X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=7aff9abeadb0d4bd740296e82e00221325062331;hb=1402060fb2ca7b2639ef98da3e22766d01149b16;hp=ca17c20d5eb358fa18f09f1b8420049680c6a881;hpb=a2a41986667a3d2f611b4e7c8432d9cdd05527a6;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ca17c20..7aff9ab 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,544 +1,1056 @@
+/*
+ * 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 org.jibble.epsgraphics.*;
+
 import java.awt.*;
 import java.awt.event.*;
+import java.awt.image.*;
 import java.awt.print.*;
 
-import com.sun.image.codec.jpeg.*;
 import java.io.*;
-import java.awt.image.*;
 
-import gnu.jpdf.*;
+import javax.imageio.*;
 
+import javax.swing.*;
 
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
-{
 
-  AlignViewport     av;
-  OverviewPanel overviewPanel;
-  SeqPanel   seqPanel;
-  IdPanel    idPanel;
-  SecondaryStructurePanel ssPanel;
-  public AlignFrame alignFrame;
-  ScalePanel scalePanel;
-  ScorePanel scorePanel;
-
-  public AlignmentPanel(AlignFrame af, final AlignViewport av)
-  {
-    alignFrame = af;
-    this.av         = av;
-    seqPanel        = new SeqPanel  (av, this);
-    idPanel         = new IdPanel   (av, this);
-
-    scalePanel = new ScalePanel(av, this);
-    scorePanel = new ScorePanel(av);
-    ssPanel = new SecondaryStructurePanel(av);
-
-    secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
-
-    idPanelHolder.add(idPanel, BorderLayout.CENTER);
-    IdwidthAdjuster iap = new IdwidthAdjuster(this);
-    idSpaceFillerPanel1.add(iap, BorderLayout.CENTER);
-
-    idPanel.idCanvas.setPreferredSize(calculateIdWidth());
-    hscrollFillerPanel.setPreferredSize(calculateIdWidth());
-
-    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
-    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-    setScrollValues(0,0);
-
-    hscroll.addAdjustmentListener(this);
-    vscroll.addAdjustmentListener(this);
-
-    addComponentListener(new ComponentAdapter()
-   {
-     public void componentResized(ComponentEvent evt)
-     {
-          RefreshPanels();
-     }
-   });
-
-
-  // hscroll.setFocusable(false);
-  // vscroll.setFocusable(false);
-   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:
-           alignFrame.cut_actionPerformed(null);
-           break;
-         case KeyEvent.VK_C:
-           alignFrame.copy_actionPerformed(null);
-           break;
-         case KeyEvent.VK_V:
-           alignFrame.paste(true);
-           break;
-         case KeyEvent.VK_A:
-           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
-           break;
-        case KeyEvent.VK_DOWN:
-          alignFrame.moveSelectedSequences(false);
-          break;
-        case KeyEvent.VK_UP:
-          alignFrame.moveSelectedSequences(true);
-          break;
-        case KeyEvent.VK_F:
-          alignFrame.findMenuItem_actionPerformed(null);
-          break;
-       }
-     }
-   });
-  }
-
-  Dimension calculateIdWidth()
-  {
-    Graphics g = this.getGraphics();
-    if(g==null)
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentPanel extends GAlignmentPanel
+    implements AdjustmentListener, Printable
+{
+    AlignViewport av;
+    OverviewPanel overviewPanel;
+    SeqPanel seqPanel;
+    IdPanel idPanel;
+    IdwidthAdjuster idwidthAdjuster;
+
+    /** DOCUMENT ME!! */
+    public AlignFrame alignFrame;
+    ScalePanel scalePanel;
+    AnnotationPanel annotationPanel;
+    AnnotationLabels alabels;
+
+    // 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)
     {
-      javax.swing.JFrame f = new javax.swing.JFrame();
-      f.addNotify();
-      g = f.getGraphics();
-    }
+        alignFrame = af;
+        this.av = av;
+        seqPanel = new SeqPanel(av, this);
+        idPanel = new IdPanel(av, this);
 
-    FontMetrics fm = g.getFontMetrics(av.font);
-    AlignmentI al = av.getAlignment();
+        scalePanel = new ScalePanel(av, this);
 
-       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();
+        idPanelHolder.add(idPanel, BorderLayout.CENTER);
+        idwidthAdjuster = new IdwidthAdjuster(this);
+        idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
 
-         if (fm.stringWidth(id) > idWidth)
-           idWidth = fm.stringWidth(id);
-         i++;
-       }
+        annotationPanel = new AnnotationPanel(this);
+        alabels = new AnnotationLabels(this);
 
-       return new Dimension(idWidth, 12);
-  }
+        annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+        annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+        annotationScroller.setViewportView(annotationPanel);
+        annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
+        fontChanged();
 
- public void highlightSearchResults(int [] results)
- {
-   seqPanel.seqCanvas.highlightSearchResults( results );
+        scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+        seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
-   // 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]);
+        setScrollValues(0, 0);
 
+        hscroll.addAdjustmentListener(this);
+        vscroll.addAdjustmentListener(this);
 
- }
+        setFocusable(true);
+        addKeyListener(new KeyAdapter()
+            {
+                public void keyPressed(KeyEvent evt)
+                {
+                    switch (evt.getKeyCode())
+                    {
+                    case 27: // escape key
+                        av.setSelectionGroup(null);
+                        repaint();
 
+                        break;
 
- public OverviewPanel getOverviewPanel()
- {
-   return overviewPanel;
- }
+                    case KeyEvent.VK_DOWN:
+                        alignFrame.moveSelectedSequences(false);
 
- public void setOverviewPanel(OverviewPanel op)
- {
-   overviewPanel = op;
- }
+                        break;
 
+                    case KeyEvent.VK_UP:
+                        alignFrame.moveSelectedSequences(true);
 
-  public void setGraphPanelVisible(boolean b)
-  {
-    idSpaceFillerPanel.setVisible(b);
-    scorePanelHolder.setVisible(b);
+                        break;
 
-    RefreshPanels();
-    // bit annoying to call this twice, can you do better?
-    RefreshPanels();
-  }
+                    case KeyEvent.VK_BACK_SPACE:
+                    case KeyEvent.VK_DELETE:
+                      alignFrame.cut_actionPerformed(null);
+                      break;
+                    }
 
-  public void setSecondaryStructureVisible(boolean b)
-  {
-    secondaryPanelHolder.setVisible(b);
-    RefreshPanels();
-  }
+                }
+            });
+    }
 
-  public void setWrapAlignment(boolean wrap)
-  {
-    scorePanelHolder.setVisible(!wrap);
-    scalePanelHolder.setVisible(!wrap);
-    secondaryPanelHolder.setVisible(!wrap);
+    /**
+     * DOCUMENT ME!
+     */
+    public void fontChanged()
+    {
+        // 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;
+        annotationPanel.adjustPanelHeight();
+
+        Dimension d = calculateIdWidth();
+        d.setSize(d.width + 4, d.height);
+        idPanel.idCanvas.setPreferredSize(d);
+        hscrollFillerPanel.setPreferredSize(d);
+        repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension calculateIdWidth()
+    {
+      Container c = new Container();
 
-    hscroll.setVisible(!wrap);
+        FontMetrics fm = c.getFontMetrics(av.font);
+        AlignmentI al = av.getAlignment();
 
- //   idSpaceFillerPanel.setVisible(!wrap);
- //   idWidthAdjusterPanel.setVisible(!wrap);
+        int i = 0;
+        int idWidth = 0;
+        String id;
 
-    RefreshPanels();
+        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);
+            }
 
-  public void setColourScheme()
-  {
-    ColourSchemeI cs = av.getGlobalColourScheme();
+            i++;
+        }
 
-    if(av.getConservationSelected())
-    {
+        // Also check annotation label widths
+        i = 0;
+
+        if (al.getAlignmentAnnotation() != null)
+        {
+            fm = c.getFontMetrics(alabels.getFont());
 
-       Alignment al = (Alignment)av.getAlignment();
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
+            while (i < al.getAlignmentAnnotation().length)
+            {
+                String label = al.getAlignmentAnnotation()[i].label;
 
-       c.calculate();
-       c.verdict(false, 100);
-       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+                if (fm.stringWidth(label) > idWidth)
+                {
+                    idWidth = fm.stringWidth(label);
+                }
 
-       av.setGlobalColourScheme( ccs );
+                i++;
+            }
+        }
 
+        return new Dimension(idWidth, 12);
     }
 
-    RefreshPanels();
-  }
-
-  public void RefreshPanels()
-  {
-              requestFocus();
-              invalidate();
-              idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
-              if(idPanel.idCanvas.getPreferredSize()!=null)
-                hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12));
-              idSpaceFillerPanel1.setPreferredSize(new Dimension(500,
-                  av.charHeight / 2 + 12));
-              scalePanelHolder.setPreferredSize(new Dimension(500,
-                  av.charHeight / 2 + 12));
-              if (av.getWrapAlignment())
-              {
-                int max = av.alignment.getWidth() /
-                    (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;
-
-                int h = (av.alignment.getHeight() + 2) * av.charHeight;
-                vextent = seqPanel.seqCanvas.getHeight() / h;
-                vscroll.setValues(0, vextent, 0, max);
-              }
-              else
-
-                setScrollValues(av.getStartRes(), av.getStartSeq());
-              av.getConsensus(true);
-              if (overviewPanel != null)
-                overviewPanel.updateOverviewImage();
-
-          validate();
-          repaint();
-  }
-  int hextent = 0;
-  int vextent = 0;
-
-
-  // return value is true if the scroll is valid
-  public boolean scrollUp(boolean up)
-  {
-    if(up)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param results DOCUMENT ME!
+     */
+    public void highlightSearchResults(int[] results)
     {
-      if(vscroll.getValue()<1)
-        return false;
-      vscroll.setValue(vscroll.getValue() - 1);
+        seqPanel.seqCanvas.highlightSearchResults(results);
+
+        // do we need to scroll the panel?
+        if (results != null)
+        {
+            SequenceI seq = av.alignment.getSequenceAt(results[0]);
+            int start = seq.findIndex(results[1]) - 1;
+            int end = seq.findIndex(results[2]) - 1;
+
+            if ((av.getStartRes() > start) || (av.getEndRes() < end) ||
+                    ((av.getStartSeq() > results[0]) ||
+                    (av.getEndSeq() < results[0])))
+            {
+                setScrollValues(start, results[0]);
+            }
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public OverviewPanel getOverviewPanel()
     {
-     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
-       return false;
-      vscroll.setValue(vscroll.getValue() + 1);
+        return overviewPanel;
     }
 
-    return true;
-  }
-
-  public boolean scrollRight(boolean right)
-  {
-    if(right)
-   {
-     if(hscroll.getValue()<1)
-       return false;
-     hscroll.setValue(hscroll.getValue() - 1);
-   }
-   else
-   {
-    if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
-      return false;
-     hscroll.setValue(hscroll.getValue() + 1);
-   }
-
-   return true;
- }
-
-
-  public void setScrollValues(int x, int y)
-  {
-    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
-    vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
-
-    if(hextent+x  >  av.getAlignment().getWidth())
-      x =  av.getAlignment().getWidth()- hextent;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param op DOCUMENT ME!
+     */
+    public void setOverviewPanel(OverviewPanel op)
+    {
+        overviewPanel = op;
+    }
 
-    if(vextent+y > av.getAlignment().getHeight())
-      y = av.getAlignment().getHeight() - vextent;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setAnnotationVisible(boolean b)
+    {
+        annotationSpaceFillerHolder.setVisible(b);
+        annotationScroller.setVisible(b);
+    }
 
-    if(y<0)
-      y = 0;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param wrap DOCUMENT ME!
+     */
+    public void setWrapAlignment(boolean wrap)
+    {
+        scalePanelHolder.setVisible(!wrap);
+        hscroll.setVisible(!wrap);
+        idwidthAdjuster.setVisible(!wrap);
 
-    if(x<0)
-      x=0;
+        av.setShowAnnotation(!wrap);
+        annotationScroller.setVisible(!wrap);
+        annotationSpaceFillerHolder.setVisible(!wrap);
+        idSpaceFillerPanel1.setVisible(!wrap);
 
-    hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
-    vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+        repaint();
+    }
 
+    /**
+     * DOCUMENT ME!
+     */
+    public void setColourScheme()
+    {
+        ColourSchemeI cs = av.getGlobalColourScheme();
 
-    repaint();
+        if (av.getConservationSelected())
+        {
+            Alignment al = (Alignment) av.getAlignment();
+            Conservation c = new Conservation("All",
+                    ResidueProperties.propHash, 3, al.getSequences(), 0,
+                    al.getWidth());
 
-  }
+            c.calculate();
+            c.verdict(false, av.ConsPercGaps);
 
+            ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
+            av.setGlobalColourScheme(ccs);
+        }
 
-    if (evt.getSource() == hscroll)
-    {
-      int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+        repaint();
     }
 
-    if (evt.getSource() == vscroll)
+    // return value is true if the scroll is valid
+    public boolean scrollUp(boolean up)
     {
-      int offy = vscroll.getValue();
-      if (av.getWrapAlignment())
-      {
-        av.setStartRes( vscroll.getValue() * av.getChunkWidth());
-      }
-      else
-      {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
-      }
-    }
-
-
-    if(overviewPanel!=null)
-      overviewPanel.setBoxPosition();
+        if (up)
+        {
+            if (vscroll.getValue() < 1)
+            {
+                return false;
+            }
+
+            fastPaint = false;
+            vscroll.setValue(vscroll.getValue() - 1);
+        }
+        else
+        {
+            if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+            {
+                return false;
+            }
 
-    repaint();
-  }
+            fastPaint = false;
+            vscroll.setValue(vscroll.getValue() + 1);
+        }
 
-  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
-  {
-    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
+        fastPaint = true;
 
-    int pwidth = (int) pf.getImageableWidth();
-    int pheight = (int) pf.getImageableHeight();
+        return true;
+    }
 
-    if (av.getWrapAlignment())
-      return printWrappedAlignment(pg, pwidth,pheight, pi);
-    else
-      return printUnwrapped(pg,pwidth, pheight,pi);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param right DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean scrollRight(boolean right)
+    {
+        if (right)
+        {
+            if (hscroll.getValue() < 1)
+            {
+                return false;
+            }
+
+            fastPaint = false;
+            hscroll.setValue(hscroll.getValue() - 1);
+        }
+        else
+        {
+            if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+            {
+                return false;
+            }
 
-  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
-  {
+            fastPaint = false;
+            hscroll.setValue(hscroll.getValue() + 1);
+        }
 
-    int idWidth = calculateIdWidth().width;
+        fastPaint = true;
 
+        return true;
+    }
 
-    pg.setColor(Color.white);
-    pg.fillRect(0,0,pwidth, pheight);
-    pg.setFont( av.getFont() );
+    /**
+     * DOCUMENT ME!
+     *
+     * @param x DOCUMENT ME!
+     * @param y DOCUMENT ME!
+     */
+    public void setScrollValues(int x, int y)
+    {
+        av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
+            1);
+
+        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();
+        }
+
+        if ((hextent + x) > av.getAlignment().getWidth())
+        {
+            x = av.getAlignment().getWidth() - hextent;
+        }
+
+        if ((vextent + y) > av.getAlignment().getHeight())
+        {
+            y = av.getAlignment().getHeight() - vextent;
+        }
+
+        if (y < 0)
+        {
+            y = 0;
+        }
+
+        if (x < 0)
+        {
+            x = 0;
+        }
+
+        hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
+        vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
+    }
 
-    ////////////////////////////////////
-    /// 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;
+    public void this_mouseWheelMoved(MouseWheelEvent e)
+    {
+      if(e.getWheelRotation()>0)
+        scrollUp(false);
+      else
+        scrollUp(true);
+    }
 
-    if (pi >= pagesWide*pagesHigh)
-     return Printable.NO_SUCH_PAGE;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
-    int startRes, endRes, startSeq, endSeq;
-    startRes = (pi % pagesWide) * totalRes;
-    endRes = startRes + totalRes-1;
-    if(endRes>av.getAlignment().getWidth())
-      endRes = av.getAlignment().getWidth();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void adjustmentValueChanged(AdjustmentEvent evt)
+    {
+        int oldX = av.getStartRes();
+        int oldY = av.getStartSeq();
+
+        if (evt.getSource() == hscroll)
+        {
+            int x = hscroll.getValue();
+            av.setStartRes(x);
+            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);
+            }
+            else
+            {
+                av.setStartSeq(offy);
+                av.setEndSeq(offy +
+                    (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+            }
+        }
+
+        if (overviewPanel != null)
+        {
+            overviewPanel.setBoxPosition();
+        }
+
+        if (av.getWrapAlignment() || !fastPaint)
+        {
+            repaint();
+        }
+        else
+        {
+            idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
+            seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
+                av.getStartSeq() - oldY);
+
+            scalePanel.repaint();
+
+            if (av.getShowAnnotation())
+            {
+                annotationPanel.fastPaint(av.getStartRes() - oldX);
+            }
+        }
+    }
 
-     startSeq = (pi / pagesWide) * totalSeq;
-     endSeq = startSeq + totalSeq;
-     if(endSeq > av.getAlignment().getHeight())
-       endSeq = av.getAlignment().getHeight();
+    /**
+     * 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();
 
-    ////////////////
-    //draw Scale
-    pg.translate(idWidth,0);
-    scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
+        if (av.getWrapAlignment())
+        {
+            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());
+        }
+    }
 
-    pg.translate(-idWidth, 30);
-    ////////////////
-    // Draw the ids
-    Color currentColor=null;
-    Color currentTextColor=null;
-    for(int i=startSeq; i<endSeq; i++)
+    /**
+     * 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
     {
-      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
-      {
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
-      }
-      else
-      {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
-        currentTextColor = Color.black;
-      }
+        pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
 
-      pg.setColor(currentColor);
-      pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
-                              idWidth,
-                              av.getCharHeight());
+        int pwidth = (int) pf.getImageableWidth();
+        int pheight = (int) pf.getImageableHeight();
 
-      pg.setColor(currentTextColor);
+        if (av.getWrapAlignment())
+        {
+            return printWrappedAlignment(pg, pwidth, pheight, pi);
+        }
+        else
+        {
+            return printUnwrapped(pg, pwidth, pheight, pi);
+        }
+    }
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId();
-      pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight
-                    (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
+    /**
+     * 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());
+
+        ////////////////////////////////////
+        /// How many sequences and residues can we fit on a printable page?
+        int totalRes = (pwidth - idWidth) / av.getCharWidth();
+
+        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;
+
+        /////////////////////////////
+        /// 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() - 1))
+        {
+            endRes = av.getAlignment().getWidth() - 1;
+        }
+
+        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.getHeight();
+        }
+
+        pagesHigh /= pheight;
+
+        if (pi >= (pagesWide * pagesHigh))
+        {
+            return Printable.NO_SUCH_PAGE;
+        }
+
+        //draw Scale
+        pg.translate(idWidth, 0);
+        scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
+        pg.translate(-idWidth, scaleHeight);
+
+        ////////////////
+        // Draw the ids
+        Color currentColor = null;
+        Color currentTextColor = null;
+
+        for (int i = startSeq; i < endSeq; i++)
+        {
+            if ((av.getSelectionGroup() != null) &&
+                    av.getSelectionGroup().sequences.contains(
+                        av.getAlignment().getSequenceAt(i)))
+            {
+                currentColor = Color.gray;
+                currentTextColor = Color.black;
+            }
+            else
+            {
+                currentColor = av.getAlignment().getSequenceAt(i).getColor();
+                currentTextColor = Color.black;
+            }
+
+            pg.setColor(currentColor);
+            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();
+            }
+
+            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);
+
+        if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+        {
+            pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight);
+            alabels.drawComponent((Graphics2D) pg);
+            pg.translate(idWidth, 0);
+            annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +
+                1);
+        }
+
+        return Printable.PAGE_EXISTS;
     }
 
-    // draw main sequence panel
-    pg.translate(idWidth,0);
-    pg.setClip(0,0,pwidth-idWidth, pheight);
-    seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
+    /**
+     * 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 resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
+                idWidth);
+        int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +
+                1) * av.charHeight;
 
-    return Printable.PAGE_EXISTS;
-  }
+        pg.setColor(Color.white);
+        pg.fillRect(0, 0, pwidth, pheight);
+        pg.setFont(av.getFont());
 
+        ////////////////
+        // Draw the ids
+        pg.setColor(Color.black);
 
-  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
-  {
+        pg.translate(0, -pi * pheight);
 
-    int idWidth = calculateIdWidth().width;
+        pg.setClip(0, pi * pheight, pwidth, pheight);
 
-    if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
-      pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
+        int ypos = 2 * av.charHeight;
 
+        do
+        {
+            for (int i = 0; i < av.alignment.getHeight(); i++)
+            {
+                SequenceI s = av.alignment.getSequenceAt(i);
+                String string = s.getName();
 
-    pg.setColor(Color.white);
-    pg.fillRect(0,0,pwidth, pheight);
-    pg.setFont( av.getFont() );
+                if (av.getShowFullId())
+                {
+                    string = s.getDisplayId();
+                }
 
-    ////////////////////////////////////
-    /// 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;
+                pg.drawString(string, 0,
+                    ((i * av.charHeight) + ypos + av.charHeight) -
+                    (av.charHeight / 5));
+            }
 
-    int noChunksOnPage = pheight / chunkHeight;
-    int totalChunks = da.getWidth() / chunkWidth;
+            ypos += ((av.alignment.getHeight() + 2) * av.charHeight);
+        }
+        while (ypos < totalHeight);
 
-    if ( pi*noChunksOnPage > totalChunks )
-     return Printable.NO_SUCH_PAGE;
+        pg.translate(idWidth, 0);
 
-    ////////////////
-    // Draw the ids
-    pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
+        seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
 
-    int row = pi*noChunksOnPage;
-    pg.setColor(Color.black);
-    for(int ypos=2*av.charHeight;
-        ypos <= pheight && row*chunkWidth<da.getWidth();
-        ypos += chunkHeight, row++ )
-    {
-      for (int i = 0; i < endy; i++)
-      {
-        SequenceI s = da.getSequenceAt(i);
-        pg.drawString(s.getDisplayId(), 0,
-                      AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
-                      av.charHeight - (av.charHeight / 5));
-      }
+        if ((pi * pheight) < totalHeight)
+        {
+            return Printable.PAGE_EXISTS;
+        }
+        else
+        {
+            return Printable.NO_SUCH_PAGE;
+        }
     }
 
-    // draw main sequence panel
-    pg.translate(idWidth,0);
-    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
-
+    /**
+     * DOCUMENT ME!
+     */
+    public void makeEPS(File epsFile)
+    {
+        if(epsFile == null)
+        {
+          jalview.io.JalviewFileChooser chooser = new jalview.io.
+              JalviewFileChooser(jalview.bin.Cache.getProperty(
+                  "LAST_DIRECTORY"), new String[]
+                                 {"eps"},
+                                 new String[]
+                                 {"Encapsulated Postscript"},
+                                 "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;
+          }
+
+          epsFile = chooser.getSelectedFile();
+
+          jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                        chooser.getSelectedFile().getParent());
+        }
+
+        int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+        int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
 
-    return Printable.PAGE_EXISTS;
+        if (av.getWrapAlignment())
+        {
+          height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
+              av.chunkHeight;
+          width = seqPanel.getWidth() + idPanel.getWidth();
+
+        }
+
+
+        if (av.getShowAnnotation())
+        {
+            height += annotationPanel.getPreferredSize().height;
+        }
+
+        try
+         {
+            FileOutputStream out = new FileOutputStream(epsFile);
+            EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
+                    height);
+
+            if (av.getWrapAlignment())
+            {
+                printWrappedAlignment(pg, width, height, 0);
+            }
+            else
+            {
+                printUnwrapped(pg, width, height, 0);
+            }
+
+            pg.flush();
+            pg.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
 
-  }
 
-  public void makeJPG(int width, int height)
-  {
-    try
+    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
+           {
+             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 (int s = 0; s < av.alignment.getHeight(); s++)
+             {
+               SequenceI seq = av.alignment.getSequenceAt(s);
+               SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+               for (int i = 0; i < groups.length; i++)
+               {
+                 int sy = s * av.charHeight + scaleHeight;
+                 for (int res = groups[i].getStartRes();
+                      res < groups[i].getEndRes() + 1; res++)
+                 {
+                   int alIndex = seq.findPosition(res);
+                   Object obj = ResidueProperties.aa2Triplet.get(
+                       seq.getCharAt(res) + "");
+                   if (obj == null)
+                     continue;
+
+                   String triplet = obj.toString();
+
+                   out.println(
+                       "<area shape=\"rect\" coords=\""
+                       + (idWidth + res * av.charWidth) + ","
+                       + sy + ","
+                       + (idWidth + (res + 1) * av.charWidth) + ","
+                       + (av.charHeight + sy) + "\""
+                       + " onMouseOver=\"toolTip('"
+                       + alIndex + " " + triplet +
+                       "<br><em>" + groups[i].getName() +
+                       "</em>')\"; onMouseOut=\"toolTip()\"; "
+                       + " href=\"#\">");
+                 }
+               }
+             }
+
+             out.println("</map></body></html>");
+             out.close();
+
+           }
+           catch (Exception ex)
+           {
+             ex.printStackTrace();
+           }
+         }///////////END OF IMAGE MAP
 
-      BufferedImage bi = new BufferedImage(width, height,
-                                           BufferedImage.TYPE_INT_RGB);
-      Graphics pg = bi.getGraphics();
+    }
 
-      try
+    /**
+     * DOCUMENT ME!
+     */
+    public void makePNG(File pngFile)
+    {
+      if(pngFile==null)
       {
-        if (av.getWrapAlignment())
-          printWrappedAlignment(pg, width, height, 0);
-        else
-          printUnwrapped(pg, width, height, 0);
+        jalview.io.JalviewFileChooser chooser = new jalview.io.
+            JalviewFileChooser(jalview.bin.Cache.getProperty(
+                "LAST_DIRECTORY"), new String[]
+                               {"png"},
+                               new String[]
+                               {"Portable network graphics"},
+                               "Portable network graphics");
+        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;
+        }
+
+        pngFile = chooser.getSelectedFile();
+
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                      chooser.getSelectedFile().getParent());
       }
-      catch (Exception ex)
-      {}
 
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"));
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create JPG image from alignment");
-      chooser.setToolTipText("Save");
 
-      int value = chooser.showSaveDialog(this);
-      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
-      {
 
-        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-        JPEGImageEncoder jie = JPEGCodec.createJPEGEncoder(out);
-        JPEGEncodeParam param = JPEGCodec.getDefaultJPEGEncodeParam(bi);
-        param.setQuality(1.0f, true);
+      int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+      int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
+
+      if (av.getWrapAlignment())
+      {
+        height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
+            av.chunkHeight;
+        width = seqPanel.getWidth() + idPanel.getWidth();
 
-        jie.encode(bi, param);
-        out.close();
       }
 
+
+        if (av.getShowAnnotation())
+        {
+            height += annotationPanel.getPreferredSize().height;
+        }
+
+        try
+        {
+
+            FileOutputStream out = new FileOutputStream(pngFile);
+
+            BufferedImage bi = new BufferedImage(width, height,
+                    BufferedImage.TYPE_INT_RGB);
+            Graphics2D png = (Graphics2D) bi.getGraphics();
+
+            png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                RenderingHints.VALUE_ANTIALIAS_ON);
+
+            if (av.getWrapAlignment())
+            {
+                printWrappedAlignment(png, width, height, 0);
+            }
+            else
+            {
+                printUnwrapped(png, width, height, 0);
+            }
+
+            ImageIO.write(bi, "png", out);
+            out.close();
+        }
+        catch(OutOfMemoryError err)
+        {
+          System.out.println("########################\n"
+                             +"OUT OF MEMORY "+pngFile+"\n"
+                             +"########################");
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
     }
-    catch (IOException ex)
+}
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+class Preview extends JFrame
+{
+    /**
+     * Creates a new Preview object.
+     *
+     * @param image DOCUMENT ME!
+     */
+    public Preview(Image image)
     {
-      System.out.println("ex Writing 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");
+        }
+    }
+}