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SciJava Common is a shared library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by both ImageJ and SCIFIO.
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/*
 * #%L
 * SciJava Common shared library for SciJava software.
 * %%
 * Copyright (C) 2009 - 2016 Board of Regents of the University of
 * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
 * Institute of Molecular Cell Biology and Genetics.
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 * 
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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package org.scijava.annotations;

import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.TreeMap;

import javax.annotation.processing.AbstractProcessor;
import javax.annotation.processing.Filer;
import javax.annotation.processing.RoundEnvironment;
import javax.annotation.processing.SupportedAnnotationTypes;
import javax.annotation.processing.SupportedSourceVersion;
import javax.lang.model.SourceVersion;
import javax.lang.model.element.AnnotationMirror;
import javax.lang.model.element.AnnotationValue;
import javax.lang.model.element.Element;
import javax.lang.model.element.ExecutableElement;
import javax.lang.model.element.Name;
import javax.lang.model.element.TypeElement;
import javax.lang.model.element.VariableElement;
import javax.lang.model.type.TypeMirror;
import javax.lang.model.util.Elements;
import javax.lang.model.util.Types;
import javax.tools.Diagnostic.Kind;
import javax.tools.FileObject;
import javax.tools.StandardLocation;

import org.scijava.annotations.AbstractIndexWriter.StreamFactory;

/**
 * The annotation processor for use with Java 6 and above.
 * 
 * @author Johannes Schindelin
 */
@SupportedSourceVersion(SourceVersion.RELEASE_6)
@SupportedAnnotationTypes("*")
public class AnnotationProcessor extends AbstractProcessor {

	private RoundEnvironment roundEnv;

	@Override
	public boolean process(final Set elements,
		final RoundEnvironment env)
	{
		roundEnv = env;

		final Writer writer = new Writer();
		for (final TypeElement element : elements) {
			writer.add(element);
		}
		try {
			writer.write(writer);
		}
		catch (final IOException e) {
			final ByteArrayOutputStream out = new ByteArrayOutputStream();
			e.printStackTrace(new PrintStream(out));
			try {
				out.close();
				processingEnv.getMessager().printMessage(Kind.ERROR, out.toString());
			}
			catch (final IOException e2) {
				processingEnv.getMessager().printMessage(Kind.ERROR,
					e2.getMessage() + " while printing " + e.getMessage());
			}
		}
		return false;
	}

	private class Writer extends AbstractIndexWriter implements StreamFactory {

		private final Map> originatingElements =
			new HashMap>();
		private final Filer filer = processingEnv.getFiler();
		private final Elements utils = processingEnv.getElementUtils();
		private final Types typeUtils = processingEnv.getTypeUtils();

		public void add(final TypeElement element) {
			final AnnotationMirror mirror = getMirror(element);
			if (mirror != null) {
				final String annotationName = utils.getBinaryName(element).toString();

				// remember originating elements
				List originating = originatingElements.get(annotationName);
				if (originating == null) {
					originating = new ArrayList();
					originatingElements.put(annotationName, originating);
				}

				for (final Element annotated : roundEnv
					.getElementsAnnotatedWith(element))
				{
					switch (annotated.getKind()) {
						case ANNOTATION_TYPE:
						case CLASS:
						case ENUM:
						case INTERFACE:
							final String className =
								utils.getBinaryName((TypeElement) annotated).toString();
							final Map values =
								adapt(annotated.getAnnotationMirrors(), element.asType());
							super.add(values, annotationName, className);
							originating.add(annotated);
							break;
						default:
							processingEnv.getMessager().printMessage(
								Kind.ERROR,
								"Cannot handle annotated element of kind " +
									annotated.getKind());
					}
				}
			}
			//
		}

		@SuppressWarnings("unchecked")
		private Map adapt(
			final List mirrors,
			final TypeMirror annotationType)
		{
			final Map result = new TreeMap();
			for (final AnnotationMirror mirror : mirrors) {
				if (typeUtils.isSameType(mirror.getAnnotationType(), annotationType)) {
					return (Map) adapt(mirror);
				}
			}
			return result;
		}

		@Override
		protected Object adapt(final Object o) {
			if (o instanceof AnnotationMirror) {
				final AnnotationMirror mirror = (AnnotationMirror) o;
				final Map result = new TreeMap();
				for (final Entry entry : mirror
					.getElementValues().entrySet())
				{
					final String key = entry.getKey().getSimpleName().toString();
					final Object value = adapt(entry.getValue().getValue());
					result.put(key, value);
				}
				return result;
			}
			else if (o instanceof List) {
				final List list = (List) o;
				final List