public void actionPerformed(ActionEvent e) {
if (readOnly) {
return;
}
JFileChooser fc = getFileChooser();
File currentDirectory = fc.getCurrentDirectory();
if (!currentDirectory.exists()) {
JOptionPane.showMessageDialog(
fc,
newFolderParentDoesntExistText,
newFolderParentDoesntExistTitleText,
JOptionPane.WARNING_MESSAGE);
return;
}
File newFolder;
try {
newFolder = fc.getFileSystemView().createNewFolder(currentDirectory);
if (fc.isMultiSelectionEnabled()) {
fc.setSelectedFiles(new File[] {newFolder});
} else {
fc.setSelectedFile(newFolder);
}
} catch (IOException exc) {
JOptionPane.showMessageDialog(
fc,
newFolderErrorText + newFolderErrorSeparator + exc,
newFolderErrorText,
JOptionPane.ERROR_MESSAGE);
return;
}
fc.rescanCurrentDirectory();
}
public File copyFileToBundle(String filename) {
File f = new File(filename);
String bundlePath = getSrcBundle();
if (f.exists()) {
try {
File newFile = FileManager.smartCopy(filename, bundlePath);
return newFile;
} catch (IOException e) {
Debug.error(
me + "copyFileToBundle: Problem while trying to save %s\n%s", filename, e.getMessage());
return f;
}
}
return null;
}
/**
* Open a file. If it's a directory, ask to open all images as a sequence in a stack or
* individually.
*/
public void openFile(File f) {
if (IJ.debugMode) IJ.log("DragAndDrop.openFile: " + f);
try {
if (null == f) return;
String path = f.getCanonicalPath();
if (f.exists()) {
if (f.isDirectory()) openDirectory(f, path);
else {
if (openAsVirtualStack && (path.endsWith(".tif") || path.endsWith(".TIF")))
(new FileInfoVirtualStack()).run(path);
else (new Opener()).openAndAddToRecent(path);
OpenDialog.setLastDirectory(f.getParent() + File.separator);
OpenDialog.setLastName(f.getName());
}
} else {
IJ.log("File not found: " + path);
}
} catch (Throwable e) {
if (!Macro.MACRO_CANCELED.equals(e.getMessage())) IJ.handleException(e);
}
}
/** 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")));
}
}
public void actionPerformed(ActionEvent e) {
if (isDirectorySelected()) {
File dir = getDirectory();
if (dir != null) {
try {
// Strip trailing ".."
dir = ShellFolder.getNormalizedFile(dir);
} catch (IOException ex) {
// Ok, use f as is
}
changeDirectory(dir);
return;
}
}
JFileChooser chooser = getFileChooser();
String filename = getFileName();
FileSystemView fs = chooser.getFileSystemView();
File dir = chooser.getCurrentDirectory();
if (filename != null) {
// Remove whitespaces from end of filename
int i = filename.length() - 1;
while (i >= 0 && filename.charAt(i) <= ' ') {
i--;
}
filename = filename.substring(0, i + 1);
}
if (filename == null || filename.length() == 0) {
// no file selected, multiple selection off, therefore cancel the approve action
resetGlobFilter();
return;
}
File selectedFile = null;
File[] selectedFiles = null;
// Unix: Resolve '~' to user's home directory
if (File.separatorChar == '/') {
if (filename.startsWith("~/")) {
filename = System.getProperty("user.home") + filename.substring(1);
} else if (filename.equals("~")) {
filename = System.getProperty("user.home");
}
}
if (chooser.isMultiSelectionEnabled()
&& filename.length() > 1
&& filename.charAt(0) == '"'
&& filename.charAt(filename.length() - 1) == '"') {
List<File> fList = new ArrayList<File>();
String[] files = filename.substring(1, filename.length() - 1).split("\" \"");
// Optimize searching files by names in "children" array
Arrays.sort(files);
File[] children = null;
int childIndex = 0;
for (String str : files) {
File file = fs.createFileObject(str);
if (!file.isAbsolute()) {
if (children == null) {
children = fs.getFiles(dir, false);
Arrays.sort(children);
}
for (int k = 0; k < children.length; k++) {
int l = (childIndex + k) % children.length;
if (children[l].getName().equals(str)) {
file = children[l];
childIndex = l + 1;
break;
}
}
}
fList.add(file);
}
if (!fList.isEmpty()) {
selectedFiles = fList.toArray(new File[fList.size()]);
}
resetGlobFilter();
} else {
selectedFile = fs.createFileObject(filename);
if (!selectedFile.isAbsolute()) {
selectedFile = fs.getChild(dir, filename);
}
// check for wildcard pattern
FileFilter currentFilter = chooser.getFileFilter();
if (!selectedFile.exists() && isGlobPattern(filename)) {
changeDirectory(selectedFile.getParentFile());
if (globFilter == null) {
globFilter = new GlobFilter();
}
try {
globFilter.setPattern(selectedFile.getName());
if (!(currentFilter instanceof GlobFilter)) {
actualFileFilter = currentFilter;
}
chooser.setFileFilter(null);
chooser.setFileFilter(globFilter);
return;
} catch (PatternSyntaxException pse) {
// Not a valid glob pattern. Abandon filter.
}
}
resetGlobFilter();
// Check for directory change action
boolean isDir = (selectedFile != null && selectedFile.isDirectory());
boolean isTrav = (selectedFile != null && chooser.isTraversable(selectedFile));
boolean isDirSelEnabled = chooser.isDirectorySelectionEnabled();
boolean isFileSelEnabled = chooser.isFileSelectionEnabled();
boolean isCtrl =
(e != null
&& (e.getModifiers() & Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()) != 0);
if (isDir && isTrav && (isCtrl || !isDirSelEnabled)) {
changeDirectory(selectedFile);
return;
} else if ((isDir || !isFileSelEnabled)
&& (!isDir || !isDirSelEnabled)
&& (!isDirSelEnabled || selectedFile.exists())) {
selectedFile = null;
}
}
if (selectedFiles != null || selectedFile != null) {
if (selectedFiles != null || chooser.isMultiSelectionEnabled()) {
if (selectedFiles == null) {
selectedFiles = new File[] {selectedFile};
}
chooser.setSelectedFiles(selectedFiles);
// Do it again. This is a fix for bug 4949273 to force the
// selected value in case the ListSelectionModel clears it
// for non-existing file names.
chooser.setSelectedFiles(selectedFiles);
} else {
chooser.setSelectedFile(selectedFile);
}
chooser.approveSelection();
} else {
if (chooser.isMultiSelectionEnabled()) {
chooser.setSelectedFiles(null);
} else {
chooser.setSelectedFile(null);
}
chooser.cancelSelection();
}
}