Uses of Interface
com.compomics.util.experiment.io.identification.IdfileReader
Package | Description |
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com.compomics.util.experiment.identification.modification.mapping |
Mapping between search engine and Utilities modifications.
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com.compomics.util.experiment.io.identification |
Experiment identification classes.
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com.compomics.util.experiment.io.identification.idfilereaders |
Experiment classes related to reading search engine files.
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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.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
TideIdfileReader
This IdfileReader reads identifications from an Tide tsv results file.class
XTandemIdfileReader
This IdfileReader reads identifications from an X! Tandem xml result file.