org.biojava3.core.sequence
Class StopCodonSequence

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.StopCodonSequence
All Implemented Interfaces:
Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>

public class StopCodonSequence
extends DNASequence

Used to map the stop codon sequence on a gene

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
 
Field Summary
 DNASequence parentGeneSequence
           
 
Constructor Summary
StopCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end)
           
 
Method Summary
 int getLength()
          Returns the length of the Sequence
 
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
 

Field Detail

parentGeneSequence

public DNASequence parentGeneSequence
Constructor Detail

StopCodonSequence

public StopCodonSequence(TranscriptSequence parentGeneSequence,
                         int begin,
                         int end)
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>