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

A

aa - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcidCollection

AbstractDataAccessController - Class in uk.ac.ebi.pridemod.controller

yperez

AbstractDataAccessController(InputStream) - Constructor for class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

Default constructor for Controllers

AbstractPTM - Class in uk.ac.ebi.pridemod.model

yperez

AbstractPTM(String, String, String, Double, Double, List<Specificity>, String) - Constructor for class uk.ac.ebi.pridemod.model.AbstractPTM

Contructor with all the fields for a general modification

add(SlimModification) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Add an slim modification to the list of modifications

add(int, SlimModification) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Add an Slim Modification in the list in an specific position (index)

addAll(Collection<? extends SlimModification>) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Add a collection of slim modifications to the current list of slim modifications.

addAll(int, Collection<? extends SlimModification>) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Add a collection of slim modifications from the index integer

altNameOrIgnore - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

AminoAcid - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for aa element declaration.

AminoAcid() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

AminoAcidCollection - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for amino_acids element declaration.

AminoAcidCollection() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.AminoAcidCollection

aminoAcids - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

approved - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

AtomComposition - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for element element declaration.

AtomComposition() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.AtomComposition

AtomElement - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for elem element declaration.

AtomElement() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

avgeMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

avgeMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

avgeMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Delta

avgeMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

avgeMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

avgeMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

avgeMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

B

biologicalSignificance - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

brick - Variable in class uk.ac.ebi.pridemod.io.unimod.model.ModBricksCollection

C

classification - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

clear() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Clear the List of modifications

compareAvg(double) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

compareId(int) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

compareId(int) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

compareMono(double) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

compareTo(Object) - Method in class uk.ac.ebi.pridemod.model.Specificity

composition - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Delta

composition - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

composition - Variable in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

composition - Variable in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

contains(Object) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Verified if a Modification exist in the List of the current modifications.

containsAll(Collection<?>) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Compare if a list of slim modifications are included in the List of modifications

createAltName(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of JAXBElement<String>}

createAminoAcid() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of AminoAcid

createAminoAcidCollection() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of AminoAcidCollection

createAtomComposition() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of AtomComposition

createAtomElement() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of AtomElement

createDelta() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of Delta

createElementCollection() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of ElementCollection

createIgnore() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of Ignore

createMiscNotes(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of JAXBElement<String>}

createModBrick() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of ModBrick

createModBricksCollection() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of ModBricksCollection

createModificationCollection() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of ModificationCollection

createNeutralLoss() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of NeutralLoss

createPepNeutralLoss() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of PepNeutralLoss

createPrideMod() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.ObjectFactory

Create an instance of PrideMod

createPrideModification() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.ObjectFactory

Create an instance of PrideModification

createPrideModifications() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.ObjectFactory

Create an instance of PrideModifications

createPsiModification() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.ObjectFactory

Create an instance of PsiModification

createPsiModifications() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.ObjectFactory

Create an instance of PsiModifications

createReference() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of Reference

createSource(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of JAXBElement<String>}

createSpecificity() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of Specificity

createText(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of JAXBElement<String>}

createUnimod() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of Unimod

createUnimodMapping() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.ObjectFactory

Create an instance of UnimodMapping

createUnimodMappings() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.ObjectFactory

Create an instance of UnimodMappings

createUnimodModification() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of UnimodModification

createUrl(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create an instance of JAXBElement<String>}

D

DataAccessController - Interface in uk.ac.ebi.pridemod.controller

DataAccessController is an Interface for all the Modification Databases.

DataAccessException - Exception in uk.ac.ebi.pridemod.exception

DataAccessException is thrown when there is an error during i/o via data access controller

User: yperez Date: 03-Feb-2010 Time: 08:45:27

DataAccessException(String) - Constructor for exception uk.ac.ebi.pridemod.exception.DataAccessException

DataAccessException(String, Throwable) - Constructor for exception uk.ac.ebi.pridemod.exception.DataAccessException

dateTimeModified - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

dateTimePosted - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Delta - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for delta element declaration.

Delta() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.Delta

delta - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

diffMono - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

E

elem - Variable in class uk.ac.ebi.pridemod.io.unimod.model.ElementCollection

element - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

element - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Delta

element - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

element - Variable in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

element - Variable in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

element - Variable in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

ElementCollection - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for elements element declaration.

ElementCollection() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.ElementCollection

elements - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

F

flag - Variable in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

fullName - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

fullName - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

fullName - Variable in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

fullName - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

G

generalModification - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

get(int) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Get a modification in the list.

getAa() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcidCollection

Gets the value of the aa property.

getAccession() - Method in class uk.ac.ebi.pridemod.model.AbstractPTM

getAccession() - Method in interface uk.ac.ebi.pridemod.model.PTM

Return the accession of a PTM.

getAccessionType(String) - Static method in class uk.ac.ebi.pridemod.utils.PRIDEModUtils

getAltNameOrIgnore() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the altNameOrIgnore property.

getAminoAcids() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Gets the value of the aminoAcids property.

getApproved() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the approved property.

getAveDeltaMass() - Method in class uk.ac.ebi.pridemod.model.AbstractPTM

getAveDeltaMass() - Method in interface uk.ac.ebi.pridemod.model.PTM

Returns the delta Average mass of the modification.

getAvgeMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Gets the value of the avgeMass property.

getAvgeMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

Gets the value of the avgeMass property.

getAvgeMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Delta

Gets the value of the avgeMass property.

getAvgeMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

Gets the value of the avgeMass property.

getAvgeMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

Gets the value of the avgeMass property.

getAvgeMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

Gets the value of the avgeMass property.

getAvgeMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

Gets the value of the avgeMass property.

getBiologicalSignificance() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Gets the value of the biologicalSignificance property.

getBrick() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBricksCollection

Gets the value of the brick property.

getbyDelta(double, double) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

This method return an object of SlimCollection with a list of the slim modifications by a given mass and small windows or error between the delta mass of the modifications and the parameter deltaMass.

getbyName(String) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Get the list of slim modifications compare only with the default specificity of each modification.

getbySpecificity(Specificity.AminoAcid) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

This method return an SlimModCollection object, a list of the slim modifications that contain an specific specificity in the list of possible specificities.

getbySpecificity(String) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

This method return an SlimModCollection object, a list of the slim modifications that contain an specific specificity in the list of possible specificities.

getbySpecificity(Specificity.AminoAcid, double, double) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

This method allow users to obtain the slim modification filtering with a delta mass a possible error (difference) and one specificity in the list of the possible specificities for each modification.

getbySpecificity(String, double, double) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

This method allow users to obtain the slim modification filtering with a delta mass a possible error (difference) and one specificity in the list of the possible specificities for each modification.

getClassForElementName(String) - Static method in class uk.ac.ebi.pridemod.io.pridemod.model.ModelConstants

getClassForElementName(String) - Static method in class uk.ac.ebi.pridemod.io.unimod.model.ModelConstants

getClassification() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Gets the value of the classification property.

getComposition() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Delta

Gets the value of the composition property.

getComposition() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

Gets the value of the composition property.

getComposition() - Method in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

Gets the value of the composition property.

getComposition() - Method in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

Gets the value of the composition property.

getDateTimeModified() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the dateTimeModified property.

getDateTimePosted() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the dateTimePosted property.

getDelta() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the delta property.

getDeltaMass() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Get the delta Mass of the Modification

getDescription() - Method in class uk.ac.ebi.pridemod.model.AbstractPTM

getDescription() - Method in interface uk.ac.ebi.pridemod.model.PTM

Returns the description of the Modification.

getDiffMono() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Gets the value of the diffMono property.

getElem() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ElementCollection

Gets the value of the elem property.

getElement() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Gets the value of the element property.

getElement() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Delta

Gets the value of the element property.

getElement() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

Gets the value of the element property.

getElement() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

Gets the value of the element property.

getElement() - Method in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

Gets the value of the element property.

getElement() - Method in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

Gets the value of the element property.

getElementNameForClass(Class) - Static method in class uk.ac.ebi.pridemod.io.pridemod.model.ModelConstants

getElementNameForClass(Class) - Static method in class uk.ac.ebi.pridemod.io.unimod.model.ModelConstants

getElements() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Gets the value of the elements property.

getFormula() - Method in class uk.ac.ebi.pridemod.model.AbstractPTM

getFormula() - Method in interface uk.ac.ebi.pridemod.model.PTM

Return the Chemical Formula of the modification

getFullName() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Gets the value of the fullName property.

getFullName() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

Gets the value of the fullName property.

getFullName() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

Gets the value of the fullName property.

getFullName() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the fullName property.

getGeneralModification() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Gets the value of the generalModification property.

getGroupOfPoster() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the groupOfPoster property.

getHidden() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Gets the value of the hidden property.

getId() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Gets the value of the id property.

getId() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Gets the value of the id property.

getId() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.UnimodMapping

Gets the value of the id property.

getIdPsiMod() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Get the PSI-Mod database identifier.

getIdUnimod() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Get Unimod database identifier.

getInstance() - Static method in class uk.ac.ebi.pridemod.io.pridemod.xml.marshaller.PrideModMarshallerFactory

getInstance() - Static method in class uk.ac.ebi.pridemod.io.pridemod.xml.unmarshaller.PrideModUnmarshallerFactory

getInstance() - Static method in class uk.ac.ebi.pridemod.io.unimod.xml.marshaller.UnimodMarshallerFactory

getInstance() - Static method in class uk.ac.ebi.pridemod.io.unimod.xml.unmarshaller.UnimodUnmarshallerFactory

getInstance() - Static method in class uk.ac.ebi.pridemod.ModReader

getListbyMassSpecificity(String, double) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModifications

getListbyMassSpecificity(String, double) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModificationCollection

getMajorVersion() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Gets the value of the majorVersion property.

getMinorVersion() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Gets the value of the minorVersion property.

getMiscNotes() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the miscNotes property.

getMiscNotesOrPepNeutralLoss() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Gets the value of the miscNotesOrPepNeutralLoss property.

getMod() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModificationCollection

Gets the value of the mod property.

getModBricks() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Gets the value of the modBricks property.

getModbyAvgMass(double) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModificationCollection

getModbyId(int) - Method in class uk.ac.ebi.pridemod.io.pridemod.extractor.PrideModExtractor

getModbyId(int) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModifications

getModbyId(int) - Method in class uk.ac.ebi.pridemod.io.unimod.extractor.UnimodExtractor

getModbyId(int) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModificationCollection

getModbyMonoMass(double) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModifications

getModifications() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Gets the value of the modifications property.

getModListbyMass(double) - Method in class uk.ac.ebi.pridemod.io.pridemod.extractor.PrideModExtractor

getModListbyMass(double) - Method in class uk.ac.ebi.pridemod.io.unimod.extractor.UnimodExtractor

getModListbyMassSepecificity(String, double) - Method in class uk.ac.ebi.pridemod.io.pridemod.extractor.PrideModExtractor

getModListbyMassSepecificity(String, double) - Method in class uk.ac.ebi.pridemod.io.unimod.extractor.UnimodExtractor

getModListbySpecificity(String) - Method in class uk.ac.ebi.pridemod.io.pridemod.extractor.PrideModExtractor

getModListbySpecificity(String) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModifications

getModListbySpecificity(String) - Method in class uk.ac.ebi.pridemod.io.unimod.extractor.UnimodExtractor

getModListbySpecificity(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModificationCollection

getMonoDeltaMass() - Method in class uk.ac.ebi.pridemod.model.AbstractPTM

getMonoDeltaMass() - Method in interface uk.ac.ebi.pridemod.model.PTM

Returns the delta MonoIsotopic mass of the modification.

getMonoMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Gets the value of the monoMass property.

getMonoMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

Gets the value of the monoMass property.

getMonoMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Delta

Gets the value of the monoMass property.

getMonoMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

Gets the value of the monoMass property.

getMonoMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

Gets the value of the monoMass property.

getMonoMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

Gets the value of the monoMass property.

getMonoMass() - Method in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

Gets the value of the monoMass property.

getName() - Method in class uk.ac.ebi.pridemod.model.AbstractPTM

getName() - Method in interface uk.ac.ebi.pridemod.model.PTM

Get the Name of the PTMs

getName() - Method in class uk.ac.ebi.pridemod.model.Specificity

Get Amino Acid Position

getNeutralLoss() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Gets the value of the neutralLoss property.

getNumber() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomComposition

Gets the value of the number property.

getObsolete() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Gets the value of the obsolete property.

getOrigin() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Gets the value of the origin property.

getParentPTMList() - Method in class uk.ac.ebi.pridemod.model.PSIModPTM

getPosition() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Gets the value of the position property.

getPosition() - Method in class uk.ac.ebi.pridemod.model.Specificity

Get Position

getPrideMod() - Method in class uk.ac.ebi.pridemod.io.pridemod.xml.PrideModReader

getPrideModification() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModifications

Gets the value of the prideModification property.

getPrideModifications() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideMod

Gets the value of the prideModifications property.

getPsiId() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

This function returns the id for a given PRIDE Mod

getPsiModDesc() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Get Name in PSI-Mod database

getPsiModification() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModifications

Gets the value of the psiModification property.

getPsiModifications() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Gets the value of the psiModifications property.

getPsiName() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

getPTMbyAccession(String) - Method in class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

Return the PTM with an specific accession.

getPTMbyAccession(String) - Method in interface uk.ac.ebi.pridemod.controller.DataAccessController

PTM accession

getPTMbyAccession(String) - Method in class uk.ac.ebi.pridemod.controller.impl.UnimodDataAccessController

We decided to put the UNIOMD: prefix in order to be compatible with the same PSI-MOD style and the mzIdentML.

getPTMbyAccession(String) - Method in class uk.ac.ebi.pridemod.ModReader

PTM accession

getPTMListByAvgDeltaMass(Double) - Method in class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

getPTMListByAvgDeltaMass(Double) - Method in interface uk.ac.ebi.pridemod.controller.DataAccessController

Get List PTMs by Average Delta Mass

getPTMListByAvgDeltaMass(Double) - Method in class uk.ac.ebi.pridemod.ModReader

getPTMListByEqualName(String) - Method in class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

getPTMListByEqualName(String) - Method in interface uk.ac.ebi.pridemod.controller.DataAccessController

Return all PTMs with the same name.

getPTMListByEqualName(String) - Method in class uk.ac.ebi.pridemod.ModReader

Return all PTMs with the same name.

getPTMListByMonoDeltaMass(Double) - Method in class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

getPTMListByMonoDeltaMass(Double) - Method in interface uk.ac.ebi.pridemod.controller.DataAccessController

Get List of PTMs by Monoisotopic delta mass

getPTMListByMonoDeltaMass(Double) - Method in class uk.ac.ebi.pridemod.ModReader

getPTMListByPatternDescription(String) - Method in class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

getPTMListByPatternDescription(String) - Method in interface uk.ac.ebi.pridemod.controller.DataAccessController

Description pattern to found PTMs with the pattern

getPTMListByPatternDescription(String) - Method in class uk.ac.ebi.pridemod.ModReader

Description pattern to found PTMs with the pattern

getPTMListByPatternName(String) - Method in class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

Return the ptm with an specific pattern in the name

getPTMListByPatternName(String) - Method in interface uk.ac.ebi.pridemod.controller.DataAccessController

String pattern present in the name.

getPTMListByPatternName(String) - Method in class uk.ac.ebi.pridemod.ModReader

String pattern present in the name.

getPTMListBySpecificity(Specificity) - Method in class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

getPTMListBySpecificity(Specificity) - Method in interface uk.ac.ebi.pridemod.controller.DataAccessController

Specificity to filter all the identifications in the

getPTMListBySpecificity(Specificity) - Method in class uk.ac.ebi.pridemod.ModReader

Specificity to filter all the identifications in the

getQNameForClass(Class) - Static method in class uk.ac.ebi.pridemod.io.pridemod.model.ModelConstants

getQNameForClass(Class) - Static method in class uk.ac.ebi.pridemod.io.unimod.model.ModelConstants

getRecordId() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the recordId property.

getShortNamePsiMod() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Get short name in PSI-Mod database

getSite() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Gets the value of the site property.

getSlimModCollection() - Method in class uk.ac.ebi.pridemod.io.pridemod.xml.PrideModReader

getSource() - Method in class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

getSource() - Method in interface uk.ac.ebi.pridemod.controller.DataAccessController

getSource() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Reference

Gets the value of the source property.

getSource() - Method in class uk.ac.ebi.pridemod.model.PSIModPTM

getSpecGroup() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Gets the value of the specGroup property.

getSpecificity() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the specificity property.

getSpecificityCollection() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Get a collection of possible specificities of the current modification.

getSpecificityCollection() - Method in class uk.ac.ebi.pridemod.model.AbstractPTM

getSpecificityCollection() - Method in interface uk.ac.ebi.pridemod.model.PTM

Return the List of AminoAcid Specificity.

getSpecificityList() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

getSpecificModification() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Gets the value of the specificModification property.

getSymbol() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomComposition

Gets the value of the symbol property.

getSynonyms() - Method in class uk.ac.ebi.pridemod.model.PSIModPTM

getTermCollection() - Method in class uk.ac.ebi.pridemod.io.psimod.PSIModReader

getTermSpec() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Gets the value of the termSpec property.

getText() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Reference

Gets the value of the text property.

getThreeLetter() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Gets the value of the threeLetter property.

getTitle() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Gets the value of the title property.

getTitle() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Gets the value of the title property.

getTitle() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Gets the value of the title property.

getTitle() - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

Gets the value of the title property.

getTitle() - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

Gets the value of the title property.

getTitle() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the title property.

getUnimodMapping() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.UnimodMappings

Gets the value of the unimodMapping property.

getUnimodMappings() - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Gets the value of the unimodMappings property.

getUnimodObject() - Method in class uk.ac.ebi.pridemod.io.unimod.xml.UnimodReader

getUniModRef() - Method in class uk.ac.ebi.pridemod.model.PRIDEModPTM

getUrl() - Method in class uk.ac.ebi.pridemod.io.unimod.model.Reference

Gets the value of the url property.

getUsernameOfPoster() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the usernameOfPoster property.

getXref() - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Gets the value of the xref property.

groupOfPoster - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

H

hidden - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

I

id - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

id - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

id - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.UnimodMapping

Ignore - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for Ignore element declaration.

Ignore() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.Ignore

indexOf(Object) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Index of the Object slim modification in the List of modifications

initializeMarshaller() - Method in class uk.ac.ebi.pridemod.io.pridemod.xml.marshaller.PrideModMarshallerFactory

initializeMarshaller() - Method in class uk.ac.ebi.pridemod.io.unimod.xml.marshaller.UnimodMarshallerFactory

initializeUnmarshaller() - Method in class uk.ac.ebi.pridemod.io.pridemod.xml.unmarshaller.PrideModUnmarshallerFactory

initializeUnmarshaller() - Method in class uk.ac.ebi.pridemod.io.unimod.xml.unmarshaller.UnimodUnmarshallerFactory

isEmpty() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Get if the modification list is Empty.

isFlag() - Method in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

Gets the value of the flag property.

isObsolete() - Method in class uk.ac.ebi.pridemod.model.PSIModPTM

isRegisteredClass(Class) - Static method in class uk.ac.ebi.pridemod.io.pridemod.model.ModelConstants

isRegisteredClass(Class) - Static method in class uk.ac.ebi.pridemod.io.unimod.model.ModelConstants

isRequired() - Method in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

Gets the value of the required property.

isSpecificity(String) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

isSpecificity(Specificity.AminoAcid) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Check if a given AminoAcid is part of the specificity of this SlimModification.

isSpecificity(Specificity.AminoAcid, double, double) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Check if a given AminoAcid is part of the specificity of this SlimModification, but only perform this check if the delta mass of this SlimModification is with the specified difference of the specified mass.

isSpecificity(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

iterator() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

An iterator through the modification List

L

lastIndexOf(Object) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Index after the element passed by parameters in the list

listIterator() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Get List of Iterator of the List of modifications

listIterator(int) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Get List of Iterator of the List of modifications from specific position

M

majorVersion - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

minorVersion - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

miscNotes - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

miscNotesOrPepNeutralLoss - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

mod - Variable in class uk.ac.ebi.pridemod.io.unimod.model.ModificationCollection

ModBrick - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for brick element declaration.

ModBrick() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

modBricks - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

ModBricksCollection - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for mod_bricks element declaration.

ModBricksCollection() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.ModBricksCollection

MODEL_PKG - Static variable in class uk.ac.ebi.pridemod.io.pridemod.model.ModelConstants

MODEL_PKG - Static variable in class uk.ac.ebi.pridemod.io.unimod.model.ModelConstants

ModelConstants - Class in uk.ac.ebi.pridemod.io.pridemod.model

User: yperez Date: 18-Julio-2011

ModelConstants() - Constructor for class uk.ac.ebi.pridemod.io.pridemod.model.ModelConstants

ModelConstants - Class in uk.ac.ebi.pridemod.io.unimod.model

Created by IntelliJ IDEA.

ModelConstants() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.ModelConstants

ModificationCollection - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for modifications element declaration.

ModificationCollection() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.ModificationCollection

modifications - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

ModReader - Class in uk.ac.ebi.pridemod

yperez

ModReader() - Constructor for class uk.ac.ebi.pridemod.ModReader

monoMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

monoMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

monoMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Delta

monoMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

monoMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

monoMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

monoMass - Variable in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

N

NeutralLoss - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for NeutralLoss element declaration.

NeutralLoss() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

neutralLoss - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

number - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AtomComposition

O

ObjectFactory - Class in uk.ac.ebi.pridemod.io.pridemod.model

This object contains factory methods for each Java content interface and Java element interface generated in the uk.ac.ebi.pridemod.model package.

ObjectFactory() - Constructor for class uk.ac.ebi.pridemod.io.pridemod.model.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: uk.ac.ebi.pridemod.model

ObjectFactory - Class in uk.ac.ebi.pridemod.io.unimod.model

This object contains factory methods for each Java content interface and Java element interface generated in the uk.ac.ebi.unimod.model package.

ObjectFactory() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: uk.ac.ebi.unimod.model

obsolete - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

origin - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

P

parseAminoAcid(String) - Static method in class uk.ac.ebi.pridemod.model.Specificity

Convert an Amino acids in the one chacter representation to the AminoAcid representation.

parsePositon(String) - Static method in class uk.ac.ebi.pridemod.model.Specificity

Convert a String to a Position object.

parseSlimModCollection() - Static method in class uk.ac.ebi.pridemod.io.PrideModController

parseSlimModification(URL) - Static method in class uk.ac.ebi.pridemod.io.slimmod.tab.ReadTabSlim

Template method that calls ReadTabSlim.processLine(String).

parseSlimModification(String) - Static method in class uk.ac.ebi.pridemod.io.slimmod.tab.ReadTabSlim

parseSlimModification(Scanner) - Static method in class uk.ac.ebi.pridemod.io.slimmod.tab.ReadTabSlim

PepNeutralLoss - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for PepNeutralLoss element declaration.

PepNeutralLoss() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

position - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

PRIDEMOD - Static variable in class uk.ac.ebi.pridemod.io.pridemod.model.ModelConstants

PrideMod - Class in uk.ac.ebi.pridemod.io.pridemod.model

Java class for anonymous complex type.

PrideMod() - Constructor for class uk.ac.ebi.pridemod.io.pridemod.model.PrideMod

PrideModController - Class in uk.ac.ebi.pridemod.io

Created by IntelliJ IDEA.

PrideModController() - Constructor for class uk.ac.ebi.pridemod.io.PrideModController

PRIDEModDataAccessController - Class in uk.ac.ebi.pridemod.controller.impl

yperez

PRIDEModDataAccessController(InputStream) - Constructor for class uk.ac.ebi.pridemod.controller.impl.PRIDEModDataAccessController

Default constructor for Controllers

PrideModExtractor - Class in uk.ac.ebi.pridemod.io.pridemod.extractor

Created by IntelliJ IDEA.

PrideModExtractor(PrideMod) - Constructor for class uk.ac.ebi.pridemod.io.pridemod.extractor.PrideModExtractor

PrideModExtractor(Unmarshaller) - Constructor for class uk.ac.ebi.pridemod.io.pridemod.extractor.PrideModExtractor

PrideModification - Class in uk.ac.ebi.pridemod.io.pridemod.model

Java class for anonymous complex type.

PrideModification() - Constructor for class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

prideModification - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModifications

prideModifications - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PrideMod

PrideModifications - Class in uk.ac.ebi.pridemod.io.pridemod.model

Java class for anonymous complex type.

PrideModifications() - Constructor for class uk.ac.ebi.pridemod.io.pridemod.model.PrideModifications

PrideModMarshallerFactory - Class in uk.ac.ebi.pridemod.io.pridemod.xml.marshaller

Created by IntelliJ IDEA.

PrideModObject - Interface in uk.ac.ebi.pridemod.io.pridemod.model

Created by IntelliJ IDEA.

PRIDEModPTM - Class in uk.ac.ebi.pridemod.model

yperez

PRIDEModPTM(String, String, String, Double, Double, List<Specificity>, Comparable, String) - Constructor for class uk.ac.ebi.pridemod.model.PRIDEModPTM

Contructor with all the fields for a general modification

PrideModReader - Class in uk.ac.ebi.pridemod.io.pridemod.xml

Created by IntelliJ IDEA.

PrideModReader(InputStream) - Constructor for class uk.ac.ebi.pridemod.io.pridemod.xml.PrideModReader

PrideModUnmarshallerFactory - Class in uk.ac.ebi.pridemod.io.pridemod.xml.unmarshaller

yperez

PRIDEModUtils - Class in uk.ac.ebi.pridemod.utils

yperez

PRIDEModUtils() - Constructor for class uk.ac.ebi.pridemod.utils.PRIDEModUtils

PRIDEModUtils.Database - Enum in uk.ac.ebi.pridemod.utils

processLine(String) - Static method in class uk.ac.ebi.pridemod.io.slimmod.tab.ReadTabSlim

PSIModDataAccessController - Class in uk.ac.ebi.pridemod.controller.impl

yperez

PSIModDataAccessController(InputStream) - Constructor for class uk.ac.ebi.pridemod.controller.impl.PSIModDataAccessController

PsiModification - Class in uk.ac.ebi.pridemod.io.pridemod.model

Java class for anonymous complex type.

PsiModification() - Constructor for class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

psiModification - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModifications

psiModifications - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

PsiModifications - Class in uk.ac.ebi.pridemod.io.pridemod.model

Java class for anonymous complex type.

PsiModifications() - Constructor for class uk.ac.ebi.pridemod.io.pridemod.model.PsiModifications

PSIModPTM - Class in uk.ac.ebi.pridemod.model

yperez.

PSIModPTM(String, String, String, Double, Double, List<Specificity>, String, List<String>, String, List<Comparable>, boolean) - Constructor for class uk.ac.ebi.pridemod.model.PSIModPTM

PSIModReader - Class in uk.ac.ebi.pridemod.io.psimod

yperez

PSIModReader(InputStream) - Constructor for class uk.ac.ebi.pridemod.io.psimod.PSIModReader

PTM - Interface in uk.ac.ebi.pridemod.model

Interface for PTMs.

ptmMap - Variable in class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

R

ReadTabSlim - Class in uk.ac.ebi.pridemod.io.slimmod.tab

User: yperez Date: 20/07/11

ReadTabSlim() - Constructor for class uk.ac.ebi.pridemod.io.slimmod.tab.ReadTabSlim

recordId - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Reference - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for xref element declaration.

Reference() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.Reference

remove(Object) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Remove an modification passed by parameters from the List of modifications

remove(int) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Remove an slim object from the list of slim modification by index.

removeAll(Collection<?>) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Remove a collection of slim modifications from the current List of slim modifications

required - Variable in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

retainAll(Collection<?>) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

S

set(int, SlimModification) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Set slim modification with the value passed by parameter element in the position index of the list.

setAminoAcids(AminoAcidCollection) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Sets the value of the aminoAcids property.

setApproved(BigInteger) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the approved property.

setAvgeMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Sets the value of the avgeMass property.

setAvgeMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

Sets the value of the avgeMass property.

setAvgeMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Delta

Sets the value of the avgeMass property.

setAvgeMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

Sets the value of the avgeMass property.

setAvgeMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

Sets the value of the avgeMass property.

setAvgeMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

Sets the value of the avgeMass property.

setAvgeMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

Sets the value of the avgeMass property.

setBiologicalSignificance(BigInteger) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Sets the value of the biologicalSignificance property.

setClassification(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Sets the value of the classification property.

setComposition(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Delta

Sets the value of the composition property.

setComposition(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

Sets the value of the composition property.

setComposition(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

Sets the value of the composition property.

setComposition(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

Sets the value of the composition property.

setDateTimeModified(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the dateTimeModified property.

setDateTimePosted(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the dateTimePosted property.

setDelta(Delta) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the delta property.

setDeltaMass(double) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Set a delta Mass of the Modification

setDiffMono(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Sets the value of the diffMono property.

setElements(ElementCollection) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Sets the value of the elements property.

setFlag(boolean) - Method in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

Sets the value of the flag property.

setFullName(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Sets the value of the fullName property.

setFullName(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

Sets the value of the fullName property.

setFullName(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

Sets the value of the fullName property.

setFullName(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the fullName property.

setGeneralModification(BigInteger) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Sets the value of the generalModification property.

setGroupOfPoster(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the groupOfPoster property.

setHidden(BigInteger) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Sets the value of the hidden property.

setId(BigInteger) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Sets the value of the id property.

setId(String) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Sets the value of the id property.

setId(BigInteger) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.UnimodMapping

Sets the value of the id property.

setIdPsiMod(String) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Set the PSI-Mod database identifier.

setIdUnimod(int) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Set Unimod database identifier.

setMajorVersion(BigInteger) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Sets the value of the majorVersion property.

setMinorVersion(BigInteger) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Sets the value of the minorVersion property.

setMiscNotes(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the miscNotes property.

setModBricks(ModBricksCollection) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Sets the value of the modBricks property.

setModifications(ModificationCollection) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Unimod

Sets the value of the modifications property.

setMonoMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Sets the value of the monoMass property.

setMonoMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

Sets the value of the monoMass property.

setMonoMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Delta

Sets the value of the monoMass property.

setMonoMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Ignore

Sets the value of the monoMass property.

setMonoMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

Sets the value of the monoMass property.

setMonoMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.NeutralLoss

Sets the value of the monoMass property.

setMonoMass(BigDecimal) - Method in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

Sets the value of the monoMass property.

setName(Specificity.AminoAcid) - Method in class uk.ac.ebi.pridemod.model.Specificity

Set Amino Acid Position

setNumber(BigInteger) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomComposition

Sets the value of the number property.

setObsolete(BigInteger) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Sets the value of the obsolete property.

setObsolete(boolean) - Method in class uk.ac.ebi.pridemod.model.PSIModPTM

setOrigin(String) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Sets the value of the origin property.

setParentPTMList(List<Comparable>) - Method in class uk.ac.ebi.pridemod.model.PSIModPTM

setPosition(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Sets the value of the position property.

setPosition(Specificity.Position) - Method in class uk.ac.ebi.pridemod.model.Specificity

Set position

setPrideModifications(PrideModifications) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideMod

Sets the value of the prideModifications property.

setPsiModDesc(String) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Set Name in PSI-Mod database

setPsiModifications(PsiModifications) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Sets the value of the psiModifications property.

setRecordId(BigInteger) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the recordId property.

setRequired(boolean) - Method in class uk.ac.ebi.pridemod.io.unimod.model.PepNeutralLoss

Sets the value of the required property.

setShortNamePsiMod(String) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Set short name in PSI-Mod database

setSite(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Sets the value of the site property.

setSource(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Reference

Sets the value of the source property.

setSource(String) - Method in class uk.ac.ebi.pridemod.model.PSIModPTM

setSpecGroup(BigInteger) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Sets the value of the specGroup property.

setSpecificityCollection(List<Specificity>) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Set a collection of possible specificities of the current modification.

setSpecificModification(BigInteger) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Sets the value of the specificModification property.

setSymbol(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomComposition

Sets the value of the symbol property.

setSynonyms(List<String>) - Method in class uk.ac.ebi.pridemod.model.PSIModPTM

setTermSpec(String) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Sets the value of the termSpec property.

setText(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Reference

Sets the value of the text property.

setThreeLetter(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Sets the value of the threeLetter property.

setTitle(String) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Sets the value of the title property.

setTitle(String) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

Sets the value of the title property.

setTitle(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

Sets the value of the title property.

setTitle(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

Sets the value of the title property.

setTitle(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

Sets the value of the title property.

setTitle(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the title property.

setUnimodMappings(UnimodMappings) - Method in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

Sets the value of the unimodMappings property.

setUniModRef(Comparable) - Method in class uk.ac.ebi.pridemod.model.PRIDEModPTM

setUrl(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.Reference

Sets the value of the url property.

setUsernameOfPoster(String) - Method in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Sets the value of the usernameOfPoster property.

site - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

size() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Get the size of the modification List.

SlimModCollection - Class in uk.ac.ebi.pridemod.io.slimmod.model

Class that contains a List and methods to retrieve the information from a List of Slim Modifications.

SlimModCollection() - Constructor for class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Constructor that create a new List of Slim modifications

SlimModCollection(List<SlimModification>) - Constructor for class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Constructor that create an instance of the SlimModCollection class and initializes the collection of slim modification with the parameter.

SlimModification - Class in uk.ac.ebi.pridemod.io.slimmod.model

Slim Modification is an object that contains the information for slim modification.

SlimModification(String, double, int, String, String, List<Specificity>) - Constructor for class uk.ac.ebi.pridemod.io.slimmod.model.SlimModification

Constructor of the Slim Modification Class using as a parameters all attributes of the class.

source - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Reference

specGroup - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Specificity

Specificity - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for specificity element declaration.

Specificity() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.Specificity

specificity - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

Specificity - Class in uk.ac.ebi.pridemod.model

Specificity is a class that contains the information of the aminoacid specificity for modifications and also specified the position of this amino acids (N-term, C-Term) or Anywhere.

Specificity(Specificity.AminoAcid, Specificity.Position) - Constructor for class uk.ac.ebi.pridemod.model.Specificity

Constructor to init the Specificity with aminoacid and position

Specificity(String, String) - Constructor for class uk.ac.ebi.pridemod.model.Specificity

Constructor to init the Specificity with aminoacid and position in String form

Specificity.AminoAcid - Enum in uk.ac.ebi.pridemod.model

To use the same notation of PSI-MOD we decide to include the X as aminoacid.

Specificity.Position - Enum in uk.ac.ebi.pridemod.model

specificModification - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

subList(int, int) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Get a collection of modification between to indexes.

symbol - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AtomComposition

T

termSpec - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

text - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Reference

threeLetter - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

title - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

title - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PsiModification

title - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AminoAcid

title - Variable in class uk.ac.ebi.pridemod.io.unimod.model.AtomElement

title - Variable in class uk.ac.ebi.pridemod.io.unimod.model.ModBrick

title - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

toArray() - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Convert the current List to an Array of Objects

toArray(T[]) - Method in class uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

U

uk.ac.ebi.pridemod - package uk.ac.ebi.pridemod

uk.ac.ebi.pridemod.controller - package uk.ac.ebi.pridemod.controller

uk.ac.ebi.pridemod.controller.impl - package uk.ac.ebi.pridemod.controller.impl

uk.ac.ebi.pridemod.exception - package uk.ac.ebi.pridemod.exception

uk.ac.ebi.pridemod.io - package uk.ac.ebi.pridemod.io

uk.ac.ebi.pridemod.io.pridemod.extractor - package uk.ac.ebi.pridemod.io.pridemod.extractor

uk.ac.ebi.pridemod.io.pridemod.model - package uk.ac.ebi.pridemod.io.pridemod.model

uk.ac.ebi.pridemod.io.pridemod.xml - package uk.ac.ebi.pridemod.io.pridemod.xml

uk.ac.ebi.pridemod.io.pridemod.xml.marshaller - package uk.ac.ebi.pridemod.io.pridemod.xml.marshaller

uk.ac.ebi.pridemod.io.pridemod.xml.unmarshaller - package uk.ac.ebi.pridemod.io.pridemod.xml.unmarshaller

uk.ac.ebi.pridemod.io.psimod - package uk.ac.ebi.pridemod.io.psimod

uk.ac.ebi.pridemod.io.slimmod.model - package uk.ac.ebi.pridemod.io.slimmod.model

uk.ac.ebi.pridemod.io.slimmod.tab - package uk.ac.ebi.pridemod.io.slimmod.tab

uk.ac.ebi.pridemod.io.unimod.extractor - package uk.ac.ebi.pridemod.io.unimod.extractor

uk.ac.ebi.pridemod.io.unimod.model - package uk.ac.ebi.pridemod.io.unimod.model

uk.ac.ebi.pridemod.io.unimod.xml - package uk.ac.ebi.pridemod.io.unimod.xml

uk.ac.ebi.pridemod.io.unimod.xml.marshaller - package uk.ac.ebi.pridemod.io.unimod.xml.marshaller

uk.ac.ebi.pridemod.io.unimod.xml.unmarshaller - package uk.ac.ebi.pridemod.io.unimod.xml.unmarshaller

uk.ac.ebi.pridemod.model - package uk.ac.ebi.pridemod.model

uk.ac.ebi.pridemod.utils - package uk.ac.ebi.pridemod.utils

UNIMOD - Static variable in class uk.ac.ebi.pridemod.io.unimod.model.ModelConstants

Unimod - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for anonymous complex type.

Unimod() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.Unimod

UnimodDataAccessController - Class in uk.ac.ebi.pridemod.controller.impl

Class to retrieve all Modifications from Unimod database.

UnimodDataAccessController(InputStream) - Constructor for class uk.ac.ebi.pridemod.controller.impl.UnimodDataAccessController

UnimodExtractor - Class in uk.ac.ebi.pridemod.io.unimod.extractor

Created by IntelliJ IDEA.

UnimodExtractor(Unimod) - Constructor for class uk.ac.ebi.pridemod.io.unimod.extractor.UnimodExtractor

UnimodExtractor(Unmarshaller) - Constructor for class uk.ac.ebi.pridemod.io.unimod.extractor.UnimodExtractor

UnimodMapping - Class in uk.ac.ebi.pridemod.io.pridemod.model

Java class for anonymous complex type.

UnimodMapping() - Constructor for class uk.ac.ebi.pridemod.io.pridemod.model.UnimodMapping

unimodMapping - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.UnimodMappings

unimodMappings - Variable in class uk.ac.ebi.pridemod.io.pridemod.model.PrideModification

UnimodMappings - Class in uk.ac.ebi.pridemod.io.pridemod.model

Java class for anonymous complex type.

UnimodMappings() - Constructor for class uk.ac.ebi.pridemod.io.pridemod.model.UnimodMappings

UnimodMarshallerFactory - Class in uk.ac.ebi.pridemod.io.unimod.xml.marshaller

Created by IntelliJ IDEA.

UnimodModification - Class in uk.ac.ebi.pridemod.io.unimod.model

Java class for mod element declaration.

UnimodModification() - Constructor for class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

UnimodObject - Interface in uk.ac.ebi.pridemod.io.unimod.model

Created by IntelliJ IDEA.

UniModPTM - Class in uk.ac.ebi.pridemod.model

yperez

UniModPTM(String, String, String, Double, Double, List<Specificity>, String) - Constructor for class uk.ac.ebi.pridemod.model.UniModPTM

Contructor with all the fields for a general modification

UnimodReader - Class in uk.ac.ebi.pridemod.io.unimod.xml

yperez

UnimodReader(InputStream) - Constructor for class uk.ac.ebi.pridemod.io.unimod.xml.UnimodReader

UnimodUnmarshallerFactory - Class in uk.ac.ebi.pridemod.io.unimod.xml.unmarshaller

url - Variable in class uk.ac.ebi.pridemod.io.unimod.model.Reference

usernameOfPoster - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

V

valueOf(String) - Static method in enum uk.ac.ebi.pridemod.model.Specificity.AminoAcid

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pridemod.model.Specificity.Position

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pridemod.utils.PRIDEModUtils.Database

Returns the enum constant of this type with the specified name.

values() - Static method in enum uk.ac.ebi.pridemod.model.Specificity.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.pridemod.model.Specificity.Position

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.ebi.pridemod.utils.PRIDEModUtils.Database

Returns an array containing the constants of this enum type, in the order they are declared.

X

xref - Variable in class uk.ac.ebi.pridemod.io.unimod.model.UnimodModification

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