Now displays sequence features

diff --git a/src/jalview/analysis/AlignmentUtil.java b/src/jalview/analysis/AlignmentUtil.java
index 1e0011a..24d23b2 100755 (executable)
--- a/src/jalview/analysis/AlignmentUtil.java
+++ b/src/jalview/analysis/AlignmentUtil.java
@@ -1,9 +1,7 @@
 package jalview.analysis;\r
 \r
 import jalview.datamodel.*;\r
-import jalview.io.*;\r
 import jalview.util.*;\r
-\r
 import java.util.*;\r
 \r
 public class AlignmentUtil {\r
@@ -226,114 +224,9 @@ public class AlignmentUtil {
          return pos;\r
     }\r
 \r
-    class FeatureThread extends Thread\r
-    {\r
-\r
-    }\r
-\r
-    public static void addUniprotFeatures(AlignmentI align)\r
+    public static void fetchSequenceFeatures(AlignmentI al, jalview.gui.AlignmentPanel ap)\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
+      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, ap);\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