JAL-1517 fix copyright for 2.8.2

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

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index e78b92c..a0e632f 100644 (file)
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,26 +1,37 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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;
 
-public class ScoreMatrix
+import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.api.analysis.ScoreModelI;
+
+public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
 {
   String name;
+  
+  @Override
+  public String getName()
+  {
+    return name;
+  }
 
   /**
    * reference to integer score matrix
@@ -31,23 +42,31 @@ public class ScoreMatrix
    * 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
+   */
   ScoreMatrix(String name, int[][] matrix, int type)
   {
     this.matrix = matrix;
     this.type = type;
+    this.name = name;
   }
 
+  @Override
   public boolean isDNA()
   {
     return type == 1;
   }
-
+  @Override
   public boolean isProtein()
   {
     return type == 0;
   }
 
+  @Override
   public int[][] getMatrix()
   {
     return matrix;
@@ -102,7 +121,7 @@ public class ScoreMatrix
     boolean header = true;
     if (html)
     {
-      sb.append("<table>");
+      sb.append("<table border=\"1\">");
     }
     for (char sym = 'A'; sym <= 'Z'; sym++)
     {