Package org.biopax.paxtools.pattern.util

Class DifferentialModificationUtil

java.lang.Object

org.biopax.paxtools.pattern.util.DifferentialModificationUtil

public class DifferentialModificationUtil
extends Object

THis class is used for comparing modification features of two PhysicalEntity objects of same EntityReference.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor	Description
DifferentialModificationUtil()

Method Summary

Modifier and Type	Method	Description
static Set<String>	collectChangedPhosphorylationSites(PhysicalEntity before, PhysicalEntity after, boolean gained)
static Set<ModificationFeature>[]	getChangedModifications(PhysicalEntity before, PhysicalEntity after)	Gets the differential features.

Methods inherited from class java.lang.Object

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

Constructor Details

DifferentialModificationUtil

public DifferentialModificationUtil()

Method Details

getChangedModifications

public static Set<ModificationFeature>[] getChangedModifications(PhysicalEntity before,
 PhysicalEntity after)

Gets the differential features.

Parameters:

before - first entity

after - second entity

Returns:

array of differential features. index 0: gained features, index 1: lost features

collectChangedPhosphorylationSites

public static Set<String> collectChangedPhosphorylationSites(PhysicalEntity before,
 PhysicalEntity after,
 boolean gained)