X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=5e5fa8d389e4ca7c16df6973f8886fc754c94481;hb=f3da4113cd7d574966523982ed5145a918c63556;hp=a0e632fcfe4d5b24f4dafc671d012357ce8c533d;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index a0e632f..5e5fa8d 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.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.
  * 
@@ -23,10 +23,11 @@ package jalview.schemes;
 import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
 import jalview.api.analysis.ScoreModelI;
 
-public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
+public class ScoreMatrix extends PairwiseSeqScoreModel implements
+        ScoreModelI
 {
   String name;
-  
+
   @Override
   public String getName()
   {
@@ -42,11 +43,15 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
    * 0 for Protein Score matrix. 1 for dna score matrix
    */
   int type;
+
   /**
    * 
-   * @param name Unique, human readable name for the matrix
-   * @param matrix Pairwise scores indexed according to appropriate symbol alphabet
-   * @param type 0 for Protein, 1 for NA
+   * @param name
+   *          Unique, human readable name for the matrix
+   * @param matrix
+   *          Pairwise scores indexed according to appropriate symbol alphabet
+   * @param type
+   *          0 for Protein, 1 for NA
    */
   ScoreMatrix(String name, int[][] matrix, int type)
   {
@@ -60,6 +65,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
   {
     return type == 1;
   }
+
   @Override
   public boolean isProtein()
   {