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OpenMS
2.4.0
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66 static void store(
const PeakMap& spectra,
69 const bool& feature_only,
70 const int& isotope_pattern_iterations,
71 const bool no_mt_info);
static void store(const PeakMap &spectra, const OpenMS::String &msfile, const FeatureMapping::FeatureToMs2Indices &feature_mapping, const bool &feature_only, const int &isotope_pattern_iterations, const bool no_mt_info)
Internal structure used in SiriusAdapter that is used for the conversion of a MzMlFile to an internal...
Base class for TOPP applications.
Definition: TOPPBase.h:150
File adapter for MzTab files.
Definition: MzTabFile.h:58
Definition: SiriusMSConverter.h:44
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:699
static bool remove(const String &file)
Removes a file (if it exists).
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
static bool exists(const String &file)
Method used to test if a file exists.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
void addMaps(const std::vector< MapType > &maps)
Add maps and balance kd-tree.
Definition: KDTreeFeatureMaps.h:81
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:450
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
static FeatureToMs2Indices assignMS2IndexToFeature(PeakMap &spectra, const KDTreeFeatureMaps &fp_map_kd, const double &precursor_mz_tolerance, const double &precursor_rt_tolerance, bool &ppm)
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
void store(const String &filename, const MzTab &mz_tab) const
static void read(const std::vector< String > &sirius_output_paths, const String &original_input_mzml, const Size &top_n_hits, MzTab &result)
Conversion of CSI:FingerID output to mzTab.
static int extract_scan_index(const String &path)
Extract scan_index from filepath.
QString toQString() const
Conversion to Qt QString.
static String path(const String &file)
Returns the path of the file (without the file name).
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
Allocate ms2 spectra to feature within the minimal distance.
Definition: FeatureMapping.h:61
A container for features.
Definition: FeatureMap.h:93
An LC-MS feature.
Definition: Feature.h:70
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
static bool empty(const String &file)
Return true if the file does not exist or the file is empty.
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
static void read(const std::vector< String > &sirius_output_paths, const String &original_input_mzml, const Size &top_n_hits, MzTab &result)
Conversion of sirius output to mzTab.
File is empty.
Definition: Exception.h:594
static bool removeDir(const QString &dir_name)
Removes the directory and all subdirectories (absolute path).
Stores a set of features, together with a 2D tree for fast search.
Definition: KDTreeFeatureMaps.h:49
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!