X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;fp=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=6cdfacbe56695b322b074d05cf90fef8565b37ea;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=efaeb430d86bc58ace6f251d11c9e9b852c33601;hpb=d1bb7a31fc091606aedbc255a5766ac79e36fa91;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index efaeb43..6cdfacb 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -36,8 +36,8 @@ import java.util.Arrays;
  * symbols. Instances of this class are immutable and thread-safe, so the same
  * object is returned from calls to getInstance().
  */
-public class ScoreMatrix extends SimilarityScoreModel implements
-        PairwiseScoreModelI
+public class ScoreMatrix extends SimilarityScoreModel
+        implements PairwiseScoreModelI
 {
   private static final char GAP_CHARACTER = Comparison.GAP_DASH;
 
@@ -98,7 +98,7 @@ public class ScoreMatrix extends SimilarityScoreModel implements
   private float minValue;
 
   private float maxValue;
-  
+
   /**
    * Constructor given a name, symbol alphabet, and matrix of scores for pairs
    * of symbols. The matrix should be square and of the same size as the
@@ -130,8 +130,8 @@ public class ScoreMatrix extends SimilarityScoreModel implements
    * @param values
    *          Pairwise scores indexed according to the symbol alphabet
    */
-  public ScoreMatrix(String theName, String theDescription,
-          char[] alphabet, float[][] values)
+  public ScoreMatrix(String theName, String theDescription, char[] alphabet,
+          float[][] values)
   {
     if (alphabet.length != values.length)
     {
@@ -454,7 +454,8 @@ public class ScoreMatrix extends SimilarityScoreModel implements
    * @param params
    * @return
    */
-  protected MatrixI findSimilarities(String[] seqs, SimilarityParamsI params)
+  protected MatrixI findSimilarities(String[] seqs,
+          SimilarityParamsI params)
   {
     double[][] values = new double[seqs.length][];
     for (int row = 0; row < seqs.length; row++)