JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 82a5871..d73bed2 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -19,7 +19,11 @@
 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;
 
 public class UserColourScheme extends ResidueColourScheme
@@ -38,7 +42,18 @@ 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) {
+      usc.schemeName = new String(schemeName);
+      usc.lowerCaseColours = new Color[lowerCaseColours.length];
+      System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0, lowerCaseColours.length);
+    }
+    return usc;
+  }
   public UserColourScheme(String colour)
   {
     super(ResidueProperties.aaIndex);
@@ -143,6 +158,7 @@ public class UserColourScheme extends ResidueColourScheme
 
   public void parseAppletParameter(String paramValue)
   {
+    // TODO: need a function to generate appletParameter colour string from a UCS
     StringTokenizer st = new StringTokenizer(paramValue, ";");
     StringTokenizer st2;
     String token = null, colour, residues;