JAL-2490 lookup features at each column position
[jalview.git] / src / jalview / gui / AlignmentPanel.java
index ad7e75c..2f6e3e4 100644 (file)
@@ -25,7 +25,8 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -33,8 +34,10 @@ 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.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -69,6 +72,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 {
   public AlignViewport av;
 
+  ViewportRanges vpRanges;
+
   OverviewPanel overviewPanel;
 
   private SeqPanel seqPanel;
@@ -76,6 +81,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   private IdPanel idPanel;
 
   private boolean headless;
+
   IdwidthAdjuster idwidthAdjuster;
 
   /** DOCUMENT ME!! */
@@ -90,15 +96,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  int hextent = 0;
+  private int hextent = 0;
 
-  int vextent = 0;
+  private int vextent = 0;
 
   /*
    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
    * true, suppresses invoking the same method recursively.
    */
-  private boolean followingComplementScroll;
+  private boolean dontScrollComplement;
+
+  private PropertyChangeListener propertyChangeListener;
+
+  private CalculationChooser calculationDialog;
 
   /**
    * Creates a new AlignmentPanel object.
@@ -110,6 +120,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     alignFrame = af;
     this.av = av;
+    vpRanges = av.getRanges();
     setSeqPanel(new SeqPanel(av, this));
     setIdPanel(new IdPanel(av, this));
 
@@ -134,8 +145,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     vscroll.addAdjustmentListener(this);
 
     final AlignmentPanel ap = this;
-    av.addPropertyChangeListener(new PropertyChangeListener()
+    propertyChangeListener = new PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
         if (evt.getPropertyName().equals("alignment"))
@@ -144,7 +156,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
           alignmentChanged();
         }
       }
-    });
+    };
+    av.addPropertyChangeListener(propertyChangeListener);
     fontChanged();
     adjustAnnotationHeight();
     updateLayout();
@@ -155,10 +168,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return av;
   }
+
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
 
+    if (getCalculationDialog() != null)
+    {
+      getCalculationDialog().validateCalcTypes();
+    }
+
     alignFrame.updateEditMenuBar();
 
     paintAlignment(true);
@@ -177,8 +196,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
             + fm.getDescent()));
     idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
-            .getCharHeight()
-            + fm.getDescent()));
+            .getCharHeight() + fm.getDescent()));
 
     getIdPanel().getIdCanvas().gg = null;
     getSeqPanel().seqCanvas.img = null;
@@ -292,7 +310,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Highlight the given results on the alignment.
    * 
    */
-  public void highlightSearchResults(SearchResults results)
+  public void highlightSearchResults(SearchResultsI results)
   {
     scrollToPosition(results);
     getSeqPanel().seqCanvas.highlightSearchResults(results);
@@ -304,7 +322,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @param results
    */
-  public boolean scrollToPosition(SearchResults results)
+  public boolean scrollToPosition(SearchResultsI results)
   {
     return scrollToPosition(results, 0, true, false);
   }
@@ -317,7 +335,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param redrawOverview
    * @return
    */
-  public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
+  public boolean scrollToPosition(SearchResultsI searchResults,
+          boolean redrawOverview)
   {
     return scrollToPosition(searchResults, 0, redrawOverview, false);
   }
@@ -336,9 +355,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          if true, try to centre the search results horizontally in the view
    * @return false if results were not found
    */
-  public boolean scrollToPosition(SearchResults results,
-          int verticalOffset,
-          boolean redrawOverview, boolean centre)
+  public boolean scrollToPosition(SearchResultsI results,
+          int verticalOffset, boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
     // TODO: properly locate search results in view when large numbers of hidden
@@ -362,8 +380,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       int start = r[0];
       int end = r[1];
-      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
       // DEBUG
+      // System.err.println(this.av.viewName + " Seq : " + seqIndex
+      // + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -371,9 +390,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       if (centre)
       {
-        int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
-        end = Math.min(end + offset, seq.getEnd() - 1);
+        end = end + offset - 1;
       }
       if (start < 0)
       {
@@ -385,11 +404,12 @@ 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;
@@ -402,9 +422,12 @@ 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 = av.getStartRes()) >= start)
+        if ((startv = vpRanges.getStartRes()) >= start)
         {
           /*
            * Scroll left to make start of search results visible
@@ -412,7 +435,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // setScrollValues(start - 1, seqIndex); // plus one residue
           setScrollValues(start, seqIndex);
         }
-        else if ((endv = av.getEndRes()) <= end)
+        else if ((endv = vpRanges.getEndRes()) <= end)
         {
           /*
            * Scroll right to make end of search results visible
@@ -420,19 +443,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
           setScrollValues(startv + end - endv, seqIndex);
         }
-        else if ((starts = av.getStartSeq()) > seqIndex)
+        else if ((starts = vpRanges.getStartSeq()) > seqIndex)
         {
           /*
            * Scroll up to make start of search results visible
            */
-          setScrollValues(av.getStartRes(), seqIndex);
+          setScrollValues(vpRanges.getStartRes(), seqIndex);
         }
-        else if ((ends = av.getEndSeq()) <= seqIndex)
+        else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
         {
           /*
            * Scroll down to make end of search results visible
            */
-          setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+          setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+                  + 1);
         }
         /*
          * Else results are already visible - no need to scroll
@@ -455,10 +479,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     int cwidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-    if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    if (res < vpRanges.getStartRes()
+            || res >= (vpRanges.getStartRes() + cwidth))
     {
       vscroll.setValue((res / cwidth));
-      av.startRes = vscroll.getValue() * cwidth;
+      vpRanges.setStartRes(vscroll.getValue() * cwidth);
     }
 
   }
@@ -504,6 +529,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * automatically adjust annotation panel height for new annotation whilst
    * ensuring the alignment is still visible.
    */
+  @Override
   public void adjustAnnotationHeight()
   {
     // TODO: display vertical annotation scrollbar if necessary
@@ -561,6 +587,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     annotationScroller.setPreferredSize(new Dimension(annotationScroller
             .getWidth(), annotationHeight));
 
+    Dimension e = idPanel.getSize();
+    alabels.setSize(new Dimension(e.width, annotationHeight));
+
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), annotationHeight));
     annotationScroller.validate();
@@ -578,7 +607,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     fontChanged();
     setAnnotationVisible(av.isShowAnnotation());
     boolean wrap = av.getWrapAlignment();
-    av.startSeq = 0;
+    vpRanges.setStartSeq(0);
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
@@ -668,14 +697,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Adjust row/column scrollers to show a visible position in the alignment.
    * 
    * @param x
-   *          visible column to scroll to DOCUMENT ME!
+   *          visible column to scroll to
    * @param y
    *          visible row to scroll to
    * 
    */
   public void setScrollValues(int x, int y)
   {
-    // System.err.println("Scroll to "+x+","+y);
     if (av == null || av.getAlignment() == null)
     {
       return;
@@ -685,12 +713,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (av.hasHiddenColumns())
     {
-      width = av.getColumnSelection().findColumnPosition(width);
+      // reset the width to exclude hidden columns
+      width = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(width);
     }
 
-    av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
-            .getCharWidth())) - 1);
-
     hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
     vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
@@ -724,7 +751,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
       x = 0;
     }
 
+    // update endRes after x has (possibly) been adjusted
+    vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+            .getCharWidth())) - 1);
+
+    /*
+     * 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);
   }
 
@@ -734,16 +772,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
+    int oldX = vpRanges.getStartRes();
+    int oldY = vpRanges.getStartSeq();
 
     if (evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+      vpRanges.setStartRes(x);
+      vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+              .getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -756,8 +796,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           int rowSize = getSeqPanel().seqCanvas
                   .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-          av.setStartRes(offy * rowSize);
-          av.setEndRes((offy + 1) * rowSize);
+          vpRanges.setStartRes(offy * rowSize);
+          vpRanges.setEndRes((offy + 1) * rowSize);
         }
         else
         {
@@ -766,18 +806,21 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // as preference setting
           SwingUtilities.invokeLater(new Runnable()
           {
+            @Override
             public void run()
             {
-              setScrollValues(av.getStartRes(), av.getStartSeq());
+              setScrollValues(vpRanges.getStartRes(),
+                      vpRanges.getStartSeq());
             }
           });
         }
       }
       else
       {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy
-                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
+        vpRanges.setStartSeq(offy);
+        vpRanges.setEndSeq(offy
+                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
+                - 1);
       }
     }
 
@@ -786,8 +829,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       overviewPanel.setBoxPosition();
     }
 
-    int scrollX = av.startRes - oldX;
-    int scrollY = av.startSeq - oldY;
+    int scrollX = vpRanges.getStartRes() - oldX;
+    int scrollY = vpRanges.getStartSeq() - oldY;
 
     if (av.getWrapAlignment() || !fastPaint)
     {
@@ -797,13 +840,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if (scrollX > av.endRes - av.startRes)
+      if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
       {
-        scrollX = av.endRes - av.startRes;
+        scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
       }
-      else if (scrollX < av.startRes - av.endRes)
+      else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
       {
-        scrollX = av.startRes - av.endRes;
+        scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
       }
 
       if (scrollX != 0 || scrollY != 0)
@@ -822,9 +865,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * If there is one, scroll the (Protein/cDNA) complementary alignment to
      * match, unless we are ourselves doing that.
      */
-    if (isFollowingComplementScroll())
+    if (isDontScrollComplement())
     {
-      setFollowingComplementScroll(false);
+      setDontScrollComplement(false);
     }
     else
     {
@@ -836,17 +879,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Repaint the alignment including the annotations and overview panels (if
    * shown).
    */
+  @Override
   public void paintAlignment(boolean updateOverview)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
-    sorter.sort(getAlignment()
-            .getAlignmentAnnotation(),
+    sorter.sort(getAlignment().getAlignmentAnnotation(),
             av.getSortAnnotationsBy());
     repaint();
 
     if (updateOverview)
     {
+      // TODO: determine if this paintAlignment changed structure colours
       av.getStructureSelectionManager().sequenceColoursChanged(this);
 
       if (overviewPanel != null)
@@ -862,6 +906,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
     invalidate();
@@ -871,13 +916,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
     hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
     validate();
 
+    /*
+     * set scroll bar positions; first suppress this being 'followed' in any
+     * complementary split pane
+     */
+    setDontScrollComplement(true);
+
     if (av.getWrapAlignment())
     {
       int maxwidth = av.getAlignment().getWidth();
 
       if (av.hasHiddenColumns())
       {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        maxwidth = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(maxwidth) - 1;
       }
 
       int canvasWidth = getSeqPanel().seqCanvas
@@ -895,7 +947,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
+      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
     }
   }
 
@@ -914,6 +966,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @throws PrinterException
    *           DOCUMENT ME!
    */
+  @Override
   public int print(Graphics pg, PageFormat pf, int pi)
           throws PrinterException
   {
@@ -924,11 +977,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (av.getWrapAlignment())
     {
-      return printWrappedAlignment(pg, pwidth, pheight, pi);
+      return printWrappedAlignment(pwidth, pheight, pi, pg);
     }
     else
     {
-      return printUnwrapped(pg, pwidth, pheight, pi);
+      return printUnwrapped(pwidth, pheight, pi, pg, pg);
     }
   }
 
@@ -949,84 +1002,103 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @throws PrinterException
    *           DOCUMENT ME!
    */
-  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+  /**
+   * Draws the alignment image, including sequence ids, sequences, and
+   * annotation labels and annotations if shown, on either one or two Graphics
+   * context.
+   * 
+   * @param pageWidth
+   * @param pageHeight
+   * @param pi
+   * @param idGraphics
+   *          the graphics context for sequence ids and annotation labels
+   * @param alignmentGraphics
+   *          the graphics context for sequences and annotations (may or may not
+   *          be the same context as idGraphics)
+   * @return
+   * @throws PrinterException
+   */
+  public int printUnwrapped(int pageWidth, int pageHeight, int pi,
+          Graphics idGraphics, Graphics alignmentGraphics)
           throws PrinterException
   {
-    int idWidth = getVisibleIdWidth(false);
-    FontMetrics fm = getFontMetrics(av.getFont());
-    int scaleHeight = av.getCharHeight() + fm.getDescent();
+    final int idWidth = getVisibleIdWidth(false);
 
-    pg.setColor(Color.white);
-    pg.fillRect(0, 0, pwidth, pheight);
-    pg.setFont(av.getFont());
-
-    // //////////////////////////////////
-    // / How many sequences and residues can we fit on a printable page?
-    int totalRes = (pwidth - idWidth) / av.getCharWidth();
+    /*
+     * Get the horizontal offset to where we draw the sequences.
+     * This is idWidth if using a single Graphics context, else zero.
+     */
+    final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
 
-    int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1;
+    FontMetrics fm = getFontMetrics(av.getFont());
+    int charHeight = av.getCharHeight();
+    int scaleHeight = charHeight + fm.getDescent();
 
-    int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
+    idGraphics.setColor(Color.white);
+    idGraphics.fillRect(0, 0, pageWidth, pageHeight);
+    idGraphics.setFont(av.getFont());
 
-    // ///////////////////////////
-    // / Only print these sequences and residues on this page
-    int startRes;
+    /*
+     * How many sequences and residues can we fit on a printable page?
+     */
+    int totalRes = (pageWidth - idWidth) / av.getCharWidth();
 
-    // ///////////////////////////
-    // / Only print these sequences and residues on this page
-    int endRes;
+    int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
 
-    // ///////////////////////////
-    // / Only print these sequences and residues on this page
-    int startSeq;
+    int alignmentWidth = av.getAlignment().getWidth();
+    int pagesWide = (alignmentWidth / totalRes) + 1;
 
-    // ///////////////////////////
-    // / Only print these sequences and residues on this page
-    int endSeq;
-    startRes = (pi % pagesWide) * totalRes;
-    endRes = (startRes + totalRes) - 1;
+    final int startRes = (pi % pagesWide) * totalRes;
+    int endRes = (startRes + totalRes) - 1;
 
-    if (endRes > (av.getAlignment().getWidth() - 1))
+    if (endRes > (alignmentWidth - 1))
     {
-      endRes = av.getAlignment().getWidth() - 1;
+      endRes = alignmentWidth - 1;
     }
 
-    startSeq = (pi / pagesWide) * totalSeq;
-    endSeq = startSeq + totalSeq;
+    final int startSeq = (pi / pagesWide) * totalSeq;
+    int endSeq = startSeq + totalSeq;
 
-    if (endSeq > av.getAlignment().getHeight())
+    int alignmentHeight = av.getAlignment().getHeight();
+    if (endSeq > alignmentHeight)
     {
-      endSeq = av.getAlignment().getHeight();
+      endSeq = alignmentHeight;
     }
 
-    int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
-            * pheight;
+    int pagesHigh = ((alignmentHeight / totalSeq) + 1)
+            * pageHeight;
 
     if (av.isShowAnnotation())
     {
       pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
     }
 
-    pagesHigh /= pheight;
+    pagesHigh /= pageHeight;
 
     if (pi >= (pagesWide * pagesHigh))
     {
       return Printable.NO_SUCH_PAGE;
     }
+    final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
+            + 3;
 
-    // draw Scale
-    pg.translate(idWidth, 0);
-    getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth,
-            scaleHeight);
-    pg.translate(-idWidth, scaleHeight);
+    /*
+     * draw the Scale at horizontal offset, then reset to top left (0, 0)
+     */
+    alignmentGraphics.translate(alignmentGraphicsOffset, 0);
+    getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
+            pageWidth - idWidth, scaleHeight);
+    alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
-    // //////////////
-    // Draw the ids
+    /*
+     * Draw the sequence ids, offset for scale height,
+     * then reset to top left (0, 0)
+     */
+    idGraphics.translate(0, scaleHeight);
+    idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
     Color currentColor = null;
     Color currentTextColor = null;
 
-    pg.setFont(getIdPanel().getIdCanvas().getIdfont());
-
     SequenceI seq;
     for (int i = startSeq; i < endSeq; i++)
     {
@@ -1034,6 +1106,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if ((av.getSelectionGroup() != null)
               && av.getSelectionGroup().getSequences(null).contains(seq))
       {
+        /*
+         * gray out ids of sequences in selection group (if any)
+         */
         currentColor = Color.gray;
         currentTextColor = Color.black;
       }
@@ -1043,46 +1118,58 @@ public class AlignmentPanel extends GAlignmentPanel implements
         currentTextColor = Color.black;
       }
 
-      pg.setColor(currentColor);
-      pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
-              av.getCharHeight());
+      idGraphics.setColor(currentColor);
+      idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
+              charHeight);
 
-      pg.setColor(currentTextColor);
+      idGraphics.setColor(currentTextColor);
 
       int xPos = 0;
+      String displayId = seq.getDisplayId(av.getShowJVSuffix());
       if (av.isRightAlignIds())
       {
-        fm = pg.getFontMetrics();
+        fm = idGraphics.getFontMetrics();
         xPos = idWidth
-                - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
+                - fm.stringWidth(displayId)
                 - 4;
       }
 
-      pg.drawString(
-              seq.getDisplayId(av.getShowJVSuffix()),
-              xPos,
-              (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
-                      - (av.getCharHeight() / 5));
+      idGraphics.drawString(displayId, xPos,
+              (((i - startSeq) * charHeight) + charHeight)
+                      - (charHeight / 5));
     }
+    idGraphics.setFont(av.getFont());
+    idGraphics.translate(0, -scaleHeight);
 
-    pg.setFont(av.getFont());
-
-    // draw main sequence panel
-    pg.translate(idWidth, 0);
-    getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+    /*
+     * draw the sequences, offset for scale height, and id width (if using a
+     * single graphics context), then reset to (0, scale height)
+     */
+    alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
+    getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
+            startSeq, endSeq, 0);
+    alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
-    if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
+    if (av.isShowAnnotation() && (endSeq == alignmentHeight))
     {
-      // draw annotation - need to offset for current scroll position
-      int offset = -getAlabels().getScrollOffset();
-      pg.translate(0, offset);
-      pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight()
-              + 3);
-      getAlabels().drawComponent(pg, idWidth);
-      pg.translate(idWidth + 3, 0);
+      /*
+       * draw annotation labels; drawComponent() translates by
+       * getScrollOffset(), so compensate for that first;
+       * then reset to (0, scale height)
+       */
+      int offset = getAlabels().getScrollOffset();
+      idGraphics.translate(0, -offset);
+      idGraphics.translate(0, alignmentDrawnHeight);
+      getAlabels().drawComponent(idGraphics, idWidth);
+      idGraphics.translate(0, -alignmentDrawnHeight);
+
+      /*
+       * draw the annotations starting at 
+       * (idOffset, alignmentHeight) from (0, scaleHeight)
+       */
+      alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
       getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
-              pg, -1, startRes, endRes + 1);
-      pg.translate(0, -offset);
+              alignmentGraphics, -1, startRes, endRes + 1);
     }
 
     return Printable.PAGE_EXISTS;
@@ -1105,8 +1192,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @throws PrinterException
    *           DOCUMENT ME!
    */
-  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
-          int pi) throws PrinterException
+  public int printWrappedAlignment(int pwidth, int pheight, int pi,
+          Graphics pg) throws PrinterException
   {
     int annotationHeight = 0;
     AnnotationLabels labels = null;
@@ -1130,7 +1217,8 @@ 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
@@ -1171,12 +1259,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       if (labels != null)
       {
-        pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.getCharHeight()));
+        pg.translate(-3,
+                ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
-        pg.translate(+3, -ypos
+        pg.translate(
+                +3,
+                -ypos
                         - (av.getAlignment().getHeight() * av
                                 .getCharHeight()));
       }
@@ -1186,8 +1276,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pg.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
-            0);
+    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+            totalHeight, 0);
 
     if ((pi * pheight) < totalHeight)
     {
@@ -1231,22 +1321,26 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (onscreen
             || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
     {
-      return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
-              : calculateIdWidth().width + 4);
+      int w = getIdPanel().getWidth();
+      return (w > 0 ? w : calculateIdWidth().width + 4);
     }
     return idwidth.intValue() + 4;
   }
 
   void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
   {
-    long progress = System.currentTimeMillis();
+    int boarderBottomOffset = 5;
+    long pSessionId = System.currentTimeMillis();
     headless = (System.getProperty("java.awt.headless") != null && System
             .getProperty("java.awt.headless").equals("true"));
     if (alignFrame != null && !headless)
     {
-      alignFrame.setProgressBar(MessageManager.formatMessage(
-              "status.saving_file", new Object[]
-              { type.getLabel() }), progress);
+      if (file != null)
+      {
+        alignFrame.setProgressBar(MessageManager.formatMessage(
+                "status.saving_file", new Object[] { type.getLabel() }),
+                pSessionId);
+      }
     }
     try
     {
@@ -1272,26 +1366,30 @@ public class AlignmentPanel extends GAlignmentPanel implements
         }
 
         im = new jalview.util.ImageMaker(this, type, imageAction,
-                aDimension.getWidth(), aDimension.getHeight(), file,
-                imageTitle);
+                aDimension.getWidth(), aDimension.getHeight()
+                        + boarderBottomOffset, file, imageTitle,
+                alignFrame, pSessionId, headless);
+        Graphics graphics = im.getGraphics();
         if (av.getWrapAlignment())
         {
-          if (im.getGraphics() != null)
+          if (graphics != null)
           {
-            printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
-                    aDimension.getHeight(), 0);
+            printWrappedAlignment(aDimension.getWidth(),
+                    aDimension.getHeight() + boarderBottomOffset, 0,
+                    graphics);
             im.writeImage();
           }
         }
         else
         {
-          if (im.getGraphics() != null)
+          if (graphics != null)
           {
-            printUnwrapped(im.getGraphics(), aDimension.getWidth(),
-                    aDimension.getHeight(), 0);
+            printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
+                    0, graphics, graphics);
             im.writeImage();
           }
         }
+
       } catch (OutOfMemoryError err)
       {
         // Be noisy here.
@@ -1305,10 +1403,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
     } finally
     {
-      if (alignFrame != null && !headless)
-      {
-        alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
-      }
+
     }
   }
 
@@ -1317,7 +1412,8 @@ 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())
@@ -1372,9 +1468,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
   }
+
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
-    // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+    // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
     // ////////////////////////////////////////////
     int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
@@ -1388,7 +1485,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
                 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
-        StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
         out.println(jalview.io.HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName
@@ -1400,17 +1496,15 @@ 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++)
           {
-            text = new StringBuffer();
+            StringBuilder text = new StringBuilder(512);
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
               triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(res)
-                      + "");
+                      .getCharAt(res) + "");
             }
             else
             {
@@ -1423,83 +1517,74 @@ 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++)
             {
               if (text.length() < 1)
               {
-                text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.getCharWidth()) + "," + sy
-                        + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + ","
-                        + (av.getCharHeight() + sy) + "\""
-                        + " onMouseOver=\"toolTip('" + alIndex + " "
-                        + triplet);
+                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 (groups[g].getStartRes() < res
                       && groups[g].getEndRes() > res)
               {
-                text.append("<br><em>" + groups[g].getName() + "</em>");
+                text.append("<br><em>").append(groups[g].getName())
+                        .append("</em>");
               }
             }
 
-            if (features != null)
+            if (text.length() < 1)
             {
-              if (text.length() < 1)
-              {
-                text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.getCharWidth()) + "," + sy
-                        + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + ","
-                        + (av.getCharHeight() + sy) + "\""
-                        + " onMouseOver=\"toolTip('" + alIndex + " "
-                        + 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.getFeatures()
+                      .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].getType().equals("disulfide bond"))
-                  {
-                    if (features[f].getBegin() == seq.findPosition(res)
-                            || features[f].getEnd() == seq
-                                    .findPosition(res))
-                    {
-                      text.append("<br>disulfide bond "
-                              + features[f].getBegin() + ":"
-                              + 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(" " + features[f].getDescription());
-                    }
-
-                    if (features[f].getValue("status") != null)
-                    {
-                      text.append(" (" + features[f].getValue("status")
-                              + ")");
-                    }
+                    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());
             }
           }
         }
@@ -1547,7 +1632,8 @@ 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;
@@ -1564,8 +1650,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
+
+    closeChildFrames();
+
+    /*
+     * try to ensure references are nulled
+     */
+    if (annotationPanel != null)
+    {
+      annotationPanel.dispose();
+    }
+
     if (av != null)
     {
+      av.removePropertyChangeListener(propertyChangeListener);
       jalview.structure.StructureSelectionManager ssm = av
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
@@ -1573,7 +1671,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       ssm.removeCommandListener(av);
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
-      av.setAlignment(null);
+      av.dispose();
       av = null;
     }
     else
@@ -1586,6 +1684,17 @@ 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()
@@ -1609,10 +1718,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public AlignmentI getAlignment()
   {
-    return av.getAlignment();
+    return av == null ? null : av.getAlignment();
   }
 
-
   @Override
   public String getViewName()
   {
@@ -1664,12 +1772,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     return new FeatureRenderer(this);
   }
-  @Override 
+
+  @Override
   public jalview.api.FeatureRenderer getFeatureRenderer()
   {
     return seqPanel.seqCanvas.getFeatureRenderer();
   }
-  public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
+
+  public void updateFeatureRenderer(
+          jalview.renderer.seqfeatures.FeatureRenderer fr)
   {
     fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
   }
@@ -1742,14 +1853,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param verticalOffset
    *          the number of visible sequences to show above the mapped region
    */
-  public void scrollToCentre(SearchResults sr, int verticalOffset)
+  public void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
     /*
      * To avoid jumpy vertical scrolling (if some sequences are gapped or not
      * mapped), we can make the scroll-to location a sequence above the one
      * actually mapped.
      */
-    SequenceI mappedTo = sr.getResultSequence(0);
+    SequenceI mappedTo = sr.getResults().get(0).getSequence();
     List<SequenceI> seqs = av.getAlignment().getSequences();
 
     /*
@@ -1777,17 +1888,59 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+   * Set a flag to say do not scroll any (cDNA/protein) complement.
    * 
    * @param b
    */
-  protected void setFollowingComplementScroll(boolean b)
+  protected void setDontScrollComplement(boolean b)
+  {
+    this.dontScrollComplement = b;
+  }
+
+  protected boolean isDontScrollComplement()
+  {
+    return this.dontScrollComplement;
+  }
+
+  /**
+   * Redraw sensibly.
+   * 
+   * @adjustHeight if true, try to recalculate panel height for visible
+   *               annotations
+   */
+  protected void refresh(boolean adjustHeight)
+  {
+    validateAnnotationDimensions(adjustHeight);
+    addNotify();
+    if (adjustHeight)
+    {
+      // sort, repaint, update overview
+      paintAlignment(true);
+    }
+    else
+    {
+      // lightweight repaint
+      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)
   {
-    this.followingComplementScroll = b;
+    calculationDialog = calculationChooser;
   }
 
-  protected boolean isFollowingComplementScroll()
+  /**
+   * Returns the reference to the PCA/Tree chooser dialog for this panel (null
+   * if none is open)
+   */
+  public CalculationChooser getCalculationDialog()
   {
-    return this.followingComplementScroll;
+    return calculationDialog;
   }
 }