chromsweep.h

/*****************************************************************************
  chromsweepBed.h

  (c) 2009 - Aaron Quinlan
  Hall Laboratory
  Department of Biochemistry and Molecular Genetics
  University of Virginia
  aaronquinlan@gmail.com

  Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#ifndef CHROMSWEEP_H
#define CHROMSWEEP_H

#include "bedFile.h"
#include <vector>
#include <queue>
#include <iostream>
#include <fstream>
#include <stdlib.h>
using namespace std;



class ChromSweep {

// public interface.
public:

    // A is the query and B is the database
    
    // constructor using existing BedFile pointers
    ChromSweep(BedFile *bedA, BedFile *bedB, bool sameStrand = false, bool diffStrand = false);
    
    // constructor using filenames
    ChromSweep(string &bedAFile, string &bedBFile);
    
    // destructor
    ~ChromSweep(void);
    
    // loads next (a pair) with the current query and it's overlaps
    //   next.first is the current query interval
    //   next.second is a vector of the current query's hits.
    // returns true if overlap
    bool Next(pair<BED, vector<BED> > &next);
    
    // Usage:
    //     ChromSweep sweep = ChromSweep(_bedA, _bedB);
    //     pair<BED, vector<BED> > hit_set;
    //     while (sweep.Next(hit_set)) 
    //     {
    //        // magic happens here!
    //        processHits(hit_set.first, hit_set.second);
    //     }
    
// private variables.
private:

    // instances of a bed file class.
    BedFile *_bedA, *_bedB;
    // do we care about strandedness.
    bool _sameStrand, _diffStrand;
    // a cache of still active features from the database file
    vector<BED> _cache;
    // the set of hits in the database for the current query
    vector<BED> _hits;
    // a queue from which we retrieve overlap results.  used by Next()
    queue< pair<BED, vector<BED> > > _results;
    BED _nullBed;
    // an empty BED vector for returning no hits for a given query
    vector<BED> _no_hits;
    // the current query and db features.
    BED _curr_qy, _curr_db;
    // a cache of the current chrom from the query. used to handle chrom changes.
    string _curr_chrom;
    // the current line status in the database and query files
    BedLineStatus _qy_status, _db_status;
    // the current line numbers in the database and query files
    int _qy_lineNum, _db_lineNum;

// private methods.
private:
    
    void ScanCache();
    bool ChromChange();
    bool IsValidHit(const BED &query, const BED &db);
};

#endif /* CHROMSWEEP_H */