org.dishevelled.bio.assembly.gfa2.Gfa2Reader.java Source code

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Here is the source code for org.dishevelled.bio.assembly.gfa2.Gfa2Reader.java

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/*
    
dsh-bio-assembly  Assemblies.
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.assembly.gfa2;

import static com.google.common.base.Preconditions.checkNotNull;

import java.io.IOException;

import java.util.LinkedList;
import java.util.List;

import javax.annotation.concurrent.Immutable;

import com.google.common.io.CharStreams;
import com.google.common.io.LineProcessor;

/**
 * Graphical Fragment Assembly (GFA) 2.0 reader.
 *
 * @author  Michael Heuer
 */
@Immutable
public final class Gfa2Reader {

    /**
     * Private no-arg constructor.
     */
    private Gfa2Reader() {
        // empty
    }

    /**
     * Read zero or more GFA 2.0 records from the specified readable.
     *
     * @param readable to read from, must not be null
     * @return zero or more GFA 2.0 records read from the specified readable
     * @throws IOException if an I/O error occurs
     */
    public static Iterable<Gfa2Record> read(final Readable readable) throws IOException {
        checkNotNull(readable);
        Collect collect = new Collect();
        stream(readable, collect);
        return collect.records();
    }

    /**
     * Stream zero or more GFA 2.0 records from the specified readable.
     *
     * @param readable readable to stream from, must not be null
     * @param listener event based listener callback, must not be null
     * @throws IOException if an I/O error occurs
     */
    public static void stream(final Readable readable, final Gfa2Listener listener) throws IOException {
        checkNotNull(readable);
        checkNotNull(listener);

        Gfa2LineProcessor lineProcessor = new Gfa2LineProcessor(listener);
        CharStreams.readLines(readable, lineProcessor);
    }

    /**
     * GFA 2.0 line processor.
     */
    private static final class Gfa2LineProcessor implements LineProcessor<Object> {
        /** Line number. */
        private long lineNumber = 0;

        /** GFA 2.0 listener. */
        private final Gfa2Listener listener;

        /**
         * Create a new GFA 2.0 line processor with the specified GFA 2.0 listener.
         *
         * @param listener GFA 2.0 listener, must not be null
         */
        private Gfa2LineProcessor(final Gfa2Listener listener) {
            checkNotNull(listener);
            this.listener = listener;
        }

        @Override
        public Object getResult() {
            return null;
        }

        @Override
        public boolean processLine(final String line) throws IOException {
            try {
                lineNumber++;
                if (line != null && !line.isEmpty()) {
                    char c = line.charAt(0);
                    if ('E' == c) {
                        return listener.record(Edge.valueOf(line));
                    } else if ('F' == c) {
                        return listener.record(Fragment.valueOf(line));
                    } else if ('G' == c) {
                        return listener.record(Gap.valueOf(line));
                    } else if ('H' == c) {
                        return listener.record(Header.valueOf(line));
                    } else if ('O' == c) {
                        return listener.record(Path.valueOf(line));
                    } else if ('S' == c) {
                        return listener.record(Segment.valueOf(line));
                    } else if ('U' == c) {
                        return listener.record(Set.valueOf(line));
                    }
                }
                // continue processing blank or unrecognized lines
                return true;
            } catch (IllegalArgumentException e) {
                throw new IOException(
                        "could not read GFA 2.0 record at line " + lineNumber + ", caught " + e.getMessage(), e);
            }
        }
    }

    /**
     * Collect.
     */
    private static class Collect implements Gfa2Listener {
        /** List of collected GFA 2.0 records. */
        private final List<Gfa2Record> records = new LinkedList<Gfa2Record>();

        @Override
        public boolean record(final Gfa2Record record) {
            records.add(record);
            return true;
        }

        /**
         * Return zero or more collected GFA 2.0 records.
         *
         * @return zero or more collected GFA 2.0 records
         */
        Iterable<Gfa2Record> records() {
            return records;
        }
    }
}