JAL-1145 patch: sequence associated annotation with graphGroups>-1 have relocated...

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e71e649..a50e724 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1781,6 +1781,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       int alwidth = 0;
+      ArrayList<Integer> newGraphGroups=new ArrayList<Integer>();
+      int fgroup=-1;
 
       if (newAlignment)
       {
@@ -1848,6 +1850,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           newDs.clear(); // tidy up
         }
+        if (alignment.getAlignmentAnnotation()!=null)
+        {
+          for (AlignmentAnnotation alan:alignment.getAlignmentAnnotation())
+          {
+            if (alan.graphGroup>fgroup)
+            {
+              fgroup=alan.graphGroup;
+            }
+          }
+        }
         if (pastedal.getAlignmentAnnotation() != null)
         {
           // Add any annotation attached to alignment.
@@ -1858,6 +1870,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
             {
               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+              if (newann.graphGroup>-1)
+              {
+                if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+                {
+                  for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+              }
+
               newann.padAnnotation(alwidth);
               alignment.addAnnotation(newann);
             }
@@ -1877,11 +1902,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (sequences[i].getAnnotation() != null)
         {
+          AlignmentAnnotation newann;
           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
           {
             annotationAdded = true;
-            sequences[i].getAnnotation()[a].adjustForAlignment();
-            sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+            newann=sequences[i].getAnnotation()[a];
+            newann.adjustForAlignment();
+            newann.padAnnotation(alwidth);
+            if (newann.graphGroup>-1)
+            {
+              if (newann.graphGroup>-1)
+              {
+                if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+                {
+                  for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+              }
+            }
             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
             // was
             // duplicated
@@ -1921,6 +1963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   newann.padAnnotation(avwidth);
                   alview[avnum].addAnnotation(newann); // annotation was
                   // duplicated earlier
+                  // TODO JAL-1145 graphGroups are not updated for sequence annotation added to several views. This may cause strangeness
                   alview[avnum].setAnnotationIndex(newann, a);
                 }
               }