OpenMS
File IO

File IO classes. More...

Collaboration diagram for File IO:

Classes

class  AbsoluteQuantitationMethodFile
 File adapter for AbsoluteQuantitationMethod files. 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. Does NOT support comment lines! 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
 File adapter for Enhanced DTA files. More...
 
class  FeatureXMLFile
 This class provides Input/Output functionality for feature maps. More...
 
class  FileHandler
 Facilitates file handling by file type recognition. 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  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  HDF5Connector
 File adapter for HDF5 files. More...
 
class  IdXMLFile
 Used to load and store idXML files. More...
 
class  InspectInfile
 Inspect input file adapter. More...
 
class  InspectOutfile
 Representation of an Inspect outfile. More...
 
class  KroenikFile
 File adapter for Kroenik (HardKloer sibling) files. More...
 
class  MascotGenericFile
 Read/write Mascot generic files (MGF). More...
 
class  MascotInfile
 Mascot input file adapter. More...
 
class  MascotXMLFile
 Used to load Mascot XML files. More...
 
class  MRMFeatureQCFile
 File adapter for MRMFeatureQC files. More...
 
class  MS2File
 MS2 input file adapter. More...
 
class  MsInspectFile
 File adapter for MsInspect files. More...
 
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  MzQuantMLFile
 File adapter for MzQuantML 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
 File adapter for OMSSACSV files. More...
 
class  OMSSAXMLFile
 Used to load OMSSAXML files. More...
 
class  PepNovoInfile
 PepNovo input file adapter. More...
 
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  ProtXMLFile
 Used to load (storing not supported, yet) ProtXML files. 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  SequestInfile
 Sequest input file adapter. More...
 
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  TextFile
 This class provides some basic file handling methods for text files. More...
 
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  XMLValidator
 Validator for XML files. More...
 
class  XMassFile
 File adapter for 'XMass Analysis (fid)' files. 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...
 

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 String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true, bool load_empty_hits=true)
 loads data from a OMSSAXML file More...
 
void load (const String &filename, std::vector< ResidueModification * > &modifications)
 loads data from unimod.xml file More...
 
void load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, ModificationDefinitionsSet &mod_def_set)
 loads data from an X! Tandem XML file More...
 

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)

Enumeration Type Documentation

◆ 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 String filename,
ProteinIdentification protein_identification,
std::vector< PeptideIdentification > &  id_data,
bool  load_proteins = true,
bool  load_empty_hits = true 
)

loads data from a OMSSAXML file

Parameters
filenameThe file to be loaded
protein_identificationProtein identifications belonging to the whole experiment
id_dataThe identifications with m/z and RT
load_proteinsIf this flag is set to false, the protein identifications are not loaded
load_empty_hitsMany 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.

Exceptions
FileNotFound
ParseError

◆ load() [2/3]

void load ( const String filename,
ProteinIdentification protein_identification,
std::vector< PeptideIdentification > &  id_data,
ModificationDefinitionsSet mod_def_set 
)

loads data from an X! Tandem XML file

Parameters
filenamethe file to be loaded
protein_identificationprotein identifications belonging to the whole experiment
id_datathe identifications with m/z and RT
mod_def_setFixed 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 String filename,
std::vector< ResidueModification * > &  modifications 
)

loads data from unimod.xml file

Parameters
filenamethe filename were the unimod xml file should be read from
modificationsthe modifications which are read from the file
Exceptions
FileNotFoundis thrown if the file could not be found
ParseErroris thrown if the given file could not be parsed