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Fix slow BEAUTi import of allignments
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@rbouckaert
rbouckaert committed Jan 30, 2014
1 parent 2f27628 commit ee543c5
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Showing 10 changed files with 162 additions and 113 deletions.
6 changes: 3 additions & 3 deletions src/beast/app/BEASTVersion.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,13 @@ public class BEASTVersion extends Version {
/**
* Version string: assumed to be in format x.x.x
*/
private static final String VERSION = "2.1.0";
private static final String VERSION = "2.1.1";

private static final String DATE_STRING = "2002-2013";
private static final String DATE_STRING = "2002-2014";

private static final boolean IS_PRERELEASE = false;

private static final String REVISION = "$Rev: 1040 $";
private static final String REVISION = "$Rev: $";

public String getVersion() {
return VERSION;
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6 changes: 3 additions & 3 deletions src/beast/app/beastapp/BeastVersion.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,13 @@ public class BeastVersion extends Version {
/**
* Version string: assumed to be in format x.x.x
*/
private static final String VERSION = "2.1.0";
private static final String VERSION = "2.1.1";

private static final String DATE_STRING = "2002-2013";
private static final String DATE_STRING = "2002-2014";

private static final boolean IS_PRERELEASE = false;

private static final String REVISION = "$Rev$";
private static final String REVISION = "$Rev: $";

public String getVersion() {
return VERSION;
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150 changes: 76 additions & 74 deletions src/beast/app/beauti/Beauti.java
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Original file line number Diff line number Diff line change
@@ -1,34 +1,29 @@
package beast.app.beauti;


import jam.framework.DocumentFrame;

import javax.swing.*;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.xml.parsers.DocumentBuilderFactory;

import org.w3c.dom.Document;
import org.w3c.dom.Element;

import beast.app.BEASTVersion;
import beast.app.beauti.BeautiDoc.ActionOnExit;
import beast.app.beauti.BeautiDoc.DOC_STATUS;
import beast.app.draw.*;
import beast.app.draw.BEASTObjectPanel;
import beast.app.draw.HelpBrowser;
import beast.app.draw.ModelBuilder;
import beast.app.draw.MyAction;
import beast.app.util.Utils;
import beast.util.AddOnManager;
import jam.framework.DocumentFrame;
import org.w3c.dom.Document;
import org.w3c.dom.Element;


import javax.swing.*;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.xml.parsers.DocumentBuilderFactory;
import java.awt.*;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.ClipboardOwner;
import java.awt.datatransfer.StringSelection;
import java.awt.datatransfer.Transferable;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.awt.event.*;
import java.io.File;
import java.lang.reflect.Method;
import java.net.URL;
Expand All @@ -52,7 +47,8 @@ public class Beauti extends JTabbedPane implements BeautiDocListener {
*/
static public final String FILE_EXT = ".xml";
static public final String FILE_EXT2 = ".json";

static final String fileSep = System.getProperty("file.separator");

/**
* document in document-view pattern. BTW this class is the view
*/
Expand Down Expand Up @@ -219,7 +215,7 @@ boolean saveAs() {
doc.setFileName(file.getAbsolutePath());// fc.getSelectedFile().toString();
String fileSep = System.getProperty("file.separator");
if (fileSep.equals("\\")) {
fileSep = "\\\\";
fileSep = "\\\\";
}
if (doc.getFileName().lastIndexOf(fileSep) > 0) {
g_sDir = doc.getFileName().substring(0,
Expand Down Expand Up @@ -268,12 +264,12 @@ class ActionLoad extends MyAction {

public ActionLoad() {
super("Load", "Load Beast File", "open", KeyEvent.VK_O);
} // c'tor
}

public ActionLoad(String sName, String sToolTipText, String sIcon,
int acceleratorKey) {
super(sName, sToolTipText, sIcon, acceleratorKey);
} // c'tor
}

public void actionPerformed(ActionEvent ae) {
File file = beast.app.util.Utils.getLoadFile("Load Beast XML File",
Expand All @@ -290,7 +286,7 @@ public void actionPerformed(ActionEvent ae) {
doc.setFileName(file.getAbsolutePath());
String fileSep = System.getProperty("file.separator");
if (fileSep.equals("\\")) {
fileSep = "\\\\";
fileSep = "\\\\";
}
if (doc.getFileName().lastIndexOf(fileSep) > 0) {
g_sDir = doc.getFileName().substring(0,
Expand Down Expand Up @@ -376,23 +372,15 @@ class ActionImport extends MyAction {
public ActionImport() {
super("Import Alignment", "Import Alignment File", "import",
KeyEvent.VK_I);
} // c'tor
}

public ActionImport(String sName, String sToolTipText, String sIcon,
int acceleratorKey) {
super(sName, sToolTipText, sIcon, acceleratorKey);
} // c'tor
}

public void actionPerformed(ActionEvent ae) {

// JFileChooser fileChooser = new JFileChooser(g_sDir);
// fileChooser.addChoosableFileFilter(ef1);
// fileChooser.addChoosableFileFilter(ef0);
// fileChooser.setMultiSelectionEnabled(true);
// fileChooser.setDialogTitle("Import alignment File");
//
// if (fileChooser.showOpenDialog(null) ==
// JFileChooser.APPROVE_OPTION) {
try {
setCursor(new Cursor(Cursor.WAIT_CURSOR));
File[] files = Utils.getLoadFiles("Import alignment File",
Expand All @@ -405,7 +393,7 @@ public void actionPerformed(ActionEvent ae) {
for (File file : files) {
String fileSep = System.getProperty("file.separator");
if (fileSep.equals("\\")) {
fileSep = "\\\\";
fileSep = "\\\\";
}
if (file.getAbsolutePath().lastIndexOf(fileSep) > 0) {
g_sDir = file.getAbsolutePath().substring(0,
Expand All @@ -427,6 +415,8 @@ public void actionPerformed(ActionEvent ae) {
doc.importXMLAlignment(file);
}
}
doc.connectModel();
doc.fireDocHasChanged();
a_save.setEnabled(true);
a_saveas.setEnabled(true);
} catch (Exception e) {
Expand Down Expand Up @@ -659,8 +649,7 @@ public void refreshPanel() {
}
}




public JMenuBar makeMenuBar() {
JMenuBar menuBar = new JMenuBar();
JMenu fileMenu = new JMenu("File");
Expand Down Expand Up @@ -771,7 +760,7 @@ public TemplateAction(File file) {
m_sFileName = file.getAbsolutePath();
String fileSep = System.getProperty("file.separator");
if (fileSep.equals("\\")) {
fileSep = "\\";
fileSep = "\\";
}
int i = m_sFileName.lastIndexOf(fileSep) + 1;
String sName = m_sFileName.substring(
Expand Down Expand Up @@ -837,7 +826,18 @@ private void getTemplateActionForDir(File dir, List<AbstractAction> actions) {
String sXML2 = BeautiDoc.load(template
.getAbsolutePath());
if (sXML2.contains("templateinfo=")) {
actions.add(new TemplateAction(template));
// String sFileName = template.getName();
// sFileName = sFileName.substring(0, sFileName.length() - 4);
// boolean duplicate = false;
// for (AbstractAction action : actions) {
// String name = action.getValue(Action.NAME).toString();
// if (name.equals(sFileName)) {
// duplicate = true;
// }
// }
// if (!duplicate) {
actions.add(new TemplateAction(template));
// }
}
} catch (Exception e) {
System.err.println(e.getMessage());
Expand Down Expand Up @@ -914,7 +914,9 @@ public void setUpPanels() throws Exception {
isInitialising = false;
}

/** record number of frames. If the last frame is closed, exit the app. **/
/**
* record number of frames. If the last frame is closed, exit the app. *
*/
static int BEAUtiIntances = 0;

public static Beauti main2(String[] args) {
Expand All @@ -933,51 +935,51 @@ public static Beauti main2(String[] args) {
if (Utils.isMac()) {
// set up application about-menu for Mac
// Mac-only stuff
try {
URL url = ClassLoader.getSystemResource(ModelBuilder.ICONPATH + "beauti.png");
Icon icon = null;
if (url != null) {
icon = new ImageIcon(url);
} else {
System.err.println("Unable to find image: " + ModelBuilder.ICONPATH + "beauti.png");
}
jam.framework.Application application = new jam.framework.MultiDocApplication(null, "BEAUti", "about" , icon) {

@Override
protected JFrame getDefaultFrame() {
return null;
try {
URL url = ClassLoader.getSystemResource(ModelBuilder.ICONPATH + "beauti.png");
Icon icon = null;
if (url != null) {
icon = new ImageIcon(url);
} else {
System.err.println("Unable to find image: " + ModelBuilder.ICONPATH + "beauti.png");
}
jam.framework.Application application = new jam.framework.MultiDocApplication(null, "BEAUti", "about", icon) {

@Override
public void doQuit() {
beauti.a_quit.actionPerformed(null);
}
@Override
protected JFrame getDefaultFrame() {
return null;
}

@Override
public void doAbout() {
beauti.a_about.actionPerformed(null);
}
@Override
public void doQuit() {
beauti.a_quit.actionPerformed(null);
}

@Override
public DocumentFrame doOpenFile(File file) {
return null;
}
@Override
public void doAbout() {
beauti.a_about.actionPerformed(null);
}

@Override
public DocumentFrame doNew() {
return null;
}
};
jam.mac.Utils.macOSXRegistration(application);
} catch (Exception e) {
// ignore
}
@Override
public DocumentFrame doOpenFile(File file) {
return null;
}

@Override
public DocumentFrame doNew() {
return null;
}
};
jam.mac.Utils.macOSXRegistration(application);
} catch (Exception e) {
// ignore
}
try {
Class<?> class_ = Class.forName("jam.maconly.OSXAdapter");
Class<?> class_ = Class.forName("jam.maconly.OSXAdapter");
Method method = class_.getMethod("enablePrefs", boolean.class);
method.invoke(null, false);
} catch (java.lang.NoSuchMethodException e) {
// ignore
// ignore
}
}
beauti.setUpPanels();
Expand Down
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