X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=5e5fa8d389e4ca7c16df6973f8886fc754c94481;hb=828bb8cde756e18e25ffae5ac47bf6832d32eeda;hp=da9896e1864a719509fa2c46aa5e8dda5e90119b;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index da9896e..5e5fa8d 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,26 +1,39 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
    */
@@ -31,22 +44,35 @@ public class ScoreMatrix
    */
   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 +127,7 @@ public class ScoreMatrix
     boolean header = true;
     if (html)
     {
-      sb.append("<table>");
+      sb.append("<table border=\"1\">");
     }
     for (char sym = 'A'; sym <= 'Z'; sym++)
     {