From dbfdb02d549e91942095e39c2a50259b1c54c256 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 15 Apr 2005 14:57:25 +0000
Subject: [PATCH] PID and conservation colouring changes

---
 src/jalview/gui/AlignFrame.java |  158 +++++++++++++++++++++------------------
 1 file changed, 86 insertions(+), 72 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9ec2f23..b00a584 100755
--- 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 );
     frame.setContentPane(fc);
     Desktop.addInternalFrame(frame, "Change Font", 480,100);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
@@ -765,106 +766,130 @@ public class AlignFrame extends GAlignFrame
 
   void changeColour(ColourSchemeI cs)
   {
+    int threshold = 0;
 
-    if(viewport.getColourAppliesToAllGroups())
+    if ( viewport.getAbovePIDThreshold() )
     {
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-        sg.cs = cs;
+      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
-        if(abovePIDThreshold.isSelected())
-          abovePIDThreshold_actionPerformed(null);
-        else if( viewport.getConservationSelected() )
-        {
-          Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.sequences, sg.getStartRes(),
-                                            sg.getEndRes());
-          c.calculate();
-          c.verdict(false, viewport.ConsPercGaps);
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-          sg.cs = ccs;
-        }
+      if (cs instanceof ResidueColourScheme)
+        ( (ResidueColourScheme) cs).setThreshold(threshold);
+      else if (cs instanceof ScoreColourScheme)
+        ( (ScoreColourScheme) cs).setThreshold(threshold);
 
-      }
+      viewport.setGlobalColourScheme(cs);
     }
+    else if (cs instanceof ResidueColourScheme)
+      ( (ResidueColourScheme) cs).setThreshold(0);
+    else if (cs instanceof ScoreColourScheme)
+      ( (ScoreColourScheme) cs).setThreshold(0);
 
 
-    if ( viewport.getAbovePIDThreshold() )
+
+    if (viewport.getConservationSelected())
     {
- //     int threshold = 0;
-   //   threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
-      Desktop.hideConservationSlider();
+      ConservationColourScheme ccs = null;
 
- //     if (cs instanceof ResidueColourScheme)
- //       ( (ResidueColourScheme) cs).setThreshold(threshold);
-  //    else if (cs instanceof ScoreColourScheme)
-   //     ( (ScoreColourScheme) cs).setThreshold(threshold);
+      Alignment al = (Alignment) viewport.alignment;
+      Conservation c = new Conservation("All",
+                                        ResidueProperties.propHash, 3,
+                                        al.getSequences(), 0,
+                                        al.getWidth() - 1);
 
-      viewport.setGlobalColourScheme(cs);
+      c.calculate();
+      c.verdict(false, viewport.ConsPercGaps);
+
+      ccs = new ConservationColourScheme(c, cs);
+
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      ccs.setConsensus( viewport.vconsensus );
+      viewport.setGlobalColourScheme(ccs);
 
     }
     else
-    if (cs instanceof ResidueColourScheme)
-      ( (ResidueColourScheme) cs).setThreshold(0);
-    else if (cs instanceof ScoreColourScheme)
-      ( (ScoreColourScheme) cs).setThreshold(0);
+    {
+        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      cs.setConsensus( viewport.vconsensus );
+      viewport.setGlobalColourScheme(cs);
+    }
 
 
+    if(viewport.getColourAppliesToAllGroups())
+    {
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 
 
-if ( viewport.getConservationSelected() )
- {
-   ConservationColourScheme ccs = null;
+        try{
+          sg.cs = (ColourSchemeI)cs.getClass().newInstance();
+        }catch(Exception ex){}
 
-   Alignment al = (Alignment) viewport.alignment;
-   Conservation c = new Conservation("All",
-                                     ResidueProperties.propHash, 3,
-                                     al.getSequences(), 0,
-                                     al.getWidth()-1);
+        if(viewport.getAbovePIDThreshold())
+        {
+          if (sg.cs instanceof ResidueColourScheme)
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+          else if (sg.cs instanceof ScoreColourScheme)
+            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
 
-   c.calculate();
-   c.verdict(false, viewport.ConsPercGaps);
+           sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+        }
 
-   ccs = new ConservationColourScheme(c, cs);
+        if( viewport.getConservationSelected() )
+        {
+          Conservation c = new Conservation("Group",
+                                            ResidueProperties.propHash, 3,
+                                            sg.sequences, 0, viewport.alignment.getWidth()-1);
+          c.calculate();
+          c.verdict(false, viewport.ConsPercGaps);
+          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs = ccs;
+        }
+        else
+        {
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+        }
+
+      }
+    }
 
-   viewport.setGlobalColourScheme(ccs);
 
-  }
-  else
-       viewport.setGlobalColourScheme( cs );
 
     alignPanel.RefreshPanels();
   }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if(viewport.getAbovePIDThreshold())
-    Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");
+      if(viewport.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+                                   "Background");
+        SliderPanel.showPIDSlider();
+      }
   }
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
     if(viewport.getConservationSelected())
-    Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme,    "Background");
+    {
+      SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
+                                        "Background");
+      SliderPanel.showConservationSlider();
+    }
   }
 
 
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
-    if(coloursChanging)
-      return;
-
-    coloursChanging = true;
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
-    Desktop.hidePIDSlider();
-    if(!viewport.getConservationSelected())
-      Desktop.hideConservationSlider();
 
    ColourSchemeI cs = viewport.getGlobalColourScheme();
    if(cs instanceof ConservationColourScheme )
@@ -872,33 +897,22 @@ if ( viewport.getConservationSelected() )
     else
       changeColour( cs );
 
-    coloursChanging = false;
   }
 
-  boolean coloursChanging = false;
+ // boolean coloursChanging = false;
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-    if(coloursChanging)
-      return;
-
-    coloursChanging = true;
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 
     conservationMenuItem.setSelected(false);
     viewport.setConservationSelected(false);
-    Desktop.hideConservationSlider();
-
-    if(!viewport.getAbovePIDThreshold())
-      Desktop.hidePIDSlider();
-
 
     ColourSchemeI cs = viewport.getGlobalColourScheme();
+
     if(cs instanceof ConservationColourScheme )
         changeColour( ((ConservationColourScheme)cs).cs );
     else
         changeColour( cs );
-
-    coloursChanging = false;
   }
 
 
@@ -919,7 +933,7 @@ if ( viewport.getConservationSelected() )
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme(viewport) );
+    changeColour(new Blosum62ColourScheme() );
   }
 
 
-- 
1.7.10.2