|
|||||||||
PREV PACKAGE NEXT PACKAGE | FRAMES NO FRAMES |
Class Summary | |
---|---|
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 | |
---|---|
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. |
|
|||||||||
PREV PACKAGE NEXT PACKAGE | FRAMES NO FRAMES |