/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.gui;
-import java.beans.*;
-import java.io.*;
-import java.util.*;
-import java.util.List;
-
-import javax.imageio.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import org.jibble.epsgraphics.*;
-import jalview.analysis.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.NJTree;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.NewickFile;
+import jalview.jbgui.GTreePanel;
+import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.imageio.ImageIO;
+import javax.swing.ButtonGroup;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+
+import org.jibble.epsgraphics.EpsGraphics2D;
/**
* DOCUMENT ME!
return treeCanvas.av.getAlignment();
}
- public AlignViewport getViewPort()
+ public AlignmentViewport getViewPort()
{
return treeCanvas.av;
}
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
}
+ @Override
public void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = false;
associateLeavesMenu.add(item);
}
- final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+ MessageManager.getString("label.all_views"));
buttonGroup.add(itemf);
itemf.setSelected(treeCanvas.applyToAllViews);
itemf.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = itemf.isSelected();
}
}
+ @Override
public void run()
{
seqs = av.getSelectionGroup().getSequencesInOrder(
av.getAlignment());
}
-
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+ 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());
+ }
+ tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+ }
+ else
+ {
+ tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+ end);
+ }
showDistances(true);
}
av.setCurrentTree(tree);
if (av.getSortByTree())
{
- sortByTree_actionPerformed(null);
+ sortByTree_actionPerformed();
}
}
}
* @param e
* DOCUMENT ME!
*/
+ @Override
public void textbox_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAsNewick_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_tree_as_newick"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
* @param e
* DOCUMENT ME!
*/
+ @Override
public void printMenu_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
treeCanvas.startPrinting();
}
+ @Override
public void originalSeqData_actionPerformed(ActionEvent e)
{
if (!tree.hasOriginalSequenceData())
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params", new String[]
- { this.title }), AlignFrame.DEFAULT_WIDTH,
+ "label.original_data_for_params",
+ new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
}
* @param e
* DOCUMENT ME!
*/
+ @Override
public void fitToWindow_actionPerformed(ActionEvent e)
{
treeCanvas.fitToWindow = fitToWindow.isSelected();
*
* @param e
*/
- public void sortByTree_actionPerformed(ActionEvent e)
+ @Override
+ public void sortByTree_actionPerformed()
{
if (treeCanvas.applyToAllViews)
public CommandI sortAlignmentIn(AlignmentPanel ap)
{
- AlignViewport av = ap.av;
+ AlignmentViewport av = ap.av;
SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
AlignmentSorter.sortByTree(av.getAlignment(), tree);
CommandI undo;
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
if (treeCanvas == null)
* @param e
* DOCUMENT ME!
*/
+ @Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowDistances(distanceMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void epsTree_actionPerformed(ActionEvent e)
{
boolean accurateText = true;
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "eps" }, new String[]
- { "Encapsulated Postscript" }, "Encapsulated Postscript");
+ { "eps" }, new String[] { "Encapsulated Postscript" },
+ "Encapsulated Postscript");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.create_eps_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pngTree_actionPerformed(ActionEvent e)
{
int width = treeCanvas.getWidth();
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "png" }, new String[]
- { "Portable network graphics" }, "Portable network graphics");
+ { "png" }, new String[] { "Portable network graphics" },
+ "Portable network graphics");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.create_png_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
tree.applyToNodes(new NodeTransformI()
{
+ @Override
public void transform(BinaryNode node)
{
if (node instanceof SequenceNode
{
// search dbrefs, features and annotation
DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
- sq.getDBRef(), new String[]
- { labelClass.toUpperCase() });
+ sq.getDBRefs(),
+ new String[] { labelClass.toUpperCase() });
if (refs != null)
{
for (int i = 0; i < refs.length; i++)
git://source.jalview.org / jalview.git / blobdiff