JAL-3521 Change grouped Jalview windows on linux taskbar to have name Jalview

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index f353d28..180467a 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -77,9 +77,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
   TreePanel tp;
 
-  AlignViewport av;
+  private AlignViewport av;
 
-  AlignmentPanel ap;
+  private AlignmentPanel ap;
 
   Font font;
 
@@ -97,7 +97,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
   int offy;
 
-  float threshold;
+  private float threshold;
 
   String longestName;
 
@@ -127,7 +127,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   {
     this.tp = tp;
     this.av = ap.av;
-    this.ap = ap;
+    this.setAssociatedPanel(ap);
     font = av.getFont();
     scrollPane = scroller;
     addMouseListener(this);
@@ -836,7 +836,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (col != null)
     {
       setColor(highlightNode, col);
-      PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+      PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
       repaint();
     }
   }
@@ -917,7 +917,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (ob instanceof SequenceI)
     {
       treeSelectionChanged((Sequence) ob);
-      PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+      PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
       repaint();
       av.sendSelection();
       return;
@@ -949,6 +949,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                     .deleteAllGroups();
             aps[a].av.getCodingComplement().clearSequenceColours();
           }
+          aps[a].av.setUpdateStructures(true);
         }
         colourGroups(groups);
 
@@ -962,7 +963,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
       }
 
-      PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+      PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
       repaint();
     }
 
@@ -1088,7 +1089,47 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      return new AlignmentPanel[] { ap };
+      return new AlignmentPanel[] { getAssociatedPanel() };
     }
   }
+
+  public AlignmentPanel getAssociatedPanel()
+  {
+    return ap;
+  }
+
+  public void setAssociatedPanel(AlignmentPanel ap)
+  {
+    this.ap = ap;
+  }
+
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public void setViewport(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public float getThreshold()
+  {
+    return threshold;
+  }
+
+  public void setThreshold(float threshold)
+  {
+    this.threshold = threshold;
+  }
+
+  public boolean isApplyToAllViews()
+  {
+    return this.applyToAllViews;
+  }
+
+  public void setApplyToAllViews(boolean applyToAllViews)
+  {
+    this.applyToAllViews = applyToAllViews;
+  }
 }