multovl  1.3
Multiple overlaps of genomic regions
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classicpipeline.hh
1 /* <LICENSE>
2 License for the MULTOVL multiple genomic overlap tools
3 
4 Copyright (c) 2007-2012, Dr Andras Aszodi,
5 Campus Science Support Facilities GmbH (CSF),
6 Dr-Bohr-Gasse 3, A-1030 Vienna, Austria, Europe.
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35 #ifndef MULTOVL_CLASSIC_PIPELINE_HEADER
36 #define MULTOVL_CLASSIC_PIPELINE_HEADER
37 
38 // == Header classicpipeline.hh ==
39 
40 // -- Own headers --
41 
42 #include "pipeline.hh"
43 #include "classicopts.hh"
44 
45 namespace multovl {
46 
47 // -- Classes --
48 
54 {
55 public:
56 
60  ClassicPipeline(int argc, char* argv[]);
61 
62  ~ClassicPipeline();
63 
64 protected:
65 
72  virtual
73  unsigned int read_input();
74 
75  // The default 1-CPU implementation is used.
76  // virtual
77  // unsigned int detect_overlaps();
78 
82  virtual
83  bool write_output();
84 
86  virtual
87  ClassicOpts* opt_ptr() { return dynamic_cast<ClassicOpts*>(opt_pimpl()); }
88 
89 private:
90 
91  unsigned int read_tracks();
92 
93  bool write_gff_output();
94  bool write_bed_output();
95  void write_comments();
96 };
97 
98 } // namespace multovl
99 
100 #endif // MULTOVL_CLASSIC_PIPELINE_HEADER
MultovlOptbase * opt_pimpl()
Definition: basepipeline.hh:132
Abstract class that provides a framework for detecting multiple overlaps using the MultiOverlap class...
Definition: pipeline.hh:57
Definition: classicpipeline.hh:53
virtual ClassicOpts * opt_ptr()
Definition: classicpipeline.hh:87
virtual unsigned int read_input()
virtual bool write_output()
ClassicPipeline(int argc, char *argv[])
Option handling for the file-based multovl tools.
Definition: classicopts.hh:56