X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=20b4b775b52281df2a364d4bd0650311560f94b4;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=1abcfbe4806becb099d50d517676e7b63162813a;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 1abcfbe..20b4b77 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,19 +1,21 @@
 /*
- * 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 2.9.0b1)
+ * 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;
@@ -21,10 +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()
   {
@@ -40,11 +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)
   {
@@ -58,6 +65,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
   {
     return type == 1;
   }
+
   @Override
   public boolean isProtein()
   {