org.dishevelled.bio.variant.vcf.header.VcfAltHeaderLine.java Source code

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Here is the source code for org.dishevelled.bio.variant.vcf.header.VcfAltHeaderLine.java

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/*
    
dsh-bio-variant  Variants.
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.variant.vcf.header;

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

import java.util.Map;

import javax.annotation.concurrent.Immutable;

import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ImmutableListMultimap;
import com.google.common.collect.ListMultimap;

/**
 * VCF ALT header line.
 *
 * @author  Michael Heuer
 */
@Immutable
public final class VcfAltHeaderLine {
    /** Header line ID. */
    private final String id;

    /** Header line description. */
    private final String description;

    /** Header line attributes. */
    private final ListMultimap<String, String> attributes;

    /**
     * Create a new VCF ALT header line.
     *
     * @param id header line ID, must not be null
     * @param description header line description, must not be null
     * @param attributes header line attributes, must not be null
     */
    VcfAltHeaderLine(final String id, final String description, final ListMultimap<String, String> attributes) {
        checkNotNull(id);
        checkNotNull(description);
        checkNotNull(attributes);

        this.id = id;
        this.description = description;
        this.attributes = ImmutableListMultimap.copyOf(attributes);
    }

    /**
     * Return the ID for this VCF ALT header line.
     *
     * @return the ID for this VCF ALT header line
     */
    public String getId() {
        return id;
    }

    /**
     * Return the description for this VCF ALT header line.
     *
     * @return the description for this VCF ALT header line
     */
    public String getDescription() {
        return description;
    }

    /**
     * Return the attributes for this VCF ALT header line.
     *
     * @return the attributes for this VCF ALT header line
     */
    public ListMultimap<String, String> getAttributes() {
        return attributes;
    }

    @Override
    public String toString() {
        StringBuilder sb = new StringBuilder();
        sb.append("##ALT=<ID=");
        sb.append(id);
        sb.append(",Description=\"");
        sb.append(description);
        sb.append("\"");
        for (Map.Entry<String, String> entry : attributes.entries()) {
            sb.append(",");
            sb.append(entry.getKey());
            sb.append("=\"");
            sb.append(entry.getValue());
            sb.append("\"");
        }
        sb.append(">");
        return sb.toString();
    }

    /**
     * Parse the specified value into a VCF ALT header line.
     *
     * @param value value, must not be null
     * @return the specified value parsed into a VCF ALT header line
     */
    public static VcfAltHeaderLine valueOf(final String value) {
        checkNotNull(value);
        checkArgument(value.startsWith("##ALT="));
        ListMultimap<String, String> entries = VcfHeaderLineParser.parseEntries(value.replace("##ALT=", ""));

        String id = VcfHeaderLineParser.requiredString("ID", entries);
        String description = VcfHeaderLineParser.requiredString("Description", entries);

        ListMultimap<String, String> attributes = ArrayListMultimap.create(entries);
        attributes.removeAll("ID");
        attributes.removeAll("Description");

        return new VcfAltHeaderLine(id, description, attributes);
    }
}