From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 25 May 2005 17:45:55 +0000 (+0000)
Subject: more clustalx bugs fixed
X-Git-Tag: Release_2_0~178
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2ece3719ca3be664ef49768ff8334d1f257720f3;p=jalview.git

more clustalx bugs fixed
---

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 1a6853b..3a707de 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -370,14 +370,35 @@ public class SeqPanel extends Panel
     av.updateConservation();
     av.updateConsensus();
 
+    // Y O Y CLUSTALX
     ColourSchemeI cs = av.getGlobalColourScheme();
     if(cs instanceof ConservationColourScheme)
-      cs = ( (ConservationColourScheme) cs).cs;
+    {
+      ConservationColourScheme ccs =  (ConservationColourScheme) cs;
+      if(ccs.cs instanceof ClustalxColourScheme)
+     {
+        jalview.analysis.Conservation c = new jalview.analysis.Conservation
+            ("All",
+            ResidueProperties.propHash, 3,
+            av.alignment.getSequences(), 0,
+            av.alignment.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, av.ConsPercGaps);
+
+        ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;
+        cxs.resetClustalX(av.alignment.getSequences(),  av.alignment.getWidth());
+        ccs = new ConservationColourScheme(c, cxs);
+        av.setGlobalColourScheme(ccs);
+     }
+    }
 
     if(cs instanceof ClustalxColourScheme)
-      cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());
+    {
+      ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
+                                    av.alignment.getWidth());
+      av.setGlobalColourScheme(cs);
+    }
 
-    ap.alignFrame.changeColour(cs);
 
   }
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ca09c97..b48861a 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -6,6 +6,7 @@ import jalview.datamodel.*;
 import javax.swing.*;
 import java.util.*;
 import jalview.schemes.*;
+import jalview.analysis.Conservation;
 
 public class SeqPanel extends JPanel
 {
@@ -374,14 +375,33 @@ public class SeqPanel extends JPanel
     av.updateConservation();
     av.updateConsensus();
 
+    // Y O Y CLUSTALX
     ColourSchemeI cs = av.getGlobalColourScheme();
     if(cs instanceof ConservationColourScheme)
-      cs = ( (ConservationColourScheme) cs).cs;
+    {
+      ConservationColourScheme ccs =  (ConservationColourScheme) cs;
+      if(ccs.cs instanceof ClustalxColourScheme)
+     {
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          av.alignment.getSequences(), 0,
+                                          av.alignment.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, av.ConsPercGaps);
+
+        ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;
+        cxs.resetClustalX(av.alignment.getSequences(),  av.alignment.getWidth());
+        ccs = new ConservationColourScheme(c, cxs);
+        av.setGlobalColourScheme(ccs);
+     }
+    }
 
     if(cs instanceof ClustalxColourScheme)
-      cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());
-
-    ap.alignFrame.changeColour(cs);
+    {
+      ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
+                                    av.alignment.getWidth());
+      av.setGlobalColourScheme(cs);
+    }
 
   }
 
@@ -496,14 +516,7 @@ public class SeqPanel extends JPanel
        repaint();
     }
     else
-    {
-      if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
-      {
-        ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;
         SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
-      }
-
-    }
 
 
     changeEndRes = false;