multovl  1.3
Multiple overlaps of genomic regions
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Protected Types | Protected Member Functions | List of all members
multovl::Pipeline Class Reference

Abstract class that provides a framework for detecting multiple overlaps using the MultiOverlap class. More...

#include "pipeline.hh"

Inheritance diagram for multovl::Pipeline:
multovl::BasePipeline multovl::ClassicPipeline

Protected Types

typedef std::map< std::string,
MultiOverlap
chrom_multovl_map
 There is one MultiOverlap object for each chromosome.
 
- Protected Types inherited from multovl::BasePipeline
typedef std::vector< Inputinput_seq_t
 

Protected Member Functions

virtual unsigned int detect_overlaps ()
 
const chrom_multovl_mapcmovl () const
 
chrom_multovl_mapcmovl ()
 
- Protected Member Functions inherited from multovl::BasePipeline
virtual unsigned int read_input ()=0
 
virtual bool write_output ()=0
 
bool set_optpimpl (MultovlOptbase *optp)
 
MultovlOptbaseopt_pimpl ()
 
virtual MultovlOptbaseopt_ptr ()=0
 
const input_seq_t & inputs () const
 
input_seq_t & inputs ()
 
void add_error (const std::string &prefix, const std::string &what)
 Adds an error message.
 
void add_all_errors (const Errors &other)
 
void add_warning (const std::string &prefix, const std::string &what)
 Adds a warning message.
 
void clear_errors ()
 Clears the errors.
 

Additional Inherited Members

- Public Member Functions inherited from multovl::BasePipeline
 BasePipeline ()
 Default init of a BasePipeline object.
 
bool run ()
 
const Errorserrors () const
 

Detailed Description

Abstract class that provides a framework for detecting multiple overlaps using the MultiOverlap class.

Member Function Documentation

const chrom_multovl_map& multovl::Pipeline::cmovl ( ) const
inlineprotected
Returns
const access to the chromosome=>multiple overlap map
chrom_multovl_map& multovl::Pipeline::cmovl ( )
inlineprotected
Returns
non-const access to the chromosome=>multiple overlap map
virtual unsigned int multovl::Pipeline::detect_overlaps ( )
protectedvirtual

Detects the overlaps. The default implementation provided here uses 1 CPU core.

Returns
the total number of overlaps found, including solitary regions.

Implements multovl::BasePipeline.


The documentation for this class was generated from the following file: