Uses of Class
uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch

Packages that use IntermediatePeptideSpectrumMatch

Package	Description
uk.ac.ebi.pride.utilities.pia.intermediate
uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl
uk.ac.ebi.pride.utilities.pia.modeller.fdr
uk.ac.ebi.pride.utilities.pia.modeller.protein.inference
uk.ac.ebi.pride.utilities.pia.modeller.psm
uk.ac.ebi.pride.utilities.pia.modeller.scores.psm

Uses of IntermediatePeptideSpectrumMatch in uk.ac.ebi.pride.utilities.pia.intermediate

Methods in uk.ac.ebi.pride.utilities.pia.intermediate that return types with arguments of type IntermediatePeptideSpectrumMatch

Modifier and Type	Method and Description
List<IntermediatePeptideSpectrumMatch>	IntermediateStructure.getAllIntermediatePSMs() Returns all intermediate PSMs of the structure
List<IntermediatePeptideSpectrumMatch>	IntermediatePeptide.getAllPeptideSpectrumMatches() Getter for the PSMs, also the ones, which do not pass the filters.
List<IntermediatePeptideSpectrumMatch>	IntermediatePeptide.getPeptideSpectrumMatches() Getter for the PSMs.
Set<IntermediatePeptideSpectrumMatch>	IntermediatePeptide.getPSMsWithScoringType(ScoringItemType type) Returns the PSMs with the given ScoringItemType, which also pass any filterings.

Methods in uk.ac.ebi.pride.utilities.pia.intermediate with parameters of type IntermediatePeptideSpectrumMatch

Modifier and Type	Method and Description
boolean	IntermediatePeptide.addPeptideSpectrumMatch(IntermediatePeptideSpectrumMatch spectrumIdentification) Adds the given spectrumIdentification to the peptide's PSMs
ScoringItemType	IntermediatePeptide.getPSMsScoringType(IntermediatePeptideSpectrumMatch psm) Returns the ScoringItemType of the PSM
void	IntermediatePeptide.setPSMsScoringType(IntermediatePeptideSpectrumMatch psm, ScoringItemType type) Sets the scoring type of the stated PSM to the given ScoringItemType.

Uses of IntermediatePeptideSpectrumMatch in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl

Subclasses of IntermediatePeptideSpectrumMatch in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl

Modifier and Type	Class and Description
class	PrideIntermediatePeptideSpectrumMatch Representation of a peptide spectrum match in the intermediate structure.

Uses of IntermediatePeptideSpectrumMatch in uk.ac.ebi.pride.utilities.pia.modeller.fdr

Method parameters in uk.ac.ebi.pride.utilities.pia.modeller.fdr with type arguments of type IntermediatePeptideSpectrumMatch

Modifier and Type	Method and Description
static int	FDRUtilities.markDecoys(List<IntermediatePeptideSpectrumMatch> psms, ProteinAccessionFilter decoysFilter) This function marks the intermediateProteins of the PSMs, which pass the given decoysFilter, as decoys for a subsequent FDR estimation.

Uses of IntermediatePeptideSpectrumMatch in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference

Methods in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference with parameters of type IntermediatePeptideSpectrumMatch

Modifier and Type	Method and Description
static Comparable	AbstractProteinInference.getPSMKey(IntermediatePeptideSpectrumMatch psm, boolean considerModifications) Returns a psm key, depending on whether the modifications are taken into account or not.

Uses of IntermediatePeptideSpectrumMatch in uk.ac.ebi.pride.utilities.pia.modeller.psm

Methods in uk.ac.ebi.pride.utilities.pia.modeller.psm that return types with arguments of type IntermediatePeptideSpectrumMatch

Modifier and Type	Method and Description
List<IntermediatePeptideSpectrumMatch>	PSMModeller.getFilesPSMs(Integer fileID) Returns the List of PSMs for the given file

Methods in uk.ac.ebi.pride.utilities.pia.modeller.psm with parameters of type IntermediatePeptideSpectrumMatch

Modifier and Type	Method and Description
boolean	PSMModeller.addPSMforFile(Integer fileID, IntermediatePeptideSpectrumMatch psm) Adds the given PSM to the end of the list of PSMs for the file specified by fileID.

Uses of IntermediatePeptideSpectrumMatch in uk.ac.ebi.pride.utilities.pia.modeller.scores.psm

Methods in uk.ac.ebi.pride.utilities.pia.modeller.scores.psm with parameters of type IntermediatePeptideSpectrumMatch

Modifier and Type	Method and Description
int	IntermediatePSMComparator.compare(IntermediatePeptideSpectrumMatch o1, IntermediatePeptideSpectrumMatch o2)