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

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

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 7caa735..bc56281 100644 (file)
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,6 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -33,7 +32,6 @@ import java.awt.Color;
 import java.util.ArrayList;
 import java.util.IdentityHashMap;
 import java.util.Map;
-import java.util.TreeMap;
 
 /**
  * Defines the color score for T-Coffee MSA
@@ -47,8 +45,7 @@ import java.util.TreeMap;
 public class TCoffeeColourScheme extends ResidueColourScheme
 {
 
-  static final Color[] colors =
-  { new Color(102, 102, 255), // #6666FF
+  static final Color[] colors = { new Color(102, 102, 255), // #6666FF
       new Color(0, 255, 0), // #00FF00
       new Color(102, 255, 0), // #66FF00
       new Color(204, 255, 0), // #CCFF00
@@ -87,7 +84,8 @@ public class TCoffeeColourScheme extends ResidueColourScheme
     // Search alignment to get all tcoffee annotation and pick one set of
     // annotation to use to colour seqs.
     seqMap = new IdentityHashMap<SequenceI, Color[]>();
-    AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
+    AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+            : alignment.getContext();
     int w = 0;
     for (AlignmentAnnotation al : alcontext
             .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
@@ -132,7 +130,7 @@ public class TCoffeeColourScheme extends ResidueColourScheme
     }
     return cols[j];
   }
-  
+
   @Override
   public ColourSchemeI applyTo(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)