From: jprocter <Jim Procter>
Date: Mon, 23 May 2005 17:45:51 +0000 (+0000)
Subject: fixed window title names for prediction on MSA or Sequence.
X-Git-Tag: Release_2_0~230
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7e58cf6fb477265076ae20f33a39e5e1b60a1e0c;p=jalview.git

fixed window title names for prediction on MSA or Sequence.
---

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index ba3186c..9f68dca 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -17,21 +17,25 @@ public class JPredClient
   int jobsRunning = 0;
   ext.vamsas.JpredSoapBindingStub server;
   WebserviceInfo wsInfo;
-
-  public JPredClient(SequenceI[] msf)
+  String altitle = "";
+  java.util.Hashtable SequenceInfo = null;
+  public JPredClient(String title, SequenceI[] msf)
   {
-    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",
+    wsInfo = new WebserviceInfo("JNet secondary structure prediction on "+title,
           "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");
 
     SequenceI seq = msf[0];
-    wsInfo.setProgressText("Job details for MSA based prediction on sequence :\nName : "
-                   + seq.getName() + "\nSequence : "
+    altitle = "JNet prediction on "+seq.getName()+" using "+title;
+    wsInfo.setProgressText("Job details for MSA based prediction ("+title+") on sequence :\n>"
+                   + seq.getName() + "\n"
                    + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
 
+    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
 
     JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
+    // JBPNote url will be set from properties
     try {
-      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
+      this.server = (JpredSoapBindingStub) loc.getjpred(new java.net.URL("http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred"));
     }
     catch (Exception ex) {
       wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"
@@ -44,16 +48,18 @@ public class JPredClient
 
   public JPredClient(SequenceI seq)
   {
-    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",
+    wsInfo = new WebserviceInfo("JNet secondary structure prediction Job",
                                 "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");
 
 
-    wsInfo.setProgressText("Job details for prediction on sequence :\nName : "
-                   + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
+    wsInfo.setProgressText("Job details for prediction on sequence :\n>"
+                   + seq.getName() + "\n" + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
+    altitle = "JNet prediction for sequence "+seq.getName();
+    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
 // TODO: put proper url in
     JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
     try {
-      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
+      this.server = (JpredSoapBindingStub) loc.getjpred(new java.net.URL("http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred")); // JBPNote will be set from properties
     }
     catch (Exception ex) {
       wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"
@@ -217,6 +223,9 @@ public class JPredClient
           FirstSeq = prediction.getQuerySeqPosition();
         }
 
+        if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al.getSequenceAt(FirstSeq), SequenceInfo))
+          throw (new Exception("Couldn't recover sequence properties for JNet Query sequence!"));
+
         AlignmentAnnotation annot;
         Annotation [] annotations = null;
         int i = 0;
@@ -224,8 +233,9 @@ public class JPredClient
 
 
         int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
+
         if (gapmap.length!=width) {
-          throw (new Exception("Jpred Client Error\nNumber of residues in supposed query sequence :\n"
+          throw (new Exception("Jnet Client Error\nNumber of residues in supposed query sequence :\n"
                                +al.getSequenceAt(FirstSeq).getName()+"\n"
                                +al.getSequenceAt(FirstSeq).getSequence()
                                +"\nDiffer from number of prediction sites in \n"+result.getPredfile()+"\n"));
@@ -293,7 +303,7 @@ public class JPredClient
 
 
         Desktop.addInternalFrame(af,
-                                 "JNet Prediction for sequence ",
+                                 altitle,
                                  AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
       }catch(Exception ex){ex.printStackTrace();}