java.lang.Iterable<NucleotideCompound>
, Accessioned
, Sequence<NucleotideCompound>
public class GeneSequence extends DNASequence
AbstractSequence.AnnotationType
DNASequence.DNAType
Constructor | Description |
---|---|
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.
|
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
|
java.util.ArrayList<ExonSequence> |
getExonSequences() |
Get the exons as an ArrayList
|
java.util.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(java.lang.String accession) |
Get the transcript sequence by accession
|
java.util.LinkedHashMap<java.lang.String,TranscriptSequence> |
getTranscripts() |
Get the collection of transcription sequences assigned to this gene
|
ExonSequence |
removeExon(java.lang.String accession) |
Remove the exon sequence
|
IntronSequence |
removeIntron(java.lang.String accession) |
Remove the intron by accession
|
TranscriptSequence |
removeTranscript(java.lang.String accession) |
Remove the transcript sequence from the gene
|
void |
setStrand(Strand strand) |
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
getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType
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 inheritpublic ChromosomeSequence getParentChromosomeSequence()
public int getLength()
Sequence
getLength
in interface Sequence<NucleotideCompound>
getLength
in class AbstractSequence<NucleotideCompound>
public void addIntronsUsingExons() throws java.lang.Exception
java.lang.Exception
public Strand getStrand()
public void setStrand(Strand strand)
strand
- the strand to setpublic TranscriptSequence getTranscript(java.lang.String accession)
accession
- public java.util.LinkedHashMap<java.lang.String,TranscriptSequence> getTranscripts()
public TranscriptSequence removeTranscript(java.lang.String accession)
accession
- public TranscriptSequence addTranscript(AccessionID accession, int begin, int end) throws java.lang.Exception
accession
- begin
- end
- java.lang.Exception
- If the accession id is already usedpublic IntronSequence removeIntron(java.lang.String accession)
accession
- public IntronSequence addIntron(AccessionID accession, int begin, int end) throws java.lang.Exception
accession
- begin
- end
- java.lang.Exception
public ExonSequence removeExon(java.lang.String accession)
accession
- public ExonSequence addExon(AccessionID accession, int begin, int end) throws java.lang.Exception
accession
- begin
- end
- java.lang.Exception
public java.util.ArrayList<ExonSequence> getExonSequences()
public java.util.ArrayList<IntronSequence> getIntronSequences()
public DNASequence getSequence5PrimeTo3Prime()