X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=7f1ce31d11bfcd6f8f88b5eae6763cc8e1e775b2;hb=e4f893546d61b043b3381c9548f0cfbf7084fd78;hp=4e5158dfacb60c3a5232e0abb8706518f5685f95;hpb=9ce64cb890f97849c5d30cd994cc682465fd7db1;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 4e5158d..7f1ce31 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;
@@ -33,6 +34,7 @@ import jalview.jbgui.GAlignmentPanel;
 import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.ViewportListenerI;
@@ -48,6 +50,8 @@ 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 +106,14 @@ 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 +148,34 @@ 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 +207,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     av.alignmentChanged(this);
 
+    if (getCalculationDialog() != null)
+    {
+      getCalculationDialog().validateCalcTypes();
+    }
+
     alignFrame.updateEditMenuBar();
 
     paintAlignment(true);
@@ -203,10 +242,6 @@ 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 +410,6 @@ 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 +417,8 @@ 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 +432,12 @@ 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 +450,6 @@ 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 +457,6 @@ 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 +464,6 @@ 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 +487,14 @@ 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!
    * 
@@ -617,75 +630,28 @@ 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 (wrap)
     {
-      if (vscroll.getValue() < 1)
-      {
-        return false;
-      }
-
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() - 1);
+      int widthInRes = getSeqPanel().seqCanvas
+              .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+      vpRanges.setViewportWidth(widthInRes);
     }
     else
     {
-      if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
-      {
-        return false;
-      }
+      int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
+              .getCharWidth()) - 1;
+      int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
+              .getCharHeight()) - 1;
 
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() + 1);
+      vpRanges.setViewportWidth(widthInRes);
+      vpRanges.setViewportHeight(heightInSeq);
     }
 
-    fastPaint = true;
+    idSpaceFillerPanel1.setVisible(!wrap);
 
-    return true;
+    repaint();
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param right
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean scrollRight(boolean right)
-  {
-    if (!right)
-    {
-      if (hscroll.getValue() < 1)
-      {
-        return false;
-      }
-
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() - 1);
-    }
-    else
-    {
-      if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
-      {
-        return false;
-      }
-
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() + 1);
-    }
-
-    fastPaint = true;
-
-    return true;
-  }
 
   /**
    * Adjust row/column scrollers to show a visible position in the alignment.
@@ -696,203 +662,171 @@ 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);
     }
-
-    hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
-    vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
-
-    if (hextent > width)
+    else
     {
-      hextent = width;
-    }
+      int width = av.getAlignment().getWidth();
+      int height = av.getAlignment().getHeight();
 
-    if (vextent > height)
-    {
-      vextent = height;
-    }
+      if (av.hasHiddenColumns())
+      {
+        // reset the width to exclude hidden columns
+        width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
+      }
 
-    if ((hextent + x) > width)
-    {
-      x = width - hextent;
-    }
+      hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+      vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
-    if ((vextent + y) > height)
-    {
-      y = height - vextent;
-    }
+      if (hextent > width)
+      {
+        hextent = width;
+      }
 
-    if (y < 0)
-    {
-      y = 0;
-    }
+      if (vextent > height)
+      {
+        vextent = height;
+      }
 
-    if (x < 0)
-    {
-      x = 0;
-    }
+      if ((hextent + x) > width)
+      {
+        x = width - hextent;
+      }
 
-    // update endRes after x has (possibly) been adjusted
-    // vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
-    // .getCharWidth())) - 1);
+      if ((vextent + y) > height)
+      {
+        y = height - vextent;
+      }
 
-    /*
-     * 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);
+      if (y < 0)
+      {
+        y = 0;
+      }
+
+      if (x < 0)
+      {
+        x = 0;
+      }
 
+      // 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 oldwidth = vpRanges.getViewportWidth();
     int oldY = vpRanges.getStartSeq();
+    int oldheight = vpRanges.getViewportHeight();
 
-    // check for horizontal scroll with wrapped alignment
-    // as this can happen via triggered events (and we don't want to hscroll
-    // when wrapped)
-    if (evt.getSource() == hscroll && !av.getWrapAlignment())
+    if (av.getWrapAlignment())
     {
-      int x = hscroll.getValue();
-      if (x == oldX)
+      if (evt.getSource() == hscroll)
       {
-        return;
+        return; // no horizontal scroll when wrapped
       }
-      // vpRanges.setStartRes(x);
-      // vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
-      // .getCharWidth())) - 1);
-      vpRanges.setStartEndRes(
-              x,
-              (x + (getSeqPanel().seqCanvas.getWidth() / av
-              .getCharWidth())) - 1);
-    }
-
-    if (evt.getSource() == vscroll)
-    {
-      int offy = vscroll.getValue();
-
-      if (av.getWrapAlignment())
+      else if (evt.getSource() == vscroll)
       {
-        if (offy == oldX)
+        int offy = vscroll.getValue();
+        int rowSize = getSeqPanel().seqCanvas
+                .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+
+        // 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 ((offy * rowSize == oldX) && (oldwidth == rowSize))
         {
           return;
         }
-        if (offy > -1)
+        else 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());
-            }
-          });
+          vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
         }
       }
       else
       {
-        if (offy == oldY)
+        // 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()
         {
-          return;
-        }
-        // vpRanges.setStartSeq(offy);
-        // vpRanges.setEndSeq(offy
-        // + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
-        // - 1);
-        vpRanges.setStartEndSeq(
-                offy,
-                offy
-                        + (getSeqPanel().seqCanvas.getHeight() / av
-                                .getCharHeight()) - 1);
+          @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);
+          }
+        });
       }
+      repaint();
     }
-
-    /*if (overviewPanel != null)
+    else
     {
-      overviewPanel.setBoxPosition();
-    }*/
-
-    // int scrollX = vpRanges.getStartRes() - oldX;
-    // int scrollY = vpRanges.getStartSeq() - oldY;
+      // horizontal scroll
+      if (evt.getSource() == hscroll)
+      {
+        int x = hscroll.getValue();
+        int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
 
-    if (av.getWrapAlignment() || !fastPaint)
-    {
-      repaint();
+        // 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 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.setViewportStartAndHeight(y, height);
+      }
+      if (!fastPaint)
+      {
+        repaint();
+      }
     }
-    /*   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();
-       }*/
   }
 
   /**
@@ -937,36 +871,39 @@ 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);
+    setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+  }
 
-    if (av.getWrapAlignment())
+  /*
+   * Set vertical scroll bar parameters for wrapped panel
+   * @param res 
+   *    the residue to scroll to
+   */
+  private void setScrollingForWrappedPanel(int res)
+  {
+    // get the width of the alignment in residues
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
     {
-      int maxwidth = av.getAlignment().getWidth();
-
-      if (av.hasHiddenColumns())
-      {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-      }
-
-      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);
-      }
+        maxwidth = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(maxwidth) - 1;
     }
-    else
+
+    // get the width of the canvas in residues
+    int canvasWidth = getSeqPanel().seqCanvas
+            .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+    if (canvasWidth > 0)
     {
-      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+      // position we want to scroll to is number of canvasWidth's to get there
+      int current = res / canvasWidth;
+
+      // max scroll position: add one because extent is 1 and scrollbar value
+      // can only be set to at most max - extent
+      int max = maxwidth / canvasWidth + 1;
+      vscroll.setUnitIncrement(1);
+      vscroll.setValues(current, 1, 0, max);
     }
   }
 
@@ -1236,7 +1173,8 @@ 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
@@ -1430,7 +1368,8 @@ 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())
@@ -1513,11 +1452,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
           sy = s * av.getCharHeight() + scaleHeight;
 
           SequenceI seq = av.getAlignment().getSequenceAt(s);
-          SequenceFeature[] features = seq.getSequenceFeatures();
           SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
-            StringBuilder text = new StringBuilder();
+            StringBuilder text = new StringBuilder(512);
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
@@ -1535,7 +1473,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
               continue;
             }
 
-            int alIndex = seq.findPosition(res);
+            int seqPos = seq.findPosition(res);
             gSize = groups.length;
             for (g = 0; g < gSize; g++)
             {
@@ -1547,7 +1485,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                         .append((idWidth + (res + 1) * av.getCharWidth()))
                         .append(",").append((av.getCharHeight() + sy))
                         .append("\"").append(" onMouseOver=\"toolTip('")
-                        .append(alIndex).append(" ").append(triplet);
+                        .append(seqPos).append(" ").append(triplet);
               }
 
               if (groups[g].getStartRes() < res
@@ -1558,61 +1496,51 @@ public class AlignmentPanel extends GAlignmentPanel implements
               }
             }
 
-            if (features != null)
+            if (text.length() < 1)
             {
-              if (text.length() < 1)
-              {
-                text.append("<area shape=\"rect\" coords=\"")
-                        .append((idWidth + res * av.getCharWidth()))
-                        .append(",").append(sy).append(",")
-                        .append((idWidth + (res + 1) * av.getCharWidth()))
-                        .append(",").append((av.getCharHeight() + sy))
-                        .append("\"").append(" onMouseOver=\"toolTip('")
-                        .append(alIndex).append(" ").append(triplet);
-              }
-              fSize = features.length;
-              for (f = 0; f < fSize; f++)
+              text.append("<area shape=\"rect\" coords=\"")
+                      .append((idWidth + res * av.getCharWidth()))
+                      .append(",").append(sy).append(",")
+                      .append((idWidth + (res + 1) * av.getCharWidth()))
+                      .append(",").append((av.getCharHeight() + sy))
+                      .append("\"").append(" onMouseOver=\"toolTip('")
+                      .append(seqPos).append(" ").append(triplet);
+            }
+            if (!Comparison.isGap(seq.getCharAt(res)))
+            {
+              List<SequenceFeature> features = seq.findFeatures(seqPos,
+                      seqPos);
+              for (SequenceFeature sf : features)
               {
-
-                if ((features[f].getBegin() <= seq.findPosition(res))
-                        && (features[f].getEnd() >= seq.findPosition(res)))
+                if (sf.isContactFeature())
                 {
-                  if (features[f].isContactFeature())
-                  {
-                    if (features[f].getBegin() == seq.findPosition(res)
-                            || features[f].getEnd() == seq
-                                    .findPosition(res))
-                    {
-                      text.append("<br>").append(features[f].getType())
-                              .append(" ").append(features[f].getBegin())
-                              .append(":").append(features[f].getEnd());
-                    }
-                  }
-                  else
+                  text.append("<br>").append(sf.getType()).append(" ")
+                          .append(sf.getBegin()).append(":")
+                          .append(sf.getEnd());
+                }
+                else
+                {
+                  text.append("<br>");
+                  text.append(sf.getType());
+                  String description = sf.getDescription();
+                  if (description != null
+                          && !sf.getType().equals(description))
                   {
-                    text.append("<br>");
-                    text.append(features[f].getType());
-                    if (features[f].getDescription() != null
-                            && !features[f].getType().equals(
-                                    features[f].getDescription()))
-                    {
-                      text.append(" ").append(features[f].getDescription());
-                    }
-
-                    if (features[f].getValue("status") != null)
-                    {
-                      text.append(" (").append(features[f].getValue("status"))
-                              .append(")");
-                    }
+                    description = description.replace("\"", "&quot;");
+                    text.append(" ").append(description);
                   }
                 }
-
+                String status = sf.getStatus();
+                if (status != null && !"".equals(status))
+                {
+                  text.append(" (").append(status).append(")");
+                }
+              }
+              if (text.length() > 1)
+              {
+                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+                out.println(text.toString());
               }
-            }
-            if (text.length() > 1)
-            {
-              text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
-              out.println(text.toString());
             }
           }
         }
@@ -1660,7 +1588,8 @@ 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;
@@ -1678,6 +1607,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
 
+    closeChildFrames();
+
     /*
      * try to ensure references are nulled
      */
@@ -1709,6 +1640,17 @@ 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()
@@ -1906,14 +1848,19 @@ 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;
   }
 
   /**
@@ -1939,11 +1886,44 @@ 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);
-    av.scrollComplementaryAlignment();
+
+    // 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;
   }
 }