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A

AbstractVisualDiffanyStyle - Class in be.svlandeg.diffany.cytoscape.vizmapper
A VisualStyle wrapper with default values for all Diffany styles.
AbstractVisualDiffanyStyle(String, Services) - Constructor for class be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
Create a new visual style and initialize it according to its type.
actionPerformed(ActionEvent) - Method in class be.svlandeg.diffany.cytoscape.actions.LoadExampleAction
 
actionPerformed(ActionEvent) - Method in class be.svlandeg.diffany.cytoscape.actions.RunProjectAction
 
actionPerformed(ActionEvent) - Method in class be.svlandeg.diffany.cytoscape.actions.UpdateVisualStyleAction
 
actionPerformed(ActionEvent) - Method in class be.svlandeg.diffany.cytoscape.gui.ExtraOptionsMenu
 
actionPerformed(ActionEvent) - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
 
ActivityFlowTest - Class in be.svlandeg.diffany.examples
Testing class that tries to simulate a range of possibilities in activity flow networks and is able to produce differential networks for them.
ActivityFlowTest() - Constructor for class be.svlandeg.diffany.examples.ActivityFlowTest
 
addArrowHead(String, EdgeStyle.ArrowHead, boolean) - Method in class be.svlandeg.diffany.core.visualstyle.TreeEdgeDrawing
Assign a specific arrowhead to a source category (and its children).
addColor(String, Color, boolean) - Method in class be.svlandeg.diffany.core.visualstyle.TreeEdgeDrawing
Assign a specific paint object to a source category (and its children).
addConsensus(ConsensusNetwork) - Method in class be.svlandeg.diffany.core.project.RunOutput
Add a consensus output network.
addCyNetwork(Network, CyRootNetwork, Services) - Static method in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
Converts a Network to a CyNetwork and registers it with Cytoscape as a CySubNetwork of the given Collection.
addDefaultPaintedParents() - Method in class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
Provide a default mapping edge type to category mapping.
addDifferential(DifferentialNetwork) - Method in class be.svlandeg.diffany.core.project.RunOutput
Add a differential output network.
addEdge(Edge) - Method in class be.svlandeg.diffany.core.networks.Network
Add an edge to this network, automatically also adding its source and target nodes if needed.
addEdgeToTree(EdgeDefinition, Set<Integer>, Map<String, EdgeComparison.IntermediateComparison>, Map<String, EdgeComparison.IntermediateComparison>) - Method in class be.svlandeg.diffany.core.algorithms.EdgeComparison
Add an edge to the set (tree) of intermediate results, by starting with the type of the edge and going up the tree.
addInteractionMappings(Set<String>, EdgeOntology, DiscreteMapping<String, Paint>, DiscreteMapping<String, Paint>, DiscreteMapping<String, ArrowShape>) - Method in class be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
Add mappings to the VizMapper according to the edges used in the project.
addInteractionMappings(Set<String>, EdgeOntology, DiscreteMapping<String, Paint>, DiscreteMapping<String, Paint>, DiscreteMapping<String, ArrowShape>) - Method in class be.svlandeg.diffany.cytoscape.vizmapper.VisualDiffStyle
 
addInteractionMappings(Set<String>, EdgeOntology, DiscreteMapping<String, Paint>, DiscreteMapping<String, Paint>, DiscreteMapping<String, ArrowShape>) - Method in class be.svlandeg.diffany.cytoscape.vizmapper.VisualSourceStyle
 
addNegSourceCat(String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Define a 'negative' category, like negative regulation
addNode(Node) - Method in class be.svlandeg.diffany.core.networks.Network
Add a new (unconnected) node to this network.
addNodeAttribute(Attribute) - Method in class be.svlandeg.diffany.core.networks.Network
Add a new required node attribute to this network.
addOne(Map<String, Integer>, String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Private method that increments a specific type in a category-to-count hashmap.
addOntologyTerm(String) - Method in class be.svlandeg.diffany.core.networks.Condition
Add a number of ontology terms to the set of previously defined terms.
addPair(OutputNetworkPair) - Method in class be.svlandeg.diffany.core.project.RunOutput
Add a pair of differential+consensus networks to this output.
addPosSourceCat(String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Define a 'positive' category, like positive regulation
addProject(CyProject) - Method in class be.svlandeg.diffany.cytoscape.Model
Add a new CyProject.
addResult(EdgeComparison.IntermediateComparison, int, double) - Method in class be.svlandeg.diffany.core.algorithms.EdgeComparison
This method adds one additional piece of support to an intermediate result.
addResult(String, double, double, double) - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionData
Add calculated scores for a certain array ID.
addRunConfiguration(ReferenceNetwork, ConditionNetwork, boolean, ProgressListener) - Method in class be.svlandeg.diffany.core.project.Project
Add a new RunConfiguration to this project.
addRunConfiguration(ReferenceNetwork, Set<ConditionNetwork>, boolean, ProgressListener) - Method in class be.svlandeg.diffany.core.project.Project
Add a new RunConfiguration to this project, automatically registering the networks to this project.
addRunConfiguration(ReferenceNetwork, Set<ConditionNetwork>, int, boolean, ProgressListener) - Method in class be.svlandeg.diffany.core.project.Project
Add a new RunConfiguration to this project, automatically registering the networks to this project.
addRunConfiguration(Set<InputNetwork>, ProgressListener) - Method in class be.svlandeg.diffany.core.project.Project
Add a new RunConfiguration to this project, automatically registering the networks to this project.
addRunConfiguration(Set<InputNetwork>, int, boolean, ProgressListener) - Method in class be.svlandeg.diffany.core.project.Project
Add a new RunConfiguration to this project, automatically registering the networks to this project.
addSourceCategories(Map<String, Boolean>, boolean) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Add a number of source categories (casing independent)
addSourceCategory(String, boolean, boolean) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Add a source category
addSourceCategoryMapping(String, String, boolean) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Create a new mapping from edge type to category.
addTicks(String, int) - Method in class be.svlandeg.diffany.core.progress.ProgressListener
Report the fact that there has been some progress, expressed by a number of ticks that were performed
adjustEdgesByFoldChanges(EdgeOntology, Set<Node>, Set<Edge>, Map<String, Double>) - Method in class be.svlandeg.diffany.study.osmotic.NetworkConstruction
Take a copy of the given set of edges and produce new ones that are weighted according to the fold changes of the DE genes.
allSourceCategories - Variable in class be.svlandeg.diffany.core.semantics.EdgeOntology
 
apply(CyNetworkView) - Method in class be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
Convenience method to apply this VisualStyle to a CyNetworkView
areEqual(Node, Node) - Static method in class be.svlandeg.diffany.core.semantics.NodeMapper
Define whether or not two nodes are equal.
Attribute - Class in be.svlandeg.diffany.core.networks
 
Attribute(String, Class<?>) - Constructor for class be.svlandeg.diffany.core.networks.Attribute
 
attributes - Variable in class be.svlandeg.diffany.core.networks.Node
 

B

Bandyopadhyay2010 - Class in be.svlandeg.diffany.examples
This class provides examples taken from the Bandyopadhyay et al, Science 2010 paper.
Bandyopadhyay2010() - Constructor for class be.svlandeg.diffany.examples.Bandyopadhyay2010
 
be.svlandeg.diffany.console - package be.svlandeg.diffany.console
 
be.svlandeg.diffany.core.algorithms - package be.svlandeg.diffany.core.algorithms
 
be.svlandeg.diffany.core.io - package be.svlandeg.diffany.core.io
 
be.svlandeg.diffany.core.networks - package be.svlandeg.diffany.core.networks
 
be.svlandeg.diffany.core.progress - package be.svlandeg.diffany.core.progress
 
be.svlandeg.diffany.core.project - package be.svlandeg.diffany.core.project
 
be.svlandeg.diffany.core.semantics - package be.svlandeg.diffany.core.semantics
 
be.svlandeg.diffany.core.visualstyle - package be.svlandeg.diffany.core.visualstyle
 
be.svlandeg.diffany.cytoscape - package be.svlandeg.diffany.cytoscape
 
be.svlandeg.diffany.cytoscape.actions - package be.svlandeg.diffany.cytoscape.actions
 
be.svlandeg.diffany.cytoscape.gui - package be.svlandeg.diffany.cytoscape.gui
 
be.svlandeg.diffany.cytoscape.internal - package be.svlandeg.diffany.cytoscape.internal
 
be.svlandeg.diffany.cytoscape.tasks - package be.svlandeg.diffany.cytoscape.tasks
 
be.svlandeg.diffany.cytoscape.vizmapper - package be.svlandeg.diffany.cytoscape.vizmapper
 
be.svlandeg.diffany.examples - package be.svlandeg.diffany.examples
 
be.svlandeg.diffany.study.osmotic - package be.svlandeg.diffany.study.osmotic
 
be.svlandeg.diffany.study.osmotic.arabidopsis - package be.svlandeg.diffany.study.osmotic.arabidopsis
 

C

calculateAllPairwiseDifferentialNetworks(Project, int, Double, boolean, boolean, int, Boolean, ProgressListener) - Method in class be.svlandeg.diffany.core.algorithms.CalculateDiff
Calculate all pairwise differential networks and/or consensus networks between the reference and each condition-specific network in the project.
calculateConsensusNetwork(Set<Network>, TreeEdgeOntology, String, int, int, boolean, double, boolean, ScheduledTask) - Method in class be.svlandeg.diffany.core.algorithms.EdgeByEdge
Calculate the consensus network between a set of networks.
CalculateDiff - Class in be.svlandeg.diffany.core.algorithms
This class serves as an abstract layer between a GUI and the actual technical implementations of various algorithms that can calculate differential networks.
CalculateDiff() - Constructor for class be.svlandeg.diffany.core.algorithms.CalculateDiff
Initialize the algorithm.
CalculateDiff(CalculateDiff.RunMode) - Constructor for class be.svlandeg.diffany.core.algorithms.CalculateDiff
Initialize the algorithm, depending on the mode parameter.
CalculateDiff.RunMode - Enum in be.svlandeg.diffany.core.algorithms
A run mode determines how differential networks will be calculated.
calculateDiffNetwork(ReferenceNetwork, Set<ConditionNetwork>, TreeEdgeOntology, String, int, int, double, ScheduledTask) - Method in class be.svlandeg.diffany.core.algorithms.EdgeByEdge
Calculate the differential network between the reference and condition-specific networks.
calculateOneDifferentialNetwork(Project, int, Double, String, String, int, int, Boolean, ProgressListener) - Method in class be.svlandeg.diffany.core.algorithms.CalculateDiff
Calculate the differential network and/or the consensus network, starting from a predefined runconfiguration in a project.
cancel() - Method in class be.svlandeg.diffany.cytoscape.tasks.LoadExampleTask
 
cancel() - Method in class be.svlandeg.diffany.cytoscape.tasks.RunProjectTask
 
cancel() - Method in class be.svlandeg.diffany.cytoscape.tasks.UpdateVisualStyleTask
 
canExecute(Model) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Checks if all necessary parameters are set to execute the algorithm.
checkInputIDs() - Method in class be.svlandeg.diffany.core.project.Run
Private method that checks whether there are no conflicting network IDs in this run.
checkoutputID(int) - Method in class be.svlandeg.diffany.core.project.Run
Private method that checks whether a specific ID of an output network can be used in this run
clean() - Method in class be.svlandeg.diffany.core.project.Logger
Clean all previous logs.
clean() - Method in class be.svlandeg.diffany.core.project.RunOutput
Clean the output.
clear() - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
Empty the table and the complete table model
clear() - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
Clears all data in the model.
commonSourceCatParent(String, String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Return the common parent of two categories, or null if there is none
commonSourceCatParent(String, String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
 
Condition - Class in be.svlandeg.diffany.core.networks
This class describes an experimental condition that can be linked to a certain network.
Condition(String, Set<String>) - Constructor for class be.svlandeg.diffany.core.networks.Condition
Create a new condition that can be linked to a network.
Condition(String) - Constructor for class be.svlandeg.diffany.core.networks.Condition
Create a new condition that can be linked to a network.
Condition(Condition) - Constructor for class be.svlandeg.diffany.core.networks.Condition
Cloning constructor
ConditionNetwork - Class in be.svlandeg.diffany.core.networks
A kind of network that is condition-specific.
ConditionNetwork(String, int, Set<Attribute>, Set<Condition>) - Constructor for class be.svlandeg.diffany.core.networks.ConditionNetwork
Create a new condition-specific network.
ConditionNetwork(String, int, Set<Attribute>, Condition) - Constructor for class be.svlandeg.diffany.core.networks.ConditionNetwork
Create a new condition-specific network.
conditionNetworks - Variable in class be.svlandeg.diffany.core.networks.DifferentialNetwork
 
conditions - Variable in class be.svlandeg.diffany.core.networks.ConditionNetwork
 
conditions - Variable in class be.svlandeg.diffany.core.project.RunDiffConfiguration
 
configuration - Variable in class be.svlandeg.diffany.core.project.Run
 
ConflictingEdgesTest - Class in be.svlandeg.diffany.examples
Testing class that simulates input networks with edge conflicts, e.g.
ConflictingEdgesTest() - Constructor for class be.svlandeg.diffany.examples.ConflictingEdgesTest
 
consensusname_default_all - Static variable in class be.svlandeg.diffany.core.algorithms.CalculateDiff
 
consensusname_pairwise_prefix - Static variable in class be.svlandeg.diffany.core.algorithms.CalculateDiff
 
consensusNet - Variable in class be.svlandeg.diffany.cytoscape.CyProject.CyNetworkPair
 
ConsensusNetwork - Class in be.svlandeg.diffany.core.networks
A consensus network is the counterpart of a differential network: containing everything but the differential edges between 2 (or more) networks, a consensus network stores the consensus or common edges between them.
ConsensusNetwork(String, int, Set<Network>) - Constructor for class be.svlandeg.diffany.core.networks.ConsensusNetwork
Create a new consensus network, referring to the original networks it was created from.
containsTableId(long) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Checks the default edge and node tables of the networks in this project for a given SUID.
createCyNetwork(Network, CyRootNetwork) - Static method in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
Creates a CyNetwork from a Network and adds it to Cytoscape.
createCyNetwork(Network, CyNetworkFactory) - Static method in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
Creates a CyNetwork from a Network and adds it to Cytoscape.
createTaskIterator() - Method in class be.svlandeg.diffany.cytoscape.tasks.LoadExampleTaskFactory
 
createTaskIterator() - Method in class be.svlandeg.diffany.cytoscape.tasks.RunProjectTaskFactory
 
createTaskIterator() - Method in class be.svlandeg.diffany.cytoscape.tasks.UpdateVisualStyleTaskFactory
 
cutoffShort - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
CyActivator - Class in be.svlandeg.diffany.cytoscape.internal
Entry point for the Diffany Cytoscape 3 App.
CyActivator() - Constructor for class be.svlandeg.diffany.cytoscape.internal.CyActivator
 
CyNetworkBridge - Class in be.svlandeg.diffany.cytoscape
Static conversion class that takes the appropriate Cytoscape Factories and uses them to create given concepts.
CyNetworkBridge() - Constructor for class be.svlandeg.diffany.cytoscape.CyNetworkBridge
 
CyNetworkBridge.NetworkType - Enum in be.svlandeg.diffany.cytoscape
To distinguish between two types of source networks
CyNetworkPair(CyNetwork, CyNetwork) - Constructor for class be.svlandeg.diffany.cytoscape.CyProject.CyNetworkPair
 
CyProject - Class in be.svlandeg.diffany.cytoscape
The CyProject keeps track of all project specific settings.
CyProject(CyRootNetwork) - Constructor for class be.svlandeg.diffany.cytoscape.CyProject
Construct empty project, named after the collection
CyProject.CyNetworkPair - Class in be.svlandeg.diffany.cytoscape
Internal class to link a differential network to its consensus counterpart.

D

date() - Method in class be.svlandeg.diffany.core.project.LogEntry
Retrieve the date of this log entry
de_attribute - Static variable in class be.svlandeg.diffany.core.networks.Node
 
def - Variable in class be.svlandeg.diffany.core.networks.Edge
 
default_ah - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
default_MIN - Variable in class be.svlandeg.diffany.core.algorithms.CalculateDiff
 
DEFAULT_NEG - Static variable in class be.svlandeg.diffany.core.networks.EdgeDefinition
 
default_paint - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
DEFAULT_SYMM - Static variable in class be.svlandeg.diffany.core.networks.EdgeDefinition
 
default_symmetry - Static variable in class be.svlandeg.diffany.core.semantics.EdgeOntology
 
DEFAULT_TYPE - Static variable in class be.svlandeg.diffany.core.networks.EdgeDefinition
 
DEFAULT_WEIGHT - Static variable in class be.svlandeg.diffany.core.networks.EdgeDefinition
 
default_weight_cutoff - Variable in class be.svlandeg.diffany.core.algorithms.CalculateDiff
 
DefaultDiffEdgeDrawing - Class in be.svlandeg.diffany.core.visualstyle
This class provides a default definition of drawing edges in a GUI for the differential network(s).
DefaultDiffEdgeDrawing(TreeEdgeOntology) - Constructor for class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
Create a new DefaultDiffEdgeDrawing object, given a specific EdgeOntology object.
DefaultEdgeOntology - Class in be.svlandeg.diffany.core.semantics
This class provides initial suggestions to the user concerning edge type-to-category mappings.
DefaultEdgeOntology() - Constructor for class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
Create a default edge ontology, with default edge categories and type-category mappings.
defaultMinOperator - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
defaultModePairwise - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
defaultReadHeader - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
defaultRunCons - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
defaultRunDiff - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
DefaultSourceEdgeDrawing - Class in be.svlandeg.diffany.core.visualstyle
This class provides a default definition of drawing edges in a GUI for the source networks.
DefaultSourceEdgeDrawing(TreeEdgeOntology) - Constructor for class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
Create a new DefaultSourceEdgeDrawing object, given a specific EdgeOntology object.
defineAllCategories() - Static method in class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
Define all categories to be used in this EdgeOntology
defineCommonAttributes(Set<Network>) - Method in class be.svlandeg.diffany.core.networks.Network
Define the node attributes by taking only those that are in common from a given set of networks.
description - Variable in class be.svlandeg.diffany.core.networks.Condition
 
DiffanyOptions - Class in be.svlandeg.diffany.console
This class defines the various options available when running the Diffany algorithms through the console.
DiffanyOptions() - Constructor for class be.svlandeg.diffany.console.DiffanyOptions
Constructor initializes the options available in Diffany
diffDraw - Variable in class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
 
DifferentialNetwork - Class in be.svlandeg.diffany.core.networks
A differential network contains differential edges between 2 (or more) networks, one of which is always a 'static' reference network.
DifferentialNetwork(String, int, ReferenceNetwork, Set<ConditionNetwork>) - Constructor for class be.svlandeg.diffany.core.networks.DifferentialNetwork
Create a new differential network, referring to exactly one static reference network and 1 or more condition-specific networks.
DifferentialNetwork(String, int, ReferenceNetwork, ConditionNetwork) - Constructor for class be.svlandeg.diffany.core.networks.DifferentialNetwork
Create a new differential network, referring to exactly one static reference network and one condition-specific network.
diffname_default_all - Static variable in class be.svlandeg.diffany.core.algorithms.CalculateDiff
 
diffname_pairwise_prefix - Static variable in class be.svlandeg.diffany.core.algorithms.CalculateDiff
 
diffNet - Variable in class be.svlandeg.diffany.cytoscape.CyProject.CyNetworkPair
 
done() - Method in class be.svlandeg.diffany.core.progress.ScheduledTask
Report that the task is finished.
downregulated - Static variable in class be.svlandeg.diffany.core.networks.Node
 

E

Edge - Class in be.svlandeg.diffany.core.networks
Class that represents an edge in a network: an edge has a source and target node and can have a certain weight.
Edge(Node, Node, EdgeDefinition) - Constructor for class be.svlandeg.diffany.core.networks.Edge
Create a new node from a certain definition and specifying source and target nodes.
Edge(String, Node, Node, boolean, double, boolean) - Constructor for class be.svlandeg.diffany.core.networks.Edge
Create a new edge with specified source and target nodes, direction and weight.
Edge(String, Node, Node, boolean, boolean) - Constructor for class be.svlandeg.diffany.core.networks.Edge
Create a new edge with default weight of 1.
Edge(String, Node, Node, boolean, double) - Constructor for class be.svlandeg.diffany.core.networks.Edge
Create a new edge, which will be defined as not negated.
Edge(String, Node, Node, boolean) - Constructor for class be.svlandeg.diffany.core.networks.Edge
Create a new edge with default weight of 1.0 and negation off.
EdgeByEdge - Class in be.svlandeg.diffany.core.algorithms
This class calculates consensus/differential networks on an edge-by-edge basis.
EdgeByEdge(Logger) - Constructor for class be.svlandeg.diffany.core.algorithms.EdgeByEdge
The constructor initializes the algorithm.
EdgeComparison - Class in be.svlandeg.diffany.core.algorithms
This class does the actual edge-by-edge comparisons, based on the semantic definitions of an ontology, structured as a tree classification system.
EdgeComparison(TreeEdgeOntology) - Constructor for class be.svlandeg.diffany.core.algorithms.EdgeComparison
Initialize this object by defining the Edge Ontology which will be used for semantically comparing edges.
EdgeComparison.IntermediateComparison - Class in be.svlandeg.diffany.core.algorithms
Private class that will be used to store intermediate calculations at all levels of the edge ontology.
EdgeDefinition - Class in be.svlandeg.diffany.core.networks
An edge definition holds all information of an edge, except its actual source and target nodes.
EdgeDefinition(String, boolean, double, boolean) - Constructor for class be.svlandeg.diffany.core.networks.EdgeDefinition
Create a new edge definition with a certain type, direction, weight and directionality
EdgeDefinition(EdgeDefinition) - Constructor for class be.svlandeg.diffany.core.networks.EdgeDefinition
Cloning constructor
EdgeDrawing - Class in be.svlandeg.diffany.core.visualstyle
This abstract class tells the GUI how to draw certain edges, depending on definitions from an EdgeOntology.
EdgeDrawing() - Constructor for class be.svlandeg.diffany.core.visualstyle.EdgeDrawing
Create a new EdgeDrawing object
EdgeFilterTableModel - Class in be.svlandeg.diffany.cytoscape.gui
Model that controls the content of the edge (interaction) filter
EdgeFilterTableModel() - Constructor for class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
 
EdgeGenerator - Class in be.svlandeg.diffany.core.networks
This class generates special edges to be used in the input/output networks, such as default edges, virtual edges or void edges.
EdgeGenerator() - Constructor for class be.svlandeg.diffany.core.networks.EdgeGenerator
 
EdgeIO - Class in be.svlandeg.diffany.core.io
This class allows reading/writing an Edge from/to File.
EdgeIO() - Constructor for class be.svlandeg.diffany.core.io.EdgeIO
 
edgeOntology - Variable in class be.svlandeg.diffany.core.project.Project
 
EdgeOntology - Class in be.svlandeg.diffany.core.semantics
This class takes care of the semantic interpretation of different edge types and their corresponding categories in the 'source' networks, i.e.
EdgeOntology() - Constructor for class be.svlandeg.diffany.core.semantics.EdgeOntology
Create an empty ontology, with no edge categories or any mapping defined
edges - Variable in class be.svlandeg.diffany.core.networks.Network
 
EdgeStyle - Class in be.svlandeg.diffany.core.visualstyle
This class defines the main visual properties of an edge, such as the color and type of arrowhead.
EdgeStyle(Color, EdgeStyle.ArrowHead) - Constructor for class be.svlandeg.diffany.core.visualstyle.EdgeStyle
Constructor: creates a visual edge style which cannot be modified
EdgeStyle.ArrowHead - Enum in be.svlandeg.diffany.core.visualstyle
 
eg - Variable in class be.svlandeg.diffany.core.algorithms.EdgeComparison
 
EMPTY_DISPLAY_NAME - Static variable in class be.svlandeg.diffany.core.algorithms.EdgeByEdge
 
EMPTY_ID - Static variable in class be.svlandeg.diffany.core.algorithms.EdgeByEdge
 
equals(Object) - Method in class be.svlandeg.diffany.core.networks.Attribute
 
example(String, String, String, String) - Method in class be.svlandeg.diffany.examples.ExampleCode
 
ExampleCode - Class in be.svlandeg.diffany.examples
This class provides example code to work with the Diffany library.
ExampleCode() - Constructor for class be.svlandeg.diffany.examples.ExampleCode
 
expandEdgeOntology(Set<Edge>, EdgeOntology) - Method in class be.svlandeg.diffany.core.algorithms.Unification
Expand an existing edge ontology to cover all interaction types from the input data.
expandNetwork(Set<String>, Set<String>, boolean, boolean, boolean) - Method in class be.svlandeg.diffany.study.osmotic.NetworkConstruction
This method defines all the nodes that will be in the Diffany networks to analyse a given set of overexpressed genes.
ExtraDiffanyVisMappings - Class in be.svlandeg.diffany.cytoscape.vizmapper
Define extra visual mappings that are not specifically needed by the Diffany algorithm.
ExtraDiffanyVisMappings(Services) - Constructor for class be.svlandeg.diffany.cytoscape.vizmapper.ExtraDiffanyVisMappings
Define the extra VizMapper settings
ExtraOptionsMenu - Class in be.svlandeg.diffany.cytoscape.gui
Menu to be placed under Apps, Diffany, Extra options
ExtraOptionsMenu(Model) - Constructor for class be.svlandeg.diffany.cytoscape.gui.ExtraOptionsMenu
Create menu and menu items
ExtraVisMappings - Interface in be.svlandeg.diffany.cytoscape.vizmapper
Define extra visual mappings that are not specifically needed by the Diffany algorithm.

F

fullCleaning(Network, EdgeOntology, ScheduledTask, boolean, boolean) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Clean an input network: Per pair of nodes, group all input edges into subclasses per root category of the EdgeOntology, unify the directionality (either all symmetric or all directed, as dicated by the edge ontology), and resolve conflicts within a root category.
fullConsensusOutputCleaning(ConsensusNetwork, EdgeOntology, ScheduledTask) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Clean an output consensus network: Remove redundant/duplicate edges in the network.
fullDifferentialOutputCleaning(Network, EdgeOntology, ScheduledTask) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Clean an output network: Remove redundant/duplicate edges in the network.
fullInputCleaning(InputNetwork, EdgeOntology, ScheduledTask) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Clean a generic input network: Per pair of nodes, group all input edges into subclasses per root category of the EdgeOntology, unify the directionality (either all symmetric or all directed, as dictated by the edge ontology), and resolve conflicts within a root category.
fullInputConditionCleaning(ConditionNetwork, EdgeOntology, ScheduledTask) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Clean an input condition-specific network: Per pair of nodes, group all input edges into subclasses per root category of the EdgeOntology, unify the directionality (either all symmetric or all directed, as dicated by the edge ontology), and resolve conflicts within a root category.
fullInputRefCleaning(ReferenceNetwork, EdgeOntology, ScheduledTask) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Clean an input reference network: Per pair of nodes, group all input edges into subclasses per root category of the EdgeOntology, unify the directionality (either all symmetric or all directed, as dicated by the edge ontology), and resolve conflicts within a root category.
FuzzyNetworks - Class in be.svlandeg.diffany.examples
This class provides examples to benchmark the fuzzy consensus functionality.
FuzzyNetworks() - Constructor for class be.svlandeg.diffany.examples.FuzzyNetworks
 
FuzzyNetworks2 - Class in be.svlandeg.diffany.examples
This class provides examples to benchmark the fuzzy consensus and differential functionality.
FuzzyNetworks2() - Constructor for class be.svlandeg.diffany.examples.FuzzyNetworks2
Constructor

G

GenePrinter - Class in be.svlandeg.diffany.study.osmotic.arabidopsis
This class allows printing Arabidopsis thaliana gene information in a human-readable format, by taking the original array ID, fetching its corresponding locus tags and Entrez Gene IDs, and gene symbols.
GenePrinter() - Constructor for class be.svlandeg.diffany.study.osmotic.arabidopsis.GenePrinter
Create a new GenePrinter, reading the mapping data.
generateRunConfiguration(Model, ProgressListener) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Generates a RunConfiguration and adds it to the Project
GENERIC_DIRECT_TYPE - Static variable in class be.svlandeg.diffany.core.networks.EdgeGenerator
 
GENERIC_DIRECTED_CAT - Variable in class be.svlandeg.diffany.core.semantics.EdgeOntology
 
GENERIC_SYMM_TYPE - Static variable in class be.svlandeg.diffany.core.networks.EdgeGenerator
 
GENERIC_SYMMETRICAL_CAT - Variable in class be.svlandeg.diffany.core.semantics.EdgeOntology
 
GenericExample - Class in be.svlandeg.diffany.examples
Generic class for printing an example to the console.
GenericExample() - Constructor for class be.svlandeg.diffany.examples.GenericExample
 
getAllArrayMappings(File) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.MapID
Obtain the mapping data between array IDs (keys) and locus IDs (values, as a set).
getAllAttributeNames() - Method in class be.svlandeg.diffany.core.networks.Node
Retrieve all attributes recorded for this node.
getAllDifferentialInteractions() - Method in class be.svlandeg.diffany.cytoscape.CyProject
Gathers the set of interactions (edge types) for all currently selected differential networks.
getAllDifferentialViews(Services) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Returns all CyNetworkViews that correspond to differential networks in this project.
getAllEdgeDefinitions(Node, Node, boolean) - Method in class be.svlandeg.diffany.core.networks.Network
Get all edge definitions in this network between two specific nodes.
getAllEdges(Node, Node) - Method in class be.svlandeg.diffany.core.networks.Network
Get all edges (both symmetric and assymetric) in this network between two specific nodes.
getAllEdges(String, String) - Method in class be.svlandeg.diffany.core.networks.Network
Get all edges (both symmetric and assymetric) in this network between two specific nodes.
getAllEquals(Network, Network) - Static method in class be.svlandeg.diffany.core.semantics.NodeMapper
Define all equal nodes in the two networks, mapping one node in network 1 to a set of nodes in network 2.
getAllEquals(Set<Network>) - Static method in class be.svlandeg.diffany.core.semantics.NodeMapper
Define all equal nodes in a set of networks, creating disjoint sets of nodes.
getAllInteractions() - Method in class be.svlandeg.diffany.cytoscape.CyProject
Iterates over all CyNetworks and creates a Set of all the used interactions, both from source as differential networks.
getAllLogMessages() - Method in class be.svlandeg.diffany.core.project.Logger
Retrieve all the logged messages.
getAllNegSourceCategories() - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Return all negative source (input) categories present in this ontology.
getAllNodeAttributes() - Method in class be.svlandeg.diffany.core.networks.Network
Get all node attributes required in this network.
getAllNodes(Set<Network>) - Static method in class be.svlandeg.diffany.core.semantics.NodeMapper
Get all nodes, without duplicating equal nodes.
getAllPosSourceCategories() - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Return all positive source (input) categories present in this ontology.
getAllSourceCategories(boolean) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Return all source (input) categories present in this ontology.
getAllSourceInteractions() - Method in class be.svlandeg.diffany.cytoscape.CyProject
Gathers the set of interactions (edge types) for all currently selected source networks.
getAllSourceViews(Services) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Returns all CyNetworkViews that correspond to the source networks (reference, conditional and consensus) in this project.
getArrayIDs() - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionData
Retrieve all IDs indexed in this dataset
getArrowHead() - Method in class be.svlandeg.diffany.core.visualstyle.EdgeStyle
Retrieve the arrowhead style
getAtReg() - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.RegData
Retrieve the URI of the regulatory data
getAttribute(String) - Method in class be.svlandeg.diffany.core.networks.Node
Retrieve the value of a certain attribute (can be null if empty or not defined).
getCanonicalForm(String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Return the canonical form of an edge type.
getCollection() - Method in class be.svlandeg.diffany.cytoscape.CyProject
 
getColor() - Method in class be.svlandeg.diffany.core.visualstyle.EdgeStyle
Retrieve the color
getColumnClass(int) - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
 
getColumnClass(int) - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
 
getColumnCount() - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
 
getColumnCount() - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
 
getColumnName(int) - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
 
getColumnName(int) - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
 
getComponent() - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
 
getConditionalNetworks() - Method in class be.svlandeg.diffany.cytoscape.CyProject
Get the set of conditional networks for this project
getConditionalNetworks() - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
Get all conditional CyNetworks in this project.
getConditionNetwork(CyNetwork, EdgeOntology) - Static method in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
Gets the CyNetwork from Cytoscape and creates a ConditionNetwork out of it.
getConditionNetworks() - Method in class be.svlandeg.diffany.core.networks.DifferentialNetwork
Get the (set of) condition-specific networks associated to this differential network
getConditionNetworks() - Method in class be.svlandeg.diffany.core.project.RunDiffConfiguration
Get the condition-dependent network(s): 1 or many.
getConditions() - Method in class be.svlandeg.diffany.core.networks.ConditionNetwork
Get the set of conditions describing the experimental environment of this network.
getConsensusEdge(List<EdgeDefinition>, List<Set<Integer>>, int, double, boolean) - Method in class be.svlandeg.diffany.core.algorithms.EdgeComparison
Method that defines the consensus edge from the corresponding edge categories in the reference and condition-specific networks.
getConsensusID(Set<Node>) - Static method in class be.svlandeg.diffany.core.semantics.NodeMapper
Return a 'consensus' ID for a set of nodes that were previously determined to be equal.
getConsensusNetwork() - Method in class be.svlandeg.diffany.core.networks.OutputNetworkPair
Retrieve the consensus network
getConsensusNetworks() - Method in class be.svlandeg.diffany.core.project.RunOutput
Retrieve all consensus networks
getConsensusNode(Node, Set<Node>, int) - Method in class be.svlandeg.diffany.core.algorithms.NodeComparison
Method that defines the consensus node from the corresponding nodes in the reference and condition-specific networks.
getCornetPPI() - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.PPIdata
Retrieve the URI of the CORNET PPI data
getCutoff() - Method in class be.svlandeg.diffany.cytoscape.Model
Get the edge cutoff.
getCyApplicationManager() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getCyLayoutAlgorithmManager() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getCyNetworkFactory() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getCyNetworkManager() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getCyNetworkViewFactory() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getCyNetworkViewManager() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getCyRootNetworkManager() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getCytoPanelName() - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
 
getDefaultEdge() - Method in class be.svlandeg.diffany.core.networks.EdgeGenerator
Obtain a default edge.
getDefaultProject() - Method in class be.svlandeg.diffany.examples.ActivityFlowTest
Get a custom project
getDefaultProject() - Method in class be.svlandeg.diffany.examples.Bandyopadhyay2010
Get a custom project.
getDefaultProject() - Method in class be.svlandeg.diffany.examples.ConflictingEdgesTest
Get a custom project.
getDefaultProject() - Method in class be.svlandeg.diffany.examples.FuzzyNetworks
Get a custom project.
getDefaultProject() - Method in class be.svlandeg.diffany.examples.FuzzyNetworks2
Get a custom project.
getDefaultProject() - Method in class be.svlandeg.diffany.examples.GenericExample
Allows subclasses to specify a default project for this example.
getDefaultProject() - Method in class be.svlandeg.diffany.examples.Ideker2011
Get a custom project.
getDefaultProject() - Method in class be.svlandeg.diffany.examples.MultipleConditionTest
Get a custom project.
getDefaultProject() - Method in class be.svlandeg.diffany.examples.OsmoticSampleTest
Get a custom project.
getDefaultProject() - Method in class be.svlandeg.diffany.examples.OsmoticUseCase
 
getDefaultProject() - Method in class be.svlandeg.diffany.examples.ProcessTest
Get a custom project.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.ActivityFlowTest
Add some custom-defined networks to the project.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.Bandyopadhyay2010
Add some custom-defined networks to the project.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.ConflictingEdgesTest
Add some custom-defined networks to the project.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.FuzzyNetworks
Add some custom-defined networks to the project: 1 reference network and 3 condition-specific.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.FuzzyNetworks2
Add some custom-defined networks to the project: 1 reference network and 3 condition-specific.
getDefaultRunConfigurationID(Project, int) - Method in class be.svlandeg.diffany.examples.FuzzyNetworks2
Add some custom-defined networks to the project: 1 reference network and 3 condition-specific.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.GenericExample
Allows subclasses to specify a default runconfig for this example.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.Ideker2011
Add some custom-defined networks to the project.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.MultipleConditionTest
Add some custom-defined networks to the project.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.OsmoticSampleTest
Add some custom-defined networks to the project: 1 reference network and 3 condition-specific.
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.OsmoticUseCase
 
getDefaultRunConfigurationID(Project) - Method in class be.svlandeg.diffany.examples.ProcessTest
Add some custom-defined networks to the project.
getDefinition() - Method in class be.svlandeg.diffany.core.networks.Edge
Get the definition of this edge
getDescription() - Method in class be.svlandeg.diffany.core.networks.Condition
Return a free-text description of the condition
getDialogTaskManager() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getDiffanyOptions() - Method in class be.svlandeg.diffany.console.DiffanyOptions
Retrieve the options object for the Diffany project
getDifferentialEdge(EdgeDefinition, List<EdgeDefinition>, List<Set<Integer>>, int, double) - Method in class be.svlandeg.diffany.core.algorithms.EdgeComparison
Method that defines the differential edge from the corresponding edge categories in the reference and condition-specific networks.
getDifferentialEdgeDrawing() - Method in class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
 
getDifferentialEdgeDrawing() - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Retrieve an EdgeDrawing object which knows how to define the visual styles in a differential network
getDifferentialNetwork() - Method in class be.svlandeg.diffany.core.networks.OutputNetworkPair
Retrieve the differential network
getDifferentialNetworks() - Method in class be.svlandeg.diffany.core.project.RunOutput
Retrieve all differential networks
getDiffStyle() - Method in class be.svlandeg.diffany.cytoscape.Model
Get the style applied to differential networks
getDirectedEdges(Node, Node) - Method in class be.svlandeg.diffany.core.networks.Network
Get all directed edges in this network between two specific nodes.
getDisplayName() - Method in class be.svlandeg.diffany.core.networks.Node
Return the name of this node.
getEdgeArrowHead(String) - Method in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
getEdgeArrowHead(String) - Method in class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
 
getEdgeArrowHead(String) - Method in class be.svlandeg.diffany.core.visualstyle.EdgeDrawing
Define the ArrowHead object of an edge by edge category.
getEdgeColor(String) - Method in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
getEdgeColor(String) - Method in class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
 
getEdgeColor(String) - Method in class be.svlandeg.diffany.core.visualstyle.EdgeDrawing
Define the Color object of an edge by edge category.
getEdgeOntology() - Method in class be.svlandeg.diffany.core.project.Project
Get the edge ontology of this project, which can translate edge types to categories and assign semantics to the categories.
getEdges() - Method in class be.svlandeg.diffany.core.networks.Network
Get the set of edges in this network.
getEdgesPerRoot(EdgeOntology, Set<String>, Set<EdgeDefinition>) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Group all input edges into subclasses per root category of the EdgeOntology.
getEdgeStyle(String) - Method in class be.svlandeg.diffany.core.visualstyle.EdgeDrawing
Define the full visual style of an edge by edge category.
getElementAt(int) - Method in class be.svlandeg.diffany.cytoscape.gui.ModeDropDownModel
 
getElementAt(int) - Method in class be.svlandeg.diffany.cytoscape.gui.ProjectDropDownModel
 
getFDR(String) - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionData
Retrieve the false discovery rate (FDR) of a certain ID
getFoldchange(String) - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionData
Retrieve the fold change of a certain ID
getHeader() - Static method in class be.svlandeg.diffany.core.io.EdgeIO
Write the header line, i.e.
getHeader(SortedSet<Attribute>) - Static method in class be.svlandeg.diffany.core.io.NodeIO
Write the header for the node file, including the custom node attribute names.
getHiddenInteractions() - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
Get a set of edge types (interactions) that should be hidden.
getHideUnconnectedNodes() - Method in class be.svlandeg.diffany.cytoscape.Model
 
getIcon() - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
 
getID() - Method in class be.svlandeg.diffany.core.networks.Network
Return the ID of this network (which should be unique within one project)
getID() - Method in class be.svlandeg.diffany.core.networks.Node
Return the unique ID of this node.
getInputNetwork(CyNetwork, EdgeOntology) - Static method in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
Gets the CyNetwork from Cytoscape and creates a InputNetwork out of it.
getInputNetworks() - Method in class be.svlandeg.diffany.core.project.RunConfiguration
Get all input network(s): 1 or many.
getKinaseInteractions() - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
Retrieve the URI of the kinase interaction data
getKinases() - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
Retrieve the URI of the kinase activity data
getLatestRunConfigID() - Method in class be.svlandeg.diffany.cytoscape.CyProject
 
getListener() - Method in class be.svlandeg.diffany.core.progress.ScheduledTask
Retrieve the progress listener object
getLocusGIDMappings(File) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.MapID
Obtain the mapping data between locus IDs (keys) and Entrez Gene IDs (values).
getLogger(int) - Method in class be.svlandeg.diffany.core.project.Project
Get the logger for a specific run ID.
getMappings() - Method in class be.svlandeg.diffany.cytoscape.vizmapper.ExtraDiffanyVisMappings
 
getMappings() - Method in interface be.svlandeg.diffany.cytoscape.vizmapper.ExtraVisMappings
Get all the extra visual mappings.
getMaxWeight() - Method in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
getMaxWeight() - Method in class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
 
getMaxWeight() - Method in class be.svlandeg.diffany.core.visualstyle.EdgeDrawing
For visualisation purposes, weights need to be scaled up to a certain maximum.
getMaxWeightedEdge(Set<EdgeDefinition>, EdgeOntology, String, Node, Node, String) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Return the edge with the highest weight, or, if there are more, the most specific one.
getMessage() - Method in class be.svlandeg.diffany.core.project.LogEntry
Retrieve the message of this log entry
getMetaOptions() - Method in class be.svlandeg.diffany.console.MetaOptions
Retrieve the options object for the meta data
getMinWeight() - Method in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
getMinWeight() - Method in class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
 
getMinWeight() - Method in class be.svlandeg.diffany.core.visualstyle.EdgeDrawing
For visualisation purposes, weights need to be scaled from a certain minimum.
getMode() - Method in class be.svlandeg.diffany.cytoscape.Model
Returns the execution mode for this project: Reference against all conditional networks, one at a time or all at once.
getName() - Method in class be.svlandeg.diffany.core.networks.Attribute
 
getName() - Method in class be.svlandeg.diffany.core.networks.Network
Return the name of this network
getName() - Method in class be.svlandeg.diffany.core.project.Project
Return the name of this project
getName() - Method in class be.svlandeg.diffany.cytoscape.CyProject
Returns the name of this project.
getName() - Method in class be.svlandeg.diffany.cytoscape.gui.NetworkEntry
Gets the default name from the network table.
getName() - Method in class be.svlandeg.diffany.examples.GenericExample
 
getName() - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionData
Return the name of this data
getNegPrefix_dir() - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve the prefix used for negative directed edges
getNegPrefix_symm() - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve the prefix used for negative symmetrical edges
getNetwork() - Method in class be.svlandeg.diffany.cytoscape.gui.NetworkEntry
The wrapped CyNetwork
getNetworkByTableId(Long) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Returns the network in this project with default (edge or node) table with given suid.
getNetworkEntry(int) - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
Get the entry at given row
getNetworkInFocus() - Method in class be.svlandeg.diffany.cytoscape.Model
The network of which the view is in focus.
getNextID() - Static method in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
 
getNodeIDs(Set<Node>) - Static method in class be.svlandeg.diffany.core.semantics.NodeMapper
Retrieve a unique set of node IDs
getNodeIDsFromEdges(Set<Edge>) - Static method in class be.svlandeg.diffany.core.semantics.NodeMapper
Retrieve a unique set of node IDs pertaining a set of edges
getNodes() - Method in class be.svlandeg.diffany.core.networks.Network
Get the set of nodes in this network
getNodesByID(Set<Node>) - Static method in class be.svlandeg.diffany.core.semantics.NodeMapper
Retrieve a mapping of the given nodes by their IDs
getNodesByLocusID(Set<String>) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.GenePrinter
Retrieve a set of nodes from their node IDs, by using the GenePrinter to search for their symbol
getNumberOfInputNetworks() - Method in class be.svlandeg.diffany.cytoscape.CyProject
 
getNumberOfRuns() - Method in class be.svlandeg.diffany.core.project.Project
Retrieve the number of runs in this project
getOntologyTerms() - Method in class be.svlandeg.diffany.core.networks.Condition
Return the corresponding ontology terms for this condition
getOutput(int) - Method in class be.svlandeg.diffany.core.project.Project
Get the output for a specific run ID.
getOutputAsPairs() - Method in class be.svlandeg.diffany.core.project.RunOutput
Retrieve the differential and consensus networks as result pairs.
getOverlapOperator() - Method in class be.svlandeg.diffany.cytoscape.Model
Get the way in which overlapping edge weights are calculated.
getOverlapSupportCutoff() - Method in class be.svlandeg.diffany.cytoscape.Model
Return the number of edges that need to be matching in the different networks in order to consider an edge a "consensus" edge.
getParentWindow() - Method in class be.svlandeg.diffany.cytoscape.Model
Get a reference to the Cytoscape main window
getPhosphat() - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
Retrieve the URI of the Phosphat data
getPosPrefix_dir() - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve the prefix used for positive directed edges
getPosPrefix_symm() - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve the prefix used for positive symmetrical edges
getProject() - Method in class be.svlandeg.diffany.cytoscape.CyProject
The actual Project that executes the algorithm.
getProjects() - Method in class be.svlandeg.diffany.cytoscape.Model
Get a list of all loaded CyProjects
getPvalue(String) - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionData
Retrieve the p-value of a certain ID
getReferenceNetwork() - Method in class be.svlandeg.diffany.core.networks.DifferentialNetwork
Get the reference network associated to this differential network
getReferenceNetwork() - Method in class be.svlandeg.diffany.core.project.RunDiffConfiguration
Get the reference network of this configuration, against which the condition dependent network(s) will be compared to.
getReferenceNetwork(CyNetwork, EdgeOntology) - Static method in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
Gets the CyNetwork from Cytoscape and creates a ReferenceNetwork out of it.
getReferenceNetwork() - Method in class be.svlandeg.diffany.cytoscape.CyProject
Gets the reference network for this project.
getReferenceNetwork() - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
Gets the CyNetwork to be used as reference network.
getRefRequired() - Method in class be.svlandeg.diffany.core.project.RunConfiguration
Retrieve whether or not the reference network needs to have an edge for it to be allowed inclusion in the consensus network
getResultNetworks() - Method in class be.svlandeg.diffany.cytoscape.CyProject
Get the set of resulting network pairs.
getRowCount() - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
 
getRowCount() - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
 
getRowNumber(CyNetwork) - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
Get the row number of a given CyNetwork
getRunConfiguration(int) - Method in class be.svlandeg.diffany.core.project.Project
Get a specific RunConfiguration by its unique run ID
getSelectedItem() - Method in class be.svlandeg.diffany.cytoscape.gui.ModeDropDownModel
 
getSelectedItem() - Method in class be.svlandeg.diffany.cytoscape.gui.ProjectDropDownModel
 
getSelectedProject() - Method in class be.svlandeg.diffany.cytoscape.Model
Returns the current CyProject.
getServices() - Method in class be.svlandeg.diffany.cytoscape.Model
Gives access to a subset of the services offered in this context, as loaded in the CyActivator
getSignificantGenes(double) - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionData
Retrieve all the significant gene IDs in this overexpression dataset, by using the threshold as a minimal cutoff of the FDR values.
getSize() - Method in class be.svlandeg.diffany.cytoscape.gui.ModeDropDownModel
 
getSize() - Method in class be.svlandeg.diffany.cytoscape.gui.ProjectDropDownModel
 
getSource() - Method in class be.svlandeg.diffany.core.networks.Edge
Get the source node of this edge.
getSourceCategory(String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Get the semantic category of a certain edge type.
getSourceEdgeDrawing() - Method in class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
 
getSourceEdgeDrawing() - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Retrieve an EdgeDrawing object which knows how to define the visual styles in an input (reference or condition-dependent) or consensus network
getSourceStyle() - Method in class be.svlandeg.diffany.cytoscape.Model
Get the style applied to source networks
getStringRepresentation() - Method in class be.svlandeg.diffany.core.networks.ConditionNetwork
 
getStringRepresentation() - Method in class be.svlandeg.diffany.core.networks.ConsensusNetwork
 
getStringRepresentation() - Method in class be.svlandeg.diffany.core.networks.DifferentialNetwork
 
getStringRepresentation() - Method in class be.svlandeg.diffany.core.networks.InputNetwork
 
getStringRepresentation() - Method in class be.svlandeg.diffany.core.networks.Network
Obtain an easy readible string representation of this network.
getStringRepresentation() - Method in class be.svlandeg.diffany.core.networks.ReferenceNetwork
 
getSupportCutoff() - Method in class be.svlandeg.diffany.core.project.RunConfiguration
Return the required number of supporting networks needed before the edge will be present in the consensus network.
getSymbolByArrayID(String) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.GenePrinter
Get the official symbol of an A.th.
getSymbolByLocusID(String) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.GenePrinter
Get the official symbol of an A.th.
getSymbolMappings(File) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.MapID
Obtain the official gene symbols (unique values) by their Entrez Gene IDs (keys).
getSynonymMappings(File) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.MapID
Obtain all synonyms (values) by their Entrez Gene IDs (keys).
getSynonymsByArrayID(String) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.GenePrinter
Get the synonyms of an A.th.
getSynonymsByLocusID(String) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.GenePrinter
Get the synonyms of an A.th.
getTarget() - Method in class be.svlandeg.diffany.core.networks.Edge
Get the target node of this edge.
getTaskManager() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getTestConfiguration(Project) - Method in class be.svlandeg.diffany.examples.OsmoticUseCase
 
getTestConfigurationWithoutReference(Project, int, boolean) - Method in class be.svlandeg.diffany.examples.FuzzyNetworks
Add some custom-defined networks to the project: 4 condition-specific networks, no reference.
getTestConfigurationWithReference(Project, int) - Method in class be.svlandeg.diffany.examples.FuzzyNetworks
Add some custom-defined networks to the project: 1 reference network and 3 condition-specific.
getTestConsensusConfiguration(Project) - Method in class be.svlandeg.diffany.examples.MultipleConditionTest
Add some custom-defined networks to the project.
getTestConsensusConfiguration(Project, int) - Method in class be.svlandeg.diffany.examples.OsmoticSampleTest
Add some custom-defined networks to the project.
getTestDiffConfiguration(Project, int) - Method in class be.svlandeg.diffany.examples.OsmoticSampleTest
Add some custom-defined networks to the project.
getTestProject() - Method in class be.svlandeg.diffany.examples.OsmoticUseCase
 
getTitle() - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
 
getTotalSupport() - Method in class be.svlandeg.diffany.core.algorithms.EdgeComparison.IntermediateComparison
 
getType() - Method in class be.svlandeg.diffany.core.networks.Attribute
 
getType() - Method in class be.svlandeg.diffany.core.networks.Edge
Get the type of this edge
getType() - Method in class be.svlandeg.diffany.core.networks.EdgeDefinition
Get the type of this edge
getUnspecifiedPrefix() - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve the prefix used for unspecified edges
getValueAt(int, int) - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
 
getValueAt(int, int) - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
 
getVisualMappingFunctionFactory(String) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getVisualMappingManager() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getVisualStyle() - Method in class be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
 
getVisualStyleFactory() - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
getVoidEdge(boolean) - Method in class be.svlandeg.diffany.core.networks.EdgeGenerator
Obtain a void edge, for the purpose of being able to compare it to existing edges.
getWeight() - Method in class be.svlandeg.diffany.core.networks.Edge
Get the weight of this edge.
getWeight() - Method in class be.svlandeg.diffany.core.networks.EdgeDefinition
Get the weight of this edge.

H

handleEvent(NetworkAddedEvent) - Method in class be.svlandeg.diffany.cytoscape.Model
 
handleEvent(NetworkDestroyedEvent) - Method in class be.svlandeg.diffany.cytoscape.Model
 
handleEvent(RowsSetEvent) - Method in class be.svlandeg.diffany.cytoscape.Model
 
handleEvent(SetCurrentNetworkViewEvent) - Method in class be.svlandeg.diffany.cytoscape.Model
 
handleEvent(SessionLoadedEvent) - Method in class be.svlandeg.diffany.cytoscape.SessionListener
 
handleEvent(SessionAboutToBeSavedEvent) - Method in class be.svlandeg.diffany.cytoscape.SessionListener
 
hasEntries() - Method in class be.svlandeg.diffany.cytoscape.gui.ProjectDropDownModel
Checks if there are any collections in the list
headerShort - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
helpShort - Static variable in class be.svlandeg.diffany.console.MetaOptions
 
hubPhos - Static variable in class be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
 
hubPPI - Static variable in class be.svlandeg.diffany.study.osmotic.arabidopsis.PPIdata
 

I

ID - Variable in class be.svlandeg.diffany.core.networks.Network
 
ID - Variable in class be.svlandeg.diffany.core.networks.Node
 
Ideker2011 - Class in be.svlandeg.diffany.examples
This class provides examples taken from the Ideker et al, Molecular Systems Biology 2011 paper.
Ideker2011() - Constructor for class be.svlandeg.diffany.examples.Ideker2011
Constructor
indexedByRawArrayIDs() - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionData
Return whether or not this dataset is indexed by array IDs (if not, they are locus IDs)
InputNetwork - Class in be.svlandeg.diffany.core.networks
A generic input network is not yet defined as a specific Diffany network type, and can at times be used to generically read input data, which still requires pre-processing.
InputNetwork(String, int, Set<Attribute>) - Constructor for class be.svlandeg.diffany.core.networks.InputNetwork
Create a new generic input network.
InputNetwork(String, int, Set<Attribute>, Set<Node>, Set<Edge>) - Constructor for class be.svlandeg.diffany.core.networks.InputNetwork
Create a new generic input network.
inputNetworks - Variable in class be.svlandeg.diffany.core.project.RunConfiguration
 
inputShort - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
insertDefaultContrasts() - Method in class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
Provide some default pos/neg categories, like positive and negative regulation.
insertDefaultMappings() - Method in class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
Provide a default mapping edge type to category mapping.
insertDefaultParents() - Method in class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
Provide some default child-parent mapping between source categories.
IntermediateComparison(String) - Constructor for class be.svlandeg.diffany.core.algorithms.EdgeComparison.IntermediateComparison
 
InvalidRunConfigurationException - Exception in be.svlandeg.diffany.cytoscape
Get throws when a CyProject doesn't have enough input data to create a new RunConfiguration
InvalidRunConfigurationException() - Constructor for exception be.svlandeg.diffany.cytoscape.InvalidRunConfigurationException
 
isCellEditable(int, int) - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
 
isCellEditable(int, int) - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
 
isConditionalNetwork(CyNetwork) - Method in class be.svlandeg.diffany.cytoscape.CyProject
 
isContained(Node, Set<Node>) - Static method in class be.svlandeg.diffany.core.semantics.NodeMapper
Define whether or not this node is already in the set.
isDefinedSourceCat(String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Check whether a certain edge category is present in this ontology.
isDefinedSourceType(String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Check whether a certain edge type is present in this ontology.
isDiffNetwork(CyNetwork) - Method in class be.svlandeg.diffany.cytoscape.CyProject
 
isDiffType(int) - Method in class be.svlandeg.diffany.core.project.Project
Get the type of the run configuration by ID: true if it can calculate differential networks, false otherwise (only consensus).
isGenerateConsensusNets() - Method in class be.svlandeg.diffany.cytoscape.Model
Are consensus networks to be generated?
isGenerateDiffNets() - Method in class be.svlandeg.diffany.cytoscape.Model
Are differential networks to be generated?
isNegated() - Method in class be.svlandeg.diffany.core.networks.Edge
Return whether or not this edge is negated (e.g.
isNegated() - Method in class be.svlandeg.diffany.core.networks.EdgeDefinition
Return whether or not this edge is negated (e.g.
isNegDirected(String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve whether or not a certain differential category can be seen as a negative, directed edge
isNegSymm(String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve whether or not a certain category can be seen as a negative, symmetrical edge
isPosDirected(String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve whether or not a certain differential category can be seen as a positive, directed edge
isPosSymm(String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve whether or not a certain category can be seen as a positive, symmetrical edge
isReady() - Method in class be.svlandeg.diffany.cytoscape.tasks.LoadExampleTaskFactory
 
isReady() - Method in class be.svlandeg.diffany.cytoscape.tasks.RunProjectTaskFactory
 
isReady() - Method in class be.svlandeg.diffany.cytoscape.tasks.UpdateVisualStyleTaskFactory
 
isReference() - Method in class be.svlandeg.diffany.cytoscape.gui.NetworkEntry
 
isReferenceNetwork(CyNetwork) - Method in class be.svlandeg.diffany.cytoscape.CyProject
 
isRefIncludedInOverlapSupportCutoff() - Method in class be.svlandeg.diffany.cytoscape.Model
When calculating only consensus networks, should the reference network be required to supply an edge?
isSelected() - Method in class be.svlandeg.diffany.cytoscape.gui.NetworkEntry
 
isSourceCatChildOf(String, String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Determine whether or not two categories are related to eachother as child (sub) - parent (super)
isSourceCatChildOf(String, String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
 
isSourceNetwork(CyNetwork) - Method in class be.svlandeg.diffany.cytoscape.CyProject
 
isSourceTypeChildOf(String, String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Determine whether or not an edge type (child) is related to a category (partent).
isSourceTypeChildOf(String, String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
 
isSymmetrical() - Method in class be.svlandeg.diffany.core.networks.Edge
Return whether or not this edge is symmetrical (if not, it goes specifically from source to target, otherwise there is no real direction)
isSymmetrical() - Method in class be.svlandeg.diffany.core.networks.EdgeDefinition
Return whether or not this edge is symmetrical (if not, it goes specifically from source to target, otherwise there is no real direction)
isSymmetricalSourceCat(String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Retrieve the symmetry state of a source edge category in this ontology
isSymmetricalSourceType(String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Retrieve the symmetry state of a source edgeType in this ontology
isValidNetworkDir(File, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Check whether this directory contains the necessary files to read a network from

K

kinase_attribute - Static variable in class be.svlandeg.diffany.core.networks.Node
 
KinaseData - Class in be.svlandeg.diffany.study.osmotic.arabidopsis
This class defines and analyses the data retrieved for Arabidopsis thaliana.
KinaseData(GenePrinter) - Constructor for class be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
Constructor: defines the gene printer that can deal with gene synonymy etc.

L

LoadExampleAction - Class in be.svlandeg.diffany.cytoscape.actions
Action that loads example CyNetworks into a Cytoscape session, based on a given Project.
LoadExampleAction(Services, String, Project, int) - Constructor for class be.svlandeg.diffany.cytoscape.actions.LoadExampleAction
Load an example Project into the current Cytoscape session.
LoadExampleAction(Services, GenericExample) - Constructor for class be.svlandeg.diffany.cytoscape.actions.LoadExampleAction
Set up the action, but don't load the example just yet.
LoadExampleTask - Class in be.svlandeg.diffany.cytoscape.tasks
Task to load example Projects into Cytoscape.
LoadExampleTask(Services, Project, int) - Constructor for class be.svlandeg.diffany.cytoscape.tasks.LoadExampleTask
Construct a new task to load networks from a Project.
LoadExampleTask(Services, GenericExample) - Constructor for class be.svlandeg.diffany.cytoscape.tasks.LoadExampleTask
Construct a new task to load networks from a Project.
LoadExampleTaskFactory - Class in be.svlandeg.diffany.cytoscape.tasks
Factory to call LoadExampleTask
LoadExampleTaskFactory(Services, Project, int) - Constructor for class be.svlandeg.diffany.cytoscape.tasks.LoadExampleTaskFactory
 
LoadExampleTaskFactory(Services, GenericExample) - Constructor for class be.svlandeg.diffany.cytoscape.tasks.LoadExampleTaskFactory
 
log - Variable in class be.svlandeg.diffany.core.algorithms.EdgeByEdge
 
log(String) - Method in class be.svlandeg.diffany.core.project.Logger
Record a log message, with the date specified to be at the time of this function call.
LogEntry - Class in be.svlandeg.diffany.core.project
A LogEntry is a logged message together with relevant meta data, used by the Logger object.
LogEntry(Date, String) - Constructor for class be.svlandeg.diffany.core.project.LogEntry
Create a new log entry at a specific date and with a specific message
Logger - Class in be.svlandeg.diffany.core.project
A Logger object records all messages that are relevant to the user of the networks algorithms.
Logger() - Constructor for class be.svlandeg.diffany.core.project.Logger
Create a new instance with an empty log file.
logger - Variable in class be.svlandeg.diffany.core.project.Run
 
logShort - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 

M

main(String[]) - Static method in class be.svlandeg.diffany.console.RunConsole
Main method that allows running the Diffany algorithms through the console.
main(String[]) - Static method in class be.svlandeg.diffany.examples.ActivityFlowTest
Testing the example
main(String[]) - Static method in class be.svlandeg.diffany.examples.Bandyopadhyay2010
Testing the example using console output (use TestExamples for the JUnit version!)
main(String[]) - Static method in class be.svlandeg.diffany.examples.ConflictingEdgesTest
Testing the example
main(String[]) - Static method in class be.svlandeg.diffany.examples.FuzzyNetworks
Testing the example using console output (use TestFuzzyConsensus for the JUnit version!)
main(String[]) - Static method in class be.svlandeg.diffany.examples.FuzzyNetworks2
Testing the example using console output (use TestFuzzyConsensus for the JUnit version!)
main(String[]) - Static method in class be.svlandeg.diffany.examples.Ideker2011
Testing the example using console output (use TestExamples for the JUnit version!)
main(String[]) - Static method in class be.svlandeg.diffany.examples.MultipleConditionTest
Testing the example
main(String[]) - Static method in class be.svlandeg.diffany.examples.OsmoticSampleTest
Testing the example
main(String[]) - Static method in class be.svlandeg.diffany.examples.OsmoticUseCase
 
main(String[]) - Static method in class be.svlandeg.diffany.examples.ProcessTest
Testing the example
main(String[]) - Static method in class be.svlandeg.diffany.study.osmotic.NetworkAnalysis
Run an analysis on specific data
main(String[]) - Static method in class be.svlandeg.diffany.study.osmotic.RunAnalysis
Run the full analysis pipeline.
makeNegated(boolean) - Method in class be.svlandeg.diffany.core.networks.EdgeDefinition
Make this edge negated or not
makeSymmetrical(boolean) - Method in class be.svlandeg.diffany.core.networks.EdgeDefinition
Make this edge symmetrical or not
mapCanSourceTypeToCategory - Variable in class be.svlandeg.diffany.core.semantics.EdgeOntology
 
MapID - Class in be.svlandeg.diffany.study.osmotic.arabidopsis
This class provides functionality to map Arabidopsis identifiers, for instance between array IDs and locus IDs
MapID() - Constructor for class be.svlandeg.diffany.study.osmotic.arabidopsis.MapID
 
max_weight - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
max_weight - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
 
MetaOptions - Class in be.svlandeg.diffany.console
This class defines the various 'meta' options available when running the Diffany jar through the console, such as the help message and the version number.
MetaOptions() - Constructor for class be.svlandeg.diffany.console.MetaOptions
Constructor initializes the meta options for this program
min_weight - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
min_weight - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
 
mode - Variable in class be.svlandeg.diffany.core.algorithms.CalculateDiff
 
ModeDropDownModel - Class in be.svlandeg.diffany.cytoscape.gui
Model for the JComboBox displaying available algorithm modes.
ModeDropDownModel() - Constructor for class be.svlandeg.diffany.cytoscape.gui.ModeDropDownModel
 
Model - Class in be.svlandeg.diffany.cytoscape
Model that keeps track of all settings and selections within the Cytoscape App.
Model(Services) - Constructor for class be.svlandeg.diffany.cytoscape.Model
Construct a new model and adds the app services to it.
Model.ComparisonMode - Enum in be.svlandeg.diffany.cytoscape
Allows for switching between algorithm execution modes.
Model.OverlapOperator - Enum in be.svlandeg.diffany.cytoscape
Operator to define the way overlapping edge weights are calculated
modeShort - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
modifyDEState(Map<String, Double>, Set<Node>) - Method in class be.svlandeg.diffany.study.osmotic.NetworkConstruction
Modify the differentially expressed status of a collection of DE nodes, using over/under expression data.
MultipleConditionTest - Class in be.svlandeg.diffany.examples
Testing class that tries to simulate a use-case of calculating a differential network from one reference network and multiple condition-specific networks.
MultipleConditionTest() - Constructor for class be.svlandeg.diffany.examples.MultipleConditionTest
 

N

name - Variable in class be.svlandeg.diffany.core.networks.Network
 
name - Variable in class be.svlandeg.diffany.core.networks.Node
 
name - Variable in class be.svlandeg.diffany.core.project.Project
 
name - Variable in class be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
Name of the visual style
neg_ah - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
neg_paint - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
negated - Variable in class be.svlandeg.diffany.core.networks.EdgeDefinition
 
NEGATED - Static variable in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
Column name for negated edges (boolean)
negSourceCats - Variable in class be.svlandeg.diffany.core.semantics.EdgeOntology
 
Network - Class in be.svlandeg.diffany.core.networks
Abstract class that represents a network: a collection of edges and nodes.
Network(String, int, Set<Attribute>, Set<Node>, Set<Edge>) - Constructor for class be.svlandeg.diffany.core.networks.Network
Create a new network with a specific name, ID, and sets of nodes and edges.
Network(String, int, Set<Attribute>) - Constructor for class be.svlandeg.diffany.core.networks.Network
Create a new network with an empty set of nodes and edges.
NetworkAnalysis - Class in be.svlandeg.diffany.study.osmotic
This class is useful for general network analyses, for instance to determine the hubs in an input network.
NetworkAnalysis() - Constructor for class be.svlandeg.diffany.study.osmotic.NetworkAnalysis
Currently empty constructor
NetworkCleaning - Class in be.svlandeg.diffany.core.algorithms
This class provides generic methods useful for network cleaning before or after applying differential algorithms.
NetworkCleaning(Logger) - Constructor for class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Create a new cleaning object, which can log important messages.
NetworkConstruction - Class in be.svlandeg.diffany.study.osmotic
This class allows to construct networks out of overexpression/coexpression values.
NetworkConstruction(GenePrinter) - Constructor for class be.svlandeg.diffany.study.osmotic.NetworkConstruction
Constructor: defines the gene printer that can deal with gene synonymy etc.
NetworkEntry - Class in be.svlandeg.diffany.cytoscape.gui
Wrapper class for CyNetworks to easily include them in GUI components by supplying a toString method returning the network name.
NetworkEntry(CyNetwork) - Constructor for class be.svlandeg.diffany.cytoscape.gui.NetworkEntry
Returns a new entry, based on given CyNetwork
NetworkIO - Class in be.svlandeg.diffany.core.io
This class allows reading or writing a Network from File.
NetworkIO() - Constructor for class be.svlandeg.diffany.core.io.NetworkIO
 
neutral_ah - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
 
neutral_paint - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
 
nextID - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
Node - Class in be.svlandeg.diffany.core.networks
Class that represents a node in a network.
Node(String, String) - Constructor for class be.svlandeg.diffany.core.networks.Node
Create a new (non-virtual) node with a specific ID and name
nodeAttributes - Variable in class be.svlandeg.diffany.core.networks.Network
 
NodeComparison - Class in be.svlandeg.diffany.core.algorithms
This class defines the nodes to be used in output (differential/consensus) networks, by transferring the node attributes and name/ID from the corresponding input nodes.
NodeComparison() - Constructor for class be.svlandeg.diffany.core.algorithms.NodeComparison
 
NodeIO - Class in be.svlandeg.diffany.core.io
This class allows reading/writing a Node from/to File.
NodeIO() - Constructor for class be.svlandeg.diffany.core.io.NodeIO
 
NodeMapper - Class in be.svlandeg.diffany.core.semantics
This abstract class allows identifying equal nodes across two networks.
NodeMapper() - Constructor for class be.svlandeg.diffany.core.semantics.NodeMapper
 
nodes - Variable in class be.svlandeg.diffany.core.networks.Network
 
not_de - Static variable in class be.svlandeg.diffany.core.networks.Node
 

O

ontologies - Variable in class be.svlandeg.diffany.core.networks.Condition
 
operatorShort - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
originalNetworks - Variable in class be.svlandeg.diffany.core.networks.ConsensusNetwork
 
OsmoticSampleTest - Class in be.svlandeg.diffany.examples
Testing class that simulates a few of the osmotic use-case edges (4 time-specific condition networks).
OsmoticSampleTest() - Constructor for class be.svlandeg.diffany.examples.OsmoticSampleTest
 
OsmoticUseCase - Class in be.svlandeg.diffany.examples
 
OsmoticUseCase() - Constructor for class be.svlandeg.diffany.examples.OsmoticUseCase
 
output - Variable in class be.svlandeg.diffany.core.project.Run
 
OutputNetworkPair - Class in be.svlandeg.diffany.core.networks
This class simply contains one differential network and its corresponding consensus network.
OutputNetworkPair(DifferentialNetwork, ConsensusNetwork) - Constructor for class be.svlandeg.diffany.core.networks.OutputNetworkPair
Create a new pair from one specific differential network and its counterpart consensus network.
outputShort - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
OverexpressionData - Class in be.svlandeg.diffany.study.osmotic
This data object stores the fold changes, p-values and FDR rates per array ID, for a certain analysis (uniquely identified by name).
OverexpressionData(String, boolean) - Constructor for class be.svlandeg.diffany.study.osmotic.OverexpressionData
Create a new object to contain overexpression values
OverexpressionIO - Class in be.svlandeg.diffany.study.osmotic
This class is used to print all calculated overexpression values to one big file.
OverexpressionIO() - Constructor for class be.svlandeg.diffany.study.osmotic.OverexpressionIO
 

P

p - Variable in class be.svlandeg.diffany.core.project.Run
 
p - Variable in class be.svlandeg.diffany.core.project.RunOutput
 
parentCatToArrowHead - Variable in class be.svlandeg.diffany.core.visualstyle.TreeEdgeDrawing
 
parentCatToColor - Variable in class be.svlandeg.diffany.core.visualstyle.TreeEdgeDrawing
 
phos_attribute - Static variable in class be.svlandeg.diffany.core.networks.Node
 
pos_ah - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
pos_paint - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
posSourceCats - Variable in class be.svlandeg.diffany.core.semantics.EdgeOntology
 
PPIdata - Class in be.svlandeg.diffany.study.osmotic.arabidopsis
This class defines and analyses the PPI data retrieved for Arabidopsis thaliana.
PPIdata(GenePrinter) - Constructor for class be.svlandeg.diffany.study.osmotic.arabidopsis.PPIdata
Constructor: defines the gene printer that can deal with gene synonymy etc.
printAllNetworks(RunDiffConfiguration) - Method in class be.svlandeg.diffany.examples.GenericExample
Print a differential run configuration
printAllNetworks(RunConfiguration) - Method in class be.svlandeg.diffany.examples.GenericExample
Print a run configuration
printAllNetworks(Project, int, boolean, boolean, boolean) - Method in class be.svlandeg.diffany.examples.GenericExample
Print an entire project.
printDatasets(String, List<OverexpressionData>, GenePrinter) - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionIO
Print all genes in the experiments and their values across all types of statistical comparisons
printNetwork(Network) - Method in class be.svlandeg.diffany.examples.GenericExample
Print a network by printing its string representation and its edges.
printNetworkStats(Network) - Method in class be.svlandeg.diffany.study.osmotic.NetworkAnalysis
Print a few generic network stats
processRawATH1mapping(File, File) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.MapID
Process the raw mapping data obtained from TAIR.
processRawMAinfo() - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.MapID
Process the raw mapping data obtained from ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_ATH1_array_elements-2010-12-20.txt Currently, the output (written to the D disk), has been stored as a resources file in Maven.
ProcessTest - Class in be.svlandeg.diffany.examples
Testing class that tries to simulate a range of possibilities in process networks and is able to produce differential networks for them.
ProcessTest() - Constructor for class be.svlandeg.diffany.examples.ProcessTest
 
ProgressListener - Class in be.svlandeg.diffany.core.progress
This interface allows to follow the progress of a differential network calculation, and as such allows to provide feedback to a waiting user.
ProgressListener() - Constructor for class be.svlandeg.diffany.core.progress.ProgressListener
Iniate a progress listener at a total of 0 ticks.
Project - Class in be.svlandeg.diffany.core.project
A project consists of a number of Diffany runs and the ontology settings within one user session.
Project(String) - Constructor for class be.svlandeg.diffany.core.project.Project
Create a new project with a default node mapper and a default edge ontology that can interpret the differential edges.
Project(String, TreeEdgeOntology) - Constructor for class be.svlandeg.diffany.core.project.Project
Create a new project with a node mapper and an edge ontology that can interpret the differential edges.
ProjectDropDownModel - Class in be.svlandeg.diffany.cytoscape.gui
Model for the JComboBox that shows the list of available CyProjects in this session.
ProjectDropDownModel(Model) - Constructor for class be.svlandeg.diffany.cytoscape.gui.ProjectDropDownModel
Create a new ComboBoxModel based on the general Model of this app and populates (refreshes) the list of network collections.
putSourceCatParent(String, String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Define a child category and its parent category.
putVisualMappingFunctionFactory(String, VisualMappingFunctionFactory) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 

R

readAllKinaseInteractions(boolean) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
Construct a set of kinase-target edges, reading input from a specified URI.
readAllPPIs(boolean) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.PPIdata
Construct a set of PPI edges, reading input from a specified URI.
readAttributesFromFile(File) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read the node attributes of a network from file.
readAttributesFromStream(InputStream) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read the node attributes of a network from stream.
readConditionNetworkFromDir(File, boolean, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read a ConditionNetwork from a directory: all edges from one File (edges.txt), and all nodes from another (nodes.txt).
readConditionNetworkFromResource(String, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read a ConditionNetwork from a resource: all edges from one File (edges.txt), and all nodes from another (nodes.txt).
readConditionsFromFile(File) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read all conditions from a file containing one tab-delimited condition per line.
readConditionsFromStream(InputStream) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read all conditions from a stream containing one tab-delimited condition per line.
readConsensusNetworkFromDir(File, ReferenceNetwork, Set<ConditionNetwork>, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read a ConsensusNetwork from a directory: all edges from one File (edges.txt), and all nodes from another (nodes.txt).
readDatasets(String, boolean) - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionIO
Read all genes and their corresponding p-values of the statistical comparisons defined by the header line
readDatasets(File, boolean) - Method in class be.svlandeg.diffany.study.osmotic.OverexpressionIO
Read all genes and their corresponding p-values of the statistical comparisons defined by the header line
readDefinitionFromTab(String) - Static method in class be.svlandeg.diffany.core.io.EdgeIO
Read an EdgeDefinition from a tab-delimited String.
readDifferentialNetworkFromDir(File, ReferenceNetwork, Set<ConditionNetwork>, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read a DifferentialNetwork from a directory: all edges from one File (edges.txt), and all nodes from another (nodes.txt).
readEdgesFromFile(File, Map<String, Node>, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read all edges from a file containing one tab-delimited edge per line.
readEdgesFromStream(InputStream, Map<String, Node>, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read all edges from a stream containing one tab-delimited edge per line.
readFromTab(String, Map<String, Node>) - Static method in class be.svlandeg.diffany.core.io.EdgeIO
Read an Edge from a tab-delimited String.
readFromTab(String, List<String>) - Static method in class be.svlandeg.diffany.core.io.NodeIO
Read a Node from a tab-delimited String.
readGenericInputNetworkFromDir(File, boolean, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read an InputNetwork from a directory: all edges from one File (edges.txt), and all nodes from another (nodes.txt).
readGenericInputNetworksFromSubdirs(File, boolean, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read a set of InputNetwork from a directory, one network per subdirectory.
readIDFromFile(File) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read the ID of a network from file.
readIDFromMap(Map<String, String>) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Return the ID of a network from stream.
readIDFromStream(InputStream) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read the ID of a network from stream.
readKinaseInteractionsByLocustags(Set<Node>, Set<Node>, Set<Node>, Set<Node>, boolean) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
Construct a set of kinase interaction edges from a certain input set of nodes, and reading input from a specified URI.
readKinaseLocusTags() - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
Read a list of (lower-case) locus tags with kinase activity.
readNameFromFile(File) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read the name of a network from file.
readNameFromStream(InputStream) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read the name of a network from a stream.
readNodesFromFile(File, boolean, List<String>) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read all nodes from a file containing one node name per line
readNodesFromStream(InputStream, boolean, List<String>) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read all nodes from a stream containing one node name per line
readPhosphorylationLocusTags(boolean) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
Read a list of (lower-case) locus tags with phosphorylation sites.
readPPIsByLocustags(Set<Node>, Set<Node>, Set<Node>, Set<Node>, boolean) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.PPIdata
Construct a set of PPI edges from two input set of nodes, and reading input from a specified URI.
readReferenceNetworkFromDir(File, boolean, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read a ReferenceNetwork from a directory: all edges from one File (edges.txt), and all nodes from another (nodes.txt).
readReferenceNetworkFromResource(String, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read a ReferenceNetwork from a directory: all edges from one File (edges.txt), and all nodes from another (nodes.txt).
readRegsByLocustags(Set<Node>, Set<Node>, boolean, boolean) - Method in class be.svlandeg.diffany.study.osmotic.arabidopsis.RegData
Construct a set of regulation edges from a certain input set of nodes, and reading input from a specified URI.
readTypeFromFile(File) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read the type of a network from file.
readTypeFromStream(InputStream) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Read the type of a network from stream.
recordMaxDepth(Map<String, Integer>, String, int) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Private method that holds the max depth value of a category mapping: each time a new depth is found, it influences the new maximum of the map
reference - Variable in class be.svlandeg.diffany.core.networks.DifferentialNetwork
 
reference - Variable in class be.svlandeg.diffany.core.project.RunDiffConfiguration
 
ReferenceNetwork - Class in be.svlandeg.diffany.core.networks
A reference network is used as comparison against condition-dependent networks.
ReferenceNetwork(String, int, Set<Attribute>) - Constructor for class be.svlandeg.diffany.core.networks.ReferenceNetwork
Create a new static reference network.
refRequired - Variable in class be.svlandeg.diffany.core.project.RunConfiguration
 
refresh(CyProject) - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
Repopulate the model with all interactions found in the currently selected CyProject
refresh() - Method in class be.svlandeg.diffany.cytoscape.gui.ProjectDropDownModel
Refreshes this model, based on the CyProjects in the Model.
refresh(CyProject) - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
Reload the NetworkEntrys based on the subnetworks from the selected network collections.
refreshCyProject() - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
Reads the selections in the GUI and reflects them in the current CyProject object.
RegData - Class in be.svlandeg.diffany.study.osmotic.arabidopsis
This class defines and analyses the regulatory data retrieved for Arabidopsis thaliana.
RegData(GenePrinter) - Constructor for class be.svlandeg.diffany.study.osmotic.arabidopsis.RegData
Constructor: defines the gene printer that can deal with gene synonymy etc.
registerConditionNetwork(CyNetwork) - Method in class be.svlandeg.diffany.cytoscape.CyProject
When a condition network gets added or is altered in any way, the Project needs to be notified of this, in order to be able to update its ontologies.
registerReferenceNetwork(CyNetwork) - Method in class be.svlandeg.diffany.cytoscape.CyProject
When a reference network gets added or is altered in any way, the Project needs to be notified of this, in order to be able to update its ontologies.
registerSourceNetwork(Network, Logger) - Method in class be.svlandeg.diffany.core.project.Project
Register a new source network to this project, updating the EdgeOntology and NodeMapper instances.
registerStyle() - Method in class be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
Registers this style with the VizMapper
removeAllCategoriesAndMappings() - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Remove all categories and type-categoryMappings
removeConditionalNetwork(CyNetwork) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Remove a conditional network from the list.
removeDestroyedNetworks() - Method in class be.svlandeg.diffany.cytoscape.CyProject
Iterates the CyNetworks in the project and removes those that have been destroyed in the Cytoscape session.
removeEdge(Edge) - Method in class be.svlandeg.diffany.core.networks.Network
Remove an edge from this network, leaving its source and target nodes otherwise untouched (and perhaps unconnected).
removeRedundantEdges(Network, EdgeOntology, ScheduledTask) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Remove redundant edges in the network, such as those that are symmetrical and represented twice (source-target and target-source), or a generic edge (e.g.
removeUnconnectedNodes() - Method in class be.svlandeg.diffany.core.networks.Network
This method removes all unconnected nodes from the network - can not be reverted!
reset(int) - Method in class be.svlandeg.diffany.core.progress.ProgressListener
Reset the progress listener to start recording a new task.
resolveToOne(Network, EdgeOntology) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
For each node pair and each semantic root category, resolve conflicts by calling NetworkCleaning.resolveToOnePerRoot(Network, EdgeOntology, Set, Set, Node, Node).
resolveToOnePerRoot(Network, EdgeOntology, Set<String>, Set<EdgeDefinition>, Node, Node) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Clean a network: Group all input edges into subclasses per root category of the EdgeOntology, resolve conflicts within a root category.
retrieveAllCommonChildren(Collection<EdgeDefinition>) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
For a set of EdgeDefinition objects, determine all their common children.
retrieveAllCommonParents(Collection<String>) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
For a set of edge types, determine all their common parents/ancestors.
retrieveAllSourceRootCats(boolean) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Retrieve all the elements in this ontology that are root (i.e.
retrieveAllSourceRootCats(boolean) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
 
retrieveCatChildren(String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Retrieve the set of child categories of a specific parent category, or an empty set if there are none and this category is thus a 'leaf'.
retrieveCatParent(String) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
Retrieve the parent category of a specific child category, or null if there is none.
retrieveCatParent(String) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
 
retrieveFirstCommonChild(Collection<EdgeDefinition>) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
For a set of EdgeDefinition objects, determine their most general common child.
retrieveFirstCommonParent(Collection<String>) - Method in class be.svlandeg.diffany.core.semantics.EdgeOntology
For a set of categories, determine their most specific common parent/ancestor.
retrieveFirstCommonParent(Collection<String>) - Method in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
 
retrieveHubs(Set<Edge>, Set<Node>, int, boolean, boolean, boolean) - Method in class be.svlandeg.diffany.study.osmotic.NetworkAnalysis
Print information about hubs in the network.
Run - Class in be.svlandeg.diffany.core.project
A run consists of a RunConfiguration which defines the networks that can be used as input for the Diffany algorithms.
Run(Project, int, RunConfiguration, Boolean, Logger) - Constructor for class be.svlandeg.diffany.core.project.Run
Create a new run, belonging to a specific project.
run(TaskMonitor) - Method in class be.svlandeg.diffany.cytoscape.tasks.LoadExampleTask
 
run(TaskMonitor) - Method in class be.svlandeg.diffany.cytoscape.tasks.RunProjectTask
 
run(TaskMonitor) - Method in class be.svlandeg.diffany.cytoscape.tasks.UpdateVisualStyleTask
 
runAnalysis(CommandLine) - Method in class be.svlandeg.diffany.console.RunProject
Run a Diffany analysis, depending on the parameters provided on the commandline.
RunAnalysis - Class in be.svlandeg.diffany.study.osmotic
This class provides the analysis pipeline for the osmotic stress application on Arabidopsis.
RunAnalysis() - Constructor for class be.svlandeg.diffany.study.osmotic.RunAnalysis
Empty constructor.
RunConfiguration - Class in be.svlandeg.diffany.core.project
A RunConfiguration defines the necessary networks needed as input for the Diffany algorithms, and should always be used in the context of a bigger Project.
RunConfiguration(Set<InputNetwork>, int, boolean) - Constructor for class be.svlandeg.diffany.core.project.RunConfiguration
Create a new configuration with a set of input networks and a required supportCutoff (between 2 and the size of the network set).
RunConfiguration(Set<InputNetwork>) - Constructor for class be.svlandeg.diffany.core.project.RunConfiguration
Create a new configuration with a set of input networks.
runCons - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
RunConsole - Class in be.svlandeg.diffany.console
This class allows to run the Diffany algorithms from the commandline, by passing the correct arguments through to RunProject.
RunConsole() - Constructor for class be.svlandeg.diffany.console.RunConsole
 
runDiff - Static variable in class be.svlandeg.diffany.console.DiffanyOptions
 
RunDiffConfiguration - Class in be.svlandeg.diffany.core.project
A RunDiffConfiguration defines the necessary networks needed as input for the differential algorithms specifically, and should always be used in the context of a bigger Project.
RunDiffConfiguration(ReferenceNetwork, Set<ConditionNetwork>) - Constructor for class be.svlandeg.diffany.core.project.RunDiffConfiguration
Create a new configuration with a reference network and a set of condition-specific networks.
RunDiffConfiguration(ReferenceNetwork, Set<ConditionNetwork>, int) - Constructor for class be.svlandeg.diffany.core.project.RunDiffConfiguration
Create a new configuration with a reference network and a set of condition-specific networks.
runFromConsole(String[], CommandLineParser) - Method in class be.svlandeg.diffany.console.RunConsole
Run the Diffany algorithms from the console input, or print the help/version statement when appropriate.
runID - Variable in class be.svlandeg.diffany.core.project.Run
 
runID - Variable in class be.svlandeg.diffany.core.project.RunOutput
 
RunOutput - Class in be.svlandeg.diffany.core.project
This class keeps the output of differential network algorithms, both differential networks as well consensus networks.
RunOutput(Project, int) - Constructor for class be.svlandeg.diffany.core.project.RunOutput
Create a new empty output object.
RunProject - Class in be.svlandeg.diffany.console
This class can run the Diffany algorithms from a CommandLine object.
RunProject() - Constructor for class be.svlandeg.diffany.console.RunProject
 
RunProjectAction - Class in be.svlandeg.diffany.cytoscape.actions
Action that runs the current CyProject.
RunProjectAction(Model, String) - Constructor for class be.svlandeg.diffany.cytoscape.actions.RunProjectAction
Run the current CyProject
RunProjectAction(Model) - Constructor for class be.svlandeg.diffany.cytoscape.actions.RunProjectAction
Run the current CyProject.
RunProjectTask - Class in be.svlandeg.diffany.cytoscape.tasks
This Task gathers information from the model and runs the Project
RunProjectTask(Model, CyProject) - Constructor for class be.svlandeg.diffany.cytoscape.tasks.RunProjectTask
Constructs a new run task.
RunProjectTaskFactory - Class in be.svlandeg.diffany.cytoscape.tasks
Factory to run RunProjectTask, followed by a UpdateVisualStyleTask
RunProjectTaskFactory(Model) - Constructor for class be.svlandeg.diffany.cytoscape.tasks.RunProjectTaskFactory
Construct a new factory.
runs - Variable in class be.svlandeg.diffany.core.project.Project
 

S

ScheduledTask - Class in be.svlandeg.diffany.core.progress
A scheduled task knows how many ticks it will take to execute in total.
ScheduledTask(ProgressListener, int) - Constructor for class be.svlandeg.diffany.core.progress.ScheduledTask
Constructor: create a new scheduled task belonging to a certain progress listener and with a pre-defined number of total ticks.
SelectionTableModel - Class in be.svlandeg.diffany.cytoscape.gui
The model for the table of available networks in the selected collection.
SelectionTableModel() - Constructor for class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
Create a new table model.
Services - Class in be.svlandeg.diffany.cytoscape.internal
Class used to gather all services from the BundleContext as loaded in the CyActivator
Services() - Constructor for class be.svlandeg.diffany.cytoscape.internal.Services
 
services - Variable in class be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
App services
SessionListener - Class in be.svlandeg.diffany.cytoscape
A listener that catches session load and save events from Cytoscape.
SessionListener(Model) - Constructor for class be.svlandeg.diffany.cytoscape.SessionListener
Construct new listener
setAttribute(String, Object) - Method in class be.svlandeg.diffany.core.networks.Node
Set the value of a certain attribute.
setConditionalNetworks(Set<CyNetwork>) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Set the set of conditional networks for this project.
setCutoff(double) - Method in class be.svlandeg.diffany.cytoscape.Model
Set the edge cutoff
setCyApplicationManager(CyApplicationManager) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setCyLayoutAlgorithmManager(CyLayoutAlgorithmManager) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setCyNetworkFactory(CyNetworkFactory) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setCyNetworkManager(CyNetworkManager) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setCyNetworkViewFactory(CyNetworkViewFactory) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setCyNetworkViewManager(CyNetworkViewManager) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setCyRootNetworkManager(CyRootNetworkManager) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setDialogTaskManager(DialogTaskManager) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setGenerateConsensusNets(boolean) - Method in class be.svlandeg.diffany.cytoscape.Model
Enable generation of consensus networks upon run
setGenerateDiffNets(boolean) - Method in class be.svlandeg.diffany.cytoscape.Model
Enable generation of differential networks upon run
setHideUnconnectedNodes(boolean) - Method in class be.svlandeg.diffany.cytoscape.Model
Should nodes with degree zero be hidden? Hidden edges are not counted.
setInputs(Set<InputNetwork>) - Method in class be.svlandeg.diffany.core.project.RunConfiguration
Set the input networks in this configuration.
setMessage(String) - Method in class be.svlandeg.diffany.core.progress.ScheduledTask
Set the message belonging to this task
setMode(Model.ComparisonMode) - Method in class be.svlandeg.diffany.cytoscape.Model
Set the execution mode for the next run.
setName(String) - Method in class be.svlandeg.diffany.examples.GenericExample
 
setNodesAndEdges(Set<Edge>) - Method in class be.svlandeg.diffany.core.networks.Network
Define a (new) set of edges for this network, overwriting previous data.
setNodesAndEdges(Set<Node>, Set<Edge>) - Method in class be.svlandeg.diffany.core.networks.Network
Define a (new) set of nodes for this network, overwriting previous data.
setOntologyTerms(Set<String>) - Method in class be.svlandeg.diffany.core.networks.Condition
Define the set of ontologies corresponding to this condition (overwrites all previously defined terms).
setOverlapOperator(Model.OverlapOperator) - Method in class be.svlandeg.diffany.cytoscape.Model
Set the way in which overlapping edge weights are calculated.
setOverlapSupportCutoff(int) - Method in class be.svlandeg.diffany.cytoscape.Model
Specify the number of edges that need to be matching in the different networks in order to consider an edge a "consensus" edge.
setParentWindow(JFrame) - Method in class be.svlandeg.diffany.cytoscape.Model
Set a reference to the Cytoscape main window
setProgress(String, int, int) - Method in class be.svlandeg.diffany.core.progress.ProgressListener
This method will be called by the differential algorithms in CalculateDiff every x clicks to allow a listener to implement e.g.
setProgress(String, int, int) - Method in class be.svlandeg.diffany.core.progress.StandardProgressListener
 
setProgress(String, int, int) - Method in class be.svlandeg.diffany.cytoscape.tasks.RunProjectTask
 
setReference(boolean) - Method in class be.svlandeg.diffany.cytoscape.gui.NetworkEntry
Toggles this network as the reference network on the next execution of the algorithm.
setReferenceNetwork(CyNetwork) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Set the referenceNetwork for this project.
setRefIncludedInOverlapSupportCutoff(boolean) - Method in class be.svlandeg.diffany.cytoscape.Model
When calculating only consensus networks, should the reference network be required to supply an edge?
setRefRequired(boolean) - Method in class be.svlandeg.diffany.core.project.RunConfiguration
Alter the fact whether or not the reference network needs to have an edge for it to be allowed inclusion in the consensus network.
setSelected(boolean) - Method in class be.svlandeg.diffany.cytoscape.gui.NetworkEntry
Toggle whether or not the network should be used with the next execution of the algorithm.
setSelectedItem(Object) - Method in class be.svlandeg.diffany.cytoscape.gui.ModeDropDownModel
 
setSelectedItem(Object) - Method in class be.svlandeg.diffany.cytoscape.gui.ProjectDropDownModel
 
setSelectedProject(CyProject) - Method in class be.svlandeg.diffany.cytoscape.Model
Set the current CyProject.
setSupportCutoff(int) - Method in class be.svlandeg.diffany.core.project.RunConfiguration
Alter the required number of supporting networks needed before an edge will be present in the consensus network.
setTaskManager(TaskManager<?, ?>) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setTaskMonitor(TaskMonitor) - Method in class be.svlandeg.diffany.examples.GenericExample
 
setType(String) - Method in class be.svlandeg.diffany.core.networks.EdgeDefinition
Set the type of the edge
setValueAt(Object, int, int) - Method in class be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
 
setValueAt(Object, int, int) - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
 
setVisualMappingManager(VisualMappingManager) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setVisualStyleFactory(VisualStyleFactory) - Method in class be.svlandeg.diffany.cytoscape.internal.Services
 
setWeight(double) - Method in class be.svlandeg.diffany.core.networks.EdgeDefinition
Set the weight of this edge (only when the value is appropriate).
signalChange() - Method in class be.svlandeg.diffany.cytoscape.Model
Let the model know something has changed.
source - Variable in class be.svlandeg.diffany.core.networks.Edge
 
sourceCatHierarchy - Variable in class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
 
sourceDraw - Variable in class be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
 
StandardProgressListener - Class in be.svlandeg.diffany.core.progress
This class implements the ProgressListener interface and prints the progress to the standard output stream, together with a time stamp.
StandardProgressListener(boolean) - Constructor for class be.svlandeg.diffany.core.progress.StandardProgressListener
Constructor which specifies whether or not to print the progress messages.
start(BundleContext) - Method in class be.svlandeg.diffany.cytoscape.internal.CyActivator
 
stateChanged(ChangeEvent) - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
 
supportCutoff - Variable in class be.svlandeg.diffany.core.project.RunConfiguration
 
SYMBOLIC_NAME - Static variable in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
Column name of an extra field to be used as preferred node label (probably the symbolic gene name)
symm_ah - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
 
symm_ah - Static variable in class be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
 
symmetrical - Variable in class be.svlandeg.diffany.core.networks.EdgeDefinition
 

T

tableChanged(TableModelEvent) - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
 
TabPane - Class in be.svlandeg.diffany.cytoscape.gui
The Control Panel for Diffany (left Cytoscape tab).
TabPane(Model) - Constructor for class be.svlandeg.diffany.cytoscape.gui.TabPane
Create JPanel and register as Observer for the model.
target - Variable in class be.svlandeg.diffany.core.networks.Edge
 
taskMonitor - Variable in class be.svlandeg.diffany.examples.GenericExample
 
teo - Variable in class be.svlandeg.diffany.core.algorithms.EdgeComparison
 
teo - Variable in class be.svlandeg.diffany.core.visualstyle.TreeEdgeDrawing
 
ticksDone(int) - Method in class be.svlandeg.diffany.core.progress.ScheduledTask
Report that a number of ticks has been done since the last report.
ticksToGo() - Method in class be.svlandeg.diffany.core.progress.ProgressListener
Obtain the number of ticks that are still to be done for this task to complete
ticksToGo() - Method in class be.svlandeg.diffany.core.progress.ScheduledTask
Return the number of ticks that still need to be done to succesfully complete this task.
toLongString() - Method in class be.svlandeg.diffany.core.networks.Node
Provide a long string of this node, including its attributes
toString() - Method in class be.svlandeg.diffany.core.algorithms.EdgeComparison.IntermediateComparison
 
toString() - Method in class be.svlandeg.diffany.core.networks.Attribute
 
toString() - Method in class be.svlandeg.diffany.core.networks.Condition
 
toString() - Method in class be.svlandeg.diffany.core.networks.Edge
 
toString() - Method in class be.svlandeg.diffany.core.networks.EdgeDefinition
 
toString() - Method in class be.svlandeg.diffany.core.networks.Node
 
toString() - Method in class be.svlandeg.diffany.core.project.LogEntry
 
toString() - Method in class be.svlandeg.diffany.cytoscape.CyProject
 
toString() - Method in class be.svlandeg.diffany.cytoscape.gui.NetworkEntry
 
toString() - Method in enum be.svlandeg.diffany.cytoscape.Model.ComparisonMode
 
totalTicks() - Method in class be.svlandeg.diffany.core.progress.ScheduledTask
Return the total number of original ticks in this task (not taking into account how many of them have already been done)
TreeEdgeDrawing - Class in be.svlandeg.diffany.core.visualstyle
This abstract class tells the GUI how to draw certain edges, depending on definitions from an TreeEdgeOntology.
TreeEdgeDrawing(TreeEdgeOntology) - Constructor for class be.svlandeg.diffany.core.visualstyle.TreeEdgeDrawing
Create a new EdgeDrawing object, given a specific TreeEdgeOntology object.
TreeEdgeOntology - Class in be.svlandeg.diffany.core.semantics
This edge ontology is implemented as a tree structure.
TreeEdgeOntology(String, String, String, String, String, Map<String, Boolean>) - Constructor for class be.svlandeg.diffany.core.semantics.TreeEdgeOntology
Create a new ontology, defining the set of categories.
type - Variable in class be.svlandeg.diffany.core.networks.EdgeDefinition
 
type - Variable in class be.svlandeg.diffany.core.project.Run
 

U

Unification - Class in be.svlandeg.diffany.core.algorithms
This class provides generic methods useful for network unification before or after applying differential algorithms.
Unification(Logger) - Constructor for class be.svlandeg.diffany.core.algorithms.Unification
Create a new unification object, which can log important messages.
unifyDirection(List<EdgeDefinition>) - Method in class be.svlandeg.diffany.core.algorithms.NetworkCleaning
Create a new list of edges by making either all input interactions directed, or all symmetrical.
unifyEdgeDirection(Set<Edge>, EdgeOntology) - Method in class be.svlandeg.diffany.core.algorithms.Unification
Use the directionality of edge types as recorded in the edge ontology to 'fix' a set of edges.
update(Services) - Method in class be.svlandeg.diffany.cytoscape.CyProject
Updates this CyProject after a run.
update(Observable, Object) - Method in class be.svlandeg.diffany.cytoscape.gui.ExtraOptionsMenu
 
update(Observable, Object) - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
 
updateInteractionMappings(Set<String>, EdgeOntology) - Method in class be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
Add visual mappings according to the networks contained in the given CyProject
UpdateVisualStyleAction - Class in be.svlandeg.diffany.cytoscape.actions
UpdateVisualStyleAction(Model) - Constructor for class be.svlandeg.diffany.cytoscape.actions.UpdateVisualStyleAction
Action that refreshes the registered visual styles and reapplies them on the Views, executing the UpdateVisualStyleTask
UpdateVisualStyleAction(Model, CyProject) - Constructor for class be.svlandeg.diffany.cytoscape.actions.UpdateVisualStyleAction
 
UpdateVisualStyleTask - Class in be.svlandeg.diffany.cytoscape.tasks
This task gathers all used interactions in a given CyProject, updates this VisualStyles and applies them to all CyNetworkViews in the CyProject.
UpdateVisualStyleTask(Model, CyProject) - Constructor for class be.svlandeg.diffany.cytoscape.tasks.UpdateVisualStyleTask
Construct a new task to update the visual styles in the model, according to the interactions in the CyNetworks contained in the CyProject.
UpdateVisualStyleTaskFactory - Class in be.svlandeg.diffany.cytoscape.tasks
Factory to run the UpdateVisualStyleTask
UpdateVisualStyleTaskFactory(Model, CyProject) - Constructor for class be.svlandeg.diffany.cytoscape.tasks.UpdateVisualStyleTaskFactory
Construct a new factory to create UpdateVisualStyleTasks
upregulated - Static variable in class be.svlandeg.diffany.core.networks.Node
 

V

valueChanged(ListSelectionEvent) - Method in class be.svlandeg.diffany.cytoscape.gui.TabPane
 
valueOf(String) - Static method in enum be.svlandeg.diffany.core.algorithms.CalculateDiff.RunMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum be.svlandeg.diffany.core.visualstyle.EdgeStyle.ArrowHead
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum be.svlandeg.diffany.cytoscape.CyNetworkBridge.NetworkType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum be.svlandeg.diffany.cytoscape.Model.ComparisonMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum be.svlandeg.diffany.cytoscape.Model.OverlapOperator
Returns the enum constant of this type with the specified name.
values() - Static method in enum be.svlandeg.diffany.core.algorithms.CalculateDiff.RunMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum be.svlandeg.diffany.core.visualstyle.EdgeStyle.ArrowHead
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum be.svlandeg.diffany.cytoscape.CyNetworkBridge.NetworkType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum be.svlandeg.diffany.cytoscape.Model.ComparisonMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum be.svlandeg.diffany.cytoscape.Model.OverlapOperator
Returns an array containing the constants of this enum type, in the order they are declared.
versionShort - Static variable in class be.svlandeg.diffany.console.MetaOptions
 
vis - Variable in class be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
The VisualStyle itself.
VisualDiffStyle - Class in be.svlandeg.diffany.cytoscape.vizmapper
VisualStyle to be applied on differential networks.
VisualDiffStyle(Services) - Constructor for class be.svlandeg.diffany.cytoscape.vizmapper.VisualDiffStyle
Construct and register new visual style for differential networks.
VisualSourceStyle - Class in be.svlandeg.diffany.cytoscape.vizmapper
VisualStyle to be applied on source and consensus networks.
VisualSourceStyle(Services) - Constructor for class be.svlandeg.diffany.cytoscape.vizmapper.VisualSourceStyle
Construct and register new visual style for source and consensus networks.

W

weight - Variable in class be.svlandeg.diffany.core.networks.EdgeDefinition
 
WEIGHT - Static variable in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
Column name for edge weight (double)
writeConditionsToFiles(ConditionNetwork, File) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Write the string representation of the conditions of a condition-specific network: call writeNetworkToFiles to write the edges edges information, nodes and network definition first.
writeDefinitionToTab(EdgeDefinition) - Static method in class be.svlandeg.diffany.core.io.EdgeIO
Get a string representation of an edge definition.
writeEdgesToTab(Set<Edge>) - Static method in class be.svlandeg.diffany.core.io.EdgeIO
Get a string representation of all edges in a collection, divided by newlines, with edges in a tabbed format.
writeNetworkToDir(Network, File, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Write the string representation of the network to (subfiles of) a directory: edges, nodes and definition all go in a separate file.
writeNetworkToFiles(Network, File, File, File, boolean) - Static method in class be.svlandeg.diffany.core.io.NetworkIO
Write the string representation of the network: All edges to one File, and all nodes to another, as specified by the parameters.
writeNodesToTab(Set<Node>, SortedSet<Attribute>) - Static method in class be.svlandeg.diffany.core.io.NodeIO
Get a string representation of all nodes in a collection, divided by newlines, with nodes in a tabbed format.
writeToTab(Edge) - Static method in class be.svlandeg.diffany.core.io.EdgeIO
Get a string representation of an edge.
writeToTab(Node, SortedSet<Attribute>) - Static method in class be.svlandeg.diffany.core.io.NodeIO
Get a string representation of a node.
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