Uses of Class
org.biopax.paxtools.query.wrapperL3.Filter

Packages that use Filter

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!

Uses of Filter in org.biopax.paxtools.query

Methods in org.biopax.paxtools.query with parameters of type Filter

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.

Uses of Filter in org.biopax.paxtools.query.wrapperL3

Subclasses of Filter in org.biopax.paxtools.query.wrapperL3

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.

Fields in org.biopax.paxtools.query.wrapperL3 with type parameters of type Filter

Modifier and Type	Field and Description
protected List<Filter>	GraphL3.filters

Constructors in org.biopax.paxtools.query.wrapperL3 with parameters of type Filter

Constructor and Description
GraphL3(Model model, Filter... filters) Constructor with the model and the IDs of the ubiquitous molecules.

Uses of Filter in org.biopax.paxtools.query.wrapperL3undirected

Fields in org.biopax.paxtools.query.wrapperL3undirected with type parameters of type Filter

Modifier and Type	Field and Description
protected List<Filter>	GraphL3Undirected.filters

Constructors in org.biopax.paxtools.query.wrapperL3undirected with parameters of type Filter

Constructor and Description
GraphL3Undirected(Model model, Filter... filters) Constructor with the model and the IDs of the ubiquitous molecules.