/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.analysis.AverageDistanceTree;
+import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
+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.SequenceI;
+import jalview.io.NewickFile;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.ScrollPane;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
public class TreePanel extends EmbmenuFrame implements ActionListener,
ItemListener
{
TreeCanvas treeCanvas;
- NJTree tree;
+ TreeModel tree;
AlignmentPanel ap;
AlignViewport av;
- public NJTree getTree()
+ public TreeModel getTree()
{
return tree;
}
+ @Override
public void finalize() throws Throwable
{
ap = null;
// yields unaligned seqs)
// or create a selection box around columns in alignment view
// test Alignment(SeqCigar[])
- if (tree.seqData != null)
+ if (tree.getOriginalData() != null)
{
char gc = '-';
try
} catch (Exception ex)
{
}
- ;
- Object[] alAndColsel = tree.seqData
+
+ Object[] alAndColsel = tree.getOriginalData()
.getAlignmentAndColumnSelection(gc);
if (alAndColsel != null && alAndColsel[0] != null)
this.newtree = newtree;
}
+ @Override
public void run()
{
if (newtree != null)
{
- if (odata == null)
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
- }
- else
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
- newtree);
- }
-
+ tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+ newtree);
}
else
{
- int start, end;
- SequenceI[] seqs;
- boolean selview = (av.getSelectionGroup() != null)
- && (av.getSelectionGroup().getSize() > 1);
- AlignmentView seqStrings = av.getAlignmentView(selview);
- if (!selview)
- {
- start = 0;
- end = av.getAlignment().getWidth();
- seqs = av.getAlignment().getSequencesArray();
- }
- else
- {
- start = av.getSelectionGroup().getStartRes();
- end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(
- av.getAlignment());
- }
-
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ ScoreModelI sm = configureScoreModel(pwtype);
+ TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
+ av, sm, SimilarityParams.Jalview)
+ : new AverageDistanceTree(av, sm, SimilarityParams.Jalview);
+ tree = new TreeModel(njtree);
}
tree.reCount(tree.getTopNode());
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == newickOutput)
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == fitToWindow)
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;
+ }
+
}