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OpenMS
2.6.0
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73 void load(
const String & filename,
ProteinIdentification & protein_identification, std::vector<PeptideIdentification> & id_data)
const;
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:273
void setProgress(SignedSize value) const
Sets the current progress.
Base class for TOPP applications.
Definition: TOPPBase.h:144
File adapter for OMSSACSV files.
Definition: OMSSACSVFile.h:54
void setMetadataOnly(bool only)
sets whether or not to load only meta data
const std::vector< EmpiricalFormula > & getNeutralLossDiffFormulas() const
returns the neutral loss diff formula (if available)
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.
Representation of a modification.
Definition: ResidueModification.h:76
void getAllOMSSANames(std::vector< String > &all_names) const
returns all the enzyme names available for OMSSA
Definition: ResidueModification.h:97
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
PeakMassType
Peak mass type.
Definition: ProteinIdentification.h:247
Iterator end()
Definition: AASequence.h:585
bool has(const Key &key) const
Test whether the map contains the given key.
Definition: Map.h:108
double getDiffAverageMass() const
returns the difference average mass, or 0.0 if not set
void setSearchEngineVersion(const String &search_engine_version)
Sets the search engine version.
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:268
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
Used to load OMSSAXML files.
Definition: OMSSAXMLFile.h:60
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
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
Definition: ResidueModification.h:99
Definition: ProteinIdentification.h:249
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
bool operator<(const QTCluster &q1, const QTCluster &q2)
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
void endProgress() const
Ends the progress display.
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:270
static String find(const String &filename, StringList directories=StringList())
Looks up the location of the file filename.
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:193
Iterator class for AASequence.
Definition: AASequence.h:256
void setModification(Size index, const String &modification)
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
const String & getIdentifier() const
Returns the identifier.
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:264
const DigestionEnzymeType * getEnzyme(const String &name) const
Definition: DigestionEnzymeDB.h:98
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Definition: ProteinIdentification.h:250
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:267
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:265
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
char getOrigin() const
Returns the origin (i.e. modified amino acid)
void setPrimaryMSRunPath(const StringList &s, bool raw=false)
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
Definition: ResidueModification.h:98
String db
The used database.
Definition: ProteinIdentification.h:261
void setNTerminalModification(const String &modification)
const std::vector< ProteinHit > & getHits() const
Returns the protein hits.
double getDiffMonoMass() const
returns the diff monoisotopic mass, or 0.0 if not set
void setCTerminalModification(const String &modification)
QString toQString() const
Conversion to Qt QString.
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:61
void setSearchParameters(const SearchParameters &search_parameters)
Sets the search parameters.
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:269
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:266
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void setSearchEngine(const String &search_engine)
Sets the search engine type.
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:271
void setModificationDefinitionsSet(const ModificationDefinitionsSet &rhs)
sets the valid modifications
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
Parse Error exception.
Definition: Exception.h:622
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...
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.
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
Logger::LogStream OpenMS_Log_info
Global static instance of a LogStream to capture messages classified as information....
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:272
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
Iterator begin()
Definition: AASequence.h:581
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
File is empty.
Definition: Exception.h:594
void setHits(const std::vector< ProteinHit > &hits)
Sets the protein hits.
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
String suffix(SizeType length) const
returns the suffix of length length
void load(const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true, bool load_empty_hits=true)
loads data from a OMSSAXML file
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
void setOptions(const PeakFileOptions &)
set options for loading/storing
TermSpecificity getTermSpecificity() const
returns terminal specificity
String taxonomy
The taxonomy restriction.
Definition: ProteinIdentification.h:263
const ResidueModification * getModification(Size index) const
Returns the modification with the given index. note: out-of-bounds check is only performed in debug m...
std::ifstream infile
Questionable file tested by TEST_FILE_EQUAL.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
static void writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
Writes all parameters to meta values.
Used to load and store idXML files.
Definition: IdXMLFile.h:63