bpp-seq3  3.0.0
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234567]
 Cbpp::AlphabetToolsUtilitary functions dealing with alphabets
 ▼Cbpp::BppApplication [external]
 Cbpp::BppSequenceApplication
 ▼Cbpp::Clonable [external]
 ►Cbpp::TemplateSequenceDataInterface< std::string >
 Cbpp::VectorPositionedContainer< bpp::Site >
 Cbpp::VectorPositionedContainer< SiteType >
 ►Cbpp::AlphabetThe Alphabet interface
 ►Cbpp::AlphabetIndex1One dimensionnal alphabet index interface
 ►Cbpp::AlphabetIndex2Two dimensionnal alphabet index interface
 ►Cbpp::AlphabetStateThis is the base class to describe states in an Alphabet
 ►Cbpp::CoreSymbolListListener< T >
 ►Cbpp::CruxSymbolListInterfaceThe CruxSymbolList interface
 Cbpp::DistanceMatrixA Matrix class to store phylogenetic distances
 ►Cbpp::GeneticCodePartial implementation of the Transliterator interface for genetic code object
 ►Cbpp::NamedContainerInterface< T >A Container template for objects that are accessible through names
 ►Cbpp::PositionedContainerInterface< T >The PositionedContainer interface
 Cbpp::SequencedValuesContainer
 ►Cbpp::StatTest [external]
 ►Cbpp::TemplateSequenceDataInterface< HashType >The SequenceData interface
 Cbpp::VectorPositionedContainer< T >The template VectorPositionedContainer class
 ▼Cbpp::Commentable
 Cbpp::TemplateSequenceDataInterface< std::string >
 Cbpp::CoreSequenceInterfaceThe core sequence interface
 ►Cbpp::SimpleCommentable
 Cbpp::TemplateSequenceDataInterface< HashType >The SequenceData interface
 ▼Cbpp::CoreSymbolListEditionEvent< T >
 Cbpp::CoreSymbolListDeletionEvent< T >
 Cbpp::CoreSymbolListInsertionEvent< T >
 Cbpp::CoreSymbolListSubstitutionEvent< T >
 ▼Cbpp::CoreWordAlphabetThe interface class for word alphabets
 Cbpp::CodonAlphabetCodon alphabet class
 Cbpp::WordAlphabetThe base class for word alphabets
 ▼Cstd::enable_shared_from_this
 Cbpp::AlphabetThe Alphabet interface
 ▼Cbpp::Exception [external]
 ►Cbpp::AlphabetExceptionThe alphabet exception base class
 Cbpp::AlphabetMismatchExceptionException thrown when two alphabets do not match
 Cbpp::EmptyContainerExceptionException thrown when an empty container is found
 ►Cbpp::SequenceExceptionThe sequence exception base class
 Cbpp::SequenceNotFoundExceptionException thrown when a sequence is not found The sequence not found exception base class
 ►Cbpp::SiteExceptionThe site exception base class
 Cbpp::SiteNotFoundExceptionThe site not found exception base class
 Cbpp::StopCodonExceptionException thrown when a stop codon is found
 Cbpp::IODistanceMatrixFactoryUtilitary class for creating distance matrix readers and writers
 ▼Cbpp::IOFormat [external]
 Cbpp::BppOAlignmentReaderFormatSequence I/O in BppO format
 Cbpp::BppOAlignmentWriterFormatSequence I/O in BppO format
 Cbpp::BppOAlphabetIndex1FormatAlphabetIndex1 I/O in BppO format
 Cbpp::BppOAlphabetIndex2FormatAlphabetIndex2 I/O in BppO format
 Cbpp::BppOSequenceReaderFormatSequence I/O in BppO format
 Cbpp::BppOSequenceStreamReaderFormatSequence I/O in BppO format
 Cbpp::BppOSequenceWriterFormatSequence I/O in BppO format
 ►Cbpp::IODistanceMatrixGeneral interface for distance matrix I/O
 ►Cbpp::IOProbabilisticSequenceThe IOProbabislisticSequence interface
 ►Cbpp::IOSequenceThe IOSequence interface
 ►Cbpp::IOSequenceStreamThe IOSequenceStream interface
 Cbpp::IoSequenceFactoryUtilitary class for creating sequence readers and writers
 Cbpp::MaseHeaderA class to store information from the header of Mase files
 Cbpp::MaseToolsUtilitary methods that deal with the Mase format
 Cbpp::NexusToolsTools for parsing Nexus files
 Cbpp::SequenceApplicationToolsThis class provides some common tools for applications
 Cbpp::SequenceContainerToolsUtilitary methods dealing with sequence containers
 ▼Cbpp::SequenceFileIndexIndex to retrieve Sequence in a file
 Cbpp::Fasta::FileIndexThe SequenceFileIndex class for Fasta format
 ▼Cbpp::SequencePositionIteratorLoop over a Sequence
 ►Cbpp::AbstractSequencePositionIteratorPartial implementation of the SequencePositionIterator interface
 Cbpp::SequenceWalkerA helper class to easily convert coordinates between sequence and alignments
 Cbpp::SequenceWithAnnotationToolsThe SequenceWithAnnotationTools static class
 Cbpp::SequenceWithQualityToolsThe SequenceWithQualityTools static class
 Cbpp::SiteContainerToolsSome utililitary methods to deal with site containers
 Cbpp::StringSequenceToolsUtilitary methods working on raw string objects
 Cbpp::SwitchDeleter< T >
 ▼Cbpp::SymbolListToolsUtilitary functions dealing with both sites and sequences
 Cbpp::CodonSiteToolsUtilitary functions for codon sites
 Cbpp::SequenceToolsSequenceTools static class
 Cbpp::SiteToolsUtilitary methods dealing with sites
 ▼Cbpp::TemplateSequenceIteratorInterface< SequenceType >Generic sequence iterator interface, allowing to loop over sequences
 Cbpp::TemplateStreamSequenceIterator< SequenceType >A sequence iterator based on a sequence stream
 Cbpp::TemplateSiteIteratorInterface< SiteType >Generic site iterator interface, allowing to loop over sites
 ▼Cbpp::TemplateSiteIteratorInterface< const SiteType >
 ►Cbpp::AbstractTemplateSiteContainerIterator< SiteType, SequenceType, HashType >Partial implementation of the SiteIterator interface, allowing to loop over a site container
 ▼Cbpp::TransliteratorInterfaceThis interface is used when translating a sequence from an alphabet to another: it gives the translation rules, eg: RNA -> DNA
 ►Cbpp::AbstractTransliteratorPartial implementation of the Transliterator interface
 ►Cbpp::ReverseTransliteratorInterfaceThe same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA;