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

Packages that use Match

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

Uses of Match in org.biopax.paxtools.pattern

Methods in org.biopax.paxtools.pattern that return types with arguments of type Match

Modifier and Type	Method	Description
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 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 List<Match>	Searcher.searchRecursive(Match match, List<MappedConst> mc, int index)	Continues searching with the mapped constraint at the given index.

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

Modifier and Type	Method	Description
Collection<BioPAXElement>	Constraint.generate(Match match, int... ind)	Generates candidate values for the variable to be generated.
Collection<BioPAXElement>	MappedConst.generate(Match match, int... outer)	Calls generate method of the constraint with index translation.
boolean	Constraint.satisfies(Match match, int... ind)	Checks if the variables in the Match satisfies this constraint.
boolean	MappedConst.satisfies(Match match, int... outer)	Directs to satisfies method of the wrapped constraint with index translation.
static List<Match>	Searcher.search(Match m, Pattern pattern)	Searches the pattern starting from the given match.
static List<Match>	Searcher.searchRecursive(Match match, List<MappedConst> mc, int index)	Continues searching with the mapped constraint at the given index.

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

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

Modifier and Type	Method	Description
Collection<BioPAXElement>	AND.generate(Match match, int... ind)	Gets intersection of the generated elements by the member constraints.
Collection<BioPAXElement>	ConstraintAdapter.generate(Match match, int... ind)	This method has to be overridden by generative constraints.
Collection<BioPAXElement>	ConstraintChain.generate(Match match, int... ind)	Chains the member constraints and returns the output of the last constraint.
Collection<BioPAXElement>	ControlToControllerER.generate(Match match, int... ind)	Navigates to the related ERs of the controllers of the given Control.
Collection<BioPAXElement>	ConversionSide.generate(Match match, int... ind)	Checks which side is the first PhysicalEntity, and gathers participants on either the other side or the same side.
Collection<BioPAXElement>	InterToPartER.generate(Match match, int... ind)	Iterated over non-taboo participants and collectes related ER.
Collection<BioPAXElement>	LinkedPE.generate(Match match, int... ind)	Gets to the linked PhysicalEntity.
Collection<BioPAXElement>	OR.generate(Match match, int... ind)	Gets the intersection of the generated values of wrapped constraints.
Collection<BioPAXElement>	Participant.generate(Match match, int... ind)	Identifies the conversion direction and gets the related participants.
Collection<BioPAXElement>	ParticipatesInConv.generate(Match match, int... ind)	Identifies the conversion direction and gets the related participants.
Collection<BioPAXElement>	PathConstraint.generate(Match match, int... ind)	Uses the encapsulated PAthAccessor to generate satisfying elements.
Collection<BioPAXElement>	RelatedControl.generate(Match match, int... ind)	According to the relation between PhysicalEntity and the Conversion, checks of the Control is relevant.
Collection<BioPAXElement>	SelfOrThis.generate(Match match, int... ind)	Gets the first mapped element along with the generated elements of wrapped constraint.
Collection<BioPAXElement>	XOR.generate(Match match, int... ind)	Gets xor of the generated elements by the member constraints.
boolean	ActivityConstraint.satisfies(Match match, int... ind)	Checks if the PhysicalEntity controls anything.
boolean	ActivityModificationChangeConstraint.satisfies(Match match, int... ind)	Checks the gained and and lost features to predict the activity change is the desired change.
boolean	AND.satisfies(Match match, int... ind)	Checks if all the constraints satisfy.
boolean	ConstraintAdapter.satisfies(Match match, int... ind)	Use this method only if constraint canGenerate, and satisfaction criteria is that simple.
boolean	ControlsNotParticipant.satisfies(Match match, int... ind)	Checks if the controlled Interaction contains a controller as a participant.
boolean	Empty.satisfies(Match match, int... ind)	Checks if the wrapped Constraint can generate any elements.
boolean	Equality.satisfies(Match match, int... ind)	Checks if the two elements are identical or not identical as desired.
boolean	Field.satisfies(Match match, int... ind)	Checks if the element in the first index has the desired value.
boolean	FieldOfMultiple.satisfies(Match match, int... ind)	Checks if the generated elements from the first mapped element has either the desired value, or has some value in common with the elements generated from second mapped element.
boolean	HasAnID.satisfies(Match match, int... ind)	Checks if the element has one of the desired IDs.
boolean	IDConstraint.satisfies(Match match, int... ind)	Checks if the element has one of the desired IDs.
boolean	ModificationChangeConstraint.satisfies(Match match, int... ind)	Checks the any of the changed modifications match to any of the desired modifications.
boolean	NonUbique.satisfies(Match match, int... ind)
boolean	NOT.satisfies(Match match, int... ind)	Negates the satisfies value of the wrapped constraint.
boolean	OR.satisfies(Match match, int... ind)	Checks if any of the wrapped constraints satisfy.
boolean	PathConstraint.satisfies(Match match, int... ind)	Checks if the PathAccessor is generating the second mapped element.
boolean	PEChainsIntersect.satisfies(Match match, int... ind)	Creates two PhysicalEntity chains with the given endpoints, and checks if they are intersecting.
boolean	SelfOrThis.satisfies(Match match, int... ind)	Checks if the last index is either generated or equal to the first element.
boolean	Size.satisfies(Match match, int... ind)	Checks if generated element size is in limits.
boolean	Type.satisfies(Match match, int... ind)	Checks if the element is assignable to a variable of the desired type.
boolean	XOR.satisfies(Match match, int... ind)	Checks if constraints satisfy in xor pattern.

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

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

Modifier and Type	Method	Description
Set<SIFInteraction>	MinerAdapter.createSIFInteraction(Match m, IDFetcher fetcher)	Creates a SIF interaction for the given match.
Set<SIFInteraction>	SIFMiner.createSIFInteraction(Match m, IDFetcher fetcher)	Creates SIF interactions for the given match.
protected Set<String>	MinerAdapter.getCellularLocations(Match m, String memLabel, String comLabel)	Gets cellular locations of the given elements in a string set.
protected PhysicalEntityChain	MinerAdapter.getChain(Match m, String memLabel, String comLabel)
protected Set<String>[]	MinerAdapter.getDeltaCompartments(Match m, String memLabel1, String comLabel1, String memLabel2, String comLabel2)	Gets delta compartments of the given two PE chains.
protected Set<String>[]	MinerAdapter.getDeltaModifications(Match m, String memLabel1, String comLabel1, String memLabel2, String comLabel2)	Gets delta modifications of the given elements in string sets.
protected String	MinerAdapter.getGeneSymbol(Match m, String label)	Searches for the gene symbol of the given EntityReference.
protected Set<String>	MinerAdapter.getIdentifiers(Match m, String label)	Uses uniprot name or gene symbol as identifier.
protected Set<String>	MinerAdapter.getModifications(Match m, String label)	Gets modifications of the given element in a string.
protected Set<String>	MinerAdapter.getModifications(Match m, String memLabel, String comLabel)	Gets modifications of the given elements in a string set.
protected String	MinerAdapter.getUniprotNameForHuman(Match m, String label)	Searches for the uniprot name of the given human EntityReference.
String	ControlsStateChangeDetailedMiner.getValue(Match m, int col)	Creates values for the result file columns.
String	MinerAdapter.getValue(Match m, int col)	This method has to be overridden if writeResultDetailed method is used.
String	UbiquitousIDMiner.getValue(Match m, int col)	Gets the ids of the small molecule reference and its physical entities.
protected boolean	MinerAdapter.labeledInactive(Match m, String simpleLabel, String complexLabel)	Checks if a PE chain is labeled as inactive.
protected int	MinerAdapter.sign(Match m, String... ctrlLabel)	Checks the cumulative sign of the chained controls.

Method parameters in org.biopax.paxtools.pattern.miner with type arguments of type Match

Modifier and Type	Method	Description
void	AbstractSIFMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out)	Writes the result as "A used-for-production-of B", where A and B are small molecule names, and whitespace is tab.
void	ControlsStateChangeDetailedMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out)	Writes the result as "A modifications-of-A B gains-of-B loss-of-B", where A and B are gene symbols, and whitespace is tab.
void	DirectedRelationMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out)	Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
void	Miner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out)	Writes the text output to the given stream.
void	RelatedGenesOfInteractionsMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out)	Writes the IDs of interaction, then gene symbols of related proteins in a line.
void	UbiquitousIDMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out)	Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
protected void	MinerAdapter.writeResultAsSIF(Map<BioPAXElement,List<Match>> matches, OutputStream out, boolean directed, String label1, String label2)	This method writes the output as pairs of gene symbols of the given two ProteinReference.
protected void	MinerAdapter.writeResultDetailed(Map<BioPAXElement,List<Match>> matches, OutputStream out, int columns)	Writes the result as a tab delimited format, where the column values are customized.
protected void	MinerAdapter.writeSIFsUsingSIFFramework(Map<BioPAXElement,List<Match>> matches, OutputStream out)	This method writes the output as pairs of gene symbols of the given two ProteinReference.