Java tutorial
/* dsh-variation Variation. Copyright (c) 2013-2014 held jointly by the individual authors. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. > http://www.fsf.org/licensing/licenses/lgpl.html > http://www.opensource.org/licenses/lgpl-license.php */ package org.dishevelled.variation.vcf; import static com.google.common.base.Preconditions.checkNotNull; import java.net.URL; import java.io.Closeable; import java.io.File; import java.io.InputStream; import java.io.InputStreamReader; import java.io.IOException; import java.util.List; import com.google.common.base.Charsets; import com.google.common.collect.Iterables; import com.google.common.collect.Lists; import com.google.common.io.InputSupplier; import com.google.common.io.Files; import com.google.common.io.Resources; /** * VCF reader. * * @author Michael Heuer */ public final class VcfReader { /** * Private no-arg constructor. */ private VcfReader() { // empty } /** * Parse the specified input supplier. * * @param supplier input supplier, must not be null * @param listener low-level event based parser callback, must not be null * @throws IOException if an I/O error occurs */ static <R extends Readable & Closeable> void parse(final InputSupplier<R> supplier, final VcfParseListener listener) throws IOException { VcfParser.parse(supplier, listener); } /** * Stream the specified input supplier. * * @param supplier input supplier, must not be null * @param listener event based reader callback, must not be null * @throws IOException if an I/O error occurs */ static <R extends Readable & Closeable> void stream(final InputSupplier<R> supplier, final VcfStreamListener listener) throws IOException { StreamingVcfParser.stream(supplier, listener); } /** * Read zero or more VCF records from the specified file. * * @param file file to read from, must not be null * @return zero or more VCF records read from the specified file * @throws IOException if an I/O error occurs */ static Iterable<VcfRecord> read(final File file) throws IOException { checkNotNull(file); Collect collect = new Collect(); stream(Files.newReaderSupplier(file, Charsets.UTF_8), collect); return collect.getResult(); } /** * Read zero or more VCF records from the specified URL. * * @param url URL to read from, must not be null * @return zero or more VCF records read from the specified URL * @throws IOException if an I/O error occurs */ static Iterable<VcfRecord> read(final URL url) throws IOException { checkNotNull(url); Collect collect = new Collect(); stream(Resources.newReaderSupplier(url, Charsets.UTF_8), collect); return collect.getResult(); } /** * Read zero or more VCF records from the specified input stream. * * @param inputStream input stream to read from, must not be null * @return zero or more VCF records read from the specified input stream * @throws IOException if an I/O error occurs */ static Iterable<VcfRecord> read(final InputStream inputStream) throws IOException { checkNotNull(inputStream); Collect collect = new Collect(); stream(new InputSupplier<InputStreamReader>() { @Override public InputStreamReader getInput() throws IOException { return new InputStreamReader(inputStream); } }, collect); return collect.getResult(); } // todo: do these all need to be here? /** * Read zero or more VCF samples from the specified input supplier. * * @param supplier input supplier to read from, must not be null * @return zero or more VCF samples read from the specified input supplier * @throws IOException if an I/O error occurs */ static <R extends Readable & Closeable> Iterable<VcfSample> samples(final InputSupplier<R> supplier) throws IOException { return VcfSampleParser.samples(supplier); } /** * Read zero or more VCF samples from the specified file. * * @param file file to read from, must not be null * @return zero or more VCF samples read from the specified file * @throws IOException if an I/O error occurs */ static Iterable<VcfSample> samples(final File file) throws IOException { checkNotNull(file); return samples(Files.newReaderSupplier(file, Charsets.UTF_8)); } /** * Read zero or more VCF samples from the specified URL. * * @param url URL to read from, must not be null * @return zero or more VCF samples read from the specified URL * @throws IOException if an I/O error occurs */ static Iterable<VcfSample> samples(final URL url) throws IOException { checkNotNull(url); return samples(Resources.newReaderSupplier(url, Charsets.UTF_8)); } /** * Read zero or more VCF samples from the specified input stream. * * @param inputStream input stream to read from, must not be null * @return zero or more VCF samples read from the specified input stream * @throws IOException if an I/O error occurs */ static Iterable<VcfSample> samples(final InputStream inputStream) throws IOException { checkNotNull(inputStream); return samples(new InputSupplier<InputStreamReader>() { @Override public InputStreamReader getInput() throws IOException { return new InputStreamReader(inputStream); } }); } /** * Collect. */ private static final class Collect implements VcfStreamListener { /** List of VCF records. */ private final List<VcfRecord> result = Lists.newLinkedList(); @Override public void record(final VcfRecord record) { result.add(record); } /** * Return the collected VCF records. * * @return the collected VCF records */ private Iterable<VcfRecord> getResult() { return Iterables.unmodifiableIterable(result); } } }