PID and conservation colouring changes

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9ec2f23..b00a584 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -581,6 +581,7 @@ public class AlignFrame extends GAlignFrame
     FontChooser fc = new FontChooser( alignPanel, frame );\r
     frame.setContentPane(fc);\r
     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
   }\r
 \r
   protected void fullSeqId_actionPerformed(ActionEvent e)\r
@@ -765,106 +766,130 @@ public class AlignFrame extends GAlignFrame
 \r
   void changeColour(ColourSchemeI cs)\r
   {\r
+    int threshold = 0;\r
 \r
-    if(viewport.getColourAppliesToAllGroups())\r
+    if ( viewport.getAbovePIDThreshold() )\r
     {\r
-      Vector groups = viewport.alignment.getGroups();\r
-      for(int i=0; i<groups.size(); i++)\r
-      {\r
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
-        sg.cs = cs;\r
+      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 \r
-        if(abovePIDThreshold.isSelected())\r
-          abovePIDThreshold_actionPerformed(null);\r
-        else if( viewport.getConservationSelected() )\r
-        {\r
-          Conservation c = new Conservation("Group",\r
-                                            ResidueProperties.propHash, 3,\r
-                                            sg.sequences, sg.getStartRes(),\r
-                                            sg.getEndRes());\r
-          c.calculate();\r
-          c.verdict(false, viewport.ConsPercGaps);\r
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-          sg.cs = ccs;\r
-        }\r
+      if (cs instanceof ResidueColourScheme)\r
+        ( (ResidueColourScheme) cs).setThreshold(threshold);\r
+      else if (cs instanceof ScoreColourScheme)\r
+        ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 \r
-      }\r
+      viewport.setGlobalColourScheme(cs);\r
     }\r
+    else if (cs instanceof ResidueColourScheme)\r
+      ( (ResidueColourScheme) cs).setThreshold(0);\r
+    else if (cs instanceof ScoreColourScheme)\r
+      ( (ScoreColourScheme) cs).setThreshold(0);\r
 \r
 \r
-    if ( viewport.getAbovePIDThreshold() )\r
+\r
+    if (viewport.getConservationSelected())\r
     {\r
- //     int threshold = 0;\r
-   //   threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
-      Desktop.hideConservationSlider();\r
+      ConservationColourScheme ccs = null;\r
 \r
- //     if (cs instanceof ResidueColourScheme)\r
- //       ( (ResidueColourScheme) cs).setThreshold(threshold);\r
-  //    else if (cs instanceof ScoreColourScheme)\r
-   //     ( (ScoreColourScheme) cs).setThreshold(threshold);\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
-      viewport.setGlobalColourScheme(cs);\r
+      c.calculate();\r
+      c.verdict(false, viewport.ConsPercGaps);\r
+\r
+      ccs = new ConservationColourScheme(c, cs);\r
+\r
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+      ccs.setConsensus( viewport.vconsensus );\r
+      viewport.setGlobalColourScheme(ccs);\r
 \r
     }\r
     else\r
-    if (cs instanceof ResidueColourScheme)\r
-      ( (ResidueColourScheme) cs).setThreshold(0);\r
-    else if (cs instanceof ScoreColourScheme)\r
-      ( (ScoreColourScheme) cs).setThreshold(0);\r
+    {\r
+        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+      cs.setConsensus( viewport.vconsensus );\r
+      viewport.setGlobalColourScheme(cs);\r
+    }\r
 \r
 \r
+    if(viewport.getColourAppliesToAllGroups())\r
+    {\r
+      Vector groups = viewport.alignment.getGroups();\r
+      for(int i=0; i<groups.size(); i++)\r
+      {\r
+        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 \r
 \r
-if ( viewport.getConservationSelected() )\r
- {\r
-   ConservationColourScheme ccs = null;\r
+        try{\r
+          sg.cs = (ColourSchemeI)cs.getClass().newInstance();\r
+        }catch(Exception ex){}\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.getAbovePIDThreshold())\r
+        {\r
+          if (sg.cs instanceof ResidueColourScheme)\r
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+          else if (sg.cs instanceof ScoreColourScheme)\r
+            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 \r
-   c.calculate();\r
-   c.verdict(false, viewport.ConsPercGaps);\r
+           sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
+        }\r
 \r
-   ccs = new ConservationColourScheme(c, cs);\r
+        if( viewport.getConservationSelected() )\r
+        {\r
+          Conservation c = new Conservation("Group",\r
+                                            ResidueProperties.propHash, 3,\r
+                                            sg.sequences, 0, viewport.alignment.getWidth()-1);\r
+          c.calculate();\r
+          c.verdict(false, viewport.ConsPercGaps);\r
+          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+\r
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+          ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+          sg.cs = ccs;\r
+        }\r
+        else\r
+        {\r
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+        }\r
+\r
+      }\r
+    }\r
 \r
-   viewport.setGlobalColourScheme(ccs);\r
 \r
-  }\r
-  else\r
-       viewport.setGlobalColourScheme( cs );\r
 \r
     alignPanel.RefreshPanels();\r
   }\r
 \r
   protected void modifyPID_actionPerformed(ActionEvent e)\r
   {\r
-    if(viewport.getAbovePIDThreshold())\r
-    Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");\r
+      if(viewport.getAbovePIDThreshold())\r
+      {\r
+        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
+                                   "Background");\r
+        SliderPanel.showPIDSlider();\r
+      }\r
   }\r
 \r
   protected void modifyConservation_actionPerformed(ActionEvent e)\r
   {\r
     if(viewport.getConservationSelected())\r
-    Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme,    "Background");\r
+    {\r
+      SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
+                                        "Background");\r
+      SliderPanel.showConservationSlider();\r
+    }\r
   }\r
 \r
 \r
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
-    if(coloursChanging)\r
-      return;\r
-\r
-    coloursChanging = true;\r
 \r
     viewport.setAbovePIDThreshold(false);\r
     abovePIDThreshold.setSelected(false);\r
-    Desktop.hidePIDSlider();\r
-    if(!viewport.getConservationSelected())\r
-      Desktop.hideConservationSlider();\r
 \r
    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
    if(cs instanceof ConservationColourScheme )\r
@@ -872,33 +897,22 @@ if ( viewport.getConservationSelected() )
     else\r
       changeColour( cs );\r
 \r
-    coloursChanging = false;\r
   }\r
 \r
-  boolean coloursChanging = false;\r
+ // boolean coloursChanging = false;\r
   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
   {\r
-    if(coloursChanging)\r
-      return;\r
-\r
-    coloursChanging = true;\r
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 \r
     conservationMenuItem.setSelected(false);\r
     viewport.setConservationSelected(false);\r
-    Desktop.hideConservationSlider();\r
-\r
-    if(!viewport.getAbovePIDThreshold())\r
-      Desktop.hidePIDSlider();\r
-\r
 \r
     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+\r
     if(cs instanceof ConservationColourScheme )\r
         changeColour( ((ConservationColourScheme)cs).cs );\r
     else\r
         changeColour( cs );\r
-\r
-    coloursChanging = false;\r
   }\r
 \r
 \r
@@ -919,7 +933,7 @@ if ( viewport.getConservationSelected() )
 \r
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
   {\r
-    changeColour(new Blosum62ColourScheme(viewport) );\r
+    changeColour(new Blosum62ColourScheme() );\r
   }\r
 \r
 \r