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OpenMS
2.4.0
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89 std::vector<CsiAdapterHit>
hits;
107 static void read(
const std::vector<String> & sirius_output_paths,
108 const String & original_input_mzml,
109 const Size & top_n_hits,
std::vector< String > pubchemids
Definition: CsiFingerIdMzTabWriter.h:79
Internal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output t...
Definition: CsiFingerIdMzTabWriter.h:70
Base class for TOPP applications.
Definition: TOPPBase.h:150
OpenMS::String smiles
Definition: CsiFingerIdMzTabWriter.h:78
int scan_index
Definition: CsiFingerIdMzTabWriter.h:86
void getAllCruxNames(std::vector< String > &all_names) const
returns all the enzyme names available for Crux
std::vector< CsiAdapterHit > hits
Definition: CsiFingerIdMzTabWriter.h:89
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:70
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
OpenMS::String inchikey2D
Definition: CsiFingerIdMzTabWriter.h:72
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
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
int scan_number
Definition: CsiFingerIdMzTabWriter.h:87
std::vector< CsiAdapterIdentification > identifications
Definition: CsiFingerIdMzTabWriter.h:94
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
OpenMS::String molecular_formula
Definition: CsiFingerIdMzTabWriter.h:75
String & simplify()
merges subsequent whitespaces to one blank character
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::String feature_id
Definition: CsiFingerIdMzTabWriter.h:88
unsigned int rank
Definition: CsiFingerIdMzTabWriter.h:74
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
QString toQString() const
Conversion to Qt QString.
Definition: CsiFingerIdMzTabWriter.h:92
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
OpenMS::String name
Definition: CsiFingerIdMzTabWriter.h:77
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::String inchi
Definition: CsiFingerIdMzTabWriter.h:73
void store(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.
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...
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:240
static String findDatabase(const String &db_name)
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.
static bool readable(const String &file)
Return true if the file exists and is readable.
Definition: CsiFingerIdMzTabWriter.h:39
ExitCodes
Exit codes.
Definition: TOPPBase.h:155
std::vector< String > links
Definition: CsiFingerIdMzTabWriter.h:80
static bool removeDirRecursively(const String &dir_name)
Removes the subdirectories of the specified directory (absolute path). Returns true if successful.
Used to load and store idXML files.
Definition: IdXMLFile.h:63
double score
Definition: CsiFingerIdMzTabWriter.h:76
Definition: CsiFingerIdMzTabWriter.h:84