A B C D E F G H I L M N O P Q R S T U V W

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(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.

addToDownstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper

Binds 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(Set<Node>, Set<Node>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.BFS

Constructor with all parameters.

BFS() - Constructor for class org.biopax.paxtools.query.algorithm.BFS

Empty constructor for other possible uses.

BLACK - Static variable in class org.biopax.paxtools.query.algorithm.BFS

Color black indicates that the node was processed.

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(Set<Node>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.CommonStreamQuery

Constructor for Common Stream with Selected Nodes.

CommonStreamQuery(Collection<Set<Node>>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.CommonStreamQuery

Constructor for Common Stream with Entity States.

ControlWrapper - Class in org.biopax.paxtools.query.wrapperL3

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 - Class in org.biopax.paxtools.query.wrapperL3undirected

Wrapper for the Control class.

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 - Enum in org.biopax.paxtools.query.algorithm

Direction is used for specifying upstream, downstream or both.

direction - Variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper

The direction that the Conversion is wrapped.

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.

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(Node, Node, Graph) - Constructor for class org.biopax.paxtools.query.wrapperL3.EdgeL3

Constructor with source and target nodes, and the owner graph.

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.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(GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.EventWrapper

Constructor with the owner graph.

EventWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected

This is the parent wrapper class for both Conversion and TemplateReaction objects.

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 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(String) - Method in class org.biopax.paxtools.query.model.AbstractGraph

Gets the wrapper object with its id (key).

getGraphObject(Object) - Method in interface org.biopax.paxtools.query.model.Graph

Gets the wrapper of the related object.

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(Object) - Method in class org.biopax.paxtools.query.model.AbstractGraph

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(Object) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3

RDF IDs of elements is used as key in the object map.

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(Object) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected

RDF IDs of elements is used as key in the object map.

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.

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, 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, boolean, 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 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.

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(PhysicalEntity, GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper

Constructor with the wrapped PhysicalEntity and the owner graph.

PhysicalEntityWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected

Wrapper for PhysicalEntity.

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.

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

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.

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.

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.

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.

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.

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.

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.

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 org.biopax.paxtools.query.algorithm.Direction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.query.algorithm.LimitType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biopax.paxtools.query.algorithm.Direction

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.query.algorithm.LimitType

Returns an array containing the constants of this enum type, 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.

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