Formatting

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

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 03b6778..69a0922 100644 (file)
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,6 +1,7 @@
 package jalview.schemes;\r
 \r
-public class ScoreMatrix {\r
+public class ScoreMatrix\r
+{\r
   String name;\r
   /**\r
    * reference to integer score matrix\r
@@ -10,36 +11,48 @@ public class ScoreMatrix {
    * 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
+  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
+   *\r
    * @param A1\r
    * @param A2\r
    * @return score for substituting first char in A1 with first char in A2\r
    */\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