Package org.biojava.nbio.core.sequence
Class CDSSequence
- java.lang.Object
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- org.biojava.nbio.core.sequence.template.AbstractSequence<NucleotideCompound>
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- org.biojava.nbio.core.sequence.DNASequence
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- org.biojava.nbio.core.sequence.CDSSequence
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- 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 parentTranscriptSequence
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}- Author:
- Scooter Willis
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Nested Class Summary
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Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.DNASequence
DNASequence.DNAType
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Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence
AbstractSequence.AnnotationType
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Constructor Summary
Constructors Constructor Description CDSSequence(TranscriptSequence parentSequence, int bioBegin, int bioEnd, int phase)
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Method Summary
All Methods Instance Methods Concrete Methods 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 Sequencejava.lang.Integer
getPhase()
Strand
getStrand()
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Methods inherited from class org.biojava.nbio.core.sequence.DNASequence
getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType
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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, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setComments, setCompoundSet, setDatabaseReferences, setDescription, setFeatureRetriever, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setReferences, setSequenceScore, setSource, setTaxonomy, setUserCollection, toString
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Constructor Detail
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CDSSequence
public CDSSequence(TranscriptSequence parentSequence, int bioBegin, int bioEnd, int phase)
- Parameters:
parentSequence
-bioBegin
-bioEnd
-phase
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Method Detail
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getLength
public int getLength()
Description copied from interface:Sequence
Returns the length of the Sequence- Specified by:
getLength
in interfaceSequence<NucleotideCompound>
- Overrides:
getLength
in classAbstractSequence<NucleotideCompound>
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getPhase
public java.lang.Integer getPhase()
- Returns:
- get the phase
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getStrand
public Strand getStrand()
- Returns:
- get the strand
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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 {@link http://www.sequenceontology.org/gff3.shtml} {@link http://biowiki.org/~yam/bioe131/GFF.ppt}- Returns:
- coding sequence
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