Package | Description |
---|---|
org.biopax.paxtools.impl.level3 |
This package contains the default implementation for BioPAX Level 3.
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org.biopax.paxtools.model.level3 |
This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
|
org.biopax.paxtools.pattern.constraint |
Package for constraints.
|
org.biopax.paxtools.pattern.util |
Package for several utility classes.
|
Modifier and Type | Method and Description |
---|---|
ConversionDirectionType |
ConversionImpl.getConversionDirection() |
Modifier and Type | Method and Description |
---|---|
void |
ConversionImpl.setConversionDirection(ConversionDirectionType spontanousType) |
Modifier and Type | Method and Description |
---|---|
ConversionDirectionType |
Conversion.getConversionDirection()
This property represents the direction of the reaction.
|
static ConversionDirectionType |
ConversionDirectionType.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static ConversionDirectionType[] |
ConversionDirectionType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
void |
Conversion.setConversionDirection(ConversionDirectionType conversionDirection)
This property represents the direction of the reaction.
|
Modifier and Type | Method and Description |
---|---|
protected ConversionDirectionType |
ConstraintAdapter.convertStepDirection(StepDirection sdir) |
protected ConversionDirectionType |
ConstraintAdapter.findDirectionInCatalysis(Conversion conv)
Searches the controlling catalysis for possible direction of the conversion.
|
protected ConversionDirectionType |
ConstraintAdapter.findDirectionInPathways(Conversion conv)
Searches pathways that contains this conversion for the possible directions.
|
protected ConversionDirectionType |
ConstraintAdapter.getCatalysisDirection(Control cont)
Gets the direction of the Control, if exists.
|
protected ConversionDirectionType |
ConstraintAdapter.getDirection(Conversion conv) |
protected ConversionDirectionType |
ConstraintAdapter.getDirection(Conversion conv,
Control cont)
Gets the direction of the Control chain the the Interaction.
|
protected ConversionDirectionType |
ConstraintAdapter.getDirection(Conversion conv,
Pathway pathway)
Gets the direction of the Control chain the the Interaction.
|
protected ConversionDirectionType |
ConstraintAdapter.getDirection(Conversion conv,
Pathway pathway,
Control cont)
Gets the direction of the Control chain the the Interaction.
|
Modifier and Type | Method and Description |
---|---|
boolean |
Blacklist.isUbique(PhysicalEntity pe,
Conversion conv,
ConversionDirectionType dir,
RelType context)
Checks if the given entity is blacklisted for the given Conversion assuming the Conversion
flows towards the given direction, and the entity is in given context.
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