X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=ec0f008a12e8e15a07986362e317e7167a92f60b;hb=6785b0c3d7bdc780e0ca1737082b82374eaf8335;hp=bf62e453b4b9e6eb8cdd9aaf6df20631a33b43ff;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index bf62e45..ec0f008 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -20,9 +20,10 @@
  */
 package jalview.schemes;
 
+import java.util.Locale;
+
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
 import jalview.util.StringUtils;
 
@@ -56,8 +57,8 @@ public class UserColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg)
   {
     return new UserColourScheme(this);
   }
@@ -107,7 +108,7 @@ public class UserColourScheme extends ResidueColourScheme
 
     if (col == null)
     {
-      System.out.println("Making colour from name: " + colour);
+      jalview.bin.Console.outPrintln("Making colour from name: " + colour);
       col = ColorUtils.createColourFromName(colour);
     }
 
@@ -216,7 +217,7 @@ public class UserColourScheme extends ResidueColourScheme
             continue;
           }
 
-          if (residue.equals(residue.toLowerCase()))
+          if (residue.equals(residue.toLowerCase(Locale.ROOT)))
           {
             if (lowerCaseColours == null)
             {
@@ -233,7 +234,7 @@ public class UserColourScheme extends ResidueColourScheme
       }
     } catch (Exception ex)
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "Error parsing userDefinedColours:\n" + token + "\n" + ex);
     }
 
@@ -307,7 +308,7 @@ public class UserColourScheme extends ResidueColourScheme
         c = lowerCaseColours[index];
         if (c != null && !c.equals(Color.white))
         {
-          residue = residue.toLowerCase();
+          residue = residue.toLowerCase(Locale.ROOT);
           if (colours.get(c) == null)
           {
             colours.put(c, new ArrayList<String>());