From d35ca06fbba0a776b65bc733ebd00b48eaf1ace6 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 10 May 2006 12:57:21 +0000
Subject: [PATCH] Annotations must createSequenceMapping if seqRef not null

---
 src/jalview/io/AnnotationReader.java |   32 +++++++++++++++++++++-----------
 src/jalview/ws/JPredClient.java      |    9 ++++++++-
 2 files changed, 29 insertions(+), 12 deletions(-)

diff --git a/src/jalview/io/AnnotationReader.java b/src/jalview/io/AnnotationReader.java
index 4325dae..d42167a 100755
--- a/src/jalview/io/AnnotationReader.java
+++ b/src/jalview/io/AnnotationReader.java
@@ -35,11 +35,13 @@ public class AnnotationReader
       String line, label, description, token;
       int graphStyle, index;
       SequenceI refSeq = null;
-      int refSeqIndex = 0;
+      int refSeqIndex = 1;
       int existingAnnotations = 0;
       if(al.getAlignmentAnnotation()!=null)
        existingAnnotations = al.getAlignmentAnnotation().length;
 
+      int alWidth = al.getWidth();
+
       StringTokenizer st;
       Annotation[] annotations;
       AlignmentAnnotation annotation = null;
@@ -100,28 +102,32 @@ public class AnnotationReader
           }
           catch(Exception ex)
           {
-            refSeqIndex = 0;
+            refSeqIndex = 1;
           }
 
           continue;
         }
 
+
         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
         label = description = st.nextToken();
 
         line = st.nextToken();
+
         st = new StringTokenizer(line, "|", true);
-        annotations = new Annotation[st.countTokens()+refSeqIndex];
-        index = refSeqIndex;
+        annotations = new Annotation[alWidth];
+
+        index = 0;
         boolean emptyColumn = true;
-        while (st.hasMoreElements())
+
+
+        while (st.hasMoreElements() && index<alWidth)
         {
           token = st.nextToken().trim();
-
           if(token.equals("|"))
           {
             if(emptyColumn)
-              annotations[index++] = parseAnnotation("");
+              index++;
 
             emptyColumn = true;
           }
@@ -139,12 +145,16 @@ public class AnnotationReader
                                           0,
                                           graphStyle);
 
-       annotation = al.addAnnotation(annotation, refSeq);
-       al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);
-      }
+       if(refSeq!=null)
+       {
+         annotation.createSequenceMapping(refSeq, refSeqIndex);
+         refSeq.addAlignmentAnnotation(annotation);
+       }
 
-       al.adjustSequenceAnnotations();
+       al.addAnnotation(annotation);
 
+       al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);
+      }
 
     }catch(Exception ex)
     {
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 8a4368c..2d49ac6 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -515,7 +515,14 @@ public class JPredClient
                                               "JNet Output", annotations);
             }
 
-            al.addAnnotation(annot, seqRef);
+            if (seqRef != null)
+            {
+              annot.createSequenceMapping(seqRef, 0);
+              seqRef.addAlignmentAnnotation(annot);
+            }
+
+            al.addAnnotation(annot);
+
 
             if (noMsa)
             {
-- 
1.7.10.2