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:

java.lang.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

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence

DNASequence.DNAType

Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence

AbstractSequence.AnnotationType

Constructor Summary

CDSSequence(TranscriptSequence parentSequence, int bioBegin, int bioEnd, int phase)

Method Summary

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()

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

CDSSequence

public CDSSequence(TranscriptSequence parentSequence,
                   int bioBegin,
                   int bioEnd,
                   int phase)

Parameters:

parentSequence -

bioBegin -

bioEnd -

phase -

Method Detail

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 java.lang.Integer getPhase()

Returns:

get the phase

getStrand

public Strand getStrand()

Returns:

get the strand

getCodingSequence

public java.lang.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