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

A

AbstractMetricClustering - Class in biggests.clustering
Title: Abstract Metric Clustering Description: Defines an abstract class for clustering methods based on distance metrics.
AbstractMetricClustering(IMatrix) - Constructor for class biggests.clustering.AbstractMetricClustering
Creates a new AbstractClustering object to perform clustering over the set of gene expression data contained in expressionMatrix.
AbstractMetricClustering(int, int, double[], double[], double[], double[], int[], int[], String, String[], String[], String[], double[][], int[][]) - Constructor for class biggests.clustering.AbstractMetricClustering
Creates a new AbstractMetricClustering object to perform clustering over the given set of expression data.
accept(File) - Method in class biggests.utils.FileFilterDirectory
Checks if a certain file is acceptable under the filter conditions.
accept(File) - Method in class biggests.utils.FileFilterDirectoryChooser
Checks if a certain file is acceptable under the filter conditions.
accept(File) - Method in class biggests.utils.FileFilterExtension
Checks if a certain file is acceptable under the filter conditions.
actionPerformed(ActionEvent) - Method in class biggests.gui.BiggestsFrame
 
addBiclusterGroupToDatasetTree(Biclustering, TreePath, GOFrontEnd) - Method in class biggests.gui.PanelBiclustering
Adds a bicluster group to the dataset tree.
addLoadedDataset(NodeInfo) - Method in class biggests.tree.DatasetTree
Adds the loaded dataset to the dataset tree and creates all additional nodes for preprocessed, discretized, biclustered and post-processed matrices of the dataset.
addLoadedDataset(NodeInfo, boolean) - Method in class biggests.tree.DatasetTree
Adds the loaded dataset to the dataset tree and creates all additional nodes for preprocessed, discretized, biclustered and post-processed matrices of the dataset.
addMessageToMessageHistory(String) - Method in class biggests.utils.ProgressBarFrame
Adds a new message to message history.
addNewNode(NodeInfo, TreePath, boolean) - Method in class biggests.tree.DatasetTree
Adds a new node to the datasets tree, associated with a node information object.
addNewNode(NodeInfo, TreePath, boolean, boolean) - Method in class biggests.tree.DatasetTree
Adds a new node to the datasets tree, associated with a node information object.
addPostProcessedBiclusterGroupToTree(Biclustering, ArrayList<String>, ArrayList<String>, TreePath) - Method in class biggests.gui.PanelPostProcessing
Adds a post-processed biclustering to the dataset tree.
addStylesToDocument(StyledDocument) - Method in class biggests.tree.NodeInfo
Adds a set of common styles to StyledDocument doc
algorithmsList_valueChanged(ListSelectionEvent) - Method in class biggests.gui.PanelBiclustering
Handles a selection change in algorithms' list.
ALL_TIME_POINTS - Static variable in class biggests.gui.PanelExpression
Constant which defines all time points expression chart type.
allowMissingsButton_mouseClicked(MouseEvent) - Method in class biggests.gui.PanelBiclustering
 
ALPHA - Static variable in class biggests.gui.PanelBiclustering
Name of the 'alpha' parameter (CC-TSB-biclustering).
alphabet - Variable in class biggests.tables.TableSymbols
The alphabet with all discretization symbols used in the discretization technique that gave rise to the set of discrete values that may appear in this symbols table.
applyBiclusteringAlgorithm() - Method in class biggests.gui.PanelBiclustering
Applies biclustering algorithm.
applyButton() - Method in class biggests.gui.PanelPreProcessing
Returns apply preprocessing options button.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelAnalyzingFunctionTable
Handles the mouse event fired when the user clicks the apply button.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelAnalyzingMatrixDendrogram
Handles the event fired when the user clicks apply button.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelBiclustering
Handles the mouse event fired when the user clicks the apply button.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelPostProcessing
Applies the post-processing criteria to the current biclusters group.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelPreProcessing
Handles the mouse event fired when the user clicks on the apply button.
applyCCCBiclusteringAlgorithm() - Method in class biggests.gui.PanelBiclustering
Applies CCC-Biclustering algorithm.
applyCCTSBBiclusteringAlgorithm() - Method in class biggests.gui.PanelBiclustering
Applies CC-TSB-biclustering algorithm.
applyECCCBiclusteringAlgorithm() - Method in class biggests.gui.PanelBiclustering
Applies e-CCC-Biclustering algorithm.
Arrow - Class in biggests.utils
Title: Arrow Description: Class that implements an Icon.
Arrow(boolean, int, int) - Constructor for class biggests.utils.Arrow
Creates a new arrow for the given sorting status, with the given size and priority.
ASCENDING - Static variable in class biggests.tables.TableSorter
The status that indicates that a specific column is sorted in ascending order.
AVERAGE_LINKAGE - Static variable in class biggests.clustering.HierarchicalClustering
Pairwise average linkage (clustering method).
averageLinkageClustering(double[][]) - Method in class biggests.clustering.HierarchicalClustering
Performs clustering using pairwise average-linking on the given distance matrix.

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