diff --git a/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java b/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
index 7eb10930daeb0e5efbde70be8b404973c82b2766..62a5b6a0821540343c8ae1f121a33f85ce67b0e7 100644
--- a/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
+++ b/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
@@ -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();
- }
-
- public void setQualifierTextArea(QualifierTextArea qualifier_text_area)
- {
- this.qualifier_text_area = qualifier_text_area;
+ createMenus();
}
- public JFrame getFrame()
+ /**
+ * Menu creation
+ */
+ private void createMenus()
{
- return (JFrame) SwingUtilities.getWindowAncestor(this);
+ 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);
+
+ final JMenuItem importURL = new JMenuItem("Import qualifiers from URL ...");
+ importURL.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent arg0)
+ {
+ 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);
+
+ 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;
+ }
+
+ /**
+ * 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(values, true);
+ 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(Qualifier q: qualifiers)
- names.add(q.getName());
+ 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)
{
- try
+ if(line.startsWith("#"))
+ continue;
+
+ if(startOfStanza(line))
{
- ins = doc.getInputStream();
- loadQualifiers(ins);
- ins.close();
+ 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));
}
- catch (IOException e)
+ else if(line.startsWith("import:"))
{
- e.printStackTrace();
+ // import OBO file from a URL
+ final URL url = new URL(line.substring(7).trim());
+ createObo(new URLDocument(url));
}
- logger4j.debug("Reading qualifiers from: "+fileName);
}
+ reader.close();
+ }
+ catch (IOException e)
+ {
+ e.printStackTrace();
}
+ return qualifiers;
}
/**
- * Load the qualifiers from an input stream.
+ * 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 void loadQualifiers(final InputStream ins)
+ private QualifierVector loadText(final InputStream ins)
{
- final BufferedReader br = new BufferedReader(new InputStreamReader(ins));
+ final BufferedReader reader = new BufferedReader(new InputStreamReader(ins));
+ final QualifierVector qualifiers = new QualifierVector();
try
{
String line;
- while((line = br.readLine()) != null)
+ 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 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);
+ }
+ }
+
+
+ /**
+ * Write or re-write properties and insert/update the user.dir property
+ * @param jemProp properties file
+ * @param uHome user working directory
+ */
+ private static void writeProperties(final String loc)
+ {
+ final String qualPath = System.getProperty("user.home") + File.separator + ".artemis.qualifiers";
+ try
+ {
+ final FileDocument doc = new FileDocument(new File(qualPath));
+ if(doc.readable())
{
- int idx = line.indexOf("name:");
- if(idx > -1)
+ final BufferedReader reader =
+ new BufferedReader(new InputStreamReader(doc.getInputStream()));
+ try
{
- String val = line.substring(idx+5).trim();
- while((line = br.readLine()) != null &&
- (idx = line.indexOf("namespace:")) > -1)
+ String line;
+ while((line = reader.readLine()) != null)
{
- String name = line.substring(idx+10).trim();
- logger4j.debug(name + "=" +val);
- qualifiers.addQualifierValues(new Qualifier(name, val));
+ 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;
+ }
}
}
- 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;
+ }
+
+ public String getDescription()
+ {
+ return descr;
}
}
- class ComboMouseListener extends MouseAdapter
+ 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)
@@ -342,7 +701,8 @@ class UserDefinedQualifier extends JPanel
public void mouseEntered(MouseEvent me)
{
- cb.setToolTipText(getWrappedStr((String) cb.getSelectedItem()));
+ if(cb.getSelectedItem() != null)
+ cb.setToolTipText(getWrappedStr((String) cb.getSelectedItem()));
}
private String getWrappedStr(String s)
@@ -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);
}