Index (Graph-Theoretic Querying 5.2.1 API)

A B C D E F G H I L M N O P Q R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values

A

AbstractEdge - Class in org.biopax.paxtools.query.model: The base class for an edge in the traversed graph.
AbstractEdge(Node, Node, Graph) - Constructor for class org.biopax.paxtools.query.model.AbstractEdge: Edges should know their source and target nodes, and their graph.
AbstractGraph - Class in org.biopax.paxtools.query.model: Adapter class for a graph that is queried.
AbstractGraph() - Constructor for class org.biopax.paxtools.query.model.AbstractGraph: Empty constructor that initializes the object map.
AbstractNode - Class in org.biopax.paxtools.query.model
AbstractNode(Graph) - Constructor for class org.biopax.paxtools.query.model.AbstractNode: Constructor with the owner graph.
addAccessor(PathAccessor, Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Adds the given PathAccessor to the list of accessors to use to get field values of objects and their related objects.
addToDownstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Binds the given PhysicalEntity to the downstream.
addToDownstream(PhysicalEntity, Graph) - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Bind the wrapper of the given PhysicalEntity to the downstream.
addToDownstream(PhysicalEntity, Graph) - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Binds the given PhysicalEntity to the downstream.
addToDownstream(PhysicalEntity, Graph) - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Bind the wrapper of the given PhysicalEntity to the downstream.
addToUpstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Bind the wrapper of the given element to the upstream.
addToUpstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Binds the given element to the upstream.
addToUpstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Bind the wrapper of the given element to the upstream.
addToUpstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Binds the given element to the upstream.
addValidValue(String) - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Adds the given valid value to the set of valid values.

B

BACKWARD - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Backward traversal direction.
banned - Variable in class org.biopax.paxtools.query.model.AbstractNode: For saying: "If the algorithm traverses this node, it cannot traverse those others".
BFS - Class in org.biopax.paxtools.query.algorithm: Implements breadth-first search.
BFS() - Constructor for class org.biopax.paxtools.query.algorithm.BFS: Empty constructor for other possible uses.
BFS(Set<Node>, Set<Node>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.BFS: Constructor with all parameters.
BLACK - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Color black indicates that the node was processed.
BOTHSTREAM - Enum constant in enum class org.biopax.paxtools.query.algorithm.Direction
breakCycles() - Method in class org.biopax.paxtools.query.algorithm.CycleBreaker: Run the algorithm.

C

clear() - Method in class org.biopax.paxtools.query.model.AbstractEdge: Does nothing yet.
clear() - Method in class org.biopax.paxtools.query.model.AbstractGraph: Clears memory of all wrapper in the object map.
clear() - Method in class org.biopax.paxtools.query.model.AbstractNode: Resets the path sign.
clear() - Method in interface org.biopax.paxtools.query.model.Graph: Should clear any analysis specific labeling on the graph.
clear() - Method in interface org.biopax.paxtools.query.model.GraphObject: This method should clear any analysis specific labels on the object.
colors - Variable in class org.biopax.paxtools.query.algorithm.BFS: Color labels.
CommonStreamQuery - Class in org.biopax.paxtools.query.algorithm: Searches common downstream or common upstream of a specified set of entities based on the given direction within the boundaries of a specified length limit.
CommonStreamQuery(Collection<Set<Node>>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.CommonStreamQuery: Constructor for Common Stream with Entity States.
CommonStreamQuery(Set<Node>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.CommonStreamQuery: Constructor for Common Stream with Selected Nodes.
ControlWrapper - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for the Control class.
ControlWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for the Control class.
ControlWrapper(Control, Graph) - Constructor for class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Constructor with the Control and the owner graph.
ControlWrapper(Control, Graph) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Constructor with the Control and the owner graph.
conv - Variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Wrapped Conversion.
ConversionWrapper - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for the Conversion class.
ConversionWrapper(Conversion, GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Constructor with the Conversion to wrap and the owner graph.
createFieldAccessors() - Method in class org.biopax.paxtools.query.wrapperL3.DataSourceFilter: Creates the accessor from Entity to its data source name.
createFieldAccessors() - Method in class org.biopax.paxtools.query.wrapperL3.OrganismFilter: Creates the accessor from PhysicalEntity to the organism of related EntityReference.
createFieldAccessors() - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: The child class should populate the list of PathAccessor object using the addAccessor method.
ctrl - Variable in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Wrapped control.
ctrl - Variable in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Wrapped control.
CycleBreaker - Class in org.biopax.paxtools.query.algorithm: When an algorithm searches for a paths between multiple source nodes, or from a source to a target node (source and targets may overlap), sometimes there comes paths from and to the same node, i.e cycles.
CycleBreaker(Set<GraphObject>, Set<Node>, int) - Constructor for class org.biopax.paxtools.query.algorithm.CycleBreaker: Constructor with the objects in the result, source and target nodes, and search limit.

D

DataSourceFilter - Class in org.biopax.paxtools.query.wrapperL3: Filter by data source.
DataSourceFilter(String[]) - Constructor for class org.biopax.paxtools.query.wrapperL3.DataSourceFilter: Constructor.
direction - Variable in class org.biopax.paxtools.query.algorithm.BFS: Whether the direction is FORWARD, it is REVERSE otherwise.
direction - Variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: The direction that the Conversion is wrapped.
Direction - Enum Class in org.biopax.paxtools.query.algorithm: Direction is used for specifying upstream, downstream or both.
dist - Variable in class org.biopax.paxtools.query.algorithm.BFS: Distance labels.
downstream - Variable in class org.biopax.paxtools.query.model.AbstractNode: Set of downstream edges.
DOWNSTREAM - Enum constant in enum class org.biopax.paxtools.query.algorithm.Direction
downstreamInited - Variable in class org.biopax.paxtools.query.model.AbstractNode: Flag to remember if downstream links were created.
DOWNWARD - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Backward traversal direction.

E

Edge - Interface in org.biopax.paxtools.query.model: Wrapper interface for edges in a graph to be queried.
EdgeL3 - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for links between L3 objects.
EdgeL3 - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for links between L3 objects.
EdgeL3(Node, Node, Graph) - Constructor for class org.biopax.paxtools.query.wrapperL3.EdgeL3: Constructor with source and target nodes, and the owner graph.
EdgeL3(Node, Node, Graph) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.EdgeL3: Constructor with source and target nodes, and the owner graph.
emptyOK - Variable in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Option to accept objects if the field is empty or null.
equals(Object) - Method in class org.biopax.paxtools.query.model.AbstractEdge
EventWrapper - Class in org.biopax.paxtools.query.wrapperL3: This is the parent wrapper class for both Conversion and TemplateReaction objects.
EventWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected: This is the parent wrapper class for both Conversion and TemplateReaction objects.
EventWrapper(GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.EventWrapper: Constructor with the owner graph.
EventWrapper(GraphL3Undirected) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Constructor with the owner graph.

F

Filter - Class in org.biopax.paxtools.query.wrapperL3: This is the base filter class that can be applied to any level 3 element.
Filter() - Constructor for class org.biopax.paxtools.query.wrapperL3.Filter
filters - Variable in class org.biopax.paxtools.query.wrapperL3.GraphL3
filters - Variable in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected
FORWARD - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Forward traversal direction.

G

getBanned() - Method in class org.biopax.paxtools.query.model.AbstractNode
getColor(Node) - Method in class org.biopax.paxtools.query.algorithm.BFS: Gets color tag of the node
getControl() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Gets the wrapped Control.
getControl() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Gets the wrapped Control.
getConversion() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
getDescription() - Method in enum class org.biopax.paxtools.query.algorithm.Direction: Gets the description.
getDirection() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
getDownstream() - Method in class org.biopax.paxtools.query.model.AbstractNode: Gets the downstream edges.
getDownstream() - Method in interface org.biopax.paxtools.query.model.Node
getDownstreamInteractions(Collection<Interaction>) - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Gets the downstream interactions among the given set.
getDownstreamNoInit() - Method in class org.biopax.paxtools.query.model.AbstractNode: This class gets the downstream links but does not initialize.
getGraph() - Method in class org.biopax.paxtools.query.model.AbstractEdge
getGraph() - Method in class org.biopax.paxtools.query.model.AbstractNode
getGraph() - Method in interface org.biopax.paxtools.query.model.GraphObject: Every graph object should have an owner graph.
getGraphObject(Object) - Method in class org.biopax.paxtools.query.model.AbstractGraph: Gets the related wrapper for the given object, creates the wrapper if not created before.
getGraphObject(Object) - Method in interface org.biopax.paxtools.query.model.Graph: Gets the wrapper of the related object.
getGraphObject(String) - Method in class org.biopax.paxtools.query.model.AbstractGraph: Gets the wrapper object with its id (key).
getInteraction() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Gets the wrapped TemplateReaction
getKey() - Method in class org.biopax.paxtools.query.model.AbstractEdge
getKey() - Method in interface org.biopax.paxtools.query.model.GraphObject: This method is used for storing the object in a Map.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: RDF ID of the Control is its key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: RDF ID of the Conversion and the direction is used for the key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: RDF ID of the PhysicalEntity is used as key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Uses RDF ID of TemplateReaction as key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: RDF ID of the Control is its key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Uses RDF ID of TemplateReaction as key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: RDF ID of the PhysicalEntity is used as key.
getKey(Object) - Method in class org.biopax.paxtools.query.model.AbstractGraph
getKey(Object) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: RDF IDs of elements is used as key in the object map.
getKey(Object) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: RDF IDs of elements is used as key in the object map.
getLabel(GraphObject) - Method in class org.biopax.paxtools.query.algorithm.BFS: Gets the distance label of the object.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.model.AbstractNode
getLowerEquivalent() - Method in interface org.biopax.paxtools.query.model.Node
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Control cannot have an equivalent.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events do not have equivalent objects.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Control cannot have an equivalent.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events do not have equivalent objects.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper
getModel() - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3
getModel() - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected
getObjectMap() - Method in class org.biopax.paxtools.query.model.AbstractGraph
getPathSign() - Method in class org.biopax.paxtools.query.model.AbstractNode
getPhysicalEntity() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
getPhysicalEntity() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper
getRelatedPhysicalEntities(BioPAXElement, Set<PhysicalEntity>) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the related PhysicalEntity objects of the given BioPAXElement, in level 3 models.
getRelatedPhysicalEntityMap(Collection<BioPAXElement>) - Static method in class org.biopax.paxtools.query.QueryExecuter: Maps each BioPAXElement to its related PhysicalEntity objects.
getReverse() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
getSeedInteractions(Collection<BioPAXElement>, Graph) - Static method in class org.biopax.paxtools.query.QueryExecuter: Extracts the querible interactions from the elements.
getSign() - Method in class org.biopax.paxtools.query.model.AbstractEdge: Edges are positive by default.
getSign() - Method in interface org.biopax.paxtools.query.model.Edge: Algorithms may need a sign for the edge.
getSign() - Method in interface org.biopax.paxtools.query.model.Node: Some nodes can have a sign (typically non-breadth nodes).
getSign() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper
getSign() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events have a positive sign.
getSign() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: PhysicalEntity have positive sign.
getSign() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper
getSign() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events have a positive sign.
getSign() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: PhysicalEntity have positive sign.
getSourceNode() - Method in class org.biopax.paxtools.query.model.AbstractEdge
getSourceNode() - Method in interface org.biopax.paxtools.query.model.Edge
getTargetNode() - Method in class org.biopax.paxtools.query.model.AbstractEdge
getTargetNode() - Method in interface org.biopax.paxtools.query.model.Edge
getTempReac() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Gets the wrapped TemplateReaction
getUpperEquivalent() - Method in class org.biopax.paxtools.query.model.AbstractNode
getUpperEquivalent() - Method in interface org.biopax.paxtools.query.model.Node
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Control cannot have an equivalent.
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events do not have equivalent objects.
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Control cannot have an equivalent.
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events do not have equivalent objects.
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper
getUpstream() - Method in class org.biopax.paxtools.query.model.AbstractNode: Gets the upstream edges.
getUpstream() - Method in interface org.biopax.paxtools.query.model.Node
getUpstreamConversions(Collection<Interaction>) - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Gets the conversions at the upstream of this PhysicalEntity.
getUpstreamNoInit() - Method in class org.biopax.paxtools.query.model.AbstractNode: This class gets the upstream links but does not initialize.
getWrappedSet(Set<? extends GraphObject>) - Method in interface org.biopax.paxtools.query.model.Graph: Gets the wrapped objects of the given wrapper set.
getWrappedSet(Set<? extends GraphObject>) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: Gets the wrapped objects of the given wrappers.
getWrappedSet(Set<? extends GraphObject>) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Gets the wrapped objects of the given wrappers.
getWrapperMap(Set<?>) - Method in interface org.biopax.paxtools.query.model.Graph: Gets a map from objects to their wrappers.
getWrapperMap(Set<?>) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: Gets an element-to-wrapper map for the given elements.
getWrapperMap(Set<?>) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Gets an element-to-wrapper map for the given elements.
getWrapperSet(Set<?>) - Method in interface org.biopax.paxtools.query.model.Graph: Gets the set of wrappers for the given wrapped object set.
getWrapperSet(Set<?>) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: Gets wrappers of given elements
getWrapperSet(Set<?>) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Gets wrappers of given elements
graph - Variable in class org.biopax.paxtools.query.model.AbstractNode: Owner graph.
Graph - Interface in org.biopax.paxtools.query.model: This graph interface is used in graph algorithms.
GraphL3 - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for L3 Graphs.
GraphL3(Model, Filter...) - Constructor for class org.biopax.paxtools.query.wrapperL3.GraphL3: Constructor with the model and the IDs of the ubiquitous molecules.
GraphL3Undirected - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for L3 Graphs.
GraphL3Undirected(Model, Filter...) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Constructor with the model and the IDs of the ubiquitous molecules.
GraphObject - Interface in org.biopax.paxtools.query.model: A graph object is the common interface for nodes and edges in a graph.
GRAY - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Color gray indicates that the node is in queue waiting to be procecessed.

H

hashCode() - Method in class org.biopax.paxtools.query.model.AbstractEdge

I

init() - Method in class org.biopax.paxtools.query.model.AbstractNode: Does nothing yet.
init() - Method in interface org.biopax.paxtools.query.model.Node: Initializes the node.
init() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Extracts the sign and the type of the Control.
init() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Extracts the direction, creates the reverse if necessary.
init() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Extracts the sign and the type of the Control.
initBanned() - Method in class org.biopax.paxtools.query.model.AbstractNode: Initializes the set of banned nodes.
initDownstream() - Method in class org.biopax.paxtools.query.model.AbstractNode: Initializes the downstream connections.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Binds the controlled objects.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Binds products.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Binds to downstream interactions.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Binds to products.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Binds the controlled objects.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Binds to participants and controllers.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Binds to downstream interactions.
initLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Finds member nodes if this is a homology node
initLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Finds member nodes if this is a homology node
initMaps() - Method in class org.biopax.paxtools.query.algorithm.BFS: Initializes maps used during query.
initUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Finds homology parent.
initUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Finds homology parent.
initUpstream() - Method in class org.biopax.paxtools.query.model.AbstractNode: Initializes the upstream connections.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Binds the controller and other Controls that controls this control.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Binds inputs and controllers.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Binds to upstream interactions.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Binds to template and controllers.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Binds the controller and other Controls that controls this control.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Binds to participants and controllers.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Binds to upstream interactions.
InteractionWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for Interaction class, excluding Control objects.
InteractionWrapper(Interaction, GraphL3Undirected) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Constructor with the Interaction and the owner graph.
isBreadthNode() - Method in interface org.biopax.paxtools.query.model.Node: This method is critical when the algorithm needs to calculate a path length.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Control is not a breadth node.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events are not breadth nodes.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: PhysicalEntity is a breadth node.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Control is not a breadth node.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events are not breadth nodes.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: PhysicalEntity is a breadth node.
isEmptyOK() - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Gets the option to accept empty fields.
isEquivalentInTheSet(Node, boolean, Set<Node>) - Method in class org.biopax.paxtools.query.algorithm.BFS: Checks if an equivalent of the given node is in the set.
isEquivalentInTheSet(Node, Set<Node>) - Method in class org.biopax.paxtools.query.algorithm.BFS: Checks if an equivalent of the given node is in the set.
isSafe(Node, Edge) - Method in class org.biopax.paxtools.query.algorithm.CycleBreaker: Checks whether an edge is on an unwanted cycle.
isTranscription() - Method in class org.biopax.paxtools.query.model.AbstractNode: Nodes are not transcription by default.
isTranscription() - Method in interface org.biopax.paxtools.query.model.Edge
isTranscription() - Method in interface org.biopax.paxtools.query.model.Node: A node may be related to a transcription and an algorithm can depend on this information.
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.EdgeL3
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Say if the event is a transcription.
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: This is transcription.
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EdgeL3
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Say if the event is a transcription.
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Being a transcription is not relevant in the undirected context.
isUbique() - Method in interface org.biopax.paxtools.query.model.Node: In biological graphs, some nodes are used ubiquitously like ATP, H2O, etc.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Controls are not ubiquitous molecules.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events are not ubiquitous molecules.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Controls are not ubiquitous molecules.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events are not ubiquitous molecules.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper

L

labelEquivRecursive(Node, boolean, int, boolean, boolean) - Method in class org.biopax.paxtools.query.algorithm.BFS: Labels equivalent nodes recursively.
LEFT_TO_RIGHT - Static variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Direction LEFT_TO_RIGHT.
limit - Variable in class org.biopax.paxtools.query.algorithm.BFS: Stop distance.
LimitType - Enum Class in org.biopax.paxtools.query.algorithm: Specifies whether the length limit is a normal limit or shortest_plus_k limit.
log - Variable in class org.biopax.paxtools.query.wrapperL3.GraphL3: Log for logging.
log - Variable in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Log for logging.
lowerEquivalent - Variable in class org.biopax.paxtools.query.model.AbstractNode: If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the child equivalents of this node.
lowerEquivalentInited - Variable in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Flag to remember if child equivalents initialized.
lowerEquivalentInited - Variable in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Flag to remember if child equivalents initialized.

M

model - Variable in class org.biopax.paxtools.query.wrapperL3.GraphL3: The model to be wrapped.
model - Variable in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: The model to be wrapped.

N

NEGATIVE - Static variable in interface org.biopax.paxtools.query.model.Node: Negative sign.
NeighborhoodQuery - Class in org.biopax.paxtools.query.algorithm: Searches the neighborhood of given source set of nodes
NeighborhoodQuery(Set<Node>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.NeighborhoodQuery: Constructor with parameters.
NEUTRAL - Static variable in interface org.biopax.paxtools.query.model.Node: Neutral sign.
Node - Interface in org.biopax.paxtools.query.model: Node interface to use in graph algorithms.
NORMAL - Enum constant in enum class org.biopax.paxtools.query.algorithm.LimitType

O

objectMap - Variable in class org.biopax.paxtools.query.model.AbstractGraph: Objects are stored in this map.
okToTraverse(Level3Element) - Method in class org.biopax.paxtools.query.wrapperL3.Filter: Checks if it is ok to traverse the given level 3 element.
okToTraverse(Level3Element) - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Checks if the related values of the object are among valid values.
okToTraverse(Level3Element) - Method in class org.biopax.paxtools.query.wrapperL3.UbiqueFilter: Checks if the ID of the given element is in the black list.
org.biopax.paxtools.query - package 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.algorithm - package org.biopax.paxtools.query.algorithm: This package contains the SIF rules for BioPAX Level 3.
org.biopax.paxtools.query.model - package org.biopax.paxtools.query.model: This package contains the SIF rules for BioPAX Level 3.
org.biopax.paxtools.query.wrapperL3 - package org.biopax.paxtools.query.wrapperL3: This package contains TODO annotate!
org.biopax.paxtools.query.wrapperL3undirected - package org.biopax.paxtools.query.wrapperL3undirected: This package contains TODO annotate!
OrganismFilter - Class in org.biopax.paxtools.query.wrapperL3: Filter by organism.
OrganismFilter(String[]) - Constructor for class org.biopax.paxtools.query.wrapperL3.OrganismFilter: Constructor.

P

PathsBetweenQuery - Class in org.biopax.paxtools.query.algorithm: Finds the paths between the specified source set of states within the boundaries of a specified length limit.
PathsBetweenQuery(Collection<Set<Node>>, int) - Constructor for class org.biopax.paxtools.query.algorithm.PathsBetweenQuery: Constructor with parameters
PathsFromToQuery - Class in org.biopax.paxtools.query.algorithm: Finds the paths from a specified source set of states or entities to a specified target set of states or entities within the boundaries of a specified length limit.
PathsFromToQuery(Set<Node>, Set<Node>, LimitType, int, boolean) - Constructor for class org.biopax.paxtools.query.algorithm.PathsFromToQuery: Constructor with parameters.
pathSign - Variable in class org.biopax.paxtools.query.model.AbstractNode: This variable can be used by algorithms that need to label nodes with a path sign (typically the current path).
pe - Variable in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Wrapped PhysicalEntity.
pe - Variable in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Wrapped PhysicalEntity.
PhysicalEntityWrapper - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for PhysicalEntity.
PhysicalEntityWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for PhysicalEntity.
PhysicalEntityWrapper(PhysicalEntity, GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Constructor with the wrapped PhysicalEntity and the owner graph.
PhysicalEntityWrapper(PhysicalEntity, GraphL3Undirected) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Constructor with the wrapped PhysicalEntity and the owner graph.
POSITIVE - Static variable in interface org.biopax.paxtools.query.model.Node: Positive sign.
prepareSingleNodeSet(Set<BioPAXElement>, Graph) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the related wrappers of the given elements in a set.
prepareSingleNodeSetFromSets(Set<Set<BioPAXElement>>, Graph) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the related wrappers of the given elements in the sets.
processNode(Node) - Method in class org.biopax.paxtools.query.algorithm.BFS: Processes a node.
processNode2(Node) - Method in class org.biopax.paxtools.query.algorithm.CycleBreaker: Continue the search from the node.
Prune - Class in org.biopax.paxtools.query.algorithm: This algorithm is used internally by PathsBetween and PathsFromTo algorithms.
Prune(Set<GraphObject>, Set<Node>) - Constructor for class org.biopax.paxtools.query.algorithm.Prune: Constructor with the input.

Q

QueryExecuter - Class in org.biopax.paxtools.query: This class provides static methods to execute graph queries.
QueryExecuter() - Constructor for class org.biopax.paxtools.query.QueryExecuter
queue - Variable in class org.biopax.paxtools.query.algorithm.BFS: BFS queue.

R

replaceXrefsWithRelatedER(Collection<BioPAXElement>) - Static method in class org.biopax.paxtools.query.QueryExecuter: Replaces Xref objects with the related EntityReference objects.
RIGHT_TO_LEFT - Static variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Direction RIGHT_TO_LEFT.
run() - Method in class org.biopax.paxtools.query.algorithm.BFS: Executes the algorithm.
run() - Method in class org.biopax.paxtools.query.algorithm.CommonStreamQuery: Method to run the query.
run() - Method in class org.biopax.paxtools.query.algorithm.NeighborhoodQuery: Executes the query.
run() - Method in class org.biopax.paxtools.query.algorithm.PathsBetweenQuery
run() - Method in class org.biopax.paxtools.query.algorithm.PathsFromToQuery: Executes the algorithm.
run() - Method in class org.biopax.paxtools.query.algorithm.Prune: Executes the algorithm.
runCommonStream(Set<BioPAXElement>, Model, Direction, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the elements in the common upstream or downstream of the seed
runCommonStreamMultiSet(Set<Set<BioPAXElement>>, Model, Direction, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the elements in the common upstream or downstream of the seed
runCommonStreamWithPOI(Set<BioPAXElement>, Model, Direction, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: First finds the common stream, then completes it with the paths between seed and common stream.
runCommonStreamWithPOIMultiSet(Set<Set<BioPAXElement>>, Model, Direction, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: First finds the common stream, then completes it with the paths between seed and common stream.
runGOI(Set<BioPAXElement>, Model, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Deprecated.
Use runPathsBetween instead
runNeighborhood(Set<BioPAXElement>, Model, int, Direction, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets neighborhood of the source set.
runNeighborhoodMultiSet(Set<Set<BioPAXElement>>, Model, int, Direction, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets neighborhood of the source set.
runPathsBetween(Set<BioPAXElement>, Model, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the graph constructed by the paths between the given seed nodes.
runPathsBetweenMultiSet(Set<Set<BioPAXElement>>, Model, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the graph constructed by the paths between the given seed nodes.
runPathsFromTo(Set<BioPAXElement>, Set<BioPAXElement>, Model, LimitType, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets paths the graph composed of the paths from a source node, and ends at a target node.
runPathsFromToMultiSet(Set<Set<BioPAXElement>>, Set<Set<BioPAXElement>>, Model, LimitType, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets paths the graph composed of the paths from a source node, and ends at a target node.

S

setBanned(Set<Node>) - Method in class org.biopax.paxtools.query.model.AbstractNode
setColor(Node, int) - Method in class org.biopax.paxtools.query.algorithm.BFS: Sets color tag
setEmptyOK(boolean) - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Sets the parameter to accept empty field values.
setLabel(GraphObject, int) - Method in class org.biopax.paxtools.query.algorithm.BFS: Sets the distance label.
setPathSign(int) - Method in class org.biopax.paxtools.query.model.AbstractNode
setTranscription(boolean) - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Make or not make this control related to a transcription.
setTranscription(boolean) - Method in class org.biopax.paxtools.query.wrapperL3.EdgeL3: Set the transcription flag.
setTranscription(boolean) - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Make or not make this control related to a transcription.
setTranscription(boolean) - Method in class org.biopax.paxtools.query.wrapperL3undirected.EdgeL3: Set the transcription flag.
setUbique(boolean) - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Set the ubique flag.
setUbique(boolean) - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Set the ubique flag.
SHORTEST_PLUS_K - Enum constant in enum class org.biopax.paxtools.query.algorithm.LimitType
sign - Variable in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Sign of the control.
sign - Variable in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Sign of the control.
sourceSet - Variable in class org.biopax.paxtools.query.algorithm.BFS: BFS starts from source nodes.
stopSet - Variable in class org.biopax.paxtools.query.algorithm.BFS: BFS will not further traverse neighbors of any node in the stopSet.
StringFieldFilter - Class in org.biopax.paxtools.query.wrapperL3: This is the base class for filters that are filtering based on values of specific fields of the objects and their related objects.
StringFieldFilter(boolean, String[]) - Constructor for class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Constructor.

T

TemplateReactionWrapper - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for TemplateReaction class.
TemplateReactionWrapper(TemplateReaction, GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Constructor with the TemplateReaction and the owner graph.
toString() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
toString() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
toString() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper
transcription - Variable in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Flag to indicate if this control is related to a transcription.
transcription - Variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Flag to say this Conversion is a transcription.
transcription - Variable in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Flag to indicate if this control is related to a transcription.

U

ubique - Variable in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Flag to say this is a ubiquitous molecule.
ubique - Variable in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Flag to say this is a ubiquitous molecule.
UbiqueFilter - Class in org.biopax.paxtools.query.wrapperL3: Filters out ubiquitous entities, whose IDs are supplied by user.
UbiqueFilter(Set<String>) - Constructor for class org.biopax.paxtools.query.wrapperL3.UbiqueFilter: Constructor.
UNDIRECTED - Enum constant in enum class org.biopax.paxtools.query.algorithm.Direction
upperEquivalent - Variable in class org.biopax.paxtools.query.model.AbstractNode: If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the parent equivalents of this node.
upperEquivalentInited - Variable in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Flag to remember if parent equivalents initialized.
upperEquivalentInited - Variable in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Flag to remember if parent equivalents initialized.
upstream - Variable in class org.biopax.paxtools.query.model.AbstractNode: Set of upstream edges.
UPSTREAM - Enum constant in enum class org.biopax.paxtools.query.algorithm.Direction
upstreamInited - Variable in class org.biopax.paxtools.query.model.AbstractNode: Flag to remember if upstream links were created.
UPWARD - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Forward traversal direction.

V

valueOf(String) - Static method in enum class org.biopax.paxtools.query.algorithm.Direction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.query.algorithm.LimitType: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.biopax.paxtools.query.algorithm.Direction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.query.algorithm.LimitType: Returns an array containing the constants of this enum class, in the order they are declared.

W

WHITE - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Color white indicates the node is not processed.
wrap(Object) - Method in class org.biopax.paxtools.query.model.AbstractGraph: Creates the wrapper for the given object.
wrap(Object) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: This method creates a wrapper for every wrappable L3 element.
wrap(Object) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: This method creates a wrapper for every wrappable L3 element.

A B C D E F G H I L M N O P Q R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values