Allowed for addition of OverviewPanel

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index cf3e3df..df0459f 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -2,13 +2,14 @@ package jalview.gui;
 \r
 import jalview.jbgui.GAlignmentPanel;\r
 import java.awt.*;\r
-import javax.swing.*;\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
   public AlignFrame alignFrame;\r
@@ -26,7 +27,9 @@ 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
     scorePanelHolder.add(scorePanel, BorderLayout.CENTER);\r
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
@@ -39,7 +42,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     addComponentListener(new ComponentAdapter()\r
    {\r
        public void componentResized(ComponentEvent evt)\r
-     {      RefreshPanels();    }\r
+     {\r
+     //  if(!initialising)\r
+     RefreshPanels();\r
+     }\r
    });\r
 \r
   }\r
@@ -63,6 +69,15 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     }\r
   }\r
 \r
+ public OverviewPanel getOverviewPanel()\r
+ {\r
+   return overviewPanel;\r
+ }\r
+\r
+ public void setOverviewPanel(OverviewPanel op)\r
+ {\r
+   overviewPanel = op;\r
+ }\r
 \r
 \r
   public void setGraphPanelVisible(boolean b)\r
@@ -72,18 +87,34 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     RefreshPanels();\r
   }\r
 \r
+  public void setColourScheme(jalview.schemes.ColourSchemeI cs)\r
+  {\r
+    seqPanel.setColourScheme(cs);\r
+    if(overviewPanel!=null)\r
+      overviewPanel.updateOverviewImage();\r
+  }\r
 \r
 \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
-    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
     validate();\r
     idPanel.idCanvas.paintFlag = true;\r
+    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
     seqPanel.seqCanvas.paintFlag = true;\r
     setScrollValues(av.getStartRes(), av.getStartSeq());\r
     av.getConsensus(true);\r
     repaint();\r
+\r
+    if(overviewPanel!=null)\r
+      overviewPanel.updateOverviewImage();\r
+\r
   }\r
 \r
   int hextent = 0;\r
@@ -108,11 +139,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 \r
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
+    seqPanel.seqCanvas.paintFlag = true;\r
+    repaint();\r
 \r
   }\r
 \r
 \r
-  public void adjustmentValueChanged(AdjustmentEvent evt) {\r
+  public void adjustmentValueChanged(AdjustmentEvent evt)\r
+  {\r
 \r
     if (evt.getSource() == hscroll)\r
     {\r
@@ -128,6 +162,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
         av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());\r
     }\r
 \r
+\r
+    if(overviewPanel!=null)\r
+      overviewPanel.setBoxPosition();\r
+\r
+\r
     repaint();\r
   }\r
 \r