From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 10 Dec 2004 14:33:08 +0000 (+0000)
Subject: Colour scheme new global implementation
X-Git-Tag: Release_2_0~853
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b455b63542dbdceadd35a6e1ba7a655aeebb410a;p=jalview.git

Colour scheme new global implementation
---

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 605450b..eda94a0 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,11 +1,12 @@
 package jalview.gui;
 
 import jalview.jbgui.GAlignmentPanel;
+import jalview.schemes.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
 import java.awt.*;
-import java.awt.image.*;
 import java.awt.event.*;
 import java.awt.print.*;
-import javax.swing.*;
 
 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
 {
@@ -90,7 +91,130 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   }
 
 
-  public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
+  public void setColourScheme()
+  {
+    ColourSchemeI cs = av.getGlobalColourScheme();
+
+    if(av.getConservationSelected())
+    {
+
+      Alignment al = (Alignment)av.getAlignment();
+      Conservation c = new Conservation("All", al.cons,
+                            ResidueProperties.propHash, 3, al.getSequences(), 0,
+                            al.getWidth() );
+
+       c.calculate();
+       c.verdict(false, 100);
+       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+
+       av.setGlobalColourScheme( ccs );
+
+    }
+    seqPanel.seqCanvas.paintFlag = true;
+    repaint();
+  }
+  /*
+    seqCanvas.paintFlag = true;
+    if (av.getSelection().size() == 0)
+    {
+      seqCanvas.globalColorScheme = cs;
+      for (int i = 0; i < av.alignment.getGroups().size();i++)
+      {
+        SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
+        sg.cs = cs;
+        if(!showConservation
+            && !(sg.cs instanceof Blosum62ColourScheme)
+            && sg.cs instanceof ConservationColourScheme)
+         {
+           // remove ConservationColouring from existing Conservation group
+           ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
+           sg.cs = ccs.cs;
+         }
+         else if(showConservation && !(sg.cs instanceof ConservationColourScheme))
+         {
+           // add ConservationColouring to new group
+           Conservation c = sg.getConservation();
+           Alignment al = (Alignment) av.getAlignment();
+           c = new Conservation("All", al.cons,
+                                ResidueProperties.propHash, 3, sg.sequences, 0,
+                                al.getWidth() );
+           c.calculate();
+           c.verdict(false, 100);
+           sg.setConservation(c);
+           sg.cs = new ConservationColourScheme(sg);
+         }
+      }
+    }
+    else
+    {
+      SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));
+
+      if( isNewSelection(sg) )
+      {
+        sg = av.getAlignment().addGroup();
+        for (int i=0; i < av.getSelection().size(); i++)
+        {
+          av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.
+              sel.sequenceAt(i)),
+                                       (Sequence) av.sel.sequenceAt(i));
+          av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));
+        }
+      }
+
+
+      sg.cs = cs;
+
+      // Selection is made, we only want to change the conservationColour for selected group
+      if(  showConservation
+           && !(sg.cs instanceof ConservationColourScheme)
+           && !(sg.cs instanceof Blosum62ColourScheme))
+      {
+        Conservation c = sg.getConservation();
+        Alignment al = (Alignment) av.getAlignment();
+
+        c = new Conservation("All", al.cons,
+                             ResidueProperties.propHash, 3, sg.sequences, 0,
+                             al.getWidth() );
+        c.calculate();
+        c.verdict(false, 100);
+        sg.setConservation(c);
+        sg.cs = new ConservationColourScheme(sg);
+    }
+    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)
+    {
+      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
+      sg.cs = ccs.cs;
+    }
+   }
+   repaint();
+  }
+
+  boolean isNewSelection(SequenceGroup sg)
+  {
+    if(sg==null)
+      return true;
+
+    if(sg.getSize()!=av.getSelection().size())
+      return true;
+
+    for(int i=0; i<sg.getSize(); i++)
+     if( !av.getSelection().contains( sg.getSequenceAt(i) ))
+       return true;
+
+    return false;
+  }
+
+
+  public ColourSchemeI getColourScheme()
+  {
+    if(av.getSelection().size()>0)
+       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
+    else
+      return seqCanvas.globalColorScheme;
+  }
+*/
+
+/*  public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
   {
     seqPanel.setColourScheme(cs, conservation);
 
@@ -100,6 +224,43 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       overviewPanel.updateOverviewImage();
   }
 
+   void updateResidueView()
+   {
+     if (viewport.getSelection().size() == 0)
+      {
+        for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
+        {
+          SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
+          sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
+          sg.setDisplayText( viewTextMenuItem.isSelected() );
+          sg.setColourText( colourTextMenuItem.isSelected() );
+        }
+      }
+      else
+      {
+        SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
+        if (alignPanel.seqPanel.isNewSelection(sg))
+        {
+          sg = viewport.getAlignment().addGroup();
+          for (int i = 0; i < viewport.getSelection().size(); i++)
+          {
+            viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
+                Sequence) viewport.sel.sequenceAt(i)),
+                                               (Sequence) viewport.sel.sequenceAt(
+                i));
+            viewport.alignment.addToGroup(sg,
+                                          (Sequence) viewport.sel.sequenceAt(i));
+          }
+        }
+
+        sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
+        sg.setDisplayText(viewTextMenuItem.isSelected());
+        sg.setColourText(colourTextMenuItem.isSelected());
+      }
+     alignPanel.RefreshPanels();
+   }*/
+
+
 
   public void RefreshPanels()
   {
@@ -109,8 +270,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
     setScrollValues(av.getStartRes(), av.getStartSeq());
     av.getConsensus(true);
-    repaint();
     validate();
+    repaint();
     if(overviewPanel!=null)
       overviewPanel.updateOverviewImage();