X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;fp=src%2Fjalview%2Fws%2FJPredClient.java;h=f503f912dd3a5aa8479d6a399febfc60aac3702c;hb=91d9dd665cd82447439e23df334a59e93647a8d0;hp=4cb8aeeb348f1c4e28c79b0cc62c732edcddd2f7;hpb=3cc7418f801593f64e73d7ccdbed3d557398aa45;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 4cb8aee..f503f91 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -57,6 +57,7 @@ public class JPredClient
       wsInfo = setWebService();
 
     SequenceI seq = msf[0];
+
     altitle = "JNet prediction on " + seq.getName() +
         " using alignment from " + title;
 
@@ -65,8 +66,10 @@ public class JPredClient
                            AlignSeq.extractGaps("-. ", seq.getSequence()) +
                            "\n");
     SequenceI aln[] = new SequenceI[msf.length];
-    for (int i=0,j=msf.length; i<j;i++)
-      aln[i] = new jalview.datamodel.Sequence(msf[i]);
+    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())
@@ -403,16 +406,17 @@ public class JPredClient
           {
             al = new Alignment(new FormatAdapter().readFile(
                 result.getAligfile(), "Paste", format));
+            SequenceI sqs[] = new SequenceI[al.getHeight()];
             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())))
+              sqs[i] = al.getSequenceAt(i);
+            }
+            if (!jalview.analysis.SeqsetUtils.deuniquify(
+                  (Hashtable) SequenceInfo,sqs))
               {
                 throw (new Exception(
-                    "Couldn't recover sequence properties for JNet "
-                    +((i==0) ? "Query sequence" : "alignment sequence ("+i+")")));
+                    "Couldn't recover sequence properties for alignment."));
               }
-            }
+
             noMsa = false;
             FirstSeq = 0;
           }