File List

Here is a list of all files with brief descriptions:

[detail level 1234]

▼ Bpp
▼ Seq
► Alphabet
AbstractAlphabet.cpp
AbstractAlphabet.h
AllelicAlphabet.cpp
AllelicAlphabet.h
Alphabet.h
AlphabetExceptions.cpp
AlphabetExceptions.h
AlphabetNumericState.h
AlphabetState.h
AlphabetTools.cpp
AlphabetTools.h
BinaryAlphabet.cpp
BinaryAlphabet.h
CaseMaskedAlphabet.cpp
CaseMaskedAlphabet.h
CodonAlphabet.cpp
CodonAlphabet.h
DefaultAlphabet.cpp
DefaultAlphabet.h
DNA.cpp
DNA.h
IntegerAlphabet.cpp
IntegerAlphabet.h
LetterAlphabet.cpp
LetterAlphabet.h
LexicalAlphabet.cpp
LexicalAlphabet.h
NucleicAlphabet.h
NucleicAlphabetState.h
NumericAlphabet.cpp
NumericAlphabet.h
ProteicAlphabet.cpp
ProteicAlphabet.h
ProteicAlphabetState.h
RNA.cpp
RNA.h
RNY.cpp
RNY.h
WordAlphabet.cpp
WordAlphabet.h
► AlphabetIndex
AAChargeIndex.h
AAChenGuHuangHydrophobicityIndex.h
AAChouFasmanAHelixIndex.h
AAChouFasmanBSheetIndex.h
AAChouFasmanTurnIndex.h
AAIndex1Entry.cpp
AAIndex1Entry.h
AAIndex2Entry.cpp
AAIndex2Entry.h
AAMassIndex.h
AASEA1030Index.h
AASEAInf10Index.h
AASEASup30Index.h
AASurfaceIndex.h
AAVolumeIndex.h
AlphabetIndex1.h
AlphabetIndex2.h
BLOSUM50.cpp
BLOSUM50.h
CodonFromProteicAlphabetIndex1.h
CodonFromProteicAlphabetIndex2.h
DefaultNucleotideScore.cpp
DefaultNucleotideScore.h
GranthamAAChemicalDistance.cpp
GranthamAAChemicalDistance.h
GranthamAAPolarityIndex.h
GranthamAAVolumeIndex.h
KD_AAHydropathyIndex.h
KleinAANetChargeIndex.h
MiyataAAChemicalDistance.cpp
MiyataAAChemicalDistance.h
SimpleIndexDistance.h
SimpleScore.cpp
SimpleScore.h
UserAlphabetIndex1.h
UserAlphabetIndex2.h
► App
BppSequenceApplication.cpp
BppSequenceApplication.h
SequenceApplicationTools.cpp
SequenceApplicationTools.h
► Container
AbstractSequenceContainer.h
AlignedSequenceContainer.h
AlignmentData.h
CompressedVectorSiteContainer.cpp
CompressedVectorSiteContainer.h
MappedNamedContainer.h
NamedContainer.h
PositionedContainer.h
PositionedNamedContainer.h
SequenceContainer.h
SequenceContainerExceptions.h
SequenceContainerIterator.h
SequenceContainerTools.h
SequenceData.h
SequencedValuesContainer.h
SiteContainer.h
SiteContainerExceptions.cpp
SiteContainerExceptions.h
SiteContainerIterator.h
SiteContainerTools.cpp
SiteContainerTools.h
VectorMappedContainer.h
VectorPositionedContainer.h
VectorSequenceContainer.h
VectorSiteContainer.h
► GeneticCode
AscidianMitochondrialGeneticCode.cpp
AscidianMitochondrialGeneticCode.h
CiliateNuclearGeneticCode.cpp
CiliateNuclearGeneticCode.h
EchinodermMitochondrialGeneticCode.cpp
EchinodermMitochondrialGeneticCode.h
GeneticCode.cpp
GeneticCode.h
InvertebrateMitochondrialGeneticCode.cpp
InvertebrateMitochondrialGeneticCode.h
MoldMitochondrialGeneticCode.cpp
MoldMitochondrialGeneticCode.h
StandardGeneticCode.cpp
StandardGeneticCode.h
VertebrateMitochondrialGeneticCode.cpp
VertebrateMitochondrialGeneticCode.h
YeastMitochondrialGeneticCode.cpp
YeastMitochondrialGeneticCode.h
► Io
AbstractIAlignment.h
AbstractISequence.h
AbstractOAlignment.h
AbstractOSequence.h
BppOAlignmentReaderFormat.cpp
BppOAlignmentReaderFormat.h
BppOAlignmentWriterFormat.cpp
BppOAlignmentWriterFormat.h
BppOAlphabetIndex1Format.cpp
BppOAlphabetIndex1Format.h
BppOAlphabetIndex2Format.cpp
BppOAlphabetIndex2Format.h
BppOSequenceReaderFormat.cpp
BppOSequenceReaderFormat.h
BppOSequenceStreamReaderFormat.cpp
BppOSequenceStreamReaderFormat.h
BppOSequenceWriterFormat.cpp
BppOSequenceWriterFormat.h
Clustal.cpp
Clustal.h
Dcse.cpp
Dcse.h
Fasta.cpp
Fasta.h
GenBank.cpp
GenBank.h
IoDistanceMatrix.h
IoDistanceMatrixFactory.cpp
IoDistanceMatrixFactory.h
IoSequence.h
IoSequenceFactory.cpp
IoSequenceFactory.h
IoSequenceStream.h
ISequence.h
ISequenceStream.h
Mase.cpp
Mase.h
MaseTools.cpp
MaseTools.h
NexusIoSequence.cpp
NexusIoSequence.h
NexusTools.cpp
NexusTools.h
OSequence.h
OSequenceStream.h
Pasta.cpp
Pasta.h
PhredPhd.cpp
PhredPhd.h
PhredPoly.cpp
PhredPoly.h
Phylip.cpp
Phylip.h
PhylipDistanceMatrixFormat.cpp
PhylipDistanceMatrixFormat.h
SequenceFileIndex.h
Stockholm.cpp
Stockholm.h
StreamSequenceIterator.h
CodonSiteTools.cpp
CodonSiteTools.h
Commentable.h
CoreSequence.h
CoreSite.h
CoreSymbolList.h
DistanceMatrix.cpp
DistanceMatrix.h
DNAToRNA.cpp
DNAToRNA.h
IntSymbolList.cpp
IntSymbolList.h
NucleicAcidsReplication.cpp
NucleicAcidsReplication.h
ProbabilisticSequence.cpp
ProbabilisticSequence.h
ProbabilisticSite.h
ProbabilisticSymbolList.cpp
ProbabilisticSymbolList.h
Sequence.cpp
Sequence.h
SequenceExceptions.h
SequenceIterator.h
SequencePositionIterators.cpp
SequencePositionIterators.h
SequenceTools.cpp
SequenceTools.h
SequenceWalker.cpp
SequenceWalker.h
SequenceWithAnnotation.cpp
SequenceWithAnnotation.h
SequenceWithAnnotationTools.cpp
SequenceWithAnnotationTools.h
SequenceWithQuality.cpp
SequenceWithQuality.h
SequenceWithQualityTools.cpp
SequenceWithQualityTools.h
Site.h
SiteExceptions.h
SiteIterator.h
SiteTools.h
StringSequenceTools.cpp
StringSequenceTools.h
SymbolList.h
SymbolListTools.cpp
SymbolListTools.h
Transliterator.cpp
Transliterator.h