Package org.biojava.nbio.core.sequence

Class CDSSequence

java.lang.Object

org.biojava.nbio.core.sequence.template.AbstractSequence<NucleotideCompound>

org.biojava.nbio.core.sequence.DNASequence

org.biojava.nbio.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

Nested Class Summary

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

DNASequence.DNAType

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

AbstractSequence.AnnotationType

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
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
Integer	getPhase()
Strand	getStrand()

Methods inherited from class org.biojava.nbio.core.sequence.DNASequence

getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, setDNAType

Methods inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence

addFeature, addFeature, addNote, countCompounds, equals, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getComments, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatureRetriever, getFeatures, getFeatures, getFeatures, getFeaturesByType, getFeaturesKeyWord, getIndexOf, getInverse, getLastIndexOf, getNotesList, getOriginalHeader, getParentSequence, getProxySequenceReader, getReferences, getSequenceAsString, getSequenceAsString, getSequenceScore, getSource, getSubSequence, getTaxonomy, getUserCollection, hashCode, initSequenceStorage, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setComments, setCompoundSet, setDatabaseReferences, setDescription, setFeatureRetriever, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setReferences, setSequenceScore, setSource, setTaxonomy, setUserCollection, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Details

CDSSequence

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

Parameters:

parentSequence -

bioBegin -

bioEnd -

phase -

Throws:

IllegalArgumentException - if parentSequence is incompatible with DNACompoundSet

Method Details

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>

Returns:

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