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OpenMS
2.4.0
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99 while (spectrum.size() < acqus.
getSize())
104 spectrum.push_back(p);
120 if (acqus.
getParam(
".IONIZATION MODE") ==
"LD+")
124 else if (acqus.
getParam(
".IONIZATION MODE") ==
"LD-")
142 source_file.
setFileType(
"Xmass analysis file (fid)");
147 software.
setName(
"FlexControl");
151 fc_ver = fc_ver.
suffix(
' ');
155 fc_ver = fc_ver.
prefix(
'>');
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)) );
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-")
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")
Description of the software used for processing.
Definition: Software.h:48
@ IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
@ MASSSPECTRUM
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
String getParam(const String ¶m)
Read param as string.
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
@ TOF
Time-of-flight.
Definition: MassAnalyzer.h:59
const Instrument & getInstrument() const
returns a const reference to the MS instrument description
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
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:77
String toUnmodifiedString() const
returns the peptide as string without any modifications
void setDateTime(const DateTime &date)
sets the date the experiment was performed
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
profile data
Definition: SpectrumSettings.h:74
double getPosition(Size index)
Conversion from index to MZ ratio using internal calibration params.
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
@ XQUESTXML
xQuest XML file format for protein-protein cross-link identifications (.xquest.xml)
Definition: FileTypes.h:111
@ DIRECT
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
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
Positive polarity.
Definition: IonSource.h:142
@ SMOOTHING
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.
Size getSize()
Get size of spectrum.
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
@ MALDI
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
@ POLNULL
Unknown.
Definition: IonSource.h:141
String toString() const
Conversion to String.
String & remove(char what)
Remove all occurrences of the character what.
int getNumberOfHits() const
Returns the total number of hits in the file.
@ NEGATIVE
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
@ ANALYZERNULL
Unknown.
Definition: MassAnalyzer.h:54
Size getIntensity()
Get intensity of current position and move to next position.
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)
Size getIndex()
Get index of current position (without position moving).
void setInstrumentSettings(const InstrumentSettings &instrument_settings)
sets the instrument settings of the current spectrum
@ INLETNULL
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
Baseline reduction.
Definition: DataProcessing.h:66
Representation of a peptide hit.
Definition: PeptideHit.h:54