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OpenMS
2.5.0
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OpenMS
2.5.0
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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... | |
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/ 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 | |
| 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
| 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.
| FileNotFound | |
| ParseError |
| 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
| 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.
| 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 |
1.8.16
