OpenMS
2.8.0
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#include <OpenMS/APPLICATIONS/OpenSwathBase.h>
Public Member Functions | |
TOPPOpenSwathBase (String name, String description, bool official=true) | |
Public Member Functions inherited from TOPPBase | |
TOPPBase ()=delete | |
No default constructor. More... | |
TOPPBase (const TOPPBase &)=delete | |
No default copy constructor. More... | |
TOPPBase (const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}, bool toolhandler_test=true) | |
Constructor. More... | |
virtual | ~TOPPBase () |
Destructor. More... | |
ExitCodes | main (int argc, const char **argv) |
Main routine of all TOPP applications. More... | |
String | getToolPrefix () const |
Returns the prefix used to identify the tool. More... | |
Protected Member Functions | |
bool | loadSwathFiles (const StringList &file_list, boost::shared_ptr< ExperimentalSettings > &exp_meta, std::vector< OpenSwath::SwathMap > &swath_maps, const bool split_file, const String &tmp, const String &readoptions, const String &swath_windows_file, const double min_upper_edge_dist, const bool force, const bool sort_swath_maps, const bool sonar, const bool prm, Interfaces::IMSDataConsumer *plugin_consumer=nullptr) |
Load the DIA files into internal data structures. More... | |
void | prepareChromOutput (Interfaces::IMSDataConsumer **chromatogramConsumer, const boost::shared_ptr< ExperimentalSettings > &exp_meta, const OpenSwath::LightTargetedExperiment &transition_exp, const String &out_chrom, const UInt64 run_id) |
Prepare chromatogram output. More... | |
OpenSwath::LightTargetedExperiment | loadTransitionList (const FileTypes::Type &tr_type, const String &tr_file, const Param &tsv_reader_param) |
Loads transition list from TraML / TSV or PQP. More... | |
TransformationDescription | performCalibration (String trafo_in, String irt_tr_file, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, Size debug_level, bool sonar, bool load_into_memory, const String &irt_trafo_out, const String &irt_mzml_out) |
Perform retention time and m/z calibration. More... | |
Protected Member Functions inherited from TOPPBase | |
virtual void | registerOptionsAndFlags_ ()=0 |
Sets the valid command line options (with argument) and flags (without argument). More... | |
String | getParamArgument_ (const Param::ParamEntry &entry) const |
Utility function that determines a suitable argument value for the given Param::ParamEntry. More... | |
std::vector< ParameterInformation > | paramToParameterInformation_ (const Param ¶m) const |
Translates the given parameter object into a vector of ParameterInformation, that can be utilized for cl parsing. More... | |
ParameterInformation | paramEntryToParameterInformation_ (const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const |
Transforms a ParamEntry object to command line parameter (ParameterInformation). More... | |
void | registerParamSubsectionsAsTOPPSubsections_ (const Param ¶m) |
void | registerFullParam_ (const Param ¶m) |
Register command line parameters for all entries in a Param object. More... | |
void | registerStringOption_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false) |
Registers a string option. More... | |
void | setValidStrings_ (const String &name, const std::vector< String > &strings) |
Sets the valid strings for a string option or a whole string list. More... | |
void | setValidStrings_ (const String &name, const std::string vstrings[], int count) |
Sets the valid strings for a string option or a whole string list. More... | |
void | registerInputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList()) |
Registers an input file option. More... | |
void | registerOutputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false) |
Registers an output file option. More... | |
void | registerOutputPrefix_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false) |
Registers an output file prefix used for tools with multiple file output. More... | |
void | setValidFormats_ (const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true) |
Sets the formats for a input/output file option or for all members of an input/output file lists. More... | |
void | registerDoubleOption_ (const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false) |
Registers a double option. More... | |
void | setMinInt_ (const String &name, Int min) |
Sets the minimum value for the integer parameter(can be a list of integers,too) name . More... | |
void | setMaxInt_ (const String &name, Int max) |
Sets the maximum value for the integer parameter(can be a list of integers,too) name . More... | |
void | setMinFloat_ (const String &name, double min) |
Sets the minimum value for the floating point parameter(can be a list of floating points,too) name . More... | |
void | setMaxFloat_ (const String &name, double max) |
Sets the maximum value for the floating point parameter(can be a list of floating points,too) name . More... | |
void | registerIntOption_ (const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false) |
Registers an integer option. More... | |
void | registerIntList_ (const String &name, const String &argument, IntList default_value, const String &description, bool required=true, bool advanced=false) |
Registers a list of integers option. More... | |
void | registerDoubleList_ (const String &name, const String &argument, DoubleList default_value, const String &description, bool required=true, bool advanced=false) |
Registers a list of doubles option. More... | |
void | registerStringList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false) |
Registers a list of strings option. More... | |
void | registerInputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList()) |
Registers a list of input files option. More... | |
void | registerOutputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false) |
Registers a list of output files option. More... | |
void | registerFlag_ (const String &name, const String &description, bool advanced=false) |
Registers a flag. More... | |
void | registerSubsection_ (const String &name, const String &description) |
Registers an allowed subsection in the INI file (usually from OpenMS algorithms). More... | |
void | registerTOPPSubsection_ (const String &name, const String &description) |
Registers an allowed subsection in the INI file originating from the TOPP tool itself. More... | |
void | addEmptyLine_ () |
Adds an empty line between registered variables in the documentation. More... | |
String | getStringOption_ (const String &name) const |
Returns the value of a previously registered string option. More... | |
double | getDoubleOption_ (const String &name) const |
Returns the value of a previously registered double option. More... | |
Int | getIntOption_ (const String &name) const |
Returns the value of a previously registered integer option. More... | |
StringList | getStringList_ (const String &name) const |
Returns the value of a previously registered StringList. More... | |
IntList | getIntList_ (const String &name) const |
Returns the value of a previously registered IntList. More... | |
DoubleList | getDoubleList_ (const String &name) const |
Returns the value of a previously registered DoubleList. More... | |
bool | getFlag_ (const String &name) const |
Returns the value of a previously registered flag. More... | |
const ParameterInformation & | findEntry_ (const String &name) const |
Finds the entry in the parameters_ array that has the name name . More... | |
Param const & | getParam_ () const |
Return all parameters relevant to this TOPP tool. More... | |
void | checkParam_ (const Param ¶m, const String &filename, const String &location) const |
Checks top-level entries of param according to the information during registration. More... | |
void | fileParamValidityCheck_ (const StringList ¶m_value, const String ¶m_name, const ParameterInformation &p) const |
checks if files of an input file list exist More... | |
void | fileParamValidityCheck_ (String ¶m_value, const String ¶m_name, const ParameterInformation &p) const |
checks if an input file exists (respecting the flags) More... | |
void | checkIfIniParametersAreApplicable_ (const Param &ini_params) |
Checks if the parameters of the provided ini file are applicable to this tool. More... | |
void | printUsage_ () |
Prints the tool-specific command line options and appends the common options. More... | |
virtual ExitCodes | main_ (int argc, const char **argv)=0 |
The actual "main" method. main_() is invoked by main(). More... | |
void | writeLog_ (const String &text) const |
Writes a string to the log file and to std::cout. More... | |
void | writeDebug_ (const String &text, UInt min_level) const |
Writes a text to the log file and to std::cout if the debug level is at least min_level . More... | |
void | writeDebug_ (const String &text, const Param ¶m, UInt min_level) const |
Writes a String followed by a Param to the log file and to std::cout if the debug level is at least min_level . More... | |
ExitCodes | runExternalProcess_ (const QString &executable, const QStringList &arguments, const QString &workdir="") const |
Runs an external process via ExternalProcess and prints its stderr output on failure or if debug_level > 4. More... | |
ExitCodes | runExternalProcess_ (const QString &executable, const QStringList &arguments, String &proc_stdout, String &proc_stderr, const QString &workdir="") const |
const String & | getIniLocation_ () const |
Returns the location of the ini file where parameters are taken from. E.g. if the command line was TOPPTool -instance 17 , then this will be "TOPPTool:17:" . Note the ':' at the end. More... | |
const String & | toolName_ () const |
Returns the tool name. More... | |
void | inputFileReadable_ (const String &filename, const String ¶m_name) const |
Checks if an input file exists, is readable and is not empty. More... | |
void | outputFileWritable_ (const String &filename, const String ¶m_name) const |
Checks if an output file is writable. More... | |
bool | parseRange_ (const String &text, double &low, double &high) const |
Parses a range string ([a]:[b]) into two variables (doubles) More... | |
bool | parseRange_ (const String &text, Int &low, Int &high) const |
Parses a range string ([a]:[b]) into two variables (integers) More... | |
void | addDataProcessing_ (ConsensusMap &map, const DataProcessing &dp) const |
Data processing setter for consensus maps. More... | |
void | addDataProcessing_ (FeatureMap &map, const DataProcessing &dp) const |
Data processing setter for feature maps. More... | |
void | addDataProcessing_ (PeakMap &map, const DataProcessing &dp) const |
Data processing setter for peak maps. More... | |
DataProcessing | getProcessingInfo_ (DataProcessing::ProcessingAction action) const |
Returns the data processing information. More... | |
DataProcessing | getProcessingInfo_ (const std::set< DataProcessing::ProcessingAction > &actions) const |
Returns the data processing information. More... | |
bool | writeCTD_ () |
Write common tool description (CTD) file. More... | |
Private Member Functions | |
void | loadSwathFiles_ (const StringList &file_list, const bool split_file, const String &tmp, const String &readoptions, boost::shared_ptr< ExperimentalSettings > &exp_meta, std::vector< OpenSwath::SwathMap > &swath_maps, Interfaces::IMSDataConsumer *plugin_consumer) |
Additional Inherited Members | |
Public Types inherited from TOPPBase | |
enum | ExitCodes { EXECUTION_OK , INPUT_FILE_NOT_FOUND , INPUT_FILE_NOT_READABLE , INPUT_FILE_CORRUPT , INPUT_FILE_EMPTY , CANNOT_WRITE_OUTPUT_FILE , ILLEGAL_PARAMETERS , MISSING_PARAMETERS , UNKNOWN_ERROR , EXTERNAL_PROGRAM_ERROR , PARSE_ERROR , INCOMPATIBLE_INPUT_DATA , INTERNAL_ERROR , UNEXPECTED_RESULT } |
Exit codes. More... | |
Static Public Member Functions inherited from TOPPBase | |
static void | setMaxNumberOfThreads (int num_threads) |
Sets the maximal number of usable threads. More... | |
Protected Attributes inherited from TOPPBase | |
String | version_ |
Version string (if empty, the OpenMS/TOPP version is printed) More... | |
String | verboseVersion_ |
Version string including additional revision/date time information. Note: This differs from version_ only if not provided by the user. More... | |
bool | official_ |
Flag indicating if this an official TOPP tool. More... | |
std::vector< Citation > | citations_ |
Papers, specific for this tool (will be shown in '–help') More... | |
bool | toolhandler_test_ |
Enable the ToolHandler tests. More... | |
ProgressLogger::LogType | log_type_ |
Type of progress logging. More... | |
bool | test_mode_ |
Test mode. More... | |
Int | debug_level_ |
Debug level set by -debug. More... | |
Static Protected Attributes inherited from TOPPBase | |
static String | topp_ini_file_ |
.TOPP.ini file for storing system default parameters More... | |
static const Citation | cite_openms_ |
The OpenMS citation. More... | |
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inline |
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inlineprotected |
Load the DIA files into internal data structures.
Loads SWATH files into the provided OpenSwath::SwathMap data structures. It uses the SwathFile class to load files from either mzML, mzXML or SqMass. The files will be either loaded into memory or cached to disk (depending on the readoptions parameter).
file_list | The input file(s) |
exp_meta | The output (meta data about experiment) |
swath_maps | The output (ptr to raw data) |
file_list | The input file(s) |
split_file | If loading a single file that contains a single SWATH window |
tmp | Temporary directory |
readoptions | Description on how to read the data ("normal", "cache") |
swath_windows_file | Provided file containing the SWATH windows which will be mapped to the experimental windows |
min_upper_edge_dist | Distance for each assay to the upper edge of the SWATH window |
force | Whether to override the sanity check |
sort_swath_maps | Whether to sort the provided windows first before mapping |
sonar | Whether data is in sonar format |
References SwathWindowLoader::annotateSwathMapsFromFile(), TOPPOpenSwathBase::loadSwathFiles_(), OPENMS_LOG_DEBUG, OPENMS_LOG_ERROR, and OPENMS_LOG_WARN.
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inlineprivate |
References FileHandler::getTypeByFileName(), SwathFile::loadMzML(), SwathFile::loadMzXML(), SwathFile::loadSplit(), SwathFile::loadSqMass(), TOPPBase::log_type_, FileTypes::MZML, FileTypes::MZXML, ProgressLogger::setLogType(), and FileTypes::SQMASS.
Referenced by TOPPOpenSwathBase::loadSwathFiles().
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inlineprotected |
Loads transition list from TraML / TSV or PQP.
tr_type | Input file type |
tr_file | Input file name |
tsv_reader_param | Parameters on how to interpret spectral data |
References TransitionPQPFile::convertPQPToTargetedExperiment(), OpenSwathDataAccessHelper::convertTargetedExp(), TransitionTSVFile::convertTSVToTargetedExperiment(), ProgressLogger::endProgress(), TraMLFile::load(), TOPPBase::log_type_, OPENMS_LOG_ERROR, FileTypes::PQP, ProgressLogger::setLogType(), DefaultParamHandler::setParameters(), ProgressLogger::startProgress(), FileTypes::TRAML, and FileTypes::TSV.
Referenced by TOPPOpenSwathBase::performCalibration().
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inlineprotected |
Perform retention time and m/z calibration.
This function will create the retention time transformation either by loading a provided .trafoXML file or determine it from the data itself by extracting the transitions specified in the irt_tr_file TraML file. It will also perform the m/z calibration.
m/z
calibration are performed by OpenMS::OpenSwathCalibrationWorkflow::performRTNormalizationtrafo_in | Input trafoXML file (if not empty, transformation will be loaded from this file) |
irt_tr_file | Input TraML file containing transitions (if trafo_in is empty, this file will be loaded and transitions will be extracted) |
swath_maps | The raw data (swath maps) |
min_rsq | Minimal R^2 value that is expected for the RT regression |
min_coverage | Minimal coverage of the chromatographic space that needs to be achieved |
feature_finder_param | Parameter set for the feature finding in chromatographic dimension |
cp_irt | Parameter set for the chromatogram extraction |
irt_detection_param | Parameter set for the detection of the iRTs (outlier detection, peptides per bin etc) |
calibration_param | Parameter for the m/z and im calibration (see SwathMapMassCorrection) |
debug_level | Debug level (writes out the RT normalization chromatograms if larger than 1) |
sonar | Whether the data is SONAR data |
load_into_memory | Whether to cache the current SWATH map in memory |
irt_trafo_out | Output trafoXML file (if not empty and no input trafoXML file is given, the transformation parameters will be stored in this file) |
irt_mzml_out | Output Chromatogram mzML containing the iRT peptides (if not empty, iRT chromatograms will be stored in this file) |
References Param::copy(), TransformationDescription::fitModel(), DefaultParamHandler::getDefaults(), TOPPBase::getParam_(), FileHandler::getType(), Param::getValue(), TransformationXMLFile::load(), TOPPOpenSwathBase::loadTransitionList(), TOPPBase::log_type_, OpenSwathCalibrationWorkflow::performRTNormalization(), ProgressLogger::setLogType(), Param::setValue(), TransformationXMLFile::store(), and ParamValue::toString().
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inlineprotected |
Prepare chromatogram output.
Sets up the chromatogram output, either sqMass or mzML (using numpress lossy compression). This assumes that 0.05 accuracy in RT is sufficient for all purposes.
chromatogramConsumer | The consumer to process chromatograms |
exp_meta | meta data about experiment |
transition_exp | The spectral library |
out_chrom | The output file for the chromatograms |
run_id | Unique identifier which links the sqMass and OSW file |
References MSDataWritingConsumer::addDataProcessing(), MSNumpressCoder::NumpressConfig::estimate_fixed_point, MzMLHandler::getOptions(), TOPPBase::getProcessingInfo_(), String::hasSuffix(), MSNumpressCoder::NumpressConfig::linear_fp_mass_acc, MSNumpressCoder::NumpressConfig::numpressErrorTolerance, PeakFileOptions::setCompression(), MSNumpressCoder::NumpressConfig::setCompression(), MSDataWritingConsumer::setExpectedSize(), MSDataWritingConsumer::setExperimentalSettings(), PeakFileOptions::setNumpressConfigurationIntensity(), PeakFileOptions::setNumpressConfigurationMassTime(), PeakFileOptions::setWriteIndex(), DataProcessing::SMOOTHING, String::toLower(), and LightTargetedExperiment::transitions.