OpenMS  3.0.0
FileHandler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
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34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
43 
44 namespace OpenMS
45 {
46  class PeakFileOptions;
47  class MSSpectrum;
48  class MSExperiment;
49  class FeatureMap;
50  class ConsensusMap;
51  class TargetedExperiment;
52 
66  class OPENMS_DLLAPI FileHandler
67  {
68 public:
77  static FileTypes::Type getType(const String& filename);
78 
79 
81  static FileTypes::Type getTypeByFileName(const String& filename);
82 
89  static bool hasValidExtension(const String& filename, const FileTypes::Type type);
90 
91 
99  static String stripExtension(const String& filename);
100 
108  static String swapExtension(const String& filename, const FileTypes::Type new_type);
109 
110 
123  static FileTypes::Type getConsistentOutputfileType(const String& output_filename, const String& requested_type);
124 
125 
131  static FileTypes::Type getTypeByContent(const String& filename);
132 
134  static bool isSupported(FileTypes::Type type);
135 
137  PeakFileOptions& getOptions();
138 
140  const PeakFileOptions& getOptions() const;
141 
143  void setOptions(const PeakFileOptions&);
144 
160  bool loadExperiment(const String& filename, MSExperiment& exp, FileTypes::Type force_type = FileTypes::UNKNOWN, ProgressLogger::LogType log = ProgressLogger::NONE, const bool rewrite_source_file = true, const bool compute_hash = true);
161 
173  void storeExperiment(const String& filename, const MSExperiment& exp, ProgressLogger::LogType log = ProgressLogger::NONE);
174 
187  bool loadFeatures(const String& filename, FeatureMap& map, FileTypes::Type force_type = FileTypes::UNKNOWN);
188 
199  bool storeFeatures(const String& filename, const FeatureMap& map);
200 
211  bool storeConsensusFeatures(const String& filename, const ConsensusMap& map);
212 
224  bool loadConsensusFeatures(const String& filename, ConsensusMap& map);
225 
226  bool loadIdentifications(const String& filename, std::vector<ProteinIdentification> additional_proteins, std::vector<PeptideIdentification> additional_peptides);
227 
238  bool storeTransitions(const String& filename, const TargetedExperiment& library);
239 
245  static String computeFileHash(const String& filename);
246 
247 private:
249 
250  };
251 
252 } //namespace
253 
IMDataConverter.h
OpenMS::FileTypes::CACHEDMZML
CachedMzML file (.cachedmzML)
Definition: FileTypes.h:71
ConsensusXMLFile.h
OpenMS::UniqueIdInterface::ensureUniqueId
Size ensureUniqueId()
Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was cha...
EDTAFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::ConsensusMap::applyMemberFunction
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all consensus features....
Definition: ConsensusMap.h:333
OpenMS::MSExperiment::getExperimentalSettings
const ExperimentalSettings & getExperimentalSettings() const
returns the meta information of this experiment (const access)
OpenMS::Precursor::SIZE_OF_ACTIVATIONMETHOD
Definition: Precursor.h:103
OpenMS::DataValue::INT_LIST
integer list
Definition: DataValue.h:73
OpenMS::FileTypes::SQMASS
SqLite format for mass and chromatograms, see SqMassFile.
Definition: FileTypes.h:101
OpenMS::MSExperiment::set2DData
void set2DData(const Container &container)
Assignment of a data container with RT and MZ to an MSExperiment.
Definition: MSExperiment.h:239
FileHandler.h
FileTypes.h
OpenMS::InstrumentSettings::SIZE_OF_SCANMODE
Definition: InstrumentSettings.h:69
TextFile.h
OpenMS::ConsensusXMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::SqMassFile::store
void store(const String &filename, MapType &map) const
Store an MSExperiment in sqMass format.
OpenMS::FileTypes::MZDATA
MzData file (.mzData)
Definition: FileTypes.h:61
OpenMS::MzDataFile
File adapter for MzData files.
Definition: MzDataFile.h:53
MapType
PeakMap MapType
Definition: PeakPickerIterative.cpp:84
ConversionHelper.h
Size
OpenMS::MSNumpressCoder::NumpressConfig::linear_fp_mass_acc
double linear_fp_mass_acc
Desired mass accuracy for *linear* encoding.
Definition: MSNumpressCoder.h:131
OpenMS::OMSFile
This class supports reading and writing of OMS files.
Definition: OMSFile.h:48
OpenMS::MSNumpressCoder::NumpressConfig::setCompression
void setCompression(const std::string &compression)
Set compression using a string mapping to enum NumpressCompression.
Definition: MSNumpressCoder.h:149
OpenMS::ConsensusXMLFile::store
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
IdentificationDataConverter.h
OpenMS::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
OpenMS::FeatureFileOptions::setMZRange
void setMZRange(const DRange< 1 > &range)
OpenMS::FeatureFileOptions::setIntensityRange
void setIntensityRange(const DRange< 1 > &range)
OpenMS::DataValue::STRING_VALUE
string value
Definition: DataValue.h:69
OpenMS::IsInIsolationWindowSizeRange
Predicate that determines if the width of the isolation window of an MSn spectrum is in the given ran...
Definition: RangeUtils.h:600
OpenMS::IonSource::Polarity
Polarity
Polarity of the ion source.
Definition: IonSource.h:140
OpenMS::MapConversion::convert
static void convert(UInt64 const input_map_index, PeakMap &input_map, ConsensusMap &output_map, Size n=-1)
Similar to convert for FeatureMaps.
OpenMS::Factory
Returns FactoryProduct* based on the name of the desired concrete FactoryProduct.
Definition: Factory.h:61
OpenMS::Param::insert
void insert(const std::string &prefix, const Param &param)
OpenMS::PeakFileOptions::setIntensity32Bit
void setIntensity32Bit(bool int_32_bit)
OpenMS::Internal::CachedMzMLHandler::readMemdump
void readMemdump(MapType &exp_reading, String filename) const
Read all spectra from a dump from the disk.
OpenMS::ConsensusMap::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position (First RT then m/z).
OpenMS::ConsensusMap::updateRanges
void updateRanges() override
OpenMS::NamesOfIMFormat
const std::string NamesOfIMFormat[(size_t) IMFormat::SIZE_OF_IMFORMAT]
Names of IMFormat.
OpenMS::ChromatogramTools
Conversion class to convert chromatograms.
Definition: ChromatogramTools.h:55
OpenMS::MascotGenericFile::store
void store(const String &filename, const PeakMap &experiment, bool compact=false)
stores the experiment data in a MascotGenericFile that can be used as input for MASCOT shell executio...
OpenMS::MSExperiment::sortSpectra
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
OpenMS::FileHandler::getTypeByFileName
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
OpenMS::HasScanPolarity
Predicate that determines if a spectrum has a certain scan polarity.
Definition: RangeUtils.h:237
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
IBSpectraFile.h
OpenMS::String::toDouble
double toDouble() const
Conversion to double.
OpenMS::Peak2D
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:54
OpenMS::FileTypes::MZML
MzML file (.mzML)
Definition: FileTypes.h:70
OpenMS::FileTypes::MZXML
MzXML file (.mzXML)
Definition: FileTypes.h:62
OpenMS::InstrumentSettings::NamesOfScanMode
static const std::string NamesOfScanMode[SIZE_OF_SCANMODE]
Names of scan modes.
Definition: InstrumentSettings.h:73
OpenMS::MSNumpressCoder::NumpressConfig::estimate_fixed_point
bool estimate_fixed_point
Whether to estimate the fixed point used for encoding (highly recommended)
Definition: MSNumpressCoder.h:123
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name, const DataValue &default_value=DataValue::EMPTY) const
Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not fo...
OpenMS::DataValue::STRING_LIST
string list
Definition: DataValue.h:72
OpenMS::EDTAFile
File adapter for Enhanced DTA files.
Definition: EDTAFile.h:84
OpenMS::ExperimentalSettings
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment::begin
Iterator begin()
Definition: MSExperiment.h:150
OpenMS::BaseFeature
A basic LC-MS feature.
Definition: BaseFeature.h:58
OpenMS::DTA2DFile::store
void store(const String &filename, const MapType &map) const
Stores a map in a DTA2D file.
Definition: DTA2DFile.h:269
OpenMS::DRange< 1 >
MzMLFile.h
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
OpenMS::FeatureFileOptions::getIntensityRange
const DRange< 1 > & getIntensityRange() const
returns the intensity range
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::FileTypes::CONSENSUSXML
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:65
OpenMS::DRange::encloses
bool encloses(const PositionType &position) const
Checks whether this range contains a certain point.
Definition: DRange.h:174
OpenMS::Exception::ConversionError
Invalid conversion exception.
Definition: Exception.h:354
IdXMLFile.h
FeatureXMLFile.h
OpenMS::Constants::c
const double c
Definition: Constants.h:209
OpenMS::ListUtils::contains
static bool contains(const std::vector< T > &container, const E &elem)
Checks whether the element elem is contained in the given container.
Definition: ListUtils.h:162
OpenMS::PeakFileOptions::setNumpressConfigurationMassTime
void setNumpressConfigurationMassTime(MSNumpressCoder::NumpressConfig config)
Get numpress configuration options for m/z or rt dimension.
OpenMS::IMFormat::NONE
no ion mobility
OpenMS::IMTypes::determineIMFormat
static IMFormat determineIMFormat(const MSExperiment &exp)
OpenMS::FileHandler::loadFeatures
bool loadFeatures(const String &filename, FeatureMap &map, FileTypes::Type force_type=FileTypes::UNKNOWN)
Loads a file into a FeatureMap.
DTA2DFile.h
ZhangSimilarityScore.h
OpenMS::MzXMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::SignalToNoiseEstimator::init
virtual void init(const Container &c)
Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimat...
Definition: SignalToNoiseEstimator.h:101
OpenMS::toIMFormat
IMFormat toIMFormat(const std::string &IM_format)
OpenMS::FileTypes::TSV
any TSV file, for example msInspect file or OpenSWATH transition file (see TransitionTSVFile)
Definition: FileTypes.h:86
MSDataCachedConsumer.h
OpenMS::DataValue::EMPTY_VALUE
empty
Definition: DataValue.h:75
OpenMS::MSNumpressCoder::NamesOfNumpressCompression
static const std::string NamesOfNumpressCompression[SIZE_OF_NUMPRESSCOMPRESSION]
Definition: MSNumpressCoder.h:81
OpenMS::AASequence::toString
String toString() const
returns the peptide as string with modifications embedded in brackets
OpenMS::IsZoomSpectrum
Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum.
Definition: RangeUtils.h:302
OpenMS::MzXMLFile
File adapter for MzXML 3.1 files.
Definition: MzXMLFile.h:52
OpenMS::AASequence::toUnmodifiedString
String toUnmodifiedString() const
returns the peptide as string without any modifications or (e.g., "PEPTIDER")
OpenMS::PeakFileOptions::setForceMQCompatability
void setForceMQCompatability(bool forceMQ)
[mzXML only!] Whether to write a scan-index and meta data to indicate a Thermo FTMS/ITMS instrument (...
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:58
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
OpenMS::IdentificationDataConverter::importFeatureIDs
static void importFeatureIDs(FeatureMap &features, bool clear_original=true)
Convert IDs from legacy peptide/protein identifications in a feature map.
OpenMS::DTA2DFile
DTA2D File adapter.
Definition: DTA2DFile.h:63
OpenMS::DataProcessing::CONVERSION_MZML
Conversion to mzML format.
Definition: DataProcessing.h:77
OpenMS::IBSpectraFile
Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantificatio...
Definition: IBSpectraFile.h:56
OpenMS::BaseFeature::getPeptideIdentifications
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
OpenMS::Peak2D::setIntensity
void setIntensity(IntensityType intensity)
Sets data point intensity (height)
Definition: Peak2D.h:172
OpenMS::MSNumpressCoder::NumpressConfig::numpressErrorTolerance
double numpressErrorTolerance
Check error tolerance after encoding.
Definition: MSNumpressCoder.h:108
OpenMS::String::hasSubstring
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
OpenMS::FileTypes::KROENIK
kroenik file (.kroenik)
Definition: FileTypes.h:90
OpenMS::Internal::CachedMzMLHandler::writeMetadata
void writeMetadata(MapType exp, String out_meta, bool addCacheMetaValue=false)
Write only the meta data of an MSExperiment.
OpenMS::BaseFeature::setPeptideIdentifications
void setPeptideIdentifications(const std::vector< PeptideIdentification > &peptides)
sets the PeptideIdentification vector
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
extractCachedMetaFilename
String extractCachedMetaFilename(const String &in)
Definition: FileConverter.cpp:143
OpenMS::InstrumentSettings::SRM
Selected reaction monitoring scan Synonyms: 'Multiple reaction monitoring scan',...
Definition: InstrumentSettings.h:59
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OpenMS::FeatureFileOptions::setRTRange
void setRTRange(const DRange< 1 > &range)
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::Exception::InvalidParameter
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:339
CachedMzML.h
UInt64
OpenMS::Peak2D::setRT
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
OpenMS::InPrecursorMZRange
Predicate that determines if a spectrum's precursor is within a certain m/z range.
Definition: RangeUtils.h:383
OMSFile.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::IBSpectraFile::store
void store(const String &filename, const ConsensusMap &cm)
Writes the contents of the ConsensusMap cm into the file named by filename.
OpenMS::FeatureMap::updateRanges
void updateRanges() override
OpenMS::MSExperiment::addSpectrum
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
OpenMS::SignalToNoiseEstimator::getSignalToNoise
virtual double getSignalToNoise(const Size index) const
Definition: SignalToNoiseEstimator.h:109
OpenMS::PeakFileOptions::setNumpressConfigurationIntensity
void setNumpressConfigurationIntensity(MSNumpressCoder::NumpressConfig config)
Get numpress configuration options for intensity dimension.
OpenMS::IonSource::NamesOfPolarity
static const std::string NamesOfPolarity[SIZE_OF_POLARITY]
Names of polarity of the ion source.
Definition: IonSource.h:148
OpenMS::MSDataCachedConsumer
Transforming and cached writing consumer of MS data.
Definition: MSDataCachedConsumer.h:54
OpenMS::DataValue::INT_VALUE
integer value
Definition: DataValue.h:70
OpenMS::FileTypes::FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:63
OpenMS::DataValue
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:58
OpenMS::MSExperiment::getChromatograms
const std::vector< MSChromatogram > & getChromatograms() const
returns the chromatogram list
ProgressLogger.h
OpenMS::HasScanMode
Predicate that determines if a spectrum has a certain scan mode.
Definition: RangeUtils.h:203
OpenMS::MzMLFile::load
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...
OpenMS::PeakFileOptions::setNumpressConfigurationFloatDataArray
void setNumpressConfigurationFloatDataArray(MSNumpressCoder::NumpressConfig config)
Get numpress configuration options for float data arrays.
OpenMS::IsEmptySpectrum
Predicate that determines if a spectrum is empty.
Definition: RangeUtils.h:272
OpenMS::EDTAFile::load
void load(const String &filename, ConsensusMap &consensus_map)
Loads a EDTA file into a consensusXML.
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::MzXMLFile::store
void store(const String &filename, const MapType &map) const
Stores a map in a MzXML file.
OpenMS::ConsensusMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
OpenMS::ChromatogramTools::convertChromatogramsToSpectra
void convertChromatogramsToSpectra(ExperimentType &exp)
converts the chromatogram to a list of spectra with instrument settings
Definition: ChromatogramTools.h:86
OpenMS::SignalToNoiseEstimatorMedian
Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram ba...
Definition: SignalToNoiseEstimatorMedian.h:81
MzXMLFile.h
OpenMS::FileHandler::loadExperiment
bool loadExperiment(const String &filename, MSExperiment &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool rewrite_source_file=true, const bool compute_hash=true)
Loads a file into an MSExperiment.
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
FeatureMap.h
OpenMS::FileTypes::CSV
general comma separated files format (might also be tab or space separated!!!), data should be regula...
Definition: FileTypes.h:93
RangeUtils.h
ProteinIdentification.h
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::FileHandler::options_
PeakFileOptions options_
Definition: FileHandler.h:248
OpenMS::MSExperiment::setChromatograms
void setChromatograms(const std::vector< MSChromatogram > &chromatograms)
sets the chromatogram list
OpenMS::IsInCollisionEnergyRange
Predicate that determines if an MSn spectrum was generated with a collision energy in the given range...
Definition: RangeUtils.h:548
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::MzXMLFile::transform
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false)
Transforms a map while loading using the supplied MSDataConsumer.
OpenMS::FileHandler::getConsistentOutputfileType
static FileTypes::Type getConsistentOutputfileType(const String &output_filename, const String &requested_type)
Useful function for TOPP tools which have an 'out_type' parameter and want to know what output format...
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::UniqueIdInterface::setUniqueId
Size setUniqueId()
Assigns a new, valid unique id. Always returns 1.
OpenMS::OMSFile::store
void store(const String &filename, const IdentificationData &id_data)
Write out an IdentificationData object to SQL-based OMS file.
OpenMS::Internal::CachedMzMLHandler::writeMemdump
void writeMemdump(const MapType &exp, const String &out) const
Write complete spectra as a dump to the disk.
OpenMS::String::split
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
OpenMS::ConsensusMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::Peak2D::setMZ
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
OpenMS::Feature::setOverallQuality
void setOverallQuality(QualityType q)
Set the overall quality.
OpenMS::Peak2D::RTLess
Comparator by RT position.
Definition: Peak2D.h:274
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::FeatureMap::applyMemberFunction
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all features (including subordinates)....
Definition: FeatureMap.h:289
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::FileTypes::PEPLIST
specArray file (.peplist)
Definition: FileTypes.h:88
MascotGenericFile.h
OpenMS::IMDataConverter::collapseFramesToSingle
static MSExperiment collapseFramesToSingle(const MSExperiment &in)
Collapses multiple MS spectra (each with its own drift time) from the same IM-frame into a single MSS...
OpenMS::ConsensusMap::setProteinIdentifications
void setProteinIdentifications(const std::vector< ProteinIdentification > &protein_identifications)
sets the protein identifications
OpenMS::FileTypes::EDTA
enhanced comma separated files (RT, m/z, Intensity, [meta])
Definition: FileTypes.h:92
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::MascotGenericFile
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:62
OpenMS::IdentificationDataConverter::exportFeatureIDs
static void exportFeatureIDs(FeatureMap &features, bool clear_original=true)
Convert IDs in a feature map to legacy peptide/protein identifications.
OpenMS::Exception::NotImplemented
Not implemented exception.
Definition: Exception.h:428
OpenMS::DataValue::valueType
DataType valueType() const
returns the type of value stored
Definition: DataValue.h:378
OpenMS::FeatureFileOptions::getMZRange
const DRange< 1 > & getMZRange() const
returns the MZ range
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:53
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::FeatureMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::IsInIsolationWindow
Predicate that determines if the isolation window covers ANY of the given m/z values.
Definition: RangeUtils.h:645
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::PeakFileOptions::setMz32Bit
void setMz32Bit(bool mz_32_bit)
OpenMS::DPosition< 1 >
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
OpenMS::IMDataConverter::splitByIonMobility
static MSExperiment splitByIonMobility(MSSpectrum im_frame, UInt number_of_bins=-1)
Split a (TimsTOF) ion mobility frame (i.e. a spectrum concatenated from multiple spectra with differe...
OpenMS::DataValue::EMPTY
static const DataValue EMPTY
Empty data value for comparisons.
Definition: DataValue.h:64
OpenMS::FileTypes::DTA2D
DTA2D file (.dta2d)
Definition: FileTypes.h:60
IMTypes.h
OpenMS::ProgressLogger::LogType
LogType
Possible log types.
Definition: ProgressLogger.h:68
OpenMS::HasPrecursorCharge
Predicate that determines if a spectrum has a certain precursor charge as given in the constructor li...
Definition: RangeUtils.h:431
PeakFileOptions.h
OpenMS::HasActivationMethod
Predicate that determines if a spectrum was generated using any activation method given in the constr...
Definition: RangeUtils.h:335
OpenMS::DataValue::DOUBLE_VALUE
double value
Definition: DataValue.h:71
OpenMS::IMFormat::CONCATENATED
ion mobility frame is stacked in a single spectrum (i.e. has an IM float data array)
OpenMS::IMFormat::MULTIPLE_SPECTRA
ion mobility is recorded as multiple spectra per frame (i.e. has one IM annotation per spectrum)
MSNumpressCoder.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
OpenMS::Feature::setQuality
void setQuality(Size index, QualityType q)
Set the quality in dimension c.
OpenMS::ConsensusMap::getColumnHeaders
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::FileTypes::MGF
Mascot Generic Format (.mgf)
Definition: FileTypes.h:66
OpenMS::PeakFileOptions::setForceTPPCompatability
void setForceTPPCompatability(bool forceTPP)
[mzML only!] Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precurso...
OpenMS::FeatureHandle
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:57
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::PlainMSDataWritingConsumer
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:240
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::PeakFileOptions::setRTRange
void setRTRange(const DRange< 1 > &range)
restricts the range of RT values for peaks to load
OpenMS::MSExperiment::end
Iterator end()
Definition: MSExperiment.h:160
OpenMS::MetaInfoInterface::metaValueExists
bool metaValueExists(const String &name) const
Returns whether an entry with the given name exists.
OpenMS::MSExperiment::getSpectra
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
OpenMS::ConsensusMap::Iterator
std::vector< ConsensusFeature >::iterator Iterator
Mutable iterator.
Definition: ConsensusMap.h:166
OpenMS::FileTypes::RAW
Thermo Raw File (.raw)
Definition: FileTypes.h:113
OpenMS::DataProcessing
Description of the applied preprocessing steps.
Definition: DataProcessing.h:51
OpenMS::MzMLFile::transform
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.
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::IMFormat
IMFormat
Different ways to represent ion mobility data in a spectrum.
Definition: IMTypes.h:66
OpenMS::ConsensusMap::sortByMZ
void sortByMZ()
Sorts the peaks to m/z position.
OpenMS::PeakFileOptions::setCompression
void setCompression(bool compress)
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenMS::MSNumpressCoder::NumpressConfig
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:88
String.h
OpenMS::Precursor::NamesOfActivationMethod
static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
Names of activation methods.
Definition: Precursor.h:106
OpenMS::MzDataFile::store
void store(const String &filename, const MapType &map) const
Stores a map in a MzData file.
MzDataFile.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::DataValue::DOUBLE_LIST
double list
Definition: DataValue.h:74
OpenMS::MSNumpressCoder::SIZE_OF_NUMPRESSCOMPRESSION
Definition: MSNumpressCoder.h:79
OpenMS::MSExperiment::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::ProgressLogger::NONE
No progress logging.
Definition: ProgressLogger.h:72
OpenMS::PeakFileOptions::setIntensityRange
void setIntensityRange(const DRange< 1 > &range)
restricts the range of intensity values for peaks to load
OpenMS::PeakFileOptions::setMZRange
void setMZRange(const DRange< 1 > &range)
restricts the range of MZ values for peaks to load
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:106
OpenMS::ChromatogramTools::convertSpectraToChromatograms
void convertSpectraToChromatograms(ExperimentType &exp, bool remove_spectra=false, bool force_conversion=false)
converts e.g. SRM spectra to chromatograms
Definition: ChromatogramTools.h:139
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::PeakFileOptions::setMSLevels
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
OpenMS::PeakFileOptions::setWriteIndex
void setWriteIndex(bool write_index)
Whether to write an index at the end of the file (e.g. indexedmzML file format)
SqMassFile.h
OpenMS::FeatureFileOptions::getRTRange
const DRange< 1 > & getRTRange() const
returns the RT range
MSDataWritingConsumer.h
PeptideIdentification.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::DataProcessing::FILTERING
Data filtering or extraction.
Definition: DataProcessing.h:71
OpenMS::FeatureMap::sortByPosition
void sortByPosition()
Sort features by position. Lexicographical comparison (first RT then m/z) is done.
OpenMS::InstrumentSettings::ScanMode
ScanMode
scan mode
Definition: InstrumentSettings.h:52
Factory.h
OpenMS::EDTAFile::store
void store(const String &filename, const ConsensusMap &map) const
Stores a ConsensusMap as an enhanced DTA file.
OpenMS::IonSource::SIZE_OF_POLARITY
Definition: IonSource.h:145
OpenMS::String::toInt
Int toInt() const
Conversion to int.
OpenMS::Internal::CachedMzMLHandler
An class that uses on-disk caching to read and write spectra and chromatograms.
Definition: CachedMzMLHandler.h:66
OpenMS::BaseFeature::setCharge
void setCharge(const ChargeType &ch)
Set charge state.
OpenMS::FeatureXMLFile::getOptions
FeatureFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::OMSFile::load
void load(const String &filename, IdentificationData &id_data)
Read in a OMS file and construct an IdentificationData object.
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::FeatureMap::clear
void clear(bool clear_meta_data=true)
Clears all data and meta data.
OpenMS::InIntensityRange
Predicate that determines if a peak lies inside/outside a specific intensity range.
Definition: RangeUtils.h:512
OpenMS::SqMassFile
An class that uses on-disk SQLite database to read and write spectra and chromatograms.
Definition: SqMassFile.h:56
ChromatogramTools.h
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.
OpenMS::FileTypes::OMS
OpenMS database file.
Definition: FileTypes.h:114
OpenMS::DTA2DFile::storeTIC
void storeTIC(const String &filename, const MapType &map) const
Stores the TIC of a map in a DTA2D file.
Definition: DTA2DFile.h:308
SignalToNoiseEstimatorMedian.h
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55
StringListUtils.h
OpenMS::IMFormat::SIZE_OF_IMFORMAT