public class PCAModel
{
- private volatile PCA pca;
-
- int top;
+ /*
+ * inputs
+ */
+ private final AlignmentView seqstrings;
- AlignmentView seqstrings;
+ private final SequenceI[] seqs;
- SequenceI[] seqs;
+ private final SimilarityParamsI similarityParams;
/*
- * Name of score model used to calculate PCA
+ * options - score model, nucleotide / protein
*/
- ScoreModelI scoreModel;
+ private ScoreModelI scoreModel;
private boolean nucleotide = false;
- private Vector<SequencePoint> points;
+ /*
+ * outputs
+ */
+ private volatile PCA pca;
- private SimilarityParamsI similarityParams;
+ int top;
+
+ private Vector<SequencePoint> points;
/**
* Constructor given sequence data, score model and score calculation
// top = pca.getM().height() - 1;
top = height - 1;
- points = new Vector<SequencePoint>();
+ points = new Vector<>();
float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
for (int i = 0; i < height; i++)