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;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
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;
- public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
- boolean nucleotide2)
- {
- seqstrings = seqstrings2;
- seqs = seqs2;
- nucleotide = nucleotide2;
- scoreModel = ScoreModels.getInstance().getDefaultModel(!nucleotide);
- }
-
- public boolean isJvCalcMode()
+ /**
+ * Constructor given sequence data, score model and score calculation
+ * parameter options.
+ *
+ * @param seqData
+ * @param sqs
+ * @param nuc
+ * @param modelName
+ * @param params
+ */
+ public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ ScoreModelI modelName, SimilarityParamsI params)
{
- return jvCalcMode;
+ seqstrings = seqData;
+ seqs = sqs;
+ nucleotide = nuc;
+ scoreModel = modelName;
+ similarityParams = params;
}
public void run()
{
- pca = new PCA(seqstrings, scoreModel);
- pca.setJvCalcMode(jvCalcMode);
+ pca = new PCA(seqstrings, scoreModel, similarityParams);
pca.run();
// Now find the component coordinates
return pts;
}
- public void setJvCalcMode(boolean state)
- {
- jvCalcMode = state;
- }
-
public String getScoreModelName()
{
return scoreModel == null ? "" : scoreModel.getName();