// Path: src/external/AlignmentToolInterface.java
// public enum AlignmentOperation
// {
// 	PREPROCESSING,
// 	ALIGNMENT,
// 	POSTPROCESSING,
// 	TOTAL,
// }


import java.util.Map;
import java.util.TreeMap;
import external.AlignmentToolInterface.AlignmentOperation;
/**
 * 
 */
package external;


public class AlignmentResults
{
	public AlignmentResults()
	{
		positives = new TreeMap<Integer, Integer>();
		negatives = new TreeMap<Integer, Integer>();
	}

	/**
	 * Quality values of alignments that are at the correct location in the
	 * genome
	 */
	public Map<Integer, Integer> positives;
	/**
	 * Quality values of alignments that are at an incorrect location in the
	 * genome.
	 */
	public Map<Integer, Integer> negatives;
	/**
	 * Number of fragments that were missing from the tool's output. Always
	 * added to false negative counts.
	 */
	public int missingFragments = 0;
	/**
	 * Stores time for each operation
	 */
// Path: src/external/AlignmentToolInterface.java
// public enum AlignmentOperation
// {
// 	PREPROCESSING,
// 	ALIGNMENT,
// 	POSTPROCESSING,
// 	TOTAL,
// }


// Path: src/external/AlignmentResults.java
import java.util.Map;
import java.util.TreeMap;
import external.AlignmentToolInterface.AlignmentOperation;

/**
 * 
 */
package external;


public class AlignmentResults
{
	public AlignmentResults()
	{
		positives = new TreeMap<Integer, Integer>();
		negatives = new TreeMap<Integer, Integer>();
	}

	/**
	 * Quality values of alignments that are at the correct location in the
	 * genome
	 */
	public Map<Integer, Integer> positives;
	/**
	 * Quality values of alignments that are at an incorrect location in the
	 * genome.
	 */
	public Map<Integer, Integer> negatives;
	/**
	 * Number of fragments that were missing from the tool's output. Always
	 * added to false negative counts.
	 */
	public int missingFragments = 0;
	/**
	 * Stores time for each operation
	 */
	public Map<AlignmentOperation, Long> timeMap;