A C D F G H I M N O R S T U V

A

AbstractCyniAlgorithm - Class in fr.systemsbiology.cyni

The AbstractCyniAlgorithm provides a basic implementation of a cyni algorithm TaskFactory.

AbstractCyniAlgorithm(String, String, boolean, CyniCategory) - Constructor for class fr.systemsbiology.cyni.AbstractCyniAlgorithm

The Constructor.

AbstractCyniMetric - Class in fr.systemsbiology.cyni

The AbstractCyniMetrics provides a basic implementation of a cyni metric TaskFactory.

AbstractCyniMetric(String, String) - Constructor for class fr.systemsbiology.cyni.AbstractCyniMetric

The Constructor.

AbstractCyniTask - Class in fr.systemsbiology.cyni

This is a basic implementation of a CyniAlgorithm Task that does some bookkeeping, but primarily delegates to the doCyniTask() method.

AbstractCyniTask(String, CyniAlgorithmContext, CyNetworkFactory, CyNetworkViewFactory, CyNetworkManager, CyNetworkViewManager, CyNetworkTableManager, CyRootNetworkManager, VisualMappingManager) - Constructor for class fr.systemsbiology.cyni.AbstractCyniTask

Constructor.

AbstractCyniTask(String, CyniAlgorithmContext) - Constructor for class fr.systemsbiology.cyni.AbstractCyniTask

This Constructor can be used for Cyni tasks that don't need to create a new network such as Discretization or Imputation algorithms

addColumns(CyNetwork, CyNetwork, CyTable, Class<? extends CyIdentifiable>, String) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Add columns that belong to a table associated to a network to a new table associated to a new network.

addTag(String) - Method in class fr.systemsbiology.cyni.AbstractCyniMetric

It adds a tags to the list of tags that define that metric

anyMissing - Variable in class fr.systemsbiology.cyni.CyniTable

C

changeOrderRowsByColumnValuesOrder(List<Object>) - Method in class fr.systemsbiology.cyni.CyniTable

Changes the order of the rows according to the values of a selected column The method supposes that the first value of the input list corresponds to the first element of the column and so on.

changeOrderRowsToRandom() - Method in class fr.systemsbiology.cyni.CyniTable

Changes the order of the rows in the table randomly

cloneEdgeRow(CyNetwork, CyRow, CyEdge) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Clone the row data to the row corresponding to an edge of the specified network

cloneNodeRow(CyNetwork, CyRow, CyNode) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Clone the row data to the row corresponding to a node of the specified network

colHasMissingValue - Variable in class fr.systemsbiology.cyni.CyniTable

colMaxValue - Variable in class fr.systemsbiology.cyni.CyniTable

colMinValue - Variable in class fr.systemsbiology.cyni.CyniTable

colNumStringsDiff - Variable in class fr.systemsbiology.cyni.CyniTable

columnHasMissingValue(int) - Method in class fr.systemsbiology.cyni.CyniTable

Tells if the specified column has a missing value.

columnLabels - Variable in class fr.systemsbiology.cyni.CyniTable

colWeights - Variable in class fr.systemsbiology.cyni.CyniTable

contextContentValid() - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

This method checks the context values to validate them.

contextHasOwnSwingPanel() - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

This method tells cytoscape if this algorithm provides its own swing Panel to display the context parameters.

copyEdgeColumns(CyNetwork, CyTable) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Copy the columns from a table to the edge table of a network.

copyNodeColumns(CyNetwork, CyTable) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Copy the columns from a table to the node table of a network.

createCyniContext(CyTable, CyCyniMetricsManager, TunableSetter, Map<String, Object>) - Method in interface fr.systemsbiology.cyni.CyCyniAlgorithm

Returns a new cyni context object.

createEdgeColumn(CyNetwork, String, Class<? extends T>, boolean) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Create a column of the specified name and the specified type in the edge table of the specified network.

createNetworkColumn(CyNetwork, String, Class<? extends T>, boolean) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Create a column of the specified name and the specified type in the network table of the specified network.

createNodeColumn(CyNetwork, String, Class<? extends T>, boolean) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Create a column of the specified name and the specified type in the node table of the specified network.

createTaskIterator(CyniAlgorithmContext, CyTable, CyNetworkFactory, CyNetworkViewFactory, CyNetworkManager, CyNetworkTableManager, CyRootNetworkManager, VisualMappingManager, CyNetworkViewManager, CyLayoutAlgorithmManager, CyCyniMetricsManager) - Method in interface fr.systemsbiology.cyni.CyCyniAlgorithm

Creates a task iterator containing the cyni tasks.

CyCyniAlgorithm - Interface in fr.systemsbiology.cyni

An interface specific to Cyni algorithms.

CyCyniAlgorithmManager - Interface in fr.systemsbiology.cyni

This class provides access to the available Cyni algorithms.

CyCyniMetric - Interface in fr.systemsbiology.cyni

An interface specific to Cyni metrics.

CyCyniMetricsManager - Interface in fr.systemsbiology.cyni

This class provides access to the available Cyni Metrics.

CyniAlgorithmAddedEvent - Class in fr.systemsbiology.cyni

This event will be fired when new Cyni Algorithm is added to CyCyniAlgorithmManager.

CyniAlgorithmAddedEvent(CyCyniAlgorithmManager, CyCyniAlgorithm) - Constructor for class fr.systemsbiology.cyni.CyniAlgorithmAddedEvent

Constructs the cyni algorithm added event.

CyniAlgorithmAddedListener - Interface in fr.systemsbiology.cyni

Listener for CyniAlgorithmAddedEvent.

CyniAlgorithmContext - Class in fr.systemsbiology.cyni

This is a class that contains several methods that are needed to display the context of a Cyni algorithm

CyniAlgorithmContext(boolean) - Constructor for class fr.systemsbiology.cyni.CyniAlgorithmContext

The constructor

CyniAlgorithmDeletedEvent - Class in fr.systemsbiology.cyni

This event will be fired when a Cyni Algorithm is deleted from CyCyniAlgorithmManager.

CyniAlgorithmDeletedEvent(CyCyniAlgorithmManager, CyCyniAlgorithm) - Constructor for class fr.systemsbiology.cyni.CyniAlgorithmDeletedEvent

Constructs the cyni algorithm deleted event.

CyniAlgorithmDeletedListener - Interface in fr.systemsbiology.cyni

Listener for CyniAlgorithmDeletedEvent.

CyniBayesianUtils - Class in fr.systemsbiology.cyni

This is a class that contains several utilities that will help creating a new bayesian network

CyniBayesianUtils(Map<Integer, ArrayList<Integer>>) - Constructor for class fr.systemsbiology.cyni.CyniBayesianUtils

Constructor.

CyniCategory - Enum in fr.systemsbiology.cyni

An enum that captures the types of Cyni Algorithms available

CyniMetricTags - Enum in fr.systemsbiology.cyni

An enum that captures the tags of the Cyni Metrics available

CyniNetworkUtils - Class in fr.systemsbiology.cyni

This is a class that contains several methods to help while creating a new network

CyniNetworkUtils(CyNetworkViewFactory, CyNetworkManager, CyNetworkViewManager, CyNetworkTableManager, CyRootNetworkManager, VisualMappingManager) - Constructor for class fr.systemsbiology.cyni.CyniNetworkUtils

Constructor.

CyniTable - Class in fr.systemsbiology.cyni

CyniTable(CyTable, String[], boolean, boolean, boolean) - Constructor for class fr.systemsbiology.cyni.CyniTable

Create a Cyni table from the current selected table.

CyniTable(CyniTable) - Constructor for class fr.systemsbiology.cyni.CyniTable

Create a cyni table from an existing one.

CyniTable(int, int) - Constructor for class fr.systemsbiology.cyni.CyniTable

Create an empty Cyni Table with the specified number of columns and rows.

D

data - Variable in class fr.systemsbiology.cyni.CyniTable

DEFAULT_Cyni_Metric_PROPERTY_NAME - Static variable in interface fr.systemsbiology.cyni.CyCyniMetricsManager

The name of the default Cyni Metric property.

displayNewNetwork(CyNetwork, CyNetwork, boolean) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

This method displays the new network and return a network view that might be used to modify the display features such as the layout

doCyniTask(TaskMonitor) - Method in class fr.systemsbiology.cyni.AbstractCyniTask

This method is designed to actually encapsulate the cyni algorithm.

doubleValue(int, int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the double value for the specified row and column combination

F

fr.systemsbiology.cyni - package fr.systemsbiology.cyni

This package has the core interfaces of Cyni Toolbox App

G

getAllAttributesLists(CyTable) - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

Returns a list of the names of the columns that contains list of strings

getAllAttributesNumbers(CyTable) - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

Returns a list of the names of the columns that contains numbers(Float,Integer,Double)

getAllAttributesStrings(CyTable) - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

Returns a list of the names of the columns that contains strings

getAllCyniAlgorithmNames(CyniCategory) - Method in interface fr.systemsbiology.cyni.CyCyniAlgorithmManager

Returns the list of names of cyni algorithms for a specified category.

getAllCyniAlgorithms(CyniCategory) - Method in interface fr.systemsbiology.cyni.CyCyniAlgorithmManager

Returns a collection of all available Cyni algorithms for the specified category.

getAllCyniMetrics() - Method in interface fr.systemsbiology.cyni.CyCyniMetricsManager

Returns a list of all available Cyni Metrics.

getAllCyniMetricsWithTags(List<String>) - Method in interface fr.systemsbiology.cyni.CyCyniMetricsManager

Returns the list of metrics that contains at least the same tags that are passed as input parameter.

getAttributeStringValues() - Method in class fr.systemsbiology.cyni.CyniTable

Returns the list of all possible strings values in the table

getCategory() - Method in class fr.systemsbiology.cyni.AbstractCyniAlgorithm

Returns the category of the Cyni Algorithm.

getCategory() - Method in interface fr.systemsbiology.cyni.CyCyniAlgorithm

A method to get the category of the algorithm

getColIndex(Object) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the index column for the specified label.

getColLabel(int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the label for the specified column.

getColLabels() - Method in class fr.systemsbiology.cyni.CyniTable

Returns the array with all column labels.

getColWeight(int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the weight for the specified column.

getColWeights() - Method in class fr.systemsbiology.cyni.CyniTable

Returns the array of weights for the columns.

getContextSwingPanel() - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

Returns the swing Panel that will be used instead of the tunables panel

getCyniAlgorithm(String, CyniCategory) - Method in interface fr.systemsbiology.cyni.CyCyniAlgorithmManager

Returns a Cyni algorithm of the specified name and category.

getCyniAlgorithm() - Method in class fr.systemsbiology.cyni.CyniAlgorithmAddedEvent

Returns the cyni algorithm added to the cyni algorithm manager.

getCyniAlgorithm() - Method in class fr.systemsbiology.cyni.CyniAlgorithmDeletedEvent

Returns the cyni algorithm deleted from the cyni algorithm manager.

getCyniMetric(String) - Method in interface fr.systemsbiology.cyni.CyCyniMetricsManager

Returns a Cyni Metric of the specified name and null if no metric exists with that name.

getCyniTable(CyTable, String[], boolean, boolean, boolean) - Method in class fr.systemsbiology.cyni.AbstractCyniMetric

It produces a CyniTable with methods specific for this metric

getCyniTable(CyTable, String[], boolean, boolean, boolean) - Method in interface fr.systemsbiology.cyni.CyCyniMetric

It produces a CyniTable with methods specific for this metric

getDefaultCyniMetric() - Method in interface fr.systemsbiology.cyni.CyCyniMetricsManager

Returns the default Cyni Metric.

getListOfAttributes(List<String>, CyTable, String, Object) - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

Fills a list with names of columns that has the same type that the one requested

getMetric(CyniTable, CyniTable, int, List<Integer>) - Method in interface fr.systemsbiology.cyni.CyCyniMetric

The implementation of the metric.

getName() - Method in class fr.systemsbiology.cyni.AbstractCyniAlgorithm

A computer readable name used to construct property strings.

getName() - Method in class fr.systemsbiology.cyni.AbstractCyniMetric

A computer readable name used to differentiate the metrics.

getName() - Method in interface fr.systemsbiology.cyni.CyCyniAlgorithm

Returns the computer-readable name of the Cyni Algorithm.

getName() - Method in interface fr.systemsbiology.cyni.CyCyniMetric

Returns the computer-readable name of the Cyni Metric.

getNetworkAssociatedToTable(CyTable) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Checks if the table is associated to a network, if so it returns the associated network otherwise it returns null

getNumPossibleStrings(int, boolean) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the number of possible/different strings stored in the defined column or row

getParentSwingComponent() - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

Returns the swing parent component of this context

getRank(int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns an array with a number for each position representing the rank of the value in the whole row

getResults(Class) - Method in class fr.systemsbiology.cyni.AbstractCyniTask

getRowIndex(Object) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the index row for the specified label.

getRowLabel(int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the label for the specified row.

getRowLabels() - Method in class fr.systemsbiology.cyni.CyniTable

Returns the array with all row labels.

getRowWeight(int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the weight for the specified row.

getRowWeights() - Method in class fr.systemsbiology.cyni.CyniTable

Returns the array of weights for the rows.

getTagsList() - Method in class fr.systemsbiology.cyni.AbstractCyniMetric

The list of tags of this metric

getTagsList() - Method in interface fr.systemsbiology.cyni.CyCyniMetric

The list of tags that define this metric

getType(int, int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the type of for the specified row and column combination.

getValue(int, int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the value for the specified row and column

H

handleEvent(CyniAlgorithmAddedEvent) - Method in interface fr.systemsbiology.cyni.CyniAlgorithmAddedListener

The method that should handle the specified event.

handleEvent(CyniAlgorithmDeletedEvent) - Method in interface fr.systemsbiology.cyni.CyniAlgorithmDeletedListener

The method that should handle the specified event.

hasAnyMissingValue() - Method in class fr.systemsbiology.cyni.CyniTable

Returns if the table has any missing value

hasValue(int, int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns if the content of the table for the specified row and column combination has a real value.

I

ignoreMissing - Variable in class fr.systemsbiology.cyni.CyniTable

indexToTypes - Variable in class fr.systemsbiology.cyni.CyniTable

initMetric() - Method in class fr.systemsbiology.cyni.AbstractCyniMetric

It initializes the metric and after this method the metric is ready to start calculating measurements.

initMetric() - Method in interface fr.systemsbiology.cyni.CyCyniMetric

It initializes the metric and after this method the metric is ready to start calculating measurements.

integerValue(int, int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the integer value for the specified row and column combination.

internalTable - Variable in class fr.systemsbiology.cyni.CyniTable

isGraphCyclic(int) - Method in class fr.systemsbiology.cyni.CyniBayesianUtils

This method allows checking if there is a cycle in a graph starting from a defined node.

isMatching(int, int, Object) - Method in class fr.systemsbiology.cyni.CyniTable

Checks whether the element in position defined by row and col parameters matches the given value.

isReady(Object) - Method in class fr.systemsbiology.cyni.AbstractCyniAlgorithm

Returns true if the task factory is ready to produce a task iterator.

isReady(Object) - Method in interface fr.systemsbiology.cyni.CyCyniAlgorithm

Returns true if the task factory is ready to produce a task iterator.

isTransposed() - Method in class fr.systemsbiology.cyni.CyniTable

Returns if the table is transposed

M

mapColLabels - Variable in class fr.systemsbiology.cyni.CyniTable

mapRowLabels - Variable in class fr.systemsbiology.cyni.CyniTable

mapRowOrder - Variable in class fr.systemsbiology.cyni.CyniTable

N

nColumns - Variable in class fr.systemsbiology.cyni.CyniTable

nColumns() - Method in class fr.systemsbiology.cyni.CyniTable

Returns the number of columns in the table.

netFactory - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

netMgr - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

netMgr - Variable in class fr.systemsbiology.cyni.CyniNetworkUtils

netTableMgr - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

newNetwork - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

This variable holds the new network that will be created if an inference algorithm is executed.

nodeParents - Variable in class fr.systemsbiology.cyni.CyniBayesianUtils

This variable maps an integer representing a node/row with a list of integers that represents a list of parents for that node/row In oder to use it correctly, this variable needs to be initialized and a previous map between a node and its corresponding integer is also required

nRows - Variable in class fr.systemsbiology.cyni.CyniTable

nRows() - Method in class fr.systemsbiology.cyni.CyniTable

Returns the number of rows in the table.

nThreads - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

Indicates the maximum number of threads that this task can use

O

outputMessage - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

This variable holds the message that will be shown after task is done

R

removeNodesWithoutEdges(CyNetwork) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Remove nodes that do not have any edge

resetOrderRows() - Method in class fr.systemsbiology.cyni.CyniTable

Changes the order to the initial internal state

rootNetMgr - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

rowHasMissingValue - Variable in class fr.systemsbiology.cyni.CyniTable

rowHasMissingValue(int) - Method in class fr.systemsbiology.cyni.CyniTable

Tells if the specified row has a missing value.

rowLabels - Variable in class fr.systemsbiology.cyni.CyniTable

rowMaxValue - Variable in class fr.systemsbiology.cyni.CyniTable

rowMinValue - Variable in class fr.systemsbiology.cyni.CyniTable

rowNumStringsDiff - Variable in class fr.systemsbiology.cyni.CyniTable

rowWeights - Variable in class fr.systemsbiology.cyni.CyniTable

run(TaskMonitor) - Method in class fr.systemsbiology.cyni.AbstractCyniTask

S

selectedOnly - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

Indicates whether to apply the algorithm to all rows or only the selected rows.

selectedOnly - Variable in class fr.systemsbiology.cyni.CyniAlgorithmContext

Indicates that only selected rows should be used.

selectedOnly - Variable in class fr.systemsbiology.cyni.CyniTable

setColLabel(int, Object) - Method in class fr.systemsbiology.cyni.CyniTable

Set the label for the specified column.

setColWeight(int, double) - Method in class fr.systemsbiology.cyni.CyniTable

Set the weight for the specified column.

setDefaultCyniMetric(String) - Method in interface fr.systemsbiology.cyni.CyCyniMetricsManager

Sets the default Cyni Metric.

setNetworkName(CyNetwork, String) - Method in class fr.systemsbiology.cyni.CyniNetworkUtils

Sets the name of the network

setParameters(Map<String, Object>) - Method in class fr.systemsbiology.cyni.AbstractCyniMetric

It sets the metric's parameters

setParameters(Map<String, Object>) - Method in interface fr.systemsbiology.cyni.CyCyniMetric

It sets the metric's parameters

setParentSwingComponent(Component) - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

Sets the parent component of this context so the context knows whether a swing UI has been created for this context

setRowLabel(int, Object) - Method in class fr.systemsbiology.cyni.CyniTable

Set the label for the specified row.

setRowWeight(int, double) - Method in class fr.systemsbiology.cyni.CyniTable

Set the weight for the specified row.

setSelectedOnly(boolean) - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

Set the flag that indicates that this algorithm should only operate on the currently selected rows.

setType(int, int, Class<?>) - Method in class fr.systemsbiology.cyni.CyniTable

Allows setting the type of for the specified row and column combination.

setUniformWeights() - Method in class fr.systemsbiology.cyni.CyniTable

Set the weights to a constant value.

setValue(int, int, Object) - Method in class fr.systemsbiology.cyni.CyniTable

Set the value for the specified row and column

stringValue(int, int) - Method in class fr.systemsbiology.cyni.CyniTable

Returns the string value for the specified row and column combination.

stringValues - Variable in class fr.systemsbiology.cyni.CyniTable

supportsSelectedOnly() - Method in class fr.systemsbiology.cyni.AbstractCyniAlgorithm

Tells if this Cyni supports doing a Cyni Algorithm on a subset of the nodes.

supportsSelectedOnly() - Method in interface fr.systemsbiology.cyni.CyCyniAlgorithm

Tells if this Cyni supports doing a Cyni Algorithm on a subset of the nodes.

T

toString() - Method in class fr.systemsbiology.cyni.AbstractCyniAlgorithm

Used to get the user-visible name of the cyni algorithm.

toString() - Method in class fr.systemsbiology.cyni.AbstractCyniMetric

Used to get the user-visible name of the cyni Metric.

transpose - Variable in class fr.systemsbiology.cyni.CyniTable

U

useSelectedOnly() - Method in class fr.systemsbiology.cyni.CyniAlgorithmContext

Returns whether the algorithm allows working with only selected rows

V

valueOf(String) - Static method in enum fr.systemsbiology.cyni.CyniCategory

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

valueOf(String) - Static method in enum fr.systemsbiology.cyni.CyniMetricTags

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

values() - Static method in enum fr.systemsbiology.cyni.CyniCategory

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

values() - Static method in enum fr.systemsbiology.cyni.CyniMetricTags

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

viewFactory - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

viewFactory - Variable in class fr.systemsbiology.cyni.CyniNetworkUtils

viewMgr - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

viewMgr - Variable in class fr.systemsbiology.cyni.CyniNetworkUtils

vmMgr - Variable in class fr.systemsbiology.cyni.AbstractCyniTask

vmMgr - Variable in class fr.systemsbiology.cyni.CyniNetworkUtils

A C D F G H I M N O R S T U V