protected Exon |
SnpEffPredictorFactoryGff.addExon(Transcript tr,
GffMarker gffMarker,
java.lang.String exonId) |
Create a new exon
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protected java.util.List<Exon> |
SnpEffPredictorFactoryGff.addExons(GffMarker gffMarker) |
Create and add a new exon
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protected Gene |
SnpEffPredictorFactoryGff.addGene(GffMarker gffMarker) |
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protected Gene |
SnpEffPredictorFactoryGff.addGene(GffMarker gffMarker,
boolean findNextGeneId) |
Create and add a gene based on GffMarker
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protected IntergenicConserved |
SnpEffPredictorFactoryGff.addIntergenicConserved(GffMarker gffMarker) |
Add an intergenic conserved region
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protected boolean |
SnpEffPredictorFactoryGff.addInterval(GffMarker gffMarker) |
Add interval based on GffMarker data
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protected IntronConserved |
SnpEffPredictorFactoryGff.addIntronConserved(GffMarker gffMarker) |
Add an intron conserved region
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protected java.util.List<Utr3prime> |
SnpEffPredictorFactoryGff.addUtr3(GffMarker gffMarker) |
Create new UTR3primes
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protected java.util.List<Utr5prime> |
SnpEffPredictorFactoryGff.addUtr5(GffMarker gffMarker) |
Create UTR5primes
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protected Exon |
SnpEffPredictorFactoryGff.findOrCreateExon(java.lang.String parentId,
GffMarker gffMarker) |
Find an exon for a given parentId
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protected Gene |
SnpEffPredictorFactoryGff.findOrCreateGene(GffMarker gffMarker) |
Find or create a gene based on GffMarker
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protected Transcript |
SnpEffPredictorFactoryGff.findOrCreateTranscript(GffMarker gffMarker) |
Create and add a transcript based on GffMarker
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