org.biopax.paxtools.pattern.miner

Class BlacklistGenerator3

java.lang.Object

org.biopax.paxtools.pattern.miner.BlacklistGenerator3

public class BlacklistGenerator3
extends Object

This class generates a blacklist for the given model. It uses a list of known ubiquitous molecule names.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
BlacklistGenerator3() Default Constructor.
BlacklistGenerator3(InputStream knownNamesIS) Constructor.

Method Summary

Modifier and Type	Method and Description
Blacklist	generateBlacklist(Model model) Generates the blacklist.

Methods inherited from class java.lang.Object

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

Constructor Detail

BlacklistGenerator3

public BlacklistGenerator3(InputStream knownNamesIS)

Constructor.

Parameters:

knownNamesIS - a special file that lists the known names of ubiquitous unwanted-to-traverse chemicals

BlacklistGenerator3

public BlacklistGenerator3()

Default Constructor. Uses the blacklisted small molecule names file from the classpath.

Method Detail

generateBlacklist

public Blacklist generateBlacklist(Model model)

Generates the blacklist.

Parameters:

model - model to use

Returns:

the blacklist