRYDYVTN
+ YDIKIYETHW RVGVYAIDNS WETLNVS-EM TSGRMGAKIN HLPRLPEQVI
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IEIY--MWGT INFKNQVMQY
+ CNYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ ----YHHQNI LID-ELYNNI ---YPAAPKK H--KFL-GVG DVGGYEIICE
+ NLFQILVVE
+
+t8 MIWSEHRKMV REG--REQAI DNK-C----- -------LIA KRVKVMSGYI
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGV VNTMAKKS-S
+ QSGIWKFNAF MC-LMRLMQG --------GD L--------- ----------
+ -CSY--PSFL GMCMFYAMVQ SKGD--LVLP DSCNEDSVSF MYIQHHSFHE
+ KRCLNPLNVG DREDSDHTKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ MGRLNVIEPE AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ FFAK-D-E-- ----ERPGIQ NAMNVPCG-- --DQWVGSIR GWCSSQHRYG
+ LANHILVHEP SKLHKTYKIN RKVGANAYDQ VSRMKAAAPV YPHIMEYAHG
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNV PCVESEDCQY EKKHASMTKL
+ MHQ-SLYLMH VNIMSKPAMG EWVGVRCRNE LTALRIVQLD VGHSGKTLGQ
+ -NIGVSKLLN DRTWLATSPL E------IGC GVISVEKKEA SPK-EFEVAA
+ DPTVIYFYRS LIIVHITDVL SAVRMDSPQE MRN------Q DVNSPSLGDN
+ NGQA--MNIV PYWVCVASGV VRKMHKD-SV EKRGQTWEAK S-DFLCPLAV
+ DQGEP---AA EQKPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ SCNGVLPLLK WQLCDSH-GD WQSLFPDSCP FA-LNAAVCG WKRELVPGL-
+ --NHSCEHLA KGVYFEPDGE -------DEG KMMLKIFGLE WCEVERSHEH
+ -SSIDDNYT- VNMLPFPNSR KDPVGHYVQD LED-AIRLIR PGT---ARSL
+ TILL-YGCQY YSGEFQDCEV -ERSQCYN-V YCEL----KQ DHKSAIIANK
+ QEQKGMDWNT GKE-MEQGPK -IILHGCLFF -------AEP NIVRQPGVSH
+ IFT-ENDARR MLICGNSMMP RHRFMREACV PFFHKLFMAA NQMRYDYVTN
+ YDIKIYETHW RVGVYAIDNS WETLNVS-EM TSGRMGAKIN HLPRLPEHVI
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IEIY--MWGT INFKNQVMQY
+ CNYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ ----YHHQNI LID-ELYNDI ---YPAAPKK H--KFL-GVG DVGGYEIICE
+ NLFQILVVE
+
+t6 MIWSEHRKMV REG--REQAI DNK-C----- -------LIA KRVKVMSGYI
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGV VNTMAKKS-S
+ QSGIWKFNAF MC-LMRLMQG --------GD L--------- ----------
+ -CSH--PSFL GMCMFYAMVQ SKGD--LVLP DSCNEDSVSF MYIQHHSFHE
+ KRCLNPLNVG DREDSDHTKE KHMRI----Y A---NIGG-H -IIIREWNDV
+ MGRLNVIEPE AEVIFPLRK- -RGQHSKPV- ---------- -------IDG
+ FFAK-D-E-- ----ERPGIQ NAMNVPCG-- --DQWVGSIR GWCSSQHRYG
+ LANHILVHEP SKLHKTYKVV RKVGANAYDQ VSRMKAAAPV YPHIMEYAHG
+ M----FNPFY GLSEPKNNAQ GNGEN-PMNV PCVESEDCQY EKKHASMTKL
+ MHQ-SLYLMH INIMSKPAMG EWVGVRCRNE LTALRIVQLD VGHSGKTLGQ
+ -NIGVSKLLN DRTWLATSPL E------IGC GVISVEKKEA SPK-EFEVAA
+ DPTVIYFYRS LIIVHITDVL SAVRMDSPQE MRN------Q DVNSPSLGDN
+ NGQA--MNIV PYWVCVASGV VRKMHKD-SV EKRGQTWEAK S-DFLCPLAV
+ DQGEP---AA EQKPAVGEKN PICKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ SCNGVLPLLK WQLCDSH-GD WQSLFPDSCP FA-LNAAVCG WKRELVPGL-
+ --NHSCEHLA KGVYFEPDGE -------DEG KMMLKIFGLE WCEVERSHER
+ -SSIDDNYT- VNMLPFPNSR KDPVGHYVQD LED-AIRLIR PGT---ARSL
+ TILL-YGCQY YSGEFQDCEV -ERSQCYN-I YCEL----KQ DHKSAIIANK
+ QEQKGMDWNT GKE-MEQGPK -IILHGCLFF -------AEP NIVRQPGVSH
+ IFI-ENDARR MLICGNSMMP RHRFMREACV PFFHKLFMAV NQMRYDYMTN
+ YDIKIYETHW RVGVYAIDNS WETLNVS-EM TSGRMGAKIN HLPRLPEQVI
+ -PPCMLTVSG LKDTM-AGMK QETEITKTPD IEIY--MWGT INFKNQVMQY
+ CNYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ ----YHHQNI LID-ELYNNI ---YPAAPKK H--KFL-GVG DVGGYEIICE
+ NLFQILVVE
+
+t58 MIWSEYRHMV REG--RDQAI DNK-C----- -------LIA ARVKVMSGYV
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGC VNTMAKKS-S
+ QSGIWKFNAF MC-LMHLMQG --------GD L--------- ----------
+ -CSH--PSFL GMCMFHAMVK SKGN--LVLP DSCNEDSVSF MYIQHHSFHE
+ KRCLNHLNVG DREDSEHIKE KHMRV----Y A---SIGG-H -IIIREWNDV
+ MGRLNHIEPG AEVTFPLRR- -RGQASKPV- ---------- -------IDG
+ FFAK-D-E-- ----DRPGIQ NAMSVPCG-- --DQWVGSVR GWCSSQHRYG
+ LAIHILVHQQ SRLHKTYNID RKNGANAYEQ DSRMKAGAPV YPHIMEYAHG
+ M----FNPFY GMSEPKNNAQ GNGEN-PMNV PCVESDDCQY EKKHASMDKQ
+ MHQ-SLYLMH MNIMSKPAMG EWVGNRCRNE LTALHVVQLD VGFSGKTLGQ
+ -NIGISELLN DRTWLATSPL E------IGC GVMAVEKKEA SPK-EFEVAA
+ DPTVIYFYRN LIIQHITDVL SAVRMDSPQE MRV------Q DVNSPSLGDN
+ NGQA--MNIV PYWVCVVSGV VRKTHKD-SV EKRGQTWTAK S-DFLCPIAV
+ NQGEP---GA EQKPAVGA-N PIVKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ SCNGVLPLLK WQLCDSH-GD WQSLFADSCP TA-VNAAVCA WKRELVPGL-
+ --NHSCEHLA KSVYFEPDGE -------DEG KMMLKIFGLD WCEVERSHEH
+ -SSVDDNYN- VNMLPFPNSR QDPVGHYVQD LED-LLRLIR PGT---ARSL
+ TVLF-YGCQY YSGQFQDCEI -ERSQLYN-V YCEL----KQ DHKSAIMANK
+ QEQKGMDWNT GKE-MEQGPK -IILHGVLFF -------AEP NVVRQPGVSH
+ IFV-GNDARR MLICGLSMMP GHRFMKEACV PFFHKLFMAV RRMRYDYMSN
+ YDIKIYETHW RPGVYALDNS WETLNVS-EM TSGRIGAKIN HLPRLPETVI
+ -PPCVLTVSG LKDTM-AGMK HGTEITKTPD IKIH--MWGT INFKNKVMQY
+ CTYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ ----YHHQNI LID-ELYSNI ---YPATPKK H--QYM-GVG DVGGYEVICE
+ NLFQILVVE
+
+t54 MIWSEYRHMV REG--RDQAI DNK-C----- -------LIA ARVKVMSGYV
+ LQVRNAPEDA L--YNFFTGH KGTRELVKY- YM-CMEGEGC VHTMAKKS-S
+ QSGIWKFNAF MC-LMHLMQG --------GD L--------- ----------
+ -CSH--PSFL GMCMFHAMVQ SKGN--LVLP DSCNEDSVSF MYIQHHSFHE
+ KRCLNHLNVG DREDSEHIKE KHMRI----Y A---SIGG-H -IIIREWNEV
+ MGRLNHIEVG AEVTFPLRR- -RGQASKPV- ---------- -------IDG
+ FFAK-D-E-- ----DRPGIQ NAMSVPCG-- --EQWVGSVR GWCSSQHRYG
+ LAIHILVHQQ SRLHKTYNID RKNGANAYDQ DSRMKAGAPV YPHIMEYAHG
+ M----FVPFY GMSEPKNNAQ GNGEN-PMNV PCVESDDCQY EKKHASMDKQ
+ MHQ-SLYLMH MNIMSKPAMG EWVGNRCRNE LTALHIVQLD VGFSGKTLGQ
+ -NIGISELLN DRTWLATSPL E------IGC GVMAVEKKEA SPK-EFEVAA
+ DPTVIYFYRN LIIQHITDVL SAVRMDSPQE MRV------Q DVNSPSLGDN
+ NGQA--MNIV PYWVCVVSGV VRKTHKD-SV EKRGQTWTAK S-DFLCPIAV
+ NQGEP---GA EQKPAVGA-D PIVKPWQFVI MNTTTFAKNI FRLLYVKDV-
+ SCNGVLPLLK WQLCDSH-GD WQSLFADSCP IA-VNAAVCA WKRELVPGL-
+ --NHSCEHLA KSVYFEPDGE -------DEG KMMLKIFGLD WCEVERSHEH
+ -SSVDDNYN- VNMLPFPNSR KDPVGHYVQD LED-LLRLIR PGT---ARSL
+ TVLF-YGCQY YSGEFQDCEI -ERSQLYN-V YCEL----KQ DHKSAIMANK
+ QEQKGMDWNT GKE-MEQGPK -IILHGVLFF -------AEP NVVRQPGVSH
+ IFV-GNDARR MLICGLSMMP GHRFMKEACV PFFHKLFMAV RRMRYDYMTN
+ YDIKIYETHW RPGVYALDNS WETLNVS-EM TSGRIGAKIN HLPRLPETVI
+ -PPCVLTVSG LKDTM-AGMK HGTEITKTPD IKIH--MWGT INFKNKVMQY
+ CTYYKENRSV R--------- --INNTGGAE LPK------- ----------
+ ----YHHQNI LID-ELYSNI ---YPATPKK H--QYM-GVG DVGGYEVICE
+ NLFQILVVE
+
+t65 MIWSEYRQMV REG--NDQSI DNK-C----- -------LIA DRVKMMSGVV
+ RQVRNAPEDA L--YNFFTGQ KGTRELIKF- YF-CMEGCGC VNTMAKNS-S
+ QSAPWKFNRF MC-LMHLMQS --------GD L--------- ----------
+ -CNS--PSFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DSQDSQHLRE KQLRI----Y G---RIGK-V -VIIKVWNAV
+ MGRLNHHEPP AEVMFPLRK- -GGQDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVKCG-- --DQWVGSIR GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECQY EHKHAAMEKL
+ MHH-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALQTVQLD VGSSGKTLGQ
+ -NIVTSKKLG DRTWLAASPL Q------IGC GVMVQEKKIA SPQ-EVEVAA
+ D---IYFYRN MVVQRLTDVV AAVRMQSPQE MRTPVLVCIQ KVDSVSLGDD
+ DPQM--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPAAV
+ NEGEH---GA EQRP-FGTQN PVCKPWRFVI MNTQTFAKNI IRLLYIKDI-
+ SCNQVLQLLD WQLCDSH-GD WQSLMADSCP NA-VNIAVCC WKRELMPGL-
+ --NHSCEHLA KSVYFKPDGE -------DEG QMTMKIFNLD WCEVEKSHEK
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQE LED-ALRLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DYKSAIIANQ
+ QEHKGMEWDT GKE-MQQGPK -VVVHLALFY APSNVLAAEP NIIGQPQVSH
+ VFV-GNDARR MLIVGVSMMP AYKFMREACV PFFRKLFMAE NQVRYDYMWN
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ -PPCILTVSG LKRTV-AGAP DETEITKSPV IHIV--MWAD IMFKNCVMQY
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDV ---YPAAQKK Y--QVM-GVG DIGGYELICE
+ DLFQILVCQ
+
+t29 MIWSEYRQMV REG--NDQSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YNFFTGQ KGTRELIKF- YF-CMEGCGC VNTMAKNS-S
+ QSAPWKFNRF MC-LMHLMQS --------GD L--------- ----------
+ -CNC--PSFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLFVG DSQDSQHQRE KQLRI----Y G---RIGK-V -VIIKVWNAA
+ MGRLNHVEPP AEVMFPLRR- -GGSDSKPF- ---------- -------LDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ LANHILIHGP SKLHRTYAIN KKMGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GQSEPKNEAQ GNGEN-PMNV PSVESGECQY ESKHAAMEKL
+ MHQ-SLYLMR VNTMPKPVMG DWDGNRCRAE LTALQTVQLD VGSSGKTLGQ
+ -NIVTSKKLG DRTWLAASPL Q------IGC GVMVQEKKIA SPQ-EVEVAA
+ D---IYFYRN MVVQRLTDVV AAVRMQSPQE MRTPVLVCIQ KVDSVSLGDD
+ DPQM--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ NEGEH---GA EQRPVFGTHN PVCKPWRFVI MHTQTFSKNI IRLLYIKDI-
+ SCNQVLQLLD WQLCDSH-GD WQSLMADSCP NA-VNIAVCC WKRELMPGL-
+ --NHSCEHLA KTVYFKPDGE -------DEG QMSQKIFNLD WCEVEKSHEK
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQE LEDSALRLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DYKSAIIANQ
+ QDHKGMEWDT GKE-MQQGPK -VVVHLALFY MPSNVLAAEP NIIGQPQVSH
+ WFV-GNDARR MLIVGVSMMP AYKFMREACV PFFRKLFMAD NQVRYDYMWN
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ -PPCILTVSG LKRTV-AGAP DETEITKSPV IHIV--MWAD IMFKNCVMQY
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDL ---YPAAPKK Y--QEM-GVG DIGGYELIVE
+ DLFQILVCE
+
+t98 MIWSEHRQMV REG--NDQSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YNFFTGQ KGTKELVKF- YF-CMEGCGC VNTMAKKS-S
+ QSAPWKFNRF MC-LMHLMQS --------GD L--------- ----------
+ -CNS--PPFL GMCMFHPQVQ MKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DSQDSQHLRE KQLRI----Y G---RIGK-V -VIIKVWNAV
+ MGRLNHHEPP AEVMFPLRR- -GGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ LANHILVHNP SRLHRTYAIN KKMGANVYQQ SSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECQY ESKHAAMEKL
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALQTVQLD VGSSEKTLGQ
+ -NIVTSKRLG DRTWLAASPL Q------IGC GVMVQEKKIA SPQ-EVEVAA
+ D---IYFYRN MVVQRHTDVV AAVRMQSPQE MRNPVLVCIQ KVDSASLGDD
+ DPQM--MKIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ NEGEH---GA EQRPVFGTQN PVCKPWRFVI MNTQTFSKNI IRLLYIKDI-
+ SCNQVLQLLD WQLCDSH-GD WQSLMADSCP PA-VNIAVCC WKRELMPGL-
+ --NHSCEHLA KTVYFKPDGE -------DEG QMTMKIFNLD WCEVEKSHEK
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQE LED-ALRLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEM FERSQLYR-V YCEI----KK DYKSAIIANQ
+ QEHKGMEWDT GKE-MQQGPK -IVVHLGLFY MPSNVLAAEP NIIGQPQVSH
+ VFV-ANDARR MLIVGVSMMP AYKFMREACV PFFRKLFMAE NQVRYDYVWN
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ -PPCDLTVSG LKRTV-AGPP DETEITKSPV IHIV--MWAD IVFKNCVMQY
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ ----YHQQNL LTD-ELYSDI ---YPAAPKK Y--QVM-GVG DIGGYELIVE
+ DLFQILVCE
+
+t83 MIWSEYRQMV REG--NDQSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YNFFTGQ KGTKELIKF- YF-CMEGCGT VNTMAKDS-S
+ QSAPWKFNRF MC-LMHLMQS --------GD L--------- ----------
+ -CNS--PSFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DSQDSQHLRE KQLRI----Y G---RIGK-V -VIIKVWNAV
+ MGRLNHHEPP AEVMFPLRR- -GGSCSKPF- ---------- -------VDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ LANHILIHNP SRLHRTYAIN KKMGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECQY ESKHAAMEKL
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALQTVQLD LGSSGKTLGQ
+ -NIVTSKKLG DRTWLAASPL Q------IGC GIMVQEKKIA SPQ-EVEVAA
+ D---IYFYRN MVVQRHTDVV AAVRMQSPQE MRNPVLVCIQ KVDSISLGDD
+ DPQM--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ NEGEH---GA EQRPVFGTQN PVCRPWRFVI MNMQTFSKNI IRLLYIKDI-
+ SCNQVLQLLD WQLCDSH-GD WQSLMADSCP PA-VNIAVCC WKRELMPGL-
+ --NHSCEHLA KTVYFKPDGE -------DEG QMTMKIFNLD WCEVEKSHEK
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQE LED-ALRLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSDM FERSQLYR-V YCEI----KK DYKSAIIANQ
+ QEHKGMEWDT GKE-MQQGPQ -IEVHLALFY MPSNVLPAEP NIIGQPQVSH
+ VFV-GNDARR MLIVGVSLMP AYKFMREACV PFFRKLFMAE NQVRYDYMWN
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ -PPCILTVSG LKRTI-AGAP DETEITKSPV IHIV--MWAD IMFKNCVMQY
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ ----YHQQNL LTD-ELYSDI ---YPAAPKK Y--QVM-GVG DIGGYELIVE
+ DLFQILVCE
+
+t95 MIWSEYRQMV REG--TDQSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YNFFTGQ KGTRELIKF- YF-CMEGCGC VNTMAKNS-S
+ QSAPWKFNRF MC-LMHLMQL --------GD L--------- ----------
+ -CNP--PSFL GMCMFHPQVR SKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYTG DSQDSQHLRE KQLRI----Y G---RIGR-V -VILQVWNAV
+ MGRLNHHEPP AEVMFPLRK- -GGSNSKPV- ---------- -------YDG
+ FF-------- ----DRPAIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN RKVGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECVY ESKHAAMEKL
+ MHQ-SLYLMR VNTMSKPVMG DWVGHRCRAE LTELQTVQLD VGSSGKTLGQ
+ -NIVTSKKLG DRTWLAASPL Q------IGC GVMVQEKKIA SPQ-QVEVAA
+ D---IYFYRN MVVQRLTDVV AAVRMQSPQE MRCRKLVCIQ KVDSPSLGDD
+ DPQM--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ NEGEH---GA EQRPVFGGQN PACKPWHFVI MNRQTFAKNM IRLLYIKDI-
+ SCNEVLQLLD WQLCDSH-GD WQSLIADSCP NA-SNIAVCC WKRELMPGL-
+ --NFSCEHLA KTVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ -SSVDDNYD- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ IILF-YGCQY YSGKFQDSEL FERSQLYR-M YCEI----KK DHKSAIIANQ
+ QEHKGMEWDT GKE-MQQGPK -VVLHHALFY APSNVLAAEP NIIGQPQVSH
+ VFV-GNDARR MLITGVSMMP AYKFMREACV PFFRKLFMAE NQVRYDYVWN
+ YDIKIYETHY RMGVYAVDNS WETLVYC-EM TSGRIGAKVN HLPRLPEQVT
+ -PPWVLTVSG LKRTV-AGAP DETEITKSPI IHII--MWEE IMFKNCVMQY
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QVM-GVG DIGGYELICE
+ DLFQILVCE
+
+t20 MIWSEYRQMV REG--TDQSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YNFFTGQ KGTRELIKF- YF-CMEGCGC VNTMAKNS-S
+ QSAPWKFNRF MC-LMHLMQL --------GD L--------- ----------
+ -CNP--PSFL GMCMFHPQVR SKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DSQDSQHLRE KQLRI----Y G---RIGR-V -VILQVWNAV
+ MGRLNHHEPP AEVMFPLRK- -GGSNSKAV- ---------- -------YDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN RKVGANVYQQ MSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PSVESGECVY ESKHAAMEKL
+ MHQ-SLYLMR VNTMSKPVMG DWVGHRCRAE LTELQTVQLD VGSSGKTLGQ
+ -NIVTSKKLG DRTWLAAPPL Q------IGC DVMVQEKKIA SPQ-QVEVAA
+ D---IYFYRN MVVQRLTDVV AAVRMQSPQE MRTPKLVCIQ KVDSPSLGDD
+ DPQC--MNIV PYWVCVCSGV VKKAEPD-SV DKRGKTWVAK S-DFLCPPAV
+ NEGEH---GA EQRPVFGGQN PACQPWHFVI MNTQTFAKNM IRLLYIKDI-
+ SCNQVLQLLD WQLCDSH-GD WQSLIADSCP NA-VNIAVCC WKRELMPGL-
+ --NFSCEHLA KTVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ -SSVDDNYD- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ IILF-YGCQY YSGKFQDSEL FERSQLYR-M YCEI----KK DHKSAIIANQ
+ QEHKGMEWDT GKE-MQQGPK -VVLHHALFY APSNVLAAEP NIIGQPQVSH
+ VFV-GDDARR MLITGVSMMP AYKFMREACV PFFRKLFMAE NQVRYDYVWN
+ YDIKIYETHY RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVT
+ -PPWVLTVSG LKRTV-AGAP DETEITKSPI IHII--MWED IMFKNCVMQY
+ CTYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QVM-GVG DIGGYELICE
+ DLFQILVCE
+
+t69 MIWSDYRQMV REG--GDDSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YNFFTGH KGTRELVKY- YH-CMEGCGC VNTMAKSS-S
+ QSAPWKFNRF MC-LMHLMQE --------GD L--------- ----------
+ -CNS--PGFL GMCMFHPQVQ RKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DNQDSQHLRE KQLRM----Y G---EIGK-V -VIIKVVNAV
+ MGRLNHVEPS AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGSIR GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ ISRMKALAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PCVESGECQY ENKHAAMEKL
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALKTGQLD VGSSGKTLGQ
+ -NIMTSKKLG DRTWLAANPL Q------IGR GVMVWEKKVA SPQ-EVEVAA
+ D---IYFYRN MVIECLTDVV RAVRMQSPQE MRAPVLVCIQ KVDSPSLGDD
+ VPQM--MNIV PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAM
+ NEGEH---GA EQRPVFGTQN PVCKPWRFVI MNTETFAKNI IRLLYVKDV-
+ SCNQVLQLLD WQLCDSH-GD WQSLVADSCP NA-VNIAVCC WKRELMPGL-
+ --NHSCQHLA KTVYFKPDGE -------DEG QMIVKIFNLD WCEVEKSHEK
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHNSAIIANQ
+ QEHKGMDWDT GKE-MQQGPK -IVVVLALFY QPSNVLAAEP NIMGQPQVSV
+ VFV-GNDGRR MLIVGCSMMP DYKFMREACV PFFRKLFMAE VQDRYDYAWN
+ YNIKIYETHF RDGVYAVDNS WETLVYV-EM ASGRIGAKIN HQPRLPEQVI
+ -PPCILTVSG LKRTI-ADEP DETEITKTPI IHIV--MWAD IMFKNCVMQY
+ CNYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QIM-GVG DIGGYELICE
+ DLFQILVCE
+
+t2 MIWSDYRQMV REG--GDDSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YNFFTGQ KGTRELVKY- YH-CMEGCGC VNTMAKSS-S
+ QSAPWKFNRF MC-LMYLMQD --------GD L--------- ----------
+ -CNS--PGFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DNQDSQHLRE KQLRM----Y G---EIGK-V -VIIKVVNAV
+ MGRLNHHEPS AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGSIK GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ ISRMKALAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PCVESGECQY ENKHAAMEKL
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALKTGQLD VGSSGKTLGQ
+ -NIMVSKKLG DRTWLAASPL Q------IGC GVMVWEKKVP SPQ-EVEVAA
+ D---IYFYRN MVIECLTDVV RAVRMQSPQE MRAPVLVCIQ KVDSPSLGDD
+ VPQM--MNIV PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAM
+ NEGEH---GA EQRPVFGTQN PVCKPWRFVI MNVETFAKNI IRLLYVKDV-
+ SCNQVLQLLD WQLCDSH-GD WQSMVADSCH NA-VNIAVCC WKRELMPGL-
+ --NHSCQHLA KTVYFKPDGE -------DEG QMMVKIFNLD WCEVEKSHEK
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHNSAIIANQ
+ QEHKGMDWDT GKE-MQQGPK -IVVVLALFY QPSNVLAAEP NIMGQPQVSV
+ VFV-GNDARR MLIVGCSMMP DYKFMREACV PFFRKLFMAE VQDRYDYNWN
+ YNIKIYETHF RVGVYAVDNS WETLVYV-EM ASGRIGAKIN HMPRLPEQVI
+ -PPCILTVSG LKRTI-ADEP DETEITKTPI IHIV--MWAD IMFKNCVMQY
+ CNYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QIM-GVG DIGGYELICE
+ DLFQILVCE
+
+t10 MIWSDYRQMV REG--GDDSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YNFFTGQ KGTRELVKY- YH-CMEGCGC VNTMAKSS-S
+ QSAPWKFNRF MC-LMYLMQD --------GD L--------- ----------
+ -CNS--PGFL GMCMFHPQVQ AKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DNQDSQHLRE KQLRM----Y G---EIGK-V -VIIKVVNAV
+ MGRLNHHEPS AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGSIK GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ ISRMKALAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ GNGEN-PMNV PCVESGECQY ENKHAAMEKL
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALKTGQLD VGSSGKTLGQ
+ -NIMVSKKLG DRTWLAASPL Q------IGC GVMVWEKKVP SPQ-EVEVAA
+ D---IYFYRN MVIECLTDVV RAVRMQSPQE MRAPVLVCIQ KVDSPSLGDD
+ VPQM--MNIV PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAM
+ NEGEH---GA EQRPVFGTQN PVCKPWRFVI MNVETFAKNI IRLLYVKDV-
+ SCNQVLQLLD WQLCDSH-GD WQSMVADSCH NA-VNIAVCC WKRELMPGL-
+ --NHSCQHLA KTVYFKPDGE -------DEG QMMVKIFNLD WCEVEKSHEK
+ -SSVDDNYN- VNMLPFMQSH GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHNSAIIANQ
+ QEHKGMDWDT GKE-MQQGPK -IVVVLALFY QPSNVLAAEP NIMGQPQVSV
+ VFV-GNDARR MLIVGCSMMP DYKFMREACV PFFRKLFMAE VQDRYDYNWN
+ YNIKIYETHF RVGVYAVDNS WETLVYV-EM ASGRIGAKIN HMPRLPEQVI
+ -PPCILTVSG LKRTI-ADEP DETEITKTPI IHIV--MWAD IMFKNCVMQY
+ CNYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDI ---YPAAPKK Y--QIM-GVG DIGGYELICE
+ DLFQILVCE
+
+t31 MIWSEYRSMV REG--ADQSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKQS-S
+ QSAPWKFNRF MC-LMHLMQN --------GD L--------- ----------
+ -CNL--PSFL GMCMFHNQVQ CKGE--LVLP DNVNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DNQDSQHLRE KQLRI----Y Q---NIGK-V -VIIKVWNAN
+ MGRLNHHEPP AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMNVPCG-- --DQWVGCIR GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ TSRMKAAAPI YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ MHQ-SLYLMR VNTMSKPVMG DWVGNRCRAE LTALKTVQLD VGSNGKTLGK
+ -NIMTPKKLG DRTWLAASPL Q------IGC GVMVQEKKVA SPQ-EVE-AA
+ D---IFFYRN MVIQRLTDVV AAVRMQSPQE MRPPVLVCIQ YVDSPSLGDD
+ TPQM--MNIA PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK A-DFLCPPAV
+ SEGEH---GA EQRPVFGMQN PACKPWRFVI MNTQTFAKNI IRLLYIKDV-
+ SCNAVLQLLD WQLCYSH-GD WQSLIADSCP TA-ANIAVCC WKRELMPGL-
+ --NHSCEHLA KTVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ -SSVDDNYH- VNMLPFAQSN RDPVGHYVQG LED-ALRLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIIANQ
+ HEVKGMDWNT GKE-MQQGPK -IVVHLALFY APSNVLAAEP NIVGQPQVSH
+ VFV-GNDARR MLIVGVSVMP SYKFMREACV PFFHKLFMAD NQVRHEYMWN
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGANIN HLPRLPEQVV
+ -PPCILTVSG LKRTI-AGSP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ STYYKENRSV R--------- --ANNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIRVM-GVG DIGGYEMICE
+ DLFQILVCE
+
+t15 MIWSEYRSMV REG--SDQSI DNH-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKNS-S
+ QSAPWKFNRF MC-LMHLMQN --------GD L--------- ----------
+ -CNS--PSFL GMCMFHNQVP NKGA--LVLP DNVNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DNQDSQHLRE KQLRI----Y P---SIGK-V -VIIKVWNAA
+ MGRLNHHEPP AEVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGCIR GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN RKMGANVYQQ TSRMKAAAPL YPHIMEYAHG
+ M----VEPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ MHQ-SLYLMR VNTMSKPVLG DWVGNRCRAE LTALKTVQLD IGNSGKTLGQ
+ -NIMTPKRLG ERTWLAASPL Q------IGC GVVVQEKKVA SPQ-EVEVAA
+ D---IYFYRN MVIQTLTDVV AAVRMQSPQE MRPPVLVCIQ DVDSVSLGDD
+ TPQM--MNIA PYWVCVCSGV VKKTQPD-SV DKRGKTWVAK S-DFLCPPAV
+ SEGEH---GA EQRPVFGMRN PICKPWRFVI MNTQTFAKNI IRLLYVKDV-
+ SCNAVLQLLD WQLCYSH-GD WQSLIADSCS TA-ANIAVCC WKRELMPGL-
+ --NHSCEHLA KTVYFKPDGE -------DEG QMIVKIFHLD WCEVEKSHEK
+ -SSVDDNYH- VNMLPFAQSN GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ VILS-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIVANQ
+ QEVKGMDWDT GKE-MQQGPK -IVVHLALFY APSNVLAAEP NIVGQPQVSH
+ VFV-GNDARR MLIVGVSVMP AYKFMREACV PFFHKLFMAE NQVRHDYMWN
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVV
+ -PPCILTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ STYYKENRSV R--------- --GNNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDV ---YPTAPKK YVIRVM-GVG DIGGYELICE
+ DLFQILVCQ
+
+t63 MIWSEYRSMV REG--SDQSI DNK-C----- -------LTA ARVKLMSGVV
+ RQVRNAPEDA L--YTFFTGQ KGKRELIKY- YF-CMEGCGC VNTMAKNS-S
+ QSAPWKFNRF MC-LMHLMQD --------GD L--------- ----------
+ -CNS--PSFL GMCMFHNQVS FKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DEQDSSHLRE KQLRL----Y A---RIGK-V -VIIKVWNAV
+ MGRLNHHEPP AAVMFPLRK- -GGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGIIR GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ DSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ MHQ-SLYLMR ANTMSKPVMG DWVGSRCRAE LTALKTVQLD VGSSGKTLGQ
+ -NIMTPKKLG DRTWLAASPL Q------IGC DVMVQEKKVA SPQ-EVEVAA
+ D---IYFYRN MVIQRLTDVV AAVRMQSPQE MRLPVLVCIQ DVDSPSLGDD
+ TPQK--MNIA PYWVCVCSGV VKKAQLD-SV EKRGKTWVAK S-DFLCPPAV
+ SEGEH---GP EQRPVFGVQN PVCKPWRFVI MNTQTFAANI IRLLYVKDV-
+ SCNAVLQLLD WQLCYSH-ED WQSLIADACP TA-VNIAVCC WKRELMPGL-
+ --NHSCEHLA KSVYFKPDGE -------DEG QMFMKIFNLD WCEVEKSHEK
+ -SSVDDNYN- VNMLPFVQSN GDPVGHYVQG LED-ALLLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIIANQ
+ QGVKGMDWDT GKE-MQQGPK -IVVHLALFY APSNVLAAEP NIIGQPQVSH
+ VFV-DNDARR MLIVGQSVMP PYKFMREACV PFFHKLFMAE NQVRHDYVWN
+ YDIKIYETHF RMGVYAIDNS WETLVYC-EM TSGRIGAKIN HQPRLPEQVV
+ -PPCVLTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ STYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIRQM-GMG DIGGYELICE
+ DLFQILVCE
+
+t50 MIWSEYRSMV REG--SDQSI DNK-C----- -------LTA ARVKLMSGVV
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKNS-S
+ QSAPWKFNHF MC-LMHLMQN --------GD L--------- ----------
+ -CNS--PSFL GMCMFHNQVS VKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DNQDSSHLRE KQLRL----Y A---RIGK-V -VIIKVWNAV
+ MGRLNHHEPP AEVMFPLRK- -CGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGVIR GWCSSQHQYG
+ LANHVLVHGP SKLHRTYAIN KKMGANVYQQ DSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ MHQ-SLYLMR ANTMSKPVMG DWVGSRCRAE LTALKTVQLD VGSSGKTLGQ
+ -NIMTPKKLG DRTWLAASPL Q------IGC DVMVQEKKVA SPQ-EVEVAA
+ D---IYFYRN MVIQRLTDVV AAVRMQSPQE MRLPVLVCIQ DVDSPSLGDD
+ TPQK--MNIA PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAV
+ SEGEH---GP EQRPVFGVQN PVCKPWRFVI MNTQT-AKNI IRLLYVKDV-
+ SCNAVLQLLD WQLCYSH-GD WQSLIADACS TA-VNIAVCC WKRELMPGL-
+ --NHSVEHLA KSVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ -SSVDDNYN- VNMLPFVQSN GDPVGHYVQG LED-ALLLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIMANQ
+ QGVKGMDWDT GKE-MQQGPK -IVMHLALFY APSNVLAAEP NIIGQPQVSH
+ VFV-DNDARR MLIVGQSVMP AYKFMREACV PFFHKLFMAE NQVRHDYVWN
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HQPRLPEQVV
+ -PPCILTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ STYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIRQM-GMG DIGGYELICE
+ DLFQILVCE
+
+t25 MIWSEYRSMV REG--SDQSI DNK-C----- -------LTA ARVKMMSGVV
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKNS-S
+ QSAPWKFNRF MC-LMHLMQN --------GD L--------- ----------
+ -CNS--PSFL GMCMFVNQVS FKGE--LVLP DNPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DNQDSSHLRE KQLRL----Y A---RIGK-V -VIIKVWNAV
+ MGRLNHHEPP AEVVFPLRK- -GGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWMGVIR GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ DSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ MHQ-SLYLMR ANTMSKPVMG DWVGSRCRAE LTALKIVQLD VGSSGKTLGQ
+ -NIMTPKKLG DRTWLAASPL Q------IGC DVMVQEKKVA SPQ-EVEVAA
+ D---IYFYRN MVIQRLTDVV AAVRMQSPQE MRLPVLVCIQ DVDSPSLGDD
+ TPQK--MNIA PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAV
+ SEGEH---GP EQRPVFGMQN PVCKPWRFVI MNTQTFAKNI IRLLYVKDV-
+ SCNAVLQLLD WQLCYSH-GD WQSLIADACP TA-VNIAVCC WKRELMPGL-
+ --NHSCEHLA KSVYFKPDGE -------DEG QMIMKIFNLD WCEVEKSHEK
+ -SSVDDNYD- VNMLPFVQSN GDPVGHYVQG LED-ALLLIR PGT---ARAL
+ VILF-YGCQY YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSTIIANQ
+ QGVKGMDWDT GKE-MQQGPK -IVVHLTLFY APSNVLAAEP NIFGQPQVSH
+ VFV-DNDARR MLIVGQSVMP AYKFMREACV PFFHKLFMAE NQVRHDYVWN
+ YDIKIYETHF RMGVYAVDNS WEALVYC-EM TSGRTGAKIN HQPRLPEQVV
+ -PPCILTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ STYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIRQM-GMG DIGGYELICE
+ DLFQILVCE
+
+t51 MIWSEYRSMV REG--SDQSI DNK-C----- -------LIA ARVKMMSGVV
+ RQVRNAPEDA L--YTFFTGQ KGTRELIKY- YF-CMEGCGC VNTMAKNS-S
+ QSAPWKFNRF MC-LMHLMQN --------GD L--------- ----------
+ -CNS--PSFL GMCMFHVQVQ FKGE--LVLP DHPNENSVEF MYRRHHSLSD
+ KRCLNLLYVG DNQDSQHLRE KQLRI----Y A---RIGK-V -VIIKVWNAV
+ MGRLNHHEPP AEVVFPLRK- -GGSDSKPF- ---------- -------IDG
+ FF-------- ----DRPGIA NAMSVPCG-- --DQWVGVIR GWCSSQHQYG
+ LANHILVHGP SKLHRTYAIN KKMGANVYQQ DSRMKAAAPL YPHIMEYAHG
+ M----VKPFY GISEPKNEAQ KNGEN-PMNV PCVESGECQY ESKHAAMEKL
+ MHQ-SLYLMR VNTMSKPIMG DWVGNRCRAD LTALKTVQLD VGSSGKTLGQ
+ -NIMTPKNLG DKTWLAASPL Q------IGC GIMVQEKKVA SPQ-EVEVAA
+ D---IYFYRN MVIQRLTDVV AAVRMQSPQE MRPPVLVCIQ DVDSPSLGDD
+ TPQM--MNIA PYWVCVCSGV VKKAQPD-SV DKRGKTWVAK S-DFLCPPAI
+ SEGEH---GA EQRPVFGMQN PVCRPWRFVI MNTQTFAKNV IRLLYVKDV-
+ SCNKVLQLLD WQLCYSH-GD WQSLIADACP AA-VNIAVCC WKRELMPGL-
+ --NHSCEHLA KTVYFKPDGE -------DEG QMIMKIFGLD WCEVEKSHEE
+ -SSVDDNYN- VNMLPFVSSN GDPVGHYVQG LED-ALRLIR PGT---ARAL
+ VILF-YGCQF YSGKFQDSEL FERSQLYR-V YCEI----KK DHKSAIIANQ
+ QGVKGMDWDT GKE-MQQGPK -IVVHLALFY APSNVLAAEP NIIGQPQVSH
+ VFV-DNDIRR MLIVGVSVMP AYKFMREACV PFFHKLFMAE NQVRHDYVWN
+ YDIKIYETHF RMGVYAVDNS WETLVYC-EM TSGRIGAKIN HLPRLPEQVF
+ -PPCILTVSG LKRTI-AGAP DETEITKTLI YHIV--MWAD IMFKNCVMQY
+ ATYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHQQNI LTD-ELYSDM ---YPAAPKK YVIREM-GVG DIGGYELICE
+ DLFQILVCE
+
+t9 MIWSECRQMV REK--TDNAI DNQ-C----- -------LIA ARVKENSGHV
+ KQVRNDSEDI L--YNHFTGK KGARELIKR- YV-CMEGHDC VNTVANVS-S
+ QSAIWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ -CSY--PSFL PMCMFVPQVL SKGE--LVLP DSSNEESISF VYLQHHSFSV
+ KRCLNYLNVG DSADSKHLKE KHLRA----E GMPGNIGK-H -VIINVWNAV
+ MGRLNHHEPP AEVVFPLRQ- -GGPDSKPM- ---------- -------IDG
+ FFDK-D-D-- ----DRPGIA NAMSVPCG-- --EQWGGPTR GWCSSQQKFG
+ LASHTLSHDP SSLHRTFAIN RKMGANVYQQ TSRMKASAPF YPHCMEYAHG
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESIDCQY ENKHATMTKL
+ MHH-SLYLMR MHTMSKPIMG DVNGNRCRAD LTALKMLQLD IGFSAKTLGQ
+ -NVVVPHLLG HRTWLATSPL Q------IGC GVMIFGNKIG SAN-EFEAAA
+ DPTVIYFYRN RIVRRLADVI STVRMNSPQE MRN------Q DVDSHSLGDD
+ DNQA--MVIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK V-DFLCPPAF
+ NQGEH---RA EQKPASKFEH PVCGPWEFVI VNYQTSAKDI ILLLYIKDV-
+ GCNCVLELLN WQLCTSH-GD WQSLVADSCV WA-HNVAVCA WKRELVPGL-
+ --NHSCERLA KHIYFQPDGE -------DEG KMVLKIFGLD WCEMEKSHQR
+ -SGVDDNYQ- VNMLPFNHSK NNPVGHYVQG LED-ALNLIR PGT---ARAL
+ NILF-YGCEV YSGEFQDSES -ERSWIYN-V YCEI----KK DHKSAIIAHK
+ YEHKGMDWDT GKE-AQQGPE -VVHHNLLFF -------AEP NIHGQPGVGH
+ IFV-GNDARR KLIAGVSFMS MVKFMCEACV PFFRKLFMAV GQMRYDYVNN
+ YDIKIWETVF RGGVYAIENS WETLVLC-EM TSGRCGAKMN HLPRLFEQVC
+ -PPCILTVSG LKETK-AGLI DGTEITKTPD IGIC--MWET IHFKNPVMQY
+ CCYYKENRSV R--------- --VNNTGGAA LPK------- ----------
+ ----YHHQNT LVD-ELYSDV ---YPAAPKK K--VCM-GVG DVGGYEVMGE
+ DLFQILVCE
+
+t47 MIWSECRQMV REK--SDNAI DNQ-C----- -------QIA ARVKRNSGHV
+ KQVRNDSEDI L-CYHHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ QSAVWNFDRF MCDLMHLMQN --------GD L--------- ----------
+ -CSY--PSFL PMCMFVSQVL SKGE--LVLP DSSNEESISF VYLQHHSFSD
+ KRCLNYLNVG DNSDSKHLKE KHLRA----Q GMPGNIGK-H -VIINVWNAV
+ MGRLNHHESP AEVVFPLRQ- -GGPDSKPM- ---------- -------IDG
+ FFDK-D-D-- ----DRPGIA NAMSVPCG-- --EQWGGPTR GWCSSQQKFG
+ LASHTLSHDP SNLHRTFAIN RKMGANVYQQ ASRMKASAPF YHHCMEYAHG
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESRDCQY ENKHATMTKL
+ MHQ-SLYLMR MHTMSKPIMG HVNGNRCRAD LTALKMLQLD IGFSAKTLCQ
+ -NIVVAHLLG HRTWLATSPL Q------IGC MVMIFGNKIG SAN-EFEAAA
+ DPTVIYFYRN RIVRRLADVI STVRMNSPQE MRE------Q DVDSHSLGDD
+ DNQA--MNIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK M-DFLCPPAF
+ NQGEH---RA EQKPALKFKH PVCGPWEFVI VNYQTSAKDI ILLLYIKDV-
+ GCNCVLELLK WQLCTSH-GD WQSLVADSCV WA-HNVAVCA WKRELVPGL-
+ --NHSCDRLA KHIYFQPDGE -------DEG KMILKIFGLD WCEMEKSHQR
+ -SGVDDNVQ- VNMLPFNHSK HNPVGHYVQG LED-ELNLIR PGT---ARAL
+ NILF-YGCEY YSGEFQDSES -ERSWIYN-V YCEI----KK DHKSAIMACK
+ YRHKGMDWDT GKE-AEQGPE -VVHHNLLFF -------AEP NIQGQPGVGH
+ IFV-GNDARR KLIAGLSFMA MMKFMCEACV PFFRKLFMAV GHMRYDYVSN
+ YDIKIWETVF RGGVYAIENS WETLVLC-EM TSGRCGAKMN HLPRLFEQVC
+ -PPCILTVSG LKETK-AGII DGTEITKTPE IGIC--MWDT IEFKNPVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNT LVD-ELYSDI ---YPAAPKK K--VCM-GVG DVGGYEVMGE
+ DLFQILVCE
+
+t60 MIWSECRQMV REK--TDNAI DNQ-C----- -------QIA ARVKENSGHV
+ KQVRNDSEDI L-CYHHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ QSAVWNFDRF MCDLMHLMQN --------GD L--------- ----------
+ -CSV--PSFL PMCMFVSQVL HKGE--LVLP DSSNEESISF VYLQHHSFSD
+ KRCLNYLNVG DNADSKHLKE KHLRA----Q GMPGNIGK-H -VIINVWNAV
+ MGRLNHHEPP AEVVFPLRQ- -GGPDSKPM- ---------- -------IDG
+ FFDK-D-D-- ----DRPGIA NAMSVPCG-- --EQWGGPTR GWCSSQQKFG
+ LASHTLSHNP SNLHRTFAIN RKMGANVYQQ TSRMKASAPF YHHCMEYAHG
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESIDCQY ESKHAAMTKL
+ MHQ-SLYLMR IHTMSKPIMG DVNGNRCRAD LTALKMLQLD IGFSAKTLGQ
+ -NIVVPHCLG HRTWLATSPL Q------IGC MVMIFGNKIG SEN-EFEAAA
+ DPTVIYFYRN RIVRRLADVI STVRMNSPQE MRN------Q DVDSHSLGDD
+ DNQA--MNIL PYVVCVCSGV VRKDHPDTSI HKRGRTWLAK V-DFLCPPAF
+ NQGEH---RA EQKPAFKFKH PVCGPWEFVI VNYQTEAKDI ILLLYIKDV-
+ GCNCVLELLE WQLCTSH-GD WQSLVADSCV WA-HNVAVCA WKRELVPGL-
+ --NHSCERLA KHIYFQPDGE -------DEG KMILKIFGLD WCEMEKSHQR
+ -SGVDDNYQ- VNMLPFNHSK HNPVGHYVQG LED-ALNLIR PGT---ARAL
+ NILF-YGCEY YSGEFQDSES -ERSWIYN-V YCEI----KK DHKSAIMAYK
+ FEHKGMDWDT GKE-AEQGPE -VVHHNLLFF -------AEP NIQGQPGVGH
+ IFV-GNDARR KLIAGVSFMA VMKFMCEACV PFFRKLFMAV GQMRYDYMNN
+ YDIKIWETFF RGGVYAIENS WETLVLC-EM TSGRCGAKMN HLPRLFEQVC
+ -PPCILTVSG LKETR-AGII EGTEITKTPD IGIC--MWDT IHFKNPVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNT LVD-ELYSDI ---YPAAPKK K--VCM-GVG EVGGYEVMGE
+ DLFQILVCE
+
+t30 MIWSECRQMV REK--TDNAI DNQ-C----- -------QIA ARVKENSGHV
+ KQVRNDSEDI L-CYHHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ QSAVWNFDRF MCDLMHLMQN --------GD L--------- ----------
+ -CSV--PSFL PMCMFVSQVL HKGE--LVLP DSSNEESISF VYLQHHSFSE
+ KRCLNYLNVG DNADSRHLKE KHLRA----Q GMPGNIGK-H -VIISVWNAV
+ MGRLNHHEPP AEVVFPLRQ- -GGPDSKPM- ---------- -------MDG
+ FFDK-D-D-- ----DRPGIA NAMSVPCG-- --EQWGGPTR GWCSSQQKFG
+ LASHTLSHTP SNLHRTFAIN RKMGANVYQQ TSRMKASAPF YHHCMEYAHG
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESIDCQY ENKHATMTKL
+ MHQ-SLYLMR MHTMSKPIMG DVNGNRCRAD LTALKMLQLD IGFSAKTLGQ
+ -NIIVPHCLG HRTWLATSPL Q------IGC MVMIVGNKIG SEN-EFEAAA
+ DPTVIYFYRN RIVRRLADVI STVRMNSPQE MRN------Q DVDSHSLGDD
+ DNQA--MNIL PYVVCVCSGV VRKEHPDTSI SKRGRTWLAK I-DFLCPPAF
+ NQGEH---RA EQKPAFKFKH PCCGPWEFVI VNYQTSAKDI ILLLYIKDV-
+ GCNCVLELLK WQLCTSH-GD WQSLVADSCV WA-HNVAVCE WKRELVPGL-
+ --NHSCERLA KHIYFQPDGE -------DEG KMILKIFGLD WCEMEKSHQR
+ -SGVDDNYQ- VNMLPFKHSK HNPVGHYVQG LED-ALNLIR PGT---ARAL
+ NILF-YGCEY YSGEFQDSES -ERSWIYN-V YCEI----KK DHKSAIMAYK
+ YEHKGMDWDT GKE-AEQGPE -VVHHNLLFF -------AEP NIHGQPGVGH
+ IFV-GNDARR HLIAGVSFMA VVKFMCEACV PFFRKLFMAV GQMRYDYVNN
+ YDIKIWETVF RGGVYAIENS WETLVLC-EM TSGRCGAKMN HLPRLFEQVC
+ -PPCILTVSG LKETR-AGII DGTEITKTPD IGIC--MWDT IHFKNPVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHDQNT LVD-ELYSDV ---YPAAPKK K--VCM-GVG DVGGYEVMGE
+ DLFQILVCE
+
+t70 MIWSECRQMV REK--NDNAI DNQ-C----- -------LIA ARVKEDSGHV
+ KQVRNASEDI M--YNHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ QSAVWKFDRF MCDLMHLMQD --------GD L--------- ----------
+ -CSY--PSFL PMCMFVAQVI AKGE--LVLP DSSTEESISF MYLQHHSFSD
+ KRCLNYLNVG DNEDSKHAKE KFLRG----D G---GIGQ-H -VIINVWNAV
+ MGRLNHHEPP PEVVFPLRQ- -GGPDSKPM- ---------- -------VDG
+ FFDK-D-D-- ----DRPGIA NAMNVPCG-- --DQWGGPIR GWCSSQHKFG
+ LAFHTLSHDP SKLHRTFAIN QKMGANVYQQ MSRMKTPAPF YPHVMEYAHG
+ V----CKPFY EHSEPKNEAQ GNGEKVPMNV PCVESMDCQY ENKHAPMAKL
+ MHQDSLYLMR MHTMSKPLMG DVNGNRCRAD LTSLKMLQLD IGFCAKTLGQ
+ -NIVVPKLLG HRTWLATAPL Q------IGC GMMIFGNKIG STQ-EFEAAA
+ DPTVIYFYRN RIVRRMADVI STVRMKSPQE MRG------Q DVDSHSLGDD
+ DNQA--MNIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK I-DFLFPPAF
+ NQGEH---HA EQKPVFGFKH PHCGPWEFVI CNYQTVAKDI ILLLYIKDV-
+ GCNCVLELLA WQLCTSH-GD WQSLVADSCI WA-HNVAVCA WKRELVPGL-
+ --NHSCEHLA KHIYFQPDGE -------DEG KMILKIFGLD WCEVERSHQR
+ -SGVDDNYK- VNMLPFSHSK HNPVGHYVQG LGD-ALRLIR PGT---ARAL
+ NILF-YGCQY CSGEFQDSEE -ERSWIYN-V YCEI----KK DHKSAILAHK
+ YKHKGMDWDT GKE-MEQGPK -VVNYNLLFY -------AEP NIHGQPRVGH
+ IFV-GNDAHR KLIAGVSFMS IMKFMCEACV PFFRKLFMAV RQMRYMYMNN
+ YDIKIWETAF RGGVYAIENS WETLVLC-EM TSGRSGAKMN HLPRLFEQVC
+ -PPCLLTVSG LKETV-AGII DGTEITKTPE IGIC--MWDT IHFKNPVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHNQNT LVD-ELYSDV ---YPAAPKK Q--HYM-GVG DVGGYEVMGE
+ DLFQILVCE
+
+t91 MIWSECRQMV REK--NDNAI DNQ-C----- -------LIA ARVKEDSGHV
+ KQVRNASEDI M--YNHFTGK KGARELIKR- YI-CMEGHDC VNTMANVS-S
+ QSAVWKFDRF MCDLMHLMQD --------GD L--------- ----------
+ -CSY--PSFL PMCMFVAQVI AKGE--LVLP DSSTEESISF MYLQHHSFSD
+ KRCLNYLNVG DNEDSKHAKE KFLRG----D G---GIGQ-H -VIINVWNAV
+ MGRLNHHEPP PEVVFPLRQ- -GGPDSKPM- ---------- -------VDG
+ FFDK-D-D-- ----DRPGIA NAMNVPCG-- --DQWGGPIR GWCSSQHKFG
+ LAFHTLSHDP SKLHRTFAIN QKMGANVYQQ MSRMKTPAPF YPHVMEYAHG
+ V----CKPFY EHSEPKNEAQ GNGEKVPMNV PCVESMDCQY ENKHAPMAKL
+ MHQ-SLYLMR MHTMSKPLMG DVNGNRCRAD LTSLKMLQLD IGFCAKTLGQ
+ -NIVVPKLLG HRTWLATAPL Q------IGC GMMIFGNKIG STQ-EFEAAA
+ DPTVIYFYRN RIVRRMADVI STVRMKSPQE MRG------Q DVDSHSLGDD
+ DNQA--MNIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK I-DFLFPPAF
+ NQGEH---HA EQKPVFGFKH PHCGPWEFVI CNYQTVAKDI ILLLYIKDV-
+ GCNCVLELLA WQLCTSH-GD WQSLVADSCI WA-HNVAVCA WKRELVPGL-
+ --NHSCEHLA KHIYFQPDGE -------DEG KMILKIFGLD WCEVERSHQR
+ -SGVDDNYK- VNMLPFSHSK HNPVGHYVQG LGD-ALRLIR PGT---ARAL
+ NILF-YGCQY CSGEFQDSEE -ERSWIYN-V YCEI----KK DHKSAILAHK
+ YKHKGMDWDT GKE-MEQGPK -VVNYNLLFY -------AEP NIHGQPRVGH
+ IFV-GNDAHR KLIAGVSFMS IMKFMCEACV PFFRKLFMAV RQMRYMYMNN
+ YDIKIWETAF RGGVYAIENS WETLVLC-EM TSGRSGAKMN HLPRLFEQVC
+ -PPCLLTVSG LKETV-AGII DGTEITKTPE IGIC--MWDT IHFKNPVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHNQNT LVD-ELYSDV ---YPAAPKK Q--HYM-GVG DVGGYEVMGE
+ DLFQILVCE
+
+t49 MIWSECRQMV REK--NDNAI DNQ-C----- -------LIA ARVKENSGHV
+ KQVRNASEDI M--YNHFTGN KGACELIKG- YV-CMEGHDC VNTMANIS-S
+ QSAVWKFDRF MCDLMHLMQD --------GD L--------- ----------
+ -CSY--PSFL PMCMFVAQVI AKGE--LVLP DSSNEESISF MYLQHHSFSD
+ KRCLNCLNVG DNEDSKHLKE KFLRA----D G---GIGQ-H -VIINMWNAV
+ MGRLNHHEPP PEVVYPLRQ- -GGPNSKPM- ---------- -------VDG
+ FFDK-D-D-- ----DRPGIA NAMNVPCG-- --DQWGGPIR GWCSSQHRFG
+ LAFHTLKHDP SKLHRTFAIN EKMGANVYQQ NSRMKASAPF YPHVMEYAHG
+ V----CKPFY EHSEPKNDAQ GNGDKVPMNV PCVESMDCQY ENKHAPMAKL
+ MHQ-SLYLMR MYTMSKPIMG DVNGNRCRAE LTSLKMLQLD IGFSAKTLGQ
+ -NIVPPKLLG HRTWLATSPL Q------IGC GVMIFGNKIG STQ-EFESAA
+ DPTVIYFYRN RIVKRMADVI STVRMKSPQE MRG------Q DVDSHSLGDD
+ DNQA--MNIL PYWVCVCSGV VRKEHPDTSI NKRGRTWLAK I-DFLFPPAF
+ NQGEH---HA EQKPVFGFKH PHCGPWEFVI CNYQTMAKDI ILLLYIKDV-
+ GCNCVLELLA WQLCTSH-GD WQSLVADSCI WA-HNVAVCA WKRELVPGL-
+ --NHSCEHLA KHIYFQPDGE -------DEG KMIIKIFGLD WCEVEKSHQR
+ -SGVDDNYK- VNMLPFSHSN HNPVGHYVQG LGD-ALRLIR PGT---ARAL
+ NILF-YGCEY YSGEFQDSEE -ERSWIYN-V YCEI----KK DHKSAIMAHK
+ YEHKGMDWDT GKE-MEQGPK -VVHHNILFY -------AEP NIHGQPRVGH
+ IFV-GNDAVR NLIAGVSFMS IMKFMCEACV PFFRKLFMAV RQMRYMYMNN
+ YDIKIWETAF RGGVYAMENS WETLVLC-EM TSGRVGARMN HLPRLFEQVC
+ -PPCILTVSG LKETV-AGVI DGTEITKTPE IGIC--MWDT IHFKNPVMQY
+ CCYYKEPRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHNFNA LVD-ELYSDV ---YPAAPKK K--HYM-GVG DVGGYEVMGE
+ DLFQILVCE
+
+t52 MIWSEERQMV REK--VDNAV DNQ-C----- -------LIA ARVKENCGHV
+ KQVRNASEDI L--YNHFTGK KGARELIKR- YI-CMEGHDC VNTMAHDS-S
+ QSATWKFDRF MCDLMHLMQG --------GD L--------- ----------
+ -CSY--PSFL PVCMFVAQVI NKGE--LVLP DSSNEESISF MYLQHHSFSE
+ KRCLNYLNVG DNEDSKHLKE KFLRA----D G---NIGQ-H -VIINMWNAV
+ MGRLNHHEPP AEVNFPLRQ- -GGPDSKPM- ---------- -------VDG
+ FFDK-D-D-- ----DSPGIA NAMNVPCG-- --DQWGGPIR GWCSSQHKFG
+ LASHTLSHDP SKLHRTFGIN KNMGANVYQQ TSRMKANAPF YPHVMEYAHG
+ V----CKPFY EHSEPKNEAQ GNGEK-PMNV PCVESIECQY ENKHATMAKL
+ MHD-SLYLMR MHTMSKPVMG DVNGHRCRAD LTALKMLQLD IGFSAKTLGQ
+ -NIVAPKLLG VRTWLATSPL Q------IGC GVMIFGNKIG STQ-EFEAAA
+ DPTVIYFYRN RIIRRVADVI STVRMKSPQE MRE------Q DVDSHSLGDD
+ DNQA--MTIL PHWVCVVSGV VRKEHPDTSI NKRGSTWLAK V-DFLCPPAF
+ NQGEH---HA EQKPVFGFKH PHVGPWEFVI CNYQTSAHDI ILLLYIKDV-
+ GCNCVLELLV WQLCTSH-GD WQSLVADSCV WA-HNVAVCA WKRELVPGL-
+ --NHSCERLA KHIYFQPDGE -------DEG KMILKIFELN WCEVEKSHQH
+ -SGVDDNYQ- VNMLPFDHCK HNPVGHYVQG LED-ALGLIR PGT---ARAL
+ NILF-YGCQY YSGEFQDSEA -ERSWIYN-V YCEI----KK DHKSGIMAHK
+ YDHKGVDWDT GKE-MEQGPK -VLHHNLLFY -------AEP NIHGQPTVGH
+ IFV-GNDARR KLIAGVSFMS VVKFMCEACV PFFRKLFMAF RQMRYDYVNN
+ YDIKIWETVF RGGVYAIENS WETLILC-EM TSGRCGAKMN HMPRLFEQVC
+ -PPCILTVSG LKETM-AGVI DGTEITKTPD IGIG--MWDS IHFKNPVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNS LVD-ELYSDV ---YPAAPKK K--HYM-GVG DVGGYEVMGE
+ DLFQILVCE
+
+t43 MIWSEVRQMV REG--SDNAI DNR-C----- -------LIA ARVKHVQGHV
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ QSAVWKFDRF MCALMHLMQK --------GD L--------- ----------
+ -CSH--PSFL GMCMFHEQVR CKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ KRCLNCLNVG DNDDSEHLKE KHLRI----Y G---QIGH-H -VIINVWNAF
+ MGRLNHHEPP AEVVYPLRK- -GGPDSK-M- ---------- -------VDG
+ FFDK-E-D-- ----DRPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVNFG
+ LANHTLVQ-P SKLHRTFKIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMECQY ENKHAIMAKL
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKVVQLD IGFSSKTLGQ
+ LNIIDCKLLG HRTWLATSPL Q------IGV DVMVMGNKIG SPS-EFEVAA
+ DPTIIWFYRN CIVHKLADTV STAKMKSPQE MRH------Q DVDSPSLGDD
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ NQGEH---ER EQRPVYGFKH PGCRPWQFVI ANYQTSAKNI IMLLYVKDV-
+ SCNGVLQLLN WHLCDSH-GD WQSLVADSCC WA-HNVAVCG WKRELVPGL-
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ -SSVDDNYL- VNMLPFLHSR QNPVGHYVQG LED-PMHLIR PGT---ARKL
+ NILF-YGCEY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVIAHK
+ HEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ VFM-GNDATR KLITGVSVMP TYKFMCGACV PFFHKLFMAV RNMRYDYNVN
+ YDIKIWETHI RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCVLTVSG LKQPM-AGYN DQTEITKTPD ICIC--TWGT IHFKNFVMQY
+ CVYYKENRSV R--------- --VNNTGGAE LPQ------- ----------
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ DLFQILVHE
+
+t1 MIWSEVRQMM REG--TDNAI DNQ-C----- -------LIA ARVKHMQGHV
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ QSAVWKFDRF MCCLMHLMQN --------GD L--------- ----------
+ -CSH--PSFL GMCMFVEQVR CKGE--LVLP DSPNEESLSF VYIQHHSFSD
+ KRCLNCLNVG DNDDSEHLKE KHLRI----Y G---QIGR-H -VIINVWNAF
+ MGRLNHHEPP AEVVYPLRK- -GGPDSKPV- ---------- -------VDG
+ FFDK-E-D-- ----DRPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVKFG
+ LANHTLVQ-P SKLHRTFKIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMECQY ENKHAIMAKL
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAK LTALKIVQLD IGFSAKTLGQ
+ LNIIDCKLLG RHTWLATSPL Q------IGC DMMVMGNKIG SPS-EFEVAA
+ DPTIIWFYRD CIVHKLADTV STAKMKAPQE MRV------Q DVDSPSLGDD
+ DQQE--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ NQGEH---EA EQRPVYGFVH PRCRPWQFVI ANYQTSAKNI IMLLYVKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ -SSVDDNYL- VNMLPFMQSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ NILF-YGCEY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ VEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ VFM-GNDATR KLITGVSVMP TYKFMCGACV QFFHKLFMAV RNMRYDYTVN
+ YDIKIWETHI RQGVYAVENS WETLITC-EM TSGRIGAKIN HLPRLPEQVV
+ -PPCILTVSG LKQPM-AGYN DETQITKTPD ICIC--TWGT IHFKNSVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ DLFQILVHE
+
+t86 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKPVQGHV
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ QSAVWKFDRF MCALMHLMQN --------GD L--------- ----------
+ -CSH--PSFL GMCMFHEQVR RKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ KRCLNCLNVG DNDDSEHLKE KHLRI----Y G---QIGR-H -VIINVWNAF
+ MGRLNHHEPP AEAVYPLRK- -GGPDSKPM- ---------- -------VDG
+ FFDK-E-D-- ----DRPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVKFG
+ LANHTLVQ-P SKLHRTFKIN KKMGANVYHQ TSRMKAEAPV YPHIMEYAHG
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMECQY ENKHAIMAKL
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVMGNKIG SPS-EFEVAA
+ DPTIIWFYRN CIVHKLADTV STAKMKAPQE MRV------Q DVDSPSLGDD
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ NQGEH---GA EQRPVYGFQH PRCRPWQFVI ANYQTFAKNI IMLLYVKDV-
+ SCNRVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ -SSVDDNYL- VNMLPFIHSR DNPVGHYVQG LED-PMHLIR PGT---ARKL
+ NILF-YGCEY YSGQFPDGEA -ERSWIYP-V YCEM----KK DHKSAVVAHK
+ AEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ VFM-GNDATR KLITGVSVMP TYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ YDIKIWETHI RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCILTVSG LKQPM-AGYN DETQITKTPD ICIC--GVGT IHFKNLVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ DLFQILVHE
+
+t72 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHVQGHV
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKVS-S
+ QSAVWKFDRF MCALMHLMQN --------GD L--------- ----------
+ -CSH--PSFL GMCMFHEQVR RKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ KRCLNCLNAG DNDDSEHLKE KHLRT----Y G---QIGR-H -VIINVWNAF
+ MGRLNHHEPP AEVVYPLRK- -GGPDSKPM- ---------- -------VDG
+ FFDK-E-D-- ----HRPGIA NAVSVPCA-- --DQVGGPLR GWCSSQVKFG
+ LANHTLVQ-P SKLHRTFKIN KKIGANVYQQ TSRMKADAPV YPHIMEYAHG
+ V----YKPFY ERSEPKNEAQ GNGEK-QGNV PCVESVECQY ENKHAIMAKL
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVMGNKIG SPS-EFEVAA
+ DPTIIWFYRN CIVHKLADTV STAKMKAPQE MRH------Q DVDSPSLGDD
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ KQGEH---EA EQRPVYGFQH PRCRPWQFVI ANYQSSAKNI IMLLYVKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ --NHSCEMLA KTVYFEPDGE -------DEG QMVLKIFELD WVEMEKSHQQ
+ -SSVDDNYL- VNMLPFIHSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ NILF-YGCEY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ VEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ VFM-GNDATR KLITGFSIMP TYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ YDIKIWETHI RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCILTVSG LKQPV-AGYN DETQITKTPD ICIC--TWGT IHFKNSVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ DLFQILVHE
+
+t96 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHVQGHV
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ QSAVWKFDRF MCALMHLMQV --------GD L--------- ----------
+ -CSH--PSFL GMCMFHEQVR RKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ KRCLNCLNVG DNDDSEHLKE KHLRV----Y G---QIGR-H -VIINVWNAF
+ MGRLNHHEPP AEVVYPLRK- -GGPDSKLM- ---------- -------VDG
+ FFDK-E-D-- ----ERPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVKFG
+ LANHTLVQ-P SKLHRTFKIN KKIGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMECQY ENKHAIMAKL
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVIGNKIG SPS-EFEIAA
+ DPTIIWFYRN CIVHKLADTV STAKMKAPQE MRV------Q DVDSPSLGDD
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ NQGEH---EA EQRPVYGFQH PRCRPWQFVI GNYQTSAKNI IMLLYVKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCM WA-HNVAVCG WKRELVPGL-
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ -SSVDDNYL- VNMLPFIRSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ NILF-YGCEY YSGQFPDAEA -ERSWIYD-V YCEM----KK DHKSAVYAHK
+ VEHKGMDWDT GKE-MNQGPK -IVLHGVLFN -------AEP NIHGQPGVSH
+ VFM-GNDATR KLISGVSVMP TYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ YDVKIWETHI RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCILTVSG LKQPM-AGYN METQITKTPD ICIC--TWGT IHFKNSVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNI LVD-ELYSDV ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ DLFQILVHG
+
+t44 MIWSEVRQMV REG--TDNAI DTR-C----- -------LIA ARVKHMQGHV
+ KQVRNANEDA L--YQNFSGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ QSAVWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ -CSH--PSFL GMCMFHEQVR CKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ KRCLNYLNVG DNDDSEHLKE KHLRI----Y G---VIGK-H -VIINVWNAF
+ MGRLNHHEPP ADVEYPLRK- -GGPDSKPM- ---------- -------VDG
+ FFDK-E-D-- ----DRPGIA NAVSVPCG-- --DQVGGPIR GWCSSQVKFG
+ LANHTLAQNP SKLHRTFKIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ V----CKPFY DRSEPKNEAQ GNGEK-QGNV PCVESMDCQY ENKHAIMAKL
+ MHP-PLYLMR METMSKPPMG YVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ LNIIDCKLLG HRTWLATSPL Q------IGC DIMVMGNKIG SPS-EFEVAA
+ DPTIIWFYRN CIVHKLADVV STAKMKSPQE MRV------Q DVDSPSLGDD
+ DQQA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK N-DFLCPPAF
+ EQGEH---EA EQCPVHGFKH PRCRPWQFVI ADYQTSAKNI IMLLYVKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVLKIFELD WVEMEKSHQQ
+ -SSVDDNYL- VNMLPFMHSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ NILF-YGCEY YSGQFPDCEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ HEHKGMDWDT GKE-MNQGPK -VVMHGVLFN -------AEP NIHGQPGVSH
+ VFM-GNDATR KLITGVSVMP TYKFMCNACV PFFHKLFMAV RNMRYDYTVN
+ YDIKIWETHM RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCILTVSG LKQPM-AGYN DETEITKTPD ICIC--TWGT IHFKNSVMQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNM LVD-ELYSDM ---YPAAPKK K--VYV-GAG DVGGYEVMSE
+ DLFQILVHA
+
+t45 MIWSEVRQMV REG--TDNAI DNC-C----- -------LIA ARVKHMQGHV
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YK-CMEGHDC VNTMAKSS-S
+ QSAVWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ -CSV--PSFL GMCMFHEQVR CKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ KRCLNYLNVG DNDDSEHLKE KHLRI----Y G---EIGK-H -VIINVWNAF
+ MGRLNHHEPP AEVMYPLRK- -GGPESKPM- ---------- -------VDG
+ FFDK-E-D-- ----DRPGIA NAVSVPCT-- --DQVGGPIR GWCSSQVKFG
+ LANHTLVHNP SKLHRTFAIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMDCQY ENKHAIMAKL
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVMGNKIG SPA-EFEVAA
+ DPTIIWFYRN CIVHKLADLV STAKMKSPQE MRV------Q DVDSPSLGDD
+ DQEA--MDIL PYWVCVMSGV VRKEQPD-SV NKRGRTWLAK K-DFLVPPAF
+ NQGEH---EA EQKPVYGFDH PRCRPWQFVI ANYQTSAKNI IMLLYVKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVHKIFELD WVEMEKSHQQ
+ -SSVDDNYL- VNMLPFFHSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ NILF-YGCQY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ HQHKGMDWDT GKE-MNQGPK -VVLHGVLFN -------AEP NIHGQPGVSH
+ VFM-GNDATR KLIPGVSVMH DYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ YDIKIWETHL RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCILTVSG LKQPM-AGFV DETEITKTPD ICIC--TWGT IHFKNSVVQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ DLFQILVHE
+
+t74 MIWSEVRQMV REG--TDNAI DNC-C----- -------LIA ARVKHMQGHV
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHDC VNTMAKPS-S
+ QSAVWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ -CSV--PSFL GMCMFHEQVR CKGE--LVLP DSPNEESVSF VYIQHHSFSD
+ KRCLNYLNVG DNDDSEHIKE KHLRI----Y G---EIGK-H -VIINVWNAF
+ MGRLNHHEPP AEVMYPLRK- -GGPESKPM- ---------- -------VDG
+ FFDK-E-D-- ----DRPGIA NAVSVPCA-- --DQVGGPIR GWCSSQVKFG
+ LANHTLVHNP SKLHRTFAIN KKMGANVYQQ TSRMKAEAPV YPHIMEYAHG
+ V----CKPFY ERSEPKNEAQ GNGEK-QGNV PCVESMDCQY ENKHAIMAKL
+ MHP-PLYLMR METMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSAKTLGQ
+ LNIIDCKLLG HRTWLATSPL Q------IGC DVMVVGNKIG SPA-GFEVAA
+ DPTIIWFYRN CIVHKLADLV STAKMKSPQE MRV------Q DVDSPSLGDD
+ DQEA--MDIL PYWVCVTSGV VRKEQPD-SV NKRGRTWLAK K-DFLVPPAF
+ NQGEH---EA EQKPVYGFDH PRCRPWQFVI ANYQTSAKNI IMLLYVKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCV WA-HNVAVCG WKRELVPGL-
+ --NHSCEMLA KTVYFEPDGE -------DEG KMVHKIFELD WVEMEKSHQQ
+ -SSVDDNYL- VNMLPFFHSR ENPVGHYVQG LED-PMHLIR PGT---ARKL
+ NILF-YGCQY YSGQFPDGEA -ERSWIYD-V YCEM----KK DHKSAVVAHK
+ HQHKGMDWDT GKE-MNQGPK -VVLHGVLFN -------AEP NIHGQPGVSH
+ VFM-GNDATR KLIPGVSVMH DYKFMCGACV PFFHKLFMAV RNMRYDYTVN
+ YDIKIWETHL RHGVYAVENS WETLVTC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCILTVSG LKQPM-AGFV DETEITKTPD ICIC--TWGT IHFKNSVVQY
+ CCYYKENRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHHQNI LVD-ELYSDM ---YPAAPKK K--HYV-GAG DVGGYEVMSE
+ DLFQILVHE
+
+t26 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHMSGHV
+ KQVRNANEDA L--YQNFTGK KGAREKIKR- YL-CMEGHEC VVTMAKNS-S
+ ISAMWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ -CSF--PSFL GMCMFHDQVR CKGE--LVLP DSKNEESVSF VYIQHHSFSD
+ KRCLNYLNVG DNEDSEHLKE KHLRV----Y G---NIGK-H -VIINSWNAM
+ MGRLNHHEPA AEVVYPLRK- -GGPESKPM- ---------- -------VDG
+ FFDK-E-D-- ----DRPGIA NAVSVPCD-- --DQWGGPVR GWCSSQHKFG
+ LADHTLIHIP SKLHRTFAIN KKMGANVYQQ TSRMKAAAPV YSHVMEYAHK
+ V----VKPFY ARSEPKNEAQ GNGEK-QWNV PCVESMDCQY ENKHATMAKL
+ MHP-PLYLMR MQTMAKPPMG DVDGHRCRAG LTALKIVQLD IGFSQKTLGQ
+ -NIIDSKHLG HRTWLATSPL Q------IGC SAMVMGNKIG SPQ-EVELAA
+ DPTVIYFYRN CIVQKMADVV STVKMKSPQE MRV------Q DVDSASLGDD
+ DQQP--MNII PYWVCVTSGV VHKEQPD-SV NKRGRTWTAK N-DFLCPDAF
+ NQGEH---GA EQKPTHGFEH PRCRPWQFVI PVYQTGAKNI ILLLYIKDV-
+ SVNGVLQLLI WQLCDSH-GD WQSLVADSCA WA-VNVAVCG WKRELVPGL-
+ --NHACEMLA KTVYFEPDGE -------DEG KMVIKIFGLD WCEIEKSHQQ
+ -SSVDDNYL- VNMLPFTHSR ETPVGHYVQG LED-PMHLMR PGT---ARAL
+ NILF-YGCEY YSGQFPDGEP -ERSWIYD-V YCEL----KK DHKNAIVAVK
+ HEHKGMDWDT GKE-MNHGPK -VIVHGVLFH -------AEP NIGGQPGVSH
+ VFV-GNDATR KLIAGVSVMP IVKFMCGACV PFFRKLFMAL RNMRYDYASN
+ YDIKIVETHL REGVYAVENS WETLVVC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCILTVSG LKQSV-SGYN DETEITKTPD IKIC--TWGT IHFKNSVMQY
+ CCYYKENRSV R--------- --LNNTGGAE LPK------- ----------
+ ----YHHQNV LVD-ELYGEA ---YPAAPKK K--HYM-GAG DVGGYEVMSE
+ DLFQILVHE
+
+t61 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHMSGHV
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHEC VNTMAKNS-S
+ VSAVWKFDQF MCDLMHLMQN --------GD L--------- ----------
+ -CSF--PSFL GMCMFHEQVR CKGE--LVLS DSKNEESVSF VYIQHPSFSD
+ KRCLNYLNVG DNEDSEHLKE KVLRV----Y G---DIGK-H -VIINVWNAM
+ MGRLNHHEPA AEVVCPLRK- -GGPDSKPM- ---------- -------VDG
+ FFDK-E-D-- ----DRPGVA NAVSVPCD-- --DQWGGPVR GWCSSQHKFG
+ LADHTLVHIP SKLHRTFAIT KKMGANVYQQ TSRMKATAPV YPHVMEYAHG
+ V----VKPFY DRSEPKNEAQ GNGEK-QWNV PCVESMDCQY ENKHATMAKL
+ MHP-PLYLVK MQTMSKPPMG DVDGHRCRAG LTALKIVQLD IGFSSKTLGQ
+ -NIIHSKLLG HRTWLATSPL Q------IGC DVMVMGNKIG SPQ-EVELAA
+ DPSVIYFYQN CIVQKMADVV STVKMKSPQE MRV------Q DVDSASLGDD
+ DQQP--MNII PYWVCVTSGV VRKEQPD-SV NKRGHTWTAK N-DFLCPPAY
+ NQGEH---GA EQKPVHGFEH PRCRPWQFVI SVYRTGAKNI NLLLYIKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCA WA-VNVAVCG WKRELVPGL-
+ --NHACEMLA KSVYFEPDGE -------DEG KMVLKIFGLD WCEIEKSHQQ
+ -SSVDDNYL- VNMLPFAHSR QTPVGHYVQG LED-PMHLMR PGT---ARAL
+ NILF-YGCEY YSGHFPDGEA -ERSWIYD-M YCEL----KK DHKSAIVAVK
+ HCHKGMDWDT GKE-MNHGPK -VIIHGLLFH -------AEP NIGGQPGVSH
+ VFV-GNDATR KLIAGASVMF IVKFMCGACV PFFRKLFMAL RNMRYDYSQN
+ YDIKIVETHL REGVYAIENS WETLVVC-EM TSGRMGAKIN HLPRLPEQVI
+ -PPCILTVSG LKRAV-NGYN DETEITKTPD IKIC--TWGT IHFKNSVMQY
+ CCYYKENRSV R--------- --FNNTGGAE LPK------- ----------
+ ----YHHQNV LVD-ELYSEL ---YPAAPKK A--HYM-GAG DIGGYEVMSE
+ DLFQILVHE
+
+t97 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHMSGHM
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGHEC VNTMAKNS-S
+ VSAVWKFDRF MCDLMHLMQN --------GD L--------- ----------
+ -CSF--PSFL GMCMFHQQVR CKGE--LVLP DSKNEESVSF VYIQHHSFND
+ KRCLNYLNVG DNEDSEHLEE KHLRV----Y G---NIGK-H -VIINVWNAM
+ MGRLNHHEPA AEVVCPLRK- -GGPDSKPM- ---------- -------VDG
+ FFDK-E-D-- ----DRPGVA NAMSVPCD-- --DQWGGPVR GWCSSQHKFG
+ LADHTLVHVP SKLHRTFPIN KKMGANVYQQ TSRMKATAPV YPHVMEYAHG
+ V----IKPFY DRSEPKNEAQ GNGEK-QWNV PCVESMDCQY ENKHATMAKL
+ MHP-PLYLVK MQTMSKPPMG DVDGHRCRAG LTALQIVQLD IGFSAKTLGQ
+ -NIIHSKLLG HRTWLATSPL Q------IGC DVVVMGNKIG SPQ-EVELAA
+ DPSVIYFYQN CIVQKMADVV STVKMKSPQE MRV------Q DVDSASLGDD
+ DQQP--MNII PYWVCVTSGV VRKEQPD-SV NKRGRTWSAK N-DFLCPPAF
+ NQGEH---GA EQKPVHEFQH PRCRPWQFVI SVYRTGAKNI NLLLYIKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLVADSCA WA-VNLAVCG WKRELVPGL-
+ --NHACEMLA KSVYFEPDGE -------DEG KMNLKIFGLD WCEIEKSHQQ
+ -SSVDDNYL- VNMLPFTHSR ETPVGHYVQD LED-PMHLMR PGT---ARAL
+ NILF-YGCEY YSGHFPDGEP -ERSWIYD-M YCEL----KK DHKSAIVAVK
+ HCHKGMDWDT GKE-MNHGPK -VIIHGVLFH -------AEP NIGGQPGVSH
+ VFV-GNDATR KLIAGVSVMP IVKFMCGACV PFFRKLFMAL RNMRYDYSQN
+ YDIKIVETHL REGVYAVENS WETLVVC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCILTVSG LKQAV-NDCN DETEITKTPD IKIC--TWPT IHFKNGMMQY
+ CCYYKENRSV R--------- --FNNTGGAE LPK------- ----------
+ ----YHHQNV LVD-ELYSEV ---YPAAPKK A--FYM-GAG DIGGYEVMSE
+ DLFQILVHK
+
+t17 MIWSEVRQMV REG--ADNAI DNR-C----- -------LIA ARVKHFSGHT
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGQDC VNTMAKSS-S
+ QSAVWKFDRF MCDLVHLMQN ---GARGSGD L--------- ----------
+ -CSF--PSFL GMCMFHEQVR CKGE--LVLP DSKNEESVSF VYIQHHSFSD
+ KRCLNELNVG DNEDSIHLKE KHLRI----Y G---NIGK-V -VIINVWNAM
+ MGRLNHHEPA AEVVYPLRK- -GGPDSKPM- ---------- -------VDG
+ FFDK-E-D-- ----DRPGIA NAVAVPCS-- --DQWGGPVR GWCSSQHKFG
+ LADHTLVHVP SLLHRTFAIN RKMGANVYQQ TSRMKAAAPV YPHMMEYAHG
+ V----VKPFY ERSEPKNEAQ GNGEK-QWNV PCVQSVDCQY ENKHATMAKL
+ MHP-PLYLMR METMSKPPMG DVDGVRCRAG LTALKIVQLD IGFSAKTLGQ
+ -NIIDSKLLG HRTWLATSPL Q------IGC DVMVVGNKIG SPQ-EFELAA
+ DPTVIYFYRN CIVQKLADVV STVKMKSPQE MRV------Q DVDSPSLGDD
+ NQQS--MNII PYWVCVHSGV VQKEQPD-SV HKRGRTWTAK N-DFLCPPAF
+ DQGEH---GA EQKPVHGFEH PRCRPWQFVI ANYQTGAKNI ILLLYVKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLSADSCA WA-HNVAVCG WKRELVPGL-
+ --NHACEMLA KTVYFEPDGE -------DEG KMVIKIFGLD WCEMEKAHQQ
+ -SSVDDNYL- VNMLPFTHSR ENPVGHYVQG LED-PMHLIR PGT---ARAL
+ NILF-YGCEY YSGQFPDGEP -ERSWIYD-V YCEL----KK DHKSAIVAVK
+ HEHKGMDWDT GKE-MNQGPK -VIIHGVLFH -------AEV NIHGQPGVSH
+ VFV-GNDATR KLIAGVSVMP FVKFMCGACV PFFRKLFMAL RNMRYDYTSN
+ YDIKIIETHL RNGVYAVENS WETLVVC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCMLTVSG LKQAM-AGVN DETEITKTPD IKIC--TWGT IHFKNFVMQY
+ CVYYKENRSV R--------- --FNNTGGAE LPK------- ----------
+ ----YHHQNA LVD-ELYSDV ---YPAAPKK K--HYM-GEG DVGGYEVMSE
+ DLFQILVHA
+
+t11 MIWSEVRQMV REG--TDNAI DNR-C----- -------LIA ARVKHFSGHT
+ KQVRNANEDA L--YQNFTGQ KGAREKIKR- YL-CMEGQDC VNTMAKSS-S
+ QSAVWKFDRF MCDLVHLMQN ---GARGSGD L--------- ----------
+ -CSF--PSFL GMCMFHEQVR CKGE--LVLP DSKNEESVSF VYIQHHSFSD
+ KRCLNSLNVG DNEDSIHLKE KHLRI----Y G---DIGK-H -VIINVWNAM
+ MGRLNHHEPA AEVVYPLRK- -GGPDSKPM- ---------- -------VDG
+ FFDK-E-D-- ----DRPGIA NAVAVPCS-- --DQWGGPVR GWCSSQHKFG
+ LADHTLVHVP SLLHRTFAIN KKMGANVYQQ TSRMKAAAPV YPHMMEYAHG
+ V----VKPFY ERSEPKNEAQ GNGEK-QWNV PCVQSVDCQY ENKHATMAKL
+ MHP-PLYLMR METMSKPPMG DVDGVRCRAG LTALKIVQLD IGFSAKTLGQ
+ -NIIDSKLLG HRTWLATSPL Q------IGC DVMVVGNKIG SPQ-EFELAA
+ DPTVIYFYRN CIVQKLADVV STVKMKSPQE MRV------Q DVDSPSLGDD
+ NQQS--MNII PYWVCVHSGV VQKEQPD-SV HKRGRTWTAK N-DFLCPPAF
+ DQGEH---GA EQKPVHGFEH PRCRPWQFVI ANYQTGAKNI ILLLYVKDV-
+ SCNGVLQLLN WQLCDSH-GD WQSLSADSCA WA-HNVAVCG WKRELVPGL-
+ --NHACEMLA KTVYFEPDGE -------DEG KMVIKIFGLD WCEMEKAHQQ
+ -SSVDDNYL- VNMLPFTHSR ENPVGHYVQG LED-PMHLIR PGT---ARAL
+ NILF-YGCEY YSGQFPDGEP -ERSWIYD-V YCEL----KK DHKSAIVAVK
+ HEHKGMDWDT GKE-MNQGPK -VIIHGILFH -------AEV NIHGQPGVSH
+ VFV-GNDATR KLIAGVSVMP FVKFMCGACV PFFRKLFMAL RNMRYDYTSN
+ YDIKIMETHL RNGVYAVENS WETLVVC-EM TSGRIGAKIN HLPRLPEQVI
+ -PPCMLTVSG LKQAM-AGVN DETEITKTPD IKIC--TWGT IHFKNFVMQY
+ CVYYKENRSV R--------- --FNNTGGAE LPK------- ----------
+ ----YHHQNV LVD-ELYSDG ---YPAAPKK K--HYM-GEG DVGGYEVMSE
+ DLFQILVHA
+
+t23 MIWSECQRML REH--EDQAI ANE-C----- -------LIA FKVKLVNGHV
+ KQVRNASEDA H--YTFFAGE KGARELIKR- YS-CMEGDGC VNTMAEGR-S
+ ESAVWKFDPF MCQLTHSMQS --------GD L--------- ----------
+ -CSV--PSFL GVCMFQRQVV MKGE--LVLP DSADEGSVSF MYIQHHSFAA
+ KRCLNVLNVG DNEDSVHLRH KQLRV----Y G---KIGK-H -VIISVPNAI
+ MGRLNHHEPS AIVVFPLRQ- -RGADSKSV- ---------- -------GDG
+ FYDK-D-E-- ----DRPGIA NAVSVPVA-- --EQWVGSVR GWYSSEHKYG
+ LANHILI-GP SKLHRTYQTT AKMGANVVKA TNRMKRPQPV YPHVMEYANG
+ V----VKPFY EVAESKNEAQ GNGEK-PVNV PCVESPDCQY ESKHARVNKL
+ MHP-SLYLMC MEAMNKPIMG DWDGNRCRSP LCLLKVIQLD MGVSGKTLGQ
+ -NIVMAKLLG ERTWLATSPL Q------IGC DVVAVGKKPE SPQ-EFECAA
+ DPTVIYFYKN LIIQQAADYV SAVQVKSPQE MRY------Q DVNSPSDGDE
+ NGQS--MHIG PYWVCVSSEV VKKSQPD-SV DKRGRTWVAK N-EFLCPPDH
+ MQGEHSIEGA EQKPFFGFAG PFPQPWQFVI VNPQTWAHNI IRLLYCKDV-
+ SCNCVLTCLN WVLCDSH-GD WHSLIADACP CA-HNVAVCG WKRELVPGL-
+ --NHSNEHMA KTIYFEPDGH -------DEG KMILNIFGLD WCEVETSHQE
+ -SSSDDNHL- VNMLPFGVSR DDPVGHYMLG LED-AIRLYR PGT---ARAL
+ NILF---VNY YSGDFQDPEL -ERSQLYN-V YCEQ----KQ DHRNAIRASK
+ NDHKGMAWDT AKD-MEQGPK -MVEHQVLFY -------AEP NMHGQPEVIH
+ IFI-GNDAMC MLIPGMSVMV HHKFMRAACM PFFNKLFMAV RYMRYDYVDN
+ YDIKIDETRY RDGVYARRNS WETANVC-EM SSGRSGAKIN HNPRLPEQVT
+ -PPRSLTVSG LKDTM-PGHP DVTEITKTPV IAIV--MWGT INLKNHVMQY
+ CCYYKETRSV R--------- --VNNTGGAE LPK------- ----------
+ ----YHYQNI LVD-ELYSND ---YPAAPKK A--QFM-GVG DVGGYEIVCE
+ DIFQILVCD
+
+t76 LSSSHEVRVV NHKSKPDEHI ADK-D----- -------MCA DAMCNGSGHT
+ GRIHNAVEGG I--VTNFHGF ---AEMPKN- HD-VMEEQGG PGTCLAPQQS
+ ADTSWPFVMF TVDLAHRCRG --------GD MPQNTGDSMT CPHLAEGLAA
+ VNS---RAFI GVSIYDLKVS HKMI--QACN PIQN------ ---DNHAFSD
+ QRCLNDLSQG VVGASFPKMQ HGVRH----Y K---K----- ---RVYENEV
+ GGRLDDAEAI DDMGVWIRW- -EGVKHAWCH PIGSCPDHLV CSLLVLQPAR
+ NFIQLS-MVR DTPHRLPKMA SAAPVYKQTC HLEQVQGTAR MWGKSGPRVV
+ LNGHMLK-TQ NTLHRQYLVD VELQATMVFV AARMKTDSSM YMSVREILHG
+ ---------- --CGIKDEAQ ADGQR-PATL IVVLSKDNKG ITEHGAVLKK
+ IHP------- ---LCKRCME NGRCLRYKND LTGDQLVQLA D----NTCAW
+ -NLFEC--LR DSKSLFGSPL FIKVDEDRGF TAP------- SK-------V
+ EPKCAQFYSK SCTHC----- ---------- -TM------C SVGSHASEED
+ ALDLYTHKPV PDAQCFVSRV ARNIPEH-SP CK-------- ----------
+ ---------- -P---CS--- ---------- ----VEEVCY CKVCDSKDVR
+ AVKNAYQDLQ VPLSKLK-AP WLSMGHCECW EEDINNILSV VKHELVDDVD
+ RMNRLTEVAA KMAYFGPDGF HWDVELWEEN DLNCDDFELG W-NLKH----
+ ---EDDHPL- LCIGSFSVHK YVSVMVYPLP MND-CVRMSQ PCHAAHAQDI
+ PTEQ---TRY QIHTFLDDSI -RRDLCNQ-G CHEENMVWRD DLKDPISTEV
+ IADKLHEWPT NVN-KENSAD ----HRQLFH -------ANS SALDKHQHNV
+ VMN-GSPCIR ALIIGGSSVG VNHFMMGPCQ EFFTDLFMMY EGLQYACVCA
+ MNITIQCLHT GEGVMCNVKC KEFLQREDEM KAGLIGIICN HLSRMIMVIL
+ -VHCLLTHAG LKSME-IGFD R-TGVVRMPL IAEP--LYLV I-YVNAVEPY
+ TDAYKKPKSM HQFQFDDCQI RYRTNTGFEE TPVGATHLTH VCVCVPHPWT
+ KGKSEILQNM GSA-VLYNDV IRDHNASEQK E--AHV-PMG DEGRISRAKD
+ EIMYIRDLE
+
+t53 LSSSHEVRVV NHKSKPDEHI ADK-D----- -------MCA DAMCNGSGHT
+ GRIHNAVEGG I--VTNFHGF ---AEMPKN- YD-VMEEQGG PGTCLAPQQS
+ ADTSWPFVMF TVDLAHRCRG --------GD IPQNTGDSMT CPHLAEGLAA
+ VNS---RAFI GVSTYDLKVS HKMI--QACN PIQN------ ---DNHAFSD
+ QRCLNDLAQG VVGASHPKMQ HGVRH----Y K---K----- ---RVYENEV
+ GGRLDDAEAI DDMGVWIRW- -EGVKHAWCH PIGSCPDHLV CSLLVLQPAR
+ NFIQLS-MVR DTPHGLPKMA SAAPVYKQTC HLEQVQGTAR MWGKSGPRVV
+ LNGHMLK-TQ NTLHRQYLVD VELGATMVFV AARMKTDLSM YMSVREILHG
+ ---------- --CGIKDEAQ ADGQR-PATL IVVLSKDNKG ITEHGAVLKK
+ IHP------- ---LCKRCME NGRCLRYKND LAGDQLVQLA D----NTCAW
+ -NLFEC--LR DSKSLFGSPL FIKVDEDRGF TAP------- SK-------V
+ EPKCAQFYSK SCTHC----- ---------- -TM------C SVGSHASEED
+ ALDLYTHRPV PDAQCFVSRV ARNIPEH-SP CK-------- ----------
+ ---------- -P---CS--- ---------- ----VEEVCY CKVCDSKDVR
+ AVKNAYQDLQ VPLSKLK-AP WLSMGHCECW EEDINNILSV VKHELVDDVD
+ RMNRLTEVAA KMAYFGPDGF HWDVELWEEN DLNCDDFELG W-NLKP----
+ ---EDDHPL- LCIGSFSVHK YVSVMVYPLP MND-CVRMSQ PCHAAHAQDI
+ PTEQ---TRY QIHTFLDDSI -RRDLCNQ-G CHEENMVWRD DLKDPISTEV
+ IADKLHEWPT NQN-KENSAD ----HRQLFH -------ANS SALDKHQHNV
+ VMN-GSPCIR ALIIGGSSVG VNHFMMGPCQ EFFTDLFMMY EGLQYACVCA
+ MNITIQCLHT GEGVVCNVKC KEFLQREDEM KAGLIGIICN HLSRMIMVIL
+ -VHCLLTHAG LKSME-IGFD R-TGVVRMPL IAEP--LYLV I-YVNAVEPY
+ TDAYKKPKSM HQFQFDDCQI RYRTNTGFEE TPMGATHLTH VCVCVPHPWT
+ KGKSEILQNM GSA-VLYNDV IRDHNASEQK E--AHV-PMG DQGRISRAKD
+ EIMYIRDLE
+
+t16 LSSSHEVRVV NHKSKPDEHI ADK-D----- -------MCA DAMCNGSGHT
+ GRIHNAVEGG I--VTNFHGF ---AEMPKN- YD-VMEEQGG PGTCLAPQQS
+ ADTSWPFVMF TVDLAHRCRG --------GD IPQNTGDSMT CPHLAEGLAA
+ VNS---RAFI GVSTYDLKVS HKMI--QACN PIQN------ ---DNHAFSD
+ QRCLNDLAQG VVGASHPKMQ HGVRH----Y K---K----- ---RVYENEV
+ GGRLDDAEAI DDMGVWIRW- -EGVKHAWCH PIGSCPDHLV CSLLVLQPAR
+ NFIQLS-MVR DTPHGLPKMA SAAPVYKQTC HLEQVQGTAR MWGKSGPRVV
+ LNGHMLK-TQ NTLHRQYLVD VELGATMVFV AARMKTDLSM YMSVREILHG
+ ---------- --CGIKDEAQ ADGQR-PATL IVVLSKDNKG ITEHGAVLKK
+ IHP------- ---LCKRCME NGRCLRYKND LAGDQLVQLA D----NTCLW
+ -NLFEC--LR DSKSLFGSPL FIKVDEDRGF TAP------- SK-------V
+ EPKCAQFYSK SCTHC----- ---------- -TM------C SVGSHASEED
+ ALDLYTHKPV PDAQCFVSRV ARNIPEH-SP CK-------- ----------
+ ---------- -P---CS--- ---------- ----VEEVCY CKVCDSKDVR
+ AVKNAYQDLQ VPLSKLK-AP WLSMGHCECW EEDINNILSV VKHELVDDVD
+ RMNRLTEVAA KMAYFGPDGF HWDVELWEEN DLNCDDFELG W-NLKP----
+ ---EDDHPL- LCIGSFSVHK YVSVMVYPLP MND-CVRMSQ PCHAAHAQDI
+ PTEQ---TRY QIHTFLDDSI -RRDLCNQ-G CHEENMVWRD DLKDPISTEV
+ IADKLHEWPT NQN-KENSAD ----HRQLFH -------ANS SALDKHQHNV
+ VMN-GSPCIR ALIIGGSSVG VNHFMMGPCQ EFFTDLFMMY EGLQYACVCA
+ MNITIQCLHT GEGVVCNVKC KEFLQREDEM KAGLIGIICN HLSRMIMVIL
+ -VHCLLTHAG LKSME-IGFD R-TGVVRMPL IAEP--LYLV I-YVNAVEPY
+ TDAYKKPKSM HQFQFDDCQI RYRTNTGFEE TPMGATHLTH VCVCVPHPWT
+ KGKSEILQNM GSA-VLYNDV IRDYNASEQK E--AHV-PMG DQGRISRAKD
+ EIMYIRDLE
+
+t42 LSSSHEMRVV HHKSKPDEEI ADQ-D----- -------LCA EEMCKGSGHT
+ GRIHSAVEGG I--WTNFHGF ---AEMPKN- YD-VMEEQGG PGTCIAPRQS
+ ADTSWPFMVF TVDLAHRCRG --------GD TPTQAGDSMT FPHLAEGLPA
+ VNS---RAFV GVSSYDLRVS HKMI--QACT LIQN------ ---DNVAFSD
+ QRPLNDLNQG CVGTSHPKMP HGVRH----Y K---K----- ---KVYENEV
+ GDRLDDAEGI DDVGVWMRW- -NGVKHAWCH IIGSCPDHLV CSLLVLQPGR
+ NFIQLS-VVH DTPHRLPKMA SAAAVFKQTC HLEQVPGTAR MWGKSGPRVR
+ LNGHVLK-NQ NILHRQYLVD VNLGATMVFV LARMKTDASM YMSHREILHG
+ GTFDAAKPFR QICGTKDEAQ PDGRR-PATL LVVLSKDNQG ITEHGAVLKH
+ VHP------- ---LCKKDCN NNRCLRCKNV LAGNQLIQLS D----VTCAW
+ -NLFEC--LG DSESLFGSPL AIKVDEDRGF TAP------- SK-------V
+ EPKCAQFYSK SCTHH----- ---------- -MM------C SVGSNASEED
+ ALELYTHKPV PDPQCFVSIV VRNIPEH-SP CK-------- ----------
+ ---------- -P---CS--- ---------- ----VEEVAY CKNCDSKDVR
+ AVQNAYQDLA VPLSKLK-AP WLSMGHCECW EEDINNILSM VKHELVVDQD
+ MVNRSPEVAA KMAYFGPDGF HWDVELCEES DLTVDDFELG W-VLKP----
+ ---EDDHPL- ICIGSFSVHK QFSVMVYPLP MND-AIRMSQ PCHAAHAQDI
+ HTDQ---DRY DVRTFLGHSI -KCHMCNQ-A CHEENIVWRD DLKDPITTEV
+ IAEKLQEWPT NQN-KENVAD ----HRQLFH -------ANS SALDKHRHNV
+ MMN-GSACIR TLIIGGSIVG VNVFMMEPCQ EFFTDLFMVY EGLQYAVVCA
+ VNIIIQCLHT NEGVVCNVKC KEFLQREEDM KSGLIGIICN HISRMCMHIL
+ -VVCLLTHCG LKAME-IPFD I-TGVVRGPL ITEP--LYLI I-YVNAVEPY
+ TDAYKKPKSM HQFQFDDVQI RYRTNTGFEE NPKLATHLVH VCVVVPHPWT
+ KGKSEILQNM ESA-HLYNAV IRDNNASEQK E--AHV-PVG DEGRISRAKN
+ EILYIRDLE
+
+t24 QSSSHEMRVV HHKSKPDEEI TDQ-D----- -------LCA EEMCKGSGHT
+ GRIHSAVEGG I--WTNFHGF ---AEMPKN- YD-VMEEQGG PGTCVAPRQS
+ ADTNWPFMVF PVELAHRCRG --------GD TP-------- FPHLAEGLPA
+ VNS---RAFI GVSSYDLKVS HKMI--QACN PIQN------ ---DNVAFSD
+ QRVLNDLSQG CVGTSHPKMP HGVRH----Y K---K----- ---RVYENEV
+ GDRLDDAEAV DDVGVWMRW- -AGVKVAVCH VIGSCPDHLV VSLLVLQPAR
+ NFIQLS-VVH DTPHRLPKMA SAAAVFKQTC HLEQVAGTAR VWGKSGPRVK
+ LNGHVLK-NQ NVLHRQYLVD VDLGATMVFV AARMKTDASM YMSHREILHG
+ GTFDAAKPFR QICGVKDEAQ PDGQR-PATL LVVLSKDNVG ITEHGAVLKH
+ VHP------- ---LCKKDCN NNRCLRCKNV LAGNQLVQLA D----ITCAW
+ -NLFEC--LG DSESLFGSPL AIKVDEDRGF TAP------- SK-------V
+ EPKCQQFYSK SCTHC----- ---------- -VM------C SVGSNASEED
+ ALELYTHKPV PDPQCFVSIV VRNIPEH-SP CK-------- ----------
+ ---------- -P---CS--- ---------- ----VEEVCY CKNCDSKDVR
+ ATQNAYQELA IPLSKLK-AP WLSMGHCECW EEGINNILSM VKHELVVDQD
+ MVNRSPEVAA KMAYFGPDGF HWDIELCEEN DLTCDDFELG W-VLKP----
+ ---EDDHPL- ICIGSFSVHK QFSVMVYPLP MND-AIRMSQ PCYAAHAQDI
+ HTDQ---DRY DIRTFLEHSI -RCHLCNQ-A CHEENIVWRD DLKDPITTEV
+ IADKLQEWPT NQN-AENVAD ----HRQLFH -------ANS SCLDRHRHNV
+ MMN-GSSCIR TLIIGGSIVG VNVFMMGPCQ EFFTDLFMVY EGLQYAVVCA
+ INIIIQVLHT NEGVVCNVKC KEFLQREDDM KSGLIGIICN HISRMCMHIL
+ -VHCLLTHCG LKAME-IPFD R-TGVVRGPL IAEP--LYLI I-YVNAVEPY
+ TDAYKKPKSM HQFQFDDVQI RYRTNTGFEE NPKLATHLVH VCVVVPHPWT
+ KGKSEILQNM ESARHLYNAV IRDNNASHQK E--AHV-PAG DQGRISRAKN
+ EILYIRDLE
+
diff --git a/test/test_alignment_scores.cpp b/test/test_alignment_scores.cpp
new file mode 100644
index 0000000..56ea6c1
--- /dev/null
+++ b/test/test_alignment_scores.cpp
@@ -0,0 +1,102 @@
+//
+// File: test_alignment_scores.cpp
+// Created by: Julien Dutheil
+// Created on: Wed Dec 14 16:35 2011
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for numerical calculus. This file is part of the Bio++ project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include <Bpp/Seq/Alphabet/RNA.h>
+#include <Bpp/Seq/Container/VectorSiteContainer.h>
+#include <Bpp/Seq/Container/SiteContainerTools.h>
+#include <Bpp/Seq/SiteTools.h>
+#include <iostream>
+
+using namespace bpp;
+using namespace std;
+
+int main() {
+ RNA* alpha = new RNA();
+ SiteContainer* sites = new VectorSiteContainer(alpha);
+ BasicSequence seq1("seq1", "----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU--", alpha);
+ BasicSequence seq2("seq2", "---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU--", alpha);
+ BasicSequence seq3("seq3", "---GAA-CCG---G-GU----UUU----VC-GACCGGAG--UUUU--", alpha);
+ sites->addSequence(seq1, false);
+ sites->addSequence(seq2, false);
+ sites->addSequence(seq3, false);
+
+ //Create alignment indexes:
+ RowMatrix<size_t> index1;
+ SiteContainerTools::getSequencePositions(*sites, index1);
+
+ vector<int> scores = SiteContainerTools::getColumnScores(index1, index1);
+ VectorTools::print(scores);
+ for (size_t i = 0; i < sites->getNumberOfSites(); ++i) {
+ if (SiteTools::isGapOnly(sites->getSite(i))) {
+ if (scores[i] != 0) return 1;
+ } else {
+ if (scores[i] != 1) return 1;
+ }
+ }
+
+ SiteContainer* sites2 = new VectorSiteContainer(alpha);
+ BasicSequence seq21("seq1", "----AUGCCGGCGU-UUUG--G-CCGACGUGUUUU", alpha);
+ BasicSequence seq22("seq2", "---GAAGGCGG-GUU-UUGC-GACCGAC--GUUUU", alpha);
+ BasicSequence seq23("seq3", "---GAA-CCGG-GUUU-UVC-GACCGGA--GUUUU", alpha);
+ sites2->addSequence(seq21, false);
+ sites2->addSequence(seq22, false);
+ sites2->addSequence(seq23, false);
+
+ RowMatrix<size_t> index2;
+ SiteContainerTools::getSequencePositions(*sites2, index2);
+
+ vector<int> scores12 = SiteContainerTools::getColumnScores(index1, index2);
+ VectorTools::print(scores12);
+
+ //Just a simple test, please check output by eye for better evaluation!
+ if (scores12.size() != index1.getNumberOfColumns()) return 1;
+
+ vector<int> scores21 = SiteContainerTools::getColumnScores(index2, index1);
+ VectorTools::print(scores21);
+
+ if (scores21.size() != index2.getNumberOfColumns()) return 1;
+
+ vector<double> sp12 = SiteContainerTools::getSumOfPairsScores(index1, index2);
+ VectorTools::print(sp12);
+
+ vector<double> sp21 = SiteContainerTools::getSumOfPairsScores(index2, index1);
+ VectorTools::print(sp21);
+
+ return 0;
+}
diff --git a/test/test_alphabets.cpp b/test/test_alphabets.cpp
new file mode 100644
index 0000000..9fc128e
--- /dev/null
+++ b/test/test_alphabets.cpp
@@ -0,0 +1,77 @@
+//
+// File: test_alphabets.cpp
+// Created by: Julien Dutheil
+// Created on: Sat Oct 30 17:10 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for numerical calculus. This file is part of the Bio++ project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include <Bpp/Seq/Alphabet/DNA.h>
+#include <Bpp/Seq/Alphabet/RNA.h>
+#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
+#include <Bpp/Seq/Alphabet/DefaultAlphabet.h>
+#include <Bpp/Seq/Alphabet/StandardCodonAlphabet.h>
+#include <Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.h>
+#include <Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.h>
+#include <Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.h>
+#include <Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.h>
+#include <iostream>
+
+using namespace bpp;
+using namespace std;
+
+int main() {
+ //This is a very simple test that instanciate all alpahabet classes.
+ NucleicAlphabet* dna = new DNA();
+ NucleicAlphabet* rna = new RNA();
+ Alphabet* pro = new ProteicAlphabet;
+ Alphabet* def = new DefaultAlphabet;
+ Alphabet* stdCdn = new StandardCodonAlphabet(rna);
+ Alphabet* vmtCdn = new VertebrateMitochondrialCodonAlphabet(rna);
+ Alphabet* imtCdn = new InvertebrateMitochondrialCodonAlphabet(rna);
+ Alphabet* emtCdn = new EchinodermMitochondrialCodonAlphabet(rna);
+ Alphabet* ymtCdn = new YeastMitochondrialCodonAlphabet(rna);
+
+ delete dna;
+ delete rna;
+ delete pro;
+ delete def;
+ delete stdCdn;
+ delete vmtCdn;
+ delete imtCdn;
+ delete emtCdn;
+ delete ymtCdn;
+
+ return (0);
+}
diff --git a/test/test_bowker.cpp b/test/test_bowker.cpp
new file mode 100644
index 0000000..8b4e24b
--- /dev/null
+++ b/test/test_bowker.cpp
@@ -0,0 +1,101 @@
+//
+// File: test_bowker.cpp
+// Created by: Julien Dutheil
+// Created on: Sat Apr 16 13:19 2009
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for numerical calculus. This file is part of the Bio++ project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include <Bpp/Seq/Alphabet/RNA.h>
+#include <Bpp/Seq/Alphabet/AlphabetTools.h>
+#include <Bpp/Seq/SequenceTools.h>
+#include <iostream>
+
+using namespace bpp;
+using namespace std;
+
+BasicSequence* getRandomSequence(const Alphabet* alphabet, unsigned int size) {
+ string seq = "";
+ for (unsigned int i = 0; i < size; ++i)
+ seq += alphabet->intToChar(RandomTools::giveIntRandomNumberBetweenZeroAndEntry(alphabet->getSize()));
+ return new BasicSequence("random seq", seq, alphabet);
+}
+
+int test(const Alphabet* alphabet, unsigned int size, unsigned int rep) {
+ double n01 = 0;
+ double n05 = 0;
+ double n10 = 0;
+ double n50 = 0;
+
+ //ofstream out("pvalues.txt", ios::out);
+ for (unsigned int i = 0; i < rep; ++i) {
+ ApplicationTools::displayGauge(i, rep-1);
+ auto_ptr<BasicSequence> seq1(getRandomSequence(alphabet, size));
+ auto_ptr<BasicSequence> seq2(getRandomSequence(alphabet, size));
+ auto_ptr<BowkerTest> test(SequenceTools::bowkerTest(*seq1, *seq2));
+ double p = test->getPValue();
+ if (p <= 0.01) n01++;
+ if (p <= 0.05) n05++;
+ if (p <= 0.10) n10++;
+ if (p <= 0.50) n50++;
+ //out << p << endl;
+ }
+ //out.close();
+
+ cout << n01 / rep <<
+ "\t" << n05 / rep <<
+ "\t" << n10 / rep <<
+ "\t" << n50 / rep << endl;
+
+ if (abs(n01*100 / rep - 1 ) > 1) return 1;
+ if (abs(n05*100 / rep - 5 ) > 1) return 1;
+ if (abs(n10*100 / rep - 10) > 1) return 1;
+ if (abs(n50*100 / rep - 50) > 1) return 1;
+ return 0;
+}
+
+int main() {
+ //ProteicAlphabet* alpha = new ProteicAlphabet;
+ RNA* alpha = new RNA();
+ BasicSequence seq1("seq1", "----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU--", alpha);
+ BasicSequence seq2("seq2", "---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU--", alpha);
+ auto_ptr<BowkerTest> btest(SequenceTools::bowkerTest(seq1, seq2));
+ cout << btest->getStatistic() << "\t" << btest->getPValue() << endl;
+ delete alpha;
+
+ test(&AlphabetTools::DNA_ALPHABET, 1000, 5000);
+ test(&AlphabetTools::PROTEIN_ALPHABET, 20000, 5000);
+
+ return 0;
+}
diff --git a/test/test_containers.cpp b/test/test_containers.cpp
new file mode 100644
index 0000000..8cdb459
--- /dev/null
+++ b/test/test_containers.cpp
@@ -0,0 +1,68 @@
+//
+// File: test_containers.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Nov 01 10:15 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for numerical calculus. This file is part of the Bio++ project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include <Bpp/Seq/Alphabet/RNA.h>
+#include <Bpp/Seq/Container/VectorSiteContainer.h>
+#include <Bpp/Seq/Container/SiteContainerTools.h>
+#include <iostream>
+
+using namespace bpp;
+using namespace std;
+
+int main() {
+ //ProteicAlphabet* alpha = new ProteicAlphabet;
+ RNA* alpha = new RNA();
+ SiteContainer* sites = new VectorSiteContainer(alpha);
+ BasicSequence seq1("seq1", "----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU--", alpha);
+ BasicSequence seq2("seq2", "---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU--", alpha);
+ sites->addSequence(seq1, false);
+ sites->addSequence(seq2, false);
+
+ cout << sites->getNumberOfSites() << endl;
+ cout << sites->toString("seq1") << endl;
+ cout << sites->toString("seq2") << endl;
+ SiteContainerTools::removeGapOnlySites(*sites);
+ cout << endl;
+
+ cout << sites->getNumberOfSites() << endl;
+ cout << sites->toString("seq1") << endl;
+ cout << sites->toString("seq2") << endl;
+
+ return (sites->getNumberOfSites() == 30 ? 0 : 1);
+}
diff --git a/test/test_io.cpp b/test/test_io.cpp
new file mode 100644
index 0000000..b8feb95
--- /dev/null
+++ b/test/test_io.cpp
@@ -0,0 +1,96 @@
+//
+// File: test_io.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Nov 01 10:16 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for numerical calculus. This file is part of the Bio++ project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
+#include <Bpp/Seq/Io/Fasta.h>
+#include <Bpp/Seq/Io/Mase.h>
+#include <Bpp/Seq/Io/Clustal.h>
+#include <Bpp/Seq/Io/Phylip.h>
+#include <iostream>
+
+using namespace bpp;
+using namespace std;
+
+int main() {
+ //This program reads a protein alignment generated using SimProt
+ //[http://www.uhnresearch.ca/labs/tillier/simprotWEB/] in various file formats
+ ProteicAlphabet* alpha = new ProteicAlphabet;
+ Fasta fasta;
+ const SiteContainer* sites1 = fasta.readAlignment("example.fasta", alpha);
+ //test number of seq
+ cout << "example.fasta contains " << sites1->getNumberOfSequences() << " sequences" << endl;
+ if (sites1->getNumberOfSequences() != 100) {
+ return 1;
+ }
+
+ Mase mase;
+ const SiteContainer* sites2 = mase.readAlignment("example.mase", alpha);
+ Clustal clustal;
+ const SiteContainer* sites3 = clustal.readAlignment("example.aln", alpha);
+ Phylip phylip(true, false);
+ const SiteContainer* sites4 = phylip.readAlignment("example.ph", alpha);
+ Phylip phylip3(true, true);
+ const SiteContainer* sites5 = phylip3.readAlignment("example.ph3", alpha);
+
+ cout << sites1->getNumberOfSequences() << "\t" << sites1->getNumberOfSites() << endl;
+ cout << sites2->getNumberOfSequences() << "\t" << sites2->getNumberOfSites() << endl;
+ cout << sites3->getNumberOfSequences() << "\t" << sites3->getNumberOfSites() << endl;
+ cout << sites4->getNumberOfSequences() << "\t" << sites4->getNumberOfSites() << endl;
+ cout << sites5->getNumberOfSequences() << "\t" << sites5->getNumberOfSites() << endl;
+
+ //Test:
+ bool test = sites1->getNumberOfSequences() == sites2->getNumberOfSequences()
+ && sites1->getNumberOfSequences() == sites3->getNumberOfSequences()
+ && sites1->getNumberOfSequences() == sites4->getNumberOfSequences()
+ && sites1->getNumberOfSequences() == sites5->getNumberOfSequences()
+ && sites1->getNumberOfSites() == sites2->getNumberOfSites()
+ && sites1->getNumberOfSites() == sites3->getNumberOfSites()
+ && sites1->getNumberOfSites() == sites4->getNumberOfSites()
+ && sites1->getNumberOfSites() == sites5->getNumberOfSites();
+
+ delete sites1;
+ delete sites2;
+ delete sites3;
+ delete sites4;
+ delete sites5;
+
+ delete alpha;
+
+ return (test ? 0 : 1);
+}
diff --git a/test/test_sequences.cpp b/test/test_sequences.cpp
new file mode 100644
index 0000000..15811d4
--- /dev/null
+++ b/test/test_sequences.cpp
@@ -0,0 +1,92 @@
+//
+// File: test_sequences.cpp
+// Created by: Julien Dutheil
+// Created on: Mon Dec 130 17:10 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for numerical calculus. This file is part of the Bio++ project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include <Bpp/Seq/Alphabet/DNA.h>
+#include <Bpp/Seq/Alphabet/AlphabetTools.h>
+#include <Bpp/Seq/SequenceTools.h>
+#include <iostream>
+
+using namespace bpp;
+using namespace std;
+
+int main() {
+ BasicSequence seq1("test DNA", "ATTTCG---TCGTT-AAAGCWCATGCATCGATC", &AlphabetTools::DNA_ALPHABET);
+ BasicSequence motif1("motif", "ATTT", &AlphabetTools::DNA_ALPHABET);
+ BasicSequence motif2("motif", "TCG", &AlphabetTools::DNA_ALPHABET);
+ BasicSequence motif3("motif", "GATC", &AlphabetTools::DNA_ALPHABET);
+ BasicSequence motif4("motif", "CGTC", &AlphabetTools::DNA_ALPHABET);
+ BasicSequence motif5("motif", "CWCAT", &AlphabetTools::DNA_ALPHABET);
+ BasicSequence motif6("motif", "CTCAT", &AlphabetTools::DNA_ALPHABET);
+ BasicSequence motif7("motif", "AAGCA", &AlphabetTools::DNA_ALPHABET);
+ size_t pos;
+
+ cout << "--- Strict match ---" << endl;
+
+ pos = SequenceTools::findFirstOf(seq1, motif1);
+ if (pos != 0) return 1;
+ cout << motif1.toString() << ": " << pos << endl;
+
+ pos = SequenceTools::findFirstOf(seq1, motif2);
+ if (pos != 3) return 1;
+ cout << motif2.toString() << ": " << pos << endl;
+
+ pos = SequenceTools::findFirstOf(seq1, motif3);
+ if (pos != 29) return 1;
+ cout << motif3.toString() << ": " << pos << endl;
+
+ pos = SequenceTools::findFirstOf(seq1, motif4);
+ if (pos != 33) return 1;
+ cout << motif4.toString() << ": " << pos << endl;
+
+ pos = SequenceTools::findFirstOf(seq1, motif5);
+ if (pos != 19) return 1;
+ cout << motif5.toString() << ": " << pos << endl;
+
+ cout << "--- Degenerated match ---" << endl;
+
+ pos = SequenceTools::findFirstOf(seq1, motif6, false);
+ if (pos != 19) return 1;
+ cout << motif6.toString() << ": " << pos << endl;
+
+ pos = SequenceTools::findFirstOf(seq1, motif7, false);
+ if (pos != 16) return 1;
+ cout << motif7.toString() << ": " << pos << endl;
+
+ return (0);
+}
diff --git a/test/test_walker.cpp b/test/test_walker.cpp
new file mode 100644
index 0000000..1757f2a
--- /dev/null
+++ b/test/test_walker.cpp
@@ -0,0 +1,119 @@
+//
+// File: test_walker.cpp
+// Created by: Julien Dutheil
+// Created on: Thu Nov 24 14:42 2011
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for numerical calculus. This file is part of the Bio++ project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include <Bpp/App/ApplicationTools.h>
+#include <Bpp/Seq/Alphabet/RNA.h>
+#include <Bpp/Seq/Sequence.h>
+#include <Bpp/Seq/SequenceWalker.h>
+#include <Bpp/Numeric/Random/RandomTools.h>
+#include <iostream>
+
+using namespace bpp;
+using namespace std;
+
+bool testSeq(SequenceWalker& walker, unsigned int pos, unsigned int truth) {
+ cout << 0 << endl;
+ cout << walker.getSequencePosition(0) << endl;
+ cout << 46 << endl;
+ cout << walker.getSequencePosition(46) << endl;;
+ for (unsigned int i = 0; i < 1000; ++i) {
+ ApplicationTools::displayGauge(i, 999, '=');
+ size_t r = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(47);
+ size_t x = walker.getSequencePosition(r);
+ if (walker.getSequencePosition(pos) != truth) {
+ cout << endl;
+ cerr << r << "\t" << x << endl;
+ cerr << walker.getSequencePosition(pos) << "<>" << truth << endl;
+ return false;
+ }
+ }
+ cout << endl;
+ return true;
+}
+
+bool testAln(SequenceWalker& walker, unsigned int pos, unsigned int truth) {
+ cout << 0 << endl;
+ cout << walker.getAlignmentPosition(0) << endl;
+ cout << 26 << endl;
+ cout << walker.getAlignmentPosition(26) << endl;
+ for (unsigned int i = 0; i < 1000; ++i) {
+ ApplicationTools::displayGauge(i, 999, '=');
+ unsigned int r = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(27);
+ walker.getAlignmentPosition(r);
+ if (walker.getAlignmentPosition(pos) != truth) {
+ cout << endl;
+ cerr << walker.getSequencePosition(pos) << "<>" << truth << endl;
+ return false;
+ }
+ }
+ cout << endl;
+ return true;
+}
+
+int main() {
+ RNA* alpha = new RNA();
+ BasicSequence seq1("seq1", "----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU--", alpha);
+ SequenceWalker walker(seq1);
+
+ for (unsigned int i = 0; i < 27; ++i) {
+ size_t j = walker.getAlignmentPosition(i);
+ cout << i << "\t" << seq1.getChar(j) << "\t" << j << endl;
+ }
+
+ cout << endl;
+
+ if (!testAln(walker, 5, 9)) return 1;
+ if (!testAln(walker, 10, 21)) return 1;
+ if (!testAln(walker, 22, 40)) return 1;
+
+ cout << "_________________________________________________" << endl;
+
+ for (unsigned int i = 0; i < seq1.size(); ++i) {
+ cout << i << "\t" << seq1.getChar(i) << "\t" << walker.getSequencePosition(i) << endl;
+ }
+
+
+ cout << endl;
+
+ if (!testSeq(walker, 9, 5)) return 1;
+ if (!testSeq(walker, 21, 10)) return 1;
+ if (!testSeq(walker, 40, 22)) return 1;
+
+ return 0;
+}
--
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