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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Field and Description |
---|---|
protected Blacklist |
ConstraintAdapter.blacklist
Blacklist to detect ubiquitous small molecules.
|
Modifier and Type | Method and 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.
|
Constructor and Description |
---|
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.
|
ParticipatingPE(RelType type,
Blacklist blacklist)
Deprecated.
Constructor with parameters.
|
RelatedControl(RelType peType,
Blacklist blacklist)
Constructor with the relation type between PhysicalEntity and Conversion, and the blacklist.
|
Modifier and Type | Method and Description |
---|---|
void |
DeltaFeatureExtractor.setBlacklist(Blacklist blacklist) |
Modifier and Type | Field and Description |
---|---|
protected Blacklist |
MinerAdapter.blacklist
Blacklist for identifying ubiquitous small molecules.
|
Modifier and Type | Method and Description |
---|---|
Blacklist |
BlacklistGenerator.generateBlacklist(Model model)
Generates the blacklist.
|
Modifier and Type | Method and Description |
---|---|
void |
SIFSearcher.setBlacklist(Blacklist blacklist)
Sets the blacklist that manages IDs of ubique molecules.
|
void |
SIFMiner.setBlacklist(Blacklist blacklist)
Sets the blacklist that can be used during the search.
|
void |
MinerAdapter.setBlacklist(Blacklist blacklist)
Sets the blacklist to use during SIF search.
|
Copyright © 2015 BioPAX. All rights reserved.