- Thread thread = new Thread(this);\r
- thread.start();\r
- }\r
- /**\r
- * creates a jalview sequence feature from a das feature document\r
- * @param dasfeature\r
- * @return sequence feature object created using dasfeature information\r
- */\r
- SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
- {\r
- try {\r
- /**\r
- * Different qNames for a DAS Feature - are string keys to the HashMaps in features\r
- * "METHOD") ||\r
- qName.equals("TYPE") ||\r
- qName.equals("START") ||\r
- qName.equals("END") ||\r
- qName.equals("NOTE") ||\r
- qName.equals("LINK") ||\r
- qName.equals("SCORE")\r
- */\r
- String desc = new String();\r
- if (dasfeature.containsKey("NOTE"))\r
- desc+=(String) dasfeature.get("NOTE");\r
-\r
-\r
- int start = 0, end = 0;\r
- float score = 0f;\r
-\r
- try{ start = Integer.parseInt( dasfeature.get("START").toString()); }\r
- catch( Exception ex){}\r
- try{ end = Integer.parseInt( dasfeature.get("END").toString()); }\r
- catch (Exception ex){}\r
- try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }\r
- catch (Exception ex){}\r
-\r
-\r
- SequenceFeature f = new SequenceFeature(\r
- (String) dasfeature.get("TYPE"),\r
- desc,\r
- start,\r
- end,\r
- score,\r
- nickname);\r
-\r
- if (dasfeature.containsKey("LINK"))\r
- {\r
- f.addLink(f.getType()+" "+f.begin+"_"+f.end\r
- +"|"+ dasfeature.get("LINK"));\r
- }\r
- // (String) dasfeature.get("ID"),\r
- //// (String) dasfeature.get("METHOD"),\r
- // (String) dasfeature.get("SCORE"),\r
- // null\r
- // );\r
-\r
- // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
- return f;\r
- }\r
- catch (Exception e) {\r
- e.printStackTrace();\r
- Cache.log.debug("Failed to parse "+dasfeature.toString(), e);\r
- return null;\r
- }\r
- }\r
- /**\r
- * fetch and add das features to a sequence using the given source URL and Id to create a feature request\r
- * @param seq\r
- * @param SourceUrl\r
- * @param id\r
- */\r
- protected void createFeatureFetcher(final Sequence seq,\r
- final String sourceUrl,\r
- String id,\r
- String nickname) {\r
- //////////////\r
- /// fetch DAS features\r
- final Das1Source source = new Das1Source();\r
- source.setUrl(sourceUrl);\r
- source.setNickname(nickname);\r
-\r
-\r
- Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
- sourceUrl);\r
- if (id != null && id.length() > 0)\r
+ int uniprotCount = 0;\r
+ for (int i = 0; i < selectedSources.size(); i++)\r
+ {\r
+ DasSource source = (DasSource) selectedSources.elementAt(i);\r
+ DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
+ for (int c = 0; c < coords.length; c++)\r
+ {\r
+ if (coords[c].getName().indexOf("UniProt") > -1)\r
+ {\r
+ uniprotCount++;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ int refCount = 0;\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ DBRefEntry[] dbref = sequences[i].getDBRef();\r
+ if (dbref != null)\r
+ {\r
+ for (int j = 0; j < dbref.length; j++)\r
+ {\r
+ if (dbref[j].getSource()\r
+ .equals(jalview.datamodel.DBRefSource.UNIPROT))\r