[med-svn] [libbpp-seq-omics] 03/10: Imported Upstream version 2.2.0
Andreas Tille
tille at debian.org
Wed Apr 13 14:56:40 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-omics.
commit e1f3f065bd09a02ebf0133dc9339a4fcdf57d8d9
Author: Andreas Tille <tille at debian.org>
Date: Wed Apr 13 16:41:20 2016 +0200
Imported Upstream version 2.2.0
---
BppSeqOmics.tag | 4984 ++++++++++++++++++++
CMakeLists.txt | 5 +-
ChangeLog | 8 +
Doxyfile | 2 +-
bpp-seq-omics.spec | 5 +-
debian/changelog | 7 +
debian/control | 6 +-
debian/copyright | 6 +-
genIncludes.sh | 35 +
src/Bpp/Seq/Feature/SequenceFeatureTools.cpp | 11 +-
src/Bpp/Seq/Feature/SequenceFeatureTools.h | 6 +-
src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp | 4 +-
...stener.cpp => CoordinatesOutputMafIterator.cpp} | 55 +-
...afIterator.h => CoordinatesOutputMafIterator.h} | 58 +-
src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp | 4 +-
src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp | 24 +-
src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp | 24 +-
src/Bpp/Seq/Io/Maf/IterationListener.cpp | 6 +-
src/Bpp/Seq/Io/Maf/MafParser.cpp | 3 +-
src/Bpp/Seq/Io/Maf/MafSequence.h | 17 +-
src/Bpp/Seq/Io/Maf/MafStatistics.cpp | 309 +-
src/Bpp/Seq/Io/Maf/MafStatistics.h | 269 +-
.../Seq/Io/Maf/OrphanSequenceFilterMafIterator.h | 9 +-
src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp | 7 +-
src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h | 4 +-
.../Seq/Io/Maf/SequenceStatisticsMafIterator.cpp | 4 +-
src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h | 6 +-
src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp | 51 +-
src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h | 25 +-
src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h | 2 +-
src/CMakeLists.txt | 2 +
31 files changed, 5794 insertions(+), 164 deletions(-)
diff --git a/BppSeqOmics.tag b/BppSeqOmics.tag
new file mode 100644
index 0000000..131b933
--- /dev/null
+++ b/BppSeqOmics.tag
@@ -0,0 +1,4984 @@
+<?xml version='1.0' encoding='UTF-8' standalone='yes' ?>
+<tagfile>
+ <compound kind="file">
+ <name>FeatureReader.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/</path>
+ <filename>FeatureReader_8h</filename>
+ <includes id="SequenceFeature_8h" name="SequenceFeature.h" local="yes" imported="no">SequenceFeature.h</includes>
+ <class kind="class">bpp::FeatureReader</class>
+ </compound>
+ <compound kind="file">
+ <name>GffFeatureReader.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/Gff/</path>
+ <filename>GffFeatureReader_8cpp</filename>
+ <includes id="GffFeatureReader_8h" name="GffFeatureReader.h" local="yes" imported="no">GffFeatureReader.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>GffFeatureReader.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/Gff/</path>
+ <filename>GffFeatureReader_8h</filename>
+ <includes id="SequenceFeature_8h" name="SequenceFeature.h" local="yes" imported="no">../SequenceFeature.h</includes>
+ <includes id="FeatureReader_8h" name="FeatureReader.h" local="yes" imported="no">../FeatureReader.h</includes>
+ <class kind="class">bpp::GffFeatureReader</class>
+ </compound>
+ <compound kind="file">
+ <name>GtfFeatureReader.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/Gtf/</path>
+ <filename>GtfFeatureReader_8cpp</filename>
+ <includes id="GtfFeatureReader_8h" name="GtfFeatureReader.h" local="yes" imported="no">GtfFeatureReader.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>GtfFeatureReader.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/Gtf/</path>
+ <filename>GtfFeatureReader_8h</filename>
+ <includes id="SequenceFeature_8h" name="SequenceFeature.h" local="yes" imported="no">../SequenceFeature.h</includes>
+ <includes id="FeatureReader_8h" name="FeatureReader.h" local="yes" imported="no">../FeatureReader.h</includes>
+ <class kind="class">bpp::GtfFeatureReader</class>
+ </compound>
+ <compound kind="file">
+ <name>SequenceFeature.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/</path>
+ <filename>SequenceFeature_8cpp</filename>
+ <includes id="SequenceFeature_8h" name="SequenceFeature.h" local="yes" imported="no">SequenceFeature.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>SequenceFeature.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/</path>
+ <filename>SequenceFeature_8h</filename>
+ <class kind="class">bpp::SeqRange</class>
+ <class kind="class">bpp::SequenceFeature</class>
+ <class kind="class">bpp::BasicSequenceFeature</class>
+ <class kind="class">bpp::SequenceFeatureSet</class>
+ </compound>
+ <compound kind="file">
+ <name>SequenceFeatureTools.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/</path>
+ <filename>SequenceFeatureTools_8cpp</filename>
+ <includes id="SequenceFeatureTools_8h" name="SequenceFeatureTools.h" local="yes" imported="no">SequenceFeatureTools.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>SequenceFeatureTools.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/</path>
+ <filename>SequenceFeatureTools_8h</filename>
+ <includes id="SequenceFeature_8h" name="SequenceFeature.h" local="yes" imported="no">SequenceFeature.h</includes>
+ <class kind="class">bpp::SequenceFeatureTools</class>
+ </compound>
+ <compound kind="file">
+ <name>Fastq.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/</path>
+ <filename>Fastq_8cpp</filename>
+ <includes id="Fastq_8h" name="Fastq.h" local="yes" imported="no">Fastq.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>Fastq.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/</path>
+ <filename>Fastq_8h</filename>
+ <class kind="class">bpp::Fastq</class>
+ </compound>
+ <compound kind="file">
+ <name>AlignmentFilterMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>AlignmentFilterMafIterator_8cpp</filename>
+ <includes id="AlignmentFilterMafIterator_8h" name="AlignmentFilterMafIterator.h" local="yes" imported="no">AlignmentFilterMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>AlignmentFilterMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>AlignmentFilterMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::AlignmentFilterMafIterator</class>
+ <class kind="class">bpp::AlignmentFilter2MafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>BlockLengthMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>BlockLengthMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::BlockLengthMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>BlockMergerMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>BlockMergerMafIterator_8cpp</filename>
+ <includes id="BlockMergerMafIterator_8h" name="BlockMergerMafIterator.h" local="yes" imported="no">BlockMergerMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>BlockMergerMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>BlockMergerMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::BlockMergerMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>BlockSizeMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>BlockSizeMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::BlockSizeMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>ChromosomeMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>ChromosomeMafIterator_8cpp</filename>
+ <includes id="ChromosomeMafIterator_8h" name="ChromosomeMafIterator.h" local="yes" imported="no">ChromosomeMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>ChromosomeMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>ChromosomeMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::ChromosomeMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>ConcatenateMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>ConcatenateMafIterator_8cpp</filename>
+ <includes id="ConcatenateMafIterator_8h" name="ConcatenateMafIterator.h" local="yes" imported="no">ConcatenateMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>ConcatenateMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>ConcatenateMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::ConcatenateMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>CoordinatesOutputMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>CoordinatesOutputMafIterator_8cpp</filename>
+ <includes id="CoordinatesOutputMafIterator_8h" name="CoordinatesOutputMafIterator.h" local="yes" imported="no">CoordinatesOutputMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>CoordinatesOutputMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>CoordinatesOutputMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::CoordinatesOutputMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>DuplicateFilterMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>DuplicateFilterMafIterator_8cpp</filename>
+ <includes id="DuplicateFilterMafIterator_8h" name="DuplicateFilterMafIterator.h" local="yes" imported="no">DuplicateFilterMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>DuplicateFilterMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>DuplicateFilterMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::DuplicateFilterMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>EntropyFilterMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>EntropyFilterMafIterator_8cpp</filename>
+ <includes id="EntropyFilterMafIterator_8h" name="EntropyFilterMafIterator.h" local="yes" imported="no">EntropyFilterMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>EntropyFilterMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>EntropyFilterMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::EntropyFilterMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>FeatureExtractorMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>FeatureExtractorMafIterator_8cpp</filename>
+ <includes id="FeatureExtractorMafIterator_8h" name="FeatureExtractorMafIterator.h" local="yes" imported="no">FeatureExtractorMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>FeatureExtractorMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>FeatureExtractorMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::FeatureExtractor</class>
+ </compound>
+ <compound kind="file">
+ <name>FeatureFilterMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>FeatureFilterMafIterator_8cpp</filename>
+ <includes id="FeatureFilterMafIterator_8h" name="FeatureFilterMafIterator.h" local="yes" imported="no">FeatureFilterMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>FeatureFilterMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>FeatureFilterMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::FeatureFilterMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>FullGapFilterMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>FullGapFilterMafIterator_8cpp</filename>
+ <includes id="FullGapFilterMafIterator_8h" name="FullGapFilterMafIterator.h" local="yes" imported="no">FullGapFilterMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>FullGapFilterMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>FullGapFilterMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::FullGapFilterMafIterator</class>
+ </compound>
+ <compound kind="file">
+ <name>IterationListener.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>IterationListener_8cpp</filename>
+ <includes id="IterationListener_8h" name="IterationListener.h" local="yes" imported="no">IterationListener.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>IterationListener.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>IterationListener_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <includes id="SequenceStatisticsMafIterator_8h" name="SequenceStatisticsMafIterator.h" local="yes" imported="no">SequenceStatisticsMafIterator.h</includes>
+ <class kind="class">bpp::IterationListener</class>
+ <class kind="class">bpp::AbstractStatisticsOutputIterationListener</class>
+ <class kind="class">bpp::CsvStatisticsOutputIterationListener</class>
+ </compound>
+ <compound kind="file">
+ <name>MafBlock.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MafBlock_8h</filename>
+ <includes id="MafSequence_8h" name="MafSequence.h" local="yes" imported="no">MafSequence.h</includes>
+ <class kind="class">bpp::MafBlock</class>
+ </compound>
+ <compound kind="file">
+ <name>MafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MafIterator_8cpp</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <includes id="IterationListener_8h" name="IterationListener.h" local="yes" imported="no">IterationListener.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>MafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MafIterator_8h</filename>
+ <includes id="MafBlock_8h" name="MafBlock.h" local="yes" imported="no">MafBlock.h</includes>
+ <class kind="class">bpp::MafIterator</class>
+ <class kind="class">bpp::AbstractMafIterator</class>
+ <class kind="class">bpp::MafTrashIterator</class>
+ <class kind="class">bpp::AbstractFilterMafIterator</class>
+ <class kind="class">bpp::TrashIteratorAdapter</class>
+ <class kind="class">bpp::MafIteratorSynchronizer</class>
+ </compound>
+ <compound kind="file">
+ <name>MafParser.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MafParser_8cpp</filename>
+ <includes id="MafParser_8h" name="MafParser.h" local="yes" imported="no">MafParser.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>MafParser.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MafParser_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::MafParser</class>
+ </compound>
+ <compound kind="file">
+ <name>MafSequence.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MafSequence_8cpp</filename>
+ <includes id="MafSequence_8h" name="MafSequence.h" local="yes" imported="no">MafSequence.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>MafSequence.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MafSequence_8h</filename>
+ <includes id="SequenceFeature_8h" name="SequenceFeature.h" local="yes" imported="no">../../Feature/SequenceFeature.h</includes>
+ <class kind="class">bpp::MafSequence</class>
+ </compound>
+ <compound kind="file">
+ <name>MafStatistics.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MafStatistics_8cpp</filename>
+ <includes id="MafStatistics_8h" name="MafStatistics.h" local="yes" imported="no">MafStatistics.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>MafStatistics.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MafStatistics_8h</filename>
+ <includes id="MafBlock_8h" name="MafBlock.h" local="yes" imported="no">MafBlock.h</includes>
+ <class kind="class">bpp::MafStatisticsResult</class>
+ <class kind="class">bpp::SimpleMafStatisticsResult</class>
+ <class kind="class">bpp::MafStatistics</class>
+ <class kind="class">bpp::AbstractMafStatistics</class>
+ <class kind="class">bpp::AbstractMafStatisticsSimple</class>
+ <class kind="class">bpp::PairwiseDivergenceMafStatistics</class>
+ <class kind="class">bpp::BlockSizeMafStatistics</class>
+ <class kind="class">bpp::BlockLengthMafStatistics</class>
+ <class kind="class">bpp::SequenceLengthMafStatistics</class>
+ <class kind="class">bpp::AlignmentScoreMafStatistics</class>
+ <class kind="class">bpp::CharacterCountsMafStatistics</class>
+ <class kind="class">bpp::AbstractSpeciesSelectionMafStatistics</class>
+ <class kind="class">bpp::AbstractSpeciesMultipleSelectionMafStatistics</class>
+ <class kind="class">bpp::SiteFrequencySpectrumMafStatistics</class>
+ <class kind="class">bpp::SiteFrequencySpectrumMafStatistics::Categorizer</class>
+ <class kind="class">bpp::FourSpeciesPatternCountsMafStatistics</class>
+ <class kind="class">bpp::SiteMafStatistics</class>
+ <class kind="class">bpp::PolymorphismMafStatistics</class>
+ <class kind="class">bpp::SequenceDiversityMafStatistics</class>
+ </compound>
+ <compound kind="file">
+ <name>MaskFilterMafIterator.cpp</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MaskFilterMafIterator_8cpp</filename>
+ <includes id="MaskFilterMafIterator_8h" name="MaskFilterMafIterator.h" local="yes" imported="no">MaskFilterMafIterator.h</includes>
+ </compound>
+ <compound kind="file">
+ <name>MaskFilterMafIterator.h</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
+ <filename>MaskFilterMafIterator_8h</filename>
+ <includes id="MafIterator_8h" name="MafIterator.h" local="yes" imported="no">MafIterator.h</includes>
+ <class kind="class">bpp::MaskFilterMafIterator</class>
+ </compound>
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+ <arglist>(double score)</arglist>
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+ <arglist>(const SequenceFeatureSet &sfs)</arglist>
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+ <arglist>()</arglist>
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+ <arglist>(size_t i) const </arglist>
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+ <arglist>() const </arglist>
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+ <arglist>(const std::string &seqId, RangeCollection< size_t > &coords) const </arglist>
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+ <arglist>(MafIterator *iterator, unsigned int minimumSize)</arglist>
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+ <arglist>(MafIterator *iterator, std::ostream *out, const std::vector< std::string > &species)</arglist>
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+ <arglist>(MafIterator *iterator, const std::string &reference)</arglist>
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+ <arglist>(MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, double maxEnt, unsigned int maxPos, bool keepTrashedBlocks, bool missingAsGap, bool ignoreGaps)</arglist>
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+ <type>virtual</type>
+ <name>~AbstractStatisticsOutputIterationListener</name>
+ <anchorfile>classbpp_1_1AbstractStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>a92bf3dcce4d658623bd8b58e3e9e4350</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="variable" protection="protected">
+ <type>SequenceStatisticsMafIterator *</type>
+ <name>statsIterator_</name>
+ <anchorfile>classbpp_1_1AbstractStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>af479520b0736101b73d75f0076e53cd3</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::CsvStatisticsOutputIterationListener</name>
+ <filename>classbpp_1_1CsvStatisticsOutputIterationListener.html</filename>
+ <base>bpp::AbstractStatisticsOutputIterationListener</base>
+ <member kind="function">
+ <type></type>
+ <name>CsvStatisticsOutputIterationListener</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>a06b59b97ff38f56204228d96cfa637b9</anchor>
+ <arglist>(SequenceStatisticsMafIterator *iterator, const std::string &refSpecies, OutputStream *output, const std::string &sep="\t")</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>CsvStatisticsOutputIterationListener</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>a26f59fcb5e87d0bd4816572209db11f9</anchor>
+ <arglist>(const CsvStatisticsOutputIterationListener &listener)</arglist>
+ </member>
+ <member kind="function">
+ <type>CsvStatisticsOutputIterationListener &</type>
+ <name>operator=</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>ae6f6d4b98c94092258795b15005c40d3</anchor>
+ <arglist>(const CsvStatisticsOutputIterationListener &listener)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~CsvStatisticsOutputIterationListener</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>a906f84f228ee54493b0c660aaa77599d</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>iterationStarts</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>a557f80a0f9b7d2eaf2911e0ddc8f3558</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>iterationMoves</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>ad524d3447493464f968878e649a8e2e9</anchor>
+ <arglist>(const MafBlock ¤tBlock)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>iterationStops</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>a99b75e6decff6d5c9dbef6c83c618705</anchor>
+ <arglist>()</arglist>
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+ <member kind="variable" protection="private">
+ <type>OutputStream *</type>
+ <name>output_</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>a0ec4c2f04700d35f73f86ec2b05fd14f</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::string</type>
+ <name>sep_</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>a7613da40c31d3a1577c296a81f424de9</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::string</type>
+ <name>refSpecies_</name>
+ <anchorfile>classbpp_1_1CsvStatisticsOutputIterationListener.html</anchorfile>
+ <anchor>a703f6ee372824c334f2eed8fd53dd004</anchor>
+ <arglist></arglist>
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+ <compound kind="class">
+ <name>bpp::MafBlock</name>
+ <filename>classbpp_1_1MafBlock.html</filename>
+ <base virtualness="virtual">bpp::Clonable</base>
+ <member kind="function">
+ <type></type>
+ <name>MafBlock</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a058642cef3fefccaa37ad94c4366a888</anchor>
+ <arglist>()</arglist>
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+ <member kind="function">
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+ <name>MafBlock</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>ae2bd5c7fdb9585536fe0d1851b7d05a6</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="function">
+ <type>MafBlock &</type>
+ <name>operator=</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a10ce330f5e6192c1f1dde10469568bab</anchor>
+ <arglist>(const MafBlock &block)</arglist>
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+ <member kind="function">
+ <type>MafBlock *</type>
+ <name>clone</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a39812e3de82ef1c7d5a68c67d627ac96</anchor>
+ <arglist>() const </arglist>
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+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~MafBlock</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a9334610bb793811865e8b1657181e7cd</anchor>
+ <arglist>()</arglist>
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+ <member kind="function">
+ <type>void</type>
+ <name>setScore</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a2bf88e7b9ebe30f2b8388006b71ed424</anchor>
+ <arglist>(double score)</arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>setPass</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a3fd86ff8e8216ff3d60483a483018605</anchor>
+ <arglist>(unsigned int pass)</arglist>
+ </member>
+ <member kind="function">
+ <type>double</type>
+ <name>getScore</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>af19c3566a11f04a49adfb30a30b8941f</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>unsigned int</type>
+ <name>getPass</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>acccf24c02a5de3496efad036c1173bba</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>AlignedSequenceContainer &</type>
+ <name>getAlignment</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a9dc1711c5607219d03bc3470ad70c91e</anchor>
+ <arglist>()</arglist>
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+ <member kind="function">
+ <type>const AlignedSequenceContainer &</type>
+ <name>getAlignment</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a78ca490c256ff0eb652eb35cb2dc016d</anchor>
+ <arglist>() const </arglist>
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+ <member kind="function">
+ <type>size_t</type>
+ <name>getNumberOfSequences</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>af2520910770075b2f938a3481a115dd2</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>size_t</type>
+ <name>getNumberOfSites</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a84d6c4b723e3a4cb6f6b981bd0f1f997</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
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+ <name>addSequence</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a9e5084810c7463855698ef5148a274ad</anchor>
+ <arglist>(const MafSequence &sequence)</arglist>
+ </member>
+ <member kind="function">
+ <type>bool</type>
+ <name>hasSequence</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a47b11e4d976f20d96641ecc00a183c4b</anchor>
+ <arglist>(const std::string &name) const </arglist>
+ </member>
+ <member kind="function">
+ <type>const MafSequence &</type>
+ <name>getSequence</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a9bcfc8036897c9a0a6cafe2031582645</anchor>
+ <arglist>(const std::string &name) const </arglist>
+ </member>
+ <member kind="function">
+ <type>const MafSequence &</type>
+ <name>getSequence</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>abed0e86dd2b81c767d96b5e37be2beb1</anchor>
+ <arglist>(size_t i) const </arglist>
+ </member>
+ <member kind="function">
+ <type>bool</type>
+ <name>hasSequenceForSpecies</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a34f41c2e154a97b0e62a3fe429f09b8f</anchor>
+ <arglist>(const std::string &species) const </arglist>
+ </member>
+ <member kind="function">
+ <type>const MafSequence &</type>
+ <name>getSequenceForSpecies</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a5c05243dba43f35ceefad861a1da8054</anchor>
+ <arglist>(const std::string &species) const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::vector< const MafSequence * ></type>
+ <name>getSequencesForSpecies</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a487ca618040aa36aa0fe216d8a6d6074</anchor>
+ <arglist>(const std::string &species) const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::vector< std::string ></type>
+ <name>getSpeciesList</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a7b75cbad1316162a4b8ab32cd6e21e4f</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>removeCoordinatesFromSequence</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>aa2f659d1b13ee936e1d0934910ab8fc1</anchor>
+ <arglist>(size_t i)</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getDescription</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>ab06518e567d9c3c067219a93b12d9d12</anchor>
+ <arglist>() const </arglist>
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+ <member kind="function">
+ <type>bool</type>
+ <name>hasProperty</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>ab96271a832032f3c389e334b339a1891</anchor>
+ <arglist>(const std::string &property) const </arglist>
+ </member>
+ <member kind="function">
+ <type>const Clonable &</type>
+ <name>getProperty</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a5503e3be030a789f0842a9dea4b9341f</anchor>
+ <arglist>(const std::string &property) const </arglist>
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+ <type>void</type>
+ <name>deleteProperty</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>ac79eb4dff19f8da3c4bc1b79d5edd268</anchor>
+ <arglist>(const std::string &property)</arglist>
+ </member>
+ <member kind="function">
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+ <name>setProperty</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>adef4e3b6e8ba60f6ce60c7dfc87ec947</anchor>
+ <arglist>(const std::string &property, Clonable *data)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>deleteProperties_</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a3a80859e3ee556ac4625a03cdcd5b051</anchor>
+ <arglist>()</arglist>
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+ <member kind="variable" protection="private">
+ <type>double</type>
+ <name>score_</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a8933ca18eb8af3a147c3c5f400deb0d4</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>unsigned int</type>
+ <name>pass_</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>aadf280962ad263acc173d7c92140429a</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>AlignedSequenceContainer</type>
+ <name>alignment_</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>ae35510d38dcf394363902d5bdbbba31e</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::map< std::string, Clonable * ></type>
+ <name>properties_</name>
+ <anchorfile>classbpp_1_1MafBlock.html</anchorfile>
+ <anchor>a8e291b1a01e3111a22e563456434ebe1</anchor>
+ <arglist></arglist>
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+ <compound kind="class">
+ <name>bpp::MafIterator</name>
+ <filename>classbpp_1_1MafIterator.html</filename>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~MafIterator</name>
+ <anchorfile>classbpp_1_1MafIterator.html</anchorfile>
+ <anchor>a4e861e99b1eb477c26048e720dee552a</anchor>
+ <arglist>()</arglist>
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+ <member kind="function" virtualness="pure">
+ <type>virtual MafBlock *</type>
+ <name>nextBlock</name>
+ <anchorfile>classbpp_1_1MafIterator.html</anchorfile>
+ <anchor>a655e98cf03ed6fbf8c0526c46d50d1b1</anchor>
+ <arglist>()=0</arglist>
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+ <member kind="function" virtualness="pure">
+ <type>virtual bool</type>
+ <name>isVerbose</name>
+ <anchorfile>classbpp_1_1MafIterator.html</anchorfile>
+ <anchor>a1ae26b9b0917ad3d1af03c7afea40c95</anchor>
+ <arglist>() const =0</arglist>
+ </member>
+ <member kind="function" virtualness="pure">
+ <type>virtual void</type>
+ <name>setVerbose</name>
+ <anchorfile>classbpp_1_1MafIterator.html</anchorfile>
+ <anchor>a5470b0384c03db196c128d5c8c742d37</anchor>
+ <arglist>(bool yn)=0</arglist>
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+ <member kind="function" virtualness="pure">
+ <type>virtual void</type>
+ <name>addIterationListener</name>
+ <anchorfile>classbpp_1_1MafIterator.html</anchorfile>
+ <anchor>a36a997ed134b35f1cddd2258d051cd13</anchor>
+ <arglist>(IterationListener *listener)=0</arglist>
+ </member>
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+ <compound kind="class">
+ <name>bpp::AbstractMafIterator</name>
+ <filename>classbpp_1_1AbstractMafIterator.html</filename>
+ <base virtualness="virtual">bpp::MafIterator</base>
+ <member kind="function">
+ <type></type>
+ <name>AbstractMafIterator</name>
+ <anchorfile>classbpp_1_1AbstractMafIterator.html</anchorfile>
+ <anchor>ac1f940e0046a3b801cd4205236645fe8</anchor>
+ <arglist>()</arglist>
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+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~AbstractMafIterator</name>
+ <anchorfile>classbpp_1_1AbstractMafIterator.html</anchorfile>
+ <anchor>a6957423e380a47d40452a800cbdccca0</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" protection="protected" virtualness="pure">
+ <type>virtual MafBlock *</type>
+ <name>analyseCurrentBlock_</name>
+ <anchorfile>classbpp_1_1AbstractMafIterator.html</anchorfile>
+ <anchor>ae9f8b210df6b5c086b5a827b8c95361c</anchor>
+ <arglist>()=0</arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::MafTrashIterator</name>
+ <filename>classbpp_1_1MafTrashIterator.html</filename>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~MafTrashIterator</name>
+ <anchorfile>classbpp_1_1MafTrashIterator.html</anchorfile>
+ <anchor>a6143ab67178dda679bf0c118b3a2faa8</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" virtualness="pure">
+ <type>virtual MafBlock *</type>
+ <name>nextRemovedBlock</name>
+ <anchorfile>classbpp_1_1MafTrashIterator.html</anchorfile>
+ <anchor>a312bfc8541e3c549132d43b74609a21d</anchor>
+ <arglist>()=0</arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::AbstractFilterMafIterator</name>
+ <filename>classbpp_1_1AbstractFilterMafIterator.html</filename>
+ <base>bpp::AbstractMafIterator</base>
+ <member kind="function">
+ <type></type>
+ <name>AbstractFilterMafIterator</name>
+ <anchorfile>classbpp_1_1AbstractFilterMafIterator.html</anchorfile>
+ <anchor>a30ab31aa8f5511572193678ca82faec5</anchor>
+ <arglist>(MafIterator *iterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type></type>
+ <name>AbstractFilterMafIterator</name>
+ <anchorfile>classbpp_1_1AbstractFilterMafIterator.html</anchorfile>
+ <anchor>a037244f472529ba57574e6f0ba988564</anchor>
+ <arglist>(const AbstractFilterMafIterator &it)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>AbstractFilterMafIterator &</type>
+ <name>operator=</name>
+ <anchorfile>classbpp_1_1AbstractFilterMafIterator.html</anchorfile>
+ <anchor>adef511408306fcaa40295771e4399fa1</anchor>
+ <arglist>(const AbstractFilterMafIterator &it)</arglist>
+ </member>
+ </compound>
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+ <name>bpp::TrashIteratorAdapter</name>
+ <filename>classbpp_1_1TrashIteratorAdapter.html</filename>
+ <base>bpp::AbstractMafIterator</base>
+ <member kind="function">
+ <type></type>
+ <name>TrashIteratorAdapter</name>
+ <anchorfile>classbpp_1_1TrashIteratorAdapter.html</anchorfile>
+ <anchor>a6022e1cc88fa0fe4ef505b44c0d53254</anchor>
+ <arglist>(MafTrashIterator *iterator)</arglist>
+ </member>
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+ <anchorfile>classbpp_1_1TrashIteratorAdapter.html</anchorfile>
+ <anchor>a86aa2583396ab3af0da05b9a439cb25f</anchor>
+ <arglist>(const TrashIteratorAdapter &iterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>TrashIteratorAdapter &</type>
+ <name>operator=</name>
+ <anchorfile>classbpp_1_1TrashIteratorAdapter.html</anchorfile>
+ <anchor>a969d3a9a7ac94941d431f1c701714904</anchor>
+ <arglist>(const TrashIteratorAdapter &iterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>MafBlock *</type>
+ <name>analyseCurrentBlock_</name>
+ <anchorfile>classbpp_1_1TrashIteratorAdapter.html</anchorfile>
+ <anchor>a238166a135b31125d7070cb04da2b9df</anchor>
+ <arglist>()</arglist>
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+ <member kind="variable" protection="private">
+ <type>MafTrashIterator *</type>
+ <name>iterator_</name>
+ <anchorfile>classbpp_1_1TrashIteratorAdapter.html</anchorfile>
+ <anchor>a8c1dcda5c92c2ea71e0102282ca659e2</anchor>
+ <arglist></arglist>
+ </member>
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+ <name>bpp::MafIteratorSynchronizer</name>
+ <filename>classbpp_1_1MafIteratorSynchronizer.html</filename>
+ <base>bpp::AbstractFilterMafIterator</base>
+ <member kind="function">
+ <type></type>
+ <name>MafIteratorSynchronizer</name>
+ <anchorfile>classbpp_1_1MafIteratorSynchronizer.html</anchorfile>
+ <anchor>ad54cee7992656809d580e5a4aee1a50d</anchor>
+ <arglist>(MafIterator *primaryIterator, MafIterator *secondaryIterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type></type>
+ <name>MafIteratorSynchronizer</name>
+ <anchorfile>classbpp_1_1MafIteratorSynchronizer.html</anchorfile>
+ <anchor>abe80193f0bf6d6494eca2be162438eb9</anchor>
+ <arglist>(const MafIteratorSynchronizer &iterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>MafIteratorSynchronizer &</type>
+ <name>operator=</name>
+ <anchorfile>classbpp_1_1MafIteratorSynchronizer.html</anchorfile>
+ <anchor>a32cd3997cdd23956c0a0b82cf0b63eae</anchor>
+ <arglist>(const MafIteratorSynchronizer &iterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>MafBlock *</type>
+ <name>analyseCurrentBlock_</name>
+ <anchorfile>classbpp_1_1MafIteratorSynchronizer.html</anchorfile>
+ <anchor>a4e8e7c63d9fbd4327b1b1e90a43f7c84</anchor>
+ <arglist>()</arglist>
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+ <member kind="variable" protection="private">
+ <type>MafIterator *</type>
+ <name>secondaryIterator_</name>
+ <anchorfile>classbpp_1_1MafIteratorSynchronizer.html</anchorfile>
+ <anchor>a282a9eb9aeba8d0a65d5dc1657750c8c</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::MafParser</name>
+ <filename>classbpp_1_1MafParser.html</filename>
+ <base>bpp::AbstractMafIterator</base>
+ <member kind="function">
+ <type></type>
+ <name>MafParser</name>
+ <anchorfile>classbpp_1_1MafParser.html</anchorfile>
+ <anchor>a14e9d405c9b4cef99e5d5ae9ab0777c6</anchor>
+ <arglist>(std::istream *stream, bool parseMask=false)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type></type>
+ <name>MafParser</name>
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+ <arglist>()</arglist>
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+ <arglist>(const std::string &name, const std::string &sequence, bool parseName=true)</arglist>
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+ <arglist>(const std::string &name, const std::string &sequence, size_t begin, char strand, size_t srcSize, bool parseName=true)</arglist>
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+ <arglist>() const </arglist>
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+ <arglist>()</arglist>
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+ <anchor>a80bace5e90262a758ccdb475312b20b8</anchor>
+ <arglist>() const </arglist>
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+ <anchor>a62f6259d2f358c6bcf6f3896c49f6432</anchor>
+ <arglist>()</arglist>
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+ <arglist>() const </arglist>
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+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a4e3165c4d25212c4b919ac85c7f935af</anchor>
+ <arglist>() const </arglist>
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+ <arglist>(bool origin=true) const </arglist>
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+ <arglist>(const std::string &name)</arglist>
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+ <anchor>ac81b6bca2f3d2bfe0d12757b85ed3de0</anchor>
+ <arglist>() const </arglist>
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+ <name>getChromosome</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a9d58952d748526cd6731186ce07b3b4e</anchor>
+ <arglist>() const </arglist>
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+ <name>getStrand</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>ae211f326bef4d97074b1cc9e0e5235d9</anchor>
+ <arglist>() const </arglist>
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+ <name>getGenomicSize</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a4eec97ae3a93ab906b03053382b0bf05</anchor>
+ <arglist>() const </arglist>
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+ <name>getSrcSize</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a5740c6b3755d61f5fcac84151be9ae70</anchor>
+ <arglist>() const </arglist>
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+ <name>setStart</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a5a55341f0e99a0e057b1c9e5a16ac63d</anchor>
+ <arglist>(size_t begin)</arglist>
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+ <member kind="function">
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+ <name>setChromosome</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a0d1711e2be7ed45aeba81f34c2c2aa9f</anchor>
+ <arglist>(const std::string &chr)</arglist>
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+ <name>setSpecies</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>adebcf474b25fdeece5df589211a32cf9</anchor>
+ <arglist>(const std::string &species)</arglist>
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+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a69a879878bd985aade72a9e06ed531de</anchor>
+ <arglist>(char s)</arglist>
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+ <member kind="function">
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+ <name>setSrcSize</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a4944a59662f180a39005e3552fe7b3f4</anchor>
+ <arglist>(size_t srcSize)</arglist>
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+ <member kind="function">
+ <type>std::string</type>
+ <name>getDescription</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a39a70085338246a6719f7874700107f6</anchor>
+ <arglist>() const </arglist>
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+ <type>MafSequence *</type>
+ <name>subSequence</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>ab5a26a37180cffffe1758a15f6043bbc</anchor>
+ <arglist>(size_t startAt, size_t length) const </arglist>
+ </member>
+ <member kind="function" static="yes">
+ <type>static void</type>
+ <name>splitNameIntoSpeciesAndChromosome</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a7fa51caf815a9fb4f3e1c4c6d8b4d90a</anchor>
+ <arglist>(const std::string &name, std::string &species, std::string &chr)</arglist>
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+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>beforeSequenceChanged</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a6ccf166612181b5ca550caa04647b65b</anchor>
+ <arglist>(const SymbolListEditionEvent &event)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>afterSequenceChanged</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>abac31fbcc1564765a807ce18b4092ea9</anchor>
+ <arglist>(const SymbolListEditionEvent &event)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>beforeSequenceInserted</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>aa98f498ab72626fa359bc2dbff5406af</anchor>
+ <arglist>(const SymbolListInsertionEvent &event)</arglist>
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+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>afterSequenceInserted</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>ab97eece6ed1fe3b9717ec32839ff9a5c</anchor>
+ <arglist>(const SymbolListInsertionEvent &event)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>beforeSequenceDeleted</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a3bc3991435b56c4d04cf82f29079f8f3</anchor>
+ <arglist>(const SymbolListDeletionEvent &event)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>afterSequenceDeleted</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a74a3d87c7f29d34325f0368de340418e</anchor>
+ <arglist>(const SymbolListDeletionEvent &event)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>beforeSequenceSubstituted</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a0aee40a3f4a537997c73eeca6adc14d6</anchor>
+ <arglist>(const SymbolListSubstitutionEvent &event)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>afterSequenceSubstituted</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>aa47a8c5b148d40e42e4ad85a79c90a74</anchor>
+ <arglist>(const SymbolListSubstitutionEvent &event)</arglist>
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+ <member kind="variable" protection="private">
+ <type>bool</type>
+ <name>hasCoordinates_</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a8ac4e06a988b4bdf2859a88fce0c8bc0</anchor>
+ <arglist></arglist>
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+ <type>size_t</type>
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+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>abecc9851c667fe43afd0cd50f2adad92</anchor>
+ <arglist></arglist>
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+ <type>std::string</type>
+ <name>species_</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
+ <anchor>a97d5ba2ab0e5add5b07ed7b73c2bff31</anchor>
+ <arglist></arglist>
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+ <type>std::string</type>
+ <name>chromosome_</name>
+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
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+ <arglist></arglist>
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+ <arglist></arglist>
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+ <arglist></arglist>
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+ <anchorfile>classbpp_1_1MafSequence.html</anchorfile>
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+ <arglist></arglist>
+ </member>
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+ <compound kind="class">
+ <name>bpp::MafStatisticsResult</name>
+ <filename>classbpp_1_1MafStatisticsResult.html</filename>
+ <member kind="function">
+ <type></type>
+ <name>MafStatisticsResult</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>a805f685860d87004239d1043216e7f3b</anchor>
+ <arglist>()</arglist>
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+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~MafStatisticsResult</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>aa769e27c1683a4e2d1a1bac9719fd388</anchor>
+ <arglist>()</arglist>
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+ <name>MafStatisticsResult</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>a8015358f69a833b5855ed94f0f9f2cfa</anchor>
+ <arglist>(const MafStatisticsResult &msr)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual const BppNumberI &</type>
+ <name>getValue</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>a9d73c0f9f40356044979b75976e8f329</anchor>
+ <arglist>(const std::string &tag) const </arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>setValue</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>a6f3e496acb5b85beb787b1b0a3855c0b</anchor>
+ <arglist>(const std::string &tag, double value)</arglist>
+ </member>
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+ <name>setValue</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>a280f1dacced87ffa52850c0e17ee39e6</anchor>
+ <arglist>(const std::string &tag, int value)</arglist>
+ </member>
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+ <name>setValue</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>a0683ba6930bca690e060223034147c62</anchor>
+ <arglist>(const std::string &tag, unsigned int value)</arglist>
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+ <member kind="function" virtualness="virtual">
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+ <name>hasValue</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>a5cc994fbd57f04423f8186b2905b54a9</anchor>
+ <arglist>(const std::string &tag) const </arglist>
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+ <member kind="function">
+ <type>std::vector< std::string ></type>
+ <name>getAvailableTags</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>ab52a414a67f2bde835576d72773cae35</anchor>
+ <arglist>() const </arglist>
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+ <member kind="variable" protection="protected">
+ <type>std::map< std::string, BppNumberI * ></type>
+ <name>values_</name>
+ <anchorfile>classbpp_1_1MafStatisticsResult.html</anchorfile>
+ <anchor>a284d7b348f475feb21e8acb48b769b2d</anchor>
+ <arglist></arglist>
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+ <name>bpp::SimpleMafStatisticsResult</name>
+ <filename>classbpp_1_1SimpleMafStatisticsResult.html</filename>
+ <base virtualness="virtual">bpp::MafStatisticsResult</base>
+ <member kind="function">
+ <type></type>
+ <name>SimpleMafStatisticsResult</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>a0817f2410982bb0fd3a818c034990864</anchor>
+ <arglist>(const std::string &name)</arglist>
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+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~SimpleMafStatisticsResult</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>a3c2faaf633b4d23c66e59d235728180a</anchor>
+ <arglist>()</arglist>
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+ <member kind="function" virtualness="virtual">
+ <type>virtual const BppNumberI &</type>
+ <name>getValue</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>a39f7aff9f0c81ae4b39eff416632df1c</anchor>
+ <arglist>(const std::string &tag) const </arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual const BppNumberI &</type>
+ <name>getValue</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>a60d3a4a8e4b5f33de60a9cfd93676d4e</anchor>
+ <arglist>() const </arglist>
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+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>setValue</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>ab215d4c3889372bbca9f7a9608f59b18</anchor>
+ <arglist>(const std::string &tag, double value)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>setValue</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>af3ffa3f2695ee951bdfc445aef8f1b57</anchor>
+ <arglist>(const std::string &tag, int value)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>setValue</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>adc979ca660759d2ee0168d674414bd2e</anchor>
+ <arglist>(const std::string &tag, unsigned int value)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>setValue</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>ab6944742ddefc104a419d5cceb22d400</anchor>
+ <arglist>(double value)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>setValue</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>a1ac5ceaaf988852af1698c0ce8d7a234</anchor>
+ <arglist>(int value)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual void</type>
+ <name>setValue</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>af23af5173245935a65cd74ac790346bc</anchor>
+ <arglist>(unsigned int value)</arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::string</type>
+ <name>name_</name>
+ <anchorfile>classbpp_1_1SimpleMafStatisticsResult.html</anchorfile>
+ <anchor>ab170c8df5e71bfe063e51da4e9598b55</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::MafStatistics</name>
+ <filename>classbpp_1_1MafStatistics.html</filename>
+ <member kind="function">
+ <type></type>
+ <name>MafStatistics</name>
+ <anchorfile>classbpp_1_1MafStatistics.html</anchorfile>
+ <anchor>a6ee688c65912465d8357ba449d1132e1</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~MafStatistics</name>
+ <anchorfile>classbpp_1_1MafStatistics.html</anchorfile>
+ <anchor>a8bf9ce95a362180b7e0d004f8c29befd</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" virtualness="pure">
+ <type>virtual std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1MafStatistics.html</anchorfile>
+ <anchor>af0c9f79bebf57fd0f91153b34befdc9f</anchor>
+ <arglist>() const =0</arglist>
+ </member>
+ <member kind="function" virtualness="pure">
+ <type>virtual std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1MafStatistics.html</anchorfile>
+ <anchor>aae4be18d0f1290cc1cf64008203fa4f4</anchor>
+ <arglist>() const =0</arglist>
+ </member>
+ <member kind="function" virtualness="pure">
+ <type>virtual const MafStatisticsResult &</type>
+ <name>getResult</name>
+ <anchorfile>classbpp_1_1MafStatistics.html</anchorfile>
+ <anchor>a6f904d5de86215b4a28f481175c62866</anchor>
+ <arglist>() const =0</arglist>
+ </member>
+ <member kind="function" virtualness="pure">
+ <type>virtual void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1MafStatistics.html</anchorfile>
+ <anchor>a3e7f72ee7b66dbb4e00699a14a920722</anchor>
+ <arglist>(const MafBlock &block)=0</arglist>
+ </member>
+ <member kind="function" virtualness="pure">
+ <type>virtual std::vector< std::string ></type>
+ <name>getSupportedTags</name>
+ <anchorfile>classbpp_1_1MafStatistics.html</anchorfile>
+ <anchor>a7ed1335b56a21160333132b8295cd12e</anchor>
+ <arglist>() const =0</arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::AbstractMafStatistics</name>
+ <filename>classbpp_1_1AbstractMafStatistics.html</filename>
+ <base virtualness="virtual">bpp::MafStatistics</base>
+ <member kind="function">
+ <type></type>
+ <name>AbstractMafStatistics</name>
+ <anchorfile>classbpp_1_1AbstractMafStatistics.html</anchorfile>
+ <anchor>a2989af09f09c425ffe6e0afa089b95a8</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~AbstractMafStatistics</name>
+ <anchorfile>classbpp_1_1AbstractMafStatistics.html</anchorfile>
+ <anchor>a433654f97397532eda746f55eba2d5f2</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>const MafStatisticsResult &</type>
+ <name>getResult</name>
+ <anchorfile>classbpp_1_1AbstractMafStatistics.html</anchorfile>
+ <anchor>af5de6f7ab3c8dcc676e1f9970e195422</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="variable" protection="protected">
+ <type>MafStatisticsResult</type>
+ <name>result_</name>
+ <anchorfile>classbpp_1_1AbstractMafStatistics.html</anchorfile>
+ <anchor>ad6c6d3d9c777683d46ac932e1c948e99</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::AbstractMafStatisticsSimple</name>
+ <filename>classbpp_1_1AbstractMafStatisticsSimple.html</filename>
+ <base>bpp::MafStatistics</base>
+ <member kind="function">
+ <type></type>
+ <name>AbstractMafStatisticsSimple</name>
+ <anchorfile>classbpp_1_1AbstractMafStatisticsSimple.html</anchorfile>
+ <anchor>adeea5a5f297b30c66b009b12960c21f2</anchor>
+ <arglist>(const std::string &name)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~AbstractMafStatisticsSimple</name>
+ <anchorfile>classbpp_1_1AbstractMafStatisticsSimple.html</anchorfile>
+ <anchor>ab3b88820011d31ab120ee688e6b07cea</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>const SimpleMafStatisticsResult &</type>
+ <name>getResult</name>
+ <anchorfile>classbpp_1_1AbstractMafStatisticsSimple.html</anchorfile>
+ <anchor>abbdc7e935065241c814f877c9f9bef62</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::vector< std::string ></type>
+ <name>getSupportedTags</name>
+ <anchorfile>classbpp_1_1AbstractMafStatisticsSimple.html</anchorfile>
+ <anchor>ac08f7bd54f98824e8fb1a65af758d54b</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="variable" protection="protected">
+ <type>SimpleMafStatisticsResult</type>
+ <name>result_</name>
+ <anchorfile>classbpp_1_1AbstractMafStatisticsSimple.html</anchorfile>
+ <anchor>aec4c989c7f91ad60817ab36904f152e5</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::PairwiseDivergenceMafStatistics</name>
+ <filename>classbpp_1_1PairwiseDivergenceMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatisticsSimple</base>
+ <member kind="function">
+ <type></type>
+ <name>PairwiseDivergenceMafStatistics</name>
+ <anchorfile>classbpp_1_1PairwiseDivergenceMafStatistics.html</anchorfile>
+ <anchor>a9b409ca2ef98c8a21b44a6a57018b8d0</anchor>
+ <arglist>(const std::string &species1, const std::string &species2)</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>~PairwiseDivergenceMafStatistics</name>
+ <anchorfile>classbpp_1_1PairwiseDivergenceMafStatistics.html</anchorfile>
+ <anchor>a9f5f17c474032e4b2319839e0842212f</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1PairwiseDivergenceMafStatistics.html</anchorfile>
+ <anchor>a19da531e09a6c81e7d030c8baf6be02c</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1PairwiseDivergenceMafStatistics.html</anchorfile>
+ <anchor>abbfb4114554df11ab5193985add95006</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1PairwiseDivergenceMafStatistics.html</anchorfile>
+ <anchor>a4911e16fa4c74d9fff5b42f8fbe0d1f3</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::string</type>
+ <name>species1_</name>
+ <anchorfile>classbpp_1_1PairwiseDivergenceMafStatistics.html</anchorfile>
+ <anchor>a36259284e5b72da0c6866e5be2724008</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::string</type>
+ <name>species2_</name>
+ <anchorfile>classbpp_1_1PairwiseDivergenceMafStatistics.html</anchorfile>
+ <anchor>a0d94ff07c725f591b9aa034c9055fd74</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::BlockSizeMafStatistics</name>
+ <filename>classbpp_1_1BlockSizeMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatisticsSimple</base>
+ <member kind="function">
+ <type></type>
+ <name>BlockSizeMafStatistics</name>
+ <anchorfile>classbpp_1_1BlockSizeMafStatistics.html</anchorfile>
+ <anchor>a98984dc9eaa0882c153bb632030b5fa8</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>~BlockSizeMafStatistics</name>
+ <anchorfile>classbpp_1_1BlockSizeMafStatistics.html</anchorfile>
+ <anchor>af055e6a8479171774697bc89d6a0974d</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1BlockSizeMafStatistics.html</anchorfile>
+ <anchor>a7c6645dab30ab4cc8cf919617e15b8f6</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1BlockSizeMafStatistics.html</anchorfile>
+ <anchor>ab429e8fac24e5d4a44d093b6bd29affa</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1BlockSizeMafStatistics.html</anchorfile>
+ <anchor>a28327d23b91bbfbab52526d4d4483f26</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::BlockLengthMafStatistics</name>
+ <filename>classbpp_1_1BlockLengthMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatisticsSimple</base>
+ <member kind="function">
+ <type></type>
+ <name>BlockLengthMafStatistics</name>
+ <anchorfile>classbpp_1_1BlockLengthMafStatistics.html</anchorfile>
+ <anchor>a61594666cfcf0cacc5bcbc976386ac1b</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>~BlockLengthMafStatistics</name>
+ <anchorfile>classbpp_1_1BlockLengthMafStatistics.html</anchorfile>
+ <anchor>a27d3b78706c46af271d83b91b909f433</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1BlockLengthMafStatistics.html</anchorfile>
+ <anchor>a9e349ef1a653a710db8f7524be338374</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1BlockLengthMafStatistics.html</anchorfile>
+ <anchor>a5e6c6cb2d61e6c489fa9ec46796e9417</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1BlockLengthMafStatistics.html</anchorfile>
+ <anchor>a2a1cbef57a606d76672b595a9709c350</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::SequenceLengthMafStatistics</name>
+ <filename>classbpp_1_1SequenceLengthMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatisticsSimple</base>
+ <member kind="function">
+ <type></type>
+ <name>SequenceLengthMafStatistics</name>
+ <anchorfile>classbpp_1_1SequenceLengthMafStatistics.html</anchorfile>
+ <anchor>ae9dd7ebe1b0773b791ac075d4c417f87</anchor>
+ <arglist>(const std::string &species)</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>~SequenceLengthMafStatistics</name>
+ <anchorfile>classbpp_1_1SequenceLengthMafStatistics.html</anchorfile>
+ <anchor>afa546d1de2369f42c6ca782cb7c2fabe</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1SequenceLengthMafStatistics.html</anchorfile>
+ <anchor>ae890cd9995965263339d3cef8f0d92f3</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1SequenceLengthMafStatistics.html</anchorfile>
+ <anchor>a80880d69a082c945d53357a05461ebd8</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1SequenceLengthMafStatistics.html</anchorfile>
+ <anchor>ad4f9677fe2d634c5d5d21f86e6c24b4b</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::string</type>
+ <name>species_</name>
+ <anchorfile>classbpp_1_1SequenceLengthMafStatistics.html</anchorfile>
+ <anchor>a92e9158724d3c3f3b90ff605f14489d0</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::AlignmentScoreMafStatistics</name>
+ <filename>classbpp_1_1AlignmentScoreMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatisticsSimple</base>
+ <member kind="function">
+ <type></type>
+ <name>AlignmentScoreMafStatistics</name>
+ <anchorfile>classbpp_1_1AlignmentScoreMafStatistics.html</anchorfile>
+ <anchor>a7e0114800a44066289f84040d733e9c5</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>~AlignmentScoreMafStatistics</name>
+ <anchorfile>classbpp_1_1AlignmentScoreMafStatistics.html</anchorfile>
+ <anchor>a3825a6c2800ebee7d20af3c0125606e1</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1AlignmentScoreMafStatistics.html</anchorfile>
+ <anchor>acc694a314a88e421d87b4faea699629f</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1AlignmentScoreMafStatistics.html</anchorfile>
+ <anchor>a84ec7c5e92aa978cc32bc79bcb65eddb</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1AlignmentScoreMafStatistics.html</anchorfile>
+ <anchor>a99f0ed2e9f311ec15f7ac131418aceae</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::CharacterCountsMafStatistics</name>
+ <filename>classbpp_1_1CharacterCountsMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatistics</base>
+ <member kind="function">
+ <type></type>
+ <name>CharacterCountsMafStatistics</name>
+ <anchorfile>classbpp_1_1CharacterCountsMafStatistics.html</anchorfile>
+ <anchor>a989027dc45de74d10760305d0fca8f78</anchor>
+ <arglist>(const Alphabet *alphabet)</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>CharacterCountsMafStatistics</name>
+ <anchorfile>classbpp_1_1CharacterCountsMafStatistics.html</anchorfile>
+ <anchor>a99935a3c2b9155c733888aef6ca3a78d</anchor>
+ <arglist>(const CharacterCountsMafStatistics &stats)</arglist>
+ </member>
+ <member kind="function">
+ <type>CharacterCountsMafStatistics &</type>
+ <name>operator=</name>
+ <anchorfile>classbpp_1_1CharacterCountsMafStatistics.html</anchorfile>
+ <anchor>ad19900ed72e16a366731b3b66128ac68</anchor>
+ <arglist>(const CharacterCountsMafStatistics &stats)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~CharacterCountsMafStatistics</name>
+ <anchorfile>classbpp_1_1CharacterCountsMafStatistics.html</anchorfile>
+ <anchor>a2213025d386ea44aa30f8d06e3ea5136</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1CharacterCountsMafStatistics.html</anchorfile>
+ <anchor>a28f9086cea1b5fee5f2085b7cbf353ba</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1CharacterCountsMafStatistics.html</anchorfile>
+ <anchor>a71269b0be58723ce8a312984fa1f0310</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1CharacterCountsMafStatistics.html</anchorfile>
+ <anchor>a9eacbc17da8bebd53b083acd417098c1</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="function">
+ <type>std::vector< std::string ></type>
+ <name>getSupportedTags</name>
+ <anchorfile>classbpp_1_1CharacterCountsMafStatistics.html</anchorfile>
+ <anchor>a42afdd3d406a7068bcd567058660592a</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>const Alphabet *</type>
+ <name>alphabet_</name>
+ <anchorfile>classbpp_1_1CharacterCountsMafStatistics.html</anchorfile>
+ <anchor>aaab64d3758855fad252977b9b2e52f42</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::AbstractSpeciesSelectionMafStatistics</name>
+ <filename>classbpp_1_1AbstractSpeciesSelectionMafStatistics.html</filename>
+ <base virtualness="virtual">bpp::MafStatistics</base>
+ <member kind="function">
+ <type></type>
+ <name>AbstractSpeciesSelectionMafStatistics</name>
+ <anchorfile>classbpp_1_1AbstractSpeciesSelectionMafStatistics.html</anchorfile>
+ <anchor>a6b2950fb90545c67ca73ecdaad92361a</anchor>
+ <arglist>(const std::vector< std::string > &species)</arglist>
+ </member>
+ <member kind="function" protection="protected">
+ <type>SiteContainer *</type>
+ <name>getSiteContainer_</name>
+ <anchorfile>classbpp_1_1AbstractSpeciesSelectionMafStatistics.html</anchorfile>
+ <anchor>a410fbce27d39d26d657791b0aa507684</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::vector< std::string ></type>
+ <name>species_</name>
+ <anchorfile>classbpp_1_1AbstractSpeciesSelectionMafStatistics.html</anchorfile>
+ <anchor>a5754e0c6c6b3adb6ebc40c995cdde14f</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::AbstractSpeciesMultipleSelectionMafStatistics</name>
+ <filename>classbpp_1_1AbstractSpeciesMultipleSelectionMafStatistics.html</filename>
+ <base virtualness="virtual">bpp::MafStatistics</base>
+ <member kind="function">
+ <type></type>
+ <name>AbstractSpeciesMultipleSelectionMafStatistics</name>
+ <anchorfile>classbpp_1_1AbstractSpeciesMultipleSelectionMafStatistics.html</anchorfile>
+ <anchor>a50f1bcbc70f5a72715925c3b2aeec5b6</anchor>
+ <arglist>(const std::vector< std::vector< std::string > > &species)</arglist>
+ </member>
+ <member kind="function" protection="protected">
+ <type>std::vector< SiteContainer * ></type>
+ <name>getSiteContainers_</name>
+ <anchorfile>classbpp_1_1AbstractSpeciesMultipleSelectionMafStatistics.html</anchorfile>
+ <anchor>a1d36351d06e344fcffcab819f0ee9d51</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::vector< std::vector< std::string > ></type>
+ <name>species_</name>
+ <anchorfile>classbpp_1_1AbstractSpeciesMultipleSelectionMafStatistics.html</anchorfile>
+ <anchor>ad13dab583b6d27748dc92529d90cc428</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::SiteFrequencySpectrumMafStatistics</name>
+ <filename>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatistics</base>
+ <base>bpp::AbstractSpeciesSelectionMafStatistics</base>
+ <class kind="class">bpp::SiteFrequencySpectrumMafStatistics::Categorizer</class>
+ <member kind="function">
+ <type></type>
+ <name>SiteFrequencySpectrumMafStatistics</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>ae2f6a5d481665cb0adb373db889cd4a3</anchor>
+ <arglist>(const Alphabet *alphabet, const std::vector< double > &bounds, const std::vector< std::string > &ingroup, const std::string outgroup="")</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>SiteFrequencySpectrumMafStatistics</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>a7868688fb97ee98ab034f0c4d994e7cd</anchor>
+ <arglist>(const SiteFrequencySpectrumMafStatistics &stats)</arglist>
+ </member>
+ <member kind="function">
+ <type>SiteFrequencySpectrumMafStatistics &</type>
+ <name>operator=</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>a8be819556927dc75ee2d4100391cd50b</anchor>
+ <arglist>(const SiteFrequencySpectrumMafStatistics &stats)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~SiteFrequencySpectrumMafStatistics</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>a395fcc489526a7d348b88bd98d3a399b</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>aff9307c3bfc864042610b88a8fc8e135</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>a726f8a04605842d2d9c2fecfab4294ed</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>aba6d33e7ff5d2387994b6bef7f5fcfc4</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="function">
+ <type>std::vector< std::string ></type>
+ <name>getSupportedTags</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>a6a0ad5c95edb09fc538c1cacac9310fe</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>const Alphabet *</type>
+ <name>alphabet_</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>a862096b71ae411bea636b2a155e6933f</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>Categorizer</type>
+ <name>categorizer_</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>ae2064f917123b646d08725fdfe911829</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::vector< unsigned int ></type>
+ <name>counts_</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>a6cff6d060f7e491fc46c7d133ec7811c</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::string</type>
+ <name>outgroup_</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics.html</anchorfile>
+ <anchor>ad98f4d9bc0ff476ad60231748e818f2f</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::SiteFrequencySpectrumMafStatistics::Categorizer</name>
+ <filename>classbpp_1_1SiteFrequencySpectrumMafStatistics_1_1Categorizer.html</filename>
+ <member kind="function">
+ <type></type>
+ <name>Categorizer</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics_1_1Categorizer.html</anchorfile>
+ <anchor>a79f492607d44ba74cd2f37d16ceab47c</anchor>
+ <arglist>(const std::vector< double > &bounds)</arglist>
+ </member>
+ <member kind="function">
+ <type>size_t</type>
+ <name>getNumberOfCategories</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics_1_1Categorizer.html</anchorfile>
+ <anchor>a462983200c5afee880b6075a665ce813</anchor>
+ <arglist>() const </arglist>
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+ <member kind="function">
+ <type>size_t</type>
+ <name>getCategory</name>
+ <anchorfile>classbpp_1_1SiteFrequencySpectrumMafStatistics_1_1Categorizer.html</anchorfile>
+ <anchor>a0b0df73f3c771f5b46712eceb494bf97</anchor>
+ <arglist>(double value) const </arglist>
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+ <type>std::vector< double ></type>
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+ <arglist></arglist>
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+ <name>bpp::FourSpeciesPatternCountsMafStatistics</name>
+ <filename>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatistics</base>
+ <base>bpp::AbstractSpeciesSelectionMafStatistics</base>
+ <member kind="function">
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+ <name>FourSpeciesPatternCountsMafStatistics</name>
+ <anchorfile>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</anchorfile>
+ <anchor>af588c889373f541860852ad7d28671cf</anchor>
+ <arglist>(const Alphabet *alphabet, const std::vector< std::string > &species)</arglist>
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+ <name>FourSpeciesPatternCountsMafStatistics</name>
+ <anchorfile>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</anchorfile>
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+ <arglist>(const FourSpeciesPatternCountsMafStatistics &stats)</arglist>
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+ <anchorfile>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</anchorfile>
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+ <arglist>(const FourSpeciesPatternCountsMafStatistics &stats)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~FourSpeciesPatternCountsMafStatistics</name>
+ <anchorfile>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</anchorfile>
+ <anchor>af8df00cc22cb71f8f941166d664ff22b</anchor>
+ <arglist>()</arglist>
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+ <anchorfile>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</anchorfile>
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+ <arglist>() const </arglist>
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+ <anchor>a1ddfd9f81fb25d22c7ff82c2fc4cf818</anchor>
+ <arglist>() const </arglist>
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+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</anchorfile>
+ <anchor>a7f8c85f64632bc5df5c619d213635e3e</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="function">
+ <type>std::vector< std::string ></type>
+ <name>getSupportedTags</name>
+ <anchorfile>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</anchorfile>
+ <anchor>a76978fc1017836266b7bd3d33f9b416f</anchor>
+ <arglist>() const </arglist>
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+ <member kind="variable" protection="private">
+ <type>const Alphabet *</type>
+ <name>alphabet_</name>
+ <anchorfile>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</anchorfile>
+ <anchor>a368a43891bf3e7f2172001affe15f02d</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::vector< unsigned int ></type>
+ <name>counts_</name>
+ <anchorfile>classbpp_1_1FourSpeciesPatternCountsMafStatistics.html</anchorfile>
+ <anchor>a04b305371745581290a21e9e64985c6f</anchor>
+ <arglist></arglist>
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+ <name>bpp::SiteMafStatistics</name>
+ <filename>classbpp_1_1SiteMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatistics</base>
+ <base>bpp::AbstractSpeciesSelectionMafStatistics</base>
+ <member kind="function">
+ <type></type>
+ <name>SiteMafStatistics</name>
+ <anchorfile>classbpp_1_1SiteMafStatistics.html</anchorfile>
+ <anchor>acedc89e53d9f3ebf7450b4358c72e0fe</anchor>
+ <arglist>(const std::vector< std::string > &species)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~SiteMafStatistics</name>
+ <anchorfile>classbpp_1_1SiteMafStatistics.html</anchorfile>
+ <anchor>a62787802e4ffeaed951e594107334e6d</anchor>
+ <arglist>()</arglist>
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+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1SiteMafStatistics.html</anchorfile>
+ <anchor>ae35c7512d74a25bb3c03e29579cc6d07</anchor>
+ <arglist>() const </arglist>
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+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1SiteMafStatistics.html</anchorfile>
+ <anchor>a2e7a8174bbe6c42d60e7b94ad1e73443</anchor>
+ <arglist>() const </arglist>
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+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1SiteMafStatistics.html</anchorfile>
+ <anchor>a2cf3ee198295e9620929d5a018916980</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="function">
+ <type>std::vector< std::string ></type>
+ <name>getSupportedTags</name>
+ <anchorfile>classbpp_1_1SiteMafStatistics.html</anchorfile>
+ <anchor>a28c0fa65dc598cdc709fef83acdf62c3</anchor>
+ <arglist>() const </arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::PolymorphismMafStatistics</name>
+ <filename>classbpp_1_1PolymorphismMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatistics</base>
+ <base>bpp::AbstractSpeciesMultipleSelectionMafStatistics</base>
+ <member kind="function">
+ <type></type>
+ <name>PolymorphismMafStatistics</name>
+ <anchorfile>classbpp_1_1PolymorphismMafStatistics.html</anchorfile>
+ <anchor>a0715353b2411ff8360eee838c6794fc1</anchor>
+ <arglist>(const std::vector< std::vector< std::string > > &species)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~PolymorphismMafStatistics</name>
+ <anchorfile>classbpp_1_1PolymorphismMafStatistics.html</anchorfile>
+ <anchor>ac13e920337739b6529c70b186e605117</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1PolymorphismMafStatistics.html</anchorfile>
+ <anchor>aeb6705645f2ee3cc7f8879c02af30455</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1PolymorphismMafStatistics.html</anchorfile>
+ <anchor>a5f2b811e967e556e17bb6a3f07a10a5c</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1PolymorphismMafStatistics.html</anchorfile>
+ <anchor>ac4b05292c9cf0d870d9cac46b4a2e379</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="function">
+ <type>std::vector< std::string ></type>
+ <name>getSupportedTags</name>
+ <anchorfile>classbpp_1_1PolymorphismMafStatistics.html</anchorfile>
+ <anchor>aa43cccd63f4cbac1cacb9eff96a19dee</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function" protection="private" static="yes">
+ <type>static std::vector< int ></type>
+ <name>getPatterns_</name>
+ <anchorfile>classbpp_1_1PolymorphismMafStatistics.html</anchorfile>
+ <anchor>a0081412ec742dcdb664f353d5a94f271</anchor>
+ <arglist>(const SiteContainer &sites)</arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::SequenceDiversityMafStatistics</name>
+ <filename>classbpp_1_1SequenceDiversityMafStatistics.html</filename>
+ <base>bpp::AbstractMafStatistics</base>
+ <base>bpp::AbstractSpeciesSelectionMafStatistics</base>
+ <member kind="function">
+ <type></type>
+ <name>SequenceDiversityMafStatistics</name>
+ <anchorfile>classbpp_1_1SequenceDiversityMafStatistics.html</anchorfile>
+ <anchor>a706b49e0dd3d8e1b2753b1683205db4c</anchor>
+ <arglist>(const std::vector< std::string > &ingroup)</arglist>
+ </member>
+ <member kind="function" virtualness="virtual">
+ <type>virtual</type>
+ <name>~SequenceDiversityMafStatistics</name>
+ <anchorfile>classbpp_1_1SequenceDiversityMafStatistics.html</anchorfile>
+ <anchor>a4a0ab3ae3326eefa76be1ad616ce9fbb</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getShortName</name>
+ <anchorfile>classbpp_1_1SequenceDiversityMafStatistics.html</anchorfile>
+ <anchor>a3b6faa127b55a52b78e7e876410e879b</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>std::string</type>
+ <name>getFullName</name>
+ <anchorfile>classbpp_1_1SequenceDiversityMafStatistics.html</anchorfile>
+ <anchor>ae1bdd5b0b5fc7636a9169394b370496d</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function">
+ <type>void</type>
+ <name>compute</name>
+ <anchorfile>classbpp_1_1SequenceDiversityMafStatistics.html</anchorfile>
+ <anchor>a32acab8424d39b1b43f42e230861a73f</anchor>
+ <arglist>(const MafBlock &block)</arglist>
+ </member>
+ <member kind="function">
+ <type>std::vector< std::string ></type>
+ <name>getSupportedTags</name>
+ <anchorfile>classbpp_1_1SequenceDiversityMafStatistics.html</anchorfile>
+ <anchor>a59981424c10368d2e823fb56bfc30f8f</anchor>
+ <arglist>() const </arglist>
+ </member>
+ <member kind="function" protection="private" static="yes">
+ <type>static std::vector< int ></type>
+ <name>getPatterns_</name>
+ <anchorfile>classbpp_1_1SequenceDiversityMafStatistics.html</anchorfile>
+ <anchor>a168e8d369d98c84ec7f6ccd4a3a53489</anchor>
+ <arglist>(const SiteContainer &sites)</arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::MaskFilterMafIterator</name>
+ <filename>classbpp_1_1MaskFilterMafIterator.html</filename>
+ <base>bpp::AbstractFilterMafIterator</base>
+ <base>bpp::MafTrashIterator</base>
+ <member kind="function">
+ <type></type>
+ <name>MaskFilterMafIterator</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>ae9ea74d39fa0864177883cb437375a21</anchor>
+ <arglist>(MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, unsigned int maxMasked, bool keepTrashedBlocks)</arglist>
+ </member>
+ <member kind="function">
+ <type>MafBlock *</type>
+ <name>nextRemovedBlock</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>a35db07285be7e18e929f7eed3b9b8763</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>MafBlock *</type>
+ <name>analyseCurrentBlock_</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>a2ccf5d991f556384965c78da3d2190f0</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::vector< std::string ></type>
+ <name>species_</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>a465cad4e30f65599a93c9afc4e42e5b0</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>unsigned int</type>
+ <name>windowSize_</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>a0b55e64e8353b3335d0a38b0533bf41b</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>unsigned int</type>
+ <name>step_</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>a58f3b29e2b09b5b6ec586d5e14058d30</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>unsigned int</type>
+ <name>maxMasked_</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>aaa47ab33500a4e7044e1f5999d980bc0</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::deque< MafBlock * ></type>
+ <name>blockBuffer_</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>af265abfe85d8edc4c3d154dfe06dacee</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::deque< MafBlock * ></type>
+ <name>trashBuffer_</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>ae6d30bc7fa4a89c00c569c2b4e2568b2</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::deque< std::vector< bool > ></type>
+ <name>window_</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>a9fa620b16952cbb2111b81ea9372474d</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>bool</type>
+ <name>keepTrashedBlocks_</name>
+ <anchorfile>classbpp_1_1MaskFilterMafIterator.html</anchorfile>
+ <anchor>af2f659815eb1af061445667dc084cdf8</anchor>
+ <arglist></arglist>
+ </member>
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+ <name>bpp::OrphanSequenceFilterMafIterator</name>
+ <filename>classbpp_1_1OrphanSequenceFilterMafIterator.html</filename>
+ <base>bpp::AbstractFilterMafIterator</base>
+ <member kind="function">
+ <type></type>
+ <name>OrphanSequenceFilterMafIterator</name>
+ <anchorfile>classbpp_1_1OrphanSequenceFilterMafIterator.html</anchorfile>
+ <anchor>af81605f32561b6298fd9292f37b9192d</anchor>
+ <arglist>(MafIterator *iterator, const std::vector< std::string > &species, bool strict=false, bool keep=false, bool rmDuplicates=false)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type></type>
+ <name>OrphanSequenceFilterMafIterator</name>
+ <anchorfile>classbpp_1_1OrphanSequenceFilterMafIterator.html</anchorfile>
+ <anchor>aa3a6c7432b4c39d575e0e12e32076c70</anchor>
+ <arglist>(const OrphanSequenceFilterMafIterator &iterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>OrphanSequenceFilterMafIterator &</type>
+ <name>operator=</name>
+ <anchorfile>classbpp_1_1OrphanSequenceFilterMafIterator.html</anchorfile>
+ <anchor>a8be37ba7ec4aa58fbe4dad24450041bc</anchor>
+ <arglist>(const OrphanSequenceFilterMafIterator &iterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>MafBlock *</type>
+ <name>analyseCurrentBlock_</name>
+ <anchorfile>classbpp_1_1OrphanSequenceFilterMafIterator.html</anchorfile>
+ <anchor>ae1e8dbdd4fc1a147acf1921e857b2f0e</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::vector< std::string ></type>
+ <name>species_</name>
+ <anchorfile>classbpp_1_1OrphanSequenceFilterMafIterator.html</anchorfile>
+ <anchor>a3c6c3a96d3d6ef6aa5fc7bdd7a93ac5a</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>bool</type>
+ <name>strict_</name>
+ <anchorfile>classbpp_1_1OrphanSequenceFilterMafIterator.html</anchorfile>
+ <anchor>a02a1d63905ac98fd08d5b61e101d8b97</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>bool</type>
+ <name>rmDuplicates_</name>
+ <anchorfile>classbpp_1_1OrphanSequenceFilterMafIterator.html</anchorfile>
+ <anchor>a4b29c4085860b78ba02afeb391b0e33a</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::OutputAlignmentMafIterator</name>
+ <filename>classbpp_1_1OutputAlignmentMafIterator.html</filename>
+ <base>bpp::AbstractFilterMafIterator</base>
+ <member kind="function">
+ <type></type>
+ <name>OutputAlignmentMafIterator</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>ade9d96da1efd0cd88c505531d8089c10</anchor>
+ <arglist>(MafIterator *iterator, std::ostream *out, OAlignment *writer, bool mask=true)</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>OutputAlignmentMafIterator</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>a9ec446d8698d108e881a0c4761d46098</anchor>
+ <arglist>(MafIterator *iterator, const std::string &file, OAlignment *writer, bool mask=true)</arglist>
+ </member>
+ <member kind="function">
+ <type></type>
+ <name>~OutputAlignmentMafIterator</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>ac0d53fd39b9216b5d5bae094bd5317a2</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type></type>
+ <name>OutputAlignmentMafIterator</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>ada902422b696a08ca824d408c41522b0</anchor>
+ <arglist>(const OutputAlignmentMafIterator &iterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>OutputAlignmentMafIterator &</type>
+ <name>operator=</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>a80cb13ede91975efd13e291addec9676</anchor>
+ <arglist>(const OutputAlignmentMafIterator &iterator)</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>MafBlock *</type>
+ <name>analyseCurrentBlock_</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>ae4dd6c31134f41a598870716b3ed28e6</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" protection="private">
+ <type>void</type>
+ <name>writeBlock</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>a4e2550764d675ba79863fe7db3da556d</anchor>
+ <arglist>(std::ostream &out, const MafBlock &block) const </arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::ostream *</type>
+ <name>output_</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>ab54f102c042558af418dae1e3b46ef55</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::string</type>
+ <name>file_</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>ac5c7949aaaaea9b22262706de4ba9949</anchor>
+ <arglist></arglist>
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+ <member kind="variable" protection="private">
+ <type>bool</type>
+ <name>mask_</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>a46e9b08feb8b2ff2ab7e14927380ada9</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>std::auto_ptr< OAlignment ></type>
+ <name>writer_</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>a4c5564c32d17ab6bab75eb960be767e7</anchor>
+ <arglist></arglist>
+ </member>
+ <member kind="variable" protection="private">
+ <type>unsigned int</type>
+ <name>currentBlockIndex_</name>
+ <anchorfile>classbpp_1_1OutputAlignmentMafIterator.html</anchorfile>
+ <anchor>ae1fdc4d109ac4c4708f57caad3b367b5</anchor>
+ <arglist></arglist>
+ </member>
+ </compound>
+ <compound kind="class">
+ <name>bpp::OutputMafIterator</name>
+ <filename>classbpp_1_1OutputMafIterator.html</filename>
+ <base>bpp::AbstractFilterMafIterator</base>
+ <member kind="function">
+ <type></type>
+ <name>OutputMafIterator</name>
+ <anchorfile>classbpp_1_1OutputMafIterator.html</anchorfile>
+ <anchor>ad7baa9048cd0093c7c54b6f0faeb7852</anchor>
+ <arglist>(MafIterator *iterator, std::ostream *out, bool mask=true)</arglist>
+ </member>
+ <member kind="function">
+ <type>MafBlock *</type>
+ <name>analyseCurrentBlock_</name>
+ <anchorfile>classbpp_1_1OutputMafIterator.html</anchorfile>
+ <anchor>a29a8161f1f06dffcc96140d5e8bc39a5</anchor>
+ <arglist>()</arglist>
+ </member>
+ <member kind="function" protection="private">
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+ <file>BlockLengthMafIterator.h</file>
+ <file>BlockMergerMafIterator.cpp</file>
+ <file>BlockMergerMafIterator.h</file>
+ <file>BlockSizeMafIterator.h</file>
+ <file>ChromosomeMafIterator.cpp</file>
+ <file>ChromosomeMafIterator.h</file>
+ <file>ConcatenateMafIterator.cpp</file>
+ <file>ConcatenateMafIterator.h</file>
+ <file>CoordinatesOutputMafIterator.cpp</file>
+ <file>CoordinatesOutputMafIterator.h</file>
+ <file>DuplicateFilterMafIterator.cpp</file>
+ <file>DuplicateFilterMafIterator.h</file>
+ <file>EntropyFilterMafIterator.cpp</file>
+ <file>EntropyFilterMafIterator.h</file>
+ <file>FeatureExtractorMafIterator.cpp</file>
+ <file>FeatureExtractorMafIterator.h</file>
+ <file>FeatureFilterMafIterator.cpp</file>
+ <file>FeatureFilterMafIterator.h</file>
+ <file>FullGapFilterMafIterator.cpp</file>
+ <file>FullGapFilterMafIterator.h</file>
+ <file>IterationListener.cpp</file>
+ <file>IterationListener.h</file>
+ <file>MafBlock.h</file>
+ <file>MafIterator.cpp</file>
+ <file>MafIterator.h</file>
+ <file>MafParser.cpp</file>
+ <file>MafParser.h</file>
+ <file>MafSequence.cpp</file>
+ <file>MafSequence.h</file>
+ <file>MafStatistics.cpp</file>
+ <file>MafStatistics.h</file>
+ <file>MaskFilterMafIterator.cpp</file>
+ <file>MaskFilterMafIterator.h</file>
+ <file>OrphanSequenceFilterMafIterator.cpp</file>
+ <file>OrphanSequenceFilterMafIterator.h</file>
+ <file>OutputAlignmentMafIterator.cpp</file>
+ <file>OutputAlignmentMafIterator.h</file>
+ <file>OutputMafIterator.cpp</file>
+ <file>OutputMafIterator.h</file>
+ <file>QualityFilterMafIterator.cpp</file>
+ <file>QualityFilterMafIterator.h</file>
+ <file>SequenceFilterMafIterator.cpp</file>
+ <file>SequenceFilterMafIterator.h</file>
+ <file>SequenceStatisticsMafIterator.cpp</file>
+ <file>SequenceStatisticsMafIterator.h</file>
+ <file>SequenceStreamToMafIterator.cpp</file>
+ <file>SequenceStreamToMafIterator.h</file>
+ <file>VcfOutputMafIterator.cpp</file>
+ <file>VcfOutputMafIterator.h</file>
+ <file>WindowSplitMafIterator.cpp</file>
+ <file>WindowSplitMafIterator.h</file>
+ </compound>
+ <compound kind="dir">
+ <name>Bpp/Seq</name>
+ <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/</path>
+ <filename>dir_a6df4600355513c0d02be2734b44b033.html</filename>
+ <dir>Bpp/Seq/Feature</dir>
+ <dir>Bpp/Seq/Io</dir>
+ </compound>
+ <compound kind="page">
+ <name>index</name>
+ <title></title>
+ <filename>index</filename>
+ </compound>
+</tagfile>
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 729e02a..75b241a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -102,9 +102,9 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-seq-omics")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.1.0")
+SET(CPACK_PACKAGE_VERSION "2.2.0")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "2")
SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Sequence-Omics library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
@@ -122,7 +122,6 @@ SET(CPACK_SOURCE_IGNORE_FILES
".*\\\\.deb"
".*\\\\.rpm"
".*\\\\.dmg"
- ".*\\\\.sh"
".*\\\\..*\\\\.swp"
"src/\\\\..*"
"src/libbpp*"
diff --git a/ChangeLog b/ChangeLog
index 240f0aa..e1885cb 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,11 @@
+22/09/14 -*- Version 2.2.0 -*-
+
+22/08/13 Julien Dutheil
+* Sequence diversity estimators (Watterson theta)
+
+12/08/13 Julien Dutheil
+* New Four species statistics
+
06/03/13 -*- Version 2.1.0 -*-
05/02/13 Julien Dutheil
diff --git a/Doxyfile b/Doxyfile
index f28d234..5c2d0d1 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -32,7 +32,7 @@ PROJECT_NAME = bpp-seq-omics
# This could be handy for archiving the generated documentation or
# if some version control system is used.
-PROJECT_NUMBER = 2.1.0
+PROJECT_NUMBER = 2.2.0
# 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
diff --git a/bpp-seq-omics.spec b/bpp-seq-omics.spec
index fbd9a28..3aab529 100644
--- a/bpp-seq-omics.spec
+++ b/bpp-seq-omics.spec
@@ -1,5 +1,5 @@
%define _basename bpp-seq-omics
-%define _version 2.1.0
+%define _version 2.2.0
%define _release 1
%define _prefix /usr
@@ -179,6 +179,9 @@ exit 0
%{_prefix}/include/*
%changelog
+* Mon Sep 22 2014 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.2.0-1
+- New statistics, including sequence diversity estimators
+- Several bugs and memory leaks fixed.
* Wed Mar 06 2013 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.1.0-1
- Maf to VCF tool added as a MafIterator.
* Tue Nov 06 2012 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.0.3-1
diff --git a/debian/changelog b/debian/changelog
index ddba212..b38ff21 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+libbpp-seq-omics (2.2.0-1) unstable; urgency=low
+
+ * New statistics, including sequence diversity estimators
+ * Several bugs and memory leaks fixed.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Mon, 22 Sep 2014 14:00:00 +0100
+
libbpp-seq-omics (2.1.0-1) unstable; urgency=low
* Maf to VCF tool added as a MafIterator.
diff --git a/debian/control b/debian/control
index d2eda1d..62aa8e5 100644
--- a/debian/control
+++ b/debian/control
@@ -4,14 +4,14 @@ 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-seq-dev (>= 2.1.0)
+ libbpp-seq-dev (>= 2.2.0)
Standards-Version: 3.9.4
Package: libbpp-seq-omics-dev
Section: libdevel
Architecture: any
Depends: libbpp-seq-omics1 (= ${binary:Version}), ${misc:Depends},
- libbpp-seq-dev (>= 2.1.0)
+ libbpp-seq-dev (>= 2.2.0)
Description: Bio++ Sequence library: genomics components.
Contains the Bio++ sequence classes dedicated to genomics.
@@ -19,7 +19,7 @@ Package: libbpp-seq-omics1
Section: libs
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends},
- libbpp-seq9 (>= 2.1.0)
+ libbpp-seq9 (>= 2.2.0)
Description: Bio++ Sequence library: genomics components.
Contains the Bio++ sequence classes dedicated to genomics.
diff --git a/debian/copyright b/debian/copyright
index 071c61f..9eb55d6 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,5 +1,5 @@
This package was debianized by Julien Dutheil <julien.dutheil at univ-montp2.fr> on
-Wed, 06 Mar 2013 14:34:00 +0100.
+Wed, 22 Sep 2014 14:00:00 +0100.
It was downloaded from <http://biopp.univ-montp2.fr/Repositories/sources>
@@ -9,7 +9,7 @@ Upstream Author:
Copyright:
- Copyright (C) 2013 Bio++ Development Team
+ Copyright (C) 2014 Bio++ Development Team
License:
@@ -30,7 +30,7 @@ License:
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
+The Debian packaging is (C) 2014, 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:
diff --git a/genIncludes.sh b/genIncludes.sh
new file mode 100755
index 0000000..56710e9
--- /dev/null
+++ b/genIncludes.sh
@@ -0,0 +1,35 @@
+#! /bin/bash
+
+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;
+}
+
+createGeneric $1
diff --git a/src/Bpp/Seq/Feature/SequenceFeatureTools.cpp b/src/Bpp/Seq/Feature/SequenceFeatureTools.cpp
index cd89876..f90a2c9 100644
--- a/src/Bpp/Seq/Feature/SequenceFeatureTools.cpp
+++ b/src/Bpp/Seq/Feature/SequenceFeatureTools.cpp
@@ -41,7 +41,7 @@ knowledge of the CeCILL license and that you accept its terms.
//From bpp-seq:
#include <Bpp/Seq/SequenceTools.h>
-#include <Bpp/Seq/Alphabet/StandardCodonAlphabet.h>
+#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
#include <Bpp/Seq/Alphabet/AlphabetTools.h>
#include <Bpp/Seq/Alphabet/AlphabetExceptions.h>
@@ -65,20 +65,21 @@ Sequence* SequenceFeatureTools::extract(const Sequence& seq, const SeqRange& ran
/******************************************************************************/
-unsigned int SequenceFeatureTools::getOrfs(const Sequence& seq, SequenceFeatureSet& featSet) {
+unsigned int SequenceFeatureTools::getOrfs(const Sequence& seq, SequenceFeatureSet& featSet, const GeneticCode& gCode)
+{
if (! AlphabetTools::isNucleicAlphabet(seq.getAlphabet())) {
throw AlphabetException("SequenceFeatureTools::getOrfs: Sequence alphabet must be nucleic!", seq.getAlphabet());
}
unsigned int orfCpt = 0;
- StandardCodonAlphabet codonAlpha(dynamic_cast<const NucleicAlphabet*>(seq.getAlphabet()));
+ const CodonAlphabet* codonAlpha = gCode.getSourceAlphabet();
std::vector< std::vector<size_t> > starts(3), stops(3);
size_t phase = 0;
for (size_t p = 0 ; p < seq.size() - 2 ; p++) {
phase = p % 3;
- if (codonAlpha.isInit(codonAlpha.getCodon(seq.getValue(p), seq.getValue(p + 1), seq.getValue(p + 2)))) {
+ if (gCode.isStart(codonAlpha->getCodon(seq.getValue(p), seq.getValue(p + 1), seq.getValue(p + 2)))) {
starts[phase].push_back(p);
//std::cerr << "Start: " << p << " (" << phase << ")" << std::endl;
- } else if (codonAlpha.isStop(codonAlpha.getCodon(seq.getValue(p), seq.getValue(p + 1), seq.getValue(p + 2)))) {
+ } else if (gCode.isStop(codonAlpha->getCodon(seq.getValue(p), seq.getValue(p + 1), seq.getValue(p + 2)))) {
stops[phase].push_back(p);
//std::cerr << "Stop: " << p << " (" << phase << ")" << std::endl;
}
diff --git a/src/Bpp/Seq/Feature/SequenceFeatureTools.h b/src/Bpp/Seq/Feature/SequenceFeatureTools.h
index cb32c80..7bbb152 100644
--- a/src/Bpp/Seq/Feature/SequenceFeatureTools.h
+++ b/src/Bpp/Seq/Feature/SequenceFeatureTools.h
@@ -44,6 +44,7 @@ knowledge of the CeCILL license and that you accept its terms.
//From bpp-seq:
#include <Bpp/Seq/Sequence.h>
+#include <Bpp/Seq/GeneticCode/GeneticCode.h>
namespace bpp {
@@ -69,10 +70,13 @@ class SequenceFeatureTools
*
* @param seq The Sequence where to find ORF. Must be a nucleic sequence.
* @param featSet A SequenceFeatureSet to fill with the annotations.
+ * @param gCode The genetic code to use.
* @return The number of ORF found.
* @author Sylvain Gaillard
*/
- static unsigned int getOrfs(const Sequence& seq, SequenceFeatureSet& featSet);
+ static unsigned int getOrfs(const Sequence& seq,
+ SequenceFeatureSet& featSet,
+ const GeneticCode& gCode);
};
diff --git a/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp b/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
index 3c1930f..9bb3886 100644
--- a/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
@@ -61,9 +61,9 @@ MafBlock* BlockMergerMafIterator::analyseCurrentBlock_() throw (Exception)
if (!seq1->hasCoordinates() || !seq2->hasCoordinates())
throw Exception("BlockMergerMafIterator::nextBlock. Species '" + species_[i] + "' is missing coordinates in at least one block.");
- if (seq1->stop() >= seq2->start())
+ if (seq1->stop() > seq2->start())
return currentBlock_;
- size_t space = seq2->start() - seq1->stop() - 1;
+ size_t space = seq2->start() - seq1->stop();
if (space > maxDist_)
return currentBlock_;
if (i == 0)
diff --git a/src/Bpp/Seq/Io/Maf/IterationListener.cpp b/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
similarity index 56%
copy from src/Bpp/Seq/Io/Maf/IterationListener.cpp
copy to src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
index 5e58ef4..305a60f 100644
--- a/src/Bpp/Seq/Io/Maf/IterationListener.cpp
+++ b/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
@@ -1,11 +1,11 @@
//
-// File: IterationListener.cpp
+// File: CoordinatesOutputMafIterator.cpp
// Authors: Julien Dutheil
-// Created: Wed Jun 27 2012
+// Created: Mon Jun 02 2014
//
/*
-Copyright or © or Copr. Bio++ Development Team, (2012)
+Copyright or © or Copr. Bio++ Development Team, (2014)
This software is a computer program whose purpose is to provide classes
for sequences analysis.
@@ -37,39 +37,38 @@ 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 "IterationListener.h"
+#include "CoordinatesOutputMafIterator.h"
-// From the STL:
-#include <vector>
-
-using namespace std;
using namespace bpp;
+using namespace std;
-void CsvStatisticsOutputIterationListener::iterationStarts()
+void CoordinatesOutputMafIterator::writeHeader_(ostream& out) const
{
- const vector<string>& header = statsIterator_->getResultsColumnNames();
- *output_ << "Chr" << sep_ << "Start" << sep_ << "Stop";
- for (size_t i = 0; i < header.size(); ++i) {
- *output_ << sep_ << header[i];
+ for (size_t i = 0; i < species_.size(); ++i) {
+ if (i > 0) out << "\t";
+ string sp = species_[i];
+ out << sp << ".chr\t" << sp << ".strand\t" << sp << ".start\t" << sp << ".stop";
}
- output_->endLine();
+ out << endl;
}
-void CsvStatisticsOutputIterationListener::iterationMoves(const MafBlock& currentBlock)
+MafBlock* CoordinatesOutputMafIterator::analyseCurrentBlock_() throw (Exception)
{
- const vector<double>& values = statsIterator_->getResults();
- if (currentBlock.hasSequenceForSpecies(refSpecies_)) {
- const MafSequence& refSeq = currentBlock.getSequenceForSpecies(refSpecies_);
- if (refSeq.hasCoordinates())
- *output_ << refSeq.getChromosome() << sep_ << refSeq.start() << sep_ << refSeq.stop();
- else
- *output_ << "NA" << sep_ << "NA" << sep_ << "NA";
- } else {
- *output_ << "NA" << sep_ << "NA" << sep_ << "NA";
- }
- for (size_t i = 0; i < values.size(); ++i) {
- *output_ << sep_ << values[i];
+ currentBlock_ = iterator_->nextBlock();
+ if (currentBlock_) {
+ for (size_t i = 0; i < species_.size(); ++i) {
+ if (i > 0) *output_ << "\t";
+ vector<const MafSequence*> seqs = currentBlock_->getSequencesForSpecies(species_[i]);
+ if (seqs.size() > 1)
+ throw Exception("CoordinatesOutputMafIterator::analyseCurrentBlock_(). There is more than one sequence for species '" + species_[i] + "' in current block.");
+ else if (seqs.size() == 0) {
+ *output_ << "NA\tNA\tNA\tNA";
+ } else {
+ *output_ << seqs[0]->getChromosome() << "\t" << seqs[0]->getStrand() << "\t" << seqs[0]->start() << "\t" << seqs[0]->stop();
+ }
+ }
+ *output_ << endl;
}
- output_->endLine();
+ return currentBlock_;
}
diff --git a/src/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h b/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
similarity index 55%
copy from src/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h
copy to src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
index 0bda4f5..0ae520c 100644
--- a/src/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
@@ -1,11 +1,11 @@
//
-// File: OrphanSequenceFilterMafIterator.h
+// File: CoordinatesOutputMafIterator.h
// Authors: Julien Dutheil
-// Created: Mon Mar 11 2013
+// Created: Mon Jun 02 2014
//
/*
-Copyright or © or Copr. Bio++ Development Team, (2013)
+Copyright or © or Copr. Bio++ Development Team, (2014)
This software is a computer program whose purpose is to provide classes
for sequences analysis.
@@ -37,66 +37,66 @@ 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 _ORPHANSEQUENCEFILTERMAFITERATOR_H_
-#define _ORPHANSEQUENCEFILTERMAFITERATOR_H_
+#ifndef _COORDINATESOUTPUTMAFITERATOR_H_
+#define _COORDINATESOUTPUTMAFITERATOR_H_
#include "MafIterator.h"
//From the STL:
#include <iostream>
#include <string>
-#include <deque>
namespace bpp {
/**
- * @brief Filter maf blocks to keep a the ones which display a specified combination of species.
+ * @brief Output each sequence coordinates for each block.
*
- * This filter is typically used to retrieve "orphan" sequences, that is sequences only present in one (set of) species.
+ * The set of species for which coordinates are output is provided as argument.
+ * The current implementation outputs results as a table to a file. Later implementation
+ * may involve a dedicated data structure for other application usage (file indexing and so one).
*/
-class OrphanSequenceFilterMafIterator:
+class CoordinatesOutputMafIterator:
public AbstractFilterMafIterator
{
private:
+ std::ostream* output_;
std::vector<std::string> species_;
- bool strict_;
- bool rmDuplicates_;
public:
/**
+ * @brief Creates a new CoordinatesOutputMafIterator object.
+ *
* @param iterator The input iterator.
- * @param species The list of species names to be retained.
- * @param strict If true, then block that do not contain all of the specified species will be discarded.
- * @param rmDuplicates If true, block that contain more than one instance for at least one species will be discarded.
+ * @param out A pointer toward the output stream. The stream will not be own by this instance, and will not be copied neither destroyed.
+ * @param species A vector of species names for which coordinates should be output. In case of missing species for one block, NA will be produced.
*/
- OrphanSequenceFilterMafIterator(MafIterator* iterator, const std::vector<std::string>& species, bool strict = false, bool keep = false, bool rmDuplicates = false) :
- AbstractFilterMafIterator(iterator),
- species_(species),
- strict_(strict),
- rmDuplicates_(rmDuplicates)
- {}
+ CoordinatesOutputMafIterator(MafIterator* iterator, std::ostream* out, const std::vector<std::string>& species):
+ AbstractFilterMafIterator(iterator), output_(out), species_(species)
+ {
+ if (output_)
+ writeHeader_(*output_);
+ }
private:
- OrphanSequenceFilterMafIterator(const OrphanSequenceFilterMafIterator& iterator) :
+ CoordinatesOutputMafIterator(const CoordinatesOutputMafIterator& iterator) :
AbstractFilterMafIterator(0),
- species_(iterator.species_),
- strict_(iterator.strict_),
- rmDuplicates_(iterator.rmDuplicates_)
+ output_(iterator.output_),
+ species_(iterator.species_)
{}
- OrphanSequenceFilterMafIterator& operator=(const OrphanSequenceFilterMafIterator& iterator)
+ CoordinatesOutputMafIterator& operator=(const CoordinatesOutputMafIterator& iterator)
{
- species_ = iterator.species_;
- strict_ = iterator.strict_;
- rmDuplicates_ = iterator.rmDuplicates_;
+ output_ = iterator.output_;
+ species_ = iterator.species_;
return *this;
}
private:
+ void writeHeader_(std::ostream& out) const;
MafBlock* analyseCurrentBlock_() throw (Exception);
};
} // end of namespace bpp.
-#endif //_ORPHANSEQUENCEFILTERMAFITERATOR_H_
+#endif //_COORDINATESOUTPUTMAFITERATOR_H_
diff --git a/src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp b/src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp
index 73dbdd3..9d5ae15 100644
--- a/src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp
@@ -107,7 +107,7 @@ MafBlock* EntropyFilterMafIterator::analyseCurrentBlock_() throw (Exception)
if (verbose_)
ApplicationTools::displayGauge(i - windowSize_, nc - windowSize_ - 1, '>');
//Evaluate current window:
- unsigned int count = std::accumulate(window_.begin(), window_.end(), 0);
+ unsigned int count = std::accumulate(window_.begin(), window_.end(), 0u);
if (count > maxPos_) {
if (pos.size() == 0) {
pos.push_back(i - windowSize_);
@@ -138,7 +138,7 @@ MafBlock* EntropyFilterMafIterator::analyseCurrentBlock_() throw (Exception)
}
//Evaluate last window:
- unsigned int count = std::accumulate(window_.begin(), window_.end(), 0);
+ unsigned int count = std::accumulate(window_.begin(), window_.end(), 0u);
if (count > maxPos_) {
if (pos.size() == 0) {
pos.push_back(i - windowSize_);
diff --git a/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp b/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
index 1b9b2e8..721dae0 100644
--- a/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
@@ -52,11 +52,12 @@ using namespace std;
MafBlock* FeatureExtractor::analyseCurrentBlock_() throw (Exception)
{
- if (blockBuffer_.size() == 0) {
+ while (blockBuffer_.size() == 0) {
//Unless there is no more block in the buffer, we need to parse more:
+ auto_ptr<MafBlock> block;
START:
- MafBlock* block = iterator_->nextBlock();
- if (!block) return 0; //No more block.
+ block.reset(iterator_->nextBlock());
+ if (!block.get()) return 0; //No more block.
//Check if the block contains the reference species:
if (!block->hasSequenceForSpecies(refSpecies_))
@@ -71,12 +72,24 @@ MafBlock* FeatureExtractor::analyseCurrentBlock_() throw (Exception)
RangeSet<size_t> ranges = mr->second;
if (completeOnly_)
- ranges.filterWithin(Range<size_t>(refSeq.start(), refSeq.stop()));
+ ranges.filterWithin(refSeq.getRange(true));
else
- ranges.restrictTo(Range<size_t>(refSeq.start(), refSeq.stop()));
+ ranges.restrictTo(refSeq.getRange(true));
if (ranges.isEmpty())
goto START;
+ //If the reference sequence is on the negative strand, then we have to correct the coordinates:
+ if (refSeq.getStrand() == '-') {
+ RangeSet<size_t> cRanges;
+ for (set<Range<size_t>*>::iterator it = ranges.getSet().begin();
+ it != ranges.getSet().end();
+ ++it)
+ {
+ cRanges.addRange(Range<size_t>(refSeq.getSrcSize() - (**it).end(), refSeq.getSrcSize() - (**it).begin()));
+ }
+ ranges = cRanges;
+ }
+
//We will need to convert to alignment positions, using a sequence walker:
SequenceWalker walker(refSeq);
@@ -118,7 +131,6 @@ MafBlock* FeatureExtractor::analyseCurrentBlock_() throw (Exception)
if (verbose_)
ApplicationTools::displayTaskDone();
- delete block;
}
MafBlock* nxtBlock = blockBuffer_.front();
diff --git a/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp b/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
index 578ed83..1e4e674 100644
--- a/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
@@ -75,15 +75,26 @@ MafBlock* FeatureFilterMafIterator::analyseCurrentBlock_() throw (Exception)
}
//else
MultiRange<size_t> mRange = mr->second;
- mRange.restrictTo(Range<size_t>(refSeq.start(), refSeq.stop() + 1));
+ //mRange.restrictTo(Range<size_t>(refSeq.start(), refSeq.stop() + 1)); jdutheil on 17/04/13: do we really need the +1 here?
+ mRange.restrictTo(refSeq.getRange(true));
if (mRange.isEmpty()) {
if (logstream_) {
(*logstream_ << "FEATURE FILTER: block " << block->getDescription() << " does not contain any feature and was kept as is.").endLine();
}
return block;
}
- std::vector<size_t> tmp = mRange.getBounds();
- std::deque<size_t> refBounds(tmp.begin(), tmp.end());
+ std::vector<size_t> tmp = mRange.getBounds();
+
+ //If the reference sequence is on the negative strand, then we have to correct the coordinates:
+ std::deque<size_t> refBounds;
+ if (refSeq.getStrand() == '-') {
+ for (size_t i = 0; i < tmp.size(); ++i)
+ {
+ refBounds.push_front(refSeq.getSrcSize() - tmp[i]);
+ }
+ } else {
+ refBounds = deque<size_t>(tmp.begin(), tmp.end());
+ }
//Now extract corresponding alignments. We use the range to split the original block.
//Only thing to watch out is the coordinates, refering to the ref species...
@@ -91,6 +102,7 @@ MafBlock* FeatureFilterMafIterator::analyseCurrentBlock_() throw (Exception)
int gap = refSeq.getAlphabet()->getGapCharacterCode();
long int refPos = static_cast<long int>(refSeq.start()) - 1;
+ //long int refPos = refSeq.getStrand() == '-' ? static_cast<long int>(refSeq.getSrcSize() - refSeq.start()) - 1 : static_cast<long int>(refSeq.start()) - 1;
std::vector<size_t> pos;
if (verbose_) {
ApplicationTools::message->endLine();
@@ -98,7 +110,7 @@ MafBlock* FeatureFilterMafIterator::analyseCurrentBlock_() throw (Exception)
}
for (size_t alnPos = 0; alnPos < refSeq.size() && refBounds.size() > 0; ++alnPos) {
if (verbose_)
- ApplicationTools::displayGauge(alnPos, refSeq.size() - 1, '>');
+ ApplicationTools::displayGauge(alnPos, refBounds.back(), '>');
if (refSeq[alnPos] != gap) {
refPos++;
//check if this position is a bound:
@@ -112,14 +124,14 @@ MafBlock* FeatureFilterMafIterator::analyseCurrentBlock_() throw (Exception)
ApplicationTools::displayTaskDone();
//Check if the last bound matches the end of the alignment:
- if (refBounds.size() > 0 && refBounds.front() == refSeq.stop() + 1) {
+ if (refBounds.size() > 0 && refBounds.front() == refSeq.stop()) {
pos.push_back(refSeq.size());
refBounds.pop_front();
}
if (refBounds.size() > 0) {
VectorTools::print(vector<size_t>(refBounds.begin(), refBounds.end()));
- throw Exception("FeatureFilterMafIterator::nextBlock(). An error occurred here, " + TextTools::toString(refBounds.size()) + " coordinates are left... this is most likely a bug, please report!");
+ throw Exception("FeatureFilterMafIterator::nextBlock(). An error occurred here, " + TextTools::toString(refBounds.size()) + " coordinates are left, in sequence " + refSeq.getDescription() + "... this is most likely a bug, please report!");
}
//Next step is simply to split the black according to the translated coordinates:
diff --git a/src/Bpp/Seq/Io/Maf/IterationListener.cpp b/src/Bpp/Seq/Io/Maf/IterationListener.cpp
index 5e58ef4..703b765 100644
--- a/src/Bpp/Seq/Io/Maf/IterationListener.cpp
+++ b/src/Bpp/Seq/Io/Maf/IterationListener.cpp
@@ -57,7 +57,7 @@ void CsvStatisticsOutputIterationListener::iterationStarts()
void CsvStatisticsOutputIterationListener::iterationMoves(const MafBlock& currentBlock)
{
- const vector<double>& values = statsIterator_->getResults();
+ const vector<const BppNumberI*>& values = statsIterator_->getResults();
if (currentBlock.hasSequenceForSpecies(refSpecies_)) {
const MafSequence& refSeq = currentBlock.getSequenceForSpecies(refSpecies_);
if (refSeq.hasCoordinates())
@@ -68,7 +68,9 @@ void CsvStatisticsOutputIterationListener::iterationMoves(const MafBlock& curren
*output_ << "NA" << sep_ << "NA" << sep_ << "NA";
}
for (size_t i = 0; i < values.size(); ++i) {
- *output_ << sep_ << values[i];
+ *output_ << sep_ << (values[i] ? values[i]->toString() : "NA");
+ //Memory cleaning:
+ if (values[i]) delete values[i];
}
output_->endLine();
}
diff --git a/src/Bpp/Seq/Io/Maf/MafParser.cpp b/src/Bpp/Seq/Io/Maf/MafParser.cpp
index 4043d51..8720977 100644
--- a/src/Bpp/Seq/Io/Maf/MafParser.cpp
+++ b/src/Bpp/Seq/Io/Maf/MafParser.cpp
@@ -88,7 +88,8 @@ MafBlock* MafParser::analyseCurrentBlock_() throw (Exception)
KeyvalTools::multipleKeyvals(line.substr(2), args, " ");
if (args.find("score") != args.end())
- block->setScore(TextTools::toDouble(args["score"]));
+ if (args["score"] != "NA")
+ block->setScore(TextTools::toDouble(args["score"]));
if (args.find("pass") != args.end())
block->setPass(TextTools::to<unsigned int>(args["pass"]));
diff --git a/src/Bpp/Seq/Io/Maf/MafSequence.h b/src/Bpp/Seq/Io/Maf/MafSequence.h
index dc4bf4a..c5278e8 100644
--- a/src/Bpp/Seq/Io/Maf/MafSequence.h
+++ b/src/Bpp/Seq/Io/Maf/MafSequence.h
@@ -109,12 +109,23 @@ class MafSequence:
}
size_t stop() const {
- if (hasCoordinates_) return begin_ + size_ - 1;
+ if (hasCoordinates_) return begin_ + size_;
else throw Exception("MafSequence::stop(). Sequence " + getName() + " does not have coordinates.");
}
- Range<size_t> getRange() const {
- if (hasCoordinates_) return Range<size_t>(start(), stop());
+ /**
+ * @return A range with cooridinates from this sequence.
+ * @param origin Tell if coorinates according to original sequence should be used.
+ * If 'yes' and the sequence is on the negative strand, the returned rang will be computed as [SrcSize-Stop, SrcSize-Start[
+ */
+ Range<size_t> getRange(bool origin=true) const {
+ if (hasCoordinates_) {
+ if (origin && strand_ == '-') {
+ return Range<size_t>(srcSize_ - stop(), srcSize_ - start());
+ } else {
+ return Range<size_t>(start(), stop());
+ }
+ }
else throw Exception("MafSequence::getRange(). Sequence " + getName() + " does not have coordinates.");
}
diff --git a/src/Bpp/Seq/Io/Maf/MafStatistics.cpp b/src/Bpp/Seq/Io/Maf/MafStatistics.cpp
index f0194a5..01b2367 100644
--- a/src/Bpp/Seq/Io/Maf/MafStatistics.cpp
+++ b/src/Bpp/Seq/Io/Maf/MafStatistics.cpp
@@ -92,7 +92,7 @@ void CharacterCountsMafStatistics::compute(const MafBlock& block)
result_.setValue("Unresolved", countUnres);
}
-SiteContainer* AbstractSpeciesSelectionMafStatistics::getSiteContainer(const MafBlock& block)
+SiteContainer* AbstractSpeciesSelectionMafStatistics::getSiteContainer_(const MafBlock& block)
{
VectorSiteContainer* alignment = new VectorSiteContainer(block.getAlignment().getAlphabet());
for (size_t i = 0; i < species_.size(); ++i) {
@@ -106,6 +106,35 @@ SiteContainer* AbstractSpeciesSelectionMafStatistics::getSiteContainer(const Maf
return alignment;
}
+AbstractSpeciesMultipleSelectionMafStatistics::AbstractSpeciesMultipleSelectionMafStatistics(const std::vector< std::vector<std::string> >& species):
+ species_(species)
+{
+ size_t n = VectorTools::vectorUnion(species).size();
+ size_t m = 0;
+ for (size_t i = 0; i < species.size(); ++i)
+ m += species_[i].size();
+ if (m != n)
+ throw Exception("AbstractSpeciesMultipleSelectionMafStatistics (constructor). Species selections must be fully distinct.");
+}
+
+vector<SiteContainer*> AbstractSpeciesMultipleSelectionMafStatistics::getSiteContainers_(const MafBlock& block)
+{
+ vector<SiteContainer*> alignments;
+ for (size_t k = 0; k < species_.size(); ++k) {
+ VectorSiteContainer* alignment = new VectorSiteContainer(block.getAlignment().getAlphabet());
+ for (size_t i = 0; i < species_[k].size(); ++i) {
+ if (block.hasSequenceForSpecies(species_[k][i])) {
+ vector<const MafSequence*> selection = block.getSequencesForSpecies(species_[k][i]);
+ for (size_t j = 0; j < selection.size(); ++j) {
+ alignment->addSequence(*selection[j]);
+ }
+ }
+ }
+ alignments.push_back(alignment);
+ }
+ return alignments;
+}
+
vector<string> SiteFrequencySpectrumMafStatistics::getSupportedTags() const
{
vector<string> tags;
@@ -125,41 +154,86 @@ void SiteFrequencySpectrumMafStatistics::compute(const MafBlock& block)
unsigned int nbIgnored = 0;
counts_.assign(categorizer_.getNumberOfCategories(), 0);
int state;
- auto_ptr<SiteContainer> alignment(getSiteContainer(block));
- if (alignment->getNumberOfSequences() > 0) {
- for (size_t i = 0; i < block.getNumberOfSites(); ++i) {
+ bool hasOutgroup = (outgroup_ != "");
+ bool isAnalyzable;
+ auto_ptr<SiteContainer> alignment;
+ const Sequence* outgroupSeq = 0;
+ if (hasOutgroup) {
+ isAnalyzable = (block.hasSequenceForSpecies(outgroup_) && block.getNumberOfSequences() > 1);
+ if (isAnalyzable) {
+ //We need to extract the outgroup sequence:
+ outgroupSeq = &block.getSequenceForSpecies(outgroup_); //Here we assume there is only one! Otherwise we take the first one...
+ alignment.reset(getSiteContainer_(block));
+ }
+ } else {
+ isAnalyzable = (block.getNumberOfSequences() > 0);
+ if (isAnalyzable)
+ alignment.reset(getSiteContainer_(block));
+ }
+ if (isAnalyzable) {
+ for (size_t i = 0; i < alignment->getNumberOfSites(); ++i) {
//Note: we do not rely on SiteTool::getCounts as it would be unefficient to count everything.
const Site& site = alignment->getSite(i);
map<int, unsigned int> counts;
- for (unsigned int j = 0; j < site.size(); ++j) {
+ bool isUnresolved = false;
+ bool isSaturated = false;
+ for (size_t j = 0; !isUnresolved && !isSaturated && j < site.size(); ++j) {
state = site[j];
if (alphabet_->isGap(state) || alphabet_->isUnresolved(state)) {
- nbUnresolved++;
- break;
+ isUnresolved = true;
} else {
counts[state]++;
if (counts.size() > 2) {
- nbSaturated++;
- break;
+ isSaturated = true;
}
}
}
- if (counts.size() > 0) {
+ if (isUnresolved) {
+ nbUnresolved++;
+ } else if (isSaturated) {
+ nbSaturated++;
+ } else if (hasOutgroup && (
+ alignment->getAlphabet()->isGap((*outgroupSeq)[i]) ||
+ alignment->getAlphabet()->isUnresolved((*outgroupSeq)[i]))) {
+ nbUnresolved++;
+ } else {
//Determine frequency class:
double count;
if (counts.size() == 1) {
- count = 0;
+ if (hasOutgroup) {
+ if (counts.begin()->first == (*outgroupSeq)[i])
+ count = 0; //This is the ancestral state.
+ else
+ count = counts.begin()->second; //This is a derived state.
+ } else {
+ count = 0; //In this case we do not know, so we put 0.
+ }
} else {
map<int, unsigned int>::iterator it = counts.begin();
unsigned int count1 = it->second;
it++;
unsigned int count2 = it->second;
- count = min(count1, count2);
+ if (hasOutgroup) {
+ if (counts.begin()->first == (*outgroupSeq)[i])
+ count = counts.rbegin()->second; //This is the ancestral state, therefore we other one is the derived state.
+ else if (counts.rbegin()->first == (*outgroupSeq)[i])
+ count = counts.begin()->second; //The second state is the ancestral one, therefore the first one is the derived state.
+ else {
+ //None of the two states are ancestral! The position is therefore discarded.
+ isSaturated = true;
+ }
+ } else {
+ count = min(count1, count2); //In this case we do not know, so we take the minimum of the two values.
+ }
}
- try {
- counts_[categorizer_.getCategory(count) - 1]++;
- } catch (OutOfRangeException& oof) {
- nbIgnored++;
+ if (isSaturated)
+ nbSaturated++;
+ else {
+ try {
+ counts_[categorizer_.getCategory(count) - 1]++;
+ } catch (OutOfRangeException& oof) {
+ nbIgnored++;
+ }
}
}
}
@@ -172,6 +246,53 @@ void SiteFrequencySpectrumMafStatistics::compute(const MafBlock& block)
}
}
+vector<string> FourSpeciesPatternCountsMafStatistics::getSupportedTags() const
+{
+ vector<string> tags;
+ tags.push_back("f1100");
+ tags.push_back("f0110");
+ tags.push_back("f1010");
+ tags.push_back("Ignored");
+ return tags;
+}
+
+void FourSpeciesPatternCountsMafStatistics::compute(const MafBlock& block)
+{
+ counts_.assign(6, 0);
+ auto_ptr<SiteContainer> alignment(getSiteContainer_(block));
+ if (alignment->getNumberOfSequences() == 4) {
+ unsigned int nbIgnored = 0;
+ for (size_t i = 0; i < block.getNumberOfSites(); ++i) {
+ const Site& site = alignment->getSite(i);
+ if (SiteTools::isComplete(site)) {
+ if (site[0] == site[1] &&
+ site[2] != site[1] &&
+ site[3] == site[2])
+ counts_[0]++;
+ else if (site[1] == site[2] &&
+ site[1] != site[0] &&
+ site[3] == site[0])
+ counts_[1]++;
+ else if (site[0] == site[2] &&
+ site[1] != site[0] &&
+ site[3] == site[1])
+ counts_[2]++;
+ } else {
+ nbIgnored++;
+ }
+ }
+ result_.setValue("f1100", counts_[0]);
+ result_.setValue("f0110", counts_[1]);
+ result_.setValue("f1010", counts_[2]);
+ result_.setValue("Ignored", nbIgnored);
+ } else {
+ result_.setValue("f1100", 0);
+ result_.setValue("f0110", 0);
+ result_.setValue("f1010", 0);
+ result_.setValue("Ignored", static_cast<double>(block.getNumberOfSites()));
+ }
+}
+
vector<string> SiteMafStatistics::getSupportedTags() const
{
vector<string> tags;
@@ -183,12 +304,12 @@ vector<string> SiteMafStatistics::getSupportedTags() const
void SiteMafStatistics::compute(const MafBlock& block)
{
- auto_ptr<SiteContainer> alignment(getSiteContainer(block));
+ auto_ptr<SiteContainer> alignment(getSiteContainer_(block));
unsigned int nbNg = 0;
unsigned int nbCo = 0;
unsigned int nbPi = 0;
if (alignment->getNumberOfSequences() > 0) {
- for (unsigned int i = 0; i < alignment->getNumberOfSites(); ++i) {
+ for (size_t i = 0; i < alignment->getNumberOfSites(); ++i) {
if (!SiteTools::hasGap(alignment->getSite(i)))
nbNg++;
if (SiteTools::isComplete(alignment->getSite(i)))
@@ -202,3 +323,155 @@ void SiteMafStatistics::compute(const MafBlock& block)
result_.setValue("NbParsimonyInformative", nbPi);
}
+vector<string> PolymorphismMafStatistics::getSupportedTags() const
+{
+ vector<string> tags;
+ tags.push_back("F");
+ tags.push_back("P");
+ tags.push_back("FP");
+ tags.push_back("PF");
+ tags.push_back("FF");
+ tags.push_back("X");
+ tags.push_back("FX");
+ tags.push_back("PX");
+ tags.push_back("XF");
+ tags.push_back("XP");
+ return tags;
+}
+
+vector<int> PolymorphismMafStatistics::getPatterns_(const SiteContainer& sites)
+{
+ vector<int> patterns(sites.getNumberOfSites());
+ for (size_t i = 0; i < sites.getNumberOfSites(); ++i) {
+ const Site& site = sites.getSite(i);
+ int s = -1; //Unresolved
+ if (SiteTools::isComplete(site)) {
+ if (SiteTools::isConstant(site)) {
+ s = site[0]; //The fixed state
+ } else {
+ s = -10; //Polymorphic.
+ }
+ }
+ patterns[i] = s;
+ }
+ return patterns;
+}
+
+void PolymorphismMafStatistics::compute(const MafBlock& block)
+{
+ vector<SiteContainer*> alignments(getSiteContainers_(block));
+ unsigned int nbF = 0;
+ unsigned int nbP = 0;
+ unsigned int nbFF = 0;
+ unsigned int nbFP = 0;
+ unsigned int nbPF = 0;
+ unsigned int nbX = 0;
+ unsigned int nbFX = 0;
+ unsigned int nbPX = 0;
+ unsigned int nbXF = 0;
+ unsigned int nbXP = 0;
+ //Get all patterns:
+ vector<int> patterns1(block.getNumberOfSites(), -1);
+ vector<int> patterns2(block.getNumberOfSites(), -1);
+ if (alignments[0]->getNumberOfSequences() > 0) {
+ patterns1 = getPatterns_(*alignments[0]);
+ }
+ if (alignments[1]->getNumberOfSequences() > 0) {
+ patterns2 = getPatterns_(*alignments[1]);
+ }
+ //Compare patterns:
+ for (size_t i = 0; i < block.getNumberOfSites(); ++i) {
+ int p1 = patterns1[i];
+ int p2 = patterns2[i];
+ switch (p1) {
+ case -1 :
+ switch (p2) {
+ case -1 :
+ nbX++;
+ break;
+ case -10 :
+ nbXP++;
+ break;
+ default :
+ nbXF++;
+ }
+ break;
+
+ case -10 :
+ switch (p2) {
+ case -1 :
+ nbPX++;
+ break;
+ case -10 :
+ nbP++;
+ break;
+ default :
+ nbPF++;
+ }
+ break;
+
+ default :
+ switch (p2) {
+ case -1 :
+ nbFX++;
+ break;
+ case -10 :
+ nbFP++;
+ break;
+ default :
+ if (p1 == p2)
+ nbF++;
+ else
+ nbFF++;
+ }
+ }
+ }
+
+ //Set results:
+ result_.setValue("F", nbF);
+ result_.setValue("P", nbP);
+ result_.setValue("FF", nbFF);
+ result_.setValue("FP", nbFP);
+ result_.setValue("PF", nbPF);
+ result_.setValue("X", nbX);
+ result_.setValue("FX", nbFX);
+ result_.setValue("PX", nbPX);
+ result_.setValue("XF", nbXF);
+ result_.setValue("XP", nbXP);
+}
+
+vector<string> SequenceDiversityMafStatistics::getSupportedTags() const
+{
+ vector<string> tags;
+ tags.push_back("NbSeggregating");
+ tags.push_back("WattersonTheta");
+ return tags;
+}
+
+void SequenceDiversityMafStatistics::compute(const MafBlock& block)
+{
+ auto_ptr<SiteContainer> alignment(getSiteContainer_(block));
+ unsigned int nbSeg = 0;
+ unsigned int nbTot = 0;
+ if (alignment->getNumberOfSequences() > 0) {
+ for (size_t i = 0; i < alignment->getNumberOfSites(); ++i) {
+ const Site& site = alignment->getSite(i);
+ if (SiteTools::isComplete(site)) {
+ nbTot++;
+ if (!SiteTools::isConstant(site))
+ nbSeg++;
+ }
+ }
+ }
+ double wt = 0;
+ if (nbSeg > 0) {
+ size_t n = alignment->getNumberOfSequences();
+ double hf = 0;
+ for (double i = 1; i < n; ++i)
+ hf += 1. / i;
+ wt = static_cast<double>(nbSeg) / (static_cast<double>(nbTot) * hf);
+ }
+ result_.setValue("NbSeggregating", nbSeg);
+ result_.setValue("WattersonTheta", wt);
+}
+
diff --git a/src/Bpp/Seq/Io/Maf/MafStatistics.h b/src/Bpp/Seq/Io/Maf/MafStatistics.h
index cbb52ca..3c89894 100644
--- a/src/Bpp/Seq/Io/Maf/MafStatistics.h
+++ b/src/Bpp/Seq/Io/Maf/MafStatistics.h
@@ -44,6 +44,8 @@ knowledge of the CeCILL license and that you accept its terms.
//From bpp-core:
#include <Bpp/Utils/MapTools.h>
+#include <Bpp/Numeric/VectorTools.h>
+#include <Bpp/Numeric/Number.h>
//From the STL:
#include <map>
@@ -54,35 +56,74 @@ namespace bpp {
/**
* @brief General interface for storing statistical results.
*
- * This interface will most likely be extended in the future...
- *
* @author Julien Dutheil
* @see MafStatistics
*/
class MafStatisticsResult
{
protected:
- mutable std::map<std::string, double> values_;
+ mutable std::map<std::string, BppNumberI*> values_;
public:
MafStatisticsResult(): values_() {}
virtual ~MafStatisticsResult() {}
+ MafStatisticsResult(const MafStatisticsResult& msr): values_()
+ {
+ for (std::map<std::string, BppNumberI*>::const_iterator it = msr.values_.begin();
+ it != msr.values_.end();
+ ++it) {
+ values_[it->first] = it->second->clone();
+ }
+ }
+
public:
- virtual double getValue(const std::string& tag) const throw (Exception) {
- std::map<std::string, double>::iterator it = values_.find(tag);
+ virtual const BppNumberI& getValue(const std::string& tag) const throw (Exception) {
+ std::map<std::string, BppNumberI*>::iterator it = values_.find(tag);
if (it != values_.end())
- return it->second;
+ return *it->second;
else
throw Exception("MafStatisticsResult::getValue(). No value found for tag: " + tag + ".");
}
+
+ /**
+ * @brief Associate a value to a certain tag. Any existing tag will be overwritten
+ *
+ * @param tag The name of the value to associate.
+ * @param value The value to associate to the tag.
+ */
+ virtual void setValue(const std::string& tag, double value) throw (Exception) {
+ if (values_[tag]) {
+ delete values_[tag];
+ }
+ values_[tag] = new BppDouble(value);
+ }
+
+ /**
+ * @brief Associate a value to a certain tag. Any existing tag will be overwritten
+ *
+ * @param tag The name of the value to associate.
+ * @param value The value to associate to the tag.
+ */
+ virtual void setValue(const std::string& tag, int value) throw (Exception) {
+ if (values_[tag]) {
+ delete values_[tag];
+ }
+ values_[tag] = new BppInteger(value);
+ }
+
/**
* @brief Associate a value to a certain tag. Any existing tag will be overwritten
*
* @param tag The name of the value to associate.
* @param value The value to associate to the tag.
*/
- virtual void setValue(const std::string& tag, double value) throw (Exception) { values_[tag] = value; }
+ virtual void setValue(const std::string& tag, unsigned int value) throw (Exception) {
+ if (values_[tag]) {
+ delete values_[tag];
+ }
+ values_[tag] = new BppUnsignedInteger(value);
+ }
/**
* @return A boolean saying whether a value is available for the given tag.
@@ -114,22 +155,45 @@ class SimpleMafStatisticsResult:
virtual ~SimpleMafStatisticsResult() {}
public:
- virtual double getValue() const { return values_[name_]; }
+ virtual const BppNumberI& getValue(const std::string& tag) const throw (Exception) { return SimpleMafStatisticsResult::getValue(tag); }
+
+ virtual const BppNumberI& getValue() const { return *values_[name_]; }
- /**
- * @brief Associate a value to a certain tag. Any existing tag will be overwritten
- *
- * @param tag The name of the value to associate.
- * @param value The value to associate to the tag.
- */
virtual void setValue(const std::string& tag, double value) throw (Exception) {
if (tag == name_)
- values_[tag] = value;
+ setValue(value);
else
throw Exception("SimpleMafStatisticsResult::setValue(). Unvalid tag name: " + tag + ".");
}
-
- virtual void setValue(double value) { values_[name_] = value; }
+
+ virtual void setValue(const std::string& tag, int value) throw (Exception) {
+ if (tag == name_)
+ setValue(value);
+ else
+ throw Exception("SimpleMafStatisticsResult::setValue(). Unvalid tag name: " + tag + ".");
+ }
+
+ virtual void setValue(const std::string& tag, unsigned int value) throw (Exception) {
+ if (tag == name_)
+ setValue(value);
+ else
+ throw Exception("SimpleMafStatisticsResult::setValue(). Unvalid tag name: " + tag + ".");
+ }
+
+ virtual void setValue(double value) {
+ if (values_[name_]) delete values_[name_];
+ values_[name_] = new BppDouble(value);
+ }
+
+ virtual void setValue(int value) {
+ if (values_[name_]) delete values_[name_];
+ values_[name_] = new BppInteger(value);
+ }
+
+ virtual void setValue(unsigned int value) {
+ if (values_[name_]) delete values_[name_];
+ values_[name_] = new BppUnsignedInteger(value);
+ }
};
@@ -342,7 +406,7 @@ class CharacterCountsMafStatistics:
/**
* @brief Partial implementation of MafStatistics for method working on a subset of species, in a site-wise manner.
*
- * This class stores a seleciton of species and create for each block the corresponding SiteContainer.
+ * This class stores a selection of species and create for each block the corresponding SiteContainer instance.
*/
class AbstractSpeciesSelectionMafStatistics:
public virtual MafStatistics
@@ -355,7 +419,27 @@ class AbstractSpeciesSelectionMafStatistics:
species_(species) {}
protected:
- SiteContainer* getSiteContainer(const MafBlock& block);
+ SiteContainer* getSiteContainer_(const MafBlock& block);
+
+};
+
+
+/**
+ * @brief Partial implementation of MafStatistics for method working on multiple distinct subsets of species, in a site-wise manner.
+ *
+ * This class stores two non-overlapping selections of species and create for each block the corresponding SiteContainer instances.
+ */
+class AbstractSpeciesMultipleSelectionMafStatistics:
+ public virtual MafStatistics
+{
+ private:
+ std::vector< std::vector<std::string> > species_;
+
+ public:
+ AbstractSpeciesMultipleSelectionMafStatistics(const std::vector< std::vector<std::string> >& species);
+
+ protected:
+ std::vector<SiteContainer*> getSiteContainers_(const MafBlock& block);
};
@@ -363,7 +447,8 @@ class AbstractSpeciesSelectionMafStatistics:
/**
* @brief Compute the Site Frequency Spectrum of a maf block.
*
- * The ancestral states are considered as unknown, so that 10000 and 11110 sites are treated equally.
+ * If no outgroup is provided, the ancestral states are considered as unknown
+ * and the unfolded spectrum is computed, so that 10000 and 11110 sites are treated equally.
*/
class SiteFrequencySpectrumMafStatistics:
public AbstractMafStatistics,
@@ -375,7 +460,8 @@ class SiteFrequencySpectrumMafStatistics:
std::vector<double> bounds_;
public:
- Categorizer(const std::vector<double>& bounds): bounds_(bounds) {
+ Categorizer(const std::vector<double>& bounds):
+ bounds_(bounds) {
std::sort(bounds_.begin(), bounds_.end());
}
@@ -398,14 +484,16 @@ class SiteFrequencySpectrumMafStatistics:
const Alphabet* alphabet_;
Categorizer categorizer_;
std::vector<unsigned int> counts_;
+ std::string outgroup_;
public:
- SiteFrequencySpectrumMafStatistics(const Alphabet* alphabet, const std::vector<double>& bounds, const std::vector<std::string>& ingroup):
+ SiteFrequencySpectrumMafStatistics(const Alphabet* alphabet, const std::vector<double>& bounds, const std::vector<std::string>& ingroup, const std::string outgroup = ""):
AbstractMafStatistics(),
AbstractSpeciesSelectionMafStatistics(ingroup),
alphabet_(alphabet),
categorizer_(bounds),
- counts_(bounds.size() - 1)
+ counts_(bounds.size() - 1),
+ outgroup_(outgroup)
{}
SiteFrequencySpectrumMafStatistics(const SiteFrequencySpectrumMafStatistics& stats):
@@ -413,7 +501,8 @@ class SiteFrequencySpectrumMafStatistics:
AbstractSpeciesSelectionMafStatistics(stats),
alphabet_(stats.alphabet_),
categorizer_(stats.categorizer_),
- counts_(stats.counts_)
+ counts_(stats.counts_),
+ outgroup_(stats.outgroup_)
{}
SiteFrequencySpectrumMafStatistics& operator=(const SiteFrequencySpectrumMafStatistics& stats) {
@@ -422,6 +511,7 @@ class SiteFrequencySpectrumMafStatistics:
alphabet_ = stats.alphabet_;
categorizer_ = stats.categorizer_;
counts_ = stats.counts_;
+ outgroup_ = stats.outgroup_;
return *this;
}
@@ -434,6 +524,66 @@ class SiteFrequencySpectrumMafStatistics:
std::vector<std::string> getSupportedTags() const;
};
+
+/**
+ * @brief Compute the frequency of site patterns for a quadruplet of species.
+ *
+ * Only parsimony informative sites are categorized.
+ * Species: A B C D
+ * P1 1 1 0 0
+ * P2 0 1 1 0
+ * P3 1 0 1 0
+ * Sites with more than two states are ignored, as well as sites containing gaps or unresolved characters.
+ */
+class FourSpeciesPatternCountsMafStatistics:
+ public AbstractMafStatistics,
+ public AbstractSpeciesSelectionMafStatistics
+{
+ private:
+ const Alphabet* alphabet_;
+ std::vector<unsigned int> counts_;
+
+ public:
+ FourSpeciesPatternCountsMafStatistics(
+ const Alphabet* alphabet,
+ const std::vector<std::string>& species):
+ AbstractMafStatistics(),
+ AbstractSpeciesSelectionMafStatistics(species),
+ alphabet_(alphabet),
+ counts_(6)
+ {
+ if (species.size() != 4)
+ throw Exception("FourSpeciesPatternCountsMafStatistics, constructor: 4 species should be provided.");
+ if (VectorTools::unique(species).size() != 4)
+ throw Exception("FourSpeciesPatternCountsMafStatistics, constructor: duplicated species name!");
+ }
+
+ FourSpeciesPatternCountsMafStatistics(const FourSpeciesPatternCountsMafStatistics& stats):
+ AbstractMafStatistics(),
+ AbstractSpeciesSelectionMafStatistics(stats),
+ alphabet_(stats.alphabet_),
+ counts_(stats.counts_)
+ {}
+
+ FourSpeciesPatternCountsMafStatistics& operator=(const FourSpeciesPatternCountsMafStatistics& stats) {
+ AbstractMafStatistics::operator=(stats);
+ AbstractSpeciesSelectionMafStatistics::operator=(stats);
+ alphabet_ = stats.alphabet_;
+ counts_ = stats.counts_;
+ return *this;
+ }
+
+ virtual ~FourSpeciesPatternCountsMafStatistics() {}
+
+ public:
+ std::string getShortName() const { return "FourSpeciesPatternCounts"; }
+ std::string getFullName() const { return "FourSpecies pattern counts."; }
+ void compute(const MafBlock& block);
+ std::vector<std::string> getSupportedTags() const;
+};
+
+
+
/**
* @brief Compute a few site statistics in a maf block.
*
@@ -461,6 +611,77 @@ class SiteMafStatistics:
std::vector<std::string> getSupportedTags() const;
};
+
+/**
+ * @brief Counts number of polymorphic / fixed sites in two populations.
+ *
+ * The two populations are defined as two distinct sets of species.
+ * The following counts are computed and returned:
+ * - P: number of sites polymorphic in both populations
+ * - F: number of sites fixed in both populations
+ * - FF: number of sites fixed in both populations, but with distinct states
+ * - PF / FP: number of sites polymorphic in one species and fixed in the other.
+ * - X: unresolved (because of gap or generic character)
+ * - FX / PX / XF / XP: unresolved in one population
+ */
+class PolymorphismMafStatistics:
+ public AbstractMafStatistics,
+ public AbstractSpeciesMultipleSelectionMafStatistics
+{
+ public:
+ PolymorphismMafStatistics(const std::vector< std::vector<std::string> >& species):
+ AbstractMafStatistics(),
+ AbstractSpeciesMultipleSelectionMafStatistics(species)
+ {
+ if (species.size() != 2)
+ throw Exception("PolymorphismStatistics: exactly two species selection should be provided.");
+ }
+
+ virtual ~PolymorphismMafStatistics() {}
+
+ public:
+ std::string getShortName() const { return "PolymorphismStatistics"; }
+ std::string getFullName() const { return "Polymorphism statistics."; }
+ void compute(const MafBlock& block);
+ std::vector<std::string> getSupportedTags() const;
+
+ private:
+ static std::vector<int> getPatterns_(const SiteContainer& sites);
+};
+
+
+
+/**
+ * @brief Provide estimates of sequence diversity.
+ *
+ * - Number of segregating sites
+ * - Watterson's theta (per site)
+ *
+ * Only fully resolved sites are analyzed (no gap, no generic character).
+ */
+class SequenceDiversityMafStatistics:
+ public AbstractMafStatistics,
+ public AbstractSpeciesSelectionMafStatistics
+{
+ public:
+ SequenceDiversityMafStatistics(const std::vector<std::string>& ingroup):
+ AbstractMafStatistics(),
+ AbstractSpeciesSelectionMafStatistics(ingroup)
+ {}
+
+ virtual ~SequenceDiversityMafStatistics() {}
+
+ public:
+ std::string getShortName() const { return "SequenceDiversityStatistics"; }
+ std::string getFullName() const { return "Sequence diversity statistics."; }
+ void compute(const MafBlock& block);
+ std::vector<std::string> getSupportedTags() const;
+
+ private:
+ static std::vector<int> getPatterns_(const SiteContainer& sites);
+};
+
+
} // end of namespace bpp
#endif //_MAFSTATISTICS_H_
diff --git a/src/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h b/src/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h
index 0bda4f5..7f37ffa 100644
--- a/src/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h
@@ -66,10 +66,15 @@ class OrphanSequenceFilterMafIterator:
/**
* @param iterator The input iterator.
* @param species The list of species names to be retained.
- * @param strict If true, then block that do not contain all of the specified species will be discarded.
+ * @param strict If true, then block that do not contain all of the specified species will be discarded.
+ * @param keep If true, then additional species sequences will be kept.
* @param rmDuplicates If true, block that contain more than one instance for at least one species will be discarded.
*/
- OrphanSequenceFilterMafIterator(MafIterator* iterator, const std::vector<std::string>& species, bool strict = false, bool keep = false, bool rmDuplicates = false) :
+ OrphanSequenceFilterMafIterator(MafIterator* iterator,
+ const std::vector<std::string>& species,
+ bool strict = false,
+ bool keep = false,
+ bool rmDuplicates = false) :
AbstractFilterMafIterator(iterator),
species_(species),
strict_(strict),
diff --git a/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp b/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
index 94e086d..a8c4228 100644
--- a/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
@@ -73,9 +73,12 @@ void OutputAlignmentMafIterator::writeBlock(std::ostream& out, const MafBlock& b
SequenceContainerTools::convertContainer<AlignedSequenceContainer, AlignedSequenceContainer, BasicSequence>(block.getAlignment(), aln);
//Format sequence names:
vector<string> names(aln.getNumberOfSequences());
- for (unsigned int i = 0; i < aln.getNumberOfSequences(); ++i) {
+ for (size_t i = 0; i < aln.getNumberOfSequences(); ++i) {
const MafSequence& mafseq = block.getSequence(i);
- names[i] = mafseq.getSpecies() + "-" + mafseq.getChromosome() + "(" + mafseq.getStrand() + ")/" + TextTools::toString(mafseq.start() + 1) + "-" + TextTools::toString(mafseq.stop() + 1);
+ if (mafseq.hasCoordinates())
+ names[i] = mafseq.getSpecies() + "-" + mafseq.getChromosome() + "(" + mafseq.getStrand() + ")/" + TextTools::toString(mafseq.start() + 1) + "-" + TextTools::toString(mafseq.stop() + 1);
+ else
+ names[i] = mafseq.getSpecies();
}
aln.setSequencesNames(names);
writer_->writeAlignment(out, aln);
diff --git a/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h b/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
index d1c2d4e..2954665 100644
--- a/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
@@ -79,7 +79,7 @@ class OutputAlignmentMafIterator:
* @param mask Tell if sequences should be printed masked (if applicable).
*/
OutputAlignmentMafIterator(MafIterator* iterator, std::ostream* out, OAlignment* writer, bool mask = true) :
- AbstractFilterMafIterator(iterator), output_(out), file_(), mask_(mask), writer_(writer), currentBlockIndex_(1)
+ AbstractFilterMafIterator(iterator), output_(out), file_(), mask_(mask), writer_(writer), currentBlockIndex_(0)
{
if (!writer)
throw Exception("OutputAlignmentMafIterator (constructor 1): sequence writer should not be a NULL pointer!");
@@ -98,7 +98,7 @@ class OutputAlignmentMafIterator:
* @param mask Tell if sequences should be printed masked (if applicable).
*/
OutputAlignmentMafIterator(MafIterator* iterator, const std::string& file, OAlignment* writer, bool mask = true) :
- AbstractFilterMafIterator(iterator), output_(0), file_(file), mask_(mask), writer_(writer), currentBlockIndex_(1)
+ AbstractFilterMafIterator(iterator), output_(0), file_(file), mask_(mask), writer_(writer), currentBlockIndex_(0)
{
if (!writer)
throw Exception("OutputAlignmentMafIterator (constructor 2): sequence writer should not be a NULL pointer!");
diff --git a/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp b/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp
index df487c9..9aa27ea 100644
--- a/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp
@@ -80,9 +80,9 @@ MafBlock* SequenceStatisticsMafIterator::analyseCurrentBlock_() throw (Exception
tags = statistics_[i]->getSupportedTags();
for (size_t j = 0; j < tags.size(); ++j) {
if (result.hasValue(tags[j])) {
- results_[k] = result.getValue(tags[j]);
+ results_[k] = result.getValue(tags[j]).clone();
} else {
- results_[k] = NumConstants::NaN();
+ results_[k] = 0;
}
k++;
}
diff --git a/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h b/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h
index e60ffba..0a23c29 100644
--- a/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h
@@ -67,13 +67,13 @@ class SequenceStatisticsMafIterator:
{
private:
std::vector<MafStatistics*> statistics_;
- std::vector<double> results_;
+ std::vector<const BppNumberI*> results_;
std::vector<std::string> names_;
public:
/**
* @param iterator The input iterator.
- * @param statistics A vector of pointers toward MafStatistics, tobe computed simultaneously for each maf block.
+ * @param statistics A vector of pointers toward MafStatistics, to be computed simultaneously for each maf block.
*/
SequenceStatisticsMafIterator(MafIterator* iterator, const std::vector<MafStatistics*> statistics);
@@ -94,7 +94,7 @@ class SequenceStatisticsMafIterator:
}
public:
- const std::vector<double>& getResults() const { return results_; }
+ const std::vector<const BppNumberI*>& getResults() const { return results_; }
const std::vector<std::string>& getResultsColumnNames() const { return names_; }
private:
diff --git a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp b/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
index 6a5cd6d..54f8397 100644
--- a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
@@ -44,6 +44,7 @@ knowledge of the CeCILL license and that you accept its terms.
#include <Bpp/Seq/SequenceWithQuality.h>
#include <Bpp/Seq/Container/VectorSiteContainer.h>
#include <Bpp/Seq/SiteTools.h>
+#include <Bpp/Seq/SequenceWalker.h>
using namespace bpp;
@@ -54,7 +55,7 @@ using namespace bpp;
using namespace std;
-void VcfOutputMafIterator::writeHeader(std::ostream& out) const
+void VcfOutputMafIterator::writeHeader_(std::ostream& out) const
{
time_t t = time(0); // get current time
struct tm* ct = localtime(&t);
@@ -63,22 +64,33 @@ void VcfOutputMafIterator::writeHeader(std::ostream& out) const
out << "##source=Bio++" << endl;
out << "##FILTER=<ID=gap,Description=\"At least one sequence contains a gap\">" << endl;
out << "##FILTER=<ID=unk,Description=\"At least one sequence contains an unresolved character\">" << endl;
+ if (genotypes_.size() > 0)
+ out << "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">" << endl;
//There are more options in the header that we may want to support...
//Now write the header line:
- out << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << endl;
+ out << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO";
+ if (genotypes_.size() > 0) {
+ out << "\tFORMAT";
+ for (size_t i = 0; i < genotypes_.size(); ++i)
+ out << "\t" << genotypes_[i];
+ }
+ out << endl;
}
-void VcfOutputMafIterator::writeBlock(std::ostream& out, const MafBlock& block) const
+void VcfOutputMafIterator::writeBlock_(std::ostream& out, const MafBlock& block) const
{
const MafSequence& refSeq = block.getSequenceForSpecies(refSpecies_);
string chr = refSeq.getChromosome();
+ SequenceWalker walker(refSeq);
size_t offset = refSeq.start();
int gap = refSeq.getAlphabet()->getGapCharacterCode();
- string chars = "";
+ map<int, string> chars;
for (int i = 0; i < static_cast<int>(AlphabetTools::DNA_ALPHABET.getNumberOfTypes()); ++i)
- chars += AlphabetTools::DNA_ALPHABET.intToChar(i);
+ chars[i] = AlphabetTools::DNA_ALPHABET.intToChar(i);
VectorSiteContainer sites(block.getAlignment());
+ //Where to store genotype information, if any:
+ vector<int> gt(genotypes_.size());
//Now we look all sites for SNPs:
for (size_t i = 0; i < sites.getNumberOfSites(); i++) {
if (refSeq[i] == gap)
@@ -100,6 +112,9 @@ void VcfOutputMafIterator::writeBlock(std::ostream& out, const MafBlock& block)
int ref = refSeq[i];
string alt = "";
string ac = "";
+
+ map<int, int> snps;
+ int c = 0;
for (int x = 0; x < 4; ++x) {
if (x != ref) {
size_t f = counts[x];
@@ -108,13 +123,35 @@ void VcfOutputMafIterator::writeBlock(std::ostream& out, const MafBlock& block)
alt += ",";
ac += ",";
}
- alt += TextTools::toString<char>(chars[x]);
+ alt += chars[x];
ac += TextTools::toString(f);
+ snps[x] = ++c;
}
+ } else {
+ snps[x] = 0;
}
}
if (ac != "") {
- out << chr << "\t" << (offset + i + 1) << "\t.\t" << chars[refSeq[i]] << "\t" << alt << "\t.\t" << filter << "\tAC=" << ac << endl;
+ out << chr << "\t" << (offset + walker.getSequencePosition(i) + 1) << "\t.\t" << chars[refSeq[i]] << "\t" << alt << "\t.\t" << filter << "\tAC=" << ac;
+ //Write genotpyes:
+ if (genotypes_.size() > 0) {
+ out << "\tGT";
+ for (size_t g = 0; g < genotypes_.size(); ++g) {
+ vector<const MafSequence*> sequences = block.getSequencesForSpecies(genotypes_[g]);
+ if (sequences.size() == 0)
+ out << "\t.";
+ else if (sequences.size() > 1)
+ throw Exception("VcfOutputMafIterator::writeBlock(). Duplicated sequence for species '" + genotypes_[g] + ",.");
+ else {
+ int state = (*sequences[0])[i];
+ if (AlphabetTools::DNA_ALPHABET.isGap(state) || AlphabetTools::DNA_ALPHABET.isUnresolved(state))
+ out << "\t.";
+ else
+ out << "\t" << snps[state];
+ }
+ }
+ }
+ out << endl;
}
}
}
diff --git a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h b/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
index 7f34292..572ebbe 100644
--- a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
@@ -60,26 +60,37 @@ class VcfOutputMafIterator:
private:
std::ostream* output_;
std::string refSpecies_;
+ std::vector<std::string> genotypes_;
public:
- VcfOutputMafIterator(MafIterator* iterator, std::ostream* out, const std::string& reference) :
- AbstractFilterMafIterator(iterator), output_(out), refSpecies_(reference)
+ /**
+ * @brief Build a new VcfOutputMafIterator object.
+ *
+ * @param iterator The input iterator.
+ * @param out The output stream where to write the VCF file.
+ * @param reference The species to use as a reference.
+ * @param genotypes A list of species for which genotype information should be written in the VCF file. There will be one extra column per genotype, +1 format column.
+ */
+ VcfOutputMafIterator(MafIterator* iterator, std::ostream* out, const std::string& reference, const std::vector<std::string>& genotypes) :
+ AbstractFilterMafIterator(iterator), output_(out), refSpecies_(reference), genotypes_(genotypes)
{
if (output_)
- writeHeader(*output_);
+ writeHeader_(*output_);
}
private:
VcfOutputMafIterator(const VcfOutputMafIterator& iterator) :
AbstractFilterMafIterator(0),
output_(iterator.output_),
- refSpecies_(iterator.refSpecies_)
+ refSpecies_(iterator.refSpecies_),
+ genotypes_(iterator.genotypes_)
{}
VcfOutputMafIterator& operator=(const VcfOutputMafIterator& iterator)
{
output_ = iterator.output_;
refSpecies_ = iterator.refSpecies_;
+ genotypes_ = iterator.genotypes_;
return *this;
}
@@ -88,13 +99,13 @@ class VcfOutputMafIterator:
MafBlock* analyseCurrentBlock_() throw (Exception) {
currentBlock_ = iterator_->nextBlock();
if (output_ && currentBlock_)
- writeBlock(*output_, *currentBlock_);
+ writeBlock_(*output_, *currentBlock_);
return currentBlock_;
}
private:
- void writeHeader(std::ostream& out) const;
- void writeBlock(std::ostream& out, const MafBlock& block) const;
+ void writeHeader_(std::ostream& out) const;
+ void writeBlock_(std::ostream& out, const MafBlock& block) const;
};
} // end of namespace bpp.
diff --git a/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h b/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
index b904ce8..bce9a87 100644
--- a/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
@@ -73,7 +73,7 @@ class WindowSplitMafIterator:
{
if (splitOption != RAGGED_LEFT && splitOption != RAGGED_RIGHT
&& splitOption != CENTER && splitOption != ADJUST)
- throw Exception("WindowSplitMafIterator: unvalid split option: " + splitOption);
+ throw Exception("WindowSplitMafIterator: unvalid split option: " + TextTools::toString(splitOption));
}
private:
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index a1ed253..084c00d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -24,6 +24,7 @@ SET(CPP_FILES
Bpp/Seq/Io/Maf/OutputMafIterator.cpp
Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
+ Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp
Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp
Bpp/Seq/Io/Maf/MafSequence.cpp
@@ -59,6 +60,7 @@ SET(H_FILES
Bpp/Seq/Io/Maf/OutputMafIterator.h
Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
+ Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h
Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
Bpp/Seq/Io/Maf/MafStatistics.h
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