Index (GC4S 1.6.0 API)

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

A

AbstractBooleanTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An abstract implementation of Test<Boolean> to apply TestOfIndependence tests on feature values sets of Boolean.
AbstractBooleanTest(TestOfIndependence) - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.AbstractBooleanTest: Creates a new AbstractBooleanTest instance for applying the specified TestOfIndependence.
AbstractCsvTableExporter - Class in org.sing_group.gc4s.visualization.table.csv: An abstract CsvTableExporter implementation.
AbstractCsvTableExporter() - Constructor for class org.sing_group.gc4s.visualization.table.csv.AbstractCsvTableExporter
AbstractInputJDialog - Class in org.sing_group.gc4s.dialog: Abstract class for creating input dialogs.
AbstractInputJDialog(Window) - Constructor for class org.sing_group.gc4s.dialog.AbstractInputJDialog: Constructs an AbstractInputJDialog.
AbstractKeyPressedListener - Class in org.sing_group.gc4s.event: An abstract implementation of KeyListener that runs action when key code returned by getKeyCode is pressed.
AbstractKeyPressedListener(Runnable) - Constructor for class org.sing_group.gc4s.event.AbstractKeyPressedListener: Constructs an AbstractKeyPressedListener with the specified action.
AbstractNumberTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An abstract implementation of Test<Number> to facilitate the application of tests on feature sets of Number.
AbstractNumberTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.AbstractNumberTest
AbstractTTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An abstract extension of AbstractNumberTest to compute t-tests.
AbstractTTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.AbstractTTest
accept(File) - Method in class org.sing_group.gc4s.genomebrowser.GPFilter
accept(File) - Method in class org.sing_group.gc4s.input.filechooser.ExtensionFileFilter
accept(Object) - Method in interface org.sing_group.gc4s.input.list.FilteredListModel.Filter
ACTION_EXPORT_CSV - Static variable in class org.sing_group.gc4s.visualization.table.csv.CsvTable
ACTION_TESTS_INFO - Static variable in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTable
actionPerformed(ActionEvent) - Method in class org.sing_group.gc4s.utilities.ExtendedAbstractAction
add(Component) - Method in class org.sing_group.gc4s.ui.CenteredJPanel
add(Action) - Method in class org.sing_group.gc4s.ui.menu.HamburgerMenu: Appends a new menu item to the end of the menu which dispatches the specified Action object.
add(JMenuItem) - Method in class org.sing_group.gc4s.ui.menu.HamburgerMenu: Appends the specified menu item to the end of this menu.
add(Component) - Method in class org.sing_group.gc4s.ui.menu.HamburgerMenu: Appends the specified component to the end of this menu.
addAction(Action) - Method in class org.sing_group.gc4s.input.list.JListPanel: Adds a button with the specified action.
addAction(Action, String) - Method in class org.sing_group.gc4s.input.list.JListPanel: Adds a button with the specified action.
addAction(Action) - Method in class org.sing_group.gc4s.visualization.table.ExtendedJXTable: Adds Action a so that it will appear in the ColumnControlButton of the table.
addChangeListener(ChangeListener) - Method in class org.sing_group.gc4s.input.RangeInputPanel
addChangeListener(ChangeListener) - Method in class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Adds the specified change listener to receive component events from this component.
addColor(Color) - Method in class org.sing_group.gc4s.input.list.ColorsListPanel: Adds the specified color to the list of selected colors.
addColors(List<Color>) - Method in class org.sing_group.gc4s.input.list.ColorsListPanel: Adds the specified colors to the list of selected colors.
addComponentWrapPanelComponent() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
addComponentWrapPanelComponent(Supplier<T>) - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
addComponentWrapPanelComponent(ComponentsListPanel<T>.ComponentWrapPanel) - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
addCsvListener(CsvListener) - Method in class org.sing_group.gc4s.input.csv.CsvPanel: Adds the specified CSV listener to receive component events from this component.
addCuadriculaAtRectangle(GridInfo, float, float, float, float) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
addCuadriculaInfo(double, double, GridInfo) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
addElements(List<E>) - Method in class org.sing_group.gc4s.input.list.ExtendedDefaultListModel: Adds all the elements to the model.
addElements(String...) - Method in class org.sing_group.gc4s.input.list.JInputList: Adds elements to the input list.
addExtendedDefaultListModelListener(ExtendedDefaultListModelListener) - Method in class org.sing_group.gc4s.input.list.ExtendedDefaultListModel: Adds the specified ExtendedDefaultListModelListener to the listeners list.
addFileChooserListener(FileChooserListener) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Adds the specified file chooser listener to receive component events from this component.
addFileChooserListener(MultipleFileChooserListener) - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Adds the specified file chooser listener to receive component events from this component.
addItemListener(ItemListener) - Method in class org.sing_group.gc4s.input.RadioButtonsPanel: Adds an ItemListener to this component to listen events occurred in the radio buttons.
addKeyBindings() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog: Establishes the dialog key bindings.
addListDataListener(ListDataListener) - Method in class org.sing_group.gc4s.input.list.ColorsListPanel: Adds a listener to the list that's notified each time a change to the data model occurs.
addListDataListener(ListDataListener) - Method in class org.sing_group.gc4s.input.list.JInputList: Adds a listener to the list that's notified each time a change to the data model occurs.
addProgressEventListener(ProgressEventListener) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTable: Adds the specified progress listener to receive component events from this component.
addSelectionPath(TreePath) - Method in class org.sing_group.gc4s.input.tree.PathCheckTreeSelectionModel
addSelectionPaths(TreePath[]) - Method in class org.sing_group.gc4s.input.tree.PathCheckTreeSelectionModel
addTab(String, Component) - Method in class org.sing_group.gc4s.ui.tabbedpane.CloseableJTabbedPane
addTab(String, Icon, Component) - Method in class org.sing_group.gc4s.ui.tabbedpane.CloseableJTabbedPane
addTab(String, Icon, Component, String) - Method in class org.sing_group.gc4s.ui.tabbedpane.CloseableJTabbedPane
addTab(String, Component) - Method in class org.sing_group.gc4s.ui.tabbedpane.ExtendedJTabbedPane
addTab(String, Icon, Component) - Method in class org.sing_group.gc4s.ui.tabbedpane.ExtendedJTabbedPane
addTab(String, Icon, Component, String) - Method in class org.sing_group.gc4s.ui.tabbedpane.ExtendedJTabbedPane
addTableModelListener(TableModelListener) - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel
addTrack(File) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Adds a track associated to the specified file.
addWizardStepListener(WizardStepListener) - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep: Adds the specified wizard step listener to receive component events from this component.
applyBackground(Component, ComponentAdapter) - Method in class org.sing_group.org.gc4s.statistics.table.ui.BooleanHighlighter
applyBackground(Component, ComponentAdapter) - Method in class org.sing_group.org.gc4s.statistics.table.ui.ConditionsSeparatorHighlighter
applyBackground(Component, ComponentAdapter) - Method in class org.sing_group.org.gc4s.statistics.table.ui.NumberHighlighter
applyRecursive(JComponent, Consumer<JComponent>) - Static method in class org.sing_group.gc4s.ui.UIUtils: Applies consumer to aComponent and all its JComponents.
asDoubleArray(List<Number>) - Method in class org.sing_group.org.gc4s.statistics.data.tests.AbstractNumberTest
asFunction(Map<Character, Color>) - Static method in class org.sing_group.gc4s.msaviewer.DefaultBaseColorScheme: Converts a map into a Function.
asPrimitiveArray(List<Double>) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Converts a list of Double into a primitive array of double.
asStringMatrix(Object[][]) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Converts matrix into a String[][].

B

backGroundColor - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
BamIntervalsPainter - Class in org.sing_group.gc4s.genomebrowser.painter: A Painter implementation to render .bam files.
BamIntervalsPainter(File) - Constructor for class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter: Creates a new BamIntervalsPainter for the specified track file.
BaseColorScheme - Interface in org.sing_group.gc4s.msaviewer: The interface that defines a color scheme used by a BaseColorSequenceAlignmentRenderer.
BaseColorSequenceAlignmentRenderer - Class in org.sing_group.gc4s.msaviewer: A DefaultSequenceAlignmentRenderer implementation that renders each sequence base using the color specified by the BaseColorScheme.
BaseColorSequenceAlignmentRenderer(BaseColorScheme) - Constructor for class org.sing_group.gc4s.msaviewer.BaseColorSequenceAlignmentRenderer: Creates a new BaseColorSequenceAlignmentRenderer with the specified colorScheme.
BasicTransferable - Class in org.sing_group.gc4s.visualization.table.csv: A custom Transferable implementation.
BasicTransferable(String, String) - Constructor for class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Creates a new BasicTransferable with the specified initial values.
beanProperties(Object) - Static method in class org.sing_group.gc4s.visualization.table.BeanTableModel
BeanTableModel<T> - Class in org.sing_group.gc4s.visualization.table: A table model for easily displaying a list of Java beans in a table, using one row for each bean and one column for each bean's property.
BeanTableModel(List<T>) - Constructor for class org.sing_group.gc4s.visualization.table.BeanTableModel: Creates a new BeanTableModel instance using the list of beans.
BindJXTextField - Class in org.sing_group.gc4s.input.text: A BindJXTextField extends a JXTextField allowing to specify a function to consume text field's value when it changes.
BindJXTextField(String, String, Consumer<String>) - Constructor for class org.sing_group.gc4s.input.text.BindJXTextField: Creates a new BindJXTextField.
BIO_SYNTAX_COLOR_SCHEME - Static variable in class org.sing_group.gc4s.msaviewer.BioSyntaxBaseColorScheme
BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST - Static variable in class org.sing_group.gc4s.msaviewer.BioSyntaxHighContrastBaseColorScheme
BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND - Static variable in class org.sing_group.gc4s.msaviewer.BioSyntaxHighContrastBaseColorScheme
BioSyntaxBaseColorScheme - Class in org.sing_group.gc4s.msaviewer: An DefaultBaseColorScheme extension that returns the bioSyntax color scheme (https://biosyntax.org/, https://doi.org/10.1186/s12859-018-2315-y).
BioSyntaxBaseColorScheme() - Constructor for class org.sing_group.gc4s.msaviewer.BioSyntaxBaseColorScheme: Creates a new BioSyntaxBaseColorScheme instance.
BioSyntaxHighContrastBaseColorScheme - Class in org.sing_group.gc4s.msaviewer: An DefaultBaseColorScheme extension that returns the bioSyntax color scheme (https://biosyntax.org/, https://doi.org/10.1186/s12859-018-2315-y).
BioSyntaxHighContrastBaseColorScheme() - Constructor for class org.sing_group.gc4s.msaviewer.BioSyntaxHighContrastBaseColorScheme
BLUE_LAVANDA - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
BLUE_PASTEL - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
BooleanFourConditionsFortySamplesTableDemo - Class in org.sing_group.org.gc4s.statistics.table
BooleanFourConditionsFortySamplesTableDemo() - Constructor for class org.sing_group.org.gc4s.statistics.table.BooleanFourConditionsFortySamplesTableDemo
BooleanFourConditionsFortySamplesTablePanelDemo - Class in org.sing_group.org.gc4s.statistics.table
BooleanFourConditionsFortySamplesTablePanelDemo() - Constructor for class org.sing_group.org.gc4s.statistics.table.BooleanFourConditionsFortySamplesTablePanelDemo
BooleanFourConditionsTwoThousandSamplesTableDemo - Class in org.sing_group.org.gc4s.statistics.table
BooleanFourConditionsTwoThousandSamplesTableDemo() - Constructor for class org.sing_group.org.gc4s.statistics.table.BooleanFourConditionsTwoThousandSamplesTableDemo
BooleanHighlighter - Class in org.sing_group.org.gc4s.statistics.table.ui: A ColorHighlighter to highlight Boolean values in tables.
BooleanHighlighter() - Constructor for class org.sing_group.org.gc4s.statistics.table.ui.BooleanHighlighter
BooleanTwoConditionsFortySamplesTableDemo - Class in org.sing_group.org.gc4s.statistics.table
BooleanTwoConditionsFortySamplesTableDemo() - Constructor for class org.sing_group.org.gc4s.statistics.table.BooleanTwoConditionsFortySamplesTableDemo
BooleanTwoConditionsTwoThousandSamplesTableDemo - Class in org.sing_group.org.gc4s.statistics.table
BooleanTwoConditionsTwoThousandSamplesTableDemo() - Constructor for class org.sing_group.org.gc4s.statistics.table.BooleanTwoConditionsTwoThousandSamplesTableDemo
BROWN_PASTEL - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
build() - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Builds the JFileChooserPanel using the introduced configuration.
build() - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder: Builds the JMultipleFileChooserPanel using the introduced configuration.
build() - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumBarChartRendererBuilder: Builds the JSparklinesBarChartTableCellRenderer using the introduced configuration.
build() - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumColoredBarChartRendererBuilder: Builds the JSparklinesBarChartTableCellRenderer using the introduced configuration.
build() - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumBarChartRendererBuilder: Builds the JSparklinesBarChartTableCellRenderer using the introduced configuration.
build() - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumColoredBarChartRendererBuilder: Builds the JSparklinesBarChartTableCellRenderer using the introduced configuration.
build() - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumXYDataSignificanceBarChartRendererBuilder: Builds the JSparklinesBarChartTableCellRenderer using the introduced configuration.
build() - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumXYDataSignificanceBarChartRendererBuilder: Builds the JSparklinesBarChartTableCellRenderer using the introduced configuration.
build() - Method in class org.sing_group.gc4s.ui.CardsPanelBuilder: Builds the CardsPanel using the introduced configuration.
build() - Method in class org.sing_group.gc4s.utilities.builder.JButtonBuilder: Builds the JButton.
build() - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Builds the instance of the toggle button.
ButtonTabComponent - Class in org.sing_group.gc4s.ui.tabbedpane: A ButtonTabComponent is a component to be used as tabComponent.
ButtonTabComponent(JTabbedPane) - Constructor for class org.sing_group.gc4s.ui.tabbedpane.ButtonTabComponent: Constructs a ButtonTabComponent.

C

calculateXYCoordinates(double, double, int) - Static method in class org.sing_group.gc4s.genomebrowser.grid.Coordinates
CANCEL - Static variable in class org.sing_group.gc4s.genomebrowser.TrackOptionsDialog
cancelButton - Variable in class org.sing_group.gc4s.dialog.AbstractInputJDialog
canceled - Variable in class org.sing_group.gc4s.dialog.AbstractInputJDialog
CardsPanel - Class in org.sing_group.gc4s.ui: A JPanel that displays different components using a CardLayout and creates a combo box to control which one should be visible.
CardsPanel(Map<Object, Component>, String) - Constructor for class org.sing_group.gc4s.ui.CardsPanel: Creates a new CardsPanel with the specified selection label and components.
CardsPanel(Map<Object, Component>, String, boolean) - Constructor for class org.sing_group.gc4s.ui.CardsPanel: Creates a new CardsPanel with the specified selection label and components.
CardsPanel(Map<Object, Component>, String, boolean, Object) - Constructor for class org.sing_group.gc4s.ui.CardsPanel: Creates a new CardsPanel with the specified selection label and components.
CardsPanelBuilder - Class in org.sing_group.gc4s.ui: A builder class for CardsPanel.
CardsPanelBuilder() - Constructor for class org.sing_group.gc4s.ui.CardsPanelBuilder
center(double[][], BiFunction<double[], Boolean, Double>, boolean) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Centers the data matrix by applying the computeCenter function to each row.
center(double[][], JHeatMapOperations.Centering, boolean) - Static method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations
centerAtCoordinate(Coordinates) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Centers the visualization range at the specified coordinates.
centerDialogOnScreen() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog: Centers the dialog in the parent component.
centerDialogOnScreen() - Method in class org.sing_group.gc4s.dialog.JProgressDialog
centerDialogOnScreen() - Method in class org.sing_group.gc4s.dialog.wizard.Wizard: Centers the dialog in the parent component.
centerDialogOnScreen() - Method in class org.sing_group.gc4s.dialog.WorkingDialog
CenteredJPanel - Class in org.sing_group.gc4s.ui: A JPanel that only accepts one Component and displays it in the center.
CenteredJPanel() - Constructor for class org.sing_group.gc4s.ui.CenteredJPanel: Creates a new CenteredJPanel.
CenteredJPanel(Component) - Constructor for class org.sing_group.gc4s.ui.CenteredJPanel: Creates a new CenteredJPanel with the specified Component.
changeCursor(int) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Changes the cursor.
changedUpdate(DocumentEvent) - Method in class org.sing_group.gc4s.event.DocumentAdapter
checkLeftListSelection() - Method in class org.sing_group.gc4s.input.list.JParallelListsPanel
checkRightListSelection() - Method in class org.sing_group.gc4s.input.list.JParallelListsPanel
Checks - Class in org.sing_group.gc4s.utilities: A class that provides additional checks to use in component constructors.
Checks() - Constructor for class org.sing_group.gc4s.utilities.Checks
clearHistogramIntervalsHashMap() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
clearSelectedFile() - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Clears the selected file.
clearSelectedFiles() - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Clears the selected files.
clearSharedLastFileFilter() - Static method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Clears the last file filter shared with other instances.
clearSharedLastFileFilter() - Static method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Clears the last file filter shared with other instances.
clockwise - Variable in class org.sing_group.gc4s.ui.text.VerticalLabelUI
CloseableJTabbedPane - Class in org.sing_group.gc4s.ui.tabbedpane: This class extends JTabbedPane to add close buttons to tabs.
CloseableJTabbedPane() - Constructor for class org.sing_group.gc4s.ui.tabbedpane.CloseableJTabbedPane
collapseAll(JTree) - Static method in class org.sing_group.gc4s.utilities.JTreeUtils: Collapses all nodes of the tree.
COLOR_BLUE - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_CYAN - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_GREEN - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_HIGH - Static variable in class org.sing_group.org.gc4s.statistics.table.ui.NumberHighlighter
COLOR_INVALID_INPUT - Static variable in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel
COLOR_INVALID_INPUT - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_LIGHT_BLUE - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_LIGHT_GREEN - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_LIGHT_ORANGE - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_LIGHT_RED - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_LOW - Static variable in class org.sing_group.org.gc4s.statistics.table.ui.NumberHighlighter
COLOR_MAGENTA - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_ORANGE - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_RED - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
COLOR_VALID_INPUT - Static variable in class org.sing_group.gc4s.input.DoubleRangeInputPanel
COLOR_VALID_INPUT - Static variable in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel
ColorIcon - Class in org.sing_group.gc4s.ui.icons: A ColorIcon draws a square of the established size and color.
ColorIcon(Color) - Constructor for class org.sing_group.gc4s.ui.icons.ColorIcon: Creates a new ColorIcon with the specified color and a size of 32x32.
ColorIcon(int, int, Color) - Constructor for class org.sing_group.gc4s.ui.icons.ColorIcon: Creates a new ColorIcon with the specified color and a size of widthxheight.
ColorKeyLegend - Class in org.sing_group.gc4s.visualization: This component draws a color key map between two colors.
ColorKeyLegend(Color, Color, double, double) - Constructor for class org.sing_group.gc4s.visualization.ColorKeyLegend: Creates a new ColorKeyPanel between the colors and the range specified.
ColorLegend - Class in org.sing_group.gc4s.visualization: A ColorLegend is a graphical component that shows a legend of colors and labels.
ColorLegend(Map<String, Color>) - Constructor for class org.sing_group.gc4s.visualization.ColorLegend: Creates a new ColorLegend with the specified colors and horizontal orientation.
ColorLegend(Map<String, Color>, ColorLegend.Orientation) - Constructor for class org.sing_group.gc4s.visualization.ColorLegend: Creates a new ColorLegend with the specified colors and orientation.
ColorLegend.Orientation - Enum in org.sing_group.gc4s.visualization
ColorListCellRenderer - Class in org.sing_group.gc4s.ui: An implementation of ListCellRenderer to show colors.
ColorListCellRenderer() - Constructor for class org.sing_group.gc4s.ui.ColorListCellRenderer
COLORS - Static variable in class org.sing_group.gc4s.utilities.ColorUtils
ColorsListPanel - Class in org.sing_group.gc4s.input.list: This class encloses a JListPanel<Color> to provide the ability of adding (Color) elements to the list.
ColorsListPanel() - Constructor for class org.sing_group.gc4s.input.list.ColorsListPanel: Creates a new empty ColorsListPanel.
ColorsListPanel(List<Color>) - Constructor for class org.sing_group.gc4s.input.list.ColorsListPanel: Creates a new ColorsListPanel containing the specified list of colors.
ColorsSelectionDialog - Class in org.sing_group.gc4s.dialog: A dialog that allows a user to select a list of colors using a ColorsListPanel.
ColorsSelectionDialog(Window, int, int) - Constructor for class org.sing_group.gc4s.dialog.ColorsSelectionDialog: Constructs a new ColorsSelectionDialog that requires the user to select a number of colors between min and max (both are inclusive).
ColorsSelectionDialog(Window, int, int, List<Color>) - Constructor for class org.sing_group.gc4s.dialog.ColorsSelectionDialog: Constructs a new ColorsSelectionDialog with the specified initial list of colors that requires the user to select a number of colors between min and max (both are inclusive).
ColorUtils - Class in org.sing_group.gc4s.utilities: Provides functionalities to deal with colors.
ColorUtils() - Constructor for class org.sing_group.gc4s.utilities.ColorUtils
ColumnSummaryTableCellRenderer - Class in org.sing_group.gc4s.visualization.table: A table cell renderer that displays a summary of all values of the column that the cell to be rendered belongs.
ColumnSummaryTableCellRenderer(TableCellRenderer, TableModel) - Constructor for class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer: Creates a new ColumnSummaryTableCellRenderer that uses defaultRenderer to render the component and add the tooltip summary for all columns.
ColumnSummaryTableCellRenderer(TableCellRenderer) - Constructor for class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer: Creates a new ColumnSummaryTableCellRenderer that uses defaultRenderer to render the component and add the tooltip summary for all columns.
ColumnSummaryTableCellRenderer(TableCellRenderer, List<Integer>, TableModel) - Constructor for class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer: Creates a new ColumnSummaryTableCellRenderer that uses defaultRenderer to render the component and add the tooltip summary for columns in summaryColumns.
ColumnSummaryTableCellRenderer(TableCellRenderer, List<Integer>) - Constructor for class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer: Creates a new ColumnSummaryTableCellRenderer that uses defaultRenderer to render the component and add the tooltip summary for columns in summaryColumns.
columnToDisplay - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
ComboBoxItem<T> - Class in org.sing_group.gc4s.input.combobox: A ComboboxItem wraps any object so that it can be easily added to JComboBox.
ComboBoxItem(T, String) - Constructor for class org.sing_group.gc4s.input.combobox.ComboBoxItem: Constructs a new ComboBoxItem wrapping item and display as the string to be displayed in the combo box.
ComponentsListPanel<T extends Component> - Class in org.sing_group.gc4s.ui: A component that allows showing a list of generic components with control buttons to add and remove them.
ComponentsListPanel(int) - Constructor for class org.sing_group.gc4s.ui.ComponentsListPanel
ComponentsListPanel.ComponentWrapPanel - Class in org.sing_group.gc4s.ui
computeHeight(GenomeBrowser) - Static method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil: Computes the height of a GenomeBrowser.
computeHeight(GenomeBrowser) - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
computeHeight(GenomeBrowser) - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
computeHeight(GenomeBrowser) - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
computeHeight(GenomeBrowser) - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Returns the track height.
computeTrackLinePosition(long, double, long) - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
conditionNames(int, int) - Static method in class org.sing_group.org.gc4s.statistics.table.TableDemoUtils
ConditionsSeparatorHighlighter<T> - Class in org.sing_group.org.gc4s.statistics.table.ui: A ColorHighlighter that draws a left border at the first sample of each condition to enhance the distinction between conditions.
ConditionsSeparatorHighlighter(StatisticsTestTable<T>) - Constructor for class org.sing_group.org.gc4s.statistics.table.ui.ConditionsSeparatorHighlighter: Creates a new ClassesSeparatorHighlighter for the specified table using a border size of 1px.
ConditionsSeparatorHighlighter(StatisticsTestTable<T>, int) - Constructor for class org.sing_group.org.gc4s.statistics.table.ui.ConditionsSeparatorHighlighter: Creates a new ClassesSeparatorHighlighter for the specified table using the specified border size.
configure(JFileChooser) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserConfiguration: Applies the configuration to fileChooser.
configureFont() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
configureTextField(JSpinner) - Method in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel
contentsChanged(ListDataEvent) - Method in class org.sing_group.gc4s.event.ListDataAdapter
contentsChanged(ListDataEvent) - Method in class org.sing_group.gc4s.input.list.event.DefaultListDataListener
convert(Object) - Method in interface org.sing_group.gc4s.visualization.table.csv.CsvTransferHandler.Converter: Converts the given value into a new representation.
Coordinates - Class in org.sing_group.gc4s.genomebrowser.grid: A class that encapsulates a pair of X and Y coordinates.
Coordinates(double, double) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.Coordinates: Creates a new Coordinates instance with the specified initial values.
createDefaultModel() - Method in class org.sing_group.gc4s.input.text.JLimitedTextField
createGradient(Color, Color, int) - Static method in class org.sing_group.gc4s.utilities.Gradient: Creates an array of Color objects for use as a gradient, using a linear interpolation between the two specified colors.
createMaxMinValuesBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it.
createMaxMinValuesBarChartRenderer(JTable, int, PlotOrientation) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default plot orientation (PlotOrientation.HORIZONTAL).
createMaxMinValuesBarChartRenderer(JTable, int, Double, Double) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default plot orientation (PlotOrientation.HORIZONTAL).
createMaxMinValuesBarChartRenderer(JTable, int, PlotOrientation, Double, Double) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it.
createMaxMinValuesColoredBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default positive and negative values colors and the default plot orientation (PlotOrientation.HORIZONTAL).
createMaxMinValuesColoredBarChartRenderer(JTable, int, PlotOrientation) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default positive and negative values colors.
createMaxMinValuesColoredBarChartRenderer(JTable, int, Color, Color) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default plot orientation (PlotOrientation.HORIZONTAL).
createMaxMinValuesColoredBarChartRenderer(JTable, int, PlotOrientation, Color, Color) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it.
createMaxMinValuesColoredBarChartRenderer(JTable, int, PlotOrientation, Double, Color, Double, Color) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it.
createMaxMinXYDataSignificanceBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer and sets it as renderer for the specified column, using default values for plot orientation, positive and negative values colors, significance level and non significant values color.
createMaxMinXYDataSignificanceBarChartRenderer(JTable, int, Color, double) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer and sets it as renderer for the specified column, using default values for plot orientation and positive and negative values colors.
createMaxMinXYDataSignificanceBarChartRenderer(JTable, int, PlotOrientation, Color, Color, Color, double) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer and sets it as renderer for the specified column.
createMaxMinXYDataSignificanceBarChartRenderer(JTable, int, PlotOrientation, Double, Double, Color, Color, Color, double) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer and sets it as renderer for the specified column.
createMaxValueBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default plot orientation (PlotOrientation.HORIZONTAL) and default large numbers are good (true).
createMaxValueBarChartRenderer(JTable, int, PlotOrientation) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default large numbers are good (true).
createMaxValueBarChartRenderer(JTable, int, boolean) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default plot orientation (PlotOrientation.HORIZONTAL).
createMaxValueBarChartRenderer(JTable, int, PlotOrientation, boolean) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it.
createMaxValueBarChartRenderer(JTable, int, PlotOrientation, Double, boolean) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it.
createMaxValueColoredBarChartRenderer(JTable, int, Color) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the specified positiveValuesColor for positive values and the default plot orientation (PlotOrientation.HORIZONTAL).
createMaxValueColoredBarChartRenderer(JTable, int, PlotOrientation, Color) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the specified positiveValuesColor for positive values.
createMaxValueColoredBarChartRenderer(JTable, int, PlotOrientation, Double, Color) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the specified positiveValuesColor for positive values.
createMaxXYDataSignificanceBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default values for plot orientation, significance level and colors.
createMaxXYDataSignificanceBarChartRenderer(JTable, int, Color, Color) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default plot orientation (PlotOrientation.HORIZONTAL) and default significance level (DEFAULT_SIGNIFICANCE_LEVEL).
createMaxXYDataSignificanceBarChartRenderer(JTable, int, Color, Color, double) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default plot orientation (PlotOrientation.HORIZONTAL).
createMaxXYDataSignificanceBarChartRenderer(JTable, int, PlotOrientation, Color, Color) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it, using the default significance level (DEFAULT_SIGNIFICANCE_LEVEL).
createMaxXYDataSignificanceBarChartRenderer(JTable, int, PlotOrientation, Color, Color, double) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer for the specified column and sets it as renderer for it.
createMaxXYDataSignificanceBarChartRenderer(JTable, int, double, Color, Color, double) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer and sets it as renderer for the specified column, using the default plot orientation (PlotOrientation.HORIZONTAL).
createMaxXYDataSignificanceBarChartRenderer(JTable, int, PlotOrientation, Double, Color, Color, double) - Static method in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory: Creates a new JSparklinesBarChartTableCellRenderer and sets it as renderer for the specified column.
createOpenJFileChooserPanel() - Static method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Returns a new JFileChooserPanelBuilder instance to build a JFileChooserPanel with Mode.OPEN, which means that the JFileChooser is shown using JFileChooser.showOpenDialog(java.awt.Component).
createOpenJMultipleFileChooserPanel() - Static method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder: Returns a new JMultipleFileChooserPanelBuilder instance to build a JMultipleFileChooserPanel with Mode.OPEN, which means that the JFileChooser is shown using JFileChooser.showOpenDialog(java.awt.Component).
createPanelAndCenterComponent(Component) - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Returns a new JPanel with component in the center.
createSaveJFileChooserPanel() - Static method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Returns a new JFileChooserPanelBuilder instance to build a JFileChooserPanel with Mode.SAVE, which means that the JFileChooser is shown using JFileChooser.showSaveDialog(java.awt.Component).
createSaveJMultipleFileChooserPanel() - Static method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder: Returns a new JMultipleFileChooserPanelBuilder instance to build a JMultipleFileChooserPanel with Mode.SAVE, which means that the JFileChooser is shown using JFileChooser.showSaveDialog(java.awt.Component).
createTransferable(JComponent) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTransferHandler: Create a Transferable to use as the source for a data transfer.
CsvFormat - Class in org.sing_group.gc4s.input.csv: A CsvFormat specifies the format of a CSV file.
CsvFormat(CsvFormat.FileFormat) - Constructor for class org.sing_group.gc4s.input.csv.CsvFormat: Constructs a new CsvFormat instance.
CsvFormat(String, char, boolean, String) - Constructor for class org.sing_group.gc4s.input.csv.CsvFormat: Constructs a new CsvFormat instance.
CsvFormat.FileFormat - Enum in org.sing_group.gc4s.input.csv
CsvListener - Interface in org.sing_group.gc4s.input.csv.event: The listener interface for receiving CSV events.
CsvPanel - Class in org.sing_group.gc4s.input.csv: A panel that allows user to configure a CSV format.
CsvPanel() - Constructor for class org.sing_group.gc4s.input.csv.CsvPanel: Creates a new CsvPanel instance.
CsvTable - Class in org.sing_group.gc4s.visualization.table.csv: An extension of JXTable to display CSV data.
CsvTable() - Constructor for class org.sing_group.gc4s.visualization.table.csv.CsvTable: Instantiates a CsvTable with a default table model, no data.
CsvTable(int, int) - Constructor for class org.sing_group.gc4s.visualization.table.csv.CsvTable: Instantiates a CsvTable for a given number of columns and rows.
CsvTable(Object[][], Object[]) - Constructor for class org.sing_group.gc4s.visualization.table.csv.CsvTable: Instantiates a CsvTable with data in a array or rows and column names.
CsvTable(TableModel, TableColumnModel, ListSelectionModel) - Constructor for class org.sing_group.gc4s.visualization.table.csv.CsvTable: Instantiates a CsvTable with a specific table model, column model, and selection model.
CsvTable(TableModel, TableColumnModel) - Constructor for class org.sing_group.gc4s.visualization.table.csv.CsvTable: Instantiates a CsvTable with specific table and column models.
CsvTable(TableModel) - Constructor for class org.sing_group.gc4s.visualization.table.csv.CsvTable: Instantiates a CsvTable with a specific table model
CsvTable(Vector<?>, Vector<?>) - Constructor for class org.sing_group.gc4s.visualization.table.csv.CsvTable: Instantiates a CsvTable with data in a vector or rows and column names.
CsvTableExporter - Interface in org.sing_group.gc4s.visualization.table.csv: The interface to export tables in CSV like formats.
CsvTransferHandler - Class in org.sing_group.gc4s.visualization.table.csv: A TransferHandler for CsvTable objects.
CsvTransferHandler() - Constructor for class org.sing_group.gc4s.visualization.table.csv.CsvTransferHandler
CsvTransferHandler.Converter - Interface in org.sing_group.gc4s.visualization.table.csv: A interface that allows the conversion of values in the transfer handler.
customColor - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter

D

DARK_GREEN_PASTEL - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
Dataset<T> - Interface in org.sing_group.org.gc4s.statistics.data: The interface for defining a dataset.
decideBooleanStatisticTest(Dataset<Boolean>) - Static method in class org.sing_group.org.gc4s.statistics.data.tests.StatisticsTestsUtils: Returns the most appropriate test for a dataset of Boolean depending on the number of conditions and samples in it.
DEFAULT_ALLOW_ALL_FILTER - Static variable in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel
DEFAULT_ALLOW_ALL_FILTER - Static variable in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel
DEFAULT_BLOCK_LENGTH - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
DEFAULT_BLOCKS_PER_LINE - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
DEFAULT_BORDER_PIXELS - Static variable in class org.sing_group.org.gc4s.statistics.table.ui.ConditionsSeparatorHighlighter
DEFAULT_BORDER_PIXELS - Static variable in class org.sing_group.org.gc4s.statistics.table.ui.StatisticsTestTableHeaderRenderer
DEFAULT_CASE_SENSITIVE - Static variable in class org.sing_group.gc4s.input.filechooser.ExtensionFileFilter
DEFAULT_CLEAR_SELECTED_FILE_ON_SHOW - Static variable in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel
DEFAULT_CLEAR_SELECTED_FILE_ON_SHOW - Static variable in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel
DEFAULT_FILE_FILTERS - Static variable in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel
DEFAULT_FILE_FILTERS - Static variable in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel
DEFAULT_FILES_LABEL - Static variable in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel
DEFAULT_FONT_SIZE - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
DEFAULT_ICON_BROWSE - Static variable in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel
DEFAULT_ICON_BROWSE - Static variable in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel
DEFAULT_ICON_CLEAR - Static variable in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel
DEFAULT_INITIAL_HEIGHT - Static variable in class org.sing_group.gc4s.dialog.wizard.Wizard
DEFAULT_INITIAL_WIDTH - Static variable in class org.sing_group.gc4s.dialog.wizard.Wizard
DEFAULT_LABEL_LENGTH - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
DEFAULT_LABEL_TAB - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
DEFAULT_LARGE_NUMBERS_ARE_GOOD - Static variable in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory
DEFAULT_NAN_COLOR - Static variable in class org.sing_group.org.gc4s.statistics.table.ui.NumberHighlighter
DEFAULT_NEGATIVES_COLOR - Static variable in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory
DEFAULT_NON_SIGNIFICANT_COLOR - Static variable in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory
DEFAULT_ORIENTATION - Static variable in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory
DEFAULT_POSITIVES_COLOR - Static variable in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory
DEFAULT_POSITIVES_COLOR_LARGE_NUMBERS - Static variable in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory
DEFAULT_SELECTION_MODE - Static variable in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel
DEFAULT_SELECTION_MODE - Static variable in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel
DEFAULT_SHOW_BOTTOM_TRACKS - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
DEFAULT_SHOW_INDEXES - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
DEFAULT_SHOW_UPPER_TRACKS - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
DEFAULT_SIGNIFICANCE_LEVEL - Static variable in class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory
DEFAULT_STEPS - Static variable in class org.sing_group.org.gc4s.statistics.table.ui.NumberHighlighter
DefaultBaseColorScheme - Class in org.sing_group.gc4s.msaviewer: The default BaseColorScheme implementation.
DefaultBaseColorScheme(Function<Character, Color>, Function<Character, Color>) - Constructor for class org.sing_group.gc4s.msaviewer.DefaultBaseColorScheme: Creates a new DefaultBaseColorScheme instance with the specified background and foreground color functions.
DefaultCsvTableExporter - Class in org.sing_group.gc4s.visualization.table.csv: Extends AbstractCsvTableExporter to provide the default table exporter for CSV.
DefaultCsvTableExporter(CsvFormat) - Constructor for class org.sing_group.gc4s.visualization.table.csv.DefaultCsvTableExporter: Creates a new DefaultCsvTableExporter configured with the specified format.
DefaultDataset<T> - Class in org.sing_group.org.gc4s.statistics.data: The default Dataset implementation.
DefaultDataset(String[], String[], T[][], String[]) - Constructor for class org.sing_group.org.gc4s.statistics.data.DefaultDataset: Creates a new DefaultDataset instance with the specified initial values.
DefaultFeatureValues<T> - Class in org.sing_group.org.gc4s.statistics.data: The default FeatureValues implementation.
DefaultFeatureValues(String, Map<String, List<T>>) - Constructor for class org.sing_group.org.gc4s.statistics.data.DefaultFeatureValues
DefaultListDataListener - Class in org.sing_group.gc4s.input.list.event: A default implementation of ListDataListener.
DefaultListDataListener() - Constructor for class org.sing_group.gc4s.input.list.event.DefaultListDataListener
DefaultSequenceAlignmentRenderer - Class in org.sing_group.gc4s.msaviewer: The default SequenceAlignmentRenderer implementation.
DefaultSequenceAlignmentRenderer() - Constructor for class org.sing_group.gc4s.msaviewer.DefaultSequenceAlignmentRenderer
DESCRIPTION_FONT_DIALOG - Static variable in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
DESCRIPTION_RANGE_DIALOG - Static variable in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
DESCRIPTION_VISIBLE_COLUMNS - Static variable in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
DESCRIPTION_VISIBLE_ROWS - Static variable in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
disableColumVisibilityActions() - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Disables the column visibility actions.
disabled() - Method in class org.sing_group.gc4s.utilities.builder.JButtonBuilder: Sets the button disabled.
disableRowSorting(JTable) - Static method in class org.sing_group.gc4s.visualization.table.TableUtils: Disables row sorting in table.
disableSelectionWithOneCard(boolean) - Method in class org.sing_group.gc4s.ui.CardsPanelBuilder: Sets whether the selection component must be disabled when there is only one card.
disableWait() - Method in class org.sing_group.gc4s.genomebrowser.ToolTipPane: Hides the wait message.
doAction() - Method in interface org.sing_group.gc4s.utilities.ExtendedAbstractAction.Action
DocumentAdapter - Class in org.sing_group.gc4s.event: An abstract adapter class for receiving text document events.
DocumentAdapter() - Constructor for class org.sing_group.gc4s.event.DocumentAdapter
doLayout() - Method in class org.sing_group.gc4s.input.combobox.ExtendedJComboBox
DoubleRange - Class in org.sing_group.gc4s.input: This class represents a range (i.e. a pair of a minimun and a maximum) of double.
DoubleRange(double, double) - Constructor for class org.sing_group.gc4s.input.DoubleRange: Creates a new DoubleRange.
DoubleRangeInputDialog - Class in org.sing_group.gc4s.input: A dialog that allows user to introduce a range of double values.
DoubleRangeInputDialog(Window, DoubleRange) - Constructor for class org.sing_group.gc4s.input.DoubleRangeInputDialog: Creates a new DoubleRangeInputDialog with the initial range.
DoubleRangeInputPanel - Class in org.sing_group.gc4s.input: A panel that allows user to type a range of double values.
DoubleRangeInputPanel() - Constructor for class org.sing_group.gc4s.input.DoubleRangeInputPanel: Creates a new DoubleRangeInputPanel with Double.MIN_VALUE and Double.MAX_VALUE as minimum and maximum values.
DoubleRangeInputPanel(double, double) - Constructor for class org.sing_group.gc4s.input.DoubleRangeInputPanel: Creates a new DoubleRangeInputPanel with the specified minimum and maximum values.
DoubleRangeInputPanel(DoubleRange) - Constructor for class org.sing_group.gc4s.input.DoubleRangeInputPanel: Creates a new DoubleRangeInputPanel with the specified range.
DoubleRangeSpinnerInputPanel - Class in org.sing_group.gc4s.input: A panel that allows user to type a range of double values by using spinners.
DoubleRangeSpinnerInputPanel(double, double, double, double, double) - Constructor for class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel: Creates a new DoubleRangeSpinnerInputPanel with the specified minimum and maximum values.
DoubleTextField - Class in org.sing_group.gc4s.input.text: An extension of JFormattedTextField to create text fields for allow the input of double values.
DoubleTextField() - Constructor for class org.sing_group.gc4s.input.text.DoubleTextField: Constructs a new DoubleTextField.
DoubleTextField(double) - Constructor for class org.sing_group.gc4s.input.text.DoubleTextField: Constructs a new DoubleTextField and sets value as input value.
DraggingPane - Class in org.sing_group.gc4s.genomebrowser: A panel to draw dragging rectangles.
DraggingPane() - Constructor for class org.sing_group.gc4s.genomebrowser.DraggingPane
drawNucleotides(Graphics2D) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
drawString(Graphics2D, String, int, TracksPanel, int) - Static method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil: Draws the specified string.

E

editColors() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
editVisibleColumns() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
editVisibleRows() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
elementsAdded(ExtendedDefaultListModel<?>) - Method in interface org.sing_group.gc4s.input.list.event.ExtendedDefaultListModelListener
EmailJXTextField - Class in org.sing_group.gc4s.input.text: An extension of JXTextField to input e-mails.
EmailJXTextField() - Constructor for class org.sing_group.gc4s.input.text.EmailJXTextField: Creates a new EmailJXTextField.
EmailJXTextField(Color, boolean) - Constructor for class org.sing_group.gc4s.input.text.EmailJXTextField: Creates a new EmailJXTextField with the specified color for invalid e-mails and whether an empty input is valid or not.
emptyColor - Variable in class org.sing_group.gc4s.input.text.ExtendedJXTextField
enableWait() - Method in class org.sing_group.gc4s.genomebrowser.ToolTipPane: Shows the wait message.
EnterKeyPressedListener - Class in org.sing_group.gc4s.event: A concrete implementation of AbstractKeyPressedListener to listen for enter key.
EnterKeyPressedListener(Runnable) - Constructor for class org.sing_group.gc4s.event.EnterKeyPressedListener: Constructs an EnterKeyPressedListener with the specified action.
equals(Object) - Method in class org.sing_group.gc4s.genomebrowser.grid.Coordinates
equals(Object) - Method in class org.sing_group.gc4s.input.combobox.ComboBoxItem
equals(Object) - Method in class org.sing_group.gc4s.input.filechooser.ExtensionFileFilter
expandAll(JTree) - Static method in class org.sing_group.gc4s.utilities.JTreeUtils: Expands all nodes of the tree.
exportAsImage() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
ExportCsvDialog - Class in org.sing_group.gc4s.dialog: An input dialog that allows the configuration of a CSV format.
ExportCsvDialog(Window) - Constructor for class org.sing_group.gc4s.dialog.ExportCsvDialog: Constructs an ExportCsvDialog.
exportSelectionToFile(File) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Exports the current table selection into the specified file.
exportToCsv() - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable
exportToHtml(Path) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Exports the view as an HTML document to the specified file.
exportToPng(Path) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Exports the view as a PNG image to the specified file.
exportViewToFile(File) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Exports the current table view into the specified file.
ExtendedAbstractAction - Class in org.sing_group.gc4s.utilities: An extension of AbstractAction to reduce verbosity when creating actions by allowing to construct actions by passing references to methods without parameters.
ExtendedAbstractAction(ExtendedAbstractAction.Action) - Constructor for class org.sing_group.gc4s.utilities.ExtendedAbstractAction: Creates a new ExtendedAbstractAction that invokes action on action performed.
ExtendedAbstractAction(String, ExtendedAbstractAction.Action) - Constructor for class org.sing_group.gc4s.utilities.ExtendedAbstractAction
ExtendedAbstractAction(String, Icon, ExtendedAbstractAction.Action) - Constructor for class org.sing_group.gc4s.utilities.ExtendedAbstractAction
ExtendedAbstractAction.Action - Interface in org.sing_group.gc4s.utilities
ExtendedDefaultListModel<E> - Class in org.sing_group.gc4s.input.list: This class extends DefaultListModel to add move down/up element and add several elements functionalities.
ExtendedDefaultListModel() - Constructor for class org.sing_group.gc4s.input.list.ExtendedDefaultListModel
ExtendedDefaultListModelListener - Interface in org.sing_group.gc4s.input.list.event: The listener interface for receiving ExtendedDefaultListModel events.
ExtendedDefaultTableModel - Class in org.sing_group.gc4s.visualization.table: An extension of the DefaultTableModel that provides an implementation of the DefaultTableModel#getColumnClass(int).
ExtendedDefaultTableModel(int, int) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedDefaultTableModel
ExtendedDefaultTableModel(Vector<?>, int) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedDefaultTableModel
ExtendedDefaultTableModel(Object[], int) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedDefaultTableModel
ExtendedDefaultTableModel(Vector<?>, Vector<?>) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedDefaultTableModel
ExtendedDefaultTableModel(Object[][], String[]) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedDefaultTableModel
ExtendedJComboBox<T> - Class in org.sing_group.gc4s.input.combobox: An extension of JComboBox that allows specifying whether the size of the combo box must be adapted to its items width when the drop down list is being displayed.
ExtendedJComboBox() - Constructor for class org.sing_group.gc4s.input.combobox.ExtendedJComboBox: Creates an ExtendedJComboBox with a default data model.
ExtendedJComboBox(T[]) - Constructor for class org.sing_group.gc4s.input.combobox.ExtendedJComboBox: Creates an ExtendedJComboBox that contains the elements in the specified array.
ExtendedJComboBox(ComboBoxModel<T>) - Constructor for class org.sing_group.gc4s.input.combobox.ExtendedJComboBox: Creates an ExtendedJComboBox that takes its items from an existing ComboBoxModel.
ExtendedJSeparator - Class in org.sing_group.gc4s.ui.menu: An extension of JSeparator that allows specifying a margin for the component.
ExtendedJSeparator(int) - Constructor for class org.sing_group.gc4s.ui.menu.ExtendedJSeparator: Creates a new ExtendedJSeparator using the specified margin and the default separator orientation.
ExtendedJSeparator(int, int) - Constructor for class org.sing_group.gc4s.ui.menu.ExtendedJSeparator: Creates a new ExtendedJSeparator using the specified margin and the orientation.
ExtendedJTabbedPane - Class in org.sing_group.gc4s.ui.tabbedpane: An extension of JTabbedPane that adds useful features such as the possibility of tell the tabbed pane to hide the tab bar when there is only one tab.
ExtendedJTabbedPane() - Constructor for class org.sing_group.gc4s.ui.tabbedpane.ExtendedJTabbedPane
ExtendedJXTable - Class in org.sing_group.gc4s.visualization.table: An extension of JXTable that allows to hide/show the column visibility actions and also facilitates adding own actions to the ColumnControlButton.
ExtendedJXTable() - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedJXTable: Instantiates an ExtendedJXTable with a default table model, no data.
ExtendedJXTable(TableModel) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedJXTable: Instantiates an ExtendedJXTable with a specific table model.
ExtendedJXTable(TableModel, TableColumnModel) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedJXTable: Instantiates an ExtendedJXTable with a specific table model.
ExtendedJXTable(TableModel, TableColumnModel, ListSelectionModel) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedJXTable: Instantiates an ExtendedJXTable with a specific table model, column model, and selection model.
ExtendedJXTable(int, int) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedJXTable: Instantiates an ExtendedJXTable for a given number of columns and rows.
ExtendedJXTable(Vector<?>, Vector<?>) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedJXTable: Instantiates an ExtendedJXTable with data in a vector or rows and column names.
ExtendedJXTable(Object[][], Object[]) - Constructor for class org.sing_group.gc4s.visualization.table.ExtendedJXTable: Instantiates an ExtendedJXTable with data in a array or rows and column names.
ExtendedJXTextField - Class in org.sing_group.gc4s.input.text: An extension of JXTextField that provides additional features.
ExtendedJXTextField(String) - Constructor for class org.sing_group.gc4s.input.text.ExtendedJXTextField: Creates a new ExtendedJXTextField with the specified prompt text.
ExtensionFileFilter - Class in org.sing_group.gc4s.input.filechooser: A concrete implementation of FileFilter that provides the possibility of filtering files based on a regular expression.
ExtensionFileFilter(String, String) - Constructor for class org.sing_group.gc4s.input.filechooser.ExtensionFileFilter: Creates a new ExtensionFileFilter instance with the regular expression and description specified.
ExtensionFileFilter(String, String, boolean) - Constructor for class org.sing_group.gc4s.input.filechooser.ExtensionFileFilter: Creates a new ExtensionFileFilter instance with the regular expression and description specified.

F

FdrCorrection - Class in org.sing_group.org.gc4s.statistics.data.tests: A PValuesCorrection that corrects p-values using the FDR approach.
FdrCorrection() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.FdrCorrection
features(int) - Static method in class org.sing_group.org.gc4s.statistics.table.TableDemoUtils
FeatureValues<T> - Interface in org.sing_group.org.gc4s.statistics.data: The interface for defining the set of values of a feature.
file - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
FileChooserListener - Interface in org.sing_group.gc4s.input.filechooser.event: The listener interface for receiving file chooser panel events.
FileDrop - Class in org.sing_group.gc4s.utilities: This class makes it easy to drag and drop files from the operating system to a Java program.
FileDrop(Component, FileDropListener) - Constructor for class org.sing_group.gc4s.utilities.FileDrop: Constructs a FileDrop with a default light-blue border and, if c is a Container, recursively sets all elements contained within as drop targets, though only the top level container will change borders.
FileDrop(Component, boolean, FileDropListener) - Constructor for class org.sing_group.gc4s.utilities.FileDrop: Constructor with a default border and the option to recursively set drop targets.
FileDrop(PrintStream, Component, FileDropListener) - Constructor for class org.sing_group.gc4s.utilities.FileDrop: Constructor with a default border and debugging optionally turned on.
FileDrop(PrintStream, Component, boolean, FileDropListener) - Constructor for class org.sing_group.gc4s.utilities.FileDrop: Constructor with a default border, debugging optionally turned on and the option to recursively set drop targets.
FileDrop(Component, Border, FileDropListener) - Constructor for class org.sing_group.gc4s.utilities.FileDrop: Constructor with a specified border.
FileDrop(Component, Border, boolean, FileDropListener) - Constructor for class org.sing_group.gc4s.utilities.FileDrop: Constructor with a specified border and the option to recursively set drop targets.
FileDrop(PrintStream, Component, Border, FileDropListener) - Constructor for class org.sing_group.gc4s.utilities.FileDrop: Constructor with a specified border and debugging optionally turned on.
FileDrop(PrintStream, Component, Border, boolean, FileDropListener) - Constructor for class org.sing_group.gc4s.utilities.FileDrop: Full constructor with a specified border and debugging optionally turned on.
FileDropListener - Interface in org.sing_group.gc4s.utilities: Interface to listen when files are dropped.
FileInfo - Class in org.sing_group.gc4s.genomebrowser.grid: A GenericInfo implementation for providing file information.
FileInfo(String) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.FileInfo: Creates a new FileInfo instance.
FILENAME - Static variable in class org.sing_group.gc4s.genomebrowser.grid.GridInfo
filesDropped(File[]) - Method in interface org.sing_group.gc4s.utilities.FileDropListener: Called when files have been successfully dropped.
fileToString(File) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
FilterableJXTable - Class in org.sing_group.gc4s.visualization.table: An extension of JXTable that allows to establish a row filter.
FilterableJXTable(String[][], String[]) - Constructor for class org.sing_group.gc4s.visualization.table.FilterableJXTable: Instantiates an FilterableJXTable with data in a array or rows and column names.
filterChanged() - Method in class org.sing_group.gc4s.input.list.JListPanel
FilteredListModel<E> - Class in org.sing_group.gc4s.input.list: This class extends AbstractListModel and allows filtering a given ListModel.
FilteredListModel(ListModel<E>) - Constructor for class org.sing_group.gc4s.input.list.FilteredListModel: Constructs a FilteredListModel to encapsulate the source ListModel.
FilteredListModel.Filter - Interface in org.sing_group.gc4s.input.list
finished(String) - Method in class org.sing_group.gc4s.dialog.JProgressDialog: Sets the progress finished.
finished(String) - Method in class org.sing_group.gc4s.dialog.WorkingDialog: Sets the progress finished.
focusGained(FocusEvent) - Method in class org.sing_group.gc4s.event.TextFieldSelectionFocusListener
FontConfigurationDialog - Class in org.sing_group.gc4s.dialog: A dialog that allows a user to select and configure a Font.
FontConfigurationDialog(Window) - Constructor for class org.sing_group.gc4s.dialog.FontConfigurationDialog: Constructs an FontConfigurationDialog.
FontConfigurationDialog(Window, Font) - Constructor for class org.sing_group.gc4s.dialog.FontConfigurationDialog: Constructs an FontConfigurationDialog using font as initial value.
FontConfigurationPanel - Class in org.sing_group.gc4s.input: A panel that allows user to configure a font.
FontConfigurationPanel() - Constructor for class org.sing_group.gc4s.input.FontConfigurationPanel: Creates a new FontConfigurationPanel.
FontUtils - Class in org.sing_group.gc4s.utilities: Provides functionalities to deal with fonts.
FontUtils() - Constructor for class org.sing_group.gc4s.utilities.FontUtils
formatter - Variable in class org.sing_group.gc4s.genomebrowser.grid.GenomeBrowserInfo

G

GenericInfo - Interface in org.sing_group.gc4s.genomebrowser.grid: The interface for providing a piece generic information that can be displayed as a tooltip.
GenomeBrowser - Class in org.sing_group.gc4s.genomebrowser: Allows user to interactively visualize a reference genome, with the possibility of adding and customizing different tracks.
GenomeBrowser(GenomeIndex) - Constructor for class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Creates a new GenomeBrowser instance to visualize the reference genome provided by the specified GenomeIndex.
GenomeBrowserInfo - Class in org.sing_group.gc4s.genomebrowser.grid: A GenericInfo implementation for providing genome browser information.
GenomeBrowserInfo(String, String, String, String) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.GenomeBrowserInfo: Creates a new GenomeBrowserInfo with the specified values.
GENOMEBROWSERINFO - Static variable in class org.sing_group.gc4s.genomebrowser.grid.GridInfo
GenomeBrowserState - Class in org.sing_group.gc4s.genomebrowser: This class encapsulates the state of a GenomeBrowser.
GenomeBrowserState() - Constructor for class org.sing_group.gc4s.genomebrowser.GenomeBrowserState: Creates a new GenomeBrowserState instance with empty values.
GenomeBrowserUtil - Class in org.sing_group.gc4s.genomebrowser: This class provides different utilities for the genome browser and its associated components.
GenomeBrowserUtil() - Constructor for class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
getActionClearSelection() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the clear selection action.
getActionMoveDown() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the move down action.
getActionMoveUp() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the move down action.
getActionRemoveElements() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the remove elements action.
getActionSelectAll() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the select all action.
getAddComponentButton() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
getAddComponentButtonLabel() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.FdrCorrection
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.MultiClassBooleanRandomizationTest
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.MultipleConditionsBooleanChiSquareTest
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.NominalChiSquareTest
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.OneWayAnovaTest
getAdditionalInfoUrl() - Method in interface org.sing_group.org.gc4s.statistics.data.tests.PValuesCorrection: Returns the additional information URL of the correction wrapped as an Optional.
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.StudentsHomocedasticTTest
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.StudentsPairedTTest
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.StudentsTTest
getAdditionalInfoUrl() - Method in interface org.sing_group.org.gc4s.statistics.data.tests.Test: Returns the additional information URL of the test wrapped as an Optional.
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.TwoConditionsBooleanFisherTest
getAdditionalInfoUrl() - Method in class org.sing_group.org.gc4s.statistics.data.tests.TwoConditionsBooleanYatesChiSquareTest
getAvailableFonts() - Static method in class org.sing_group.gc4s.utilities.FontUtils: Returns an array containing all available fonts in system.
getBackground() - Method in class org.sing_group.gc4s.msaviewer.SequenceBaseRenderingInfo
getBackgroundColor() - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
getBackgroundColor() - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
getBackgroundColor() - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
getBackgroundColor() - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Returns the background color.
getBaseBackgroundColorFunction() - Method in interface org.sing_group.gc4s.msaviewer.BaseColorScheme: Returns a function that returns a background Color for each sequence base Character.
getBaseBackgroundColorFunction() - Method in class org.sing_group.gc4s.msaviewer.DefaultBaseColorScheme
getBaseForegroundColorFunction() - Method in interface org.sing_group.gc4s.msaviewer.BaseColorScheme: Returns a function that returns a foreground Color for each sequence base Character.
getBaseForegroundColorFunction() - Method in class org.sing_group.gc4s.msaviewer.DefaultBaseColorScheme
getBlockLength() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
getBlockLength() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
getBlocksPerLine() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
getBlocksPerLine() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
getBottomTracks() - Method in interface org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentTracksModel: Returns the list of tracks that must be placed below the sequences.
getBoxLayoutOrientation() - Method in enum org.sing_group.gc4s.ui.Orientation: Returns the integer for the corresponding orientation in BoxLayout.
getBrowseAction() - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Returns the browse action.
getBrowseAction() - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Returns the browse action.
getBtnClearSelection() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the clear selection button.
getBtnMoveDown() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the move down button.
getBtnMoveUp() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the move up button.
getBtnRemoveElements() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the remove elements button.
getBtnSelectAll() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the select all button.
getButtonActions() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerControl
getButtonsPane() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog: Returns the buttons panel of the dialog.
getButtonsPanel() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerControl
getCellRenderer(int, int) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable
getCenterComponent() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
getCentering() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapDataOperationsDialog
getChr() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
getColor() - Method in class org.sing_group.gc4s.input.JColorChooserButton: Returns the current selected color.
getColorMap(Set<String>) - Static method in class org.sing_group.gc4s.utilities.ColorUtils: Maps each string in the input set of values into a color, using the color constants defined in this class.
getColors() - Static method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil: Returns a map of correspondences between nucleotides and their associated colors.
getColumnCellRenderer(int) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Returns the TableCellRenderer associated with the specified column.
getColumnClass(int) - Method in class org.sing_group.gc4s.visualization.table.BeanTableModel
getColumnClass(int) - Method in class org.sing_group.gc4s.visualization.table.ExtendedDefaultTableModel
getColumnClass(int) - Method in class org.sing_group.gc4s.visualization.table.MapTableModel
getColumnClass(int) - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel
getColumnClass(int) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel
getColumnCount() - Method in class org.sing_group.gc4s.visualization.table.BeanTableModel
getColumnCount() - Method in class org.sing_group.gc4s.visualization.table.MapTableModel
getColumnCount() - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel
getColumnCount() - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel
getColumnName(int) - Method in class org.sing_group.gc4s.visualization.table.BeanTableModel
getColumnName(int) - Method in class org.sing_group.gc4s.visualization.table.MapTableModel
getColumnName(int) - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel
getColumnName(int) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel
getColumnNames() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns a list with the column names.
getColumnNames() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapModel: Returns an array with the column names.
getColumnNames() - Method in class org.sing_group.gc4s.visualization.table.ExtendedJXTable
getColumnSeparator() - Method in class org.sing_group.gc4s.input.csv.CsvFormat: Returns the column separator.
getColumnSeparator() - Method in interface org.sing_group.gc4s.visualization.table.csv.CsvTableExporter: Returns the column separator.
getColumnSeparator() - Method in class org.sing_group.gc4s.visualization.table.csv.DefaultCsvTableExporter
getColumnSummary(TableModel, int) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getComplementaryColor(Color) - Static method in class org.sing_group.gc4s.utilities.ColorUtils: Returns the complementary color of the specified color.
getComponentButtonBrowse() - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Returns the browse button component.
getComponentFileName() - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Returns the file name text field component.
getComponentLabelFile() - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Returns the file label.
getComponentsList() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel: Returns the actual list of T components being shown.
getCondition(String) - Method in interface org.sing_group.org.gc4s.statistics.data.Dataset: Returns the name of the condition associated with the specified sample.
getCondition(String) - Method in class org.sing_group.org.gc4s.statistics.data.DefaultDataset
getConditionNames() - Method in interface org.sing_group.org.gc4s.statistics.data.Dataset: Returns an array with the conditions of each sample in the dataset.
getConditionNames() - Method in class org.sing_group.org.gc4s.statistics.data.DefaultDataset
getConditionNames() - Method in class org.sing_group.org.gc4s.statistics.data.DefaultFeatureValues
getConditionNames() - Method in interface org.sing_group.org.gc4s.statistics.data.FeatureValues: Returns an array containing the names of the conditions in this set of feature values
getConditionValues(String) - Method in class org.sing_group.org.gc4s.statistics.data.DefaultFeatureValues
getConditionValues(String) - Method in interface org.sing_group.org.gc4s.statistics.data.FeatureValues: Returns a list containing the values associated with the specified condition.
getConfiguration() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentControlConfigurationDialog: Returns a new MultipleSequenceAlignmentViewerConfiguration object with the values introduced by the user.
getConfiguration() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel: Returns a new MultipleSequenceAlignmentViewerConfiguration object with the values introduced by the user.
getConfiguration() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Returns the current MultipleSequenceAlignmentViewerConfiguration.
getContent() - Method in interface org.sing_group.gc4s.msaviewer.Track: Returns the track content.
getConverter(int) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Returns the Converter of a model column.
getConverter(int) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTransferHandler: Returns the Converter of a model column.
getCoordinates() - Method in class org.sing_group.gc4s.genomebrowser.grid.GridInfo: Returns the Coordinates.
getCsvFormat() - Method in class org.sing_group.gc4s.input.csv.CsvPanel: Return the CsvFormat based on the configuration selected by the user.
getCsvListeners() - Method in class org.sing_group.gc4s.input.csv.CsvPanel: Returns an array of all the CSV listeners registered on this component.
getCurrentSequence() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the current sequence.
getData() - Method in class org.sing_group.gc4s.genomebrowser.grid.GridInfo: Returns the GenericInfo.
getData() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns the data matrix.
getData() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapModel: Returns the input data matrix.
getData() - Method in class org.sing_group.gc4s.visualization.table.ExtendedJXTable
getDataset() - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel: Returns the Dataset<T> associated with this model.
getDecimalFormatter() - Method in class org.sing_group.gc4s.input.csv.CsvFormat: Returns the decimal formatter.
getDecimalFormatter() - Method in class org.sing_group.gc4s.visualization.table.csv.AbstractCsvTableExporter: Return a DecimalFormat object to format decimal values.
getDecimalFormatter() - Method in class org.sing_group.gc4s.visualization.table.csv.DefaultCsvTableExporter
getDecimalSeparator() - Method in class org.sing_group.gc4s.input.csv.CsvFormat: Returns the decimal separator character.
getDescription() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog
getDescription() - Method in class org.sing_group.gc4s.dialog.ColorsSelectionDialog
getDescription() - Method in class org.sing_group.gc4s.dialog.ExportCsvDialog
getDescription() - Method in class org.sing_group.gc4s.dialog.FontConfigurationDialog
getDescription() - Method in class org.sing_group.gc4s.dialog.ListSelectionDialog
getDescription() - Method in class org.sing_group.gc4s.genomebrowser.GPFilter
getDescription() - Method in enum org.sing_group.gc4s.input.csv.CsvFormat.FileFormat
getDescription() - Method in class org.sing_group.gc4s.input.DoubleRangeInputDialog
getDescription() - Method in class org.sing_group.gc4s.input.filechooser.ExtensionFileFilter
getDescription() - Method in class org.sing_group.gc4s.input.ItemSelectionDialog
getDescription() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentControlConfigurationDialog
getDescription() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapDataOperationsDialog
getDescription() - Method in interface org.sing_group.org.gc4s.statistics.data.tests.PValuesCorrection: Returns the description of the correction wrapped as an Optional.
getDescription() - Method in interface org.sing_group.org.gc4s.statistics.data.tests.Test: Returns the description of the test wrapped as an Optional.
getDescriptionPane() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog
getDialogTitle() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog
getDialogTitle() - Method in class org.sing_group.gc4s.dialog.ColorsSelectionDialog
getDialogTitle() - Method in class org.sing_group.gc4s.dialog.ExportCsvDialog
getDialogTitle() - Method in class org.sing_group.gc4s.dialog.FontConfigurationDialog
getDialogTitle() - Method in class org.sing_group.gc4s.dialog.ListSelectionDialog
getDialogTitle() - Method in class org.sing_group.gc4s.input.DoubleRangeInputDialog
getDialogTitle() - Method in class org.sing_group.gc4s.input.ItemSelectionDialog
getDialogTitle() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentControlConfigurationDialog
getDialogTitle() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapDataOperationsDialog
getDoubleBuffer() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getDoubleListSummary(List<Double>, String) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getDraggingPane() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the DraggingPane.
getElementAt(int) - Method in class org.sing_group.gc4s.input.list.FilteredListModel: Returns the element at the specified index.
getExtendedDefaultListModelListeners() - Method in class org.sing_group.gc4s.input.list.ExtendedDefaultListModel: Returns the list of all registered ExtendedDefaultListModelListeners.
getFeatures() - Method in interface org.sing_group.org.gc4s.statistics.data.Dataset: Returns an array with the names of the features in the dataset.
getFeatures() - Method in class org.sing_group.org.gc4s.statistics.data.DefaultDataset
getFeatureValues(String) - Method in interface org.sing_group.org.gc4s.statistics.data.Dataset: Returns a FeatureValues object that represents the values of the specified feature.
getFeatureValues(String) - Method in class org.sing_group.org.gc4s.statistics.data.DefaultDataset
getFileChooser() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog: Returns the dialog filechooser.
getFilechooser() - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Returns the browse action.
getFilechooser() - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Returns the browse action.
getFileChooser() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerControl
getFileChooserListeners() - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Returns an array of all the file chooser listeners registered on this component.
getFileChooserListeners() - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Returns an array of all the file chooser listeners registered on this component.
getFileColumnSummary(TableModel, int) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getFiles() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the current list of file tracks.
getFiles() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
getFileSelectionMode() - Method in enum org.sing_group.gc4s.input.filechooser.SelectionMode
getFinalPosition() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the the actual final position being visualized.
getFinalPosition() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
getFloatColumnSummary(TableModel, int) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getFontSize() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
getFontSize() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
getForeground() - Method in class org.sing_group.gc4s.msaviewer.SequenceBaseRenderingInfo
getFormat(int) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Returns the format of a model column.
getFormatter() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getFunction() - Method in enum org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations.Centering
getFunction() - Method in enum org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations.Transform
getGenericComponent() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
getGenomeIndex() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the GenomeIndex.
getHeader() - Method in interface org.sing_group.gc4s.msaviewer.Sequence: The sequence header.
getHeatmapFont() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns the heat map font.
getHeatmapFont() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel: Returns the heat map font.
getHeight() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getHeight(String) - Method in class org.sing_group.gc4s.utilities.StringMetrics: Returns the height of message.
getHelpLabel() - Method in class org.sing_group.gc4s.input.InputParameter
getHelpLabel() - Method in class org.sing_group.gc4s.input.InputParameterSeparator
getHighColor() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns the high color of the gradient.
getHighValue() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns the high value of the heatmap.
getHistogramIntervals() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getHTMLData() - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Fetch the data in a text/html format
getIcon() - Method in enum org.sing_group.gc4s.ui.menu.HamburgerMenu.Size
getIconHeight() - Method in class org.sing_group.gc4s.ui.icons.ColorIcon
getIconWidth() - Method in class org.sing_group.gc4s.ui.icons.ColorIcon
getInitialPosition() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the actual initial position being visualized.
getInitialPosition() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
getInput() - Method in class org.sing_group.gc4s.input.InputParameter
getInput() - Method in class org.sing_group.gc4s.input.InputParameterSeparator
getInputComponentsPane() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog
getInputComponentsPane() - Method in class org.sing_group.gc4s.dialog.ColorsSelectionDialog
getInputComponentsPane() - Method in class org.sing_group.gc4s.dialog.ExportCsvDialog
getInputComponentsPane() - Method in class org.sing_group.gc4s.dialog.FontConfigurationDialog
getInputComponentsPane() - Method in class org.sing_group.gc4s.dialog.ListSelectionDialog
getInputComponentsPane() - Method in class org.sing_group.gc4s.input.DoubleRangeInputDialog
getInputComponentsPane() - Method in class org.sing_group.gc4s.input.ItemSelectionDialog
getInputComponentsPane() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentControlConfigurationDialog
getInputComponentsPane() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapDataOperationsDialog
getInputItems() - Method in class org.sing_group.gc4s.input.list.JInputList: Returns a list with the items introduced.
getIntegerColumnSummary(TableModel, int) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getItem() - Method in class org.sing_group.gc4s.input.combobox.ComboBoxItem: Returns the wrapped item.
getItemListeners() - Method in class org.sing_group.gc4s.input.RadioButtonsPanel: Returns an array of all the ItemListeners added to this component with addItemListener().
getJComponents(JComponent) - Static method in class org.sing_group.gc4s.ui.UIUtils: Returns a List of the JComponents inside aComponent.
getKeyCode() - Method in class org.sing_group.gc4s.event.AbstractKeyPressedListener
getKeyCode() - Method in class org.sing_group.gc4s.event.EnterKeyPressedListener
getLabel() - Method in class org.sing_group.gc4s.input.InputParameter
getLabelLength() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
getLabelLenth() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
getLabelTab() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
getLabelTab() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
getLayeredPane() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the JLayeredPane.
getLeftListPanel() - Method in class org.sing_group.gc4s.input.list.JParallelListsPanel
getLineBreak() - Method in class org.sing_group.gc4s.input.csv.CsvFormat: Returns the line break.
getLineBreak() - Method in interface org.sing_group.gc4s.visualization.table.csv.CsvTableExporter: Returns the line break.
getLineBreak() - Method in class org.sing_group.gc4s.visualization.table.csv.DefaultCsvTableExporter
getLines() - Method in class org.sing_group.gc4s.genomebrowser.grid.FileInfo
getLines() - Method in interface org.sing_group.gc4s.genomebrowser.grid.GenericInfo: Returns the list of lines to display in the tooltip.
getLines() - Method in class org.sing_group.gc4s.genomebrowser.grid.GenomeBrowserInfo
getLines() - Method in class org.sing_group.gc4s.genomebrowser.grid.IntervalInfo
getLines() - Method in class org.sing_group.gc4s.genomebrowser.grid.PileupInfo
getLines() - Method in class org.sing_group.gc4s.genomebrowser.grid.TrackPositionInfo
getList() - Method in class org.sing_group.gc4s.input.list.JListPanel: Returns the wrapped JList.
getListCellRendererComponent(JList<? extends Color>, Color, int, boolean, boolean) - Method in class org.sing_group.gc4s.ui.ColorListCellRenderer
getListPanel() - Method in class org.sing_group.gc4s.input.list.JInputList: Returns the enclosed JListPanel<String>.
getLongColumnSummary(TableModel, int) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getLowColor() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns the low color of the gradient.
getLowValue() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns the low value of the heatmap.
getMax() - Method in class org.sing_group.gc4s.input.DoubleRange: Return the maximum value of the range.
getMaxColumnValue(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.util.TableUtils: Returns the maximum value of the specified column in table.
getMaxDoubleValue(List<Double>) - Static method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil: Returns the maximum value in the specified list of doubles.
getMaxHistogramValue() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getMaxIntegerValue(List<Integer>) - Static method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil: Returns the maximum value in the specified list of integers.
getMaxValue() - Method in class org.sing_group.gc4s.input.RangeInputPanel: Returns the maximum value introduced.
getMaxValue() - Method in class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Returns the maximum value introduced.
getMessage() - Method in class org.sing_group.gc4s.dialog.JOptionPaneMessage: Returns an Object to pass to the JOptionPane methods.
getMin() - Method in class org.sing_group.gc4s.input.DoubleRange: Return the minimum value of the range.
getMinColumnValue(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.util.TableUtils: Returns the minimum value of the specified column in table.
getMinValue() - Method in class org.sing_group.gc4s.input.RangeInputPanel: Returns the minimum value introduced.
getMinValue() - Method in class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Returns the minimum value introduced.
getName() - Method in interface org.sing_group.gc4s.genomebrowser.TrackOption: Returns the option name.
getName() - Method in interface org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentTracksModel: Returns the name associated to this model.
getName() - Method in interface org.sing_group.gc4s.msaviewer.Track: Returns the track name.
getName() - Method in enum org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations.Centering
getName() - Method in enum org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations.Transform
getName() - Method in class org.sing_group.org.gc4s.statistics.data.DefaultFeatureValues
getName() - Method in interface org.sing_group.org.gc4s.statistics.data.FeatureValues: Returns the feature name.
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.FdrCorrection
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.MultiClassBooleanRandomizationTest
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.MultipleConditionsBooleanChiSquareTest
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.NominalChiSquareTest
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.OneWayAnovaTest
getName() - Method in interface org.sing_group.org.gc4s.statistics.data.tests.PValuesCorrection: Returns the name of the correction.
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.StudentsHomocedasticTTest
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.StudentsPairedTTest
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.StudentsTTest
getName() - Method in interface org.sing_group.org.gc4s.statistics.data.tests.Test: Returns the name of the test.
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.TwoConditionsBooleanFisherTest
getName() - Method in class org.sing_group.org.gc4s.statistics.data.tests.TwoConditionsBooleanYatesChiSquareTest
getNoModelsMessage() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerControl
getNoModelsMessage() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel
getNorthComponent() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
getNucleotideColor(char) - Static method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil: Returns the color associated to a nucleotide.
getNumberOfIntervals() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
getOptions() - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
getOptions() - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
getOptions() - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
getOptions() - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Returns the collection of configurable TrackOptions.
getPainter(Painter) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the file associated to the specified painter.
getPainter(File) - Static method in class org.sing_group.gc4s.genomebrowser.painter.PainterFactory: Returns an adequate painter implementation for the specified file type based on the file extension.
getPainters() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the current list of Painters.
getPainters() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
getPlainData() - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Fetch the data in a text/plain format.
getPreferredSize(JComponent) - Method in class org.sing_group.gc4s.ui.text.VerticalLabelUI
getProgress() - Method in class org.sing_group.org.gc4s.statistics.table.progress.ProgressEvent: Returns the progress value.
getProgressEventListenerListeners() - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTable: Returns an array of all the progress listeners registered on this component.
getPropertyDescriptors(Object) - Static method in class org.sing_group.gc4s.visualization.table.BeanTableModel
getRange() - Method in class org.sing_group.gc4s.input.DoubleRangeInputPanel: Returns the DoubleRange introduced by the user.
getRange() - Method in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel: Returns the DoubleRange introduced by the user.
getRemoveAllComponentsButton() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
getRemoveAllComponentsButtonLabel() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
getRicherData(DataFlavor) - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable
getRicherFlavors() - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Some subclasses will have flavors that are more descriptive than HTML or plain text.
getRightListPanel() - Method in class org.sing_group.gc4s.input.list.JParallelListsPanel
getRowCount() - Method in class org.sing_group.gc4s.visualization.table.BeanTableModel
getRowCount() - Method in class org.sing_group.gc4s.visualization.table.MapTableModel
getRowCount() - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel
getRowCount() - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel
getRowFilter() - Method in class org.sing_group.gc4s.visualization.table.FilterableJXTable
getRowNames() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns a list with the row names.
getRowNames() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapModel: Returns an array with the row names.
getRules() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
getSampleCondition(int) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel: Returns the name of the condition associated to the sample located at the specified column index.
getSamples() - Method in interface org.sing_group.org.gc4s.statistics.data.Dataset: Returns an array with the names of the samples in the dataset.
getSamples() - Method in class org.sing_group.org.gc4s.statistics.data.DefaultDataset
getScaledIcon(ImageIcon, int, int) - Static method in class org.sing_group.gc4s.ui.icons.Icons: Scales icon to width and height.
getScroll() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the JScrollPane.
getSelectedCard() - Method in class org.sing_group.gc4s.ui.CardsPanel: Returns the current visible component.
getSelectedColors() - Method in class org.sing_group.gc4s.dialog.ColorsSelectionDialog: Returns a list containing the Colors selected by the user.
getSelectedColors() - Method in class org.sing_group.gc4s.input.list.ColorsListPanel: Returns a list containing the Colors selected by the user.
getSelectedCsvFormat() - Method in class org.sing_group.gc4s.dialog.ExportCsvDialog: Return the CsvFormat based on the configuration selected by the user.
getSelectedFile() - Method in class org.sing_group.gc4s.dialog.ExportCsvDialog: Returns the selected file.
getSelectedFile() - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Returns the selected file.
getSelectedFiles() - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Returns the selected files.
getSelectedFont() - Method in class org.sing_group.gc4s.dialog.FontConfigurationDialog: Returns the Font configured by the user.
getSelectedFont() - Method in class org.sing_group.gc4s.input.FontConfigurationPanel: Returns the Font configured by the user.
getSelectedItem() - Method in class org.sing_group.gc4s.input.RadioButtonsPanel: Returns the selected item.
getSelectedItems() - Method in class org.sing_group.gc4s.dialog.ListSelectionDialog: Returns the selected elements.
getSelectedItems() - Method in class org.sing_group.gc4s.input.ItemSelectionDialog
getSelectedItems() - Method in class org.sing_group.gc4s.input.ItemSelectionPanel: Returns the list of n selected items.
getSelectedRange() - Method in class org.sing_group.gc4s.input.DoubleRangeInputDialog: Returns the DoubleRange introduced.
getSelectionLabel() - Method in class org.sing_group.gc4s.input.tree.JTreeSelectionPanel: Returns the selection label component.
getSelectionLabelFont() - Method in class org.sing_group.gc4s.input.tree.JTreeSelectionPanel: Returns the font of the selected item text label.
getSelectionLabelMinimumSize() - Method in class org.sing_group.gc4s.input.tree.JTreeSelectionPanel: Returns the minimum size of the selected item text label.
getSequence() - Method in interface org.sing_group.gc4s.msaviewer.Sequence: Returns the sequence content.
getSequences() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the available sequences.
getSize() - Method in class org.sing_group.gc4s.input.combobox.ExtendedJComboBox
getSize() - Method in class org.sing_group.gc4s.input.list.FilteredListModel
getSource() - Method in class org.sing_group.gc4s.dialog.wizard.event.WizardStepEvent
getSourceActions(JComponent) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTransferHandler
getSourceListModel() - Method in class org.sing_group.gc4s.input.list.FilteredListModel: Returns the enclosed ListModel.
getSpinnerValue(JSpinner) - Static method in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel
getSquareWidth() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getStatisticsTestTableModel() - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTable: Returns the StatisticsTestTableModel<T> used by the table.
getStatus() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the current GenomeBrowserState.
getStatus() - Method in class org.sing_group.gc4s.genomebrowser.SortTracksDialog
getStatus() - Method in class org.sing_group.gc4s.genomebrowser.TrackOptionsDialog
getStepComponent() - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep: Returns the JComponent that shows the step.
getSteps() - Method in class org.sing_group.gc4s.dialog.wizard.Wizard
getStepTitle() - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep: Returns the title of the step.
getStringColumnSummary(TableModel, int) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getStringValuesSummary(Set<String>, String) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getTable() - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTablePanel: Returns the StatisticsTestTable shown in this component.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.sing_group.org.gc4s.statistics.table.ui.StatisticsTestTableHeaderRenderer
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.sing_group.org.gc4s.statistics.table.ui.YesNoTableCellRenderer
getTooltip(JTable, int) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
getToolTipColor() - Method in class org.sing_group.gc4s.genomebrowser.grid.FileInfo
getToolTipColor() - Method in interface org.sing_group.gc4s.genomebrowser.grid.GenericInfo: Return the color for the tooltip.
getToolTipColor() - Method in class org.sing_group.gc4s.genomebrowser.grid.GenomeBrowserInfo
getToolTipColor() - Method in class org.sing_group.gc4s.genomebrowser.grid.IntervalInfo
getToolTipColor() - Method in class org.sing_group.gc4s.genomebrowser.grid.PileupInfo
getToolTipColor() - Method in class org.sing_group.gc4s.genomebrowser.grid.TrackPositionInfo
getToolTipsPane() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the ToolTipPane.
getTrackColor() - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
getTrackColor() - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
getTrackColor() - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
getTrackColor() - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Returns the track color.
getTrackFile() - Method in interface org.sing_group.gc4s.genomebrowser.TrackFileProvider: Returns the track file.
getTrackName() - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
getTrackName() - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
getTrackName() - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
getTrackName() - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Returns the track name.
getTrackOptions(Painter) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
getTracksPanel() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Returns the TracksPanel.
getTransferData(DataFlavor) - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Returns an object which represents the data to be transferred.
getTransferDataFlavors() - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Returns an array of DataFlavor objects indicating the flavors the data can be provided in.
getTransform() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapDataOperationsDialog
getType() - Method in class org.sing_group.gc4s.genomebrowser.grid.GridInfo: Returns the type of the information contained.
getType() - Method in interface org.sing_group.gc4s.genomebrowser.TrackOption: Returns the option class.
getUniqueConditionNames() - Method in interface org.sing_group.org.gc4s.statistics.data.Dataset: Returns a set containing the unique condition names.
getUniqueConditionNames() - Method in class org.sing_group.org.gc4s.statistics.data.DefaultDataset
getUnselectedItems() - Method in class org.sing_group.gc4s.dialog.ListSelectionDialog: Returns the unselected elements.
getUpperTracks() - Method in interface org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentTracksModel: Returns the list of tracks that must be placed above the sequences.
getValue() - Method in interface org.sing_group.gc4s.genomebrowser.TrackOption: Returns the option value.
getValue() - Method in class org.sing_group.gc4s.input.text.DoubleTextField
getValue() - Method in class org.sing_group.gc4s.input.text.JIntegerTextField
getValue(String, String) - Method in interface org.sing_group.org.gc4s.statistics.data.Dataset: Returns the value associated with the specified sample and feature.
getValue(String, String) - Method in class org.sing_group.org.gc4s.statistics.data.DefaultDataset
getValueAt(int, int) - Method in class org.sing_group.gc4s.visualization.table.BeanTableModel
getValueAt(int, int) - Method in class org.sing_group.gc4s.visualization.table.MapTableModel
getValueAt(int, int) - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel
getValueAt(int, int) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel
getVisibleColumnNames() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns a list with the column names that are currently visible.
getVisibleRowNames() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Returns a list with the row names that are currently visible.
getVisibleRows() - Method in class org.sing_group.gc4s.visualization.table.FilterableJXTable
getWidth() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getWidth(String) - Method in class org.sing_group.gc4s.utilities.StringMetrics: Returns the width of message.
getWizardStepListeners() - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep: Returns the list of all registered wizard step listeners.
getWrappedComponent() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel.ComponentWrapPanel
getX() - Method in class org.sing_group.gc4s.genomebrowser.grid.Coordinates
getX(int) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getxStart() - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
getxStop() - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
getY() - Method in class org.sing_group.gc4s.genomebrowser.grid.Coordinates
getY(int) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getY(int, int) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
getyStart() - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
getyStop() - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
GPFilter - Class in org.sing_group.gc4s.genomebrowser: A FileFilter implementation to obtain the supported files.
GPFilter() - Constructor for class org.sing_group.gc4s.genomebrowser.GPFilter
GPPainter - Class in org.sing_group.gc4s.genomebrowser.painter: A Painter implementation to render generic genomic position files.
GPPainter(File) - Constructor for class org.sing_group.gc4s.genomebrowser.painter.GPPainter: Creates a new GPPainter for the specified track file.
Gradient - Class in org.sing_group.gc4s.utilities: Class that generates color gradients.
Gradient() - Constructor for class org.sing_group.gc4s.utilities.Gradient
GRAY_1 - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
GRAY_2 - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
GREEN_APPLE - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
GREEN_M - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
GridInfo - Class in org.sing_group.gc4s.genomebrowser.grid: A class that encapsulates a GenericInfo associated to a specific Coordinates location.
GridInfo(GenericInfo, int) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.GridInfo: Creates a new GridInfo instance with the specified initial values.

H

HamburgerMenu - Class in org.sing_group.gc4s.ui.menu: A hamburger button to display a menu.
HamburgerMenu() - Constructor for class org.sing_group.gc4s.ui.menu.HamburgerMenu: Creates a new HamburgerMenu using the 24 pixel icon.
HamburgerMenu(HamburgerMenu.Size) - Constructor for class org.sing_group.gc4s.ui.menu.HamburgerMenu: Creates a new HamburgerMenu using the specified size icon.
HamburgerMenu.Size - Enum in org.sing_group.gc4s.ui.menu: The possible sizes of the hamburguer icon.
hashCode() - Method in class org.sing_group.gc4s.genomebrowser.grid.Coordinates
histogramIntervals - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
htmlData - Variable in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable

I

ICON_ACCEPT - Static variable in class org.sing_group.gc4s.dialog.AbstractInputJDialog
ICON_ADD - Static variable in class org.sing_group.gc4s.input.list.JInputList
ICON_ADD_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ADD_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ADD_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_DOWN - Static variable in class org.sing_group.gc4s.input.list.JListPanel
ICON_ARROW_DOWN_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_DOWN_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_DOWN_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_LEFT - Static variable in class org.sing_group.gc4s.input.list.JParallelListsPanel
ICON_ARROW_LEFT_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_LEFT_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_LEFT_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_RIGHT - Static variable in class org.sing_group.gc4s.input.list.JParallelListsPanel
ICON_ARROW_RIGHT_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_RIGHT_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_RIGHT_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_UP - Static variable in class org.sing_group.gc4s.input.list.JListPanel
ICON_ARROW_UP_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_UP_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROW_UP_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_DOWN_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_DOWN_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_DOWN_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_LEFT_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_LEFT_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_LEFT_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_RIGHT_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_RIGHT_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_RIGHT_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_UP_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_UP_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ARROWS_UP_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_BAR_CHART_1_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_BAR_CHART_1_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_BAR_CHART_1_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_BAR_CHART_2_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_BAR_CHART_2_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_BAR_CHART_2_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_BROWSE_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_BROWSE_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_BROWSE_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CANCEL - Static variable in class org.sing_group.gc4s.dialog.AbstractInputJDialog
ICON_CANCEL_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CANCEL_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CANCEL_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CASE_SENSITIVE_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CASE_SENSITIVE_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CASE_SENSITIVE_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CHARACTER_MAP_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CHARACTER_MAP_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CHARACTER_MAP_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CLEAR - Static variable in class org.sing_group.gc4s.input.list.JListPanel
ICON_CLOUD_DOWNLOAD_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CLOUD_DOWNLOAD_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CLOUD_DOWNLOAD_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CLOUD_UPLOAD_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CLOUD_UPLOAD_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_CLOUD_UPLOAD_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_COLOR_CMYK_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_COLOR_CMYK_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_COLOR_CMYK_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_COLOR_WHEEL_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_COLOR_WHEEL_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_COLOR_WHEEL_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_COLUMN_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_COLUMN_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_COLUMN_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_1_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_1_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_1_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_2_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_2_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_2_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_3_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_3_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_3_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_4_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_4_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_DOWNLOAD_4_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EDIT_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EDIT_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EDIT_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EXPORT_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EXPORT_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EXPORT_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EYE_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EYE_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EYE_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EYE_HIDDEN_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EYE_HIDDEN_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_EYE_HIDDEN_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FILES_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FILES_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FILES_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FIND_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FIND_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FIND_2_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FIND_2_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FIND_2_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FIND_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FOLDER_BLACK_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FOLDER_BLACK_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FOLDER_BLACK_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FONT_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FONT_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_FONT_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_HARD_DISK_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_HARD_DISK_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_HARD_DISK_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_HELP - Static variable in class org.sing_group.gc4s.dialog.AbstractInputJDialog
ICON_IMAGE_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_IMAGE_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_IMAGE_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_INFO_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_INFO_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_INFO_2_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_INFO_2_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_INFO_2_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_INFO_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_LINK_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_LINK_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_LINK_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_LOOKUP_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_LOOKUP_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_LOOKUP_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_MERGE_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_MERGE_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_MERGE_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_OK_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_OK_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_OK_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_OK_COLOR_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_OK_COLOR_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_OK_COLOR_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_PAINT_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_PAINT_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_PAINT_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_PAINT_BRUSH_1_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_PAINT_BRUSH_1_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_PAINT_BRUSH_1_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_PAINT_BRUSH_2_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_PAINT_BRUSH_2_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_PAINT_BRUSH_2_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_2_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_2_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_2_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_3_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_3_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_3_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_4_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_4_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_4_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_5_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_5_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_QUESTION_5_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_RAM_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_RAM_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_RAM_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_RANGE_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_RANGE_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_RANGE_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_RECENT_FILES_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_RECENT_FILES_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_RECENT_FILES_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REFRESH_1_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REFRESH_1_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REFRESH_1_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REFRESH_2_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REFRESH_2_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REFRESH_2_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REFRESH_3_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REFRESH_3_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REFRESH_3_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_REMOVE - Static variable in class org.sing_group.gc4s.input.list.JListPanel
ICON_ROW_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ROW_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ROW_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_SELECT_ALL - Static variable in class org.sing_group.gc4s.input.list.JListPanel
ICON_SETTINGS_1_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_SETTINGS_1_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_SETTINGS_1_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_SETTINGS_2_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_SETTINGS_2_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_SETTINGS_2_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_SPECIAL_CHARACTER_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_SPECIAL_CHARACTER_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_SPECIAL_CHARACTER_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_TABLE_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_TABLE_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_TABLE_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_TRASH_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_TRASH_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_TRASH_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_1_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_1_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_1_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_2_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_2_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_2_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_3_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_3_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_3_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_4_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_4_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_UPLOAD_4_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_WARNING_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_WARNING_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_WARNING_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_WARNING_COLOR_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_WARNING_COLOR_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_WARNING_COLOR_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ZOOM_IN_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ZOOM_IN_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ZOOM_IN_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ZOOM_OUT_16 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ZOOM_OUT_24 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
ICON_ZOOM_OUT_32 - Static variable in class org.sing_group.gc4s.ui.icons.Icons
Icons - Class in org.sing_group.gc4s.ui.icons: Provides a set of icons in different sizes.
Icons() - Constructor for class org.sing_group.gc4s.ui.icons.Icons
IconsPanel - Class in org.sing_group.gc4s.ui.icons: Shows all icons in the Icons class.
IconsPanel() - Constructor for class org.sing_group.gc4s.ui.icons.IconsPanel
ImageIOUtils - Class in org.sing_group.gc4s.utilities: Provides functionalities to deal with ImageIO.
ImageIOUtils() - Constructor for class org.sing_group.gc4s.utilities.ImageIOUtils
init(GenomeBrowser) - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
init(GenomeBrowser) - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
init(GenomeBrowser) - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
init(GenomeBrowser) - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Initializes the track painter.
init() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
initData() - Method in class org.sing_group.gc4s.visualization.table.BeanTableModel
InputParameter - Class in org.sing_group.gc4s.input: This class encapsulates three components of an input parameter: a description label, a JComponent to use to retrieve user input, and a label to use as help for this parameter.
InputParameter(String, JComponent, String) - Constructor for class org.sing_group.gc4s.input.InputParameter
InputParameterSeparator - Class in org.sing_group.gc4s.input: An InputParameterSeparator represents a separator in an InputParametersPanel.
InputParameterSeparator(int) - Constructor for class org.sing_group.gc4s.input.InputParameterSeparator: Creates an InputParameterSeparator with the specified height.
InputParameterSeparator(String, int) - Constructor for class org.sing_group.gc4s.input.InputParameterSeparator: Creates an InputParameterSeparator with the specified height and label.
InputParametersPanel - Class in org.sing_group.gc4s.input: An InputParametersPanel takes one or more InputParameter and properly arranges them using a GroupLayout.
InputParametersPanel(InputParameter...) - Constructor for class org.sing_group.gc4s.input.InputParametersPanel: Creates a new InputParametersPanel using the list of parameters.
InputParametersPanel(InputParametersPanel.DescriptionAlignment, InputParameter...) - Constructor for class org.sing_group.gc4s.input.InputParametersPanel: Creates a new InputParametersPanel using the list of parameters.
InputParametersPanel.DescriptionAlignment - Enum in org.sing_group.gc4s.input
insertUpdate(DocumentEvent) - Method in class org.sing_group.gc4s.event.DocumentAdapter
insertUpdate(DocumentEvent) - Method in class org.sing_group.gc4s.event.RunnableDocumentAdapter
IntegerRangeInputPanel - Class in org.sing_group.gc4s.input.text: A panel that allows user typing a range defined by values, taking into account that the minimum value should always be lower or equal to the maximum value.
IntegerRangeInputPanel(int, int) - Constructor for class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Constructs a new IntegerRangeInputPanel instance using min and max as minimum and maximum initial values.
IntegerRangeInputPanel(int, int, String, String) - Constructor for class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Constructs a new IntegerRangeInputPanel instance using min and max as minimum and maximum initial values.
IntegerRangeInputPanel(int, int, String, String, Orientation) - Constructor for class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Constructs a new IntegerRangeInputPanel instance using min and max as minimum and maximum initial values.
intervalAdded(ListDataEvent) - Method in class org.sing_group.gc4s.event.ListDataAdapter
intervalAdded(ListDataEvent) - Method in class org.sing_group.gc4s.input.list.event.DefaultListDataListener
INTERVALINFO - Static variable in class org.sing_group.gc4s.genomebrowser.grid.GridInfo
IntervalInfo - Class in org.sing_group.gc4s.genomebrowser.grid: A GenericInfo implementation for providing interval information.
IntervalInfo(String, String, String) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.IntervalInfo: Creates a new IntervalInfo started with the specified values.
IntervalInfo(String, String, String, Color) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.IntervalInfo: Creates a new IntervalInfo started with the specified values.
intervalRemoved(ListDataEvent) - Method in class org.sing_group.gc4s.event.ListDataAdapter
intervalRemoved(ListDataEvent) - Method in class org.sing_group.gc4s.input.list.event.DefaultListDataListener
IntervalsPainter - Class in org.sing_group.gc4s.genomebrowser.painter: A Painter implementation to render intervals files.
IntervalsPainter(File) - Constructor for class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter: Creates a new IntervalsPainter for the specified track file.
invalidEmailColor - Variable in class org.sing_group.gc4s.input.text.EmailJXTextField
isBold() - Method in class org.sing_group.gc4s.msaviewer.SequenceBaseRenderingInfo
isCanceled() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog: Returns whether the dialog has been canceled.
isCanceled() - Method in class org.sing_group.gc4s.dialog.wizard.Wizard: Returns true if the dialog has been canceled and false otherwise.
isCellEditable(int, int) - Method in class org.sing_group.gc4s.visualization.table.MapTableModel
isCellEditable(int, int) - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel
isCellEditable(int, int) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel
isCompletePileup(File) - Static method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil: Returns true if the specified file contains a complete pileup and false otherwise.
isDataFlavorSupported(DataFlavor) - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Returns whether or not the specified data flavor is supported for this object.
isFirstSampleColumn(int) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel: Returns true if the specified columnIndex corresponds to the first sample of a condition and false otherwise.
isHTMLFlavor(DataFlavor) - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Returns whether or not the specified data flavor is an HTML flavor that is supported.
isHTMLSupported() - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Should the HTML flavors be offered?
isItalic() - Method in class org.sing_group.gc4s.msaviewer.SequenceBaseRenderingInfo
isLiveUpdate() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentControlConfigurationDialog: Returns true if the live update option is selected and false if it is not.
isPlainFlavor(DataFlavor) - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Returns whether or not the specified data flavor is an plain flavor that is supported.
isPlainSupported() - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Should the plain text flavors be offered?
isQuoteFields() - Method in class org.sing_group.gc4s.input.csv.CsvFormat: Returns true if fields must be delimited by duoble quotes.
isRicherFlavor(DataFlavor) - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable
isSampleColumn(int) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel: Returns true if the specified columnIndex corresponds to a sample and false otherwise.
isShowBottomTracks() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
isShowBottomTracks() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
isShowIndexes() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
isShowIndexes() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
isShowUpperTracks() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
isShowUpperTracks() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
isStepCompleted() - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep: Returns true if the step is completed and false otherwise.
isStringFlavor(DataFlavor) - Method in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable: Returns whether or not the specified data flavor is a String flavor that is supported.
isValidFormat() - Method in class org.sing_group.gc4s.input.csv.CsvPanel: Returns true if the format introduced is valid and false otherwise.
isValidInput() - Method in class org.sing_group.gc4s.input.text.EmailJXTextField: Returns true if the current input is valid and false otherwise.
isValidLine(String, GenomeBrowser) - Method in class org.sing_group.gc4s.genomebrowser.painter.PileupPainter
isValidRange() - Method in class org.sing_group.gc4s.input.DoubleRangeInputPanel: Returns true if the minimum value is lower than the maximum value and false otherwise.
isValidRange() - Method in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel: Returns true if the minimum value is lower or equal than the maximum value and false otherwise.
isValidRange() - Method in class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Returns true if the minimum value is lower or equal to the maximum value and false otherwise.
isValidSelection() - Method in class org.sing_group.gc4s.input.RadioButtonsPanel: Returns true it the selection is valid and false otherwise.
ItemSelectionDialog<T> - Class in org.sing_group.gc4s.input: An ItemSelectionDialog allows users choosing n items from different combo boxes using an ItemSelectionPanel.
ItemSelectionDialog(Window, List<T>, int) - Constructor for class org.sing_group.gc4s.input.ItemSelectionDialog
ItemSelectionDialog(Window, List<T>, int, Function<T, String>, boolean) - Constructor for class org.sing_group.gc4s.input.ItemSelectionDialog
ItemSelectionPanel<T> - Class in org.sing_group.gc4s.input: An ItemSelectionPanel allows users choosing n items from different combo boxes.
ItemSelectionPanel(List<T>, int) - Constructor for class org.sing_group.gc4s.input.ItemSelectionPanel: Creates a new ItemSelectionPanel with n combo boxes to select items.
ItemSelectionPanel(List<T>, int, Function<T, String>) - Constructor for class org.sing_group.gc4s.input.ItemSelectionPanel: Creates a new ItemSelectionPanel with n combo boxes to select items.
itemStateChanged(ItemEvent) - Method in class org.sing_group.gc4s.input.RadioButtonsPanel

J

JButtonBuilder - Class in org.sing_group.gc4s.utilities.builder: A builder class for JButton.
JColorChooserButton - Class in org.sing_group.gc4s.input: A button that allows users selecting a color by using a JColorChooser.
JColorChooserButton() - Constructor for class org.sing_group.gc4s.input.JColorChooserButton: Constructs a new JColorChooserButton with the default color.
JColorChooserButton(Color) - Constructor for class org.sing_group.gc4s.input.JColorChooserButton: Constructs a new JColorChooserButton with the specified color.
JFileChooserConfiguration - Class in org.sing_group.gc4s.input.filechooser: A class that encapsulates the configuration of a JFileChooser, providing the method JFileChooserConfiguration.configure(JFileChooser) to configure a given JFileChooser.
JFileChooserConfiguration(int) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserConfiguration: Creates a new JFileChooserConfiguration with the specified JFileChooser selection mode.
JFileChooserConfiguration(int, List<FileFilter>) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserConfiguration: Creates a new JFileChooserConfiguration with the specified JFileChooser selection mode.
JFileChooserConfiguration(int, List<FileFilter>, boolean, boolean) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserConfiguration: Creates a new JFileChooserConfiguration with the specified JFileChooser selection mode.
JFileChooserPanel - Class in org.sing_group.gc4s.input.filechooser: A JFileChooserPanel displays a text field together a browse button that allows users to select a file.
JFileChooserPanel(Mode) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Constructs a JFileChooserPanel with the specified mode}.
JFileChooserPanel(Mode, String) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Constructs a JFileChooserPanel with the specified mode} and requiredExtension.
JFileChooserPanel(Mode, JFileChooser, String) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Constructs a JFileChooserPanel with the specified mode} and filechooser.
JFileChooserPanel(Mode, SelectionMode, JFileChooser) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Constructs a JFileChooserPanel with the specified mode}, selectionMode and filechooser.
JFileChooserPanel(Mode, JFileChooser) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Constructs a JFileChooserPanel with the specified mode} and filechooser.
JFileChooserPanel(Mode, JFileChooser, String, SelectionMode) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Constructs a JFileChooserPanel with the specified mode}, filechooser, labelFiletext and selectionMode.
JFileChooserPanel(Mode, JFileChooser, ImageIcon, String, String, SelectionMode) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Constructs a JFileChooserPanel with the specified mode}, selectionMode, filechooser, browseIcon, labelFiletext and requiredFileExtension.
JFileChooserPanel(Mode, JFileChooser, ImageIcon, String, String, SelectionMode, boolean, boolean, List<FileFilter>) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Constructs a JFileChooserPanel with the specified mode}, filechooser, selectionMode, browseIcon, labelFiletext and requiredFileExtension.
JFileChooserPanelBuilder - Class in org.sing_group.gc4s.input.filechooser: A builder class for JFileChooserPanel.
JFileChooserPanelBuilder(Mode) - Constructor for class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder
JHeatMap - Class in org.sing_group.gc4s.visualization.heatmap: A JHeatMap provides a heatmap representation for a double matrix.
JHeatMap(JHeatMapModel) - Constructor for class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Constructs a new JHeatMap taking model as data source.
JHeatMap(double[][], String[], String[]) - Constructor for class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Constructs a new JHeatMap taking data as input data matrix and rowNames/columNames as names for rows and columns.
JHeatMapDataOperationsDialog - Class in org.sing_group.gc4s.visualization.heatmap: An input dialog that shows the different operations that can be applied to a heat map.
JHeatMapDataOperationsDialog(Window) - Constructor for class org.sing_group.gc4s.visualization.heatmap.JHeatMapDataOperationsDialog
JHeatMapModel - Class in org.sing_group.gc4s.visualization.heatmap: This class encapsulates the data needed by JHeatMap.
JHeatMapModel(double[][], String[], String[]) - Constructor for class org.sing_group.gc4s.visualization.heatmap.JHeatMapModel: Constructs a new JHeatMapModel.
JHeatMapOperations - Class in org.sing_group.gc4s.visualization.heatmap: This class stores different types operations that can be applied to heatmap data.
JHeatMapOperations() - Constructor for class org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations
JHeatMapOperations.Centering - Enum in org.sing_group.gc4s.visualization.heatmap
JHeatMapOperations.Transform - Enum in org.sing_group.gc4s.visualization.heatmap
JHeatMapPanel - Class in org.sing_group.gc4s.visualization.heatmap: A JHeatMapPanel wraps a JHeatMap, adding a toolbar with options to manipulate it.
JHeatMapPanel(JHeatMap) - Constructor for class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel: Constructs a new JHeatMapPanel wrapping heatmap.
JInputList - Class in org.sing_group.gc4s.input.list: This class encloses a JListPanel<String> to provide the ability of adding (String) elements to the list.
JInputList() - Constructor for class org.sing_group.gc4s.input.list.JInputList: Creates a new JInputList instance with JListPanel functionalities disabled and without allowing repeated elements.
JInputList(boolean, boolean, boolean) - Constructor for class org.sing_group.gc4s.input.list.JInputList: Creates a new JInputList instance.
JIntegerTextField - Class in org.sing_group.gc4s.input.text: This class extends JFormattedTextField and only accepts integers as input.
JIntegerTextField() - Constructor for class org.sing_group.gc4s.input.text.JIntegerTextField: Creates a new JIntegerTextField.
JIntegerTextField(Integer) - Constructor for class org.sing_group.gc4s.input.text.JIntegerTextField: Creates a new JIntegerTextField and initializes it with the specified value.
JLimitedTextField - Class in org.sing_group.gc4s.input.text: A JLimitedTextField is an extension of JTextField that allows specifying the maximum extension of the document (Integer.MAX_VALUE by default).
JLimitedTextField(int) - Constructor for class org.sing_group.gc4s.input.text.JLimitedTextField: Constructs a new instance of JLimitedTextField.
JLimitedTextField(String) - Constructor for class org.sing_group.gc4s.input.text.JLimitedTextField: Constructs a new instance of JLimitedTextField.
JLimitedTextField(String, int) - Constructor for class org.sing_group.gc4s.input.text.JLimitedTextField: Constructs a new instance of JLimitedTextField.
JLimitedTextField(String, int, int) - Constructor for class org.sing_group.gc4s.input.text.JLimitedTextField: Constructs a new instance of JLimitedTextField.
JListPanel<E> - Class in org.sing_group.gc4s.input.list: This class encloses a JList based on a ExtendedDefaultListModel to provide common list functionalities (moving elements, select all, clear selection, filtering elements).
JListPanel(JList<E>) - Constructor for class org.sing_group.gc4s.input.list.JListPanel: Constructs a JListPanel within the button actions and the filter visible.
JListPanel(JList<E>, boolean, boolean) - Constructor for class org.sing_group.gc4s.input.list.JListPanel: Constructs a JListPanel.
JMultipleFileChooserPanel - Class in org.sing_group.gc4s.input.filechooser: A JMultipleFileChooserPanel displays a JList along with a browse button that allows users to select several files.
JMultipleFileChooserPanel(Mode) - Constructor for class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Constructs a JMultipleFileChooserPanel with the specified mode}.
JMultipleFileChooserPanel(Mode, JFileChooser) - Constructor for class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Constructs a JMultipleFileChooserPanel with the specified mode} and filechooser.
JMultipleFileChooserPanel(Mode, SelectionMode, JFileChooser) - Constructor for class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Constructs a JMultipleFileChooserPanel with the specified mode}, selectionMode and filechooser.
JMultipleFileChooserPanel(Mode, JFileChooser, ImageIcon, SelectionMode) - Constructor for class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Constructs a JMultipleFileChooserPanel with the specified mode}, selectionMode, filechooser and browseIcon.
JMultipleFileChooserPanel(Mode, JFileChooser, ImageIcon, SelectionMode, boolean, boolean, List<FileFilter>) - Constructor for class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Constructs a JMultipleFileChooserPanel with the specified mode}, filechooser, browseIcon, and labelFiletext.
JMultipleFileChooserPanelBuilder - Class in org.sing_group.gc4s.input.filechooser: A builder class for JMultipleFileChooserPanel.
JMultipleFileChooserPanelBuilder(Mode) - Constructor for class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder
JOptionPaneMessage - Class in org.sing_group.gc4s.dialog: A JOptionPaneMessage object represents a message for a JOptionPane and adds a check box to allow the user to not show the message again.
JOptionPaneMessage(String) - Constructor for class org.sing_group.gc4s.dialog.JOptionPaneMessage: Creates a new JOptionPaneMessage with the specified message.
JParallelListsPanel<E> - Class in org.sing_group.gc4s.input.list: A JParallelListsPanel displays two parallel JListPanels, allowing to move elements between them.
JParallelListsPanel(JList<E>, JList<E>) - Constructor for class org.sing_group.gc4s.input.list.JParallelListsPanel: Creates a new JParallelListsPanel with left and right lists.
JParallelListsPanel(JList<E>, JList<E>, boolean, boolean) - Constructor for class org.sing_group.gc4s.input.list.JParallelListsPanel: Creates a new JParallelListsPanel with left and right lists.
JParallelListsPanel(JList<E>, JList<E>, String, String, boolean, boolean) - Constructor for class org.sing_group.gc4s.input.list.JParallelListsPanel: Creates a new JParallelListsPanel with left and right lists.
JPopupMenuActionsVisibility - Class in org.sing_group.gc4s.ui.menu: This component extends JPopupMenu so that it only becomes visible if there is at least one JMenuItem enabled.
JPopupMenuActionsVisibility() - Constructor for class org.sing_group.gc4s.ui.menu.JPopupMenuActionsVisibility
JProgressDialog - Class in org.sing_group.gc4s.dialog: A JProgressDialog facilitates the creation of progress dialogs based on fixed task lists.
JProgressDialog(Window, String, List<String>) - Constructor for class org.sing_group.gc4s.dialog.JProgressDialog: Constructs a new ProgressDialog instance with the specified parameters.
JProgressDialog(Window, String, List<String>, String) - Constructor for class org.sing_group.gc4s.dialog.JProgressDialog: Constructs a new ProgressDialog instance with the specified parameters.
JProgressDialog(Window, String, List<String>, String, String) - Constructor for class org.sing_group.gc4s.dialog.JProgressDialog: Constructs a new ProgressDialog instance with the specified parameters.
JSparklinesBarChartTableCellRendererBuilderFactory - Class in org.sing_group.gc4s.jsparklines.builders: This factory provides methods to create renderer builder objects for bar charts.
JSparklinesBarChartTableCellRendererBuilderFactory() - Constructor for class org.sing_group.gc4s.jsparklines.builders.JSparklinesBarChartTableCellRendererBuilderFactory
JSparklinesBarChartTableCellRendererFactory - Class in org.sing_group.gc4s.jsparklines: This factory provides methods to create different types of JSparkLines bar chart renderers.
JSparklinesBarChartTableCellRendererFactory() - Constructor for class org.sing_group.gc4s.jsparklines.JSparklinesBarChartTableCellRendererFactory
JToggleButtonBuilder<T extends JToggleButton> - Class in org.sing_group.gc4s.utilities.builder: A builder class to construct toggle buttons.
JTreePopupMenu(JTree) - Constructor for class org.sing_group.gc4s.input.tree.JTreeSelectionPanel.JTreePopupMenu: Constructs a new JTreePopupMenu with the specified tree.
JTreePopupMenu(JTree, boolean, boolean, boolean) - Constructor for class org.sing_group.gc4s.input.tree.JTreeSelectionPanel.JTreePopupMenu
JTreeSelectionPanel - Class in org.sing_group.gc4s.input.tree: A component to select an element from a JTree.
JTreeSelectionPanel(JTree) - Constructor for class org.sing_group.gc4s.input.tree.JTreeSelectionPanel: Constructs a new JTreeSelectionPanel with the specified tree and default values for the rest of the parameters.
JTreeSelectionPanel(JTree, String, boolean, boolean, boolean, boolean) - Constructor for class org.sing_group.gc4s.input.tree.JTreeSelectionPanel: Constructs a new JTreeSelectionPanel with the specified tree.
JTreeSelectionPanel.JTreePopupMenu - Class in org.sing_group.gc4s.input.tree: An extension of JPopupMenu that show a JTree when it becomes visible.
JTreeUtils - Class in org.sing_group.gc4s.utilities: Utility methods for manipulating JTree objects.
JTreeUtils() - Constructor for class org.sing_group.gc4s.utilities.JTreeUtils

K

keyPressed(KeyEvent) - Method in class org.sing_group.gc4s.event.AbstractKeyPressedListener
keyReleased(KeyEvent) - Method in class org.sing_group.gc4s.event.AbstractKeyPressedListener
keyTyped(KeyEvent) - Method in class org.sing_group.gc4s.event.AbstractKeyPressedListener

L

largeNumbersAreGood(boolean) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumBarChartRendererBuilder: Sets whether large numbers are good or not.
LIGHT_BLACK - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
ListDataAdapter - Class in org.sing_group.gc4s.event: An abstract adapter class for receiving data list events.
ListDataAdapter() - Constructor for class org.sing_group.gc4s.event.ListDataAdapter
ListSelectionDialog<E> - Class in org.sing_group.gc4s.dialog: A ListSelectionDialog displays two parallel JListPanels, allowing to move elements between them.
ListSelectionDialog(Window, List<E>, List<E>) - Constructor for class org.sing_group.gc4s.dialog.ListSelectionDialog: Creates a new ListSelectionDialog with selected and unselected lists.
ListSelectionDialog(Window, List<E>, List<E>, String, String) - Constructor for class org.sing_group.gc4s.dialog.ListSelectionDialog: Creates a new ListSelectionDialog with selected and unselected lists.

M

main(String[]) - Static method in class org.sing_group.org.gc4s.statistics.table.BooleanFourConditionsFortySamplesTableDemo
main(String[]) - Static method in class org.sing_group.org.gc4s.statistics.table.BooleanFourConditionsFortySamplesTablePanelDemo
main(String[]) - Static method in class org.sing_group.org.gc4s.statistics.table.BooleanFourConditionsTwoThousandSamplesTableDemo
main(String[]) - Static method in class org.sing_group.org.gc4s.statistics.table.BooleanTwoConditionsFortySamplesTableDemo
main(String[]) - Static method in class org.sing_group.org.gc4s.statistics.table.BooleanTwoConditionsTwoThousandSamplesTableDemo
main(String[]) - Static method in class org.sing_group.org.gc4s.statistics.table.MinimalTableDemo
main(String[]) - Static method in class org.sing_group.org.gc4s.statistics.table.NominalTableDemo
main(String[]) - Static method in class org.sing_group.org.gc4s.statistics.table.ThreeConditionsMeasurementsTableDemo
main(String[]) - Static method in class org.sing_group.org.gc4s.statistics.table.TwoConditionsMeasurementsTableDemo
MapTableModel<K,V> - Class in org.sing_group.gc4s.visualization.table: A table model for easily displaying all the entries of a map.
MapTableModel(Map<K, V>) - Constructor for class org.sing_group.gc4s.visualization.table.MapTableModel: Creates a new MapTableModel for the specified map.
MapTableViewer<K,V> - Class in org.sing_group.gc4s.visualization.table: A component that allows showing the entries of a map in a table using a MapTableModel, which provides one row for each entry with the key in the first column and the value in the second column.
MapTableViewer(Map<K, V>) - Constructor for class org.sing_group.gc4s.visualization.table.MapTableViewer: Creates a new MapTableViewer for the specified map.
MapTableViewer(MapTableModel<K, V>) - Constructor for class org.sing_group.gc4s.visualization.table.MapTableViewer: Creates a new MapTableViewer for the specified model.
MatrixUtils - Class in org.sing_group.gc4s.utilities: Provides functionalities to deal with data matrices.
MatrixUtils() - Constructor for class org.sing_group.gc4s.utilities.MatrixUtils
max(double[][]) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Return the maximum value in data ignoring missing values (Double.NaN).
max(double[]) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Return the maximum value in data ignoring missing values (Double.NaN).
maxHistogramValue - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
maximize() - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog: Maximizes the dialog.
MaximumBarChartRendererBuilder - Class in org.sing_group.gc4s.jsparklines.builders.barchartrenderer: A builder class for the creation of simple JSparkLines bar chart renderers that only account for the maximum column value.
MaximumBarChartRendererBuilder(JTable, int) - Constructor for class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumBarChartRendererBuilder: Creates a new MaximumBarChartRendererBuilder for the specified table and column.
MaximumColoredBarChartRendererBuilder - Class in org.sing_group.gc4s.jsparklines.builders.barchartrenderer: A builder class for the creation of JSparkLines bar chart renderers that only account for the maximum column value and allow the usage of a custom color for the bars.
MaximumColoredBarChartRendererBuilder(JTable, int) - Constructor for class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumColoredBarChartRendererBuilder: Creates a new MaximumColoredBarChartRendererBuilder for the specified table and column.
MaximumMinimumBarChartRendererBuilder - Class in org.sing_group.gc4s.jsparklines.builders.barchartrenderer: A builder class for the creation of JSparkLines bar chart renderers that account for both the maximum and minimum column values.
MaximumMinimumBarChartRendererBuilder(JTable, int) - Constructor for class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumBarChartRendererBuilder: Creates a new MaximumMinimumBarChartRendererBuilder for the specified table and column.
MaximumMinimumColoredBarChartRendererBuilder - Class in org.sing_group.gc4s.jsparklines.builders.barchartrenderer: A builder class for the creation of JSparkLines bar chart renderers that account for both the maximum and minimum column values and allow the usage of custom colors for the bars.
MaximumMinimumColoredBarChartRendererBuilder(JTable, int) - Constructor for class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumColoredBarChartRendererBuilder: Creates a new MaximumMinimumColoredBarChartRendererBuilder for the specified table and column.
MaximumMinimumXYDataSignificanceBarChartRendererBuilder - Class in org.sing_group.gc4s.jsparklines.builders.barchartrenderer: A builder class for the creation of JSparkLines bar chart renderers for columns of XYDataPoint values that account for both maximum and minimum column values.
MaximumMinimumXYDataSignificanceBarChartRendererBuilder(JTable, int) - Constructor for class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumXYDataSignificanceBarChartRendererBuilder: Creates a new MaximumMinimumXYDataSignificanceBarChartRendererBuilder for the specified table and column.
MaximumXYDataSignificanceBarChartRendererBuilder - Class in org.sing_group.gc4s.jsparklines.builders.barchartrenderer: A builder class for the creation of JSparkLines bar chart renderers for columns of XYDataPoint values that account for maximum column values.
MaximumXYDataSignificanceBarChartRendererBuilder(JTable, int) - Constructor for class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumXYDataSignificanceBarChartRendererBuilder: Creates a new MaximumXYDataSignificanceBarChartRendererBuilder for the specified table and column.
mean(double[], boolean) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Returns the mean value of data.
median(double[], boolean) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Returns the median value of data.
min(double[][]) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Return the minimum value in data ignoring missing values (Double.NaN).
min(double[]) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Return the minimum value in data ignoring missing values (Double.NaN).
MinimalTableDemo - Class in org.sing_group.org.gc4s.statistics.table
MinimalTableDemo() - Constructor for class org.sing_group.org.gc4s.statistics.table.MinimalTableDemo
Mode - Enum in org.sing_group.gc4s.input.filechooser: The mode to open a JFileChooser.
modelToHtml() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel
mouseClicked(MouseEvent) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
mouseDragged(MouseEvent) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
mouseEntered(MouseEvent) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
mouseExited(MouseEvent) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
mouseMoved(MouseEvent) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
mousePressed(MouseEvent) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
mouseReleased(MouseEvent) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
moveDown(int) - Method in class org.sing_group.gc4s.input.list.ExtendedDefaultListModel: Moves down the element at index and returns true.
moveLeftSelectedElement() - Method in class org.sing_group.gc4s.input.list.JParallelListsPanel
moveRightSelectedElement() - Method in class org.sing_group.gc4s.input.list.JParallelListsPanel
moveUp(int) - Method in class org.sing_group.gc4s.input.list.ExtendedDefaultListModel: Moves up the element at index and returns true.
MultiClassBooleanRandomizationTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An AbstractBooleanTest to compute the randomization test of independence on a feature values set with two or more conditions.
MultiClassBooleanRandomizationTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.MultiClassBooleanRandomizationTest: Creates a new MultiClassBooleanRandomizationTest instance.
MultilineLabel - Class in org.sing_group.gc4s.ui.text: An extension of JTextArea configured as multiline label.
MultilineLabel(String) - Constructor for class org.sing_group.gc4s.ui.text.MultilineLabel: Creates a new MultilineLabel to show the specified text.
MultipleConditionsBooleanChiSquareTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An AbstractBooleanTest to compute the Chi-squared test of independence on a feature values set with two or more conditions.
MultipleConditionsBooleanChiSquareTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.MultipleConditionsBooleanChiSquareTest: Creates a new MultipleConditionsBooleanChiSquareTest instance.
MultipleFileChooserListener - Interface in org.sing_group.gc4s.input.filechooser.event: The listener interface for receiving multiple file chooser panel events.
MultipleSequenceAlignmentControlConfigurationDialog - Class in org.sing_group.gc4s.msaviewer: A dialog that allows user to set the values of a MultipleSequenceAlignmentViewerConfiguration.
MultipleSequenceAlignmentControlConfigurationDialog(Window, MultipleSequenceAlignmentViewerConfiguration) - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentControlConfigurationDialog: Creates a new dialog with the controls initialized with the values specified by configuration.
MultipleSequenceAlignmentTracksModel - Interface in org.sing_group.gc4s.msaviewer: An interface for the definition of multiple sequence alignment tracks.
MultipleSequenceAlignmentViewerConfiguration - Class in org.sing_group.gc4s.msaviewer: This class stores the configuration of the MultipleSequenceAlignmentViewerPanel.
MultipleSequenceAlignmentViewerConfiguration() - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration: Creates a new MultipleSequenceAlignmentViewerConfiguration initialized with the default values.
MultipleSequenceAlignmentViewerConfiguration(int, int, int, int, int, boolean, boolean, boolean) - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration: Creates a new MultipleSequenceAlignmentViewerConfiguration initialized with the specified values.
MultipleSequenceAlignmentViewerConfigurationPanel - Class in org.sing_group.gc4s.msaviewer: A panel that allows to set the values for a MultipleSequenceAlignmentViewerConfiguration.
MultipleSequenceAlignmentViewerConfigurationPanel(MultipleSequenceAlignmentViewerConfiguration) - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel: Creates a new dialog with the controls initialized with the values specified by configuration.
MultipleSequenceAlignmentViewerControl - Class in org.sing_group.gc4s.msaviewer: A panel that wraps a MultipleSequenceAlignmentViewerPanel and allows the selection of different models and configuring the visual display settings.
MultipleSequenceAlignmentViewerControl(List<Sequence>, List<MultipleSequenceAlignmentTracksModel>, Map<MultipleSequenceAlignmentTracksModel, SequenceAlignmentRenderer>, MultipleSequenceAlignmentViewerConfiguration) - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerControl: Creates a new MultipleSequenceAlignmentViewerControl with the specified sequences, configuration, tracks models and sequence alignment renderers.
MultipleSequenceAlignmentViewerPanel - Class in org.sing_group.gc4s.msaviewer: A panel that displays the aligned sequences.
MultipleSequenceAlignmentViewerPanel(List<Sequence>) - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Creates a new MultipleSequenceAlignmentViewerPanel with the specified sequences and default values for configuration, tracks model and sequence alignment renderer.
MultipleSequenceAlignmentViewerPanel(List<Sequence>, MultipleSequenceAlignmentViewerConfiguration) - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Creates a new MultipleSequenceAlignmentViewerPanel with the specified sequences and configuration and default values for tracks model and sequence alignment renderer.
MultipleSequenceAlignmentViewerPanel(List<Sequence>, MultipleSequenceAlignmentTracksModel) - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Creates a new MultipleSequenceAlignmentViewerPanel with the specified sequences and tracks model and default values for configuration and sequence alignment renderer.
MultipleSequenceAlignmentViewerPanel(List<Sequence>, MultipleSequenceAlignmentTracksModel, SequenceAlignmentRenderer) - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Creates a new MultipleSequenceAlignmentViewerPanel with the specified sequences, tracks model and sequence alignment renderer and default values for configuration.
MultipleSequenceAlignmentViewerPanel(List<Sequence>, MultipleSequenceAlignmentTracksModel, SequenceAlignmentRenderer, MultipleSequenceAlignmentViewerConfiguration) - Constructor for class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Creates a new MultipleSequenceAlignmentViewerPanel with the specified sequences, configuration, tracks model and sequence alignment renderer.

N

newBuilder() - Static method in class org.sing_group.gc4s.ui.CardsPanelBuilder: Returns a new CardsPanelBuilder instance to build a CardsPanel.
newJButtonBuilder() - Static method in class org.sing_group.gc4s.utilities.builder.JButtonBuilder: Returns a new JButtonBuilder instance.
newJToggleButton() - Static method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Creates a new JToggleButtonBuilder to construct a JToggleButton.
newJToggleButton(Supplier<T>) - Static method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Creates a new JToggleButtonBuilder to construct a JToggleButton.
newMaximumBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.builders.JSparklinesBarChartTableCellRendererBuilderFactory: Returns a new MaximumBarChartRendererBuilder for the specified table and column.
newMaximumColoredBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.builders.JSparklinesBarChartTableCellRendererBuilderFactory: Returns a new MaximumColoredBarChartRendererBuilder for the specified table and column.
newMaximumMinimumBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.builders.JSparklinesBarChartTableCellRendererBuilderFactory: Returns a new MaximumMinimumBarChartRendererBuilder for the specified table and column.
newMaximumMinimumColoredBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.builders.JSparklinesBarChartTableCellRendererBuilderFactory: Returns a new MaximumMinimumColoredBarChartRendererBuilder for the specified table and column.
newMaximumMinimumXYDataSignificanceBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.builders.JSparklinesBarChartTableCellRendererBuilderFactory: Returns a new MaximumMinimumXYDataSignificanceBarChartRendererBuilder for the specified table and column.
newMaximumXYDataSignificanceBarChartRenderer(JTable, int) - Static method in class org.sing_group.gc4s.jsparklines.builders.JSparklinesBarChartTableCellRendererBuilderFactory: Returns a new MaximumXYDataSignificanceBarChartRendererBuilder for the specified table and column.
nextTask() - Method in class org.sing_group.gc4s.dialog.JProgressDialog: Sets next task in the label and increments the progress.
NominalChiSquareTest - Class in org.sing_group.org.gc4s.statistics.data.tests: A Test<String> implementation to compute the Chi-squared test on feature values of string, that is, with nominal values.
NominalChiSquareTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.NominalChiSquareTest
NominalTableDemo - Class in org.sing_group.org.gc4s.statistics.table
NominalTableDemo() - Constructor for class org.sing_group.org.gc4s.statistics.table.NominalTableDemo
notifyWizardStepCompleted(WizardStepEvent) - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep
notifyWizardStepNextButtonTooltipChanged(String) - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep
notifyWizardStepStatus() - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep
notifyWizardStepUncompleted(WizardStepEvent) - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep
NumberHighlighter - Class in org.sing_group.org.gc4s.statistics.table.ui: A ColorHighlighter to highlight Number values in tables by creating a gradient of colors (like in heat map representations).
NumberHighlighter(StatisticsTestTable<Number>) - Constructor for class org.sing_group.org.gc4s.statistics.table.ui.NumberHighlighter: Creates a new NumberHighlighter for the specified table using the default colors for the lowest and highest values.
NumberHighlighter(StatisticsTestTable<Number>, Color, Color) - Constructor for class org.sing_group.org.gc4s.statistics.table.ui.NumberHighlighter: Creates a new NumberHighlighter for the specified table using the specified colors.

O

offset - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
OK - Static variable in class org.sing_group.gc4s.genomebrowser.TrackOptionsDialog
okButton - Variable in class org.sing_group.gc4s.dialog.AbstractInputJDialog
OneWayAnovaTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An AbstractNumberTest to compute the One-way ANOVA test on a feature values set with two or more conditions.
OneWayAnovaTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.OneWayAnovaTest
onFileChoosed(ChangeEvent) - Method in interface org.sing_group.gc4s.input.filechooser.event.FileChooserListener
onFileRemoved(ChangeEvent) - Method in interface org.sing_group.gc4s.input.filechooser.event.MultipleFileChooserListener
onFinish() - Method in class org.sing_group.org.gc4s.statistics.table.progress.ProgressEventAdapter
onFinish() - Method in interface org.sing_group.org.gc4s.statistics.table.progress.ProgressEventListener: Invoked when the process is finished.
onFinish() - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTablePanel
onFormatEdited(ChangeEvent) - Method in interface org.sing_group.gc4s.input.csv.event.CsvListener
onOkButtonEvent(ActionEvent) - Method in class org.sing_group.gc4s.dialog.AbstractInputJDialog
onProgress(ProgressEvent) - Method in class org.sing_group.org.gc4s.statistics.table.progress.ProgressEventAdapter
onProgress(ProgressEvent) - Method in interface org.sing_group.org.gc4s.statistics.table.progress.ProgressEventListener: Invoked when a progress is made.
onProgress(ProgressEvent) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTablePanel
onStart() - Method in class org.sing_group.org.gc4s.statistics.table.progress.ProgressEventAdapter
onStart() - Method in interface org.sing_group.org.gc4s.statistics.table.progress.ProgressEventListener: Invoked when the process is started.
onStart() - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTablePanel
options - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
org.sing_group.gc4s.dialog - package org.sing_group.gc4s.dialog: Provides components related to the creation of different types of dialogs.
org.sing_group.gc4s.dialog.wizard - package org.sing_group.gc4s.dialog.wizard: Provides components related with to creation of Wizard dialogs or assistants.
org.sing_group.gc4s.dialog.wizard.event - package org.sing_group.gc4s.dialog.wizard.event: Provides extensions of interfaces and classes related to different types of events fired by Wizard dialogs.
org.sing_group.gc4s.event - package org.sing_group.gc4s.event: Provides extensions of interfaces and classes related to different types of events fired by AWT components.
org.sing_group.gc4s.genomebrowser - package org.sing_group.gc4s.genomebrowser: Provides the main classes related with the genome browser.
org.sing_group.gc4s.genomebrowser.grid - package org.sing_group.gc4s.genomebrowser.grid: Provides classes related with the grid tooltip information.
org.sing_group.gc4s.genomebrowser.painter - package org.sing_group.gc4s.genomebrowser.painter: Provides classes related with the track painters.
org.sing_group.gc4s.input - package org.sing_group.gc4s.input: Provides components related to the retrieval of different types of user inputs.
org.sing_group.gc4s.input.combobox - package org.sing_group.gc4s.input.combobox: Provides components related to the retrieval of user input using combo boxes.
org.sing_group.gc4s.input.csv - package org.sing_group.gc4s.input.csv: Provides components related to the retrieval of CSV (comma-separated values) configurations.
org.sing_group.gc4s.input.csv.event - package org.sing_group.gc4s.input.csv.event: Provides interfaces and classes related to different types of events fired by CSV related components.
org.sing_group.gc4s.input.filechooser - package org.sing_group.gc4s.input.filechooser: Provides components related to file selection.
org.sing_group.gc4s.input.filechooser.event - package org.sing_group.gc4s.input.filechooser.event: Provides interfaces and classes frelated to different types of events fired by file chooser components.
org.sing_group.gc4s.input.list - package org.sing_group.gc4s.input.list: Provides components related to the retrieval of user input using lists.
org.sing_group.gc4s.input.list.event - package org.sing_group.gc4s.input.list.event: Provides interfaces and classes related to different types of events fired by list components.
org.sing_group.gc4s.input.text - package org.sing_group.gc4s.input.text: Provides components related to the retrieval of user input using text fields.
org.sing_group.gc4s.input.tree - package org.sing_group.gc4s.input.tree
org.sing_group.gc4s.jsparklines - package org.sing_group.gc4s.jsparklines: Provides components related to the creation of different types of JSparkLines renderers.
org.sing_group.gc4s.jsparklines.builders - package org.sing_group.gc4s.jsparklines.builders: Provides components related to the creation of builder classes for different types of JSparkLines renderers.
org.sing_group.gc4s.jsparklines.builders.barchartrenderer - package org.sing_group.gc4s.jsparklines.builders.barchartrenderer: Provides components related to the creation of builder classes for JSparkLines bar chart renderers.
org.sing_group.gc4s.jsparklines.util - package org.sing_group.gc4s.jsparklines.util: Provides utility classes for other packages in this module.
org.sing_group.gc4s.msaviewer - package org.sing_group.gc4s.msaviewer: Provides components related to the visualization of multiple alignment sequences.
org.sing_group.gc4s.ui - package org.sing_group.gc4s.ui: Provides components related to the creation of user interfaces and layouts.
org.sing_group.gc4s.ui.icons - package org.sing_group.gc4s.ui.icons: Provides icons and utilities to deal with icons.
org.sing_group.gc4s.ui.menu - package org.sing_group.gc4s.ui.menu: Provides components related to the creation of menus.
org.sing_group.gc4s.ui.tabbedpane - package org.sing_group.gc4s.ui.tabbedpane: Provides components related to the creation of tabbed panes.
org.sing_group.gc4s.ui.text - package org.sing_group.gc4s.ui.text: Provides components related to the creation of text components.
org.sing_group.gc4s.utilities - package org.sing_group.gc4s.utilities: Provides classes offering different functionalities that cannot be grouped in other packages (dialog, event, input, ui or visualization).
org.sing_group.gc4s.utilities.builder - package org.sing_group.gc4s.utilities.builder: Provides builder classes to facilitate the creation of components.
org.sing_group.gc4s.visualization - package org.sing_group.gc4s.visualization: Provides components related to data visualization.
org.sing_group.gc4s.visualization.heatmap - package org.sing_group.gc4s.visualization.heatmap: Provides components related to heat map visualization.
org.sing_group.gc4s.visualization.table - package org.sing_group.gc4s.visualization.table: Provides components related to table visualization.
org.sing_group.gc4s.visualization.table.csv - package org.sing_group.gc4s.visualization.table.csv: Provides components related to table visualization of CSV data.
org.sing_group.org.gc4s.statistics.data - package org.sing_group.org.gc4s.statistics.data: Provides classes related with data representations.
org.sing_group.org.gc4s.statistics.data.tests - package org.sing_group.org.gc4s.statistics.data.tests: Provides classes related with statistical tests.
org.sing_group.org.gc4s.statistics.data.util - package org.sing_group.org.gc4s.statistics.data.util: Provides utility classes for other packages in this module.
org.sing_group.org.gc4s.statistics.table - package org.sing_group.org.gc4s.statistics.table: Provides components related to the visualization of statistical tests tables.
org.sing_group.org.gc4s.statistics.table.progress - package org.sing_group.org.gc4s.statistics.table.progress: Provides classes related with progress events at the statistical tests tables.
org.sing_group.org.gc4s.statistics.table.ui - package org.sing_group.org.gc4s.statistics.table.ui: Provides classes related to the customization of the statistical tests tables.
Orientation - Enum in org.sing_group.gc4s.ui: An enumeration that defines possible orientation of components.

P

paint(Graphics2D, GenomeBrowser, int) - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
paint(Graphics2D, GenomeBrowser, int) - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
paint(Graphics2D, GenomeBrowser, int) - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
paint(Graphics2D, GenomeBrowser, int) - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Paints the track at Graphics2D with the specified track offset.
paint(Graphics2D, GenomeBrowser, int) - Method in class org.sing_group.gc4s.genomebrowser.painter.PileupPainter
paint(Graphics, JComponent) - Method in class org.sing_group.gc4s.ui.text.VerticalLabelUI
paint(Graphics) - Method in class org.sing_group.gc4s.visualization.ColorKeyLegend
paintComponent(Graphics) - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
paintComponent(Graphics) - Method in class org.sing_group.gc4s.genomebrowser.ToolTipPane
paintComponent(Graphics) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
Painter - Interface in org.sing_group.gc4s.genomebrowser.painter: The interface that defines a track painter.
PainterFactory - Class in org.sing_group.gc4s.genomebrowser.painter: A factory to create the appropriate Painter for each file type.
PainterFactory() - Constructor for class org.sing_group.gc4s.genomebrowser.painter.PainterFactory
paintIcon(Component, Graphics, int, int) - Method in class org.sing_group.gc4s.ui.icons.ColorIcon
parent - Variable in class org.sing_group.gc4s.dialog.AbstractInputJDialog
parsePileupLine(String) - Method in class org.sing_group.gc4s.genomebrowser.grid.PileupInfo
parseValue(Object) - Method in class org.sing_group.gc4s.visualization.table.csv.AbstractCsvTableExporter
parseValue(Object) - Method in interface org.sing_group.gc4s.visualization.table.csv.CsvTableExporter: Returns an String representation of the specified value.
PathCheckTreeSelectionModel - Class in org.sing_group.gc4s.input.tree
PathCheckTreeSelectionModel() - Constructor for class org.sing_group.gc4s.input.tree.PathCheckTreeSelectionModel
PILEUPINFO - Static variable in class org.sing_group.gc4s.genomebrowser.grid.GridInfo
PileupInfo - Class in org.sing_group.gc4s.genomebrowser.grid: A GenericInfo implementation for providing pileup information.
PileupInfo(String, Color, boolean) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.PileupInfo: Creates a new PileupInfo instance for the pileup line.
PileupPainter - Class in org.sing_group.gc4s.genomebrowser.painter: A GPPainter extension to render pileup files.
PileupPainter(File) - Constructor for class org.sing_group.gc4s.genomebrowser.painter.PileupPainter: Creates a new PileupPainter for the specified track file.
plainData - Variable in class org.sing_group.gc4s.visualization.table.csv.BasicTransferable
PopupMenuAdapter - Class in org.sing_group.gc4s.event: An abstract adapter class for receiving popup menu events.
PopupMenuAdapter() - Constructor for class org.sing_group.gc4s.event.PopupMenuAdapter
popupMenuCanceled(PopupMenuEvent) - Method in class org.sing_group.gc4s.event.PopupMenuAdapter
popupMenuWillBecomeInvisible(PopupMenuEvent) - Method in class org.sing_group.gc4s.event.PopupMenuAdapter
popupMenuWillBecomeVisible(PopupMenuEvent) - Method in class org.sing_group.gc4s.event.PopupMenuAdapter
printChar(StringBuilder, Optional<SequenceBaseRenderingInfo>, char) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel
PROGRESS_EVENT_LISTENER - Static variable in class org.sing_group.org.gc4s.statistics.table.TableDemoUtils
ProgressEvent - Class in org.sing_group.org.gc4s.statistics.table.progress: An object that represents the progress of a process.
ProgressEvent(float) - Constructor for class org.sing_group.org.gc4s.statistics.table.progress.ProgressEvent: Creates a new ProgressEvent with the specified progres value.
ProgressEventAdapter - Class in org.sing_group.org.gc4s.statistics.table.progress: An adapter class for receiving progress events.
ProgressEventAdapter() - Constructor for class org.sing_group.org.gc4s.statistics.table.progress.ProgressEventAdapter
ProgressEventListener - Interface in org.sing_group.org.gc4s.statistics.table.progress: The listener interface for receiving progress events.
properties() - Static method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel: Returns a set containing the specific properties of this component that can be notified with property changes.
PROPERTY_BLOCK_LENGTH - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
PROPERTY_BLOCKS_PER_LINE - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
PROPERTY_FONT_SIZE - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
PROPERTY_LABEL_LENGTH - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
PROPERTY_LABEL_TAB - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
PROPERTY_RANGE - Static variable in class org.sing_group.gc4s.input.DoubleRangeInputPanel
PROPERTY_RANGE - Static variable in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel
PROPERTY_SELECTION - Static variable in class org.sing_group.gc4s.input.ItemSelectionPanel
PROPERTY_SHOW_BOTTOM_TRACKS - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
PROPERTY_SHOW_INDEXES - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
PROPERTY_SHOW_UPPER_TRACKS - Static variable in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfigurationPanel
PROPERTY_VISIBLE_CARD - Static variable in class org.sing_group.gc4s.ui.CardsPanel
PURPLE_PASTEL - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
PValuesCorrection - Interface in org.sing_group.org.gc4s.statistics.data.tests: The interface that defines a statistical correction that is applied to correct a set of p-values.

Q

quoteFields() - Method in interface org.sing_group.gc4s.visualization.table.csv.CsvTableExporter: Returns true if fields must be quoted and false otherwise.
quoteFields() - Method in class org.sing_group.gc4s.visualization.table.csv.DefaultCsvTableExporter

R

RadioButtonsPanel<T> - Class in org.sing_group.gc4s.input: A component that allows users selecting a single item from a list of items using radio buttons.
RadioButtonsPanel(T[]) - Constructor for class org.sing_group.gc4s.input.RadioButtonsPanel: Creates a RadioButtonsPanel that contains the elements in the specified array.
RadioButtonsPanel(List<T>) - Constructor for class org.sing_group.gc4s.input.RadioButtonsPanel: Creates a RadioButtonsPanel that contains the elements in the specified list.
RadioButtonsPanel(T[], int, int) - Constructor for class org.sing_group.gc4s.input.RadioButtonsPanel: Creates a RadioButtonsPanel that contains the elements in the specified array.
RadioButtonsPanel(List<T>, int, int) - Constructor for class org.sing_group.gc4s.input.RadioButtonsPanel: Creates a RadioButtonsPanel that contains the elements in the specified list.
randomValues(int, int, int) - Static method in class org.sing_group.org.gc4s.statistics.data.util.StatisticsTestsDataUtils
randomValues(int, int) - Static method in class org.sing_group.org.gc4s.statistics.data.util.StatisticsTestsDataUtils
randomValues(int, int, List<String>) - Static method in class org.sing_group.org.gc4s.statistics.data.util.StatisticsTestsDataUtils
RangeInputPanel - Class in org.sing_group.gc4s.input: A panel that allows user selecting a range of values, taking into account that the minimum value should always be lower or equal to the maximum value.
RangeInputPanel(int, int) - Constructor for class org.sing_group.gc4s.input.RangeInputPanel: Constructs a new RangeInputPanel instance using min and max as minimum and maximum values for the input sliders.
RangeInputPanel(int, int, String, String) - Constructor for class org.sing_group.gc4s.input.RangeInputPanel: Constructs a new RangeInputPanel instance using min and max as minimum and maximum values for the input sliders.
RED_PASTEL - Static variable in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil
remove(Component) - Static method in class org.sing_group.gc4s.utilities.FileDrop: Removes the drag-and-drop hooks from the component and optionally from the all children.
remove(PrintStream, Component, boolean) - Static method in class org.sing_group.gc4s.utilities.FileDrop: Removes the drag-and-drop hooks from the component and optionally from the all children.
removeAllComponents() - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
removeAllElements() - Method in class org.sing_group.gc4s.input.list.JInputList: Removes all elements from the input list.
removeChangeListener(ChangeListener) - Method in class org.sing_group.gc4s.input.RangeInputPanel
removeChangeListener(ChangeListener) - Method in class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Removes the specified change listener.
removeColumn(int, Object[][]) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Removes column at the specified index from data matrix.
removeComponentWrapPanel(ComponentsListPanel<T>.ComponentWrapPanel) - Method in class org.sing_group.gc4s.ui.ComponentsListPanel
removeConverter(int) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Removes the Converter of a model column.
removeConverter(int) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTransferHandler: Removes the Converter of a model column.
removeElements(List<E>) - Method in class org.sing_group.gc4s.input.list.ExtendedDefaultListModel: Removes all the elements from the model.
removeExtendedDefaultListModelListener(ExtendedDefaultListModelListener) - Method in class org.sing_group.gc4s.input.list.ExtendedDefaultListModel: Removes the specified ExtendedDefaultListModelListener to the listeners list.
removeFile(File) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Removes the painter associated to the specified file.
removeFormat(int) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Removes the format of a model column.
removeItemListener(ItemListener) - Method in class org.sing_group.gc4s.input.RadioButtonsPanel: Removes an ItemListener from this component.
removeListDataListener(ListDataListener) - Method in class org.sing_group.gc4s.input.list.ColorsListPanel: Removes a listener from the list that's notified each time a change to the data model occurs.
removePainter(Painter) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Removes the specified painter.
removeProgressEventListener(ProgressEventListener) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTable: Removes the specified progress listener to stop receiving component events from this component.
removeTabAt(int) - Method in class org.sing_group.gc4s.ui.tabbedpane.ExtendedJTabbedPane
removeTableModelListener(TableModelListener) - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel
RemoveTrackJMenuItem(String) - Constructor for class org.sing_group.gc4s.genomebrowser.TracksPanel.RemoveTrackJMenuItem
RemoveTracksDialog - Class in org.sing_group.gc4s.genomebrowser: A dialog that allows users to remove tracks.
RemoveTracksDialog(GenomeBrowser) - Constructor for class org.sing_group.gc4s.genomebrowser.RemoveTracksDialog: Creates a new RemoveTracksDialog for removing tracks at the specified GenomeBrowser.
removeUpdate(DocumentEvent) - Method in class org.sing_group.gc4s.event.DocumentAdapter
removeUpdate(DocumentEvent) - Method in class org.sing_group.gc4s.event.RunnableDocumentAdapter
removeWizardStepListener(WizardStepListener) - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep: Removes the specified wizard step listener to stop receiving component events from this component.
render(Sequence, int) - Method in class org.sing_group.gc4s.msaviewer.BaseColorSequenceAlignmentRenderer
render(Sequence, int) - Method in class org.sing_group.gc4s.msaviewer.DefaultSequenceAlignmentRenderer
render(Sequence, int) - Method in interface org.sing_group.gc4s.msaviewer.SequenceAlignmentRenderer: Returns the SequenceBaseRenderingInfo that must be used to render the specified sequence at the specified position.
renderNucleotides(Graphics2D, File, int, Color, GenomeBrowser) - Method in class org.sing_group.gc4s.genomebrowser.painter.PileupPainter
renderTrack(Track, int) - Method in class org.sing_group.gc4s.msaviewer.DefaultSequenceAlignmentRenderer
renderTrack(Track, int) - Method in interface org.sing_group.gc4s.msaviewer.SequenceAlignmentRenderer: Returns the SequenceBaseRenderingInfo that must be used to render the specified track at the specified position.
repaintGenomeBrowser() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Tells the genome browser to repaint.
repaintTracks() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
requireSameLengthSequences(List<Sequence>) - Static method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Throws an IllegalArgumentException if not all sequences have the same length.
requireStrictPositive(int, String) - Static method in class org.sing_group.gc4s.utilities.Checks: Checks if the provided number is greater than 0.
requireStrictPositive(int) - Static method in class org.sing_group.gc4s.utilities.Checks: Checks if the provided number is greater than or 0.
reset() - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
reset() - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
reset() - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
reset() - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
reset() - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Resets the track painter.
reset() - Method in class org.sing_group.gc4s.genomebrowser.painter.PileupPainter
reset() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration: Sets the default values.
resetToDefault() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel
RowHeaderCell(Object) - Constructor for class org.sing_group.gc4s.visualization.table.RowHeaderTableModel.RowHeaderCell
RowHeaderExtendedJXTable - Class in org.sing_group.gc4s.visualization.table: A RowHeaderExtendedJXTable extends a ExtendedJXTable to allow users creating tables within a row names column.
RowHeaderExtendedJXTable(Object[][], Object[], Object[]) - Constructor for class org.sing_group.gc4s.visualization.table.RowHeaderExtendedJXTable: Instantiates an RowHeaderExtendedJXTable with data in a array or rows, column names and row names.
RowHeaderTableModel - Class in org.sing_group.gc4s.visualization.table: A RowHeaderTableModel wraps a TableModel adding row names.
RowHeaderTableModel(TableModel, Object[]) - Constructor for class org.sing_group.gc4s.visualization.table.RowHeaderTableModel: Creates a new RowHeaderTableModel to wrap m and add row names.
RowHeaderTableModel.RowHeaderCell - Class in org.sing_group.gc4s.visualization.table
RunnableDocumentAdapter - Class in org.sing_group.gc4s.event: A DocumentAdapter implementation that calls the run method of a Runnable every time insertUpdate or removeUpdate are called.
RunnableDocumentAdapter(Runnable) - Constructor for class org.sing_group.gc4s.event.RunnableDocumentAdapter: Creates a new RunnableDocumentAdapter with the specified Runnable.

S

samples(int) - Static method in class org.sing_group.org.gc4s.statistics.table.TableDemoUtils
saveAsPNG(TracksPanel) - Static method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserUtil: Saves the specified TracksPanel as a PNG image.
saveStatus(GenomeBrowser) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState: Updates the variables in this object to store the current status of the specified GenomeBrowser.
seek - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
seekButtonAction() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser
seekCoordinates(int, int) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Sets the visualization range to the one obtained by the specified component graphical coordinates.
seekPositions(long, long) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Sets the visualization range to the one obtained by the specified genomic positions.
SELECTED_FONT - Static variable in class org.sing_group.gc4s.input.FontConfigurationPanel
SelectionMode - Enum in org.sing_group.gc4s.input.filechooser: The selection mode of a JFileChooser.
Sequence - Interface in org.sing_group.gc4s.msaviewer: The interface for defining a sequence.
SequenceAlignmentRenderer - Interface in org.sing_group.gc4s.msaviewer: The interface for rendering sequence alignments.
SequenceBaseRenderingInfo - Class in org.sing_group.gc4s.msaviewer: This class encloses the information used by the SequenceAlignmentRenderer to render a single base of a sequence alignment or track alignment.
SequenceBaseRenderingInfo(Color, Color, boolean, boolean) - Constructor for class org.sing_group.gc4s.msaviewer.SequenceBaseRenderingInfo: Creates a new SequenceBaseRenderingInfo with the specified initial values.
setAllRowsVisible() - Method in class org.sing_group.gc4s.visualization.table.FilterableJXTable: Sets all rows visible (i.e. removes the current row filter).
setAutoAdjustWidth(boolean) - Method in class org.sing_group.gc4s.input.combobox.ExtendedJComboBox: Sets whether the size of the combo box must be adapted to its items width or not.
setBackground(Color) - Method in class org.sing_group.gc4s.ui.ColorListCellRenderer
setBackgroundColorRecursive(JComponent, Color) - Static method in class org.sing_group.gc4s.ui.UIUtils: Sets the background color to aComponent and all its JComponents.
setBlockLength(int) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
setBlocksPerLine(int) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
setChanged() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
setChr(String) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
setClearSelectedFileActionEnabled(boolean) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Establishes whether the clear selected file action should be enabled or not.
setColor(Color) - Method in class org.sing_group.gc4s.input.JColorChooserButton: Sets the component selected color.
setColors(Color, Color) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Establishes the low and high colors of the gradient.
setColumnCellRenderer(int, TableCellRenderer) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Sets the TableCellRenderer for the specified column.
setColumVisibilityActionsEnabled(boolean) - Method in class org.sing_group.gc4s.visualization.table.ExtendedJXTable: Sets the visibility of the column visibility actions at the ColumnControlButton.
setConfiguration(MultipleSequenceAlignmentViewerConfiguration) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Sets the new MultipleSequenceAlignmentViewerConfiguration value.
setConverter(int, CsvTransferHandler.Converter) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Sets the Converter of a model column.
setConverter(int, CsvTransferHandler.Converter) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTransferHandler: Sets the Converter of a model column.
setCoordinates(Coordinates) - Method in class org.sing_group.gc4s.genomebrowser.grid.GridInfo: Sets the component coordinates in which the information should be shown.
setCuadriculaInfo(GridInfo) - Method in class org.sing_group.gc4s.genomebrowser.ToolTipPane: Sets the current GridInfo.
setData(double[][]) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Establishes the data matrix of the heatmap.
setDecimalFormat(DecimalFormat) - Method in class org.sing_group.gc4s.visualization.ColorKeyLegend: Sets the decimal format to format gradient values.
setDecimalFormat(DecimalFormat) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Sets the decimal format.
setElementIntroductionEnabled(boolean) - Method in class org.sing_group.gc4s.input.list.JInputList: Enables or disables the introduction of new elements to the list.
setEmptyTextFieldColor(Color) - Method in class org.sing_group.gc4s.input.text.ExtendedJXTextField: Sets the color that must be set when the text field is empty.
setEnabled(boolean) - Method in class org.sing_group.gc4s.input.RadioButtonsPanel
setEnabled(boolean) - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Sets the enabled status of the toggle button.
setEndLabel(String) - Method in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel: Sets the range end label.
setFilter(FilteredListModel.Filter) - Method in class org.sing_group.gc4s.input.list.FilteredListModel: Sets the model Filter.
setFinalPosition(long) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
setFocusable(Boolean) - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Sets the focusable feature of the toggle button.
setFont(Font) - Method in class org.sing_group.gc4s.visualization.ColorKeyLegend
setFontPreviewVisible(boolean) - Method in class org.sing_group.gc4s.input.FontConfigurationPanel: Sets the visibility of the font preview area.
setFontSize(int) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
setFormat(int, String) - Method in class org.sing_group.gc4s.visualization.table.csv.CsvTable: Sets the format of a model column.
setHeatmapFont(Font) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Sets the heat map font.
setHeatmapRange() - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapPanel
setHideTabBarWhenSingleTab(boolean) - Method in class org.sing_group.gc4s.ui.tabbedpane.ExtendedJTabbedPane: Sets whether the tab bar should be shown when there is only one tab.
setHighColor(Color) - Method in class org.sing_group.gc4s.visualization.ColorKeyLegend: Sets the low high of the gradient.
setHighColor(Color) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Establishes the high color of the gradient.
setHighValue(double) - Method in class org.sing_group.gc4s.visualization.ColorKeyLegend: Sets the high value of the gradient.
setInitialPosition(long) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
setLabelLength(int) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
setLabelTab(int) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
setLeftListElements(List<E>) - Method in class org.sing_group.gc4s.input.list.JParallelListsPanel: Sets the elements that must appear in the left list.
setLowColor(Color) - Method in class org.sing_group.gc4s.visualization.ColorKeyLegend: Sets the low color of the gradient.
setLowColor(Color) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Establishes the low color of the gradient.
setLowValue(double) - Method in class org.sing_group.gc4s.visualization.ColorKeyLegend: Sets the low value of the gradient.
setMaxHistogramValue(int) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
setMaxValue(int) - Method in class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Sets the maximum value.
setMinValue(int) - Method in class org.sing_group.gc4s.input.text.IntegerRangeInputPanel: Sets the minimum value.
setModelAndRenderer(MultipleSequenceAlignmentTracksModel, SequenceAlignmentRenderer) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Sets the new tracks model and alignment renderer.
setMouseZoomEnabled(boolean) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel: Sets whether the scroll mouse zoom should be enabled or not.
setMouseZoomEnabled(boolean) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Sets whether the scroll mouse zoom should be enabled or not.
setNanColor(Color) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Establishes the color for missing values (Double.NaN).
setNimbusKeepAlternateRowColor() - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Sets the value of the property Nimbus.keepAlternateRowColor in UIManager to true.
setNimbusKeepAlternateRowColor(boolean) - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Sets the value of the property Nimbus.keepAlternateRowColor in UIManager.
setNimbusLookAndFeel() - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Sets the Nimbus look and feel.
setNumberOfIntervals(int) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowserState
setOpaqueRecursive(JComponent, boolean) - Static method in class org.sing_group.gc4s.ui.UIUtils: Sets the opacity to aComponent and all its JComponents.
setOptions(Collection<TrackOption>) - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
setOptions(Collection<TrackOption>) - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
setOptions(Collection<TrackOption>) - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
setOptions(Collection<TrackOption>) - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Sets the track painter options.
setOptions(Collection<TrackOption>) - Method in class org.sing_group.gc4s.genomebrowser.painter.PileupPainter
setOptionTrackButtonEnabled(boolean) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Enables (or disables) the track options button.
setPileupColumnsFiltersChanged(boolean) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
setPvalues(Map<String, Double>) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel: Sets the values for the p-values column.
setQvalues(Map<String, Double>) - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel: Sets the values for the q-values column.
setRange(DoubleRange) - Method in class org.sing_group.gc4s.input.DoubleRangeInputPanel: Establishes the range.
setRemoveTrackButtonEnabled(boolean) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Enables (or disables) the remove tracks button.
setRightListElements(List<E>) - Method in class org.sing_group.gc4s.input.list.JParallelListsPanel: Sets the elements that must appear in the right list.
setSelected(Boolean) - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Sets the selection status of the toggle button.
setSelectedCard(Object) - Method in class org.sing_group.gc4s.ui.CardsPanel: Sets the selected card.
setSelectedCsvFileFormat(CsvFormat.FileFormat) - Method in class org.sing_group.gc4s.dialog.ExportCsvDialog: Establishes the selected CsvFormat.FileFormat.
setSelectedCsvFileFormat(CsvFormat.FileFormat) - Method in class org.sing_group.gc4s.input.csv.CsvPanel: Establishes the selected CsvFormat.FileFormat.
setSelectedFile(File) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Sets the selected file.
setSelectedFiles(File[]) - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Sets the selected files.
setSelectedFont(Font) - Method in class org.sing_group.gc4s.input.FontConfigurationPanel: Establishes the selected Font.
setSelectedItem(T) - Method in class org.sing_group.gc4s.input.RadioButtonsPanel: Sets selected the radio button associated to item.
setSelectedRange(DoubleRange) - Method in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel: Sets the specified range in the spinner controls.
setSelectionPath(TreePath) - Method in class org.sing_group.gc4s.input.tree.PathCheckTreeSelectionModel
setSelectionPaths(TreePath[]) - Method in class org.sing_group.gc4s.input.tree.PathCheckTreeSelectionModel
setSequence(String) - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser: Sets the active sequence.
setShowBottomTracks(boolean) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
setShowIndexes(boolean) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
setShowUpperTracks(boolean) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration
setStartLabel(String) - Method in class org.sing_group.gc4s.input.DoubleRangeSpinnerInputPanel: Sets the range start label.
setTrackColor(Color) - Method in class org.sing_group.gc4s.genomebrowser.painter.BamIntervalsPainter
setTrackColor(Color) - Method in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
setTrackColor(Color) - Method in class org.sing_group.gc4s.genomebrowser.painter.IntervalsPainter
setTrackColor(Color) - Method in interface org.sing_group.gc4s.genomebrowser.painter.Painter: Sets the track color.
setUseSharedLastFileFilter(boolean) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanel: Establishes whether the last file filter selected by the user should be shared with other instances or not.
setUseSharedLastFileFilter(boolean) - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanel: Establishes whether the last file filter selected by the user should be shared with other instances or not.
setValue(Object) - Method in interface org.sing_group.gc4s.genomebrowser.TrackOption: Sets the option value.
setValueAt(Object, int, int) - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel
setValuesRange(DoubleRange) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Sets the range of values used to draw the heatmap.
setVisible(boolean) - Method in class org.sing_group.gc4s.dialog.FontConfigurationDialog
setVisible(boolean) - Method in class org.sing_group.gc4s.dialog.ListSelectionDialog
setVisible(InputParameter, boolean) - Method in class org.sing_group.gc4s.input.InputParametersPanel: Makes the specified parameter visible or invisible.
setVisible(boolean) - Method in class org.sing_group.gc4s.input.ItemSelectionDialog
setVisible(boolean) - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentControlConfigurationDialog
setVisible(boolean) - Method in class org.sing_group.gc4s.ui.menu.JPopupMenuActionsVisibility
setVisible(boolean) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapDataOperationsDialog
setVisibleColumnNames(List<String>) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Sets the visible column names.
setVisibleRowNames(List<String>) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Sets the visible row names.
setVisibleRows(List<Integer>) - Method in class org.sing_group.gc4s.visualization.table.FilterableJXTable: Sets visible only row indexes specified in visibleRows.
setxStart(int) - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
setxStop(int) - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
setYCoordinate(double) - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel.RemoveTrackJMenuItem
setYCoordinate() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel.RemoveTrackJMenuItem
setyStart(int) - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
setyStop(int) - Method in class org.sing_group.gc4s.genomebrowser.DraggingPane
shouldBeShown() - Method in class org.sing_group.gc4s.dialog.JOptionPaneMessage: Returns true if the message should be shown.
showComponent(Component, int) - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Shows a JFrame containing the specified component and frame extended state.
showComponent(Component, String, int) - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Shows a JFrame containing the specified component, title and frame extended state.
showComponent(Component, Dimension) - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Shows a JFrame containing the specified component and size
showComponent(Component, String) - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Shows a JFrame containing the specified component and title.
showComponent(Component) - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Shows a JFrame containing the specified component.
showDialog() - Method in class org.sing_group.gc4s.input.JColorChooserButton
showDialog(JDialog) - Static method in class org.sing_group.gc4s.visualization.VisualizationUtils: Shows dialog and ends the application after it is closed.
sortRows(Set<K>) - Method in class org.sing_group.gc4s.visualization.table.MapTableModel
SortTracksDialog - Class in org.sing_group.gc4s.genomebrowser: A dialog that allows users to sort tracks.
SortTracksDialog(GenomeBrowser) - Constructor for class org.sing_group.gc4s.genomebrowser.SortTracksDialog: Creates a new SortTracksDialog for sorting tracks at the specified GenomeBrowser.
statisticalSort() - Method in class org.sing_group.org.gc4s.statistics.table.StatisticsTestTable
StatisticsTestsDataUtils - Class in org.sing_group.org.gc4s.statistics.data.util: A utility class to generate lists of random values.
StatisticsTestsDataUtils() - Constructor for class org.sing_group.org.gc4s.statistics.data.util.StatisticsTestsDataUtils
StatisticsTestsUtils - Class in org.sing_group.org.gc4s.statistics.data.tests: A utility class to help with the usage of tests.
StatisticsTestsUtils() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.StatisticsTestsUtils
StatisticsTestTable<T> - Class in org.sing_group.org.gc4s.statistics.table: A StatisticsTestTable displays the data in a given Dataset<T> and applies the specified Test<T> to each feature (i.e. row) in the dataset.
StatisticsTestTable(Dataset<T>, Test<T>) - Constructor for class org.sing_group.org.gc4s.statistics.table.StatisticsTestTable: Creates a new StatisticsTestTable with the specified dataset and statistic test, without correction.
StatisticsTestTable(Dataset<T>, Test<T>, PValuesCorrection) - Constructor for class org.sing_group.org.gc4s.statistics.table.StatisticsTestTable: Creates a new StatisticsTestTable with the specified dataset, statistic test and correction.
StatisticsTestTableHeaderRenderer - Class in org.sing_group.org.gc4s.statistics.table.ui: A DefaultTableCellRenderer table cell renderer used to display sample names in table headers using different colors.
StatisticsTestTableHeaderRenderer(TableCellRenderer) - Constructor for class org.sing_group.org.gc4s.statistics.table.ui.StatisticsTestTableHeaderRenderer: Creates a new StatisticsTestTableHeaderRenderer that uses the specified default renderer to obtain each table cell.
StatisticsTestTableHeaderRenderer(TableCellRenderer, int) - Constructor for class org.sing_group.org.gc4s.statistics.table.ui.StatisticsTestTableHeaderRenderer: Creates a new StatisticsTestTableHeaderRenderer that uses the specified default renderer to obtain each table cell.
StatisticsTestTableModel<T> - Class in org.sing_group.org.gc4s.statistics.table: The table model for the StatisticsTestTable.
StatisticsTestTableModel(Dataset<T>, boolean) - Constructor for class org.sing_group.org.gc4s.statistics.table.StatisticsTestTableModel: Creates a new StatisticsTestTableModel for the specified dataset.
StatisticsTestTablePanel<T> - Class in org.sing_group.org.gc4s.statistics.table: A panel that shows a StatisticsTestTable along with a progress bar to display the progress of the computation of the p-values.
StatisticsTestTablePanel(Dataset<T>, Test<T>) - Constructor for class org.sing_group.org.gc4s.statistics.table.StatisticsTestTablePanel: Creates a new StatisticsTestTablePanel with the specified dataset and statistic test, without correction.
StatisticsTestTablePanel(Dataset<T>, Test<T>, PValuesCorrection) - Constructor for class org.sing_group.org.gc4s.statistics.table.StatisticsTestTablePanel: Creates a new StatisticsTestTablePanel with the specified dataset, statistic test and correction.
STATUS_ACCEPT - Static variable in class org.sing_group.gc4s.genomebrowser.SortTracksDialog
STATUS_CANCEL - Static variable in class org.sing_group.gc4s.genomebrowser.SortTracksDialog
stepEntered() - Method in class org.sing_group.gc4s.dialog.wizard.WizardStep: This method is invoked when the step is entered.
StringMetrics - Class in org.sing_group.gc4s.utilities: An utility class to compute the size of a String given a Graphics2D and a Font.
StringMetrics(Graphics2D, Font) - Constructor for class org.sing_group.gc4s.utilities.StringMetrics: Creates a new StringMetrics.
StudentsHomocedasticTTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An implementation of AbstractTTest to compute the two-sample t-test under the hypothesis of equal subpopulation variances.
StudentsHomocedasticTTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.StudentsHomocedasticTTest
StudentsPairedTTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An implementation of AbstractTTest to compute the two-sample, paired, two-tailed t-test statistic.
StudentsPairedTTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.StudentsPairedTTest
StudentsTTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An implementation of AbstractTTest to compute the two-sample, two-tailed t-test statistic.
StudentsTTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.StudentsTTest

T

tableChanged(TableModelEvent) - Method in class org.sing_group.gc4s.visualization.table.ColumnSummaryTableCellRenderer
TableDemoUtils - Class in org.sing_group.org.gc4s.statistics.table
TableDemoUtils() - Constructor for class org.sing_group.org.gc4s.statistics.table.TableDemoUtils
TableUtils - Class in org.sing_group.gc4s.jsparklines.util: This class provides utility methods to deal with JTables.
TableUtils() - Constructor for class org.sing_group.gc4s.jsparklines.util.TableUtils
TableUtils - Class in org.sing_group.gc4s.visualization.table: Provides functionalities to deal with tables.
TableUtils() - Constructor for class org.sing_group.gc4s.visualization.table.TableUtils
test(FeatureValues<Boolean>) - Method in class org.sing_group.org.gc4s.statistics.data.tests.AbstractBooleanTest
test(FeatureValues<Number>) - Method in class org.sing_group.org.gc4s.statistics.data.tests.AbstractTTest
test(double[], double[]) - Method in class org.sing_group.org.gc4s.statistics.data.tests.AbstractTTest
test(FeatureValues<String>) - Method in class org.sing_group.org.gc4s.statistics.data.tests.NominalChiSquareTest
test(FeatureValues<Number>) - Method in class org.sing_group.org.gc4s.statistics.data.tests.OneWayAnovaTest
test(double[], double[]) - Method in class org.sing_group.org.gc4s.statistics.data.tests.StudentsHomocedasticTTest
test(double[], double[]) - Method in class org.sing_group.org.gc4s.statistics.data.tests.StudentsPairedTTest
test(double[], double[]) - Method in class org.sing_group.org.gc4s.statistics.data.tests.StudentsTTest
Test<T> - Interface in org.sing_group.org.gc4s.statistics.data.tests: The interface that defines a statistical test that is applied to a FeatureValues object.
test(FeatureValues<T>) - Method in interface org.sing_group.org.gc4s.statistics.data.tests.Test: Returns the p-value that results of the application of the statistical test to the specified values.
TextFieldSelectionFocusListener - Class in org.sing_group.gc4s.event: A FocusAdapter implementation that selects all text in a JTextField when it gains focus.
TextFieldSelectionFocusListener() - Constructor for class org.sing_group.gc4s.event.TextFieldSelectionFocusListener
thatDoes(Action) - Method in class org.sing_group.gc4s.utilities.builder.JButtonBuilder: Sets the button action.
thatDoes(Consumer<ItemEvent>) - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Sets an action to be executed when the button is activated.
ThreeConditionsMeasurementsTableDemo - Class in org.sing_group.org.gc4s.statistics.table
ThreeConditionsMeasurementsTableDemo() - Constructor for class org.sing_group.org.gc4s.statistics.table.ThreeConditionsMeasurementsTableDemo
tmpValues - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
toImage(JComponent, String, File) - Static method in class org.sing_group.gc4s.utilities.ImageIOUtils: Exports the given component as a image into file.
toImage(String, File, Component...) - Static method in class org.sing_group.gc4s.utilities.ImageIOUtils: Exports the given components as a image into file.
TOOLTIP_COLOR - Static variable in class org.sing_group.gc4s.genomebrowser.grid.FileInfo
TOOLTIP_COLOR - Static variable in class org.sing_group.gc4s.genomebrowser.grid.GenomeBrowserInfo
ToolTipPane - Class in org.sing_group.gc4s.genomebrowser: A panel to display GridInfo as tooltips.
ToolTipPane(GenomeBrowser) - Constructor for class org.sing_group.gc4s.genomebrowser.ToolTipPane: Creates a new ToolTipPane for displaying tooltips at the specified GenomeBrowser.
toPngImage(File) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Exports the heatmap as a png image.
toString() - Method in class org.sing_group.gc4s.genomebrowser.GenomeBrowser
toString() - Method in class org.sing_group.gc4s.genomebrowser.grid.Coordinates
toString() - Method in class org.sing_group.gc4s.genomebrowser.grid.FileInfo
toString() - Method in interface org.sing_group.gc4s.genomebrowser.grid.GenericInfo: Return a string representation.
toString() - Method in class org.sing_group.gc4s.genomebrowser.grid.GenomeBrowserInfo
toString() - Method in class org.sing_group.gc4s.genomebrowser.grid.IntervalInfo
toString() - Method in class org.sing_group.gc4s.genomebrowser.grid.PileupInfo
toString() - Method in class org.sing_group.gc4s.genomebrowser.grid.TrackPositionInfo
toString() - Method in class org.sing_group.gc4s.input.combobox.ComboBoxItem
toString() - Method in enum org.sing_group.gc4s.input.csv.CsvFormat.FileFormat
toString() - Method in class org.sing_group.gc4s.input.DoubleRange
toString() - Method in class org.sing_group.gc4s.visualization.table.RowHeaderTableModel.RowHeaderCell
Track - Interface in org.sing_group.gc4s.msaviewer: The interface for defining a track.
trackColor - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
TrackFileProvider - Interface in org.sing_group.gc4s.genomebrowser: An interface for providing track files.
trackHeight - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
TRACKINFO - Static variable in class org.sing_group.gc4s.genomebrowser.grid.GridInfo
trackName - Variable in class org.sing_group.gc4s.genomebrowser.painter.GPPainter
TrackOption - Interface in org.sing_group.gc4s.genomebrowser: An interface for describing track options
TrackOptionsDialog - Class in org.sing_group.gc4s.genomebrowser: A dialog to configure one or more TrackOptions.
TrackOptionsDialog(Collection<TrackOption>) - Constructor for class org.sing_group.gc4s.genomebrowser.TrackOptionsDialog: Creates a new {OptionsDialog for the specified track options.
TRACKPOSITION - Static variable in class org.sing_group.gc4s.genomebrowser.grid.GridInfo
TrackPositionInfo - Class in org.sing_group.gc4s.genomebrowser.grid: A GenericInfo implementation for providing information about track positions.
TrackPositionInfo(String, long) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.TrackPositionInfo: Creates a new TrackPositionInfo instance at the specified base.
TrackPositionInfo(String, long, Color) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.TrackPositionInfo: Creates a new TrackPositionInfo instance at the specified base.
TrackPositionInfo(int, Color) - Constructor for class org.sing_group.gc4s.genomebrowser.grid.TrackPositionInfo: Creates a new TrackPositionInfo.
TracksPanel - Class in org.sing_group.gc4s.genomebrowser: A panel for managing tracks and track painters.
TracksPanel(GenomeBrowser) - Constructor for class org.sing_group.gc4s.genomebrowser.TracksPanel: Creates a new TracksPanel instance for the specified GenomeBrowser.
TracksPanel.RemoveTrackJMenuItem - Class in org.sing_group.gc4s.genomebrowser
transform(double[][], Function<Double, Double>) - Static method in class org.sing_group.gc4s.utilities.MatrixUtils: Transforms the data matrix by applying the transformation function to each single value.
transform(double[][], JHeatMapOperations.Transform) - Static method in class org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations
TwoConditionsBooleanFisherTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An AbstractBooleanTest to compute the Fischer's exact test of independence on a feature values set with two conditions.
TwoConditionsBooleanFisherTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.TwoConditionsBooleanFisherTest: Creates a new TwoConditionsBooleanFisherTest instance.
TwoConditionsBooleanYatesChiSquareTest - Class in org.sing_group.org.gc4s.statistics.data.tests: An AbstractBooleanTest to compute the Chi-squared test of independence with Yates' correction on a feature values set with two conditions.
TwoConditionsBooleanYatesChiSquareTest() - Constructor for class org.sing_group.org.gc4s.statistics.data.tests.TwoConditionsBooleanYatesChiSquareTest: Creates a new TwoConditionsBooleanYatesChiSquareTest instance.
TwoConditionsMeasurementsTableDemo - Class in org.sing_group.org.gc4s.statistics.table
TwoConditionsMeasurementsTableDemo() - Constructor for class org.sing_group.org.gc4s.statistics.table.TwoConditionsMeasurementsTableDemo

U

UIUtils - Class in org.sing_group.gc4s.ui: Provides functionalities to deal with UI components.
UIUtils() - Constructor for class org.sing_group.gc4s.ui.UIUtils
updateDoubleBuffer() - Method in class org.sing_group.gc4s.genomebrowser.TracksPanel
updateHtml() - Method in class org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerPanel

V

valueOf(String) - Static method in enum org.sing_group.gc4s.input.csv.CsvFormat.FileFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sing_group.gc4s.input.filechooser.Mode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sing_group.gc4s.input.filechooser.SelectionMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sing_group.gc4s.input.InputParametersPanel.DescriptionAlignment: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sing_group.gc4s.ui.menu.HamburgerMenu.Size: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sing_group.gc4s.ui.Orientation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sing_group.gc4s.visualization.ColorLegend.Orientation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations.Centering: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations.Transform: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.sing_group.gc4s.input.csv.CsvFormat.FileFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sing_group.gc4s.input.filechooser.Mode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sing_group.gc4s.input.filechooser.SelectionMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sing_group.gc4s.input.InputParametersPanel.DescriptionAlignment: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sing_group.gc4s.ui.menu.HamburgerMenu.Size: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sing_group.gc4s.ui.Orientation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sing_group.gc4s.visualization.ColorLegend.Orientation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations.Centering: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sing_group.gc4s.visualization.heatmap.JHeatMapOperations.Transform: Returns an array containing the constants of this enum type, in the order they are declared.
VerticalLabelUI - Class in org.sing_group.gc4s.ui.text: To rotate a JLabel‘s text vertically, you only need to use this class and pass it as a parameter to the JLabel‘s setUI() method.
VerticalLabelUI(boolean) - Constructor for class org.sing_group.gc4s.ui.text.VerticalLabelUI: Constructs a new VerticalLabelUI with the given orientation.
VisualizationUtils - Class in org.sing_group.gc4s.visualization: Utility methods for showing components.
VisualizationUtils() - Constructor for class org.sing_group.gc4s.visualization.VisualizationUtils

W

withAllowAllFilter(boolean) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Sets whether the "All files" file filter should be used or not.
withAllowAllFilter(boolean) - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder: Sets whether the "All files" file filter should be used or not.
withBrowseIcon(ImageIcon) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Sets the ImageIcon for the browse button.
withBrowseIcon(ImageIcon) - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder: Sets the ImageIcon for the browse button.
withCard(Object, Component) - Method in class org.sing_group.gc4s.ui.CardsPanelBuilder: Adds a new Component as card with the specified label.
withClearSelectedFileOnShow(boolean) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Sets whether to clear the selected file when the file chooser is shown or not.
withClearSelectedFileOnShow(boolean) - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder: Sets whether to clear the selected file when the file chooser is shown or not.
withFileChooser(JFileChooser) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Sets the JFileChooser that will be opened.
withFileChooser(JFileChooser) - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder: Sets the JFileChooser that will be opened.
withFileChooserSelectionMode(SelectionMode) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Sets the JFileChooser selection mode.
withFileChooserSelectionMode(SelectionMode) - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder: Sets the JFileChooser selection mode.
withFileFilters(List<FileFilter>) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Sets the list of FileFilter to use in the file chooser.
withFileFilters(List<FileFilter>) - Method in class org.sing_group.gc4s.input.filechooser.JMultipleFileChooserPanelBuilder: Sets the list of FileFilter to use in the file chooser.
withIcon(Icon) - Method in class org.sing_group.gc4s.utilities.builder.JButtonBuilder: Sets the button icon.
withLabel(String) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Sets the text for the label file.
withLabel(String) - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Sets the label of the toggle button.
withMaxValue(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumBarChartRendererBuilder: Sets the maximum value of the column that must be used.
withMaxValue(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumColoredBarChartRendererBuilder: Sets the maximum value of the column that must be used.
withMaxValue(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumBarChartRendererBuilder: Sets the maximum value of the column that must be used.
withMaxValue(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumColoredBarChartRendererBuilder: Sets the maximum value of the column that must be used.
withMaxValue(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumXYDataSignificanceBarChartRendererBuilder: Sets the maximum value of the column that must be used.
withMaxValue(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumXYDataSignificanceBarChartRendererBuilder: Sets the maximum value of the column that must be used.
withMinValue(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumBarChartRendererBuilder: Sets the minimum value of the column that must be used.
withMinValue(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumColoredBarChartRendererBuilder: Sets the minimum value of the column that must be used.
withMinValue(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumXYDataSignificanceBarChartRendererBuilder: Sets the minimum value of the column that must be used.
withNegativeValuesColor(Color) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumColoredBarChartRendererBuilder: Sets the color that must be used for negative values.
withNegativeValuesColor(Color) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumXYDataSignificanceBarChartRendererBuilder: Sets the color that must be used for negative values.
withNonSignificanteValuesColor(Color) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumXYDataSignificanceBarChartRendererBuilder: Sets the color that must be used for non significant values.
withNonSignificanteValuesColor(Color) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumXYDataSignificanceBarChartRendererBuilder: Sets the color that must be used for non significant values.
withPlotOrientation(PlotOrientation) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumBarChartRendererBuilder
withPlotOrientation(PlotOrientation) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumColoredBarChartRendererBuilder: Sets the plot orientation.
withPlotOrientation(PlotOrientation) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumBarChartRendererBuilder: Sets the plot orientation.
withPlotOrientation(PlotOrientation) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumColoredBarChartRendererBuilder: Sets the plot orientation.
withPlotOrientation(PlotOrientation) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumXYDataSignificanceBarChartRendererBuilder: Sets the plot orientation.
withPlotOrientation(PlotOrientation) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumXYDataSignificanceBarChartRendererBuilder: Sets the plot orientation.
withPositiveValuesColor(Color) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumColoredBarChartRendererBuilder: Sets the color that must be used for positive values.
withPositiveValuesColor(Color) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumColoredBarChartRendererBuilder: Sets the color that must be used for positive values.
withPositiveValuesColor(Color) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumXYDataSignificanceBarChartRendererBuilder: Sets the color that must be used for positive values.
withPositiveValuesColor(Color) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumXYDataSignificanceBarChartRendererBuilder: Sets the color that must be used for positive values.
withRequiredFileSaveExtension(String) - Method in class org.sing_group.gc4s.input.filechooser.JFileChooserPanelBuilder: Only for Mode.SAVE, sets the extension that file must have (e.g.: "txt").
withSelectedCard(String) - Method in class org.sing_group.gc4s.ui.CardsPanelBuilder: Sets the name of the card that must be selected by default.
withSelectedIcon(ImageIcon) - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Sets the selected icon status of the toggle button.
withSelectionLabel(String) - Method in class org.sing_group.gc4s.ui.CardsPanelBuilder: Sets the selection label shown to the user in the main panel.
withSignificanceLevel(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumMinimumXYDataSignificanceBarChartRendererBuilder: Sets the significance level that must be used by the renderer.
withSignificanceLevel(Double) - Method in class org.sing_group.gc4s.jsparklines.builders.barchartrenderer.MaximumXYDataSignificanceBarChartRendererBuilder: Sets the significance level that must be used by the renderer.
withText(String) - Method in class org.sing_group.gc4s.utilities.builder.JButtonBuilder: Sets the button text.
withTooltip(String) - Method in class org.sing_group.gc4s.utilities.builder.JButtonBuilder: Sets the button tooltip.
withTooltip(String) - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Sets the tooltip of the toggle button.
withTooltip(Function<Boolean, String>) - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Sets a function that generates the tooltip of the toggle button using the selection state of the toggle button.
withUnselectedIcon(ImageIcon) - Method in class org.sing_group.gc4s.utilities.builder.JToggleButtonBuilder: Sets the unselection icon of the toggle button.
Wizard - Class in org.sing_group.gc4s.dialog.wizard: A wizard dialog that allows showing a list of WizardStep.
Wizard(Window, String, List<WizardStep>) - Constructor for class org.sing_group.gc4s.dialog.wizard.Wizard: Creates a new Wizard with the specified title and WizardSteps.
wizardFinished() - Method in class org.sing_group.gc4s.dialog.wizard.Wizard
WizardStep - Class in org.sing_group.gc4s.dialog.wizard: An abstract class that represents a step in a Wizard.
WizardStep() - Constructor for class org.sing_group.gc4s.dialog.wizard.WizardStep
WizardStepAdapter - Class in org.sing_group.gc4s.dialog.wizard.event: An abstract adapter class for receiving wizard step events.
WizardStepAdapter() - Constructor for class org.sing_group.gc4s.dialog.wizard.event.WizardStepAdapter
wizardStepCompleted(WizardStepEvent) - Method in class org.sing_group.gc4s.dialog.wizard.event.WizardStepAdapter
wizardStepCompleted(WizardStepEvent) - Method in interface org.sing_group.gc4s.dialog.wizard.event.WizardStepListener: Invoked when the wizard step is completed.
wizardStepCompleted(WizardStepEvent) - Method in class org.sing_group.gc4s.dialog.wizard.Wizard
WizardStepEvent - Class in org.sing_group.gc4s.dialog.wizard.event: A WizardStepEvent is used to notify interested parties that state has changed in the WizardStep source.
WizardStepEvent(WizardStep) - Constructor for class org.sing_group.gc4s.dialog.wizard.event.WizardStepEvent
WizardStepListener - Interface in org.sing_group.gc4s.dialog.wizard.event: The listener interface for receiving wizard step events.
wizardStepNextButtonTooltipChanged(String) - Method in class org.sing_group.gc4s.dialog.wizard.event.WizardStepAdapter
wizardStepNextButtonTooltipChanged(String) - Method in interface org.sing_group.gc4s.dialog.wizard.event.WizardStepListener: Invoked when the wizard step wants to change the next button tooltip.
wizardStepNextButtonTooltipChanged(String) - Method in class org.sing_group.gc4s.dialog.wizard.Wizard
wizardStepUncompleted(WizardStepEvent) - Method in class org.sing_group.gc4s.dialog.wizard.event.WizardStepAdapter
wizardStepUncompleted(WizardStepEvent) - Method in interface org.sing_group.gc4s.dialog.wizard.event.WizardStepListener: Invoked when the wizard step is uncompleted.
wizardStepUncompleted(WizardStepEvent) - Method in class org.sing_group.gc4s.dialog.wizard.Wizard
WorkingDialog - Class in org.sing_group.gc4s.dialog: A WorkingDialog shows a progress in work dialog with an indeterminate progress bar and a label.
WorkingDialog(Window, String, String) - Constructor for class org.sing_group.gc4s.dialog.WorkingDialog: Constructs a new WorkingDialog instance with the specified parameters.
WorkingDialog(Window, String, String, ImageIcon) - Constructor for class org.sing_group.gc4s.dialog.WorkingDialog: Constructs a new WorkingDialog instance with the specified parameters.

Y

YesNoTableCellRenderer - Class in org.sing_group.org.gc4s.statistics.table.ui: A DefaultTableCellRenderer extension to display boolean values as YES (for true) and NO (false).
YesNoTableCellRenderer() - Constructor for class org.sing_group.org.gc4s.statistics.table.ui.YesNoTableCellRenderer

Z

zoomIn(double) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Zooms in the heatmap by a factor of scale.
zoomOut(double) - Method in class org.sing_group.gc4s.visualization.heatmap.JHeatMap: Zooms out the heatmap by a factor of scale.

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