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

F

fCharHeight - Variable in class biggests.utils.VerticalTextIcon
The width and height of the label, character height and descent.
fCharStrings - Variable in class biggests.utils.VerticalTextIcon
The label parsed into one-char strings.
fCharWidths - Variable in class biggests.utils.VerticalTextIcon
The characters widths.
fComponent - Variable in class biggests.utils.VerticalTextIcon
The component in which the label will be drawn.
fDescent - Variable in class biggests.utils.VerticalTextIcon
The width and height of the label, character height and descent.
fHeight - Variable in class biggests.utils.VerticalTextIcon
The width and height of the label, character height and descent.
FileFilterDirectory - Class in biggests.utils
Title: File Filter with directory exclusion.
FileFilterDirectory(String[], String) - Constructor for class biggests.utils.FileFilterDirectory
Creates a new directory file filter, with a specific valid file extension and some invalid directory paths.
FileFilterDirectoryChooser - Class in biggests.utils
Title: Description:
FileFilterDirectoryChooser(String[]) - Constructor for class biggests.utils.FileFilterDirectoryChooser
 
FileFilterExtension - Class in biggests.utils
Title: File Filter by extension.
FileFilterExtension(String) - Constructor for class biggests.utils.FileFilterExtension
Creates a new extension file filter, to filter files based on their extensions.
FILL_NEIGHBORS - Static variable in class biggests.gui.PanelPreProcessing
'Number of neighbors' parameter name.
FILL_VALUE - Static variable in class biggests.gui.PanelPreProcessing
'Value to fill missings' parameter name;
fillAverageRowButton_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user selects the fill missings with average over the same row radio button.
fillCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing
 
fillKNeighborsButton_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user selects the fill missings with average over the k-neighbors radio button.
fillValueButton_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user selects the fill missings with a given value radio button.
FILTER_ACV - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with an ACV value below a given threshold' option.
FILTER_ACV_ARV - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter trivial biclusters and biclusters with ACV and ARV values below given thresholds' option.
FILTER_ARV - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with an ARV value below a given threshold' option.
FILTER_CONDITIONS - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with less than a given number of conditions' option.
FILTER_CONDITIONS_GENES_ARV_ACV - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with less than given numbers of genes and conditions and with ARV and ACV values below given thresholds' option.
FILTER_CONDITIONS_GENES_ARV_ACV_MSR - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with less than given numbers of genes and conditions and with ARV, ACV and MSR values below given thresholds' option.
FILTER_CONSTANT_PATTERN - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with constant pattern' option.
filter_CONSTANT_PATTERN(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with a constant pattern and a % of overlapping conditions below two given thresholds.
FILTER_GENES - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with less than a given number of genes' option.
FILTER_GENES_CONDITIONS - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with less than a given number of genes and less than a given number of conditions' option.
FILTER_MSR - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with an MSR value below a given threshold' option.
FILTER_OVERLAPPING_GENES - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with a row similarity below a given threshold' option.
FILTER_OVERLAPPING_GENES_CONDITIONS - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters with row and column similarities below given thresholds' option.
FILTER_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT - Static variable in class biggests.gui.PanelPostProcessing
 
filter_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Filters the biclusters of the given biclusters' group (BiclusteringInDiscretizedMatrix) for which the pattern p-value with columns is not significant.
FILTER_PATTERN_PVALUE_NOT_SIGNIFICANT - Static variable in class biggests.gui.PanelPostProcessing
 
filter_PATTERN_PVALUE_NOT_SIGNIFICANT(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Filters the biclusters of the given biclusters' group (BiclusteringInDiscretizedMatrix) for which the pattern p-value is not significant.
FILTER_PERCENTAGE - Static variable in class biggests.gui.PanelPreProcessing
'Percentage of genes to filter' parameter name.
FILTER_SIZE - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters smaller than a given size' option.
FILTER_SIZE_ARV_ACV - Static variable in class biggests.gui.PanelPostProcessing
The index of 'filter biclusters smaller than a given size and with ARV and ACV values below given thresholds' option.
FILTER_TRIVIAL - Static variable in class biggests.gui.PanelPostProcessing
The index of filter trivial biclusters option.
filter_TRIVIAL(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs trivial biclusters filtering algorithm.
filterBy_ACV_ARV_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with ACV and ARV below two given thresholds.
filterBy_ACV_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with an ACV below a given threshold.
filterBy_ARV_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with an ARV below a given threshold.
filterBy_MSR_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with a MSR below a given threshold.
filterBy_NR_CONDITIONS(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with less than a given number of conditions.
filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_MSR_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with a number of conditions, a number of genes, ACV, ARV and MSR below five given thresholds.
filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with a number of conditions, a number of genes, ACV and ARV below four given thresholds.
filterBy_NR_GENES(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with less than a given number of genes.
filterBy_NR_GENES_NR_CONDITIONS(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with less than a given number of genes and a given number of conditions.
filterBy_OVERLAPPING_GENES_CONDITIONS_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with a % of overlapping genes and a % of overlapping conditions below two given thresholds.
filterBy_OVERLAPPING_GENES_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with a % of overlapping genes below a given threshold.
filterBy_SIZE_ARV_ACV_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with size, ACV and ARV below three given thresholds.
filterBy_SIZE_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs filtering of biclusters with size below a given threshold.
filterCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPostProcessing
Handles changes on filter check box selection.
filterCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing
 
filterCriteriaList_valueChanged(ListSelectionEvent) - Method in class biggests.gui.PanelPostProcessing
Handles a selection change on filter criteria list.
filterCriteriaList_valueChanged() - Method in class biggests.gui.PanelPostProcessing
Handles a selection change on filter criteria list.
filterPercentGenesButton_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user selects the filter genes with more than a % of missing values radio button.
findAnnotationFileExtensionForOrganism(String) - Static method in class biggests.gui.PanelFunctionAnalysis
Finds and returns the corresponding annotation file extension for a given organism.
findBiclusterNodeByIDinSetOfBiclustersNodes(Enumeration, int) - Method in class biggests.tree.DatasetTree
Looks for a NodeInfo object of a bicluster or post-processed bicluster object with a specific id.
findClosestPair(int, double[][], int[], int[]) - Static method in class biggests.clustering.HierarchicalClustering
Searches the distance matrix to find the pair with the shortest distance between them.
findFileExtensionInDirectoryPath(String, String) - Static method in class biggests.gui.BiggestsIO
Finds the first file with a specific file extension in some specific directory.
findFileInDirectoryPath(String, String) - Static method in class biggests.gui.BiggestsIO
Finds for a specific filename in a specific directory path.
findGeneAssociationFileName(String, boolean) - Static method in class biggests.gui.PanelFunctionAnalysis
Finds a specific filename or extension for a given organism.
findInfoString(String) - Method in class biggests.tree.NodeInfo
Finds a specific information string.
finishTaskInLabelContext(String) - Method in class biggests.gui.BiggestsFrame
 
fLabel - Variable in class biggests.utils.VerticalTextIcon
The label to rotate.
fPosition - Variable in class biggests.utils.VerticalTextIcon
The position of the characters.
fRotation - Variable in class biggests.utils.VerticalTextIcon
The rotation of the label.
functionGroupTable_mouseClicked(MouseEvent) - Method in class biggests.gui.PanelAnalyzingFunctionTable
Handles the event fired when the mouse is clicked on a function group table's row.
fWidth - Variable in class biggests.utils.VerticalTextIcon
The width and height of the label, character height and descent.

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