Merge branch 'efficiency/JAL-2034_JAL-1421' into develop

[jalview.git] / src / jalview / appletgui / SeqPanel.java

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 31bf6a4..02172d6 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -919,6 +919,21 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   Tooltip tooltip;
 
+  /**
+   * set when the current UI interaction has resulted in a change that requires
+   * overview shading to be recalculated. this could be changed to something
+   * more expressive that indicates what actually has changed, so selective
+   * redraws can be applied
+   */
+  private boolean needOverviewUpdate; // TODO: refactor to avcontroller
+
+  /**
+   * set if av.getSelectionGroup() refers to a group that is defined on the
+   * alignment view, rather than a transient selection
+   */
+  private boolean editingDefinedGroup = false; // TODO: refactor to avcontroller
+                                               // or viewModel
+
   @Override
   public void mouseDragged(MouseEvent evt)
   {
@@ -1421,10 +1436,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
               && res < stretchGroup.getEndRes())
       {
         av.setSelectionGroup(stretchGroup);
+        editingDefinedGroup = true;
       }
       else
       {
         stretchGroup = null;
+        editingDefinedGroup = false;
       }
     }
 
@@ -1444,6 +1461,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                   && allGroups[i].getEndRes() >= res)
           {
             stretchGroup = allGroups[i];
+            editingDefinedGroup = true;
             break;
           }
         }
@@ -1499,6 +1517,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
+      editingDefinedGroup = false;
       stretchGroup = sg;
 
       if (av.getConservationSelected())
@@ -1521,9 +1540,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       return;
     }
-
-    stretchGroup.recalcConservation(); // always do this - annotation has own
-                                       // state
+    // always do this - annotation has own state
+    // but defer colourscheme update until hidden sequences are passed in
+    boolean vischange = stretchGroup.recalcConservation(true);
+    needOverviewUpdate |= vischange && editingDefinedGroup;
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1540,11 +1560,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                 stretchGroup.getName());
       }
     }
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
+    ap.paintAlignment(needOverviewUpdate);
+    needOverviewUpdate =false;
+    editingDefinedGroup = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    PaintRefresher.Refresh(ap, av.getSequenceSetId());
-    ap.paintAlignment(true);
     av.sendSelection();
   }
 
@@ -1596,6 +1618,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
+        needOverviewUpdate |= editingDefinedGroup;
       }
     }
     else if (changeStartRes)
@@ -1603,6 +1626,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
+        needOverviewUpdate |= editingDefinedGroup;
       }
     }
 
@@ -1636,6 +1660,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
+        needOverviewUpdate |= editingDefinedGroup;
       }
       else
       {
@@ -1645,6 +1670,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
+        needOverviewUpdate |= editingDefinedGroup;
       }
     }