import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.ViewBasedAnalysisI;
-import jalview.bin.Cache;
import jalview.datamodel.Alignment;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.io.NewickFile;
import jalview.util.MessageManager;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
-public class TreePanel extends EmbmenuFrame implements ActionListener,
- ItemListener
+public class TreePanel extends EmbmenuFrame
+ implements ActionListener, ItemListener, AutoCloseable
{
SequenceI[] seq;
}
@Override
- public void finalize() throws Throwable
+ public void close()
{
ap = null;
av = null;
- super.finalize();
+ super.close();
}
/**
* Creates a new TreePanel object.
- *
- * @param av
- * DOCUMENT ME!
- * @param seqVector
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
- * @param pwtype
- * DOCUMENT ME!
- * @param s
- * DOCUMENT ME!
- * @param e
- * DOCUMENT ME!
*/
- public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ public TreePanel(AlignmentPanel alignPanel, String type, String pwtype)
{
try
{
ex.printStackTrace();
}
- initTreePanel(ap, type, pwtype, null);
+ initTreePanel(alignPanel, type, pwtype, null);
}
/**
* Creates a new TreePanel object.
*
- * @param av
- * DOCUMENT ME!
- * @param seqVector
- * DOCUMENT ME!
- * @param newtree
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
- * @param pwtype
- * DOCUMENT ME!
*/
public TreePanel(AlignmentPanel ap, String type, String pwtype,
NewickFile newtree)
}
Object[] alAndColsel = tree.getOriginalData()
- .getAlignmentAndColumnSelection(gc);
+ .getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
AlignFrame af = new AlignFrame(al, av.applet,
"Original Data for Tree", false);
- af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
+ af.viewport.getAlignment()
+ .setHiddenColumns((HiddenColumns) alAndColsel[1]);
}
}
else
{
- System.out.println("Original Tree Data not available");
+ jalview.bin.Console.outPrintln("Original Tree Data not available");
}
}
}
else
{
- ScoreModelI sm = configureScoreModel(pwtype);
- TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
- av, sm, SimilarityParams.Jalview)
+ ScoreModelI sm1 = ScoreModels.getInstance().getScoreModel(pwtype,
+ treeCanvas.ap);
+ ScoreModelI sm = sm1;
+ TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING)
+ ? new NJTree(av, sm, SimilarityParams.Jalview)
: new AverageDistanceTree(av, sm, SimilarityParams.Jalview);
tree = new TreeModel(njtree);
}
bootstrapMenu.setState(showBoots);
treeCanvas.setShowBootstrap(showBoots);
treeCanvas.setShowDistances(showDist);
- treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
- "showUnlinkedTreeNodes", false));
+ treeCanvas.setMarkPlaceholders(av.applet
+ .getDefaultParameter("showUnlinkedTreeNodes", false));
}
treeCanvas.repaint();
jMenu2.setLabel(MessageManager.getString("action.view"));
fontSize.setLabel(MessageManager.getString("action.font"));
fontSize.addActionListener(this);
- bootstrapMenu.setLabel(MessageManager
- .getString("label.show_bootstrap_values"));
+ bootstrapMenu.setLabel(
+ MessageManager.getString("label.show_bootstrap_values"));
bootstrapMenu.addItemListener(this);
distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
distanceMenu.addItemListener(this);
- placeholdersMenu.setLabel(MessageManager
- .getString("label.mark_unassociated_leaves"));
+ placeholdersMenu.setLabel(
+ MessageManager.getString("label.mark_unassociated_leaves"));
placeholdersMenu.addItemListener(this);
fitToWindow.setState(true);
fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
inputData.addActionListener(this);
}
- /**
- * Gets the score model for the given name. If the score model is one that
- * requires to get state data from the current view, allow it to do so
- *
- * @param sm
- * @return
- */
- protected ScoreModelI configureScoreModel(String modelName)
- {
- ScoreModelI sm = ScoreModels.getInstance().forName(modelName);
- if (sm instanceof ViewBasedAnalysisI)
- {
- try
- {
- sm = sm.getClass().newInstance();
- ((ViewBasedAnalysisI) sm).configureFromAlignmentView(treeCanvas.ap);
- } catch (Exception q)
- {
- Cache.log.error("Couldn't create a scoremodel instance for "
- + sm.getName());
- }
- }
- return sm;
- }
-
}