UserDefinedQualifiers.java 24.96 KiB
/* UserDefinedQualifier
* This file is part of Artemis
*
* Copyright(C) 2013 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.
*
*/
package uk.ac.sanger.artemis.components;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Enumeration;
import java.util.Vector;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.UIManager;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
import javax.swing.filechooser.FileFilter;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.components.genebuilder.JExtendedComboBox;
import uk.ac.sanger.artemis.components.genebuilder.cv.DatePanel;
import uk.ac.sanger.artemis.editor.MultiLineToolTipUI;import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.FileDocument;
import uk.ac.sanger.artemis.util.LinePushBackReader;
import uk.ac.sanger.artemis.util.ReadOnlyException;
import uk.ac.sanger.artemis.util.StringVector;
import uk.ac.sanger.artemis.util.URLDocument;
/**
* Load and make available qualifiers from a list in a file
* of tag=value pairs and from OBO files.
*/
class UserDefinedQualifiers extends JFrame
{
private static final long serialVersionUID = 1L;
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(UserDefinedQualifiers.class);
/* collection of loaded files */
private Vector<QualifierList> obos = new Vector<QualifierList>();
/* component containing list of available values */
private Box qualifierBox = Box.createHorizontalBox();
/* listener for adding qualifiers **/
private ActionListener addListener;
/* text area in the feature editor to add qualifiers to */
private QualifierTextArea qualifier_text_area;
private Selection selection;
private JPanel mainPanel;
/* line pattern for tag=value */
private static Pattern TAG_VALUE_PATTERN = Pattern.compile("^/?(\\w+) ?= ?([^\\n\\r]+)$");
UserDefinedQualifiers()
{
mainPanel = (JPanel) getContentPane();
MultiLineToolTipUI.initialize();
read();
createComponentToAddCvTerm();
createMenus();
}
/**
* Menu creation
*/
private void createMenus()
{
final JMenuBar menuBar = new JMenuBar();
final JMenu fileMenu = new JMenu("File");
menuBar.add(fileMenu);
final JMenuItem importFile = new JMenuItem("Import qualifiers from file ...");
importFile.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
importFromFile();
}
});
fileMenu.add(importFile);
final JMenuItem importURL = new JMenuItem("Import qualifiers from URL ...");
importURL.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
importFromUrl();
}
}); fileMenu.add(importURL);
final JMenuItem pasteQualifiers = new JMenuItem("Paste qualifiers ...");
pasteQualifiers.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
final QualifierTextArea qualifierText = new QualifierTextArea();
int status = JOptionPane.showConfirmDialog(UserDefinedQualifiers.this,
qualifierText, "Paste in qualifier lists in the format: name = value",
JOptionPane.OK_CANCEL_OPTION);
if(status == JOptionPane.OK_OPTION)
{
QualifierList obo = new QualifierList();
obo.qualifiers = loadText(new ByteArrayInputStream(qualifierText.getText().getBytes()));
obos.add(obo);
createComponentToAddCvTerm();
mainPanel.revalidate();
writeQualifierList(qualifierText.getText());
}
}
});
fileMenu.add(pasteQualifiers);
fileMenu.addSeparator();
final JMenu removeFile = new JMenu("Qualifier source(s)");
removeFile.addMenuListener(new MenuListener(){
public void menuCanceled(MenuEvent e){}
public void menuDeselected(MenuEvent e){}
public void menuSelected(MenuEvent e)
{
removeFile.removeAll();
for(final QualifierList obo: obos)
{
final JCheckBoxMenuItem oboMenu =
new JCheckBoxMenuItem(obo.doc.getName(), obo.isAcive);
removeFile.add(oboMenu);
oboMenu.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
{
obo.isAcive = oboMenu.isSelected();
createComponentToAddCvTerm();
mainPanel.revalidate();
mainPanel.repaint();
}
});
}
}
});
fileMenu.add(removeFile);
setJMenuBar(menuBar);
}
/**
* Add components to the panel for adding CvTerm's to
* the annotation.
*/
private void createComponentToAddCvTerm()
{
mainPanel.removeAll();
mainPanel.setLayout(new GridBagLayout());
final GridBagConstraints c = new GridBagConstraints();
final JCheckBox ignoreCase = new JCheckBox("Ignore case",true);
final Vector<String> names = getQualiferNames();
final JComboBox nameCombo = new JComboBox(names);
final JButton addButton = new JButton("ADD"); final JCheckBox addToAllSelected = new JCheckBox("add to all selected features", false);
final JTextField keyWord = new JTextField(45);
final Dimension d = new Dimension(500, ignoreCase.getPreferredSize().height);
final Dimension d2 = new Dimension(300, ignoreCase.getPreferredSize().height);
int row = 0;
c.gridx = 0;
c.gridy = row;
c.anchor = GridBagConstraints.EAST;
if(names.size() < 1)
{
c.gridwidth = 2;
mainPanel.add(new JLabel("Import a list of qualifiers from the File menu."), c);
c.gridwidth = 1;
ignoreCase.setEnabled(false);
nameCombo.setEnabled(false);
addButton.setEnabled(false);
addToAllSelected.setEnabled(false);
keyWord.setEnabled(false);
}
else
{
mainPanel.add(new JLabel("Name: "), c);
c.gridx = 1;
c.anchor = GridBagConstraints.WEST;
mainPanel.add(nameCombo, c);
}
c.gridx = 2;
mainPanel.add(Box.createHorizontalStrut(150), c);
// keyword
keyWord.setSelectionStart(0);
keyWord.setSelectionEnd(keyWord.getText().length());
keyWord.setSelectedTextColor(Color.blue);
keyWord.setMinimumSize(d2);
keyWord.addActionListener(new ActionListener(){
// carry out search when enter key is pressed
public void actionPerformed(ActionEvent event)
{
searchQualifiers(keyWord.getText(), nameCombo,
ignoreCase.isSelected(), addButton, addToAllSelected, d);
}
});
c.gridy = ++row;
c.gridx = 0;
c.anchor = GridBagConstraints.EAST;
mainPanel.add(new JLabel("Keywords: "),c);
c.gridx = 1;
c.anchor = GridBagConstraints.WEST;
mainPanel.add(keyWord,c);
c.gridy = ++row;
mainPanel.add(ignoreCase,c);
// search button
c.gridx = 0;
c.gridy = ++row;
c.anchor = GridBagConstraints.WEST;
final JButton search = new JButton("SEARCH");
search.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
searchQualifiers(keyWord.getText(), nameCombo,
ignoreCase.isSelected(), addButton, addToAllSelected, d);
}
});
mainPanel.add(search,c);
c.gridx = 0;
c.gridy = ++row;
c.gridwidth = 3;
qualifierBox.add(Box.createVerticalStrut(25));
mainPanel.add(qualifierBox, c);
c.gridx = 0;
c.gridy = ++row;
c.gridwidth = 1;
mainPanel.add(addButton, c);
c.gridx = 1;
final JButton closeButton = new JButton("CLOSE");
mainPanel.add(closeButton, c);
closeButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
dispose();
}
});
c.gridx = 0;
c.gridy = ++row;
c.gridwidth = 2;
mainPanel.add(addToAllSelected,c);
c.gridy = ++row;
mainPanel.add(Box.createVerticalStrut(15), c);
}
private StringVector searchOboQualifiers(final QualifierList obo,
final String qName,
final String keyWord,
final boolean ignoreCase)
{
final Qualifier q = obo.qualifiers.getQualifierByName(qName);
if(q == null)
return null;
final StringVector values = q.getValues();
if(keyWord != null && !keyWord.trim().equals(""))
{
final String keyWordLC = keyWord.toLowerCase();
final StringVector tmp = values.copy();
for(String val: tmp)
{
if(ignoreCase)
{
if(val.toLowerCase().indexOf(keyWordLC) == -1)
values.remove(val);
}
else if(val.indexOf(keyWord) == -1)
values.remove(val);
}
}
return values;
}
/**
* Search the qualifiers for the selected qualifier name and value.
*/
private void searchQualifiers(final String keyWord,
final JComboBox nameCombo,
final boolean ignoreCase,
final JButton addButton,
final JCheckBox addToAllSelected,
final Dimension d)
{
final String qName = (String) nameCombo.getSelectedItem();
final StringVector results = new StringVector(); for(QualifierList obo: obos)
{
if(!obo.isAcive)
continue;
StringVector oboResult = searchOboQualifiers(obo, qName, keyWord, ignoreCase);
if(oboResult != null)
results.add(oboResult);
}
final JExtendedComboBox valuesList = new JExtendedComboBox(results, true);
valuesList.getEditor().getEditorComponent().addMouseListener(
new ComboMouseListener(valuesList));
valuesList.setPreferredSize(d);
valuesList.setMaximumSize(d);
if(valuesList.getSelectedItem() != null &&
valuesList.getSelectedItem().equals("") &&
valuesList.getItemCount() > 2)
valuesList.setSelectedIndex(1);
qualifierBox.removeAll();
qualifierBox.add(valuesList);
if(addListener != null)
addButton.removeActionListener(addListener);
addListener = new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
String qval = (String) valuesList.getSelectedItem();
if(qName.equals("biological_process"))
qval = "/GO=aspect=P;"+qval+";date="+DatePanel.getDate();
else if(qName.equals("molecular_function"))
qval = "/GO=aspect=F;"+qval+";date="+DatePanel.getDate();
else if(qName.equals("cellular_component"))
qval = "/GO=aspect=C;"+qval+";date="+DatePanel.getDate();
else
qval = "/"+qName+"="+qval;
if(addToAllSelected.isSelected())
{
final FeatureVector features = selection.getAllFeatures();
if(!Options.isBlackBeltMode() && features.size() > 1)
{
int status = JOptionPane.showConfirmDialog(UserDefinedQualifiers.this,
"Add "+qName+" to "+features.size()+" selected features?",
"Add Qualifier To Selected Features",
JOptionPane.OK_CANCEL_OPTION);
if(status == JOptionPane.CANCEL_OPTION)
return;
}
final int idx = qval.indexOf("=");
final Qualifier q = new Qualifier(qval.substring(1, idx), qval.substring( idx+1 ));
try
{
for(int i=0; i<features.size(); i++)
features.elementAt(i).addQualifierValues(q);
}
catch (ReadOnlyException e)
{
e.printStackTrace();
}
catch (EntryInformationException e)
{
e.printStackTrace();
}
}
else
qualifier_text_area.append(qval+"\n"); }
};
addButton.addActionListener(addListener);
mainPanel.revalidate();
}
/**
* Return a list of the qualifier names.
* @return
*/
private Vector<String> getQualiferNames()
{
final Vector<String> names = new Vector<String>();
for(QualifierList obo: obos)
{
if(!obo.isAcive)
continue;
QualifierVector qualifiers = obo.qualifiers;
for(Qualifier q: qualifiers)
if(!names.contains(q.getName()))
names.add(q.getName());
}
return names;
}
/**
* Read qualifier lists
*/
private void read()
{
URL url = ClassLoader.getSystemResource("etc/artemis.qualifiers");
if(url != null)
{
Document doc = new URLDocument(
ClassLoader.getSystemResource("etc/artemis.qualifiers"));
createObo(doc);
}
final String [] qualFiles =
{
"artemis.qualifiers",
System.getProperty("user.home") + File.separator + ".artemis.qualifiers"
};
for(String fileName: qualFiles)
{
Document doc = new FileDocument(new File(fileName));
if(doc.readable())
createObo(doc);
}
}
/**
* Load the qualifiers from an input stream.
* @param ins
* @throws IOException
*/
private QualifierVector loadQualifiers(final Document doc) throws IOException
{
QualifierVector qualifiers = loadObo(doc.getInputStream());
if(qualifiers.size() == 0)
qualifiers = loadText(doc.getInputStream());
return qualifiers;
}
/**
* Load in qualifiers from an input stream that are in OBO format.
* @param ins
* @return */
private QualifierVector loadObo(final InputStream ins)
{
final LinePushBackReader reader = new LinePushBackReader(
new BufferedReader(new InputStreamReader(ins)));
final QualifierVector qualifiers = new QualifierVector();
try
{
String line;
while((line = reader.readLine()) != null)
{
if(line.startsWith("#"))
continue;
if(startOfStanza(line))
{
String val = null;
String name = null;
String id = null;
while((line = reader.readLine()) != null &&
!startOfStanza(line) &&
line.indexOf("import:") == -1)
{
if(line.startsWith("namespace:"))
name = line.substring(10).trim();
else if(line.startsWith("name:"))
val = line.substring(5).trim();
else if(line.startsWith("id:"))
id = line.substring(3).trim();
}
if(line != null)
reader.pushBack(line);
if(id != null)
{
if( name != null &&
(name.equals("biological_process") ||
name.equals("molecular_function") ||
name.equals("cellular_component")))
val = "term="+val+"; GOid="+id;
else
val = "term="+val+"; id="+id;
}
if(name != null)
qualifiers.addQualifierValues(new Qualifier(name, val));
}
else if(line.startsWith("import:"))
{
// import OBO file from a URL
final URL url = new URL(line.substring(7).trim());
createObo(new URLDocument(url));
}
}
reader.close();
}
catch (IOException e)
{
e.printStackTrace();
}
return qualifiers;
}
/**
* Each unit of the OBO file starts with one of the three supported stanza
* types: [Term], [Typedef], and [Instance]. Parsers/serializers will round-trip
* (successfully load and save) unrecognized stanzas.
* @param line
* @return
*/ private boolean startOfStanza(final String line)
{
return line.startsWith("[");
}
/**
* Load in qualifiers from an input stream that are in the format:
* name=value
* @param ins
* @return
*/
private QualifierVector loadText(final InputStream ins)
{
final BufferedReader reader = new BufferedReader(new InputStreamReader(ins));
final QualifierVector qualifiers = new QualifierVector();
try
{
String line;
while((line = reader.readLine()) != null)
{
Matcher m = TAG_VALUE_PATTERN.matcher(line);
if(m.matches())
qualifiers.addQualifierValues(new Qualifier(m.group(1), m.group(2)));
}
reader.close();
}
catch (IOException e)
{
e.printStackTrace();
}
return qualifiers;
}
/**
* Import OBO
*/
private void importFromFile()
{
final StickyFileChooser fc = new StickyFileChooser();
//final JCheckBox autoImport = new JCheckBox("Automatically import", true);
//fc.setAccessory(autoImport);
OboFileFilter oboFilter = new OboFileFilter(new String[]{"obo", "OBO"}, "OBO files");
fc.addChoosableFileFilter(oboFilter);
fc.setFileFilter(oboFilter);
int status = fc.showOpenDialog(UserDefinedQualifiers.this);
if(status != StickyFileChooser.APPROVE_OPTION)
return;
final FileDocument doc = new FileDocument(fc.getSelectedFile());
if(!doc.readable())
{
JOptionPane.showMessageDialog(UserDefinedQualifiers.this,
"Cannot read file "+doc.getName(),
"Problem reading file", JOptionPane.WARNING_MESSAGE);
return;
}
createObo(doc);
createComponentToAddCvTerm();
mainPanel.revalidate();
mainPanel.repaint();
//if(autoImport.isSelected())
writeQualifierList(fc.getSelectedFile().getAbsolutePath());
}
private void importFromUrl()
{
String s = (String)JOptionPane.showInputDialog( UserDefinedQualifiers.this,
"URL:", "Import Qualifiers",
JOptionPane.PLAIN_MESSAGE,
null, null,
"http://www.geneontology.org/GO_slims/goslim_generic.obo");
if(s == null || s.trim().equals("") || s.trim().equals("http://"))
return;
try
{
String urlStr = s.trim();
createObo(new URLDocument(new URL(urlStr)));
createComponentToAddCvTerm();
mainPanel.revalidate();
mainPanel.repaint();
writeQualifierList(urlStr);
}
catch (MalformedURLException e)
{
e.printStackTrace();
}
}
private void createObo(Document doc)
{
try
{
logger4j.debug("Reading qualifiers from: "+doc.getName());
final QualifierList obo = new QualifierList();
obo.doc = doc;
obo.qualifiers = loadQualifiers(doc);
obos.add(obo);
}
catch (IOException e)
{
logger4j.error(e.getMessage());
JOptionPane.showMessageDialog(UserDefinedQualifiers.this,
"Problem Loading:\n"+doc.getName()+"\n"+
e.getMessage(), "Problem Loading",
JOptionPane.ERROR_MESSAGE);
}
}
/**
* Write or append to artemis qualifiers list
* @param loc
* @param isOBO
*/
private static void writeQualifierList(final String loc)
{
int status = JOptionPane.showConfirmDialog(
null,
"Automatically import:\n"+loc+"\nbetween session?",
"Import Option", JOptionPane.YES_NO_OPTION);
if(status != JOptionPane.YES_OPTION)
return;
final boolean isOBO;
if(loc.toLowerCase().endsWith(".obo"))
isOBO = true;
else
{
File f = new File(loc);
if(f.exists())
isOBO = true;
else
isOBO = false;
}
final String qualPath = System.getProperty("user.home") + File.separator + ".artemis.qualifiers";
try
{
final FileDocument doc = new FileDocument(new File(qualPath));
if(doc.readable())
{
final BufferedReader reader =
new BufferedReader(new InputStreamReader(doc.getInputStream()));
try
{
String line;
while((line = reader.readLine()) != null)
{
if(line.startsWith("import: file://"+loc))
{
System.out.println("Import line already exists :\n"+line);
return;
}
else if(line.startsWith("import: "+loc))
{
System.out.println("Import line already exists :\n"+line);
return;
}
}
}
finally
{
reader.close();
}
}
final File qualFile = new File(qualPath);
final boolean exists = qualFile.exists();
final BufferedWriter bufferedwriter = new BufferedWriter(
new FileWriter(qualFile, true));
if(!exists)
{
bufferedwriter.append("# User defined list of qualifiers in the format of:\n");
bufferedwriter.append("# name=value\n");
bufferedwriter.append("# The qualifiers are separated by lines.\n");
bufferedwriter.append("# OBO files can be used by defining import statements:\n");
bufferedwriter.append("#import: http://www.geneontology.org/GO_slims/goslim_generic.obo\n\n");
}
if(isOBO)
{
if(loc.startsWith("http://"))
bufferedwriter.append("\nimport: "+loc+"\n");
else
bufferedwriter.append("\nimport: file://"+loc+"\n");
}
else
bufferedwriter.append(loc+"\n");
bufferedwriter.close();
}
catch (FileNotFoundException filenotfoundexception)
{
System.err.println(qualPath+" read error");
}
catch (IOException e)
{
System.err.println(qualPath+" i/o error");
}
}
private class OboFileFilter extends FileFilter
{ private String[] suffix;
private String descr;
OboFileFilter(final String[] suffix, final String descr)
{
this.suffix = suffix;
this.descr = descr;
}
public boolean accept(final File file)
{
if(file.isDirectory())
return true;
for(String s: suffix)
{
if(file.getName().endsWith("." + s) )
return true;
}
return false;
}
public String getDescription()
{
return descr;
}
}
protected void setQualifierTextArea(final QualifierTextArea qualifier_text_area)
{
this.qualifier_text_area = qualifier_text_area;
}
protected void setSelection(final Selection selection)
{
this.selection = selection;
}
private class ComboMouseListener extends MouseAdapter
{
private JComboBox cb;
ComboMouseListener(JComboBox cb)
{
this.cb = cb;
}
public void mouseEntered(MouseEvent me)
{
if(cb.getSelectedItem() != null)
cb.setToolTipText(getWrappedStr((String) cb.getSelectedItem()));
}
private String getWrappedStr(String s)
{
final StringBuilder buff = new StringBuilder();
final int lineLen = 60;
for(int k=0; k<s.length(); k+=lineLen)
{
int end = k + lineLen;
if(end > s.length())
end = s.length();
buff.append ( s.substring(k,end) ).append("\n");
}
return buff.toString();
}
}
private class QualifierList
{
Document doc; QualifierVector qualifiers;
boolean isAcive = true;
}
public static void main(String args[])
{
final javax.swing.plaf.FontUIResource font_ui_resource =
Options.getOptions().getFontUIResource();
final Enumeration<Object> keys = UIManager.getDefaults().keys();
while(keys.hasMoreElements())
{
Object key = keys.nextElement();
Object value = UIManager.get(key);
if(value instanceof javax.swing.plaf.FontUIResource)
UIManager.put(key, font_ui_resource);
}
final JFrame f = new UserDefinedQualifiers();
f.pack();
f.setVisible(true);
}
}