Merge branch 'features/JAL-2360colourSchemeApplicability' into

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

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 57e8458..aa20121 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -20,9 +20,12 @@
  */
 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!
@@ -84,42 +87,6 @@ public class ScoreColourScheme extends ResidueColourScheme
   /**
    * DOCUMENT ME!
    * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param j
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @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))
-    {
-      return Color.white;
-    }
-
-    Color currentColour = colors[ResidueProperties.aaIndex[c]];
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param c
    *          DOCUMENT ME!
    * 
@@ -135,4 +102,15 @@ public class ScoreColourScheme extends ResidueColourScheme
   {
     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);
+  }
 }