OpenMS  3.0.0
CsiFingerIdMzTabWriter.h
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31 // $Maintainer: Oliver Alka $
32 // $Authors: Oliver Alka $
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34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41  class OPENMS_DLLAPI CsiFingerIdMzTabWriter
42  {
43  public:
44 
73  {
74  public:
77  unsigned int rank = 0;
78  unsigned int formula_rank = 0;
81  double score = 0.;
86  std::vector<String> pubchemids;
87  std::vector<String> links;
88 
89  };
90 
92  {
93  public:
94  double mz = 0.;
95  double rt = 0.;
97  int scan_index = -1;
98  int scan_number = -1;
100  std::vector<CsiAdapterHit> hits;
101  };
102 
104  {
105  public:
106  std::vector <CsiAdapterIdentification> identifications;
107  };
108 
119  static void read(const std::vector<String>& sirius_output_paths,
120  const String& original_input_mzml,
121  const Size& top_n_hits,
122  MzTab& result);
123 
124  };
125 }
DefaultParamHandler.h
OpenMS::ProteinIdentification::SearchParameters::digestion_enzyme
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:273
MzTabFile.h
FileHandler.h
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun::identifications
std::vector< CsiAdapterIdentification > identifications
Definition: CsiFingerIdMzTabWriter.h:106
OpenMS::IdXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
OpenMS::DigestionEnzymeDB::getInstance
static InstanceType * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
OpenMS::StringUtils::toQString
static QString toQString(const String &this_s)
Definition: StringUtils.h:201
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::smiles
OpenMS::String smiles
Definition: CsiFingerIdMzTabWriter.h:83
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::inchikey2D
OpenMS::String inchikey2D
Definition: CsiFingerIdMzTabWriter.h:75
OpenMS::ProteinIdentification::SearchParameters::missed_cleavages
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:268
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::String::trim
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
MzMLFile.h
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification::native_ids
OpenMS::StringList native_ids
Definition: CsiFingerIdMzTabWriter.h:96
SearchEngineBase.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification::feature_id
OpenMS::String feature_id
Definition: CsiFingerIdMzTabWriter.h:99
OpenMS::MzTab
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:477
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::name
OpenMS::String name
Definition: CsiFingerIdMzTabWriter.h:82
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::adduct
OpenMS::String adduct
Definition: CsiFingerIdMzTabWriter.h:79
MSDataCachedConsumer.h
OpenMS::String::hasPrefix
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::pubchemids
std::vector< String > pubchemids
Definition: CsiFingerIdMzTabWriter.h:86
OpenMS::String::simplify
String & simplify()
merges subsequent whitespaces to one blank character
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance_ppm
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:270
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::molecular_formula
OpenMS::String molecular_formula
Definition: CsiFingerIdMzTabWriter.h:80
OpenMS::ListUtils::concatenate
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:209
OpenMS::ProteinIdentification::SearchParameters::charges
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:264
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::inchi
OpenMS::String inchi
Definition: CsiFingerIdMzTabWriter.h:76
OpenMS::MzIdentMLFile
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit
Internal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output t...
Definition: CsiFingerIdMzTabWriter.h:72
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification
Definition: CsiFingerIdMzTabWriter.h:91
OpenMS::ProteinIdentification::SearchParameters::variable_modifications
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:267
ProteaseDB.h
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::dbflags
OpenMS::String dbflags
Definition: CsiFingerIdMzTabWriter.h:85
OpenMS::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:261
ModificationDefinitionsSet.h
OpenMS::ProteinIdentification::SearchParameters::db_version
String db_version
The database version.
Definition: ProteinIdentification.h:262
OpenMS::String::split
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:269
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::SearchEngineBase
Base class for Search Engine Adapters.
Definition: SearchEngineBase.h:54
OpenMS::ProteinIdentification::SearchParameters::fixed_modifications
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:266
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::links
std::vector< String > links
Definition: CsiFingerIdMzTabWriter.h:87
OpenMS::MzIdentMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:271
OpenMS::Constants::UserParam::ISOTOPE_ERROR
const std::string ISOTOPE_ERROR
Definition: Constants.h:327
OpenMS::File::TempDir
Class representing a temporary directory.
Definition: File.h:64
OpenMS::String::substr
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
OpenMS::PlainMSDataWritingConsumer
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:240
OpenMS::MzMLFile::transform
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false)
Transforms a map while loading using the supplied MSDataConsumer.
OpenMS::CsiFingerIdMzTabWriter
Definition: CsiFingerIdMzTabWriter.h:41
OpenMS::TOPPBase::ExitCodes
ExitCodes
Exit codes.
Definition: TOPPBase.h:152
String.h
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification::hits
std::vector< CsiAdapterHit > hits
Definition: CsiFingerIdMzTabWriter.h:100
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance_ppm
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:272
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::xlogp
OpenMS::String xlogp
Definition: CsiFingerIdMzTabWriter.h:84
MSDataWritingConsumer.h
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::DefaultParamHandler::writeParametersToMetaValues
static void writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
Writes all parameters to meta values.
OpenMS::ProteinIdentification::SearchParameters::taxonomy
String taxonomy
The taxonomy restriction.
Definition: ProteinIdentification.h:263
StandardTypes.h
File.h
MzIdentMLFile.h
OpenMS::DigestionEnzyme::getName
const String & getName() const
returns the name of the enzyme
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun
Definition: CsiFingerIdMzTabWriter.h:103
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68