From 7bf593f3593a0392fb01d78644f7bfd75762a87e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 29 Aug 2005 17:23:19 +0000
Subject: [PATCH] Reset all colour schemes after gaps removed

---
 src/jalview/appletgui/AlignFrame.java |   31 +++++++++++++++++++++++++++----
 src/jalview/gui/AlignFrame.java       |   33 ++++++++++++++++++++++++++++-----
 2 files changed, 55 insertions(+), 9 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dc8f72b..38aea52 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -172,6 +172,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    resetAllColourSchemes();
   }
 
   protected void redoMenuItem_actionPerformed(ActionEvent e)
@@ -180,6 +181,7 @@ public class AlignFrame
     restoreHistoryItem(hi);
     updateEditMenuBar();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     alignPanel.repaint();
     alignPanel.repaint();
   }
@@ -608,7 +610,7 @@ public class AlignFrame
 
     viewport.updateConservation();
     viewport.updateConsensus();
-    resetAllClustalSchemes();
+    resetAllColourSchemes();
     alignPanel.repaint();
   }
 
@@ -660,14 +662,32 @@ public class AlignFrame
     }
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
-    resetAllClustalSchemes();
     viewport.updateConservation();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     alignPanel.repaint();
   }
 
-  void resetAllClustalSchemes()
+  void resetAllColourSchemes()
   {
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
+    {
+        cs.setConsensus(viewport.vconsensus);
+        if(cs.conservationApplied())
+        {
+          Alignment al = (Alignment) viewport.alignment;
+          Conservation c = new Conservation("All",
+                                            ResidueProperties.propHash, 3,
+                                            al.getSequences(), 0,
+                                            al.getWidth() - 1);
+          c.calculate();
+          c.verdict(false, viewport.ConsPercGaps);
+
+          cs.setConservation(c);
+        }
+    }
+
     if(viewport.getGlobalColourScheme()!=null
        && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
     {
@@ -680,10 +700,13 @@ public class AlignFrame
     for(s=0; s<sSize; s++)
     {
       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
-      if(sg.cs instanceof ClustalxColourScheme)
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
       {
         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
       }
+
+      sg.recalcConservation();
+
     }
   }
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bdca06c..efe8e63 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -410,6 +410,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    resetAllColourSchemes();
   }
 
   /**
@@ -423,7 +424,7 @@ public class AlignFrame
     restoreHistoryItem(hi);
     updateEditMenuBar();
     viewport.updateConsensus();
-    alignPanel.repaint();
+    resetAllColourSchemes();
     alignPanel.repaint();
   }
 
@@ -969,7 +970,7 @@ public class AlignFrame
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
-    resetAllClustalSchemes();
+    resetAllColourSchemes();
     viewport.updateConservation();
     viewport.updateConsensus();
     alignPanel.repaint();
@@ -1034,15 +1035,34 @@ public class AlignFrame
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
-    resetAllClustalSchemes();
 
     viewport.updateConservation();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     alignPanel.repaint();
   }
 
-  void resetAllClustalSchemes()
+
+  void resetAllColourSchemes()
   {
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
+    {
+        cs.setConsensus(viewport.vconsensus);
+        if(cs.conservationApplied())
+        {
+          Alignment al = (Alignment) viewport.alignment;
+          Conservation c = new Conservation("All",
+                                            ResidueProperties.propHash, 3,
+                                            al.getSequences(), 0,
+                                            al.getWidth() - 1);
+          c.calculate();
+          c.verdict(false, viewport.ConsPercGaps);
+
+          cs.setConservation(c);
+        }
+    }
+
     if(viewport.getGlobalColourScheme()!=null
        && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
     {
@@ -1055,10 +1075,13 @@ public class AlignFrame
     for(s=0; s<sSize; s++)
     {
       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
-      if(sg.cs instanceof ClustalxColourScheme)
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
       {
         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
       }
+
+      sg.recalcConservation();
+
     }
   }
 
-- 
1.7.10.2