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:

java.lang.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.template.AbstractSequence
  AbstractSequence.AnnotationType
- Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.DNASequence
  DNASequence.DNAType

Constructor Summary

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type Method Description

int getLength()
Returns the length of the Sequence
- 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 org.biojava.nbio.core.sequence.DNASequence
  getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType
- Methods inherited from interface java.lang.Iterable
  forEach, spliterator
- Methods inherited from class java.lang.Object
  clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getLength()`	Returns the length of the Sequence

- 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>

Class ExonSequence

Nested Class Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from interface java.lang.Iterable

Methods inherited from class java.lang.Object

Constructor Detail

ExonSequence

Method Detail

getLength