44 class KDTreeFeatureMaps;
63 const String& getTmpDir()
const;
64 const String& getTmpOutDir()
const;
65 const String& getTmpMsFile()
const;
89 static void preprocessingSirius(
const String& featureinfo,
91 std::vector<FeatureMap>& v_fp,
106 static void checkFeatureSpectraNumber(
const String& featureinfo,
124 const static std::vector<String> callSiriusQProcess(
const String& tmp_ms_file,
125 const String& tmp_out_dir,
127 const String& out_csifingerid,
132 String getNoMasstraceInfoIsotopePattern();
133 int getIsotopePatternIterations();
166 void updateMembers_()
override;
String auto_charge_
Definition: SiriusAdapterAlgorithm.h:161
Struct for temporary folder structure.
Definition: SiriusAdapterAlgorithm.h:53
String feature_only_
Definition: SiriusAdapterAlgorithm.h:146
int debug_level_
Definition: SiriusAdapterAlgorithm.h:68
String isotope_
Definition: SiriusAdapterAlgorithm.h:154
String tmp_dir_
Definition: SiriusAdapterAlgorithm.h:70
double precursor_mz_tolerance_
Definition: SiriusAdapterAlgorithm.h:141
String most_intense_ms2_
Definition: SiriusAdapterAlgorithm.h:164
Definition: SiriusAdapterAlgorithm.h:46
int isotope_pattern_iterations_
Definition: SiriusAdapterAlgorithm.h:144
String tmp_ms_file_
Definition: SiriusAdapterAlgorithm.h:71
int tree_timeout_
Definition: SiriusAdapterAlgorithm.h:157
String ion_tree_
Definition: SiriusAdapterAlgorithm.h:162
int noise_
Definition: SiriusAdapterAlgorithm.h:152
String no_masstrace_info_isotope_pattern_
Definition: SiriusAdapterAlgorithm.h:147
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Stores a set of features, together with a 2D tree for fast search.
Definition: KDTreeFeatureMaps.h:49
String database_
Definition: SiriusAdapterAlgorithm.h:151
Definition: FeatureMapping.h:48
int top_n_hits_
Definition: SiriusAdapterAlgorithm.h:158
int compound_timeout_
Definition: SiriusAdapterAlgorithm.h:156
String no_recalibration_
Definition: SiriusAdapterAlgorithm.h:163
int candidates_
Definition: SiriusAdapterAlgorithm.h:150
int ppm_max_
Definition: SiriusAdapterAlgorithm.h:153
unsigned int filter_by_num_masstraces_
Definition: SiriusAdapterAlgorithm.h:140
String precursor_mz_tolerance_unit_
Definition: SiriusAdapterAlgorithm.h:142
double precursor_rt_tolerance_
Definition: SiriusAdapterAlgorithm.h:143
A more convenient string class.
Definition: String.h:58
String profile_
Definition: SiriusAdapterAlgorithm.h:149
String elements_
Definition: SiriusAdapterAlgorithm.h:155
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
String tmp_out_dir_
Definition: SiriusAdapterAlgorithm.h:72
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
int cores_
Definition: SiriusAdapterAlgorithm.h:159