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

S

saveButton_actionPerformed(ActionEvent) - Method in class biggests.gui.SaveChartImageDialog
Handles the event fired when the user clicks save button.
saveChartAsPDF(File, JFreeChart, int, int, FontMapper) - Static method in class biggests.gui.SaveChartImageDialog
Saves a chart to a PDF file.
saveChartAsSVG(File, JFreeChart, int, int) - Static method in class biggests.gui.SaveChartImageDialog
Saves a chart as a SVG document.
SaveChartImageDialog - Class in biggests.gui
Title: Save Chart Image Dialog Description: Dialog suited for prompting the user to provide the width, height and file format to export a chart as an image.
SaveChartImageDialog(Frame, Component, String, boolean, int, int) - Constructor for class biggests.gui.SaveChartImageDialog
Creates a save chart image dialog.
saveCurrentSession(boolean) - Method in class biggests.gui.BiggestsFrame
Saves current session to a zip archive file.
saveGraph_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
Handles the user click on the save graph button.
saveSession(DatasetTree, String, String) - Static method in class biggests.gui.BiggestsIO
Saves a session to a .zip archive file.
saveSession2(DatasetTree, String, String) - Static method in class biggests.gui.BiggestsIO
Saves a session to a .zip archive file.
SCROLL_BAR_INCREMENT - Static variable in class biggests.gui.BiggestsFrame
 
SEMICOLON - Static variable in class biggests.gui.PanelLoading
Data delimiter: semicolon.
serialVersionUID - Static variable in class biggests.tree.Dataset
 
serialVersionUID - Static variable in class biggests.tree.DatasetTree
 
serialVersionUID - Static variable in class biggests.tree.NodeInfo
 
sessionExit_actionPerformed(ActionEvent) - Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user clicks Session -> Exit item menu.
sessionLoadDataset_actionPerformed(ActionEvent) - Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user clicks the menu item Session -> Load Dataset.
sessionLoadSession_actionPerformed(ActionEvent) - Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user clicks the menu item Session -> Load Session.
sessionSaveSession_actionPerformed(ActionEvent) - Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user clicks the menu item Session -> Save Session.
setBackAndForegroundHighlightColors(JComponent) - Static method in class biggests.utils.HeatmapColorScheme
 
setColumnComparator(Class, Comparator) - Method in class biggests.tables.TableSorter
Sets the given comparator for the given objects' type.
setDiscretizeCheckBoxSelected(boolean) - Method in class biggests.gui.PanelPreProcessing
Sets the discretize check box selected/deselected, enabling/disabling the corresponding discretize options.
setDistance(double) - Method in class biggests.clustering.ClusterTreeNode
Sets the distance between left and right sons.
setEvenRowsColor(Color) - Method in class biggests.tables.TableFunctionGroup
Sets a new color to mark even rows that are not selected.
setEvenRowsColor(Color) - Method in class biggests.tables.TableFunctionIndividual
Sets a new color to mark even rows that are not selected.
setFilterCheckBoxSelected(boolean) - Method in class biggests.gui.PanelPostProcessing
Sets filter check box selected/deselected.
setFilterCheckBoxSelected(boolean) - Method in class biggests.gui.PanelPreProcessing
Sets the filter check box selected/deselected, enabling/disabling the corresponding filter options.
setGeneIDCheckBoxSelected(boolean) - Method in class biggests.gui.PanelLoading
Sets gene ID check box selected/deselected.
setGeneShiftsCheckBoxSelected(boolean) - Method in class biggests.gui.PanelBiclustering
Sets gene shifts check box selected/deselected, along with the corresponding enabling/disabling of shifts label and input text field.
setHeatmapColorScheme(int) - Static method in class biggests.utils.HeatmapColorScheme
 
setInfoStrings(ArrayList<String>) - Method in class biggests.tree.NodeInfo
Sets information strings.
setInfoStyles(ArrayList<String>) - Method in class biggests.tree.NodeInfo
Sets information styles.
setLabel(String) - Method in class biggests.utils.VerticalTextIcon
Sets the fLabel to the given label string, updating the orientation as needed and invalidating the layout if the size changes.
setLeft(int) - Method in class biggests.clustering.ClusterTreeNode
Sets the index for left son.
setNormalizeCheckBoxSelected(boolean) - Method in class biggests.gui.PanelPreProcessing
Sets the normalize check box selected/deselected, enabling/disabling the corresponding normalize options.
setNumberOfDendrograms(int) - Static method in class biggests.gui.PanelAnalyzingMatrixDendrogram
 
setOddRowsColor(Color) - Method in class biggests.tables.TableFunctionGroup
Sets a new color to mark odd rows that are not selected.
setOddRowsColor(Color) - Method in class biggests.tables.TableFunctionIndividual
Sets a new color to mark odd rows that are not selected.
setPathToDOT(String) - Static method in class biggests.gui.BiggestsFrame
 
setPreviewEnabled(boolean) - Method in class biggests.gui.PanelLoading
Sets preview option enabled/disabled.
setRestrictedErrorsECCCCheckBoxSelected(boolean) - Method in class biggests.gui.PanelBiclustering
Sets restricted errors for e-CCC-Biclustering algorithm check box selected/deselected, along with the corresponding enabling/disabling of neighbors label and text field.
setRight(int) - Method in class biggests.clustering.ClusterTreeNode
Sets the index for right son.
setSignificantColor(Color) - Method in class biggests.tables.TableFunctionGroup
Sets a new color to mark significant terms.
setSignificantColor(Color) - Method in class biggests.tables.TableFunctionIndividual
Sets a new color to mark significant terms.
setSmoothCheckBoxSelected(boolean) - Method in class biggests.gui.PanelPreProcessing
Sets the smooth check box selected/deselected, enabling/disabling the corresponding smooth options.
setSortCheckBoxSelected(boolean) - Method in class biggests.gui.PanelPostProcessing
Sets sort check box selected/deselected.
setSortingStatus(int, int) - Method in class biggests.tables.TableSorter
Sets the sorting status for a given column.
setStop(boolean) - Static method in class biggests.gui.BiggestsIO
Sets stop flag.
setString(String) - Method in class biggests.utils.ProgressBarFrame
Sets the message displayed by the progress bar.
setStringsAndStyles(Biclustering) - Method in class biggests.gui.PanelBiclustering
Sets strings and styles attributes according to the type and parameters of biclustering object.
setStringsAndStylesCCC(CCC_Biclustering) - Method in class biggests.gui.PanelBiclustering
Sets strings and styles attributes according to the parameters of the CCC_Biclustering object.
setStringsAndStylesCCTSB(CC_TSB_Biclustering) - Method in class biggests.gui.PanelBiclustering
Sets strings and styles attributes according to the parameters of the CC_TSB_Biclustering object.
setStringsAndStylesECCC(E_CCC_Biclustering) - Method in class biggests.gui.PanelBiclustering
Sets strings and styles attributes according to the parameters of the E_CCC_Biclustering object.
setTabbedPaneAnalyzingEnabledTabs(boolean, boolean, boolean) - Method in class biggests.gui.BiggestsFrame
Enables/disables tabs on the analyzing tabbed pane.
setTabbedPaneAnalyzingMatrixEnabledTabs(boolean, boolean, boolean, boolean) - Method in class biggests.gui.BiggestsFrame
Enables/disables tabs on the matrix analysis tabbed pane.
setTabbedPaneEnabledTabs(boolean, boolean, boolean, boolean, boolean, boolean) - Method in class biggests.gui.BiggestsFrame
Enables/disables tabs on the main tabbed pane.
setTableHeader(JTableHeader) - Method in class biggests.tables.TableSorter
Sets the table header.
setTableHeader(JTableHeader) - Method in class biggests.tables.TableSorterVerticalHeader
 
setTableModel(TableModel) - Method in class biggests.tables.TableSorter
Sets the table model.
setTree(DatasetTree) - Method in class biggests.gui.BiggestsFrame
Sets a new dataset tree.
setValue(Object) - Method in class biggests.tables.TableFunctionGroup.FloatCellRenderer
Overrides DefaultTableCellRenderer's setValue method.
setValue(Object) - Method in class biggests.tables.TableFunctionIndividual.FloatCellRenderer
Overrides DefaultTableCellRenderer's setValue method.
setValue(Object) - Method in class biggests.tables.TableValues.FloatCellRenderer
Overrides DefaultTableCellRenderer's setValue method.
setValueAt(Object, int, int) - Method in class biggests.tables.TableSorter
Sets the element of the cell with row and column) indexes.
SHIFTS - Static variable in class biggests.gui.PanelBiclustering
Name of the 'shifts' parameter for CCC-Biclustering and e-CCC-Biclustering algorithms.
showDendrogram(String, String) - Method in class biggests.gui.PanelAnalyzingMatrixDendrogram
 
showDiscretizeErrorMessage(String) - Method in class biggests.gui.PanelPreProcessing
Shows the discretization error message.
signChangesCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelBiclustering
 
SIGNIFICANT_COLOR - Static variable in class biggests.tables.TableFunctionGroup
Default color to mark rows that contain biclusters with significant terms.
SIGNIFICANT_COLOR - Static variable in class biggests.tables.TableFunctionIndividual
Default color for significant terms.
SINGLE_LINKAGE - Static variable in class biggests.clustering.HierarchicalClustering
Pairwise single-linkage (clustering method).
singleLinkageClustering(double[][], int[][], double[], double[][], char, boolean) - Method in class biggests.clustering.HierarchicalClustering
Performs single-linkage hierarchical clustering, using either the distance matrix directly, if available, or by calculating the distances from the expression data matrix.
SMOOTH_WINDOW - Static variable in class biggests.gui.PanelPreProcessing
'Smoothing window' parameter name.
smoothCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user selects/deselects the smooth check box.
SORT_ACV - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their ACV values' option.
SORT_ARV - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their ARV values' option.
SORT_ARV_ACV_DIFF - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by the differences between their ARV and ACV values' option.
SORT_ARV_MSR_DIFF - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by the differences between their ARV and MSR values' option.
SORT_BEST_GO_BONFERRONI_PVALUE - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their best GO Bonferroni corrected p-value' option.
SORT_BEST_GO_PVALUE - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their best GO p-value' option.
SORT_CONDITIONS - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their number of conditions' option.
SORT_GENES - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their number of genes' option.
SORT_MSR - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their MSR values' option.
SORT_PATTERN_COLUMNS_PVALUE - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by the p-value for their pattern with columns' option.
SORT_PATTERN_PVALUE - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their pattern p-value' option.
SORT_SIZE - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their size' option.
SORT_VARIANCE - Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their variance' option.
sortBy_ACV(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their ACV.
sortBy_ARV(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their ARV.
sortBy_ARV_ACV_DIFF(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by the difference of their ARV and ACV (ARV-ACV).
sortBy_ARV_MSR_DIFF(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by the difference of their ARV and MSR (ARV-MSR).
sortBy_BEST_GO_BONFERRONI_PVALUE(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their best GO Bonferroni corrected p-values in ascending order.
sortBy_BEST_GO_PVALUE(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their best GO p-values in ascending order.
sortBy_MSR(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their MSR.
sortBy_NR_CONDITIONS(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their number of conditions.
sortBy_NR_GENES(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their number of genes.
sortBy_PATTERN_PVALUE(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their pattern p-value in ascending order.
sortBy_PATTERN_WITH_COLUMNS_PVALUE(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their pattern with columns p-value in ascending order.
sortBy_SIZE(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their sizes.
sortBy_VARIANCE(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their variances.
sortCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPostProcessing
Handles changes on sort check box selection.
sortClusteringTree(boolean, double[], double[], int[], ClusterTreeNode[]) - Method in class biggests.clustering.HierarchicalClustering
Sorts the nodes of the tree based on the tree's structure.
sortCriteriaList_valueChanged(ListSelectionEvent) - Method in class biggests.gui.PanelPostProcessing
Handles a selection change on sort criteria list.
sortCriteriaList_valueChanged() - Method in class biggests.gui.PanelPostProcessing
Handles a selection change on sort criteria list.
sortIndexes(double[], int[]) - Static method in class biggests.clustering.AbstractMetricClustering
Sets up an index table given the data, such that data[indexes[i]], with i = 0, ..., data.length is in increasing order.
SPACE - Static variable in class biggests.gui.PanelLoading
Data delimiter: space.
SPEARMAN_RANK_CORRELATION - Static variable in class biggests.clustering.AbstractMetricClustering
Spearman's rank correlation (distance metric).
spearmansRankCorrelation(double[][], double[][], int[][], int[][], double[], int, int, boolean) - Static method in class biggests.clustering.AbstractMetricClustering
Calculates the Spearman distance between two genes/rows or conditions/columns.
springLayout() - Method in class biggests.gui.PanelFunctionAnalysis
Returns the layout for this panel.
startTaskInLabelContext(String) - Method in class biggests.gui.BiggestsFrame
 
SVG - Static variable in class biggests.gui.BiggestsIO
Image format: SVG
SVG - Static variable in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
SVG image type.
SVG - Static variable in class biggests.gui.SaveChartImageDialog
SVG document file extension.
SYMBOLS - Static variable in class biggests.gui.PanelAnalyzingMatrixTables
The type for symbols tables.
SYMBOLS - Static variable in class biggests.tree.NodeInfo
The symbol values matrix data type.

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