1 #ifndef BALL_FORMAT_COMMANDLINEPARSER_H
2 #define BALL_FORMAT_COMMANDLINEPARSER_H
154 void printHelp(
const std::set<String>& parameter_names = std::set<String>(),
bool show_manual =
true);
168 void replaceEscapedCharacters_(
String& parameter_value);
172 void checkAndRegisterFlag(
String name,
String description,
bool default_gui_value =
false,
bool perform_check =
true,
bool hidden=
false);
174 void validateRegisteredFilesHaveFormats();
177 void checkParameterName(
const String& name,
const bool perform_check =
true);
180 std::set<String> reserved_params_;
183 std::list<std::pair<String, String> > escaped_chars_;
184 std::map<String, list<String> > parameter_map_;
185 std::map<String, ParamFile::ParameterDescription> registered_parameters_;
187 std::map<String, ParamFile::ParameterDescription> registered_flags_;
188 typedef std::map<String, ParamFile::ParameterDescription>::iterator MapIterator;
189 std::list<MapIterator> original_parameter_order_;
190 std::list<MapIterator> original_flag_order_;
191 Size max_parname_length_;
192 Size max_flagname_length_;
const String & getStartTime()
void registerMandatoryOutputFileList(const String &name, const String &description)
void setParameterRestrictions(String category, String par_name, int min_value, int max_value)
CommandlineParser(String tool_name, String tool_description, String tool_version, String build_date, String category="")
void registerMandatoryGalaxyOutputFolder(const String &name, const String &description)
void setParameterRestrictions(String category, String par_name, list< String > &allowed_values)
void registerOptionalIntegerListParameter(const String &name, const String &description, const std::vector< int > &default_values=vector< int >())
void setParameterRestrictions(String par_name, list< String > &allowed_values)
void registerFlag(String name, String description, bool default_gui_value=false, bool hidden=false)
void registerOptionalStringParameter(const String &name, const String &description, const String &default_value="")
const String & getStartCommand()
void registerMandatoryDoubleParameter(const String &name, const String &description)
void setParameterAsHidden(String name)
void registerOptionalInputFileList(const String &name, const String &description, const std::vector< String > &default_values=vector< String >())
void setToolManual(const String &manual)
void registerMandatoryGalaxyOutputId(const String &name, const String &description)
void registerMandatoryInputFile(const String &name, const String &description)
void setSupportedFormats(String category, String par_name, String supported_formats)
void setParameterAsAdvanced(String name)
void registerMandatoryIntegerParameter(const String &name, const String &description)
void registerOptionalDoubleListParameter(const String &name, const String &description, const std::vector< double > &default_values=vector< double >())
void registerMandatoryStringParameter(const String &name, const String &description)
void setSupportedFormats(String par_name, String supported_formats)
static const String NOT_FOUND
void registerOptionalGalaxyOutputId(const String &name, const String &description, const String &default_value="")
void registerOptionalGalaxyOutputFolder(const String &name, const String &description, const String &default_value="")
const String & get(String name)
void copyAdvancedParametersToOptions(Options &options)
void registerOptionalOutputFileList(const String &name, const String &description, const std::vector< String > &default_values=vector< String >())
void registerMandatoryOutputFile(const String &name, const String &description)
void registerMandatoryStringListParameter(const String &name, const String &description)
static const list< String > EMTPY_LIST
void registerOptionalStringListParameter(const String &name, const String &description, const std::vector< String > &default_values=vector< String >())
void registerMandatoryIntegerListParameter(const String &name, const String &description)
void setParameterRestrictions(String par_name, double min_value, double max_value)
void registerOptionalOutputFile(const String &name, const String &description, const String &default_value="")
void registerOptionalInputFile(const String &name, const String &description, const String &default_value="")
void registerMandatoryDoubleListParameter(const String &name, const String &description)
void registerOptionalIntegerParameter(const String &name, const String &description, int default_value=0)
const list< String > & getList(String name)
void setParameterRestrictions(String par_name, int min_value, int max_value)
void registerOptionalDoubleParameter(const String &name, const String &description, double default_value=0.0)
void printHelp(const std::set< String > ¶meter_names=std::set< String >(), bool show_manual=true)
void registerMandatoryInputFileList(const String &name, const String &description)
void setParameterRestrictions(String category, String par_name, double min_value, double max_value)
void parse(int argc, char *argv[])
void registerAdvancedParameters(Options &options)