Package | Description |
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org.biopax.paxtools.pattern.miner |
Package for pattern miner utility.
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Modifier and Type | Class and Description |
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class |
SIFEnum
Enum for representing supported SIF edge types.
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Modifier and Type | Field and Description |
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SIFType |
SIFInteraction.type |
Modifier and Type | Method and Description |
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SIFType |
SIFMiner.getSIFType()
Gets the type of the interaction.
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SIFType |
AbstractSIFMiner.getSIFType() |
Modifier and Type | Method and Description |
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static boolean[][] |
SIFInteraction.convertToAdjacencyMatrix(Collection<SIFInteraction> sifInts,
SIFType... type)
Converts the given collection of interactions into an adjacency matrix.
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static List<String> |
SIFInteraction.getSortedGeneNames(Collection<SIFInteraction> sifInts,
SIFType... type)
Collects and sorts sourceID and targetID of the given collection of sif interactions.
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void |
AbstractSIFMiner.setType(SIFType type) |
Constructor and Description |
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AbstractSIFMiner(SIFType type)
Constructor with interaction type.
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AbstractSIFMiner(SIFType type,
String supplName,
String supplDesc)
Constructor with interaction type, supplementary name, supplementary description, and ubiquitous IDs.
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ConsumptionControlledByMiner(SIFType type)
Constructor for extension purposes.
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ControlsStateChangeOfMiner(SIFType type)
Constructor for extension purposes.
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SIFInteraction(String sourceID,
String targetID,
BioPAXElement sourceER,
BioPAXElement targetER,
SIFType type,
Set<BioPAXElement> mediators,
Set<BioPAXElement> sourcePEs,
Set<BioPAXElement> targetPEs) |
SIFSearcher(IDFetcher idFetcher,
SIFType... types)
Constructor with ID fetcher and binary interaction types.
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SIFSearcher(SIFType... types)
Constructor with binary interaction types.
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