org.dishevelled.bio.assembly.gfa1.Path.java Source code

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Here is the source code for org.dishevelled.bio.assembly.gfa1.Path.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.gfa1;

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

import java.util.List;
import java.util.Map;
import java.util.Objects;

import java.util.stream.Collectors;

import javax.annotation.Nullable;

import javax.annotation.concurrent.Immutable;

import com.google.common.base.Joiner;
import com.google.common.base.Splitter;

import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMap;

import org.dishevelled.bio.assembly.gfa.Reference;
import org.dishevelled.bio.assembly.gfa.Tag;

/**
 * Path GFA 1.0 record.
 *
 * @author  Michael Heuer
 */
@Immutable
public final class Path extends Gfa1Record {
    /** Name for this path. */
    private final String name;

    /** List of segment references for this path. */
    private final List<Reference> segments;

    /** List of overlaps for this path. */
    private final List<String> overlaps;

    /** Cached hash code. */
    private final int hashCode;

    /**
     * Create a new path GFA 1.0 record.
     *
     * @param name name, must not be null
     * @param segments list of segment references, must not be null
     * @param overlaps list of overlaps, if any
     * @param tags tags, must not be null
     */
    public Path(final String name, final List<Reference> segments, @Nullable final List<String> overlaps,
            final Map<String, Tag> tags) {

        super(tags);
        checkNotNull(name);
        checkNotNull(segments);

        this.name = name;
        this.segments = ImmutableList.copyOf(segments);
        this.overlaps = overlaps == null ? null : ImmutableList.copyOf(overlaps);

        hashCode = Objects.hash(this.name, this.segments, this.overlaps, getTags());
    }

    /**
     * Return the name for this path.
     *
     * @return the name for this path
     */
    public String getName() {
        return name;
    }

    /**
     * Return an immutable list of segment references for this path.
     *
     * @return an immutable list of segment references for this path
     */
    public List<Reference> getSegments() {
        return segments;
    }

    /**
     * Return true if this path has any overlaps.
     *
     * @return true if this path has any overlaps
     */
    public boolean hasOverlaps() {
        return overlaps != null;
    }

    /**
     * Return an immutable list of overlaps in cigar format for this path,
     * or null if none exist.
     *
     * @return an immutable list of overlaps in cigar format for this path,
     *    or null if none exist
     */
    public List<String> getOverlaps() {
        return overlaps;
    }

    @Override
    public int hashCode() {
        return hashCode;
    }

    @Override
    public boolean equals(final Object o) {
        if (o == this) {
            return true;
        }
        if (!(o instanceof Path)) {
            return false;
        }
        Path p = (Path) o;

        return Objects.equals(name, p.getName()) && Objects.equals(segments, p.getSegments())
                && Objects.equals(overlaps, p.getOverlaps()) && Objects.equals(getTags(), p.getTags());
    }

    @Override
    public String toString() {
        Joiner joiner = Joiner.on("\t");
        StringBuilder sb = new StringBuilder();
        joiner.appendTo(sb, "P", name, Joiner.on(",").join(segments), Joiner.on(",").join(overlaps));
        if (!getTags().isEmpty()) {
            sb.append("\t");
            joiner.appendTo(sb, getTags().values());
        }
        return sb.toString();
    }

    /**
     * Parse a path GFA 1.0 record from the specified value.
     *
     * @param value value, must not be null
     * @return a path GFA 1.0 record parsed from the specified value
     */
    public static Path valueOf(final String value) {
        checkNotNull(value);
        checkArgument(value.startsWith("P"), "value must start with P");
        List<String> tokens = Splitter.on("\t").splitToList(value);
        if (tokens.size() < 4) {
            throw new IllegalArgumentException("value must have at least four tokens, was " + tokens.size());
        }
        String name = tokens.get(1);

        List<Reference> segments = Splitter.on(",").splitToList(tokens.get(2)).stream().map(Reference::valueOf)
                .collect(Collectors.toList());

        List<String> overlaps = "*".equals(tokens.get(3)) ? null
                : ImmutableList.copyOf(Splitter.on(",").split(tokens.get(3)));

        ImmutableMap.Builder<String, Tag> tags = ImmutableMap.builder();
        for (int i = 4; i < tokens.size(); i++) {
            Tag tag = Tag.valueOf(tokens.get(i));
            tags.put(tag.getName(), tag);
        }

        return new Path(name, segments, overlaps, tags.build());
    }
}