/*
 *                    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.core.search.io;

import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import org.biojava.nbio.core.sequence.template.Sequence;

/**
 * This class models a search result.
 * You will find one of this for every query sequence specified in the run.
 *
 * Designed by Paolo Pavan.
 * You may want to find my contacts on Github and LinkedIn for code info
 * or discuss major changes.
 * https://github.com/paolopavan
 *
 * @author Paolo Pavan
 */

public abstract class Result implements Iterable<Hit>{
	private String program;
	private String version;
	private String reference;
	private String dbFile;

	private HashMap<String,String> programSpecificParameters;

	private int iterationNumber;
	private String queryID;
	private String queryDef;
	private int queryLength;
	private Sequence querySequence;
	private List<Hit> hits;
	private int hitCounter = -1;

	public Result(String program, String version, String reference, String dbFile, HashMap<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
		this.program = program;
		this.version = version;
		this.reference = reference;
		this.dbFile = dbFile;
		this.programSpecificParameters = programSpecificParameters;
		this.iterationNumber = iterationNumber;
		this.queryID = queryID;
		this.queryDef = queryDef;
		this.queryLength = queryLength;
		this.hits = hits;
		this.querySequence = querySequence;
	}

	@Override
	public int hashCode() {
		int hash = 7;
		hash = 29 * hash + (this.queryID != null ? this.queryID.hashCode() : 0);
		hash = 29 * hash + (this.queryDef != null ? this.queryDef.hashCode() : 0);
		hash = 29 * hash + (this.hits != null ? this.hits.hashCode() : 0);
		return hash;
	}
	/**
	 * Experimental.
	 * Wants to return an hashcode designed to allow conceptual comparisons of search results.
	 * Wants to implement conceptual comparisons of search results.
	 * Fields unrelated to search are deliberately not considered.
	 * @return
	 */
	@Override
	public boolean equals(Object obj) {
		if (obj == null) {
			return false;
		}
		if (getClass() != obj.getClass()) {
			return false;
		}
		final Result other = (Result) obj;
		if ((this.queryID == null) ? (other.queryID != null) : !this.queryID.equals(other.queryID)) {
			return false;
		}
		if ((this.queryDef == null) ? (other.queryDef != null) : !this.queryDef.equals(other.queryDef)) {
			return false;
		}
		if (this.hits != other.hits && (this.hits == null || !this.hits.equals(other.hits))) {
			return false;
		}
		return true;
	}

	public int getIterationNumber() {
		return iterationNumber;
	}

	public String getQueryID() {
		return queryID;
	}

	public String getQueryDef() {
		return queryDef;
	}

	public int getQueryLength() {
		return queryLength;
	}

	public int getHitCounter() {
		return hitCounter;
	}

	public String getProgram() {
		return program;
	}

	public String getVersion() {
		return version;
	}

	public String getReference() {
		return reference;
	}

	public String getDbFile() {
		return dbFile;
	}

	public Set<String> getProgramSpecificParametersList() {
		return programSpecificParameters.keySet();
	}

	public String getProgramSpecificParameter(String key) {
		return programSpecificParameters.get(key);
	}
	/**
	 * returns the reference to the original and whole sequence used to query the database.
	 * Available only if the ResultFactory implements setQueryReferences and
	 * it was used before the parsing with SearchIO
	 * @return Sequence object
	 */
	public Sequence getQuerySequence() {
		return querySequence;
	}

	@Override
	public Iterator<Hit> iterator() {
		return new Iterator<Hit>() {
			int currentResult = 0;
			@Override
			public boolean hasNext() {
				return currentResult < hits.size();
			}

			@Override
			public Hit next() {
				return hits.get(currentResult++);
			}

			@Override
			public void remove() {
				throw new UnsupportedOperationException("The remove operation is not supported by this iterator");
			}
		};
	}
}
