- // TODO can we allow PCA on unaligned data given choice of
- // similarity measure parameters?
- if (!checkAligned(seqstrings))
- {
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.getString("label.pca_sequences_not_aligned"),
- MessageManager.getString("label.sequences_not_aligned"),
- JvOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
- pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
- SimilarityParams.SeqSpace);
+ ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel(
+ modelName, ap);
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+ params);