package org.seqcode.deepseq;

import org.seqcode.genome.Genome;

import org.seqcode.genome.location.ScoredStrandedPoint;

import org.seqcode.genome.location.ScoredStrandedRegion;

/**

* StrandedBaseCount represents the sum of hit weights at a stranded base position in the genome.

* The same class was called StrandedBase previously (renaming to reduce confusion)

* Coordinate is the 5' end of the read.

* We do not store chromomosome info here because this class is always used

* in the context of a chromosome or a region, no need to differentiate.

* It records the number of reads mapped to this base position.

*

* @author yguo

*

*/

public class StrandedBaseCount implements Comparable<StrandedBaseCount>{

private char strand;

private int coordinate;

private float count;

public StrandedBaseCount(char strand, int coord, float count){

this.setStrand(strand);

this.setCoordinate(coord);

this.setCount(count);

}

public void setStrand(char strand) {

this.strand = strand;

}

public char getStrand() {

return strand;

}

public void setCoordinate(int coordinate) {

this.coordinate = coordinate;

}

public int getCoordinate() {

return coordinate;

}

public void setCount(float count) {

this.count = count;

}

public float getCount() {

return count;

}

// sort according to coordinate, considering strand

public int compareTo(StrandedBaseCount b) {

double diff = coordinate-b.coordinate;

return diff==0?

(strand==b.strand?0:strand=='+'?1:-1): // same coord, compare strand

(diff<0?-1:1); // diff coord

}

public String toString(){

return coordinate+" "+strand+" "+count;

}

//Makes this into a regular Region-derived object

public ScoredStrandedPoint toScoredStrandedPoint(Genome g, String chr){

return new ScoredStrandedPoint(g, chr, coordinate, count, strand);

}

//Makes the pseudo extended read into a regular Region-derived object

public ScoredStrandedRegion expandToScoredStrandedRegion(Genome g, String chr, int upstreamext, int downstreamext){

return (new ScoredStrandedPoint(g, chr, coordinate, count, strand).expand(upstreamext, downstreamext));

}

}