JAL-1517 fix copyright for 2.8.2

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index d363764..8bb1acd 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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;
 
@@ -59,13 +62,17 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
   }
 
-  public ClustalxColourScheme(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps)
+  public ClustalxColourScheme(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    alignmentChanged(alignment,hiddenReps);
+    alignmentChanged(alignment, hiddenReps);
   }
-  public void alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps) {
-    int maxWidth=alignment.getWidth();
-    List<SequenceI> seqs=alignment.getSequences(hiddenReps);
+
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    int maxWidth = alignment.getWidth();
+    List<SequenceI> seqs = alignment.getSequences(hiddenReps);
     cons2 = new int[maxWidth][24];
     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
     // get the current setting of the
@@ -86,7 +93,7 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     int j = 0;
     char[] seq;
 
-    for (SequenceI sq: seqs)
+    for (SequenceI sq : seqs)
     {
       seq = sq.getSequence();
 
@@ -322,6 +329,14 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
   {
     this.includeGaps = includeGaps;
   }
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    ClustalxColourScheme css= new ClustalxColourScheme(sg, hiddenRepSequences);
+    css.includeGaps = includeGaps;
+    return css;
+  }
 }
 
 class ConsensusColour