org.biojava3.core.sequence
Class CDSSequence

java.lang.Object
  extended by org.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>
      extended by org.biojava3.core.sequence.DNASequence
          extended by 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

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
 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.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 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