ConBox (Paxtools 4.3.1 API)

java.lang.Object
- org.biopax.paxtools.pattern.constraint.ConBox

```
public class ConBox
extends Object
```
Some predefined constraints.

Author:

Ozgun Babur

Constructor Summary

Constructors
Constructor and Description

ConBox()

Constructors
Constructor and Description
`ConBox()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static Constraint`	`complexes()` From PhysicalEntity to its parent Complex recursively.
`static Constraint`	`complexMembers()` From Complex to its members recursively (also getting member of the inner complexes).
`static Constraint`	`compToER()` From Complex or SimplePhysicalEntity to the related EntityReference.
`static Constraint`	`controlled()` From Control to the controlled Process
`static Constraint`	`controllerPE()` From Control to the controller PhysicalEntity
`static Constraint`	`controlsConv()` From PhysicalEntity to the controlled Conversion, skipping the middle Control.
`static Constraint`	`controlsInteraction()` From PhysicalEntity to the controlled Interaction, skipping the middle Control.
`static Constraint`	`controlToConv()` From Control to the controlled Conversion, traversing downstream Controls recursively.
`static Constraint`	`controlToInter()` From Control to the controlled Interaction, traversing downstream Controls recursively.
`static Constraint`	`controlToTempReac()` From Control to the controlled TemplateReaction, traversing downstream Controls recursively.
`static Constraint`	`convToControl()` From Conversion to the upstream Control (and its upstream Control recursively).
`static Constraint`	`convToController()` From Conversion to the controller of the upstream Control (and its upstream Control recursively).
`static Constraint`	`differentialActivity(boolean activating)` Gets a constraint to ensure that ensures only one of the two PhysicalEntities has an activity.
`static Constraint`	`equal(boolean equal)` Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
`static Constraint`	`erToPE()` From EntityReference to the member PhysicalEntity
`static Constraint`	`genericEquiv()` From PhysicalEntity to its generic equivalents, i.e.
`static Constraint`	`hasDifferentCompartments()` Checks if two physical entities have non-empty and different compartments.
`static Constraint`	`hasXref(String xrefID)` Makes sure that the object has an Xref with the given ID.
`static Constraint`	`inSamePathway()` Makes sure that the two interactions are members of the same pathway.
`static Constraint`	`interToControl()` From Interaction to the upstream Control (and its upstream Control recursively).
`static Constraint`	`interToController()` From Interaction to the controlling Controls recursively, and their controller PEs.
`static Constraint`	`interToPE()` From Interaction to the related PhysicalEntity.
`static Constraint`	`isBait()` Checks if the molecule is a bait of a Y2H experiment.
`static Constraint`	`isHuman()` Makes sure the EntityReference or the PhysicalEntity belongs to human.
`static Constraint`	`isPrey()` Checks if the molecule is a prey of a Y2H experiment.
`static Constraint`	`left()` From Conversion to its left participants.
`static Constraint`	`linkedER(boolean up)`
`static Constraint`	`linkToComplex()` Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
`static Constraint`	`linkToComplex(Blacklist blacklist)` Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
`static Constraint`	`linkToSimple(Blacklist blacklist)` Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
`static Constraint`	`linkToSpecific()` Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
`static Constraint`	`maxDegree(int limit)` Makes sure the participant degree (number of Conversions that this is a participant) of the PhysicalEntity is less than or equal to the parameter.
`static Constraint`	`modificationConstraint(String modifTerm)` Makes sure that the PhysicalEntity or any linked PE contains the modification term.
`static Constraint`	`moreControllerThanParticipant()` Makes sure that the PhysicalEntity is controlling more reactions than it participates (excluding complex assembly).
`static Constraint`	`nameEquals(String... name)` Filters Named to contain a name from the input set.
`static Constraint`	`nameEquals(String name)` Filters Named to contain a specific name.
`static Constraint`	`nextInteraction()` Starts from an Interaction and gets next Interactions in temporal order, if ever defined in a Pathway.
`static Constraint`	`notAParticipant()` Makes sure that the second element (PhysicalEntity) is not a participant of the first element (Interaction).
`static Constraint`	`notControlled()` Makes sure the Interaction has no Control
`static Constraint`	`notControlsThis()` Makes sure the second element (Control) is not a controller to the first element (Interaction).
`static Constraint`	`notGeneric()` Makes sure that the PhysicalEntity do not have member physical entities..
`static Constraint`	`notLabeledInactive()` Makes sure a PhysicalEntity of any linked member PhysicalEntities toward members are not labeled as inactive.
`static Constraint`	`participant()` From Interaction to its PhysicalEntity participants.
`static Constraint`	`participantER()` From Interaction to the related EntityReference of its participants.
`static Constraint`	`participatesInConv()` From PhysicalEntity to the Conversion that it participates.
`static Constraint`	`participatesInInter()` From PhysicalEntity to the Interaction that it participates.
`static Constraint`	`peNotRelatedToER()` Makes sure that the given physical entity is not related to the entity reference.
`static Constraint`	`peToControl()` From PhysicalEntity to the downstream Control
`static Constraint`	`peToControlledConv()` From PhysicalEntity to the downstream Conversion.
`static Constraint`	`peToControlledInter()` From PhysicalEntity to the downstream Interaction.
`static Constraint`	`peToER()` From SimplePhysicalEntity to its EntityReference.
`static Constraint`	`peToInter()` From PhysicalEntity to the related Interaction.
`static Constraint`	`product()` From TemplateReaction to its products.
`static Constraint`	`right()` From Conversion to its right participants.
`static Constraint`	`simpleMembers()` From complex to its simple members (members which are of type SimplePhysicalEntity) recursively.
`static Constraint`	`simplePEToConv(RelType type)` From simple PhysicalEntity to related Conversion.
`static Constraint`	`source(String dbname)`
`static Constraint`	`type(Class<? extends BioPAXElement> clazz)` Creates an element type constraint.
`static Constraint`	`withComplexes()` From PhysicalEntity to parent Complex recursively, or to itself.
`static Constraint`	`withComplexMembers()` From Complex to its members, or the complex itself.
`static Constraint`	`withSimpleMembers()` From complex to its simple members recursively, or the Complex itself

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - ConBox
```
public ConBox()
```
- Method Detail
  - erToPE
```
public static Constraint erToPE()
```
    From EntityReference to the member PhysicalEntity
    
    Returns:
    
    generative constraint to get to the member PhysicalEntity of the EntityReference
  - peToER
```
public static Constraint peToER()
```
    From SimplePhysicalEntity to its EntityReference.
    
    Returns:
    
    generative constraint to get the EntityReference of the SimplePhysicalEntity
  - peToControl
```
public static Constraint peToControl()
```
    From PhysicalEntity to the downstream Control
    
    Returns:
    
    generative constraint to get the Control that the PhysicalEntity is a controller
  - peToControlledConv
```
public static Constraint peToControlledConv()
```
    From PhysicalEntity to the downstream Conversion.
    
    Returns:
    
    generative constraint to get the Conversion that the PhysicalEntity is a controller
  - peToControlledInter
```
public static Constraint peToControlledInter()
```
    From PhysicalEntity to the downstream Interaction.
    
    Returns:
    
    generative constraint to get the Interaction that the PhysicalEntity is a controller
  - peToInter
```
public static Constraint peToInter()
```
    From PhysicalEntity to the related Interaction.
    
    Returns:
    
    generative constraint to get the Interaction that the PhysicalEntity is a controller
  - simplePEToConv
```
public static Constraint simplePEToConv(RelType type)
```
    From simple PhysicalEntity to related Conversion. The relation can be through complexes and generics.
    
    Parameters:
    
    type - relationship type
    
    Returns:
    
    generative constraint
  - interToPE
```
public static Constraint interToPE()
```
    From Interaction to the related PhysicalEntity.
    
    Returns:
    
    the constraint
  - controlled
```
public static Constraint controlled()
```
    From Control to the controlled Process
    
    Returns:
    
    generative constraint to get the controlled Process of the Control
  - controllerPE
```
public static Constraint controllerPE()
```
    From Control to the controller PhysicalEntity
    
    Returns:
    
    generative constraint to get the controller PhysicalEntity of the Control
  - controlToConv
```
public static Constraint controlToConv()
```
    From Control to the controlled Conversion, traversing downstream Controls recursively.
    
    Returns:
    
    generative constraint to get the downstream (controlled) Conversion of the Control
  - controlToTempReac
```
public static Constraint controlToTempReac()
```
    From Control to the controlled TemplateReaction, traversing downstream Controls recursively.
    
    Returns:
    
    generative constraint to get the downstream (controlled) TemplateReaction of the Control
  - controlToInter
```
public static Constraint controlToInter()
```
    From Control to the controlled Interaction, traversing downstream Controls recursively.
    
    Returns:
    
    generative constraint to get the downstream (controlled) Interaction of the Control
  - convToControl
```
public static Constraint convToControl()
```
    From Conversion to the upstream Control (and its upstream Control recursively).
    
    Returns:
    
    generative constraint to get the upstream Controls of the Conversion
  - convToController
```
public static Constraint convToController()
```
    From Conversion to the controller of the upstream Control (and its upstream Control recursively).
    
    Returns:
    
    the constraint
  - interToControl
```
public static Constraint interToControl()
```
    From Interaction to the upstream Control (and its upstream Control recursively).
    
    Returns:
    
    generative constraint to get the upstream Controls of the Interaction
  - controlsConv
```
public static Constraint controlsConv()
```
    From PhysicalEntity to the controlled Conversion, skipping the middle Control.
    
    Returns:
    
    generative constraint to get the Conversion that the PhysicalEntity controls
  - controlsInteraction
```
public static Constraint controlsInteraction()
```
    From PhysicalEntity to the controlled Interaction, skipping the middle Control.
    
    Returns:
    
    generative constraint to get the Interaction that the PhysicalEntity controls
  - nextInteraction
```
public static Constraint nextInteraction()
```
    Starts from an Interaction and gets next Interactions in temporal order, if ever defined in a Pathway.
    
    Returns:
    
    generative constraint
  - genericEquiv
```
public static Constraint genericEquiv()
```
    From PhysicalEntity to its generic equivalents, i.e. either parent PhysicalEntity recursively or member PhysicalEntity recursively. Note that another member of the parent is not a generic equivalent.
    
    Returns:
    
    generative constraint to get the generic equivalents of the PhysicalEntity
  - complexMembers
```
public static Constraint complexMembers()
```
    From Complex to its members recursively (also getting member of the inner complexes).
    
    Returns:
    
    generative constraint to get the members of the Complex
  - simpleMembers
```
public static Constraint simpleMembers()
```
    From complex to its simple members (members which are of type SimplePhysicalEntity) recursively.
    
    Returns:
    
    generative constraint to get the simple members of the Complex recursively
  - withComplexMembers
```
public static Constraint withComplexMembers()
```
    From Complex to its members, or the complex itself.
    
    Returns:
    
    generative constraint to get the members of a complex and to itself
  - withSimpleMembers
```
public static Constraint withSimpleMembers()
```
    From complex to its simple members recursively, or the Complex itself
    
    Returns:
    
    generative constraint to get the simple members of the Complex recursively, or the Complex itself
  - complexes
```
public static Constraint complexes()
```
    From PhysicalEntity to its parent Complex recursively.
    
    Returns:
    
    generative constraint to get the parent Complex of the PhysicalEntity recursively
  - withComplexes
```
public static Constraint withComplexes()
```
    From PhysicalEntity to parent Complex recursively, or to itself.
    
    Returns:
    
    generative constraint to get the parent Complex of PhysicalEntity recursively, ot to itself
  - left
```
public static Constraint left()
```
    From Conversion to its left participants.
    
    Returns:
    
    generative constraint to get the left participants of the Conversion
  - right
```
public static Constraint right()
```
    From Conversion to its right participants.
    
    Returns:
    
    generative constraint to get the right participants of the Conversion
  - participatesInConv
```
public static Constraint participatesInConv()
```
    From PhysicalEntity to the Conversion that it participates.
    
    Returns:
    
    generative constraint to get the Conversions that the PhysicalEntity is a participant of
  - participatesInInter
```
public static Constraint participatesInInter()
```
    From PhysicalEntity to the Interaction that it participates.
    
    Returns:
    
    generative constraint to get the Interactions that the PhysicalEntity is a participant of
  - interToController
```
public static Constraint interToController()
```
    From Interaction to the controlling Controls recursively, and their controller PEs.
    
    Returns:
    
    the constraint
  - compToER
```
public static Constraint compToER()
```
    From Complex or SimplePhysicalEntity to the related EntityReference. If Complex, then EntityReference of simple members (recursively) are related.
    
    Returns:
    
    generative constraint to get the related EntityReference of the Complex or SimplePhysicalEntity
  - nameEquals
```
public static Constraint nameEquals(String name)
```
    Filters Named to contain a specific name.
    
    Parameters:
    
    name - name to require
    
    Returns:
    
    constraint to check if the name exists in among names
  - nameEquals
```
public static Constraint nameEquals(String... name)
```
    Filters Named to contain a name from the input set.
    
    Parameters:
    
    name - name to require
    
    Returns:
    
    constraint
  - differentialActivity
```
public static Constraint differentialActivity(boolean activating)
```
    Gets a constraint to ensure that ensures only one of the two PhysicalEntities has an activity. Size of this constraint is 2.
    
    Parameters:
    
    activating - true/false (TODO explain)
    
    Returns:
    
    constraint to make sure only one of the PhysicalEntity has an activity
  - participant
```
public static Constraint participant()
```
    From Interaction to its PhysicalEntity participants.
    
    Returns:
    
    generative constraint to get the participants of the Interaction
  - participantER
```
public static Constraint participantER()
```
    From Interaction to the related EntityReference of its participants.
    
    Returns:
    
    generative constraint to get the related PhysicalEntity of the participants of an Interaction
  - product
```
public static Constraint product()
```
    From TemplateReaction to its products.
    
    Returns:
    
    generative constraint to get the products of the TemplateReaction
  - notControlled
```
public static Constraint notControlled()
```
    Makes sure the Interaction has no Control
    
    Returns:
    
    constraint to filter out Interactions with a Control
  - isHuman
```
public static Constraint isHuman()
```
    Makes sure the EntityReference or the PhysicalEntity belongs to human. Please note that this check depends on the display name of the related BioSource object to be "Homo sapiens". If that is not the case, the constraint won't work.
    
    Returns:
    
    constraint to make sure the EntityReference or the PhysicalEntity belongs to human
  - hasXref
```
public static Constraint hasXref(String xrefID)
```
    Makes sure that the object has an Xref with the given ID. This id is not an RDF ID, it is the value of the Xref, like gene symbol.
    
    Parameters:
    
    xrefID - xref id
    
    Returns:
    
    constraint
  - notAParticipant
```
public static Constraint notAParticipant()
```
    Makes sure that the second element (PhysicalEntity) is not a participant of the first element (Interaction).
    
    Returns:
    
    constraint to make sure that the PhysicalEntity in second index is not a participant of the Interaction in first index
  - peNotRelatedToER
```
public static Constraint peNotRelatedToER()
```
    Makes sure that the given physical entity is not related to the entity reference.
    
    Returns:
    
    the constraint todo: method not tested
  - notControlsThis
```
public static Constraint notControlsThis()
```
    Makes sure the second element (Control) is not a controller to the first element (Interaction).
    
    Returns:
    
    constraint to filter out cases where the Control at the second index is controlling the Interaction at the first index.
  - notLabeledInactive
```
public static Constraint notLabeledInactive()
```
    Makes sure a PhysicalEntity of any linked member PhysicalEntities toward members are not labeled as inactive.
    
    Returns:
    
    constraint to filter out PhysicalEntity labeled as inactive.
  - modificationConstraint
```
public static Constraint modificationConstraint(String modifTerm)
```
    Makes sure that the PhysicalEntity or any linked PE contains the modification term. Size = 1.
    
    Parameters:
    
    modifTerm - term to check
    
    Returns:
    
    constraint to filter out PhysicalEntity not associated to a modification term
  - linkToSpecific
```
public static Constraint linkToSpecific()
```
    Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
    
    Returns:
    
    the constraint
  - linkToComplex
```
public static Constraint linkToComplex()
```
    Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
    
    Returns:
    
    the constraint
  - linkedER
```
public static Constraint linkedER(boolean up)
```
  - linkToSimple
```
public static Constraint linkToSimple(Blacklist blacklist)
```
    Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
    
    Parameters:
    
    blacklist - used to detect ubiquitous small molecules
    
    Returns:
    
    the constraint
  - linkToComplex
```
public static Constraint linkToComplex(Blacklist blacklist)
```
    Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
    
    Parameters:
    
    blacklist - used to detect ubiquitous small molecules
    
    Returns:
    
    the constraint
  - equal
```
public static Constraint equal(boolean equal)
```
    Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
    
    Parameters:
    
    equal - true/false (TODO explain)
    
    Returns:
    
    the constraint
  - type
```
public static Constraint type(Class<? extends BioPAXElement> clazz)
```
    Creates an element type constraint.
    
    Parameters:
    
    clazz - a BioPAX type, i.e., corresponding interface class
    
    Returns:
    
    the constraint
  - notGeneric
```
public static Constraint notGeneric()
```
    Makes sure that the PhysicalEntity do not have member physical entities..
    
    Returns:
    
    the constraint
  - maxDegree
```
public static Constraint maxDegree(int limit)
```
    Makes sure the participant degree (number of Conversions that this is a participant) of the PhysicalEntity is less than or equal to the parameter.
    
    Parameters:
    
    limit - max degree limit
    
    Returns:
    
    the constraint
  - source
```
public static Constraint source(String dbname)
```
  - inSamePathway
```
public static Constraint inSamePathway()
```
    Makes sure that the two interactions are members of the same pathway.
    
    Returns:
    
    non-generative constraint
  - moreControllerThanParticipant
```
public static Constraint moreControllerThanParticipant()
```
    Makes sure that the PhysicalEntity is controlling more reactions than it participates (excluding complex assembly).
    
    Returns:
    
    non-generative constraint
  - hasDifferentCompartments
```
public static Constraint hasDifferentCompartments()
```
    Checks if two physical entities have non-empty and different compartments.
    
    Returns:
    
    the constraint
  - isPrey
```
public static Constraint isPrey()
```
    Checks if the molecule is a prey of a Y2H experiment.
    
    Returns:
    
    the constraint
  - isBait
```
public static Constraint isBait()
```
    Checks if the molecule is a bait of a Y2H experiment.
    
    Returns:
    
    the constraint

Class ConBox

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ConBox

Method Detail

erToPE

peToER

peToControl

peToControlledConv

peToControlledInter

peToInter

simplePEToConv

interToPE

controlled

controllerPE

controlToConv

controlToTempReac

controlToInter

convToControl

convToController

interToControl

controlsConv

controlsInteraction

nextInteraction

genericEquiv

complexMembers

simpleMembers

withComplexMembers

withSimpleMembers

complexes

withComplexes

left

right

participatesInConv

participatesInInter

interToController

compToER

nameEquals

nameEquals

differentialActivity

participant

participantER

product

notControlled

isHuman

hasXref

notAParticipant

peNotRelatedToER

notControlsThis

notLabeledInactive

modificationConstraint

linkToSpecific

linkToComplex

linkedER

linkToSimple

linkToComplex

equal

type

notGeneric

maxDegree

source

inSamePathway

moreControllerThanParticipant

hasDifferentCompartments

isPrey

isBait