JAL-1517 update copyright to version 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 da9896e..1abcfbe 100644 (file)
--- 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.
  * 
@@ -14,12 +14,22 @@
  * 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/>.
+ * 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
@@ -30,23 +40,31 @@ 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;
@@ -101,7 +119,7 @@ public class ScoreMatrix
     boolean header = true;
     if (html)
     {
-      sb.append("<table>");
+      sb.append("<table border=\"1\">");
     }
     for (char sym = 'A'; sym <= 'Z'; sym++)
     {