Package 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 Details

    • 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 Details

    • generateBlacklist

      public Blacklist generateBlacklist(Model model)
      Generates the blacklist.
      Parameters:
      model - model to use
      Returns:
      the blacklist