X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;fp=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=04de50b2c3ebc255a65b8f7e4f12fda1910cf10b;hb=0288494d034d48dd8ce0c5a8654ac2ee695b4573;hp=8ade5d690648ee799b1b4b6c8e31970f63019770;hpb=7451c6419c9c94627f79d044228db55b90e9b4cf;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 8ade5d6..04de50b 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -106,6 +106,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   private PropertyChangeListener propertyChangeListener;
 
+  private CalculationChooser calculationDialog;
+
   /**
    * Creates a new AlignmentPanel object.
    * 
@@ -169,6 +171,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     av.alignmentChanged(this);
 
+    if (getCalculationDialog() != null)
+    {
+      getCalculationDialog().validateCalcTypes();
+    }
+
     alignFrame.updateEditMenuBar();
 
     paintAlignment(true);
@@ -1647,6 +1654,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
 
+    closeChildFrames();
+
     /*
      * try to ensure references are nulled
      */
@@ -1678,6 +1687,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
+   * Close any open dialogs that would be orphaned when this one is closed
+   */
+  protected void closeChildFrames()
+  {
+    if (calculationDialog != null)
+    {
+      calculationDialog.closeFrame();
+    }
+  }
+
+  /**
    * hides or shows dynamic annotation rows based on groups and av state flags
    */
   public void updateAnnotation()
@@ -1906,4 +1926,24 @@ public class AlignmentPanel extends GAlignmentPanel implements
       repaint();
     }
   }
+
+  /**
+   * Set the reference to the PCA/Tree chooser dialog for this panel. This
+   * reference should be nulled when the dialog is closed.
+   * 
+   * @param calculationChooser
+   */
+  public void setCalculationDialog(CalculationChooser calculationChooser)
+  {
+    calculationDialog = calculationChooser;
+  }
+
+  /**
+   * Returns the reference to the PCA/Tree chooser dialog for this panel (null
+   * if none is open)
+   */
+  public CalculationChooser getCalculationDialog()
+  {
+    return calculationDialog;
+  }
 }