/**
* @return an instanciation of the given content-type class name, or null if class wasn't found
*/
public static ContentType getContentTypeFromClassName(String contentTypeClassName) {
if (contentTypeClassName == null)
contentTypeClassName = getAvailableContentTypes()[DEFAULT_CONTENT_TYPE_INDEX];
ContentType ct = null;
try {
Class clazz = Class.forName(contentTypeClassName);
ct = (ContentType) clazz.newInstance();
} catch (ClassNotFoundException cnfex) {
if (jpicedt.Log.DEBUG) cnfex.printStackTrace();
JPicEdt.getMDIManager()
.showMessageDialog(
"The pluggable content-type you asked for (class "
+ cnfex.getLocalizedMessage()
+ ") isn't currently installed, using default instead...",
Localizer.currentLocalizer().get("msg.LoadingContentTypeClass"),
JOptionPane.ERROR_MESSAGE);
} catch (Exception ex) {
if (jpicedt.Log.DEBUG) ex.printStackTrace();
JPicEdt.getMDIManager()
.showMessageDialog(
ex.getLocalizedMessage(),
Localizer.currentLocalizer().get("msg.LoadingContentTypeClass"),
JOptionPane.ERROR_MESSAGE);
}
return ct;
}
/** Determine whether the current user has Windows administrator privileges. */
public static boolean isWinAdmin() {
if (!isWinPlatform()) return false;
// for (String group : new com.sun.security.auth.module.NTSystem().getGroupIDs()) {
// if (group.equals("S-1-5-32-544")) return true; // "S-1-5-32-544" is a well-known
// security identifier in Windows. If the current user has it then he/she/it is an
// administrator.
// }
// return false;
try {
Class<?> ntsys = Class.forName("com.sun.security.auth.module.NTSystem");
if (ntsys != null) {
Object groupObj =
SystemUtils.invoke(
ntsys.newInstance(), ntsys.getDeclaredMethod("getGroupIDs"), (Object[]) null);
if (groupObj instanceof String[]) {
for (String group : (String[]) groupObj) {
if (group.equals("S-1-5-32-544"))
return true; // "S-1-5-32-544" is a well-known security identifier in Windows. If the
// current user has it then he/she/it is an administrator.
}
}
}
} catch (ReflectiveOperationException e) {
System.err.println(e);
}
return false;
}
public static Field makeAccessible(Class<?> target, String fieldName) {
try {
final Field field = target.getDeclaredField(fieldName);
return (Field)
AccessController.doPrivileged(
new PrivilegedExceptionAction<Object>() {
public Object run() throws IllegalAccessException, InvocationTargetException {
if (!field.isAccessible()) field.setAccessible(true);
return field;
}
});
} catch (NoSuchFieldException | PrivilegedActionException e) {
System.out.print("");
} // keep quiet IError.printStackTrace(e); }
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");
}
/**
* Creates the customizer component for the node.
*
* @return the component, or null if there is no customizer
*/
@Override
protected Component createCustomizer() {
Class customizerClass = component.getBeanInfo().getBeanDescriptor().getCustomizerClass();
if (customizerClass == null) {
if (javax.swing.JTable.class.isAssignableFrom(component.getBeanClass())) {
customizerClass = TableCustomizer.class;
} else {
return null;
}
}
Object customizerObject;
try {
customizerObject = customizerClass.newInstance();
} catch (InstantiationException e) {
ErrorManager.getDefault().notify(ErrorManager.WARNING, e);
return null;
} catch (IllegalAccessException e) {
ErrorManager.getDefault().notify(ErrorManager.WARNING, e);
return null;
}
if (!(customizerObject instanceof Component) || !(customizerObject instanceof Customizer))
return null;
if (customizerObject instanceof NodeCustomizer)
((NodeCustomizer) customizerObject).attach(component.getNodeReference());
// Issue 203352 - default values of properties must be initialized
// before the customizer is shown/used
component.ensureDefaultPropertyValuesInitialization();
Customizer customizer = (Customizer) customizerObject;
customizer.setObject(component.getBeanInstance());
if (customizerObject instanceof FormAwareEditor) {
// Hack - returns some property
Node.Property prop = component.getProperties()[0].getProperties()[0];
((FormAwareEditor) customizerObject)
.setContext(component.getFormModel(), (FormProperty) prop);
}
customizer.addPropertyChangeListener(
new PropertyChangeListener() {
@Override
public void propertyChange(PropertyChangeEvent evt) {
FormProperty[] properties;
if (evt.getPropertyName() != null) {
FormProperty changedProperty = component.getBeanProperty(evt.getPropertyName());
if (changedProperty != null) properties = new FormProperty[] {changedProperty};
else return; // non-existing property?
} else {
properties = component.getAllBeanProperties();
evt = null;
}
updatePropertiesFromCustomizer(properties, evt);
}
});
// [undo/redo for customizer probably does not work...]
return (Component) customizerObject;
}