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Clean up BEAST code and some BEAUti code #6
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@rbouckaert
rbouckaert committed Sep 14, 2022
1 parent 9eb3c1f commit 095eff4
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Showing 6 changed files with 16 additions and 620 deletions.
308 changes: 0 additions & 308 deletions src/beastfx/app/beast/BeastMCMC.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,6 @@



import beastfx.app.util.ExtensionFileFilter;
import beast.base.core.BEASTVersion2;
import beast.base.core.Log;
import beast.base.core.ProgramStatus;
Expand All @@ -39,23 +38,16 @@
import beast.base.util.FileUtils;
import beast.base.util.Randomizer;
import beast.pkgmgmt.PackageManager;
import beast.pkgmgmt.Version;
import org.json.JSONException;
import org.json.JSONObject;
import org.xml.sax.SAXException;

import javax.swing.*;
import javax.swing.border.EtchedBorder;
import javax.swing.filechooser.FileFilter;
import javax.xml.parsers.ParserConfigurationException;
import java.awt.*;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.net.URL;
import java.util.*;
import java.util.List;
import java.util.concurrent.Executors;

/**
Expand Down Expand Up @@ -124,10 +116,6 @@ public void parseArgs(String[] args) throws IOException, XMLParserException, JSO
ProgramStatus.m_nThreads = Integer.parseInt(args[i + 1]);
ProgramStatus.g_exec = Executors.newFixedThreadPool(ProgramStatus.m_nThreads);
i += 2;
// use BEAST environment variable to set Beast directories as colon separated list
// } else if (args[i].equals("-beastlib")) {
// ClassDiscovery.setJarPath(args[i + 1]);
// i += 2;
} else if (args[i].equals("-prefix")) {
System.setProperty("file.name.prefix", args[i + 1].trim());
i += 2;
Expand Down Expand Up @@ -199,79 +187,6 @@ public void parseArgs(String[] args) throws IOException, XMLParserException, JSO

if (beastFile == null) {
// Not resuming so get starting options...

List<String> MCMCargs = new ArrayList<>();
Version version = new BEASTVersion2();
String titleString = "<html><center><p>Bayesian Evolutionary Analysis Sampling Trees<br>" +
"Version " + version.getVersionString() + ", " + version.getDateString() + "</p></center></html>";
//javax.swing.Icon icon = IconUtils.getIcon(BeastMain.class, "images/beast.png");
String nameString = "BEAST " + version.getVersionString();

// BeastDialog dialog = new BeastDialog(new JFrame(), titleString, icon);
//
// if (!dialog.showDialog(nameString, m_nSeed)) {
// return;
// }
//
// switch (dialog.getLogginMode()) {
// case 0:/* do not ovewrite */
// break;
// case 1:
// MCMCargs.add("-overwrite");
// break;
// case 2:
// MCMCargs.add("-resume");
// break;
// }
// MCMCargs.add("-seed");
// MCMCargs.add(dialog.getSeed() + "");
//
// if (dialog.getThreadPoolSize() > 0) {
// MCMCargs.add("-threads");
// MCMCargs.add(dialog.getThreadPoolSize() + "");
// }
//
// boolean useBeagle = dialog.useBeagle();
// boolean beagleShowInfo = false;
// long beagleFlags = 0;
// if (useBeagle) {
// beagleShowInfo = dialog.showBeagleInfo();
// if (dialog.preferBeagleCPU()) {
// beagleFlags |= BeagleFlag.PROCESSOR_CPU.getMask();
// }
// if (dialog.preferBeagleSSE()) {
// beagleFlags |= BeagleFlag.VECTOR_SSE.getMask();import jam.util.IconUtils;

// }
// if (dialog.preferBeagleGPU()) {
// beagleFlags |= BeagleFlag.PROCESSOR_GPU.getMask();
// }
// if (dialog.preferBeagleDouble()) {
// beagleFlags |= BeagleFlag.PRECISION_DOUBLE.getMask();
// }
// if (dialog.preferBeagleSingle()) {
// beagleFlags |= BeagleFlag.PRECISION_SINGLE.getMask();
// }
// }
// if (beagleFlags != 0) {
// System.setProperty("beagle.preferred.flags", Long.toString(beagleFlags));
// }
// if (!useBeagle) {
// System.setProperty("java.only", "true");
// }
//
// File inputFile = dialog.getInputFile();
// if (!beagleShowInfo && inputFile == null) {
// System.err.println("No input file specified");
// System.exit(1);
// }
// MCMCargs.add(inputFile.getAbsolutePath());
//
//// BeastStartDialog dlg = new BeastStartDialog();
//// if (dlg.m_bOK) {
//// parseArgs(dlg.getArgs());
//// }
// parseArgs(MCMCargs.toArray(new String[0]));
return;
}

Expand Down Expand Up @@ -338,39 +253,6 @@ public static String getUsage() {
"-beastlib <path> : Colon separated list of directories. All jar files in the path are loaded. (default 'beastlib')";
} // getUsage

/**
* open file dialog for prompting the user to specify an xml script file to process *
*/
String getFileNameByDialog() {
JFileChooser fc = new JFileChooser(System.getProperty("user.dir"));
fc.addChoosableFileFilter(new FileFilter() {
@Override
public boolean accept(File f) {
if (f.isDirectory()) {
return true;
}
String name = f.getName().toLowerCase();
if (name.endsWith(".xml")) {
return true;
}
return false;
}

// The description of this filter
@Override
public String getDescription() {
return "xml files";
}
});

fc.setDialogTitle("Load xml file");
int rval = fc.showOpenDialog(null);

if (rval == JFileChooser.APPROVE_OPTION) {
return fc.getSelectedFile().toString();
}
return null;
} // getFileNameByDialog

public void run() throws Exception {
ProgramStatus.g_exec = Executors.newFixedThreadPool(ProgramStatus.m_nThreads);
Expand All @@ -380,205 +262,15 @@ public void run() throws Exception {
} // run


/**
* class for starting Beast with a dialog *
*/
class BeastStartDialog extends JDialog {
private static final long serialVersionUID = 1L;
boolean m_bOK = false;
JTextField m_fileEntry;
JTextField m_seedEntry;
JCheckBox m_bUseGPU;
JComboBox<String> m_mode;

public BeastStartDialog() {
setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
setModalityType(DEFAULT_MODALITY_TYPE);
init();
setVisible(true);
}

String[] getArgs() {
List<String> args = new ArrayList<>();
args.add("-seed");
args.add(m_seedEntry.getText());
switch (m_mode.getSelectedIndex()) {
case 0:
break;
case 1:
args.add("-overwrite");
break;
case 2:
args.add("-resume");
break;
}
// if (m_bUseGPU.isSelected()) {
// args.add("-useGPU");
// }
args.add(m_fileEntry.getText());
return args.toArray(new String[0]);
}

void init() {
try {
setTitle("Beast Start Dialog");
Box box = Box.createVerticalBox();

box.add(createHeader());
box.add(Box.createVerticalStrut(10));
box.add(createFileInput());
box.add(Box.createVerticalStrut(10));
box.add(Box.createVerticalBox());
box.add(Box.createVerticalStrut(10));
box.add(createSeedInput());
// box.add(Box.createVerticalStrut(10));
// box.add(createBeagleInput());
box.add(Box.createVerticalStrut(10));
box.add(createModeInput());

box.add(Box.createVerticalGlue());
box.add(createRunQuitButtons());
add(box);
int size = UIManager.getFont("Label.font").getSize();
setSize(600 * size / 13, 500 * size / 13);
} catch (Exception e) {
e.printStackTrace();
JOptionPane.showMessageDialog(this, "Could not create dialog: " + e.getMessage());
}
} // BeastStartDialog::init

private Component createHeader() {
Box box = Box.createHorizontalBox();

String iconLocation = "beast/app/draw/icons/beast.png";
ImageIcon icon = null;
try {
URL url = BeastMCMC.class.getClassLoader().getResource(iconLocation);
if (url == null) {
System.err.println("Cannot find icon " + iconLocation);
return null;
}
icon = new ImageIcon(url);
} catch (Exception e) {
System.err.println("Cannot load icon " + iconLocation + " " + e.getMessage());
return null;
}


JLabel label = new JLabel(icon);
label.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10));
box.add(label, BorderLayout.WEST);
label = new JLabel("<html><center>BEAST<br>Version: " + VERSION + "<br>Developers: " + DEVELOPERS + "<br>Copyright: " + COPYRIGHT + "</html>");
label.setHorizontalAlignment(SwingConstants.CENTER);
box.add(label);
return box;
} // BeastStartDialog::createHeader

private Component createFileInput() {
Box box = Box.createHorizontalBox();
box.add(new JLabel("Beast XML File: "));
m_fileEntry = new JTextField();
int fontsize = m_fileEntry.getFont().getSize();
Dimension size = new Dimension(300 * fontsize / 13, 20 * fontsize / 13);
m_fileEntry.setMinimumSize(size);
m_fileEntry.setPreferredSize(size);
m_fileEntry.setSize(size);
m_fileEntry.setToolTipText("Enter file name of Beast 2 XML file");
m_fileEntry.setMaximumSize(new Dimension(1024 * fontsize / 13, 20 * fontsize / 13));
box.add(m_fileEntry);
//box.add(Box.createHorizontalGlue());

JButton button = new JButton("Choose file");
button.addActionListener(e -> {
JFileChooser fileChooser = new JFileChooser(ProgramStatus.g_sDir);
File file = new File(m_fileEntry.getText());
if (file.exists())
fileChooser.setSelectedFile(file);
fileChooser.addChoosableFileFilter(new ExtensionFileFilter(".xml", "Beast xml file (*.xml)"));
fileChooser.setDialogTitle("Select Beast 2 XML file");
int rval = fileChooser.showOpenDialog(null);
if (rval == JFileChooser.APPROVE_OPTION) {
String fileName = fileChooser.getSelectedFile().toString();
if (fileName.lastIndexOf(File.separator) > 0) {
ProgramStatus.setCurrentDir(fileName.substring(0, fileName.lastIndexOf(File.separator)));
}
m_fileEntry.setText(fileName);
}
});
box.add(button);

return box;
} // BeastStartDialog::createFileInput

private Component createSeedInput() {
Box box = Box.createHorizontalBox();
box.add(new JLabel("Random number seed: "));
m_seedEntry = new JTextField("127");
m_seedEntry.setHorizontalAlignment(SwingConstants.RIGHT);
Dimension size = new Dimension(100, 20);
m_seedEntry.setMinimumSize(size);
m_seedEntry.setPreferredSize(size);
m_seedEntry.setSize(size);
m_seedEntry.setToolTipText("Enter seed number used for initialising the random number generator");
int fontsize = m_seedEntry.getFont().getSize();
m_seedEntry.setMaximumSize(new Dimension(1024 * fontsize / 13, 20 * fontsize / 13));
box.add(m_seedEntry);
box.add(Box.createHorizontalGlue());
return box;
} // BeastStartDialog::createSeedInput

private Component createModeInput() {
Box box = Box.createHorizontalBox();
box.add(new JLabel("Mode of running: "));
m_mode = new JComboBox<>(new String[]{"default: only write new log files",
"overwrite: overwrite log files",
"resume: appends log to existing files (if any)"});
Dimension size = new Dimension(350, 20);
m_mode.setMinimumSize(size);
m_mode.setPreferredSize(size);
m_mode.setSize(size);
m_mode.setMaximumSize(size);

m_mode.setSelectedIndex(0);
box.add(m_mode);
box.add(Box.createHorizontalGlue());
return box;
} // BeastStartDialog::createModeInput

Component createRunQuitButtons() {
Box cancelOkBox = Box.createHorizontalBox();
cancelOkBox.setBorder(new EtchedBorder());
JButton okButton = new JButton("Run");
okButton.addActionListener(e -> {
m_bOK = true;
dispose();
});
JButton cancelButton = new JButton("Quit");
cancelButton.addActionListener(e -> {
dispose();
System.exit(0);
});
cancelOkBox.add(Box.createHorizontalGlue());
cancelOkBox.add(cancelButton);
cancelOkBox.add(Box.createHorizontalStrut(20));
cancelOkBox.add(okButton);
cancelOkBox.add(Box.createHorizontalStrut(20));
return cancelOkBox;
} // BeastStartDialog::createRunQuitButtons

} // class BeastStartDialog


public static void main(String[] args) {
try {
System.setProperty("beast.debug", "true");
BeastMCMC app = new BeastMCMC();
app.parseArgs(args);

app.run();
} catch (XMLParserException e) {
System.out.println(e.getMessage());
//e.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
System.out.println(BeastMCMC.getUsage());
Expand Down
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