X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=d55ffbfb06d0c55e7bbea3e92c1eac1fca0b955f;hb=675982336ef7772ca635baca391c48fb868501b7;hp=b86250ac6e0935114ddb8a4090d0f2369e07d511;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index b86250a..d55ffbf 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);
   }
@@ -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)
             {
@@ -287,7 +288,7 @@ public class UserColourScheme extends ResidueColourScheme
     /*
      * step 1: build a map from colours to the symbol(s) that have the colour
      */
-    Map<Color, List<String>> colours = new HashMap<Color, List<String>>();
+    Map<Color, List<String>> colours = new HashMap<>();
 
     for (char symbol = 'A'; symbol <= 'Z'; symbol++)
     {
@@ -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>());
@@ -320,7 +321,7 @@ public class UserColourScheme extends ResidueColourScheme
     /*
      * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
      */
-    List<String> residueColours = new ArrayList<String>();
+    List<String> residueColours = new ArrayList<>();
     for (Entry<Color, List<String>> cols : colours.entrySet())
     {
       boolean first = true;
@@ -350,4 +351,10 @@ public class UserColourScheme extends ResidueColourScheme
     Collections.sort(residueColours);
     return StringUtils.listToDelimitedString(residueColours, ";");
   }
+
+  @Override
+  public boolean hasGapColour()
+  {
+    return (findColour(' ') != null);
+  }
 }