- 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.
- 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.
- 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
-
- 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 CyNetworkView
s 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
CyNetwork
s 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 CyNetworkView
s 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 CyNetwork
s in this project.
- getConditionNetwork(CyNetwork, EdgeOntology) - Static method in class be.svlandeg.diffany.cytoscape.CyNetworkBridge
-
- 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
-
- 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
-
- 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
-
- 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.
- 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
-
- 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
- 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
-
- refresh(CyProject) - Method in class be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
-
Reload the
NetworkEntry
s 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 CyNetwork
s 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
-
- 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
-
- RunProjectAction(Model, String) - Constructor for class be.svlandeg.diffany.cytoscape.actions.RunProjectAction
-
- RunProjectAction(Model) - Constructor for class be.svlandeg.diffany.cytoscape.actions.RunProjectAction
-
- 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
-
- 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
-