X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=69a0922e37c55c2e3f32efe72109b574825ea9a1;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=03b6778cf32828bef78cdbc71423111c633c6f2a;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 03b6778..69a0922 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,6 +1,7 @@
 package jalview.schemes;
 
-public class ScoreMatrix {
+public class ScoreMatrix
+{
   String name;
   /**
    * reference to integer score matrix
@@ -10,36 +11,48 @@ public class ScoreMatrix {
    * 0 for Protein Score matrix. 1 for dna score matrix
    */
   int type;
-  ScoreMatrix(String name, int[][] matrix, int type) {
-    this.matrix=matrix;
-    this.type=type;
+  ScoreMatrix(String name, int[][] matrix, int type)
+  {
+    this.matrix = matrix;
+    this.type = type;
   }
-  public boolean isDNA() {
-    return type==1;
+
+  public boolean isDNA()
+  {
+    return type == 1;
   }
-  public boolean isProtein() {
-    return type==0;
+
+  public boolean isProtein()
+  {
+    return type == 0;
   }
-  public int[][] getMatrix() {
+
+  public int[][] getMatrix()
+  {
     return matrix;
   }
+
   /**
-   * 
+   *
    * @param A1
    * @param A2
    * @return score for substituting first char in A1 with first char in A2
    */
   public int getPairwiseScore(String A1, String A2)
   {
-    return getPairwiseScore(A1.charAt(0),A2.charAt(0));
+    return getPairwiseScore(A1.charAt(0), A2.charAt(0));
   }
-  public int getPairwiseScore(char c, char d) {
+
+  public int getPairwiseScore(char c, char d)
+  {
     int pog = 0;
 
     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];
     }