Option handling for the file-based multovl tools.
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#include "classicopts.hh"
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const std::string & | source () const |
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const std::string & | outformat () const |
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const std::string & | save_to () const |
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const std::string & | load_from () const |
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std::vector< std::string > | input_files () const |
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virtual std::string | param_str () const |
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virtual std::ostream & | print_help (std::ostream &out) const |
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unsigned int | minmult () const |
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unsigned int | maxmult () const |
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bool | solitary () const |
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bool | nointrack () const |
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unsigned int | ovlen () const |
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bool | uniregion () const |
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bool | timing () const |
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virtual std::ostream & | print_version (std::ostream &out) const |
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void | process_commandline (int argc, char *argv[]) |
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bool | parse_check (int argc, char *argv[]) |
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std::vector< std::string > | pos_opts () const |
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bool | error_status () const |
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std::string | error_messages () const |
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bool | version_needed () const |
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bool | help_needed () const |
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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") |
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template<typename Opttype > |
void | add_option (const std::string &name, Opttype *optvarp, const Opttype &defval, const std::string &descr, const char nm= '\0') |
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void | add_bool_switch (const std::string &name, bool *varp, const std::string &descr, const char nm= '\0') |
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template<typename Opttype > |
void | add_mandatory_option (const std::string &name, const std::string &descr, const char nm= '\0') |
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bool | perform_parsing (int argc, char *argv[]) |
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bool | option_seen (const std::string &optnm) const |
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template<typename Opttype > |
Opttype | fetch_value (const std::string &optnm) const |
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void | add_error (const std::string &msg) |
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void | error_reset () |
| Reset the error status to "no error".
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Option handling for the file-based multovl tools.
virtual bool multovl::ClassicOpts::check_variables |
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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.
std::vector<std::string> multovl::ClassicOpts::input_files |
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const |
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inline |
- Returns
- a vector of input file names provided as positional arguments on the command line.
const std::string& multovl::ClassicOpts::load_from |
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const |
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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 |
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const |
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inline |
- Returns
- the desired output format. May be {BED,GFF}, case-insensitive, default GFF
virtual std::ostream& multovl::ClassicOpts::print_help |
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std::ostream & |
out | ) |
const |
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virtual |
Prints help, using the facilities provided by boost::program_options
- Parameters
-
out | this 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 |
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const |
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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 |
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const |
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inline |
- Returns
- the definition for the "source" column in the GFF output.
The documentation for this class was generated from the following file: