private static <T> List<T> createAnnotations(
PluginManager<T> pluginManager,
List<String> annotationGroupsToUse,
List<String> annotationsToUse) {
// get the instances
List<T> annotations = new ArrayList<T>();
// get the classes from the provided groups (interfaces)
// create a map for all annotation classes which implement our top-level interfaces
HashMap<String, Class> classMap = new HashMap<String, Class>();
for (Class c : pluginManager.getPlugins()) classMap.put(c.getSimpleName(), c);
for (Class c : annotationTypePluginManager.getInterfaces()) classMap.put(c.getSimpleName(), c);
// use a TreeSet so that classes are returned deterministically (the plugin manager apparently
// isn't deterministic)
TreeSet<Class> classes =
new TreeSet<Class>(
new Comparator<Class>() {
public int compare(Class o1, Class o2) {
return o1.getSimpleName().compareTo(o2.getSimpleName());
}
});
if (annotationGroupsToUse.size() != 1 || !"none".equals(annotationGroupsToUse.get(0))) {
for (String group : annotationGroupsToUse) {
Class interfaceClass = classMap.get(group);
if (interfaceClass == null) interfaceClass = classMap.get(group + "Annotation");
if (interfaceClass != null)
classes.addAll(pluginManager.getPluginsImplementing(interfaceClass));
}
}
// get the specific classes provided
for (String annotation : annotationsToUse) {
Class annotationClass = classMap.get(annotation);
if (annotationClass == null) annotationClass = classMap.get(annotation + "Annotation");
if (annotationClass != null) classes.add(annotationClass);
}
// note that technically an annotation can work on both the INFO and FORMAT fields
for (Class c : classes) annotations.add(pluginManager.createByType(c));
return annotations;
}
public static void validateAnnotations(
List<String> annotationGroupsToUse, List<String> annotationsToUse) {
HashMap<String, Class> classMap = new HashMap<String, Class>();
for (Class c : infoFieldAnnotationPluginManager.getPlugins())
classMap.put(c.getSimpleName(), c);
for (Class c : genotypeAnnotationPluginManager.getPlugins()) classMap.put(c.getSimpleName(), c);
for (Class c : annotationTypePluginManager.getInterfaces()) classMap.put(c.getSimpleName(), c);
if (annotationGroupsToUse.size() != 1 || !"none".equals(annotationGroupsToUse.get(0))) {
for (String group : annotationGroupsToUse) {
Class interfaceClass = classMap.get(group);
if (interfaceClass == null) interfaceClass = classMap.get(group + "Annotation");
if (interfaceClass == null)
throw new UserException.BadArgumentValue(
"group",
"Annotation group "
+ group
+ " was not found; please check that you have specified the group name correctly");
}
}
// validate the specific classes provided
for (String annotation : annotationsToUse) {
Class annotationClass = classMap.get(annotation);
if (annotationClass == null) annotationClass = classMap.get(annotation + "Annotation");
if (annotationClass == null) {
if (DeprecatedToolChecks.isDeprecatedAnnotation(annotation)) {
throw new UserException.DeprecatedAnnotation(
annotation, DeprecatedToolChecks.getAnnotationDeprecationInfo(annotation));
} else {
throw new UserException.BadArgumentValue(
"annotation",
"Annotation "
+ annotation
+ " was not found; please check that you have specified the annotation name correctly");
}
}
}
}
public static List<GenotypeAnnotation> createAllGenotypeAnnotations() {
return genotypeAnnotationPluginManager.createAllTypes();
}
public static List<InfoFieldAnnotation> createAllInfoFieldAnnotations() {
return infoFieldAnnotationPluginManager.createAllTypes();
}