X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=d353b512371d39890fbf9226c77cf7723ac10b69;hb=4944c2f33bb34b4f262fd2f3ae40dcdc2a825557;hp=f503f912dd3a5aa8479d6a399febfc60aac3702c;hpb=58e82de6951f919828899de75b908cd1114d8511;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index f503f91..d353b51 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -399,7 +399,7 @@ public class JPredClient
         {
           jalview.bin.Cache.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(),
+          String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(),
               "Paste");
 
           if (jalview.io.FormatAdapter.formats.contains(format))
@@ -439,6 +439,7 @@ public class JPredClient
           }
         }
 
+        al.setDataset(null);
 
         AlignmentAnnotation annot;
         Annotation[] annotations = null;
@@ -460,6 +461,8 @@ public class JPredClient
         // JBPNote Should also rename the query sequence sometime...
         i = 0;
 
+        SequenceI seqRef = al.getSequenceAt(FirstSeq);
+
         while (i < preds.length)
         {
           String id = preds[i].getName().toUpperCase();
@@ -503,7 +506,8 @@ public class JPredClient
             {
               annot = new AlignmentAnnotation(preds[i].getName(),
                                               "JNet Output", annotations, 0f,
-                                              10f, 1);
+                                              10f,
+                                              AlignmentAnnotation.BAR_GRAPH);
             }
             else
             {
@@ -511,7 +515,7 @@ public class JPredClient
                                               "JNet Output", annotations);
             }
 
-            al.addAnnotation(annot);
+            al.addAnnotation(annot, seqRef);
 
             if (noMsa)
             {
@@ -544,8 +548,7 @@ public class JPredClient
       }
       catch (Exception ex)
       {
-        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.");
-        jalview.bin.Cache.log.debug("Exception: ",ex);
+        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.",ex);
       }
     }
   }