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... | |
| 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. 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 | 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... | |
Functions | |
| void | load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=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... | |
File IO classes.
This module contains all classes that are involved in file IO. Take a look at the FileHandler class!
Implement reading of pepXML and protXML (Andreas)
Allow reading of zipped XML files (David, Hiwi)
| 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 | |
| void load | ( | const String & | filename, |
| std::vector< ResidueModification * > & | modifications | ||
| ) |
loads data from unimod.xml file
| filename | the filename were the unimod xml file should be read from |
| modifications | the modifications which are read from the file |
| FileNotFound | is thrown if the file could not be found |
| ParseError | is 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
| filename | the file to be loaded |
| protein_identification | protein identifications belonging to the whole experiment |
| id_data | the 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 |
||
| ) |
loads data from a OMSSAXML file
| 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 |
This class serves to read in a OMSSAXML file. The information can be retrieved via the load function.
| FileNotFound | |
| ParseError |
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5 |