Package org.biojava.nbio.core.sequence

Class TranscriptSequence

java.lang.Object

org.biojava.nbio.core.sequence.template.AbstractSequence<NucleotideCompound>

org.biojava.nbio.core.sequence.DNASequence

org.biojava.nbio.core.sequence.TranscriptSequence

All Implemented Interfaces:

Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>

public class TranscriptSequence
extends DNASequence

This is the sequence if you want to go from a gene sequence to a protein sequence. Need to start with a ChromosomeSequence then getting a GeneSequence and then a TranscriptSequence

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
TranscriptSequence(GeneSequence parentDNASequence, int begin, int end)	Deprecated.
TranscriptSequence(GeneSequence parentDNASequence, AccessionID accessionID, int begin, int end)

Method Summary

Modifier and Type	Method	Description
CDSSequence	addCDS(AccessionID accession, int begin, int end, int phase)	Add a Coding Sequence region with phase to the transcript sequence
void	addStartCodonSequence(AccessionID accession, int begin, int end)	Sets the start codon sequence at given begin / end location.
void	addStopCodonSequence(AccessionID accession, int begin, int end)	Sets the stop codon sequence at given begin / end location.
LinkedHashMap<String,CDSSequence>	getCDSSequences()	Get the CDS sequences that have been added to the TranscriptSequences
DNASequence	getDNACodingSequence()	Get the stitched together CDS sequences then maps to the cDNA
int	getLength()	Returns the length of the Sequence
ArrayList<ProteinSequence>	getProteinCDSSequences()	Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet.
ProteinSequence	getProteinSequence()	Get the protein sequence
ProteinSequence	getProteinSequence(TranscriptionEngine engine)	Get the protein sequence with user defined TranscriptEngine
StartCodonSequence	getStartCodonSequence()
StopCodonSequence	getStopCodonSequence()
Strand	getStrand()
CDSSequence	removeCDS(String accession)	Remove a CDS or coding sequence from the transcript sequence

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

getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, 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, initSequenceStorage, 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

TranscriptSequence

public TranscriptSequence(GeneSequence parentDNASequence,
                          int begin,
                          int end)

Deprecated.

Use public TranscriptSequence(GeneSequence parentDNASequence, AccessionID accessionID, int begin, int end) that requires an explicit accessionID

TranscriptSequence

public TranscriptSequence(GeneSequence parentDNASequence,
                          AccessionID accessionID,
                          int begin,
                          int end)

Parameters:

parentDNASequence -

accessionID -

begin -

end - inclusive of end

Throws:

IllegalArgumentException - if the parentDNASequence is incompatible with DNACompoundSet

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>

getStrand

public Strand getStrand()

Returns:

the strand

removeCDS

public CDSSequence removeCDS(String accession)

Remove a CDS or coding sequence from the transcript sequence

Parameters:

accession -

Returns:

getCDSSequences

public LinkedHashMap<String,CDSSequence> getCDSSequences()

Get the CDS sequences that have been added to the TranscriptSequences

Returns:

addCDS

public CDSSequence addCDS(AccessionID accession,
                          int begin,
                          int end,
                          int phase)
                   throws Exception

Add a Coding Sequence region with phase to the transcript sequence

Parameters:

accession -

begin -

end -

phase - 0,1,2

Returns:

Throws:

Exception

getProteinCDSSequences

public ArrayList<ProteinSequence> getProteinCDSSequences()

Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet. This can be used to map a CDS/exon region of a protein sequence back to the DNA sequence If you have a protein sequence and a predicted gene you can take the predict CDS protein sequences and align back to the protein sequence. If you have errors in mapping the predicted protein CDS regions to an the known protein sequence then you can identify possible errors in the prediction

Returns:

getDNACodingSequence

public DNASequence getDNACodingSequence()

Get the stitched together CDS sequences then maps to the cDNA

Returns:

getProteinSequence

public ProteinSequence getProteinSequence()

Get the protein sequence

Returns:

getProteinSequence

public ProteinSequence getProteinSequence(TranscriptionEngine engine)

Get the protein sequence with user defined TranscriptEngine

Parameters:

engine -

Returns:

getStartCodonSequence

public StartCodonSequence getStartCodonSequence()

Returns:

the startCodonSequence

addStartCodonSequence

public void addStartCodonSequence(AccessionID accession,
                                  int begin,
                                  int end)

Sets the start codon sequence at given begin / end location. Note that calling this method multiple times will replace any existing value.

Parameters:

accession -

begin -

end -

getStopCodonSequence

public StopCodonSequence getStopCodonSequence()

Returns:

the stopCodonSequence

addStopCodonSequence

public void addStopCodonSequence(AccessionID accession,
                                 int begin,
                                 int end)

Sets the stop codon sequence at given begin / end location. Note that calling this method multiple times will replace any existing value.

Parameters:

accession -

begin -

end -