X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=e31251080e9bbf895d6e1f31b365933cda7cefad;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=fcb5a57a4849009c96b240c5f8ce0ffc9b584276;hpb=bfdb9a55949b38a89878959278a8b8ed82a55e49;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index fcb5a57..e312510 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,416 +1,1057 @@
+/*
+ * 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.*;
 
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
-{
+import java.io.*;
 
-  AlignViewport     av;
-  OverviewPanel overviewPanel;
-  SeqPanel   seqPanel;
-  IdPanel    idPanel;
-  public AlignFrame alignFrame;
-  ScalePanel scalePanel;
-  ScorePanel scorePanel;
-
-  public AlignmentPanel(AlignFrame af, 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);
-
-    idPanelHolder.add(idPanel, BorderLayout.CENTER);
-    idPanel.addNotify();
-    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();
-     }
-   });
-  }
-
- public void highlightSearchResults(int [] results)
- {
-   seqPanel.seqCanvas.highlightSearchResults( results );
-
-   // 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]);
-
-
- }
-
-
- public OverviewPanel getOverviewPanel()
- {
-   return overviewPanel;
- }
-
- public void setOverviewPanel(OverviewPanel op)
- {
-   overviewPanel = op;
- }
-
-
-  public void setGraphPanelVisible(boolean b)
-  {
-    scorePanelHolder.setVisible(b);
-    idSpaceFillerPanel.setVisible(b);
-    RefreshPanels();
-  }
-
-  public void setWrapAlignment(boolean wrap)
-  {
-      scalePanelHolder.setVisible(!wrap);
-      scorePanelHolder.setVisible(!wrap);
-
-      hscroll.setVisible(!wrap);
-      idSpaceFillerPanel.setVisible(!wrap);
-      idSpaceFillerPanel1.setVisible(!wrap);
-  }
-
-
-  public void setColourScheme()
-  {
-    ColourSchemeI cs = av.getGlobalColourScheme();
-
-    if(av.getConservationSelected())
+import javax.imageio.*;
+
+import javax.swing.*;
+
+
+/**
+ * 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)
     {
+        alignFrame = af;
+        this.av = av;
+        seqPanel = new SeqPanel(av, this);
+        idPanel = new IdPanel(av, this);
+
+        scalePanel = new ScalePanel(av, this);
+
+        idPanelHolder.add(idPanel, BorderLayout.CENTER);
+        idwidthAdjuster = new IdwidthAdjuster(this);
+        idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+
+        annotationPanel = new AnnotationPanel(this);
+        alabels = new AnnotationLabels(this);
 
-      Alignment al = (Alignment)av.getAlignment();
-      Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
+        annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+        annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+        annotationScroller.setViewportView(annotationPanel);
+        annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
-       c.calculate();
-       c.verdict(false, 100);
-       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+        fontChanged();
 
-       av.setGlobalColourScheme( ccs );
+        scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+        seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
+        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;
+
+                    case KeyEvent.VK_DOWN:
+                        alignFrame.moveSelectedSequences(false);
+
+                        break;
+
+                    case KeyEvent.VK_UP:
+                        alignFrame.moveSelectedSequences(true);
+
+                        break;
+                    }
+                }
+            });
     }
-    seqPanel.seqCanvas.paintFlag = true;
-    repaint();
-  }
-  /*
-    seqCanvas.paintFlag = true;
-    if (av.getSelection().size() == 0)
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void fontChanged()
     {
-      seqCanvas.globalColorScheme = cs;
-      for (int i = 0; i < av.alignment.getGroups().size();i++)
-      {
-        SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
-        sg.cs = cs;
-        if(!showConservation
-            && !(sg.cs instanceof Blosum62ColourScheme)
-            && sg.cs instanceof ConservationColourScheme)
-         {
-           // remove ConservationColouring from existing Conservation group
-           ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-           sg.cs = ccs.cs;
-         }
-         else if(showConservation && !(sg.cs instanceof ConservationColourScheme))
-         {
-           // add ConservationColouring to new group
-           Conservation c = sg.getConservation();
-           Alignment al = (Alignment) av.getAlignment();
-           c = new Conservation("All", al.cons,
-                                ResidueProperties.propHash, 3, sg.sequences, 0,
-                                al.getWidth() );
-           c.calculate();
-           c.verdict(false, 100);
-           sg.setConservation(c);
-           sg.cs = new ConservationColourScheme(sg);
-         }
-      }
+        // 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();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension calculateIdWidth()
     {
-      SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));
+        Graphics g = this.getGraphics();
 
-      if( isNewSelection(sg) )
-      {
-        sg = av.getAlignment().addGroup();
-        for (int i=0; i < av.getSelection().size(); i++)
+        if (g == null)
         {
-          av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.
-              sel.sequenceAt(i)),
-                                       (Sequence) av.sel.sequenceAt(i));
-          av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));
+            javax.swing.JFrame f = new javax.swing.JFrame();
+            f.addNotify();
+            g = f.getGraphics();
         }
-      }
 
+        FontMetrics fm = g.getFontMetrics(av.font);
+        AlignmentI al = av.getAlignment();
 
-      sg.cs = cs;
+        int i = 0;
+        int idWidth = 0;
+        String id;
 
-      // Selection is made, we only want to change the conservationColour for selected group
-      if(  showConservation
-           && !(sg.cs instanceof ConservationColourScheme)
-           && !(sg.cs instanceof Blosum62ColourScheme))
-      {
-        Conservation c = sg.getConservation();
-        Alignment al = (Alignment) av.getAlignment();
-
-        c = new Conservation("All", al.cons,
-                             ResidueProperties.propHash, 3, sg.sequences, 0,
-                             al.getWidth() );
-        c.calculate();
-        c.verdict(false, 100);
-        sg.setConservation(c);
-        sg.cs = new ConservationColourScheme(sg);
+        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);
     }
-    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param results DOCUMENT ME!
+     */
+    public void highlightSearchResults(int[] results)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-      sg.cs = ccs.cs;
+        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]);
+            }
+        }
     }
-   }
-   repaint();
-  }
 
-  boolean isNewSelection(SequenceGroup sg)
-  {
-    if(sg==null)
-      return true;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public OverviewPanel getOverviewPanel()
+    {
+        return overviewPanel;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param op DOCUMENT ME!
+     */
+    public void setOverviewPanel(OverviewPanel op)
+    {
+        overviewPanel = op;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setAnnotationVisible(boolean b)
+    {
+        annotationSpaceFillerHolder.setVisible(b);
+        annotationScroller.setVisible(b);
+    }
 
-    if(sg.getSize()!=av.getSelection().size())
-      return true;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param wrap DOCUMENT ME!
+     */
+    public void setWrapAlignment(boolean wrap)
+    {
+        scalePanelHolder.setVisible(!wrap);
+        hscroll.setVisible(!wrap);
+        idwidthAdjuster.setVisible(!wrap);
 
-    for(int i=0; i<sg.getSize(); i++)
-     if( !av.getSelection().contains( sg.getSequenceAt(i) ))
-       return true;
+        av.setShowAnnotation(!wrap);
+        annotationScroller.setVisible(!wrap);
+        annotationSpaceFillerHolder.setVisible(!wrap);
+        idSpaceFillerPanel1.setVisible(!wrap);
 
-    return false;
-  }
+        repaint();
+    }
 
+    /**
+     * DOCUMENT ME!
+     */
+    public void setColourScheme()
+    {
+        ColourSchemeI cs = av.getGlobalColourScheme();
 
-  public ColourSchemeI getColourScheme()
-  {
-    if(av.getSelection().size()>0)
-       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
-    else
-      return seqCanvas.globalColorScheme;
-  }
-*/
+        if (av.getConservationSelected())
+        {
+            Alignment al = (Alignment) av.getAlignment();
+            Conservation c = new Conservation("All",
+                    ResidueProperties.propHash, 3, al.getSequences(), 0,
+                    al.getWidth());
 
-/*  public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
-  {
-    seqPanel.setColourScheme(cs, conservation);
+            c.calculate();
+            c.verdict(false, av.ConsPercGaps);
 
-    av.setGlobalColourScheme(cs);
+            ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
-  }
+            av.setGlobalColourScheme(ccs);
+        }
 
-   void updateResidueView()
-   {
-     if (viewport.getSelection().size() == 0)
-      {
-        for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
+        repaint();
+    }
+
+    // return value is true if the scroll is valid
+    public boolean scrollUp(boolean up)
+    {
+        if (up)
         {
-          SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
-          sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
-          sg.setDisplayText( viewTextMenuItem.isSelected() );
-          sg.setColourText( colourTextMenuItem.isSelected() );
+            if (vscroll.getValue() < 1)
+            {
+                return false;
+            }
+
+            fastPaint = false;
+            vscroll.setValue(vscroll.getValue() - 1);
         }
-      }
-      else
-      {
-        SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
-        if (alignPanel.seqPanel.isNewSelection(sg))
+        else
         {
-          sg = viewport.getAlignment().addGroup();
-          for (int i = 0; i < viewport.getSelection().size(); i++)
-          {
-            viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
-                Sequence) viewport.sel.sequenceAt(i)),
-                                               (Sequence) viewport.sel.sequenceAt(
-                i));
-            viewport.alignment.addToGroup(sg,
-                                          (Sequence) viewport.sel.sequenceAt(i));
-          }
+            if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+            {
+                return false;
+            }
+
+            fastPaint = false;
+            vscroll.setValue(vscroll.getValue() + 1);
         }
 
-        sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
-        sg.setDisplayText(viewTextMenuItem.isSelected());
-        sg.setColourText(colourTextMenuItem.isSelected());
-      }
-     alignPanel.RefreshPanels();
-   }*/
+        fastPaint = true;
+
+        return true;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param right DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean scrollRight(boolean right)
+    {
+        if (right)
+        {
+            if (hscroll.getValue() < 1)
+            {
+                return false;
+            }
 
+            fastPaint = false;
+            hscroll.setValue(hscroll.getValue() - 1);
+        }
+        else
+        {
+            if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+            {
+                return false;
+            }
 
+            fastPaint = false;
+            hscroll.setValue(hscroll.getValue() + 1);
+        }
 
-  public void RefreshPanels()
-  {
-    invalidate();
-    seqPanel.seqCanvas.paintFlag = true;
-    idPanel.idCanvas.paintFlag = true;
-    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
-    setScrollValues(av.getStartRes(), av.getStartSeq());
-    av.getConsensus(true);
-    validate();
-    repaint();
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
+        fastPaint = true;
 
-  }
+        return true;
+    }
 
-  int hextent = 0;
-  int vextent = 0;
+    /**
+     * 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);
 
-  public void setScrollValues(int x, int y)
-  {
-    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
-    vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
+        hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+        vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
 
-    if(hextent+x  >  av.getAlignment().getWidth())
-      x =  av.getAlignment().getWidth()- hextent;
+        if (hextent > av.alignment.getWidth())
+        {
+            hextent = av.alignment.getWidth();
+        }
 
-    if(vextent+y > av.getAlignment().getHeight())
-      y = av.getAlignment().getHeight() - vextent;
+        if (vextent > av.alignment.getHeight())
+        {
+            vextent = av.alignment.getHeight();
+        }
 
-    if(y<0)
-      y = 0;
+        if ((hextent + x) > av.getAlignment().getWidth())
+        {
+            x = av.getAlignment().getWidth() - hextent;
+        }
 
-    if(x<0)
-      x=0;
+        if ((vextent + y) > av.getAlignment().getHeight())
+        {
+            y = av.getAlignment().getHeight() - vextent;
+        }
 
-    hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
-    vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
-    repaint();
+        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());
+    }
+
+    public void this_mouseWheelMoved(MouseWheelEvent e)
+    {
+      if(e.getWheelRotation()>0)
+        scrollUp(false);
+      else
+        scrollUp(true);
+    }
+
+
+    /**
+     * 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);
+            }
+        }
+    }
 
-  }
+    /**
+     * 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();
 
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
+        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());
+        }
+    }
 
-    if (evt.getSource() == hscroll)
+    /**
+     * 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
     {
-      int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+        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);
+        }
+        else
+        {
+            return printUnwrapped(pg, pwidth, pheight, pi);
+        }
     }
 
-    if (evt.getSource() == vscroll)
+    /**
+     * 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 offy = vscroll.getValue();
-        av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());
+        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;
     }
 
+    /**
+     * 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;
+
+        pg.setColor(Color.white);
+        pg.fillRect(0, 0, pwidth, pheight);
+        pg.setFont(av.getFont());
+
+        ////////////////
+        // Draw the ids
+        pg.setColor(Color.black);
+
+        pg.translate(0, -pi * pheight);
+
+        pg.setClip(0, pi * pheight, pwidth, pheight);
 
-    if(overviewPanel!=null)
-      overviewPanel.setBoxPosition();
+        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();
+
+                if (av.getShowFullId())
+                {
+                    string = s.getDisplayId();
+                }
+
+                pg.drawString(string, 0,
+                    ((i * av.charHeight) + ypos + av.charHeight) -
+                    (av.charHeight / 5));
+            }
+
+            ypos += ((av.alignment.getHeight() + 2) * av.charHeight);
+        }
+        while (ypos < totalHeight);
+
+        pg.translate(idWidth, 0);
+
+        seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+
+        if ((pi * pheight) < totalHeight)
+        {
+            return Printable.PAGE_EXISTS;
+        }
+        else
+        {
+            return Printable.NO_SUCH_PAGE;
+        }
+    }
 
-    seqPanel.seqCanvas.paintFlag=true;
-    repaint();
-  }
+    /**
+     * 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();
 
-  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
-  {
+          jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                        chooser.getSelectedFile().getParent());
+        }
 
-    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
+        int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+        int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
 
-    int pwidth = (int)pf.getImageableWidth();
-    int pheight = (int)pf.getImageableHeight();
-    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+        if (av.getWrapAlignment())
+        {
+          height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
+              av.chunkHeight;
+          width = seqPanel.getWidth() + idPanel.getWidth();
 
-    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 - 30)/av.getCharHeight())-1;
-    int pagesWide = av.getAlignment().getWidth() / totalRes +1;
-    int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
 
-    if (pi >= pagesWide*pagesHigh)
-     return Printable.NO_SUCH_PAGE;
+        if (av.getShowAnnotation())
+        {
+            height += annotationPanel.getPreferredSize().height;
+        }
 
-    /////////////////////////////
-    /// 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();
+        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();
+        }
+    }
 
-     startSeq = (pi / pagesWide) * totalSeq;
-     endSeq = startSeq + totalSeq;
-     if(endSeq > av.getAlignment().getHeight())
-       endSeq = av.getAlignment().getHeight();
 
+    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
 
-    ////////////////
-    //draw Scale
-    pg.translate(idWidth,0);
-    scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
+    }
 
-    pg.translate(-idWidth, 30);
-    ////////////////
-    // Draw the ids
-    Color currentColor=null;
-    Color currentTextColor=null;
-    for(int i=startSeq; i<endSeq; i++)
+    /**
+     * DOCUMENT ME!
+     */
+    public void makePNG(File pngFile)
     {
-      if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
+      if(pngFile==null)
       {
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
+        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());
       }
-      else
+
+
+
+      int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+      int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
+
+      if (av.getWrapAlignment())
       {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
-        currentTextColor = Color.black;
+        height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
+            av.chunkHeight;
+        width = seqPanel.getWidth() + idPanel.getWidth();
+
       }
 
-      pg.setColor(currentColor);
-      pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
-                              idWidth,
-                              av.getCharHeight());
 
-      pg.setColor(currentTextColor);
+        if (av.getShowAnnotation())
+        {
+            height += annotationPanel.getPreferredSize().height;
+        }
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId();
-      pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight
-                    (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
-    }
+        try
+        {
+
+            FileOutputStream out = new FileOutputStream(pngFile);
 
-    // 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);
+            BufferedImage bi = new BufferedImage(width, height,
+                    BufferedImage.TYPE_INT_RGB);
+            Graphics2D png = (Graphics2D) bi.getGraphics();
 
-    return Printable.PAGE_EXISTS;
-  }
+            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();
+        }
+    }
 }
 
 
+/**
+ * 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");
+        }
+    }
+}