public class SIFSearcher extends Object
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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SIFSearcher(SIFMiner... miners)
Constructor with miners.
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SIFSearcher(SIFType... types)
Constructor with binary interaction types.
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Modifier and Type | Method and Description |
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Set<SIFInteraction> |
searchSIF(Model model)
Searches the given model with the contained miners.
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boolean |
searchSIF(Model model,
OutputStream out)
Searches the given model with the contained miners.
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boolean |
searchSIF(Model model,
OutputStream out,
boolean withMediators)
Searches the given model with the contained miners.
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boolean |
searchSIF(Model model,
OutputStream out,
SIFToText stt)
Searches the given model with the contained miners.
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AdjacencyMatrix |
searchSIFGetMatrix(Model model)
Searches the given model with the contained miners.
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void |
setBlacklist(Blacklist blacklist)
Sets the blacklist that manages IDs of ubique molecules.
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public SIFSearcher(SIFType... types)
types
- sif typespublic SIFSearcher(SIFMiner... miners)
miners
- sif minerspublic SIFSearcher(IDFetcher idFetcher, SIFType... types)
idFetcher
- ID fetchertypes
- sif typespublic SIFSearcher(IDFetcher idFetcher, SIFMiner... miners)
idFetcher
- ID fetcherminers
- sif minerspublic void setBlacklist(Blacklist blacklist)
blacklist
- for identifying ubiquitous small moleculespublic AdjacencyMatrix searchSIFGetMatrix(Model model)
model
- model to searchpublic Set<SIFInteraction> searchSIF(Model model)
model
- model to searchpublic boolean searchSIF(Model model, OutputStream out)
model
- model to searchout
- stream to writepublic boolean searchSIF(Model model, OutputStream out, boolean withMediators)
model
- model to searchout
- stream to writewithMediators
- whether to write the IDs of the mediator elements to the outputpublic boolean searchSIF(Model model, OutputStream out, SIFToText stt)
model
- model to searchout
- stream to writestt
- sif to text converterCopyright © 2015 BioPAX. All rights reserved.