JAL-2428 Javadoc

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

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 969e6b3..8e58c20 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -73,7 +73,7 @@ public class UserColourScheme extends ResidueColourScheme
     schemeName = from.schemeName;
     if (from.lowerCaseColours != null)
     {
-      lowerCaseColours = new Color[lowerCaseColours.length];
+      lowerCaseColours = new Color[from.lowerCaseColours.length];
       System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0,
               from.lowerCaseColours.length);
     }
@@ -238,36 +238,6 @@ public class UserColourScheme extends ResidueColourScheme
 
   }
 
-  @Override
-  public Color findColour(char c, int j, SequenceI seq)
-  {
-    Color currentColour;
-    int index = ResidueProperties.aaIndex[c];
-
-    if ((threshold == 0) || aboveThreshold(c, j))
-    {
-      if (lowerCaseColours != null && 'a' <= c && c <= 'z')
-      {
-        currentColour = lowerCaseColours[index];
-      }
-      else
-      {
-        currentColour = colors[index];
-      }
-    }
-    else
-    {
-      currentColour = Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-
   public void setLowerCaseColours(Color[] lcolours)
   {
     lowerCaseColours = lcolours;