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Classes | Enumerations | Functions
File IO

File IO classes. More...

Classes

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
 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  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
 Mascot input file adapter. More...
 
class  MascotInfile
 Mascot input file adapter. More...
 
class  MascotXMLFile
 Used to load MascotXML 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  MzDataFile
 File adapter for MzData files. More...
 
class  MzIdentMLFile
 File adapter for MzIdentML files. More...
 
class  MzMLFile
 File adapter for MzML files. More...
 
class  MzQuantMLFile
 File adapter for MzQuantML 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...
 
class  MzXMLFile
 File adapter for MzXML 2.1 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...
 
struct  PepXMLFile::AminoAcidModification
 
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...
 
struct  QcMLFile::QualityParameter
 Representation of a quality parameter. More...
 
struct  QcMLFile::Attachment
 Representation of an attachment. More...
 
class  QcMLFile
 File adapter for 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  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  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  XTandemInfile
 XTandem input file. More...
 
class  XTandemXMLFile
 Used to load XTandemXML files. More...
 

Enumerations

enum  Type {
  UNKNOWN, DTA, DTA2D, MZDATA,
  MZXML, FEATUREXML, IDXML, CONSENSUSXML,
  MGF, INI, TOPPAS, TRANSFORMATIONXML,
  MZML, MS2, PEPXML, PROTXML,
  MZIDENTML, MZQUANTML, QCML, GELML,
  TRAML, MSP, OMSSAXML, MASCOTXML,
  PNG, XMASS, TSV, PEPLIST,
  HARDKLOER, KROENIK, FASTA, EDTA,
  CSV, TXT, OBO, HTML,
  XML, ANALYSISXML, XSD, PSQ,
  MRM, PSMS, SIZE_OF_TYPE
}
 Actual file types enum. More...
 
enum  MzTabCellStateType {
  MZTAB_CELLSTATE_DEFAULT, MZTAB_CELLSTATE_NULL, MZTAB_CELLSTATE_NAN, MZTAB_CELLSTATE_INF,
  SIZE_OF_MZTAB_CELLTYPE
}
 Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...
 
enum  ErrorUnit { DALTONS = 0, PPM }
 error unit, either Da or ppm More...
 
enum  MassType { MONOISOTOPIC = 0, AVERAGE }
 Mass type of the precursor, either monoisotopic or average. 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)
 loads data from a XTandemXML 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

enum ErrorUnit

error unit, either Da or ppm

Enumerator
DALTONS 
PPM 
enum MassType

Mass type of the precursor, either monoisotopic or average.

Enumerator
MONOISOTOPIC 
AVERAGE 
enum MzTabCellStateType

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

Enumerator
MZTAB_CELLSTATE_DEFAULT 
MZTAB_CELLSTATE_NULL 
MZTAB_CELLSTATE_NAN 
MZTAB_CELLSTATE_INF 
SIZE_OF_MZTAB_CELLTYPE 
enum Type

Actual file types enum.

Enumerator
UNKNOWN 

Unknown file extension.

DTA 

DTA file (.dta)

DTA2D 

DTA2D file (.dta2d)

MZDATA 

MzData file (.mzData)

MZXML 

MzXML file (.mzXML)

FEATUREXML 

OpenMS feature file (.featureXML)

IDXML 

OpenMS identification format (.idXML)

CONSENSUSXML 

OpenMS consensus map format (.consensusXML)

MGF 

Mascot Generic Format (.mgf)

INI 

OpenMS parameters file (.ini)

TOPPAS 

OpenMS parameters file with workflow information (.toppas)

TRANSFORMATIONXML 

Transformation description file (.trafoXML)

MZML 

MzML file (.mzML)

MS2 

MS2 file (.ms2)

PEPXML 

TPP pepXML file (.pepXML)

PROTXML 

TPP protXML file (.protXML)

MZIDENTML 

mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)

MZQUANTML 

mzQuantML (HUPO PSI AnalysisXML followup format) (.mzq)

QCML 

qcML (will undergo standardisation maybe) (.qcml)

GELML 

GelML (HUPO PSI format) (.gelML)

TRAML 

TraML (HUPO PSI format) for transitions (.traML)

MSP 

NIST spectra library file format (.msp)

OMSSAXML 

OMSSA XML file format for peptide identifications (.xml)

MASCOTXML 

Mascot XML file format for peptide identifications (.xml)

PNG 

Portable Network Graphics (.png)

XMASS 

XMass Analysis file (fid)

TSV 

msInspect file (.tsv)

PEPLIST 

specArray file (.peplist)

HARDKLOER 

hardkloer file (.hardkloer)

KROENIK 

kroenik file (.kroenik)

FASTA 

FASTA file (.fasta)

EDTA 

enhanced comma separated files (RT, m/z, Intensity, [meta])

CSV 

general comma separated files format (might also be tab or space separated!!!), data should be regular, i.e. matrix form

TXT 

any text format, which has only loose definition of what it actually contains – thus it is usually hard to say where the file actually came from (e.g. PepNovo).

OBO 

Controlled Vocabulary format.

HTML 

any HTML format

XML 

any XML format

ANALYSISXML 

analysisXML format

XSD 

XSD schema format.

PSQ 

NCBI binary blast db.

MRM 

SpectraST MRM List.

PSMS 

Percolator tab-delimited output (PSM level)

SIZE_OF_TYPE 

No file type. Simply stores the number of types.

Function Documentation

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

loads data from a XTandemXML file

Parameters
filenamethe file to be loaded
protein_identificationprotein identifications belonging to the whole experiment
id_datathe identifications with m/z and RT

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

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

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:57 using doxygen 1.8.9.1