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

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Here is the source code for org.dishevelled.bio.assembly.gfa2.Segment.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.checkArgument;
import static com.google.common.base.Preconditions.checkNotNull;

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

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.ImmutableMap;

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

/**
 * Segment GFA 2.0 record.
 *
 * @author  Michael Heuer
 */
@Immutable
public final class Segment extends Gfa2Record {
    /** Identifier for this segment. */
    private final String id;

    /** Length for this segment. */
    private final int length;

    /** Optional sequence for this segment. */
    private final String sequence;

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

    /**
     * Create a new segment GFA 2.0 record.
     *
     * @param id identifier, must not be null
     * @param length length, must be at least zero
     * @param sequence sequence, if any
     * @param tags tags, must not be null
     */
    public Segment(final String id, final int length, @Nullable final String sequence,
            final Map<String, Tag> tags) {

        super(tags);
        checkNotNull(id);
        checkArgument(length >= 0, "length must be at least zero");

        this.id = id;
        this.length = length;
        this.sequence = sequence;

        hashCode = Objects.hash(this.id, this.length, this.sequence, getTags());
    }

    /**
     * Return the identifier for this segment.
     *
     * @return the identifier for this segment
     */
    public String getId() {
        return id;
    }

    /**
     * Return the length for this segment.
     *
     * @return the length for this segment
     */
    public int getLength() {
        return length;
    }

    /**
     * Return the sequence for this segment, if any.
     *
     * @return the sequence for this segment, if any
     */
    public String getSequence() {
        return sequence;
    }

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

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

        return Objects.equals(id, s.getId()) && Objects.equals(length, s.getLength())
                && Objects.equals(sequence, s.getSequence()) && Objects.equals(getTags(), s.getTags());
    }

    @Override
    public String toString() {
        Joiner joiner = Joiner.on("\t");
        StringBuilder sb = new StringBuilder();
        joiner.appendTo(sb, "S", id, length, sequence == null ? "*" : sequence);
        if (!getTags().isEmpty()) {
            sb.append("\t");
            joiner.appendTo(sb, getTags().values());
        }
        return sb.toString();
    }

    /**
     * Parse a segment GFA 2.0 record from the specified value.
     *
     * @param value value, must not be null
     * @return a segment GFA 2.0 record parsed from the specified value
     */
    public static Segment valueOf(final String value) {
        checkNotNull(value);
        checkArgument(value.startsWith("S"), "value must start with S");
        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());
        }

        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 Segment(tokens.get(1), Integer.parseInt(tokens.get(2)), tokens.get(3), tags.build());
    }
}