From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 15 Feb 2005 10:45:46 +0000 (+0000)
Subject: add applytoallgroups colouring option
X-Git-Tag: Release_2_0~660
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d7b6fc2a38b90786ce62ea4e8a418e05b24e5352;p=jalview.git

add applytoallgroups colouring option
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3a38769..686ecbc 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -635,171 +635,187 @@ public class AlignFrame extends GAlignFrame
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( null );
-    changeColour();
+    changeColour( null );
   }
 
 
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(
-      new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
     abovePIDThreshold.setSelected(false);
-    changeColour();
+    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new ZappoColourScheme() );
-    changeColour();
+    changeColour(new ZappoColourScheme());
   }
 
   public void taylorColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new TaylorColourScheme() );
-    changeColour();
+    changeColour(new TaylorColourScheme());
   }
 
 
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
-    changeColour();
+    changeColour( new HydrophobicColourScheme() );
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new HelixColourScheme()  );
-    changeColour();
+    changeColour(new HelixColourScheme() );
   }
 
 
   public void strandColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new StrandColourScheme() );
-    changeColour();
+    changeColour(new StrandColourScheme());
   }
 
 
   public void turnColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new TurnColourScheme() );
-    changeColour();
+    changeColour(new TurnColourScheme());
   }
 
 
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new BuriedColourScheme() );
-    changeColour();
+    changeColour(new BuriedColourScheme() );
   }
 
   public void nucleotideColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new NucleotideColourScheme() );
-    changeColour();
+    changeColour(new NucleotideColourScheme());
   }
 
 
-  void changeColour()
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
-    if(abovePIDThreshold.isSelected())
-      abovePIDThreshold_actionPerformed(null);
-    else if(conservationMenuItem.isSelected())
-      conservationMenuItem_actionPerformed(null);
-
-    alignPanel.RefreshPanels();
+    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
   }
 
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+
+  void changeColour(ColourSchemeI cs)
   {
-   if(abovePIDThreshold.isSelected())
-   {
-     abovePIDThreshold.setSelected(false);
-     Desktop.hidePIDSlider();
-   }
 
-   viewport.setConservationSelected(conservationMenuItem.isSelected());
+    if(viewport.getColourAppliesToAllGroups())
+    {
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+        sg.cs = cs;
+
+        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, 100);
+          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+
+          sg.cs = ccs;
+        }
+
+      }
+    }
+
+
+    if ( viewport.getAbovePIDThreshold())
+    {
+      int threshold = 0;
+      threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
+      Desktop.hideConservationSlider();
+
+      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);
+
+
 
-   ColourSchemeI oldCs = viewport.getGlobalColourScheme();
 
+if ( viewport.getConservationSelected() )
+ {
    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());
+   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);
+   ccs = new ConservationColourScheme(c, cs);
 
+   int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
+       "Background");
 
-         int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");
+   ccs.inc = threshold;
 
-         ccs.inc = threshold;
+   viewport.setGlobalColourScheme(ccs);
 
-         if (ccs.cs instanceof ResidueColourScheme)
-           ((ResidueColourScheme) ccs.cs).setThreshold(0);
-         else if (ccs.cs instanceof ScoreColourScheme)
-           ((ScoreColourScheme)ccs.cs).setThreshold(0);
+  }
+  else
+       viewport.setGlobalColourScheme( cs );
 
-         viewport.setGlobalColourScheme(ccs);
+    alignPanel.RefreshPanels();
+  }
 
 
-       }
-       else if (oldCs instanceof ConservationColourScheme)
-       {
-         /// ie, if we remove ConservationColourScheme from backgroundColour
-         oldCs = ccs.cs;
-         viewport.setGlobalColourScheme(oldCs);
-         Desktop.hideConservationSlider();
-       }
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
 
-       if(e!=null)
-         alignPanel.RefreshPanels();
+    viewport.setAbovePIDThreshold(false);
+    abovePIDThreshold.setSelected(false);
+    Desktop.hidePIDSlider();
+    if(!viewport.getConservationSelected())
+      Desktop.hideConservationSlider();
+
+   ColourSchemeI cs = viewport.getGlobalColourScheme();
+   if(cs instanceof ConservationColourScheme )
+     changeColour( ((ConservationColourScheme)cs).cs );
+    else
+      changeColour( cs );
   }
 
 
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-      if(conservationMenuItem.isSelected())
-        conservationMenuItem.setSelected(false);
+    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 
-      ColourSchemeI oldCs = viewport.getGlobalColourScheme();
-      int threshold = 0;
-      if (oldCs instanceof ConservationColourScheme)
-     {
-       ConservationColourScheme ccs = (ConservationColourScheme) oldCs;
-       oldCs = ccs.cs;
-     }
+    conservationMenuItem.setSelected(false);
+    viewport.setConservationSelected(false);
+    Desktop.hideConservationSlider();
 
-     if(abovePIDThreshold.isSelected())
-     {
-       threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");
-       Desktop.hideConservationSlider();
-     }
-     else
-       Desktop.hidePIDSlider();
+    if(!viewport.getAbovePIDThreshold())
+      Desktop.hidePIDSlider();
 
-      if (oldCs instanceof ResidueColourScheme)
-          ((ResidueColourScheme) oldCs).setThreshold(threshold);
-      else if (oldCs instanceof ScoreColourScheme)
-          ((ScoreColourScheme)oldCs).setThreshold(threshold);
 
-    viewport.setGlobalColourScheme(oldCs);
-     if(e!=null)
-        alignPanel.RefreshPanels();
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
+    if(cs instanceof ConservationColourScheme )
+        changeColour( ((ConservationColourScheme)cs).cs );
+    else
+        changeColour( cs );
+
   }
 
 
@@ -817,15 +833,13 @@ public class AlignFrame extends GAlignFrame
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new PIDColourScheme() );
-    alignPanel.setColourScheme( );
+    changeColour( new PIDColourScheme() );
   }
 
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
-    changeColour();
+    changeColour(new Blosum62ColourScheme(viewport) );
   }
 
 
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 11d1ff3..093c233 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -89,6 +89,7 @@ public class GAlignFrame extends JInternalFrame
   JMenu jMenu1 = new JMenu();
   JMenuItem pasteNew = new JMenuItem();
   JMenuItem pasteThis = new JMenuItem();
+  protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
 
@@ -670,6 +671,15 @@ public class GAlignFrame extends JInternalFrame
         pasteThis_actionPerformed(e);
       }
     });
+    applyToAllGroups.setText("Apply colour to all groups");
+    applyToAllGroups.setState(true);
+    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        applyToAllGroups_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -717,6 +727,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(consensusGraphMenuItem);
     viewMenu.add(overviewMenuItem);
     viewMenu.add(sequenceFeatures);
+    colourMenu.add(applyToAllGroups);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(zappoColour);
@@ -1091,6 +1102,11 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+  {
+
+  }
+
 
 
 }