Java tutorial
/* dsh-bio-alignment Aligments. Copyright (c) 2013-2019 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.bio.alignment.sam; import static com.google.common.base.Preconditions.checkNotNull; import java.net.URL; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.InputStream; import java.io.InputStreamReader; import java.io.IOException; import java.util.ArrayList; import java.util.List; import javax.annotation.concurrent.Immutable; import com.google.common.base.Charsets; import com.google.common.io.Resources; /** * SAM reader. * * @since 1.1 * @author Michael Heuer */ @Immutable public final class SamReader { /** * Private no-arg constructor. */ private SamReader() { // empty } // callback methods /** * Parse the specified readable. * * @param readable readable to parse, must not be null * @param listener low-level event based parser callback, must not be null * @throws IOException if an I/O error occurs */ public static void parse(final Readable readable, final SamParseListener listener) throws IOException { SamParser.parse(readable, listener); } /** * Stream the specified readable. * * @param readable readable to stream, must not be null * @param listener event based reader callback, must not be null * @throws IOException if an I/O error occurs */ public static void stream(final Readable readable, final SamStreamListener listener) throws IOException { StreamingSamParser.stream(readable, listener); } // collect methods /** * Read the SAM header from the specified readable. * * @param readable readable to read from, must not be null * @return the SAM header read from the specified readable * @throws IOException if an I/O error occurs */ public static SamHeader header(final Readable readable) throws IOException { return SamHeaderParser.header(readable); } /** * Read zero or more SAM records from the specified readable. * * @param readable readable to read from, must not be null * @return zero or more SAM records read from the specified readable * @throws IOException if an I/O error occurs */ public static Iterable<SamRecord> records(final Readable readable) throws IOException { Collect collect = new Collect(); StreamingSamParser.stream(readable, collect); return collect.getRecords(); } /** * Collect. */ private static final class Collect extends SamStreamAdapter { /** Arbitrary large capacity for list of SAM records. */ private static final int CAPACITY = 10000000; /** List of SAM records. */ private final List<SamRecord> records = new ArrayList<SamRecord>(CAPACITY); @Override public void record(final SamRecord record) { records.add(record); } /** * Return the list of SAM records. * * @return the list of SAM records */ List<SamRecord> getRecords() { return records; } } // convenience methods /** * Read the SAM header from the specified file. * * @param file file to read from, must not be null * @return the SAM header read from the specified file * @throws IOException if an I/O error occurs */ public static SamHeader header(final File file) throws IOException { checkNotNull(file); // could also use Files.asCharSource(file, Charsets.UTF_8).openBufferedStream() try (BufferedReader reader = new BufferedReader(new FileReader(file))) { return header(reader); } } /** * Read the SAM header from the specified URL. * * @param url URL to read from, must not be null * @return the SAM header read from the specified URL * @throws IOException if an I/O error occurs */ public static SamHeader header(final URL url) throws IOException { checkNotNull(url); try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) { return header(reader); } } /** * Read the SAM header from the specified input stream. * * @param inputStream input stream to read from, must not be null * @return the SAM header read from the specified input stream * @throws IOException if an I/O error occurs */ public static SamHeader header(final InputStream inputStream) throws IOException { checkNotNull(inputStream); try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) { return header(reader); } } /** * Read zero or more SAM records from the specified file. * * @param file file to read from, must not be null * @return zero or more SAM records read from the specified file * @throws IOException if an I/O error occurs */ public static Iterable<SamRecord> records(final File file) throws IOException { checkNotNull(file); try (BufferedReader reader = new BufferedReader(new FileReader(file))) { return records(reader); } } /** * Read zero or more SAM records from the specified URL. * * @param url URL to read from, must not be null * @return zero or more SAM records read from the specified URL * @throws IOException if an I/O error occurs */ public static Iterable<SamRecord> records(final URL url) throws IOException { checkNotNull(url); try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) { return records(reader); } } /** * Read zero or more SAM records from the specified input stream. * * @param inputStream input stream to read from, must not be null * @return zero or more SAM records read from the specified input stream * @throws IOException if an I/O error occurs */ public static Iterable<SamRecord> records(final InputStream inputStream) throws IOException { checkNotNull(inputStream); try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) { return records(reader); } } }