merge from 2_4_Release branch

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

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 69a0922..a5a5ed3 100644 (file)
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,16 +1,37 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program 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 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
 package jalview.schemes;\r
 \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
+\r
   ScoreMatrix(String name, int[][] matrix, int type)\r
   {\r
     this.matrix = matrix;\r
@@ -33,7 +54,7 @@ public class ScoreMatrix
   }\r
 \r
   /**\r
-   *\r
+   * \r
    * @param A1\r
    * @param A2\r
    * @return score for substituting first char in A1 with first char in A2\r
@@ -49,16 +70,15 @@ public class ScoreMatrix
 \r
     try\r
     {\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
+      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