JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 9b01332..89f3eed 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,25 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
-import java.util.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-import java.awt.*;
+import java.awt.Color;
+import java.util.Map;
+import java.util.StringTokenizer;
 
 public class UserColourScheme extends ResidueColourScheme
 {
@@ -29,15 +36,33 @@ public class UserColourScheme extends ResidueColourScheme
 
   public UserColourScheme()
   {
+    super(ResidueProperties.aaIndex);
   }
 
   public UserColourScheme(Color[] newColors)
   {
+    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);
     Color col = getColourFromString(colour);
 
     if (col == null)
@@ -139,6 +164,8 @@ 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;
@@ -201,7 +228,8 @@ public class UserColourScheme extends ResidueColourScheme
 
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
     int index = ResidueProperties.aaIndex[c];