org.biopax.paxtools.pattern.miner

Class SIFSearcher

java.lang.Object

org.biopax.paxtools.pattern.miner.SIFSearcher

public class SIFSearcher
extends Object

Searches a model and generates SIF network using the pattern matches.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
SIFSearcher(IDFetcher idFetcher, SIFMiner... miners) Constructor with ID fetcher and miners.
SIFSearcher(IDFetcher idFetcher, SIFType... types) Constructor with ID fetcher and binary interaction types.
SIFSearcher(SIFMiner... miners) Constructor with miners.
SIFSearcher(SIFType... types) Constructor with binary interaction types.

Method Summary

Modifier and Type	Method and Description
Set<SIFInteraction>	searchSIF(Model model) Searches the given model with the contained miners.
boolean	searchSIF(Model model, OutputStream out) Searches the given model with the contained miners.
boolean	searchSIF(Model model, OutputStream out, boolean withMediators) Searches the given model with the contained miners.
boolean	searchSIF(Model model, OutputStream out, SIFToText stt) Searches the given model with the contained miners.
AdjacencyMatrix	searchSIFGetMatrix(Model model) Searches the given model with the contained miners.
void	setBlacklist(Blacklist blacklist) Sets the blacklist that manages IDs of ubique molecules.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SIFSearcher

public SIFSearcher(SIFType... types)

Constructor with binary interaction types.

Parameters:

types - sif types

SIFSearcher

public SIFSearcher(SIFMiner... miners)

Constructor with miners.

Parameters:

miners - sif miners

SIFSearcher

public SIFSearcher(IDFetcher idFetcher,
                   SIFType... types)

Constructor with ID fetcher and binary interaction types.

Parameters:

idFetcher - ID fetcher

types - sif types

SIFSearcher

public SIFSearcher(IDFetcher idFetcher,
                   SIFMiner... miners)

Constructor with ID fetcher and miners.

Parameters:

idFetcher - ID fetcher

miners - sif miners

Method Detail

setBlacklist

public void setBlacklist(Blacklist blacklist)

Sets the blacklist that manages IDs of ubique molecules. This is not mandatory but need if ubiquitous small molecules are needed to be handled.

Parameters:

blacklist - for identifying ubiquitous small molecules

searchSIFGetMatrix

public AdjacencyMatrix searchSIFGetMatrix(Model model)

Searches the given model with the contained miners.

Parameters:

model - model to search

Returns:

sif interactions

searchSIF

public Set<SIFInteraction> searchSIF(Model model)

Searches the given model with the contained miners.

Parameters:

model - model to search

Returns:

sif interactions

searchSIF

public boolean searchSIF(Model model,
                         OutputStream out)

Searches the given model with the contained miners. Writes the textual result to the given output stream. Closes the stream at the end. Produces simplest version of SIF format.

Parameters:

model - model to search

out - stream to write

Returns:

true if any output produced successfully

searchSIF

public boolean searchSIF(Model model,
                         OutputStream out,
                         boolean withMediators)

Searches the given model with the contained miners. Writes the textual result to the given output stream. Closes the stream at the end.

Parameters:

model - model to search

out - stream to write

withMediators - whether to write the IDs of the mediator elements to the output

Returns:

true if any output produced successfully

searchSIF

public boolean searchSIF(Model model,
                         OutputStream out,
                         SIFToText stt)

Searches the given model with the contained miners. Writes the textual result to the given output stream. Closes the stream at the end.

Parameters:

model - model to search

out - stream to write

stt - sif to text converter

Returns:

true if any output produced successfully