| AccessionID |
Used in Sequences as the unique identifier.
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| BasicSequence<C extends Compound> |
Bare bones version of the Sequence object to be used sparingly.
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| CDSComparator |
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| CDSSequence |
Represents a exon or coding sequence in a gene.
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| ChromosomeSequence |
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
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| DNASequence |
This is class should model the attributes associated with a DNA sequence
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| ExonComparator |
Sort 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.
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| ExonSequence |
A gene contains a collection of Exon sequences
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| GeneSequence |
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| IntronSequence |
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| MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound> |
Implements a minimal data structure for reading and writing a sequence alignment.
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| ProteinSequence |
The representation of a ProteinSequence
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| RNASequence |
RNASequence where RNACompoundSet are the allowed values
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| SequenceComparator |
Used to sort sequences in ascending order of bioBegin property.
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| SequenceOptimizationHints |
A static class that provides optimization hints for memory or performance handling of sequence data.
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| StartCodonSequence |
Used to map the start codon feature on a gene
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| StopCodonSequence |
Used to map the stop codon sequence on a gene
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| TaxonomyID |
A sequence can be associated with a species or Taxonomy ID
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| TranscriptSequence |
This is the sequence if you want to go from a gene sequence to a protein sequence.
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