X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=0c8afaa6bba9d3c7fa8a0eb7a30afdd75d3c245a;hb=a60611ba87555ed0e135eb4a3b858d5768ff0506;hp=7e383a9a57fc41e25f8cc293b298d95b83432f8e;hpb=8f1b417b654a575bf7a368b4edeffee813042a5c;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 7e383a9..0c8afaa 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * 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/>.
+ * 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;
@@ -212,6 +214,27 @@ 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 +244,13 @@ 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 +259,22 @@ 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);
         }
-
       }
     }
 
@@ -299,13 +308,15 @@ 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
@@ -1306,7 +1317,7 @@ 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())
@@ -1370,15 +1381,15 @@ public abstract class AlignmentViewport implements AlignViewportI
       {
         conservation = new AlignmentAnnotation("Conservation",
                 "Conservation of total alignment less than "
-                        + getConsPercGaps() + "% gaps",
-                new Annotation[1], 0f, 11f,
-                AlignmentAnnotation.BAR_GRAPH);
+                        + getConsPercGaps() + "% gaps", new Annotation[1],
+                0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
         alignment.addAnnotation(conservation);
       }
     }
   }
+
   private void initQuality()
   {
     if (showQuality)
@@ -1387,21 +1398,20 @@ public abstract class AlignmentViewport implements AlignViewportI
       {
         quality = new AlignmentAnnotation("Quality",
                 "Alignment Quality based on Blosum62 scores",
-                new Annotation[1], 0f, 11f,
-                AlignmentAnnotation.BAR_GRAPH);
+                new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         quality.hasText = true;
         quality.autoCalculated = true;
         alignment.addAnnotation(quality);
       }
     }
   }
+
   private void initRNAStructure()
   {
-    if (alignment.hasRNAStructure() && strucConsensus==null)
+    if (alignment.hasRNAStructure() && strucConsensus == null)
     {
       strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-              new Annotation[1], 0f, 100f,
-              AlignmentAnnotation.BAR_GRAPH);
+              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       strucConsensus.hasText = true;
       strucConsensus.autoCalculated = true;
 
@@ -1411,6 +1421,7 @@ public abstract class AlignmentViewport implements AlignViewportI
       }
     }
   }
+
   /*
    * (non-Javadoc)
    * 
@@ -1511,7 +1522,7 @@ public abstract class AlignmentViewport implements AlignViewportI
         if (aan[an].autoCalculated && aan[an].groupRef != null)
         {
           oldrfs.add(aan[an].groupRef);
-          alignment.deleteAnnotation(aan[an],false);
+          alignment.deleteAnnotation(aan[an], false);
         }
       }
     }
@@ -1551,11 +1562,12 @@ public abstract class AlignmentViewport implements AlignViewportI
   @Override
   public Color getSequenceColour(SequenceI seq)
   {
-    Color sqc=Color.white;
+    Color sqc = Color.white;
     if (sequenceColours != null)
     {
       sqc = (Color) sequenceColours.get(seq);
-      if (sqc == null) {
+      if (sqc == null)
+      {
         sqc = Color.white;
       }
     }