/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-import java.util.Hashtable;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-
-public class TreePanel
- extends EmbmenuFrame implements ActionListener, ItemListener
+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.datamodel.Alignment;
+import jalview.datamodel.HiddenColumns;
+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
{
SequenceI[] seq;
+
String type;
+
String pwtype;
+
int start;
+
int end;
+
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;
+ av = null;
+ super.finalize();
+ }
+
/**
* 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(AlignViewport av, String type, String pwtype)
+ public TreePanel(AlignmentPanel alignPanel, String type, String pwtype)
{
try
{
jbInit();
this.setMenuBar(jMenuBar1);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
- initTreePanel(av, 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(AlignViewport av,
- String type,
- String pwtype,
- NewickFile newtree)
+ public TreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newtree)
{
try
{
jbInit();
this.setMenuBar(jMenuBar1);
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
- initTreePanel(av, type, pwtype, newtree);
+ initTreePanel(ap, type, pwtype, newtree);
}
- void initTreePanel(AlignViewport av,
- String type,
- String pwtype,
- NewickFile newTree)
+
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newTree)
{
- this.av = av;
+ this.ap = ap;
+ this.av = ap.av;
this.type = type;
this.pwtype = pwtype;
-
- treeCanvas = new TreeCanvas(av, scrollPane);
+ treeCanvas = new TreeCanvas(ap, scrollPane);
TreeLoader tl = new TreeLoader(newTree);
tl.start();
embedMenuIfNeeded(treeCanvas);
scrollPane.add(treeCanvas, BorderLayout.CENTER);
}
+
void showOriginalData()
{
- // decide if av alignment is sufficiently different to original data to warrant a new window to be created
- // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+ // decide if av alignment is sufficiently different to original data to
+ // warrant a new window to be created
+ // create new alignmnt window with hidden regions (unhiding hidden regions
+ // 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 {
+ try
+ {
// we try to get the associated view's gap character
// but this may fail if the view was closed...
- gc = av.
- getGapCharacter();
- } catch (Exception ex) {};
- Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
+ gc = av.getGapCharacter();
+ } catch (Exception ex)
+ {
+ }
+
+ Object[] alAndColsel = tree.getOriginalData()
+ .getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
- Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
- AlignFrame af = new AlignFrame(al,
- av.applet,
- "Original Data for Tree",
- false);
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ 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
}
}
- class TreeLoader
- extends Thread
+ class TreeLoader extends Thread
{
NewickFile newtree;
+
jalview.datamodel.AlignmentView odata = null;
public TreeLoader(NewickFile newtree)
this.newtree = newtree;
}
+ @Override
public void run()
{
if (newtree != null)
{
- if (odata == null)
- {
- tree = new NJTree(av.alignment.getSequencesArray(),
- newtree);
- }
- else
- {
- tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
- }
-
+ tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+ newtree);
}
else
{
- int start, end;
- SequenceI[] seqs;
- AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
- if (av.getSelectionGroup() == null)
- {
- start = 0;
- end = av.alignment.getWidth();
- seqs = av.alignment.getSequencesArray();
- }
- else
- {
- start = av.getSelectionGroup().getStartRes();
- end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
- }
-
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ 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);
}
tree.reCount(tree.getTopNode());
treeCanvas.setTree(tree);
if (newtree != null)
{
- distanceMenu.setState(newtree.HasDistances());
- bootstrapMenu.setState(newtree.HasBootstrap());
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());
- treeCanvas.setShowDistances(newtree.HasDistances());
+ // Set default view, paying lip service to any overriding tree view
+ // parameter settings
+ boolean showDist = newtree.HasDistances()
+ && av.applet.getDefaultParameter("showTreeDistances",
+ newtree.HasDistances());
+ boolean showBoots = newtree.HasBootstrap()
+ && av.applet.getDefaultParameter("showTreeBootstraps",
+ newtree.HasBootstrap());
+ distanceMenu.setState(showDist);
+ bootstrapMenu.setState(showBoots);
+ treeCanvas.setShowBootstrap(showBoots);
+ treeCanvas.setShowDistances(showDist);
+ treeCanvas.setMarkPlaceholders(av.applet
+ .getDefaultParameter("showUnlinkedTreeNodes", false));
}
treeCanvas.repaint();
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == newickOutput)
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == fitToWindow)
public void newickOutput_actionPerformed()
{
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(
+ tree.getTopNode());
String output = fout.print(false, true);
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
cap.setText(output);
}
BorderLayout borderLayout1 = new BorderLayout();
+
protected ScrollPane scrollPane = new ScrollPane();
+
MenuBar jMenuBar1 = new MenuBar();
+
Menu jMenu2 = new Menu();
+
protected MenuItem fontSize = new MenuItem();
+
protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
+
protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
+
protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
+
protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
+
Menu fileMenu = new Menu();
+
MenuItem newickOutput = new MenuItem();
+
MenuItem inputData = new MenuItem();
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
setLayout(borderLayout1);
this.setBackground(Color.white);
this.setFont(new java.awt.Font("Verdana", 0, 12));
- jMenu2.setLabel("View");
- fontSize.setLabel("Font...");
+ jMenu2.setLabel(MessageManager.getString("action.view"));
+ fontSize.setLabel(MessageManager.getString("action.font"));
fontSize.addActionListener(this);
- bootstrapMenu.setLabel("Show Bootstrap Values");
+ bootstrapMenu.setLabel(
+ MessageManager.getString("label.show_bootstrap_values"));
bootstrapMenu.addItemListener(this);
- distanceMenu.setLabel("Show Distances");
+ distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
distanceMenu.addItemListener(this);
- placeholdersMenu.setLabel("Mark Unassociated Leaves");
+ placeholdersMenu.setLabel(
+ MessageManager.getString("label.mark_unassociated_leaves"));
placeholdersMenu.addItemListener(this);
fitToWindow.setState(true);
- fitToWindow.setLabel("Fit To Window");
+ fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
fitToWindow.addItemListener(this);
- fileMenu.setLabel("File");
- newickOutput.setLabel("Newick Format");
+ fileMenu.setLabel(MessageManager.getString("action.file"));
+ newickOutput.setLabel(MessageManager.getString("label.newick_format"));
newickOutput.addActionListener(this);
- inputData.setLabel("Input Data...");
+ inputData.setLabel(MessageManager.getString("label.input_data"));
add(scrollPane, BorderLayout.CENTER);
jMenuBar1.add(fileMenu);
git://source.jalview.org / jalview.git / blobdiff