/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
package jalview.schemes;
-public class ScoreMatrix
+import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.api.analysis.ScoreModelI;
+
+public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
{
String name;
+
+ @Override
+ public String getName()
+ {
+ return name;
+ }
/**
* reference to integer score matrix
* 0 for Protein Score matrix. 1 for dna score matrix
*/
int type;
-
+ /**
+ *
+ * @param name Unique, human readable name for the matrix
+ * @param matrix Pairwise scores indexed according to appropriate symbol alphabet
+ * @param type 0 for Protein, 1 for NA
+ */
ScoreMatrix(String name, int[][] matrix, int type)
{
this.matrix = matrix;
this.type = type;
+ this.name = name;
}
+ @Override
public boolean isDNA()
{
return type == 1;
}
-
+ @Override
public boolean isProtein()
{
return type == 0;
}
+ @Override
public int[][] getMatrix()
{
return matrix;