File IO classes. More...

Collaboration diagram for File IO:

Namespaces
namespace	OpenMS::ArrowIOHelpers
	Public helpers for writing and concatenating Arrow tables to Parquet files.

Classes
class	SpectrumAccessOpenMSCached
	OpenSwath::ISpectrumAccess implementation backed by an on-disk OpenMS::CachedmzML cache. More...

class	SpectrumAccessOpenMSInMemory
	OpenSwath::ISpectrumAccess implementation that holds the complete spectrum / chromatogram payload in memory. More...

class	SpectrumAccessSqMass
	OpenSwath::ISpectrumAccess implementation backed by an sqMass (SQLite) spectrum store. More...

class	TransitionParquetFile
	Read OpenSwath Parquet library input (.oswpq) into LightTargetedExperiment. More...

class	AbsoluteQuantitationMethodFile
	File adapter for AbsoluteQuantitationMethod files. More...

class	Bzip2Ifstream
	Streaming decompressor for bzip2 (.bz2) files. More...

class	CachedmzML
	Random-access reader/writer for the OpenMS on-disk cache format. More...

class	CompressedInputSource
	Xerces `InputSource` that opens a bzip2-, zip- or gzip-compressed file on demand. More...

class	ConsensusMapArrowExport
	Export ConsensusMap feature data to Apache Arrow format following QPX feature schema. More...

class	ConsensusMapArrowIO
	Import and export ConsensusMap data to/from Apache Arrow format. More...

class	ConsensusXMLFile
	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More...

class	CsvFile
	This class handles csv files. Currently only loading is implemented. More...

class	CVMappingFile
	Used to load CvMapping files. More...

class	DTA2DFile
	DTA2D File adapter. More...

class	DTAFile
	File adapter for DTA files. More...

class	EDTAFile

class	FeatureMapArrowIO
	Import and export FeatureMap data to/from Apache Arrow format. More...

class	FeatureXMLFile
	This class provides Input/Output functionality for feature maps. More...

class	FileHandler
	Facilitates file handling by file type recognition. More...

class	FileInfo
	Library-level equivalent of the FileInfo tool. More...

struct	FileTypes
	Centralizes the file types recognized by FileHandler. More...

class	FLASHDeconvFeatureFile
	FLASHDeconv feature level output .tsv, .ms1ft (for Promex), *.feature (for TopPIC) file formats. More...

class	FLASHDeconvSpectrumFile
	FLASHDeconv Spectrum level output .tsv, .msalign (for TopPIC) file formats. More...

class	GNPSMetaValueFile
	Writer for the meta-value (.TSV) table consumed by GNPS Feature-Based Molecular Networking. More...

class	GNPSMGFFile
	Writer for the consensus-spectrum MGF file consumed by GNPS Feature-Based / Ion-Identity Molecular Networking. More...

class	GNPSQuantificationFile
	Writer for the feature-quantification (.TXT) table required by GNPS Feature-Based Molecular Networking. More...

class	ConsensusXMLHandler
	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More...

class	FeatureXMLHandler
	This class provides Input/Output functionality for feature maps. More...

class	ImzMLHandler
	SAX2 handler for imzML 1.1.0 files, extending OpenMS MzMLHandler. More...

struct	ImzMLMeta
	Dataset-level metadata for imzML mass spectrometry imaging files. More...

struct	ImzMLSpectrumIndex
	Per-spectrum binary index entry for an imzML dataset. More...

class	ImzMLBinaryIO
	Shared .ibd binary array decode utilities for imzML handlers. More...

class	ImzMLWriter
	Writer for imzML 1.1.0 files (.imzML + companion .ibd). More...

class	MzMLSqliteSwathHandler
	Read-only accessor for SWATH/DIA spectrum indices stored in an sqMass file. More...

class	HDF5Connector
	File adapter for HDF5 files. More...

class	IdXMLFile
	Used to load and store idXML files. More...

class	ImzMLFile
	File adapter for imzML 1.1.0 mass spectrometry imaging data. More...

class	InspectInfile
	Inspect input file adapter. More...

class	KroenikFile
	File adapter for Kroenik (HardKloer sibling) files. More...

class	MascotGenericFile
	Read/write Mascot generic files (MGF). More...

class	MascotXMLFile
	Used to load Mascot XML files. More...

class	MRMFeaturePickerFile
	Loads MRM component and component-group parameter sets from a comma-separated file. More...

class	MRMFeatureQCFile
	File adapter for MRMFeatureQC files. More...

class	MS2File

class	MSExperimentArrowExport
	Export MSExperiment data to Apache Arrow format. More...

class	MsInspectFile

class	MSPFile
	File adapter for MSP files (NIST spectra library) More...

class	MSstatsFile
	File adapter for MSstats files. More...

class	MzDataFile
	File adapter for MzData files. More...

class	MzIdentMLFile
	File adapter for MzIdentML files. More...

class	MzMLFile
	File adapter for MzML files. More...

class	MzQCFile
	File adapter for mzQC files used to load and store mzQC files. More...

class	MzTabModification
	Data model of MzTab files. More...

class	MzTab
	Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...

class	MzTabFile
	File adapter for MzTab files. More...

struct	CompareMzTabMMatchRef
	Data model of MzTabM files. Please see the official MzTabM specification at https://github.com/HUPO-PSI/mzTab/tree/master/specification_document-releases/2_0-Metabolomics-Release. More...

class	MzTabMFile
	File adapter for MzTab-M files. More...

class	MzXMLFile
	File adapter for MzXML 3.1 files. More...

class	OMSSACSVFile

class	OMSSAXMLFile
	Used to load OMSSAXML files. More...

class	FeatureFileOptions
	Options for loading files containing features. More...

class	ParquetFile
	Shared utilities for reading, writing, and packaging Parquet-based file formats. More...

class	PEFFFile
	This class serves for reading and writing PEFF (PSI Extended FASTA Format) files. More...

class	PepNovoInfile

class	PepNovoOutfile
	Representation of a PepNovo output file. More...

class	PepXMLFile
	Used to load and store PepXML files. More...

class	PepXMLFileMascot
	Used to load Mascot PepXML files. More...

class	ProteinGroupArrowExport
	Export protein group data to Apache Arrow format following QPX pg schema. More...

class	ProteinIdentificationArrowIO
	Import and export ProteinIdentification data to/from Apache Arrow format. More...

class	ProtXMLFile
	Used to load (storing not supported, yet) ProtXML files. More...

class	PSMArrowIO
	Read and write OpenMS identification data as a parquet bundle (.idparquet). More...

class	PTMXMLFile
	Used to load and store PTMXML files. More...

class	QcMLFile
	File adapter for QcML files used to load and store QcML files. More...

class	QPXFile
	Export PSM (Peptide Spectrum Match) data to Apache Arrow format following QPX PSM schema. More...

class	SequestInfile

class	SequestOutfile
	Representation of a Sequest output file. More...

class	SpecArrayFile
	File adapter for SpecArray (.pepList) files. More...

class	SqliteConnector
	File adapter for Sqlite files. More...

class	SqMassFile
	Read and write mass-spectrometry data in the on-disk `sqMass` (SQLite) format. More...

class	TextFile

class	ToolDescriptionFile
	File adapter for ToolDescriptor files. More...

class	TraMLFile
	File adapter for HUPO PSI TraML files. More...

class	TransformationXMLFile
	Used to load and store TransformationXML files. More...

class	TriqlerFile
	File adapter for Triqler files. More...

class	UnimodXMLFile
	Used to load XML files from unimod.org files. More...

class	MzDataValidator
	Semantic validator for mzData files. More...

class	MzIdentMLValidator
	Semantic validator for mzIdentML files. More...

class	MzMLValidator
	Semantic validator for mzML files. More...

class	XMLValidator
	Validator for XML files. More...

class	XMassFile

class	XMLFile
	Base class for loading and storing XML files via Xerces, with optional schema validation and transparent gzip / bzip2 / zip decompression on load. More...

class	XQuestResultXMLFile
	Used to load and store xQuest result files. More...

class	XTandemInfile
	XTandem input file. More...

class	XTandemXMLFile
	Used to load XTandemXML files. More...

class	ZipIfstream
	Streaming reader for the single non-directory entry of a ZIP archive. More...

class	ZlibCompression
	Compresses and uncompresses arbitrary byte buffers using zlib. More...

Enumerations
enum	MzTabCellStateType { MZTAB_CELLSTATE_DEFAULT , MZTAB_CELLSTATE_NULL , MZTAB_CELLSTATE_NAN , MZTAB_CELLSTATE_INF , SIZE_OF_MZTAB_CELLTYPE }
	Base functionality to for MzTab data models. More...

Functions
void	load (const std::string &filename, ProteinIdentification &protein_identification, PeptideIdentificationList &id_data, bool load_proteins=true, bool load_empty_hits=true)
	loads data from a OMSSAXML file

void	load (const std::string &filename, std::vector< ResidueModification * > &modifications)
	loads data from unimod.xml file

void	load (const std::string &filename, ProteinIdentification &protein_identification, PeptideIdentificationList &id_data, ModificationDefinitionsSet &mod_def_set)
	loads data from an X! Tandem XML file

Detailed Description

File IO classes.

This module contains all classes that are involved in file IO. Take a look at the FileHandler class!

Todo:

Implement reading of pepXML and protXML (Andreas)

Allow reading of zipped XML files (David, Hiwi)

Class Documentation

◆ OpenMS::ImzMLMeta

struct OpenMS::ImzMLMeta

Dataset-level metadata for imzML mass spectrometry imaging files.

imzML (HUPO-PSI standard v1.1.0) extends mzML with a companion binary file (.ibd) and IMS ontology CV terms (IMS:*) that describe the imaging geometry, binary layout, and file checksum.

ImzMLFile::load stores these fields on the loaded MSExperiment as MetaValues (see ImzMLFile documentation).

See also: ImzMLFile, OnDiscImzMLExperiment, Internal::ImzMLHandler

Collaboration diagram for ImzMLMeta:

[legend]

Class Members
string	ibd_file_path	Absolute path to the .ibd file.
string	ibd_md5	MD5 checksum (IMS:1000090), empty if absent.
string	ibd_sha1	SHA-1 checksum (IMS:1000091), empty if absent.
string	imaging_mode	"continuous" (shared m/z array) or "processed" (per-spectrum m/z).
string	int_data_type	same set as mz_data_type
string	line_scan_direction	"left-right" \| "right-left" (IMS:1000491/492)
uint32_t	max_count_x {0}	Max pixel column (IMS:1000042)
uint32_t	max_count_y {0}	Max pixel row (IMS:1000043)
uint32_t	max_count_z {1}	Max depth slice (usually 1 for 2-D datasets)
double	max_dim_x {0}	Physical x extent in µm (IMS:1000044)
double	max_dim_y {0}	Physical y extent in µm (IMS:1000045)
string	mz_data_type	"float32" \| "float64" \| "int32" \| "int64"
double	pixel_size_x {0}	Physical pixel width in µm (IMS:1000046)
double	pixel_size_y {0}	Physical pixel height in µm (IMS:1000047)
string	polarity	"positive" \| "negative" (MS:1000130/129)
string	scan_direction	"flyback" \| "meander" \| "horizontal" \| "vertical"
string	scan_pattern	"top down" \| "bottom up" (IMS:1000401/402)
string	uuid	Dataset UUID (IMS:1000080)

Enumeration Type Documentation

◆ MzTabCellStateType

enum MzTabCellStateType

Base functionality to for MzTab data models.

MzTab supports null, NaN, Inf for cells with Integer or Double values. MzTabCellType explicitly defines the state of the cell for these types.

Enumerator
MZTAB_CELLSTATE_DEFAULT
MZTAB_CELLSTATE_NULL
MZTAB_CELLSTATE_NAN
MZTAB_CELLSTATE_INF
SIZE_OF_MZTAB_CELLTYPE

Function Documentation

◆ load() [1/3]

void load	(	const std::string &	filename,
		ProteinIdentification &	protein_identification,
		PeptideIdentificationList &	id_data,
		bool	load_proteins = `true`,
		bool	load_empty_hits = `true`
	)

loads data from a OMSSAXML file

Parameters

[in]	filename	The file to be loaded
[in]	protein_identification	Protein identifications belonging to the whole experiment
[in]	id_data	The identifications with m/z and RT
[in]	load_proteins	If this flag is set to false, the protein identifications are not loaded
[in]	load_empty_hits	Many spectra will not return a hit. Report empty peptide identifications?

This class serves to read in a OMSSAXML file. The information can be retrieved via the load function.

@exception FileNotFound
@exception ParseError

◆ load() [2/3]

void load	(	const std::string &	filename,
		ProteinIdentification &	protein_identification,
		PeptideIdentificationList &	id_data,
		ModificationDefinitionsSet &	mod_def_set
	)

loads data from an X! Tandem XML file

Parameters

[in]	filename	the file to be loaded
[in]	protein_identification	protein identifications belonging to the whole experiment
[in]	id_data	the identifications with m/z and RT
[in]	mod_def_set	Fixed and variable modifications defined for the search. May be extended with additional (X! Tandem default) modifications if those are found in the file.

This class serves to read in an X! Tandem XML file. The information can be retrieved via the load function.

◆ load() [3/3]

void load	(	const std::string &	filename,
		std::vector< ResidueModification * > &	modifications
	)

loads data from unimod.xml file

@param[in] filename the filename were the unimod xml file should be read from
@param[in] modifications the modifications which are read from the file
@throw FileNotFound is thrown if the file could not be found
@throw ParseError is thrown if the given file could not be parsed

Namespaces

Classes

Enumerations

Functions