Uses of Interface
com.compomics.util.experiment.io.identification.IdfileReader

Packages that use IdfileReader

Package	Description
com.compomics.util.experiment.identification.modification.mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.io.identification	Experiment identification classes.
com.compomics.util.experiment.io.identification.idfilereaders	Experiment classes related to reading search engine files.

Uses of IdfileReader in com.compomics.util.experiment.identification.modification.mapping

Methods in com.compomics.util.experiment.identification.modification.mapping with parameters of type IdfileReader

Modifier and Type	Method	Description
static double	ModificationMassMapper.getMass(String searchEngineModificationName, IdfileReader idfileReader, SearchParameters searchParameters, ModificationProvider modificationProvider)	Returns the mass indicated by the identification algorithm for the given modification.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNames(Peptide peptide, ModificationMatch modificationMatch, IdfileReader idfileReader, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modification names.
static void	ModificationLocalizationMapper.modificationLocalization(Peptide peptide, HashMap<Integer,ArrayList<String>> expectedNames, HashMap<ModificationMatch,ArrayList<String>> modNames, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider)	Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications.

Uses of IdfileReader in com.compomics.util.experiment.identification.modification.search_engine_mapping

Methods in com.compomics.util.experiment.identification.modification.search_engine_mapping with parameters of type IdfileReader

Modifier and Type	Method	Description
static double	ModificationMassMapper.getMass(String searchEngineModificationName, IdfileReader idfileReader, SearchParameters searchParameters, ModificationProvider modificationProvider)	Returns the mass indicated by the identification algorithm for the given modification.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNames(Peptide peptide, ModificationMatch modificationMatch, IdfileReader idfileReader, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modification names from a search engine modification indexed by site.
static void	ModificationLocalizationMapper.modificationLocalization(Peptide peptide, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider, SequenceProvider sequenceProvider)	Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications.

Uses of IdfileReader in com.compomics.util.experiment.io.identification

Methods in com.compomics.util.experiment.io.identification that return IdfileReader

Modifier and Type	Method	Description
IdfileReader	IdfileReaderFactory.getFileReader(File aFile)	This method returns the proper identification file reader depending on the format of the provided file.

Uses of IdfileReader in com.compomics.util.experiment.io.identification.idfilereaders

Classes in com.compomics.util.experiment.io.identification.idfilereaders that implement IdfileReader

Modifier and Type	Class	Description
class	AndromedaIdfileReader	This IdfileReader reads identifications from an Andromeda result file.
class	CossIdfileReader	This IdfileReader reads identifications from a COSS tsv result file.
class	DirecTagIdfileReader	An identification file reader for Direct tag results.
class	MascotIdfileReader	This IdfileReader reads identifications from a Mascot results file.
class	MsAmandaIdfileReader	This IdfileReader reads identifications from an MS Amanda csv result file.
class	MzIdentMLIdfileReader	This IdfileReader reads identifications from an mzIdentML result file.
class	NovorIdfileReader	This IdfileReader reads identifications from a Novor csv result file.
class	OnyaseIdfileReader	Id file reader for the scripts in Onyase.
class	PepNovoIdfileReader	This class can be used to parse PepNovo identification files.
class	PepxmlIdfileReader	Simple IdfileReader for Pepxml files.
class	PNovoIdfileReader	This class can be used to parse pNovo identification files.
class	SageIdfileReader	This IdfileReader reads identifications from a Sage tsv file.
class	TideIdfileReader	This IdfileReader reads identifications from an Tide tsv results file.
class	XTandemIdfileReader	This IdfileReader reads identifications from an X! Tandem xml result file.