Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 123456]

bpp::Alphabet	The Alphabet interface
bpp::AbstractAlphabet	A partial implementation of the Alphabet interface
bpp::BinaryAlphabet	The BinaryAlphabet class, letters are 0 and 1
bpp::LetterAlphabet	Specialized partial implementation of Alphabet using single letters
bpp::CaseMaskedAlphabet	Case-sensitive letter alphabet
bpp::DefaultAlphabet	The DefaultAlphabet class
bpp::NucleicAlphabet	The abstract base class for nucleic alphabets
bpp::DNA	This alphabet is used to deal with DNA sequences
bpp::RNA	This alphabet is used to deal with RNA sequences
bpp::ProteicAlphabet	This alphabet is used to deal with proteins
bpp::RNY
bpp::WordAlphabet	The base class for word alphabets
bpp::CodonAlphabet	The abstract base class for codon alphabets
bpp::EchinodermMitochondrialCodonAlphabet	This class implements the Echinoderm and Faltworms Mitochondrial codon alphabet as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG9
bpp::InvertebrateMitochondrialCodonAlphabet	This class implements the Invertebrate
bpp::StandardCodonAlphabet	This class implements the standard codon alphabet as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
bpp::VertebrateMitochondrialCodonAlphabet	This class implements the vertebrate mitochondrial codon alphabet as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2
bpp::YeastMitochondrialCodonAlphabet	This class implements the Yeast
bpp::AlphabetTools	Utilitary functions dealing with alphabets
bpp::Clonable [external]
bpp::AlphabetIndex1	One dimensionnal alphabet index interface
bpp::AAChargeIndex	Charge of each amino acid
bpp::AAChenGuHuangHydrophobicityIndex	Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 2006
bpp::AAChouFasmanAHelixIndex	A-Helix score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm
bpp::AAChouFasmanBSheetIndex	B-sheet score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm
bpp::AAChouFasmanTurnIndex	Turn score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm
bpp::AAIndex1Entry	Create a AlphabetIndex1 object from an AAIndex2 entry
bpp::AAMassIndex	Mass (dalton) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html
bpp::AASEA1030Index	Percentage of amino acids having a Solvent Exposed Area between 10 and 30 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm
bpp::AASEAInf10Index	Percentage of amino acids having a Solvent Exposed Area below 10 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm
bpp::AASEASup30Index	Percentage of amino acids having a Solvent Exposed Area above 30 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm
bpp::AASurfaceIndex	Surface (Angström^2) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html
bpp::AAVolumeIndex	Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html
bpp::GranthamAAPolarityIndex	Polarity index used in Grantham (1974)
bpp::GranthamAAVolumeIndex	Volume index used in Grantham (1974)
bpp::KleinAANetChargeIndex	Charge of each amino acid
bpp::AlphabetIndex2	Two dimensionnal alphabet index interface
bpp::AAIndex2Entry	Create a AlphabetIndex2 object from an AAIndex2 entry
bpp::BLOSUM50	BLOSUM 50 Substitution Matrix
bpp::DefaultNucleotideScore	Default Substitution Matrix for nucleotide alignments
bpp::GranthamAAChemicalDistance	Grantham (1974) Amino-Acid chemical distance
bpp::MiyataAAChemicalDistance	Miyata et al. (1979) Amino-Acid chemical distance
bpp::SimpleIndexDistance	Simple dissimilarity distance
bpp::SimpleScore	Simple Substitution Matrix, with match and mismatch penalties
bpp::AlphabetState	This is the base class to describe states in an Alphabet
bpp::NucleicAlphabetState	This is the base class to describe states in a NucleicAlphabet
bpp::ProteicAlphabetState	This is the base class to describe states in a ProteicAlphabet
bpp::Matrix< Scalar > [external]
bpp::RowMatrix< double > [external]
bpp::DistanceMatrix	A Matrix class to store phylogenetic distances
bpp::SequenceContainer	The SequenceContainer interface
bpp::OrderedSequenceContainer	The OrderedSequenceContainer interface
bpp::AbstractSequenceContainer	Partial implementation of the OrderedSequenceContainer interface
bpp::CompressedVectorSiteContainer	A low memory, yet restricted, version of the VectorSiteContainer class
bpp::MapSequenceContainer	MapSequenceContainer class
bpp::VectorSequenceContainer	The VectorSequenceContainer class
bpp::AlignedSequenceContainer	Aligned sequences container
bpp::VectorSiteContainer	The VectorSiteContainer class
bpp::SiteContainer	The SiteContainer interface
bpp::AlignedSequenceContainer	Aligned sequences container
bpp::CompressedVectorSiteContainer	A low memory, yet restricted, version of the VectorSiteContainer class
bpp::VectorSiteContainer	The VectorSiteContainer class
bpp::StatTest [external]
bpp::BowkerTest	Bowker's homogeneity test results class
bpp::SymbolList	The SymbolList interface
bpp::BasicSymbolList	A basic SymbolList object
bpp::BasicSequence	A basic implementation of the Sequence interface
bpp::Site	The Site class
bpp::EdSymbolList	A event-driven SymbolList object
bpp::SequenceWithAnnotation	An implementation of the Sequence interface that supports annotation
bpp::SequenceWithQuality	A SequenceWithAnnotation class with quality scores attached
bpp::Sequence	The sequence interface
bpp::BasicSequence	A basic implementation of the Sequence interface
bpp::SequenceWithAnnotation	An implementation of the Sequence interface that supports annotation
bpp::SymbolListListener
bpp::SequenceAnnotation	Interface for sequence annotations
bpp::SequenceMask
bpp::SequenceQuality	The SequenceQuality class
bpp::ConstSequenceIterator	Generic const sequence iterator interface, allowing to loop over const sequences
bpp::AbstractSequenceContainerIterator	Partial implementation of the SequenceIterator interface, allowing to loop over an ordered sequence container
bpp::SimpleSequenceContainerIterator	Loop over all sequences in a SequenceContainer
bpp::ConstSequenceWithQualityIterator	Generic const sequence iterator interface, allowing to loop over const sequences with quality scores
bpp::ConstSiteIterator	Generic const site iterator interface, allowing to loop over const sites
bpp::AbstractSiteContainerIterator	Partial implementation of the SiteIterator interface, allowing to loop over a site container
bpp::CompleteSiteContainerIterator	Loop over all complete sites in a SiteContainer (i.e. sites without gap and unresolved characters)
bpp::NoGapSiteContainerIterator	Loop over all sites without gaps in a SiteContainer
bpp::SimpleSiteContainerIterator	Loop over all sites in a SiteContainer
bpp::Exception [external]
bpp::AlphabetException	The alphabet exception base class
bpp::BadCharException	An alphabet exception thrown when trying to specify a bad char to the alphabet
bpp::BadIntException	An alphabet exception thrown when trying to specify a bad int to the alphabet
bpp::CharStateNotSupportedException	Exception thrown in case no character is available for a certain state in an alphabet
bpp::AlphabetMismatchException	Exception thrown when two alphabets do not match
bpp::EmptyContainerException	Exception thrown when an empty container is found
bpp::SequenceException	The sequence exception base class
bpp::EmptySequenceException	Exception thrown when a sequence is found to be empty and it should not
bpp::SequenceNotAlignedException	Exception thrown when a sequence is not align with others
bpp::SequenceWithGapException	Exception thrown when a sequence is found to have gap and it should not
bpp::SequenceNotFoundException	Exception thrown when a sequence is not found The sequence not found exception base class
bpp::SiteException	The site exception base class
bpp::EmptySiteException	Exception sent when a empty site is found
bpp::SiteWithGapException	Exception sent when a site containing gap is found
bpp::SiteNotFoundException	The site not found exception base class
bpp::StopCodonException	Exception thrown when a stop codon is found
bpp::IOFormat [external]
bpp::BppOAlignmentReaderFormat	Sequence I/O in BppO format
bpp::BppOAlignmentWriterFormat	Sequence I/O in BppO format
bpp::BppOAlphabetIndex1Format	AlphabetIndex1 I/O in BppO format
bpp::BppOAlphabetIndex2Format	AlphabetIndex2 I/O in BppO format
bpp::BppOSequenceReaderFormat	Sequence I/O in BppO format
bpp::BppOSequenceStreamReaderFormat	Sequence I/O in BppO format
bpp::BppOSequenceWriterFormat	Sequence I/O in BppO format
bpp::IOSequence	The IOSequence interface
bpp::IAlignment	The IAlignment interface
bpp::AbstractIAlignment	Partial implementation of the IAlignment interface, dedicated to alignment readers
bpp::Clustal	The clustal sequence file format
bpp::DCSE	Support for the Dedicated Comparative Sequence Editor format
bpp::Fasta	The fasta sequence file format
bpp::Mase	The mase sequence file format
bpp::NexusIOSequence	The Nexus format reader for sequences
bpp::Phylip	The Phylip & co format
bpp::ISequence	The ISequence interface
bpp::AbstractISequence	Partial implementation of the ISequence interface
bpp::Fasta	The fasta sequence file format
bpp::GenBank	The GenBank sequence file format
bpp::Mase	The mase sequence file format
bpp::Clustal	The clustal sequence file format
bpp::DCSE	Support for the Dedicated Comparative Sequence Editor format
bpp::NexusIOSequence	The Nexus format reader for sequences
bpp::Phylip	The Phylip & co format
bpp::OAlignment	The OAlignment interface
bpp::AbstractOAlignment	Partial implementation of the OAlignment interface
bpp::Clustal	The clustal sequence file format
bpp::Phylip	The Phylip & co format
bpp::Stockholm	The Stockholm alignment file format
bpp::AbstractOSequence	Partial implementation of the OSequence and OAlignment interfaces
bpp::Fasta	The fasta sequence file format
bpp::Mase	The mase sequence file format
bpp::OSequence	The OSequence interface
bpp::AbstractOSequence	Partial implementation of the OSequence and OAlignment interfaces
bpp::IOSequenceStream	The IOSequenceStream interface
bpp::ISequenceStream	The ISequenceStream interface
bpp::Fasta	The fasta sequence file format
bpp::PhredPhd	The phd sequence file format from phred software
bpp::PhredPoly	The poly sequence file format from phred software
bpp::OSequenceStream	The OSequenceStream interface
bpp::Fasta	The fasta sequence file format
bpp::IoSequenceFactory	Utilitary class for creating sequence readers and writers
bpp::MaseHeader	A class to store information from the header of Mase files
bpp::MaseTools	Utilitary methods that deal with the Mase format
bpp::NexusTools	Tools for parsing Nexus files
bpp::SequenceApplicationTools	This class provides some common tools for applications
bpp::SequenceContainerTools	Utilitary methods dealing with sequence containers
bpp::SequenceFileIndex	Index to retrieve Sequence in a file
bpp::Fasta::FileIndex	The SequenceFileIndex class for Fasta format
bpp::SequenceIterator	Generic sequence iterator interface, allowing to loop over sequences
bpp::SequenceWithQualityIterator	Generic sequence iterator interface, allowing to loop over sequences with quality scores
bpp::StreamSequenceWithQualityIterator	A sequence iterator based on a sequence stream
bpp::StreamSequenceIterator	A sequence iterator based on a sequence stream
bpp::SequencePositionIterator	Loop over a Sequence
bpp::AbstractSequencePositionIterator	Partial implementation of the SequencePositionIterator interface
bpp::SimpleSequencePositionIterator	Loop over all positions in a Sequence
bpp::SequenceWalker	A helper class to easily convert coordinates between sequence and alignments
bpp::SequenceWithAnnotationTools	The SequenceWithAnnotationTools static class
bpp::SequenceWithQualityTools	The SequenceWithQualityTools static class
bpp::SiteContainerTools	Some utililitary methods to deal with site containers
bpp::SiteIterator	Generic site iterator interface, allowing to loop over sites
bpp::StringSequenceTools	Utilitary methods working on raw string objects
bpp::SymbolListEditionEvent
bpp::SymbolListDeletionEvent
bpp::SymbolListInsertionEvent
bpp::SymbolListSubstitutionEvent
bpp::SymbolListTools	Utilitary functions dealing with both sites and sequences
bpp::CodonSiteTools	Utilitary functions for codon sites
bpp::SequenceTools	SequenceTools static class
bpp::SiteTools	Utilitary methods dealing with sites
bpp::Transliterator	This interface is used when translating a sequence from an alphabet to another: it gives the translation rules, eg: RNA -> DNA
bpp::AbstractTransliterator	Partial implementation of the Transliterator interface
bpp::AbstractReverseTransliterator	Partial implementation of the ReverseTransliterator interface
bpp::DNAToRNA	Reverse iterator to convert RNA to DNA
bpp::GeneticCode	Partial implementation of the Transliterator interface for genetic code object
bpp::EchinodermMitochondrialGeneticCode	This class implements the Echinoderm and Faltworms Mitochondrial genetic code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG9
bpp::InvertebrateMitochondrialGeneticCode	This class implements the Invertebrate Mitochondrial genetic code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG5
bpp::StandardGeneticCode	This class implements the standard genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
bpp::VertebrateMitochondrialGeneticCode	This class implements the vertebrate mitochondrial genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2
bpp::YeastMitochondrialGeneticCode	This class implements the Invertebrate Mitochondrial genetic code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG3
bpp::ReverseTransliterator	The same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA;
bpp::AbstractReverseTransliterator	Partial implementation of the ReverseTransliterator interface
bpp::NucleicAcidsReplication	Replication between to nucleic acids