CDSSequence (biojava 6.0.0 API)

java.lang.Object
- org.biojava.nbio.core.sequence.template.AbstractSequence<NucleotideCompound>
- - org.biojava.nbio.core.sequence.DNASequence
  - - org.biojava.nbio.core.sequence.CDSSequence

All Implemented Interfaces:

Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>
```
public class CDSSequence
extends DNASequence
```
Represents a exon or coding sequence in a gene. It has a parent TranscriptSequence where a TranscriptSequence is the child of a GeneSequence Not important for protein construction but the phase is used if outputting the gene to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}

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

CDSSequence(TranscriptSequence parentSequence, int bioBegin, int bioEnd, int phase)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`String`	`getCodingSequence()`	A CDS sequence if negative stranded needs to be reverse complement to represent the actual coding sequence.
`int`	`getLength()`	Returns the length of the Sequence
`Integer`	`getPhase()`
`Strand`	`getStrand()`

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
  - CDSSequence
```
public CDSSequence(TranscriptSequence parentSequence,
                   int bioBegin,
                   int bioEnd,
                   int phase)
```
    Parameters:
    
    parentSequence -
    
    bioBegin -
    
    bioEnd -
    
    phase -
- 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>
  - getPhase
```
public Integer getPhase()
```
    Returns:
    
    get the phase
  - getStrand
```
public Strand getStrand()
```
    Returns:
    
    get the strand
  - getCodingSequence
```
public String getCodingSequence()
```
    A CDS sequence if negative stranded needs to be reverse complement to represent the actual coding sequence. When getting a ProteinSequence from a TranscriptSequence this method is callled for each CDSSequence {@link http://www.sequenceontology.org/gff3.shtml} {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
    
    Returns:
    
    coding sequence