update author list in license for (JAL-826)

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

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 03b6778..f5d30a9 100644 (file)
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,28 +1,57 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
 package jalview.schemes;\r
 \r
-public class ScoreMatrix {\r
+public class ScoreMatrix\r
+{\r
   String name;\r
+\r
   /**\r
    * reference to integer score matrix\r
    */\r
   int[][] matrix;\r
+\r
   /**\r
    * 0 for Protein Score matrix. 1 for dna score matrix\r
    */\r
   int type;\r
-  ScoreMatrix(String name, int[][] matrix, int type) {\r
-    this.matrix=matrix;\r
-    this.type=type;\r
+\r
+  ScoreMatrix(String name, int[][] matrix, int type)\r
+  {\r
+    this.matrix = matrix;\r
+    this.type = type;\r
   }\r
-  public boolean isDNA() {\r
-    return type==1;\r
+\r
+  public boolean isDNA()\r
+  {\r
+    return type == 1;\r
   }\r
-  public boolean isProtein() {\r
-    return type==0;\r
+\r
+  public boolean isProtein()\r
+  {\r
+    return type == 0;\r
   }\r
-  public int[][] getMatrix() {\r
+\r
+  public int[][] getMatrix()\r
+  {\r
     return matrix;\r
   }\r
+\r
   /**\r
    * \r
    * @param A1\r
@@ -31,21 +60,24 @@ public class ScoreMatrix {
    */\r
   public int getPairwiseScore(String A1, String A2)\r
   {\r
-    return getPairwiseScore(A1.charAt(0),A2.charAt(0));\r
+    return getPairwiseScore(A1.charAt(0), A2.charAt(0));\r
   }\r
-  public int getPairwiseScore(char c, char d) {\r
+\r
+  public int getPairwiseScore(char c, char d)\r
+  {\r
     int pog = 0;\r
 \r
     try\r
     {\r
-      int a = (type==0) ? ResidueProperties.aaIndex[c] : ResidueProperties.nucleotideIndex[c];\r
-      int b = (type==0) ? ResidueProperties.aaIndex[d] : ResidueProperties.nucleotideIndex[d];\r
+      int a = (type == 0) ? ResidueProperties.aaIndex[c]\r
+              : ResidueProperties.nucleotideIndex[c];\r
+      int b = (type == 0) ? ResidueProperties.aaIndex[d]\r
+              : ResidueProperties.nucleotideIndex[d];\r
 \r
       pog = matrix[a][b];\r
-    }\r
-    catch (Exception e)\r
+    } catch (Exception e)\r
     {\r
-      //System.out.println("Unknown residue in " + A1 + " " + A2);\r
+      // System.out.println("Unknown residue in " + A1 + " " + A2);\r
     }\r
 \r
     return pog;\r