/** 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;
}
/**
* Transfer selected qualifiers to the list of features defined by the selected names.
*
* @param qualifierCheckBoxes - list of qualifier check boxes
* @param geneNameTextArea - text with a list of feature names to transfer to
* @param feature - feature to copy from
* @param entryGroup
* @param sameKey
* @param overwrite
*/
protected static int transferAnnotation(
final Hashtable<JCheckBox, Vector<JCheckBox>> qualifierCheckBoxes,
final Vector<JCheckBox> geneNameCheckBoxes,
final Feature orginatingFeature,
final EntryGroup entryGroup,
final boolean sameKey,
final boolean overwrite,
final boolean setEvidenceAndWithFrom,
final StringBuffer buff,
final StringBuffer genesUpdated) {
// transfer selected annotation to genes
final QualifierVector qualifiers = orginatingFeature.getQualifiers();
final QualifierVector qualifiersToTransfer = new QualifierVector();
Enumeration<JCheckBox> enumQualifiers = qualifierCheckBoxes.keys();
while (enumQualifiers.hasMoreElements()) {
JCheckBox cb = enumQualifiers.nextElement();
if (cb.isSelected()) {
Vector<JCheckBox> qualifierValuesCheckBox = qualifierCheckBoxes.get(cb);
final StringVector values = qualifiers.getQualifierByName(cb.getText()).getValues();
StringVector valuesToTransfer = new StringVector(values);
logger4j.debug("TRANSFER " + cb.getText());
for (int i = 0; i < qualifierValuesCheckBox.size(); i++) {
JCheckBox valuesCb = qualifierValuesCheckBox.get(i);
if (!valuesCb.isSelected()) {
valuesToTransfer.remove(valuesCb.getText());
logger4j.debug("NOT TRANSFERING " + valuesCb.getText());
}
}
if (valuesToTransfer.size() < 1) continue;
valuesToTransfer =
new StringVector(
getTransferValues(
setEvidenceAndWithFrom, orginatingFeature, cb.getText(), valuesToTransfer));
qualifiersToTransfer.addElement(new Qualifier(cb.getText(), valuesToTransfer));
}
}
int count = 0;
for (int i = 0; i < geneNameCheckBoxes.size(); i++) {
if (geneNameCheckBoxes.get(i).isSelected()) count++;
}
if (count < 1) {
JOptionPane.showMessageDialog(
null, "No genes selected.", "Warning", JOptionPane.WARNING_MESSAGE);
return -1;
}
String geneNames[] = new String[count];
count = 0;
for (int i = 0; i < geneNameCheckBoxes.size(); i++) {
JCheckBox cb = geneNameCheckBoxes.get(i);
if (cb.isSelected()) {
geneNames[count] = cb.getText();
logger4j.debug("TRANSFER ANNOTATION TO " + geneNames[count]);
count++;
}
}
final String key = orginatingFeature.getKey().getKeyString();
final FeatureVector features = entryGroup.getAllFeatures();
// transfer selected annotation
entryGroup.getActionController().startAction();
geneNames =
transfer(
features,
qualifiersToTransfer,
key,
sameKey,
overwrite,
GeneUtils.isDatabaseEntry(entryGroup),
geneNames,
genesUpdated);
entryGroup.getActionController().endAction();
//
// Commit changes to genes not in Artemis but in the database
//
Vector<String> genesNotFound = null;
if (geneNames != null
&& orginatingFeature.getEntry().getEMBLEntry() instanceof DatabaseDocumentEntry) {
DatabaseDocumentEntry db_entry =
(DatabaseDocumentEntry) orginatingFeature.getEntry().getEMBLEntry();
DatabaseDocument doc = (DatabaseDocument) db_entry.getDocument();
for (int i = 0; i < geneNames.length; i++) {
DatabaseDocumentEntry newDbEntry = GeneEdit.makeGeneEntry(null, geneNames[i], doc, null);
if (newDbEntry == null) {
if (genesNotFound == null) genesNotFound = new Vector<String>();
genesNotFound.add(geneNames[i]);
continue;
}
char[] c = new char[1];
PartialSequence ps = new PartialSequence(c, 100, 0, null, null);
newDbEntry.setPartialSequence(ps);
Entry entry = null;
try {
entry = new Entry(newDbEntry);
} catch (Exception e) {
e.printStackTrace();
}
SimpleEntryGroup entry_group = new SimpleEntryGroup();
entry_group.addElement(entry);
ChadoTransactionManager ctm = new ChadoTransactionManager();
entry_group.addFeatureChangeListener(ctm);
entry_group.addEntryChangeListener(ctm);
ctm.setEntryGroup(entry_group);
transfer(
entry.getAllFeatures(),
qualifiersToTransfer,
key,
sameKey,
overwrite,
true,
geneNames,
genesUpdated);
for (int j = 0; j < ctm.getTransactionCount(); j++)
buff.append(ctm.getTransactionAt(j).getLogComment() + "\n");
ChadoTransactionManager.commit((DatabaseDocument) newDbEntry.getDocument(), false, ctm);
entry_group.removeFeatureChangeListener(ctm);
entry_group.removeEntryChangeListener(ctm);
// if(newDbEntry != null)
// GeneEdit.showGeneEditor(null, geneNames[i], newDbEntry);
}
}
if (genesNotFound != null)
JOptionPane.showMessageDialog(
null,
"Gene(s) Not Found:\n" + genesNotFound.toString(),
"Gene(s) Not Found",
JOptionPane.WARNING_MESSAGE);
return 0;
}
/** 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");
}
}
}
/**
* Create a new FeatureListFrame component. The constructor does not call setVisible (true).
*
* @param title The title to use for the new JFrame.
* @param feature_list The FeatureList to show.
* @param selection The Selection that the commands in the menus will operate on.
* @param entry_group The EntryGroup object where new features/entries will be added.
* @param goto_event_source The object that the menu item will call makeBaseVisible() on.
*/
public FeatureListFrame(
final String title,
final Selection selection,
final GotoEventSource goto_event_source,
final EntryGroup entry_group,
final BasePlotGroup base_plot_group) {
super(title);
this.entry_group = entry_group;
feature_list = new FeatureList(entry_group, selection, goto_event_source, base_plot_group);
final Font default_font = Options.getOptions().getFont();
setFont(default_font);
final JMenuBar menu_bar = new JMenuBar();
menu_bar.setFont(default_font);
setJMenuBar(menu_bar);
final JMenu file_menu = new JMenu("File");
final JMenuItem close = new JMenuItem("Close");
close.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent event) {
setVisible(false);
FeatureListFrame.this.dispose();
feature_list.stopListening();
}
});
file_menu.add(close);
menu_bar.add(file_menu);
final JMenu select_menu =
new SelectMenu(this, selection, goto_event_source, entry_group, base_plot_group);
menu_bar.add(select_menu);
final JMenu view_menu =
new ViewMenu(this, selection, goto_event_source, entry_group, base_plot_group);
menu_bar.add(view_menu);
final JMenu goto_menu = new GotoMenu(this, selection, goto_event_source, entry_group);
menu_bar.add(goto_menu);
if (Options.readWritePossible()) {
final JMenu edit_menu =
new EditMenu(this, selection, goto_event_source, entry_group, base_plot_group, null);
menu_bar.add(edit_menu);
final JMenu write_menu = new WriteMenu(this, selection, entry_group);
menu_bar.add(write_menu);
final JMenu run_menu = new RunMenu(this, selection);
menu_bar.add(run_menu);
}
final JScrollPane jsp_feature_list = new JScrollPane(feature_list);
getContentPane().add(jsp_feature_list, "Center");
final JPanel panel = new JPanel();
final JButton close_button = new JButton("Close");
panel.add(close_button);
close_button.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
setVisible(false);
FeatureListFrame.this.dispose();
feature_list.stopListening();
}
});
getContentPane().add(panel, "South");
pack();
addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent event) {
setVisible(false);
entry_group.removeEntryGroupChangeListener(FeatureListFrame.this);
FeatureListFrame.this.dispose();
feature_list.stopListening();
}
});
entry_group.addEntryGroupChangeListener(this);
final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
int screen_height = screen.height;
int screen_width = screen.width;
if (screen_width <= 700 || screen_height <= 400)
setSize(screen_width * 9 / 10, screen_height * 9 / 10);
else setSize(700, 400);
final int hgt = entry_group.getAllFeaturesCount() * feature_list.getLineHeight();
feature_list.setPreferredSize(new Dimension(getSize().width * 4, hgt));
jsp_feature_list.getVerticalScrollBar().setUnitIncrement(feature_list.getLineHeight());
setLocation(
new Point((screen.width - getSize().width) / 2, (screen.height - getSize().height) / 2));
}