| ►Nbpp | This alphabet is used to deal NumericAlphabet |
| NIntegerTools | |
| NTextTools | |
| CAbstractAlphabet | A partial implementation of the Alphabet interface |
| ►CAllelicAlphabet | The base class for allelic alphabets |
| CAllelicTransliterator | |
| CAlphabet | The Alphabet interface |
| CAlphabetException | The alphabet exception base class |
| CBadCharException | An alphabet exception thrown when trying to specify a bad char to the alphabet |
| CBadIntException | An alphabet exception thrown when trying to specify a bad int to the alphabet |
| CAlphabetMismatchException | Exception thrown when two alphabets do not match |
| CCharStateNotSupportedException | Exception thrown in case no character is available for a certain state in an alphabet |
| CAlphabetNumericState | States that do have a double value |
| CAlphabetState | This is the base class to describe states in an Alphabet |
| CAlphabetTools | Utilitary functions dealing with alphabets |
| CBinaryAlphabet | The BinaryAlphabet class, letters are 0 and 1 |
| CCaseMaskedAlphabet | Case-sensitive letter alphabet |
| CCodonAlphabet | Codon alphabet class |
| CDefaultAlphabet | The DefaultAlphabet class |
| CDNA | This alphabet is used to deal with DNA sequences |
| CIntegerAlphabet | The Integer Alphabet class, letters are from 0 to a given number, MAX |
| CLetterAlphabet | Specialized partial implementation of Alphabet using single letters |
| CLexicalAlphabet | Alphabet made of given words |
| CNucleicAlphabet | The abstract base class for nucleic alphabets |
| CNucleicAlphabetState | This is the base class to describe states in a NucleicAlphabet |
| CNumericAlphabet | |
| CProteicAlphabet | This alphabet is used to deal with proteins |
| CProteicAlphabetState | This is the base class to describe states in a ProteicAlphabet |
| CRNA | This alphabet is used to deal with RNA sequences |
| CRNY | |
| CCoreWordAlphabet | The interface class for word alphabets |
| CWordAlphabet | The base class for word alphabets |
| CAAChargeIndex | Charge of each amino acid |
| CAAChenGuHuangHydrophobicityIndex | Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 2006 |
| CAAChouFasmanAHelixIndex | A-Helix score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm |
| CAAChouFasmanBSheetIndex | B-sheet score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm |
| CAAChouFasmanTurnIndex | Turn score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm |
| CAAIndex1Entry | Create a AlphabetIndex1 object from an AAIndex2 entry |
| CAAIndex2Entry | Create a AlphabetIndex2 object from an AAIndex2 entry |
| CAAMassIndex | Mass (dalton) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html |
| CAASEA1030Index | 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 |
| CAASEAInf10Index | 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 |
| CAASEASup30Index | 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 |
| CAASurfaceIndex | Surface (Angström^2) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html |
| CAAVolumeIndex | Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html (Note: original webpage is not available anymore) |
| CAlphabetIndex1 | One dimensionnal alphabet index interface |
| CProteicAlphabetIndex1 | |
| CAlphabetIndex2 | Two dimensionnal alphabet index interface |
| CProteicAlphabetIndex2 | Virtual AlphabetIndex2 for proteic alphabet |
| CBLOSUM50 | BLOSUM 50 Substitution Matrix |
| CCodonFromProteicAlphabetIndex1 | AlphabetIndex1 for codon based on ProteicAlphabetIndex1 |
| CCodonFromProteicAlphabetIndex2 | |
| CDefaultNucleotideScore | Default Substitution Matrix for nucleotide alignments |
| CGranthamAAChemicalDistance | Grantham (1974) Amino-Acid chemical distance |
| CGranthamAAPolarityIndex | Polarity index used in Grantham (1974) |
| CGranthamAAVolumeIndex | Volume index used in Grantham (1974) |
| CKD_AAHydropathyIndex | Hydropathy index defined in Kyte & Doolitle (1982) |
| CKleinAANetChargeIndex | Charge of each amino acid |
| CMiyataAAChemicalDistance | Miyata et al. (1979) Amino-Acid chemical distance |
| CSimpleIndexDistance | Simple dissimilarity distance |
| CSimpleScore | Simple Substitution Matrix, with match and mismatch penalties |
| CUserAlphabetIndex1 | Alphabet index given by user |
| CUserAlphabetIndex2 | Alphabet index given by user |
| CBppSequenceApplication | |
| CSequenceApplicationTools | This class provides some common tools for applications |
| CCodonSiteTools | Utilitary functions for codon sites |
| CCommentable | |
| CSimpleCommentable | |
| CAbstractTemplateSequenceContainer | Partial implementation of the SequenceContainer interface |
| CTemplateAlignedSequenceContainer | The AlignedSequencesContainer class |
| CTemplateAlignmentDataInterface | The Container of Aligned Values interface |
| CCompressedVectorSiteContainer | A low memory, yet restricted, version of the VectorSiteContainer class |
| CMappedNamedContainer | MappedNamedContainer class |
| CNamedContainerInterface | A Container template for objects that are accessible through names |
| CPositionedContainerInterface | The PositionedContainer interface |
| CPositionedNamedContainerInterface | The template PositionedNamedContainer interface, that links position & name containers |
| CTemplateSequenceContainerInterface | The SequenceContainer interface |
| CSwitchDeleter | |
| CSequenceNotFoundException | Exception thrown when a sequence is not found The sequence not found exception base class |
| CEmptyContainerException | Exception thrown when an empty container is found |
| CSequenceContainerTools | Utilitary methods dealing with sequence containers |
| CTemplateSequenceDataInterface | The SequenceData interface |
| CSequencedValuesContainer | |
| CTemplateSiteContainerInterface | The SiteContainer interface |
| CSiteNotFoundException | The site not found exception base class |
| CAbstractTemplateSiteContainerIterator | Partial implementation of the SiteIterator interface, allowing to loop over a site container |
| CSimpleTemplateSiteContainerIterator | Loop over all sites in a SiteContainer |
| CNoGapTemplateSiteContainerIterator | Loop over all sites without gaps in a SiteContainer |
| CCompleteTemplateSiteContainerIterator | Loop over all complete sites in a SiteContainer (i.e. sites without gap and unresolved characters) |
| CSiteContainerTools | Some utililitary methods to deal with site containers |
| CVectorMappedContainer | The template VectorMappedContainer class |
| CVectorPositionedContainer | The template VectorPositionedContainer class |
| CTemplateVectorSequenceContainer | The VectorSequenceContainer class |
| CTemplateVectorSiteContainer | The VectorSiteContainer class |
| CCoreSequenceInterface | The core sequence interface |
| CAbstractCoreSequence | A partial implementation of the CoreSequence interface |
| CCoreSiteInterface | The core site interface |
| CAbstractCoreSite | A partial implementation of the CoreSite interface |
| CCruxSymbolListInterface | The CruxSymbolList interface |
| CTemplateCoreSymbolListInterface | The CoreSymbolList interface |
| CCoreSymbolListEditionEvent | |
| CCoreSymbolListInsertionEvent | |
| CCoreSymbolListDeletionEvent | |
| CCoreSymbolListSubstitutionEvent | |
| CCoreSymbolListListener | |
| CTemplateEventDrivenCoreSymbolListInterface | Interface for event-driven CoreSymbolList objects |
| CDistanceMatrix | A Matrix class to store phylogenetic distances |
| CDNAToRNA | Reverse iterator to convert RNA to DNA |
| CAscidianMitochondrialGeneticCode | This class implements the ascidian mitochondrial genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG13 |
| CCiliateNuclearGeneticCode | This class implements the mold, protozoan, and coelenterate mitochondrial code and the Mycoplasma/Spiroplasma code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG4 |
| CEchinodermMitochondrialGeneticCode | 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 |
| CStopCodonException | Exception thrown when a stop codon is found |
| CGeneticCode | Partial implementation of the Transliterator interface for genetic code object |
| CInvertebrateMitochondrialGeneticCode | 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 |
| CMoldMitochondrialGeneticCode | This class implements the mold, protozoan, and coelenterate mitochondrial code and the Mycoplasma/Spiroplasma code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG4 |
| CStandardGeneticCode | 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 |
| CVertebrateMitochondrialGeneticCode | 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 |
| CYeastMitochondrialGeneticCode | 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 |
| CIntSymbolListInterface | The specific IntSymbolList interface |
| CIntSymbolList | A basic IntSymbolList object |
| CEventDrivenIntSymbolList | A event-driven IntSymbolList object |
| CAbstractIAlignment | Partial implementation of the IAlignment interface, dedicated to alignment readers |
| CAbstractIAlignment2 | Partial implementation of the IAlignment and ISequence interface, dedicated to alignment readers |
| CAbstractIProbabilisticAlignment | |
| CAbstractIProbabilisticAlignment2 | |
| CAbstractISequence | Partial implementation of the ISequence interface |
| CAbstractIProbabilisticSequence | Partial implementation of the IProbabilisticSequence interface |
| CAbstractOAlignment | Partial implementation of the OAlignment interface |
| CAbstractOProbabilisticAlignment | Partial implementation of the OProbabilisticAlignment interface |
| CAbstractOSequence | Partial implementation of the OSequence interface |
| CAbstractOSequence2 | Partial implementation of the OAlignment interface |
| CAbstractOProbabilisticSequence | Partial implementation of the OProbabilisticSequence interface |
| CAbstractOProbabilisticSequence2 | Partial implementation of the OProbabilisticAlignment interface |
| CBppOAlignmentReaderFormat | Sequence I/O in BppO format |
| CBppOAlignmentWriterFormat | Sequence I/O in BppO format |
| CBppOAlphabetIndex1Format | AlphabetIndex1 I/O in BppO format |
| CBppOAlphabetIndex2Format | AlphabetIndex2 I/O in BppO format |
| CBppOSequenceReaderFormat | Sequence I/O in BppO format |
| CBppOSequenceStreamReaderFormat | Sequence I/O in BppO format |
| CBppOSequenceWriterFormat | Sequence I/O in BppO format |
| CClustal | The clustal sequence file format |
| CDCSE | Support for the Dedicated Comparative Sequence Editor format |
| ►CFasta | The fasta sequence file format |
| CFileIndex | The SequenceFileIndex class for Fasta format |
| CGenBank | The GenBank sequence file format |
| CIODistanceMatrix | General interface for distance matrix I/O |
| CIDistanceMatrix | General interface for distance matrix readers |
| CODistanceMatrix | General interface for distance matrix writers |
| CAbstractIDistanceMatrix | Partial implementation of the IDistanceMatrix interface |
| CAbstractODistanceMatrix | Partial implementation of the ODistanceMatrix interface |
| CIODistanceMatrixFactory | Utilitary class for creating distance matrix readers and writers |
| CIOSequence | The IOSequence interface |
| CIOProbabilisticSequence | The IOProbabislisticSequence interface |
| CIoSequenceFactory | Utilitary class for creating sequence readers and writers |
| CIOSequenceStream | The IOSequenceStream interface |
| CISequence | The ISequence interface |
| CIAlignment | The IAlignment interface |
| CIProbabilisticSequence | The IProbabilisticSequence interface |
| CIProbabilisticAlignment | The IProbabilisticSequence interface |
| CTemplateISequenceStream | The ISequenceStream interface |
| CMaseHeader | A class to store information from the header of Mase files |
| CMase | The mase sequence file format |
| CMaseTools | Utilitary methods that deal with the Mase format |
| CNexusIOSequence | The Nexus format reader for sequences |
| CNexusTools | Tools for parsing Nexus files |
| COSequence | The OSequence interface |
| COAlignment | The OAlignment interface |
| COProbabilisticSequence | The OProbabilisticSequence interface |
| COProbabilisticAlignment | The OProbabilisticAlignment interface |
| CTemplateOSequenceStream | The OSequenceStream interface |
| CPasta | The Pasta sequence file format |
| CPhredPhd | The phd sequence file format from phred software |
| CPhredPoly | The poly sequence file format from phred software |
| CPhylip | The Phylip & co format |
| CPhylipDistanceMatrixFormat | Distance matrix I/O in Phylip format |
| CSequenceFileIndex | Index to retrieve Sequence in a file |
| CStockholm | The Stockholm alignment file format |
| CTemplateStreamSequenceIterator | A sequence iterator based on a sequence stream |
| CNucleicAcidsReplication | Replication between to nucleic acids |
| CProbabilisticSequenceInterface | The probabilistic sequence interface |
| CProbabilisticSequence | A basic implementation of the ProbabilisticSequence interface |
| CProbabilisticSiteInterface | The ProbabilisticSite interface |
| CProbabilisticSite | |
| CProbabilisticSymbolListInterface | The ProbabilisticSymbolList interface |
| CProbabilisticSymbolList | ProbabilisticSymbolList object |
| CSequenceInterface | The sequence interface |
| CSequence | A basic implementation of the Sequence interface |
| CSequenceException | The sequence exception base class |
| CEmptySequenceException | Exception thrown when a sequence is found to be empty and it should not |
| CSequenceWithGapException | Exception thrown when a sequence is found to have gap and it should not |
| CSequenceNotAlignedException | Exception thrown when a sequence is not align with others |
| CTemplateSequenceIteratorInterface | Generic sequence iterator interface, allowing to loop over sequences |
| CSequencePositionIterator | Loop over a Sequence |
| CAbstractSequencePositionIterator | Partial implementation of the SequencePositionIterator interface |
| CSimpleSequencePositionIterator | Loop over all positions in a Sequence |
| CBowkerTest | Bowker's homogeneity test results class |
| CSequenceTools | SequenceTools static class |
| CSequenceWalker | A helper class to easily convert coordinates between sequence and alignments |
| CSequenceAnnotation | Interface for sequence annotations |
| CSequenceWithAnnotation | An implementation of the Sequence interface that supports annotation |
| CSequenceMask | |
| CSequenceWithAnnotationTools | The SequenceWithAnnotationTools static class |
| CSequenceQuality | The SequenceQuality class |
| CSequenceWithQuality | A SequenceWithAnnotation class with quality scores attached |
| CSequenceWithQualityTools | The SequenceWithQualityTools static class |
| CSiteInterface | The site interface |
| CSite | The Site class |
| CSiteException | The site exception base class |
| CEmptySiteException | Exception sent when a empty site is found |
| CSiteWithGapException | Exception sent when a site containing gap is found |
| CTemplateSiteIteratorInterface | Generic site iterator interface, allowing to loop over sites |
| CSiteTools | Utilitary methods dealing with sites |
| CStringSequenceTools | Utilitary methods working on raw string objects |
| CAbstractTemplateSymbolList | A partial implementation of a SymbolList object |
| CAbstractTemplateEventDrivenSymbolList | A partial implementation of a EventDrivenSymbolList object |
| CSymbolListTools | Utilitary functions dealing with both sites and sequences |
| CTransliteratorInterface | This interface is used when translating a sequence from an alphabet to another: it gives the translation rules, eg: RNA -> DNA |
| CReverseTransliteratorInterface | The same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA; |
| CAbstractTransliterator | Partial implementation of the Transliterator interface |
| CAbstractReverseTransliterator | Partial implementation of the ReverseTransliterator interface |
1.9.1