Index (PIA core library 0.0.5-SNAPSHOT API)

A B C D E F G H I L M N O P R S T U V

A

AbstractFilter - Class in uk.ac.ebi.pride.utilities.pia.modeller.filter
AbstractFilter() - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter
AbstractProteinInference - Class in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference: This abstract class define the main methods for each ProteinInference methods.
AbstractProteinInference(IntermediateStructure, PeptideScoring, ProteinScoring, List<AbstractFilter>, Integer) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: The constructor works using a DataAccessController.
addChild(IntermediateGroup) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Adds a child to the set of children.
addCluster(Collection<IntermediateGroup>) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructure: Adds the given cluster to the clusters in the structure.
addCluster(Collection<IntermediateGroup>) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: Adds the given cluster information into the intermediate structure.
addFile(String) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Adds a file to the input files.
addFileAndImportSpectra(String, List<AbstractFilter>) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Adds a file to the input files and adds the filtered PSMs to the structure creator.
addFileAndImportSpectra(String, List<AbstractFilter>, String) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Adds a file to the input files and adds the filtered PSMs to the structure creator.
addFilter(AbstractFilter) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: adds a new filter to the inference filters.
addParent(IntermediateGroup) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Adds a new group to the set of parents.
addPeptide(IntermediatePeptide) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Adds a single peptide to the group.
addPeptide(IntermediatePeptide) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: adds the given peptide to the peptides map
addPeptide(IntermediatePeptide) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Adds one IntermediatePeptide to the map of peptides
addPeptides(Collection<IntermediatePeptide>) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Adds a collection of IntermediatePeptides to the map of peptides
addPeptideSpectrumMatch(IntermediatePeptideSpectrumMatch) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Adds the given spectrumIdentification to the peptide's PSMs
addPeptideToProteinConnection(Comparable, String) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: Connects the peptide with the protein.
addPrideControllerAsInput(DataAccessController) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Adds a DataAccessController as source for import.
addProtein(IntermediateProtein) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Adds a new protein to the map of proteins.
addProtein(IntermediateProtein) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: adds the given protein to the proteins map
addProtein(IntermediateProtein) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Adds one protein to the set of proteins
addProteinInformation(String, IntermediateProtein) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: potentially adds further information to a protein, coming from e.g.
addProteinsSpectrumIdentificationsToStructCreator(Comparable, List<AbstractFilter>, String) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController: Adds the spectrum identifications of a single protein to the structure creator.
addPSMforFile(Integer, IntermediatePeptideSpectrumMatch) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller: Adds the given PSM to the end of the list of PSMs for the file specified by fileID.
addSpectrumIdentificationsToStructCreator(List<AbstractFilter>) - Method in interface uk.ac.ebi.pride.utilities.pia.intermediate.DataImportController: Adds the filtered PSMs to the IntermediateStructureCreator.
addSpectrumIdentificationsToStructCreator(List<AbstractFilter>, String) - Method in interface uk.ac.ebi.pride.utilities.pia.intermediate.DataImportController: Adds the filtered PSMs to the IntermediateStructureCreator.
addSpectrumIdentificationsToStructCreator(List<AbstractFilter>) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController
addSpectrumIdentificationsToStructCreator(List<AbstractFilter>, String) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController
addSubgroup(InferenceProteinGroup) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Adds a protein group to the subGroups of this group
addToReports(List<InferenceProteinGroup>) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorInference: Adds the proteinGroups to the list of reported ProteinGroups.
allowedThreads - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: the number of allowed threads (smaller 1 = all available)

B

baseScoreAccession - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoring: accession of the base score
buildIntermediateStructure() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: After the peptide and dbSeqeunce data is loaded, this method creates the intermediate structure.
buildIntermediateStructure() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: This method builds the intermediate structure with the data of the input files.

C

calculateAllFDR() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller: Calculates the FDR of the PSMs for all files
calculateFDR(List<T>, String) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRUtilities: Calculate the FDR on the given score sorted List of FDRComputableByDecoys objects.
calculateFDR(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller: Calculates the FDR of the PSMs for the file selected by its ID
calculateFDRScore(List<T>, String, boolean) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRUtilities: Calculates the FDR score of the report.
calculateInference(boolean) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: calculateInference is the method of the abstract class which allows the class to compute the protein groups and create the List of different groups.
calculateInference(boolean) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorInference
calculateInference(boolean) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.ReportAllInference
calculatePeptideScore(IntermediatePeptide) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoring: Calculates the peptide score for the intermediate peptide.
calculatePeptideScore(IntermediatePeptide) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoringUseBestPSM
calculateProteinScore(InferenceProteinGroup) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.protein.ProteinScoring: Calculates the protein score for the inference group.
calculateProteinScore(InferenceProteinGroup) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.protein.ProteinScoringAdditive
calculateProteinScore(InferenceProteinGroup) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.protein.ProteinScoringMultiplicative
close() - Method in interface uk.ac.ebi.pride.utilities.pia.intermediate.DataImportController: Some controllers should be closed after usage.
close() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController
close() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: As some controllers should be closed, do this here.
comparator - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter
compare(IntermediatePeptide, IntermediatePeptide) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.IntermediatePeptideComparator
compare(IntermediatePeptideSpectrumMatch, IntermediatePeptideSpectrumMatch) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.psm.IntermediatePSMComparator
compareValues(Double, Double) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.IntermediatePeptideComparator: Compares the values of two peptide scores.
compareValues(Double, Double) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.psm.IntermediatePSMComparator: Compares the values of two PSM scores.
compareValues(Double, Double, boolean) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.ScoreUtilities: Compares the values of two values considered to be scores.
computeID(String) - Static method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Returns the ID computed by the given arguments.
convertCvParams(List<CvParam>) - Static method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideUtilities: Converts a PRIDE-CvParam into a jMzIdentML CvParam
convertInferenceProteinGroup(InferenceProteinGroup, boolean, boolean) - Static method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideUtilities: Converts a InferenceProteinGroup from any protein inference into a PRIDE ProteinGroup.
convertIntermediateProtein(PrideIntermediateProtein, boolean) - Static method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideUtilities: Converts a PrideIntermediateProtein into a PRIDE Protein
convertUserParams(List<UserParam>) - Static method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideUtilities: Converts a PRIDE-UserParam into a jMzIdentML-UserParam
countSpectrumOnce - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.scores.protein.ProteinScoring: use a spectrum only once for protein scoring
createClustersFilteredPeptidesMap(Set<IntermediateGroup>, boolean) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: This method creates a Map from the groups' IDs to the associated IntermediatePeptides of the given cluster, which satisfy the currently set filters.
createFilteredPeptidesMap(boolean) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: This method creates a Map from the groups' IDs to the associated IntermediatePeptides, which satisfy the currently set filters.
createProteinAmbiguityGroupID(IntermediateGroup) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: Ceates a unique ID for a ProteinAmbiguityGroup from the group ID
CvScore - Enum in uk.ac.ebi.pride.utilities.pia.modeller.scores: Enumeration of known CV terms for scores
CVUtilities - Class in uk.ac.ebi.pride.utilities.pia.psisupport: Class containing some helpers for the CV managing in the PSI formats
CVUtilities.CVs - Enum in uk.ac.ebi.pride.utilities.pia.psisupport

D

DataImportController - Interface in uk.ac.ebi.pride.utilities.pia.intermediate: An interface for the data import controllers for PIA input files.
directlyConnectedToProtein(IntermediateProtein) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Returns true, if the group is directly connected to the dbSequence.
doFileRefinement(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: performs the file refinement an the given object and returns the refined object.

E

equals(Object) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup
equals(Object) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide
equals(Object) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch
equals(Object) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
equals(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup

F

FDRComputableByDecoys - Interface in uk.ac.ebi.pride.utilities.pia.modeller.fdr: Interface used for calculation of FDR estimation by usage of decoys.
FDRUtilities - Class in uk.ac.ebi.pride.utilities.pia.modeller.fdr: This class provides functionality for the FDR estimation using decoy proteins
FDRUtilities() - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRUtilities
FilterComparator - Enum in uk.ac.ebi.pride.utilities.pia.modeller.filter: This enum contains the comparator types used by the filters.
filteringName - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
filterPSMs(List<AbstractFilter>) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Filters the PSMs using the given filters.
filters - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: list of the settings.
FilterType - Enum in uk.ac.ebi.pride.utilities.pia.modeller.filter
filterType - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
FilterUtilities - Class in uk.ac.ebi.pride.utilities.pia.modeller.filter: Some helper methods for the filtering.
findAccessionInObo(String) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.ScoreUtilities: Checks the PSI-MS obo and returns the name of the accession.

G

getAccession() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein: getter for the Protein accession
getAccession() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediateProtein
getAccession() - Method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.CvScore
getAllChildren() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Getter for all children groups of this group, including children's children and so on.
getAllIntermediatePSMs() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructure: Returns all intermediate PSMs of the structure
getAllPeptideChildren() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Getter for all children groups of this group that have at least one peptide, recursive, i.e.
getAllPeptides() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: getter for all peptides, including all children's peptides.
getAllPeptideSpectrumMatches() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Getter for the PSMs, also the ones, which do not pass the filters.
getAllProteins() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Getter for the intermediateProtein of this group and all the parents.
getAllProteins() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Returns all proteins (if the group is assigned)
getAvailableComparators() - Method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterType: Returns a List of the available FilterComparators for this FilterType.
getAvailableComparators(String) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterUtilities: gets the available comparators for the filter given by the short name
getBaseScoreAccessions() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Returns the basic scores of this PSM.
getBaseScoreAccessions() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getByRepresentingName(String) - Static method in class uk.ac.ebi.pride.utilities.pia.psisupport.CVUtilities: Retrieves the CV which is represented by the given name.
getCharge() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the charge.
getCharge() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getChildren() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Getter for the children set
getCliShort() - Method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterComparator: returns the short form for the command line
getCluster(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructure: Returns the cluster given by the clusterNr
getClusters() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructure: Returns the clusters
getComparatorRegexes() - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterComparator: Builds a regex to extract the comparator from the command line
getController() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController: Returns the actual controller.
getControllerID() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Returns the ID of the used controller for importing.
getControllerID() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getCV() - Method in enum uk.ac.ebi.pride.utilities.pia.psisupport.CVUtilities.CVs: return the CV representative
getCvLabel() - Method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.CvScore
getCvRefByAccession(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.CvScore: Get Cv score by accession.
getDeltaMass() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the mass-delta (NOT m/z) between measured and theoretical mass value (measured - theoretical)
getDeltaMass() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getExperimentalMassToCharge() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the PSM's measured experimental m/z
getExperimentalMassToCharge() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getFDR() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch
getFDR() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
getFDR() - Method in interface uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRComputableByDecoys: Gets the local FDR value.
getFDRScore() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch
getFDRScore() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
getFDRScore() - Method in interface uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRComputableByDecoys: Gets the smoothed FDRScore value.
getFdrScoreAccession(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller: Getter for the score set for FDR estimation of the file given by fileID
getFilesMainScoreAccession(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller: Returns the main score of the file given by its ID.
getFilesPSMs(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller: Returns the List of PSMs for the given file
getFilterComparator() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: getter for the filter's comparator
getFilterComparatorByCLI(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterComparator: gets the FilterArgument given by the CLI short, or null, if the short is not found.
getFilterComparatorByName(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterComparator: gets the FilterArgument given by the name, or null, if the name is not found.
getFilteringName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: returns the human readable name, which can be used in a drop-down menu (shorter than getName)
getFilteringName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide.PeptideNrPSMsFilter
getFilteringName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinAccessionFilter
getFilteringName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinNrPSMsFilter
getFilteringName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMAccessionsFilter
getFilteringName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMDecoyFilter
getFilteringName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMQValueFilter
getFilteringName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
getFilterNegate() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: returns, whether this filter is negating or not
getFilters() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: Returns a List of all filter settings for this inference filter.
getFilterType() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: returns the type of the filter, i.e.
getFilterType(String) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterUtilities: Returns the FilterType of the given filter.
getFilterType() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide.PeptideNrPSMsFilter
getFilterType() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinAccessionFilter
getFilterType() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinNrPSMsFilter
getFilterType() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMAccessionsFilter
getFilterType() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMDecoyFilter
getFilterType() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMQValueFilter
getFilterType() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
getFilterValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: returns the value, against which is filtered
getFilterValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide.PeptideNrPSMsFilter
getFilterValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinAccessionFilter
getFilterValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinNrPSMsFilter
getFilterValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMAccessionsFilter
getFilterValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMDecoyFilter
getFilterValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMQValueFilter
getFilterValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
getGroup() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: returns the group of this peptide
getGroup() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein: returns the group of this protein
getHigherScoreBetter() - Method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.CvScore
getID() - Method in interface uk.ac.ebi.pride.utilities.pia.intermediate.DataImportController: Returns the ID of the controller.
getID() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Getter for the ID.
getID() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Returns an identifier for the peptide
getID() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Returns an ID of the peptideSpectrumMatch
getID() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController
getID() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getID() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup
getImportController(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Returns the DataImportController of the given file.
getImportControllerIds() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Returns the IDs of the input controllers
getInferredProteins() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.ProteinModeller: Returns a list of the inferred protein groups.
getInputFileName() - Method in interface uk.ac.ebi.pride.utilities.pia.intermediate.DataImportController: Returns the file name which is handled by this controller
getInputFileName() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController
getIntermediateStructure() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Returns the IntermediateStructure created or loaded by this modeller.
getIsDecoy() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the isDecoy flag.
getIsDecoy() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
getIsDecoy() - Method in interface uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRComputableByDecoys: Returns true, if the item is a decoy, or false, if not.
getIsMainScore() - Method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.CvScore
getIsUnique() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Returns whether the PSM is unique for only one protein (given the database)
getLabel() - Method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterComparator: returns the label used for the SelectItems
getMissedCleavages() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the number of missed cleavages
getMissedCleavages() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getModifications() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the modifications
getModifications() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: returns the human readable long name of the filter
getName() - Method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterComparator: returns the name used as the SelectItem's value
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide.PeptideNrPSMsFilter
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinAccessionFilter
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinNrPSMsFilter
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMAccessionsFilter
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMDecoyFilter
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMQValueFilter
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: Get the human readable name of the inference method.
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorInference
getName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.ReportAllInference
getName() - Method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.CvScore
getNextCluster() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: Returns the next cluster in the clustered mapping of peptides to proteins.
getNextCluster() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorInference: Returns the next cluster in the intermediate structure null, if no more clusters are available.
getNrClusters() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructure: Returns the number of trees
getNrGroups() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructure: Returns the number of total groups
getNrPeptides() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructure: Returns the total number of peptides
getNrPeptides() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator
getNrProteins() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructure: Returns the total number of proteins
getNrProteins() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator
getNrPSMs(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller: Returns the number of PSMs for the given file.
getNrSpectrumIdentifications() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator
getNumberOfPeptideSpectrumMatches() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Getter for the number of PSMs.
getObjectsValue(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: returns the value of the Object o, which will be used for filtering.
getObjectsValue(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide.PeptideNrPSMsFilter
getObjectsValue(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinAccessionFilter
getObjectsValue(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinNrPSMsFilter
getObjectsValue(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMAccessionsFilter
getObjectsValue(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMDecoyFilter
getObjectsValue(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMQValueFilter
getObjectsValue(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
getParams() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for additional CV and user params (like sourceID, spectrum title...)
getParams() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getParents() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Getter for the parents.
getPeptide() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the peptide.
getPeptide(Comparable) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: getter for the peptide from the map with the given ID
getPeptideKey(IntermediatePeptide, boolean) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: Return a peptide key, depending on whether the modifications are taken into account or not.
getPeptides() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Getter for the peptides.
getPeptides() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Returns the set of IntermediatePeptides
getPeptideSpectrumMatches() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Getter for the PSMs.
getPeptidesScoringType(IntermediatePeptide) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Returns the ScoringItemType of the peptide
getPeptidesWithScoringType(ScoringItemType) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Returns the peptides with the given ScoringItemType
getPrideProtein() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediateProtein: Getter for the complete PRIDE protein
getPrideProteinID() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediateProtein: Getter for the PRIDE protein ID
getProgressValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: If polling of inference is performed, return the current state of the progress (between 0 and 100 progress in percent, <0 inference aborted, >100 inference is done).
getProgressValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorInference
getProgressValue() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.ReportAllInference
getProtein(Comparable) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: getter for the protein from the map with the given ID
getProteinModeller() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Returns the associated ProteinModeller
getProteins() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Getter for the proteins.
getProteins() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Returns the set of proteins
getProteinScore() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein: Returns the proteinScore or null, if it is not yet calculated.
getProteinSequence() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein: getter for the protein sequence.
getProteinSequence() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediateProtein
getPSMKey(IntermediatePeptideSpectrumMatch, boolean) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: Returns a psm key, depending on whether the modifications are taken into account or not.
getPSMModeller() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Returns the associated PSMModeller
getPSMsScoringType(IntermediatePeptideSpectrumMatch) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Returns the ScoringItemType of the PSM
getPSMsWithScoringType(ScoringItemType) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Returns the PSMs with the given ScoringItemType, which also pass any filterings.
getQValue() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch
getQValue() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
getQValue() - Method in interface uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRComputableByDecoys: Getter for the qValue.
getRepresentations() - Method in enum uk.ac.ebi.pride.utilities.pia.psisupport.CVUtilities.CVs: Returns a list of string representations which may be used by this CV
getRetentionTime() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the PSMs' retention time.
getRetentionTime() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getScore() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Getter for the peptide score.
getScore(String) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Returns the score value of the score with the given accession.
getScore(String) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein: Returns the score value of the score with the given accession.
getScore(String) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getScore(String) - Method in interface uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRComputableByDecoys: Returns the score value of the score with the given accession.
getScore() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Getter for the protein score.
getScoreAccessions() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Returns the accessions of the available scores of this PSM, including calculated scores.
getSequence() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Getter for the sequence.
getSequence() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the sequence.
getSequence() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: returns the machine readable name of the filter
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide.PeptideNrPSMsFilter
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinAccessionFilter
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinNrPSMsFilter
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMAccessionsFilter
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMDecoyFilter
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMQValueFilter
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: Get the unique machine readable short name of the inference method.
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorInference
getShortName() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.ReportAllInference
getSpectrumId() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Getter for the spectrum id (as in mzIdentML's SpectrumIdentificationResult)
getSpectrumId() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
getSubGroups() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Returns the set of sub-groups
getTreeID() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Getter for the group's treeID.
groupHasDirectReportPeptides(IntermediateGroup, Map<Integer, Set<IntermediatePeptide>>) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: Tests for the given group, if it has any direct IntermediatePeptides, in the given Map.
groupHasReportPeptides(IntermediateGroup, Map<Integer, Set<IntermediatePeptide>>) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: Tests for the given group, if it has any IntermediatePeptides, whether direct or in the peptideChildren, in the given Map.

H

hasAccession(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.CvScore: Check whether the accession exists in the enum.
hashCode() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup
hashCode() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide
hashCode() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch
hashCode() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
hashCode() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup
higherScoreBetter - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoring: whether higher value of the base score is better than a lower value

I

importAllDataFromFile(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Imports all spectrum identifications from the file to the structure creator.
importAllDataFromFile(Integer, String) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Imports all spectrum identifications from the file to the structure creator.
importDataFromFile(Integer, List<AbstractFilter>) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Imports the filtered PSMs and adds them to the structure creator.
importDataFromFile(Integer, List<AbstractFilter>, String) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Imports the filtered PSMs and adds them to the structure creator.
InferenceProteinGroup - Class in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference: This group bundles the information about an inferred protein group.
InferenceProteinGroup(String, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Basic constructor
infereProteins(PeptideScoring, ProteinScoring, Class<? extends AbstractProteinInference>, List<AbstractFilter>, boolean) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.ProteinModeller: Runs the protein inference with the given settings and stores the protein groups in a list, which can be returned by ProteinModeller.getInferredProteins()
insertIntoMap(IntermediatePeptide, Set<IntermediateProtein>, Map<Integer, IntermediateGroup>) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreatorWorkerThread: Inserts the given peptide with its accessions into the intermediate format, which is then build up by the groups in subGroups.
IntermediateGroup - Class in uk.ac.ebi.pride.utilities.pia.intermediate
IntermediateGroup(int) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Basic Constructor, sets all the maps to null and score to NaN.
IntermediatePeptide - Class in uk.ac.ebi.pride.utilities.pia.intermediate: A peptide class, which is used in the intermediate structure.
IntermediatePeptide(String) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Basic constructor, only initializes the sequence
IntermediatePeptideComparator - Class in uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide: Compares the scores of IntermediatePeptides.
IntermediatePeptideComparator(boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.IntermediatePeptideComparator: Creates the comparator with the given value for higherScoreBetter.
IntermediatePeptideComparator(PeptideScoring) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.IntermediatePeptideComparator: Creates the comparator and gets the value for higherScoreBetter from the given PeptideScoring.
IntermediatePeptideSpectrumMatch - Class in uk.ac.ebi.pride.utilities.pia.intermediate: Representation of a peptide spectrum match in the intermediate structure.
IntermediatePeptideSpectrumMatch() - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch
IntermediateProtein - Class in uk.ac.ebi.pride.utilities.pia.intermediate: An intermediate class, which represents a protein in the intermediate structure.
IntermediateProtein() - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
IntermediatePSMComparator - Class in uk.ac.ebi.pride.utilities.pia.modeller.scores.psm: Compares the scores of IntermediatePeptideSpectrumMatches
IntermediatePSMComparator(String, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.scores.psm.IntermediatePSMComparator
IntermediateStructure - Class in uk.ac.ebi.pride.utilities.pia.intermediate: This class is a container for the intermediate structure created before PIAs protein inference.
IntermediateStructure() - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructure
intermediateStructure - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: the PIA intermediate structure
IntermediateStructureCreator - Class in uk.ac.ebi.pride.utilities.pia.intermediate: This class creates the intermediate structure needed for fast data access during protein inference.
IntermediateStructureCreator(int) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator
IntermediateStructureCreatorWorkerThread - Class in uk.ac.ebi.pride.utilities.pia.intermediate: This thread builds up the intermediate structure given the peptide to dbSequence mapping.
IntermediateStructureCreatorWorkerThread(int, IntermediateStructureCreator) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreatorWorkerThread
isHigherScoreBetter(String, boolean) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.scores.ScoreUtilities: Returns for a given score accession, whether a higher score is better.

L

logger - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterUtilities

M

markDecoys(List<IntermediatePeptideSpectrumMatch>, ProteinAccessionFilter) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRUtilities: This function marks the intermediateProteins of the PSMs, which pass the given decoysFilter, as decoys for a subsequent FDR estimation.

N

name - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
name - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorInference: the human readable name of this filter
name - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.ReportAllInference: the human readable name of this filter
negate - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter
newInferenceFor(Class) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: Returns, whether a new inference on the level, where this filter is applied, is necessary.

O

OccamsRazorInference - Class in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference: This inference filter reports all the PIA IntermediateGroups as protein, which together fulfill the Occam's Razor constraints.
OccamsRazorInference(IntermediateStructure, PeptideScoring, ProteinScoring, List<AbstractFilter>, Integer) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorInference
OccamsRazorWorkerThread - Class in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference
OccamsRazorWorkerThread(int, OccamsRazorInference, List<AbstractFilter>, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorWorkerThread

P

PeptideModeller - Class in uk.ac.ebi.pride.utilities.pia.modeller.peptide: This class handles the peptides and their inference in a given IntermediateStructure.
PeptideModeller(IntermediateStructure) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.peptide.PeptideModeller
PeptideNrPSMsFilter - Class in uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide: Filters for the number of PSMs on peptide level.
PeptideNrPSMsFilter(FilterComparator, Integer, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide.PeptideNrPSMsFilter
peptidesContains(Comparable) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: returns true, if the peptides map already contains a peptide with the given ID
peptideScoring - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: the currently set peptide scoring
PeptideScoring - Class in uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide
PeptideScoring(String, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoring: Creates a new scoring object and determines (if appropriate), if a higher value is better for the given base-score.
peptideScoring - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.scores.protein.ProteinScoring: the peptide scoring used
PeptideScoringUseBestPSM - Class in uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide: This class uses the PSM with the best score for scoring of a peptide.
PeptideScoringUseBestPSM(String, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoringUseBestPSM
PIAModeller - Class in uk.ac.ebi.pride.utilities.pia.modeller: This modeller handles all PIA data, started by the import of identifications, intermediate structure creation and displaying of PSMs, peptides and proteins.
PIAModeller() - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Creates a modeller for the new creation of a intermediate structure using as many threads as processors are available.
PIAModeller(int, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Creates a modeller for the new creation of a intermediate structure using only the specified number of threads
PIAModeller(String) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Creates a modeller which loads the intermediate structure from a file using as many threads as processors are available.
PIAModeller(String, int, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller: Creates a modeller which loads the intermediate structure from a file using only the specified number of threads
prefix - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
PrideImportController - Class in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl
PrideImportController(File, PrideImportController.InputFileType, IntermediateStructureCreator) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController: Creates an import controller for the given file type.
PrideImportController(File, IntermediateStructureCreator) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController: Creates an import controller guessing the file type
PrideImportController(DataAccessController, IntermediateStructureCreator) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController: Creates an import controller for the given DataAccessController
PrideImportController.InputFileType - Enum in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl: Defines the input file type
PrideIntermediatePeptideSpectrumMatch - Class in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl: Representation of a peptide spectrum match in the intermediate structure.
PrideIntermediatePeptideSpectrumMatch(DataAccessController, Comparable, Comparable) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch
PrideIntermediatePeptideSpectrumMatch(DataAccessController, Comparable, Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediatePeptideSpectrumMatch: creates a new PRIDE intermediate PSM and caches the score given by the accession (this requires some mor memory, but is much faster)
PrideIntermediateProtein - Class in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl: An intermediate class, which represents a protein
PrideIntermediateProtein(DataAccessController, Comparable) - Constructor for class uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideIntermediateProtein: Basic constructor, only initializes the representative
PrideUtilities - Class in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl: This class contains some helper functions for the pride import
ProteinAccessionFilter - Class in uk.ac.ebi.pride.utilities.pia.modeller.filter.protein: Filters for accessions on PSM level.
ProteinAccessionFilter(FilterComparator, String, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinAccessionFilter
ProteinModeller - Class in uk.ac.ebi.pride.utilities.pia.modeller.protein: This class handles the proteins and their inference in a given IntermediateStructure.
ProteinModeller(IntermediateStructure, int) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.protein.ProteinModeller
ProteinNrPSMsFilter - Class in uk.ac.ebi.pride.utilities.pia.modeller.filter.protein: Filters for the number of PSMs on protein level.
ProteinNrPSMsFilter(FilterComparator, Integer, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinNrPSMsFilter
proteinsContains(String) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreator: returns true, if the proteins map already contains a protein with the given accessions
proteinScoring - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: the currently set protein scoring
ProteinScoring - Class in uk.ac.ebi.pride.utilities.pia.modeller.scores.protein
ProteinScoring(boolean, PeptideScoring) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.scores.protein.ProteinScoring
ProteinScoringAdditive - Class in uk.ac.ebi.pride.utilities.pia.modeller.scores.protein: Calculates the score of the protein by adding up the scores of peptides.
ProteinScoringAdditive(boolean, PeptideScoring) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.scores.protein.ProteinScoringAdditive
ProteinScoringMultiplicative - Class in uk.ac.ebi.pride.utilities.pia.modeller.scores.protein: Calculates the score of the protein by multiplying up the scores of peptides and returning the -log10 of the score (log for numeric reasons, minus to get higherScoreBetter)
ProteinScoringMultiplicative(boolean, PeptideScoring) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.scores.protein.ProteinScoringMultiplicative
psiCV - Static variable in enum uk.ac.ebi.pride.utilities.pia.psisupport.CVUtilities.CVs: represents the PSI-CV
PSMAccessionsFilter - Class in uk.ac.ebi.pride.utilities.pia.modeller.filter.psm: Filters for accessions on PSM level.
PSMAccessionsFilter(FilterComparator, String, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMAccessionsFilter
psmComparator - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoringUseBestPSM: the used score comparator
PSMDecoyFilter - Class in uk.ac.ebi.pride.utilities.pia.modeller.filter.psm: Filter for decoys on PSM level.
PSMDecoyFilter(FilterComparator, Boolean, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMDecoyFilter
PSMModeller - Class in uk.ac.ebi.pride.utilities.pia.modeller.psm: This class handles the PSMs, originating from different importers (i.e.
PSMModeller(Integer, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller
PSMQValueFilter - Class in uk.ac.ebi.pride.utilities.pia.modeller.filter.psm: Filters for accessions on PSM level.
PSMQValueFilter(FilterComparator, Double, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMQValueFilter
PSMScoreFilter - Class in uk.ac.ebi.pride.utilities.pia.modeller.filter.psm: Filters for a score on PSM level.
PSMScoreFilter(FilterComparator, Double, boolean, String, boolean) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter

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removeAllScoringInformation() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Removes all information about which PSMs were used for scoring.
removeAllScoringInformation() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Removes all information about which peptides were used for scoring.
removeFilter(int) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.AbstractProteinInference: Removes the filter at the given index
removeProtein(IntermediateProtein) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Removes the given dbSequence from the directly connected dbSequences
ReportAllInference - Class in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference: This inference reports all the PIA IntermediateGroups as one protein.
ReportAllInference(IntermediateStructure, PeptideScoring, ProteinScoring, List<AbstractFilter>, Integer) - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.ReportAllInference
run() - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateStructureCreatorWorkerThread
run() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorWorkerThread

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satisfiesFilter(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: compares the given object and the filter value with the filter comparator and thus returns, whether the object satisfies the filter.
satisfiesFilterList(Object, List<AbstractFilter>) - Static method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterUtilities: Checks whether all the filters in the given List are satisfied for the given object.
ScoreUtilities - Class in uk.ac.ebi.pride.utilities.pia.modeller.scores
ScoreUtilities() - Constructor for class uk.ac.ebi.pride.utilities.pia.modeller.scores.ScoreUtilities
ScoringItemType - Enum in uk.ac.ebi.pride.utilities.pia.modeller.scores
setDecoyFilter(ProteinAccessionFilter) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller: Sets the filter for decoy identification.
setFDR(Double) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch
setFDR(Double) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
setFDR(Double) - Method in interface uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRComputableByDecoys: Sets the local FDR value.
setFDRScore(Double) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch
setFDRScore(Double) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
setFDRScore(Double) - Method in interface uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRComputableByDecoys: Sets the smoothed FDRScore value.
setFdrScoreAccession(Integer, String) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.psm.PSMModeller: Sets the given accession as the accession used for FDR calculation of the file given by fileID.
setGroup(IntermediateGroup) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: sets the group of this peptide
setGroup(IntermediateGroup) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein: sets the group of this protein
setID(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Setter for the ID.
setIsDecoy(Boolean) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Deprecated.
setIsDecoy(Boolean) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein: Setter for the isDecoy flag, may overwrite the initial setting.
setIsUnique(Boolean) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Sets the isUnique flag, should only be done by importers.
setPeptide(IntermediatePeptide) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch: Setter for the peptide (called while parsing the PIA XML file).
setPeptides(Collection<IntermediatePeptide>) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Setter for the peptides.
setPeptidesScoringType(IntermediatePeptide, ScoringItemType) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Sets the scoring type of the stated peptide to the given ScoringItemType.
setProteinScore(Double) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein: Setter for the protein score
setPSMsScoringType(IntermediatePeptideSpectrumMatch, ScoringItemType) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Sets the scoring type of the stated PSM to the given ScoringItemType.
setQValue(Double) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptideSpectrumMatch
setQValue(Double) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein
setQValue(Double) - Method in interface uk.ac.ebi.pride.utilities.pia.modeller.fdr.FDRComputableByDecoys: Setter for the qValue.
setScore(Double) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediatePeptide: Sets the score of the peptide.
setScore(Double) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup: Sets the score of the protein.
setTreeID(Integer) - Method in class uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateGroup: Setter for the treeID.
shortName - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide.PeptideNrPSMsFilter
shortName - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinAccessionFilter
shortName - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinNrPSMsFilter
shortName - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMAccessionsFilter
shortName - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMDecoyFilter
shortName - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMQValueFilter
shortName - Variable in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter
shortName - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.OccamsRazorInference: the machine readable name of the filter
shortName - Static variable in class uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.ReportAllInference: the machine readable name of the filter
supportsClass(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: Returns, whether the class of the given object is valid for an instance of this filter.
supportsClass(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide.PeptideNrPSMsFilter
supportsClass(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinAccessionFilter
supportsClass(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.protein.ProteinNrPSMsFilter
supportsClass(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMAccessionsFilter
supportsClass(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMDecoyFilter
supportsClass(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMQValueFilter
supportsClass(Object) - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter

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toString() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter
toString() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.psm.PSMScoreFilter

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uk.ac.ebi.pride.utilities.pia.intermediate - package uk.ac.ebi.pride.utilities.pia.intermediate
uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl - package uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl
uk.ac.ebi.pride.utilities.pia.modeller - package uk.ac.ebi.pride.utilities.pia.modeller
uk.ac.ebi.pride.utilities.pia.modeller.fdr - package uk.ac.ebi.pride.utilities.pia.modeller.fdr
uk.ac.ebi.pride.utilities.pia.modeller.filter - package uk.ac.ebi.pride.utilities.pia.modeller.filter
uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide - package uk.ac.ebi.pride.utilities.pia.modeller.filter.peptide
uk.ac.ebi.pride.utilities.pia.modeller.filter.protein - package uk.ac.ebi.pride.utilities.pia.modeller.filter.protein
uk.ac.ebi.pride.utilities.pia.modeller.filter.psm - package uk.ac.ebi.pride.utilities.pia.modeller.filter.psm
uk.ac.ebi.pride.utilities.pia.modeller.peptide - package uk.ac.ebi.pride.utilities.pia.modeller.peptide
uk.ac.ebi.pride.utilities.pia.modeller.protein - package uk.ac.ebi.pride.utilities.pia.modeller.protein
uk.ac.ebi.pride.utilities.pia.modeller.protein.inference - package uk.ac.ebi.pride.utilities.pia.modeller.protein.inference
uk.ac.ebi.pride.utilities.pia.modeller.psm - package uk.ac.ebi.pride.utilities.pia.modeller.psm
uk.ac.ebi.pride.utilities.pia.modeller.scores - package uk.ac.ebi.pride.utilities.pia.modeller.scores
uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide - package uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide
uk.ac.ebi.pride.utilities.pia.modeller.scores.protein - package uk.ac.ebi.pride.utilities.pia.modeller.scores.protein
uk.ac.ebi.pride.utilities.pia.modeller.scores.psm - package uk.ac.ebi.pride.utilities.pia.modeller.scores.psm
uk.ac.ebi.pride.utilities.pia.psisupport - package uk.ac.ebi.pride.utilities.pia.psisupport
unimodCV - Static variable in enum uk.ac.ebi.pride.utilities.pia.psisupport.CVUtilities.CVs: represents the UNIMOD
uoCV - Static variable in enum uk.ac.ebi.pride.utilities.pia.psisupport.CVUtilities.CVs: represents the UnitOntology CV

V

valueNeedsFileRefinement() - Method in class uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter: returns true, if the objects need file refinement (e.g.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController.InputFileType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterComparator: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.CvScore: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.ScoringItemType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.pia.psisupport.CVUtilities.CVs: Returns the enum constant of this type with the specified name.
values() - Static method in enum uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController.InputFileType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterComparator: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.filter.FilterType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.CvScore: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.pride.utilities.pia.modeller.scores.ScoringItemType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.pride.utilities.pia.psisupport.CVUtilities.CVs: Returns an array containing the constants of this enum type, in the order they are declared.

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