From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 1 Feb 2005 19:02:28 +0000 (+0000)
Subject: Conservation and PID colouring methods updated
X-Git-Tag: Release_2_0~709
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f202be793ee0fd5027b8e602761f9860d7eb1ddd;p=jalview.git

Conservation and PID colouring methods updated
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5173fed..9a87b90 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -39,6 +39,9 @@ public class AlignFrame extends GAlignFrame
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
     fontNameMenuItem.setText(viewport.getFont().getName());
     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
+
+    clustalColour.setSelected(true);
+    clustalColour_actionPerformed(null);
   }
 
   protected void saveAs_actionPerformed(ActionEvent e)
@@ -478,8 +481,8 @@ public class AlignFrame extends GAlignFrame
 
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
-    conservationMenuItem.setSelected(false);
+    viewport.setGlobalColourScheme(
+      new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
     abovePIDThreshold.setSelected(false);
     changeColour();
   }
@@ -544,119 +547,98 @@ public class AlignFrame extends GAlignFrame
     else if(conservationMenuItem.isSelected())
       conservationMenuItem_actionPerformed(null);
 
-
-     alignPanel.RefreshPanels();
+    alignPanel.RefreshPanels();
   }
 
-  void addConservationOrPIDColour()
+
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
-    int x=0, y=0, threshold = 70;
+   if(abovePIDThreshold.isSelected())
+   {
+     abovePIDThreshold.setSelected(false);
+     Desktop.hidePIDSlider();
+   }
 
-    if(sliderFrame!=null)
-       try
-       {
-         x = sliderFrame.getX();
-         y = sliderFrame.getY();
-         SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
-         threshold = sp.getValue();
-         sliderFrame.setClosed(true);
-       }
-       catch (Exception ex)
-       {    ex.printStackTrace();   }
+   viewport.setConservationSelected(conservationMenuItem.isSelected());
 
-     ColourSchemeI oldCs = viewport.getGlobalColourScheme();
+   ColourSchemeI oldCs = viewport.getGlobalColourScheme();
 
-     ConservationColourScheme ccs = null;
-     if (oldCs instanceof ConservationColourScheme)
-       ccs = (ConservationColourScheme) oldCs;
+   ConservationColourScheme ccs = null;
+   if (oldCs instanceof ConservationColourScheme)
+         ccs = (ConservationColourScheme) oldCs;
 
-     if(conservationMenuItem.isSelected())
-     {
-       Alignment al = (Alignment)viewport.alignment;
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
+       if (conservationMenuItem.isSelected())
+       {
+         Alignment al = (Alignment) viewport.alignment;
+         Conservation c = new Conservation("All",
+                                           ResidueProperties.propHash, 3,
+                                           al.getSequences(), 0,
+                                           al.getWidth());
 
-       c.calculate();
-       c.verdict(false, 100);
+         c.calculate();
+         c.verdict(false, 100);
 
-       if(ccs!=null)
-         ccs = new ConservationColourScheme(c, ccs.cs);
-       else
-         ccs = new ConservationColourScheme(c, oldCs);
+         if (ccs != null)
+           ccs = new ConservationColourScheme(c, ccs.cs);
+         else
+           ccs = new ConservationColourScheme(c, oldCs);
 
-        viewport.setGlobalColourScheme( ccs );
 
-     }
-     else if(oldCs instanceof ConservationColourScheme)
-     {
-       oldCs = ccs.cs;
-       viewport.setGlobalColourScheme( oldCs );
-     }
+         int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");
 
+         ccs.inc = threshold;
+
+         if (ccs.cs instanceof ResidueColourScheme)
+           ((ResidueColourScheme) ccs.cs).setThreshold(0);
+         else if (ccs.cs instanceof ScoreColourScheme)
+           ((ScoreColourScheme)ccs.cs).setThreshold(0);
+
+         viewport.setGlobalColourScheme(ccs);
 
-     if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
-     {
-       sliderFrame = new JInternalFrame();
-       sliderFrame.setMaximizable(false);
-       sliderFrame.setResizable(false);
 
-       SliderPanel sp = null;
-       if (conservationMenuItem.isSelected())
-       {
-        if(threshold > 50)
-          threshold = 30;
-        sp = new SliderPanel(alignPanel, threshold, true,ccs);
-        Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);
-        threshold = 0;
        }
-       else if (abovePIDThreshold.isSelected())
+       else if (oldCs instanceof ConservationColourScheme)
        {
-         sp = new SliderPanel(alignPanel, threshold, false, oldCs);
-         sp.cs = oldCs;
-         Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
+         /// ie, if we remove ConservationColourScheme from backgroundColour
+         oldCs = ccs.cs;
+         viewport.setGlobalColourScheme(oldCs);
+         Desktop.hideConservationSlider();
        }
 
-       sliderFrame.setContentPane(sp);
-       if(x!=0 && y!=0)
-               sliderFrame.setLocation(x,y);
+       if(e!=null)
+         alignPanel.RefreshPanels();
+  }
 
-     }
-     else
-       threshold = 0;
 
+  public void abovePIDThreshold_actionPerformed(ActionEvent e)
+  {
+      if(conservationMenuItem.isSelected())
+        conservationMenuItem.setSelected(false);
 
-     if (oldCs instanceof ResidueColourScheme)
+      ColourSchemeI oldCs = viewport.getGlobalColourScheme();
+      int threshold = 0;
+      if (oldCs instanceof ConservationColourScheme)
      {
-       ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
-       rcs.setThreshold(threshold);
+       ConservationColourScheme ccs = (ConservationColourScheme) oldCs;
+       oldCs = ccs.cs;
      }
-     else if (oldCs instanceof ScoreColourScheme)
+
+     if(abovePIDThreshold.isSelected())
      {
-       ScoreColourScheme scs = (ScoreColourScheme) oldCs;
-       scs.setThreshold(threshold);
+       threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");
+       Desktop.hideConservationSlider();
      }
+     else
+       Desktop.hidePIDSlider();
 
+      if (oldCs instanceof ResidueColourScheme)
+          ((ResidueColourScheme) oldCs).setThreshold(threshold);
+      else if (oldCs instanceof ScoreColourScheme)
+          ((ScoreColourScheme)oldCs).setThreshold(threshold);
 
-  }
-
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-   if(abovePIDThreshold.isSelected())
-    abovePIDThreshold.setSelected(false);
-
-   viewport.setConservationSelected(conservationMenuItem.isSelected());
-
-   addConservationOrPIDColour();
-  }
-
-  JInternalFrame sliderFrame;
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)
-  {
-      if(conservationMenuItem.isSelected())
-        conservationMenuItem.setSelected(false);
-
-      addConservationOrPIDColour();
+    viewport.setGlobalColourScheme(oldCs);
+     if(e!=null)
+        alignPanel.RefreshPanels();
   }
 
 
@@ -682,7 +664,7 @@ public class AlignFrame extends GAlignFrame
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
-    alignPanel.setColourScheme();
+    changeColour();
   }
 
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 464ec59..2c475fa 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -12,6 +12,7 @@ package jalview.gui;
 import jalview.gui.*;
 import jalview.io.*;
 import jalview.datamodel.*;
+import jalview.schemes.*;
 import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
@@ -261,4 +262,86 @@ public class Desktop extends jalview.jbgui.GDesktop
    }
  }
 
+ static JInternalFrame conservationSlider;
+ static JInternalFrame PIDSlider;
+ public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
+ {
+   SliderPanel sp = null;
+
+   if(conservationSlider == null)
+   {
+     sp = new SliderPanel(ap, 30, true, cs);
+     conservationSlider = new JInternalFrame();
+     conservationSlider.setContentPane(sp);
+     conservationSlider.setResizable(false);
+     addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90);
+     conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+                  {
+                    public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)
+                    {
+                      conservationSlider = null;
+                    }
+                  });
+   }
+   else
+   {
+       conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");
+       sp = (SliderPanel)conservationSlider.getContentPane();
+       sp.cs = cs;
+   }
+
+   if(ap.av.alignment.getGroups()!=null)
+     sp.setAllGroupsCheckEnabled( true );
+   else
+     sp.setAllGroupsCheckEnabled( false);
+
+   return sp.getValue();
+
+ }
+
+ public static void hideConservationSlider()
+ {
+  try{
+    conservationSlider.setClosed(true);
+    conservationSlider = null;
+  }catch(Exception ex){}
+}
+
+
+ public static void hidePIDSlider()
+ {
+   try{
+     PIDSlider.setClosed(true);
+     PIDSlider = null;
+   }catch(Exception ex){}
+ }
+
+ public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
+ {
+   SliderPanel pid = null;
+   if(PIDSlider == null)
+   {
+     pid = new SliderPanel(ap, 50, false, cs);
+     PIDSlider = new JInternalFrame();
+     PIDSlider.setContentPane(pid);
+     PIDSlider.setResizable(false);
+     addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);
+   }
+   else
+   {
+       PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
+       pid = (SliderPanel)PIDSlider.getContentPane();
+       pid.cs = cs;
+   }
+
+   if (ap.av.alignment.getGroups() != null)
+     pid.setAllGroupsCheckEnabled(true);
+   else
+     pid.setAllGroupsCheckEnabled(false);
+
+
+   return pid.getValue();
+
+ }
+
 }