From 42f46263655185b0a436356c37295ec82d091dce Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 8 Feb 2005 18:39:50 +0000
Subject: [PATCH] new class

---
 src/jalview/io/WSWUBlastClient.java |  119 +++++++++++++++++++++++++++++++++++
 1 file changed, 119 insertions(+)
 create mode 100755 src/jalview/io/WSWUBlastClient.java

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
new file mode 100755
index 0000000..ed29f89
--- /dev/null
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -0,0 +1,119 @@
+package jalview.io;
+
+import org.apache.axis.client.*;
+import javax.xml.namespace.QName;
+import java.util.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import javax.swing.*;
+
+public class WSWUBlastClient
+{
+  CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+
+  public WSWUBlastClient(AlignmentI al, ArrayList ids)
+  {
+    JInternalFrame frame = new JInternalFrame();
+    cap.formatForOutput();
+    frame.setContentPane(cap);
+    cap.setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
+                +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");
+    Desktop.addInternalFrame(frame, "BLASTing for unidentified sequences ", 800,300);
+
+    for(int i=0; i<ids.size(); i++)
+    {
+     SequenceI sequence =  al.findName( ids.get(i).toString() );
+     StringBuffer nonGapped = new StringBuffer();
+      for (int n = 0; n < sequence.getSequence().length(); n++)
+      {
+        if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))
+          nonGapped.append(sequence.getCharAt(n));
+      }
+
+     BlastThread thread = new BlastThread(ids.get(i).toString(),  nonGapped.toString());
+     thread.start();
+     }
+
+  }
+
+  class BlastThread extends Thread
+  {
+    String sequence;
+    String id;
+    BlastThread(String id, String sequence)
+    {
+      this.sequence = sequence;
+      this.id = id;
+    }
+
+    public void run()
+    {
+      FindUniprotIDFromUnknownSequence(id, sequence);
+    }
+  }
+
+  public void FindUniprotIDFromUnknownSequence (String id, String s)
+  {
+        HashMap params = new HashMap();
+        params.put("database", "uniprot");
+        params.put("sensitivity","low");
+        params.put("sort","totalscore");
+        params.put("matrix","pam10");
+        params.put("program","blastp");
+        params.put("alignments","5");
+        params.put("outformat","xml");
+        byte[] sequence = s.getBytes();
+
+        try {
+            Call call = (Call) new Service().createCall();
+            call.setTargetEndpointAddress (new java.net.URL("http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
+            call.setOperationName(new QName("WSWUBlast", "doWUBlast"));
+
+            String result = (String) call.invoke(new Object[] {params,sequence});
+            parseResult(id, result);
+            }
+        catch (Exception exp) {
+             System.err.println ("ERROR:\n" + exp.toString());
+            exp.printStackTrace();
+        }
+    }
+
+    void parseResult(String id1, String res)
+    {
+      StringTokenizer st = new StringTokenizer(res, "\n");
+      String data;
+      String id2;
+      int maxFound = 90;
+      StringBuffer buffer = new StringBuffer("\n\n"+id1+" :");
+
+      while( st.hasMoreTokens() )
+      {
+        data = st.nextToken();
+
+        if(data.indexOf("database=\"uniprot\" id=")>-1)
+        {
+          int index =  data.indexOf("database=\"uniprot\" id=")+ 23;
+          id2 = data.substring( index, data.indexOf("\"", index) );
+          while( data.indexOf("</alignment>")==-1)
+          {
+            data = st.nextToken();
+            if(data.indexOf("<identity>")>-1)
+            {
+              int value = Integer.parseInt( data.substring(data.indexOf("<identity>")+10, data.indexOf("</identity>")));
+              if(value>=maxFound)
+              {
+                maxFound = value;
+                buffer.append(" "+ id2 + " " + value+"%; ");
+              }
+            }
+          }
+
+        }
+
+
+      }
+
+      cap.setText(cap.getText()+buffer.toString());
+    }
+
+}
-- 
1.7.10.2