import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
+ ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+ false);
+ pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
}
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
+ ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+ true);
+ pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
}
}
;
Object[] alAndColsel = pcaModel.getSeqtrings()
- .getAlignmentAndColumnSelection(gc);
+ .getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
AlignFrame af = new AlignFrame(al, av.applet,
"Original Data for PCA", false);
- af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
+ af.viewport.getAlignment().setHiddenColumns(
+ (HiddenColumns) alAndColsel[1]);
}
}