From 503023b56eda1ae799c73b4189921bb2d60cc5d7 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 22 Aug 2005 15:41:39 +0000
Subject: [PATCH] tidied client and fixed non-unique msa bug (lead to Hmmer
 error)

---
 src/jalview/ws/JPredClient.java |   40 ++++++++++++++++++++++++++++-----------
 1 file changed, 29 insertions(+), 11 deletions(-)

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 04a6101..65f0325 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -63,15 +63,17 @@ public class JPredClient
                            title + ") on sequence :\n>" + seq.getName() + "\n" +
                            AlignSeq.extractGaps("-. ", seq.getSequence()) +
                            "\n");
-
-    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+    SequenceI aln[] = new SequenceI[msf.length];
+    for (int i=0,j=msf.length; i<j;i++)
+      aln[i] = new jalview.datamodel.Sequence(msf[i]);
+    SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
 
     if (!locateWebService())
     {
       return;
     }
 
-    JPredThread jthread = new JPredThread(msf);
+    JPredThread jthread = new JPredThread(aln);
     jthread.start();
   }
 
@@ -350,21 +352,24 @@ public class JPredClient
         OutputHeader += ("\n" + result.getAligfile());
       }
 
-      wsInfo.setProgressText(OutputHeader);
+      wsInfo.setProgressText(OutputHeader+"Parsing...");
 
       try
       {
+        jalview.bin.Jalview.log.debug("Parsing output from JNet job.");
         // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
         jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
             getPredfile(),
             "Paste");
         SequenceI[] preds = prediction.getSeqsAsArray();
+        jalview.bin.Jalview.log.debug("Got prediction profile.");
         Alignment al;
         int FirstSeq; // the position of the query sequence in Alignment al
         boolean noMsa = true; // set if no MSA has been returned by JPred
 
         if ( (this.msa != null) && (result.getAligfile() != null))
         {
+          jalview.bin.Jalview.log.debug("Getting associated alignment.");
           // we ignore the returned alignment if we only predicted on a single sequence
           String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),
               "Paste");
@@ -373,6 +378,16 @@ public class JPredClient
           {
             al = new Alignment(jalview.io.FormatAdapter.readFile(
                 result.getAligfile(), "Paste", format));
+            for (int i=0, j=al.getHeight(); i<j; i++) {
+              SequenceI sq = al.getSequenceAt(i);
+              if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+                  sq, (Hashtable) SequenceInfo.get(sq.getName())))
+              {
+                throw (new Exception(
+                    "Couldn't recover sequence properties for JNet "
+                    +((i==0) ? "Query sequence" : "alignment sequence ("+i+")")));
+              }
+            }
             noMsa = false;
             FirstSeq = 0;
           }
@@ -387,14 +402,14 @@ public class JPredClient
         {
           al = new Alignment(preds);
           FirstSeq = prediction.getQuerySeqPosition();
+          if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+              al.getSequenceAt(FirstSeq), SequenceInfo))
+          {
+            throw (new Exception(
+                "Couldn't recover sequence properties for JNet Query sequence!"));
+          }
         }
 
-        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;
@@ -489,6 +504,9 @@ public class JPredClient
           addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
                               "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
          */
+
+        wsInfo.setProgressText(OutputHeader);
+        jalview.bin.Jalview.log.debug("Finished parsing output.");
         AlignFrame af = new AlignFrame(al);
 
         Desktop.addInternalFrame(af, altitle,
@@ -498,7 +516,7 @@ public class JPredClient
       catch (Exception ex)
       {
         jalview.bin.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction.");
-        jalview.bin.Jalview.log.debug(ex);
+        jalview.bin.Jalview.log.debug("Exception: ",ex);
       }
     }
   }
-- 
1.7.10.2