Uses of Class
org.biopax.paxtools.pattern.miner.SIFInteraction

Packages that use SIFInteraction

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

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

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

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.
Set<SIFInteraction>	SIFSearcher.searchSIF(Model model)	Searches the given model with the contained miners.

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

Modifier and Type	Method	Description
String	CustomFormat.convert(SIFInteraction inter)	Prepares the line in the output file for the given interaction.
String	SIFToText.convert(SIFInteraction inter)	Creates the textual data corresponding to the given binary interaction.
String	OutputColumn.getColumnValue(SIFInteraction inter)	Get the string to write in the output file.
void	SIFInteraction.mergeWith(SIFInteraction equivalent)	Merges publications of the parameter equivalent sif with this one.

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

Modifier and Type	Method	Description
static boolean[][]	SIFInteraction.convertToAdjacencyMatrix(Collection<SIFInteraction> sifInts, SIFType... type)	Converts the given collection of interactions into an adjacency matrix.
static List<String>	SIFInteraction.getSortedGeneNames(Collection<SIFInteraction> sifInts, SIFType... type)	Collects and sorts sourceID and targetID of the given collection of sif interactions.
static boolean	ExtendedSIFWriter.write(Set<SIFInteraction> inters, OutputStream out)	Writes down the given inferred binary interactions into the output stream using the Pathway Commons one-file EXTENDED_BINARY_SIF format, where edges (interactions) are written first, followed by a single blank line, followed by the nodes section (participant details and annotations).
static boolean	ExtendedSIFWriter.writeInteractions(Set<SIFInteraction> inters, OutputStream out)	Writes down the given interactions into the given "edges" output stream.
static boolean	ExtendedSIFWriter.writeParticipants(Set<SIFInteraction> inters, OutputStream out)	Writes down the interaction participants' (nodes) details to the given output stream.