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