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OpenMS
2.4.0
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99 while (spectrum.size() < acqus.getSize())
104 spectrum.push_back(p);
111 spectrum.
setName(
"Xmass analysis file " + acqus.getParam(
"$ID_raw"));
113 spectrum.
setNativeID(
"spectrum=xsd:" + acqus.getParam(
"$ID_raw").remove(
'<').remove(
'>'));
120 if (acqus.getParam(
".IONIZATION MODE") ==
"LD+")
124 else if (acqus.getParam(
".IONIZATION MODE") ==
"LD-")
141 source_file.
setFileSize(4.0 * acqus.getSize() / 1024 / 1024);
142 source_file.
setFileType(
"Xmass analysis file (fid)");
147 software.
setName(
"FlexControl");
148 String fc_ver = acqus.getParam(
"$FCVer");
151 fc_ver = fc_ver.
suffix(
' ');
155 fc_ver = fc_ver.
prefix(
'>');
158 software.
setMetaValue(
"Acquisition method",
DataValue(acqus.getParam(
"$ACQMETH").remove(
'<').remove(
'>')));
160 std::set<DataProcessing::ProcessingAction> actions;
167 std::vector< boost::shared_ptr< DataProcessing> > data_processing_vector;
168 data_processing_vector.push_back( boost::shared_ptr< DataProcessing>(
new DataProcessing(data_processing)) );
186 Instrument & instrument = experimental_settings.getInstrument();
187 instrument.
setName(acqus.getParam(
"SPECTROMETER/DATASYSTEM"));
188 instrument.
setVendor(acqus.getParam(
"ORIGIN"));
189 instrument.
setModel(acqus.getParam(
"$InstrID").remove(
'<').remove(
'>'));
191 std::vector<IonSource> & ionSourceList = instrument.
getIonSources();
192 ionSourceList.clear();
193 ionSourceList.resize(1);
194 if (acqus.getParam(
".INLET") ==
"DIRECT")
203 if (acqus.getParam(
".IONIZATION MODE") ==
"LD+")
207 else if (acqus.getParam(
".IONIZATION MODE") ==
"LD-")
215 ionSourceList[0].setMetaValue(
"MALDI target reference",
DataValue(acqus.getParam(
"$TgIDS").remove(
'<').remove(
'>')));
216 ionSourceList[0].setOrder(0);
218 std::vector<MassAnalyzer> & massAnalyzerList = instrument.
getMassAnalyzers();
219 massAnalyzerList.clear();
220 massAnalyzerList.resize(1);
221 if (acqus.getParam(
".SPECTROMETER TYPE") ==
"TOF")
231 date.
set(acqus.getParam(
"$AQ_DATE").remove(
'<').remove(
'>'));
232 experimental_settings.setDateTime(date);
Description of the software used for processing.
Definition: Software.h:48
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
general spectrum type
Definition: InstrumentSettings.h:55
Description of the settings a MS Instrument was run with.
Definition: InstrumentSettings.h:47
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.
const ExperimentalSettings & getExperimentalSettings() const
returns the meta information of this experiment (const access)
void setName(const String &name)
sets the name of the software
void setModel(const String &model)
sets the instrument model
void setPathToFile(const String &path_path_to_file)
sets the file path
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:52
Time-of-flight.
Definition: MassAnalyzer.h:59
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
void setPolarity(IonSource::Polarity polarity)
sets the polarity
void setVendor(const String &vendor)
sets the instrument vendor
void setIdentifier(const String &id)
sets the identifier
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
void setNameOfFile(const String &name_of_file)
sets the file name
const std::vector< MassAnalyzer > & getMassAnalyzers() const
returns a const reference to the mass analyzer list
const std::vector< IonSource > & getIonSources() const
returns a const reference to the ion source list
void load(const String &filename, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids)
Load the content of the xquest.xml file into the provided data structures.
Description of the experimental settings.
Definition: ExperimentalSettings.h:58
A more convenient string class.
Definition: String.h:57
const std::string PRECURSOR_ERROR_PPM_USERPARAM
File not found exception.
Definition: Exception.h:523
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
#define LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:446
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
void setType(SpectrumType type)
sets the spectrum type
String prefix(SizeType length) const
returns the prefix of length length
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:110
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:77
String toUnmodifiedString() const
returns the peptide as string without any modifications
void load(const String &filename, MSSpectrum &spectrum)
Loads a spectrum from a XMass file.
Definition: XMassFile.h:83
void setDataProcessing(const std::vector< DataProcessingPtr > &data_processing)
sets the description of the applied processing
void setCompletionTime(const DateTime &completion_time)
sets the time of completion taking a DateTime object
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
profile data
Definition: SpectrumSettings.h:74
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
void setVersion(const String &version)
sets the software version
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
static DateTime now()
Returns the current date and time.
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
Description of a MS instrument.
Definition: Instrument.h:63
void setFileSize(float file_size)
sets the file size in MB
void setComment(const String &comment)
sets the free-text comment
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Representation of a histogram.
Definition: Histogram.h:63
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
void setSourceFile(const SourceFile &source_file)
sets the source file
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
#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
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
Type
Actual file types enum.
Definition: FileTypes.h:58
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
xQuest XML file format for protein-protein cross-link identifications (.xquest.xml)
Definition: FileTypes.h:111
Direct.
Definition: IonSource.h:54
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
void setScanMode(ScanMode scan_mode)
sets the scan mode
void setPosition(PositionType const &position)
Mutable access to the position.
Definition: Peak1D.h:149
File adapter for 'XMass Analysis (fid)' files.
Definition: XMassFile.h:66
void clear(bool clear_meta_data)
Clears all data and meta data.
void setMSLevel(UInt ms_level)
Sets the MS level.
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
Not implemented exception.
Definition: Exception.h:436
void set(UInt month, UInt day, UInt year, UInt hour, UInt minute, UInt second)
sets data from six integers
Calibration of m/z positions.
Definition: DataProcessing.h:69
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
static void getCumulativeHistogram(DataIterator begin, DataIterator end, bool complement, bool inclusive, Histogram< ValueType, BinSizeType > &histogram)
Definition: Histogram.h:249
void setMethodOfCombination(const String &method_of_combination)
sets the method of combination
void setSoftware(const Software &software)
sets the software used for processing
void setProcessingActions(const std::set< ProcessingAction > &actions)
sets the description of the applied processing
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
Positive polarity.
Definition: IonSource.h:142
Smoothing of the signal to reduce noise.
Definition: DataProcessing.h:63
void setZoomScan(bool zoom_scan)
sets if this scan is a zoom (enhanced resolution) scan
const std::vector< PeptideEvidence > & getPeptideEvidences() const
returns information on peptides (potentially) identified by this PSM
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.
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
void setName(const String &name)
sets the name of the instrument
Description of the applied preprocessing steps.
Definition: DataProcessing.h:51
Read-only fid File handler for XMass Analysis.
Definition: FidHandler.h:51
Matrix-assisted laser desorption ionization.
Definition: IonSource.h:106
void setName(const String &name)
Sets the name.
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:46
Unknown.
Definition: IonSource.h:141
String toString() const
Conversion to String.
int getNumberOfHits() const
Returns the total number of hits in the file.
Negative polarity.
Definition: IonSource.h:143
void setAcquisitionInfo(const AcquisitionInfo &acquisition_info)
sets the acquisition info
Centralizes the file types recognized by FileHandler.
Definition: FileTypes.h:53
const String & getProteinAccession() const
get the protein accession the peptide matches to. If not available the empty string is returned.
void setFileType(const String &file_type)
sets the file type
Unknown.
Definition: MassAnalyzer.h:54
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
void store(const String &, const MSSpectrum &)
Stores a spectrum in a XMass file (not available)
Definition: XMassFile.h:240
Search parameters of the DB search.
Definition: ProteinIdentification.h:103
String suffix(SizeType length) const
returns the suffix of length length
void setRT(double rt)
Sets the absolute retention time (in seconds)
void setInstrumentSettings(const InstrumentSettings &instrument_settings)
sets the instrument settings of the current spectrum
Unknown.
Definition: IonSource.h:53
DateTime Class.
Definition: DateTime.h:54
Read-only acqus File handler for XMass Analysis.
Definition: AcqusHandler.h:52
Used to load and store idXML files.
Definition: IdXMLFile.h:63
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
void importExperimentalSettings(const String &filename, PeakMap &exp)
Import settings from a XMass file.
Definition: XMassFile.h:180
Baseline reduction.
Definition: DataProcessing.h:66
Representation of a peptide hit.
Definition: PeptideHit.h:54