Package org.biopax.paxtools.pattern.util

package org.biopax.paxtools.pattern.util

Package for several utility classes.

Related Packages

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.

Class	Description
AdjacencyMatrix	Adjacency matrix representation of a graph.
Blacklist	A blacklist is used for not using ubiquitous small molecules in patterns.
ChemicalNameNormalizer	This class is used for finding a standard name for a small molecule.
DifferentialModificationUtil	THis class is used for comparing modification features of two PhysicalEntity objects of same EntityReference.
HGNC	This class provides a mapping between HGNC IDs and Symbols.
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.
ProgressWatcher	This interface is to use for tracking progress of a process.
RelType	Distinguishes between input and output.