multovl
1.3
Multiple overlaps of genomic regions
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Option handling for the file-based multovl tools. More...
#include "probopts.hh"
Public Types | |
typedef std::vector< std::string > | filenames_t |
Public Member Functions | |
ProbOpts () | |
Initialize. | |
const std::string & | free_file () const |
const filenames_t & | fixed_files () const |
unsigned int | fixed_filecnt () const |
bool | file_is_fixed (const std::string &filename) const |
filenames_t | shuffle_files () const |
unsigned int | reshufflings () const |
unsigned int | random_seed () const |
bool | progress () const |
virtual std::string | param_str () const |
virtual std::ostream & | print_help (std::ostream &out) const |
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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 |
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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 () |
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virtual std::ostream & | version_info (std::ostream &out) const |
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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". | |
Option handling for the file-based multovl tools.
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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.
Reimplemented in multovl::prob::ParProbOpts.
bool multovl::prob::ProbOpts::file_is_fixed | ( | const std::string & | filename | ) | const |
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Convenience method to see whether fixed files have been defined at all.
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Prints help, using the facilities provided by boost::program_options
out | this is the stream the help text is printed to. |
Reimplemented from multovl::Polite.
Reimplemented in multovl::prob::ParProbOpts.
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