From 1fbd8cb915ebe49b9d214731b810484a96081528 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 7 Feb 2005 17:05:18 +0000
Subject: [PATCH] Now displays sequence features

---
 src/jalview/analysis/AlignmentUtil.java |  111 +------------------------------
 1 file changed, 2 insertions(+), 109 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtil.java b/src/jalview/analysis/AlignmentUtil.java
index 1e0011a..24d23b2 100755
--- a/src/jalview/analysis/AlignmentUtil.java
+++ b/src/jalview/analysis/AlignmentUtil.java
@@ -1,9 +1,7 @@
 package jalview.analysis;
 
 import jalview.datamodel.*;
-import jalview.io.*;
 import jalview.util.*;
-
 import java.util.*;
 
 public class AlignmentUtil {
@@ -226,114 +224,9 @@ public class AlignmentUtil {
          return pos;
     }
 
-    class FeatureThread extends Thread
-    {
-
-    }
-
-    public static void addUniprotFeatures(AlignmentI align)
+    public static void fetchSequenceFeatures(AlignmentI al, jalview.gui.AlignmentPanel ap)
     {
-      EBIFetchClient ebi = new EBIFetchClient();
-      int seqIndex = 0;
-      Vector sequences = align.getSequences();
-      SequenceI sequence;
-
-      while (seqIndex < sequences.size())
-      {
-        StringBuffer ids = new StringBuffer("uniprot:");
-        for (int i=0; seqIndex<sequences.size() && i<50; seqIndex++, i++)
-        {
-          sequence = (SequenceI) sequences.get(seqIndex);
-          ids.append(sequence.getName() + ";");
-        }
-
-        String[] result = ebi.fetchData(ids.toString(), "xml", null);
-        sequence = null;
-        Vector features = null;
-        String type, description, status, start, end, pdb = null;
-
-        for (int r = 0; r < result.length; r++)
-        {
-          if(sequence==null && result[r].indexOf("<name>")>-1)
-          {
-            sequence = align.findName( parseElement( result[r], "<name>" )) ;
-            features = new Vector();
-            type=""; start="0"; end="0"; description=""; status=""; pdb="";
-          }
-
-          if(sequence==null)
-            continue;
-
-           if( result[r].indexOf("<property type=\"pdb accession\"")>-1)
-           {
-             pdb = parseValue( result[r], "value=" );
-             sequence.setPDBId(pdb);
-           }
-
-           if(result[r].indexOf("feature type")>-1)
-           {
-             type = parseValue( result[r], "type=" );
-             description = parseValue( result[r], "description=" );
-             status = parseValue ( result[r], "status=");
-
-             while( result[r].indexOf("<location>")==-1)
-             {
-                 r++;  //<location>
-             }
-             r++;
-             if(result[r].indexOf("begin")>-1)
-             {
-               start = parseValue( result[r], "position=" );
-               end = parseValue( result[++r], "position=" );
-             }
-             else
-             {
-               start = parseValue( result[r], "position=" );
-               end = parseValue(   result[r], "position=" );
-             }
-             int sstart = Integer.parseInt(start);
-             int eend = Integer.parseInt(end);
-
-             if(sstart>=sequence.getStart() && eend<=sequence.getEnd())
-             {
-               SequenceFeature sf = new SequenceFeature(type,
-                   sstart,
-                   eend,
-                   description,
-                   status);
-               features.add(sf);
-             }
-           }
-
-           if(result[r].indexOf("</entry>")>-1)
-           {
-             sequence.setSequenceFeatures( features );
-             features = null;
-             sequence = null;
-           }
-        }
-      }
+      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, ap);
     }
 
-    static String parseValue(String line, String tag)
-    {
-
-      int index = line.indexOf(tag)+tag.length()+1;
-      if(index==tag.length())
-        return "";
-
-      return line.substring( index, line.indexOf("\"", index+1) );
-    }
-
-
-    static String parseElement(String line, String tag)
-    {
-      int index = line.indexOf(tag)+tag.length();
-      return line.substring( index, line.indexOf("</") ) ;
-    }
-
-
-
-
-
 }
-- 
1.7.10.2