JAL-3206 strict above/below threshold test restored

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

diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index e451135..1b36f30 100644 (file)
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -24,7 +24,6 @@ import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
-import java.awt.Color;
 import java.util.Map;
 
 /**
@@ -40,58 +39,7 @@ public class PurinePyrimidineColourScheme extends ResidueColourScheme
   public PurinePyrimidineColourScheme()
   {
     super(ResidueProperties.purinepyrimidineIndex,
-            ResidueProperties.purinepyrimidine, 0);
-  }
-
-  /**
-   * Finds the corresponding color for the type of character inputed
-   * 
-   * @param c
-   *          Character in sequence
-   * 
-   * @return Color from purinepyrimidineIndex in
-   *         jalview.schemes.ResidueProperties
-   */
-  @Override
-  public Color findColour(char c)
-  {
-    return colors[ResidueProperties.purinepyrimidineIndex[c]];
-  }
-
-  /**
-   * Returns color based on conservation
-   * 
-   * @param c
-   *          Character in sequence
-   * @param j
-   *          Threshold
-   * 
-   * @return Color in RGB
-   */
-  public Color findColour(char c, int j)
-  {
-    Color currentColour;
-    if ((threshold == 0) || aboveThreshold(c, j))
-    {
-      try
-      {
-        currentColour = colors[ResidueProperties.purinepyrimidineIndex[c]];
-      } catch (Exception ex)
-      {
-        return Color.white;
-      }
-    }
-    else
-    {
-      return Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
+            ResidueProperties.purinepyrimidine);
   }
 
   @Override