#include <OpenMS/ANALYSIS/ID/SiriusAdapterAlgorithm.h>
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static void | preprocessingSirius (const String &featureinfo, const MSExperiment &spectra, std::vector< FeatureMap > &v_fp, KDTreeFeatureMaps &fp_map_kd, const SiriusAdapterAlgorithm &sirius_algo, FeatureMapping::FeatureToMs2Indices &feature_mapping) |
| Preprocessing needed for SIRIUS. More...
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static void | checkFeatureSpectraNumber (const String &featureinfo, const FeatureMapping::FeatureToMs2Indices &feature_mapping, const MSExperiment &spectra, const SiriusAdapterAlgorithm &sirius_algo) |
| logs number of features and spectra used More...
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const static std::vector< String > | callSiriusQProcess (const String &tmp_ms_file, const String &tmp_out_dir, String &executable, const String &out_csifingerid, const SiriusAdapterAlgorithm &sirius_algo) |
| Call SIRIUS with QProcess. More...
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◆ SiriusAdapterAlgorithm()
◆ callSiriusQProcess()
Call SIRIUS with QProcess.
- Returns
- Vector with paths to a compound
- Parameters
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tmp_ms_file | path to temporary .ms file |
tmp_out_dir | path to temporary output folder |
executable | path to executable |
out_csifingerid | path to CSI:FingerID output (can be empty). |
sirius_algo | Parameters needed for SIRIUS |
◆ checkFeatureSpectraNumber()
logs number of features and spectra used
Prints the number of features and spectra used (OPENMS_LOG_INFO)
- Parameters
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featureinfo | Path to featureXML |
feature_mapping | FeatureToMs2Indices with feature mapping |
spectra | Input of MSExperiment with spectra information |
sirius_algo | Parameters needed for preprocessing |
◆ getCandidates()
◆ getFeatureOnly()
◆ getIsotopePatternIterations()
int getIsotopePatternIterations |
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◆ getNoMasstraceInfoIsotopePattern()
String getNoMasstraceInfoIsotopePattern |
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◆ getTopNHits()
◆ preprocessingSirius()
Preprocessing needed for SIRIUS.
- Returns
- FeatureToMS2Indices
Filter number of masstraces and perform feature mapping.
- Parameters
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featureinfo | Path to featureXML |
spectra | Input of MSExperiment with spectra information |
fp_map_kd | KDTree used for query and match spectra with features |
sirius_algo | Parameters needed for preprocessing |
feature_mapping | Empty FeatureToMs2Indices |
◆ updateMembers_()
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
◆ auto_charge_
◆ candidates_
◆ compound_timeout_
◆ cores_
◆ database_
◆ elements_
◆ feature_only_
◆ filter_by_num_masstraces_
unsigned int filter_by_num_masstraces_ |
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◆ ion_tree_
◆ isotope_
◆ isotope_pattern_iterations_
int isotope_pattern_iterations_ |
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◆ most_intense_ms2_
◆ no_masstrace_info_isotope_pattern_
String no_masstrace_info_isotope_pattern_ |
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protected |
◆ no_recalibration_
◆ noise_
◆ ppm_max_
◆ precursor_mz_tolerance_
double precursor_mz_tolerance_ |
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◆ precursor_mz_tolerance_unit_
String precursor_mz_tolerance_unit_ |
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◆ precursor_rt_tolerance_
double precursor_rt_tolerance_ |
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◆ profile_
◆ top_n_hits_
◆ tree_timeout_