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Move CombineAnnotations into the appropriate package
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
1 parent 0b61306 commit 6a9ce00

2 files changed

Lines changed: 187 additions & 107 deletions

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‎src/main/java/org/scijava/annotations/CombineAnnotations.java‎

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/*
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* #%L
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* SciJava Common shared library for SciJava software.
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* %%
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* Copyright (C) 2009 - 2013 Board of Regents of the University of
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* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
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* Institute of Molecular Cell Biology and Genetics.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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*
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* The views and conclusions contained in the software and documentation are
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* those of the authors and should not be interpreted as representing official
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* policies, either expressed or implied, of any organization.
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* #L%
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*/
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package org.scijava.annotations;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.lang.annotation.Annotation;
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import java.net.URL;
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import java.util.Enumeration;
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import java.util.HashSet;
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import java.util.Set;
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import org.scijava.util.FileUtils;
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/**
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* Combines SezPoz annotations from all JAR files on the classpath.
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*
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* @author Curtis Rueden
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*/
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public class CombineAnnotations extends AbstractIndexWriter {
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private static final String PREFIX = "META-INF/json/";
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private static final String LEGACY_PREFIX = "META-INF/annotations/";
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private final String OUTPUT_DIR;
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private final Set<String> annotationFiles;
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public CombineAnnotations() throws IOException {
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this(null);
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}
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public CombineAnnotations(final String outputDir) throws IOException {
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if (outputDir != null) {
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OUTPUT_DIR = outputDir;
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} else {
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OUTPUT_DIR = "src/main/assembly/all";
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}
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annotationFiles = getAnnotationFiles();
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}
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/** Reads in annotations from all available resources and combines them. */
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public void combine() throws IOException, ClassNotFoundException {
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final ClassLoader loader = Thread.currentThread().getContextClassLoader();
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log("");
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log("Writing annotations to " + new File(OUTPUT_DIR).getAbsolutePath());
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new File(OUTPUT_DIR, PREFIX).mkdirs();
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for (final String annotationFile : annotationFiles) {
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final String annotationName = annotationFile.substring(PREFIX.length());
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@SuppressWarnings("unchecked")
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final Class<? extends Annotation> annotation =
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(Class<? extends Annotation>) loader.loadClass(annotationName);
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for (IndexItem<? extends Annotation> item : Index.load(annotation, loader)) {
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add(adapt(item.annotation()), annotationName, item.className());
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}
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}
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write(new StreamFactory() {
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@Override
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public InputStream openInput(String annotationName)
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throws IOException {
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return null;
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}
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@Override
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public OutputStream openOutput(String annotationName)
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throws IOException {
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final File file = new File(OUTPUT_DIR, PREFIX + annotationName);
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return new FileOutputStream(file);
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}
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@Override
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public boolean isClassObsolete(String className) {
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return false;
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}
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});
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}
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/** Scans for annotations files in every resource on the classpath. */
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public Set<String> getAnnotationFiles() throws IOException {
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final HashSet<String> files = new HashSet<String>();
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for (final String prefix : new String[] { PREFIX, LEGACY_PREFIX }) {
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final Enumeration<URL> directories = Thread.currentThread()
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.getContextClassLoader().getResources(prefix);
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while (directories.hasMoreElements()) {
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final URL url = directories.nextElement();
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for (final URL annotationIndexURL : FileUtils.listContents(url)) {
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String string = annotationIndexURL.toString();
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if (string.endsWith("/")) {
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continue;
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}
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final int length = string.length();
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add(files, PREFIX + string.substring(
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string.lastIndexOf('/', length - 1) + 1, length));
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}
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}
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}
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return files;
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}
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public static void main(final String[] args) throws Exception {
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new CombineAnnotations(args.length > 0 ? args[0] : null).combine();
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}
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// -- Helper methods --
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private void add(final HashSet<String> set, final String item) {
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log("\t" + item);
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set.add(item);
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}
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private void log(final String msg) {
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System.out.println(msg);
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}
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}

‎src/main/java/org/scijava/util/CombineAnnotations.java‎

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package org.scijava.util;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.lang.annotation.Annotation;
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import java.net.URL;
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import java.util.Enumeration;
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import java.util.HashSet;
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import java.util.Set;
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import org.scijava.annotations.AbstractIndexWriter;
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import org.scijava.annotations.Index;
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import org.scijava.annotations.IndexItem;
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/**
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* Combines SezPoz annotations from all JAR files on the classpath.
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*
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* @author Curtis Rueden
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* @deprecated Use {@link org.scijava.annotations.CombineAnnotations} instead.
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*/
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public class CombineAnnotations extends AbstractIndexWriter {
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private static final String PREFIX = "META-INF/json/";
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private static final String LEGACY_PREFIX = "META-INF/annotations/";
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private final String OUTPUT_DIR;
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private final Set<String> annotationFiles;
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public CombineAnnotations() throws IOException {
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this(null);
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}
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public CombineAnnotations(final String outputDir) throws IOException {
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if (outputDir != null) {
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OUTPUT_DIR = outputDir;
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} else {
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OUTPUT_DIR = "src/main/assembly/all";
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}
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annotationFiles = getAnnotationFiles();
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}
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/** Reads in annotations from all available resources and combines them. */
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@Deprecated
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public class CombineAnnotations extends
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org.scijava.annotations.CombineAnnotations
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{
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/**
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* @deprecated Use {@link org.scijava.annotations.CombineAnnotations#CombineAnnotations()} instead.
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*/
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@Deprecated
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public CombineAnnotations() throws IOException {}
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/**
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* @deprecated Use {@link org.scijava.annotations.CombineAnnotations#combine()} instead.
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*/
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@Deprecated
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@Override
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public void combine() throws IOException, ClassNotFoundException {
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final ClassLoader loader = Thread.currentThread().getContextClassLoader();
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log("");
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log("Writing annotations to " + new File(OUTPUT_DIR).getAbsolutePath());
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new File(OUTPUT_DIR, PREFIX).mkdirs();
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for (final String annotationFile : annotationFiles) {
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final String annotationName = annotationFile.substring(PREFIX.length());
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@SuppressWarnings("unchecked")
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final Class<? extends Annotation> annotation =
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(Class<? extends Annotation>) loader.loadClass(annotationName);
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for (IndexItem<? extends Annotation> item : Index.load(annotation, loader)) {
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add(adapt(item.annotation()), annotationName, item.className());
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}
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}
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write(new StreamFactory() {
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@Override
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public InputStream openInput(String annotationName)
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throws IOException {
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return null;
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}
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@Override
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public OutputStream openOutput(String annotationName)
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throws IOException {
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final File file = new File(OUTPUT_DIR, PREFIX + annotationName);
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return new FileOutputStream(file);
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}
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@Override
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public boolean isClassObsolete(String className) {
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return false;
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}
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});
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super.combine();
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}
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/** Scans for annotations files in every resource on the classpath. */
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/**
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* @deprecated Use {@link org.scijava.annotations.CombineAnnotations#getAnnotationFiles()} instead.
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*/
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@Deprecated
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@Override
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public Set<String> getAnnotationFiles() throws IOException {
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final HashSet<String> files = new HashSet<String>();
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for (final String prefix : new String[] { PREFIX, LEGACY_PREFIX }) {
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final Enumeration<URL> directories = Thread.currentThread()
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.getContextClassLoader().getResources(prefix);
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while (directories.hasMoreElements()) {
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final URL url = directories.nextElement();
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for (final URL annotationIndexURL : FileUtils.listContents(url)) {
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String string = annotationIndexURL.toString();
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if (string.endsWith("/")) {
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continue;
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}
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final int length = string.length();
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add(files, PREFIX + string.substring(
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string.lastIndexOf('/', length - 1) + 1, length));
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}
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}
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}
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return files;
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return super.getAnnotationFiles();
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}
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/**
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* @deprecated Use {@link org.scijava.annotations.CombineAnnotations#main(String[])} instead.
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*/
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@Deprecated
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public static void main(final String[] args) throws Exception {
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new CombineAnnotations(args.length > 0 ? args[0] : null).combine();
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}
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// -- Helper methods --
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private void add(final HashSet<String> set, final String item) {
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log("\t" + item);
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set.add(item);
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}
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private void log(final String msg) {
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System.out.println(msg);
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new org.scijava.annotations.CombineAnnotations(args.length > 0 ? args[0]
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: null).combine();
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}
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}

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