public class TranscriptModelBuilder extends Object
TranscriptModel
objects field-by-field.
In this sense, it is similar to StringBuilder
for building String
objects.
Usage:
TranscriptModelBuilder
builder = new TranscriptInfoBuilder(); builder.setStrand
('-'); builder.setAccession
("<accession>"); // ...TranscriptModel
transcript = builder.build
();
Constructor and Description |
---|
TranscriptModelBuilder() |
Modifier and Type | Method and Description |
---|---|
void |
addExonRegion(GenomeInterval exonRegion) |
TranscriptModel |
build() |
void |
clearAltGeneIDs()
Clear alternative geneIDs map
|
void |
clearExonRegions()
Clear exon regions list
|
String |
getAccession() |
Map<String,String> |
getAltGeneIDs() |
GenomeInterval |
getCDSRegion() |
ArrayList<GenomeInterval> |
getExonRegions() |
String |
getGeneID() |
String |
getGeneSymbol() |
String |
getSequence() |
Strand |
getStrand() |
int |
getTranscriptSupportLevel() |
GenomeInterval |
getTXRegion() |
void |
reset()
Reset the builder into the state after initialization.
|
void |
setAccession(String accession) |
void |
setCDSRegion(GenomeInterval cdsRegion) |
void |
setGeneID(String geneID) |
void |
setGeneSymbol(String geneSymbol) |
void |
setSequence(String sequence) |
void |
setStrand(Strand strand) |
void |
setTranscriptSupportLevel(int transcriptSupportLevel) |
void |
setTXRegion(GenomeInterval txRegion) |
public void reset()
public TranscriptModel build()
TranscriptModel
with the currently set configuration.public Strand getStrand()
public void setStrand(Strand strand)
strand
- the strand to setpublic String getAccession()
public void setAccession(String accession)
accession
- the accession to setpublic String getGeneSymbol()
public void setGeneSymbol(String geneSymbol)
geneSymbol
- the geneSymbol to setpublic GenomeInterval getTXRegion()
public void setTXRegion(GenomeInterval txRegion)
txRegion
- the txRegion to setpublic GenomeInterval getCDSRegion()
public void setCDSRegion(GenomeInterval cdsRegion)
cdsRegion
- the cdsRegion to setpublic ArrayList<GenomeInterval> getExonRegions()
public void clearExonRegions()
public void clearAltGeneIDs()
public void addExonRegion(GenomeInterval exonRegion)
exonRegion
- interval to appendpublic String getSequence()
public void setSequence(String sequence)
sequence
- the sequence to setpublic String getGeneID()
public void setGeneID(String geneID)
geneID
- the geneID to setpublic int getTranscriptSupportLevel()
TranscriptSupportLevels
public void setTranscriptSupportLevel(int transcriptSupportLevel)
transcriptSupportLevel
- set transcript resource levelTranscriptSupportLevels
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