org.biojava3.core.sequence
Class ExonSequence

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.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.biojava3.core.sequence.DNASequence
DNASequence.DNAType
 
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence
AbstractSequence.AnnotationType
 
Constructor Summary
ExonSequence(GeneSequence parentGeneSequence, int bioBegin, int bioEnd)
          Need a parent gene sequence and the bioBegin and bioEnd.
 
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
 

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>