java.lang.Iterable<NucleotideCompound>
, Accessioned
, Sequence<NucleotideCompound>
public class TranscriptSequence extends DNASequence
AbstractSequence.AnnotationType
DNASequence.DNAType
Constructor | Description |
---|---|
TranscriptSequence(GeneSequence parentDNASequence,
int begin,
int end) |
Modifier and Type | Method | Description |
---|---|---|
CDSSequence |
addCDS(AccessionID accession,
int begin,
int end,
int phase) |
Add a Coding Sequence region with phase to the transcript sequence
|
void |
addStartCodonSequence(AccessionID accession,
int begin,
int end) |
|
void |
addStopCodonSequence(AccessionID accession,
int begin,
int end) |
|
java.util.LinkedHashMap<java.lang.String,CDSSequence> |
getCDSSequences() |
Get the CDS sequences that have been added to the TranscriptSequences
|
DNASequence |
getDNACodingSequence() |
Get the stitched together CDS sequences then maps to the cDNA
|
int |
getLength() |
Returns the length of the Sequence
|
java.util.ArrayList<ProteinSequence> |
getProteinCDSSequences() |
Return a list of protein sequences based on each CDS sequence
where the phase shift between two CDS sequences is assigned to the
CDS sequence that starts the triplet.
|
ProteinSequence |
getProteinSequence() |
Get the protein sequence
|
ProteinSequence |
getProteinSequence(TranscriptionEngine engine) |
Get the protein sequence with user defined TranscriptEngine
|
StartCodonSequence |
getStartCodonSequence() |
|
StopCodonSequence |
getStopCodonSequence() |
|
Strand |
getStrand() |
|
CDSSequence |
removeCDS(java.lang.String accession) |
Remove a CDS or coding sequence from the transcript sequence
|
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 TranscriptSequence(GeneSequence parentDNASequence, int begin, int end)
parentDNASequence
- begin
- end
- inclusive of endpublic int getLength()
Sequence
getLength
in interface Sequence<NucleotideCompound>
getLength
in class AbstractSequence<NucleotideCompound>
public Strand getStrand()
public CDSSequence removeCDS(java.lang.String accession)
accession
- public java.util.LinkedHashMap<java.lang.String,CDSSequence> getCDSSequences()
public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase) throws java.lang.Exception
accession
- begin
- end
- phase
- 0,1,2java.lang.Exception
public java.util.ArrayList<ProteinSequence> getProteinCDSSequences()
public DNASequence getDNACodingSequence()
public ProteinSequence getProteinSequence()
public ProteinSequence getProteinSequence(TranscriptionEngine engine)
engine
- public StartCodonSequence getStartCodonSequence()
public void addStartCodonSequence(AccessionID accession, int begin, int end)
startCodonSequence
- the startCodonSequence to setpublic StopCodonSequence getStopCodonSequence()
public void addStopCodonSequence(AccessionID accession, int begin, int end)
stopCodonSequence
- the stopCodonSequence to set