Package org.biojava.nbio.core.sequence

Class StopCodonSequence

java.lang.Object

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

org.biojava.nbio.core.sequence.DNASequence

org.biojava.nbio.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.biojava.nbio.core.sequence.DNASequence

DNASequence.DNAType

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

AbstractSequence.AnnotationType

Field Summary

Fields

Modifier and Type	Field	Description
DNASequence	parentGeneSequence

Constructor Summary

Constructors

Constructor	Description
StopCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end)

Method Summary

Modifier and Type	Method	Description
int	getLength()	Returns the length of the Sequence

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

getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, 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, 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

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>