From da18eb63c94018e134fb60d70e6de43e99bbff50 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 29 Aug 2005 15:18:11 +0000
Subject: [PATCH] Reset ClustalX after removing gaps

---
 src/jalview/appletgui/AlignFrame.java |   24 ++++++++++++++++++++++++
 src/jalview/appletgui/SeqPanel.java   |    6 +++---
 src/jalview/gui/AlignFrame.java       |   24 ++++++++++++++++++++++++
 src/jalview/gui/SeqPanel.java         |    5 +++--
 4 files changed, 54 insertions(+), 5 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index fae50d9..80e8438 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -599,6 +599,7 @@ public class AlignFrame
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();
+    resetAllClustalSchemes();
     alignPanel.repaint();
   }
 
@@ -644,11 +645,34 @@ public class AlignFrame
       while(j < end && j < jSize) ;
     }
 
+    resetAllClustalSchemes();
     viewport.updateConservation();
     viewport.updateConsensus();
     alignPanel.repaint();
   }
 
+  void resetAllClustalSchemes()
+  {
+    if(viewport.getGlobalColourScheme()!=null
+       && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
+    {
+      ((ClustalxColourScheme)viewport.getGlobalColourScheme()).
+          resetClustalX(viewport.alignment.getSequences(),
+                        viewport.alignment.getWidth());
+    }
+
+    int s, sSize = viewport.alignment.getGroups().size();
+    for(s=0; s<sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+      if(sg.cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+      }
+    }
+  }
+
+
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9a5863f..ee7676c 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -535,9 +535,9 @@ public class SeqPanel
 
         if (cs instanceof ClustalxColourScheme)
         {
-          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
-          cxs.resetClustalX(av.alignment.getSequences(),
-                            av.alignment.getWidth());
+          ((ClustalxColourScheme)cs).
+              resetClustalX(av.alignment.getSequences(),
+                                av.alignment.getWidth());
           cs.setConservation(c);
           av.setGlobalColourScheme(cs);
         }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bdcea36..084ad7d 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -961,6 +961,7 @@ public class AlignFrame
                                    viewport.alignment, HistoryItem.HIDE));
 
     viewport.getAlignment().removeGaps();
+    resetAllClustalSchemes();
     viewport.updateConservation();
     viewport.updateConsensus();
     alignPanel.repaint();
@@ -1017,11 +1018,34 @@ public class AlignFrame
       while (j < end && j < jSize);
     }
 
+    resetAllClustalSchemes();
+
     viewport.updateConservation();
     viewport.updateConsensus();
     alignPanel.repaint();
   }
 
+  void resetAllClustalSchemes()
+  {
+    if(viewport.getGlobalColourScheme()!=null
+       && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
+    {
+      ((ClustalxColourScheme)viewport.getGlobalColourScheme()).
+          resetClustalX(viewport.alignment.getSequences(),
+                        viewport.alignment.getWidth());
+    }
+
+    int s, sSize = viewport.alignment.getGroups().size();
+    for(s=0; s<sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+      if(sg.cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+      }
+    }
+  }
+
   /**
    * DOCUMENT ME!
    *
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 444b6bb..de1a533 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -650,9 +650,10 @@ public class SeqPanel extends JPanel
 
             if (cs instanceof ClustalxColourScheme)
             {
-              ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
-              cxs.resetClustalX(av.alignment.getSequences(),
+              ((ClustalxColourScheme)cs).
+                  resetClustalX(av.alignment.getSequences(),
                                 av.alignment.getWidth());
+
               cs.setConservation(c);
               av.setGlobalColourScheme(cs);
             }
-- 
1.7.10.2