From 52c82458a18df360ea80de64e03aca1fe473f813 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 1 Feb 2005 19:03:56 +0000
Subject: [PATCH] Update PID or conservationSlider if necessary

---
 src/jalview/gui/SeqPanel.java |   66 ++++++++++++++++++++++++++++++++++++-----
 1 file changed, 59 insertions(+), 7 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 7b3fae3..ab2e1ef 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -12,7 +12,7 @@ public class SeqPanel extends JPanel
 {
 
   public    SeqCanvas         seqCanvas;
-  public    AlignmentPanel    parent;
+  public    AlignmentPanel    ap;
 
   protected int startres;
   protected int lastres;
@@ -33,7 +33,7 @@ public class SeqPanel extends JPanel
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
-    parent = p;
+    ap = p;
 
     addMouseMotionListener( new MouseMotionAdapter()
     {
@@ -86,13 +86,13 @@ public class SeqPanel extends JPanel
 
     seqEditOccurred = -1;
 
-    parent.RefreshPanels();
+    ap.RefreshPanels();
     repaint();
 
   }
 
   public void doMousePressed(MouseEvent evt) {
-    parent.alignFrame.addHistoryItem("sequence edit");
+    ap.alignFrame.addHistoryItem("sequence edit");
     int seq;
     int res;
 
@@ -168,7 +168,7 @@ public class SeqPanel extends JPanel
     if(aa!="")
       text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
 
-    parent.alignFrame.statusBar.setText(text.toString());
+    ap.alignFrame.statusBar.setText(text.toString());
 
   }
 
@@ -362,10 +362,21 @@ public class SeqPanel extends JPanel
       sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );
       av.setRubberbandGroup( sg );
       stretchGroup = sg;
+
+      if(av.getConservationSelected())
+        Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");
+      else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())
+      {
+        ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();
+        int threshold = rcs.getThreshold();
+        if (threshold > 0)
+          Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
+      }
+
     }
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-        jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( parent , null);
+        jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
         pop.show(this, evt.getX(), evt.getY());
 
     // edit the properties of existing group
@@ -393,6 +404,47 @@ public class SeqPanel extends JPanel
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
+
+    if(stretchGroup.cs instanceof ClustalxColourScheme)
+    {
+      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
+      seqCanvas.paintFlag = true;
+      repaint();
+    }
+
+    else if(stretchGroup.cs instanceof ConservationColourScheme)
+    {
+      ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
+
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3, stretchGroup.sequences, 0,
+                                        av.alignment.getWidth() );
+
+       c.calculate();
+       c.verdict(false, 100);
+       ccs = new ConservationColourScheme(c, ccs.cs);
+
+       stretchGroup.cs = ccs;
+
+
+       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
+
+       seqCanvas.paintFlag = true;
+       repaint();
+    }
+    else
+    {
+      if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
+      {
+        ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;
+        int threshold = rcs.getThreshold();
+        if(threshold>0)
+          Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
+      }
+
+    }
+
+
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -411,7 +463,7 @@ public class SeqPanel extends JPanel
       changeEndRes = true;
 
     else if(stretchGroup.getStartRes()==res)
-      // Edit end res position of selected group
+      // Edit start res position of selected group
       changeStartRes = true;
 
 
-- 
1.7.10.2