X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=f5d30a940e06b2135cf1af1b81d503617456c8bb;hb=3e51d4b043f8ac3e262f9b3660ec1f8561d1db93;hp=69a0922e37c55c2e3f32efe72109b574825ea9a1;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 69a0922..f5d30a9 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,16 +1,36 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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.
+ * 
+ * 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/>.
+ */
 package jalview.schemes;
 
 public class ScoreMatrix
 {
   String name;
+
   /**
    * reference to integer score matrix
    */
   int[][] matrix;
+
   /**
    * 0 for Protein Score matrix. 1 for dna score matrix
    */
   int type;
+
   ScoreMatrix(String name, int[][] matrix, int type)
   {
     this.matrix = matrix;
@@ -33,7 +53,7 @@ public class ScoreMatrix
   }
 
   /**
-   *
+   * 
    * @param A1
    * @param A2
    * @return score for substituting first char in A1 with first char in A2
@@ -49,16 +69,15 @@ public class ScoreMatrix
 
     try
     {
-      int a = (type == 0) ? ResidueProperties.aaIndex[c] :
-          ResidueProperties.nucleotideIndex[c];
-      int b = (type == 0) ? ResidueProperties.aaIndex[d] :
-          ResidueProperties.nucleotideIndex[d];
+      int a = (type == 0) ? ResidueProperties.aaIndex[c]
+              : ResidueProperties.nucleotideIndex[c];
+      int b = (type == 0) ? ResidueProperties.aaIndex[d]
+              : ResidueProperties.nucleotideIndex[d];
 
       pog = matrix[a][b];
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
-      //System.out.println("Unknown residue in " + A1 + " " + A2);
+      // System.out.println("Unknown residue in " + A1 + " " + A2);
     }
 
     return pog;