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JAL-2738 use complement base for a VCF variant on reverse strand gene
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblGene.java
diff --git
a/src/jalview/ext/ensembl/EnsemblGene.java
b/src/jalview/ext/ensembl/EnsemblGene.java
index
f975ac8
..
45e8e34
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblGene.java
+++ b/
src/jalview/ext/ensembl/EnsemblGene.java
@@
-429,7
+429,7
@@
public class EnsemblGene extends EnsemblSeqProxy
protected void mapTranscriptToChromosome(Sequence transcript,
SequenceI gene, MapList mapping)
{
protected void mapTranscriptToChromosome(Sequence transcript,
SequenceI gene, MapList mapping)
{
- GeneLoci loci = ((Sequence) gene).getGeneLoci();
+ GeneLoci loci = gene.getGeneLoci();
if (loci == null)
{
return;
if (loci == null)
{
return;
@@
-448,8
+448,9
@@
public class EnsemblGene extends EnsemblSeqProxy
List<int[]> exons = mapping.getFromRanges();
List<int[]> transcriptLoci = new ArrayList<>();
List<int[]> exons = mapping.getFromRanges();
List<int[]> transcriptLoci = new ArrayList<>();
-
- for (int[] exon : exons) {
+
+ for (int[] exon : exons)
+ {
transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
}
transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
}