X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=a4a38f98fce7e525a23ce6edd9dbe425ad520b45;hb=76b5c58c65413e8b239dbf71999f500600ef0f95;hp=73cee2d7fefd691fa2c83a007479c257519409b3;hpb=7ee3b5a7f099858cdde2318c719121b39d9e466e;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 73cee2d..a4a38f9 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,27 +1,54 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.jbgui.GAlignmentPanel;
-import jalview.schemes.*;
-import jalview.analysis.*;
 import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
+
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
+
 import java.io.*;
-import java.awt.image.*;
-import org.jibble.epsgraphics.*;
-import javax.imageio.*;
 
+import javax.swing.*;
 
 
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentPanel extends GAlignmentPanel
+    implements AdjustmentListener, Printable
 {
-
-  AlignViewport     av;
+  public AlignViewport av;
   OverviewPanel overviewPanel;
-  SeqPanel   seqPanel;
-  IdPanel    idPanel;
+  SeqPanel seqPanel;
+  IdPanel idPanel;
   IdwidthAdjuster idwidthAdjuster;
+
+  /** DOCUMENT ME!! */
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
   AnnotationPanel annotationPanel;
@@ -29,13 +56,21 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
+  int hextent = 0;
+  int vextent = 0;
 
+  /**
+   * Creates a new AlignmentPanel object.
+   *
+   * @param af DOCUMENT ME!
+   * @param av DOCUMENT ME!
+   */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     alignFrame = af;
-    this.av         = av;
-    seqPanel        = new SeqPanel  (av, this);
-    idPanel         = new IdPanel   (av, this);
+    this.av = av;
+    seqPanel = new SeqPanel(av, this);
+    idPanel = new IdPanel(av, this);
 
     scalePanel = new ScalePanel(av, this);
 
@@ -46,321 +81,555 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     annotationPanel = new AnnotationPanel(this);
     alabels = new AnnotationLabels(this);
 
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+
     annotationScroller.setViewportView(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
-    Dimension d = calculateIdWidth();
-    d.setSize( d.width+4, d.height);
-    idPanel.idCanvas.setPreferredSize( d );
-    hscrollFillerPanel.setPreferredSize( d );
+    fontChanged();
 
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
+    setScrollValues(0, 0);
 
-    if(seqPanel.seqCanvas.getWidth()==0)
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-     {
-       public void run()
-       {
-         setScrollValues(0,0);
-         Dimension d = calculateIdWidth();
-         d.setSize( d.width+4, d.height);
-         idPanel.idCanvas.setPreferredSize( d );
-         RefreshPanels();
-       }
-    });
+    adjustAnnotationHeight();
 
+    setAnnotationVisible(av.getShowAnnotation());
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
-    addComponentListener(new ComponentAdapter()
-   {
-     public void componentResized(ComponentEvent evt)
-     {
-          RefreshPanels();
-     }
-   });
-
-   setFocusable(true);
-   addKeyListener(new KeyAdapter()
-   {
-     public void keyPressed(KeyEvent evt)
-     {
-       switch(evt.getKeyCode())
-       {
-         case  27: // escape key
-           av.setSelectionGroup(null);
-           RefreshPanels();
-           break;
-         case KeyEvent.VK_X:
-           if(evt.isControlDown())
-           alignFrame.cut_actionPerformed(null);
-           break;
-         case KeyEvent.VK_C:
-         if(evt.isControlDown())
-           alignFrame.copy_actionPerformed(null);
-           break;
-         case KeyEvent.VK_V:
-          if(evt.isControlDown())
-           alignFrame.paste(true);
-           break;
-         case KeyEvent.VK_A:
-         if(evt.isControlDown())
-           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
+    af.addKeyListener(new KeyAdapter()
+    {
+      public void keyPressed(KeyEvent evt)
+      {
+        if(av.cursorMode
+           && evt.getKeyCode()>=KeyEvent.VK_0
+           && evt.getKeyCode()<=KeyEvent.VK_9)
+        {
+          seqPanel.numberPressed(evt.getKeyChar());
+        }
+
+        switch (evt.getKeyCode())
+        {
+          case 27: // escape key
+            alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);
+
+            break;
+
+          case KeyEvent.VK_DOWN:
+            if(av.cursorMode)
+            {
+              seqPanel.moveCursor(0,1);
+            }
+            else
+              alignFrame.moveSelectedSequences(false);
+            break;
+
+          case KeyEvent.VK_UP:
+            if (av.cursorMode)
+            {
+              seqPanel.moveCursor(0,-1);
+            }
+            else
+              alignFrame.moveSelectedSequences(true);
+            break;
+
+          case KeyEvent.VK_LEFT:
+            if(av.cursorMode)
+            {
+              seqPanel.moveCursor(-1,0);
+            }
+            break;
+
+          case KeyEvent.VK_RIGHT:
+            if (av.cursorMode)
+            {
+              seqPanel.moveCursor(1,0);
+            }
+            break;
+
+          case KeyEvent.VK_SPACE:
+            if(av.cursorMode)
+            {
+              seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown());
+            }
+            break;
+
+          case KeyEvent.VK_DELETE:
+          case KeyEvent.VK_BACK_SPACE:
+            if(!av.cursorMode)
+            {
+              alignFrame.cut_actionPerformed(null);
+            }
+            else
+              seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
+
+            break;
+
+          case KeyEvent.VK_S:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorRow();
+            }
+            break;
+          case KeyEvent.VK_C:
+            if(av.cursorMode && !evt.isControlDown())
+            {
+              seqPanel.setCursorColumn();
+            }
+            break;
+          case KeyEvent.VK_P:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorPosition();
+            }
+            break;
+
+          case KeyEvent.VK_ENTER:
+          case KeyEvent.VK_COMMA:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorRowAndColumn();
+            }
+            break;
+
+          case KeyEvent.VK_Q:
+            if(av.cursorMode)
+            {
+              seqPanel.setSelectionAreaAtCursor(true);
+            }
+            break;
+          case KeyEvent.VK_M:
+            if(av.cursorMode)
+            {
+              seqPanel.setSelectionAreaAtCursor(false);
+            }
+            break;
+
+         case KeyEvent.VK_F2:
+           av.cursorMode = ! av.cursorMode;
+           alignFrame.statusBar.setText("Keyboard editing mode is "+
+               (av.cursorMode ? "on" : "off"));
+           if(av.cursorMode)
+           {
+             seqPanel.seqCanvas.cursorX = av.startRes;
+             seqPanel.seqCanvas.cursorY = av.startSeq;
+           }
+           seqPanel.seqCanvas.repaint();
            break;
-        case KeyEvent.VK_DOWN:
-          alignFrame.moveSelectedSequences(false);
-          break;
-        case KeyEvent.VK_UP:
-          alignFrame.moveSelectedSequences(true);
-          break;
-        case KeyEvent.VK_F:
-         if(evt.isControlDown())
-          alignFrame.findMenuItem_actionPerformed(null);
-          break;
-       }
-     }
-   });
+
+          case KeyEvent.VK_F1:
+            try
+            {
+              ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+              java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+              javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+              javax.help.HelpBroker hb = hs.createHelpBroker();
+              hb.setCurrentID("home");
+              hb.setDisplayed(true);
+            }
+            catch (Exception ex)
+            {
+              ex.printStackTrace();
+            }
+            break;
+          case KeyEvent.VK_H:
+          {
+            boolean toggleSeqs = !evt.isControlDown();
+            boolean toggleCols = !evt.isShiftDown();
+
+            boolean hide = false;
+
+            SequenceGroup sg = av.getSelectionGroup();
+            if(toggleSeqs)
+             {
+               if(sg != null && sg.getSize(false) != av.alignment.getHeight())
+               {
+                 alignFrame.hideSelSequences_actionPerformed(null);
+                 hide = true;
+               }
+               else if (!(toggleCols && av.colSel.getSelected().size() > 0))
+                 alignFrame.showAllSeqs_actionPerformed(null);
+             }
+
+             if (toggleCols)
+             {
+               if(av.colSel.getSelected().size() > 0)
+               {
+                 alignFrame.hideSelColumns_actionPerformed(null);
+                 if(!toggleSeqs)
+                   av.selectionGroup = sg;
+               }
+               else if(!hide)
+                 alignFrame.showAllColumns_actionPerformed(null);
+             }
+            break;
+          }
+
+        }
+      }
+    });
   }
 
-  Dimension calculateIdWidth()
+  /**
+   * DOCUMENT ME!
+   */
+  public void fontChanged()
   {
-    Graphics g = this.getGraphics();
-    if(g==null)
+    // set idCanvas bufferedImage to null
+    // to prevent drawing old image
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    scalePanelHolder.setPreferredSize(new Dimension(10,
+        av.charHeight + fm.getDescent()));
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
+        av.charHeight + fm.getDescent()));
+
+    idPanel.idCanvas.gg = null;
+    seqPanel.seqCanvas.img = null;
+    annotationPanel.adjustPanelHeight();
+
+    Dimension d = calculateIdWidth();
+    d.setSize(d.width + 4, d.height);
+    idPanel.idCanvas.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(d);
+
+    if (av.getWrapAlignment())
     {
-      javax.swing.JFrame f = new javax.swing.JFrame();
-      f.addNotify();
-      g = f.getGraphics();
+      int max = av.alignment.getWidth() /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+      vscroll.setMaximum(max);
+      vscroll.setUnitIncrement(1);
+      vscroll.setVisibleAmount(1);
+    }
+    else
+    {
+      setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-    FontMetrics fm = g.getFontMetrics(av.font);
-    AlignmentI al = av.getAlignment();
+    if (overviewPanel != null)
+      overviewPanel.setBoxPosition();
 
-       int i   = 0;
-       int idWidth = 0;
-       String id;
-       while (i < al.getHeight() && al.getSequenceAt(i) != null)
-       {
-         SequenceI s   = al.getSequenceAt(i);
-         if(av.getShowFullId())
-           id   = s.getDisplayId();
-         else
-           id = s.getName();
-
-         if (fm.stringWidth(id) > idWidth)
-           idWidth = fm.stringWidth(id);
-         i++;
-       }
-
-       // Also check annotation label widths
-       i=0;
-       if(al.getAlignmentAnnotation()!=null)
-       {
-         fm = g.getFontMetrics(alabels.getFont());
-         while (i < al.getAlignmentAnnotation().length)
-         {
-           String label = al.getAlignmentAnnotation()[i].label;
-           if (fm.stringWidth(label) > idWidth)
-             idWidth = fm.stringWidth(label);
-           i++;
-         }
-       }
-
-       return new Dimension(idWidth, 12);
+    repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension calculateIdWidth()
+  {
+    Container c = new Container();
+
+    FontMetrics fm = c.getFontMetrics(av.font);
+    AlignmentI al = av.getAlignment();
+
+    int i = 0;
+    int idWidth = 0;
+    String id;
 
- public void highlightSearchResults(int [] results)
- {
-   seqPanel.seqCanvas.highlightSearchResults( results );
+    while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
+    {
+      SequenceI s = al.getSequenceAt(i);
 
-   // do we need to scroll the panel?
-   if(results!=null && (av.getStartSeq()>results[0]
-                        || av.getEndSeq()<results[0]
-                        || av.getStartRes()>results[1]
-                        || av.getEndRes()<results[2]))
-       setScrollValues(results[1], results[0]);
+      id = s.getDisplayId(av.getShowJVSuffix());
 
+      if (fm.stringWidth(id) > idWidth)
+      {
+        idWidth = fm.stringWidth(id);
+      }
 
- }
+      i++;
+    }
 
+    // Also check annotation label widths
+    i = 0;
 
- public OverviewPanel getOverviewPanel()
- {
-   return overviewPanel;
- }
+    if (al.getAlignmentAnnotation() != null)
+    {
+      fm = c.getFontMetrics(alabels.getFont());
 
- public void setOverviewPanel(OverviewPanel op)
- {
-   overviewPanel = op;
- }
+      while (i < al.getAlignmentAnnotation().length)
+      {
+        String label = al.getAlignmentAnnotation()[i].label;
 
+        if (fm.stringWidth(label) > idWidth)
+        {
+          idWidth = fm.stringWidth(label);
+        }
 
-  public void setAnnotationVisible(boolean b)
-  {
-    annotationSpaceFillerHolder.setVisible(b);
-    annotationScroller.setVisible(b);
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-     {
-       public void run()
-       {
-         RefreshPanels();
-       }
-    });
+        i++;
+      }
+    }
 
+    return new Dimension(idWidth, 12);
   }
 
-
-  public void setWrapAlignment(boolean wrap)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param results DOCUMENT ME!
+   */
+  public void highlightSearchResults(SearchResults results)
   {
-    scalePanelHolder.setVisible(!wrap);
-    hscroll.setVisible(!wrap);
-    idwidthAdjuster.setVisible(!wrap);
+    seqPanel.seqCanvas.highlightSearchResults(results);
 
-    av.setShowAnnotation(!wrap);
-    annotationScroller.setVisible(!wrap);
-    annotationSpaceFillerHolder.setVisible(!wrap);
-    idSpaceFillerPanel1.setVisible(!wrap);
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-     {
-       public void run()
-       {
-         RefreshPanels();
-       }
-    });
+    // do we need to scroll the panel?
+    if (results != null)
+    {
+      SequenceI seq = results.getResultSequence(0);
+      int seqIndex = av.alignment.findIndex(seq);
+      int start = seq.findIndex(results.getResultStart(0)) - 1;
+      int end = seq.findIndex(results.getResultEnd(0)) - 1;
 
+      if(!av.wrapAlignment)
+      {
+        if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
+           ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+        {
+          setScrollValues(start, seqIndex);
+        }
+      }
+      else
+      {
+        scrollToWrappedVisible(start);
+      }
+    }
   }
 
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+    if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
 
-  public void setColourScheme()
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public OverviewPanel getOverviewPanel()
   {
-    ColourSchemeI cs = av.getGlobalColourScheme();
+    return overviewPanel;
+  }
 
-    if(av.getConservationSelected())
+  /**
+   * DOCUMENT ME!
+   *
+   * @param op DOCUMENT ME!
+   */
+  public void setOverviewPanel(OverviewPanel op)
+  {
+    overviewPanel = op;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setAnnotationVisible(boolean b)
+  {
+    if (!av.wrapAlignment)
     {
+      annotationSpaceFillerHolder.setVisible(b);
+      annotationScroller.setVisible(b);
+    }
+    repaint();
+  }
 
-       Alignment al = (Alignment)av.getAlignment();
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
+  public void adjustAnnotationHeight()
+  {
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+          while(alignFrame.getHeight()==0)
+          {
+            Thread.yield();
+          }
 
-       c.calculate();
-       c.verdict(false, 100);
-       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+        int height = annotationPanel.adjustPanelHeight();
 
-       av.setGlobalColourScheme( ccs );
+        if (height > alignFrame.getHeight() / 2)
+        {
+          height = alignFrame.getHeight() / 2;
+        }
 
-    }
+        annotationScroller.setPreferredSize(
+            new Dimension(annotationScroller.getWidth(),
+                          height));
 
-    RefreshPanels();
-  }
+        annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            annotationSpaceFillerHolder.getWidth(),
+            height));
 
+        annotationPanel.repaint();
+      }
+    });
+  }
 
-  public void RefreshPanels()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param wrap DOCUMENT ME!
+   */
+  public void setWrapAlignment(boolean wrap)
   {
-    requestFocus();
-    invalidate();
-
-    Dimension d = idPanel.idCanvas.getPreferredSize();
-    idPanelHolder.setPreferredSize(d);
-    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+    av.startSeq = 0;
+    scalePanelHolder.setVisible(!wrap);
+    hscroll.setVisible(!wrap);
+    idwidthAdjuster.setVisible(!wrap);
 
-    if (av.getWrapAlignment())
+    if (wrap)
     {
-      int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-      vscroll.setValues(0, 1, 0, max);
+      annotationScroller.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
     }
-    else
+    else if (av.showAnnotation)
     {
-      if (overviewPanel != null)
-        overviewPanel.updateOverviewImage();
-      setScrollValues(av.getStartRes(), av.getStartSeq());
+      annotationScroller.setVisible(true);
+      annotationSpaceFillerHolder.setVisible(true);
     }
 
-    validate();
+    idSpaceFillerPanel1.setVisible(!wrap);
+
     repaint();
   }
 
-  int hextent = 0;
-  int vextent = 0;
-
   // return value is true if the scroll is valid
   public boolean scrollUp(boolean up)
   {
-    if(up)
+    if (up)
     {
-      if(vscroll.getValue()<1)
+      if (vscroll.getValue() < 1)
+      {
         return false;
-      fastPaint  = false;
+      }
+
+      fastPaint = false;
       vscroll.setValue(vscroll.getValue() - 1);
     }
     else
     {
-     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
-       return false;
-      fastPaint  = false;
+      if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+      {
+        return false;
+      }
+
+      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 (!right)
     {
       if (hscroll.getValue() < 1)
+      {
         return false;
+      }
+
       fastPaint = false;
       hscroll.setValue(hscroll.getValue() - 1);
     }
     else
     {
-      if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+      if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+      {
         return false;
+      }
+
       fastPaint = false;
       hscroll.setValue(hscroll.getValue() + 1);
     }
+
     fastPaint = true;
+
     return true;
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param x DOCUMENT ME!
+   * @param y DOCUMENT ME!
+   */
   public void setScrollValues(int x, int y)
   {
-    hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
-    vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
 
-    if(hextent > av.alignment.getWidth())
-      hextent = av.alignment.getWidth();
-    if(vextent > av.alignment.getHeight())
-      vextent = av.alignment.getHeight();
+    int width = av.alignment.getWidth();
+    int height = av.alignment.getHeight();
 
-    if(hextent+x  >  av.getAlignment().getWidth())
-      x =  av.getAlignment().getWidth()- hextent;
+    if(av.hasHiddenColumns)
+     width = av.getColumnSelection().findColumnPosition(width);
 
-    if(vextent+y > av.getAlignment().getHeight())
-      y = av.getAlignment().getHeight() - vextent;
+    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
 
-    if(y<0)
-      y = 0;
+    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
 
-    if(x<0)
-      x=0;
+    if (hextent > width)
+    {
+      hextent = width;
+    }
 
-    hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
-    vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+    if (vextent > height)
+    {
+      vextent = height;
+    }
 
-  }
+    if ( (hextent + x) > width)
+    {
+      x = width - hextent;
+    }
+
+    if ( (vextent + y) > height)
+    {
+      y = height - vextent;
+    }
+
+    if (y < 0)
+    {
+      y = 0;
+    }
 
+    if (x < 0)
+    {
+      x = 0;
+    }
 
+    hscroll.setValues(x, hextent, 0, width);
+    vscroll.setValues(y, vextent, 0, height);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
+
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
@@ -368,103 +637,246 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+      av.setEndRes( (x +
+                     (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
     {
       int offy = vscroll.getValue();
+
       if (av.getWrapAlignment())
       {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-        av.setStartRes( vscroll.getValue() * rowSize );
-        av.setEndRes( (vscroll.getValue()+1) * rowSize );
+        if(offy>-1)
+        {
+          int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
+              seqCanvas.getWidth());
+          av.setStartRes(offy * rowSize);
+          av.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()
+              {
+                public void run()
+                {
+                  setScrollValues(av.getStartRes(), av.getStartSeq());
+                }
+              });
+        }
       }
       else
       {
         av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
+        av.setEndSeq(offy +
+                     (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
       }
     }
 
-
-    if(overviewPanel!=null)
+    if (overviewPanel != null)
+    {
       overviewPanel.setBoxPosition();
+    }
+
+    int scrollX = av.startRes - oldX;
+    int scrollY = av.startSeq - oldY;
 
-    if(av.getWrapAlignment() || !fastPaint)
+    if (av.getWrapAlignment() || !fastPaint)
+    {
       repaint();
+    }
     else
     {
-      seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
-                                   av.getStartSeq() - oldY);
-      idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
-      scalePanel.repaint();
-      if (av.getShowAnnotation())
-        annotationPanel.fastPaint(av.getStartRes() - oldX);
+      // Make sure we're not trying to draw a panel
+      // larger than the visible window
+      if(scrollX>av.endRes-av.startRes)
+        scrollX = av.endRes-av.startRes;
+      else if(scrollX<av.startRes-av.endRes)
+        scrollX = av.startRes - av.endRes;
+
+      if(scrollX!=0 || scrollY!=0)
+      {
+        idPanel.idCanvas.fastPaint(scrollY);
+        seqPanel.seqCanvas.fastPaint(scrollX,
+                                     scrollY);
+        scalePanel.repaint();
+
+        if (av.getShowAnnotation())
+        {
+          annotationPanel.fastPaint(scrollX);
+        }
+      }
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    invalidate();
+
+    Dimension d = idPanel.idCanvas.getPreferredSize();
+    idPanelHolder.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+    validate();
+
+    if (av.getWrapAlignment())
+    {
+      int maxwidth = av.alignment.getWidth();
+
+      if (av.hasHiddenColumns)
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+      int max = maxwidth /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +
+          1;
+
+
+      vscroll.setMaximum(max);
+      vscroll.setUnitIncrement(1);
+      vscroll.setVisibleAmount(1);
+    }
+    else
+    {
+      setScrollValues(av.getStartRes(), av.getStartSeq());
+    }
+
+    if( this.getVisibleRect().getBounds() == g.getClipBounds()
+        && overviewPanel != null)
+        overviewPanel.updateOverviewImage();
 
   }
 
-  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
+  /**
+   * DOCUMENT ME!
+   *
+   * @param pg DOCUMENT ME!
+   * @param pf DOCUMENT ME!
+   * @param pi DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   *
+   * @throws PrinterException DOCUMENT ME!
+   */
+  public int print(Graphics pg, PageFormat pf, int pi)
+      throws PrinterException
   {
-    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
+    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
 
     int pwidth = (int) pf.getImageableWidth();
     int pheight = (int) pf.getImageableHeight();
 
     if (av.getWrapAlignment())
-      return printWrappedAlignment(pg, pwidth,pheight, pi);
+    {
+      return printWrappedAlignment(pg, pwidth, pheight, pi);
+    }
     else
-      return printUnwrapped(pg,pwidth, pheight,pi);
+    {
+      return printUnwrapped(pg, pwidth, pheight, pi);
+    }
   }
 
-  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+  /**
+   * DOCUMENT ME!
+   *
+   * @param pg DOCUMENT ME!
+   * @param pwidth DOCUMENT ME!
+   * @param pheight DOCUMENT ME!
+   * @param pi DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   *
+   * @throws PrinterException DOCUMENT ME!
+   */
+  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+      throws PrinterException
   {
-
     int idWidth = calculateIdWidth().width + 4;
-
+    FontMetrics fm = getFontMetrics(av.getFont());
+    int scaleHeight = av.charHeight + fm.getDescent();
 
     pg.setColor(Color.white);
-    pg.fillRect(0,0,pwidth, pheight);
-    pg.setFont( av.getFont() );
+    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();
-    int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
-    int pagesWide = av.getAlignment().getWidth() / totalRes +1;
-    int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
+    int totalRes = (pwidth - idWidth) / av.getCharWidth();
 
-    if (pi >= pagesWide*pagesHigh)
-     return Printable.NO_SUCH_PAGE;
+    int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
+        1;
+
+    int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
 
     /////////////////////////////
     /// Only print these sequences and residues on this page
-    int startRes, endRes, startSeq, endSeq;
+    int startRes;
+
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int endRes;
+
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int startSeq;
+
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int endSeq;
     startRes = (pi % pagesWide) * totalRes;
-    endRes = startRes + totalRes-1;
-    if(endRes>av.getAlignment().getWidth())
-      endRes = av.getAlignment().getWidth();
+    endRes = (startRes + totalRes) - 1;
+
+    if (endRes > (av.getAlignment().getWidth() - 1))
+    {
+      endRes = av.getAlignment().getWidth() - 1;
+    }
 
-     startSeq = (pi / pagesWide) * totalSeq;
-     endSeq = startSeq + totalSeq;
-     if(endSeq > av.getAlignment().getHeight())
-       endSeq = av.getAlignment().getHeight();
+    startSeq = (pi / pagesWide) * totalSeq;
+    endSeq = startSeq + totalSeq;
 
+    if (endSeq > av.getAlignment().getHeight())
+    {
+      endSeq = av.getAlignment().getHeight();
+    }
+
+    int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
+
+    if (av.showAnnotation)
+    {
+      pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+    }
+
+    pagesHigh /= pheight;
+
+    if (pi >= (pagesWide * pagesHigh))
+    {
+      return Printable.NO_SUCH_PAGE;
+    }
 
-    ////////////////
     //draw Scale
-    pg.translate(idWidth,0);
-    scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
+    pg.translate(idWidth, 0);
+    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
+    pg.translate( -idWidth, scaleHeight);
 
-    pg.translate(-idWidth, 30);
     ////////////////
     // Draw the ids
-    Color currentColor=null;
-    Color currentTextColor=null;
-    for(int i=startSeq; i<endSeq; i++)
+    Color currentColor = null;
+    Color currentTextColor = null;
+
+    pg.setFont(new Font(av.getFont().getName(),
+                        Font.ITALIC,
+                        av.getFont().getSize()));
+    for (int i = startSeq; i < endSeq; i++)
     {
-      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
+      if ( (av.getSelectionGroup() != null) &&
+          av.getSelectionGroup().getSequences(false).contains(
+              av.getAlignment().getSequenceAt(i)))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -476,196 +888,469 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       }
 
       pg.setColor(currentColor);
-      pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
-                              idWidth,
-                              av.getCharHeight());
+      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+                  av.getCharHeight());
 
       pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getName();
-      if(av.getShowFullId())
-        string = av.getAlignment().getSequenceAt(i).getDisplayId();
+      String string = av.getAlignment().getSequenceAt(i).getDisplayId
+          ( av.getShowJVSuffix());
 
-      pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight
-                    (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
+      pg.drawString(string, 0,
+                    ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
+                    (av.getCharHeight() / 5));
     }
 
-    // draw main sequence panel
-    pg.translate(idWidth,0);
-    seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
+    pg.setFont(av.getFont());
 
+    // draw main sequence panel
+    pg.translate(idWidth, 0);
+    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
 
-    if(av.getShowAnnotation())
-      {
-        pg.translate(-idWidth,(endSeq-startSeq)*av.charHeight);
-        alabels.drawComponent((Graphics2D)pg);
-        pg.translate(idWidth,0);
-        annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes+1);
-      }
+    if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+    {
+      pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
+      alabels.drawComponent( (Graphics2D) pg, idWidth);
+      pg.translate(idWidth+3, 0);
+      annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
+                                    1);
+    }
 
     return Printable.PAGE_EXISTS;
   }
 
-
-  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+  /**
+   * DOCUMENT ME!
+   *
+   * @param pg DOCUMENT ME!
+   * @param pwidth DOCUMENT ME!
+   * @param pheight DOCUMENT ME!
+   * @param pi DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   *
+   * @throws PrinterException DOCUMENT ME!
+   */
+  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
+                                   int pi)
+      throws PrinterException
   {
 
-    int idWidth = calculateIdWidth().width+4;
+    int annotationHeight = 0;
+    AnnotationLabels labels = null;
+    if (av.showAnnotation)
+    {
+      annotationHeight = annotationPanel.adjustPanelHeight();
+      labels = new AnnotationLabels(av);
+    }
 
-    if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
-      pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+      hgap += av.charHeight;
 
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap
+        + annotationHeight;
 
-    pg.setColor(Color.white);
-    pg.fillRect(0,0,pwidth, pheight);
-    pg.setFont( av.getFont() );
+    int idWidth = calculateIdWidth().width + 4;
 
-    ////////////////////////////////////
-    /// How many sequences and residues can we fit on a printable page?
-    AlignmentI da = av.alignment;
-    int endy   = da.getHeight();
-    int chunkHeight =  (da.getHeight() + 2)*av.charHeight;
-    int chunkWidth  =   (pwidth-idWidth)/av.charWidth;
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
 
-    int noChunksOnPage = pheight / chunkHeight;
-    int totalChunks = da.getWidth() / chunkWidth;
 
-    if ( pi*noChunksOnPage > totalChunks )
-     return Printable.NO_SUCH_PAGE;
+    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
+        idWidth);
+
+    int totalHeight = cHeight * (maxwidth / resWidth + 1);
+
+    pg.setColor(Color.white);
+    pg.fillRect(0, 0, pwidth, pheight);
+    pg.setFont(av.getFont());
 
     ////////////////
     // Draw the ids
-    pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
-
-    int row = pi*noChunksOnPage;
     pg.setColor(Color.black);
-    for(int ypos=2*av.charHeight;
-        ypos <= pheight && row*chunkWidth<da.getWidth();
-        ypos += chunkHeight, row++ )
+
+    pg.translate(0, -pi * pheight);
+
+    pg.setClip(0, pi * pheight, pwidth, pheight);
+
+    int ypos = hgap;
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                           av.getFont().getSize());
+    pg.setFont(italic);
+
+    do
     {
-      for (int i = 0; i < endy; i++)
+      for (int i = 0; i < av.alignment.getHeight(); i++)
       {
-        SequenceI s = da.getSequenceAt(i);
-        String string = s.getName();
-        if (av.getShowFullId())
-          string = s.getDisplayId();
+        SequenceI s = av.alignment.getSequenceAt(i);
+        String string = s.getDisplayId( av.getShowJVSuffix());
 
         pg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
-                      av.charHeight - (av.charHeight / 5));
+                      ( (i * av.charHeight) + ypos + av.charHeight) -
+                      (av.charHeight / 5));
       }
+      if (labels != null)
+      {
+        pg.translate(-3,
+                     ypos +
+                     (av.getAlignment().getHeight() * av.charHeight));
+
+        pg.setFont(av.getFont());
+        labels.drawComponent(pg, idWidth);
+        pg.setFont(italic);
+        pg.translate(+3,
+                     -ypos -
+                     (av.getAlignment().getHeight() * av.charHeight));
+      }
+
+      ypos += cHeight;
     }
+    while (ypos < totalHeight);
 
-    // draw main sequence panel
-    pg.translate(idWidth,0);
-    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
+    pg.translate(idWidth, 0);
 
+    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
 
-    return Printable.PAGE_EXISTS;
+    if ( (pi * pheight) < totalHeight)
+    {
+      return Printable.PAGE_EXISTS;
 
+    }
+    else
+    {
+      return Printable.NO_SUCH_PAGE;
+    }
   }
 
-
-  public void makeEPS()
+  void makeAlignmentImage(int type, File file)
   {
-    int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
-    int width = seqPanel.getWidth() + idPanel.getWidth();
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
 
-    if (!av.getWrapAlignment())
+    int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+    int width = idPanel.getWidth() + (maxwidth * av.charWidth);
+    if (idPanel.getWidth() == 0)
     {
-      height = (av.alignment.getHeight()+1) * av.charHeight + 30;
-      width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
+      width += calculateIdWidth().getWidth() + 4;
     }
-    if(av.getShowAnnotation())
-   {
-     height += annotationPanel.getPreferredSize().height;
-   }
 
-    try
+    if (av.getWrapAlignment())
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from alignment");
-      chooser.setToolTipText("Save");
-
-      int value = chooser.showSaveDialog(this);
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-        return;
+      height = getWrappedHeight();
+      if (System.getProperty("java.awt.headless") != null
+          && System.getProperty("java.awt.headless").equals("true"))
+      {
+        width = alignFrame.getWidth() - 22;
+      }
+      else
+        width = seqPanel.getWidth() + idPanel.getWidth();
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-      EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
+    }
+    else if (av.getShowAnnotation())
+    {
+      height += annotationPanel.adjustPanelHeight() + 3;
+    }
 
-        if (av.getWrapAlignment())
-          printWrappedAlignment(pg, width, height, 0);
-        else
-          printUnwrapped(pg, width, height, 0);
+    jalview.util.ImageMaker im;
+    if(type==jalview.util.ImageMaker.PNG)
+      im  = new jalview.util.ImageMaker(this,
+                                        jalview.util.ImageMaker.PNG,
+                                        "Create PNG image from alignment",
+                                        width, height, file, null);
+    else
+      im = new jalview.util.ImageMaker(this,
+                                        jalview.util.ImageMaker.EPS,
+                                       "Create EPS file from alignment",
+                                        width, height, file, alignFrame.getTitle() );
 
+    try
+    {
+      if (av.getWrapAlignment())
+      {
+        if(im.getGraphics()!=null)
+        {
+          printWrappedAlignment(im.getGraphics(), width, height, 0);
+          im.writeImage();
+        }
+      }
+      else
+      {
+        if(im.getGraphics()!=null)
+        {
+          printUnwrapped(im.getGraphics(), width, height, 0);
+          im.writeImage();
+        }
+      }
+    }
+    catch (OutOfMemoryError err)
+    {
+      System.out.println("########################\n"
+                         + "OUT OF MEMORY " + file + "\n"
+                         + "########################");
+
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "Out of Memory Creating Image!!"
+                                            +
+                                            "\nSee help files for increasing Java Virtual Machine memory."
+                                            , "Out of memory",
+                                            JOptionPane.WARNING_MESSAGE);
+      System.out.println("Create IMAGE: " + err);
+      System.gc();
 
-        pg.flush();
-        pg.close();
     }
     catch (Exception ex)
     {
       ex.printStackTrace();
     }
   }
+  /**
+   * DOCUMENT ME!
+   */
+  public void makeEPS(File epsFile)
+  {
+    makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+  }
 
-  public void makePNG()
+  /**
+   * DOCUMENT ME!
+   */
+  public void makePNG(File pngFile)
   {
-      int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
-      int width = seqPanel.getWidth() + idPanel.getWidth();
+    makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+  }
 
-      if (!av.getWrapAlignment())
+  public void makePNGImageMap(File imgMapFile, String imageName)
+  {
+    ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+    //////////////////////////////////////////////
+    int idWidth = calculateIdWidth().width + 4;
+    FontMetrics fm = getFontMetrics(av.getFont());
+    int scaleHeight = av.charHeight + fm.getDescent();
+
+    // Gen image map
+    //////////////////////////////////
+    if (imgMapFile != null)
+    {
+      try
       {
-        height = (av.alignment.getHeight()+1) * av.charHeight + 30;
-        width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
-      }
+        int s, sSize = av.alignment.getHeight(),
+            res, alwidth = av.alignment.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 +
+                    "\" border=\"0\" usemap=\"#Map\" >"
+                    + "<map name=\"Map\">");
+
+        for (s = 0; s < sSize; s++)
+        {
+          sy = s * av.charHeight + scaleHeight;
+
+          SequenceI seq = av.alignment.getSequenceAt(s);
+          SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
+          SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+          for(res =0; res<alwidth; res++)
+          {
+            text = new StringBuffer();
+            Object obj = null;
+            if(av.alignment.isNucleotide())
+              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
+            else
+              obj = ResidueProperties.aa2Triplet.get(
+                    seq.getCharAt(res) + "");
+
+              if (obj == null)
+                  continue;
+
+            String triplet = obj.toString();
+            int alIndex = 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.charWidth) + ","
+                  + sy + ","
+                  + (idWidth + (res + 1) * av.charWidth) + ","
+                  + (av.charHeight + sy) + "\""
+                  + " onMouseOver=\"toolTip('"
+                  + alIndex + " " + triplet );
+              }
+
+              if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
+                text.append("<br><em>" + groups[g].getName() + "</em>");
+            }
+
+            if (features != null)
+            {
+              if(text.length()<1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
+                  + (idWidth + res * av.charWidth) + ","
+                  + sy + ","
+                  + (idWidth + (res + 1) * av.charWidth) + ","
+                  + (av.charHeight + sy) + "\""
+                  + " onMouseOver=\"toolTip('"
+                  + alIndex + " " + triplet );
+              }
+                fSize = features.length;
+                for (f = 0; f < fSize; f++)
+                {
+
+                  if ( (features[f].getBegin() <= seq.findPosition(res)) &&
+                      (features[f].getEnd() >= seq.findPosition(res)))
+                  {
+                    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>");
+                      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") + ")");
+                      }
+                    }
+                  }
+
+                }
+              }
+              if(text.length()>1)
+              {
+                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+                out.println(text.toString());
+              }
+            }
+          }
+        out.println("</map></body></html>");
+        out.close();
 
-      if(av.getShowAnnotation())
+      }
+      catch (Exception ex)
       {
-        height += annotationPanel.getPreferredSize().height;
+        ex.printStackTrace();
       }
+    } ///////////END OF IMAGE MAP
 
+  }
 
-System.out.println(width +" "+height);
+  int getWrappedHeight()
+  {
+    int seqPanelWidth = seqPanel.seqCanvas.getWidth();
 
-    try
+    //If headless, seqPanel will have 0 width
+    if (System.getProperty("java.awt.headless") != null
+              && System.getProperty("java.awt.headless").equals("true"))
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from alignment");
-      chooser.setToolTipText("Save");
+      int idWidth = calculateIdWidth().width + 4;
+      seqPanelWidth = alignFrame.getWidth() - idWidth;
+    }
 
-      int value = chooser.showSaveDialog(this);
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-        return;
+    int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
+        seqPanelWidth
+          );
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+      hgap += av.charHeight;
 
-      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
-      Graphics png = bi.getGraphics();
+    int annotationHeight = 0;
+    if (av.showAnnotation)
+    {
+      annotationHeight = annotationPanel.adjustPanelHeight();
+    }
 
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap
+        + annotationHeight;
 
-        if (av.getWrapAlignment())
-          printWrappedAlignment(png, width, height, 0);
-        else
-          printUnwrapped(png, width, height, 0);
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
 
-        ImageIO.write(bi, "png", out);
-        out.close();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
 
-}
+    int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
 
+    return height;
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @author $author$
+   * @version $Revision$
+   */
+  class Preview
+      extends JFrame
+  {
+    /**
+     * Creates a new Preview object.
+     *
+     * @param image DOCUMENT ME!
+     */
+    public Preview(Image image)
+    {
+      setResizable(true);
+      setSize(image.getWidth(this), image.getHeight(this));
+      setVisible(true);
+      getContentPane().setLayout(new BorderLayout());
+      getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
+      validate();
+      repaint();
+    }
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @author $author$
+   * @version $Revision$
+   */
+  class PreviewPanel
+      extends JPanel
+  {
+    Image image;
+
+    /**
+     * Creates a new PreviewPanel object.
+     *
+     * @param image DOCUMENT ME!
+     */
+    public PreviewPanel(Image image)
+    {
+      this.image = image;
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
+    {
+      if (image != null)
+      {
+        g.drawImage(image, 0, 0, this);
+      }
+      else
+      {
+        System.out.println("DEBUG:image is null");
+      }
+    }
+  }
+}