JAL-2393 code tidy and comments, PIDDistanceModel deprecated

[jalview.git] / src / jalview / analysis / scoremodels / ScoreMatrix.java

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 8b7fc42..a4b8343 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -79,21 +79,21 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * of symbols. The matrix should be square and of the same size as the
    * alphabet, for example 20x20 for a 20 symbol alphabet.
    * 
-   * @param name
+   * @param theName
    *          Unique, human readable name for the matrix
    * @param alphabet
    *          the symbols to which scores apply
-   * @param matrix
+   * @param values
    *          Pairwise scores indexed according to the symbol alphabet
    */
-  public ScoreMatrix(String name, char[] alphabet, float[][] matrix)
+  public ScoreMatrix(String theName, char[] alphabet, float[][] values)
   {
-    if (alphabet.length != matrix.length)
+    if (alphabet.length != values.length)
     {
       throw new IllegalArgumentException(
               "score matrix size must match alphabet size");
     }
-    for (float[] row : matrix)
+    for (float[] row : values)
     {
       if (row.length != alphabet.length)
       {
@@ -102,8 +102,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
       }
     }
 
-    this.matrix = matrix;
-    this.name = name;
+    this.matrix = values;
+    this.name = theName;
     this.symbols = alphabet;
 
     symbolIndex = buildSymbolIndex(alphabet);