From 49901c2879a03b48fafb84a251e976230459c77f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 16 Nov 2004 15:15:56 +0000
Subject: [PATCH] halfway to wrap alignment

---
 src/jalview/gui/AlignmentPanel.java |   38 +++++++++++++++++++----------------
 1 file changed, 21 insertions(+), 17 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index df0459f..11c9e2b 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -3,18 +3,17 @@ package jalview.gui;
 import jalview.jbgui.GAlignmentPanel;
 import java.awt.*;
 import java.awt.event.*;
-import java.io.*;
 
 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener
 {
 
   AlignViewport     av;
   OverviewPanel overviewPanel;
-  public SeqPanel   seqPanel;
-  public IdPanel    idPanel;
+  SeqPanel   seqPanel;
+  IdPanel    idPanel;
   public AlignFrame alignFrame;
-  public ScalePanel scalePanel;
-  public ScorePanel scorePanel;
+  ScalePanel scalePanel;
+  ScorePanel scorePanel;
 
   public boolean    groupEdit = false;
 
@@ -27,7 +26,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     scalePanel = new ScalePanel(av);
     scorePanel = new ScorePanel(av);
 
-
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idPanel.addNotify();
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
@@ -43,8 +41,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    {
        public void componentResized(ComponentEvent evt)
      {
-     //  if(!initialising)
-     RefreshPanels();
+          RefreshPanels();
      }
    });
 
@@ -58,7 +55,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   public void selectAll(boolean flag) {
     int i = 0;
     if (flag) {
-      while (i < seqPanel.align.getHeight()) {
+      while (i < av.getAlignment().getHeight()) {
         if (! av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
           av.getSelection().addElement(av.getAlignment().getSequenceAt(i));
         }
@@ -87,9 +84,22 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     RefreshPanels();
   }
 
-  public void setColourScheme(jalview.schemes.ColourSchemeI cs)
+  public void setWrapAlignment(boolean wrap)
+  {
+
+      scalePanelHolder.setVisible(!wrap);
+      scorePanelHolder.setVisible(!wrap);
+
+      hscroll.setVisible(!wrap);
+      idSpaceFillerPanel.setVisible(!wrap);
+      idSpaceFillerPanel1.setVisible(!wrap);
+
+  }
+
+
+  public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
   {
-    seqPanel.setColourScheme(cs);
+    seqPanel.setColourScheme(cs, conservation);
     if(overviewPanel!=null)
       overviewPanel.updateOverviewImage();
   }
@@ -97,12 +107,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void RefreshPanels()
   {
-
-  /*  try{
-      ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream("dump.dat"));
-      out.writeObject( (jalview.datamodel.Alignment)av.getAlignment() );
-    }catch(IOException ex){ex.printStackTrace();}*/
-
     invalidate();
     validate();
     idPanel.idCanvas.paintFlag = true;
-- 
1.7.10.2