+ }\r
+ }\r
+ }\r
+ Iterator<List<String>> idset = ids.iterator();\r
+ Iterator<List<DBRefEntry>> idobjset = idobj.iterator();\r
+ Iterator<Map<String, SequenceI>> seqset = sqset.iterator();\r
+ for (jalviewSourceI source : srcobj)\r
+ {\r
+ processResponse(seqset.next(), source, idset.next(), idobjset.next(),\r
+ results.get(source.getSourceURL()),\r
+ errors.get(source.getSourceURL()));\r
+ }\r
+ }\r
+\r
+ private void processResponse(Map<String, SequenceI> sequencemap,\r
+ jalviewSourceI jvsource, List<String> ids,\r
+ List<DBRefEntry> idobj, Map<List<String>, DasGFFAdapter> results,\r
+ Map<List<String>, Exception> errors)\r
+ {\r
+ Set<SequenceI> sequences = new HashSet<SequenceI>();\r
+ String source = jvsource.getSourceURL();\r
+ // process features\r
+ DasGFFAdapter result = (results == null) ? null : results.get(ids);\r
+ Exception error = (errors == null) ? null : errors.get(ids);\r
+ if (result == null)\r
+ {\r
+ debug("das source " + source + " could not be contacted. "\r
+ + (error == null ? "" : error.toString()));\r
+ }\r
+ else\r
+ {\r
+\r
+ GFFAdapter gff = result.getGFF();\r
+ List<SEGMENT> segments = gff.getSegments();\r
+ List<ERRORSEGMENT> errorsegs = gff.getErrorSegments();\r
+ List<UNKNOWNFEATURE> unkfeats = gff.getUnknownFeatures();\r
+ List<UNKNOWNSEGMENT> unksegs = gff.getUnknownSegments();\r
+ debug("das source " + source + " returned " + gff.getTotal()\r
+ + " responses. " + (errorsegs != null ? errorsegs.size() : 0)\r
+ + " were incorrect segment queries, "\r
+ + (unkfeats != null ? unkfeats.size() : 0)\r
+ + " were unknown features "\r
+ + (unksegs != null ? unksegs.size() : 0)\r
+ + " were unknown segments and "\r
+ + (segments != null ? segments.size() : 0)\r
+ + " were segment responses.");\r
+ Iterator<DBRefEntry> dbr = idobj.iterator();\r
+ if (segments != null)\r
+ {\r
+ for (SEGMENT seg : segments)\r
+ {\r
+ String id = seg.getId();\r
+ DBRefEntry dbref = idobj.get(ids.indexOf(id));\r
+ SequenceI sequence = sequencemap.get(id);\r
+ boolean added = false;\r
+ sequences.add(sequence);\r
+\r
+ for (FEATURE feat : seg.getFEATURE())\r
+ {\r
+ // standard DAS feature-> jalview sequence feature transformation\r
+ SequenceFeature f = newSequenceFeature(feat, jvsource.getTitle());\r
+ if (!parseSeqFeature(sequence, f, feat, jvsource))\r
+ {\r
+ if (dbref.getMap() != null && f.getBegin() > 0\r
+ && f.getEnd() > 0)\r
+ {\r
+ debug("mapping from " + f.getBegin() + " - " + f.getEnd());\r
+ SequenceFeature vf[] = null;\r
+\r
+ try\r
+ {\r
+ vf = dbref.getMap().locateFeature(f);\r
+ } catch (Exception ex)\r
+ {\r
+ Cache.log\r
+ .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");\r
+ Cache.log.info("Mapping feature from " + f.getBegin()\r
+ + " to " + f.getEnd() + " in dbref "\r
+ + dbref.getAccessionId() + " in "\r
+ + dbref.getSource());\r
+ Cache.log.info("using das Source " + source);\r
+ Cache.log.info("Exception", ex);\r
+ }\r
+\r
+ if (vf != null)\r
+ {\r
+ for (int v = 0; v < vf.length; v++)\r
+ {\r
+ debug("mapping to " + v + ": " + vf[v].getBegin()\r
+ + " - " + vf[v].getEnd());\r
+ sequence.addSequenceFeature(vf[v]);\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ sequence.addSequenceFeature(f);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ featuresAdded(sequences);\r
+ }\r
+ else\r
+ {\r
+ // System.out.println("No features found for " + seq.getName()\r
+ // + " from: " + e.getDasSource().getNickname());\r
+ }\r