X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=e25818e4cd8022791d5e2b816f3afbeb3f16c106;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=d49572d8f3dbfee689d64fdb9fe53bd3cf868dc1;hpb=c346dab4e1569fab50bf4107868ed043d9e4a0a3;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d49572d..e25818e 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -212,6 +212,24 @@ public abstract class AlignmentViewport implements AlignViewportI
     // calculation till later or to do all calculations in thread.
     // via changecolour
     globalColourScheme = cs;
+    boolean recalc=false;
+    if (cs!=null)
+    {
+      cs.setConservationApplied(recalc = getConservationSelected());
+      if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme)
+      {
+        recalc = true;
+        cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
+      } else {
+        cs.setThreshold(0, ignoreGapsInConsensusCalculation);
+      }
+      if (recalc)
+      {
+        cs.setConsensus(hconsensus);
+        cs.setConservation(hconservation);
+      }
+      cs.alignmentChanged(alignment, hiddenRepSequences);
+    }
     if (getColourAppliesToAllGroups())
     {
       for (SequenceGroup sg : getAlignment().getGroups())
@@ -221,29 +239,13 @@ public abstract class AlignmentViewport implements AlignViewportI
           sg.cs = null;
           continue;
         }
-        if (cs instanceof ClustalxColourScheme)
-        {
-          sg.cs = new ClustalxColourScheme(sg, getHiddenRepSequences());
-        }
-        else
-        {
-          try
-          {
-            sg.cs = cs.getClass().newInstance();
-          } catch (Exception ex)
-          {
-            ex.printStackTrace();
-            sg.cs = cs;
-          }
-        }
-
+        sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+        sg.setConsPercGaps(ConsPercGaps);
         if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
                 || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
-          sg.cs.setConsensus(AAFrequency.calculate(
-                  sg.getSequences(getHiddenRepSequences()), 0,
-                  sg.getWidth()));
+          recalc=true;
         }
         else
         {
@@ -252,20 +254,19 @@ public abstract class AlignmentViewport implements AlignViewportI
 
         if (getConservationSelected())
         {
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3,
-                  sg.getSequences(getHiddenRepSequences()), 0,
-                  getAlignment().getWidth() - 1);
-          c.calculate();
-          c.verdict(false, getConsPercGaps());
-          sg.cs.setConservation(c);
+          sg.cs.setConservationApplied(true);
+          recalc=true;
         }
         else
         {
           sg.cs.setConservation(null);
-          sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+          // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+        }
+        if (recalc) {
+          sg.recalcConservation();
+        } else {
+          sg.cs.alignmentChanged(sg, hiddenRepSequences);
         }
-
       }
     }
 
@@ -299,7 +300,13 @@ public abstract class AlignmentViewport implements AlignViewportI
    * view
    */
   protected Hashtable[] hStrucConsensus = null;
-
+  
+  protected Conservation hconservation = null;
+  @Override
+  public void setConservation(Conservation cons)
+  {
+    hconservation = cons;
+  }
   /**
    * percentage gaps allowed in a column before all amino acid properties should
    * be considered unconserved
@@ -1300,7 +1307,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     ColourSchemeI cs = globalColourScheme;
     if (cs != null)
     {
-      cs.alignmentChanged(alignment, null);
+      cs.alignmentChanged(alignment, hiddenRepSequences);
 
       cs.setConsensus(hconsensus);
       if (cs.conservationApplied())