From 58c1349375691d2285976352f6947a835e745c7c Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 21 Sep 2017 16:27:01 +0100
Subject: [PATCH] JAL-2738 add chromosome coordinate mappings to transcripts

---
 src/jalview/ext/ensembl/EnsemblGene.java |   48 ++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 365c1c2..32b7c7c 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -23,6 +23,7 @@ package jalview.ext.ensembl;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GeneLoci;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -401,6 +402,8 @@ public class EnsemblGene extends EnsemblSeqProxy
     cdna.transferFeatures(gene.getFeatures().getPositionalFeatures(),
             transcript.getDatasetSequence(), mapping, parentId);
 
+    mapTranscriptToChromosome(transcript, gene, mapping);
+
     /*
      * fetch and save cross-references
      */
@@ -415,6 +418,51 @@ public class EnsemblGene extends EnsemblSeqProxy
   }
 
   /**
+   * If the gene has a mapping to chromosome coordinates, derive the transcript
+   * chromosome regions and save on the transcript sequence
+   * 
+   * @param transcript
+   * @param gene
+   * @param mapping
+   *          the mapping from gene to transcript positions
+   */
+  protected void mapTranscriptToChromosome(Sequence transcript,
+          SequenceI gene, MapList mapping)
+  {
+    GeneLoci loci = ((Sequence) gene).getGeneLoci();
+    if (loci == null)
+    {
+      return;
+    }
+
+    /*
+     * patch to ensure gene to chromosome mapping is complete
+     * (in case created before gene length was known)
+     */
+    MapList geneMapping = loci.getMapping();
+    if (geneMapping.getFromRanges().get(0)[1] == 0)
+    {
+      geneMapping.getFromRanges().get(0)[0] = gene.getStart();
+      geneMapping.getFromRanges().get(0)[1] = gene.getEnd();
+    }
+
+    List<int[]> exons = mapping.getFromRanges();
+    List<int[]> transcriptLoci = new ArrayList<>();
+    
+    for (int[] exon : exons) {
+      transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
+    }
+
+    List<int[]> transcriptRange = Arrays.asList(new int[] {
+        transcript.getStart(), transcript.getEnd() });
+    MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
+    GeneLoci gl = new GeneLoci(loci.getSpecies(), loci.getReference(),
+            loci.getChromosome(), mapList, loci.isForwardStrand());
+
+    transcript.setGeneLoci(gl);
+  }
+
+  /**
    * Returns the 'transcript_id' property of the sequence feature (or null)
    * 
    * @param feature
-- 
1.7.10.2