/**
* Handle the -biojava option
*
* <p>Command line syntax: art -biojava org.biojava.bio.seq.io.EmblLikeFormat foo.embl
*
* <p>BioJava formats: EmblLikeFormat, FastaFormat, GAMEFormat, GenbankFormat, PhredFormat
*/
private void handleBioJava(final String[] args) {
if (args.length == 3) {
final String class_name = args[1];
final String location = args[2];
final Document location_document = DocumentFactory.makeDocument(location);
try {
final Object biojava_object = Class.forName(class_name).newInstance();
final EntryInformation entry_information = Options.getArtemisEntryInformation();
final uk.ac.sanger.artemis.io.BioJavaEntry emblEntry;
if (biojava_object instanceof SequenceFormat) {
final SequenceFormat sequence_format = (SequenceFormat) biojava_object;
emblEntry =
new uk.ac.sanger.artemis.io.BioJavaEntry(
entry_information, location_document, sequence_format);
final Entry new_entry = new Entry(emblEntry);
final EntryEdit new_entry_edit = makeEntryEdit(new_entry);
new_entry_edit.setVisible(true);
} else new MessageDialog(this, "not a SequenceFormat: " + class_name);
} catch (IllegalAccessException e) {
new MessageDialog(this, "cannot create class: " + class_name + " - IllegalAccessException");
} catch (ClassNotFoundException e) {
new MessageDialog(this, "cannot find class: " + class_name);
} catch (ClassCastException e) {
new MessageDialog(this, class_name + " is not a sub-class of " + "SequenceFormat");
} catch (IOException e) {
new MessageDialog(this, "I/O error while reading from " + location + ": " + e.getMessage());
} catch (NoSequenceException e) {
new MessageDialog(this, location + " contained no sequence");
} catch (InstantiationException e) {
new MessageDialog(this, "cannot instantiate " + class_name);
} catch (OutOfRangeException e) {
new MessageDialog(
this,
"read failed: one of the features in "
+ location
+ " has an out of range location: "
+ e.getMessage());
}
} else new MessageDialog(this, "the -biojava option needs two arguments");
}
/**
* Get the String residing on the clipboard.
*
* @return any text found on the Clipboard; if none found, return an empty String.
*/
public void openClipboardContents() {
Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
// odd: the Object param of getContents is not currently used
Transferable contents = clipboard.getContents(null);
boolean hasTransferableText =
(contents != null) && contents.isDataFlavorSupported(DataFlavor.stringFlavor);
if (hasTransferableText) {
TextDocument entry_document = new TextDocument();
final InputStreamProgressListener progress_listener = getInputStreamProgressListener();
entry_document.addInputStreamProgressListener(progress_listener);
final EntryInformation artemis_entry_information = Options.getArtemisEntryInformation();
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
return;
try {
final Entry entry = new Entry(new_embl_entry);
EntryEdit last_entry_edit = makeEntryEdit(entry);
addEntryEdit(last_entry_edit);
getStatusLabel().setText("");
last_entry_edit.setVisible(true);
} catch (OutOfRangeException e) {
new MessageDialog(
this,
"read failed: one of the features in "
+ " cut and paste has an out of range "
+ "location: "
+ e.getMessage());
} catch (NoSequenceException e) {
new MessageDialog(this, "read failed: " + " cut and paste contains no sequence");
}
}
}
/** 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");
}
}
}
/** 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")));
}
}