Package org.biojava.nbio.core.sequence

Class GeneSequence

java.lang.Object

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

org.biojava.nbio.core.sequence.DNASequence

org.biojava.nbio.core.sequence.GeneSequence

All Implemented Interfaces:

Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>

public class GeneSequence
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
GeneSequence(ChromosomeSequence parentSequence, int begin, int end, Strand strand)	Deprecated.
GeneSequence(ChromosomeSequence parentSequence, AccessionID accessionId, int begin, int end, Strand strand)	A class that keeps track of the details of a GeneSequence which is difficult to properly model.

Method Summary

Modifier and Type	Method	Description
ExonSequence	addExon(AccessionID accession, int begin, int end)	Add an ExonSequence mainly used to mark as a feature
IntronSequence	addIntron(AccessionID accession, int begin, int end)	Add an Intron Currently used to mark an IntronSequence as a feature
void	addIntronsUsingExons()	Once everything has been added to the gene sequence where you might have added exon sequences only then you can infer the intron sequences and add them.
TranscriptSequence	addTranscript(AccessionID accession, int begin, int end)	Add a transcription sequence to a gene which describes a ProteinSequence
ArrayList<ExonSequence>	getExonSequences()	Get the exons as an ArrayList.
ArrayList<IntronSequence>	getIntronSequences()	Get the introns as an ArrayList.
int	getLength()	Returns the length of the Sequence
ChromosomeSequence	getParentChromosomeSequence()	The parent ChromosomeSequence which contains the actual DNA sequence data
DNASequence	getSequence5PrimeTo3Prime()	Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction Returns the DNASequence representative of the 5' and 3' reading based on strand
Strand	getStrand()	A gene should have Strand
TranscriptSequence	getTranscript(String accession)	Get the transcript sequence by accession
LinkedHashMap<String,TranscriptSequence>	getTranscripts()	Get the collection of transcription sequences assigned to this gene
ExonSequence	removeExon(String accession)	Remove the exon sequence
IntronSequence	removeIntron(String accession)	Remove the intron by accession
TranscriptSequence	removeTranscript(String accession)	Remove the transcript sequence from the gene
void	setStrand(Strand strand)

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

GeneSequence

public GeneSequence(ChromosomeSequence parentSequence,
                    int begin,
                    int end,
                    Strand strand)

Deprecated.

Use GeneSequence(ChromosomeSequence parentSequence, AccessionID accessionId, int begin, int end, Strand strand) which mandates an accessionID.

Parameters:

parentSequence -

begin -

end - inclusive of end

strand - force a gene to have strand and transcription sequence will inherit

GeneSequence

public GeneSequence(ChromosomeSequence parentSequence,
                    AccessionID accessionId,
                    int begin,
                    int end,
                    Strand strand)

A class that keeps track of the details of a GeneSequence which is difficult to properly model. Two important concepts that is difficult to make everything flexible but still work. You can have GFF features that only describe Exons or Exons/Introns or CDS regions and one or more Transcriptions. You can have exon sequences but that does not imply transcription to the actual protein. The GeneSequence will keep track of Exons and Introns but to get a Protein sequence you need to start with a TranscriptSequence and then add CDS sequences. This is also a key class in the biojava-3-genome module for reading and writing GFF3 files

Parameters:

parentSequence -

accessionId - An identifier for the gene.

begin -

end -

strand - force a gene to have strand and transcription sequence will inherit

Method Detail

getParentChromosomeSequence

public ChromosomeSequence getParentChromosomeSequence()

The parent ChromosomeSequence which contains the actual DNA sequence data

Returns:

Chromosome sequence

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>

addIntronsUsingExons

public void addIntronsUsingExons()
                          throws Exception

Once everything has been added to the gene sequence where you might have added exon sequences only then you can infer the intron sequences and add them. You may also have the case where you only added one or more TranscriptSequences and from that you can infer the exon sequences and intron sequences. Currently not implement

Throws:

Exception

getStrand

public Strand getStrand()

A gene should have Strand

Returns:

the strand

setStrand

public void setStrand(Strand strand)

Parameters:

strand - the strand to set

getTranscript

public TranscriptSequence getTranscript(String accession)

Get the transcript sequence by accession

Parameters:

accession -

Returns:

the transcript

getTranscripts

public LinkedHashMap<String,TranscriptSequence> getTranscripts()

Get the collection of transcription sequences assigned to this gene

Returns:

transcripts

removeTranscript

public TranscriptSequence removeTranscript(String accession)

Remove the transcript sequence from the gene

Parameters:

accession -

Returns:

transcriptsequence

addTranscript

public TranscriptSequence addTranscript(AccessionID accession,
                                        int begin,
                                        int end)
                                 throws Exception

Add a transcription sequence to a gene which describes a ProteinSequence

Parameters:

accession -

begin -

end -

Returns:

transcript sequence

Throws:

Exception - If the accession id is already used

removeIntron

public IntronSequence removeIntron(String accession)

Remove the intron by accession

Parameters:

accession -

Returns:

the removed intron sequence, or null if no intron with that accession exists.

addIntron

public IntronSequence addIntron(AccessionID accession,
                                int begin,
                                int end)
                         throws Exception

Add an Intron Currently used to mark an IntronSequence as a feature

Parameters:

accession -

begin -

end -

Returns:

intron sequence

Throws:

Exception

removeExon

public ExonSequence removeExon(String accession)

Remove the exon sequence

Parameters:

accession -

Returns:

exon sequence

addExon

public ExonSequence addExon(AccessionID accession,
                            int begin,
                            int end)

Add an ExonSequence mainly used to mark as a feature

Parameters:

accession -

begin -

end -

Returns:

exon sequence

Throws:

IllegalArgumentException - if accessionID is already added.

getExonSequences

public ArrayList<ExonSequence> getExonSequences()

Get the exons as an ArrayList. Modifying this list will not modify the underlying collection

Returns:

exons

getIntronSequences

public ArrayList<IntronSequence> getIntronSequences()

Get the introns as an ArrayList. Modifying this list will not modify the underlying collection

Returns:

introns

getSequence5PrimeTo3Prime

public DNASequence getSequence5PrimeTo3Prime()

Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction Returns the DNASequence representative of the 5' and 3' reading based on strand

Returns:

dna sequence or null if sequence could not be generated.