Remove ref in PaintRefresher on close, changeColour updated

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