Serialized Form (Paxtools Core (BioPAX object model, I/O API, implementation and extras) 5.1.0 API)

Package org.biopax.paxtools.impl
- Class org.biopax.paxtools.impl.BioPAXElementImpl extends Object implements Serializable
  - Serialized Fields
    - uri
```
String uri
```
    - annotations
```
Map<K,V> annotations
```
- Class org.biopax.paxtools.impl.ModelImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -2087521863213381434L
  - Serialized Fields
    - idMap
```
Map<K,V> idMap
```
    - nameSpacePrefixMap
```
Map<K,V> nameSpacePrefixMap
```
    - level
```
BioPAXLevel level
```
    - addDependencies
```
boolean addDependencies
```
    - xmlBase
```
String xmlBase
```
    - uri
```
String uri
```
    - name
```
String name
```
Package org.biopax.paxtools.impl.level3
- Class org.biopax.paxtools.impl.level3.BindingFeatureImpl extends EntityFeatureImpl implements Serializable
  - Serialized Fields
    - bindsTo
```
BindingFeature bindsTo
```
    - intramolecular
```
Boolean intramolecular
```
- Class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl extends PathwayStepImpl implements Serializable
  - Serialized Fields
    - stepConversion
```
Conversion stepConversion
```
    - stepDirection
```
StepDirection stepDirection
```
    - stepProcess
```
Set<E> stepProcess
```
    - log
```
org.slf4j.Logger log
```
- Class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl extends ConversionImpl implements Serializable
  - Serialized Fields
    - deltaS
```
Set<E> deltaS
```
    - kEQ
```
Set<E> kEQ
```
    - deltaH
```
Set<E> deltaH
```
    - deltaG
```
Set<E> deltaG
```
    - eCNumber
```
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
```
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.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 extends L3ElementImpl implements Serializable
  - Serialized Fields
    - structureFormat
```
StructureFormatType structureFormat
```
    - structureData
```
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
```
Set<E> component
```
    - componentStoichiometry
```
Set<E> componentStoichiometry
```
- Class org.biopax.paxtools.impl.level3.ControlImpl extends InteractionImpl implements Serializable
  - Serialized Fields
    - controlType
```
ControlType controlType
```
    - pathwayController
```
Set<E> pathwayController
```
    - peController
```
Set<E> peController
```
    - controlled
```
Set<E> controlled
```
- Class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl extends XReferrableImpl implements Serializable
  - Serialized Fields
    - term
```
Set<E> term
```
- Class org.biopax.paxtools.impl.level3.ConversionImpl extends InteractionImpl implements Serializable
  - Serialized Fields
    - right
```
Set<E> right
```
    - left
```
Set<E> left
```
    - conversionDirection
```
ConversionDirectionType conversionDirection
```
    - participantStoichiometry
```
Set<E> participantStoichiometry
```
    - spontaneous
```
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 ChemicalConstantImpl implements Serializable
  - Serialized Fields
    - deltaGPrime0
```
float deltaGPrime0
```
- 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
    - evidence
```
Set<E> evidence
```
    - ownerEntityReference
```
EntityReference ownerEntityReference
```
    - featureOf
```
Set<E> featureOf
```
    - notFeatureOf
```
Set<E> notFeatureOf
```
    - featureLocation
```
SequenceLocation featureLocation
```
    - memberFeature
```
Set<E> memberFeature
```
    - featureLocationType
```
SequenceRegionVocabulary featureLocationType
```
    - memberFeatureOf
```
Set<E> memberFeatureOf
```
- Class org.biopax.paxtools.impl.level3.EntityImpl extends NamedImpl implements Serializable
  - Serialized Fields
    - participantOf
```
Set<E> participantOf
```
    - availability
```
Set<E> availability
```
      This Set keeps statements describing the availability of this data (e.g. a copyright statement).
    - dataSource
```
Set<E> dataSource
```
      This Set keeps statements describing the data sources for this data.
    - evidence
```
Set<E> evidence
```
      This Set keeps evidence related to this entity
- Class org.biopax.paxtools.impl.level3.EntityReferenceImpl extends NamedImpl implements Serializable
  - Serialized Fields
    - entityFeature
```
Set<E> entityFeature
```
    - entityReferenceOf
```
Set<E> entityReferenceOf
```
    - evidence
```
Set<E> evidence
```
    - entityReferenceType
```
Set<E> entityReferenceType
```
    - memberEntityReference
```
Set<E> memberEntityReference
```
    - ownerEntityReference
```
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
```
Set<E> experimentalForm
```
    - confidence
```
Set<E> confidence
```
    - evidenceCode
```
Set<E> evidenceCode
```
- Class org.biopax.paxtools.impl.level3.ExperimentalFormImpl extends L3ElementImpl implements Serializable
  - Serialized Fields
    - experimentalFormEntity
```
Entity experimentalFormEntity
```
    - experimentalFormDescription
```
Set<E> experimentalFormDescription
```
    - experimentalFeature
```
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
```
Set<E> participant
```
    - interactionType
```
Set<E> interactionType
```
    - log
```
org.slf4j.Logger log
```
- Class org.biopax.paxtools.impl.level3.InteractionVocabularyImpl extends ControlledVocabularyImpl implements Serializable
- Class org.biopax.paxtools.impl.level3.KPrimeImpl extends ChemicalConstantImpl implements Serializable
  - Serialized Fields
    - kPrime
```
float kPrime
```
- Class org.biopax.paxtools.impl.level3.L3ElementImpl extends BioPAXElementImpl implements Serializable
  - Serialized Fields
    - comment
```
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
```
String standardName
```
    - displayName
```
String displayName
```
    - allNames
```
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
```
Set<E> subRegion
```
- Class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl extends NucleicAcidReferenceImpl implements Serializable
  - Serialized Fields
    - absoluteRegion
```
SequenceLocation absoluteRegion
```
    - regionType
```
Set<E> regionType
```
    - subRegionOf
```
Set<E> subRegionOf
```
- Class org.biopax.paxtools.impl.level3.PathwayImpl extends ProcessImpl implements Serializable
  - Serialized Fields
    - pathwayComponent
```
Set<E> pathwayComponent
```
    - pathwayOrder
```
Set<E> pathwayOrder
```
    - organism
```
BioSource organism
```
    - controllerOf
```
Set<E> controllerOf
```
- Class org.biopax.paxtools.impl.level3.PathwayStepImpl extends L3ElementImpl implements Serializable
  - Serialized Fields
    - stepProcess
```
Set<E> stepProcess
```
    - nextStep
```
Set<E> nextStep
```
    - nextStepOf
```
Set<E> nextStepOf
```
    - pathwayOrderOf
```
Pathway pathwayOrderOf
```
    - evidence
```
Set<E> evidence
```
- Class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl extends ControlledVocabularyImpl implements Serializable
  - Serialized Fields
    - patoData
```
String patoData
```
- Class org.biopax.paxtools.impl.level3.PhysicalEntityImpl extends EntityImpl implements Serializable
  - Serialized Fields
    - cellularLocation
```
CellularLocationVocabulary cellularLocation
```
    - memberPhysicalEntity
```
Set<E> memberPhysicalEntity
```
    - componentOf
```
Set<E> componentOf
```
    - feature
```
Set<E> feature
```
    - notFeature
```
Set<E> notFeature
```
    - controllerOf
```
Set<E> controllerOf
```
    - memberPhysicalEntityOf
```
Set<E> memberPhysicalEntityOf
```
- Class org.biopax.paxtools.impl.level3.ProcessImpl extends EntityImpl implements Serializable
  - Serialized Fields
    - controlledOf
```
Set<E> controlledOf
```
    - stepProcessOf
```
Set<E> stepProcessOf
```
    - pathwayComponentOf
```
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
```
String title
```
    - url
```
Set<E> url
```
    - source
```
Set<E> source
```
    - author
```
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
- Class org.biopax.paxtools.impl.level3.ScoreImpl extends XReferrableImpl implements Serializable
  - Serialized Fields
    - value
```
String value
```
    - scoreSource
```
Provenance scoreSource
```
- Class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl extends EntityReferenceImpl implements Serializable
  - Serialized Fields
    - organism
```
BioSource organism
```
    - sequence
```
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
```
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
```
- 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
```
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
```
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
```
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
```
String db
```
    - dbVersion
```
String dbVersion
```
    - idVersion
```
String idVersion
```
    - refId
```
String refId
```
    - xrefOf
```
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.AccessibleSet extends HashSet<E> implements Serializable
- Class org.biopax.paxtools.util.BioPaxIOException extends RuntimeException implements Serializable
- Class org.biopax.paxtools.util.IllegalBioPAXArgumentException extends IllegalArgumentException implements Serializable

Serialized Form

Package org.biopax.paxtools.impl

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

Serialized Fields

uri

annotations

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

Serialized Fields

idMap

nameSpacePrefixMap

level

addDependencies

xmlBase

uri

name

Package org.biopax.paxtools.impl.level3

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

Serialized Fields

bindsTo

intramolecular

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

Serialized Fields

stepConversion

stepDirection

stepProcess

log

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

Serialized Fields

deltaS

kEQ

deltaH

deltaG

eCNumber

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

Serialized Fields

celltype

tissue

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

Serialized Fields

catalysisDirection

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.ChemicalConstantImpl extends L3ElementImpl implements Serializable

Serialized Fields

ionicStrength

ph

pMg

temperature

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

Serialized Fields

structureFormat

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

componentStoichiometry

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

Serialized Fields

controlType

pathwayController

peController

controlled

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

Serialized Fields

term

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

Serialized Fields

right

left

conversionDirection

participantStoichiometry

spontaneous

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

Serialized Fields

modificationType

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

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

Serialized Fields