Class Summary Class Description AccessionIDUsed in Sequences as the unique identifier. BasicSequence<C extends Compound>Bare bones version of the Sequence object to be used sparingly. CDSComparator CDSSequenceRepresents a exon or coding sequence in a gene. ChromosomeSequenceA ChromosomeSequence is a DNASequence but keeps track of geneSequences DNASequenceThis is class should model the attributes associated with a DNA sequence ExonComparatorSort Exon where it is a little confusing if exons should always be ordered left to right where a negative stranded gene should go the other direction. ExonSequenceA gene contains a collection of Exon sequences GeneSequence IntronSequence MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound>Implements a minimal data structure for reading and writing a sequence alignment. ProteinSequenceThe representation of a ProteinSequence RNASequenceRNASequence where RNACompoundSet are the allowed values SequenceComparatorUsed to sort sequences in ascending order of bioBegin property. SequenceOptimizationHintsA static class that provides optimization hints for memory or performance handling of sequence data. StartCodonSequenceUsed to map the start codon feature on a gene StopCodonSequenceUsed to map the stop codon sequence on a gene TaxonomyIDA sequence can be associated with a species or Taxonomy ID TranscriptSequenceThis is the sequence if you want to go from a gene sequence to a protein sequence.
Enum Summary Enum Description DataSourceGenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT UNIPROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier DNASequence.DNATypeThe type of DNA sequence SequenceOptimizationHints.SequenceCollection SequenceOptimizationHints.SequenceUsage StrandProvides a way of representing the strand of a sequence, location hit or feature.