X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=44ecf76ff963122941be68503119d9ef9e295cc6;hb=279af6f3b1803de7a1e467b83a7205df18e70d48;hp=cceff8614e027cf8c22a1b8f77abc59b6f7e69d5;hpb=7c581704d0ce30ffad302f199e0f44f689cd32fb;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index cceff86..44ecf76 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.viewmodel;
 
@@ -42,6 +43,7 @@ import jalview.workers.StrucConsensusThread;
 
 import java.awt.Color;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -210,6 +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())
@@ -219,29 +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
         {
@@ -250,20 +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);
         }
-
       }
     }
 
@@ -297,7 +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
@@ -1298,7 +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())
@@ -1416,7 +1425,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     int charHeight = getCharHeight();
     if (aa != null)
     {
-      boolean graphgrp[] = null;
+      BitSet graphgrp = new BitSet();
       for (int i = 0; i < aa.length; i++)
       {
         if (aa[i] == null)
@@ -1430,17 +1439,13 @@ public abstract class AlignmentViewport implements AlignViewportI
         }
         if (aa[i].graphGroup > -1)
         {
-          if (graphgrp == null)
-          {
-            graphgrp = new boolean[aa.length];
-          }
-          if (graphgrp[aa[i].graphGroup])
+          if (graphgrp.get(aa[i].graphGroup))
           {
             continue;
           }
           else
           {
-            graphgrp[aa[i].graphGroup] = true;
+            graphgrp.set(aa[i].graphGroup);
           }
         }
         aa[i].height = 0;
@@ -1507,8 +1512,7 @@ public abstract class AlignmentViewport implements AlignViewportI
         if (aan[an].autoCalculated && aan[an].groupRef != null)
         {
           oldrfs.add(aan[an].groupRef);
-          alignment.deleteAnnotation(aan[an]);
-          aan[an] = null;
+          alignment.deleteAnnotation(aan[an],false);
         }
       }
     }