- /*
- * Build new mappings - from the same protein regions, but now to contiguous
- * exons
- */
- List<int[]> exonRange = new ArrayList<int[]>();
- exonRange.add(new int[]
- { 1, newSequence.length() });
- MapList map = new MapList(exonRange, mapping.getMap().getToRanges(), 3, 1);
- newMapping.addMap(exon.getDatasetSequence(), mapping.getTo(), map);
+ /*
+ * Build new mappings - from the same protein regions, but now to
+ * contiguous exons
+ */
+ List<int[]> exonRange = new ArrayList<int[]>();
+ exonRange.add(new int[]
+ { 1, newSequence.length() });
+ MapList map = new MapList(exonRange, seqMapping.getMap()
+ .getToRanges(),
+ 3, 1);
+ newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
+ MapList cdsToDnaMap = new MapList(dnaExonRanges, exonRange, 1, 1);
+ newMapping.addMap(dnaSeq, exon.getDatasetSequence(), cdsToDnaMap);