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1 /*****************************************************************************
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2 chromsweepBed.h
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3
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4 (c) 2009 - Aaron Quinlan
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licenced under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #ifndef CHROMSWEEP_H
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13 #define CHROMSWEEP_H
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14
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15 #include "bedFile.h"
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16 #include <vector>
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17 #include <queue>
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18 #include <iostream>
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19 #include <fstream>
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20 #include <stdlib.h>
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21 using namespace std;
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22
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23
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24
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25 class ChromSweep {
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26
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27 // public interface.
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28 public:
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29
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30 // A is the query and B is the database
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31
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32 // constructor using existing BedFile pointers
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33 ChromSweep(BedFile *bedA, BedFile *bedB, bool sameStrand = false, bool diffStrand = false);
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34
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35 // constructor using filenames
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36 ChromSweep(string &bedAFile, string &bedBFile);
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37
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38 // destructor
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39 ~ChromSweep(void);
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40
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41 // loads next (a pair) with the current query and it's overlaps
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42 // next.first is the current query interval
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43 // next.second is a vector of the current query's hits.
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44 // returns true if overlap
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45 bool Next(pair<BED, vector<BED> > &next);
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46
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47 // Usage:
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48 // ChromSweep sweep = ChromSweep(_bedA, _bedB);
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49 // pair<BED, vector<BED> > hit_set;
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50 // while (sweep.Next(hit_set))
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51 // {
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52 // // magic happens here!
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53 // processHits(hit_set.first, hit_set.second);
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54 // }
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55
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56 // private variables.
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57 private:
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58
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59 // instances of a bed file class.
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60 BedFile *_bedA, *_bedB;
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61 // do we care about strandedness.
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62 bool _sameStrand, _diffStrand;
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63 // a cache of still active features from the database file
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64 vector<BED> _cache;
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65 // the set of hits in the database for the current query
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66 vector<BED> _hits;
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67 // a queue from which we retrieve overlap results. used by Next()
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68 queue< pair<BED, vector<BED> > > _results;
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69 BED _nullBed;
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70 // an empty BED vector for returning no hits for a given query
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71 vector<BED> _no_hits;
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72 // the current query and db features.
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73 BED _curr_qy, _curr_db;
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74 // a cache of the current chrom from the query. used to handle chrom changes.
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75 string _curr_chrom;
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76 // the current line status in the database and query files
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77 BedLineStatus _qy_status, _db_status;
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78 // the current line numbers in the database and query files
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79 int _qy_lineNum, _db_lineNum;
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80
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81 // private methods.
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82 private:
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83
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84 void ScanCache();
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85 bool ChromChange();
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86 bool IsValidHit(const BED &query, const BED &db);
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87 };
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88
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89 #endif /* CHROMSWEEP_H */
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