X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=6850d79f7c78f765417e87e7a9af99f0895d5bb3;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=116bbd8a52edc277e1e52410834bd6a6c1130dee;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 116bbd8..6850d79 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,25 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.schemes;
 
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
+import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -48,9 +55,10 @@ public class ScoreColourScheme extends ResidueColourScheme
    * @param max
    *          DOCUMENT ME!
    */
-  public ScoreColourScheme(double[] scores, double min, double max)
+  public ScoreColourScheme(int symbolIndex[], double[] scores, double min,
+          double max)
   {
-    super();
+    super(symbolIndex);
 
     this.scores = scores;
     this.min = min;
@@ -90,27 +98,12 @@ public class ScoreColourScheme extends ResidueColourScheme
   @Override
   public Color findColour(char c, int j, SequenceI seq)
   {
-    if (threshold > 0)
-    {
-      if (!aboveThreshold(c, j))
-      {
-        return Color.white;
-      }
-    }
-
-    if (jalview.util.Comparison.isGap(c))
+    if (Comparison.isGap(c))
     {
       return Color.white;
     }
 
-    Color currentColour = colors[ResidueProperties.aaIndex[c]];
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
+    return colors[ResidueProperties.aaIndex[c]];
   }
 
   /**
@@ -125,4 +118,21 @@ public class ScoreColourScheme extends ResidueColourScheme
   {
     return new Color(c, (float) 0.0, (float) 1.0 - c);
   }
+
+  @Override
+  public String getSchemeName()
+  {
+    return "Score";
+  }
+
+  /**
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
+   */
+  @Override
+  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+          Map<SequenceI, SequenceCollectionI> hrs)
+  {
+    return new ScoreColourScheme(symbolIndex, scores, min, max);
+  }
 }