halfway to wrap alignment

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