multovl  1.3
Multiple overlaps of genomic regions
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multovl::ClassicOpts Class Reference

Option handling for the file-based multovl tools. More...

#include "classicopts.hh"

Inheritance diagram for multovl::ClassicOpts:
multovl::MultovlOptbase multovl::Polite

Public Member Functions

const std::string & source () const
 
const std::string & outformat () const
 
const std::string & save_to () const
 
const std::string & load_from () const
 
std::vector< std::string > input_files () const
 
virtual std::string param_str () const
 
virtual std::ostream & print_help (std::ostream &out) const
 
- Public Member Functions inherited from multovl::MultovlOptbase
unsigned int minmult () const
 
unsigned int maxmult () const
 
bool solitary () const
 
bool nointrack () const
 
unsigned int ovlen () const
 
bool uniregion () const
 
bool timing () const
 
virtual std::ostream & print_version (std::ostream &out) const
 
- Public Member Functions inherited from multovl::Polite
void process_commandline (int argc, char *argv[])
 
bool parse_check (int argc, char *argv[])
 
std::vector< std::string > pos_opts () const
 
bool error_status () const
 
std::string error_messages () const
 
bool version_needed () const
 
bool help_needed () const
 

Protected Member Functions

virtual bool check_variables ()
 
- Protected Member Functions inherited from multovl::MultovlOptbase
virtual std::ostream & version_info (std::ostream &out) const
 
- Protected Member Functions inherited from multovl::Polite
 Polite (const std::string &descr="Options")
 
template<typename Opttype >
void add_option (const std::string &name, Opttype *optvarp, const Opttype &defval, const std::string &descr, const char nm= '\0')
 
void add_bool_switch (const std::string &name, bool *varp, const std::string &descr, const char nm= '\0')
 
template<typename Opttype >
void add_mandatory_option (const std::string &name, const std::string &descr, const char nm= '\0')
 
bool perform_parsing (int argc, char *argv[])
 
bool option_seen (const std::string &optnm) const
 
template<typename Opttype >
Opttype fetch_value (const std::string &optnm) const
 
void add_error (const std::string &msg)
 
void error_reset ()
 Reset the error status to "no error".
 

Detailed Description

Option handling for the file-based multovl tools.

Member Function Documentation

virtual bool multovl::ClassicOpts::check_variables ( )
protectedvirtual

Derived classes must override this method so that first an appropriate base class version is invoked to process the base class' commandline variables and then additional processing must be done on the derived class' variables if /true/ was returned, like this:-

bool DerivedOpts::check_variables()
{
        bool ok = BaseOpts::check_variables();  // don't invoke Polite::check_variables() !
        if (ok) {
                // e.g. check some variables here
                if (option_seen("opt") > 0)
                {
                        int opt = fetch_value<int>("opt");
                        if (opt < 1) opt = 1;
                        // ...
                        ok = true;
                }
                else
                {
                    add_error("opt must be present");
                    ok = false;
  }
        }
        return ok;
}

Reimplemented from multovl::MultovlOptbase.

std::vector<std::string> multovl::ClassicOpts::input_files ( ) const
inline
Returns
a vector of input file names provided as positional arguments on the command line.
const std::string& multovl::ClassicOpts::load_from ( ) const
inline
Returns
the archive file name to load (deserialize) the status of the program from. The file is to be created by a previous saving operation. If this option is chosen, then no track input files are read. Empty string by default, meaning tracks are read from files given as positional arguments on the command line.
const std::string& multovl::ClassicOpts::outformat ( ) const
inline
Returns
the desired output format. May be {BED,GFF}, case-insensitive, default GFF
virtual std::ostream& multovl::ClassicOpts::print_help ( std::ostream &  out) const
virtual

Prints help, using the facilities provided by boost::program_options

Parameters
outthis is the stream the help text is printed to.
Returns
/out/ is returned here

Reimplemented from multovl::Polite.

const std::string& multovl::ClassicOpts::save_to ( ) const
inline
Returns
the archive file name to save (serialize) the status of the program to. Empty string by default meaning no status is to be saved.
const std::string& multovl::ClassicOpts::source ( ) const
inline
Returns
the definition for the "source" column in the GFF output.

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