From c20c49427b35c709b8a7d58c6f5b556efc801fb2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 23 Aug 2005 16:49:16 +0000
Subject: [PATCH] Remove ref in PaintRefresher on close, changeColour updated

---
 src/jalview/appletgui/AlignFrame.java |  103 +++++++++++++++------------------
 1 file changed, 47 insertions(+), 56 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 010c73d..83c66ec 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -39,15 +39,6 @@ public class AlignFrame
   public static final int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
 
-  public AlignFrame(AlignmentI al)
-  {
-    this.applet = null;
-    viewport = new AlignViewport(al, null);
-    alignPanel = new AlignmentPanel(this, viewport);
-    add(alignPanel);
-    alignPanel.validate();
-  }
-
   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
   {
     this.applet = applet;
@@ -82,6 +73,15 @@ public class AlignFrame
       }
     }
 
+    this.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent e)
+          {
+            closeMenuItem_actionPerformed(null);
+          }
+    });
+
+
 
   }
 
@@ -108,6 +108,7 @@ public class AlignFrame
 
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
+    PaintRefresher.components.remove(viewport.alignment);
     dispose();
   }
 
@@ -804,49 +805,48 @@ public class AlignFrame
   {
     int threshold = 0;
 
-    if (viewport.getAbovePIDThreshold())
+    if(cs!=null)
     {
-      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
-
-      cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+      if (viewport.getAbovePIDThreshold())
+      {
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
-      viewport.setGlobalColourScheme(cs);
-    }
-    else
-    {
-      cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-    }
+        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 
-    if (viewport.getConservationSelected())
-    {
+        viewport.setGlobalColourScheme(cs);
+      }
+      else
+      {
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+      }
 
-      Alignment al = (Alignment) viewport.alignment;
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth() - 1);
+      if (viewport.getConservationSelected())
+      {
 
-      c.calculate();
-      c.verdict(false, viewport.ConsPercGaps);
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
 
-      cs.setConservation(c);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
 
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      cs.setConsensus(viewport.vconsensus);
-      viewport.setGlobalColourScheme(cs);
+        cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(alignPanel, cs, "Background");
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
 
-    }
-    else
-    {
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      if (cs != null)
+      }
+      else
       {
-        cs.setConsensus(viewport.vconsensus);
+        cs.setConservation(null);
       }
-      viewport.setGlobalColourScheme(cs);
+
+      cs.setConsensus(viewport.vconsensus);
+
     }
+    viewport.setGlobalColourScheme(cs);
 
     if (viewport.getColourAppliesToAllGroups())
     {
@@ -862,9 +862,7 @@ public class AlignFrame
         }
         if (cs instanceof ClustalxColourScheme)
         {
-          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
-          cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
-          sg.cs = cxs;
+          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
         else
         {
@@ -886,6 +884,8 @@ public class AlignFrame
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
         }
+        else
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
 
         if (viewport.getConservationSelected())
         {
@@ -895,21 +895,16 @@ public class AlignFrame
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
-
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
-          sg.cs = cs;
+          sg.cs.setConservation(c);
         }
         else
         {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs.setConservation(null);
         }
 
       }
     }
 
-    updateCSConsensus();
 
     if (alignPanel.getOverviewPanel() != null)
     {
@@ -919,15 +914,11 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
-  public void updateCSConsensus()
-  {
-    //Colour schemes must have their consensus updated
 
-  }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold())
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
                                      "Background");
@@ -937,7 +928,7 @@ public class AlignFrame
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected())
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
                                         "Background");
-- 
1.7.10.2