java.lang.Iterable<NucleotideCompound>
, Accessioned
, Sequence<NucleotideCompound>
public class CDSSequence extends DNASequence
TranscriptSequence
where a TranscriptSequence is the child of a GeneSequence
Not important for protein construction but the phase is used if outputting the gene
to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}AbstractSequence.AnnotationType
DNASequence.DNAType
Constructor | Description |
---|---|
CDSSequence(TranscriptSequence parentSequence,
int bioBegin,
int bioEnd,
int phase) |
Modifier and Type | Method | Description |
---|---|---|
java.lang.String |
getCodingSequence() |
A CDS sequence if negative stranded needs to be reverse complement
to represent the actual coding sequence.
|
int |
getLength() |
Returns the length of the Sequence
|
java.lang.Integer |
getPhase() |
|
Strand |
getStrand() |
addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatureRetriever, getFeatures, getFeatures, getFeatures, getFeaturesByType, getFeaturesKeyWord, getIndexOf, getInverse, getLastIndexOf, getNotesList, getOriginalHeader, getParentSequence, getProxySequenceReader, getSequenceAsString, getSequenceAsString, getSequenceScore, getSource, getSubSequence, getTaxonomy, getUserCollection, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setCompoundSet, setDatabaseReferences, setDescription, setFeatureRetriever, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection, toString
getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType
public CDSSequence(TranscriptSequence parentSequence, int bioBegin, int bioEnd, int phase)
parentSequence
- bioBegin
- bioEnd
- phase
- public int getLength()
Sequence
getLength
in interface Sequence<NucleotideCompound>
getLength
in class AbstractSequence<NucleotideCompound>
public java.lang.Integer getPhase()
public Strand getStrand()
public java.lang.String getCodingSequence()