SequenceFeature display added

[jalview.git] / src / jalview / analysis / AlignmentUtil.java

diff --git a/src/jalview/analysis/AlignmentUtil.java b/src/jalview/analysis/AlignmentUtil.java
index 5a773a0..1e0011a 100755 (executable)
--- a/src/jalview/analysis/AlignmentUtil.java
+++ b/src/jalview/analysis/AlignmentUtil.java
@@ -226,4 +226,114 @@ public class AlignmentUtil {
          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