org.biojava.nbio.core.sequence.IntronSequence

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

public class IntronSequence extends DNASequence

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

Description

IntronSequence(GeneSequence parentGeneSequence, int begin, int end)

Place holder for Intron sequence features
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, 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, toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Constructor Details
- IntronSequence
  
  public IntronSequence(GeneSequence parentGeneSequence, int begin, int end)
  
  Place holder for Intron sequence features
  
  Parameters:
  
  parentGeneSequence -
  
  begin -
  
  end -
Method Details
- 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>

Class IntronSequence

Nested Class Summary

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

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

Constructor Summary

Method Summary

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

Methods inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Details

IntronSequence

Method Details

getLength