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Viewing changes to src/Bpp/Seq/Io/Stockholm.cpp

Committer: Package Import Robot
Author(s): Julien Dutheil
Date: 2013-03-05 14:31:00 UTC
mfrom: (1.1.2)
Revision ID: package-import@ubuntu.com-20130305143100-2jox395vr1ghao46

Tags: 2.1.0-1

* 'omics' tools now in bpp-seq-omics
* Extended BppO support
* StateProperties renamed to AlphabetIndex

files added:
.pc

.pc/.quilt_patches

.pc/.quilt_series

.pc/.version

.pc/applied-patches

bpp-seq.spec

debian/postinst

debian/postrm

debian/prerm

src/Bpp/Seq/AlphabetIndex

src/Bpp/Seq/AlphabetIndex/AAChargeIndex.h

src/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h

src/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h

src/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h

src/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h

src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp

src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h

src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp

src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h

src/Bpp/Seq/AlphabetIndex/AAMassIndex.h

src/Bpp/Seq/AlphabetIndex/AASEA1030Index.h

src/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h

src/Bpp/Seq/AlphabetIndex/AASEASup30Index.h

src/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h

src/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h

src/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h

src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h

src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp

src/Bpp/Seq/AlphabetIndex/BLOSUM50.h

src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp

src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h

src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp

src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h

src/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h

src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h

src/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h

src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp

src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h

src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h

src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp

src/Bpp/Seq/AlphabetIndex/SimpleScore.h

src/Bpp/Seq/AlphabetIndex/__BLOSUM50MatrixCode

src/Bpp/Seq/AlphabetIndex/__GranthamMatrixCode

src/Bpp/Seq/AlphabetIndex/__MiyataMatrixCode

src/Bpp/Seq/Container/SequenceContainerIterator.cpp

src/Bpp/Seq/Container/SequenceContainerIterator.h

src/Bpp/Seq/Container/SiteContainerIterator.cpp

src/Bpp/Seq/Container/SiteContainerIterator.h

src/Bpp/Seq/Io/AbstractIAlignment.h

src/Bpp/Seq/Io/AbstractOAlignment.h

src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp

src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h

src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp

src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h

src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp

src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h

src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp

src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h

src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp

src/Bpp/Seq/Io/BppOSequenceReaderFormat.h

src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp

src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h

src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp

src/Bpp/Seq/Io/BppOSequenceWriterFormat.h

src/Bpp/Seq/Io/StreamSequenceIterator.cpp

src/Bpp/Seq/Io/StreamSequenceIterator.h

src/Bpp/Seq/SequenceIterator.h

src/Bpp/Seq/SiteIterator.h

files removed:
Seq.spec

src/Bpp/Seq.all

src/Bpp/Seq/Alphabet.all

src/Bpp/Seq/App.all

src/Bpp/Seq/Container.all

src/Bpp/Seq/Container/SiteIterator.cpp

src/Bpp/Seq/Container/SiteIterator.h

src/Bpp/Seq/Feature

src/Bpp/Seq/Feature/Gff

src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp

src/Bpp/Seq/Feature/Gff/GffFeatureReader.h

src/Bpp/Seq/Feature/SequenceFeature.cpp

src/Bpp/Seq/Feature/SequenceFeature.h

src/Bpp/Seq/GeneticCode.all

src/Bpp/Seq/Io.all

src/Bpp/Seq/Io/AbstractISequence2.h

src/Bpp/Seq/Io/Fastq.cpp

src/Bpp/Seq/Io/Fastq.h

src/Bpp/Seq/Io/MafAlignmentParser.cpp

src/Bpp/Seq/Io/MafAlignmentParser.h

src/Bpp/Seq/Io/MafIterator.cpp

src/Bpp/Seq/Io/MafIterator.h

src/Bpp/Seq/StateProperties

src/Bpp/Seq/StateProperties.all

src/Bpp/Seq/StateProperties/AAChargeIndex.h

src/Bpp/Seq/StateProperties/AAChenGuHuangHydrophobicityIndex.h

src/Bpp/Seq/StateProperties/AAChouFasmanAHelixIndex.h

src/Bpp/Seq/StateProperties/AAChouFasmanBSheetIndex.h

src/Bpp/Seq/StateProperties/AAChouFasmanTurnIndex.h

src/Bpp/Seq/StateProperties/AAIndex1Entry.cpp

src/Bpp/Seq/StateProperties/AAIndex1Entry.h

src/Bpp/Seq/StateProperties/AAIndex2Entry.cpp

src/Bpp/Seq/StateProperties/AAIndex2Entry.h

src/Bpp/Seq/StateProperties/AAMassIndex.h

src/Bpp/Seq/StateProperties/AASEA1030Index.h

src/Bpp/Seq/StateProperties/AASEAInf10Index.h

src/Bpp/Seq/StateProperties/AASEASup30Index.h

src/Bpp/Seq/StateProperties/AASurfaceIndex.h

src/Bpp/Seq/StateProperties/AAVolumeIndex.h

src/Bpp/Seq/StateProperties/AlphabetIndex1.h

src/Bpp/Seq/StateProperties/AlphabetIndex2.h

src/Bpp/Seq/StateProperties/BLOSUM50.cpp

src/Bpp/Seq/StateProperties/BLOSUM50.h

src/Bpp/Seq/StateProperties/ChenGuHuangAAHydrophobicityIndex.h

src/Bpp/Seq/StateProperties/DefaultNucleotideScore.cpp

src/Bpp/Seq/StateProperties/DefaultNucleotideScore.h

src/Bpp/Seq/StateProperties/GranthamAAChemicalDistance.cpp

src/Bpp/Seq/StateProperties/GranthamAAChemicalDistance.h

src/Bpp/Seq/StateProperties/GranthamAAPolarityIndex.h

src/Bpp/Seq/StateProperties/GranthamAAVolumeIndex.h

src/Bpp/Seq/StateProperties/KleinAANetChargeIndex.h

src/Bpp/Seq/StateProperties/MiyataAAChemicalDistance.cpp

src/Bpp/Seq/StateProperties/MiyataAAChemicalDistance.h

src/Bpp/Seq/StateProperties/SimpleIndexDistance.h

src/Bpp/Seq/StateProperties/SimpleScore.cpp

src/Bpp/Seq/StateProperties/SimpleScore.h

src/Bpp/Seq/StateProperties/__BLOSUM50MatrixCode

src/Bpp/Seq/StateProperties/__GranthamMatrixCode

src/Bpp/Seq/StateProperties/__MiyataMatrixCode

test/test_fastq.cpp

test/test_gff.cpp

files modified:
CMakeLists.txt

ChangeLog

Doxyfile

debian/changelog

debian/control

debian/copyright

debian/rules

src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp

src/Bpp/Seq/Alphabet/AbstractAlphabet.h

src/Bpp/Seq/Alphabet/Alphabet.h

src/Bpp/Seq/Alphabet/AlphabetState.h

src/Bpp/Seq/Alphabet/AlphabetTools.cpp

src/Bpp/Seq/Alphabet/AlphabetTools.h

src/Bpp/Seq/Alphabet/CodonAlphabet.cpp

src/Bpp/Seq/Alphabet/DNA.cpp

src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp

src/Bpp/Seq/Alphabet/DefaultAlphabet.h

src/Bpp/Seq/Alphabet/LetterAlphabet.h

src/Bpp/Seq/Alphabet/NucleicAlphabet.h

src/Bpp/Seq/Alphabet/NucleicAlphabetState.h

src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp

src/Bpp/Seq/Alphabet/ProteicAlphabet.h

src/Bpp/Seq/Alphabet/RNA.cpp

src/Bpp/Seq/Alphabet/RNY.cpp

src/Bpp/Seq/Alphabet/RNY.h

src/Bpp/Seq/Alphabet/WordAlphabet.cpp

src/Bpp/Seq/Alphabet/WordAlphabet.h

src/Bpp/Seq/App/SequenceApplicationTools.cpp

src/Bpp/Seq/App/SequenceApplicationTools.h

src/Bpp/Seq/CodonSiteTools.cpp

src/Bpp/Seq/CodonSiteTools.h

src/Bpp/Seq/Container/AbstractSequenceContainer.cpp

src/Bpp/Seq/Container/AbstractSequenceContainer.h

src/Bpp/Seq/Container/AlignedSequenceContainer.cpp

src/Bpp/Seq/Container/AlignedSequenceContainer.h

src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp

src/Bpp/Seq/Container/CompressedVectorSiteContainer.h

src/Bpp/Seq/Container/MapSequenceContainer.cpp

src/Bpp/Seq/Container/MapSequenceContainer.h

src/Bpp/Seq/Container/OrderedSequenceContainer.h

src/Bpp/Seq/Container/SequenceContainer.h

src/Bpp/Seq/Container/SequenceContainerTools.cpp

src/Bpp/Seq/Container/SequenceContainerTools.h

src/Bpp/Seq/Container/SiteContainer.h

src/Bpp/Seq/Container/SiteContainerTools.cpp

src/Bpp/Seq/Container/SiteContainerTools.h

src/Bpp/Seq/Container/VectorSequenceContainer.cpp

src/Bpp/Seq/Container/VectorSequenceContainer.h

src/Bpp/Seq/Container/VectorSiteContainer.cpp

src/Bpp/Seq/Container/VectorSiteContainer.h

src/Bpp/Seq/DNAToRNA.cpp

src/Bpp/Seq/DistanceMatrix.cpp

src/Bpp/Seq/DistanceMatrix.h

src/Bpp/Seq/GeneticCode/GeneticCode.cpp

src/Bpp/Seq/GeneticCode/GeneticCode.h

src/Bpp/Seq/Io/AbstractISequence.h

src/Bpp/Seq/Io/AbstractOSequence.h

src/Bpp/Seq/Io/Clustal.cpp

src/Bpp/Seq/Io/Clustal.h

src/Bpp/Seq/Io/Dcse.cpp

src/Bpp/Seq/Io/Dcse.h

src/Bpp/Seq/Io/Fasta.cpp

src/Bpp/Seq/Io/Fasta.h

src/Bpp/Seq/Io/GenBank.cpp

src/Bpp/Seq/Io/GenBank.h

src/Bpp/Seq/Io/ISequence.h

src/Bpp/Seq/Io/ISequenceStream.h

src/Bpp/Seq/Io/IoSequenceFactory.cpp

src/Bpp/Seq/Io/IoSequenceFactory.h

src/Bpp/Seq/Io/Mase.cpp

src/Bpp/Seq/Io/Mase.h

src/Bpp/Seq/Io/MaseTools.cpp

src/Bpp/Seq/Io/MaseTools.h

src/Bpp/Seq/Io/NexusIoSequence.cpp

src/Bpp/Seq/Io/NexusIoSequence.h

src/Bpp/Seq/Io/OSequence.h

src/Bpp/Seq/Io/Phylip.cpp

src/Bpp/Seq/Io/Phylip.h

src/Bpp/Seq/Io/SequenceFileIndex.h

src/Bpp/Seq/Io/Stockholm.cpp

src/Bpp/Seq/Io/Stockholm.h

src/Bpp/Seq/NucleicAcidsReplication.cpp

src/Bpp/Seq/NucleicAcidsReplication.h

src/Bpp/Seq/Sequence.cpp

src/Bpp/Seq/Sequence.h

src/Bpp/Seq/SequenceExceptions.cpp

src/Bpp/Seq/SequenceExceptions.h

src/Bpp/Seq/SequencePositionIterators.cpp

src/Bpp/Seq/SequencePositionIterators.h

src/Bpp/Seq/SequenceTools.cpp

src/Bpp/Seq/SequenceTools.h

src/Bpp/Seq/SequenceWalker.cpp

src/Bpp/Seq/SequenceWalker.h

src/Bpp/Seq/SequenceWithAnnotation.cpp

src/Bpp/Seq/SequenceWithAnnotation.h

src/Bpp/Seq/SequenceWithAnnotationTools.h

src/Bpp/Seq/SequenceWithQuality.cpp

src/Bpp/Seq/SequenceWithQuality.h

src/Bpp/Seq/SequenceWithQualityTools.cpp

src/Bpp/Seq/Site.cpp

src/Bpp/Seq/Site.h

src/Bpp/Seq/SiteExceptions.cpp

src/Bpp/Seq/SiteExceptions.h

src/Bpp/Seq/SiteTools.cpp

src/Bpp/Seq/SiteTools.h

src/Bpp/Seq/StringSequenceTools.cpp

src/Bpp/Seq/StringSequenceTools.h

src/Bpp/Seq/SymbolList.cpp

src/Bpp/Seq/SymbolList.h

src/Bpp/Seq/SymbolListTools.cpp

src/Bpp/Seq/SymbolListTools.h

src/CMakeLists.txt

test/CMakeLists.txt

test/test_alignment_scores.cpp

test/test_alphabets.cpp

test/test_bowker.cpp

test/test_containers.cpp

test/test_io.cpp

test/test_sequences.cpp

test/test_walker.cpp

Show diffs side-by-side

added added

removed removed

src/Bpp/Seq/Io/Stockholm.cpp

/******************************************************************************/

void Stockholm::write(ostream& output, const SiteContainer& sc) const throw (Exception)

void Stockholm::writeAlignment(ostream& output, const SiteContainer& sc) const throw (Exception)

{

if (!output)

throw IOException("Stockholm::write: can't write to ostream output");

throw IOException("Stockholm::writeAlignment: can't write to ostream output");

output << "# STOCKHOLM 1.0" << endl;

// Loop for all general comments

for (unsigned int i = 0; i < sc.getGeneralComments().size(); ++i)

for (size_t i = 0; i < sc.getGeneralComments().size(); ++i)

{

output << "#=GF CC " << sc.getGeneralComments()[i] << endl;

}

// Main loop : for all sequences in vector container

vector<string> names = sc.getSequencesNames();

unsigned int maxSize = 0;

size_t maxSize = 0;

for(unsigned int i = 0; i < names.size(); ++i)

{

names[i] = TextTools::removeWhiteSpaces(names[i]);

if (names[i].size() > maxSize) maxSize = names[i].size();

}

if (maxSize > 255) maxSize = 255;

for (unsigned int i = 0; i < sc.getNumberOfSequences(); ++i)

for (size_t i = 0; i < sc.getNumberOfSequences(); ++i)

{

output << TextTools::resizeRight(names[i], maxSize) << " " << sc.getSequence(i).toString() << endl;

}

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