JAL-2446 merged to spike branch

[jalview.git] / src / jalview / schemes / ScoreColourScheme.java

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 8198ff1..aa20121 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,26 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 java.awt.Color;
+import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -82,49 +87,30 @@ public class ScoreColourScheme extends ResidueColourScheme
   /**
    * DOCUMENT ME!
    * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param j
+   * @param c
    *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  @Override
-  public Color findColour(char c, int j, SequenceI seq)
+  public Color makeColour(float c)
   {
-    if (threshold > 0)
-    {
-      if (!aboveThreshold(c, j))
-      {
-        return Color.white;
-      }
-    }
-
-    if (jalview.util.Comparison.isGap(c))
-    {
-      return Color.white;
-    }
-
-    Color currentColour = colors[ResidueProperties.aaIndex[c]];
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
+    return new Color(c, (float) 0.0, (float) 1.0 - c);
+  }
 
-    return currentColour;
+  @Override
+  public String getSchemeName()
+  {
+    return "Score";
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param c
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
    */
-  public Color makeColour(float c)
+  @Override
+  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+          Map<SequenceI, SequenceCollectionI> hrs)
   {
-    return new Color(c, (float) 0.0, (float) 1.0 - c);
+    return new ScoreColourScheme(symbolIndex, scores, min, max);
   }
 }