SearchParams.java

/*
 * Genoogle: Similar DNA Sequences Searching Engine and Tools. (http://genoogle.pih.bio.br)
 * Copyright (C) 2008,2009  Felipe Fernandes Albrecht (felipe.albrecht@gmail.com)
 *
 * For further information check the LICENSE file.
 */

package bio.pih.genoogle.search;

import java.lang.reflect.Field;
import java.util.Map;
import java.util.Map.Entry;

import org.apache.log4j.Logger;

import bio.pih.genoogle.io.XMLConfigurationReader;
import bio.pih.genoogle.seq.SymbolList;

import com.google.common.collect.Maps;

/**
 * A class to hold parameters for a search. Now it is a bit useless, but when more parameters will
 * be added, they should be stored here.
 * 
 * @author albrecht
 */
public final class SearchParams {

	private static Logger logger = Logger.getLogger(SearchParams.class.getCanonicalName());

	private final SymbolList query;
	private final String databankName;
	private int maxSubSequencesDistance;
	private int sequencesExtendDropoff;
	private int minHspLength;
	private int maxHitsResults;
	private int maxThreadsIndexSearch;
	private int maxThreadsExtendAlign;
	private int minQuerySliceLength;
	private int querySplitQuantity;
	private int matchScore;
	private int mismatchScore;


	/**
	 * Default maximum distance between two sub-sequences of a sequence to be considered at same
	 * area.
	 */
	public static final int MAX_SUB_SEQUENCE_DISTANCE = XMLConfigurationReader.getMaxSubSequenceDistance();

	/**
	 * Drop off for sequences extension.
	 */
	public static final int SEQUENCES_EXTEND_DROPOFF = XMLConfigurationReader.getExtendDropoff();

	/**
	 * Minimum value for E-Value
	 */
	public static final int MIN_HSP_LENGTH = XMLConfigurationReader.getMinHspLength();

	/**
	 * Quantity of hits that will be processed and shown.
	 */
	public static final int MAX_HITS_RESULTS = XMLConfigurationReader.getMaxResults();

	public static final int MAX_THREADS_INDEX_SEARCH = XMLConfigurationReader.getMaxThreadsIndexSearch();
	
	public static final int MAX_THREADS_EXTEND_ALIGN = XMLConfigurationReader.getMaxThreadsExtendAlign();

	public static final int MIN_QUERY_SLICE_LENGTH = XMLConfigurationReader.getMinQuerySliceLength();

	public static final int QUERY_SPLIT_QUANTITY = XMLConfigurationReader.getQuerySplitQuantity();

	public static final int MATCH_SCORE = XMLConfigurationReader.getMatchScore();

	public static final int MISMATCH_SCORE = XMLConfigurationReader.getMismatchScore();

	public SearchParams(SymbolList query, String databankName) {
		this(query, databankName, MATCH_SCORE, MISMATCH_SCORE, 
				MAX_SUB_SEQUENCE_DISTANCE, SEQUENCES_EXTEND_DROPOFF, MIN_HSP_LENGTH, MAX_HITS_RESULTS, 
				MAX_THREADS_INDEX_SEARCH, MAX_THREADS_EXTEND_ALIGN, MIN_QUERY_SLICE_LENGTH, QUERY_SPLIT_QUANTITY);
	}

	public enum Parameter {
		MAX_SUB_SEQUENCE_DISTANCE("MaxSubSequenceDistance", Integer.class),
		SEQUENCES_EXTEND_DROPOFF("SequencesExtendDropoff", Integer.class),
		MIN_HSP_LENGTH("MinHspLength", Integer.class),
		MAX_HITS_RESULTS("MaxHitsResults", Integer.class),
		MAX_THREADS_INDEX_SEARCH("MaxThreadsIndexSearch", Integer.class),
		MAX_THREADS_EXTEND_ALIGN("MaxThreadsExtendAlign", Integer.class),
		MIN_QUERY_SLICE_LENGTH("MinQuerySliceLength", Integer.class),
		QUERY_SPLIT_QUANTITY("QuerySplitQuantity", Integer.class),
		MATCH_SCORE("MatchScore", Integer.class),
		MISMATCH_SCORE("MismatchScore", Integer.class);

		private String name;
		private Class<?> clazz;

		Parameter(String name, Class<?> clazz) {
			this.name = name;
			this.clazz = clazz;
		}

		public String getName() {
			return name;
		}

		public Class<?> getClazz() {
			return clazz;
		}

		public static Parameter getParameterByName(String name) {
			for (Parameter param : values()) {
				if (param.getName().equals(name) || param.name().equals(name)) {
					return param;
				}
			}
			return null;
		}

		public Object convertValue(String value) {
			if (this.getClazz().equals(Integer.class)) {
				return new Integer(value);
			} else if (this.getClazz().equals(Double.class)) {
				return new Double(value);
			}
			return null;
		}
	}

	public SearchParams(SymbolList query, String databankName, Map<Parameter, Object> parameters) {
		this(query, databankName, MATCH_SCORE, MISMATCH_SCORE, MAX_SUB_SEQUENCE_DISTANCE, SEQUENCES_EXTEND_DROPOFF, MIN_HSP_LENGTH, MAX_HITS_RESULTS, MAX_THREADS_INDEX_SEARCH, MAX_THREADS_EXTEND_ALIGN, MIN_QUERY_SLICE_LENGTH, QUERY_SPLIT_QUANTITY);

		for (Entry<Parameter, Object> paramEntry : parameters.entrySet()) {
			Object v = paramEntry.getValue();
			switch (paramEntry.getKey()) {
			case MAX_SUB_SEQUENCE_DISTANCE:
				this.maxSubSequencesDistance = (Integer) v;
				break;
			case SEQUENCES_EXTEND_DROPOFF:
				this.sequencesExtendDropoff = (Integer) v;
				break;
			case MIN_HSP_LENGTH:
				this.minHspLength = (Integer) v;
				break;
			case MAX_HITS_RESULTS:
				this.maxHitsResults = (Integer) v;
				break;
			case MAX_THREADS_INDEX_SEARCH:
				this.maxThreadsIndexSearch = (Integer) v;
				break;
			case MAX_THREADS_EXTEND_ALIGN:
				this.maxThreadsExtendAlign = (Integer) v;
				break;
			case MIN_QUERY_SLICE_LENGTH:
				this.minQuerySliceLength = (Integer) v;
				break;
			case QUERY_SPLIT_QUANTITY:
				this.querySplitQuantity = (Integer) v;
				break;
			case MATCH_SCORE:
				this.matchScore = (Integer) v;
				break;
			case MISMATCH_SCORE:
				this.mismatchScore = (Integer) v;
				break;
			}
		}
	}

	public SearchParams(SymbolList query, String databankName, int matchScore, int mismatchScore,
			int maxSubSequencesDistance, int sequencesExtendDropoff, int minHspLength, int maxHitsResults,
			int maxThreadsIndexSearch, int maxThreadsExtendAlign, int minQuerySliceLength, int querySplitQuantity) {
		this.query = query;
		this.databankName = databankName;
		this.matchScore = matchScore;
		this.mismatchScore = mismatchScore;
		this.maxSubSequencesDistance = maxSubSequencesDistance;
		this.sequencesExtendDropoff = sequencesExtendDropoff;
		this.minHspLength = minHspLength;
		this.maxHitsResults = maxHitsResults;
		this.maxThreadsIndexSearch = maxThreadsIndexSearch;
		this.maxThreadsExtendAlign = maxThreadsExtendAlign;
		this.minQuerySliceLength = minQuerySliceLength;
		this.querySplitQuantity = querySplitQuantity;
	}

	/**
	 * @return the query of the search
	 */
	public SymbolList getQuery() {
		return query;
	}

	/**
	 * @return the data bank where the search will be performed
	 */
	public String getDatabank() {
		return databankName;
	}

	/**
	 * @return value when has a match between two bases.
	 */
	public int getMatchScore() {
		return matchScore;
	}

	/**
	 * @return value when has a mismatch between two bases.
	 */
	public int getMismatchScore() {
		return mismatchScore;
	}

	/**
	 * @return maximum distance between two sub-sequences to be considered at same area.
	 */
	public int getMaxSubSequencesDistance() {
		return maxSubSequencesDistance;
	}

	/**
	 * @return drop off for sequences extension.
	 */
	public int getSequencesExtendDropoff() {
		return sequencesExtendDropoff;
	}

	/**
	 * @return the minimum length of a HSP to be keep to the next search phase.
	 */
	public int getMinHspLength() {
		return minHspLength;
	}

	/**
	 * @return the quantity of hits that will be processed and shown.
	 */
	public int getMaxHitsResults() {
		return maxHitsResults;
	}

	/**
	 * @return quantity of threads which will be used to perform the index search of the input query
	 *         sub-sequences.
	 */
	public int getMaxThreadsIndexSearch() {
		return maxThreadsIndexSearch;
	}
	
	/**
	 * @return quantity of threads which will be used to extend and align the HSPs.
	 */
	public int getMaxThreadsExtendAlign() {
		return maxThreadsExtendAlign;
	}

	/**
	 * @return quantity of slices which the input query will be divided.
	 */
	public int getQuerySplitQuantity() {
		return querySplitQuantity;
	}

	/**
	 * @return the minimum slice length when the input query is divided.
	 */
	public int getMinQuerySliceLength() {
		return minQuerySliceLength;
	}

	/**
	 * Get a {@link Map} with all parameters and their values.
	 * 
	 * @return {@link Map} indexed by {@link Parameter} containing the parameters and their values.
	 */
	public static Map<Parameter, Object> getSearchParamsMap() {
		Map<Parameter, Object> searchParameters = Maps.newHashMap();
		try {
			for (SearchParams.Parameter param : SearchParams.Parameter.values()) {
				Field field;
				field = SearchParams.class.getDeclaredField(param.toString());
				int value = field.getInt(SearchParams.class);
				searchParameters.put(param, value);
			}
		} catch (Exception e) {
			logger.fatal("Fatal error while loading the search parameters.", e);
		} 
		return searchParameters;
	}

}