Package org.biopax.paxtools.pattern.util

Class PhysicalEntityChain

java.lang.Object

org.biopax.paxtools.pattern.util.PhysicalEntityChain

public class PhysicalEntityChain
extends Object

This class takes two PhysicalEntity objects linked with generic or complex member relationships, and prepares an array of PEs that link those.

Author:

Ozgun Babur

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	PhysicalEntityChain.Activity	Values for activity.

Field Summary

Fields

Modifier and Type	Field	Description
protected static final PathAccessor	PE2FEAT	Accessor to the modification term.
protected static final PathAccessor	PE2TERM	Accessor to the modification term.
PhysicalEntity[]	pes	Array that links two ends of the chain.

Constructor Summary

Constructors

Constructor	Description
PhysicalEntityChain(PhysicalEntity small, PhysicalEntity big)	Constructor with endpoints.

Method Summary

Modifier and Type	Method	Description
PhysicalEntityChain.Activity	checkActivityLabel()	Checks if the chain has a member with an activity label.
protected PhysicalEntity[]	fillArray(PhysicalEntity parent, PhysicalEntity target, int depth, int dir)	Creates the chain that links the given endpoints.
Set<String>	getCellularLocations()	Retrieves the cellular location of the PhysicalEntity.
Set<ModificationFeature>	getModifications()	Collects modifications from the elements of the chain.
boolean	intersects(PhysicalEntityChain rpeh)	Checks if two chains intersect without ignoring endpoint intersection.
boolean	intersects(PhysicalEntityChain rpeh, boolean ignoreEndPoints)	Checks if two chains intersect.

Methods inherited from class java.lang.Object

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

Field Details

pes

public PhysicalEntity[] pes

Array that links two ends of the chain.

PE2TERM

protected static final PathAccessor PE2TERM

Accessor to the modification term.

PE2FEAT

protected static final PathAccessor PE2FEAT

Accessor to the modification term.

Constructor Details

PhysicalEntityChain

public PhysicalEntityChain(PhysicalEntity small,
 PhysicalEntity big)

Constructor with endpoints. The end points are differentiated with the terms small and big. This refers to a hierarchy in the relation. Small means you will get to this end while going towards MEMBER direction, and big means this end is at the COMPLEX direction. To understand this please see the directions in LinkedPE.

Parameters:

small - member end of the chain

big - complex end of the chain

See Also:

• LinkedPE

Method Details

fillArray

protected PhysicalEntity[] fillArray(PhysicalEntity parent,
 PhysicalEntity target,
 int depth,
 int dir)

Creates the chain that links the given endpoints.

Parameters:

parent - current element

target - target at the member end

depth - current depth

dir - current direction to traverse homologies

Returns:

array of entities

getCellularLocations

public Set<String> getCellularLocations()

Retrieves the cellular location of the PhysicalEntity.

Returns:

cellular location of the PhysicalEntity

intersects

public boolean intersects(PhysicalEntityChain rpeh)

Checks if two chains intersect without ignoring endpoint intersection.

Parameters:

rpeh - second chain

Returns:

true if they intersect

intersects

public boolean intersects(PhysicalEntityChain rpeh,
 boolean ignoreEndPoints)

Checks if two chains intersect.

Parameters:

rpeh - second chain

ignoreEndPoints - flag to ignore intersections at the endpoints of the chains

Returns:

true if they intersect

checkActivityLabel

public PhysicalEntityChain.Activity checkActivityLabel()

Checks if the chain has a member with an activity label.

Returns:

the activity status found

getModifications

public Set<ModificationFeature> getModifications()

Collects modifications from the elements of the chain.

Returns:

modifications