void lookUpTaxonID(String taxonID) {
URI url;
try {
// We should look up the miITIS_TSN status, but since we don't
// have any options there ...
url =
new URI(
"http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value="
+ taxonID);
} catch (URISyntaxException e) {
throw new RuntimeException(e);
}
try {
Desktop desktop = Desktop.getDesktop();
desktop.browse(url);
} catch (IOException e) {
MessageBox.messageBox(
mainFrame,
"Could not open URL '" + url + "'",
"The following error occurred while looking up URL '" + url + "': " + e.getMessage(),
MessageBox.ERROR);
}
}
void searchName(String nameToMatch) {
URI url;
try {
// We should look up the miITIS_TSN status, but since we don't
// have any options there ...
url = new URI("http", "www.google.com", "/search", "q=" + nameToMatch);
// I think the URI handles the URL encoding?
} catch (URISyntaxException e) {
throw new RuntimeException(e);
}
try {
Desktop desktop = Desktop.getDesktop();
desktop.browse(url);
} catch (IOException e) {
MessageBox.messageBox(
mainFrame,
"Could not open URL '" + url + "'",
"The following error occurred while looking up URL '" + url + "': " + e.getMessage(),
MessageBox.ERROR);
}
}
public File getCurrentFile(boolean shouldSave) {
if (shouldSave && _editingFile == null && isDirty()) {
try {
saveAsFile(Settings.isMac());
} catch (IOException e) {
Debug.error(
me + "getCurrentFile: Problem while trying to save %s\n%s",
_editingFile.getAbsolutePath(),
e.getMessage());
}
}
return _editingFile;
}
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;
}
/**
* 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");
}
private void jMenuItemLoadProjectActionPerformed(
java.awt.event.ActionEvent evt) // GEN-FIRST:event_jMenuItemLoadProjectActionPerformed
{ // GEN-HEADEREND:event_jMenuItemLoadProjectActionPerformed
JFileChooser jfc = new JFileChooser();
if (lastPath != null) {
jfc.setCurrentDirectory(lastPath);
}
int fileDialogReturnVal = jfc.showOpenDialog(this);
if (fileDialogReturnVal == JFileChooser.APPROVE_OPTION) {
try {
File inputFile = jfc.getSelectedFile();
FileInputStream fis = new FileInputStream(inputFile);
ObjectInputStream ois = new ObjectInputStream(fis);
this.theProject = (Project) ois.readObject();
this.currentResults = (LSAResults) ois.readObject();
lastPath = new File(jfc.getSelectedFile().getPath());
} catch (IOException e) {
if (this.theProject == null) {
log.log(Log.ERROR, "Failed to load project");
}
if (this.currentResults == null) {
log.log(Log.WARNING, "Failed to load results");
}
log.log(Log.WARNING, e.getMessage());
} catch (ClassNotFoundException e) {
log.log(Log.ERROR, "Class not found error, version mismatch");
}
}
if (this.theProject != null) {
jMenuItemViewDocuments.setEnabled(true);
jMenuItemSaveProject.setEnabled(true);
this.setTitle(theProject.getProjectName());
log.log(Log.INFO, "Project Loaded");
}
if (this.currentResults != null) {
log.log(Log.INFO, "Results loaded");
}
} // GEN-LAST:event_jMenuItemLoadProjectActionPerformed
private void jMenuItemSaveLSAResultsActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_jMenuItemSaveLSAResultsActionPerformed
if (this.currentResults != null) {
JFileChooser jfc = new JFileChooser();
int fileDialogReturnVal = jfc.showSaveDialog(this);
if (fileDialogReturnVal == JFileChooser.APPROVE_OPTION) {
try {
File outputFile = jfc.getSelectedFile();
FileOutputStream fos = new FileOutputStream(outputFile);
ObjectOutputStream oos = new ObjectOutputStream(fos);
oos.writeObject(this.currentResults);
} catch (IOException e) {
System.out.println("IOexception");
System.out.println(e.getMessage());
}
}
}
} // GEN-LAST:event_jMenuItemSaveLSAResultsActionPerformed
private void jMenuItemLoadLSAResultsActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_jMenuItemLoadLSAResultsActionPerformed
JFileChooser jfc = new JFileChooser();
int fileDialogReturnVal = jfc.showOpenDialog(this);
if (fileDialogReturnVal == JFileChooser.APPROVE_OPTION) {
try {
File inputFile = jfc.getSelectedFile();
FileInputStream fis = new FileInputStream(inputFile);
ObjectInputStream ois = new ObjectInputStream(fis);
this.currentResults = (LSAResults) ois.readObject();
} catch (IOException e) {
log.log(Log.ERROR, "Failed to load LSA results\n" + e.getMessage());
} catch (ClassNotFoundException e) {
log.log(Log.ERROR, "Class not found : Error loading LSA results due to version mismatch");
}
System.out.println(currentResults == null);
}
} // GEN-LAST:event_jMenuItemLoadLSAResultsActionPerformed
private void jMenuItemSaveProjectActionPerformed(
java.awt.event.ActionEvent evt) // GEN-FIRST:event_jMenuItemSaveProjectActionPerformed
{ // GEN-HEADEREND:event_jMenuItemSaveProjectActionPerformed
if (this.theProject != null) {
JFileChooser jfc = new JFileChooser();
int fileDialogReturnVal = jfc.showSaveDialog(this);
if (fileDialogReturnVal == JFileChooser.APPROVE_OPTION) {
try {
File outputFile = jfc.getSelectedFile();
FileOutputStream fos = new FileOutputStream(outputFile);
ObjectOutputStream oos = new ObjectOutputStream(fos);
oos.writeObject(this.theProject);
if (this.currentResults != null) {
oos.writeObject(this.currentResults);
}
} catch (IOException e) {
log.log(Log.ERROR, "Failed to save file\n" + e.getMessage());
}
}
}
} // GEN-LAST:event_jMenuItemSaveProjectActionPerformed