Serialized Form

Package org.biopax.paxtools.impl

Class org.biopax.paxtools.impl.BioPAXElementImpl

class BioPAXElementImpl extends Object implements Serializable

Serialized Fields

annotations

Map<String,Object> annotations

uri

String uri

Class org.biopax.paxtools.impl.ModelImpl

class ModelImpl extends Object implements Serializable

serialVersionUID:

-2087521863213381434L

Serialized Fields

addDependencies

boolean addDependencies

idMap

Map<String,BioPAXElement> idMap

level

BioPAXLevel level

name

String name

nameSpacePrefixMap

Map<String,String> nameSpacePrefixMap

uri

String uri

xmlBase

String xmlBase

Package org.biopax.paxtools.impl.level3

Class org.biopax.paxtools.impl.level3.BindingFeatureImpl

class BindingFeatureImpl extends EntityFeatureImpl implements Serializable

Serialized Fields

bindsTo

BindingFeature bindsTo

intramolecular

Boolean intramolecular

Class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl

class BiochemicalPathwayStepImpl extends PathwayStepImpl implements Serializable

Serialized Fields

log

org.slf4j.Logger log

stepConversion

Conversion stepConversion

stepDirection

StepDirection stepDirection

stepProcess

Set<Process> stepProcess

Class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

class BiochemicalReactionImpl extends ConversionImpl implements Serializable

Serialized Fields

deltaG

Set<DeltaG> deltaG

deltaH

Set<Float> deltaH

deltaS

Set<Float> deltaS

eCNumber

Set<String> eCNumber

kEQ

Set<KPrime> kEQ

Class org.biopax.paxtools.impl.level3.BioSourceImpl

class BioSourceImpl extends NamedImpl implements Serializable

Serialized Fields

celltype

CellVocabulary celltype

tissue

TissueVocabulary tissue

Class org.biopax.paxtools.impl.level3.CatalysisImpl

class CatalysisImpl extends ControlImpl implements Serializable

Serialized Fields

catalysisDirection

CatalysisDirectionType catalysisDirection

cofactor

Set<PhysicalEntity> cofactor

Class org.biopax.paxtools.impl.level3.CellularLocationVocabularyImpl

class CellularLocationVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.CellVocabularyImpl

class CellVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.ChemicalConstantImpl

class ChemicalConstantImpl extends L3ElementImpl implements Serializable

Serialized Fields

ionicStrength

float ionicStrength

ph

float ph

pMg

float pMg

temperature

float temperature

Class org.biopax.paxtools.impl.level3.ChemicalStructureImpl

class ChemicalStructureImpl extends L3ElementImpl implements Serializable

Serialized Fields

structureData

String structureData

structureFormat

StructureFormatType structureFormat

Class org.biopax.paxtools.impl.level3.ComplexAssemblyImpl

class ComplexAssemblyImpl extends ConversionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.ComplexImpl

class ComplexImpl extends PhysicalEntityImpl implements Serializable

Serialized Fields

component

Set<PhysicalEntity> component

componentStoichiometry

Set<Stoichiometry> componentStoichiometry

Class org.biopax.paxtools.impl.level3.ControlImpl

class ControlImpl extends InteractionImpl implements Serializable

Serialized Fields

controlled

Set<Process> controlled

controlType

ControlType controlType

pathwayController

Set<Pathway> pathwayController

peController

Set<PhysicalEntity> peController

Class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl

class ControlledVocabularyImpl extends XReferrableImpl implements Serializable

Serialized Fields

term

Set<String> term

Class org.biopax.paxtools.impl.level3.ConversionImpl

class ConversionImpl extends InteractionImpl implements Serializable

Serialized Fields

conversionDirection

ConversionDirectionType conversionDirection

left

Set<PhysicalEntity> left

participantStoichiometry

Set<Stoichiometry> participantStoichiometry

right

Set<PhysicalEntity> right

spontaneous

Boolean spontaneous

Class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl

class CovalentBindingFeatureImpl extends BindingFeatureImpl implements Serializable

Serialized Fields

modificationType

SequenceModificationVocabulary modificationType

Class org.biopax.paxtools.impl.level3.DegradationImpl

class DegradationImpl extends ConversionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.DeltaGImpl

class DeltaGImpl extends ChemicalConstantImpl implements Serializable

Serialized Fields

deltaGPrime0

float deltaGPrime0

Class org.biopax.paxtools.impl.level3.DnaImpl

class DnaImpl extends NucleicAcidImpl implements Serializable

Class org.biopax.paxtools.impl.level3.DnaReferenceImpl

class DnaReferenceImpl extends NucleicAcidReferenceImpl implements Serializable

Class org.biopax.paxtools.impl.level3.DnaRegionImpl

class DnaRegionImpl extends NucleicAcidImpl implements Serializable

Class org.biopax.paxtools.impl.level3.DnaRegionReferenceImpl

class DnaRegionReferenceImpl extends NucleicAcidRegionReferenceImpl implements Serializable

Class org.biopax.paxtools.impl.level3.EntityFeatureImpl

class EntityFeatureImpl extends L3ElementImpl implements Serializable

Serialized Fields

evidence

Set<Evidence> evidence

featureLocation

SequenceLocation featureLocation

featureLocationType

SequenceRegionVocabulary featureLocationType

featureOf

Set<PhysicalEntity> featureOf

memberFeature

Set<EntityFeature> memberFeature

memberFeatureOf

Set<EntityFeature> memberFeatureOf

notFeatureOf

Set<PhysicalEntity> notFeatureOf

ownerEntityReference

EntityReference ownerEntityReference

Class org.biopax.paxtools.impl.level3.EntityImpl

class EntityImpl extends NamedImpl implements Serializable

Serialized Fields

availability

Set<String> availability

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

dataSource

Set<Provenance> dataSource

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

evidence

Set<Evidence> evidence

This Set keeps evidence related to this entity

participantOf

Set<Interaction> participantOf

Class org.biopax.paxtools.impl.level3.EntityReferenceImpl

class EntityReferenceImpl extends NamedImpl implements Serializable

Serialized Fields

entityFeature

Set<EntityFeature> entityFeature

entityReferenceOf

Set<SimplePhysicalEntity> entityReferenceOf

entityReferenceType

Set<EntityReferenceTypeVocabulary> entityReferenceType

evidence

Set<Evidence> evidence

memberEntityReference

Set<EntityReference> memberEntityReference

ownerEntityReference

Set<EntityReference> ownerEntityReference

Class org.biopax.paxtools.impl.level3.EntityReferenceTypeVocabularyImpl

class EntityReferenceTypeVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.EvidenceCodeVocabularyImpl

class EvidenceCodeVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.EvidenceImpl

class EvidenceImpl extends XReferrableImpl implements Serializable

Serialized Fields

confidence

Set<Score> confidence

evidenceCode

Set<EvidenceCodeVocabulary> evidenceCode

experimentalForm

Set<ExperimentalForm> experimentalForm

Class org.biopax.paxtools.impl.level3.ExperimentalFormImpl

class ExperimentalFormImpl extends L3ElementImpl implements Serializable

Serialized Fields

experimentalFeature

Set<EntityFeature> experimentalFeature

experimentalFormDescription

Set<ExperimentalFormVocabulary> experimentalFormDescription

experimentalFormEntity

Entity experimentalFormEntity

Class org.biopax.paxtools.impl.level3.ExperimentalFormVocabularyImpl

class ExperimentalFormVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.FragmentFeatureImpl

class FragmentFeatureImpl extends EntityFeatureImpl implements Serializable

Class org.biopax.paxtools.impl.level3.GeneImpl

class GeneImpl extends EntityImpl implements Serializable

Serialized Fields

organism

BioSource organism

Class org.biopax.paxtools.impl.level3.GeneticInteractionImpl

class GeneticInteractionImpl extends InteractionImpl implements Serializable

Serialized Fields

interactionScore

Score interactionScore

phenotype

PhenotypeVocabulary phenotype

Class org.biopax.paxtools.impl.level3.InteractionImpl

class InteractionImpl extends ProcessImpl implements Serializable

Serialized Fields

interactionType

Set<InteractionVocabulary> interactionType

log

org.slf4j.Logger log

participant

Set<Entity> participant

Class org.biopax.paxtools.impl.level3.InteractionVocabularyImpl

class InteractionVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.KPrimeImpl

class KPrimeImpl extends ChemicalConstantImpl implements Serializable

Serialized Fields

kPrime

float kPrime

Class org.biopax.paxtools.impl.level3.L3ElementImpl

class L3ElementImpl extends BioPAXElementImpl implements Serializable

Serialized Fields

comment

Set<String> comment

Class org.biopax.paxtools.impl.level3.ModificationFeatureImpl

class ModificationFeatureImpl extends EntityFeatureImpl implements Serializable

Serialized Fields

modificationType

SequenceModificationVocabulary modificationType

Class org.biopax.paxtools.impl.level3.ModulationImpl

class ModulationImpl extends ControlImpl implements Serializable

Class org.biopax.paxtools.impl.level3.MolecularInteractionImpl

class MolecularInteractionImpl extends InteractionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.NamedImpl

class NamedImpl extends XReferrableImpl implements Serializable

Serialized Fields

allNames

Set<String> allNames

displayName

String displayName

standardName

String standardName

Class org.biopax.paxtools.impl.level3.NucleicAcidImpl

class NucleicAcidImpl extends SimplePhysicalEntityImpl implements Serializable

Class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl

class NucleicAcidReferenceImpl extends SequenceEntityReferenceImpl implements Serializable

Serialized Fields

subRegion

Set<NucleicAcidRegionReference> subRegion

Class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl

class NucleicAcidRegionReferenceImpl extends NucleicAcidReferenceImpl implements Serializable

Serialized Fields

absoluteRegion

SequenceLocation absoluteRegion

regionType

Set<SequenceRegionVocabulary> regionType

subRegionOf

Set<NucleicAcidReference> subRegionOf

Class org.biopax.paxtools.impl.level3.PathwayImpl

class PathwayImpl extends ProcessImpl implements Serializable

Serialized Fields

controllerOf

Set<Control> controllerOf

organism

BioSource organism

pathwayComponent

Set<Process> pathwayComponent

pathwayOrder

Set<PathwayStep> pathwayOrder

Class org.biopax.paxtools.impl.level3.PathwayStepImpl

class PathwayStepImpl extends L3ElementImpl implements Serializable

Serialized Fields

evidence

Set<Evidence> evidence

nextStep

Set<PathwayStep> nextStep

nextStepOf

Set<PathwayStep> nextStepOf

pathwayOrderOf

Pathway pathwayOrderOf

stepProcess

Set<Process> stepProcess

Class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl

class PhenotypeVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Serialized Fields

patoData

String patoData

Class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

class PhysicalEntityImpl extends EntityImpl implements Serializable

Serialized Fields

cellularLocation

CellularLocationVocabulary cellularLocation

componentOf

Set<Complex> componentOf

controllerOf

Set<Control> controllerOf

feature

Set<EntityFeature> feature

memberPhysicalEntity

Set<PhysicalEntity> memberPhysicalEntity

memberPhysicalEntityOf

Set<PhysicalEntity> memberPhysicalEntityOf

notFeature

Set<EntityFeature> notFeature

Class org.biopax.paxtools.impl.level3.ProcessImpl

class ProcessImpl extends EntityImpl implements Serializable

Serialized Fields

controlledOf

Set<Control> controlledOf

pathwayComponentOf

Set<Pathway> pathwayComponentOf

stepProcessOf

Set<PathwayStep> stepProcessOf

Class org.biopax.paxtools.impl.level3.ProteinImpl

class ProteinImpl extends SimplePhysicalEntityImpl implements Serializable

Class org.biopax.paxtools.impl.level3.ProteinReferenceImpl

class ProteinReferenceImpl extends SequenceEntityReferenceImpl implements Serializable

Class org.biopax.paxtools.impl.level3.ProvenanceImpl

class ProvenanceImpl extends NamedImpl implements Serializable

Class org.biopax.paxtools.impl.level3.PublicationXrefImpl

class PublicationXrefImpl extends XrefImpl implements Serializable

Serialized Fields

author

Set<String> author

source

Set<String> source

title

String title

url

Set<String> url

year

int year

Class org.biopax.paxtools.impl.level3.RelationshipTypeVocabularyImpl

class RelationshipTypeVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.RelationshipXrefImpl

class RelationshipXrefImpl extends XrefImpl implements Serializable

Serialized Fields

relationshipType

RelationshipTypeVocabulary relationshipType

Class org.biopax.paxtools.impl.level3.RnaImpl

class RnaImpl extends NucleicAcidImpl implements Serializable

Class org.biopax.paxtools.impl.level3.RnaReferenceImpl

class RnaReferenceImpl extends NucleicAcidReferenceImpl implements Serializable

Class org.biopax.paxtools.impl.level3.RnaRegionImpl

class RnaRegionImpl extends NucleicAcidImpl implements Serializable

Class org.biopax.paxtools.impl.level3.RnaRegionReferenceImpl

class RnaRegionReferenceImpl extends NucleicAcidRegionReferenceImpl implements Serializable

Class org.biopax.paxtools.impl.level3.ScoreImpl

class ScoreImpl extends XReferrableImpl implements Serializable

Serialized Fields

scoreSource

Provenance scoreSource

value

String value

Class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl

class SequenceEntityReferenceImpl extends EntityReferenceImpl implements Serializable

Serialized Fields

organism

BioSource organism

sequence

String sequence

Class org.biopax.paxtools.impl.level3.SequenceIntervalImpl

class SequenceIntervalImpl extends SequenceLocationImpl implements Serializable

Serialized Fields

sequenceIntervalBegin

SequenceSite sequenceIntervalBegin

sequenceIntervalEnd

SequenceSite sequenceIntervalEnd

Class org.biopax.paxtools.impl.level3.SequenceLocationImpl

class SequenceLocationImpl extends L3ElementImpl implements Serializable

Serialized Fields

regionType

Set<SequenceRegionVocabulary> regionType

Class org.biopax.paxtools.impl.level3.SequenceModificationVocabularyImpl

class SequenceModificationVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.SequenceRegionVocabularyImpl

class SequenceRegionVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.SequenceSiteImpl

class SequenceSiteImpl extends SequenceLocationImpl implements Serializable

Serialized Fields

positionStatus

PositionStatusType positionStatus

sequencePosition

int sequencePosition

Class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl

class SimplePhysicalEntityImpl extends PhysicalEntityImpl implements Serializable

Serialized Fields

entityReference

EntityReference entityReference

Class org.biopax.paxtools.impl.level3.SmallMoleculeImpl

class SmallMoleculeImpl extends SimplePhysicalEntityImpl implements Serializable

Class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl

class SmallMoleculeReferenceImpl extends EntityReferenceImpl implements Serializable

Serialized Fields

chemicalFormula

String chemicalFormula

molecularWeight

float molecularWeight

structure

ChemicalStructure structure

Class org.biopax.paxtools.impl.level3.StoichiometryImpl

class StoichiometryImpl extends L3ElementImpl implements Serializable

Serialized Fields

physicalEntity

PhysicalEntity physicalEntity

stoichiometricCoefficient

float stoichiometricCoefficient

Class org.biopax.paxtools.impl.level3.TemplateReactionImpl

class TemplateReactionImpl extends InteractionImpl implements Serializable

Serialized Fields

product

Set<PhysicalEntity> product

template

NucleicAcid template

templateDirection

TemplateDirectionType templateDirection

Class org.biopax.paxtools.impl.level3.TemplateReactionRegulationImpl

class TemplateReactionRegulationImpl extends ControlImpl implements Serializable

Class org.biopax.paxtools.impl.level3.TissueVocabularyImpl

class TissueVocabularyImpl extends ControlledVocabularyImpl implements Serializable

Class org.biopax.paxtools.impl.level3.TransportImpl

class TransportImpl extends ConversionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.TransportWithBiochemicalReactionImpl

class TransportWithBiochemicalReactionImpl extends BiochemicalReactionImpl implements Serializable

Class org.biopax.paxtools.impl.level3.UnificationXrefImpl

class UnificationXrefImpl extends XrefImpl implements Serializable

Class org.biopax.paxtools.impl.level3.XReferrableImpl

class XReferrableImpl extends L3ElementImpl implements Serializable

Serialized Fields

xref

Set<Xref> xref

This variable stores the external references to the owner object.

Class org.biopax.paxtools.impl.level3.XrefImpl

class XrefImpl extends L3ElementImpl implements Serializable

Serialized Fields

db

String db

dbVersion

String dbVersion

idVersion

String idVersion

refId

String refId

xrefOf

Set<XReferrable> 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.AccessibleSet

class AccessibleSet extends HashSet<E> implements Serializable

Exception Class org.biopax.paxtools.util.BioPaxIOException

class BioPaxIOException extends RuntimeException implements Serializable

Exception Class org.biopax.paxtools.util.IllegalBioPAXArgumentException

class IllegalBioPAXArgumentException extends IllegalArgumentException implements Serializable