- 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