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OpenMS
2.4.0
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53 #include <boost/lexical_cast.hpp>
79 static void concatMULTISEPeptideIds(std::vector<PeptideIdentification>& all_peptide_ids, std::vector<PeptideIdentification>& new_peptide_ids,
String search_engine);
89 static void mergeMULTISEPeptideIds(std::vector<PeptideIdentification>& all_peptide_ids, std::vector<PeptideIdentification>& new_peptide_ids,
String search_engine);
98 static void mergeMULTISEProteinIds(std::vector<ProteinIdentification>& all_protein_ids, std::vector<ProteinIdentification>& new_protein_ids);
108 static void addMSGFFeatures(std::vector<PeptideIdentification>& peptide_ids,
StringList& feature_set);
117 static void addXTANDEMFeatures(std::vector<PeptideIdentification>& peptide_ids,
StringList& feature_set);
126 static void addCOMETFeatures(std::vector<PeptideIdentification>& peptide_ids,
StringList& feature_set);
135 static void addMASCOTFeatures(std::vector<PeptideIdentification>& peptide_ids,
StringList& feature_set);
147 static void addMULTISEFeatures(std::vector<PeptideIdentification>& peptide_ids,
StringList& search_engines_used,
StringList& feature_set,
bool complete_only =
true,
bool limits_imputation =
false);
157 static void addCONCATSEFeatures(std::vector<PeptideIdentification>& peptide_id_list,
StringList& search_engines_used,
StringList& feature_set);
166 static void checkExtraFeatures(
const std::vector<PeptideHit> &psms,
StringList& extra_features);
171 static double rescaleFragmentFeature_(
double featureValue,
int NumMatchedMainIons);
174 static void assignDeltaScore_(std::vector<PeptideHit>& hits,
String score_ref,
String output_ref);
177 static String getScanMergeKey_(std::vector<PeptideIdentification>::iterator it, std::vector<PeptideIdentification>::iterator start);
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:118
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
Base class for TOPP applications.
Definition: TOPPBase.h:150
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a MzIdentML file.
void addLine(const StringType &line)
Definition: TextFile.h:112
For accession dependent sorting of PeptideEvidences.
Definition: PercolatorFeatureSetHelper.h:189
Percolator feature set and integration helper.
Definition: PercolatorFeatureSetHelper.h:67
static void mergeMULTISEProteinIds(std::vector< ProteinIdentification > &all_protein_ids, std::vector< ProteinIdentification > &new_protein_ids)
mergeMULTISEProteinIds
This class serves for reading in and writing OpenSWATH OSW files.
Definition: OSWFile.h:62
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
void write(const std::string &in_osw, const std::string &osw_level, const std::map< std::string, std::vector< double > > &features)
Updates an OpenSWATH OSW SQLite files with the MS1-, MS2- or transition-level results of Percolator.
A more convenient string class.
Definition: String.h:57
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
String & removeWhitespaces()
removes whitespaces (space, tab, line feed, carriage return)
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Representation of a protein hit.
Definition: ProteinHit.h:53
with N-terminus and C-terminus
Definition: Residue.h:152
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
String prefix(SizeType length) const
returns the prefix of length length
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:77
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:106
Unknown file extension.
Definition: FileTypes.h:60
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
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:175
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:109
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
const String & getAccession() const
returns the accession of the protein
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:112
#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
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
Type
Actual file types enum.
Definition: FileTypes.h:58
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
QString toQString() const
Conversion to Qt QString.
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:114
void read(const std::string &in_osw, const std::string &osw_level, std::stringstream &pin_output, const double &ipf_max_peakgroup_pep, const double &ipf_max_transition_isotope_overlap, const double &ipf_min_transition_sn)
Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level as stringstream TXT i...
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:111
OpenSWATH OpenSWATH report (OSW) SQLite DB.
Definition: FileTypes.h:105
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
This class handles csv files. Currently only loading is implemented.
Definition: CsvFile.h:49
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:116
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.
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
For accession dependent sorting of ProteinHits.
Definition: PercolatorFeatureSetHelper.h:180
ExitCodes
Exit codes.
Definition: TOPPBase.h:155
static Type nameToType(const String &name)
Converts a file type name into a Type.
String toString() const
Conversion to String.
void store(const String &filename)
Writes the data to a file.
const String & getProteinAccession() const
get the protein accession the peptide matches to. If not available the empty string is returned.
const double C13C12_MASSDIFF_U
Search parameters of the DB search.
Definition: ProteinIdentification.h:103
String suffix(SizeType length) const
returns the suffix of length length
float toFloat() const
Conversion to float.
Used to load and store idXML files.
Definition: IdXMLFile.h:63
Representation of a peptide hit.
Definition: PeptideHit.h:54