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

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 2d44a0f..8ebcc87 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -825,6 +825,20 @@ public class SeqPanel extends JPanel implements MouseListener,
   String lastTooltip;
 
   /**
+   * 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 = false; // 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
+
+  /**
    * Set status message in alignment panel
    * 
    * @param sequence
@@ -1568,10 +1582,12 @@ public class SeqPanel extends JPanel implements MouseListener,
               && (res < stretchGroup.getEndRes()))
       {
         av.setSelectionGroup(stretchGroup);
+        editingDefinedGroup = true;
       }
       else
       {
         stretchGroup = null;
+        editingDefinedGroup = false;
       }
     }
     else if (!stretchGroup.getSequences(null).contains(sequence)
@@ -1590,6 +1606,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                   && (allGroups[i].getEndRes() >= res))
           {
             stretchGroup = allGroups[i];
+            editingDefinedGroup = true;
             break;
           }
         }
@@ -1639,7 +1656,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
-
+      editingDefinedGroup = false;
       stretchGroup = sg;
 
       if (av.getConservationSelected())
@@ -1682,9 +1699,10 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       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,
@@ -1702,8 +1720,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
     PaintRefresher.Refresh(this, av.getSequenceSetId());
-    ap.paintAlignment(true);
-
+    ap.paintAlignment(needOverviewUpdate);
+    needOverviewUpdate =false;
+    editingDefinedGroup = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1757,6 +1776,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
+        needOverviewUpdate |= editingDefinedGroup;
       }
     }
     else if (changeStartRes)
@@ -1764,6 +1784,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
+        needOverviewUpdate |= editingDefinedGroup;
       }
     }
 
@@ -1797,6 +1818,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
+        needOverviewUpdate |= editingDefinedGroup;
       }
       else
       {
@@ -1806,6 +1828,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
+        needOverviewUpdate |= editingDefinedGroup;
       }
     }