org.biojava3.core.sequence
Class CDSSequence
java.lang.Object
org.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>
org.biojava3.core.sequence.DNASequence
org.biojava3.core.sequence.CDSSequence
- All Implemented Interfaces:
- Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>
public class CDSSequence
- extends DNASequence
Represents a exon or coding sequence in a gene. It has a parent 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. http://www.sequenceontology.org/gff3.shtml
- Author:
- Scooter Willis
Methods inherited from class org.biojava3.core.sequence.DNASequence |
getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType |
Methods inherited from class org.biojava3.core.sequence.template.AbstractSequence |
addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, 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, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection, toString |
CDSSequence
public CDSSequence(TranscriptSequence parentSequence,
int bioBegin,
int bioEnd,
int phase)
- Parameters:
parentSequence
- bioBegin
- bioEnd
- phase
-
getLength
public int getLength()
- Description copied from interface:
Sequence
- Returns the length of the Sequence
- Specified by:
getLength
in interface Sequence<NucleotideCompound>
- Overrides:
getLength
in class AbstractSequence<NucleotideCompound>
getPhase
public Integer getPhase()
- Returns:
- get the phase
getStrand
public Strand getStrand()
- Returns:
- get the strand
getCodingSequence
public String getCodingSequence()
- A CDS sequence if negative stranded needs to be reverse complement
to represent the actual coding sequence. When getting a ProteinSequence
from a TranscriptSequence this method is callled for each CDSSequence
http://www.sequenceontology.org/gff3.shtml
http://biowiki.org/~yam/bioe131/GFF.ppt
- Returns:
- coding sequence