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

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Here is the source code for org.dishevelled.bio.assembly.gfa2.Set.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 com.google.common.collect.ImmutableSet;

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

/**
 * Set GFA 2.0 record.
 *
 * @author  Michael Heuer
 */
@Immutable
public final class Set extends Gfa2Record {
    /** Optional identifier for this set. */
    private final String id;

    /** Unordered set of identifiers for this set. */
    private final java.util.Set<String> ids;

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

    /**
     * Create a new set GFA 2.0 record.
     *
     * @param id identifier, if any
     * @param ids unordered set of identifiers, must not be null
     * @param tags tags, must not be null
     */
    public Set(@Nullable final String id, final java.util.Set<String> ids, final Map<String, Tag> tags) {

        super(tags);
        checkNotNull(ids);

        this.id = id;
        this.ids = ImmutableSet.copyOf(ids);

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

    /**
     * Return the identifier for this set, if any.
     *
     * @return the identifier for this set, if any
     */
    public String getId() {
        return id;
    }

    /**
     * Return an immutable unordered set of identifiers for this set.
     *
     * @return an immutable unordered set of identifiers for this set
     */
    public java.util.Set<String> getIds() {
        return ids;
    }

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

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

        return Objects.equals(id, s.getId()) && Objects.equals(ids, s.getIds())
                && Objects.equals(getTags(), s.getTags());
    }

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

    /**
     * Parse a set GFA 2.0 record from the specified value.
     *
     * @param value value, must not be null
     * @return a set GFA 2.0 record parsed from the specified value
     */
    public static Set valueOf(final String value) {
        checkNotNull(value);
        checkArgument(value.startsWith("U"), "value must start with U");
        List<String> tokens = Splitter.on("\t").splitToList(value);
        if (tokens.size() < 3) {
            throw new IllegalArgumentException("value must have at least three tokens, was " + tokens.size());
        }
        String id = "*".equals(tokens.get(1)) ? null : tokens.get(1);
        java.util.Set<String> ids = ImmutableSet.copyOf(Splitter.on(" ").split(tokens.get(2)));

        ImmutableMap.Builder<String, Tag> tags = ImmutableMap.builder();
        for (int i = 3; i < tokens.size(); i++) {
            Tag tag = Tag.valueOf(tokens.get(i));
            tags.put(tag.getName(), tag);
        }

        return new Set(id, ids, tags.build());
    }
}