org.biopax.paxtools.query

Class QueryExecuter

java.lang.Object

org.biopax.paxtools.query.QueryExecuter

public class QueryExecuter
extends Object

This class provides static methods to execute graph queries. These cover only the most frequent use cases. Users can use these methods as example for executing the query they need.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
QueryExecuter()

Method Summary

Modifier and Type	Method and Description
static Set<PhysicalEntity>	getRelatedPhysicalEntities(BioPAXElement element, Set<PhysicalEntity> pes) Gets the related PhysicalEntity objects of the given BioPAXElement, in level 3 models.
static Map<BioPAXElement,Set<PhysicalEntity>>	getRelatedPhysicalEntityMap(Collection<BioPAXElement> elements) Maps each BioPAXElement to its related PhysicalEntity objects.
static Set<Node>	getSeedInteractions(Collection<BioPAXElement> elements, Graph graph) Extracts the querible interactions from the elements.
static Set<Node>	prepareSingleNodeSet(Set<BioPAXElement> elements, Graph graph) Gets the related wrappers of the given elements in a set.
protected static void	replaceXrefsWithRelatedER(Collection<BioPAXElement> elements) Replaces Xref objects with the related EntityReference objects.
static Set<BioPAXElement>	runCommonStream(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Filter... filters) Gets the elements in the common upstream or downstream of the seed
static Set<BioPAXElement>	runCommonStreamWithPOI(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Filter... filters) First finds the common stream, then completes it with the paths between seed and common stream.
static Set<BioPAXElement>	runGOI(Set<BioPAXElement> sourceSet, Model model, int limit, Filter... filters) Deprecated. Use runPathsBetween instead
static Set<BioPAXElement>	runNeighborhood(Set<BioPAXElement> sourceSet, Model model, int limit, Direction direction, Filter... filters) Gets neighborhood of the source set.
static Set<BioPAXElement>	runPathsBetween(Set<BioPAXElement> sourceSet, Model model, int limit, Filter... filters) Gets the graph constructed by the paths between the given seed nodes.
static Set<BioPAXElement>	runPathsFromTo(Set<BioPAXElement> sourceSet, Set<BioPAXElement> targetSet, Model model, LimitType limitType, int limit, Filter... filters) Gets paths the graph composed of the paths from a source node, and ends at a target node.

Methods inherited from class java.lang.Object

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

Constructor Detail

QueryExecuter

public QueryExecuter()

Method Detail

runNeighborhood

public static Set<BioPAXElement> runNeighborhood(Set<BioPAXElement> sourceSet,
                                                 Model model,
                                                 int limit,
                                                 Direction direction,
                                                 Filter... filters)

Gets neighborhood of the source set.

Parameters:

sourceSet - seed to the query

model - BioPAX model

limit - neigborhood distance to get

direction - UPSTREAM, DOWNSTREAM or BOTHSTREAM

filters - for filtering graph elements

Returns:

BioPAX elements in the result set

runPathsBetween

public static Set<BioPAXElement> runPathsBetween(Set<BioPAXElement> sourceSet,
                                                 Model model,
                                                 int limit,
                                                 Filter... filters)

Gets the graph constructed by the paths between the given seed nodes. Does not get paths between physical entities that belong the same entity reference.

Parameters:

sourceSet - Seed to the query

model - BioPAX model

limit - Length limit for the paths to be found

filters - optional filters - for filtering graph elements

Returns:

BioPAX elements in the result

runGOI

public static Set<BioPAXElement> runGOI(Set<BioPAXElement> sourceSet,
                                        Model model,
                                        int limit,
                                        Filter... filters)

Deprecated. Use runPathsBetween instead

Gets paths between the seed nodes.

Parameters:

sourceSet - Seed to the query

model - BioPAX model

limit - Length limit for the paths to be found

filters - for filtering graph elements

Returns:

BioPAX elements in the result

runPathsFromTo

public static Set<BioPAXElement> runPathsFromTo(Set<BioPAXElement> sourceSet,
                                                Set<BioPAXElement> targetSet,
                                                Model model,
                                                LimitType limitType,
                                                int limit,
                                                Filter... filters)

Gets paths the graph composed of the paths from a source node, and ends at a target node.

Parameters:

sourceSet - Seeds for start points of paths

targetSet - Seeds for end points of paths

model - BioPAX model

limitType - either NORMAL or SHORTEST_PLUS_K

limit - Length limit fothe paths to be found

filters - for filtering graph elements

Returns:

BioPAX elements in the result

runCommonStream

public static Set<BioPAXElement> runCommonStream(Set<BioPAXElement> sourceSet,
                                                 Model model,
                                                 Direction direction,
                                                 int limit,
                                                 Filter... filters)

Gets the elements in the common upstream or downstream of the seed

Parameters:

sourceSet - Seed to the query

model - BioPAX model

direction - UPSTREAM or DOWNSTREAM

limit - Length limit for the search

filters - for filtering graph elements

Returns:

BioPAX elements in the result

runCommonStreamWithPOI

public static Set<BioPAXElement> runCommonStreamWithPOI(Set<BioPAXElement> sourceSet,
                                                        Model model,
                                                        Direction direction,
                                                        int limit,
                                                        Filter... filters)

First finds the common stream, then completes it with the paths between seed and common stream.

Parameters:

sourceSet - Seed to the query

model - BioPAX model

direction - UPSTREAM or DOWNSTREAM

limit - Length limit for the search

filters - for filtering graph elements

Returns:

BioPAX elements in the result

prepareSingleNodeSet

public static Set<Node> prepareSingleNodeSet(Set<BioPAXElement> elements,
                                             Graph graph)

Gets the related wrappers of the given elements in a set.

Parameters:

elements - Elements to get the related wrappers

graph - Owner graph

Returns:

Related wrappers in a set

getRelatedPhysicalEntityMap

public static Map<BioPAXElement,Set<PhysicalEntity>> getRelatedPhysicalEntityMap(Collection<BioPAXElement> elements)

Maps each BioPAXElement to its related PhysicalEntity objects.

Parameters:

elements - Elements to map

Returns:

The mapping

replaceXrefsWithRelatedER

protected static void replaceXrefsWithRelatedER(Collection<BioPAXElement> elements)

Replaces Xref objects with the related EntityReference objects. This is required for the use case when user provides multiple xrefs that point to the same ER.

Parameters:

elements - elements to send to a query as source or target

getRelatedPhysicalEntities

public static Set<PhysicalEntity> getRelatedPhysicalEntities(BioPAXElement element,
                                                             Set<PhysicalEntity> pes)

Gets the related PhysicalEntity objects of the given BioPAXElement, in level 3 models.

Parameters:

element - Element to get related PhysicalEntity objects

pes - Result set. If not supplied, a new set will be initialized.

Returns:

Related PhysicalEntity objects

getSeedInteractions

public static Set<Node> getSeedInteractions(Collection<BioPAXElement> elements,
                                            Graph graph)

Extracts the querible interactions from the elements.

Parameters:

elements - BioPAX elements to search

graph - graph model

Returns:

Querible Interactions (nodes)