  bpp | |
   AbstractAlphabet | A partial implementation of the Alphabet interface |
| Alphabet | The Alphabet interface |
| AlphabetException | The alphabet exception base class |
| BadCharException | An alphabet exception thrown when trying to specify a bad char to the alphabet |
| BadIntException | An alphabet exception thrown when trying to specify a bad int to the alphabet |
| AlphabetMismatchException | Exception thrown when two alphabets do not match |
| CharStateNotSupportedException | Exception thrown in case no character is available for a certain state in an alphabet |
| AlphabetState | This is the base class to describe states in an Alphabet |
| AlphabetTools | Utilitary functions dealing with alphabets |
| BinaryAlphabet | The BinaryAlphabet class, letters are 0 and 1 |
| CaseMaskedAlphabet | Case-sensitive letter alphabet |
| CodonAlphabet | The abstract base class for codon alphabets |
| DefaultAlphabet | The DefaultAlphabet class |
| DNA | This alphabet is used to deal with DNA sequences |
| 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 |
| InvertebrateMitochondrialCodonAlphabet | This class implements the Invertebrate |
| LetterAlphabet | Specialized partial implementation of Alphabet using single letters |
| NucleicAlphabet | The abstract base class for nucleic alphabets |
| NucleicAlphabetState | This is the base class to describe states in a NucleicAlphabet |
| ProteicAlphabet | This alphabet is used to deal with proteins |
| ProteicAlphabetState | This is the base class to describe states in a ProteicAlphabet |
| RNA | This alphabet is used to deal with RNA sequences |
| RNY | |
| 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 |
| 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 |
| WordAlphabet | The base class for word alphabets |
| YeastMitochondrialCodonAlphabet | This class implements the Yeast |
| AAChargeIndex | Charge of each amino acid |
| AAChenGuHuangHydrophobicityIndex | Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 2006 |
| AAChouFasmanAHelixIndex | A-Helix score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm |
| AAChouFasmanBSheetIndex | B-sheet score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm |
| AAChouFasmanTurnIndex | Turn score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm |
| AAIndex1Entry | Create a AlphabetIndex1 object from an AAIndex2 entry |
| AAIndex2Entry | Create a AlphabetIndex2 object from an AAIndex2 entry |
| AAMassIndex | Mass (dalton) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html |
| 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 |
| 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 |
| 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 |
| AASurfaceIndex | Surface (Angström^2) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html |
| AAVolumeIndex | Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html |
| AlphabetIndex1 | One dimensionnal alphabet index interface |
| AlphabetIndex2 | Two dimensionnal alphabet index interface |
| BLOSUM50 | BLOSUM 50 Substitution Matrix |
| DefaultNucleotideScore | Default Substitution Matrix for nucleotide alignments |
| GranthamAAChemicalDistance | Grantham (1974) Amino-Acid chemical distance |
| GranthamAAPolarityIndex | Polarity index used in Grantham (1974) |
| GranthamAAVolumeIndex | Volume index used in Grantham (1974) |
| KleinAANetChargeIndex | Charge of each amino acid |
| MiyataAAChemicalDistance | Miyata et al. (1979) Amino-Acid chemical distance |
| SimpleIndexDistance | Simple dissimilarity distance |
| SimpleScore | Simple Substitution Matrix, with match and mismatch penalties |
| SequenceApplicationTools | This class provides some common tools for applications |
| CodonSiteTools | Utilitary functions for codon sites |
| AbstractSequenceContainer | Partial implementation of the OrderedSequenceContainer interface |
| AlignedSequenceContainer | Aligned sequences container |
| CompressedVectorSiteContainer | A low memory, yet restricted, version of the VectorSiteContainer class |
| MapSequenceContainer | MapSequenceContainer class |
| OrderedSequenceContainer | The OrderedSequenceContainer interface |
| SequenceContainer | The SequenceContainer interface |
| SequenceNotFoundException | Exception thrown when a sequence is not found The sequence not found exception base class |
| EmptyContainerException | Exception thrown when an empty container is found |
| AbstractSequenceContainerIterator | Partial implementation of the SequenceIterator interface, allowing to loop over an ordered sequence container |
| SimpleSequenceContainerIterator | Loop over all sequences in a SequenceContainer |
| SequenceContainerTools | Utilitary methods dealing with sequence containers |
| SiteContainer | The SiteContainer interface |
| SiteNotFoundException | The site not found exception base class |
| AbstractSiteContainerIterator | Partial implementation of the SiteIterator interface, allowing to loop over a site container |
| SimpleSiteContainerIterator | Loop over all sites in a SiteContainer |
| NoGapSiteContainerIterator | Loop over all sites without gaps in a SiteContainer |
| CompleteSiteContainerIterator | Loop over all complete sites in a SiteContainer (i.e. sites without gap and unresolved characters) |
| SiteContainerTools | Some utililitary methods to deal with site containers |
| VectorSequenceContainer | The VectorSequenceContainer class |
| VectorSiteContainer | The VectorSiteContainer class |
| DistanceMatrix | A Matrix class to store phylogenetic distances |
| DNAToRNA | Reverse iterator to convert RNA to DNA |
| 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 |
| StopCodonException | Exception thrown when a stop codon is found |
| GeneticCode | Partial implementation of the Transliterator interface for genetic code object |
| 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 |
| 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 |
| 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 |
| 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 |
| AbstractIAlignment | Partial implementation of the IAlignment interface, dedicated to alignment readers |
| AbstractISequence | Partial implementation of the ISequence interface |
| AbstractOAlignment | Partial implementation of the OAlignment interface |
| AbstractOSequence | Partial implementation of the OSequence and OAlignment interfaces |
| BppOAlignmentReaderFormat | Sequence I/O in BppO format |
| BppOAlignmentWriterFormat | Sequence I/O in BppO format |
| BppOAlphabetIndex1Format | AlphabetIndex1 I/O in BppO format |
| BppOAlphabetIndex2Format | AlphabetIndex2 I/O in BppO format |
| BppOSequenceReaderFormat | Sequence I/O in BppO format |
| BppOSequenceStreamReaderFormat | Sequence I/O in BppO format |
| BppOSequenceWriterFormat | Sequence I/O in BppO format |
| Clustal | The clustal sequence file format |
| DCSE | Support for the Dedicated Comparative Sequence Editor format |
 Fasta | The fasta sequence file format |
  FileIndex | The SequenceFileIndex class for Fasta format |
| GenBank | The GenBank sequence file format |
| IOSequence | The IOSequence interface |
| IoSequenceFactory | Utilitary class for creating sequence readers and writers |
| IOSequenceStream | The IOSequenceStream interface |
| ISequence | The ISequence interface |
| IAlignment | The IAlignment interface |
| ISequenceStream | The ISequenceStream interface |
| MaseHeader | A class to store information from the header of Mase files |
| Mase | The mase sequence file format |
| MaseTools | Utilitary methods that deal with the Mase format |
| NexusIOSequence | The Nexus format reader for sequences |
| NexusTools | Tools for parsing Nexus files |
| OSequence | The OSequence interface |
| OAlignment | The OAlignment interface |
| OSequenceStream | The OSequenceStream interface |
| PhredPhd | The phd sequence file format from phred software |
| PhredPoly | The poly sequence file format from phred software |
| Phylip | The Phylip & co format |
| SequenceFileIndex | Index to retrieve Sequence in a file |
| Stockholm | The Stockholm alignment file format |
| StreamSequenceIterator | A sequence iterator based on a sequence stream |
| StreamSequenceWithQualityIterator | A sequence iterator based on a sequence stream |
| NucleicAcidsReplication | Replication between to nucleic acids |
| Sequence | The sequence interface |
| BasicSequence | A basic implementation of the Sequence interface |
| SequenceException | The sequence exception base class |
| EmptySequenceException | Exception thrown when a sequence is found to be empty and it should not |
| SequenceWithGapException | Exception thrown when a sequence is found to have gap and it should not |
| SequenceNotAlignedException | Exception thrown when a sequence is not align with others |
| SequenceIterator | Generic sequence iterator interface, allowing to loop over sequences |
| ConstSequenceIterator | Generic const sequence iterator interface, allowing to loop over const sequences |
| SequenceWithQualityIterator | Generic sequence iterator interface, allowing to loop over sequences with quality scores |
| ConstSequenceWithQualityIterator | Generic const sequence iterator interface, allowing to loop over const sequences with quality scores |
| SequencePositionIterator | Loop over a Sequence |
| AbstractSequencePositionIterator | Partial implementation of the SequencePositionIterator interface |
| SimpleSequencePositionIterator | Loop over all positions in a Sequence |
| BowkerTest | Bowker's homogeneity test results class |
| SequenceTools | SequenceTools static class |
| SequenceWalker | A helper class to easily convert coordinates between sequence and alignments |
| SequenceAnnotation | Interface for sequence annotations |
| SequenceWithAnnotation | An implementation of the Sequence interface that supports annotation |
| SequenceMask | |
| SequenceWithAnnotationTools | The SequenceWithAnnotationTools static class |
| SequenceQuality | The SequenceQuality class |
| SequenceWithQuality | A SequenceWithAnnotation class with quality scores attached |
| SequenceWithQualityTools | The SequenceWithQualityTools static class |
| Site | The Site class |
| SiteException | The site exception base class |
| EmptySiteException | Exception sent when a empty site is found |
| SiteWithGapException | Exception sent when a site containing gap is found |
| SiteIterator | Generic site iterator interface, allowing to loop over sites |
| ConstSiteIterator | Generic const site iterator interface, allowing to loop over const sites |
| SiteTools | Utilitary methods dealing with sites |
| StringSequenceTools | Utilitary methods working on raw string objects |
| SymbolList | The SymbolList interface |
| BasicSymbolList | A basic SymbolList object |
| SymbolListEditionEvent | |
| SymbolListInsertionEvent | |
| SymbolListDeletionEvent | |
| SymbolListSubstitutionEvent | |
| SymbolListListener | |
| EdSymbolList | A event-driven SymbolList object |
| SymbolListTools | Utilitary functions dealing with both sites and sequences |
| Transliterator | This interface is used when translating a sequence from an alphabet to another: it gives the translation rules, eg: RNA -> DNA |
| ReverseTransliterator | The same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA; |
| AbstractTransliterator | Partial implementation of the Transliterator interface |
| AbstractReverseTransliterator | Partial implementation of the ReverseTransliterator interface |
1.8.3.1-20130209 
