/*
* inputs
*/
- private final AlignmentView seqstrings;
+ private AlignmentView inputData;
private final SequenceI[] seqs;
public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
ScoreModelI modelName, SimilarityParamsI params)
{
- seqstrings = seqData;
+ inputData = seqData;
seqs = sqs;
nucleotide = nuc;
scoreModel = modelName;
*/
public void calculate()
{
- pca = new PCA(seqstrings, scoreModel, similarityParams);
+ pca = new PCA(inputData, scoreModel, similarityParams);
pca.run(); // executes in same thread, wait for completion
// Now find the component coordinates
return pca.getDetails();
}
- public AlignmentView getSeqtrings()
+ public AlignmentView getInputData()
{
- return seqstrings;
+ return inputData;
+ }
+
+ public void setInputData(AlignmentView data)
+ {
+ inputData = data;
}
public String getPointsasCsv(boolean transformed, int xdim, int ydim,