public class QueryExecuter extends Object
Constructor and Description |
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QueryExecuter() |
Modifier and Type | Method and Description |
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static Set<PhysicalEntity> |
getRelatedPhysicalEntities(BioPAXElement element,
Set<PhysicalEntity> pes)
Gets the related PhysicalEntity objects of the given BioPAXElement, in level 3 models.
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static Map<BioPAXElement,Set<PhysicalEntity>> |
getRelatedPhysicalEntityMap(Collection<BioPAXElement> elements)
Maps each BioPAXElement to its related PhysicalEntity objects.
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static Set<Node> |
getSeedInteractions(Collection<BioPAXElement> elements,
Graph graph)
Extracts the querible interactions from the elements.
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static Set<Node> |
prepareSingleNodeSet(Set<BioPAXElement> elements,
Graph graph)
Gets the related wrappers of the given elements in a set.
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protected static void |
replaceXrefsWithRelatedER(Collection<BioPAXElement> elements)
Replaces Xref objects with the related EntityReference objects.
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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
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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.
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static Set<BioPAXElement> |
runGOI(Set<BioPAXElement> sourceSet,
Model model,
int limit,
Filter... filters)
Deprecated.
Use runPathsBetween instead
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static Set<BioPAXElement> |
runNeighborhood(Set<BioPAXElement> sourceSet,
Model model,
int limit,
Direction direction,
Filter... filters)
Gets neighborhood of the source set.
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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.
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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.
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public QueryExecuter()
public static Set<BioPAXElement> runNeighborhood(Set<BioPAXElement> sourceSet, Model model, int limit, Direction direction, Filter... filters)
sourceSet
- seed to the querymodel
- BioPAX modellimit
- neigborhood distance to getdirection
- UPSTREAM, DOWNSTREAM or BOTHSTREAMfilters
- for filtering graph elementspublic static Set<BioPAXElement> runPathsBetween(Set<BioPAXElement> sourceSet, Model model, int limit, Filter... filters)
sourceSet
- Seed to the querymodel
- BioPAX modellimit
- Length limit for the paths to be foundfilters
- optional filters - for filtering graph elementspublic static Set<BioPAXElement> runGOI(Set<BioPAXElement> sourceSet, Model model, int limit, Filter... filters)
sourceSet
- Seed to the querymodel
- BioPAX modellimit
- Length limit for the paths to be foundfilters
- for filtering graph elementspublic static Set<BioPAXElement> runPathsFromTo(Set<BioPAXElement> sourceSet, Set<BioPAXElement> targetSet, Model model, LimitType limitType, int limit, Filter... filters)
sourceSet
- Seeds for start points of pathstargetSet
- Seeds for end points of pathsmodel
- BioPAX modellimitType
- either NORMAL or SHORTEST_PLUS_Klimit
- Length limit fothe paths to be foundfilters
- for filtering graph elementspublic static Set<BioPAXElement> runCommonStream(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Filter... filters)
sourceSet
- Seed to the querymodel
- BioPAX modeldirection
- UPSTREAM or DOWNSTREAMlimit
- Length limit for the searchfilters
- for filtering graph elementspublic static Set<BioPAXElement> runCommonStreamWithPOI(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Filter... filters)
sourceSet
- Seed to the querymodel
- BioPAX modeldirection
- UPSTREAM or DOWNSTREAMlimit
- Length limit for the searchfilters
- for filtering graph elementspublic static Set<Node> prepareSingleNodeSet(Set<BioPAXElement> elements, Graph graph)
elements
- Elements to get the related wrappersgraph
- Owner graphpublic static Map<BioPAXElement,Set<PhysicalEntity>> getRelatedPhysicalEntityMap(Collection<BioPAXElement> elements)
elements
- Elements to mapprotected static void replaceXrefsWithRelatedER(Collection<BioPAXElement> elements)
elements
- elements to send to a query as source or targetpublic static Set<PhysicalEntity> getRelatedPhysicalEntities(BioPAXElement element, Set<PhysicalEntity> pes)
element
- Element to get related PhysicalEntity objectspes
- Result set. If not supplied, a new set will be initialized.public static Set<Node> getSeedInteractions(Collection<BioPAXElement> elements, Graph graph)
elements
- BioPAX elements to searchgraph
- graph modelCopyright © 2015 BioPAX. All rights reserved.