Package | Description |
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org.biopax.paxtools.pattern.constraint |
Package for constraints.
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org.biopax.paxtools.pattern.miner |
Package for pattern miner utility.
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Constructor and Description |
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HasAnID(IDFetcher fetcher,
Map<BioPAXElement,Set<String>> idMap)
Constructor with the ID fetcher.
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Modifier and Type | Class and Description |
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class |
CommonIDFetcher
Tries to get gene symbols or uniprot IDs for genes and display names for small molecules.
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Modifier and Type | Field and Description |
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protected IDFetcher |
MinerAdapter.idFetcher
ID fetcher is used for skipping objects that cannot generate a valid ID during the search.
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Modifier and Type | Method and Description |
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Set<SIFInteraction> |
SIFMiner.createSIFInteraction(Match m,
IDFetcher fetcher)
Creates SIF interactions for the given match.
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Set<SIFInteraction> |
MinerAdapter.createSIFInteraction(Match m,
IDFetcher fetcher)
Creates a SIF interaction for the given match.
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protected Set<String> |
MinerAdapter.fetchIDs(BioPAXElement ele,
IDFetcher fetcher) |
void |
SIFMiner.setIDFetcher(IDFetcher idFetcher)
Sets the idFetcher that helps to fasten the search.
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void |
MinerAdapter.setIDFetcher(IDFetcher idFetcher)
Sets the ID fetcher to use during SIF search.
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Constructor and Description |
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SIFSearcher(IDFetcher idFetcher,
SIFMiner... miners)
Constructor with ID fetcher and miners.
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SIFSearcher(IDFetcher idFetcher,
SIFType... types)
Constructor with ID fetcher and binary interaction types.
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