package jalview.viewmodel;
import jalview.analysis.PCA;
-import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.RotatableCanvasI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
private SimilarityParamsI similarityParams;
/**
- * Constructor given sequence data and score calculation parameter options.
- * The initial state is to compute PCA using a default score model (BLOSUM62
- * for peptide, DNA for nucleotide).
+ * Constructor given sequence data, score model and score calculation
+ * parameter options.
*
* @param seqData
* @param sqs
* @param nuc
+ * @param sm
* @param params
*/
- public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc, ScoreModelI sm,
SimilarityParamsI params)
{
seqstrings = seqData;
seqs = sqs;
nucleotide = nuc;
- scoreModel = ScoreModels.getInstance().getDefaultModel(!nucleotide);
+ scoreModel = sm;
similarityParams = params;
}