Uses of Class
org.biopax.paxtools.pattern.util.Blacklist

Packages that use Blacklist

Package	Description
org.biopax.paxtools.pattern	Main package.
org.biopax.paxtools.pattern.constraint	Package for constraints.
org.biopax.paxtools.pattern.example
org.biopax.paxtools.pattern.miner	Package for pattern miner utility.

Uses of Blacklist in org.biopax.paxtools.pattern

Methods in org.biopax.paxtools.pattern with parameters of type Blacklist

Modifier and Type	Method	Description
static Pattern	PatternBox.catalysisPrecedes(Blacklist blacklist)	Pattern for detecting two EntityReferences are controlling consecutive reactions, where output of one reaction is input to the other.
static Pattern	PatternBox.chemicalAffectsProteinThroughBinding(Blacklist blacklist)	A small molecule is in a complex with a protein.
static Pattern	PatternBox.controlsMetabolicCatalysis(Blacklist blacklist, boolean consumption)	Pattern for a Protein controlling a reaction whose participant is a small molecule.
static Pattern	PatternBox.controlsStateChangeThroughBindingSmallMolecule(Blacklist blacklist)	Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.
static Pattern	PatternBox.controlsStateChangeThroughControllerSmallMolecule(Blacklist blacklist)	Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.
static Pattern	PatternBox.controlsTransportOfChemical(Blacklist blacklist)	Pattern for a ProteinReference has a member PhysicalEntity that is controlling a reaction that changes cellular location of a small molecule.
static Pattern	PatternBox.reactsWith(Blacklist blacklist)	Constructs a pattern where first and last small molecules are substrates to the same biochemical reaction.
static Pattern	PatternBox.usedToProduce(Blacklist blacklist)	Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.

Uses of Blacklist in org.biopax.paxtools.pattern.constraint

Fields in org.biopax.paxtools.pattern.constraint declared as Blacklist

Modifier and Type	Field	Description
protected Blacklist	ConstraintAdapter.blacklist	Blacklist to detect ubiquitous small molecules.

Methods in org.biopax.paxtools.pattern.constraint with parameters of type Blacklist

Modifier and Type	Method	Description
static Constraint	ConBox.linkToComplex(Blacklist blacklist)	Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
static Constraint	ConBox.linkToSimple(Blacklist blacklist)	Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.

Constructors in org.biopax.paxtools.pattern.constraint with parameters of type Blacklist

Modifier	Constructor	Description
protected	ConstraintAdapter(int size, Blacklist blacklist)	Constructor with size.
	ConversionSide(ConversionSide.Type type, Blacklist blacklist, RelType relType)	Constructor.
	LinkedPE(LinkedPE.Type type, Blacklist blacklist)	Constructor with the linking type.
	NonUbique(Blacklist blacklist)
	Participant(RelType type, Blacklist blacklist)	Constructor with parameters.
	Participant(RelType type, Blacklist blacklist, boolean considerControl)	Constructor with parameters.
	Participant(RelType type, Blacklist blacklist, boolean considerControl, boolean considerPathway)	Constructor with parameters.
	ParticipatesInConv(RelType type, Blacklist blacklist)	Constructor with parameters.
	RelatedControl(RelType peType, Blacklist blacklist)	Constructor with the relation type between PhysicalEntity and Conversion, and the blacklist.

Uses of Blacklist in org.biopax.paxtools.pattern.example

Methods in org.biopax.paxtools.pattern.example with parameters of type Blacklist

Modifier and Type	Method	Description
void	DeltaFeatureExtractor.setBlacklist(Blacklist blacklist)

Uses of Blacklist in org.biopax.paxtools.pattern.miner

Fields in org.biopax.paxtools.pattern.miner declared as Blacklist

Modifier and Type	Field	Description
protected Blacklist	MinerAdapter.blacklist	Blacklist for identifying ubiquitous small molecules.

Methods in org.biopax.paxtools.pattern.miner that return Blacklist

Modifier and Type	Method	Description
Blacklist	BlacklistGenerator.generateBlacklist(Model model)	Generates the blacklist.
Blacklist	BlacklistGenerator2.generateBlacklist(Model model)	Generates the blacklist.
Blacklist	BlacklistGenerator3.generateBlacklist(Model model)	Generates the blacklist.

Methods in org.biopax.paxtools.pattern.miner with parameters of type Blacklist

Modifier and Type	Method	Description
void	MinerAdapter.setBlacklist(Blacklist blacklist)	Sets the blacklist to use during SIF search.
void	SIFMiner.setBlacklist(Blacklist blacklist)	Sets the blacklist that can be used during the search.
void	SIFSearcher.setBlacklist(Blacklist blacklist)	Sets the blacklist that manages IDs of ubique molecules.