org.biopax.paxtools.util
Class Level2Helper

java.lang.Object
  org.biopax.paxtools.util.Level2Helper

public class Level2Helper
extends java.lang.Object

This class has static methods for doing some calculations on biopax level 2 model members. These methods may be considered to be included in the utility methods of the model objects themselves. However, most of these methods are based on very weak assumptions, and most times they work because of the common missuse of biopax by data providers.

Author:

Ozgun Babur Date: Mar 27, 2008 Time: 4:33:57 PM

Constructor Summary

Level2Helper()

Method Summary

static java.util.Collection<java.util.List<physicalEntityParticipant>>	groupParticipants(physicalEntity pe, boolean includeComplexMemberships)
static boolean	hasLeftToRightEvidence(conversion conv, control cont)
static boolean	hasRightToLeftEvidence(conversion conv, control cont)
static boolean	isActiveComplex(complex cmp)
static boolean	isInactiveComplex(complex cmp)
static boolean	isNegative(control cont)
static java.util.Collection<java.util.List<physicalEntityParticipant>>	selectFunctionalSets(java.util.Collection<java.util.List<physicalEntityParticipant>> parts)
static java.util.Collection<java.util.List<physicalEntityParticipant>>	selectInactiveSets(java.util.Collection<java.util.List<physicalEntityParticipant>> parts)

Methods inherited from class java.lang.Object

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

Constructor Detail

Level2Helper

public Level2Helper()

Method Detail

hasLeftToRightEvidence

public static boolean hasLeftToRightEvidence(conversion conv,
                                             control cont)

hasRightToLeftEvidence

public static boolean hasRightToLeftEvidence(conversion conv,
                                             control cont)

isNegative

public static boolean isNegative(control cont)

groupParticipants

public static java.util.Collection<java.util.List<physicalEntityParticipant>> groupParticipants(physicalEntity pe,
                                                                                                boolean includeComplexMemberships)

selectFunctionalSets

public static java.util.Collection<java.util.List<physicalEntityParticipant>> selectFunctionalSets(java.util.Collection<java.util.List<physicalEntityParticipant>> parts)

selectInactiveSets

public static java.util.Collection<java.util.List<physicalEntityParticipant>> selectInactiveSets(java.util.Collection<java.util.List<physicalEntityParticipant>> parts)

isActiveComplex

public static boolean isActiveComplex(complex cmp)

isInactiveComplex

public static boolean isInactiveComplex(complex cmp)