From 5504aa5ac8a832f1c437b38ada4681545ed639f3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 14 Jan 2005 15:46:53 +0000
Subject: [PATCH] Various color bugs sorted out

---
 src/jalview/gui/AlignFrame.java |  187 +++++++++++++++++++++------------------
 1 file changed, 102 insertions(+), 85 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ede7eac..f7b4ac5 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -459,6 +459,8 @@ public class AlignFrame extends GAlignFrame
   public void clustalColour_actionPerformed(ActionEvent e)
   {
     viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
+    conservationMenuItem.setSelected(false);
+    abovePIDThreshold.setSelected(false);
     changeColour();
   }
 
@@ -511,110 +513,125 @@ public class AlignFrame extends GAlignFrame
   void changeColour()
   {
     if(abovePIDThreshold.isSelected())
-    {
       abovePIDThreshold_actionPerformed(null);
-      alignPanel.setColourScheme( );
-    }
     else if(conservationMenuItem.isSelected())
       conservationMenuItem_actionPerformed(null);
-    else
-      alignPanel.setColourScheme( );
 
+     alignPanel.seqPanel.seqCanvas.paintFlag = true;
+     alignPanel.repaint();
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  void addConservationOrPIDColour()
   {
-    viewport.setConservationSelected(conservationMenuItem.isSelected());
+    int x=0, y=0, threshold = 70;
 
-    alignPanel.setColourScheme();
-    ColourSchemeI oldCs = viewport.getGlobalColourScheme();
+    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();   }
 
-    if(conservationMenuItem.isSelected())
-    {
-      if(sliderPanel!=null)
-      {
-        sliderPanel.cs = oldCs;
-      }
+     ColourSchemeI oldCs = viewport.getGlobalColourScheme();
 
-      else
-      {
-        sliderPanel = new SliderPanel(alignPanel, 30, true,
-                                      viewport.getGlobalColourScheme());
-        JInternalFrame frame = new JInternalFrame();
-        frame.setContentPane(sliderPanel);
-        Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,
-                                 90);
-        frame.setMaximizable(false);
-        frame.setResizable(false);
-        frame.addInternalFrameListener(new javax.swing.event.
-                                       InternalFrameAdapter()
-        {
-          public void internalFrameClosed(javax.swing.event.InternalFrameEvent
-                                          evt)
-          {
-            sliderPanel = null;
-          };
-        });
-      }
-    }
-    else
-    {
-        if(oldCs instanceof ConservationColourScheme)
-        {
-          ConservationColourScheme ccs = (ConservationColourScheme)oldCs;
-          viewport.setGlobalColourScheme( ccs.cs );
-        }
-        alignPanel.setColourScheme();
-    }
+     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() );
 
-  SliderPanel sliderPanel;
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)
-  {
-    ColourSchemeI oldCs = viewport.getGlobalColourScheme();
-    int threshold = 0;
+       c.calculate();
+       c.verdict(false, 100);
 
-    if(abovePIDThreshold.isSelected())
-    {
-      if(sliderPanel!=null)
-        sliderPanel.cs = oldCs;
+       if(ccs!=null)
+         ccs = new ConservationColourScheme(c, ccs.cs);
+       else
+         ccs = new ConservationColourScheme(c, oldCs);
 
-      else
-      {
-        sliderPanel = new SliderPanel(alignPanel, 70, false, oldCs);
-        JInternalFrame frame = new JInternalFrame();
-        frame.setContentPane(sliderPanel);
-        Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400,
-                                 90);
-        frame.setMaximizable(false);
-        frame.setResizable(false);
-        frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-        {
-          public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
-          {
-            sliderPanel = null;
-          };
-        });
+        viewport.setGlobalColourScheme( ccs );
 
-      }
+     }
+     else if(oldCs instanceof ConservationColourScheme)
+     {
+       oldCs = ccs.cs;
+       viewport.setGlobalColourScheme( oldCs );
+     }
 
-      threshold = sliderPanel.getValue();
-    }
 
-    if (oldCs instanceof ResidueColourScheme)
-    {
-      ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
-      rcs.setThreshold(threshold);
-    }
-    else if (oldCs instanceof ScoreColourScheme)
-    {
-      ScoreColourScheme scs = (ScoreColourScheme) oldCs;
-      scs.setThreshold(threshold);
-    }
+     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())
+       {
+         sp = new SliderPanel(alignPanel, threshold, false, oldCs);
+         sp.cs = oldCs;
+         Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
+       }
+
+       sliderFrame.setContentPane(sp);
+       if(x!=0 && y!=0)
+               sliderFrame.setLocation(x,y);
 
-    alignPanel.setColourScheme();
+     }
+     else
+       threshold = 0;
+
+
+     if (oldCs instanceof ResidueColourScheme)
+     {
+       ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
+       rcs.setThreshold(threshold);
+     }
+     else if (oldCs instanceof ScoreColourScheme)
+     {
+       ScoreColourScheme scs = (ScoreColourScheme) oldCs;
+       scs.setThreshold(threshold);
+     }
+
+     alignPanel.seqPanel.seqCanvas.paintFlag = true;
+     alignPanel.repaint();
+
+  }
+
+  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();
   }
 
 
-- 
1.7.10.2