/* ArtemisMain.java
*
* created: Wed Feb 23 2000
*
* This file is part of Artemis
*
* Copyright(C) 2000 Genome Research Limited
*
* 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
* 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.
*
* 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.33 2008-12-10 16:43:38 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
import uk.ac.sanger.artemis.components.database.DatabaseJPanel;
import uk.ac.sanger.artemis.components.filetree.FileManager;
import uk.ac.sanger.artemis.components.filetree.LocalAndRemoteFileManager;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.TextDocument;
import uk.ac.sanger.artemis.util.DocumentFactory;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.io.EntryInformation;
import org.biojava.bio.seq.io.SequenceFormat;
import java.awt.event.*;
import java.awt.Toolkit;
import java.io.*;
import java.awt.datatransfer.*;
import javax.swing.JFrame;
import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
/**
* The main window for the Artemis sequence editor.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
* @version $Id: ArtemisMain.java,v 1.33 2008-12-10 16:43:38 tjc Exp $
**/
public class ArtemisMain extends Splash
{
/** */
private static final long serialVersionUID = 1L;
/** Version String use for banner messages and title bars. */
public static final String version = "Release 9";
/** A vector containing all EntryEdit object we have created. */
private EntryEditVector entry_edit_objects = new EntryEditVector();
protected static FileManager filemanager = null;
private LocalAndRemoteFileManager fm;
/**
* The constructor creates all the components for the main Artemis
* window and sets up all the menu callbacks.
**/
public ArtemisMain(final String args[])
{
super("Artemis", "Artemis", version);
ActionListener menu_listener = new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
if(filemanager == null)
filemanager = new FileManager(ArtemisMain.this);
else
filemanager.setVisible(true);
}
};
makeMenuItem(file_menu, "Open File Manager ...", menu_listener);
ActionListener menu_listener_ssh = new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
if(fm == null)
fm = new LocalAndRemoteFileManager(ArtemisMain.this);
else
fm.setVisible(true);
}
};
if(System.getProperty("chado") != null)
makeMenuItem(file_menu, "Open Database and SSH File Manager ...", menu_listener_ssh);
else
makeMenuItem(file_menu, "Open SSH File Manager ...", menu_listener_ssh);
final EntrySourceVector entry_sources = getEntrySources(this);
for(int source_index=0; source_index<entry_sources.size();
++source_index)
{
final EntrySource this_entry_source =
entry_sources.elementAt(source_index);
String entry_source_name = this_entry_source.getSourceName();
String menu_name = null;
if(entry_source_name.equals("Filesystem"))
menu_name = "Open ...";
else
menu_name = "Open from " + entry_source_name + " ...";
menu_listener = new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
getEntryEditFromEntrySource(this_entry_source);
}
};
makeMenuItem(file_menu, menu_name, menu_listener);
}
menu_listener = new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
launchDatabaseJFrame();
}
};
//final boolean sanger_options =
// Options.getOptions().getPropertyTruthValue("sanger_options");
//makeMenuItem(file_menu, "Database Entry ...", menu_listener);
menu_listener = new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
exit();
}
};
makeMenuItem(file_menu, "Quit", menu_listener);
getCanvas().addMouseListener(new MouseAdapter()
{
/**
* Listen for mouse press events so that we can do popup menus and
* selection.
**/
public void mousePressed(MouseEvent event)
{
handleCanvasMousePress(event);
}
});
}
/**
* Handle a mouse press event on the drawing canvas - select on click,
* select and broadcast it on double click.
**/
private void handleCanvasMousePress(MouseEvent event)
{
if(event.getID() != MouseEvent.MOUSE_PRESSED)
return;
if((event.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
{
openClipboardContents();
}
}
/**
* Get the String residing on the clipboard.
*
* @return any text found on the Clipboard; if none found, return an
* empty String.
*/
public void openClipboardContents()
{
Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
//odd: the Object param of getContents is not currently used
Transferable contents = clipboard.getContents(null);
boolean hasTransferableText = (contents != null) &&
contents.isDataFlavorSupported(DataFlavor.stringFlavor);
if(hasTransferableText)
{
TextDocument entry_document = new TextDocument();
final InputStreamProgressListener progress_listener =
getInputStreamProgressListener();
entry_document.addInputStreamProgressListener(progress_listener);
final EntryInformation artemis_entry_information =
Options.getArtemisEntryInformation();
final uk.ac.sanger.artemis.io.Entry new_embl_entry =
EntryFileDialog.getEntryFromFile(this, entry_document,
artemis_entry_information,
false);
if(new_embl_entry == null) // the read failed
return;
try
{
final Entry entry = new Entry(new_embl_entry);
EntryEdit last_entry_edit = makeEntryEdit(entry);
addEntryEdit(last_entry_edit);
getStatusLabel().setText("");
last_entry_edit.setVisible(true);
}
catch(OutOfRangeException e)
{
new MessageDialog(this, "read failed: one of the features in " +
" cut and paste has an out of range " +
"location: " + e.getMessage());
}
catch(NoSequenceException e)
{
new MessageDialog(this, "read failed: " +
" cut and paste contains no sequence");
}
}
}
/**
*
* Launch database manager window
*
*/
private void launchDatabaseJFrame()
{
SwingWorker entryWorker = new SwingWorker()
{
public Object construct()
{
getStatusLabel().setText("Connecting ...");
DatabaseEntrySource entry_source = new DatabaseEntrySource();
boolean promptUser = true;
if(System.getProperty("read_only") != null)
promptUser = false;
if(!entry_source.setLocation(promptUser))
return null;
JFrame frame = new JFrame("Organism List");
final DatabaseJPanel pane = new DatabaseJPanel(entry_source,
ArtemisMain.this);
frame.getContentPane().add(pane);
frame.pack();
Utilities.rightJustifyFrame(frame);
frame.setVisible(true);
//frame.setJMenuBar(pane.makeMenuBar(entry_source, ArtemisMain.this));
getStatusLabel().setText("");
return null;
}
};
entryWorker.start();
}
/**
* Read the entries named in args and in the diana.ini file.
**/
protected void readArgsAndOptions(final String [] args)
{
if(args.length == 0)
{
if(System.getProperty("chado") != null &&
(args.length < 1 || args[0].indexOf(':') == -1))
fm = new LocalAndRemoteFileManager(ArtemisMain.this);
// open the entries given in the options file(diana.ini)
readDefaultEntries();
return;
}
if(args[0].equals("-biojava"))
{
handleBioJava(args);
return;
}
final EntryInformation artemis_entry_information =
Options.getArtemisEntryInformation();
EntryEdit last_entry_edit = null;
boolean seen_plus = false;
for(int i = 0 ; i<args.length ; ++i)
{
String new_entry_name = args[i];
if(new_entry_name.length() == 0)
continue;
if(new_entry_name.equals("+"))
{
seen_plus = true;
continue;
}
if(new_entry_name.startsWith("+") && last_entry_edit != null ||
seen_plus)
{
// new feature file
final Document entry_document;
if(seen_plus)
entry_document = DocumentFactory.makeDocument(new_entry_name);
else
entry_document =
DocumentFactory.makeDocument(new_entry_name.substring(1));
final InputStreamProgressListener progress_listener =
getInputStreamProgressListener();
entry_document.addInputStreamProgressListener(progress_listener);
final uk.ac.sanger.artemis.io.Entry new_embl_entry =
EntryFileDialog.getEntryFromFile(this, entry_document,
artemis_entry_information,
false);
if(new_embl_entry == null) // the read failed
break;
try
{
final Entry new_entry =
new Entry(last_entry_edit.getEntryGroup().getBases(),
new_embl_entry);
last_entry_edit.getEntryGroup().add(new_entry);
}
catch(OutOfRangeException e)
{
new MessageDialog(this, "read failed: one of the features in " +
new_entry_name + " has an out of range " +
"location: " + e.getMessage());
}
seen_plus = false; // reset
}
else if(System.getProperty("chado") != null && new_entry_name.indexOf(':')>-1)
{
// open from database e.g. Pfalciparum:Pf3D7_09:95000..150000
Splash.logger4j.info("OPEN ENTRY "+new_entry_name);
getStatusLabel().setText("Connecting ...");
DatabaseEntrySource entry_source = new DatabaseEntrySource();
boolean promptUser = true;
if(System.getProperty("read_only") != null)
{
promptUser = false;
entry_source.setReadOnly(true);
}
if(!entry_source.setLocation(promptUser))
return;
last_entry_edit =
DatabaseJPanel.show(entry_source, this,
getInputStreamProgressListener(), new_entry_name);
}
else
{
// new sequence file
if(last_entry_edit != null)
{
last_entry_edit.setVisible(true);
last_entry_edit = null;
}
if (new_entry_name.indexOf ("://") == -1)
{
File file = new File (new_entry_name);
if(!file.exists())
{
JOptionPane.showMessageDialog(null, "File "+
new_entry_name +" not found.\n"+
"Check the file name.", "File Not Found",
JOptionPane.WARNING_MESSAGE);
}
}
final Document entry_document =
DocumentFactory.makeDocument(new_entry_name);
entry_document.addInputStreamProgressListener(getInputStreamProgressListener());
final uk.ac.sanger.artemis.io.Entry new_embl_entry =
EntryFileDialog.getEntryFromFile(this, entry_document,
artemis_entry_information,
false);
if(new_embl_entry == null) // the read failed
break;
try
{
final Entry entry = new Entry(new_embl_entry);
last_entry_edit = makeEntryEdit(entry);
addEntryEdit(last_entry_edit);
getStatusLabel().setText("");
}
catch(OutOfRangeException e)
{
new MessageDialog(this, "read failed: one of the features in " +
new_entry_name + " has an out of range " +
"location: " + e.getMessage());
break;
}
catch(NoSequenceException e)
{
new MessageDialog(this, "read failed: " +
new_entry_name + " contains no sequence");
break;
}
}
}
if(System.getProperty("offset") != null)
last_entry_edit.getGotoEventSource().gotoBase(
Integer.parseInt(System.getProperty("offset")));
last_entry_edit.setVisible(true);
for(int entry_index=0; entry_index<entry_edit_objects.size();
++entry_index)
{
if(System.getProperty("offset") != null)
entry_edit_objects.elementAt(entry_index).getGotoEventSource().gotoBase(
Integer.parseInt(System.getProperty("offset")));
}
}
/**
*
* Handle the -biojava option
*
* Command line syntax:
* art -biojava org.biojava.bio.seq.io.EmblLikeFormat foo.embl
*
* BioJava formats:
* EmblLikeFormat, FastaFormat, GAMEFormat, GenbankFormat, PhredFormat
*
**/
private void handleBioJava(final String [] args)
{
if(args.length == 3)
{
final String class_name = args[1];
final String location = args[2];
final Document location_document =
DocumentFactory.makeDocument(location);
try
{
final Object biojava_object =
Class.forName(class_name).newInstance();
final EntryInformation entry_information =
Options.getArtemisEntryInformation();
final uk.ac.sanger.artemis.io.BioJavaEntry emblEntry;
if(biojava_object instanceof SequenceFormat)
{
final SequenceFormat sequence_format = (SequenceFormat)biojava_object;
emblEntry =
new uk.ac.sanger.artemis.io.BioJavaEntry(entry_information,
location_document,
sequence_format);
final Entry new_entry = new Entry(emblEntry);
final EntryEdit new_entry_edit = makeEntryEdit(new_entry);
new_entry_edit.setVisible(true);
}
else
new MessageDialog(this, "not a SequenceFormat: " + class_name);
}
catch(IllegalAccessException e)
{
new MessageDialog(this, "cannot create class: " + class_name +
" - IllegalAccessException");
}
catch(ClassNotFoundException e)
{
new MessageDialog(this, "cannot find class: " + class_name);
}
catch(ClassCastException e)
{
new MessageDialog(this, class_name + " is not a sub-class of " +
"SequenceFormat");
}
catch(IOException e)
{
new MessageDialog(this, "I/O error while reading from " +
location + ": " + e.getMessage());
}
catch(NoSequenceException e)
{
new MessageDialog(this, location + " contained no sequence");
}
catch(InstantiationException e)
{
new MessageDialog(this, "cannot instantiate " + class_name);
}
catch(OutOfRangeException e)
{
new MessageDialog(this, "read failed: one of the features in " +
location +
" has an out of range location: " +
e.getMessage());
}
}
else
new MessageDialog(this, "the -biojava option needs two arguments");
}
/**
* Read the entries given in the uk.ac.sanger.artemis.ini file.
**/
private void readDefaultEntries()
{
final EntryInformation artemis_entry_information =
Options.getArtemisEntryInformation();
final String default_sequence_file_name =
Options.getOptions().getDefaultSequenceFileName();
final String default_feature_file_name =
Options.getOptions().getDefaultFeatureFileName();
if(default_sequence_file_name != null)
{
final String default_sequence_file_name_embl =
default_sequence_file_name + "_embl";
uk.ac.sanger.artemis.io.Entry new_embl_entry = null;
// try opening the default sequence file with "_embl" added to the name
// if that fails try the plain sequence file name
final Document entry_document =
DocumentFactory.makeDocument(default_sequence_file_name_embl);
final InputStreamProgressListener progress_listener =
getInputStreamProgressListener();
entry_document.addInputStreamProgressListener(progress_listener);
if(entry_document.readable())
{
new_embl_entry =
EntryFileDialog.getEntryFromFile(this,
entry_document,
artemis_entry_information,
false);
}
if(new_embl_entry == null || new_embl_entry.getSequence() == null ||
new_embl_entry.getSequence().length() == 0)
{
final File entry_file = new File(default_sequence_file_name);
if(entry_file.exists())
{
new_embl_entry =
EntryFileDialog.getEntryFromFile(this,
entry_document,
artemis_entry_information,
false);
}
else
{
// read failed
System.err.println("file does not exist: " +
default_sequence_file_name +
"(given in options files)");
return;
}
}
if(new_embl_entry == null || new_embl_entry.getSequence() == null ||
new_embl_entry.getSequence().length() == 0)
{
// read failed
System.err.println("failed to read " + default_sequence_file_name +
"(given in options files)");
return;
}
getStatusLabel().setText("");
try
{
final Entry entry = new Entry(new_embl_entry);
final EntryEdit new_entry_edit = makeEntryEdit(entry);
new_entry_edit.setVisible(true);
if(default_feature_file_name != null)
{
final Document feature_document =
DocumentFactory.makeDocument(default_feature_file_name);
final uk.ac.sanger.artemis.io.Entry new_embl_table_entry =
EntryFileDialog.getEntryFromFile(this,
feature_document,
artemis_entry_information,
false);
if(new_embl_table_entry == null) // open failed
return;
final EntryGroup entry_group = new_entry_edit.getEntryGroup();
final Entry new_table_entry =
new Entry(entry.getBases(), new_embl_table_entry);
entry_group.add(new_table_entry);
}
} catch(OutOfRangeException e) {
new MessageDialog(this, "read failed: one of the features in " +
default_feature_file_name +
" has an out of range location: " +
e.getMessage());
} catch(NoSequenceException e) {
new MessageDialog(this, "read failed: " +
new_embl_entry.getName() +
" contains no sequence");
}
}
}
/**
* Make an EntryEdit component from the given Entry.
**/
public static EntryEdit makeEntryEdit(final Entry entry)
{
final Bases bases = entry.getBases();
final EntryGroup entry_group = new SimpleEntryGroup(bases);
entry_group.add(entry);
final EntryEdit entry_edit = new EntryEdit(entry_group);
return entry_edit;
}
/**
* This method gets rid of an EntryEdit object and it's frame. Each object
* removed with this method must have been added previously with
* addEntryEdit().
* @param entry_edit The object to get rid of.
**/
public void entryEditFinished(EntryEdit entry_edit)
{
if(null == entry_edit)
throw new Error("entryEditFinished() was passed a null object");
if(!entry_edit_objects.removeElement(entry_edit))
throw new Error("entryEditFinished() - could not remove a " +
"object from an empty vector");
entry_edit.setVisible(false);
entry_edit.dispose();
}
/**
* Add an EntryEdit object to our list of objects.
* @param entry_edit The object to add.
**/
public synchronized void addEntryEdit(EntryEdit entry_edit)
{
entry_edit_objects.addElement(entry_edit);
}
/**
* Read an Entry from the given EntrySource and make a new EntryEdit
* component for the Entry.
**/
private void getEntryEditFromEntrySource(final EntrySource entry_source)
{
SwingWorker entryWorker = new SwingWorker()
{
EntryEdit entry_edit;
public Object construct()
{
try
{
final Entry entry = entry_source.getEntry(true);
if(entry == null)
return null;
final EntryGroup entry_group =
new SimpleEntryGroup(entry.getBases());
entry_group.add(entry);
entry_edit = new EntryEdit(entry_group);
}
catch(OutOfRangeException e)
{
new MessageDialog(ArtemisMain.this, "read failed: one of the features in " +
" the entry has an out of range " +
"location: " + e.getMessage());
}
catch(NoSequenceException e)
{
new MessageDialog(ArtemisMain.this, "read failed: entry contains no sequence");
}
catch(IOException e)
{
new MessageDialog(ArtemisMain.this, "read failed due to IO error: " + e);
}
return null;
}
public void finished()
{
if(entry_edit != null)
entry_edit.setVisible(true);
}
};
entryWorker.start();
}
/**
* Retrieve a live vector containing all the EntryEdit object we have created.
*/
protected EntryEditVector get_entry_edit_objects() {
return entry_edit_objects;
}
/**
* Close the main frame and all EntryEdit frames and then this frame,
* then exit.
**/
protected void exit()
{
Splash.exitApp();
// for(int i=0 ; i<entry_edit_objects.size() ;++i)
// entryEditFinished(entry_edit_objects.elementAt(i));
// if(filemanager != null)
// filemanager.setVisible(false);
// setVisible(false);
// dispose();
// System.gc();
}
/**
* Main entry point for the stand-alone version of Artemis.
**/
public static void main(final String [] args)
{
SwingUtilities.invokeLater(new Runnable()
{
public void run()
{
final ArtemisMain main_window = new ArtemisMain(args);
main_window.setVisible(true);
main_window.readArgsAndOptions(args);
}
});
}
}