Merge remote-tracking branch 'origin/develop' into feature/2588

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 0d53172..395f6b3 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -25,6 +25,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -110,6 +111,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   private PropertyChangeListener propertyChangeListener;
 
+  private CalculationChooser calculationDialog;
+
   /**
    * Creates a new AlignmentPanel object.
    * 
@@ -203,6 +206,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     av.alignmentChanged(this);
 
+    if (getCalculationDialog() != null)
+    {
+      getCalculationDialog().validateCalcTypes();
+    }
+
     alignFrame.updateEditMenuBar();
 
     paintAlignment(true);
@@ -408,7 +416,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       if (centre)
       {
-        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
+                - 1;
         start = Math.max(start - offset, 0);
         end = end + offset - 1;
       }
@@ -422,11 +431,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       if (av.hasHiddenColumns())
       {
-        start = av.getColumnSelection().findColumnPosition(start);
-        end = av.getColumnSelection().findColumnPosition(end);
+        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+        start = hidden.findColumnPosition(start);
+        end = hidden.findColumnPosition(end);
         if (start == end)
         {
-          if (!av.getColumnSelection().isVisible(r[0]))
+          if (!hidden.isVisible(r[0]))
           {
             // don't scroll - position isn't visible
             return false;
@@ -673,7 +683,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (av.hasHiddenColumns())
       {
         // reset the width to exclude hidden columns
-        width = av.getColumnSelection().findColumnPosition(width);
+        width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
       }
 
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@@ -876,7 +886,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        maxwidth = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(maxwidth) - 1;
     }
 
     // get the width of the canvas in residues
@@ -1161,7 +1172,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
@@ -1355,7 +1367,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth);
     }
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
@@ -1585,7 +1598,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     int height = ((maxwidth / chunkWidth) + 1) * cHeight;
@@ -1603,6 +1617,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
 
+    closeChildFrames();
+
     /*
      * try to ensure references are nulled
      */
@@ -1634,6 +1650,17 @@ 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()
@@ -1889,4 +1916,24 @@ public class AlignmentPanel extends GAlignmentPanel implements
       setToScrollComplementPanel(true);
     }
   }
+
+  /**
+   * 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;
+  }
 }