35 #ifndef OPENMS_APPLICATIONS_TOPPBASE_H 36 #define OPENMS_APPLICATIONS_TOPPBASE_H 73 BaseException(file, line, function,
"UnregisteredParameter", parameter)
85 BaseException(file, line, function,
"WrongParameterType", parameter)
97 BaseException(file, line, function,
"RequiredParameterNotGiven", parameter)
162 TOPPBase(
const String& name,
const String& description,
bool official =
true,
bool id_tag_support =
false,
bool require_args =
true,
const String& version =
"");
177 static void setMaxNumberOfThreads(
int num_threads);
237 void enableLogging_()
const;
251 virtual Param getSubsectionDefaults_(
const String& section)
const;
260 Param getSubsectionDefaults_()
const;
281 Param parseCommandLine_(
const int argc,
const char** argv,
const String& misc =
"misc",
const String& unknown =
"unknown");
299 Int getParamAsInt_(
const String& key,
Int default_value = 0)
const;
306 double getParamAsDouble_(
const String& key,
double default_value = 0)
const;
338 bool getParamAsBool_(
const String& key)
const;
361 Param getDefaultParameters_()
const;
386 return ini_location_;
390 const String& toolName_()
const;
412 virtual void registerOptionsAndFlags_() = 0;
418 std::vector<ParameterInformation> paramToParameterInformation_(
const Param& param)
const;
431 void registerParamSubsectionsAsTOPPSubsections_(
const Param& param);
434 void registerFullParam_(
const Param& param);
446 void registerStringOption_(
const String& name,
const String& argument,
const String& default_value,
const String& description,
bool required =
true,
bool advanced =
false);
454 void setValidStrings_(
const String& name,
const std::vector<String>& strings);
486 void registerOutputFile_(
const String& name,
const String& argument,
const String& default_value,
const String& description,
bool required =
true,
bool advanced =
false);
498 void setValidFormats_(
const String& name,
const std::vector<String>& formats,
const bool force_OpenMS_format =
true);
511 void registerDoubleOption_(
const String& name,
const String& argument,
double default_value,
const String& description,
bool required =
true,
bool advanced =
false);
518 void setMinInt_(
const String& name,
Int min);
524 void setMaxInt_(
const String& name,
Int max);
530 void setMinFloat_(
const String& name,
double min);
536 void setMaxFloat_(
const String& name,
double max);
548 void registerIntOption_(
const String& name,
const String& argument,
549 Int default_value,
const String& description,
550 bool required =
true,
bool advanced =
false);
563 void registerIntList_(
const String& name,
const String& argument,
IntList default_value,
const String& description,
bool required =
true,
bool advanced =
false);
575 void registerDoubleList_(
const String& name,
const String& argument,
DoubleList default_value,
const String& description,
bool required =
true,
bool advanced =
false);
587 void registerStringList_(
const String& name,
const String& argument,
StringList default_value,
const String& description,
bool required =
true,
bool advanced =
false);
602 void registerInputFileList_(
const String& name,
const String& argument,
StringList default_value,
const String& description,
bool required =
true,
bool advanced =
false);
617 void registerOutputFileList_(
const String& name,
const String& argument,
StringList default_value,
const String& description,
bool required =
true,
bool advanced =
false);
620 void registerFlag_(
const String& name,
const String& description,
bool advanced =
false);
629 void registerSubsection_(
const String& name,
const String& description);
640 void registerTOPPSubsection_(
const String& name,
const String& description);
644 void addEmptyLine_();
665 double getDoubleOption_(
const String& name)
const;
675 Int getIntOption_(
const String& name)
const;
708 bool getFlag_(
const String& name)
const;
722 Param const& getParam_()
const;
737 void checkParam_(
const Param& param,
const String& filename,
const String& location)
const;
747 void checkIfIniParametersAreApplicable_(
const Param& ini_params);
754 virtual ExitCodes main_(
int argc,
const char** argv) = 0;
758 void writeLog_(
const String& text)
const;
762 void writeDebug_(
const String& text,
UInt min_level)
const;
765 void writeDebug_(
const String& text,
const Param& param,
UInt min_level)
const;
793 void inputFileReadable_(
const String& filename,
const String& param_name)
const;
805 void outputFileWritable_(
const String& filename,
const String& param_name)
const;
809 void parseRange_(
const String& text,
double& low,
double& high)
const;
812 void parseRange_(
const String& text,
Int& low,
Int& high)
const;
827 template <
typename PeakType,
typename CT>
830 for (
Size i = 0; i < map.
size(); ++i)
832 map[i].getDataProcessing().push_back(dp);
844 DataProcessing getProcessingInfo_(
const std::set<DataProcessing::ProcessingAction>& actions)
const;
882 void addText_(
const String& text);
897 #endif //OPENMS_APPLICATIONS_TOPPBASE_H String verboseVersion_
Version string including additional revision/date time information. Note: This differs from version_ ...
Definition: TOPPBase.h:372
Definition: TOPPBase.h:139
Description of the applied preprocessing steps.
Definition: DataProcessing.h:51
std::map< String, String > subsections_TOPP_
Storage location and description for allowed subsections from TOPP tool's command-line parameters...
Definition: TOPPBase.h:266
An unregistered parameter was accessed.
Definition: TOPPBase.h:68
const std::vector< DataProcessing > & getDataProcessing() const
returns a const reference to the description of the applied processing
Definition: TOPPBase.h:132
Definition: TOPPBase.h:135
A more convenient string class.
Definition: String.h:57
Size size() const
Definition: MSExperiment.h:117
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:66
LogType
Possible log types.
Definition: ProgressLogger.h:71
UnregisteredParameter(const char *file, int line, const char *function, const String ¶meter)
Definition: TOPPBase.h:72
RequiredParameterNotGiven(const char *file, int line, const char *function, const String ¶meter)
Definition: TOPPBase.h:96
std::ofstream log_
Log file stream. Use the writeLog_() and writeDebug_() methods to access it.
Definition: TOPPBase.h:227
A container for features.
Definition: FeatureMap.h:93
bool official_
Flag indicating if this an official TOPP tool.
Definition: TOPPBase.h:375
Parameter entry used to store the actual information inside of a Param entry.
Definition: Param.h:80
A container for consensus elements.
Definition: ConsensusMap.h:72
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:59
Definition: TOPPBase.h:140
Definition: TOPPBase.h:136
std::map< String, String > subsections_
Storage location and description for allowed subsections.
Definition: TOPPBase.h:263
const String & getIniLocation_() const
Returns the location of the ini file where parameters are taken from. E.g. if the command line was TO...
Definition: TOPPBase.h:384
Definition: TOPPBase.h:142
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
bool test_mode_
Test mode.
Definition: TOPPBase.h:868
Definition: TOPPBase.h:141
Base class for TOPP applications.
Definition: TOPPBase.h:125
static GlobalExceptionHandler & getInstance()
The accessor for the singleton. It also serves as a replacement for the constructor.
Definition: GlobalExceptionHandler.h:89
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:57
const char * tool_name
Definition: TOPPAS.cpp:92
Definition: TOPPBase.h:138
A parameter was accessed with the wrong type.
Definition: TOPPBase.h:80
Definition: TOPPBase.h:137
Param param_cmdline_
Parameters from command line.
Definition: TOPPBase.h:215
Tags OpenMS file containers with a DocumentID.
Definition: DocumentIDTagger.h:55
Param param_common_tool_
Parameters from common section with tool name.
Definition: TOPPBase.h:221
MSChromatogram< ChromatogramPeakType > & getChromatogram(Size id)
returns a single chromatogram
Definition: MSExperiment.h:796
ProcessingAction
Definition: DataProcessing.h:58
bool id_tag_support_
Tool indicates it supports assignment of unique DocumentID from IDPool.
Definition: TOPPBase.h:188
Definition: TOPPBase.h:143
Definition: TOPPBase.h:144
bool require_args_
Require at least one command line argument, exit immediately otherwise. GUI tools should disable this...
Definition: TOPPBase.h:191
Size getNrChromatograms() const
get the total number of chromatograms available
Definition: MSExperiment.h:814
Exception base class.
Definition: Exception.h:90
Param param_common_
Parameters from common section without tool name.
Definition: TOPPBase.h:224
String version_
Version string (if empty, the OpenMS/TOPP version is printed)
Definition: TOPPBase.h:369
DocumentIDTagger id_tagger_
Instance of DocumentIDTagger, which can be accessed using getDocumentIDTagger_()
Definition: TOPPBase.h:194
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:74
Management and storage of parameters / INI files.
Definition: Param.h:75
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:69
WrongParameterType(const char *file, int line, const char *function, const String ¶meter)
Definition: TOPPBase.h:84
Definition: TOPPBase.h:134
static void setMessage(const std::string &message)
String const tool_name_
Tool name. This is assigned once and for all in the constructor.
Definition: TOPPBase.h:182
Param param_
All parameters relevant to this invocation of the program.
Definition: TOPPBase.h:209
Definition: TOPPBase.h:133
std::vector< ParameterInformation > parameters_
Storage location for parameter information.
Definition: TOPPBase.h:240
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
ExitCodes
Exit codes.
Definition: TOPPBase.h:130
String const ini_location_
Location in the ini file where to look for parameters.
Definition: TOPPBase.h:200
String const tool_description_
Tool description. This is assigned once and for all in the constructor.
Definition: TOPPBase.h:185
Param param_inifile_
All parameters specified in the ini file.
Definition: TOPPBase.h:212
int Int
Signed integer type.
Definition: Types.h:96
Param param_instance_
Parameters from instance section.
Definition: TOPPBase.h:218
void addDataProcessing_(MSExperiment< PeakType, CT > &map, const DataProcessing &dp) const
Data processing setter for peak maps.
Definition: TOPPBase.h:828
Int debug_level_
Debug level set by -debug.
Definition: TOPPBase.h:874
ProgressLogger::LogType log_type_
Type of progress logging.
Definition: TOPPBase.h:815
Int const instance_number_
Instance number.
Definition: TOPPBase.h:197
static String topp_ini_file_
.TOPP.ini file for storing system default parameters
Definition: TOPPBase.h:871
A required parameter was not given.
Definition: TOPPBase.h:92