OpenMS  3.0.0
OpenSwathOSWWriter.h
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31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger $
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34 
35 #pragma once
36 
37 // Interfaces
39 
41 
43 
44 #include <fstream>
45 
46 namespace OpenMS
47 {
48 
115  class OPENMS_DLLAPI OpenSwathOSWWriter
116  {
120  bool doWrite_;
122  bool sonar_;
124 
125  public:
126 
127  OpenSwathOSWWriter(const String& output_filename,
128  const UInt64 run_id,
129  const String& input_filename = "inputfile",
130  bool ms1_scores = false,
131  bool sonar = false,
132  bool uis_scores = false);
133 
134  bool isActive() const;
135 
140  void writeHeader();
141 
153  String getScore(const Feature& feature, std::string score_name) const;
154 
166  std::vector<String> getSeparateScore(const Feature& feature, std::string score_name) const;
167 
182  String prepareLine(const OpenSwath::LightCompound& /* pep */,
183  const OpenSwath::LightTransition* /* transition */,
184  const FeatureMap& output, const String& id) const;
185 
199  void writeLines(const std::vector<String>& to_osw_output);
200 
201  };
202 
203 }
204 
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::FileTypes::SQMASS
SqLite format for mass and chromatograms, see SqMassFile.
Definition: FileTypes.h:101
FileHandler.h
FileTypes.h
OpenMS::SqMassFile::store
void store(const String &filename, MapType &map) const
Store an MSExperiment in sqMass format.
MapType
PeakMap MapType
Definition: PeakPickerIterative.cpp:84
Size
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
OpenMS::Internal::CachedMzMLHandler::readMemdump
void readMemdump(MapType &exp_reading, String filename) const
Read all spectra from a dump from the disk.
OpenMS::FileHandler::getTypeByFileName
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::FileTypes::MZML
MzML file (.mzML)
Definition: FileTypes.h:70
OpenMS::OpenSwathOSWWriter::run_id_
OpenMS::UInt64 run_id_
Definition: OpenSwathOSWWriter.h:119
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MSDataSqlConsumer.h
OpenMS::SqMassFile::load
void load(const String &filename, MapType &map) const
OpenMS::OpenSwathOSWWriter
Class to write out an OpenSwath OSW SQLite output (PyProphet input).
Definition: OpenSwathOSWWriter.h:115
MzMLFile.h
TransitionExperiment.h
OpenMS::OpenSwathOSWWriter::doWrite_
bool doWrite_
Definition: OpenSwathOSWWriter.h:120
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
MSDataCachedConsumer.h
OpenMS::SqMassFile::SqMassConfig::linear_fp_mass_acc
double linear_fp_mass_acc
desired mass accuracy for numpress linear encoding (-1 no effect, use 0.0001 for 0....
Definition: SqMassFile.h:69
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:58
OpenMS::Internal::CachedMzMLHandler::writeMetadata
void writeMetadata(MapType exp, String out_meta, bool addCacheMetaValue=false)
Write only the meta data of an MSExperiment.
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::ChromatogramSettings::getDataProcessing
std::vector< DataProcessingPtr > & getDataProcessing()
returns a mutable reference to the description of the applied processing
OpenMS::SqMassFile::SqMassConfig::use_lossy_numpress
bool use_lossy_numpress
use lossy numpress compression
Definition: SqMassFile.h:68
CachedMzML.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenSwath::LightCompound
Definition: TransitionExperiment.h:160
UniqueIdGenerator.h
OpenMS::MetaInfoInterface::removeMetaValue
void removeMetaValue(const String &name)
Removes the DataValue corresponding to name if it exists.
OpenMS::MSDataCachedConsumer
Transforming and cached writing consumer of MS data.
Definition: MSDataCachedConsumer.h:54
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
OpenMS::MSExperiment::getChromatograms
const std::vector< MSChromatogram > & getChromatograms() const
returns the chromatogram list
ProgressLogger.h
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::MSDataSqlConsumer
A data consumer that inserts MS data into a SQLite database.
Definition: MSDataSqlConsumer.h:60
CachedMzMLHandler.h
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
OpenMS::SqMassFile::setConfig
void setConfig(const SqMassConfig &config)
Definition: SqMassFile.h:100
FeatureMap.h
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::MSExperiment::setChromatograms
void setChromatograms(const std::vector< MSChromatogram > &chromatograms)
sets the chromatogram list
OpenMS::MSExperiment::getNrChromatograms
Size getNrChromatograms() const
get the total number of chromatograms available
OpenMS::OpenSwathOSWWriter::input_filename_
String input_filename_
Definition: OpenSwathOSWWriter.h:118
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::Internal::CachedMzMLHandler::writeMemdump
void writeMemdump(const MapType &exp, const String &out) const
Write complete spectra as a dump to the disk.
OpenMS::OpenSwathOSWWriter::output_filename_
String output_filename_
Definition: OpenSwathOSWWriter.h:117
OpenMS::OpenSwathOSWWriter::sonar_
bool sonar_
Definition: OpenSwathOSWWriter.h:122
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::OpenSwathOSWWriter::enable_uis_scoring_
bool enable_uis_scoring_
Definition: OpenSwathOSWWriter.h:123
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
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::MSExperiment::getChromatogram
MSChromatogram & getChromatogram(Size id)
returns a single chromatogram
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::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
OpenMS::SqMassFile::SqMassConfig::write_full_meta
bool write_full_meta
write full meta data
Definition: SqMassFile.h:67
SqMassFile.h
OpenMS::SqMassFile::transform
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false) const
MSDataWritingConsumer.h
OpenSwath::LightTransition
Definition: TransitionExperiment.h:45
OpenMS::MzMLFile::setOptions
void setOptions(const PeakFileOptions &)
set options for loading/storing
OpenMS::PeakFileOptions::setMaxDataPoolSize
void setMaxDataPoolSize(Size size)
Set maximal size of the data pool.
OpenMS::OpenSwathOSWWriter::use_ms1_traces_
bool use_ms1_traces_
Definition: OpenSwathOSWWriter.h:121
OpenMS::SqMassFile::SqMassConfig
Configuration class for SqMassFile.
Definition: SqMassFile.h:65
OpenMS::Internal::CachedMzMLHandler
An class that uses on-disk caching to read and write spectra and chromatograms.
Definition: CachedMzMLHandler.h:66
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::SqMassFile
An class that uses on-disk SQLite database to read and write spectra and chromatograms.
Definition: SqMassFile.h:56
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.