X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=e62707fc82618c2a964fdac443222e04f341a7cf;hb=ddbcb3e33e1a8d4c644472cfa3d28b193da97064;hp=4863659f64250610c06587b149eabdefb6474c14;hpb=6cd58958becb397f90c6609f5f525de04fc98a2b;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 4863659..e62707f 100644
--- 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;
@@ -48,6 +49,8 @@ import java.awt.Graphics;
 import java.awt.Insets;
 import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
 import java.awt.print.PageFormat;
 import java.awt.print.Printable;
 import java.awt.print.PrinterException;
@@ -102,12 +105,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /*
    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
-   * true, suppresses invoking the same method recursively.
+   * false, suppresses invoking the same method recursively.
    */
-  private boolean dontScrollComplement;
+  private boolean scrollComplementaryPanel = true;
 
   private PropertyChangeListener propertyChangeListener;
 
+  private CalculationChooser calculationDialog;
+
   /**
    * Creates a new AlignmentPanel object.
    * 
@@ -142,6 +147,34 @@ public class AlignmentPanel extends GAlignmentPanel implements
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
+    addComponentListener(new ComponentAdapter()
+    {
+      @Override
+      public void componentResized(ComponentEvent evt)
+      {
+        // reset the viewport ranges when the alignment panel is resized
+        // in particular, this initialises the end residue value when Jalview
+        // is initialised
+        if (av.getWrapAlignment())
+        {
+          int widthInRes = getSeqPanel().seqCanvas
+                  .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+          vpRanges.setViewportWidth(widthInRes);
+        }
+        else
+        {
+          int widthInRes = getSeqPanel().seqCanvas.getWidth()
+                  / av.getCharWidth();
+          int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+                  / av.getCharHeight();
+          
+          vpRanges.setViewportWidth(widthInRes);
+          vpRanges.setViewportHeight(heightInSeq);
+        }
+      }
+
+    });
+
     final AlignmentPanel ap = this;
     propertyChangeListener = new PropertyChangeListener()
     {
@@ -173,6 +206,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     av.alignmentChanged(this);
 
+    if (getCalculationDialog() != null)
+    {
+      getCalculationDialog().validateCalcTypes();
+    }
+
     alignFrame.updateEditMenuBar();
 
     paintAlignment(true);
@@ -203,10 +241,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     getIdPanel().getIdCanvas().setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
-    if (overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
-    }
     if (this.alignFrame.getSplitViewContainer() != null)
     {
       ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
@@ -375,9 +409,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       int start = r[0];
       int end = r[1];
-      // DEBUG
-      // System.err.println(this.av.viewName + " Seq : " + seqIndex
-      // + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -385,7 +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;
       }
@@ -399,11 +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;
@@ -416,9 +449,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       seqIndex = Math.max(0, seqIndex - verticalOffset);
 
-      // System.out.println("start=" + start + ", end=" + end + ", startv="
-      // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
-      // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
         if ((startv = vpRanges.getStartRes()) >= start)
@@ -426,7 +456,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
           /*
            * Scroll left to make start of search results visible
            */
-          // setScrollValues(start - 1, seqIndex); // plus one residue
           setScrollValues(start, seqIndex);
         }
         else if ((endv = vpRanges.getEndRes()) <= end)
@@ -434,7 +463,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
           /*
            * Scroll right to make end of search results visible
            */
-          // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
           setScrollValues(startv + end - endv, seqIndex);
         }
         else if ((starts = vpRanges.getStartSeq()) > seqIndex)
@@ -458,30 +486,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       else
       {
-        scrollToWrappedVisible(start);
+        vpRanges.scrollToWrappedVisible(start);
       }
     }
-    if (redrawOverview && overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
-    }
+
     paintAlignment(redrawOverview);
     return true;
   }
 
-  void scrollToWrappedVisible(int res)
-  {
-    int cwidth = getSeqPanel().seqCanvas
-            .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-    if (res < vpRanges.getStartRes()
-            || res >= (vpRanges.getStartRes() + cwidth))
-    {
-      vscroll.setValue((res / cwidth));
-      // vpRanges.setStartRes(vscroll.getValue() * cwidth);
-    }
-
-  }
-
   /**
    * DOCUMENT ME!
    * 
@@ -617,76 +629,32 @@ public class AlignmentPanel extends GAlignmentPanel implements
       annotationSpaceFillerHolder.setVisible(true);
     }
 
-    idSpaceFillerPanel1.setVisible(!wrap);
-
-    repaint();
-  }
-
-  // return value is true if the scroll is valid
-  public boolean scrollUp(boolean up)
-  {
-    if (up)
-    {
-      if (vscroll.getValue() < 1)
-      {
-        return false;
-      }
-
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() - 1);
-    }
-    else
-    {
-      if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+    int canvasWidth = getSeqPanel().seqCanvas.getWidth();
+    if (canvasWidth > 0)
+    { // may not yet be laid out
+      if (wrap)
       {
-        return false;
+        int widthInRes = getSeqPanel().seqCanvas
+                .getWrappedCanvasWidth(canvasWidth);
+        vpRanges.setViewportWidth(widthInRes);
       }
-
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() + 1);
-    }
-
-    fastPaint = true;
-
-    return true;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param right
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean scrollRight(boolean right)
-  {
-    if (!right)
-    {
-      if (hscroll.getValue() < 1)
+      else
       {
-        return false;
-      }
+        int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
+        int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
+                .getCharHeight()) - 1;
 
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() - 1);
-    }
-    else
-    {
-      if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
-      {
-        return false;
+        vpRanges.setViewportWidth(widthInRes);
+        vpRanges.setViewportHeight(heightInSeq);
       }
-
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() + 1);
     }
 
-    fastPaint = true;
+    idSpaceFillerPanel1.setVisible(!wrap);
 
-    return true;
+    repaint();
   }
 
+
   /**
    * Adjust row/column scrollers to show a visible position in the alignment.
    * 
@@ -696,199 +664,185 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          visible row to scroll to
    * 
    */
-  public void setScrollValues(int x, int y)
+  public void setScrollValues(int xpos, int ypos)
   {
+    int x = xpos;
+    int y = ypos;
+
     if (av == null || av.getAlignment() == null)
     {
       return;
     }
-    int width = av.getAlignment().getWidth();
-    int height = av.getAlignment().getHeight();
 
-    if (av.hasHiddenColumns())
+    if (av.getWrapAlignment())
     {
-      // reset the width to exclude hidden columns
-      width = av.getColumnSelection().findColumnPosition(width);
+      setScrollingForWrappedPanel(x);
     }
+    else
+    {
+      int width = av.getAlignment().getWidth();
+      int height = av.getAlignment().getHeight();
 
-    hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
-    vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+      if (av.hasHiddenColumns())
+      {
+        // reset the width to exclude hidden columns
+        width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
+      }
 
-    if (hextent > width)
-    {
-      hextent = width;
-    }
+      hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+      vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
-    if (vextent > height)
-    {
-      vextent = height;
-    }
+      if (hextent > width)
+      {
+        hextent = width;
+      }
 
-    if ((hextent + x) > width)
-    {
-      x = width - hextent;
-    }
+      if (vextent > height)
+      {
+        vextent = height;
+      }
 
-    if ((vextent + y) > height)
-    {
-      y = height - vextent;
-    }
+      if ((hextent + x) > width)
+      {
+        x = width - hextent;
+      }
 
-    if (y < 0)
-    {
-      y = 0;
-    }
+      if ((vextent + y) > height)
+      {
+        y = height - vextent;
+      }
 
-    if (x < 0)
-    {
-      x = 0;
-    }
+      if (y < 0)
+      {
+        y = 0;
+      }
 
-    // update endRes after x has (possibly) been adjusted
-    vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
-            .getCharWidth())) - 1);
+      if (x < 0)
+      {
+        x = 0;
+      }
 
-    /*
-     * each scroll adjustment triggers adjustmentValueChanged, which resets the
-     * 'do not scroll complement' flag; ensure it is the same for both
-     * operations
-     */
-    // boolean flag = isDontScrollComplement();
-    hscroll.setValues(x, hextent, 0, width);
-    // setDontScrollComplement(flag);
-    vscroll.setValues(y, vextent, 0, height);
+      // update the scroll values
+      hscroll.setValues(x, hextent, 0, width);
+      vscroll.setValues(y, vextent, 0, height);
+    }
   }
 
   /**
-   * DOCUMENT ME!
+   * Respond to adjustment event when horizontal or vertical scrollbar is
+   * changed
    * 
    * @param evt
-   *          DOCUMENT ME!
+   *          adjustment event encoding whether hscroll or vscroll changed
    */
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    int oldX = vpRanges.getStartRes();
-    int oldY = vpRanges.getStartSeq();
+    if (av.getWrapAlignment())
+    {
+      adjustScrollingWrapped(evt);
+      return;
+    }
 
     if (evt.getSource() == hscroll)
     {
+      int oldX = vpRanges.getStartRes();
+      int oldwidth = vpRanges.getViewportWidth();
       int x = hscroll.getValue();
-      if (x == oldX)
+      int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+
+      // if we're scrolling to the position we're already at, stop
+      // this prevents infinite recursion of events when the scroll/viewport
+      // ranges values are the same
+      if ((x == oldX) && (width == oldwidth))
+      {
+        return;
+      }
+      vpRanges.setViewportStartAndWidth(x, width);
+    }
+    else if (evt.getSource() == vscroll)
+    {
+      int oldY = vpRanges.getStartSeq();
+      int oldheight = vpRanges.getViewportHeight();
+      int y = vscroll.getValue();
+      int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+
+      // if we're scrolling to the position we're already at, stop
+      // this prevents infinite recursion of events when the scroll/viewport
+      // ranges values are the same
+      if ((y == oldY) && (height == oldheight))
       {
         return;
       }
-      // vpRanges.setStartRes(x);
-      // vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
-      // .getCharWidth())) - 1);
-      vpRanges.setStartEndRes(
-              x,
-              (x + (getSeqPanel().seqCanvas.getWidth() / av
-              .getCharWidth())) - 1);
+      vpRanges.setViewportStartAndHeight(y, height);
     }
+    if (!fastPaint)
+    {
+      repaint();
+    }
+  }
 
+  /**
+   * Responds to a scroll change by setting the start position of the viewport.
+   * Does
+   * 
+   * @param evt
+   */
+  protected void adjustScrollingWrapped(AdjustmentEvent evt)
+  {
+    if (evt.getSource() == hscroll)
+    {
+      return; // no horizontal scroll when wrapped
+    }
     if (evt.getSource() == vscroll)
     {
-      int offy = vscroll.getValue();
+      int newY = vscroll.getValue();
 
-      if (av.getWrapAlignment())
+      /*
+       * if we're scrolling to the position we're already at, stop
+       * this prevents infinite recursion of events when the scroll/viewport
+       * ranges values are the same
+       */
+      int oldX = vpRanges.getStartRes();
+      int oldY = vpRanges.getWrappedScrollPosition(oldX);
+      if (oldY == newY)
       {
-        if (offy == oldX)
-        {
-          return;
-        }
-        if (offy > -1)
-        {
-          int rowSize = getSeqPanel().seqCanvas
-                  .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-          vpRanges.setStartEndRes(offy * rowSize, (offy + 1) * rowSize);
-          // vpRanges.setStartRes(offy * rowSize);
-          // vpRanges.setEndRes((offy + 1) * rowSize);
-
-        }
-        else
-        {
-          // This is only called if file loaded is a jar file that
-          // was wrapped when saved and user has wrap alignment true
-          // as preference setting
-          SwingUtilities.invokeLater(new Runnable()
-          {
-            @Override
-            public void run()
-            {
-              setScrollValues(vpRanges.getStartRes(),
-                      vpRanges.getStartSeq());
-            }
-          });
-        }
+        return;
       }
-      else
+      if (newY > -1)
       {
-        if (offy == oldY)
-        {
-          return;
-        }
-        // vpRanges.setStartSeq(offy);
-        // vpRanges.setEndSeq(offy
-        // + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
-        // - 1);
-        vpRanges.setStartEndSeq(
-                offy,
-                offy
-                        + (getSeqPanel().seqCanvas.getHeight() / av
-                                .getCharHeight()) - 1);
+        /*
+         * limit page up/down to one width's worth of positions
+         */
+        int rowSize = vpRanges.getViewportWidth();
+        int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
+        vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
       }
     }
-
-    /*if (overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
-    }*/
-
-    // int scrollX = vpRanges.getStartRes() - oldX;
-    // int scrollY = vpRanges.getStartSeq() - oldY;
-
-    if (av.getWrapAlignment() || !fastPaint)
+    else
     {
-      repaint();
+      // This is only called if file loaded is a jar file that
+      // was wrapped when saved and user has wrap alignment true
+      // as preference setting
+      SwingUtilities.invokeLater(new Runnable()
+      {
+        @Override
+        public void run()
+      {
+          // When updating scrolling to use ViewportChange events, this code
+          // could not be validated and it is not clear if it is now being
+          // called. Log warning here in case it is called and unforeseen
+          // problems occur
+          Cache.log
+                  .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+
+          // scroll to start of panel
+          vpRanges.setStartRes(0);
+          vpRanges.setStartSeq(0);
+        }
+      });
     }
-    /*   else
-       {
-         // Make sure we're not trying to draw a panel
-         // larger than the visible window
-         if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
-         {
-           scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
-         }
-         else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
-         {
-           scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
-         }
-
-         if (scrollX != 0 || scrollY != 0)
-         {
-           getIdPanel().getIdCanvas().fastPaint(scrollY);
-           getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
-           getScalePanel().repaint();
-
-           if (av.isShowAnnotation() && scrollX != 0)
-           {
-             getAnnotationPanel().fastPaint(scrollX);
-           }
-         }
-       }
-       /*
-        * If there is one, scroll the (Protein/cDNA) complementary alignment to
-        * match, unless we are ourselves doing that.
-        */
-    /*   if (isDontScrollComplement())
-       {
-         setDontScrollComplement(false);
-       }
-       else
-       {
-         av.scrollComplementaryAlignment();
-       }*/
+    repaint();
   }
 
   /**
@@ -933,37 +887,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
     validate();
 
     /*
-     * set scroll bar positions; first suppress this being 'followed' in any
-     * complementary split pane
+     * set scroll bar positions
      */
-    setDontScrollComplement(true);
-
-    if (av.getWrapAlignment())
-    {
-      int maxwidth = av.getAlignment().getWidth();
+    setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+  }
 
-      if (av.hasHiddenColumns())
-      {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-      }
+  /**
+   * Set vertical scroll bar position, and number of increments, for wrapped
+   * panel
+   * 
+   * @param topLeftColumn
+   *          the column position at top left (0..)
+   */
+  private void setScrollingForWrappedPanel(int topLeftColumn)
+  {
+    int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
+    int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
 
-      int canvasWidth = getSeqPanel().seqCanvas
-              .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-      if (canvasWidth > 0)
-      {
-        int max = maxwidth
-                / getSeqPanel().seqCanvas
-                        .getWrappedCanvasWidth(getSeqPanel().seqCanvas
-                                .getWidth()) + 1;
-        vscroll.setMaximum(max);
-        vscroll.setUnitIncrement(1);
-        vscroll.setVisibleAmount(1);
-      }
-    }
-    else
-    {
-      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
-    }
+    /*
+     * a scrollbar's value can be set to at most (maximum-extent)
+     * so we add extent (1) to the maxScroll value
+     */
+    vscroll.setUnitIncrement(1);
+    vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
   }
 
   /**
@@ -1232,7 +1178,8 @@ 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
@@ -1426,7 +1373,8 @@ 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())
@@ -1656,7 +1604,8 @@ 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;
@@ -1674,6 +1623,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
 
+    closeChildFrames();
+
     /*
      * try to ensure references are nulled
      */
@@ -1705,6 +1656,17 @@ 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()
@@ -1902,14 +1864,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @param b
    */
-  protected void setDontScrollComplement(boolean b)
+  protected void setToScrollComplementPanel(boolean b)
   {
-    this.dontScrollComplement = b;
+    this.scrollComplementaryPanel = b;
   }
 
-  protected boolean isDontScrollComplement()
+  /**
+   * Get whether to scroll complement panel
+   * 
+   * @return true if cDNA/protein complement panels should be scrolled
+   */
+  protected boolean isSetToScrollComplementPanel()
   {
-    return this.dontScrollComplement;
+    return this.scrollComplementaryPanel;
   }
 
   /**
@@ -1935,11 +1902,44 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   @Override
+  /**
+   * Property change event fired when a change is made to the viewport ranges 
+   * object associated with this alignment panel's viewport
+   */
   public void propertyChange(PropertyChangeEvent evt)
   {
+    // update this panel's scroll values based on the new viewport ranges values
     int x = vpRanges.getStartRes();
     int y = vpRanges.getStartSeq();
     setScrollValues(x, y);
 
+    // now update any complementary alignment (its viewport ranges object
+    // is different so does not get automatically updated)
+    if (isSetToScrollComplementPanel())
+    {
+      setToScrollComplementPanel(false);
+      av.scrollComplementaryAlignment();
+      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;
   }
 }