X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=43fb5fac17366c74ad8740bb2dec6d27385d3d0a;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=b339e5165f97191d5e122dbdb11927c52bac271f;hpb=5150ffd5baa1f58bb6b4059616bc6b9050326553;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index b339e51..43fb5fa 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,28 +1,54 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.jbgui.GAlignmentPanel;
-import jalview.schemes.*;
-import jalview.analysis.*;
 import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
+
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
+
 import java.io.*;
-import java.awt.image.*;
-import org.jibble.epsgraphics.*;
-import javax.imageio.*;
-import javax.swing.*;
 
+import javax.swing.*;
 
 
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentPanel extends GAlignmentPanel
+    implements AdjustmentListener, Printable
 {
-
-  AlignViewport     av;
+  public AlignViewport av;
   OverviewPanel overviewPanel;
-  SeqPanel   seqPanel;
-  IdPanel    idPanel;
+  SeqPanel seqPanel;
+  IdPanel idPanel;
   IdwidthAdjuster idwidthAdjuster;
+
+  /** DOCUMENT ME!! */
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
   AnnotationPanel annotationPanel;
@@ -30,13 +56,21 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
+  int hextent = 0;
+  int vextent = 0;
 
+  /**
+   * Creates a new AlignmentPanel object.
+   *
+   * @param af DOCUMENT ME!
+   * @param av DOCUMENT ME!
+   */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     alignFrame = af;
-    this.av         = av;
-    seqPanel        = new SeqPanel  (av, this);
-    idPanel         = new IdPanel   (av, this);
+    this.av = av;
+    seqPanel = new SeqPanel(av, this);
+    idPanel = new IdPanel(av, this);
 
     scalePanel = new ScalePanel(av, this);
 
@@ -47,7 +81,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     annotationPanel = new AnnotationPanel(this);
     alabels = new AnnotationLabels(this);
 
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
+                                                 getPreferredSize());
     annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
     annotationScroller.setViewportView(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
@@ -59,256 +94,357 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     setScrollValues(0, 0);
 
+    annotationPanel.adjustPanelHeight();
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
+                                                 getPreferredSize());
+    annotationScroller.setPreferredSize(annotationPanel.
+                                        getPreferredSize());
+    setAnnotationVisible(av.getShowAnnotation());
+
     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;
-       }
-     }
-   });
+    af.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;
+
+          case KeyEvent.VK_BACK_SPACE:
+          case KeyEvent.VK_DELETE:
+            alignFrame.cut_actionPerformed(null);
+            break;
+
+          case KeyEvent.VK_P:
+            seqPanel.seqCanvas.increaseAARatio();
+            break;
+          case KeyEvent.VK_L:
+            seqPanel.seqCanvas.decreaseAARation();
+            break;
+        }
+      }
+    });
   }
 
+  /**
+   * 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()));
+    scalePanelHolder.setPreferredSize(new Dimension(10,
+        av.charHeight + fm.getDescent()));
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
+        av.charHeight + fm.getDescent()));
 
     idPanel.idCanvas.gg = null;
+    seqPanel.seqCanvas.img = null;
     annotationPanel.adjustPanelHeight();
+
     Dimension d = calculateIdWidth();
     d.setSize(d.width + 4, d.height);
     idPanel.idCanvas.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
-    repaint();
-  }
 
-
-  Dimension calculateIdWidth()
-  {
-    Graphics g = this.getGraphics();
-    if(g==null)
+    if (av.getWrapAlignment())
+    {
+      int max = av.alignment.getWidth() /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+      vscroll.setMaximum(max);
+      vscroll.setUnitIncrement(1);
+      vscroll.setVisibleAmount(1);
+    }
+    else
     {
-      javax.swing.JFrame f = new javax.swing.JFrame();
-      f.addNotify();
-      g = f.getGraphics();
+      setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-    FontMetrics fm = g.getFontMetrics(av.font);
-    AlignmentI al = av.getAlignment();
+    if (overviewPanel != null)
+      overviewPanel.setBoxPosition();
 
-       int i   = 0;
-       int idWidth = 0;
-       String id;
-       while (i < al.getHeight() && al.getSequenceAt(i) != null)
-       {
-         SequenceI s   = al.getSequenceAt(i);
-         if(av.getShowFullId())
-           id   = s.getDisplayId();
-         else
-           id = s.getName();
-
-         if (fm.stringWidth(id) > idWidth)
-           idWidth = fm.stringWidth(id);
-         i++;
-       }
-
-       // Also check annotation label widths
-       i=0;
-       if(al.getAlignmentAnnotation()!=null)
-       {
-         fm = g.getFontMetrics(alabels.getFont());
-         while (i < al.getAlignmentAnnotation().length)
-         {
-           String label = al.getAlignmentAnnotation()[i].label;
-           if (fm.stringWidth(label) > idWidth)
-             idWidth = fm.stringWidth(label);
-           i++;
-         }
-       }
-
-       return new Dimension(idWidth, 12);
+    repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension calculateIdWidth()
+  {
+    Container c = new Container();
+
+    FontMetrics fm = c.getFontMetrics(av.font);
+    AlignmentI al = av.getAlignment();
 
- public void highlightSearchResults(int [] results)
- {
-   seqPanel.seqCanvas.highlightSearchResults( results );
+    int i = 0;
+    int idWidth = 0;
+    String id;
 
-   // do we need to scroll the panel?
-   if(results!=null)
+    while ( (i < al.getHeight()) && (al.getSequenceAt(i) != 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]);
+      SequenceI s = al.getSequenceAt(i);
+
+      id = s.getDisplayId(av.getShowJVSuffix());
+
+      if (fm.stringWidth(id) > idWidth)
+      {
+        idWidth = fm.stringWidth(id);
+      }
+
+      i++;
     }
 
- }
+    // Also check annotation label widths
+    i = 0;
 
+    if (al.getAlignmentAnnotation() != null)
+    {
+      fm = c.getFontMetrics(alabels.getFont());
 
- public OverviewPanel getOverviewPanel()
- {
-   return overviewPanel;
- }
+      while (i < al.getAlignmentAnnotation().length)
+      {
+        String label = al.getAlignmentAnnotation()[i].label;
 
- public void setOverviewPanel(OverviewPanel op)
- {
-   overviewPanel = op;
- }
+        if (fm.stringWidth(label) > idWidth)
+        {
+          idWidth = fm.stringWidth(label);
+        }
 
+        i++;
+      }
+    }
 
-  public void setAnnotationVisible(boolean b)
-  {
-    annotationSpaceFillerHolder.setVisible(b);
-    annotationScroller.setVisible(b);
+    return new Dimension(idWidth, 12);
   }
 
-
-  public void setWrapAlignment(boolean wrap)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param results DOCUMENT ME!
+   */
+  public void highlightSearchResults(int[] results)
   {
-    scalePanelHolder.setVisible(!wrap);
-    hscroll.setVisible(!wrap);
-    idwidthAdjuster.setVisible(!wrap);
-
-    av.setShowAnnotation(!wrap);
-    annotationScroller.setVisible(!wrap);
-    annotationSpaceFillerHolder.setVisible(!wrap);
-    idSpaceFillerPanel1.setVisible(!wrap);
+    seqPanel.seqCanvas.highlightSearchResults(results);
 
-    repaint();
+    // 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]);
+      }
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public OverviewPanel getOverviewPanel()
+  {
+    return overviewPanel;
+  }
 
-  public void setColourScheme()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param op DOCUMENT ME!
+   */
+  public void setOverviewPanel(OverviewPanel op)
   {
-    ColourSchemeI cs = av.getGlobalColourScheme();
+    overviewPanel = op;
+  }
 
-    if(av.getConservationSelected())
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setAnnotationVisible(boolean b)
+  {
+    if (!av.wrapAlignment)
     {
+      annotationSpaceFillerHolder.setVisible(b);
+      annotationScroller.setVisible(b);
+    }
+    repaint();
+  }
 
-       Alignment al = (Alignment)av.getAlignment();
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
-
-       c.calculate();
-       c.verdict(false, av.ConsPercGaps);
-       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
-
-       av.setGlobalColourScheme( ccs );
+  /**
+   * 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();
   }
 
-
-  int hextent = 0;
-  int vextent = 0;
-
   // return value is true if the scroll is valid
   public boolean scrollUp(boolean up)
   {
-    if(up)
+    if (up)
     {
-      if(vscroll.getValue()<1)
+      if (vscroll.getValue() < 1)
+      {
         return false;
-      fastPaint  = false;
+      }
+
+      fastPaint = false;
       vscroll.setValue(vscroll.getValue() - 1);
     }
     else
     {
-     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
-       return false;
-      fastPaint  = false;
+      if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+      {
+        return false;
+      }
+
+      fastPaint = false;
       vscroll.setValue(vscroll.getValue() + 1);
     }
+
     fastPaint = true;
+
     return true;
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param right DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
   public boolean scrollRight(boolean right)
   {
-
     if (right)
     {
       if (hscroll.getValue() < 1)
+      {
         return false;
+      }
+
       fastPaint = false;
       hscroll.setValue(hscroll.getValue() - 1);
     }
     else
     {
-      if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+      if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+      {
         return false;
+      }
+
       fastPaint = false;
       hscroll.setValue(hscroll.getValue() + 1);
     }
+
     fastPaint = true;
+
     return true;
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param x DOCUMENT ME!
+   * @param y DOCUMENT ME!
+   */
   public void setScrollValues(int x, int y)
   {
-    av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
+                 1);
 
-    hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
-    vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
+    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
 
-    if(hextent > av.alignment.getWidth())
+    if (hextent > av.alignment.getWidth())
+    {
       hextent = av.alignment.getWidth();
-    if(vextent > av.alignment.getHeight())
+    }
+
+    if (vextent > av.alignment.getHeight())
+    {
       vextent = av.alignment.getHeight();
+    }
 
-    if(hextent+x  >  av.getAlignment().getWidth())
-      x =  av.getAlignment().getWidth()- hextent;
+    if ( (hextent + x) > av.getAlignment().getWidth())
+    {
+      x = av.getAlignment().getWidth() - hextent;
+    }
 
-    if(vextent+y > av.getAlignment().getHeight())
+    if ( (vextent + y) > av.getAlignment().getHeight())
+    {
       y = av.getAlignment().getHeight() - vextent;
+    }
 
-    if(y<0)
+    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() );
-
-
+    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();
 
@@ -316,47 +452,69 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+      av.setEndRes( (x +
+                     (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
     {
       int offy = vscroll.getValue();
+
       if (av.getWrapAlignment())
       {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-        av.setStartRes( vscroll.getValue() * rowSize );
-        av.setEndRes( (vscroll.getValue()+1) * rowSize );
+        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();
+    }
 
-    if(av.getWrapAlignment() || !fastPaint)
+    int xShift = av.getStartRes() - oldX;
+    int yShift = av.getStartSeq() - oldY;
+
+    if ( (xShift != 0 && yShift != 0) ||
+        (Math.abs(xShift) > av.getEndRes() - av.getStartRes()
+         || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())
+        || av.getWrapAlignment()
+        || !fastPaint)
+    {
+      // Either no shift at all, or shift greater than visible amount
       repaint();
+    }
     else
     {
-      idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
-      seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
-                                   av.getStartSeq() - oldY);
+      idPanel.idCanvas.fastPaint(yShift);
+      seqPanel.seqCanvas.fastPaint(xShift, yShift);
 
       scalePanel.repaint();
+
       if (av.getShowAnnotation())
-        annotationPanel.fastPaint(av.getStartRes() - oldX);
+      {
+        annotationPanel.fastPaint(xShift);
+      }
     }
-
   }
 
-
+  /**
+   * 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));
@@ -364,7 +522,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+      int max = av.alignment.getWidth() /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);
@@ -375,313 +534,507 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     }
 
 
-
+    if( this.getVisibleRect().getBounds() == g.getClipBounds() )
+    {
+      if (overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+    }
   }
 
-  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
+  /**
+   * DOCUMENT ME!
+   *
+   * @param pg DOCUMENT ME!
+   * @param pf DOCUMENT ME!
+   * @param pi DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   *
+   * @throws PrinterException DOCUMENT ME!
+   */
+  public int print(Graphics pg, PageFormat pf, int pi)
+      throws PrinterException
   {
-    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
+    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
 
     int pwidth = (int) pf.getImageableWidth();
     int pheight = (int) pf.getImageableHeight();
 
     if (av.getWrapAlignment())
-      return printWrappedAlignment(pg, pwidth,pheight, pi);
+    {
+      return printWrappedAlignment(pg, pwidth, pheight, pi);
+    }
     else
-      return printUnwrapped(pg,pwidth, pheight,pi);
+    {
+      return printUnwrapped(pg, pwidth, pheight, pi);
+    }
   }
 
-  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+  /**
+   * DOCUMENT ME!
+   *
+   * @param pg DOCUMENT ME!
+   * @param pwidth DOCUMENT ME!
+   * @param pheight DOCUMENT ME!
+   * @param pi DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   *
+   * @throws PrinterException DOCUMENT ME!
+   */
+  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+      throws PrinterException
   {
+    int idWidth = calculateIdWidth().width + 4;
+    FontMetrics fm = getFontMetrics(av.getFont());
+    int scaleHeight = av.charHeight + fm.getDescent();
 
-      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.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();
+    ////////////////////////////////////
+    /// 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 totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
+        1;
 
-      int pagesWide = av.getAlignment().getWidth() / totalRes + 1;
+    int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
 
-      /////////////////////////////
-      /// 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()-1)
-        endRes = av.getAlignment().getWidth()-1;
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int startRes;
 
-      startSeq = (pi / pagesWide) * totalSeq;
-      endSeq = startSeq + totalSeq;
-      if (endSeq > av.getAlignment().getHeight())
-        endSeq = av.getAlignment().getHeight();
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int endRes;
 
-      int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int startSeq;
 
-      if (av.showAnnotation)
-        pagesHigh += annotationPanel.getHeight();
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int endSeq;
+    startRes = (pi % pagesWide) * totalRes;
+    endRes = (startRes + totalRes) - 1;
 
-      pagesHigh /= pheight;
+    if (endRes > (av.getAlignment().getWidth() - 1))
+    {
+      endRes = av.getAlignment().getWidth() - 1;
+    }
 
-      if (pi >= pagesWide * pagesHigh)
-        return Printable.NO_SUCH_PAGE;
+    startSeq = (pi / pagesWide) * totalSeq;
+    endSeq = startSeq + totalSeq;
 
-        //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;
-        }
+    if (endSeq > av.getAlignment().getHeight())
+    {
+      endSeq = av.getAlignment().getHeight();
+    }
 
-        pg.setColor(currentColor);
-        pg.fillRect(0,
-                    jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
-            av.getCharHeight()),
-                    idWidth,
-                    av.getCharHeight());
+    int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
 
-        pg.setColor(currentTextColor);
+    if (av.showAnnotation)
+    {
+      pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+    }
 
-        String string = av.getAlignment().getSequenceAt(i).getName();
-        if (av.getShowFullId())
-          string = av.getAlignment().getSequenceAt(i).getDisplayId();
+    pagesHigh /= pheight;
 
-        pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
-                      (startSeq, i, av.getCharHeight()) + av.getCharHeight() -
-                      (av.getCharHeight() / 5));
-      }
+    if (pi >= (pagesWide * pagesHigh))
+    {
+      return Printable.NO_SUCH_PAGE;
+    }
 
-      // draw main sequence panel
-      pg.translate(idWidth, 0);
-      seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
-                                   startRes, startSeq, 0);
+    //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;
 
-      if (av.showAnnotation && endSeq == av.alignment.getHeight())
+    for (int i = startSeq; i < endSeq; i++)
+    {
+      if ( (av.getSelectionGroup() != null) &&
+          av.getSelectionGroup().sequences.contains(
+              av.getAlignment().getSequenceAt(i)))
       {
-        pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
-        alabels.drawComponent( (Graphics2D) pg);
-        pg.translate(idWidth, 0);
-        annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes+1);
+        currentColor = Color.gray;
+        currentTextColor = Color.black;
+      }
+      else
+      {
+        currentColor = av.getAlignment().getSequenceAt(i).getColor();
+        currentTextColor = Color.black;
       }
 
-      return Printable.PAGE_EXISTS;
+      pg.setColor(currentColor);
+      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+                  av.getCharHeight());
 
-  }
+      pg.setColor(currentTextColor);
+
+      String string = av.getAlignment().getSequenceAt(i).getDisplayId
+          ( av.getShowJVSuffix());
+
+      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 + 3);
+      alabels.drawComponent( (Graphics2D) pg, idWidth);
+      pg.translate(idWidth, 0);
+      annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
+                                    1);
+    }
+
+    return Printable.PAGE_EXISTS;
+  }
 
-  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+  /**
+   * DOCUMENT ME!
+   *
+   * @param pg DOCUMENT ME!
+   * @param pwidth DOCUMENT ME!
+   * @param pheight DOCUMENT ME!
+   * @param pi DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   *
+   * @throws PrinterException DOCUMENT ME!
+   */
+  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
+                                   int pi)
+      throws PrinterException
   {
-      int idWidth = calculateIdWidth().width + 4;
 
-      int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth);
-      int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
-          ( (av.alignment.getWidth()
-             / resWidth) + 1) * av.charHeight;
+    int annotationHeight = 0;
+    AnnotationLabels labels = null;
+    if (av.showAnnotation)
+    {
+      annotationHeight = annotationPanel.adjustPanelHeight();
+      labels = new AnnotationLabels(av);
+    }
 
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+      hgap += av.charHeight;
 
-      pg.setColor(Color.white);
-      pg.fillRect(0, 0, pwidth, pheight);
-      pg.setFont(av.getFont());
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap
+        + annotationHeight;
 
-      ////////////////
-      // Draw the ids
-      pg.setColor(Color.black);
+    int idWidth = calculateIdWidth().width + 4;
 
-      pg.translate(0, -pi * pheight);
+    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
+        idWidth);
 
-      pg.setClip(0,pi*pheight,pwidth, pheight);
+    int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
 
-      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.setColor(Color.white);
+    pg.fillRect(0, 0, pwidth, pheight);
+    pg.setFont(av.getFont());
 
-          pg.drawString(string, 0,
-                        AlignmentUtil.getPixelHeight(0, i, av.charHeight) +
-                        ypos +
-                        av.charHeight - (av.charHeight / 5));
+    ////////////////
+    // Draw the ids
+    pg.setColor(Color.black);
 
-        }
+    pg.translate(0, -pi * pheight);
 
-        ypos += (av.alignment.getHeight() + 2) * av.charHeight;
+    pg.setClip(0, pi * pheight, pwidth, pheight);
 
-      }
-      while (ypos < totalHeight);
+    int ypos = hgap;
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                           av.getFont().getSize());
+    pg.setFont(italic);
 
-      pg.translate(idWidth, 0);
+    do
+    {
+      for (int i = 0; i < av.alignment.getHeight(); i++)
+      {
+        SequenceI s = av.alignment.getSequenceAt(i);
+        String string = s.getDisplayId( av.getShowJVSuffix());
 
-      seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+        pg.drawString(string, 0,
+                      ( (i * av.charHeight) + ypos + av.charHeight) -
+                      (av.charHeight / 5));
+      }
+      if (labels != null)
+      {
+        pg.translate(0,
+                     ypos +
+                     (av.getAlignment().getHeight() * av.charHeight));
+
+        pg.setFont(av.getFont());
+        labels.drawComponent(pg, idWidth);
+        pg.setFont(italic);
+        pg.translate(0,
+                     -ypos -
+                     (av.getAlignment().getHeight() * av.charHeight));
+      }
 
-      if (pi * pheight < totalHeight)
-        return Printable.PAGE_EXISTS;
-      else
-        return Printable.NO_SUCH_PAGE;
+      ypos += cHeight;
+    }
+    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;
+    }
+  }
 
-  public void makeEPS()
+  void makeAlignmentImage(int type, File file)
   {
-    int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
-    int width = seqPanel.getWidth() + idPanel.getWidth();
+    int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+    int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
 
-    if (!av.getWrapAlignment())
+    if (av.getWrapAlignment())
     {
-      height = (av.alignment.getHeight()+1) * av.charHeight + 30;
-      width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
+      height = getWrappedHeight();
+      width = seqPanel.getWidth() + idPanel.getWidth();
     }
-    if(av.getShowAnnotation())
-   {
-     height += annotationPanel.getPreferredSize().height;
-   }
-
-    try
+    else if (av.getShowAnnotation())
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from alignment");
-      chooser.setToolTipText("Save");
-
-      int value = chooser.showSaveDialog(this);
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-        return;
+      height += annotationPanel.adjustPanelHeight() + 3;
+    }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-      EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
+    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() );
 
-        if (av.getWrapAlignment())
-          printWrappedAlignment(pg, width, height, 0);
-        else
-          printUnwrapped(pg, width, height, 0);
+    try
+    {
+      if (av.getWrapAlignment())
+      {
+        if(im.getGraphics()!=null)
+          printWrappedAlignment(im.getGraphics(), width, height, 0);
+      }
+      else
+      {
+        if(im.getGraphics()!=null)
+          printUnwrapped(im.getGraphics(), width, height, 0);
+      }
 
+      im.writeImage();
+    }
+    catch (OutOfMemoryError err)
+    {
+      System.out.println("########################\n"
+                         + "OUT OF MEMORY " + file + "\n"
+                         + "########################");
+
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "Out of Memory Creating Image!!"
+                                            +
+                                            "\nSee help files for increasing Java Virtual Machine memory."
+                                            , "Out of memory",
+                                            JOptionPane.WARNING_MESSAGE);
+      System.out.println("Create IMAGE: " + err);
+      System.gc();
 
-        pg.flush();
-        pg.close();
     }
     catch (Exception ex)
     {
       ex.printStackTrace();
     }
   }
+  /**
+   * DOCUMENT ME!
+   */
+  public void makeEPS(File epsFile)
+  {
+    makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+  }
 
-  public void makePNG()
+  /**
+   * DOCUMENT ME!
+   */
+  public void makePNG(File pngFile)
   {
-      int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
-      int width = seqPanel.getWidth() + idPanel.getWidth();
+    makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+  }
 
-      if (!av.getWrapAlignment())
-      {
-        height = (av.alignment.getHeight()+1) * av.charHeight + 30;
-        width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
-      }
+  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();
 
-      if(av.getShowAnnotation())
+    // Gen image map
+    //////////////////////////////////
+    if (imgMapFile != null)
+    {
+      try
       {
-        height += annotationPanel.getPreferredSize().height;
-      }
-
+        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=\"#\">");
+            }
+          }
+        }
 
-    try
-    {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from alignment");
-      chooser.setToolTipText("Save");
+        out.println("</map></body></html>");
+        out.close();
 
-      int value = chooser.showSaveDialog(this);
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-        return;
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    } ///////////END OF IMAGE MAP
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+  }
 
-      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
-      Graphics2D png = (Graphics2D)bi.getGraphics();
+  int getWrappedHeight()
+  {
 
-      png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
+    int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
+        seqPanel.seqCanvas.getWidth());
 
-        if (av.getWrapAlignment())
-          printWrappedAlignment(png, width, height, 0);
-        else
-          printUnwrapped(png, width, height, 0);
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+      hgap += av.charHeight;
 
-        ImageIO.write(bi, "png", out);
-        out.close();
-    }
-    catch (Exception ex)
+    int annotationHeight = 0;
+    if (av.showAnnotation)
     {
-      ex.printStackTrace();
+      annotationHeight = annotationPanel.adjustPanelHeight();
     }
-  }
 
-}
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap
+        + annotationHeight;
 
-class Preview extends JFrame
-{
+    int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
 
-  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();
+    return height;
   }
-}
 
-class PreviewPanel extends JPanel
-{
-  Image image;
-  public PreviewPanel(Image image)
+  /**
+   * DOCUMENT ME!
+   *
+   * @author $author$
+   * @version $Revision$
+   */
+  class Preview
+      extends JFrame
   {
-    this.image = image;
+    /**
+     * 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();
+    }
   }
-  public void paintComponent(Graphics g)
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @author $author$
+   * @version $Revision$
+   */
+  class PreviewPanel
+      extends JPanel
   {
-    if(image!=null)
-      g.drawImage(image,0,0,this);
-    else
-      System.out.println("image is null");
+    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");
+      }
+    }
   }
 }
-
-
-
-