X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=81b999f009ad9875d1db939f254bace5eb9c65f1;hb=e78af69b55f5b95978094c6643ce884ba78efad2;hp=2b101fd17626b254a6229e65be828f8f849f3afa;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 2b101fd..81b999f 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,19 +1,36 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
 package jalview.appletgui;
 
-import jalview.jbappletgui.GAlignmentPanel;
-import jalview.schemes.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
 import java.awt.*;
 import java.awt.event.*;
 
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener
+import jalview.datamodel.*;
+
+public class AlignmentPanel extends Panel implements AdjustmentListener
 {
 
-  AlignViewport     av;
+  AlignViewport av;
   OverviewPanel overviewPanel;
-  SeqPanel   seqPanel;
-  IdPanel    idPanel;
+  SeqPanel seqPanel;
+  IdPanel idPanel;
   IdwidthAdjuster idwidthAdjuster;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
@@ -23,17 +40,30 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
+  boolean MAC = false;
+
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    if(System.getProperty("os.name").startsWith("Mac"))
+      MAC = true;
+
     alignFrame = af;
-    this.av         = av;
-    seqPanel        = new SeqPanel  (av, this);
-    idPanel         = new IdPanel   (av, this);
-    scalePanel      = new ScalePanel(av, this);
+    this.av = av;
+    seqPanel = new SeqPanel(av, this);
+    idPanel = new IdPanel(av, this);
+    scalePanel = new ScalePanel(av, this);
     idwidthAdjuster = new IdwidthAdjuster(this);
     annotationPanel = new AnnotationPanel(this);
-    alabels         = new AnnotationLabels(this);
-
+    alabels = new AnnotationLabels(this);
 
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
@@ -48,56 +78,66 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
-   seqPanel.seqCanvas.addKeyListener( new MyKeyAdapter() );
-   idPanel.idCanvas.addKeyListener( new MyKeyAdapter() );
+    seqPanel.seqCanvas.addKeyListener(new MyKeyAdapter());
+    idPanel.idCanvas.addKeyListener(new MyKeyAdapter());
 
-   addComponentListener(new ComponentAdapter()
-     {
-       public void componentResized(ComponentEvent evt)
-       {
-         setScrollValues(av.getStartRes(), av.getStartSeq());
-         repaint();
-       }
-     });
+    addComponentListener(new ComponentAdapter()
+    {
+      public void componentResized(ComponentEvent evt)
+      {
+        setScrollValues(av.getStartRes(), av.getStartSeq());
+        repaint();
+      }
+    });
 
-     Dimension d = calculateIdWidth();
-     idPanel.idCanvas.setSize(d);
+    Dimension d = calculateIdWidth();
+    idPanel.idCanvas.setSize(d);
 
-     hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
-     annotationScroller.setSize(annotationPanel.getSize());
+    hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
+    annotationScroller.setSize(annotationPanel.getSize());
 
-     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
-     annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
-     alabels.setSize(d.width,annotationPanel.getSize().height);
+    idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+    annotationSpaceFillerHolder.setSize(d.width,
+                                        annotationPanel.getSize().height);
+    alabels.setSize(d.width, annotationPanel.getSize().height);
 
   }
 
-  class MyKeyAdapter extends KeyAdapter
+  class MyKeyAdapter
+      extends KeyAdapter
   {
-     public void keyPressed(KeyEvent evt)
-     {
-       switch(evt.getKeyCode())
-       {
-         case  27: // escape key
-           av.setSelectionGroup(null);
-           alignFrame.alignPanel.repaint();
-           break;
-         case KeyEvent.VK_X:
-           if(evt.isControlDown())
-           alignFrame.cut_actionPerformed(null);
-           break;
-         case KeyEvent.VK_C:
-         if(evt.isControlDown())
-           alignFrame.copy_actionPerformed(null);
-           break;
-         case KeyEvent.VK_V:
-          if(evt.isControlDown())
-           alignFrame.paste(true);
-           break;
-         case KeyEvent.VK_A:
-         if(evt.isControlDown())
-           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
-           break;
+    public void keyPressed(KeyEvent evt)
+    {
+      // System.out.println(evt.getKeyCode()); log.
+      switch (evt.getKeyCode())
+      {
+        case 27: // escape key
+          alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);
+          break;
+        case KeyEvent.VK_X:
+          if (evt.isControlDown())
+          {
+            alignFrame.cut_actionPerformed(null);
+          }
+          break;
+        case KeyEvent.VK_C:
+          if (evt.isControlDown())
+          {
+            alignFrame.copy_actionPerformed(null);
+          }
+          break;
+        case KeyEvent.VK_V:
+          if (evt.isControlDown())
+          {
+            alignFrame.paste(true);
+          }
+          break;
+        case KeyEvent.VK_A:
+          if (evt.isControlDown())
+          {
+            alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
+          }
+          break;
         case KeyEvent.VK_DOWN:
           alignFrame.moveSelectedSequences(false);
           break;
@@ -105,11 +145,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
           alignFrame.moveSelectedSequences(true);
           break;
         case KeyEvent.VK_F:
-         if(evt.isControlDown())
-          alignFrame.findMenuItem_actionPerformed(null);
+          if (evt.isControlDown())
+          {
+            alignFrame.findMenuItem_actionPerformed(null);
+          }
           break;
-       }
-     }
+        case KeyEvent.VK_BACK_SPACE:
+        case KeyEvent.VK_DELETE:
+          alignFrame.cut_actionPerformed(null);
+          break;
+
+      }
+    }
   }
 
   public void fontChanged()
@@ -118,8 +165,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     // to prevent drawing old image
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    scalePanel.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
-    idwidthAdjuster.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
+    scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
+    idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
 
     annotationPanel.adjustPanelHeight();
     annotationPanel.repaint();
@@ -129,21 +176,25 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     hscrollFillerPanel.setSize(d);
 
     alignFrame.pack();
+
+    if(overviewPanel!=null)
+          overviewPanel.updateOverviewImage();
   }
 
   public void setIdWidth(int w, int h)
   {
-    idPanel.idCanvas.setSize(w,h);
-    idPanelHolder.setSize(w,idPanelHolder.getSize().height);
-    alabels.setSize(w,alabels.getSize().height);
+    idPanel.idCanvas.setSize(w, h);
+    idPanelHolder.setSize(w, idPanelHolder.getSize().height);
+    alabels.setSize(w, alabels.getSize().height);
     validate();
   }
+
   Dimension calculateIdWidth()
   {
     Frame frame = new Frame();
     frame.addNotify();
     Graphics g = frame.getGraphics();
-    if(g==null)
+    if (g == null)
     {
       Frame f = new Frame();
       f.addNotify();
@@ -153,110 +204,105 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     FontMetrics fm = g.getFontMetrics(av.font);
     AlignmentI al = av.getAlignment();
 
-       int i   = 0;
-       int idWidth = 0;
-       String id;
-       while (i < al.getHeight() && al.getSequenceAt(i) != null)
-       {
-         SequenceI s   = al.getSequenceAt(i);
-         if(av.getShowFullId())
-           id   = s.getDisplayId();
-         else
-           id = s.getName();
-
-         if (fm.stringWidth(id) > idWidth)
-           idWidth = fm.stringWidth(id);
-         i++;
-       }
-
-       // Also check annotation label widths
-       i=0;
-       if(al.getAlignmentAnnotation()!=null)
-       {
-         fm = g.getFontMetrics(frame.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, idPanel.idCanvas.getSize().height);
-  }
-
+    int i = 0;
+    int idWidth = 0;
+    String id;
+    while (i < al.getHeight() && al.getSequenceAt(i) != null)
+    {
+      SequenceI s = al.getSequenceAt(i);
+      id = s.getDisplayId(av.getShowJVSuffix());
 
- public void highlightSearchResults(int [] results)
- {
-   seqPanel.seqCanvas.highlightSearchResults( results );
+      if (fm.stringWidth(id) > idWidth)
+      {
+        idWidth = fm.stringWidth(id);
+      }
+      i++;
+    }
 
-   // 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]);
+    // Also check annotation label widths
+    i = 0;
+    if (al.getAlignmentAnnotation() != null)
+    {
+      fm = g.getFontMetrics(frame.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, idPanel.idCanvas.getSize().height);
+  }
 
- }
+  public void highlightSearchResults(int[] results)
+  {
+    seqPanel.seqCanvas.highlightSearchResults(results);
 
+    // do we need to scroll the panel?
+    if (results != null)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(results[0]);
+      int start = seq.findIndex(results[1]) - 1;
+      int end = seq.findIndex(results[2]) - 1;
+      if (av.getStartRes() > start
+          || av.getEndRes() < end
+          || (av.getStartSeq() > results[0]
+              || av.getEndSeq() < results[0]))
+      {
+        setScrollValues(start, results[0]);
+      }
+    }
 
- public OverviewPanel getOverviewPanel()
- {
-   return overviewPanel;
- }
+  }
 
- public void setOverviewPanel(OverviewPanel op)
- {
-   overviewPanel = op;
- }
+  public OverviewPanel getOverviewPanel()
+  {
+    return overviewPanel;
+  }
 
+  public void setOverviewPanel(OverviewPanel op)
+  {
+    overviewPanel = op;
+  }
 
   public void setAnnotationVisible(boolean b)
   {
-    annotationSpaceFillerHolder.setVisible(b);
-    annotationScroller.setVisible(b);
+    if (!av.wrapAlignment)
+    {
+      annotationSpaceFillerHolder.setVisible(b);
+      annotationScroller.setVisible(b);
+    }
+    validate();
+    repaint();
   }
 
-
   public void setWrapAlignment(boolean wrap)
   {
+    av.startSeq = 0;
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
 
-    av.setShowAnnotation(!wrap);
-    annotationScroller.setVisible(!wrap);
-    annotationSpaceFillerHolder.setVisible(!wrap);
-    idSpaceFillerPanel1.setVisible(!wrap);
-
-    repaint();
-
-  }
-
-
-  public void setColourScheme()
-  {
-    ColourSchemeI cs = av.getGlobalColourScheme();
-
-    if(av.getConservationSelected())
+    if (wrap)
     {
-
-       Alignment al = (Alignment)av.getAlignment();
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
-
-       c.calculate();
-       c.verdict(false, av.ConsPercGaps);
-       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
-
-       av.setGlobalColourScheme( ccs );
-
+      annotationScroller.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
+    else if (av.showAnnotation)
+    {
+      annotationScroller.setVisible(true);
+      annotationSpaceFillerHolder.setVisible(true);
     }
 
+    idSpaceFillerPanel1.setVisible(!wrap);
+
+    validate();
     repaint();
+
   }
 
 
@@ -266,18 +312,22 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   // return value is true if the scroll is valid
   public boolean scrollUp(boolean up)
   {
-    if(up)
+    if (up)
     {
-      if(vscroll.getValue()<1)
+      if (vscroll.getValue() < 1)
+      {
         return false;
-      fastPaint  = false;
+      }
+      fastPaint = false;
       vscroll.setValue(vscroll.getValue() - 1);
     }
     else
     {
-     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
-       return false;
-      fastPaint  = false;
+      if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
+      {
+        return false;
+      }
+      fastPaint = false;
       vscroll.setValue(vscroll.getValue() + 1);
     }
     fastPaint = true;
@@ -290,14 +340,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     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);
     }
@@ -305,47 +359,57 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     return true;
   }
 
-
   public void setScrollValues(int x, int y)
   {
 
     av.setStartRes(x);
     av.setStartSeq(y);
-    av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
+    av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);
 
-    hextent = seqPanel.seqCanvas.getSize().width/av.charWidth;
-    vextent = seqPanel.seqCanvas.getSize().height/av.charHeight;
+    hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
+    vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
 
-    if(hextent > av.alignment.getWidth())
+    if (hextent > av.alignment.getWidth())
+    {
       hextent = av.alignment.getWidth();
-    if(vextent > av.alignment.getHeight())
+    }
+    if (vextent > av.alignment.getHeight())
+    {
       vextent = av.alignment.getHeight();
+    }
 
-    if(hextent+x  >  av.getAlignment().getWidth())
-      x =  av.getAlignment().getWidth()- hextent;
+    if (hextent + x > av.getAlignment().getWidth())
+    {
+      x = av.getAlignment().getWidth() - hextent;
+    }
 
-    if(vextent+y > av.getAlignment().getHeight())
+    if (vextent + y > av.getAlignment().getHeight())
+    {
       y = av.getAlignment().getHeight() - vextent;
+    }
 
-    if(y<0)
+    if (y < 0)
+    {
       y = 0;
+    }
 
-    if(x<0)
-      x=0;
-
+    if (x < 0)
+    {
+      x = 0;
+    }
 
     int endSeq = y + vextent;
-    if(endSeq>av.alignment.getHeight())
+    if (endSeq > av.alignment.getHeight())
+    {
       endSeq = av.alignment.getHeight();
+    }
 
-
-    av.setEndSeq( endSeq );
-    hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
-    vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+    av.setEndSeq(endSeq);
+    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
+    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
 
   }
 
-
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     int oldX = av.getStartRes();
@@ -355,7 +419,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
+      av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
+                   1);
     }
 
     if (evt.getSource() == vscroll)
@@ -363,22 +428,28 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       int offy = vscroll.getValue();
       if (av.getWrapAlignment())
       {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-        av.setStartRes( vscroll.getValue() * rowSize );
-        av.setEndRes( (vscroll.getValue()+1) * rowSize );
+        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
+            seqCanvas.getSize().width);
+        av.setStartRes(vscroll.getValue() * rowSize);
+        av.setEndRes( (vscroll.getValue() + 1) * rowSize);
       }
       else
       {
         av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height / av.getCharHeight());
+        av.setEndSeq(offy +
+                     seqPanel.seqCanvas.getSize().height / av.getCharHeight());
       }
     }
 
-    if(overviewPanel!=null)
+    if (overviewPanel != null)
+    {
       overviewPanel.setBoxPosition();
+    }
 
-    if(av.getWrapAlignment() || !fastPaint)
+    if (av.getWrapAlignment() || !fastPaint || MAC)
+    {
       repaint();
+    }
     else
     {
       idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
@@ -387,34 +458,32 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
       scalePanel.repaint();
       if (av.getShowAnnotation())
+      {
         annotationPanel.fastPaint(av.getStartRes() - oldX);
+      }
     }
 
   }
 
   public void update(Graphics g)
   {
-    paint (g);
+    paint(g);
   }
 
-
   public void paint(Graphics g)
   {
     Dimension d = idPanel.idCanvas.getSize();
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
-    annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
-    alabels.setSize(d.width,annotationPanel.getSize().height);
-
-    alabels.repaint();
-    idPanel.idCanvas.repaint();
-    seqPanel.seqCanvas.repaint();
-    scalePanel.repaint();
-    annotationPanel.repaint();
+    annotationSpaceFillerHolder.setSize(d.width,
+                                        annotationPanel.getSize().height);
 
+    alabels.setSize(d.width, annotationPanel.getSize().height);
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+      int max = av.alignment.getWidth() /
+          seqPanel.seqCanvas.
+          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1;
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);
@@ -424,7 +493,86 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
+    alabels.repaint();
+    idPanel.idCanvas.repaint();
+    seqPanel.seqCanvas.repaint();
+    scalePanel.repaint();
+    annotationPanel.repaint();
+
+    if (getBounds() == g.getClipBounds())
+    {
+      if (overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+    }
 
+  }
 
+  protected Panel sequenceHolderPanel = new Panel();
+  protected Scrollbar vscroll = new Scrollbar();
+  protected Scrollbar hscroll = new Scrollbar();
+  protected Panel seqPanelHolder = new Panel();
+  BorderLayout borderLayout1 = new BorderLayout();
+  BorderLayout borderLayout3 = new BorderLayout();
+  protected Panel scalePanelHolder = new Panel();
+  protected Panel idPanelHolder = new Panel();
+  BorderLayout borderLayout5 = new BorderLayout();
+  protected Panel idSpaceFillerPanel1 = new Panel();
+  public Panel annotationSpaceFillerHolder = new Panel();
+  BorderLayout borderLayout6 = new BorderLayout();
+  BorderLayout borderLayout7 = new BorderLayout();
+  Panel hscrollHolder = new Panel();
+  BorderLayout borderLayout10 = new BorderLayout();
+  protected Panel hscrollFillerPanel = new Panel();
+  BorderLayout borderLayout11 = new BorderLayout();
+  public Panel annotationScroller = new Panel();
+  BorderLayout borderLayout4 = new BorderLayout();
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  private void jbInit() throws Exception {
+      //  idPanelHolder.setPreferredSize(new Dimension(70, 10));
+      this.setLayout(borderLayout7);
+
+      //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+      sequenceHolderPanel.setLayout(borderLayout3);
+      seqPanelHolder.setLayout(borderLayout1);
+      scalePanelHolder.setBackground(Color.white);
+
+      // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
+      scalePanelHolder.setLayout(borderLayout6);
+      idPanelHolder.setLayout(borderLayout5);
+      idSpaceFillerPanel1.setBackground(Color.white);
+
+      //  idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+      idSpaceFillerPanel1.setLayout(borderLayout11);
+      annotationSpaceFillerHolder.setBackground(Color.white);
+
+      //  annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+      annotationSpaceFillerHolder.setLayout(borderLayout4);
+      hscroll.setOrientation(Scrollbar.HORIZONTAL);
+      hscrollHolder.setLayout(borderLayout10);
+      hscrollFillerPanel.setBackground(Color.white);
+
+      //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+      hscrollHolder.setBackground(Color.white);
+
+      //    annotationScroller.setPreferredSize(new Dimension(10, 80));
+      //  this.setPreferredSize(new Dimension(220, 166));
+      seqPanelHolder.setBackground(Color.white);
+      idPanelHolder.setBackground(Color.white);
+      annotationScroller.setLayout(borderLayout2);
+      sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
+      sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
+      seqPanelHolder.add(vscroll, BorderLayout.EAST);
+      sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
+
+      //  Panel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
+      this.add(idPanelHolder, BorderLayout.WEST);
+      idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
+      idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
+      this.add(hscrollHolder, BorderLayout.SOUTH);
+      hscrollHolder.add(hscroll, BorderLayout.CENTER);
+      hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
+      this.add(sequenceHolderPanel, BorderLayout.CENTER);
   }
+
 }