Package org.biopax.paxtools.pattern.constraint

Class ModificationChangeConstraint

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint

All Implemented Interfaces:

Constraint

public class ModificationChangeConstraint
extends ConstraintAdapter

This class checks if there exists a desired type of modification change among two PhysicalEntity. var0: First simple PhysicalEntity Var1: Second simple PhysicalEntity

Author:

Ozgun Babur

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ModificationChangeConstraint.Type

Field Summary

Fields

Modifier and Type	Field	Description
protected String[]	featureSubstring	Partial names of the features to be considered.
protected ModificationChangeConstraint.Type	type	Gain or loss?

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

blacklist, size

Constructor Summary

Constructors

Constructor	Description
ModificationChangeConstraint(ModificationChangeConstraint.Type type, String... featureSubstring)	Constructor with the desired change and maps to activating and inactivating features.

Method Summary

Modifier and Type	Method	Description
boolean	satisfies(Match match, int... ind)	Checks the any of the changed modifications match to any of the desired modifications.

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

featureSubstring

protected String[] featureSubstring

Partial names of the features to be considered.

type

protected ModificationChangeConstraint.Type type

Gain or loss?

Constructor Details

ModificationChangeConstraint

public ModificationChangeConstraint(ModificationChangeConstraint.Type type,
 String... featureSubstring)

Constructor with the desired change and maps to activating and inactivating features. If the feature substrings are not provided, any feature is qualified.

Parameters:

type - either gain, loss, or any

featureSubstring - partial names of the features desired to be changed

Method Details

satisfies

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

Checks the any of the changed modifications match to any of the desired modifications.

Specified by:

satisfies in interface Constraint

Overrides:

satisfies in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

true if a modification change is among desired modifications