org.biopax.paxtools.pattern.util

Class Blacklist

java.lang.Object

org.biopax.paxtools.pattern.util.Blacklist

public class Blacklist
extends Object

A blacklist is used for not using ubiquitous small molecules in patterns. This class knows how to read itself from an InputStream, and can write itself to an OutputStream.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
Blacklist() Constructor for a blank blacklist.
Blacklist(InputStream is) Constructor with resource input stream.
Blacklist(String filename) Constructor with resource file name.

Method Summary

Modifier and Type	Method and Description
void	addEntry(String id, int score, RelType context) Adds a new blacklisted ID.
RelType	getContext(String id) Gets the context of the ubiquity of the ID.
Set<String>	getListed() Gets the IDs of the blacklisted molecules.
Set	getNonUbiqueObjects(Set objects)
Set<PhysicalEntity>	getNonUbiques(Set<PhysicalEntity> entities, RelType ctx) Gets the non-ubiquitous physical entities in the given set and in the given context.
Collection<SmallMolecule>	getUbiques(Set<PhysicalEntity> entities, RelType context) Gets the ubiquitous small molecules among the given set and in the given context.
boolean	isUbique(PhysicalEntity pe) Checks if the given entity is blacklisted in at least one context.
boolean	isUbique(PhysicalEntity pe, Conversion conv, ConversionDirectionType dir, RelType context) Checks if the given entity is blacklisted for the given Conversion assuming the Conversion flows towards the given direction, and the entity is in given context.
boolean	isUbiqueInBothContexts(PhysicalEntity pe) Checks if the given entity is blacklisted in both context together.
void	write(OutputStream os) Dumps data to the given output stream.
void	write(String filename) Dumps data to the given file.

Methods inherited from class java.lang.Object

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

Constructor Detail

Blacklist

public Blacklist()

Constructor for a blank blacklist.

Blacklist

public Blacklist(String filename)

Constructor with resource file name.

Parameters:

filename - file path to import the blacklist entries from

Blacklist

public Blacklist(InputStream is)

Constructor with resource input stream.

Parameters:

is - input stream to read/init the blacklist from

Method Detail

addEntry

public void addEntry(String id,
                     int score,
                     RelType context)

Adds a new blacklisted ID.

Parameters:

id - ID of the blacklisted molecule

score - the ubiquity score

context - context of ubiquity

getListed

public Set<String> getListed()

Gets the IDs of the blacklisted molecules.

Returns:

IDs

write

public void write(String filename)

Dumps data to the given file.

Parameters:

filename - output file name

write

public void write(OutputStream os)

Dumps data to the given output stream.

Parameters:

os - output stream

getContext

public RelType getContext(String id)

Gets the context of the ubiquity of the ID. Be careful with the result. If the result is null, then either the ID may not be ubique, or the ID may be ubique without a context (which means in both contexts).

Parameters:

id - ID to check

Returns:

context of ubiquity

isUbique

public boolean isUbique(PhysicalEntity pe)

Checks if the given entity is blacklisted in at least one context.

Parameters:

pe - physical entity BioPAX object

Returns:

true/false

isUbiqueInBothContexts

public boolean isUbiqueInBothContexts(PhysicalEntity pe)

Checks if the given entity is blacklisted in both context together.

Parameters:

pe - physical entity BioPAX object

Returns:

true/false

isUbique

public boolean isUbique(PhysicalEntity pe,
                        Conversion conv,
                        ConversionDirectionType dir,
                        RelType context)

Checks if the given entity is blacklisted for the given Conversion assuming the Conversion flows towards the given direction, and the entity is in given context.

Parameters:

pe - physical entity BioPAX object

conv - conversion interaction (BioPAX)

dir - conversion direction

context - relationship type - context

Returns:

true/false

getUbiques

public Collection<SmallMolecule> getUbiques(Set<PhysicalEntity> entities,
                                            RelType context)

Gets the ubiquitous small molecules among the given set and in the given context. It is assumed that the given set is either left or right of a Conversion. If there is no non-ubiquitous element in the set, then the least ubique(s) are removed from the result.

Parameters:

entities - left or right of a conversion

context - are these entities input or output

Returns:

ubiquitous small molecules in the given context

getNonUbiques

public Set<PhysicalEntity> getNonUbiques(Set<PhysicalEntity> entities,
                                         RelType ctx)

Gets the non-ubiquitous physical entities in the given set and in the given context. It is assumed that the given set is either left or right of a Conversion. If there is no non-ubiquitous element in the set, then the least ubique(s) are added to the result.

Parameters:

entities - left or right of a conversion

ctx - are these entities input or output

Returns:

non-ubiquitous physical entities in the given context

getNonUbiqueObjects

public Set getNonUbiqueObjects(Set objects)