new class

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