org.biojava.nbio.core.sequence

Class ExonSequence

java.lang.Object

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

org.biojava.nbio.core.sequence.DNASequence

org.biojava.nbio.core.sequence.ExonSequence

All Implemented Interfaces:

Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>

public class ExonSequence
extends DNASequence

A gene contains a collection of Exon sequences

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 and Description
ExonSequence(GeneSequence parentGeneSequence, int bioBegin, int bioEnd) Need a parent gene sequence and the bioBegin and bioEnd.

Method Summary

Modifier and Type	Method and 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

Constructor Detail

ExonSequence

public ExonSequence(GeneSequence parentGeneSequence,
                    int bioBegin,
                    int bioEnd)

Need a parent gene sequence and the bioBegin and bioEnd. An Exon sequence doesn't actually imply what the protein coding sequence will be. This is a little difficult to model and have it make sense. A gene has a collection of Exon and Intron sequences where the Exon sequences will join up. A gene sequences has a collection of different possible isoform proteins based on the transcription rules. A TranscriptionSequence will contain CDSSequence where the CDSSequence will be contained in the ExonSequence. Thus a ExonSequence is the union of overlapping CDSSequences.

Parameters:

parentGeneSequence -

bioBegin -

bioEnd -

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>