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java.lang.Objectorg.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>
org.biojava3.core.sequence.DNASequence
org.biojava3.core.sequence.GeneSequence
public class GeneSequence
Nested Class Summary |
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Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence |
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DNASequence.DNAType |
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence |
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AbstractSequence.AnnotationType |
Constructor Summary | |
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GeneSequence(ChromosomeSequence parentSequence,
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 | |
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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)
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Methods inherited from class org.biojava3.core.sequence.DNASequence |
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getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public GeneSequence(ChromosomeSequence parentSequence, int begin, int end, Strand strand)
parentDNASequence
- begin
- end
- inclusive of endstrand
- force a gene to have strand and transcription sequence will inheritMethod Detail |
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public ChromosomeSequence getParentChromosomeSequence()
public int getLength()
Sequence
getLength
in interface Sequence<NucleotideCompound>
getLength
in class AbstractSequence<NucleotideCompound>
public void addIntronsUsingExons() throws Exception
Exception
public Strand getStrand()
public void setStrand(Strand strand)
strand
- the strand to setpublic TranscriptSequence getTranscript(String accession)
accession
-
public LinkedHashMap<String,TranscriptSequence> getTranscripts()
public TranscriptSequence removeTranscript(String accession)
accession
-
public TranscriptSequence addTranscript(AccessionID accession, int begin, int end) throws Exception
accession
- begin
- end
-
Exception
- If the accession id is already usedpublic IntronSequence removeIntron(String accession)
accession
-
public IntronSequence addIntron(AccessionID accession, int begin, int end) throws Exception
accession
- begin
- end
-
Exception
public ExonSequence removeExon(String accession)
accession
-
public ExonSequence addExon(AccessionID accession, int begin, int end) throws Exception
accession
- begin
- end
-
Exception
public ArrayList<ExonSequence> getExonSequences()
public ArrayList<IntronSequence> getIntronSequences()
public DNASequence getSequence5PrimeTo3Prime()
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