Package org.biojava.nbio.core.sequence

Class Summary

Class	Description
AccessionID	Used in Sequences as the unique indentifier.
BasicSequence<C extends Compound>	Bare bones version of the Sequence object to be used sparingly.
CDSComparator
CDSSequence	Represents a exon or coding sequence in a gene.
ChromosomeSequence	A ChromosomeSequence is a DNASequence but keeps track of geneSequences
DNASequence	This is class should model the attributes associated with a DNA sequence
ExonComparator	Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction.
ExonSequence	A 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.
ProteinSequence	The representation of a ProteinSequence
RNASequence	RNASequence where RNACompoundSet are the allowed values
SequenceComparator	Used to sort sequences
SequenceOptimizationHints	A static class that provides optimization hints for memory or performance handling of sequence data.
StartCodonSequence	Used to map the start codon feature on a gene
StopCodonSequence	Used to map the stop codon sequence on a gene
TaxonomyID	A sequence can be associated with a species or Taxonomy ID
TranscriptSequence	This is the sequence if you want to go from a gene sequence to a protein sequence.

Enum Summary

Enum	Description
DataSource	GenBank 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.DNAType	The type of DNA sequence
SequenceOptimizationHints.SequenceCollection
SequenceOptimizationHints.SequenceUsage
Strand	Provides a way of representing the strand of a sequence, location hit or feature.