JAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF for GRAPHLINE statements

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index bd536f3..4abd768 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -624,11 +624,13 @@ public class AnnotationFile
   }
   long nlinesread=0;
   String lastread="";
+  private static String GRAPHLINE="GRAPHLINE", COMBINE="COMBINE"; 
   public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
           throws Exception
   {
     nlinesread = 0;
     ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
+    ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<Object[]>();
     boolean modified = false;
     String groupRef = null;
     Hashtable groupRefRows = new Hashtable();
@@ -712,7 +714,7 @@ public class AnnotationFile
           continue;
         }
 
-        else if (token.equalsIgnoreCase("COMBINE"))
+        else if (token.equalsIgnoreCase(COMBINE))
         {
           // keep a record of current state and resolve groupRef at end
           combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef});
@@ -725,9 +727,10 @@ public class AnnotationFile
           modified = true;
           continue;
         }
-        else if (token.equalsIgnoreCase("GRAPHLINE"))
+        else if (token.equalsIgnoreCase(GRAPHLINE))
         {
-          addLine(al, st);
+          // resolve at end
+          deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st, refSeq, groupRef});
           modified = true;
           continue;
         }
@@ -970,6 +973,21 @@ public class AnnotationFile
         }
         ((Vector) groupRefRows.get(groupRef)).removeAllElements();
       }
+      // process any deferred attribute settings for each context
+      for (Object[] _deferred_args : deferredAnnotation_calls)
+      {
+        if (_deferred_args[0] == GRAPHLINE)
+        {
+          addLine(al,
+                  (StringTokenizer) _deferred_args[1], // st
+                  (SequenceI) _deferred_args[2], // refSeq
+                  (_deferred_args[3] == null) ? null : groupRefLookup
+                          .get((String) _deferred_args[3]) // the reference
+                                                           // group, or null
+          );
+        }
+      }      
+
       // finally, combine all the annotation rows within each context.
       /**
        * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
@@ -983,7 +1001,6 @@ public class AnnotationFile
                 (_combine_args[2]==null) ? null : groupRefLookup.get((String)_combine_args[2]) // the reference group, or null
                 );
       }
-
     }
     return modified;
   }
@@ -1194,19 +1211,26 @@ public class AnnotationFile
     }
   }
 
-  void addLine(AlignmentI al, StringTokenizer st)
+  void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
   {
     String group = st.nextToken();
     AlignmentAnnotation annotation = null, alannot[] = al
             .getAlignmentAnnotation();
+    float value = new Float(st.nextToken()).floatValue();
+    String label = st.hasMoreTokens() ? st.nextToken() : null;
+    java.awt.Color colour = null;
+    if (st.hasMoreTokens())
+    {
+      UserColourScheme ucs = new UserColourScheme(st.nextToken());
+      colour = ucs.findColour('A');
+    }
     if (alannot != null)
     {
       for (int i = 0; i < alannot.length; i++)
       {
-        if (alannot[i].label.equalsIgnoreCase(group))
+        if (alannot[i].label.equalsIgnoreCase(group) && (seqRef==null || alannot[i].sequenceRef==seqRef) && (groupRef==null || alannot[i].groupRef==groupRef))
         {
-          annotation = alannot[i];
-          break;
+          alannot[i].setThreshold(new GraphLine(value, label, colour));
         }
       }
     }
@@ -1214,16 +1238,6 @@ public class AnnotationFile
     {
       return;
     }
-    float value = new Float(st.nextToken()).floatValue();
-    String label = st.hasMoreTokens() ? st.nextToken() : null;
-    java.awt.Color colour = null;
-    if (st.hasMoreTokens())
-    {
-      UserColourScheme ucs = new UserColourScheme(st.nextToken());
-      colour = ucs.findColour('A');
-    }
-
-    annotation.setThreshold(new GraphLine(value, label, colour));
   }
 
   void addGroup(AlignmentI al, StringTokenizer st)