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java.lang.Object org.biopax.paxtools.query.QueryExecuter
public class QueryExecuter
Constructor Summary | |
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QueryExecuter()
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Method Summary | |
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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. |
static Map<BioPAXElement,Set<PhysicalEntity>> |
getRelatedPhysicalEntityMap(Collection<BioPAXElement> elements)
Maps each BioPAXElement to its related PhysicalEntity objects. |
static Set<Node> |
prepareSingleNodeSet(Set<BioPAXElement> elements,
Graph graph)
Gets the related physical entities and wraps in a single node set. |
static Set<BioPAXElement> |
runCommonStream(Set<BioPAXElement> sourceSet,
Model model,
Direction direction,
int limit)
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static Set<BioPAXElement> |
runCommonStream(Set<BioPAXElement> sourceSet,
Model model,
Direction direction,
int limit,
Set<String> ubiqueIDs)
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)
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static Set<BioPAXElement> |
runCommonStreamWithPOI(Set<BioPAXElement> sourceSet,
Model model,
Direction direction,
int limit,
Set<String> ubiqueIDs)
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)
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static Set<BioPAXElement> |
runGOI(Set<BioPAXElement> sourceSet,
Model model,
int limit,
Set<String> ubiqueIDs)
Gets paths between the seed nodes. |
static Set<BioPAXElement> |
runNeighborhood(Set<BioPAXElement> sourceSet,
Model model,
int limit,
Direction direction)
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static Set<BioPAXElement> |
runNeighborhood(Set<BioPAXElement> sourceSet,
Model model,
int limit,
Direction direction,
Set<String> ubiqueIDs)
Gets neighborhood of the source set. |
static Set<BioPAXElement> |
runPathsBetween(Set<BioPAXElement> sourceSet,
Model model,
int limit)
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static Set<BioPAXElement> |
runPathsBetween(Set<BioPAXElement> sourceSet,
Model model,
int limit,
Set<String> ubiqueIDs)
Gets the graph constructed by the paths between the given seed nodes. |
static Set<BioPAXElement> |
runPOI(Set<BioPAXElement> sourceSet,
Set<BioPAXElement> targetSet,
Model model,
LimitType limitType,
int limit)
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static Set<BioPAXElement> |
runPOI(Set<BioPAXElement> sourceSet,
Set<BioPAXElement> targetSet,
Model model,
LimitType limitType,
int limit,
Set<String> ubiqueIDs)
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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public QueryExecuter()
Method Detail |
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public static Set<BioPAXElement> runNeighborhood(Set<BioPAXElement> sourceSet, Model model, int limit, Direction direction)
runNeighborhood(java.util.Set, org.biopax.paxtools.model.Model, int, org.biopax.paxtools.query.algorithm.Direction)
public static Set<BioPAXElement> runNeighborhood(Set<BioPAXElement> sourceSet, Model model, int limit, Direction direction, Set<String> ubiqueIDs)
sourceSet
- seed to the querymodel
- BioPAX modellimit
- neigborhood distance to getdirection
- UPSTREAM, DOWNSTREAM or BOTHSTREAMubiqueIDs
- RDF IDs of ubiquitous entity references. can be null
public static Set<BioPAXElement> runPathsBetween(Set<BioPAXElement> sourceSet, Model model, int limit)
runPathsBetween(java.util.Set, org.biopax.paxtools.model.Model, int)
public static Set<BioPAXElement> runPathsBetween(Set<BioPAXElement> sourceSet, Model model, int limit, Set<String> ubiqueIDs)
sourceSet
- Seed to the querymodel
- BioPAX modellimit
- Length limit for the paths to be foundubiqueIDs
- RDF IDs of ubiquitous PEs. Can be null
public static Set<BioPAXElement> runGOI(Set<BioPAXElement> sourceSet, Model model, int limit)
runGOI(java.util.Set, org.biopax.paxtools.model.Model, int)
public static Set<BioPAXElement> runGOI(Set<BioPAXElement> sourceSet, Model model, int limit, Set<String> ubiqueIDs)
sourceSet
- Seed to the querymodel
- BioPAX modellimit
- Length limit for the paths to be foundubiqueIDs
- RDF IDs of the ubiquitous physical entities. Can be null
public static Set<BioPAXElement> runPOI(Set<BioPAXElement> sourceSet, Set<BioPAXElement> targetSet, Model model, LimitType limitType, int limit)
runPOI(java.util.Set, java.util.Set, org.biopax.paxtools.model.Model, org.biopax.paxtools.query.algorithm.LimitType, int)
public static Set<BioPAXElement> runPOI(Set<BioPAXElement> sourceSet, Set<BioPAXElement> targetSet, Model model, LimitType limitType, int limit, Set<String> ubiqueIDs)
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 foundubiqueIDs
- RDF IDs of the ubiquitous physical entities. Can be null
public static Set<BioPAXElement> runCommonStream(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit)
runCommonStream(java.util.Set, org.biopax.paxtools.model.Model, org.biopax.paxtools.query.algorithm.Direction, int)
public static Set<BioPAXElement> runCommonStream(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Set<String> ubiqueIDs)
sourceSet
- Seed to the querymodel
- BioPAX modeldirection
- UPSTREAM or DOWNSTREAMlimit
- Length limit for the searchubiqueIDs
- RDF IDs of the ubiquitous physical entities. Can be null
public static Set<BioPAXElement> runCommonStreamWithPOI(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit)
runCommonStreamWithPOI(java.util.Set, org.biopax.paxtools.model.Model, org.biopax.paxtools.query.algorithm.Direction, int, java.util.Set)
public static Set<BioPAXElement> runCommonStreamWithPOI(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Set<String> ubiqueIDs)
sourceSet
- Seed to the querymodel
- BioPAX modeldirection
- UPSTREAM or DOWNSTREAMlimit
- Length limit for the searchubiqueIDs
- RDF IDs of the ubiquitous physical entities. Can be null
public static Set<Node> prepareSingleNodeSet(Set<BioPAXElement> elements, Graph graph)
elements
- graph
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public static Map<BioPAXElement,Set<PhysicalEntity>> getRelatedPhysicalEntityMap(Collection<BioPAXElement> elements)
elements
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public static Set<PhysicalEntity> getRelatedPhysicalEntities(BioPAXElement element, Set<PhysicalEntity> pes)
element
- to get related PhysicalEntity objectspes
- result set. if not supplied, a new set will be initialized.
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