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Commit a7507bca authored by tcarver's avatar tcarver
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updates

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uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
+ 459
− 93
View file @ a7507bca
......@@ -29,61 +29,142 @@ 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.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.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
import javax.swing.filechooser.FileFilter;
import uk.ac.sanger.artemis.Options;
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.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.StringVector;
import uk.ac.sanger.artemis.util.URLDocument;
class UserDefinedQualifier extends JPanel
/**
* Load and make available qualifiers from a list in a file
* of tag=value pairs and from OBO files.
*/
class UserDefinedQualifier extends JFrame
{
private static final long serialVersionUID = 1L;
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(UserDefinedQualifier.class);
private QualifierVector qualifiers = new QualifierVector();
/* collection of loaded files */
private Vector<OBO> obos = new Vector<OBO>();
/* component containing list of available values */
private Box qualifierBox = Box.createHorizontalBox();
private JButton addButton = new JButton("ADD");
/* listener for adding qualifiers **/
private ActionListener addListener;
/* text area in the feature editor to add qualifiers to */
private QualifierTextArea qualifier_text_area;
private JPanel mainPanel;
/* line pattern for tag=value */
private static Pattern TAG_VALUE_PATTERN = Pattern.compile("^/?(\\w+) ?= ?([^\\n\\r]+)$");
UserDefinedQualifier()
{
mainPanel = (JPanel) getContentPane();
MultiLineToolTipUI.initialize();
read();
createComponentToAddCvTerm();
createMenus();
}
public void setQualifierTextArea(QualifierTextArea qualifier_text_area)
/**
* Menu creation
*/
private void createMenus()
{
this.qualifier_text_area = qualifier_text_area;
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)
{
importObo();
}
});
fileMenu.add(importFile);
public JFrame getFrame()
final JMenuItem importURL = new JMenuItem("Import qualifiers from URL ...");
importURL.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
return (JFrame) SwingUtilities.getWindowAncestor(this);
importFromUrl();
}
});
fileMenu.add(importURL);
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 OBO 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();
mainPanel.removeAll();
createComponentToAddCvTerm();
mainPanel.revalidate();
mainPanel.repaint();
}
});
}
}
});
fileMenu.add(removeFile);
setJMenuBar(menuBar);
}
/**
......@@ -92,30 +173,29 @@ class UserDefinedQualifier extends JPanel
*/
private void createComponentToAddCvTerm()
{
setLayout(new GridBagLayout());
mainPanel.setLayout(new GridBagLayout());
final GridBagConstraints c = new GridBagConstraints();
final JCheckBox ignoreCase = new JCheckBox("Ignore case",true);
final JComboBox nameCombo = new JComboBox(getQualiferNames());
final Dimension d = new Dimension(500, nameCombo.getPreferredSize().height);
final Dimension d2 = new Dimension(300, nameCombo.getPreferredSize().height);
final JButton addButton = new JButton("ADD");
//final JScrollPane jspNames = new JScrollPane(nameCombo);
int row = 0;
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;
add(new JLabel("Name: "), c);
mainPanel.add(new JLabel("Name: "), c);
c.gridx = 1;
c.weightx = 0.5d;
c.anchor = GridBagConstraints.WEST;
add(nameCombo, c);
c.weightx = 0.d;
mainPanel.add(nameCombo, c);
c.gridx = 2;
c.weightx = 0.5d;
add(Box.createHorizontalStrut(150), c);
mainPanel.add(Box.createHorizontalStrut(150), c);
// keyword
final JTextField keyWord = new JTextField(45);
......@@ -127,19 +207,20 @@ class UserDefinedQualifier extends JPanel
// carry out search when enter key is pressed
public void actionPerformed(ActionEvent event)
{
searchQualifiers(keyWord.getText(), nameCombo, ignoreCase.isSelected(), d);
searchQualifiers(keyWord.getText(), nameCombo,
ignoreCase.isSelected(), addButton, d);
}
});
c.gridy = ++row;
c.gridx = 0;
c.anchor = GridBagConstraints.EAST;
add(new JLabel("Keywords: "),c);
mainPanel.add(new JLabel("Keywords: "),c);
c.gridx = 1;
c.anchor = GridBagConstraints.WEST;
add(keyWord,c);
mainPanel.add(keyWord,c);
c.gridy = ++row;
add(ignoreCase,c);
mainPanel.add(ignoreCase,c);
// search button
c.gridx = 0;
......@@ -149,49 +230,46 @@ class UserDefinedQualifier extends JPanel
search.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
searchQualifiers(keyWord.getText(), nameCombo, ignoreCase.isSelected(), d);
searchQualifiers(keyWord.getText(), nameCombo,
ignoreCase.isSelected(), addButton, d);
}
});
add(search,c);
mainPanel.add(search,c);
c.gridx = 0;
c.gridy = ++row;
c.gridwidth = 3;
qualifierBox.add(Box.createVerticalStrut(25));
add(qualifierBox, c);
mainPanel.add(qualifierBox, c);
c.gridx = 0;
c.gridy = ++row;
c.gridwidth = 1;
add(addButton, c);
mainPanel.add(addButton, c);
c.gridx = 1;
final JButton closeButton = new JButton("CLOSE");
add(closeButton, c);
mainPanel.add(closeButton, c);
closeButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
final JFrame topFrame =
(JFrame) SwingUtilities.getWindowAncestor(UserDefinedQualifier.this);
topFrame.dispose();
dispose();
}
});
c.gridy = ++row;
add(Box.createVerticalStrut(15), c);
mainPanel.add(Box.createVerticalStrut(15), c);
}
/**
* Search the qualifiers for the selected qualifier name and value.
*/
private void searchQualifiers(final String keyWord,
final JComboBox nameCombo,
final boolean ignoreCase,
final Dimension d)
private StringVector searchOboQualifiers(final OBO obo,
final String qName,
final String keyWord,
final boolean ignoreCase)
{
final String qName = (String) nameCombo.getSelectedItem();
final StringVector values = qualifiers.getQualifierByName(qName).getValues();
final Qualifier q = obo.qualifiers.getQualifierByName(qName);
if(q == null)
return null;
final StringVector values = q.getValues();
if(keyWord != null && !keyWord.trim().equals(""))
{
......@@ -208,8 +286,30 @@ class UserDefinedQualifier extends JPanel
values.remove(val);
}
}
return values;
}
final JExtendedComboBox valuesList = new JExtendedComboBox(values, true);
/**
* 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 Dimension d)
{
final String qName = (String) nameCombo.getSelectedItem();
final StringVector results = new StringVector();
for(OBO 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));
......@@ -229,12 +329,22 @@ class UserDefinedQualifier extends JPanel
addListener = new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
qualifier_text_area.append("/"+qName+"="+valuesList.getSelectedItem()+"\n");
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;
qualifier_text_area.append(qval+"\n");
}
};
addButton.addActionListener(addListener);
revalidate();
mainPanel.revalidate();
}
/**
......@@ -244,28 +354,30 @@ class UserDefinedQualifier extends JPanel
private Vector<String> getQualiferNames()
{
final Vector<String> names = new Vector<String>();
for(OBO 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()
{
InputStream ins =
this.getClass().getClassLoader().getResourceAsStream("etc/artemis.qualifiers");
try
URL url = ClassLoader.getSystemResource("etc/artemis.qualifiers");
if(url != null)
{
if(ins != null)
{
loadQualifiers(ins);
ins.close();
}
}
catch (IOException e)
{
e.printStackTrace();
Document doc = new URLDocument(
ClassLoader.getSystemResource("etc/artemis.qualifiers"));
createObo(doc);
}
catch (NullPointerException e2) {}
final String [] qualFiles =
{
......@@ -275,64 +387,311 @@ class UserDefinedQualifier extends JPanel
for(String fileName: qualFiles)
{
final Document doc = new FileDocument(new File(fileName));
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
{
ins = doc.getInputStream();
loadQualifiers(ins);
ins.close();
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();
}
logger4j.debug("Reading qualifiers from: "+fileName);
return qualifiers;
}
/**
* Import OBO
*/
private void importObo()
{
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(UserDefinedQualifier.this);
if(status != StickyFileChooser.APPROVE_OPTION)
return;
final FileDocument doc = new FileDocument(fc.getSelectedFile());
if(!doc.readable())
{
JOptionPane.showMessageDialog(UserDefinedQualifier.this,
"Cannot read file "+doc.getName(),
"Problem reading file", JOptionPane.WARNING_MESSAGE);
return;
}
createObo(doc);
mainPanel.removeAll();
createComponentToAddCvTerm();
mainPanel.revalidate();
if(autoImport.isSelected())
writeProperties(fc.getSelectedFile().getAbsolutePath());
}
private void importFromUrl()
{
String s = (String)JOptionPane.showInputDialog(
UserDefinedQualifier.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)));
mainPanel.removeAll();
createComponentToAddCvTerm();
mainPanel.revalidate();
int status = JOptionPane.showConfirmDialog(
UserDefinedQualifier.this,
"Automatically import:\n"+urlStr+"\nbetween session?",
"Import Option", JOptionPane.YES_NO_OPTION);
if(status == JOptionPane.YES_OPTION)
writeProperties(urlStr);
}
catch (MalformedURLException e)
{
e.printStackTrace();
}
}
private void createObo(Document doc)
{
try
{
logger4j.debug("Reading qualifiers from: "+doc.getName());
OBO obo = new OBO();
obo.doc = doc;
obo.qualifiers = loadQualifiers(doc);
obos.add(obo);
}
catch (IOException e)
{
logger4j.error(e.getMessage());
JOptionPane.showMessageDialog(UserDefinedQualifier.this,
"Problem Loading:\n"+doc.getName()+"\n"+
e.getMessage(), "Problem Loading",
JOptionPane.ERROR_MESSAGE);
}
}
/**
* Load the qualifiers from an input stream.
* @param ins
* Write or re-write properties and insert/update the user.dir property
* @param jemProp properties file
* @param uHome user working directory
*/
private void loadQualifiers(final InputStream ins)
private static void writeProperties(final String loc)
{
final String qualPath = System.getProperty("user.home") + File.separator + ".artemis.qualifiers";
try
{
final BufferedReader br = new BufferedReader(new InputStreamReader(ins));
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 = br.readLine()) != null)
while((line = reader.readLine()) != null)
{
int idx = line.indexOf("name:");
if(idx > -1)
if(line.startsWith("import: file://"+loc))
{
String val = line.substring(idx+5).trim();
while((line = br.readLine()) != null &&
(idx = line.indexOf("namespace:")) > -1)
System.out.println("Import line already exists :\n"+line);
return;
}
else if(line.startsWith("import: "+loc))
{
String name = line.substring(idx+10).trim();
logger4j.debug(name + "=" +val);
qualifiers.addQualifierValues(new Qualifier(name, val));
System.out.println("Import line already exists :\n"+line);
return;
}
}
}
else if((idx = line.indexOf("import:")) > -1)
finally
{
// import OBO file from a URL
final URL url = new URL(line.substring(idx+7).trim());
final Document doc = new URLDocument(url);
loadQualifiers(doc.getInputStream());
reader.close();
}
}
final BufferedWriter bufferedwriter = new BufferedWriter(
new FileWriter(new File(qualPath), true));
if(loc.startsWith("http://"))
bufferedwriter.append("\nimport: "+loc+"\n");
else
bufferedwriter.append("\nimport: file://"+loc+"\n");
bufferedwriter.close();
}
catch (FileNotFoundException filenotfoundexception)
{
System.err.println(qualPath+" read error");
}
catch (IOException e)
{
e.printStackTrace();
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;
}
class ComboMouseListener extends MouseAdapter
public String getDescription()
{
return descr;
}
}
protected void setQualifierTextArea(QualifierTextArea qualifier_text_area)
{
this.qualifier_text_area = qualifier_text_area;
}
private class ComboMouseListener extends MouseAdapter
{
private JComboBox cb;
ComboMouseListener(JComboBox cb)
......@@ -342,6 +701,7 @@ class UserDefinedQualifier extends JPanel
public void mouseEntered(MouseEvent me)
{
if(cb.getSelectedItem() != null)
cb.setToolTipText(getWrappedStr((String) cb.getSelectedItem()));
}
......@@ -360,6 +720,13 @@ class UserDefinedQualifier extends JPanel
}
}
private class OBO
{
Document doc;
QualifierVector qualifiers;
boolean isAcive = true;
}
public static void main(String args[])
{
final javax.swing.plaf.FontUIResource font_ui_resource =
......@@ -374,8 +741,7 @@ class UserDefinedQualifier extends JPanel
UIManager.put(key, font_ui_resource);
}
final JFrame f = new JFrame("User Defined Qualifiers");
f.getContentPane().add(new UserDefinedQualifier());
final JFrame f = new UserDefinedQualifier();
f.pack();
f.setVisible(true);
}
......
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