 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 |