X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=9ae14cac7145a2897e3ced7a7b226fa8b0ea301f;hb=8c9072337270d0e4c26c569346d5ba1f829e08d3;hp=89ed91bbd72c29f86f0db9adb97e4c74f639c49d;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 89ed91b..9ae14ca 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,14 +20,14 @@
  */
 package jalview.schemes;
 
-import java.awt.Color;
-import java.util.Map;
-import java.util.StringTokenizer;
-
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
+import java.awt.Color;
+import java.util.Map;
+import java.util.StringTokenizer;
+
 public class UserColourScheme extends ResidueColourScheme
 {
   Color[] lowerCaseColours;
@@ -44,18 +44,22 @@ public class UserColourScheme extends ResidueColourScheme
     super(ResidueProperties.aaIndex);
     colors = newColors;
   }
+
   @Override
   public ColourSchemeI applyTo(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     UserColourScheme usc = new UserColourScheme(colors);
-    if (lowerCaseColours!=null) {
+    if (lowerCaseColours != null)
+    {
       usc.schemeName = new String(schemeName);
       usc.lowerCaseColours = new Color[lowerCaseColours.length];
-      System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0, lowerCaseColours.length);
+      System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
+              lowerCaseColours.length);
     }
     return usc;
   }
+
   public UserColourScheme(String colour)
   {
     super(ResidueProperties.aaIndex);
@@ -63,7 +67,7 @@ public class UserColourScheme extends ResidueColourScheme
 
     if (col == null)
     {
-      System.out.println("Unknown colour!! " + colour);
+      System.out.println("Making colour from name: " + colour);
       col = createColourFromName(colour);
     }
 
@@ -95,8 +99,12 @@ public class UserColourScheme extends ResidueColourScheme
     return schemeName;
   }
 
-  public Color getColourFromString(String colour)
+  public static Color getColourFromString(String colour)
   {
+    if (colour == null)
+    {
+      return null;
+    }
     colour = colour.trim();
 
     Color col = null;
@@ -132,7 +140,7 @@ public class UserColourScheme extends ResidueColourScheme
 
   }
 
-  public Color createColourFromName(String name)
+  public static Color createColourFromName(String name)
   {
     int r, g, b;
 
@@ -160,7 +168,8 @@ public class UserColourScheme extends ResidueColourScheme
 
   public void parseAppletParameter(String paramValue)
   {
-    // TODO: need a function to generate appletParameter colour string from a UCS
+    // TODO: need a function to generate appletParameter colour string from a
+    // UCS
     StringTokenizer st = new StringTokenizer(paramValue, ";");
     StringTokenizer st2;
     String token = null, colour, residues;