A C D E G H I M N O P R S T U

A

abstractingModeler - Variable in class org.isb.metanodes.actions.CollapseSelectedNodesAction

abstractingModeler - Variable in class org.isb.metanodes.actions.UncollapseSelectedNodesAction

AbstractMetaNodeAttsHandler - Class in org.isb.metanodes.data

Specialized version of SimpleMetaNodeAttributesHandler.
1.

AbstractMetaNodeAttsHandler() - Constructor for class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

Constructor.

AbstractMetaNodeModeler - Class in org.isb.metanodes.model

This class models meta-nodes by abstracting the graphs that compose meta-nodes into single nodes that can be 'collapsed' or 'expanded'.

AbstractMetaNodeModeler(RootGraph) - Constructor for class org.isb.metanodes.model.AbstractMetaNodeModeler

Since there should only be one AbstractMetaNodeModeler per/Cytoscape, the constructor is protected; use MetaNodeModelerFactory.getCytoscapeAbstractMetaNodeModeler(); to get an instance.

abstractModeler - Static variable in class org.isb.metanodes.MetaNodeUtils

The object that modifies the network model to collapse and expand metanodes, not recommended to use unless you know what you are doing

ActionFactory - Class in org.isb.metanodes.actions

This class creates and returns AbstractActions that can be added to GUI elements for applying meta-node operations to a graph.

ActionFactory() - Constructor for class org.isb.metanodes.actions.ActionFactory

actionPerformed(ActionEvent) - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Implements AbstractAction.actionPerformed by calling CollapseSelectedNodesAction.collapseSelectedNodes

actionPerformed(ActionEvent) - Method in class org.isb.metanodes.actions.UncollapseSelectedNodesAction

Implements AbstractAction.actionPerformed by calling uncollapseSelectedNodes

apply(int, int) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler.CopyEdgeAttr

applyModel() - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Applies the model to the CyNetwork TODO: Why does this not take a CyNetwork????

applyModel(CyNetwork, CyNode) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Applies the model to the given CyNode.

applyModel(CyNetwork, CyNode, List) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Applies the model to the given CyNode.

assignDefaultName - Variable in class org.isb.metanodes.model.GPMetaNodeFactory

Specifies whether or not this class should assign a name to newly created meta-nodes

assignDefaultName(CyNetwork, CyNode) - Method in class org.isb.metanodes.model.GPMetaNodeFactory

Creates a new name of the form MetaNode_ and adds an object-name mapping in the node attributes contained in CyNetwork for the given node.

assignDefaultNames(boolean) - Method in class org.isb.metanodes.model.GPMetaNodeFactory

Sets whether or not a default name for newly created meta-nodes should be given

assignDefaultNames(boolean) - Static method in class org.isb.metanodes.model.MetaNodeFactory

Sets whether or not a default name for newly created meta-nodes should be given and added to the node attributes.

assignName(CyNetwork, CyNode) - Method in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

Assigns a canonical name and a common name to the given node.

assignName(CyNetwork, CyNode) - Method in interface org.isb.metanodes.data.MetaNodeAttributesHandler

Creates a unique name for the CyNode and registers this name and node into Cytoscape

assignName(CyNetwork, CyNode) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

Transfers all children names to meta node name

attributesHandler - Variable in class org.isb.metanodes.model.GPMetaNodeFactory

The MetaNodeAttributesHandler that names newly created meta-nodes

C

CHILD_OF_EDGE_INTERACTION - Static variable in class org.isb.metanodes.model.AbstractMetaNodeModeler

clear() - Method in class org.isb.metanodes.model.GPMetaNodeFactory

Clears the Factory, right now it does nothing...

clear() - Static method in class org.isb.metanodes.model.MetaNodeFactory

Clears this Factory (useful if a new RootGraph is loaded, but this is not supposed to happen in Cytoscape, so don't use it for now).

collapseAll - Variable in class org.isb.metanodes.actions.CollapseSelectedNodesAction

collapseExistentParents - Variable in class org.isb.metanodes.actions.CollapseSelectedNodesAction

collapseMetaNode(CyNetwork, CyNode, boolean, boolean) - Static method in class org.isb.metanodes.MetaNodeUtils

Collapses the given metanode in the given network

collapseRecursively - Variable in class org.isb.metanodes.actions.CollapseSelectedNodesAction

collapseSelectedNodes(AbstractMetaNodeModeler, boolean, boolean, boolean, boolean, boolean) - Static method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Collapses into a meta-node(s) a set of selected nodes in the current CyNetwork.

CollapseSelectedNodesAction - Class in org.isb.metanodes.actions

Use metaNodeViewer.actions.ActionFactory to get an instance of this class.

CollapseSelectedNodesAction(AbstractMetaNodeModeler, boolean, boolean, boolean, boolean, String) - Constructor for class org.isb.metanodes.actions.CollapseSelectedNodesAction

Use metaNodeViewer.actions.ActionFactory instead

compare(Object, Object) - Method in class org.isb.metanodes.data.IntraDegreeComparator

convertToMetaNode(CyNode, CyNetwork, List) - Static method in class org.isb.metanodes.model.MetaNodeFactory

Sets the children nodes of a given node to convert it into a metanode

countIntraDegrees(CyNetwork, int[]) - Static method in class org.isb.metanodes.data.IntraDegreeComparator

For each node in the array it counts how many edges it has to other nodes within the array, and puts it in a map where the key is the node's RootGraph index, and the value is its intra-degree.

createCollapseSelectedNodesAction(boolean, boolean, boolean, boolean, String) - Static method in class org.isb.metanodes.actions.ActionFactory

Creates and returns an AbstractAction to collapse nodes that are selected in the current CyNetwork.

createMetaEdge(CyNode, CyNode, String) - Static method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Creates a new CyEdge between the given nodes, the interaction type is META_EDGE_INTERACTION.
This method allows to have several edges between the same pair of nodes with the same interaction type.

createMetaNode(CyNetwork, CyNetwork, MetaNodeAttributesHandler) - Static method in class org.isb.metanodes.MetaNodeUtils

Creates a metanode that represents the given child-network in the given network

createMetaNode(CyNetwork, CyNetwork) - Static method in class org.isb.metanodes.MetaNodeUtils

Creates a metanode that represents the given child-network in the given network

createMetaNode(CyNetwork, ArrayList) - Method in class org.isb.metanodes.model.GPMetaNodeFactory

Creates a meta-node within CyNetwork's RootGraph, a default name is given to the meta-node by this.attributesHandler (if getAssignDefaultNames() is true).

createMetaNode(CyNetwork, ArrayList, MetaNodeAttributesHandler) - Method in class org.isb.metanodes.model.GPMetaNodeFactory

Creates a meta-node within CyNetwork's RootGraph, a default name is given to the meta-node by the given MetaNodeAttributesHandler (if getAssignDefaultNames() is true).

createMetaNode(CyNetwork, ArrayList) - Static method in class org.isb.metanodes.model.MetaNodeFactory

Creates a meta-node within the CyNetwork's RootGraph, a default name is given to the meta-node if getAssignDefaultNames() is true.

createMetaNode(CyNetwork, ArrayList, MetaNodeAttributesHandler) - Static method in class org.isb.metanodes.model.MetaNodeFactory

Creates a meta-node within the CyNetwork's RootGraph, a name is given to the meta-node (if getAssignDefaultNames() is true) by invoking attributes_handler.assigName().

createMetaNodeAlias(CyNetwork, int) - Method in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

createMetaNodeUI(int) - Method in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

createMetaRelationshipEdges - Variable in class org.isb.metanodes.actions.CollapseSelectedNodesAction

createUncollapseSelectedNodesAction(boolean, boolean, boolean, String) - Static method in class org.isb.metanodes.actions.ActionFactory

Creates and returns an AbstractAction that uncollapses selected meta-nodes in the current CyNetwork.

CYTOSCAPE_ABSTRACT_MODELER - Static variable in class org.isb.metanodes.model.MetaNodeModelerFactory

The AbstractMetaNodeModeler for all networks in Cytoscape.

D

DEBUG - Static variable in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

DEBUG - Static variable in class org.isb.metanodes.data.IntraDegreeComparator

DEBUG - Static variable in class org.isb.metanodes.model.AbstractMetaNodeModeler

DEBUG - Static variable in class org.isb.metanodes.model.GPMetaNodeFactory

DEFAULT_MN_ATTRIBUTES_HANDLER - Static variable in class org.isb.metanodes.model.MetaNodeModelerFactory

The default attributes handler for meta-nodes.

DEFAULT_NODE_LABEL_ATTRIBUTE - Static variable in interface org.isb.metanodes.data.MetaNodeAttributesHandler

The default attribute that is used to label nodes, this is not the same as the unique ID of nodes which are internal keys to nodes

defaultAttributesHandler - Variable in class org.isb.metanodes.model.AbstractMetaNodeModeler

The default MetaNodeAttributesHandler.

E

edgeConnectsDescendants(int, int) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

expandMetaNode(CyNetwork, CyNode, boolean) - Static method in class org.isb.metanodes.MetaNodeUtils

Expands the metanode in the given network

G

getAllMetaNodeIDs(CyNetwork) - Static method in class org.isb.metanodes.MetaNodeUtils

Returns indices of nodes that are metanodes in the given network, whether they are collapsed or expanded

getAllMetaNodes(CyNetwork) - Static method in class org.isb.metanodes.MetaNodeUtils

Returns all CyNodes that are metanodes in the given network, whether they are collapsed or expanded

getAssignDefaultNames() - Method in class org.isb.metanodes.model.GPMetaNodeFactory

Whether or not default names are being assigned to newly created meta-nodes

getAssignDefaultNames() - Static method in class org.isb.metanodes.model.MetaNodeFactory

Whether or not default names are being assigned to newly created meta-nodes

getCanonicalMetaName(CyNode) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

Method to encapsulate the canonical naming of meta nodes and edges

getChildNetwork(CyNode) - Static method in class org.isb.metanodes.MetaNodeUtils

Returns the child-network of the given metanode, or null if the node is not a metanode

getChildren(CyNode) - Static method in class org.isb.metanodes.MetaNodeUtils

Finds the immediate children nodes of the meta-node and returns them

getCollapseAll() - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

getCollapseExistentParents() - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

getCollapseRecursively() - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

getCommonMetaName(CyNode, CyNetwork) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

getCreateMetaRelationshipEdges() - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Gets whether or not "sharedMember" edges between meta-nodes and "childOf" edges between meta-nodes and their children are to be created

getCreateMetaRelationshipEdges() - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Gets wether or not edges that represent meta-relationships should be created.

getCytoscapeAbstractMetaNodeModeler() - Static method in class org.isb.metanodes.model.MetaNodeModelerFactory

It returns a AbstractMetaNodeModeler for the RootGraph obtained through Cytoscape.getRootGraph()

getCytoscapeAbstractMetaNodeModeler(MetaNodeAttributesHandler) - Static method in class org.isb.metanodes.model.MetaNodeModelerFactory

It returns a AbstractMetaNodeModeler for the RootGraph obtained through Cytoscape.getRootGraph()

getDescendantIndices(CyNode) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

getDescendants(CyNode, ArrayList) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Stores in the given ArrayList the nodes that are descendants of the given node, descendants are nodes that are direct children, or children of children, etc.

getDescendants(CyNode) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

getIntraDegree(int) - Method in class org.isb.metanodes.data.IntraDegreeComparator

Given a CyNode, it returns its intradegree.

getLeafChildren(CyNode) - Static method in class org.isb.metanodes.MetaNodeUtils

Returns the descendant nodes of the given metanode that are not meta-nodes themselves

getMultipleEdges() - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

getMultipleEdges() - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

getNetworkAttributesHandler(CyNetwork) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Gets the MetaNodeAttributesHandler that is being used to transfer node and edge attributes from children nodes and edges to meta-nodes for the given CyNetwork

getNodeLabelAttribute() - Method in interface org.isb.metanodes.data.MetaNodeAttributesHandler

Gets the name of the node attribute to which meta-node names should be assigned to, if not set, it is DEFAULT_NODE_LABEL_ATTRIBUTE

getNodeLabelAttribute() - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

Gets the name of the node attribute to which meta-node names should be assigned to, if not set, it is DEFAULT_NODE_LABEL_ATTRIBUTE

getNodesInCyNet(CyNetwork) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

getParents(CyNetwork, CyNode) - Static method in class org.isb.metanodes.MetaNodeUtils

Finds and returns the immediate parents of the given child node

getRootGraph() - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

getRootParents(CyNetwork, CyNode) - Static method in class org.isb.metanodes.MetaNodeUtils

Finds and returns the top level parents of the given child node

getSizeProportionalToNumChildren() - Method in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

Gets whether or not to set the size of a metanode proportional to its number of children

GPMetaNodeFactory - Class in org.isb.metanodes.model

Creates meta-nodes for a given CyNetwork and keeps track of which meta-nodes belong to which network (since all CyNetworks share a RootGraoh).

GPMetaNodeFactory() - Constructor for class org.isb.metanodes.model.GPMetaNodeFactory

Constructor.

GPMetaNodeFactory(MetaNodeAttributesHandler) - Constructor for class org.isb.metanodes.model.GPMetaNodeFactory

Constructor.

GPMetaNodeFactory(MetaNodeAttributesHandler, boolean) - Constructor for class org.isb.metanodes.model.GPMetaNodeFactory

Constructor.

H

hasParents(CyNetwork, CyNode) - Static method in class org.isb.metanodes.MetaNodeUtils

Returns true if the given node has parent metanodes in the given network, false otherwise

I

IntraDegreeComparator - Class in org.isb.metanodes.data

A Comparator for CyNodes that compares the given nodes depending on their intra-degrees.

IntraDegreeComparator(CyNetwork, boolean, int[]) - Constructor for class org.isb.metanodes.data.IntraDegreeComparator

Constructor.

intraDegrees - Variable in class org.isb.metanodes.data.IntraDegreeComparator

isCollapsed(CyNetwork, CyNode) - Static method in class org.isb.metanodes.MetaNodeUtils

Returns true if the given metanode is collapsed in the given network, false if it is expanded, or if it is not a metanode at all

isMetaNode(CyNode) - Static method in class org.isb.metanodes.MetaNodeUtils

Returns true if the given node is a metanode, false otherwise

isMetaNode(CyNode) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

M

makeMetaNode(CyNetwork, CyNode, List) - Method in class org.isb.metanodes.model.GPMetaNodeFactory

Converts the given node into a metanode

MetaNodeAttributesHandler - Interface in org.isb.metanodes.data

An interface for classes that handle the node and edge attributes of meta-nodes.

MetaNodeFactory - Class in org.isb.metanodes.model

A class with easy to use static methods for creating meta-nodes for CyNetworks.

MetaNodeFactory() - Constructor for class org.isb.metanodes.model.MetaNodeFactory

MetaNodeModelerFactory - Class in org.isb.metanodes.model

A class that contains all the meta-node modelers (implementations of metaNodeViewer.model.GPMetaNodeModel) for Cytoscape.

MetaNodeModelerFactory() - Constructor for class org.isb.metanodes.model.MetaNodeModelerFactory

METANODES_CHILDREN - Static variable in class org.isb.metanodes.model.MetaNodeFactory

METANODES_HINTS - Static variable in class org.isb.metanodes.model.MetaNodeFactory

METANODES_IN_NETWORK - Static variable in class org.isb.metanodes.model.MetaNodeFactory

The key to obtain a cern.colt.list.IntArrayList that contains RootGraph indices of meta-nodes for a given CyNetwork through Cytoscape.getNetworkAttributes(String key) This is necessary because all CyNetworks belong to the same RootGraph which contains the meta-nodes, so we need to know which meta-nodes belong to which CyNetworks.

MetaNodeUtils - Class in org.isb.metanodes

Class with easy to use static methods for metanode operations.

MetaNodeUtils() - Constructor for class org.isb.metanodes.MetaNodeUtils

multipleEdges - Variable in class org.isb.metanodes.actions.CollapseSelectedNodesAction

N

network - Variable in class org.isb.metanodes.data.IntraDegreeComparator

networkToAttsHandler - Variable in class org.isb.metanodes.model.AbstractMetaNodeModeler

A Map from CyNetworks to MetaNodeAttributesHandlers that are used to assign names and attribute values to meta-nodes.

newNetwork - Variable in class org.isb.metanodes.actions.UncollapseSelectedNodesAction

nodeLabelAttribute - Variable in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

The name of the node attribute to which meta-node names should be assigned to

nodesAreInNetwork - Variable in class org.isb.metanodes.data.IntraDegreeComparator

nodesAreInNetwork(CyNetwork, int[]) - Static method in class org.isb.metanodes.data.IntraDegreeComparator

O

org.isb.metanodes - package org.isb.metanodes

org.isb.metanodes.actions - package org.isb.metanodes.actions

org.isb.metanodes.data - package org.isb.metanodes.data

org.isb.metanodes.model - package org.isb.metanodes.model

P

prepareNodeForModel(CyNetwork, CyNode) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Creates edges between the given CyNode and other nodes so that when the CyNode is collapsed (applyModel) or expanded (undoModel) the needed edges (between meta-nodes and non-meta-nodes, or meta-nodes and meta-nodes), will be there for hiding or unhiding as necessary.

R

recursive - Variable in class org.isb.metanodes.actions.UncollapseSelectedNodesAction

removeFromAttributes(CyNetwork, CyNode, ArrayList) - Method in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

Removes attributes for the given meta-node.

removeFromAttributes(CyNetwork, CyNode, ArrayList) - Method in interface org.isb.metanodes.data.MetaNodeAttributesHandler

Removes all attributes created for the given meta-node.

removeFromAttributes(CyNetwork, CyNode, ArrayList) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

removeMetaEdgesFromAttributes(CyNetwork, CyNode, ArrayList) - Method in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

Removes attributes created for meta-edges.

removeMetaEdgesFromAttributes(CyNetwork, CyNode, ArrayList) - Method in interface org.isb.metanodes.data.MetaNodeAttributesHandler

Remove attributes for the gicen meta-edges in CyNetwork, but leave the attributes for the meta-node as they are.

removeMetaEdgesFromAttributes(CyNetwork, CyNode, ArrayList) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

removeMetaNode(CyNetwork, CyNode, boolean) - Static method in class org.isb.metanodes.MetaNodeUtils

Expands and then permanently removes the given metanode from the network

removeMetaNode(CyNetwork, CyNode, boolean) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Removes the edges that were created by prepareNodeForModel() that are connected to the given CyNode and their attributes in the given CyNetwork.

REPORT_TIME - Static variable in class org.isb.metanodes.actions.CollapseSelectedNodesAction

REPORT_TIME - Static variable in class org.isb.metanodes.model.AbstractMetaNodeModeler

rootGraph - Variable in class org.isb.metanodes.model.AbstractMetaNodeModeler

The RootGraph of all CyNetworks for which this modeler will be applied.

S

setAssignDefaultNames(boolean) - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Sets whether or not default names should be assigned to newly created metanodes

setAttributes(CyNetwork, CyNode, ArrayList, AbstractIntIntMap) - Method in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

Sets the node and edge attributes of the given meta-node and assigns a unique name to it

setAttributes(CyNetwork, CyNode, ArrayList, AbstractIntIntMap) - Method in interface org.isb.metanodes.data.MetaNodeAttributesHandler

Sets the node and edge attributes of the meta-node

setAttributes(CyNetwork, CyNode, ArrayList, AbstractIntIntMap) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

Simply calls separate methods for nodes then edges

setChildNetwork(CyNode, CyNetwork, CyNetwork) - Static method in class org.isb.metanodes.MetaNodeUtils

Sets a network as a child-network for an existing CyNode that after this call becomes a metanode

setCollapseAll(boolean) - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Sets whether or not the to collapse all meta-nodes

setCollapseExistentParents(boolean) - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Sets whether or not the existent meta-node parents of the selected nodes should be collapsed instead of creating new meta-nodes for them

setCollapseRecursively(boolean) - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Sets whether or not the top-level meta-node parents of the selected nodes should be found and collapsed.

setCreateMetaRelationshipEdges(boolean) - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Sets whether or not "sharedMember" edges between meta-nodes and "childOf" edges between meta-nodes and their children should be created

setCreateMetaRelationshipEdges(boolean) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Sets wether or not edges that represent meta-relationships should be created.

setDefaultAttributesHandler(MetaNodeAttributesHandler) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Sets the default MetaNodeAttributesHandler, by default, this handler is MetaNodeModelerFactory.DEFAULT_MN_ATTRIBUTES_HANDLER.

setEdgeAttributes(CyNetwork, CyNode, AbstractIntIntMap) - Method in interface org.isb.metanodes.data.MetaNodeAttributesHandler

Sets the edge attributes of the meta-node

setEdgeAttributes(CyNetwork, CyNode, AbstractIntIntMap) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

Copies all edge attributes from child to meta edges

setMetaNodeAttributesHandler(MetaNodeAttributesHandler) - Static method in class org.isb.metanodes.actions.ActionFactory

Sets the default MetaNodeAttributesHandler that should be used to transfer node and edge attributes from children nodes and edges to meta-nodes.

setMultipleEdges(boolean) - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Sets whether multiple edges between meta-nodes and other nodes should be created

setMultipleEdges(boolean) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Sets whether or not multiple edges between a meta-node and another node (meta or not meta) should be created when abstracting the meta-node, true by default

setNetworkAttributesHandler(CyNetwork, MetaNodeAttributesHandler) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Sets the MetaNodeAttributesHandler that should be used from now on to transfer node and edge attributes from children nodes and edges to meta-nodes in the given CyNetwork

setNewNetwork(boolean) - Method in class org.isb.metanodes.actions.UncollapseSelectedNodesAction

Sets whether or not this uncollapse will open a new network

setNodeAttributes(CyNetwork, CyNode, ArrayList) - Method in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

Sets the node attributes of the meta-node

setNodeAttributes(CyNetwork, CyNode, ArrayList) - Method in interface org.isb.metanodes.data.MetaNodeAttributesHandler

Sets the node attributes of the meta-node

setNodeAttributes(CyNetwork, CyNode, ArrayList) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

takes union of all children attributes, treating canonical and common name as special cases

setNodeLabelAttribute(String) - Method in interface org.isb.metanodes.data.MetaNodeAttributesHandler

Sets the name of the node attribute to which meta-node names should be assigned to, if not set, it is DEFAULT_NODE_LABEL_ATTRIBUTE

setNodeLabelAttribute(String) - Method in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

Sets the name of the node attribute to which meta-node names should be assigned to, if not set, it is DEFAULT_NODE_LABEL_ATTRIBUTE

setRecursiveUncollapse(boolean) - Method in class org.isb.metanodes.actions.UncollapseSelectedNodesAction

Sets whether or not this uncollapse should be recursive (uncollapse to the bottom level of the graph).

setRootGraph(RootGraph) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Sets the RootGraph whose CyNetworks will be changed so that their meta-nodes can be collapsed and expanded.

setSizeProportionalToNumChildren(boolean) - Method in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

Whether or not to set the size of a metanode proportional to its number of children

setTemporaryUncollapse(boolean) - Method in class org.isb.metanodes.actions.UncollapseSelectedNodesAction

Sets whether or not this uncollapse is temporary or not.

setUseDefaultMetanodeSizer(boolean) - Method in class org.isb.metanodes.actions.CollapseSelectedNodesAction

Sets whether or not to use the default sizer

SHARED_CHILD_INTERACTION - Static variable in class org.isb.metanodes.model.AbstractMetaNodeModeler

SimpleMetaNodeAttributesHandler - Class in org.isb.metanodes.data

Implementation of MetaNodesAttributesHandler that transfers the union of all attributes on the child nodes to the parent meta-nodes.

SimpleMetaNodeAttributesHandler() - Constructor for class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

SimpleMetaNodeAttributesHandler.CopyEdgeAttr - Class in org.isb.metanodes.data

Procedure class to copy over edge attributes

SimpleMetaNodeAttributesHandler.CopyEdgeAttr() - Constructor for class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler.CopyEdgeAttr

sizeProportionalToNumChildren - Variable in class org.isb.metanodes.data.AbstractMetaNodeAttsHandler

Whether or not to set the size of a metanode proportional to its number of children
True by default

sortNodes(CyNetwork, int[]) - Static method in class org.isb.metanodes.data.IntraDegreeComparator

Sorts the nodes with the given RootGraph indices according to their intradegree.

T

temporaryUncollapse - Variable in class org.isb.metanodes.actions.UncollapseSelectedNodesAction

TRANSFERRED_EDGE_INTERACTION - Static variable in class org.isb.metanodes.model.AbstractMetaNodeModeler

U

uncollapseSelectedNodes(AbstractMetaNodeModeler, boolean, boolean, boolean) - Static method in class org.isb.metanodes.actions.UncollapseSelectedNodesAction

Uncollapses the selected nodes in the current CyNetwork.

UncollapseSelectedNodesAction - Class in org.isb.metanodes.actions

Use metaNodeViewer.actions.ActionFactory to get an instance of this class.

UncollapseSelectedNodesAction(AbstractMetaNodeModeler, boolean, boolean, boolean, String) - Constructor for class org.isb.metanodes.actions.UncollapseSelectedNodesAction

Use metaNodeViewer.actions.ActionFactory instead.

undoModel(boolean) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

Undos the changes made to CyNetwork in order to apply the model.

undoModel(CyNetwork, CyNode, boolean, boolean) - Method in class org.isb.metanodes.model.AbstractMetaNodeModeler

It undos the model for the given CyNode.

usedEdgeNames - Variable in class org.isb.metanodes.data.SimpleMetaNodeAttributesHandler

Tracks the edge names that have been examined so far

useDefaultMetanodeSizer - Static variable in class org.isb.metanodes.actions.CollapseSelectedNodesAction

A C D E G H I M N O P R S T U