| OpenMS 2.5.0

Classes | Enumerations | Functions
File IO
Format

File IO classes. More...

## 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. 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 | 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 MzTab 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 | 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 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 | 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 }
| Data model of MzTab files. 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

enum MzTabCellStateType

Data model of MzTab files.

Please see the official MzTab specification at https://code.google.com/p/mztab/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,
|  | std::vector< ResidueModification *> & | modifications
| ) |  |

loads data from unimod.xml file

Parameters

  filename | the filename were the unimod xml file should be read from
  modifications | the modifications which are read from the file

Exceptions

  FileNotFound | is thrown if the file could not be found
  ParseError | is thrown if the given file could not be parsed

## ◆ 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

  filename | the file to be loaded
  protein_identification | protein identifications belonging to the whole experiment
  id_data | the identifications with m/z and RT
  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 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

  filename | The file to be loaded
  protein_identification | Protein identifications belonging to the whole experiment
  id_data | The identifications with m/z and RT
  load_proteins | If this flag is set to false, the protein identifications are not loaded
  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.

Exceptions

  FileNotFound |
  ParseError |