PNG and EPS in ImageMaker
authoramwaterhouse <Andrew Waterhouse>
Fri, 11 Nov 2005 18:17:29 +0000 (18:17 +0000)
committeramwaterhouse <Andrew Waterhouse>
Fri, 11 Nov 2005 18:17:29 +0000 (18:17 +0000)
src/MCview/PDBViewer.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/TreePanel.java
src/jalview/util/ImageMaker.java [new file with mode: 0755]

index 49c1b11..95d4b35 100755 (executable)
@@ -7,13 +7,6 @@ import jalview.gui.*;
 import jalview.io.EBIFetchClient;\r
 import java.awt.event.ActionListener;\r
 import java.awt.event.ActionEvent;\r
-import java.io.FileOutputStream;\r
-import org.jibble.epsgraphics.EpsGraphics2D;\r
-import javax.imageio.ImageIO;\r
-import java.awt.image.BufferedImage;\r
-import java.awt.Graphics;\r
-import java.awt.Graphics2D;\r
-import java.awt.RenderingHints;\r
 \r
 public class PDBViewer extends JInternalFrame implements Runnable\r
 {\r
@@ -41,11 +34,15 @@ public class PDBViewer extends JInternalFrame implements Runnable
     pdbcanvas = new PDBCanvas(seqcanvas, seq);\r
 \r
     setContentPane(pdbcanvas);\r
-    Desktop.addInternalFrame(this,\r
-                         sequence.getName() + ":" + pdb.getId()\r
-                         + " Method: " + pdb.getProperty().get("method")\r
-                         + " Chain:" + pdb.getProperty().get("chains"),\r
-                         400, 400);\r
+    StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());\r
+    if(pdb.getProperty()!=null)\r
+    {\r
+      title.append( " Method: " );\r
+      title.append(pdb.getProperty().get("method"));\r
+      title.append( " Chain:" );\r
+      title.append( pdb.getProperty().get("chains"));\r
+    }\r
+    Desktop.addInternalFrame(this,title.toString(),400, 400);\r
 \r
      Thread worker = new Thread(this);\r
      worker.start();\r
@@ -215,126 +212,52 @@ public class PDBViewer extends JInternalFrame implements Runnable
   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
   JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();\r
 \r
-  public void png_actionPerformed(ActionEvent e)\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  public void eps_actionPerformed(ActionEvent e)\r
   {\r
-    int width =  pdbcanvas.getWidth();\r
-    int height = pdbcanvas.getHeight();\r
-\r
-    try\r
-    {\r
-        jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
-                    "LAST_DIRECTORY"), new String[] { "png" },\r
-                new String[] { "Portable network graphics" },\r
-                "Portable network graphics");\r
-\r
-        chooser.setFileView(new jalview.io.JalviewFileView());\r
-        chooser.setDialogTitle("Create PNG Image of Molecule");\r
-        chooser.setToolTipText("Save");\r
-\r
-        int value = chooser.showSaveDialog(this);\r
-\r
-        if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
-        {\r
-            return;\r
-        }\r
-\r
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
-            chooser.getSelectedFile().getParent());\r
-\r
-        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
-\r
-        BufferedImage bi = new BufferedImage(width, height,\r
-                BufferedImage.TYPE_INT_RGB);\r
-        Graphics png = bi.getGraphics();\r
-        Graphics2D ig2 = (Graphics2D) png;\r
-        ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
-                                 RenderingHints.VALUE_ANTIALIAS_ON);\r
-\r
-\r
-        pdbcanvas.drawAll(png, width, height);\r
-\r
-        ImageIO.write(bi, "png", out);\r
-        out.close();\r
-    }\r
-    catch (Exception ex)\r
-    {\r
-        ex.printStackTrace();\r
-    }\r
+    makePDBImage(jalview.util.ImageMaker.EPS);\r
   }\r
 \r
-  public void eps_actionPerformed(ActionEvent e)\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  public void png_actionPerformed(ActionEvent e)\r
   {\r
-    boolean accurateText = true;\r
-\r
-    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
-        "Prompt each time");\r
-\r
-  // If we need to prompt, and if the GUI is visible then\r
-  // Prompt for EPS rendering style\r
-    if (renderStyle.equalsIgnoreCase("Prompt each time")\r
-        && !\r
-        (System.getProperty("java.awt.headless") != null\r
-         && System.getProperty("java.awt.headless").equals("true")))\r
-    {\r
-      EPSOptions eps = new EPSOptions();\r
-      renderStyle = eps.getValue();\r
-\r
-      if (renderStyle==null || eps.cancelled)\r
-        return;\r
-\r
+     makePDBImage(jalview.util.ImageMaker.PNG);\r
+  }\r
 \r
-    }\r
+  void makePDBImage(int type)\r
+  {\r
+    int width = pdbcanvas.getWidth();\r
+    int height = pdbcanvas.getHeight();\r
 \r
-    if (renderStyle.equalsIgnoreCase("text"))\r
+    jalview.util.ImageMaker im;\r
+\r
+    if (type == jalview.util.ImageMaker.PNG)\r
+      im = new jalview.util.ImageMaker(this,\r
+                                       jalview.util.ImageMaker.PNG,\r
+                                       "Make PNG image from view",\r
+                                       width, height,\r
+                                       null, null);\r
+    else\r
+      im = new jalview.util.ImageMaker(this,\r
+                                       jalview.util.ImageMaker.EPS,\r
+                                       "Make EPS file from view",\r
+                                       width, height,\r
+                                       null, this.getTitle());\r
+\r
+    if (im.getGraphics() != null)\r
     {\r
-      accurateText = false;\r
+      pdbcanvas.drawAll(im.getGraphics(), width, height);\r
+      im.writeImage();\r
     }\r
-\r
-      int width = getWidth();\r
-      int height = getHeight();\r
-\r
-      try\r
-      {\r
-          jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
-                      "LAST_DIRECTORY"), new String[] { "eps" },\r
-                  new String[] { "Encapsulated Postscript" },\r
-                  "Encapsulated Postscript");\r
-          chooser.setFileView(new jalview.io.JalviewFileView());\r
-          chooser.setDialogTitle("Create EPS file from tree");\r
-          chooser.setToolTipText("Save");\r
-\r
-          int value = chooser.showSaveDialog(this);\r
-\r
-          if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
-          {\r
-              return;\r
-          }\r
-\r
-          jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
-                                        chooser.getSelectedFile().getParent());\r
-\r
-          FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
-          EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
-                                               height);\r
-          Graphics2D ig2 = (Graphics2D) pg;\r
-          ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
-                         RenderingHints.VALUE_ANTIALIAS_ON);\r
-\r
-\r
-          pg.setAccurateTextMode(accurateText);\r
-\r
-          pdbcanvas.drawAll(pg, width, height);\r
-\r
-          pg.flush();\r
-          pg.close();\r
-      }\r
-      catch (Exception ex)\r
-      {\r
-          ex.printStackTrace();\r
-        }\r
-\r
   }\r
-\r
   public void charge_actionPerformed(ActionEvent e)\r
   {\r
     clearButtonGroup();\r
index fc4c688..ecdf741 100755 (executable)
@@ -24,17 +24,12 @@ import jalview.jbgui.*;
 \r
 import jalview.schemes.*;\r
 \r
-import org.jibble.epsgraphics.*;\r
-\r
 import java.awt.*;\r
 import java.awt.event.*;\r
-import java.awt.image.*;\r
 import java.awt.print.*;\r
 \r
 import java.io.*;\r
 \r
-import javax.imageio.*;\r
-\r
 import javax.swing.*;\r
 \r
 \r
@@ -47,1072 +42,939 @@ import javax.swing.*;
 public class AlignmentPanel extends GAlignmentPanel\r
     implements AdjustmentListener, Printable\r
 {\r
-    public AlignViewport av;\r
-    OverviewPanel overviewPanel;\r
-    SeqPanel seqPanel;\r
-    IdPanel idPanel;\r
-    IdwidthAdjuster idwidthAdjuster;\r
-\r
-    /** DOCUMENT ME!! */\r
-    public AlignFrame alignFrame;\r
-    ScalePanel scalePanel;\r
-    AnnotationPanel annotationPanel;\r
-    AnnotationLabels alabels;\r
-\r
-    // this value is set false when selection area being dragged\r
-    boolean fastPaint = true;\r
-    int hextent = 0;\r
-    int vextent = 0;\r
-\r
-    /**\r
-     * Creates a new AlignmentPanel object.\r
-     *\r
-     * @param af DOCUMENT ME!\r
-     * @param av DOCUMENT ME!\r
-     */\r
-    public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
+  public AlignViewport av;\r
+  OverviewPanel overviewPanel;\r
+  SeqPanel seqPanel;\r
+  IdPanel idPanel;\r
+  IdwidthAdjuster idwidthAdjuster;\r
+\r
+  /** DOCUMENT ME!! */\r
+  public AlignFrame alignFrame;\r
+  ScalePanel scalePanel;\r
+  AnnotationPanel annotationPanel;\r
+  AnnotationLabels alabels;\r
+\r
+  // this value is set false when selection area being dragged\r
+  boolean fastPaint = true;\r
+  int hextent = 0;\r
+  int vextent = 0;\r
+\r
+  /**\r
+   * Creates a new AlignmentPanel object.\r
+   *\r
+   * @param af DOCUMENT ME!\r
+   * @param av DOCUMENT ME!\r
+   */\r
+  public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
+  {\r
+    alignFrame = af;\r
+    this.av = av;\r
+    seqPanel = new SeqPanel(av, this);\r
+    idPanel = new IdPanel(av, this);\r
+\r
+    scalePanel = new ScalePanel(av, this);\r
+\r
+    idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
+    idwidthAdjuster = new IdwidthAdjuster(this);\r
+    idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
+\r
+    annotationPanel = new AnnotationPanel(this);\r
+    alabels = new AnnotationLabels(this);\r
+\r
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
+                                                 getPreferredSize());\r
+    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
+    annotationScroller.setViewportView(annotationPanel);\r
+    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
+\r
+    fontChanged();\r
+\r
+    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
+    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
+\r
+    setScrollValues(0, 0);\r
+\r
+    annotationPanel.adjustPanelHeight();\r
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
+                                                 getPreferredSize());\r
+    annotationScroller.setPreferredSize(annotationPanel.\r
+                                        getPreferredSize());\r
+    setAnnotationVisible(av.getShowAnnotation());\r
+\r
+    hscroll.addAdjustmentListener(this);\r
+    vscroll.addAdjustmentListener(this);\r
+\r
+    af.addKeyListener(new KeyAdapter()\r
     {\r
-        alignFrame = af;\r
-        this.av = av;\r
-        seqPanel = new SeqPanel(av, this);\r
-        idPanel = new IdPanel(av, this);\r
+      public void keyPressed(KeyEvent evt)\r
+      {\r
+        switch (evt.getKeyCode())\r
+        {\r
+          case 27: // escape key\r
+            av.setSelectionGroup(null);\r
+            repaint();\r
 \r
-        scalePanel = new ScalePanel(av, this);\r
+            break;\r
 \r
-        idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
-        idwidthAdjuster = new IdwidthAdjuster(this);\r
-        idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
+          case KeyEvent.VK_DOWN:\r
+            alignFrame.moveSelectedSequences(false);\r
 \r
-        annotationPanel = new AnnotationPanel(this);\r
-        alabels = new AnnotationLabels(this);\r
+            break;\r
 \r
-        annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());\r
-        annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
-        annotationScroller.setViewportView(annotationPanel);\r
-        annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
+          case KeyEvent.VK_UP:\r
+            alignFrame.moveSelectedSequences(true);\r
 \r
-        fontChanged();\r
+            break;\r
 \r
-        scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
-        seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
+          case KeyEvent.VK_BACK_SPACE:\r
+          case KeyEvent.VK_DELETE:\r
+            alignFrame.cut_actionPerformed(null);\r
+            break;\r
 \r
-        setScrollValues(0, 0);\r
+          case KeyEvent.VK_P:\r
+            seqPanel.seqCanvas.increaseAARatio();\r
+            break;\r
+          case KeyEvent.VK_L:\r
+            seqPanel.seqCanvas.decreaseAARation();\r
+            break;\r
+        }\r
+      }\r
+    });\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   */\r
+  public void fontChanged()\r
+  {\r
+    // set idCanvas bufferedImage to null\r
+    // to prevent drawing old image\r
+    FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+    scalePanelHolder.setPreferredSize(new Dimension(10,\r
+        av.charHeight + fm.getDescent()));\r
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10,\r
+        av.charHeight + fm.getDescent()));\r
+\r
+    idPanel.idCanvas.gg = null;\r
+    seqPanel.seqCanvas.img = null;\r
+    annotationPanel.adjustPanelHeight();\r
+\r
+    Dimension d = calculateIdWidth();\r
+    d.setSize(d.width + 4, d.height);\r
+    idPanel.idCanvas.setPreferredSize(d);\r
+    hscrollFillerPanel.setPreferredSize(d);\r
+\r
+    if (av.getWrapAlignment())\r
+    {\r
+      int max = av.alignment.getWidth() /\r
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+      vscroll.setMaximum(max);\r
+      vscroll.setUnitIncrement(1);\r
+      vscroll.setVisibleAmount(1);\r
+    }\r
+    else\r
+    {\r
+      setScrollValues(av.getStartRes(), av.getStartSeq());\r
+    }\r
 \r
-        annotationPanel.adjustPanelHeight();\r
-        annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());\r
-        annotationScroller.setPreferredSize(annotationPanel.\r
-                                            getPreferredSize());\r
-        setAnnotationVisible(av.getShowAnnotation());\r
+    if (overviewPanel != null)\r
+      overviewPanel.setBoxPosition();\r
 \r
+    repaint();\r
+  }\r
 \r
-        hscroll.addAdjustmentListener(this);\r
-        vscroll.addAdjustmentListener(this);\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
+  public Dimension calculateIdWidth()\r
+  {\r
+    Container c = new Container();\r
 \r
-        af.addKeyListener(new KeyAdapter()\r
-            {\r
-                public void keyPressed(KeyEvent evt)\r
-                {\r
-                    switch (evt.getKeyCode())\r
-                    {\r
-                    case 27: // escape key\r
-                        av.setSelectionGroup(null);\r
-                        repaint();\r
-\r
-                        break;\r
-\r
-                    case KeyEvent.VK_DOWN:\r
-                        alignFrame.moveSelectedSequences(false);\r
-\r
-                        break;\r
-\r
-                    case KeyEvent.VK_UP:\r
-                        alignFrame.moveSelectedSequences(true);\r
-\r
-                        break;\r
-\r
-                    case KeyEvent.VK_BACK_SPACE:\r
-                    case KeyEvent.VK_DELETE:\r
-                      alignFrame.cut_actionPerformed(null);\r
-                      break;\r
-\r
-                    case KeyEvent.VK_P:\r
-                      seqPanel.seqCanvas.increaseAARatio();\r
-                      break;\r
-                    case KeyEvent.VK_L:\r
-                      seqPanel.seqCanvas.decreaseAARation();\r
-                      break;\r
-                    }\r
-                }\r
-            });\r
-    }\r
+    FontMetrics fm = c.getFontMetrics(av.font);\r
+    AlignmentI al = av.getAlignment();\r
 \r
+    int i = 0;\r
+    int idWidth = 0;\r
+    String id;\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     */\r
-    public void fontChanged()\r
+    while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))\r
     {\r
-        // set idCanvas bufferedImage to null\r
-        // to prevent drawing old image\r
-        FontMetrics fm = getFontMetrics(av.getFont());\r
-\r
-        scalePanelHolder.setPreferredSize(new Dimension(10,\r
-                av.charHeight + fm.getDescent()));\r
-        idSpaceFillerPanel1.setPreferredSize(new Dimension(10,\r
-                av.charHeight + fm.getDescent()));\r
+      SequenceI s = al.getSequenceAt(i);\r
 \r
-        idPanel.idCanvas.gg = null;\r
-        seqPanel.seqCanvas.img = null;\r
-        annotationPanel.adjustPanelHeight();\r
-\r
-        Dimension d = calculateIdWidth();\r
-        d.setSize(d.width + 4, d.height);\r
-        idPanel.idCanvas.setPreferredSize(d);\r
-        hscrollFillerPanel.setPreferredSize(d);\r
-\r
-        if (av.getWrapAlignment())\r
-        {\r
-          int max = av.alignment.getWidth() /\r
-              seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
-          vscroll.setMaximum(max);\r
-          vscroll.setUnitIncrement(1);\r
-          vscroll.setVisibleAmount(1);\r
-        }\r
-        else\r
-        {\r
-          setScrollValues(av.getStartRes(), av.getStartSeq());\r
-        }\r
+      id = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
 \r
-        if(overviewPanel!=null)\r
-          overviewPanel.setBoxPosition();\r
+      if (fm.stringWidth(id) > idWidth)\r
+      {\r
+        idWidth = fm.stringWidth(id);\r
+      }\r
 \r
-        repaint();\r
+      i++;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public Dimension calculateIdWidth()\r
-    {\r
-      Container c = new Container();\r
+    // Also check annotation label widths\r
+    i = 0;\r
 \r
-        FontMetrics fm = c.getFontMetrics(av.font);\r
-        AlignmentI al = av.getAlignment();\r
+    if (al.getAlignmentAnnotation() != null)\r
+    {\r
+      fm = c.getFontMetrics(alabels.getFont());\r
 \r
-        int i = 0;\r
-        int idWidth = 0;\r
-        String id;\r
+      while (i < al.getAlignmentAnnotation().length)\r
+      {\r
+        String label = al.getAlignmentAnnotation()[i].label;\r
 \r
-        while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))\r
+        if (fm.stringWidth(label) > idWidth)\r
         {\r
-            SequenceI s = al.getSequenceAt(i);\r
-\r
-            id = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
-\r
-            if (fm.stringWidth(id) > idWidth)\r
-            {\r
-                idWidth = fm.stringWidth(id);\r
-            }\r
-\r
-            i++;\r
+          idWidth = fm.stringWidth(label);\r
         }\r
 \r
-        // Also check annotation label widths\r
-        i = 0;\r
-\r
-        if (al.getAlignmentAnnotation() != null)\r
-        {\r
-            fm = c.getFontMetrics(alabels.getFont());\r
+        i++;\r
+      }\r
+    }\r
 \r
-            while (i < al.getAlignmentAnnotation().length)\r
-            {\r
-                String label = al.getAlignmentAnnotation()[i].label;\r
+    return new Dimension(idWidth, 12);\r
+  }\r
 \r
-                if (fm.stringWidth(label) > idWidth)\r
-                {\r
-                    idWidth = fm.stringWidth(label);\r
-                }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param results DOCUMENT ME!\r
+   */\r
+  public void highlightSearchResults(int[] results)\r
+  {\r
+    seqPanel.seqCanvas.highlightSearchResults(results);\r
 \r
-                i++;\r
-            }\r
-        }\r
+    // do we need to scroll the panel?\r
+    if (results != null)\r
+    {\r
+      SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
+      int start = seq.findIndex(results[1]) - 1;\r
+      int end = seq.findIndex(results[2]) - 1;\r
 \r
-        return new Dimension(idWidth, 12);\r
+      if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||\r
+          ( (av.getStartSeq() > results[0]) ||\r
+           (av.getEndSeq() < results[0])))\r
+      {\r
+        setScrollValues(start, results[0]);\r
+      }\r
     }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param results DOCUMENT ME!\r
-     */\r
-    public void highlightSearchResults(int[] results)\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
+  public OverviewPanel getOverviewPanel()\r
+  {\r
+    return overviewPanel;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param op DOCUMENT ME!\r
+   */\r
+  public void setOverviewPanel(OverviewPanel op)\r
+  {\r
+    overviewPanel = op;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param b DOCUMENT ME!\r
+   */\r
+  public void setAnnotationVisible(boolean b)\r
+  {\r
+    if (!av.wrapAlignment)\r
     {\r
-        seqPanel.seqCanvas.highlightSearchResults(results);\r
-\r
-        // do we need to scroll the panel?\r
-        if (results != null)\r
-        {\r
-            SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
-            int start = seq.findIndex(results[1]) - 1;\r
-            int end = seq.findIndex(results[2]) - 1;\r
-\r
-            if ((av.getStartRes() > start) || (av.getEndRes() < end) ||\r
-                    ((av.getStartSeq() > results[0]) ||\r
-                    (av.getEndSeq() < results[0])))\r
-            {\r
-                setScrollValues(start, results[0]);\r
-            }\r
-        }\r
+      annotationSpaceFillerHolder.setVisible(b);\r
+      annotationScroller.setVisible(b);\r
     }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public OverviewPanel getOverviewPanel()\r
+    repaint();\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param wrap DOCUMENT ME!\r
+   */\r
+  public void setWrapAlignment(boolean wrap)\r
+  {\r
+    av.startSeq = 0;\r
+    scalePanelHolder.setVisible(!wrap);\r
+    hscroll.setVisible(!wrap);\r
+    idwidthAdjuster.setVisible(!wrap);\r
+\r
+    if (wrap)\r
     {\r
-        return overviewPanel;\r
+      annotationScroller.setVisible(false);\r
+      annotationSpaceFillerHolder.setVisible(false);\r
     }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param op DOCUMENT ME!\r
-     */\r
-    public void setOverviewPanel(OverviewPanel op)\r
+    else if (av.showAnnotation)\r
     {\r
-        overviewPanel = op;\r
+      annotationScroller.setVisible(true);\r
+      annotationSpaceFillerHolder.setVisible(true);\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param b DOCUMENT ME!\r
-     */\r
-    public void setAnnotationVisible(boolean b)\r
+    idSpaceFillerPanel1.setVisible(!wrap);\r
+\r
+    repaint();\r
+  }\r
+\r
+  // return value is true if the scroll is valid\r
+  public boolean scrollUp(boolean up)\r
+  {\r
+    if (up)\r
     {\r
-      if (!av.wrapAlignment)\r
+      if (vscroll.getValue() < 1)\r
       {\r
-        annotationSpaceFillerHolder.setVisible(b);\r
-        annotationScroller.setVisible(b);\r
+        return false;\r
       }\r
-      repaint();\r
-    }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param wrap DOCUMENT ME!\r
-     */\r
-    public void setWrapAlignment(boolean wrap)\r
-    {\r
-        av.startSeq = 0;\r
-        scalePanelHolder.setVisible(!wrap);\r
-        hscroll.setVisible(!wrap);\r
-        idwidthAdjuster.setVisible(!wrap);\r
-\r
-       if(wrap)\r
-       {\r
-         annotationScroller.setVisible(false);\r
-         annotationSpaceFillerHolder.setVisible(false);\r
-       }\r
-       else if(av.showAnnotation)\r
-       {\r
-         annotationScroller.setVisible(true);\r
-         annotationSpaceFillerHolder.setVisible(true);\r
-       }\r
-\r
-       idSpaceFillerPanel1.setVisible(!wrap);\r
-\r
-        repaint();\r
+      fastPaint = false;\r
+      vscroll.setValue(vscroll.getValue() - 1);\r
     }\r
-\r
-\r
-    // return value is true if the scroll is valid\r
-    public boolean scrollUp(boolean up)\r
+    else\r
     {\r
-        if (up)\r
-        {\r
-            if (vscroll.getValue() < 1)\r
-            {\r
-                return false;\r
-            }\r
-\r
-            fastPaint = false;\r
-            vscroll.setValue(vscroll.getValue() - 1);\r
-        }\r
-        else\r
-        {\r
-            if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())\r
-            {\r
-                return false;\r
-            }\r
-\r
-            fastPaint = false;\r
-            vscroll.setValue(vscroll.getValue() + 1);\r
-        }\r
-\r
-        fastPaint = true;\r
+      if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())\r
+      {\r
+        return false;\r
+      }\r
 \r
-        return true;\r
+      fastPaint = false;\r
+      vscroll.setValue(vscroll.getValue() + 1);\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param right DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public boolean scrollRight(boolean right)\r
+    fastPaint = true;\r
+\r
+    return true;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param right DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
+  public boolean scrollRight(boolean right)\r
+  {\r
+    if (right)\r
     {\r
-        if (right)\r
-        {\r
-            if (hscroll.getValue() < 1)\r
-            {\r
-                return false;\r
-            }\r
-\r
-            fastPaint = false;\r
-            hscroll.setValue(hscroll.getValue() - 1);\r
-        }\r
-        else\r
-        {\r
-            if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())\r
-            {\r
-                return false;\r
-            }\r
-\r
-            fastPaint = false;\r
-            hscroll.setValue(hscroll.getValue() + 1);\r
-        }\r
-\r
-        fastPaint = true;\r
+      if (hscroll.getValue() < 1)\r
+      {\r
+        return false;\r
+      }\r
 \r
-        return true;\r
+      fastPaint = false;\r
+      hscroll.setValue(hscroll.getValue() - 1);\r
     }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param x DOCUMENT ME!\r
-     * @param y DOCUMENT ME!\r
-     */\r
-    public void setScrollValues(int x, int y)\r
+    else\r
     {\r
-        av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -\r
-            1);\r
-\r
-        hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
-        vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;\r
-\r
-        if (hextent > av.alignment.getWidth())\r
-        {\r
-            hextent = av.alignment.getWidth();\r
-        }\r
+      if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())\r
+      {\r
+        return false;\r
+      }\r
 \r
-        if (vextent > av.alignment.getHeight())\r
-        {\r
-            vextent = av.alignment.getHeight();\r
-        }\r
+      fastPaint = false;\r
+      hscroll.setValue(hscroll.getValue() + 1);\r
+    }\r
 \r
-        if ((hextent + x) > av.getAlignment().getWidth())\r
-        {\r
-            x = av.getAlignment().getWidth() - hextent;\r
-        }\r
+    fastPaint = true;\r
 \r
-        if ((vextent + y) > av.getAlignment().getHeight())\r
-        {\r
-            y = av.getAlignment().getHeight() - vextent;\r
-        }\r
+    return true;\r
+  }\r
 \r
-        if (y < 0)\r
-        {\r
-            y = 0;\r
-        }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param x DOCUMENT ME!\r
+   * @param y DOCUMENT ME!\r
+   */\r
+  public void setScrollValues(int x, int y)\r
+  {\r
+    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -\r
+                 1);\r
 \r
-        if (x < 0)\r
-        {\r
-            x = 0;\r
-        }\r
+    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
+    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;\r
 \r
-        hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
-        vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
+    if (hextent > av.alignment.getWidth())\r
+    {\r
+      hextent = av.alignment.getWidth();\r
     }\r
 \r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param evt DOCUMENT ME!\r
-     */\r
-    public void adjustmentValueChanged(AdjustmentEvent evt)\r
+    if (vextent > av.alignment.getHeight())\r
     {\r
-\r
-        int oldX = av.getStartRes();\r
-        int oldY = av.getStartSeq();\r
-\r
-        if (evt.getSource() == hscroll)\r
-        {\r
-            int x = hscroll.getValue();\r
-            av.setStartRes(x);\r
-            av.setEndRes((x +\r
-                (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);\r
-        }\r
-\r
-        if (evt.getSource() == vscroll)\r
-        {\r
-            int offy = vscroll.getValue();\r
-\r
-            if (av.getWrapAlignment())\r
-            {\r
-                int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
-                av.setStartRes(vscroll.getValue() * rowSize);\r
-                av.setEndRes((vscroll.getValue() + 1) * rowSize);\r
-            }\r
-            else\r
-            {\r
-                av.setStartSeq(offy);\r
-                av.setEndSeq(offy +\r
-                    (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));\r
-            }\r
-        }\r
-\r
-        if (overviewPanel != null)\r
-        {\r
-            overviewPanel.setBoxPosition();\r
-        }\r
-\r
-        int xShift = av.getStartRes() - oldX;\r
-        int yShift = av.getStartSeq() - oldY;\r
-\r
-        if ( (xShift != 0 && yShift != 0) ||\r
-            (Math.abs(xShift) > av.getEndRes() - av.getStartRes()\r
-             || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())\r
-             || av.getWrapAlignment()\r
-             || !fastPaint)\r
-        {\r
-          // Either no shift at all, or shift greater than visible amount\r
-          repaint();\r
-        }\r
-        else\r
-        {\r
-            idPanel.idCanvas.fastPaint(yShift);\r
-            seqPanel.seqCanvas.fastPaint(xShift, yShift);\r
-\r
-            scalePanel.repaint();\r
-\r
-            if (av.getShowAnnotation())\r
-            {\r
-                annotationPanel.fastPaint(xShift);\r
-            }\r
-        }\r
+      vextent = av.alignment.getHeight();\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param g DOCUMENT ME!\r
-     */\r
-    public void paintComponent(Graphics g)\r
+    if ( (hextent + x) > av.getAlignment().getWidth())\r
     {\r
-        invalidate();\r
-\r
-        Dimension d = idPanel.idCanvas.getPreferredSize();\r
-        idPanelHolder.setPreferredSize(d);\r
-        hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
-        validate();\r
-\r
-        if (av.getWrapAlignment())\r
-        {\r
-            int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
-            vscroll.setMaximum(max);\r
-            vscroll.setUnitIncrement(1);\r
-            vscroll.setVisibleAmount(1);\r
-        }\r
-        else\r
-        {\r
-            setScrollValues(av.getStartRes(), av.getStartSeq());\r
-        }\r
+      x = av.getAlignment().getWidth() - hextent;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param pg DOCUMENT ME!\r
-     * @param pf DOCUMENT ME!\r
-     * @param pi DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     *\r
-     * @throws PrinterException DOCUMENT ME!\r
-     */\r
-    public int print(Graphics pg, PageFormat pf, int pi)\r
-        throws PrinterException\r
+    if ( (vextent + y) > av.getAlignment().getHeight())\r
     {\r
-        pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());\r
-\r
-        int pwidth = (int) pf.getImageableWidth();\r
-        int pheight = (int) pf.getImageableHeight();\r
-\r
-        if (av.getWrapAlignment())\r
-        {\r
-            return printWrappedAlignment(pg, pwidth, pheight, pi);\r
-        }\r
-        else\r
-        {\r
-            return printUnwrapped(pg, pwidth, pheight, pi);\r
-        }\r
+      y = av.getAlignment().getHeight() - vextent;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param pg DOCUMENT ME!\r
-     * @param pwidth DOCUMENT ME!\r
-     * @param pheight DOCUMENT ME!\r
-     * @param pi DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     *\r
-     * @throws PrinterException DOCUMENT ME!\r
-     */\r
-    public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
-        throws PrinterException\r
+    if (y < 0)\r
     {\r
-        int idWidth = calculateIdWidth().width + 4;\r
-        FontMetrics fm = getFontMetrics(av.getFont());\r
-        int scaleHeight = av.charHeight + fm.getDescent();\r
-\r
-        pg.setColor(Color.white);\r
-        pg.fillRect(0, 0, pwidth, pheight);\r
-        pg.setFont(av.getFont());\r
-\r
-        ////////////////////////////////////\r
-        /// How many sequences and residues can we fit on a printable page?\r
-        int totalRes = (pwidth - idWidth) / av.getCharWidth();\r
-\r
-        int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -\r
-            1;\r
-\r
-        int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;\r
-\r
-        /////////////////////////////\r
-        /// Only print these sequences and residues on this page\r
-        int startRes;\r
+      y = 0;\r
+    }\r
 \r
-        /////////////////////////////\r
-        /// Only print these sequences and residues on this page\r
-        int endRes;\r
+    if (x < 0)\r
+    {\r
+      x = 0;\r
+    }\r
 \r
-        /////////////////////////////\r
-        /// Only print these sequences and residues on this page\r
-        int startSeq;\r
+    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
+    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
+  }\r
 \r
-        /////////////////////////////\r
-        /// Only print these sequences and residues on this page\r
-        int endSeq;\r
-        startRes = (pi % pagesWide) * totalRes;\r
-        endRes = (startRes + totalRes) - 1;\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param evt DOCUMENT ME!\r
+   */\r
+  public void adjustmentValueChanged(AdjustmentEvent evt)\r
+  {\r
 \r
-        if (endRes > (av.getAlignment().getWidth() - 1))\r
-        {\r
-            endRes = av.getAlignment().getWidth() - 1;\r
-        }\r
+    int oldX = av.getStartRes();\r
+    int oldY = av.getStartSeq();\r
 \r
-        startSeq = (pi / pagesWide) * totalSeq;\r
-        endSeq = startSeq + totalSeq;\r
+    if (evt.getSource() == hscroll)\r
+    {\r
+      int x = hscroll.getValue();\r
+      av.setStartRes(x);\r
+      av.setEndRes( (x +\r
+                     (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);\r
+    }\r
 \r
-        if (endSeq > av.getAlignment().getHeight())\r
-        {\r
-            endSeq = av.getAlignment().getHeight();\r
-        }\r
+    if (evt.getSource() == vscroll)\r
+    {\r
+      int offy = vscroll.getValue();\r
 \r
-        int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;\r
+      if (av.getWrapAlignment())\r
+      {\r
+        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+            seqCanvas.getWidth());\r
+        av.setStartRes(vscroll.getValue() * rowSize);\r
+        av.setEndRes( (vscroll.getValue() + 1) * rowSize);\r
+      }\r
+      else\r
+      {\r
+        av.setStartSeq(offy);\r
+        av.setEndSeq(offy +\r
+                     (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));\r
+      }\r
+    }\r
 \r
-        if (av.showAnnotation)\r
-        {\r
-            pagesHigh += annotationPanel.adjustPanelHeight()+3;\r
-        }\r
+    if (overviewPanel != null)\r
+    {\r
+      overviewPanel.setBoxPosition();\r
+    }\r
 \r
-        pagesHigh /= pheight;\r
+    int xShift = av.getStartRes() - oldX;\r
+    int yShift = av.getStartSeq() - oldY;\r
 \r
-        if (pi >= (pagesWide * pagesHigh))\r
-        {\r
-            return Printable.NO_SUCH_PAGE;\r
-        }\r
+    if ( (xShift != 0 && yShift != 0) ||\r
+        (Math.abs(xShift) > av.getEndRes() - av.getStartRes()\r
+         || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())\r
+        || av.getWrapAlignment()\r
+        || !fastPaint)\r
+    {\r
+      // Either no shift at all, or shift greater than visible amount\r
+      repaint();\r
+    }\r
+    else\r
+    {\r
+      idPanel.idCanvas.fastPaint(yShift);\r
+      seqPanel.seqCanvas.fastPaint(xShift, yShift);\r
 \r
-        //draw Scale\r
-        pg.translate(idWidth, 0);\r
-        scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
-        pg.translate(-idWidth, scaleHeight);\r
+      scalePanel.repaint();\r
 \r
-        ////////////////\r
-        // Draw the ids\r
-        Color currentColor = null;\r
-        Color currentTextColor = null;\r
+      if (av.getShowAnnotation())\r
+      {\r
+        annotationPanel.fastPaint(xShift);\r
+      }\r
+    }\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param g DOCUMENT ME!\r
+   */\r
+  public void paintComponent(Graphics g)\r
+  {\r
+    invalidate();\r
+\r
+    Dimension d = idPanel.idCanvas.getPreferredSize();\r
+    idPanelHolder.setPreferredSize(d);\r
+    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
+    validate();\r
+\r
+    if (av.getWrapAlignment())\r
+    {\r
+      int max = av.alignment.getWidth() /\r
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+      vscroll.setMaximum(max);\r
+      vscroll.setUnitIncrement(1);\r
+      vscroll.setVisibleAmount(1);\r
+    }\r
+    else\r
+    {\r
+      setScrollValues(av.getStartRes(), av.getStartSeq());\r
+    }\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param pg DOCUMENT ME!\r
+   * @param pf DOCUMENT ME!\r
+   * @param pi DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   *\r
+   * @throws PrinterException DOCUMENT ME!\r
+   */\r
+  public int print(Graphics pg, PageFormat pf, int pi)\r
+      throws PrinterException\r
+  {\r
+    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());\r
+\r
+    int pwidth = (int) pf.getImageableWidth();\r
+    int pheight = (int) pf.getImageableHeight();\r
+\r
+    if (av.getWrapAlignment())\r
+    {\r
+      return printWrappedAlignment(pg, pwidth, pheight, pi);\r
+    }\r
+    else\r
+    {\r
+      return printUnwrapped(pg, pwidth, pheight, pi);\r
+    }\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param pg DOCUMENT ME!\r
+   * @param pwidth DOCUMENT ME!\r
+   * @param pheight DOCUMENT ME!\r
+   * @param pi DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   *\r
+   * @throws PrinterException DOCUMENT ME!\r
+   */\r
+  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
+      throws PrinterException\r
+  {\r
+    int idWidth = calculateIdWidth().width + 4;\r
+    FontMetrics fm = getFontMetrics(av.getFont());\r
+    int scaleHeight = av.charHeight + fm.getDescent();\r
+\r
+    pg.setColor(Color.white);\r
+    pg.fillRect(0, 0, pwidth, pheight);\r
+    pg.setFont(av.getFont());\r
+\r
+    ////////////////////////////////////\r
+    /// How many sequences and residues can we fit on a printable page?\r
+    int totalRes = (pwidth - idWidth) / av.getCharWidth();\r
+\r
+    int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -\r
+        1;\r
+\r
+    int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;\r
+\r
+    /////////////////////////////\r
+    /// Only print these sequences and residues on this page\r
+    int startRes;\r
+\r
+    /////////////////////////////\r
+    /// Only print these sequences and residues on this page\r
+    int endRes;\r
+\r
+    /////////////////////////////\r
+    /// Only print these sequences and residues on this page\r
+    int startSeq;\r
+\r
+    /////////////////////////////\r
+    /// Only print these sequences and residues on this page\r
+    int endSeq;\r
+    startRes = (pi % pagesWide) * totalRes;\r
+    endRes = (startRes + totalRes) - 1;\r
+\r
+    if (endRes > (av.getAlignment().getWidth() - 1))\r
+    {\r
+      endRes = av.getAlignment().getWidth() - 1;\r
+    }\r
 \r
-        for (int i = startSeq; i < endSeq; i++)\r
-        {\r
-            if ((av.getSelectionGroup() != null) &&\r
-                    av.getSelectionGroup().sequences.contains(\r
-                        av.getAlignment().getSequenceAt(i)))\r
-            {\r
-                currentColor = Color.gray;\r
-                currentTextColor = Color.black;\r
-            }\r
-            else\r
-            {\r
-                currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
-                currentTextColor = Color.black;\r
-            }\r
+    startSeq = (pi / pagesWide) * totalSeq;\r
+    endSeq = startSeq + totalSeq;\r
 \r
-            pg.setColor(currentColor);\r
-            pg.fillRect(0, (i-startSeq) * av.charHeight, idWidth,\r
-                av.getCharHeight());\r
+    if (endSeq > av.getAlignment().getHeight())\r
+    {\r
+      endSeq = av.getAlignment().getHeight();\r
+    }\r
 \r
-            pg.setColor(currentTextColor);\r
+    int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;\r
 \r
-            String string = av.getAlignment().getSequenceAt(i).getDisplayId\r
-                (av.getShowDBPrefix(), av.getShowJVSuffix());\r
+    if (av.showAnnotation)\r
+    {\r
+      pagesHigh += annotationPanel.adjustPanelHeight() + 3;\r
+    }\r
 \r
-            pg.drawString(string, 0,\r
-                (((i-startSeq) * av.charHeight) + av.getCharHeight()) -\r
-                (av.getCharHeight() / 5));\r
-        }\r
+    pagesHigh /= pheight;\r
 \r
-        // draw main sequence panel\r
-        pg.translate(idWidth, 0);\r
-        seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
-            startRes, startSeq, 0);\r
+    if (pi >= (pagesWide * pagesHigh))\r
+    {\r
+      return Printable.NO_SUCH_PAGE;\r
+    }\r
 \r
-        if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
-        {\r
-            pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight +3);\r
-            alabels.drawComponent((Graphics2D) pg, idWidth);\r
-            pg.translate(idWidth, 0);\r
-            annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +\r
-                1);\r
-        }\r
+    //draw Scale\r
+    pg.translate(idWidth, 0);\r
+    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
+    pg.translate( -idWidth, scaleHeight);\r
 \r
-        return Printable.PAGE_EXISTS;\r
-    }\r
+    ////////////////\r
+    // Draw the ids\r
+    Color currentColor = null;\r
+    Color currentTextColor = null;\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param pg DOCUMENT ME!\r
-     * @param pwidth DOCUMENT ME!\r
-     * @param pheight DOCUMENT ME!\r
-     * @param pi DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     *\r
-     * @throws PrinterException DOCUMENT ME!\r
-     */\r
-    public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
-        int pi) throws PrinterException\r
+    for (int i = startSeq; i < endSeq; i++)\r
     {\r
-\r
-      int annotationHeight = 0;\r
-      AnnotationLabels labels = null;\r
-      if (av.showAnnotation)\r
+      if ( (av.getSelectionGroup() != null) &&\r
+          av.getSelectionGroup().sequences.contains(\r
+              av.getAlignment().getSequenceAt(i)))\r
       {\r
-        annotationHeight = annotationPanel.adjustPanelHeight();\r
-        labels = new AnnotationLabels(av);\r
+        currentColor = Color.gray;\r
+        currentTextColor = Color.black;\r
+      }\r
+      else\r
+      {\r
+        currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
+        currentTextColor = Color.black;\r
       }\r
 \r
-      int hgap = av.charHeight;\r
-      if (av.scaleAboveWrapped)\r
-        hgap += av.charHeight;\r
-\r
-      int cHeight = av.getAlignment().getHeight() * av.charHeight\r
-          + hgap\r
-          + annotationHeight;\r
-\r
-\r
-      int idWidth = calculateIdWidth().width + 4;\r
+      pg.setColor(currentColor);\r
+      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,\r
+                  av.getCharHeight());\r
 \r
-        int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
-                idWidth);\r
+      pg.setColor(currentTextColor);\r
 \r
-        int totalHeight = cHeight * (av.alignment.getWidth() / resWidth +1);\r
+      String string = av.getAlignment().getSequenceAt(i).getDisplayId\r
+          (av.getShowDBPrefix(), av.getShowJVSuffix());\r
 \r
-        pg.setColor(Color.white);\r
-        pg.fillRect(0, 0, pwidth, pheight);\r
-        pg.setFont(av.getFont());\r
+      pg.drawString(string, 0,\r
+                    ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -\r
+                    (av.getCharHeight() / 5));\r
+    }\r
 \r
+    // draw main sequence panel\r
+    pg.translate(idWidth, 0);\r
+    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
+                                 startRes, startSeq, 0);\r
 \r
-        ////////////////\r
-        // Draw the ids\r
-        pg.setColor(Color.black);\r
+    if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
+    {\r
+      pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight + 3);\r
+      alabels.drawComponent( (Graphics2D) pg, idWidth);\r
+      pg.translate(idWidth, 0);\r
+      annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
+                                    1);\r
+    }\r
 \r
-        pg.translate(0, -pi * pheight);\r
+    return Printable.PAGE_EXISTS;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param pg DOCUMENT ME!\r
+   * @param pwidth DOCUMENT ME!\r
+   * @param pheight DOCUMENT ME!\r
+   * @param pi DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   *\r
+   * @throws PrinterException DOCUMENT ME!\r
+   */\r
+  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
+                                   int pi)\r
+      throws PrinterException\r
+  {\r
+\r
+    int annotationHeight = 0;\r
+    AnnotationLabels labels = null;\r
+    if (av.showAnnotation)\r
+    {\r
+      annotationHeight = annotationPanel.adjustPanelHeight();\r
+      labels = new AnnotationLabels(av);\r
+    }\r
 \r
-        pg.setClip(0, pi * pheight, pwidth, pheight);\r
+    int hgap = av.charHeight;\r
+    if (av.scaleAboveWrapped)\r
+      hgap += av.charHeight;\r
 \r
-        int ypos = hgap;\r
-        Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
-                             av.getFont().getSize());\r
-        pg.setFont(italic);\r
+    int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+        + hgap\r
+        + annotationHeight;\r
 \r
+    int idWidth = calculateIdWidth().width + 4;\r
 \r
-        do\r
-        {\r
-          for (int i = 0; i < av.alignment.getHeight(); i++)\r
-          {\r
-            SequenceI s = av.alignment.getSequenceAt(i);\r
-            String string = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
+    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
+        idWidth);\r
 \r
-            pg.drawString(string, 0,\r
-                          ( (i * av.charHeight) + ypos + av.charHeight) -\r
-                          (av.charHeight / 5));\r
-          }\r
-            if (labels != null)\r
-            {\r
-              pg.translate(0,\r
-                           ypos +\r
-                           (av.getAlignment().getHeight() * av.charHeight));\r
-\r
-              pg.setFont(av.getFont());\r
-              labels.drawComponent( pg, idWidth );\r
-              pg.setFont(italic);\r
-              pg.translate(0,\r
-                           -ypos -\r
-                           (av.getAlignment().getHeight() * av.charHeight));\r
-            }\r
+    int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);\r
 \r
-            ypos += cHeight;\r
-        }\r
-        while (ypos < totalHeight);\r
+    pg.setColor(Color.white);\r
+    pg.fillRect(0, 0, pwidth, pheight);\r
+    pg.setFont(av.getFont());\r
 \r
-        pg.translate(idWidth, 0);\r
+    ////////////////\r
+    // Draw the ids\r
+    pg.setColor(Color.black);\r
 \r
-        seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
+    pg.translate(0, -pi * pheight);\r
 \r
-        if ((pi * pheight) < totalHeight)\r
-        {\r
-            return Printable.PAGE_EXISTS;\r
+    pg.setClip(0, pi * pheight, pwidth, pheight);\r
 \r
-        }\r
-     else\r
-        {\r
-            return Printable.NO_SUCH_PAGE;\r
-        }\r
-    }\r
+    int ypos = hgap;\r
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+                           av.getFont().getSize());\r
+    pg.setFont(italic);\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     */\r
-    public void makeEPS(File epsFile)\r
+    do\r
     {\r
-      boolean accurateText = true;\r
-\r
-      String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
-          "Prompt each time");\r
-\r
-      // If we need to prompt, and if the GUI is visible then\r
-      // Prompt for EPS rendering style\r
-      if (renderStyle.equalsIgnoreCase("Prompt each time")\r
-          && !\r
-          (System.getProperty("java.awt.headless") != null\r
-           && System.getProperty("java.awt.headless").equals("true")))\r
+      for (int i = 0; i < av.alignment.getHeight(); i++)\r
       {\r
-        EPSOptions eps = new EPSOptions();\r
-        renderStyle = eps.getValue();\r
+        SequenceI s = av.alignment.getSequenceAt(i);\r
+        String string = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
 \r
-        if(eps.cancelled || renderStyle==null)\r
-          return;\r
-\r
-        renderStyle = eps.getValue();\r
+        pg.drawString(string, 0,\r
+                      ( (i * av.charHeight) + ypos + av.charHeight) -\r
+                      (av.charHeight / 5));\r
       }\r
-\r
-      if (renderStyle.equalsIgnoreCase("text"))\r
+      if (labels != null)\r
       {\r
-        accurateText = false;\r
-      }\r
-\r
-\r
-        if(epsFile == null)\r
-        {\r
-          jalview.io.JalviewFileChooser chooser = new jalview.io.\r
-              JalviewFileChooser(jalview.bin.Cache.getProperty(\r
-                  "LAST_DIRECTORY"), new String[]\r
-                                 {"eps"},\r
-                                 new String[]\r
-                                 {"Encapsulated Postscript"},\r
-                                 "Encapsulated Postscript");\r
-          chooser.setFileView(new jalview.io.JalviewFileView());\r
-          chooser.setDialogTitle("Create EPS file from alignment");\r
-          chooser.setToolTipText("Save");\r
-\r
-          int value = chooser.showSaveDialog(this);\r
-\r
-          if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
-          {\r
-            return;\r
-          }\r
-\r
-          epsFile = chooser.getSelectedFile();\r
-\r
-          jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
-                                        chooser.getSelectedFile().getParent());\r
-        }\r
-\r
-\r
-        int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
-        int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
+        pg.translate(0,\r
+                     ypos +\r
+                     (av.getAlignment().getHeight() * av.charHeight));\r
 \r
+        pg.setFont(av.getFont());\r
+        labels.drawComponent(pg, idWidth);\r
+        pg.setFont(italic);\r
+        pg.translate(0,\r
+                     -ypos -\r
+                     (av.getAlignment().getHeight() * av.charHeight));\r
+      }\r
 \r
-        if (av.getWrapAlignment())\r
-        {\r
-          height = getWrappedHeight();\r
-          width = seqPanel.getWidth() + idPanel.getWidth();\r
-        }\r
-        else if (av.getShowAnnotation())\r
-        {\r
-          height += annotationPanel.adjustPanelHeight()+3;\r
-        }\r
-\r
+      ypos += cHeight;\r
+    }\r
+    while (ypos < totalHeight);\r
 \r
-        try\r
-         {\r
-           FileOutputStream out = new FileOutputStream(epsFile);\r
-           EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,\r
-                                                height);\r
+    pg.translate(idWidth, 0);\r
 \r
-           pg.setAccurateTextMode(accurateText);\r
+    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
 \r
-           if (av.getWrapAlignment())\r
-           {\r
-                printWrappedAlignment(pg, width, height, 0);\r
-            }\r
-            else\r
-            {\r
-                printUnwrapped(pg, width, height, 0);\r
-            }\r
+    if ( (pi * pheight) < totalHeight)\r
+    {\r
+      return Printable.PAGE_EXISTS;\r
 \r
-            pg.flush();\r
-            pg.close();\r
-          }\r
-          catch (OutOfMemoryError err)\r
-          {\r
-            System.out.println("########################\n"\r
-                               + "OUT OF MEMORY " + epsFile + "\n"\r
-                               + "########################");\r
-\r
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-                                                  "Out of memory creating EPS file!!"\r
-                                                  +\r
-                                                  "\nSee help files for increasing Java Virtual Machine memory."\r
-                                                  , "Out of memory",\r
-                                                  JOptionPane.WARNING_MESSAGE);\r
-            System.out.println("Create EPS: " + err);\r
-            System.gc();\r
-          }\r
-        catch (Exception ex)\r
-        {\r
-            ex.printStackTrace();\r
-        }\r
     }\r
+    else\r
+    {\r
+      return Printable.NO_SUCH_PAGE;\r
+    }\r
+  }\r
 \r
+  void makeAlignmentImage(int type, File file)\r
+  {\r
+    int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+    int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
 \r
-    public void makePNGImageMap(File imgMapFile, String imageName)\r
+    if (av.getWrapAlignment())\r
     {\r
-      ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS\r
-      //////////////////////////////////////////////\r
-      int idWidth = calculateIdWidth().width + 4;\r
-      FontMetrics fm = getFontMetrics(av.getFont());\r
-      int scaleHeight = av.charHeight + fm.getDescent();\r
-\r
-        // Gen image map\r
-         //////////////////////////////////\r
-         if(imgMapFile!=null)\r
-         {\r
-           try\r
-           {\r
-             PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));\r
-             out.println(jalview.io.HTMLOutput.getImageMapHTML());\r
-             out.println("<img src=\"" + imageName +\r
-                       "\" border=\"0\" usemap=\"#Map\" >"\r
-                       +"<map name=\"Map\">");\r
-\r
-             for (int s = 0; s < av.alignment.getHeight(); s++)\r
-             {\r
-               SequenceI seq = av.alignment.getSequenceAt(s);\r
-               SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
-               for (int i = 0; i < groups.length; i++)\r
-               {\r
-                 int sy = s * av.charHeight + scaleHeight;\r
-                 for (int res = groups[i].getStartRes();\r
-                      res < groups[i].getEndRes() + 1; res++)\r
-                 {\r
-                   int alIndex = seq.findPosition(res);\r
-                   Object obj = ResidueProperties.aa2Triplet.get(\r
-                       seq.getCharAt(res) + "");\r
-                   if (obj == null)\r
-                     continue;\r
-\r
-                   String triplet = obj.toString();\r
-\r
-                   out.println(\r
-                       "<area shape=\"rect\" coords=\""\r
-                       + (idWidth + res * av.charWidth) + ","\r
-                       + sy + ","\r
-                       + (idWidth + (res + 1) * av.charWidth) + ","\r
-                       + (av.charHeight + sy) + "\""\r
-                       + " onMouseOver=\"toolTip('"\r
-                       + alIndex + " " + triplet +\r
-                       "<br><em>" + groups[i].getName() +\r
-                       "</em>')\"; onMouseOut=\"toolTip()\"; "\r
-                       + " href=\"#\">");\r
-                 }\r
-               }\r
-             }\r
-\r
-             out.println("</map></body></html>");\r
-             out.close();\r
-\r
-           }\r
-           catch (Exception ex)\r
-           {\r
-             ex.printStackTrace();\r
-           }\r
-         }///////////END OF IMAGE MAP\r
-\r
+      height = getWrappedHeight();\r
+      width = seqPanel.getWidth() + idPanel.getWidth();\r
     }\r
-\r
-    int getWrappedHeight()\r
+    else if (av.getShowAnnotation())\r
     {\r
+      height += annotationPanel.adjustPanelHeight() + 3;\r
+    }\r
 \r
-      int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
-        seqPanel.seqCanvas.getWidth());\r
-\r
-      int hgap = av.charHeight;\r
-      if (av.scaleAboveWrapped)\r
-        hgap += av.charHeight;\r
-\r
-      int annotationHeight = 0;\r
-      if (av.showAnnotation)\r
+    jalview.util.ImageMaker im;\r
+    if(type==jalview.util.ImageMaker.PNG)\r
+      im  = new jalview.util.ImageMaker(this,\r
+                                        jalview.util.ImageMaker.PNG,\r
+                                        "Create PNG image from alignment",\r
+                                        width, height, file, null);\r
+    else\r
+      im = new jalview.util.ImageMaker(this,\r
+                                        jalview.util.ImageMaker.EPS,\r
+                                       "Create EPS file from alignment",\r
+                                        width, height, file, alignFrame.getTitle() );\r
+\r
+    try\r
+    {\r
+      if (av.getWrapAlignment())\r
       {\r
-        annotationHeight = annotationPanel.adjustPanelHeight();\r
+        if(im.getGraphics()!=null)\r
+          printWrappedAlignment(im.getGraphics(), width, height, 0);\r
+      }\r
+      else\r
+      {\r
+        if(im.getGraphics()!=null)\r
+          printUnwrapped(im.getGraphics(), width, height, 0);\r
       }\r
 \r
-      int cHeight = av.getAlignment().getHeight() * av.charHeight\r
-          + hgap\r
-          + annotationHeight;\r
-\r
-\r
-      int height =  ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
-\r
-      return height;\r
+      im.writeImage();\r
     }\r
+    catch (OutOfMemoryError err)\r
+    {\r
+      System.out.println("########################\n"\r
+                         + "OUT OF MEMORY " + file + "\n"\r
+                         + "########################");\r
+\r
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                                            "Out of Memory Creating Image!!"\r
+                                            +\r
+                                            "\nSee help files for increasing Java Virtual Machine memory."\r
+                                            , "Out of memory",\r
+                                            JOptionPane.WARNING_MESSAGE);\r
+      System.out.println("Create IMAGE: " + err);\r
+      System.gc();\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     */\r
-    public void makePNG(File pngFile)\r
+    }\r
+    catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+    }\r
+  }\r
+  /**\r
+   * DOCUMENT ME!\r
+   */\r
+  public void makeEPS(File epsFile)\r
+  {\r
+    makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   */\r
+  public void makePNG(File pngFile)\r
+  {\r
+    makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);\r
+  }\r
+\r
+  public void makePNGImageMap(File imgMapFile, String imageName)\r
+  {\r
+    ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS\r
+    //////////////////////////////////////////////\r
+    int idWidth = calculateIdWidth().width + 4;\r
+    FontMetrics fm = getFontMetrics(av.getFont());\r
+    int scaleHeight = av.charHeight + fm.getDescent();\r
+\r
+    // Gen image map\r
+    //////////////////////////////////\r
+    if (imgMapFile != null)\r
     {\r
-      if(pngFile==null)\r
+      try\r
       {\r
-        jalview.io.JalviewFileChooser chooser = new jalview.io.\r
-            JalviewFileChooser(jalview.bin.Cache.getProperty(\r
-                "LAST_DIRECTORY"), new String[]\r
-                               {"png"},\r
-                               new String[]\r
-                               {"Portable network graphics"},\r
-                               "Portable network graphics");\r
-        chooser.setFileView(new jalview.io.JalviewFileView());\r
-        chooser.setDialogTitle("Create EPS file from alignment");\r
-        chooser.setToolTipText("Save");\r
-\r
-        int value = chooser.showSaveDialog(this);\r
-\r
-        if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+        PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));\r
+        out.println(jalview.io.HTMLOutput.getImageMapHTML());\r
+        out.println("<img src=\"" + imageName +\r
+                    "\" border=\"0\" usemap=\"#Map\" >"\r
+                    + "<map name=\"Map\">");\r
+\r
+        for (int s = 0; s < av.alignment.getHeight(); s++)\r
         {\r
-          return;\r
+          SequenceI seq = av.alignment.getSequenceAt(s);\r
+          SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
+          for (int i = 0; i < groups.length; i++)\r
+          {\r
+            int sy = s * av.charHeight + scaleHeight;\r
+            for (int res = groups[i].getStartRes();\r
+                 res < groups[i].getEndRes() + 1; res++)\r
+            {\r
+              int alIndex = seq.findPosition(res);\r
+              Object obj = ResidueProperties.aa2Triplet.get(\r
+                  seq.getCharAt(res) + "");\r
+              if (obj == null)\r
+                continue;\r
+\r
+              String triplet = obj.toString();\r
+\r
+              out.println(\r
+                  "<area shape=\"rect\" coords=\""\r
+                  + (idWidth + res * av.charWidth) + ","\r
+                  + sy + ","\r
+                  + (idWidth + (res + 1) * av.charWidth) + ","\r
+                  + (av.charHeight + sy) + "\""\r
+                  + " onMouseOver=\"toolTip('"\r
+                  + alIndex + " " + triplet +\r
+                  "<br><em>" + groups[i].getName() +\r
+                  "</em>')\"; onMouseOut=\"toolTip()\"; "\r
+                  + " href=\"#\">");\r
+            }\r
+          }\r
         }\r
 \r
-        pngFile = chooser.getSelectedFile();\r
+        out.println("</map></body></html>");\r
+        out.close();\r
 \r
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
-                                      chooser.getSelectedFile().getParent());\r
       }\r
-\r
-\r
-\r
-      int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
-      int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
-\r
-      if (av.getWrapAlignment())\r
+      catch (Exception ex)\r
       {\r
-        height = getWrappedHeight();\r
-        width = seqPanel.getWidth() + idPanel.getWidth();\r
+        ex.printStackTrace();\r
       }\r
-      else if (av.getShowAnnotation())\r
-        {\r
-            height += annotationPanel.adjustPanelHeight()+3;\r
-        }\r
+    } ///////////END OF IMAGE MAP\r
 \r
-        try\r
-        {\r
+  }\r
 \r
-            FileOutputStream out = new FileOutputStream(pngFile);\r
+  int getWrappedHeight()\r
+  {\r
 \r
-            BufferedImage bi = new BufferedImage(width, height,\r
-                    BufferedImage.TYPE_INT_RGB);\r
-            Graphics2D png = (Graphics2D) bi.getGraphics();\r
+    int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
+        seqPanel.seqCanvas.getWidth());\r
 \r
-            png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
-                RenderingHints.VALUE_ANTIALIAS_ON);\r
+    int hgap = av.charHeight;\r
+    if (av.scaleAboveWrapped)\r
+      hgap += av.charHeight;\r
 \r
-            if (av.getWrapAlignment())\r
-            {\r
-                printWrappedAlignment(png, width, height, 0);\r
-            }\r
-            else\r
-            {\r
-                printUnwrapped(png, width, height, 0);\r
-            }\r
+    int annotationHeight = 0;\r
+    if (av.showAnnotation)\r
+    {\r
+      annotationHeight = annotationPanel.adjustPanelHeight();\r
+    }\r
 \r
-            ImageIO.write(bi, "png", out);\r
-            out.close();\r
-        }\r
-        catch (OutOfMemoryError err)\r
-        {\r
-          System.out.println("########################\n"\r
-                             + "OUT OF MEMORY " + pngFile + "\n"\r
-                             + "########################");\r
-\r
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-                                                "Out of memory creating PNG!!"\r
-                                                +\r
-                                                "\nSee help files for increasing Java Virtual Machine memory."\r
-                                                , "Out of memory",\r
-                                                JOptionPane.WARNING_MESSAGE);\r
-          System.out.println("Create PNG: " + err);\r
-          System.gc();\r
+    int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+        + hgap\r
+        + annotationHeight;\r
 \r
-        }\r
-        catch (Exception ex)\r
-        {\r
-            ex.printStackTrace();\r
-        }\r
-    }\r
-}\r
+    int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
 \r
+    return height;\r
+  }\r
 \r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-class Preview extends JFrame\r
-{\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @author $author$\r
+   * @version $Revision$\r
+   */\r
+  class Preview\r
+      extends JFrame\r
+  {\r
     /**\r
      * Creates a new Preview object.\r
      *\r
@@ -1120,25 +982,25 @@ class Preview extends JFrame
      */\r
     public Preview(Image image)\r
     {\r
-        setResizable(true);\r
-        setSize(image.getWidth(this), image.getHeight(this));\r
-        setVisible(true);\r
-        getContentPane().setLayout(new BorderLayout());\r
-        getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);\r
-        validate();\r
-        repaint();\r
+      setResizable(true);\r
+      setSize(image.getWidth(this), image.getHeight(this));\r
+      setVisible(true);\r
+      getContentPane().setLayout(new BorderLayout());\r
+      getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);\r
+      validate();\r
+      repaint();\r
     }\r
-}\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-class PreviewPanel extends JPanel\r
-{\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @author $author$\r
+   * @version $Revision$\r
+   */\r
+  class PreviewPanel\r
+      extends JPanel\r
+  {\r
     Image image;\r
 \r
     /**\r
@@ -1148,7 +1010,7 @@ class PreviewPanel extends JPanel
      */\r
     public PreviewPanel(Image image)\r
     {\r
-        this.image = image;\r
+      this.image = image;\r
     }\r
 \r
     /**\r
@@ -1158,13 +1020,14 @@ class PreviewPanel extends JPanel
      */\r
     public void paintComponent(Graphics g)\r
     {\r
-        if (image != null)\r
-        {\r
-            g.drawImage(image, 0, 0, this);\r
-        }\r
-        else\r
-        {\r
-            System.out.println("DEBUG:image is null");\r
-        }\r
+      if (image != null)\r
+      {\r
+        g.drawImage(image, 0, 0, this);\r
+      }\r
+      else\r
+      {\r
+        System.out.println("DEBUG:image is null");\r
+      }\r
     }\r
+  }\r
 }\r
index 71891aa..e680dde 100755 (executable)
@@ -29,10 +29,6 @@ import java.awt.event.*;
 \r
 import java.util.*;\r
 import javax.swing.*;\r
-import java.io.FileOutputStream;\r
-import org.jibble.epsgraphics.EpsGraphics2D;\r
-import javax.imageio.ImageIO;\r
-import java.awt.image.BufferedImage;\r
 import java.awt.print.*;\r
 \r
 \r
@@ -313,7 +309,6 @@ public class PCAPanel extends GPCAPanel implements Runnable
 \r
 \r
 \r
-\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -321,79 +316,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
      */\r
     public void eps_actionPerformed(ActionEvent e)\r
     {\r
-      boolean accurateText = true;\r
-\r
-      String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
-          "Prompt each time");\r
-\r
-  // If we need to prompt, and if the GUI is visible then\r
-  // Prompt for EPS rendering style\r
-      if (renderStyle.equalsIgnoreCase("Prompt each time")\r
-          && !\r
-          (System.getProperty("java.awt.headless") != null\r
-           && System.getProperty("java.awt.headless").equals("true")))\r
-      {\r
-        EPSOptions eps = new EPSOptions();\r
-        renderStyle = eps.getValue();\r
-\r
-        if (renderStyle == null || eps.cancelled)\r
-          return;\r
-\r
-      }\r
-\r
-      if (renderStyle.equalsIgnoreCase("text"))\r
-      {\r
-        accurateText = false;\r
-      }\r
-\r
-      int width = rc.getWidth();\r
-      int height = rc.getHeight();\r
-\r
-      try\r
-      {\r
-        jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
-            jalview.bin.Cache.getProperty(\r
-                "LAST_DIRECTORY"), new String[]\r
-            {"eps"},\r
-            new String[]\r
-            {"Encapsulated Postscript"},\r
-            "Encapsulated Postscript");\r
-        chooser.setFileView(new jalview.io.JalviewFileView());\r
-        chooser.setDialogTitle("Create EPS file from PCA");\r
-        chooser.setToolTipText("Save");\r
-\r
-        int value = chooser.showSaveDialog(this);\r
-\r
-        if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
-        {\r
-          return;\r
-        }\r
-\r
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
-                                      chooser.getSelectedFile().getParent());\r
-\r
-        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
-        EpsGraphics2D pg = new EpsGraphics2D("PCA", out, 0, 0, width,\r
-                                             height);\r
-\r
-        pg.setAccurateTextMode(accurateText);\r
-\r
-        rc.drawBackground(pg, rc.bgColour);\r
-        rc.drawScene(pg);\r
-\r
-        if (rc.drawAxes == true)\r
-        {\r
-          rc.drawAxes(pg);\r
-        }\r
-\r
-\r
-        pg.flush();\r
-        pg.close();\r
-      }\r
-      catch (Exception ex)\r
-      {\r
-        ex.printStackTrace();\r
-      }\r
+      makePCAImage(jalview.util.ImageMaker.EPS);\r
     }\r
 \r
     /**\r
@@ -403,48 +326,38 @@ public class PCAPanel extends GPCAPanel implements Runnable
      */\r
     public void png_actionPerformed(ActionEvent e)\r
     {\r
+       makePCAImage(jalview.util.ImageMaker.PNG);\r
+    }\r
+\r
+    void makePCAImage(int type)\r
+    {\r
       int width = rc.getWidth();\r
       int height = rc.getHeight();\r
 \r
-      try\r
-      {\r
-        jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
-            jalview.bin.Cache.getProperty(\r
-                "LAST_DIRECTORY"), new String[]\r
-            {"png"},\r
-            new String[]\r
-            {"Portable network graphics"},\r
-            "Portable network graphics");\r
-\r
-        chooser.setFileView(new jalview.io.JalviewFileView());\r
-        chooser.setDialogTitle("Create PNG image from PCA");\r
-        chooser.setToolTipText("Save");\r
-\r
-        int value = chooser.showSaveDialog(this);\r
+      jalview.util.ImageMaker im;\r
 \r
-        if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
-        {\r
-          return;\r
-        }\r
-\r
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
-                                      chooser.getSelectedFile().getParent());\r
-\r
-        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
-\r
-        BufferedImage bi = new BufferedImage(width, height,\r
-                                             BufferedImage.TYPE_INT_RGB);\r
-        Graphics big = bi.getGraphics();\r
-\r
-        big.drawImage(rc.img,0,0,this);\r
-\r
-        ImageIO.write(bi, "png", out);\r
-        out.close();\r
-      }\r
-      catch (Exception ex)\r
-      {\r
-        ex.printStackTrace();\r
-      }\r
+      if(type == jalview.util.ImageMaker.PNG)\r
+        im = new jalview.util.ImageMaker(this,\r
+                                         jalview.util.ImageMaker.PNG,\r
+                                         "Make PNG image from PCA",\r
+                                         width, height,\r
+                                         null, null);\r
+        else\r
+          im = new jalview.util.ImageMaker(this,\r
+                                 jalview.util.ImageMaker.EPS,\r
+                                 "Make EPS file from PCA",\r
+                                 width, height,\r
+                                 null, this.getTitle());\r
+\r
+      if(im.getGraphics()!=null)\r
+       {\r
+         rc.drawBackground(im.getGraphics(), Color.black);\r
+         rc.drawScene(im.getGraphics());\r
+         if (rc.drawAxes == true)\r
+         {\r
+           rc.drawAxes(im.getGraphics());\r
+         }\r
+         im.writeImage();\r
+       }\r
     }\r
-\r
   }\r
index 7677cf8..1c70c24 100755 (executable)
@@ -26,18 +26,14 @@ import jalview.io.*;
 \r
 import jalview.jbgui.*;\r
 \r
-import org.jibble.epsgraphics.*;\r
 \r
 import java.awt.*;\r
 import java.awt.event.*;\r
-import java.awt.image.*;\r
 \r
 import java.io.*;\r
 \r
 import java.util.*;\r
 \r
-import javax.imageio.*;\r
-\r
 import java.beans.PropertyChangeEvent;\r
 \r
 \r
@@ -391,70 +387,7 @@ public class TreePanel extends GTreePanel
      */\r
     public void epsTree_actionPerformed(ActionEvent e)\r
     {\r
-      boolean accurateText = true;\r
-\r
-      String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
-          "Prompt each time");\r
-\r
-    // If we need to prompt, and if the GUI is visible then\r
-    // Prompt for EPS rendering style\r
-      if (renderStyle.equalsIgnoreCase("Prompt each time")\r
-          && !\r
-          (System.getProperty("java.awt.headless") != null\r
-           && System.getProperty("java.awt.headless").equals("true")))\r
-      {\r
-        EPSOptions eps = new EPSOptions();\r
-        renderStyle = eps.getValue();\r
-\r
-        if (renderStyle==null || eps.cancelled)\r
-          return;\r
-\r
-\r
-      }\r
-\r
-      if (renderStyle.equalsIgnoreCase("text"))\r
-      {\r
-        accurateText = false;\r
-      }\r
-\r
-        int width = treeCanvas.getWidth();\r
-        int height = treeCanvas.getHeight();\r
-\r
-        try\r
-        {\r
-            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
-                        "LAST_DIRECTORY"), new String[] { "eps" },\r
-                    new String[] { "Encapsulated Postscript" },\r
-                    "Encapsulated Postscript");\r
-            chooser.setFileView(new jalview.io.JalviewFileView());\r
-            chooser.setDialogTitle("Create EPS file from tree");\r
-            chooser.setToolTipText("Save");\r
-\r
-            int value = chooser.showSaveDialog(this);\r
-\r
-            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
-            {\r
-                return;\r
-            }\r
-\r
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
-                                          chooser.getSelectedFile().getParent());\r
-\r
-            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
-            EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
-                                                 height);\r
-\r
-            pg.setAccurateTextMode(accurateText);\r
-\r
-            treeCanvas.draw(pg, width, height);\r
-\r
-            pg.flush();\r
-            pg.close();\r
-        }\r
-        catch (Exception ex)\r
-        {\r
-            ex.printStackTrace();\r
-        }\r
+      makeTreeImage(jalview.util.ImageMaker.EPS);\r
     }\r
 \r
     /**\r
@@ -464,44 +397,34 @@ public class TreePanel extends GTreePanel
      */\r
     public void pngTree_actionPerformed(ActionEvent e)\r
     {\r
-        int width = treeCanvas.getWidth();\r
-        int height = treeCanvas.getHeight();\r
-\r
-        try\r
-        {\r
-            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
-                        "LAST_DIRECTORY"), new String[] { "png" },\r
-                    new String[] { "Portable network graphics" },\r
-                    "Portable network graphics");\r
-\r
-            chooser.setFileView(new jalview.io.JalviewFileView());\r
-            chooser.setDialogTitle("Create PNG image from tree");\r
-            chooser.setToolTipText("Save");\r
-\r
-            int value = chooser.showSaveDialog(this);\r
-\r
-            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
-            {\r
-                return;\r
-            }\r
-\r
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
-                chooser.getSelectedFile().getParent());\r
+       makeTreeImage(jalview.util.ImageMaker.PNG);\r
+    }\r
 \r
-            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+    void makeTreeImage(int type)\r
+    {\r
+      int width = treeCanvas.getWidth();\r
+      int height = treeCanvas.getHeight();\r
 \r
-            BufferedImage bi = new BufferedImage(width, height,\r
-                    BufferedImage.TYPE_INT_RGB);\r
-            Graphics png = bi.getGraphics();\r
+      jalview.util.ImageMaker im;\r
 \r
-            treeCanvas.draw(png, width, height);\r
+      if(type == jalview.util.ImageMaker.PNG)\r
+        im = new jalview.util.ImageMaker(this,\r
+                                         jalview.util.ImageMaker.PNG,\r
+                                         "Make PNG image from tree",\r
+                                         width, height,\r
+                                         null, null);\r
+        else\r
+          im = new jalview.util.ImageMaker(this,\r
+                                 jalview.util.ImageMaker.EPS,\r
+                                 "Make EPS file from tree",\r
+                                 width, height,\r
+                                 null, this.getTitle());\r
 \r
-            ImageIO.write(bi, "png", out);\r
-            out.close();\r
-        }\r
-        catch (Exception ex)\r
-        {\r
-            ex.printStackTrace();\r
-        }\r
+      if(im.getGraphics()!=null)\r
+      {\r
+        treeCanvas.draw(im.getGraphics(), width, height);\r
+        im.writeImage();\r
+      }\r
     }\r
+\r
 }\r
diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java
new file mode 100755 (executable)
index 0000000..02427f2
--- /dev/null
@@ -0,0 +1,165 @@
+package jalview.util;\r
+\r
+import java.awt.event.ActionEvent;\r
+import java.awt.RenderingHints;\r
+import javax.imageio.ImageIO;\r
+import org.jibble.epsgraphics.EpsGraphics2D;\r
+import jalview.gui.EPSOptions;\r
+import java.awt.Graphics2D;\r
+import java.io.*;\r
+import java.awt.image.BufferedImage;\r
+import java.awt.Graphics;\r
+import jalview.io.*;\r
+import java.awt.*;\r
+\r
+\r
+public class ImageMaker\r
+{\r
+  public static final int EPS = 0;\r
+  public static final int PNG = 1;\r
+  int type = -1;\r
+\r
+  EpsGraphics2D pg;\r
+  Graphics graphics;\r
+  FileOutputStream out;\r
+  BufferedImage bi;\r
+\r
+  public ImageMaker(Component parent, int type, String title,\r
+                           int width, int height, File file, String EPStitle)\r
+  {\r
+    this.type = type;\r
+\r
+    if (file == null)\r
+    {\r
+      JalviewFileChooser chooser;\r
+      chooser = type == EPS ? getEPSChooser() : getPNGChooser();\r
+\r
+      chooser.setFileView(new jalview.io.JalviewFileView());\r
+      chooser.setDialogTitle(title);\r
+      chooser.setToolTipText("Save");\r
+\r
+      int value = chooser.showSaveDialog(parent);\r
+\r
+      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+      {\r
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+                                      chooser.getSelectedFile().getParent());\r
+\r
+        file = chooser.getSelectedFile();\r
+      }\r
+    }\r
+\r
+    try\r
+    {\r
+      out = new FileOutputStream(file);\r
+\r
+      if (type == EPS)\r
+        setupEPS(width, height, EPStitle);\r
+      else\r
+        setupPNG(width, height);\r
+    }\r
+    catch (Exception ex)\r
+    {\r
+      System.out.println("Error creating " + (type == EPS ? "EPS" : "PNG") +\r
+                         " file.");\r
+    }\r
+  }\r
+\r
+  public Graphics getGraphics()\r
+  {\r
+    return graphics;\r
+  }\r
+\r
+\r
+  void setupPNG(int width, int height)\r
+  {\r
+        bi = new BufferedImage(width, height,\r
+                BufferedImage.TYPE_INT_RGB);\r
+        graphics  = bi.getGraphics();\r
+        Graphics2D ig2 = (Graphics2D) graphics;\r
+        ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+                                 RenderingHints.VALUE_ANTIALIAS_ON);\r
+  }\r
+\r
+  public void writeImage()\r
+  {\r
+    try{\r
+      switch(type)\r
+      {\r
+        case EPS:\r
+          pg.flush();\r
+          pg.close();\r
+          break;\r
+        case PNG:\r
+          ImageIO.write(bi, "png", out);\r
+          out.close();\r
+          break;\r
+      }\r
+    }\r
+    catch (Exception ex)\r
+    {\r
+        ex.printStackTrace();\r
+    }\r
+  }\r
+\r
+  void setupEPS(int width, int height, String title)\r
+  {\r
+    boolean accurateText = true;\r
+\r
+    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
+        "Prompt each time");\r
+\r
+    // If we need to prompt, and if the GUI is visible then\r
+    // Prompt for EPS rendering style\r
+    if (renderStyle.equalsIgnoreCase("Prompt each time")\r
+        && !\r
+        (System.getProperty("java.awt.headless") != null\r
+         && System.getProperty("java.awt.headless").equals("true")))\r
+    {\r
+      EPSOptions eps = new EPSOptions();\r
+      renderStyle = eps.getValue();\r
+\r
+      if (renderStyle == null || eps.cancelled)\r
+        return;\r
+    }\r
+\r
+    if (renderStyle.equalsIgnoreCase("text"))\r
+    {\r
+      accurateText = false;\r
+    }\r
+\r
+    try   {\r
+      pg = new EpsGraphics2D(title, out, 0, 0, width,\r
+                                           height);\r
+      Graphics2D ig2 = (Graphics2D) pg;\r
+      ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+                           RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
+      pg.setAccurateTextMode(accurateText);\r
+\r
+      graphics = pg;\r
+    }\r
+    catch (Exception ex) {  }\r
+  }\r
+\r
+\r
+  JalviewFileChooser getPNGChooser()\r
+  {\r
+    return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+        "LAST_DIRECTORY"), new String[]\r
+                                             {"png"},\r
+                                             new String[]\r
+                                             {"Portable network graphics"},\r
+                                             "Portable network graphics");\r
+  }\r
+\r
+  JalviewFileChooser getEPSChooser()\r
+  {\r
+    return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+        "LAST_DIRECTORY"), new String[]\r
+                                             {"eps"},\r
+                                             new String[]\r
+                                             {"Encapsulated Postscript"},\r
+                                             "Encapsulated Postscript");\r
+  }\r
+}\r