import jalview.analysis.TreeBuilder;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.AlignViewportI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
pca = new JRadioButton(
MessageManager.getString("label.principal_component_analysis"));
pca.setOpaque(false);
+
neighbourJoining = new JRadioButton(
MessageManager.getString("label.tree_calc_nj"));
neighbourJoining.setSelected(true);
+ neighbourJoining.setOpaque(false);
+
averageDistance = new JRadioButton(
MessageManager.getString("label.tree_calc_av"));
- neighbourJoining.setOpaque(false);
+ averageDistance.setOpaque(false);
JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
calcChoicePanel.setOpaque(false);
};
});
+ validateCalcTypes();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
* gui validation shouldn't allow insufficient sequences here, but leave
* this check in in case this method gets exposed programmatically in future
*/
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
SequenceGroup sg = viewport.getSelectionGroup();
if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
{
*/
protected void openPcaPanel(String modelName, SimilarityParamsI params)
{
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
/*
* gui validation shouldn't allow insufficient sequences here, but leave