Index (PRIDE Utilities Library 2.0.4 API)

A B C D E F G H I M N O P Q R S T U V W X Y Z

A

A_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
A_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
AbstractPrecursorIon - Class in uk.ac.ebi.pride.utilities.iongen.impl: Implement most of methods of PrecursorIon.
AbstractPrecursorIon(Peptide, int) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.AbstractPrecursorIon
AbstractProductIon - Class in uk.ac.ebi.pride.utilities.iongen.impl: Implement most of methods of ProductIon interface.
AbstractProductIon(PrecursorIon, ProductIonType, int, Peptide, int) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.AbstractProductIon: Create product ion instance.
addALLModification(Map<Integer, PTModification>) - Method in class uk.ac.ebi.pride.utilities.mol.Peptide: If patch add modifications, we will rollback to the point of before patch add.
addAminoAcid(AminoAcid) - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Add a new amino acid to the end of the Peptide.
addAminoAcids(Collection<AminoAcid>) - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Add a collection of amino acids to the end of the Peptide.
addModification(Integer, PTModification) - Method in class uk.ac.ebi.pride.utilities.mol.Peptide: Add a modification into peptide.
AMBIGUOUS_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
AMBIGUOUS_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
AminoAcid - Enum in uk.ac.ebi.pride.utilities.mol: Enumeration of 20 amino acids.
AminoAcidSequence - Class in uk.ac.ebi.pride.utilities.mol: Peptide represents a list of AminoAcid
AminoAcidSequence() - Constructor for class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Default constructor, this will make a empty Peptide object
AminoAcidSequence(AminoAcid...) - Constructor for class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Constructor to ake a Peptide object with specified amino acids.
AMMONIA_LOSS - Static variable in class uk.ac.ebi.pride.utilities.mol.NeutralLoss
ApproximateComparator - Class in uk.ac.ebi.pride.utilities.util: In double add, minus, compare operator, can not get exact 0.
ApproximateComparator() - Constructor for class uk.ac.ebi.pride.utilities.util.ApproximateComparator
ApproximateComparator(int) - Constructor for class uk.ac.ebi.pride.utilities.util.ApproximateComparator
Atom - Enum in uk.ac.ebi.pride.utilities.mol: Atom is an enum which stores all chemical elements.

B

B_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
B_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor

C

C_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
C_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
calculate(String) - Static method in class uk.ac.ebi.pride.utilities.mol.GraviUtilities
calculate(String) - Method in class uk.ac.ebi.pride.utilities.mol.IsoelectricPointUtils.BjellpI
calculate(String) - Static method in class uk.ac.ebi.pride.utilities.mol.IsoelectricPointUtils
calculateAvgMass(Mass...) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: calculate the sum of the average masses.
calculateDeltaMz(String, double, int, List<Double>) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: Calculate the mono delta m/z for the given sequence, precursor m/z and precursor charge If invalid, -1 will be returned.
calculateDeltaMz(double, double) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: Calculate the mono delta m/z for the given sequence, based on theoretical and experimental mass
calculateMonoMass(Mass...) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: calculate the sum of the mono-isotopic masses.
calculatePeptideAvgMass(AminoAcidSequence, List<PTModification>, double...) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: Calculate peptide's average mass.
calculatePeptideMonoMass(AminoAcidSequence, List<PTModification>, double...) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: Calculate peptide's monoisotopic mass.
calculateTheoreticalMass(String, double...) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: Calculates the theoretical mass taking into account the mono-mass of every AminoAcid of the sequence and the array of masses passed
check() - Static method in class uk.ac.ebi.pride.utilities.util.InternetChecker: Default method to check internet, test on google.
check(String) - Static method in class uk.ac.ebi.pride.utilities.util.InternetChecker: Test internet on a specified url string.
checkFormat(File) - Static method in enum uk.ac.ebi.pride.utilities.util.file.MassSpecFileFormat: Detect mass spec file format
checkFormat(URL) - Static method in enum uk.ac.ebi.pride.utilities.util.file.MassSpecFileFormat: Detect mass spec file format
clearModifications() - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
clone() - Method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
clone() - Method in class uk.ac.ebi.pride.utilities.mol.NeutralLoss
CO - Static variable in class uk.ac.ebi.pride.utilities.mol.Group: CO group used in calcute the mass of a and x ion.
CO_ELUTING_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
CO_ELUTING_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
compare(double, double) - Method in class uk.ac.ebi.pride.utilities.util.ApproximateComparator
compareTo(ProductIon) - Method in class uk.ac.ebi.pride.utilities.iongen.impl.AbstractProductIon: Based on ascending order of product ion cleavage position.
compareTo(ImmoniumIon) - Method in class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon
compareTo(Peak) - Method in class uk.ac.ebi.pride.utilities.iongen.model.Peak: Based on m/z ascent order and intensity descent order.
containsPeptideQuantification(QuantCvTermReference) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference: Checks whether the passed quantification method contains peptide quantification values Quatitation Methods (O18, AQUA, ICAT, ICPL, SILAC, TMT, ITRAQ,TIC)
containsProteinQuantification(QuantCvTermReference) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference: Checks whether the passed quantification method contains protein quantification values
convertURLToFile(URL) - Static method in class uk.ac.ebi.pride.utilities.util.IOUtilities: Convert a url to a file object
createDefaultProductIons(PrecursorIon, ProductIonType, int) - Static method in class uk.ac.ebi.pride.utilities.util.ProductIonFactory
createImmoniumProductIons(PrecursorIon, int) - Static method in class uk.ac.ebi.pride.utilities.util.ProductIonFactory
CvTermReference - Enum in uk.ac.ebi.pride.utilities.term: CvTerms contain a list of controlled vocabularies.

D

D_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType: d ions from partial side chain fragmentation of a ions
D_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
DefaultPeptideIon - Class in uk.ac.ebi.pride.utilities.iongen.impl
DefaultPeptideIon(Peptide, int) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon: Create a peptide ion.
DefaultPrecursorIon - Class in uk.ac.ebi.pride.utilities.iongen.impl: Provide different construct methods to create precursor ion.
DefaultPrecursorIon(Peptide, int) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPrecursorIon
DefaultPrecursorIon(Peptide) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPrecursorIon: Default charge is 2, that means this type of precursor ion can generate product ions which charges up to +2.
DefaultPrecursorIon(String, int) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPrecursorIon
DefaultPrecursorIon(String) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPrecursorIon: Default charge is 2, that means this type of precursor ion can generate product ions which charges up to +2.
DefaultProductIon - Class in uk.ac.ebi.pride.utilities.iongen.impl: Default implement of AbstractProductIon.
DefaultProductIon(PrecursorIon, ProductIonType, int, Peptide, int) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.DefaultProductIon: Create product ion instance.
DOT - Static variable in class uk.ac.ebi.pride.utilities.util.file.FileUtil

E

Element - Enum in uk.ac.ebi.pride.utilities.mol: Chemical element, this is a enum class.
EMAIL_ADDRESS_PATTERN - Static variable in class uk.ac.ebi.pride.utilities.util.RegExUtilities: regular expression pattern for email address
equals(Object) - Method in class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon
equals(Object) - Method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
equals(Object) - Method in class uk.ac.ebi.pride.utilities.iongen.model.Peak
equals(Object) - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence
equals(Object) - Method in class uk.ac.ebi.pride.utilities.mol.Group
equals(Object) - Method in class uk.ac.ebi.pride.utilities.mol.NeutralLoss
equals(Object) - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
equals(Object) - Method in class uk.ac.ebi.pride.utilities.mol.PTModification
equals(Object) - Method in class uk.ac.ebi.pride.utilities.util.Triple
equals(Object) - Method in class uk.ac.ebi.pride.utilities.util.Tuple

F

FileUtil - Class in uk.ac.ebi.pride.utilities.util.file: Utility class for file access
findMinMax(double[]) - Static method in class uk.ac.ebi.pride.utilities.util.Math.MathUtils
findParamByName(String) - Static method in enum uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference: Tries to guess which search engine is described by the passed name.
FragmentIonType - Class in uk.ac.ebi.pride.utilities.iongen.ion: FragmentIonType defines different type of fragment ion annotations.
FragmentIonTypeColor - Class in uk.ac.ebi.pride.utilities.iongen.ion: FragmentIonTypeColor stores all the color for each FragmentIonType.
FragmentIonTypeColor() - Constructor for class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
FragmentIonUtilities - Class in uk.ac.ebi.pride.utilities.iongen.ion: Collection of methods for FragmentIonType
FragmentIonUtilities() - Constructor for class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonUtilities

G

getAccession() - Method in enum uk.ac.ebi.pride.utilities.term.CvTermReference
getAccession() - Method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getAccession() - Method in enum uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference
getAccession() - Method in enum uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference
getAcid() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon
getAminoAcid(char) - Static method in enum uk.ac.ebi.pride.utilities.mol.AminoAcid
getAminoAcid(int) - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Returns the amino acid with specified index
getAminoacid(char) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: Converts a chart to an AminoAcid if it matches with one of them
getAminoAcids() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Returns a new list of amino acids
getAminoAcids() - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
getAvgMass() - Method in enum uk.ac.ebi.pride.utilities.mol.AminoAcid
getAvgMass() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Get the sum of average mass.
getAvgMass() - Method in enum uk.ac.ebi.pride.utilities.mol.Atom
getAvgMass() - Method in interface uk.ac.ebi.pride.utilities.mol.Mass
getAvgMass() - Method in class uk.ac.ebi.pride.utilities.mol.NeutralLoss
getAvgMass() - Method in enum uk.ac.ebi.pride.utilities.mol.NuclearParticle
getAvgMassDeltas() - Method in class uk.ac.ebi.pride.utilities.mol.PTModification
getByCvTermReference(CvTermReference) - Static method in enum uk.ac.ebi.pride.utilities.engine.SearchEngineType: Deprecated.
getByName(String) - Static method in enum uk.ac.ebi.pride.utilities.engine.SearchEngineType: Deprecated.

Return A SearchEngineType using the name of the SearchEngine
getCharge() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon
getCharge() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon
getCharge() - Method in interface uk.ac.ebi.pride.utilities.iongen.model.PeptideIon
getCharge() - Method in interface uk.ac.ebi.pride.utilities.iongen.model.ProductIon
getCharge() - Method in enum uk.ac.ebi.pride.utilities.mol.Atom
getCharge() - Method in enum uk.ac.ebi.pride.utilities.mol.NuclearParticle
getChemicalFormula() - Method in enum uk.ac.ebi.pride.utilities.mol.AminoAcid
getChildAccessions() - Method in enum uk.ac.ebi.pride.utilities.term.CvTermReference
getChildAccessions() - Method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getColor(FragmentIonType) - Static method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor: Get the color according to the input ion type.
getCTerminalGroup() - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
getCvLabel() - Method in enum uk.ac.ebi.pride.utilities.term.CvTermReference
getCvLabel() - Method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getCvLabel() - Method in enum uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference
getCvLabel() - Method in enum uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference
getCvRefByAccession(String) - Static method in enum uk.ac.ebi.pride.utilities.term.CvTermReference: Get Cv term by accession.
getCvRefByAccession(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference: Get Cv term by accession.
getDecompressedFileName(File) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil
getDefaultCvTerm(String) - Static method in enum uk.ac.ebi.pride.utilities.engine.SearchEngineType: Deprecated.
getDepthPeakSetList(int, int) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore: Peak set was first separated into windows of splitSize m/z units.
getElements() - Method in class uk.ac.ebi.pride.utilities.mol.Group
getFileExtension(File) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil: Get file extension for a given file
getFileExtension(String) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil
getFileExtension() - Method in enum uk.ac.ebi.pride.utilities.util.file.MassSpecFileFormat
getFileInputStream(File) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil
getFirst() - Method in class uk.ac.ebi.pride.utilities.util.Triple
getFormula() - Method in enum uk.ac.ebi.pride.utilities.mol.Atom
getFormula() - Method in enum uk.ac.ebi.pride.utilities.mol.NuclearParticle
getFragmentIonNeutralLoss(String) - Static method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonUtilities: Return NeutralLoss object based on the input string.
getFragmentIonType(String) - Static method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonUtilities: Use pride ontology to map ion type.
getFullPath(Class) - Static method in class uk.ac.ebi.pride.utilities.util.IOUtilities: This method return the installation path of the input cs
getFullPath(Class, String) - Static method in class uk.ac.ebi.pride.utilities.util.IOUtilities: This method return the full path of specified subPath
getGroup() - Method in enum uk.ac.ebi.pride.utilities.mol.ProductIonType
getInstance(double[], double[]) - Static method in class uk.ac.ebi.pride.utilities.iongen.model.PeakSet: Translate the m/z Array and intensity Array into a set of peaks.
getIntensity() - Method in class uk.ac.ebi.pride.utilities.iongen.model.Peak
getIntensityArray() - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeakSet
getIntensityParamIndex(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getIonPair() - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
getIsotopeLabellingMethodParam(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getKey() - Method in class uk.ac.ebi.pride.utilities.util.Tuple
getLabel() - Method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
getLabel() - Method in class uk.ac.ebi.pride.utilities.mol.PTModification
getLabelFreeMethod(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getLength() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Return the length of the peptide.
getLength() - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
getLoss() - Method in enum uk.ac.ebi.pride.utilities.mol.ProductIonType
getMass() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.AbstractProductIon
getMass() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon
getMass() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon
getMass() - Method in interface uk.ac.ebi.pride.utilities.iongen.model.PeptideIon
getMass() - Method in enum uk.ac.ebi.pride.utilities.mol.Element
getMass() - Method in class uk.ac.ebi.pride.utilities.mol.Group
getMassOverCharge() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon
getMassOverCharge() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon
getMassOverCharge() - Method in interface uk.ac.ebi.pride.utilities.iongen.model.PeptideIon
getMatchedSet(ProductIonSet, PeakSet) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore: match the peak set to fragment ion list with an ion tolerance of [-tolerance, +tolerance]
getMatchedString(Pattern, String, int) - Static method in class uk.ac.ebi.pride.utilities.util.RegExUtilities
getMaxIntensityPeak() - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeakSet
getMonoMass() - Method in enum uk.ac.ebi.pride.utilities.mol.AminoAcid
getMonoMass() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Get the sum of monoisotopic mass.
getMonoMass() - Method in enum uk.ac.ebi.pride.utilities.mol.Atom
getMonoMass() - Method in interface uk.ac.ebi.pride.utilities.mol.Mass
getMonoMass() - Method in class uk.ac.ebi.pride.utilities.mol.NeutralLoss
getMonoMass() - Method in enum uk.ac.ebi.pride.utilities.mol.NuclearParticle
getMonoMassDeltas() - Method in class uk.ac.ebi.pride.utilities.mol.PTModification
getMz() - Method in class uk.ac.ebi.pride.utilities.iongen.model.Peak
getMzArray() - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeakSet
getName() - Method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
getName() - Method in enum uk.ac.ebi.pride.utilities.mol.AminoAcid
getName() - Method in enum uk.ac.ebi.pride.utilities.mol.Atom
getName() - Method in enum uk.ac.ebi.pride.utilities.mol.Element
getName() - Method in class uk.ac.ebi.pride.utilities.mol.Group: User can get the group name based on the elements name which are included in the chemical group.
getName() - Method in class uk.ac.ebi.pride.utilities.mol.NeutralLoss
getName() - Method in enum uk.ac.ebi.pride.utilities.mol.NuclearParticle
getName() - Method in enum uk.ac.ebi.pride.utilities.mol.ProductIonType
getName() - Method in class uk.ac.ebi.pride.utilities.mol.PTModification
getName() - Method in enum uk.ac.ebi.pride.utilities.term.CvTermReference
getName() - Method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getName() - Method in enum uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference
getName() - Method in enum uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference
getNTerminalGroup() - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
getNumberOfAminoAcids() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Return the number of amino acids
getOneLetterCode() - Method in enum uk.ac.ebi.pride.utilities.mol.AminoAcid
getOneLetterCodeString() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Get the string of peptide in one letter format.
getPair() - Method in enum uk.ac.ebi.pride.utilities.mol.ProductIonType
getParentAccessions() - Method in enum uk.ac.ebi.pride.utilities.term.CvTermReference
getParentAccessions() - Method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getPeptide() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon
getPeptide() - Method in interface uk.ac.ebi.pride.utilities.iongen.model.PeptideIon
getPosition() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.AbstractProductIon
getPosition() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon
getPosition() - Method in interface uk.ac.ebi.pride.utilities.iongen.model.ProductIon
getPrecursorIon() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.AbstractProductIon
getPrecursorIon() - Method in interface uk.ac.ebi.pride.utilities.iongen.model.ProductIon
getProbability(int, int) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore: probability of success.
getProductIon(ProductIonType, int, int) - Method in class uk.ac.ebi.pride.utilities.iongen.impl.AbstractPrecursorIon: A precursor ion can cleavage different type of product ions.
getProductIon(ProductIonType, int, int) - Method in interface uk.ac.ebi.pride.utilities.iongen.model.PrecursorIon: A precursor ion can cleavage different type of product ions.
getProductIonSet() - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
getPTM() - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
getQuantitativeMethodParam(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getReagent(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getReagentByShortAccessionLabel(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getReagentByShortNameLabel(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getReagentShortLabel(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getRealFileName(String) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil
getScore(ProductIonSet, int, int) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore: get a peptide score based on peakDepth.
getScore() - Method in enum uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference
getSearchEngineParam() - Method in enum uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference
getSearchEngineScoreParamByAccession(String) - Static method in enum uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference
getSearchEngineScoreParamByName(String) - Static method in enum uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference
getSearchEngineScores() - Method in enum uk.ac.ebi.pride.utilities.engine.SearchEngineType: Deprecated.
getSecond() - Method in class uk.ac.ebi.pride.utilities.util.Triple
getSequence() - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
getSign() - Method in class uk.ac.ebi.pride.utilities.mol.NeutralLoss
getStandardDeviationParamIndex(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getStandardErrorParamIndex(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getThird() - Method in class uk.ac.ebi.pride.utilities.util.Triple
getThreeLetterCode() - Method in enum uk.ac.ebi.pride.utilities.mol.AminoAcid
getThreeLetterCodeString() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Get the string of peptide in three letter format.
getTolerance() - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
getTopIntensityPeak(int) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeakSet
getType() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.AbstractProductIon
getType() - Method in interface uk.ac.ebi.pride.utilities.iongen.model.ProductIon
getType() - Method in class uk.ac.ebi.pride.utilities.mol.PTModification
getTypeName() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon
getUnit(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
getValue() - Method in enum uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference
getValue() - Method in class uk.ac.ebi.pride.utilities.util.Tuple
getWeightedAvgScore(ProductIonSet, int, double[]) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore: get a weighted average peptide score.
GraviUtilities - Class in uk.ac.ebi.pride.utilities.mol
GraviUtilities() - Constructor for class uk.ac.ebi.pride.utilities.mol.GraviUtilities
Group - Class in uk.ac.ebi.pride.utilities.mol: Chemical Group, which including at least one Element.
Group(Element...) - Constructor for class uk.ac.ebi.pride.utilities.mol.Group: A chemical group maybe include more than one chemical elements.

H

H - Static variable in class uk.ac.ebi.pride.utilities.mol.Group
H2O - Static variable in class uk.ac.ebi.pride.utilities.mol.Group: Water group.
hasAccession(String) - Static method in enum uk.ac.ebi.pride.utilities.term.CvTermReference: Check whether the accession exists in the enum.
hasAccession(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference: Check whether the accession exists in the enum.
hashCode() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon
hashCode() - Method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
hashCode() - Method in class uk.ac.ebi.pride.utilities.iongen.model.Peak
hashCode() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence
hashCode() - Method in class uk.ac.ebi.pride.utilities.mol.Group
hashCode() - Method in class uk.ac.ebi.pride.utilities.mol.NeutralLoss
hashCode() - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
hashCode() - Method in class uk.ac.ebi.pride.utilities.mol.PTModification
hashCode() - Method in class uk.ac.ebi.pride.utilities.util.Triple
hashCode() - Method in class uk.ac.ebi.pride.utilities.util.Tuple

I

IllegalAminoAcidSequenceException - Exception in uk.ac.ebi.pride.utilities.exception: Exception class for throwing an illegal AminoAcid sequence error
IllegalAminoAcidSequenceException() - Constructor for exception uk.ac.ebi.pride.utilities.exception.IllegalAminoAcidSequenceException
IllegalAminoAcidSequenceException(String) - Constructor for exception uk.ac.ebi.pride.utilities.exception.IllegalAminoAcidSequenceException
IllegalAminoAcidSequenceException(String, Throwable) - Constructor for exception uk.ac.ebi.pride.utilities.exception.IllegalAminoAcidSequenceException
IllegalAminoAcidSequenceException(Throwable) - Constructor for exception uk.ac.ebi.pride.utilities.exception.IllegalAminoAcidSequenceException
IMMONIUM_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
IMMONIUM_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
ImmoniumIon - Class in uk.ac.ebi.pride.utilities.iongen.impl: Creator: Qingwei-XU Date: ${DATE} Version: 0.1-SNAPSHOT
ImmoniumIon(PrecursorIon, int) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon: the position from [0..length-1]
ImmoniumIon(PrecursorIon, int, int) - Constructor for class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon
IN_SOURCE_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
IN_SOURCE_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
InternetChecker - Class in uk.ac.ebi.pride.utilities.util: InternetChecker checks the availability of internet on local computer
InternetChecker() - Constructor for class uk.ac.ebi.pride.utilities.util.InternetChecker
IonCleavageException - Exception in uk.ac.ebi.pride.utilities.iongen.model: During the process of PrecursorIon cleavage into different type of ProductIon.
IonCleavageException(String) - Constructor for exception uk.ac.ebi.pride.utilities.iongen.model.IonCleavageException
IOUtilities - Class in uk.ac.ebi.pride.utilities.util: IOUtilities provides a list of convenient methods to perform io operations.
IOUtilities() - Constructor for class uk.ac.ebi.pride.utilities.util.IOUtilities
isAminoAcidSequence(String) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: Check if the sequence is valid in terms of the letters contained
isBackboneFragmentIonType(FragmentIonType) - Static method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonUtilities: Retrun true if the ion is a, b, c, x, y, z.
isBinaryFile(File) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil: Check whether a given file is a binary file
isChild(String, String) - Static method in enum uk.ac.ebi.pride.utilities.term.CvTermReference: Check whether two accessions are parent-child relationship.
isChild(String, String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference: Check whether two accessions are parent-child relationship.
isCTerminalFragmentation(FragmentIonType) - Static method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonUtilities: Check whether the fragment ion type is C-Terminal fragment ions.
isCTerminalSideChainFragmentation(FragmentIonType) - Static method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonUtilities: Check whether the fragment ion type is C-Terminal side chain fragment ions.
isEmpty(String) - Static method in class uk.ac.ebi.pride.utilities.util.StringUtils: Check if an string is empty.
isFileEmpty(File) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil
isFileFormat() - Method in enum uk.ac.ebi.pride.utilities.util.file.MassSpecFileFormat
isGzipped(File) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil
isImmoniumFragmentation(FragmentIonType) - Static method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonUtilities: Check wether the fragment ion type is Immonium fragment ion.
isInteger(String) - Static method in class uk.ac.ebi.pride.utilities.util.NumberUtilities: Check whether an string is an integer.
isIntensityParam(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
isIsotopeLabellingMethodParam(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
isLabelFreeMethod(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
isMassSpecDataFolder(File) - Static method in enum uk.ac.ebi.pride.utilities.util.file.MassSpecFileFormat: Check whether a folder is a recognized mass spec data folder
isNonNegativeInteger(String) - Static method in class uk.ac.ebi.pride.utilities.util.NumberUtilities: Check whether an string is a non-negative integer.
isNTerminalFragmentation(FragmentIonType) - Static method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonUtilities: Check whether the fragment ion type is N-Terminal fragment ions.
isNTerminalSideChainFragmentation(FragmentIonType) - Static method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonUtilities: Check whether the fragment ion type is N-Terminal fragment ions.
isNumber(String) - Static method in class uk.ac.ebi.pride.utilities.util.NumberUtilities: Check whether a string is a number
IsoelectricPointUtils - Class in uk.ac.ebi.pride.utilities.mol: IsoelectricPointUtils is used to calculate the theoretical isoelectric point of a peptide
At the moment we only support one method, and the peptide PTMs are not taken into account
IsoelectricPointUtils() - Constructor for class uk.ac.ebi.pride.utilities.mol.IsoelectricPointUtils
IsoelectricPointUtils.BjellpI - Class in uk.ac.ebi.pride.utilities.mol
IsoelectricPointUtils.BjellpI() - Constructor for class uk.ac.ebi.pride.utilities.mol.IsoelectricPointUtils.BjellpI
isQuantitativeMethodParam(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
isQuantitativeParam(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference: Checks whether the passed accession describes a QuantificationCvParam.
isReagent(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
isShowAmmoniaLoss() - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
isShowWaterLoss() - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
isStandardDeviationParam(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
isStandardErrorParam(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
isSubSampleDescription(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
isUnit(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference
isValidEmail(String) - Static method in class uk.ac.ebi.pride.utilities.util.RegExUtilities: Check whether email is a valid email address.
isZipped(File) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil

M

main(String[]) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities
Mass - Interface in uk.ac.ebi.pride.utilities.mol: Mass provides a set of interfaces to get monoisotopic mass and average mass.
MassSpecFileFormat - Enum in uk.ac.ebi.pride.utilities.util.file: Different mass spec file format, also include support methods for detecting the format
MassSpecFileRegx - Class in uk.ac.ebi.pride.utilities.util.file: This utility class contains regular expressions for recognizing mass spec file format
MathUtils - Class in uk.ac.ebi.pride.utilities.util.Math
MathUtils() - Constructor for class uk.ac.ebi.pride.utilities.util.Math.MathUtils
MoleculeUtilities - Class in uk.ac.ebi.pride.utilities.mol: Utility class for Molecule operations
MoleculeUtilities() - Constructor for class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities
MZDATA_PATTERN - Static variable in class uk.ac.ebi.pride.utilities.util.file.MassSpecFileRegx
MZIDENTML_PATTERN - Static variable in class uk.ac.ebi.pride.utilities.util.file.MassSpecFileRegx
MZML_PATTERN - Static variable in class uk.ac.ebi.pride.utilities.util.file.MassSpecFileRegx
MZXML_PATTERN - Static variable in class uk.ac.ebi.pride.utilities.util.file.MassSpecFileRegx

N

NeutralLoss - Class in uk.ac.ebi.pride.utilities.mol: neutral losses
NeutralLoss(String, String, double, double) - Constructor for class uk.ac.ebi.pride.utilities.mol.NeutralLoss
NH - Static variable in class uk.ac.ebi.pride.utilities.mol.Group: NH group used in calcute the mass of z ion.
NH3 - Static variable in class uk.ac.ebi.pride.utilities.mol.Group: Ammonia group
NON_IDENTIFIED_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
NON_IDENTIFIED_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
NuclearParticle - Enum in uk.ac.ebi.pride.utilities.mol: NuclearParticle is an enum which stores all the nuclear particles.
NumberUtilities - Class in uk.ac.ebi.pride.utilities.util: NumberUtilities provides methods for number handling.
NumberUtilities() - Constructor for class uk.ac.ebi.pride.utilities.util.NumberUtilities

O

OH - Static variable in class uk.ac.ebi.pride.utilities.mol.Group

P

Peak - Class in uk.ac.ebi.pride.utilities.iongen.model: Peak including m/z and intensity double value.
Peak(double, double) - Constructor for class uk.ac.ebi.pride.utilities.iongen.model.Peak
PeakSet - Class in uk.ac.ebi.pride.utilities.iongen.model: Creator: Qingwei-XU Date: 02/11/12
PeakSet() - Constructor for class uk.ac.ebi.pride.utilities.iongen.model.PeakSet
PeakSet(SortedSet<Peak>) - Constructor for class uk.ac.ebi.pride.utilities.iongen.model.PeakSet
Peptide - Class in uk.ac.ebi.pride.utilities.mol: A peptide including three parts: N terminal group, C terminal group and a couple of AminoAcids.
Peptide(String) - Constructor for class uk.ac.ebi.pride.utilities.mol.Peptide: Create a peptide without PTM.
Peptide(String, Group, Group) - Constructor for class uk.ac.ebi.pride.utilities.mol.Peptide: Create a peptide without PTM.
Peptide(String, Map<Integer, PTModification>) - Constructor for class uk.ac.ebi.pride.utilities.mol.Peptide: Create a peptide with PTM.
Peptide(String, Group, Group, Map<Integer, PTModification>) - Constructor for class uk.ac.ebi.pride.utilities.mol.Peptide: Create a peptide with PTM.
Peptide(List<AminoAcid>) - Constructor for class uk.ac.ebi.pride.utilities.mol.Peptide: Create a peptide without PTM.
Peptide(List<AminoAcid>, Group, Group) - Constructor for class uk.ac.ebi.pride.utilities.mol.Peptide: Create a peptide without PTM.
Peptide(List<AminoAcid>, Map<Integer, PTModification>) - Constructor for class uk.ac.ebi.pride.utilities.mol.Peptide: Create a peptide with PTM.
Peptide(List<AminoAcid>, Group, Group, Map<Integer, PTModification>) - Constructor for class uk.ac.ebi.pride.utilities.mol.Peptide: Create a peptide with PTM.
PeptideIon - Interface in uk.ac.ebi.pride.utilities.iongen.model: When a peptide with charges, we call it peptide ion.
PeptideScore - Class in uk.ac.ebi.pride.utilities.iongen.model
PeptideScore(PrecursorIon, PeakSet, ProductIonPair, double, boolean, boolean) - Constructor for class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
PeptideScore(PrecursorIon, PeakSet) - Constructor for class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
PRECURSOR_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
PRECURSOR_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
PrecursorIon - Interface in uk.ac.ebi.pride.utilities.iongen.model: A kind of PeptideIon, which can cleavage different types of product ions.
PRIDE_XML_PATTERN - Static variable in class uk.ac.ebi.pride.utilities.util.file.MassSpecFileRegx
ProductIon - Interface in uk.ac.ebi.pride.utilities.iongen.model: A kind of PeptideIon, which have one PrecursorIon.
ProductIonFactory - Class in uk.ac.ebi.pride.utilities.util: This is a general interface for most users to get theoretical m/z values list of product ions and immonium ions.
ProductIonFactory() - Constructor for class uk.ac.ebi.pride.utilities.util.ProductIonFactory
ProductIonPair - Enum in uk.ac.ebi.pride.utilities.mol: This is enum class.
ProductIonSet - Class in uk.ac.ebi.pride.utilities.iongen.model
ProductIonSet() - Constructor for class uk.ac.ebi.pride.utilities.iongen.model.ProductIonSet
ProductIonType - Enum in uk.ac.ebi.pride.utilities.mol: Creator: Qingwei-XU Date: 23/10/12
PTModification - Class in uk.ac.ebi.pride.utilities.mol: PTModification stores modification details, this class is not enum because there are many different types of modifications.
PTModification(String, String, String, List<Double>, List<Double>) - Constructor for class uk.ac.ebi.pride.utilities.mol.PTModification

Q

QuantCvTermReference - Enum in uk.ac.ebi.pride.utilities.term: Holds the cvParams to report quantitative information in PRIDE XML files.

R

RegExUtilities - Class in uk.ac.ebi.pride.utilities.util: RegExUtilities provides convenient methods for handling regular expressions.
RegExUtilities() - Constructor for class uk.ac.ebi.pride.utilities.util.RegExUtilities
remove(int) - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Remove amino acid at the index.
removeAll() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: Remove all amino acid
removeModification(int) - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
removeModification(PTModification) - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
replaceSpecialAA(String) - Static method in class uk.ac.ebi.pride.utilities.mol.IsoelectricPointUtils

S

scaleDouble(double, int) - Static method in class uk.ac.ebi.pride.utilities.util.NumberUtilities: Returns the value scaled to the indicated decimal places
SearchEngineCvTermReference - Enum in uk.ac.ebi.pride.utilities.term
SearchEngineScoreCvTermReference - Enum in uk.ac.ebi.pride.utilities.term
SearchEngineType - Enum in uk.ac.ebi.pride.utilities.engine: Deprecated.
searchForAminoAcid(double, double, boolean) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: Search within a mass window (inclusive).
searchForPeptide(double, double, boolean, int) - Static method in class uk.ac.ebi.pride.utilities.mol.MoleculeUtilities: Search and return a combination of amino acid according the number of residue specified.
setFirst(K) - Method in class uk.ac.ebi.pride.utilities.util.Triple
setIonPair(ProductIonPair) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
setKey(K) - Method in class uk.ac.ebi.pride.utilities.util.Tuple
setSecond(V) - Method in class uk.ac.ebi.pride.utilities.util.Triple
setShowAmmoniaLoss(boolean) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
setShowWaterLoss(boolean) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
setThird(T) - Method in class uk.ac.ebi.pride.utilities.util.Triple
setTolerance(double) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeptideScore
setValue(V) - Method in class uk.ac.ebi.pride.utilities.util.Tuple
splitWindow(int) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeakSet: split the whole peaks into list of subsets.
splitWindow(int) - Method in class uk.ac.ebi.pride.utilities.iongen.model.ProductIonSet: split the whole fragment ion list into list of subsets.
StringUtils - Class in uk.ac.ebi.pride.utilities.util: General functions for all libraries in PRIDE Related with String handling
StringUtils() - Constructor for class uk.ac.ebi.pride.utilities.util.StringUtils
subSet(double, double) - Method in class uk.ac.ebi.pride.utilities.iongen.model.PeakSet: Create a subset of peak set.

T

tail(File, int) - Static method in class uk.ac.ebi.pride.utilities.util.file.FileUtil
toString() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon
toString() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.DefaultProductIon
toString() - Method in class uk.ac.ebi.pride.utilities.iongen.impl.ImmoniumIon
toString() - Method in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
toString() - Method in class uk.ac.ebi.pride.utilities.iongen.model.Peak
toString() - Method in class uk.ac.ebi.pride.utilities.mol.AminoAcidSequence: This method calls getOneLetterCodeString()
toString() - Method in enum uk.ac.ebi.pride.utilities.mol.Element
toString() - Method in class uk.ac.ebi.pride.utilities.mol.Group
toString() - Method in class uk.ac.ebi.pride.utilities.mol.NeutralLoss
toString() - Method in class uk.ac.ebi.pride.utilities.mol.Peptide
Triple<K,V,T> - Class in uk.ac.ebi.pride.utilities.util: Data structure contains three elements
Triple(K, V, T) - Constructor for class uk.ac.ebi.pride.utilities.util.Triple
Tuple<K,V> - Class in uk.ac.ebi.pride.utilities.util: Tuple stores two elements.
Tuple(K, V) - Constructor for class uk.ac.ebi.pride.utilities.util.Tuple

U

uk.ac.ebi.pride.utilities.engine - package uk.ac.ebi.pride.utilities.engine
uk.ac.ebi.pride.utilities.exception - package uk.ac.ebi.pride.utilities.exception
uk.ac.ebi.pride.utilities.iongen.impl - package uk.ac.ebi.pride.utilities.iongen.impl
uk.ac.ebi.pride.utilities.iongen.ion - package uk.ac.ebi.pride.utilities.iongen.ion
uk.ac.ebi.pride.utilities.iongen.model - package uk.ac.ebi.pride.utilities.iongen.model
uk.ac.ebi.pride.utilities.mol - package uk.ac.ebi.pride.utilities.mol
uk.ac.ebi.pride.utilities.term - package uk.ac.ebi.pride.utilities.term
uk.ac.ebi.pride.utilities.util - package uk.ac.ebi.pride.utilities.util
uk.ac.ebi.pride.utilities.util.file - package uk.ac.ebi.pride.utilities.util.file
uk.ac.ebi.pride.utilities.util.Math - package uk.ac.ebi.pride.utilities.util.Math

V

V_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType: v ions from complete side chain fragmentation of y ions
V_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.engine.SearchEngineType: Deprecated.

Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.mol.AminoAcid: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.mol.Atom: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.mol.Element: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.mol.NuclearParticle: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.mol.ProductIonPair: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.mol.ProductIonType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.term.CvTermReference: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.term.QuantCvTermReference: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.util.file.MassSpecFileFormat: Returns the enum constant of this type with the specified name.
values() - Static method in enum uk.ac.ebi.pride.utilities.engine.SearchEngineType: Deprecated.

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.mol.AminoAcid: 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.mol.Atom: 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.mol.Element: 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.mol.NuclearParticle: 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.mol.ProductIonPair: 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.mol.ProductIonType: 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.term.CvTermReference: 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.term.QuantCvTermReference: 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.term.SearchEngineCvTermReference: 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.term.SearchEngineScoreCvTermReference: 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.util.file.MassSpecFileFormat: Returns an array containing the constants of this enum type, in the order they are declared.

W

W_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType: w ions from partial side chain fragmentation of z ions
W_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor
WATER_LOSS - Static variable in class uk.ac.ebi.pride.utilities.mol.NeutralLoss

X

X_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
X_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor

Y

Y_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
Y_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor

Z

Z_ION - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonType
Z_ION_COLOR - Static variable in class uk.ac.ebi.pride.utilities.iongen.ion.FragmentIonTypeColor

A B C D E F G H I M N O P Q R S T U V W X Y Z