Serialized Form

Package org.biopax.paxtools.impl

Class org.biopax.paxtools.impl.BioPAXElementImpl extends java.lang.Object implements Serializable

Serialized Fields

uri

java.lang.String uri

proxyId

java.lang.Long proxyId

version

java.lang.Integer version

annotations

java.util.Map<K,V> annotations

Class org.biopax.paxtools.impl.ModelImpl extends java.lang.Object implements Serializable

serialVersionUID: -2087521863213381434L

Serialized Fields

idMap

java.util.Map<K,V> idMap

nameSpacePrefixMap

java.util.Map<K,V> nameSpacePrefixMap

level

BioPAXLevel level

addDependencies

boolean addDependencies

Package org.biopax.paxtools.impl.level3

Class org.biopax.paxtools.impl.level3.BindingFeatureImpl extends EntityFeatureImpl implements Serializable

Serialized Fields

bindsTo

BindingFeature bindsTo

intramolecular

java.lang.Boolean intramolecular

Class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl extends PathwayStepImpl implements Serializable

Serialized Fields

stepConversion

Conversion stepConversion

stepDirection

StepDirection stepDirection

Class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl extends ConversionImpl implements Serializable

Serialized Fields

deltaS

java.util.Set<E> deltaS

kEQ

java.util.Set<E> kEQ

deltaH

java.util.Set<E> deltaH

deltaG

java.util.Set<E> deltaG

eCNumber

java.util.Set<E> eCNumber

Class org.biopax.paxtools.impl.level3.BioSourceImpl extends NamedImpl implements Serializable

Serialized Fields

celltype

CellVocabulary celltype

tissue

TissueVocabulary tissue

Class org.biopax.paxtools.impl.level3.CatalysisImpl extends ControlImpl implements Serializable

Serialized Fields

catalysisDirection

CatalysisDirectionType catalysisDirection

cofactor

java.util.Set<E> cofactor

Class org.biopax.paxtools.impl.level3.CellularLocationVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.CellVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.ChemicalStructureImpl extends L3ElementImpl implements Serializable

Serialized Fields

structureFormat

StructureFormatType structureFormat

structureData

java.lang.String structureData

Class org.biopax.paxtools.impl.level3.ComplexAssemblyImpl extends ConversionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.ComplexImpl extends PhysicalEntityImpl implements Serializable

Serialized Fields

component

java.util.Set<E> component

componentStoichiometry

java.util.Set<E> componentStoichiometry

Class org.biopax.paxtools.impl.level3.ControlImpl extends InteractionImpl implements Serializable

Serialized Fields

controlType

ControlType controlType

pathwayController

java.util.Set<E> pathwayController

peController

java.util.Set<E> peController

controlled

java.util.Set<E> controlled

Class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl extends XReferrableImpl implements Serializable

Serialized Fields

term

java.util.Set<E> term

Class org.biopax.paxtools.impl.level3.ConversionImpl extends InteractionImpl implements Serializable

Serialized Fields

right

java.util.Set<E> right

left

java.util.Set<E> left

conversionDirection

ConversionDirectionType conversionDirection

participantStoichiometry

java.util.Set<E> participantStoichiometry

spontaneous

java.lang.Boolean spontaneous

Class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl extends BindingFeatureImpl implements Serializable

Serialized Fields

modificationType

SequenceModificationVocabulary modificationType

Class org.biopax.paxtools.impl.level3.DegradationImpl extends ConversionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.DeltaGImpl extends L3ElementImpl implements Serializable

Serialized Fields

deltaGPrime0

float deltaGPrime0

temperature

float temperature

ionicStrength

float ionicStrength

ph

float ph

pMg

float pMg

Class org.biopax.paxtools.impl.level3.DnaImpl extends NucleicAcidImpl implements Serializable

Class org.biopax.paxtools.impl.level3.DnaReferenceImpl extends NucleicAcidReferenceImpl implements Serializable

Class org.biopax.paxtools.impl.level3.DnaRegionImpl extends NucleicAcidImpl implements Serializable

Class org.biopax.paxtools.impl.level3.DnaRegionReferenceImpl extends NucleicAcidRegionReferenceImpl implements Serializable

Class org.biopax.paxtools.impl.level3.EntityFeatureImpl extends L3ElementImpl implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

evidence

java.util.Set<E> evidence

ownerEntityReference

EntityReference ownerEntityReference

featureOf

java.util.Set<E> featureOf

notFeatureOf

java.util.Set<E> notFeatureOf

featureLocation

SequenceLocation featureLocation

memberFeature

java.util.Set<E> memberFeature

featureLocationType

SequenceRegionVocabulary featureLocationType

memberFeatureOf

java.util.Set<E> memberFeatureOf

Class org.biopax.paxtools.impl.level3.EntityImpl extends NamedImpl implements Serializable

Serialized Fields

participantOf

java.util.Set<E> participantOf

availability

java.util.Set<E> availability

This Set keeps statements describing the availability of this data (e.g. a copyright statement).

dataSource

java.util.Set<E> dataSource

This Set keeps statements describing the data sources for this data.

evidence

java.util.Set<E> evidence

This Set keeps evidence related to this entity

Class org.biopax.paxtools.impl.level3.EntityReferenceImpl extends NamedImpl implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

entityFeature

java.util.Set<E> entityFeature

entityReferenceOf

java.util.Set<E> entityReferenceOf

evidence

java.util.Set<E> evidence

entityReferenceType

java.util.Set<E> entityReferenceType

memberEntity

java.util.Set<E> memberEntity

ownerEntityReference

java.util.Set<E> ownerEntityReference

Class org.biopax.paxtools.impl.level3.EntityReferenceTypeVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.EvidenceCodeVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.EvidenceImpl extends XReferrableImpl implements Serializable

Serialized Fields

experimentalForm

java.util.Set<E> experimentalForm

confidence

java.util.Set<E> confidence

evidenceCode

java.util.Set<E> evidenceCode

Class org.biopax.paxtools.impl.level3.ExperimentalFormImpl extends L3ElementImpl implements Serializable

Serialized Fields

experimentalFormEntity

Entity experimentalFormEntity

experimentalFormDescription

java.util.Set<E> experimentalFormDescription

experimentalFeature

java.util.Set<E> experimentalFeature

Class org.biopax.paxtools.impl.level3.ExperimentalFormVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.FragmentFeatureImpl extends EntityFeatureImpl implements Serializable

Class org.biopax.paxtools.impl.level3.GeneImpl extends EntityImpl implements Serializable

Serialized Fields

organism

BioSource organism

Class org.biopax.paxtools.impl.level3.GeneticInteractionImpl extends InteractionImpl implements Serializable

Serialized Fields

phenotype

PhenotypeVocabulary phenotype

interactionScore

Score interactionScore

Class org.biopax.paxtools.impl.level3.InteractionImpl extends ProcessImpl implements Serializable

Serialized Fields

participant

java.util.Set<E> participant

interactionType

java.util.Set<E> interactionType

log

org.apache.commons.logging.Log log

Class org.biopax.paxtools.impl.level3.InteractionVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.KPrimeImpl extends L3ElementImpl implements Serializable

Serialized Fields

ionicStrength

float ionicStrength

kPrime

float kPrime

ph

float ph

pMg

float pMg

temperature

float temperature

Class org.biopax.paxtools.impl.level3.L3ElementImpl extends BioPAXElementImpl implements Serializable

Serialized Fields

comment

java.util.Set<E> comment

Class org.biopax.paxtools.impl.level3.ModificationFeatureImpl extends EntityFeatureImpl implements Serializable

Serialized Fields

modificationType

SequenceModificationVocabulary modificationType

Class org.biopax.paxtools.impl.level3.ModulationImpl extends ControlImpl implements Serializable

Class org.biopax.paxtools.impl.level3.MolecularInteractionImpl extends InteractionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.NamedImpl extends XReferrableImpl implements Serializable

Serialized Fields

standardName

java.lang.String standardName

displayName

java.lang.String displayName

allNames

java.util.Set<E> allNames

Class org.biopax.paxtools.impl.level3.NucleicAcidImpl extends SimplePhysicalEntityImpl implements Serializable

Class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl extends SequenceEntityReferenceImpl implements Serializable

Serialized Fields

subRegion

java.util.Set<E> subRegion

Class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl extends NucleicAcidReferenceImpl implements Serializable

Serialized Fields

absoluteRegion

SequenceLocation absoluteRegion

regionType

java.util.Set<E> regionType

containerEntityReference

NucleicAcidReference containerEntityReference

subRegionOf

java.util.Set<E> subRegionOf

Class org.biopax.paxtools.impl.level3.PathwayImpl extends ProcessImpl implements Serializable

Serialized Fields

pathwayComponent

java.util.Set<E> pathwayComponent

pathwayOrder

java.util.Set<E> pathwayOrder

organism

BioSource organism

controllerOf

java.util.Set<E> controllerOf

Class org.biopax.paxtools.impl.level3.PathwayStepImpl extends L3ElementImpl implements Serializable

Serialized Fields

stepProcess

java.util.Set<E> stepProcess

nextStep

java.util.Set<E> nextStep

nextStepOf

java.util.Set<E> nextStepOf

pathwayOrderOf

Pathway pathwayOrderOf

evidence

java.util.Set<E> evidence

Class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Serialized Fields

patoData

java.lang.String patoData

Class org.biopax.paxtools.impl.level3.PhysicalEntityImpl extends EntityImpl implements Serializable

Serialized Fields

cellularLocation

CellularLocationVocabulary cellularLocation

memberPhysicalEntity

java.util.Set<E> memberPhysicalEntity

componentOf

java.util.Set<E> componentOf

feature

java.util.Set<E> feature

notFeature

java.util.Set<E> notFeature

controllerOf

java.util.Set<E> controllerOf

log

org.apache.commons.logging.Log log

memberPhysicalEntityOf

java.util.Set<E> memberPhysicalEntityOf

Class org.biopax.paxtools.impl.level3.ProcessImpl extends EntityImpl implements Serializable

Serialized Fields

controlledOf

java.util.Set<E> controlledOf

stepProcessOf

java.util.Set<E> stepProcessOf

pathwayComponentOf

java.util.Set<E> pathwayComponentOf

Class org.biopax.paxtools.impl.level3.ProteinImpl extends SimplePhysicalEntityImpl implements Serializable

Class org.biopax.paxtools.impl.level3.ProteinReferenceImpl extends SequenceEntityReferenceImpl implements Serializable

Class org.biopax.paxtools.impl.level3.ProvenanceImpl extends NamedImpl implements Serializable

Class org.biopax.paxtools.impl.level3.PublicationXrefImpl extends XrefImpl implements Serializable

Serialized Fields

title

java.lang.String title

url

java.util.Set<E> url

source

java.util.Set<E> source

author

java.util.Set<E> author

year

int year

Class org.biopax.paxtools.impl.level3.RelationshipTypeVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.RelationshipXrefImpl extends XrefImpl implements Serializable

Serialized Fields

relationshipType

RelationshipTypeVocabulary relationshipType

Class org.biopax.paxtools.impl.level3.RnaImpl extends NucleicAcidImpl implements Serializable

Class org.biopax.paxtools.impl.level3.RnaReferenceImpl extends NucleicAcidReferenceImpl implements Serializable

Class org.biopax.paxtools.impl.level3.RnaRegionImpl extends NucleicAcidImpl implements Serializable

Class org.biopax.paxtools.impl.level3.RnaRegionReferenceImpl extends NucleicAcidRegionReferenceImpl implements Serializable

Serialized Fields

rnaRegionReference

RnaRegionReference rnaRegionReference

sequenceLocation

SequenceLocation sequenceLocation

Class org.biopax.paxtools.impl.level3.ScoreImpl extends XReferrableImpl implements Serializable

Serialized Fields

value

java.lang.String value

scoreSource

Provenance scoreSource

Class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl extends EntityReferenceImpl implements Serializable

Serialized Fields

organism

BioSource organism

sequence

java.lang.String sequence

Class org.biopax.paxtools.impl.level3.SequenceIntervalImpl extends SequenceLocationImpl implements Serializable

Serialized Fields

sequenceIntervalBegin

SequenceSite sequenceIntervalBegin

sequenceIntervalEnd

SequenceSite sequenceIntervalEnd

Class org.biopax.paxtools.impl.level3.SequenceLocationImpl extends L3ElementImpl implements Serializable

Serialized Fields

regionType

java.util.Set<E> regionType

Class org.biopax.paxtools.impl.level3.SequenceModificationVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.SequenceRegionVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.SequenceSiteImpl extends SequenceLocationImpl implements Serializable

Serialized Fields

positionStatus

PositionStatusType positionStatus

sequencePosition

int sequencePosition

Class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl extends PhysicalEntityImpl implements Serializable

Serialized Fields

entityReference

EntityReference entityReference

log

org.apache.commons.logging.Log log

Class org.biopax.paxtools.impl.level3.SmallMoleculeImpl extends SimplePhysicalEntityImpl implements Serializable

Class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl extends EntityReferenceImpl implements Serializable

Serialized Fields

chemicalFormula

java.lang.String chemicalFormula

molecularWeight

float molecularWeight

structure

ChemicalStructure structure

Class org.biopax.paxtools.impl.level3.StoichiometryImpl extends L3ElementImpl implements Serializable

Serialized Fields

stoichiometricCoefficient

float stoichiometricCoefficient

physicalEntity

PhysicalEntity physicalEntity

Class org.biopax.paxtools.impl.level3.TemplateReactionImpl extends InteractionImpl implements Serializable

Serialized Fields

product

java.util.Set<E> product

template

NucleicAcid template

templateDirection

TemplateDirectionType templateDirection

Class org.biopax.paxtools.impl.level3.TemplateReactionRegulationImpl extends ControlImpl implements Serializable

Class org.biopax.paxtools.impl.level3.TissueVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.TransportImpl extends ConversionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.TransportWithBiochemicalReactionImpl extends BiochemicalReactionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.UnificationXrefImpl extends XrefImpl implements Serializable

Class org.biopax.paxtools.impl.level3.XReferrableImpl extends L3ElementImpl implements Serializable

Serialized Fields

xref

java.util.Set<E> xref

This variable stores the external references to the owner object.

Class org.biopax.paxtools.impl.level3.XrefImpl extends L3ElementImpl implements Serializable

Serialized Fields

db

java.lang.String db

dbVersion

java.lang.String dbVersion

idVersion

java.lang.String idVersion

refId

java.lang.String refId

xrefOf

java.util.Set<E> xrefOf

Package org.biopax.paxtools.model

Package org.biopax.paxtools.model.level2

Package org.biopax.paxtools.model.level3

Package org.biopax.paxtools.util

Class org.biopax.paxtools.util.BidirectionalLinkViolationException extends IllegalBioPAXArgumentException implements Serializable

Class org.biopax.paxtools.util.BioPaxIOException extends java.lang.RuntimeException implements Serializable

Class org.biopax.paxtools.util.IllegalBioPAXArgumentException extends java.lang.IllegalArgumentException implements Serializable

Class org.biopax.paxtools.util.IllegalRDFIDException extends java.lang.IllegalArgumentException implements Serializable