JAL-2034 moved ‘isDefinedGroup’ flag to a test method on AlignViewportI so controller...

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 8343f0b..df57cc0 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -397,4 +397,12 @@ public interface AlignViewportI extends ViewStyleI
 
 
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+  /**
+   * check if current selection group is defined on the view, or is simply a
+   * temporary group.
+   * 
+   * @return true if group is defined on the alignment
+   */
+  boolean isSelectionDefinedGroup();
 }

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 02172d6..a437960 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -927,13 +927,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    */
   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)
   {
@@ -1436,12 +1429,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
               && res < stretchGroup.getEndRes())
       {
         av.setSelectionGroup(stretchGroup);
-        editingDefinedGroup = true;
       }
       else
       {
         stretchGroup = null;
-        editingDefinedGroup = false;
       }
     }
 
@@ -1461,7 +1452,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                   && allGroups[i].getEndRes() >= res)
           {
             stretchGroup = allGroups[i];
-            editingDefinedGroup = true;
             break;
           }
         }
@@ -1517,7 +1507,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
-      editingDefinedGroup = false;
       stretchGroup = sg;
 
       if (av.getConservationSelected())
@@ -1543,7 +1532,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // 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;
+    // here we rely on stretchGroup == av.getSelection()
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1563,7 +1553,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     PaintRefresher.Refresh(ap, av.getSequenceSetId());
     ap.paintAlignment(needOverviewUpdate);
     needOverviewUpdate =false;
-    editingDefinedGroup = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1618,7 +1607,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1626,7 +1615,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1660,7 +1649,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1670,7 +1659,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index f476d41..348c21c 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -836,7 +836,8 @@ public class SeqPanel extends JPanel implements MouseListener,
    * 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
+  // private boolean editingDefinedGroup = false; // TODO: refactor to
+  // avcontroller or viewModel
 
   /**
    * Set status message in alignment panel
@@ -1583,12 +1584,10 @@ 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)
@@ -1607,7 +1606,6 @@ public class SeqPanel extends JPanel implements MouseListener,
                   && (allGroups[i].getEndRes() >= res))
           {
             stretchGroup = allGroups[i];
-            editingDefinedGroup = true;
             break;
           }
         }
@@ -1657,7 +1655,6 @@ public class SeqPanel extends JPanel implements MouseListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
-      editingDefinedGroup = false;
       stretchGroup = sg;
 
       if (av.getConservationSelected())
@@ -1703,7 +1700,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     // 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;
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1723,7 +1720,6 @@ public class SeqPanel extends JPanel implements MouseListener,
     PaintRefresher.Refresh(this, av.getSequenceSetId());
     ap.paintAlignment(needOverviewUpdate);
     needOverviewUpdate =false;
-    editingDefinedGroup = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1777,7 +1773,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1785,7 +1781,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1819,7 +1815,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1829,7 +1825,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 19ebf45..457f2c5 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2782,5 +2782,31 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
+  /**
+   * hold status of current selection group - defined on alignment or not.
+   */
+  private boolean selectionIsDefinedGroup = false;
 
+  @Override
+  public boolean isSelectionDefinedGroup()
+  {
+    if (selectionGroup == null)
+    {
+      return false;
+    }
+    if (isSelectionGroupChanged(true))
+    {
+      selectionIsDefinedGroup = false;
+      List<SequenceGroup> gps = alignment.getGroups();
+      if (gps == null || gps.size() == 0)
+      {
+        selectionIsDefinedGroup = false;
+      }
+      else
+      {
+        selectionIsDefinedGroup = gps.contains(selectionGroup);
+      }
+    }
+    return selectionIsDefinedGroup;
+  }
 }