OpenMS  2.4.0
SiriusMSConverter.h
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31 // $Maintainer: Oliver Alka $
32 // $Authors: Oliver Alka $
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34 
35 #pragma once
36 
40 
41 namespace OpenMS
42 {
43 
44  class OPENMS_DLLAPI SiriusMSFile
45  {
46 public:
47 
65  // preprocessing e.g. feature information
66  static void store(const PeakMap& spectra,
67  const OpenMS::String& msfile,
68  const FeatureMapping::FeatureToMs2Indices& feature_mapping,
69  const bool& feature_only,
70  const int& isotope_pattern_iterations,
71  const bool no_mt_info);
72 
73  };
74 
75 }
76 
OpenMS::SiriusMSFile::store
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...
MzTabFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
OpenMS::MzTabFile
File adapter for MzTab files.
Definition: MzTabFile.h:58
OpenMS::SiriusMSFile
Definition: SiriusMSConverter.h:44
KDTreeFeatureMaps.h
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:57
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
FeatureXMLFile.h
OpenMS::MzTab
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:699
CsiFingerIdMzTabWriter.h
OpenMS::File::remove
static bool remove(const String &file)
Removes a file (if it exists).
OpenMS::File::getUniqueName
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
ListUtils.h
Element.h
OpenMS::File::exists
static bool exists(const String &file)
Method used to test if a file exists.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
LOG_DEBUG
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
OpenMS::KDTreeFeatureMaps::addMaps
void addMaps(const std::vector< MapType > &maps)
Add maps and balance kd-tree.
Definition: KDTreeFeatureMaps.h:81
LOG_WARN
#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
OpenMS::MzMLFile::load
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...
OpenMS::FeatureMapping::assignMS2IndexToFeature
static FeatureToMs2Indices assignMS2IndexToFeature(PeakMap &spectra, const KDTreeFeatureMaps &fp_map_kd, const double &precursor_mz_tolerance, const double &precursor_rt_tolerance, bool &ppm)
SiriusMSConverter.h
QProcess
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
SpectrumLookup.h
OpenMS::MzTabFile::store
void store(const String &filename, const MzTab &mz_tab) const
OpenMS::CsiFingerIdMzTabWriter::read
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.
OpenMS::SiriusMzTabWriter::extract_scan_index
static int extract_scan_index(const String &path)
Extract scan_index from filepath.
SiriusMzTabWriter.h
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::File::path
static String path(const String &file)
Returns the path of the file (without the file name).
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::FeatureMapping::FeatureToMs2Indices
Allocate ms2 spectra to feature within the minimal distance.
Definition: FeatureMapping.h:61
FeatureMapping.h
EmpiricalFormula.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:93
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::File::empty
static bool empty(const String &file)
Return true if the file does not exist or the file is empty.
OpenMS::File::getTempDirectory
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
OpenMS::SiriusMzTabWriter::read
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.
OpenMS::Exception::FileEmpty
File is empty.
Definition: Exception.h:594
StandardTypes.h
OpenMS::File::removeDir
static bool removeDir(const QString &dir_name)
Removes the directory and all subdirectories (absolute path).
OpenMS::KDTreeFeatureMaps
Stores a set of features, together with a 2D tree for fast search.
Definition: KDTreeFeatureMaps.h:49
File.h
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h