X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=fdd01d3d09a8514ddd5083ca334a5a16978a8ab1;hb=3a455483336b530b45d449270069815a933151d2;hp=da68ab9020f62b11a5bc55d98bab0716c414ba05;hpb=3f578998521236c208e9d3c7790d4d5ac4da0a50;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index da68ab9..fdd01d3 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,389 +1,684 @@
+/*
+ * 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 com.sun.image.codec.jpeg.*;
 import java.io.*;
-import java.awt.image.*;
 
+import javax.swing.*;
 
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
-{
 
-  AlignViewport     av;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentPanel extends GAlignmentPanel
+    implements AdjustmentListener, Printable
+{
+  public AlignViewport av;
   OverviewPanel overviewPanel;
-  SeqPanel   seqPanel;
-  IdPanel    idPanel;
-  SecondaryStructurePanel ssPanel;
+  SeqPanel seqPanel;
+  IdPanel idPanel;
+  IdwidthAdjuster idwidthAdjuster;
+
+  /** DOCUMENT ME!! */
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
-  ScorePanel scorePanel;
+  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);
+    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);
-    idPanel.addNotify();
+    idwidthAdjuster = new IdwidthAdjuster(this);
+    idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
 
-    javax.swing.JFrame f = new javax.swing.JFrame();
-    f.addNotify();
-    FontMetrics fm = f.getGraphics().getFontMetrics(av.font);
-    AlignmentI al = av.getAlignment();
+    annotationPanel = new AnnotationPanel(this);
+    alabels = new AnnotationLabels(this);
 
-    int i   = 0;
-    int idWidth = 0;
-    while (i < al.getHeight() && al.getSequenceAt(i) != null)
-    {
-      SequenceI s   = al.getSequenceAt(i);
-      String str   = s.getDisplayId();
-      if (fm.stringWidth(str) > idWidth)
-        idWidth = fm.stringWidth(str);
-      i++;
-    }
-    hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
+
+    annotationScroller.setViewportView(annotationPanel);
+    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+
+    fontChanged();
 
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-    setScrollValues(0,0);
+
+    setScrollValues(0, 0);
+
+    annotationPanel.adjustPanelHeight();
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
+                                                 getPreferredSize());
+    annotationScroller.setPreferredSize(annotationPanel.
+                                        getPreferredSize());
+    setAnnotationVisible(av.getShowAnnotation());
 
     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;
-       }
-     }
-   });
-  }
+    af.addKeyListener(new KeyAdapter()
+    {
+      public void keyPressed(KeyEvent evt)
+      {
+        switch (evt.getKeyCode())
+        {
+          case 27: // escape key
+            av.setSelectionGroup(null);
+            repaint();
 
+            break;
 
- public void highlightSearchResults(int [] results)
- {
-   seqPanel.seqCanvas.highlightSearchResults( results );
+          case KeyEvent.VK_DOWN:
+            alignFrame.moveSelectedSequences(false);
 
-   // 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]);
+            break;
 
+          case KeyEvent.VK_UP:
+            alignFrame.moveSelectedSequences(true);
 
- }
+            break;
 
+          case KeyEvent.VK_BACK_SPACE:
+          case KeyEvent.VK_DELETE:
+            alignFrame.cut_actionPerformed(null);
+            break;
 
- public OverviewPanel getOverviewPanel()
- {
-   return overviewPanel;
- }
+          case KeyEvent.VK_P:
+            seqPanel.seqCanvas.increaseAARatio();
+            break;
+          case KeyEvent.VK_L:
+            seqPanel.seqCanvas.decreaseAARation();
+            break;
+        }
+      }
+    });
+  }
 
- public void setOverviewPanel(OverviewPanel op)
- {
-   overviewPanel = op;
- }
+  /**
+   * 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()));
 
-  public void setGraphPanelVisible(boolean b)
-  {
-    idSpaceFillerPanel.setVisible(b);
-    scorePanelHolder.setVisible(b);
+    idPanel.idCanvas.gg = null;
+    seqPanel.seqCanvas.img = null;
+    annotationPanel.adjustPanelHeight();
 
-    RefreshPanels();
-    // bit annoying to call this twice, can you do better?
-    RefreshPanels();
-  }
+    Dimension d = calculateIdWidth();
+    d.setSize(d.width + 4, d.height);
+    idPanel.idCanvas.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(d);
 
-  public void setSecondaryStructureVisible(boolean b)
-  {
-    secondaryPanelHolder.setVisible(b);
-    RefreshPanels();
+    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 (overviewPanel != null)
+      overviewPanel.setBoxPosition();
+
+    repaint();
   }
 
-  public void setWrapAlignment(boolean wrap)
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension calculateIdWidth()
   {
-    scorePanelHolder.setVisible(!wrap);
-    scalePanelHolder.setVisible(!wrap);
-    secondaryPanelHolder.setVisible(!wrap);
+    Container c = new Container();
 
-    hscroll.setVisible(!wrap);
+    FontMetrics fm = c.getFontMetrics(av.font);
+    AlignmentI al = av.getAlignment();
 
-    idSpaceFillerPanel.setVisible(!wrap);
-    idSpaceFillerPanel1.setVisible(!wrap);
+    int i = 0;
+    int idWidth = 0;
+    String id;
 
-    RefreshPanels();
+    while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
+    {
+      SequenceI s = al.getSequenceAt(i);
 
-  }
+      id = s.getDisplayId(av.getShowJVSuffix());
 
+      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;
 
-       Alignment al = (Alignment)av.getAlignment();
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
+    if (al.getAlignmentAnnotation() != null)
+    {
+      fm = c.getFontMetrics(alabels.getFont());
 
-       c.calculate();
-       c.verdict(false, 100);
-       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+      while (i < al.getAlignmentAnnotation().length)
+      {
+        String label = al.getAlignmentAnnotation()[i].label;
 
-       av.setGlobalColourScheme( ccs );
+        if (fm.stringWidth(label) > idWidth)
+        {
+          idWidth = fm.stringWidth(label);
+        }
 
+        i++;
+      }
     }
 
-    RefreshPanels();
+    return new Dimension(idWidth, 12);
   }
 
-  public void RefreshPanels()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param results DOCUMENT ME!
+   */
+  public void highlightSearchResults(int[] results)
   {
-              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;
+    seqPanel.seqCanvas.highlightSearchResults(results);
 
-                int h = (av.alignment.getHeight() + 2) * av.charHeight;
-                vextent = seqPanel.seqCanvas.getHeight() / h;
-                vscroll.setValues(0, vextent, 0, max);
-              }
-              else
+    // 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;
 
-                setScrollValues(av.getStartRes(), av.getStartSeq());
-              av.getConsensus(true);
-              if (overviewPanel != null)
-                overviewPanel.updateOverviewImage();
+      if(!av.wrapAlignment)
+      {
+        if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
+            ( (av.getStartSeq() > results[0]) ||
+             (av.getEndSeq() < results[0])))
+        {
+          setScrollValues(start, results[0]);
+        }
+      }
+      else
+      {
+        int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+        if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
+        {
+          vscroll.setValue(start / cwidth);
+        }
+      }
+    }
+  }
 
-          validate();
-          repaint();
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public OverviewPanel getOverviewPanel()
+  {
+    return overviewPanel;
   }
-  int hextent = 0;
-  int vextent = 0;
 
+  /**
+   * 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();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param wrap DOCUMENT ME!
+   */
+  public void setWrapAlignment(boolean wrap)
+  {
+    av.startSeq = 0;
+    scalePanelHolder.setVisible(!wrap);
+    hscroll.setVisible(!wrap);
+    idwidthAdjuster.setVisible(!wrap);
+
+    if (wrap)
+    {
+      annotationScroller.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
+    else if (av.showAnnotation)
+    {
+      annotationScroller.setVisible(true);
+      annotationSpaceFillerHolder.setVisible(true);
+    }
+
+    idSpaceFillerPanel1.setVisible(!wrap);
+
+    repaint();
+  }
 
   // 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;
       vscroll.setValue(vscroll.getValue() - 1);
     }
     else
     {
-     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
-       return 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(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;
- }
+    if (right)
+    {
+      if (hscroll.getValue() < 1)
+      {
+        return false;
+      }
 
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() - 1);
+    }
+    else
+    {
+      if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+      {
+        return false;
+      }
 
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() + 1);
+    }
+
+    fastPaint = true;
+
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param x DOCUMENT ME!
+   * @param y DOCUMENT ME!
+   */
   public void setScrollValues(int x, int y)
   {
-    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
-    vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
+    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
+                 1);
 
-    if(hextent+x  >  av.getAlignment().getWidth())
-      x =  av.getAlignment().getWidth()- hextent;
+    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
 
-    if(vextent+y > av.getAlignment().getHeight())
-      y = av.getAlignment().getHeight() - vextent;
+    if (hextent > av.alignment.getWidth())
+    {
+      hextent = av.alignment.getWidth();
+    }
 
-    if(y<0)
-      y = 0;
+    if (vextent > av.alignment.getHeight())
+    {
+      vextent = av.alignment.getHeight();
+    }
 
-    if(x<0)
-      x=0;
+    if ( (hextent + x) > av.getAlignment().getWidth())
+    {
+      x = av.getAlignment().getWidth() - hextent;
+    }
 
-    hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
-    vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+    if ( (vextent + y) > av.getAlignment().getHeight())
+    {
+      y = av.getAlignment().getHeight() - vextent;
+    }
 
+    if (y < 0)
+    {
+      y = 0;
+    }
 
-    repaint();
+    if (x < 0)
+    {
+      x = 0;
+    }
 
+    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
+    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
   }
 
-
+  /**
+   * 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);
+      av.setEndRes( (x +
+                     (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
     {
       int offy = vscroll.getValue();
+
       if (av.getWrapAlignment())
       {
-        av.setStartRes( vscroll.getValue() * av.getChunkWidth());
+        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());
+        av.setEndSeq(offy +
+                     (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
       }
     }
 
-
-    if(overviewPanel!=null)
+    if (overviewPanel != null)
+    {
       overviewPanel.setBoxPosition();
+    }
 
-    repaint();
+    int scrollX = av.startRes - oldX;
+    int scrollY = av.startSeq - oldY;
+
+    if (av.getWrapAlignment() || !fastPaint)
+    {
+      repaint();
+    }
+    else
+    {
+      // 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);
+        }
+      }
+    }
   }
 
-  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
   {
-    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
+    invalidate();
 
-    int pwidth = (int) pf.getImageableWidth();
-    int pheight = (int) pf.getImageableHeight();
+    Dimension d = idPanel.idCanvas.getPreferredSize();
+    idPanelHolder.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+    validate();
 
     if (av.getWrapAlignment())
-      return printWrappedAlignment(pg, pwidth,pheight, pi);
+    {
+      int max = av.alignment.getWidth() /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
+      vscroll.setMaximum(max);
+      vscroll.setUnitIncrement(1);
+      vscroll.setVisibleAmount(1);
+    }
     else
-      return printUnwrapped(pg,pwidth, pheight,pi);
+    {
+      setScrollValues(av.getStartRes(), av.getStartSeq());
+    }
+
+
+    if( this.getVisibleRect().getBounds() == g.getClipBounds() )
+    {
+      if (overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+    }
   }
 
-  public int printUnwrapped(Graphics pg, int pwidth, int pheight, 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());
 
-    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+    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);
+    }
+  }
+
+  /**
+   * 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();
+
+    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;
 
-    if (pi >= pagesWide*pagesHigh)
-     return Printable.NO_SUCH_PAGE;
+    /////////////////////////////
+    /// 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 startRes, endRes, startSeq, endSeq;
+    int endSeq;
     startRes = (pi % pagesWide) * totalRes;
-    endRes = startRes + totalRes-1;
-    if(endRes>av.getAlignment().getWidth())
-      endRes = av.getAlignment().getWidth();
+    endRes = (startRes + totalRes) - 1;
 
-     startSeq = (pi / pagesWide) * totalSeq;
-     endSeq = startSeq + totalSeq;
-     if(endSeq > av.getAlignment().getHeight())
-       endSeq = av.getAlignment().getHeight();
+    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.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().sequences.contains(
+              av.getAlignment().getSequenceAt(i)))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -395,126 +690,441 @@ 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).getDisplayId();
-      pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight
-                    (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
+      String string = av.getAlignment().getSequenceAt(i).getDisplayId
+          ( av.getShowJVSuffix());
+
+      pg.drawString(string, 0,
+                    ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
+                    (av.getCharHeight() / 5));
     }
 
+    pg.setFont(av.getFont());
+
     // 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);
+    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-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 = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+    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 resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
+        idWidth);
 
-    int noChunksOnPage = pheight / chunkHeight;
-    int totalChunks = da.getWidth() / chunkWidth;
+    int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
 
-    if ( pi*noChunksOnPage > totalChunks )
-     return Printable.NO_SUCH_PAGE;
+    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);
-        pg.drawString(s.getDisplayId(), 0,
-                      AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
-                      av.charHeight - (av.charHeight / 5));
+        SequenceI s = av.alignment.getSequenceAt(i);
+        String string = s.getDisplayId( av.getShowJVSuffix());
+
+        pg.drawString(string, 0,
+                      ( (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 makeJPG(int width, int height)
+  void makeAlignmentImage(int type, File file)
   {
-    try
+    int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+    int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
+
+    if (idPanel.getWidth() == 0)
     {
+      width += calculateIdWidth().getWidth() + 4;
+    }
 
-      BufferedImage bi = new BufferedImage(width, height,
-                                           BufferedImage.TYPE_INT_RGB);
-      Graphics pg = bi.getGraphics();
+    if (av.getWrapAlignment())
+    {
+      height = getWrappedHeight();
+      width = seqPanel.getWidth() + idPanel.getWidth();
+    }
+    else if (av.getShowAnnotation())
+    {
+      height += annotationPanel.adjustPanelHeight() + 3;
+    }
 
-      try
+    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 (av.getWrapAlignment())
-          printWrappedAlignment(pg, width, height, 0);
-        else
-          printUnwrapped(pg, width, height, 0);
+        if(im.getGraphics()!=null)
+        {
+          printWrappedAlignment(im.getGraphics(), width, height, 0);
+          im.writeImage();
+        }
       }
-      catch (Exception ex)
-      {}
+      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();
+
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+  /**
+   * DOCUMENT ME!
+   */
+  public void makeEPS(File epsFile)
+  {
+    makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+  }
 
-      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");
+  /**
+   * DOCUMENT ME!
+   */
+  public void makePNG(File pngFile)
+  {
+    makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+  }
 
-      int value = chooser.showSaveDialog(this);
-      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+  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
       {
+        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);
+          java.util.Vector 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 );
+              }
 
-        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-        JPEGImageEncoder jie = JPEGCodec.createJPEGEncoder(out);
-        JPEGEncodeParam param = JPEGCodec.getDefaultJPEGEncodeParam(bi);
-        param.setQuality(1.0f, true);
+              if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
+                text.append("<br><em>" + groups[g].getName() + "</em>");
+            }
 
-        jie.encode(bi, param);
+            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.size();
+                for (f = 0; f < fSize; f++)
+                {
+                  SequenceFeature sf = (SequenceFeature) features.elementAt(f);
+
+                  if ( (sf.getBegin() <= seq.findPosition(res)) &&
+                      (sf.getEnd() >= seq.findPosition(res)))
+                  {
+                    if (sf.getType().equals("disulfide bond"))
+                    {
+                      if (sf.getBegin() == seq.findPosition(res)
+                          || sf.getEnd() == seq.findPosition(res))
+                      {
+                        text.append("<br>disulfide bond " + sf.getBegin() + ":" +
+                                       sf.getEnd());
+                      }
+                    }
+                    else
+                    {
+                      text.append("<br>");
+                      text.append(sf.getType());
+                      if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription()))
+                        text.append(" " + sf.getDescription());
+
+                      if (sf.getStatus() != null && sf.getStatus().length()>0)
+                      {
+                        text.append(" (" + sf.getStatus() + ")");
+                      }
+                    }
+                  }
+
+                }
+              }
+              if(text.length()>1)
+              {
+                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+                out.println(text.toString());
+              }
+            }
+          }
+        out.println("</map></body></html>");
         out.close();
+
       }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    } ///////////END OF IMAGE MAP
 
-    }
-    catch (IOException ex)
+  }
+
+  int getWrappedHeight()
+  {
+
+    int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
+        seqPanel.seqCanvas.getWidth());
+
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+      hgap += av.charHeight;
+
+    int annotationHeight = 0;
+    if (av.showAnnotation)
     {
-      System.out.println("ex Writing image ");
+      annotationHeight = annotationPanel.adjustPanelHeight();
     }
-  }
 
-}
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap
+        + annotationHeight;
+
+    int height = ( (av.alignment.getWidth() / 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");
+      }
+    }
+  }
+}