Package | Description |
---|---|
org.biopax.paxtools.query |
Graph-theoretic querying module in Paxtools is used for identifying paths between molecules or identifying other
molecules that is reachable through some specific paths using the BioPAX data model.
|
org.biopax.paxtools.query.wrapperL3 |
This package contains TODO annotate!
|
org.biopax.paxtools.query.wrapperL3undirected |
This package contains TODO annotate!
|
Modifier and Type | Method and Description |
---|---|
static Set<BioPAXElement> |
QueryExecuter.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> |
QueryExecuter.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> |
QueryExecuter.runGOI(Set<BioPAXElement> sourceSet,
Model model,
int limit,
Filter... filters)
Deprecated.
Use runPathsBetween instead
|
static Set<BioPAXElement> |
QueryExecuter.runNeighborhood(Set<BioPAXElement> sourceSet,
Model model,
int limit,
Direction direction,
Filter... filters)
Gets neighborhood of the source set.
|
static Set<BioPAXElement> |
QueryExecuter.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> |
QueryExecuter.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.
|
Modifier and Type | Class and Description |
---|---|
class |
DataSourceFilter
Filter by data source.
|
class |
OrganismFilter
Filter by organism.
|
class |
StringFieldFilter
This is the base class for filters that are filtering based on values of specific fields of the
objects and their related objects.
|
class |
UbiqueFilter
Filters out ubiquitous entities, whose IDs are supplied by user.
|
Modifier and Type | Field and Description |
---|---|
protected List<Filter> |
GraphL3.filters |
Constructor and Description |
---|
GraphL3(Model model,
Filter... filters)
Constructor with the model and the IDs of the ubiquitous molecules.
|
Modifier and Type | Field and Description |
---|---|
protected List<Filter> |
GraphL3Undirected.filters |
Constructor and Description |
---|
GraphL3Undirected(Model model,
Filter... filters)
Constructor with the model and the IDs of the ubiquitous molecules.
|
Copyright © 2015 BioPAX. All rights reserved.