GPSPeak.java

package org.seqcode.gsebricks.verbs.chipseq;

import org.seqcode.genome.Genome;
import org.seqcode.genome.location.Point;

public class GPSPeak extends Point{
	double strength;
	double controlStrength;
	double expectedStrength;
	double qvalue;
	double pvalue;
	double pois_pvalue;
	double IPvsEMP;
	double IPvsCTR;
	private boolean jointEvent;		// 1 for joint event, 0 for unary, etc
	String nearestGene;
	int distance;
	Point EM_position;
	String kmer;
	int kmerGroupCount;
	char kmerStrand;
	double kmerStrength;
	String boundSequence;
	public String getKmer() {return kmer;}
	public void setKmer(String km) {kmer=km;}
	public int getKmerGroupCount() {	return kmerGroupCount;}
	public double getKmerStrength() {return kmerStrength;}
	public char getKmerStrand() {return kmerStrand;}
	public String getBoundSequence() {return boundSequence;}
	public void setBoundSequence(String bs) {boundSequence=bs;}

	public GPSPeak(Genome g, String chr, int pos, double ipStrength, 
			double controlStrength, double qvalue, double pvalue, double IPvsEMP, 
			int joint, String nearestGene, int distance){
		super(g, chr.replaceFirst("chr", ""), pos);
		this.strength = ipStrength;
		this.controlStrength = controlStrength;
		this.qvalue = qvalue;
		this.pvalue = pvalue;
		this.IPvsEMP = IPvsEMP;
		this.IPvsCTR = 0;
		this.jointEvent = joint==1;
		this.nearestGene = nearestGene;
		this.distance = distance;
		this.EM_position = this;
	}

	public GPSPeak(Genome g, String chr, int pos, double ipStrength, 
			double controlStrength, double qvalue, double pvalue, double IPvsEMP, double IPvsCTR, 
			int joint, String nearestGene, int distance){
		super(g, chr.replaceFirst("chr", ""), pos);
		this.strength = ipStrength;
		this.controlStrength = controlStrength;
		this.qvalue = qvalue;
		this.pvalue = pvalue;
		this.IPvsEMP = IPvsEMP;
		this.IPvsCTR = IPvsCTR;
		this.jointEvent = joint==1;
		this.nearestGene = nearestGene;
		this.distance = distance;
		this.EM_position = this;
	}
	
	public GPSPeak(Genome g, String chr, int pos, double ipStrength, 
			double ctrlStrength, double qvalue, double pvalue, double IPvsEMP){
		super(g, chr.replaceFirst("chr", ""), pos);
		this.strength = ipStrength;
		this.controlStrength = ctrlStrength;
		this.qvalue = qvalue;
		this.pvalue = pvalue;
		this.IPvsEMP = IPvsEMP;
		this.IPvsCTR = 0;
		this.EM_position = this;
	}
	// GPS output format 2010-11-10	
	// Position	   IP	Control	   Fold	Q_-lg10	P_-lg10	IPvsEMP	IPvsCTR
	public GPSPeak(Genome g, String chr, int pos, double ipStrength, 
			double ctrlStrength, double qvalue, double pvalue, double IPvsEMP, double IPvsCTR){
		super(g, chr.replaceFirst("chr", ""), pos);
		this.strength = ipStrength;
		this.controlStrength = ctrlStrength;
		this.qvalue = qvalue;
		this.pvalue = pvalue;
		this.IPvsEMP = IPvsEMP;
		this.IPvsCTR = IPvsCTR;
		this.EM_position = this;
	}
	// GPS output format 2011-01-30	
	// Position	     IP	Control	   Fold	Q_-lg10	P_-lg10	IPvsEMP	IPvsCTR	Kmer	KmerCount	KmerStrength	BoundSequence
	public GPSPeak(Genome g, String chr, int pos, double ipStrength, double ctrlStrength, 
			double qvalue, double pvalue, double IPvsEMP, double IPvsCTR, 
			String kmer, int kmerCount, double kmerStrength, String boundSequence){
		super(g, chr.replaceFirst("chr", ""), pos);
		this.strength = ipStrength;
		this.controlStrength = ctrlStrength;
		this.qvalue = qvalue;
		this.pvalue = pvalue;
		this.IPvsEMP = IPvsEMP;
		this.IPvsCTR = IPvsCTR;
		this.EM_position = this;
		this.kmer = kmer;
		this.kmerGroupCount = kmerCount;
		this.kmerStrength = kmerStrength;
		this.boundSequence = boundSequence;
	}
	// GPS output format 2011-07-25	
	// Position	     IP	Control	   Fold	Expectd	Q_-lg10	P_-lg10	P_poiss	IPvsEMP	IPvsCTR	
	public GPSPeak(Genome g, String chr, int pos, double ipStrength, double expectedStrength,
			double ctrlStrength, double qvalue, double pvalue, double pois_pvalue, double IPvsEMP, double IPvsCTR){
		super(g, chr.replaceFirst("chr", ""), pos);
		this.strength = ipStrength;
		this.controlStrength = ctrlStrength;
		this.expectedStrength = expectedStrength;
		this.qvalue = qvalue;
		this.pvalue = pvalue;
		this.pois_pvalue = pois_pvalue;
		this.IPvsEMP = IPvsEMP;
		this.IPvsCTR = IPvsCTR;
		this.EM_position = this;
	}
	// GPS output format 2011-07-25	
	// Position	     IP	Control	   Fold	Expectd	Q_-lg10	P_-lg10	P_poiss	IPvsEMP	IPvsCTR	Kmer	Count	Strength	BoundSequence	EnrichedHGP
	public GPSPeak(Genome g, String chr, int pos, double ipStrength, double ctrlStrength, double expectedStrength,
			double qvalue, double pvalue, double pois_pvalue, double IPvsEMP, double IPvsCTR, 
			String kmer, int kmerCount, char kmerStrand, String boundSequence){
		super(g, chr.replaceFirst("chr", ""), pos);
		this.strength = ipStrength;
		this.controlStrength = ctrlStrength;
		this.expectedStrength = expectedStrength;
		this.qvalue = qvalue;
		this.pvalue = pvalue;
		this.pois_pvalue = pois_pvalue;
		this.IPvsEMP = IPvsEMP;
		this.IPvsCTR = IPvsCTR;
		this.EM_position = this;
		this.kmer = kmer;
		this.kmerGroupCount = kmerCount;
		this.kmerStrand = kmerStrand;
		this.boundSequence = boundSequence;
	}
	
	public boolean isJointEvent() {
		return jointEvent;
	}

	public double getStrength() {
		return strength;
	}
	public double getControlStrength() {
		return controlStrength;
	}
	public Point getEM_position() {
		return EM_position;
	}
	public double getQvalue() {
		return qvalue;
	}
	public double getPvalue() {
		return pvalue;
	}
	public double getShape() {
		return IPvsEMP;
	}
	public double getIPvsCTR() {
		return IPvsCTR;
	}
	public void setStrength(double strength) {
		this.strength = strength;
	}
	public void setControlStrength(double controlStrength) {
		this.controlStrength = controlStrength;
	}
	public void setEM_position(Point em_position) {
		EM_position = em_position;
	}
	public void setQvalue(double qvalue) {
		this.qvalue = qvalue;
	}
	public void setShape(double shape) {
		this.IPvsEMP = shape;
	}

	public String getNearestGene() {
		return nearestGene;
	}
	public int getDistance() {
		return distance;
	}
	public void setNearestGene(String nearestGene) {
		this.nearestGene = nearestGene;
	}
	public void setDistance(int distance) {
		this.distance = distance;
	}
	public int compareByPValue(GPSPeak p) {
		double diff = getPvalue()- p.getPvalue();
		return	diff==0?0:(diff<0)?-1:1;	//p-value: ascending
	}
	public int compareByIPStrength(GPSPeak p) {
		double diff = getStrength()- p.getStrength();
		return	diff==0?0:(diff<0)?1:-1;	//ip strength: descending
	}
	public String toGPS(){
		return toString()+"\t"+strength+"\t"+controlStrength+"\t"+qvalue+"\t"+pvalue
		+"\t"+IPvsEMP+"\t"+jointEvent+"\t"+nearestGene+"\t"+distance;
	}
	
	public static String toGPS_Header(){
		return "GPS Event\tIP\tControl\tQ_-lg10\tP_-lg10\t"+
		"Shape\tJoint\tNearestGene\tDistance";
	}
	
	public String toGPS_short(){
		double fold = controlStrength==0 ? 9999:strength/controlStrength;
		String out = String.format("%s\t%.1f\t%.1f\t%.1f\t%.3f\t%.3f\t%.3f", 
				toString(), strength, controlStrength, fold, qvalue, pvalue, IPvsEMP);
		return out;
	}
	
	public static String toGPS_short_Header(){
		return "Event Location\tIP\tControl\tIP/Ctrl\tQ_-lg10\tP_-lg10\tShape";
	}
	
	public String toGPS_motifShort(){
	  return toString()+"\t"+nearestGene+"\t"+distance+"\t"+strength+"\t"
	  +controlStrength;//+"\t"+qvalue+"\t"+shape+"\t"+shapeZ;
	}
}