Package org.biopax.paxtools.pattern.constraint

Class ActivityModificationChangeConstraint

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint

All Implemented Interfaces:

Constraint

public class ActivityModificationChangeConstraint
extends ConstraintAdapter

This is a very specialized constraint that checks if two PhysicalEntity of the same EntityReference have differential features, such that we can predict an activity change based on gain or loss of these features. To use this constraint, user should be able to supply maps that categorize features as activating or inhibiting.

Author:

Ozgun Babur

Field Summary

Fields

Modifier and Type	Field	Description
protected static final String[]	general	Some general modification sub-strings to use if exact terms are not conclusive.

Fields inherited from class org.biopax.paxtools.pattern.constraint.ConstraintAdapter

blacklist, size

Constructor Summary

Constructors

Constructor	Description
ActivityModificationChangeConstraint(boolean activating, Map<EntityReference,Set<ModificationFeature>> activityFeat, Map<EntityReference,Set<ModificationFeature>> inactivityFeat)	Constructor with the desired change and maps to activating and inactivating features,

Method Summary

Modifier and Type	Method	Description
protected Map<EntityReference,Set<String>>	extractModifNames(Map mfMap)	Extracts the modification terms from the moficiation features.
protected Set<String>	extractModifNames(Set mfSet)	Extracts terms of the modification features.
boolean	satisfies(Match match, int... ind)	Checks the gained and and lost features to predict the activity change is the desired change.
protected boolean	setContainsGeneralTerm(Set<String> set, String term)	Checks if any element in the set contains the term.

Methods inherited from class org.biopax.paxtools.pattern.constraint.ConstraintAdapter

assertIndLength, canGenerate, convertStepDirection, findDirectionInCatalysis, findDirectionInPathways, generate, getCatalysisDirection, getControlChain, getConvParticipants, getDirection, getDirection, getDirection, getDirection, getVariableSize, setSize

Methods inherited from class java.lang.Object

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

Field Details

general

protected static final String[] general

Some general modification sub-strings to use if exact terms are not conclusive.

Constructor Details

ActivityModificationChangeConstraint

public ActivityModificationChangeConstraint(boolean activating,
 Map<EntityReference,Set<ModificationFeature>> activityFeat,
 Map<EntityReference,Set<ModificationFeature>> inactivityFeat)

Constructor with the desired change and maps to activating and inactivating features,

Parameters:

activating - desired change

activityFeat - map from EntityReference to the activating features

inactivityFeat - map from EntityReference to the inactivating features

Method Details

satisfies

public boolean satisfies(Match match,
 int... ind)

Checks the gained and and lost features to predict the activity change is the desired change. If exact matching (terms with locations) is not conclusive, then terms without locations are checked. If still not conclusive, then approximate matching is used.

Specified by:

satisfies in interface Constraint

Overrides:

satisfies in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

true if the modification gain or loss is mapped to the desired change

extractModifNames

protected Map<EntityReference,Set<String>> extractModifNames(Map mfMap)

Extracts the modification terms from the moficiation features.

Parameters:

mfMap - map for the features

Returns:

map from EntityReference to the set of the extracted terms

extractModifNames

protected Set<String> extractModifNames(Set mfSet)

Extracts terms of the modification features.

Parameters:

mfSet - set of modification features

Returns:

set of extracted terms

setContainsGeneralTerm

protected boolean setContainsGeneralTerm(Set<String> set,
 String term)

Checks if any element in the set contains the term.

Parameters:

set - set to check

term - term to search for

Returns:

true if any element contains the term