import java.util.HashMap;


public class PARCLIPread {
	private String _chromosome;
	private char _strand;
	private long _startPosition;
	private long _endPosition;
	private boolean _unique = true;
	private byte _numberOfMismatches;
    //	private HashMap<Byte, Integer> _conversionMap;
    private HashMap<Byte, Integer> _conversionMap; //MR02012018
	private int _readCount;
	
	public PARCLIPread(String chromosome, char strand, long startPosition, long endPosition, int readCount, byte numberOfMismatches, HashMap<Byte, Integer> conversionMap ) {
		_chromosome = chromosome;
		_strand = strand;
		_startPosition = startPosition;
		_endPosition = endPosition;
		_readCount = readCount;
		_numberOfMismatches = numberOfMismatches;
		_conversionMap = conversionMap;
		_unique = true;
	}
	public String getChromosome() {
		return _chromosome;
	}
	public char getStrand() {
		return _strand;
	}
	public long getStartPosition() {
		return _startPosition;
	}
	public long getEndPosition() {
		return _endPosition;
	}
	public int getLength() {
		return (int) (_endPosition - _startPosition + 1);
	}
	public HashMap<Byte, Integer> getConversionMap() {
		return _conversionMap;
	}
	public boolean isUnique() {
		return _unique;
	}
	public void setUnique( boolean unique ) {
		_unique = unique;
	}
	public byte getNumberOfMismatches() {
		return _numberOfMismatches;
	}
	public int getReadCount() {
		return _readCount;
	}
}