return pos;\r
}\r
\r
+ class FeatureThread extends Thread\r
+ {\r
+\r
+ }\r
+\r
+ public static void addUniprotFeatures(AlignmentI align)\r
+ {\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ int seqIndex = 0;\r
+ Vector sequences = align.getSequences();\r
+ SequenceI sequence;\r
+\r
+ while (seqIndex < sequences.size())\r
+ {\r
+ StringBuffer ids = new StringBuffer("uniprot:");\r
+ for (int i=0; seqIndex<sequences.size() && i<50; seqIndex++, i++)\r
+ {\r
+ sequence = (SequenceI) sequences.get(seqIndex);\r
+ ids.append(sequence.getName() + ";");\r
+ }\r
+\r
+ String[] result = ebi.fetchData(ids.toString(), "xml", null);\r
+ sequence = null;\r
+ Vector features = null;\r
+ String type, description, status, start, end, pdb = null;\r
+\r
+ for (int r = 0; r < result.length; r++)\r
+ {\r
+ if(sequence==null && result[r].indexOf("<name>")>-1)\r
+ {\r
+ sequence = align.findName( parseElement( result[r], "<name>" )) ;\r
+ features = new Vector();\r
+ type=""; start="0"; end="0"; description=""; status=""; pdb="";\r
+ }\r
+\r
+ if(sequence==null)\r
+ continue;\r
+\r
+ if( result[r].indexOf("<property type=\"pdb accession\"")>-1)\r
+ {\r
+ pdb = parseValue( result[r], "value=" );\r
+ sequence.setPDBId(pdb);\r
+ }\r
+\r
+ if(result[r].indexOf("feature type")>-1)\r
+ {\r
+ type = parseValue( result[r], "type=" );\r
+ description = parseValue( result[r], "description=" );\r
+ status = parseValue ( result[r], "status=");\r
+\r
+ while( result[r].indexOf("<location>")==-1)\r
+ {\r
+ r++; //<location>\r
+ }\r
+ r++;\r
+ if(result[r].indexOf("begin")>-1)\r
+ {\r
+ start = parseValue( result[r], "position=" );\r
+ end = parseValue( result[++r], "position=" );\r
+ }\r
+ else\r
+ {\r
+ start = parseValue( result[r], "position=" );\r
+ end = parseValue( result[r], "position=" );\r
+ }\r
+ int sstart = Integer.parseInt(start);\r
+ int eend = Integer.parseInt(end);\r
+\r
+ if(sstart>=sequence.getStart() && eend<=sequence.getEnd())\r
+ {\r
+ SequenceFeature sf = new SequenceFeature(type,\r
+ sstart,\r
+ eend,\r
+ description,\r
+ status);\r
+ features.add(sf);\r
+ }\r
+ }\r
+\r
+ if(result[r].indexOf("</entry>")>-1)\r
+ {\r
+ sequence.setSequenceFeatures( features );\r
+ features = null;\r
+ sequence = null;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ static String parseValue(String line, String tag)\r
+ {\r
+\r
+ int index = line.indexOf(tag)+tag.length()+1;\r
+ if(index==tag.length())\r
+ return "";\r
+\r
+ return line.substring( index, line.indexOf("\"", index+1) );\r
+ }\r
+\r
+\r
+ static String parseElement(String line, String tag)\r
+ {\r
+ int index = line.indexOf(tag)+tag.length();\r
+ return line.substring( index, line.indexOf("</") ) ;\r
+ }\r
+\r
+\r
+\r
+\r
+\r
}\r