Uses of Package
org.biopax.paxtools.pattern.util

Packages that use org.biopax.paxtools.pattern.util

Package	Description
org.biopax.paxtools.pattern	Main package.
org.biopax.paxtools.pattern.constraint	Package for constraints.
org.biopax.paxtools.pattern.example
org.biopax.paxtools.pattern.miner	Package for pattern miner utility.
org.biopax.paxtools.pattern.util	Package for several utility classes.

Classes in org.biopax.paxtools.pattern.util used by org.biopax.paxtools.pattern

Class and Description
Blacklist A blacklist is used for not using ubiquitous small molecules in patterns.
ProgressWatcher This interface is to use for tracking progress of a process.

Classes in org.biopax.paxtools.pattern.util used by org.biopax.paxtools.pattern.constraint

Class and Description
Blacklist A blacklist is used for not using ubiquitous small molecules in patterns.
RelType Distinguishes between input and output.

Classes in org.biopax.paxtools.pattern.util used by org.biopax.paxtools.pattern.example

Class and Description
Blacklist A blacklist is used for not using ubiquitous small molecules in patterns.

Classes in org.biopax.paxtools.pattern.util used by org.biopax.paxtools.pattern.miner

Class and Description
AdjacencyMatrix Adjacency matrix representation of a graph.
Blacklist A blacklist is used for not using ubiquitous small molecules in patterns.
PhysicalEntityChain This class takes two PhysicalEntity objects linked with generic or complex member relationships, and prepares an array of PEs that link those.

Classes in org.biopax.paxtools.pattern.util used by org.biopax.paxtools.pattern.util

Class and Description
PhysicalEntityChain This class takes two PhysicalEntity objects linked with generic or complex member relationships, and prepares an array of PEs that link those.
PhysicalEntityChain.Activity Values for activity.
RelType Distinguishes between input and output.