Package 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>
A gene contains a collection of Exon sequences
- Author:
- Scooter Willis
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Nested Class Summary
Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.DNASequence
DNASequence.DNATypeNested classes/interfaces inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence
AbstractSequence.AnnotationType -
Constructor Summary
ConstructorsConstructorDescriptionExonSequence(GeneSequence parentGeneSequence, int bioBegin, int bioEnd) Need a parent gene sequence and the bioBegin and bioEnd. -
Method Summary
Methods inherited from class org.biojava.nbio.core.sequence.DNASequence
getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNATypeMethods inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence
addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatureRetriever, 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, setFeatureRetriever, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection, toStringMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitMethods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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ExonSequence
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-
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Method Details
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getLength
public int getLength()Description copied from interface:SequenceReturns the length of the Sequence- Specified by:
getLengthin interfaceSequence<NucleotideCompound>- Overrides:
getLengthin classAbstractSequence<NucleotideCompound>
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