/**
* 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 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());
}
} 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")));
}
}