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/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.genome.parsers.gff;

import java.util.HashMap;

/**
 * A feature on a sequence (for example, an exon or a gene), defined by a location
 * and a set of attributes encoded as key/value pairs.
 *
 * @author Hanno Hinsch
 */
public interface FeatureI
{

	/**
	 * Get the location of the feature.
	 *
	 * @return The location.
	 */
	public Location location();

	/**
	 * Get the group id of the feature. The group id is defined in the GFF1
	 * format; features that share a common group id are presumed to be part
	 * of some logical group. For example, a gene might be represented by several
	 * exon features that all share the same group id.
	 *


	 * The exact meaning of a feature's group id, or even its existence, is not guaranteed
	 * by this interface. An understanding of a particular file's data format is necessary to properly
	 * interpret the group id.
	 *
	 * @return The group id. This may be an empty string.
	 */
	public String group();

	/**
	 * Get the feature type, for example, "exon", "CDS", etc.
	 *
	 * @return The type.
	 */
	public String type();

	/**
	 * Get the sequence name.
	 *
	 * @return Sequence name.
	 */
	public String seqname();

	/**
	 * Get the attribute value for this key.
	 *
	 * @param key The key.
	 * @return The corresponding value. Null if the key has no value defined .
	 */
	public String getAttribute( String key );


	/**
	 * Check if the feature has a value defined for the specified key.
	 *
	 * @param key The key.
	 * @return True if a value is defined for this key.
	 */
	public boolean hasAttribute( String key );

	/**
	 * Check if the feature attributes include the specified key/value pair.
	 *
	 * @param key The key.
	 * @param value The value.
	 * @return True if the feature's value for this key matches the specified value.
	 */
	public boolean hasAttribute( String key, String value );

	/**
	 * A string representation of the feature.
	 *
	 * @return The string.
	 */
	@Override
	public String toString();

	/**
	 * Get HashMap of user data.
	 *
	 * @return The user HashMap.
	 */
	public  HashMap userData();

	public HashMap getAttributes();

}