SequenceI[] seqs;
/*
- * Score model used to calculate PCA
+ * Name of score model used to calculate PCA
*/
ScoreModelI scoreModel;
private Vector<SequencePoint> points;
- private boolean jvCalcMode = true;
-
private SimilarityParamsI similarityParams;
/**
* @param seqData
* @param sqs
* @param nuc
- * @param sm
+ * @param modelName
* @param params
*/
- public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc, ScoreModelI sm,
- SimilarityParamsI params)
+ public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ ScoreModelI modelName, SimilarityParamsI params)
{
seqstrings = seqData;
seqs = sqs;
nucleotide = nuc;
- scoreModel = sm;
+ scoreModel = modelName;
similarityParams = params;
}
return pts;
}
- public void setJvCalcMode(boolean state)
- {
- jvCalcMode = state;
- }
-
public String getScoreModelName()
{
return scoreModel == null ? "" : scoreModel.getName();