Uses of Class
org.biopax.paxtools.pattern.Pattern

Packages that use Pattern

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

Uses of Pattern in org.biopax.paxtools.pattern

Methods in org.biopax.paxtools.pattern that return Pattern

Modifier and Type	Method	Description
static Pattern	PatternBox.actChange(boolean activating, Map<EntityReference,Set<ModificationFeature>> activityFeat, Map<EntityReference,Set<ModificationFeature>> inactivityFeat)	Pattern for the activity of an EntityReference is changed through a Conversion.
static Pattern	PatternBox.bindsTo()	Finds two Protein that appear together in a Complex.
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.chemicalAffectsProteinThroughControl()	A small molecule controls an interaction of which the protein is a participant.
static Pattern	PatternBox.controlsDegradationIndirectly()	Finds cases where protein A changes state of B, and B is then degraded.
static Pattern	PatternBox.controlsExpressionWithConversion()	Finds the cases where transcription relation is shown using a Conversion instead of a TemplateReaction.
static Pattern	PatternBox.controlsExpressionWithTemplateReac()	Finds transcription factors that trans-activate or trans-inhibit an entity.
static Pattern	PatternBox.controlsMetabolicCatalysis(Blacklist blacklist, boolean consumption)	Pattern for a Protein controlling a reaction whose participant is a small molecule.
static Pattern	PatternBox.controlsPhosphorylation()
static Pattern	PatternBox.controlsStateChange()	Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
static Pattern	PatternBox.controlsStateChangeBothControlAndPart()	Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
static Pattern	PatternBox.controlsStateChangeButIsParticipant()	Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
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.controlsStateChangeThroughDegradation()	Finds cases where proteins affect their degradation.
static Pattern	PatternBox.controlsTransport()	Pattern for a ProteinReference has a member PhysicalEntity that is controlling a transportation of another ProteinReference.
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.hasNonSelfEffect()	Pattern for detecting PhysicalEntity that controls a Conversion whose participants are not associated with the EntityReference of the initial PhysicalEntity.
static Pattern	PatternBox.inComplexWith()	Two proteins have states that are members of the same complex.
static Pattern	PatternBox.inSameActiveComplex()	Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has an activity.
static Pattern	PatternBox.inSameComplex()	Pattern for two different EntityReference have member PhysicalEntity in the same Complex.
static Pattern	PatternBox.inSameComplexEffectingConversion()	Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex is controlling a Conversion.
static Pattern	PatternBox.inSameComplexHavingTransActivity()	Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has transcriptional activity.
static Pattern	PatternBox.modifiedPESimple()	Pattern for an EntityReference has distinct PhysicalEntities associated with both left and right of a Conversion.
static Pattern	PatternBox.modifierConv()	Pattern for finding Conversions that an EntityReference is participating.
static Pattern	PatternBox.molecularInteraction()	Constructs a pattern where first and last molecules are participants of a MolecularInteraction.
static Pattern	PatternBox.neighborOf()	Constructs a pattern where first and last proteins are related through an interaction.
static Pattern	PatternBox.peInOut()
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.relatedProteinRefOfInter(Class<? extends Interaction>... seedType)	Finds ProteinsReference related to an interaction.
static Pattern	PatternBox.stateChange(Pattern p, String ctrlLabel)	Pattern for a Conversion has an input PhysicalEntity and another output PhysicalEntity that belongs to the same EntityReference.
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.

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

Modifier and Type	Method	Description
void	Pattern.add(Pattern p)	Appends the constraints in the parameter pattern to the desired location.
List<BioPAXElement>	Match.get(String[] label, Pattern p)	Gets elements corresponding to the given labels in the pattern.
BioPAXElement	Match.get(String label, Pattern p)	Gets element corresponding to the given label in the pattern.
boolean	Searcher.hasSolution(Pattern p, BioPAXElement... ele)	Checks if there is any match for the given pattern if search starts from the given element.
static Map<BioPAXElement,List<Match>>	Searcher.search(Collection<? extends BioPAXElement> eles, Pattern pattern)	Searches the given pattern starting from the given elements.
static List<Match>	Searcher.search(BioPAXElement ele, Pattern pattern)	Searches the pattern starting from the given element.
static Map<BioPAXElement,List<Match>>	Searcher.search(Model model, Pattern pattern)	Searches the given pattern in the given model.
static Map<BioPAXElement,List<Match>>	Searcher.search(Model model, Pattern pattern, ProgressWatcher prg)	Searches the given pattern in the given model.
static List<Match>	Searcher.search(Match m, Pattern pattern)	Searches the pattern starting from the given match.
static <T extends BioPAXElement> Set<T>	Searcher.searchAndCollect(Collection<? extends BioPAXElement> eles, Pattern pattern, int index, Class<T> c)	Searches the given pattern starting from the given elements, then collects the specified elements of the matches and returns.
static <T extends BioPAXElement> Set<T>	Searcher.searchAndCollect(BioPAXElement ele, Pattern pattern, int index, Class<T> c)	Searches the given pattern starting from the given element, then collects the specified elements of the matches and returns.
static <T extends BioPAXElement> Set<T>	Searcher.searchAndCollect(Model model, Pattern pattern, int index, Class<T> c)	Searches a model for the given pattern, then collects the specified elements of the matches and returns.
static void	Searcher.searchInFile(Pattern p, String inFile, String outFile)	Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns.
static void	Searcher.searchInFile(Pattern p, String inFile, String outFile, int seedLimit, int graphPerSeed)	Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns.
static List<Match>	Searcher.searchPlain(Collection<? extends BioPAXElement> eles, Pattern pattern)	Searches the pattern starting from given elements, but instead of a match map, returns all matches in a list.
static List<Match>	Searcher.searchPlain(Model model, Pattern pattern)	Searches the pattern in a given model, but instead of a match map, returns all matches in a list.
static Pattern	PatternBox.stateChange(Pattern p, String ctrlLabel)	Pattern for a Conversion has an input PhysicalEntity and another output PhysicalEntity that belongs to the same EntityReference.

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

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

Modifier and Type	Method	Description
Pattern	CatalysisPrecedesMiner.constructPattern()	Constructs the pattern.
Pattern	ChemicalAffectsThroughBindingMiner.constructPattern()	Constructs the pattern.
Pattern	ChemicalAffectsThroughControlMiner.constructPattern()	Constructs the pattern.
Pattern	ConsumptionControlledByMiner.constructPattern()	Constructs the pattern.
Pattern	ControlsDegradationIndirectMiner.constructPattern()	Constructs the pattern.
Pattern	ControlsExpressionMiner.constructPattern()	Constructs the pattern.
Pattern	ControlsExpressionWithConvMiner.constructPattern()	Constructs the pattern.
Pattern	ControlsPhosphorylationMiner.constructPattern()	Constructs the pattern.
Pattern	ControlsProductionOfMiner.constructPattern()	Constructs the pattern.
Pattern	ControlsStateChangeDetailedMiner.constructPattern()	Constructs the pattern.
Pattern	ControlsStateChangeOfMiner.constructPattern()	Constructs the pattern.
Pattern	ControlsTransportMiner.constructPattern()	Constructs the pattern.
Pattern	ControlsTransportOfChemicalMiner.constructPattern()	Constructs the pattern.
Pattern	CSCOBothControllerAndParticipantMiner.constructPattern()	Constructs the pattern.
Pattern	CSCOButIsParticipantMiner.constructPattern()	Constructs the pattern.
Pattern	CSCOThroughBindingSmallMoleculeMiner.constructPattern()	Constructs the pattern.
Pattern	CSCOThroughControllingSmallMoleculeMiner.constructPattern()	Constructs the pattern.
Pattern	CSCOThroughDegradationMiner.constructPattern()	Constructs the pattern.
Pattern	DirectedRelationMiner.constructPattern()	Constructs the pattern.
Pattern	InComplexWithMiner.constructPattern()	Constructs the pattern.
Pattern	InteractsWithMiner.constructPattern()	Constructs the pattern.
abstract Pattern	MinerAdapter.constructPattern()	Constructs the pattern to use for mining.
Pattern	NeighborOfMiner.constructPattern()	Constructs the pattern.
Pattern	ReactsWithMiner.constructPattern()	Constructs the pattern.
Pattern	RelatedGenesOfInteractionsMiner.constructPattern()	Constructs the pattern.
Pattern	UbiquitousIDMiner.constructPattern()	Constructs the pattern.
Pattern	UsedToProduceMiner.constructPattern()	Constructs the pattern.
Pattern	Miner.getPattern()	Gets the pattern to use for mining the graph.
Pattern	MinerAdapter.getPattern()	Gets the pattern, constructs if null.