X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=364be5df454f5960a2744079f9e5c07ad3586ca7;hb=5a74e4957b86821f2fd0752d1d9bc46ebb3cfdc6;hp=068d605ba00d31b1772a21f3ea96e0f92d377e0b;hpb=71019ada6142e8a449dfcec0a9c87eb00efbefaf;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 068d605..364be5d 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -18,39 +18,53 @@
  */
 package jalview.gui;
 
-import java.io.*;
-import javax.imageio.*;
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.awt.image.*;
 import java.awt.print.*;
+
+import java.io.*;
+
 import javax.swing.*;
 
-import org.jibble.epsgraphics.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
 
-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;
   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 = false;
+  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;
@@ -67,9 +81,7 @@ public class AlignmentPanel
     annotationPanel = new AnnotationPanel(this);
     alabels = new AnnotationLabels(this);
 
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
-                                                 getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+
     annotationScroller.setViewportView(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
@@ -80,14 +92,27 @@ public class AlignmentPanel
 
     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()
+    af.addKeyListener(new KeyAdapter()
     {
       public void keyPressed(KeyEvent evt)
       {
+        if(av.cursorMode
+           && evt.getKeyCode()>=KeyEvent.VK_0
+           && evt.getKeyCode()<=KeyEvent.VK_9)
+        {
+          seqPanel.numberPressed(evt.getKeyChar());
+        }
+
         switch (evt.getKeyCode())
         {
           case 27: // escape key
@@ -97,19 +122,133 @@ public class AlignmentPanel
             break;
 
           case KeyEvent.VK_DOWN:
-            alignFrame.moveSelectedSequences(false);
-
+            if(av.cursorMode)
+            {
+              seqPanel.moveCursor(0,1);
+            }
+            else
+              alignFrame.moveSelectedSequences(false);
             break;
 
           case KeyEvent.VK_UP:
-            alignFrame.moveSelectedSequences(true);
+            if (av.cursorMode)
+            {
+              seqPanel.moveCursor(0,-1);
+            }
+            else
+              alignFrame.moveSelectedSequences(true);
+            break;
+
+          case KeyEvent.VK_LEFT:
+            if(av.cursorMode)
+            {
+              seqPanel.moveCursor(-1,0);
+            }
+            break;
 
+          case KeyEvent.VK_RIGHT:
+            if (av.cursorMode)
+            {
+              seqPanel.moveCursor(1,0);
+            }
             break;
+
+          case KeyEvent.VK_SPACE:
+            if(av.cursorMode)
+            {
+              seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown());
+            }
+            break;
+
+          case KeyEvent.VK_DELETE:
+          case KeyEvent.VK_BACK_SPACE:
+            if(!av.cursorMode)
+            {
+              alignFrame.cut_actionPerformed(null);
+              seqPanel.seqCanvas.repaint();
+            }
+            else
+              seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
+
+            break;
+
+          case KeyEvent.VK_S:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorRow();
+            }
+            break;
+          case KeyEvent.VK_C:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorColumn();
+            }
+            break;
+          case KeyEvent.VK_P:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorPosition();
+            }
+            break;
+
+          case KeyEvent.VK_ENTER:
+          case KeyEvent.VK_COMMA:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorRowAndColumn();
+            }
+            break;
+
+          case KeyEvent.VK_Q:
+            if(av.cursorMode)
+            {
+              seqPanel.setSelectionAreaAtCursor(true);
+            }
+            break;
+          case KeyEvent.VK_M:
+            if(av.cursorMode)
+            {
+              seqPanel.setSelectionAreaAtCursor(false);
+            }
+            break;
+
+         case KeyEvent.VK_F2:
+           av.cursorMode = ! av.cursorMode;
+           alignFrame.statusBar.setText("Keyboard editing mode is "+
+               (av.cursorMode ? "on" : "off"));
+           if(av.cursorMode)
+           {
+             seqPanel.seqCanvas.cursorX = av.startRes;
+             seqPanel.seqCanvas.cursorY = av.startSeq;
+           }
+           seqPanel.seqCanvas.repaint();
+           break;
+
+          case KeyEvent.VK_F1:
+            try
+            {
+              ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+              java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+              javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+              javax.help.HelpBroker hb = hs.createHelpBroker();
+              hb.setCurrentID("home");
+              hb.setDisplayed(true);
+            }
+            catch (Exception ex)
+            {
+              ex.printStackTrace();
+            }
+            break;
+
         }
       }
     });
   }
 
+  /**
+   * DOCUMENT ME!
+   */
   public void fontChanged()
   {
     // set idCanvas bufferedImage to null
@@ -122,27 +261,43 @@ public class AlignmentPanel
         av.charHeight + fm.getDescent()));
 
     idPanel.idCanvas.gg = null;
+    seqPanel.seqCanvas.img = null;
     annotationPanel.adjustPanelHeight();
 
     Dimension d = calculateIdWidth();
     d.setSize(d.width + 4, d.height);
     idPanel.idCanvas.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
+
+    if (av.getWrapAlignment())
+    {
+      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();
   }
 
-  Dimension calculateIdWidth()
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension calculateIdWidth()
   {
-    Graphics g = this.getGraphics();
+    Container c = new Container();
 
-    if (g == null)
-    {
-      javax.swing.JFrame f = new javax.swing.JFrame();
-      f.addNotify();
-      g = f.getGraphics();
-    }
-
-    FontMetrics fm = g.getFontMetrics(av.font);
+    FontMetrics fm = c.getFontMetrics(av.font);
     AlignmentI al = av.getAlignment();
 
     int i = 0;
@@ -153,14 +308,7 @@ public class AlignmentPanel
     {
       SequenceI s = al.getSequenceAt(i);
 
-      if (av.getShowFullId())
-      {
-        id = s.getDisplayId();
-      }
-      else
-      {
-        id = s.getName();
-      }
+      id = s.getDisplayId(av.getShowJVSuffix());
 
       if (fm.stringWidth(id) > idWidth)
       {
@@ -175,7 +323,7 @@ public class AlignmentPanel
 
     if (al.getAlignmentAnnotation() != null)
     {
-      fm = g.getFontMetrics(alabels.getFont());
+      fm = c.getFontMetrics(alabels.getFont());
 
       while (i < al.getAlignmentAnnotation().length)
       {
@@ -193,76 +341,108 @@ public class AlignmentPanel
     return new Dimension(idWidth, 12);
   }
 
-  public void highlightSearchResults(int[] results)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param results DOCUMENT ME!
+   */
+  public void highlightSearchResults(SearchResults results)
   {
     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;
+      SequenceI seq = results.getResultSequence(0);
+      int seqIndex = av.alignment.findIndex(seq);
+      int start = seq.findIndex(results.getResultStart(0)) - 1;
+      int end = seq.findIndex(results.getResultEnd(0)) - 1;
 
-      if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
-          ( (av.getStartSeq() > results[0]) ||
-           (av.getEndSeq() < results[0])))
+      if(!av.wrapAlignment)
+      {
+        if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
+           ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+        {
+          setScrollValues(start, seqIndex);
+        }
+      }
+      else
       {
-        setScrollValues(start, results[0]);
+        scrollToWrappedVisible(start);
       }
     }
   }
 
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+    if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
+
+  /**
+   * 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 (!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);
 
-    av.setShowAnnotation(!wrap);
-    annotationScroller.setVisible(!wrap);
-    annotationSpaceFillerHolder.setVisible(!wrap);
-    idSpaceFillerPanel1.setVisible(!wrap);
-
-    repaint();
-  }
-
-  public void setColourScheme()
-  {
-    ColourSchemeI cs = av.getGlobalColourScheme();
-
-    if (av.getConservationSelected())
+    if (wrap)
     {
-      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);
+      annotationScroller.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
+    else if (av.showAnnotation)
+    {
+      annotationScroller.setVisible(true);
+      annotationSpaceFillerHolder.setVisible(true);
     }
 
+    idSpaceFillerPanel1.setVisible(!wrap);
+
     repaint();
   }
 
@@ -295,9 +475,16 @@ public class AlignmentPanel
     return true;
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param right DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
   public boolean scrollRight(boolean right)
   {
-    if (right)
+    if (!right)
     {
       if (hscroll.getValue() < 1)
       {
@@ -323,32 +510,44 @@ public class AlignmentPanel
     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);
+
+    int width = av.alignment.getWidth();
+    int height = av.alignment.getHeight();
+
+    if(av.hasHiddenColumns)
+     width = av.getColumnSelection().findColumnPosition(width);
+
+    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
 
     hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
     vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
 
-    if (hextent > av.alignment.getWidth())
+    if (hextent > width)
     {
-      hextent = av.alignment.getWidth();
+      hextent = width;
     }
 
-    if (vextent > av.alignment.getHeight())
+    if (vextent > height)
     {
-      vextent = av.alignment.getHeight();
+      vextent = height;
     }
 
-    if ( (hextent + x) > av.getAlignment().getWidth())
+    if ( (hextent + x) > width)
     {
-      x = av.getAlignment().getWidth() - hextent;
+      x = width - hextent;
     }
 
-    if ( (vextent + y) > av.getAlignment().getHeight())
+    if ( (vextent + y) > height)
     {
-      y = av.getAlignment().getHeight() - vextent;
+      y = height - vextent;
     }
 
     if (y < 0)
@@ -361,10 +560,15 @@ public class AlignmentPanel
       x = 0;
     }
 
-    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
-    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
+    hscroll.setValues(x, hextent, 0, width);
+    vscroll.setValues(y, vextent, 0, height);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     int oldX = av.getStartRes();
@@ -402,25 +606,42 @@ public class AlignmentPanel
       overviewPanel.setBoxPosition();
     }
 
+    int scrollX = av.startRes - oldX;
+    int scrollY = av.startSeq - oldY;
+
     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())
+      // 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)
       {
-        annotationPanel.fastPaint(av.getStartRes() - oldX);
+        idPanel.idCanvas.fastPaint(scrollY);
+        seqPanel.seqCanvas.fastPaint(scrollX,
+                                     scrollY);
+        scalePanel.repaint();
+
+        if (av.getShowAnnotation())
+        {
+          annotationPanel.fastPaint(scrollX);
+        }
       }
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
   public void paintComponent(Graphics g)
   {
     invalidate();
@@ -433,7 +654,9 @@ public class AlignmentPanel
     if (av.getWrapAlignment())
     {
       int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
+
+
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);
@@ -442,8 +665,24 @@ public class AlignmentPanel
     {
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
+
+    if( this.getVisibleRect().getBounds() == g.getClipBounds()
+        && overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+
   }
 
+  /**
+   * 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
   {
@@ -462,6 +701,18 @@ public class AlignmentPanel
     }
   }
 
+  /**
+   * 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
   {
@@ -517,7 +768,7 @@ public class AlignmentPanel
 
     if (av.showAnnotation)
     {
-      pagesHigh += annotationPanel.getHeight();
+      pagesHigh += annotationPanel.adjustPanelHeight() + 3;
     }
 
     pagesHigh /= pheight;
@@ -537,6 +788,9 @@ public class AlignmentPanel
     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) &&
@@ -553,35 +807,30 @@ public class AlignmentPanel
       }
 
       pg.setColor(currentColor);
-      pg.fillRect(0,
-                  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
-          av.getCharHeight()), idWidth, av.getCharHeight());
+      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+                  av.getCharHeight());
 
       pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getName();
-
-      if (av.getShowFullId())
-      {
-        string = av.getAlignment().getSequenceAt(i).getDisplayId();
-      }
+      String string = av.getAlignment().getSequenceAt(i).getDisplayId
+          ( av.getShowJVSuffix());
 
       pg.drawString(string, 0,
-                    (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
-          av.getCharHeight()) + av.getCharHeight()) -
+                    ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
                     (av.getCharHeight() / 5));
     }
 
+    pg.setFont(av.getFont());
+
     // draw main sequence panel
     pg.translate(idWidth, 0);
-    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
-                                 startRes, startSeq, 0);
+    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
 
     if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
     {
-      pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
-      alabels.drawComponent( (Graphics2D) pg);
-      pg.translate(idWidth, 0);
+      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);
     }
@@ -589,17 +838,45 @@ public class AlignmentPanel
     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 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;
+
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap
+        + annotationHeight;
+
     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 totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
 
     pg.setColor(Color.white);
     pg.fillRect(0, 0, pwidth, pheight);
@@ -613,26 +890,37 @@ public class AlignmentPanel
 
     pg.setClip(0, pi * pheight, pwidth, pheight);
 
-    int ypos = 2 * av.charHeight;
+    int ypos = hgap;
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                           av.getFont().getSize());
+    pg.setFont(italic);
 
     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();
-        }
+        String string = s.getDisplayId( av.getShowJVSuffix());
 
         pg.drawString(string, 0,
-                      (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
-                       av.charHeight) - (av.charHeight / 5));
+                      ( (i * av.charHeight) + ypos + av.charHeight) -
+                      (av.charHeight / 5));
+      }
+      if (labels != null)
+      {
+        pg.translate(-3,
+                     ypos +
+                     (av.getAlignment().getHeight() * av.charHeight));
+
+        pg.setFont(av.getFont());
+        labels.drawComponent(pg, idWidth);
+        pg.setFont(italic);
+        pg.translate(+3,
+                     -ypos -
+                     (av.getAlignment().getHeight() * av.charHeight));
       }
 
-      ypos += ( (av.alignment.getHeight() + 2) * av.charHeight);
+      ypos += cHeight;
     }
     while (ypos < totalHeight);
 
@@ -643,6 +931,7 @@ public class AlignmentPanel
     if ( (pi * pheight) < totalHeight)
     {
       return Printable.PAGE_EXISTS;
+
     }
     else
     {
@@ -650,172 +939,307 @@ public class AlignmentPanel
     }
   }
 
-  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 (idPanel.getWidth() == 0)
     {
-      height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
-      width = idPanel.getWidth() +
-          (av.alignment.getWidth() * av.charWidth);
+      width += calculateIdWidth().getWidth() + 4;
     }
 
-    if (av.getShowAnnotation())
+    if (av.getWrapAlignment())
     {
-      height += annotationPanel.getPreferredSize().height;
+      height = getWrappedHeight();
+      width = seqPanel.getWidth() + idPanel.getWidth();
     }
-
-    try
+    else if (av.getShowAnnotation())
     {
-      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;
-      }
-
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+      height += annotationPanel.adjustPanelHeight() + 3;
+    }
 
-      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() );
 
+    try
+    {
       if (av.getWrapAlignment())
       {
-        printWrappedAlignment(pg, width, height, 0);
+        if(im.getGraphics()!=null)
+        {
+          printWrappedAlignment(im.getGraphics(), width, height, 0);
+          im.writeImage();
+        }
       }
       else
       {
-        printUnwrapped(pg, width, height, 0);
+        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();
     }
   }
-
-  public void makePNG()
+  /**
+   * DOCUMENT ME!
+   */
+  public void makeEPS(File epsFile)
   {
-    int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
-        av.chunkHeight;
-    int width = seqPanel.getWidth() + idPanel.getWidth();
+    makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+  }
 
-    if (!av.getWrapAlignment())
-    {
-      height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
-      width = idPanel.getWidth() +
-          (av.alignment.getWidth() * av.charWidth);
-    }
+  /**
+   * DOCUMENT ME!
+   */
+  public void makePNG(File pngFile)
+  {
+    makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+  }
 
-    if (av.getShowAnnotation())
-    {
-      height += annotationPanel.getPreferredSize().height;
-    }
+  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();
 
-    try
+    // Gen image map
+    //////////////////////////////////
+    if (imgMapFile != null)
     {
-      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);
+      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);
+          SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
+          SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+          for(res =0; res<alwidth; res++)
+          {
+            text = new StringBuffer();
+            Object obj = null;
+            if(av.alignment.isNucleotide())
+              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
+            else
+              obj = ResidueProperties.aa2Triplet.get(
+                    seq.getCharAt(res) + "");
+
+              if (obj == null)
+                  continue;
+
+            String triplet = obj.toString();
+            int alIndex = seq.findPosition(res);
+            gSize = groups.length;
+            for (g = 0; g < gSize; g++)
+            {
+              if(text.length()<1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
+                  + (idWidth + res * av.charWidth) + ","
+                  + sy + ","
+                  + (idWidth + (res + 1) * av.charWidth) + ","
+                  + (av.charHeight + sy) + "\""
+                  + " onMouseOver=\"toolTip('"
+                  + alIndex + " " + triplet );
+              }
+
+              if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
+                text.append("<br><em>" + groups[g].getName() + "</em>");
+            }
+
+            if (features != null)
+            {
+              if(text.length()<1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
+                  + (idWidth + res * av.charWidth) + ","
+                  + sy + ","
+                  + (idWidth + (res + 1) * av.charWidth) + ","
+                  + (av.charHeight + sy) + "\""
+                  + " onMouseOver=\"toolTip('"
+                  + alIndex + " " + triplet );
+              }
+                fSize = features.length;
+                for (f = 0; f < fSize; f++)
+                {
+
+                  if ( (features[f].getBegin() <= seq.findPosition(res)) &&
+                      (features[f].getEnd() >= seq.findPosition(res)))
+                  {
+                    if (features[f].getType().equals("disulfide bond"))
+                    {
+                      if (features[f].getBegin() == seq.findPosition(res)
+                          || features[f].getEnd() == seq.findPosition(res))
+                      {
+                        text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
+                                       features[f].getEnd());
+                      }
+                    }
+                    else
+                    {
+                      text.append("<br>");
+                      text.append(features[f].getType());
+                      if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
+                        text.append(" " + features[f].getDescription());
+
+                      if (features[f].getStatus() != null && features[f].getStatus().length()>0)
+                      {
+                        text.append(" (" + features[f].getStatus() + ")");
+                      }
+                    }
+                  }
+
+                }
+              }
+              if(text.length()>1)
+              {
+                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+                out.println(text.toString());
+              }
+            }
+          }
+        out.println("</map></body></html>");
+        out.close();
 
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      }
+      catch (Exception ex)
       {
-        return;
+        ex.printStackTrace();
       }
+    } ///////////END OF IMAGE MAP
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
-
-      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();
     }
-  }
-}
 
-class Preview
-    extends JFrame
-{
-  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();
-  }
-}
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap
+        + annotationHeight;
 
-class PreviewPanel
-    extends JPanel
-{
-  Image image;
+    int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
 
-  public PreviewPanel(Image image)
+    return height;
+  }
+
+  /**
+   * 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)
+    Image image;
+
+    /**
+     * Creates a new PreviewPanel object.
+     *
+     * @param image DOCUMENT ME!
+     */
+    public PreviewPanel(Image image)
     {
-      g.drawImage(image, 0, 0, this);
+      this.image = image;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      System.out.println("DEBUG:image is null");
+      if (image != null)
+      {
+        g.drawImage(image, 0, 0, this);
+      }
+      else
+      {
+        System.out.println("DEBUG:image is null");
+      }
     }
   }
 }