multovl  1.3
Multiple overlaps of genomic regions
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pipeline.hh
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2 License for the MULTOVL multiple genomic overlap tools
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5 Campus Science Support Facilities GmbH (CSF),
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35 #ifndef MULTOVL_PIPELINE_HEADER
36 #define MULTOVL_PIPELINE_HEADER
37 
38 // == Header pipeline.hh ==
39 
40 // -- Own headers --
41 
42 #include "basepipeline.hh"
43 #include "multioverlap.hh"
44 
45 // -- Boost headers --
46 
47 // -- Standard headers --
48 
49 #include <map>
50 #include <string>
51 
52 namespace multovl {
53 
54 // -- Classes --
55 
57 class Pipeline: public BasePipeline
58 {
59 
60 protected:
61 
63  typedef std::map<std::string, MultiOverlap> chrom_multovl_map;
64 
68  virtual
69  unsigned int detect_overlaps();
70 
72  const chrom_multovl_map& cmovl() const { return _cmovl; }
73 
75  chrom_multovl_map& cmovl() { return _cmovl; }
76 
77 private:
78 
79  chrom_multovl_map _cmovl;
80 };
81 
82 } // namespace multovl
83 
84 #endif // MULTOVL_PIPELINE_HEADER
std::map< std::string, MultiOverlap > chrom_multovl_map
There is one MultiOverlap object for each chromosome.
Definition: pipeline.hh:63
Abstract class that provides a framework for detecting multiple overlaps using the MultiOverlap class...
Definition: pipeline.hh:57
virtual unsigned int detect_overlaps()
Multiple genomic region overlaps.
const chrom_multovl_map & cmovl() const
Definition: pipeline.hh:72
Definition: basepipeline.hh:69
chrom_multovl_map & cmovl()
Definition: pipeline.hh:75