Merge remote-tracking branch 'origin/develop' into

[jalview.git] / src / jalview / datamodel / BinarySequence.java

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 62ee974..b7e15a6 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -20,8 +20,8 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
 
 /**
  * Encode a sequence as a numeric vector using either classic residue binary
@@ -112,23 +112,23 @@ public class BinarySequence extends Sequence
   /**
    * ancode using substitution matrix given in matrix
    * 
-   * @param matrix
+   * @param smtrx
    */
-  public void matrixEncode(final ScoreMatrix matrix)
+  public void matrixEncode(final ScoreMatrix smtrx)
           throws InvalidSequenceTypeException
   {
-    if (isNa != matrix.isDNA())
+    if (isNa != smtrx.isDNA())
     {
       throw new InvalidSequenceTypeException("matrix "
-              + matrix.getClass().getCanonicalName()
+              + smtrx.getClass().getCanonicalName()
               + " is not a valid matrix for "
               + (isNa ? "nucleotide" : "protein") + "sequences");
     }
-    matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
-            : ResidueProperties.aaIndex, matrix.getMatrix());
+    matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
+            : ResidueProperties.aaIndex, smtrx.getMatrix());
   }
 
-  private void matrixEncode(final int[] aaIndex, final int[][] matrix)
+  private void matrixEncode(final int[] aaIndex, final float[][] matrix)
   {
     int nores = initMatrixGetNoRes();