Add Annotation to specific sequence

[jalview.git] / src / jalview / ws / JPredClient.java

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index f503f91..6fd0a4a 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -439,6 +439,7 @@ public class JPredClient
           }\r
         }\r
 \r
+        al.setDataset(null);\r
 \r
         AlignmentAnnotation annot;\r
         Annotation[] annotations = null;\r
@@ -460,6 +461,8 @@ public class JPredClient
         // JBPNote Should also rename the query sequence sometime...\r
         i = 0;\r
 \r
+        SequenceI seqRef = al.getSequenceAt(FirstSeq);\r
+\r
         while (i < preds.length)\r
         {\r
           String id = preds[i].getName().toUpperCase();\r
@@ -503,7 +506,8 @@ public class JPredClient
             {\r
               annot = new AlignmentAnnotation(preds[i].getName(),\r
                                               "JNet Output", annotations, 0f,\r
-                                              10f, 1);\r
+                                              10f,\r
+                                              AlignmentAnnotation.BAR_GRAPH);\r
             }\r
             else\r
             {\r
@@ -511,7 +515,7 @@ public class JPredClient
                                               "JNet Output", annotations);\r
             }\r
 \r
-            al.addAnnotation(annot);\r
+            al.addAnnotation(annot, seqRef);\r
 \r
             if (noMsa)\r
             {\r
@@ -544,8 +548,7 @@ public class JPredClient
       }\r
       catch (Exception ex)\r
       {\r
-        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.");\r
-        jalview.bin.Cache.log.debug("Exception: ",ex);\r
+        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.",ex);\r
       }\r
     }\r
   }\r