X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=b339e5165f97191d5e122dbdb11927c52bac271f;hb=5150ffd5baa1f58bb6b4059616bc6b9050326553;hp=506fb0967b8e4dc6d61b410413fe0838b7ed2613;hpb=46be82307a1be9c637e0f3e2a34631692731eeb7;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 506fb09..b339e51 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -11,6 +11,7 @@ import java.io.*;
 import java.awt.image.*;
 import org.jibble.epsgraphics.*;
 import javax.imageio.*;
+import javax.swing.*;
 
 
 
@@ -22,10 +23,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   SeqPanel   seqPanel;
   IdPanel    idPanel;
   IdwidthAdjuster idwidthAdjuster;
-  SecondaryStructurePanel ssPanel;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
-  ScorePanel scorePanel;
+  AnnotationPanel annotationPanel;
+  AnnotationLabels alabels;
+
+  // this value is set false when selection area being dragged
+  boolean fastPaint = true;
 
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
@@ -35,51 +39,29 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     idPanel         = new IdPanel   (av, this);
 
     scalePanel = new ScalePanel(av, this);
-    scorePanel = new ScorePanel(av);
-    ssPanel = new SecondaryStructurePanel(av);
-
-    secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
 
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idwidthAdjuster = new IdwidthAdjuster(this);
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
 
-    Dimension d = calculateIdWidth();
-    d.setSize( d.width+4, d.height);
-    idPanel.idCanvas.setPreferredSize( d );
-    hscrollFillerPanel.setPreferredSize( d );
+    annotationPanel = new AnnotationPanel(this);
+    alabels = new AnnotationLabels(this);
 
-    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
-    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationScroller.setViewportView(annotationPanel);
+    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
+    fontChanged();
 
-    if(seqPanel.seqCanvas.getWidth()==0)
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-     {
-       public void run()
-       {
-         setScrollValues(0,0);
-         Dimension d = calculateIdWidth();
-         d.setSize( d.width+4, d.height);
-         idPanel.idCanvas.setPreferredSize( d );
-         hscrollFillerPanel.setPreferredSize( d );
-         RefreshPanels();
-       }
-    });
+    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
+    setScrollValues(0, 0);
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
-    addComponentListener(new ComponentAdapter()
-   {
-     public void componentResized(ComponentEvent evt)
-     {
-          RefreshPanels();
-     }
-   });
-
    setFocusable(true);
    addKeyListener(new KeyAdapter()
    {
@@ -89,34 +71,39 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
        {
          case  27: // escape key
            av.setSelectionGroup(null);
-           RefreshPanels();
-           break;
-         case KeyEvent.VK_X:
-           alignFrame.cut_actionPerformed(null);
-           break;
-         case KeyEvent.VK_C:
-           alignFrame.copy_actionPerformed(null);
-           break;
-         case KeyEvent.VK_V:
-           alignFrame.paste(true);
-           break;
-         case KeyEvent.VK_A:
-           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
+           repaint();
            break;
+
         case KeyEvent.VK_DOWN:
           alignFrame.moveSelectedSequences(false);
           break;
         case KeyEvent.VK_UP:
           alignFrame.moveSelectedSequences(true);
           break;
-        case KeyEvent.VK_F:
-          alignFrame.findMenuItem_actionPerformed(null);
-          break;
        }
      }
    });
   }
 
+  public void fontChanged()
+  {
+    // set idCanvas bufferedImage to null
+    // to prevent drawing old image
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));
+
+    idPanel.idCanvas.gg = null;
+    annotationPanel.adjustPanelHeight();
+    Dimension d = calculateIdWidth();
+    d.setSize(d.width + 4, d.height);
+    idPanel.idCanvas.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(d);
+    repaint();
+  }
+
+
   Dimension calculateIdWidth()
   {
     Graphics g = this.getGraphics();
@@ -146,6 +133,20 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
          i++;
        }
 
+       // Also check annotation label widths
+       i=0;
+       if(al.getAlignmentAnnotation()!=null)
+       {
+         fm = g.getFontMetrics(alabels.getFont());
+         while (i < al.getAlignmentAnnotation().length)
+         {
+           String label = al.getAlignmentAnnotation()[i].label;
+           if (fm.stringWidth(label) > idWidth)
+             idWidth = fm.stringWidth(label);
+           i++;
+         }
+       }
+
        return new Dimension(idWidth, 12);
   }
 
@@ -155,12 +156,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    seqPanel.seqCanvas.highlightSearchResults( results );
 
    // do we need to scroll the panel?
-   if(results!=null && (av.getStartSeq()>results[0]
-                        || av.getEndSeq()<results[0]
-                        || av.getStartRes()>results[1]
-                        || av.getEndRes()<results[2]))
-       setScrollValues(results[1], results[0]);
-
+   if(results!=null)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(results[0]);
+      int start = seq.findIndex( results[1] )-1;
+      int end = seq.findIndex( results[2] )-1;
+      if( av.getStartRes() > start
+          || av.getEndRes() < end
+          || (av.getStartSeq() > results[0]
+          || av.getEndSeq() < results[0]))
+        setScrollValues(start, results[0]);
+    }
 
  }
 
@@ -176,35 +182,25 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
  }
 
 
-  public void setGraphPanelVisible(boolean b)
+  public void setAnnotationVisible(boolean b)
   {
-    idSpaceFillerPanel.setVisible(b);
-    scorePanelHolder.setVisible(b);
-
-    RefreshPanels();
-    // bit annoying to call this twice, can you do better?
-    RefreshPanels();
+    annotationSpaceFillerHolder.setVisible(b);
+    annotationScroller.setVisible(b);
   }
 
-  public void setSecondaryStructureVisible(boolean b)
-  {
-    secondaryPanelHolder.setVisible(b);
-    RefreshPanels();
-  }
 
   public void setWrapAlignment(boolean wrap)
   {
-    scorePanelHolder.setVisible(!wrap);
     scalePanelHolder.setVisible(!wrap);
-    secondaryPanelHolder.setVisible(!wrap);
-
     hscroll.setVisible(!wrap);
-
     idwidthAdjuster.setVisible(!wrap);
-    idSpaceFillerPanel.setVisible(!wrap);
+
+    av.setShowAnnotation(!wrap);
+    annotationScroller.setVisible(!wrap);
+    annotationSpaceFillerHolder.setVisible(!wrap);
     idSpaceFillerPanel1.setVisible(!wrap);
 
-    RefreshPanels();
+    repaint();
 
   }
 
@@ -222,46 +218,16 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
                             al.getWidth() );
 
        c.calculate();
-       c.verdict(false, 100);
+       c.verdict(false, av.ConsPercGaps);
        ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
        av.setGlobalColourScheme( ccs );
 
     }
 
-    RefreshPanels();
+    repaint();
   }
 
-  public void RefreshPanels()
-  {
-
-              requestFocus();
-              invalidate();
-              idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
-              if(idPanel.idCanvas.getPreferredSize()!=null)
-                hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12));
-              idSpaceFillerPanel1.setPreferredSize(new Dimension(500,
-                  av.charHeight / 2 + 12));
-              scalePanelHolder.setPreferredSize(new Dimension(500,
-                  av.charHeight / 2 + 12));
-
-              if (av.getWrapAlignment())
-              {
-                int max = av.alignment.getWidth() /
-                    (seqPanel.seqCanvas.getWidth() / av.charWidth)+1 ;
-
-                vscroll.setValues(0, 1, 0, max);
-              }
-              else
-              {
-                av.getConsensus(true);
-                if (overviewPanel != null)
-                  overviewPanel.updateOverviewImage();
-                 setScrollValues(av.getStartRes(), av.getStartSeq());
-              }
-
-          repaint();
-  }
 
   int hextent = 0;
   int vextent = 0;
@@ -273,39 +239,46 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       if(vscroll.getValue()<1)
         return false;
+      fastPaint  = false;
       vscroll.setValue(vscroll.getValue() - 1);
     }
     else
     {
      if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
        return false;
+      fastPaint  = false;
       vscroll.setValue(vscroll.getValue() + 1);
     }
-
+    fastPaint = true;
     return true;
   }
 
   public boolean scrollRight(boolean right)
   {
-    if(right)
-   {
-     if(hscroll.getValue()<1)
-       return false;
-     hscroll.setValue(hscroll.getValue() - 1);
-   }
-   else
-   {
-    if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
-      return false;
-     hscroll.setValue(hscroll.getValue() + 1);
-   }
 
-   return true;
- }
+    if (right)
+    {
+      if (hscroll.getValue() < 1)
+        return false;
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() - 1);
+    }
+    else
+    {
+      if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+        return false;
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() + 1);
+    }
+    fastPaint = true;
+    return true;
+  }
 
 
   public void setScrollValues(int x, int y)
   {
+    av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+
     hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
     vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
 
@@ -329,13 +302,15 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
 
-    repaint();
+
 
   }
 
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
+    int oldX = av.getStartRes();
+    int oldY = av.getStartSeq();
 
     if (evt.getSource() == hscroll)
     {
@@ -349,7 +324,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       int offy = vscroll.getValue();
       if (av.getWrapAlignment())
       {
-        av.setStartRes( vscroll.getValue() * av.getChunkWidth());
+        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+        av.setStartRes( vscroll.getValue() * rowSize );
+        av.setEndRes( (vscroll.getValue()+1) * rowSize );
       }
       else
       {
@@ -358,11 +335,47 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       }
     }
 
-
     if(overviewPanel!=null)
       overviewPanel.setBoxPosition();
 
-    repaint();
+    if(av.getWrapAlignment() || !fastPaint)
+      repaint();
+    else
+    {
+      idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
+      seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
+                                   av.getStartSeq() - oldY);
+
+      scalePanel.repaint();
+      if (av.getShowAnnotation())
+        annotationPanel.fastPaint(av.getStartRes() - oldX);
+    }
+
+  }
+
+
+  public void paintComponent(Graphics g)
+  {
+    invalidate();
+    Dimension d = idPanel.idCanvas.getPreferredSize();
+    idPanelHolder.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+    validate();
+
+    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());
+    }
+
+
+
   }
 
   public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
@@ -381,139 +394,159 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
   {
 
-    int idWidth = calculateIdWidth().width;
+      int idWidth = calculateIdWidth().width + 4;
+      FontMetrics fm = getFontMetrics(av.getFont());
+      int scaleHeight = av.charHeight + fm.getDescent();
 
+      pg.setColor(Color.white);
+      pg.fillRect(0, 0, pwidth, pheight);
+      pg.setFont(av.getFont());
 
-    pg.setColor(Color.white);
-    pg.fillRect(0,0,pwidth, pheight);
-    pg.setFont( av.getFont() );
+      ////////////////////////////////////
+      /// How many sequences and residues can we fit on a printable page?
+      int totalRes = (pwidth - idWidth) / av.getCharWidth();
 
-    ////////////////////////////////////
-    /// How many sequences and residues can we fit on a printable page?
-    int totalRes = (pwidth - idWidth)/av.getCharWidth();
-    int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
-    int pagesWide = av.getAlignment().getWidth() / totalRes +1;
-    int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
+      int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - 1;
 
-    if (pi >= pagesWide*pagesHigh)
-     return Printable.NO_SUCH_PAGE;
+      int pagesWide = av.getAlignment().getWidth() / totalRes + 1;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
-    int startRes, endRes, startSeq, endSeq;
-    startRes = (pi % pagesWide) * totalRes;
-    endRes = startRes + totalRes-1;
-    if(endRes>av.getAlignment().getWidth())
-      endRes = av.getAlignment().getWidth();
+      /////////////////////////////
+      /// Only print these sequences and residues on this page
+      int startRes, endRes, startSeq, endSeq;
+      startRes = (pi % pagesWide) * totalRes;
+      endRes = startRes + totalRes - 1;
+      if (endRes > av.getAlignment().getWidth()-1)
+        endRes = av.getAlignment().getWidth()-1;
 
-     startSeq = (pi / pagesWide) * totalSeq;
-     endSeq = startSeq + totalSeq;
-     if(endSeq > av.getAlignment().getHeight())
-       endSeq = av.getAlignment().getHeight();
+      startSeq = (pi / pagesWide) * totalSeq;
+      endSeq = startSeq + totalSeq;
+      if (endSeq > av.getAlignment().getHeight())
+        endSeq = av.getAlignment().getHeight();
 
+      int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
 
-    ////////////////
-    //draw Scale
-    pg.translate(30,0);
-    scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
+      if (av.showAnnotation)
+        pagesHigh += annotationPanel.getHeight();
 
-    pg.translate(-30, 30);
-    ////////////////
-    // Draw the ids
-    Color currentColor=null;
-    Color currentTextColor=null;
-    for(int i=startSeq; i<endSeq; i++)
-    {
-      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
-      {
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
-      }
-      else
+      pagesHigh /= pheight;
+
+      if (pi >= pagesWide * pagesHigh)
+        return Printable.NO_SUCH_PAGE;
+
+        //draw Scale
+      pg.translate(idWidth, 0);
+      scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
+      pg.translate( -idWidth, scaleHeight);
+      ////////////////
+      // Draw the ids
+      Color currentColor = null;
+      Color currentTextColor = null;
+      for (int i = startSeq; i < endSeq; i++)
       {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
-        currentTextColor = Color.black;
-      }
+        if (av.getSelectionGroup() != null &&
+            av.getSelectionGroup().sequences.
+            contains(av.getAlignment().getSequenceAt(i)))
+        {
+          currentColor = Color.gray;
+          currentTextColor = Color.black;
+        }
+        else
+        {
+          currentColor = av.getAlignment().getSequenceAt(i).getColor();
+          currentTextColor = Color.black;
+        }
+
+        pg.setColor(currentColor);
+        pg.fillRect(0,
+                    jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
+            av.getCharHeight()),
+                    idWidth,
+                    av.getCharHeight());
 
-      pg.setColor(currentColor);
-      pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
-                              idWidth,
-                              av.getCharHeight());
+        pg.setColor(currentTextColor);
 
-      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).getName();
-      if(av.getShowFullId())
-        string = av.getAlignment().getSequenceAt(i).getDisplayId();
+        pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
+                      (startSeq, i, av.getCharHeight()) + av.getCharHeight() -
+                      (av.getCharHeight() / 5));
+      }
 
-      pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight
-                    (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
-    }
+      // draw main sequence panel
+      pg.translate(idWidth, 0);
+      seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
+                                   startRes, startSeq, 0);
 
-    // draw main sequence panel
-    pg.translate(idWidth+4,0);
-    pg.setClip(0,0,pwidth-idWidth, pheight);
-    seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
 
-    return Printable.PAGE_EXISTS;
+      if (av.showAnnotation && endSeq == av.alignment.getHeight())
+      {
+        pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
+        alabels.drawComponent( (Graphics2D) pg);
+        pg.translate(idWidth, 0);
+        annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes+1);
+      }
+
+      return Printable.PAGE_EXISTS;
+
   }
 
 
   public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
   {
+      int idWidth = calculateIdWidth().width + 4;
+
+      int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth);
+      int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
+          ( (av.alignment.getWidth()
+             / resWidth) + 1) * av.charHeight;
 
-    int idWidth = calculateIdWidth().width;
 
-    if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
-      pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
+      pg.setColor(Color.white);
+      pg.fillRect(0, 0, pwidth, pheight);
+      pg.setFont(av.getFont());
 
+      ////////////////
+      // Draw the ids
+      pg.setColor(Color.black);
 
-    pg.setColor(Color.white);
-    pg.fillRect(0,0,pwidth, pheight);
-    pg.setFont( av.getFont() );
+      pg.translate(0, -pi * pheight);
 
-    ////////////////////////////////////
-    /// How many sequences and residues can we fit on a printable page?
-    AlignmentI da = av.alignment;
-    int endy   = da.getHeight();
-    int chunkHeight =  (da.getHeight() + 2)*av.charHeight;
-    int chunkWidth  =   (pwidth-idWidth)/av.charWidth;
+      pg.setClip(0,pi*pheight,pwidth, pheight);
 
-    int noChunksOnPage = pheight / chunkHeight;
-    int totalChunks = da.getWidth() / chunkWidth;
+      int ypos = 2 * av.charHeight;
+      do
+      {
+        for (int i = 0; i < av.alignment.getHeight(); i++)
+        {
+          SequenceI s = av.alignment.getSequenceAt(i);
+          String string = s.getName();
+          if (av.getShowFullId())
+            string = s.getDisplayId();
 
-    if ( pi*noChunksOnPage > totalChunks )
-     return Printable.NO_SUCH_PAGE;
+          pg.drawString(string, 0,
+                        AlignmentUtil.getPixelHeight(0, i, av.charHeight) +
+                        ypos +
+                        av.charHeight - (av.charHeight / 5));
 
-    ////////////////
-    // Draw the ids
-    pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
+        }
 
-    int row = pi*noChunksOnPage;
-    pg.setColor(Color.black);
-    for(int ypos=2*av.charHeight;
-        ypos <= pheight && row*chunkWidth<da.getWidth();
-        ypos += chunkHeight, row++ )
-    {
-      for (int i = 0; i < endy; i++)
-      {
-        SequenceI s = da.getSequenceAt(i);
-        String string = s.getName();
-        if (av.getShowFullId())
-          string = s.getDisplayId();
+        ypos += (av.alignment.getHeight() + 2) * av.charHeight;
 
-        pg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
-                      av.charHeight - (av.charHeight / 5));
       }
-    }
+      while (ypos < totalHeight);
+
+      pg.translate(idWidth, 0);
 
-    // draw main sequence panel
-    pg.translate(idWidth+4,0);
-    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
+      seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+
+      if (pi * pheight < totalHeight)
+        return Printable.PAGE_EXISTS;
+      else
+        return Printable.NO_SUCH_PAGE;
 
 
-    return Printable.PAGE_EXISTS;
 
   }
 
@@ -528,6 +561,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       height = (av.alignment.getHeight()+1) * av.charHeight + 30;
       width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
     }
+    if(av.getShowAnnotation())
+   {
+     height += annotationPanel.getPreferredSize().height;
+   }
 
     try
     {
@@ -571,6 +608,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
         width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
       }
 
+      if(av.getShowAnnotation())
+      {
+        height += annotationPanel.getPreferredSize().height;
+      }
+
 
 
     try
@@ -589,8 +631,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 
       BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
-      Graphics png = bi.getGraphics();
+      Graphics2D png = (Graphics2D)bi.getGraphics();
 
+      png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
 
         if (av.getWrapAlignment())
           printWrappedAlignment(png, width, height, 0);
@@ -608,6 +651,37 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
 }
 
+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();
+  }
+}
+
+class PreviewPanel extends JPanel
+{
+  Image image;
+  public PreviewPanel(Image image)
+  {
+    this.image = image;
+  }
+  public void paintComponent(Graphics g)
+  {
+    if(image!=null)
+      g.drawImage(image,0,0,this);
+    else
+      System.out.println("image is null");
+  }
+}
+