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

## A

actionPerformed(ActionEvent) - Method in class RNAstructure_java_interface.source.windows.InternalWindow
actionPerformed(ActionEvent) - Method in class RNAstructure_java_utilities.RNAstructureMenu
activate() - Method in class RNAstructure_java_interface.source.windows.MultilignWindow
activate() - Method in class RNAstructure_java_interface.source.windows.MultiWindow
  Activate data input for this window.
activate() - Method in class RNAstructure_java_interface.source.windows.TurboFoldWindow
activateMultilign() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
activateTurboFold() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
addAnnotationProbability(String) - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
addAnnotationSHAPE(String) - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
addBackendTuple(String, String) - Method in class RNAstructure_java_interface.source.windows.MultilignWindow
addBackendTuple(String, String) - Method in class RNAstructure_java_interface.source.windows.MultiWindow
  Add a tuple to the calculation back end.
addBackendTuple(String, String) - Method in class RNAstructure_java_interface.source.windows.TurboFoldWindow
addCheckBoxMenuItem(String, String) - Method in class RNAstructure_java_utilities.RNAstructureMenu
  Add a check box menu item with rollover text.
addClosingListener(JDialog) - Method in class RNAstructure_java_drawing.source.runners.RunnerTemplate
  Add a listener to the dialog spawned by this template that exits the application when the dialog is closed.
addGeneralSection() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Add a menu section of general constraints commands.
addMaxPairingDistanceSection() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Add a menu section that handles maximum pairing distance.
addMenuItem(String, String) - Method in class RNAstructure_java_utilities.RNAstructureMenu
  Add a plain text menu item with rollover text.
addMenuItem(String, String, char) - Method in class RNAstructure_java_utilities.RNAstructureMenu
  Add a plain text menu item with rollover text and a key stroke which can activate it.
addMenuItem(String, String, String) - Method in class RNAstructure_java_utilities.RNAstructureMenu
  Add a plain text menu item with rollover text and a key stroke which can activate it.
addMultilignTuple(String, String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
addSaveRestoreSection() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Add a menu section that handles saving and restoring constraints.
addSHAPESection() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Add a menu section that handles SHAPE constraints.
addShowResetSection() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Add a menu section that handles showing and resetting constraints.
addTurboFoldTuple(String, String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
ALWAYS - Static variable in class RNAstructure_java_utilities.ScrollerPane
  A generic constant symbolizing that a scroll bar must always be used.
AnnotationMenu - Class in RNAstructure_java_drawing.source.menus
  A class that handles a menu which can annotate a drawn structure.
AnnotationMenu(StructureDialog) - Constructor for class RNAstructure_java_drawing.source.menus.AnnotationMenu
  Constructor.
ApplicationRootFrame - Class in RNAstructure_java_interface.source.startup
  A class that creates the application frame of the RNAstructure GUI.
ApplicationRootFrame() - Constructor for class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Constructor.
areas - Variable in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  The array of text areas in this window.

## B

backend - Variable in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  The back end object that reads data for dot plots.
backend - Variable in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  The back end object that reads data for structures.
backend - Variable in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  The back end calculator that's linked to this menu.
backend - Variable in class RNAstructure_java_interface.source.windows.InternalWindow
  The back end calculator that's linked to this window.
bar - Variable in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  The main RNAstructure toolbar.
BorderBuilder - Class in RNAstructure_java_utilities
  A class that places a border type on a specified component type.
BorderBuilder() - Constructor for class RNAstructure_java_utilities.BorderBuilder
BorderedButtonPanel - Class in RNAstructure_java_utilities
  A class that produces a panel which contains a button with a border around it.
BorderedButtonPanel(ActionListener, String) - Constructor for class RNAstructure_java_utilities.BorderedButtonPanel
  Text Constructor.
BorderedButtonPanel(ActionListener, String, int) - Constructor for class RNAstructure_java_utilities.BorderedButtonPanel
  Border Constructor.
buildAllSubDataStructure(String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildBackPanel() - Method in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Create the gray back panel that fills the main frame.
buildBifoldDataStructure(String, String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildBipartitionDataStructure(String, String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildButtonPanel() - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  Make the button panel at the bottom of the window.
buildDialog(String, NumberField...) - Method in class RNAstructure_java_utilities.ValueSelectionDialog
  Build the value selection dialog.
buildDynalignAlignmentMenu() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Build a complete menu that handles Dynalign alignment constraints.
buildDynalignDataStructure(String, String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildEfn2DataStructure(String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildFoldDataStructure(String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildInfoLabel() - Method in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Create the label at the bottom of the main frame.
buildInputRegion(int, String) - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  Build a text input region for this window.
buildLegend(String...) - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Build the legend grid for this panel.
buildMaxExpectDataStructure(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildMaxLoopMenu() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Build a complete menu that handles maximum loop size.
buildOligoScreenDataStructure() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildOligoWalkDataStructure(String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildPartitionDataStructure(String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildProbKnotDataStructure(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildRefoldDynalignDataStructure(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildRefoldSingleDataStructure(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildRemovePseudoknotsDataStructure(String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildResultsWindow(String, int, int, int) - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow
  Build the results window for this OligoWalk calculation.
buildSpecificOptionsPanel() - Method in class RNAstructure_java_interface.source.windows.MultilignWindow
buildSpecificOptionsPanel() - Method in class RNAstructure_java_interface.source.windows.MultiWindow
  Build an input options box specific to this window.
buildSpecificOptionsPanel() - Method in class RNAstructure_java_interface.source.windows.TurboFoldWindow
buildStochasticDataStructure(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
buildTemperatureMenu() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Build a complete menu that handles temperature.
buildToolBar() - Method in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Build the main RNAstructure toolbar.
buildUnimolecularMenu() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Build a complete menu that handles if unimolecular pairs are allowed.

## C

canFoldOligoOligo(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
canFoldOligoSelf(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
cards - Variable in class RNAstructure_java_interface.source.windows.TurboFoldWindow
  The layout that holds the dynamic options applicable to a mode.
checkOS() - Static method in class RNAstructure_java_utilities.MacChecker
  Check the OS to see if it's a Mac, and if it is, set a few system properties to make things more "Mac-like."
checkValue() - Method in class RNAstructure_java_utilities.NumberField
  Check the value of a field to make sure it's valid.
checkValue() - Method in class RNAstructure_java_utilities.NumberField.DoubleField
checkValue() - Method in class RNAstructure_java_utilities.NumberField.FloatField
checkValue() - Method in class RNAstructure_java_utilities.NumberField.IntegerField
CIRCLED_NUCS - Static variable in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Boolean that tells whether a structure's nucleotides are circled.
clearAnnotation() - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Clear annotation from this dialog.
clearDynalignAlignmentConstraints() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
clearFoldingConstraints(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
CLOCKWISE_STRUCTURE - Static variable in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Boolean that tells whether a structure is rendered clockwise.
columnWidth - Variable in class RNAstructure_java_interface.source.windows.MultiWindow
  The width of each column of the window (input controls in column 1, sequence set in column 2).
combineFileNames(String, String, String) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Combine two file names into a new file name.
components - Variable in class RNAstructure_java_utilities.FieldPanel
  The components on this panel (buttons or labels).
constraints - Variable in class RNAstructure_java_interface.source.windows.ModuleWindow
  The GridBagConstraints for this window.
ConstraintsMenu - Class in RNAstructure_java_interface.source.menus
  A class that creates a folding constraints menu.
ConstraintsMenu(RNAstructureBackendCalculator) - Constructor for class RNAstructure_java_interface.source.menus.ConstraintsMenu
  General Constructor.
ConstraintsMenu.NucOrHelixDialog - Class in RNAstructure_java_interface.source.menus
  An inner class which creates a dialog that sets constraints on single nucleotides or helices.
ConstraintsMenu.NucOrHelixDialog(String, String) - Constructor for class RNAstructure_java_interface.source.menus.ConstraintsMenu.NucOrHelixDialog
  Constructor.
convertToolTips() - Method in class RNAstructure_java_interface.source.menus.RolloverMenu
  Convert tooltips to rollover text.
createAdditionalControls() - Method in class RNAstructure_java_drawing.source.menus.DotsMenu.RangeDialog
createAdditionalControls() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.OligoSelectionDialog
createAdditionalControls() - Method in class RNAstructure_java_utilities.ValueSelectionDialog
  Create any additional controls that need to show up on this dialog.
createDefaultMenuBar(RNAstructureMenu...) - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Create the image dialog's default menu bar.
createDisabled(String) - Static method in class RNAstructure_java_utilities.FileField
  Create a disabled file input field.
createDNA() - Static method in class RNAstructure_java_interface.source.menus.NucleicAcidMenu
  Create a DNA menu.
createDrawnImage(Graphics2D) - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Create the image drawn on this panel.
createDrawnImage(Graphics2D) - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
createDrawnImage(Graphics2D) - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
createEmptyBox(String) - Static method in class RNAstructure_java_utilities.HTMLCheckBox
  Create an empty check box.
createEnabled(String) - Static method in class RNAstructure_java_utilities.FileField
  Create an enabled file input field.
createInputPanel() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow
  Create the panel which holds input controls.
createResultsPanel() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow
  Create the panel which holds results data.
createRNA() - Static method in class RNAstructure_java_interface.source.menus.NucleicAcidMenu
  Create a RNA menu.
createSelectedBox(String) - Static method in class RNAstructure_java_utilities.HTMLCheckBox
  Create a selected check box.
createSelectionAction() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog.ZoomDialog
createSelectionAction() - Method in class RNAstructure_java_drawing.source.menus.DotsMenu.ColorDialog
createSelectionAction() - Method in class RNAstructure_java_drawing.source.menus.DotsMenu.RangeDialog
createSelectionAction() - Method in class RNAstructure_java_drawing.source.menus.StructureMenu.MoveDialog
createSelectionAction() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu.NucOrHelixDialog
createSelectionAction() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.OligoSelectionDialog
createSelectionAction() - Method in class RNAstructure_java_utilities.ValueSelectionDialog
  Create the action that occurs once values are selected.
currentColor - Variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow.BarButton
  The current color painted on this button.

## D

data - Variable in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  The array of data for a particular structure.
defaultColor - Variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow.BarButton
  The default color forthis button.
defaultFile - Variable in class RNAstructure_java_utilities.FileChooser
  The default file name for this file chooser, if necessary.
delete() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
delete() - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
delete() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
delete_DotPlotBackend(long) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
delete_RNAstructureBackendCalculator(long) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
delete_StructureBackend(long) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
deleteBackendTuple(int) - Method in class RNAstructure_java_interface.source.windows.MultilignWindow
deleteBackendTuple(int) - Method in class RNAstructure_java_interface.source.windows.MultiWindow
  Delete a tuple from the calculation back end.
deleteBackendTuple(int) - Method in class RNAstructure_java_interface.source.windows.TurboFoldWindow
deleteMultilignTuple(long) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
deleteTurboFoldTuple(long) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
deselect() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.BarButton
  Deselect this button.
determineOligoMaximum(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
dialog - Variable in class RNAstructure_java_drawing.source.menus.AnnotationMenu
  The structure panel connected to this menu.
dialog - Variable in class RNAstructure_java_drawing.source.menus.DotsMenu
  The structure dialog connected to this menu.
dialog - Variable in class RNAstructure_java_drawing.source.menus.PlotMenu
  The plot dialog connected to this menu.
dialog - Variable in class RNAstructure_java_drawing.source.menus.StructureMenu
  The structure dialog connected to this menu.
dialog - Variable in class RNAstructure_java_interface.source.windows.DrawingWindow
  The image dialog connected to this window.
dialogHandler - Variable in class RNAstructure_java_interface.source.windows.InternalWindow
  A dialog handler to show any simple dialog messages that pop up from this window.
doActions(String) - Method in class RNAstructure_java_interface.source.windows.DrawingWindow
  Do any actions specific to this window.
doActions(String) - Method in class RNAstructure_java_interface.source.windows.InternalWindow
  Do any actions specific to this window.
doActions(String) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
doActions(String) - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
doAdditionalCheck(char) - Method in class RNAstructure_java_utilities.NumberField
  Do any additional necessary checks on a key character to make sure it's valid to be output.
doAdditionalCheck(char) - Method in class RNAstructure_java_utilities.NumberField.DoubleField
doAdditionalCheck(char) - Method in class RNAstructure_java_utilities.NumberField.FloatField
doMenuActions(String) - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog.PrintMenu
doMenuActions(String) - Method in class RNAstructure_java_drawing.source.menus.AnnotationMenu
doMenuActions(String) - Method in class RNAstructure_java_drawing.source.menus.DotsMenu
doMenuActions(String) - Method in class RNAstructure_java_drawing.source.menus.PlotMenu
doMenuActions(String) - Method in class RNAstructure_java_drawing.source.menus.StructureMenu
doMenuActions(String) - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
doMenuActions(String) - Method in class RNAstructure_java_interface.source.menus.FileMenu
doMenuActions(String) - Method in class RNAstructure_java_interface.source.menus.HelpMenu
doMenuActions(String) - Method in class RNAstructure_java_interface.source.menus.NucleicAcidMenu
doMenuActions(String) - Method in class RNAstructure_java_interface.source.menus.RolloverMenu
doMenuActions(String) - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.OligoWalkResultsMenu
doMenuActions(String) - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow.EditMenu
doMenuActions(String) - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow.ReadMenu
doMenuActions(String) - Method in class RNAstructure_java_utilities.RNAstructureMenu
  Do any actions specific to this menu.
doOpen() - Static method in class RNAstructure_java_utilities.FileChooser
  Create a file chooser that selects a file to open.
doRevalidate() - Method in class RNAstructure_java_interface.source.windows.DrawingWindow
  Revalidate the drawing window.
doSave() - Static method in class RNAstructure_java_utilities.FileChooser
  Create a file chooser that selects a file to save.
doSave(String) - Static method in class RNAstructure_java_utilities.FileChooser
  Create a file chooser that selects a file to save, and will have a default file filled in.
DotPlotBackend - Class in RNAstructure_java_drawing.source.proxy
DotPlotBackend(long, boolean) - Constructor for class RNAstructure_java_drawing.source.proxy.DotPlotBackend
DotPlotBackend() - Constructor for class RNAstructure_java_drawing.source.proxy.DotPlotBackend
DotPlotBackend_getBounds(long, DotPlotBackend) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getColors(long, DotPlotBackend) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getCurrentMax(long, DotPlotBackend) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getCurrentMin(long, DotPlotBackend) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getDefaultMax(long, DotPlotBackend) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getDefaultMin(long, DotPlotBackend) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getDotData(long, DotPlotBackend, int, int) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getDotDataByLocation(long, DotPlotBackend, int, int, double) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getGridLine(long, DotPlotBackend, int) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getLegendData(long, DotPlotBackend) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getLength(long, DotPlotBackend) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_readData(long, DotPlotBackend, String, int) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_setColors(long, DotPlotBackend, int) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_setRange(long, DotPlotBackend, double, double) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_writePostscriptFile(long, DotPlotBackend, String) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_writeStructuresFile(long, DotPlotBackend, String, String) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_writeSVGFile(long, DotPlotBackend, String) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackend_writeTextFile(long, DotPlotBackend, String) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotPlotBackendProxyJNI - Class in RNAstructure_java_drawing.source.proxy
DotPlotBackendProxyJNI() - Constructor for class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
DotsMenu - Class in RNAstructure_java_drawing.source.menus
  A class that handles a menu which can manipulate a drawn dot plot.
DotsMenu(PlotDialog) - Constructor for class RNAstructure_java_drawing.source.menus.DotsMenu
  Constructor.
DotsMenu.ColorDialog - Class in RNAstructure_java_drawing.source.menus
  An inner class which creates a dialog that sets the number of colors in a dot plot.
DotsMenu.ColorDialog() - Constructor for class RNAstructure_java_drawing.source.menus.DotsMenu.ColorDialog
  Constructor.
DotsMenu.RangeDialog - Class in RNAstructure_java_drawing.source.menus
  An inner class which creates a dialog that sets the range of values in a dot plot.
DotsMenu.RangeDialog() - Constructor for class RNAstructure_java_drawing.source.menus.DotsMenu.RangeDialog
  Constructor.
DrawingWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for displaying a drawing window.
DrawingWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.DrawingWindow
  File Constructor.
DrawingWindow(String, int) - Constructor for class RNAstructure_java_interface.source.windows.DrawingWindow
  Strand Constructor.
DynalignFoldWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the Dynalign module, which calculates common structures for two strands of nucleic acids.
DynalignFoldWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.DynalignFoldWindow
  Constructor.
DynalignRefoldWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the Dynalign refold module, which refolds a previous Dynalign calculation from a save file.
DynalignRefoldWindow() - Constructor for class RNAstructure_java_interface.source.windows.DynalignRefoldWindow
  Constructor.
DynamicMenuBar - Class in RNAstructure_java_interface.source.menus
  A class that creates a menu bar.
DynamicMenuBar(InternalWindow, RolloverMenu...) - Constructor for class RNAstructure_java_interface.source.menus.DynamicMenuBar
  Constructor.

## E

edited - Variable in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  A boolean, true if the sequence has been edited, false if not.
Efn2Window - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the efn2 (Energy Function 2) module, which calculates the folding free energy of structures.
Efn2Window(String) - Constructor for class RNAstructure_java_interface.source.windows.Efn2Window
  Constructor.
enableMenus() - Method in class RNAstructure_java_interface.source.menus.DynamicMenuBar
  Enable the menus on this menu bar.
error - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The error message generated while building this panel, if any.
error - Variable in class RNAstructure_java_interface.source.windows.DrawingWindow
  True if an error occurred building this window, false if not.
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.DynalignFoldWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.DynalignRefoldWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.Efn2Window
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.FoldDoubleWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.FoldSingleWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.FoldSuboptimalWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.MaxExpectWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Execute an action within a particular module.
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.MultilignWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.MultiWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.OligoScreenWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.PartitionDoubleWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.PartitionSingleWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.ProbKnotWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.PseudoknotWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.RefoldWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.StochasticWindow
executeModuleAction(String) - Method in class RNAstructure_java_interface.source.windows.TurboFoldWindow

## F

FieldPanel - Class in RNAstructure_java_utilities
  A class that creates a panel which holds aligned input fields.
FieldPanel(JTextField[]) - Constructor for class RNAstructure_java_utilities.FieldPanel
  Constructor.
FieldPanel.FilePanel - Class in RNAstructure_java_utilities
  An inner class that handles a panel which contains file fields.
FieldPanel.FilePanel(ActionListener, FileField...) - Constructor for class RNAstructure_java_utilities.FieldPanel.FilePanel
  Constructor.
FieldPanel.NumberPanel - Class in RNAstructure_java_utilities
  An inner class that handles a panel which contains numeric data fields.
FieldPanel.NumberPanel(NumberField...) - Constructor for class RNAstructure_java_utilities.FieldPanel.NumberPanel
  Constructor.
fields - Variable in class RNAstructure_java_utilities.ValueSelectionDialog
  The array of number fields this dialog holds.
file - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The file that is drawn in some way on this panel.
FileChooser - Class in RNAstructure_java_utilities
  A class that creates a file chooser so the user can select a file to open or save.
FileChooser(FileChooser.Types, String) - Constructor for class RNAstructure_java_utilities.FileChooser
  Constructor.
FileChooser.Types - Enum in RNAstructure_java_utilities
  An enum that holds the possible values for the file chooser type.
FileChooser.Types() - Constructor for enum RNAstructure_java_utilities.FileChooser.Types
FileField - Class in RNAstructure_java_utilities
  A class that creates a text field which holds a file name.
FileField(String, boolean) - Constructor for class RNAstructure_java_utilities.FileField
  Constructor.
FileMenu - Class in RNAstructure_java_interface.source.menus
  A class that creates a "File" menu.
FileMenu(InternalWindow) - Constructor for class RNAstructure_java_interface.source.menus.FileMenu
  Constructor.
finalize() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
finalize() - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
finalize() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
finishModule(String) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Handle finishing of a module.
flip() - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Flip the structure image horizontally.
flip() - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
FoldDoubleWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the bifold module, which folds two strands of nucleic acids into their likely hybrid structure.
FoldDoubleWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.FoldDoubleWindow
  Constructor.
foldOligo(String, int, boolean, boolean, String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
FoldSingleWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the Fold module, which folds a strand of nucleic acids into their likely lowest free energy structure.
FoldSingleWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.FoldSingleWindow
  Constructor.
FoldSuboptimalWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the AllSub module, which calculates the free energy of a varied group of suboptimal structures.
FoldSuboptimalWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.FoldSuboptimalWindow
  Constructor.
formatSequence() - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  Format the sequence in the text area.

## G

getAlignment() - Method in class RNAstructure_java_utilities.FileChooser
  Select an alignment file.
getAllOligoData(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getArea(int) - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  Get a text area from this window.
getBounds() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getBracket() - Method in class RNAstructure_java_utilities.FileChooser
  Select a dot bracket file.
getColors() - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Get the range of colors allowed in this dialog.
getColors() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getConstraints() - Method in class RNAstructure_java_utilities.FileChooser
  Select a constraints file.
getCPtr(DotPlotBackend) - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getCPtr(StructureBackend) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackend
getCPtr(RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getCT() - Method in class RNAstructure_java_utilities.FileChooser
  Select a CT file.
getCurrentBounds() - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Get the current bounds allowed in this dialog.
getCurrentMax() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getCurrentMin() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getDefaultBounds() - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Get the default bounds allowed in this dialog.
getDefaultMax() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getDefaultMin() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getDisplayedOligo(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getDotData(int, int) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getDotDataByLocation(int, int, double) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getDotPlot() - Method in class RNAstructure_java_utilities.FileChooser
  Select a dot plot file.
getDynalign() - Method in class RNAstructure_java_utilities.FileChooser
  Select a Dynalign save file.
getDynalignAlignmentConstraints() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getDynalignAlignmentWindowSize() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getDynalignStructureWindowSize() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getField(int) - Method in class RNAstructure_java_utilities.FieldPanel.NumberPanel
  Get a particular input field.
getFile() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Get the file drawn on this dialog.
getFile(int) - Method in class RNAstructure_java_utilities.FieldPanel.FilePanel
  Get a file name from a particular input field.
getFile() - Method in class RNAstructure_java_utilities.FileField
  Get the file name in the field.
getFolding() - Method in class RNAstructure_java_utilities.FileChooser
  Select a folding save file.
getFoldingConstraints(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getFoldWindowSize() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getFrame() - Static method in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Get the top frame of the application.
getGraphRegionBegin() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getGraphRegionEnd() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getGridLine(int) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getHelix() - Method in class RNAstructure_java_utilities.FileChooser
  Select a structure helix file.
getImage(String) - Static method in class RNAstructure_java_utilities.ImageGrabber
  Create an image.
getImageData() - Method in class RNAstructure_java_interface.source.windows.DrawingWindow
  Get the data from a dialog to put in this window.
getImageIcon(String) - Static method in class RNAstructure_java_utilities.ImageGrabber
  Create an image icon.
getImageLabel(String) - Static method in class RNAstructure_java_utilities.ImageGrabber
  Create an image label.
getInputControl(int) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Get a particular input control from the content pane.
getInputControl(Container, int) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Get a particular input control from a given container.
getLegendData() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getLength() - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
getList() - Method in class RNAstructure_java_utilities.FileChooser
  Select an oligo list file.
getMaxConstraintIndex(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getMaxLoop() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getMaxPair() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getMostRecentFrame() - Method in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Get the most recent internal frame in the application.
getMostStableOligo() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getMultilignCT(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getMultilignMaxPairs() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getMultilignSequenceSetData() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getNumMultilignSequences() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getNumSequences() - Method in class RNAstructure_java_interface.source.windows.MultilignWindow
getNumSequences() - Method in class RNAstructure_java_interface.source.windows.MultiWindow
  Get the number of sequences this window handles.
getNumSequences() - Method in class RNAstructure_java_interface.source.windows.TurboFoldWindow
getNumTurboFoldSequences() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getOligoLabelData(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getOligoTargetLength() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getOligoTargetSequence() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getOUT() - Method in class RNAstructure_java_utilities.FileChooser
  Select a general OUT file.
getPartition() - Method in class RNAstructure_java_utilities.FileChooser
  Select a partition function save file.
getPostscript() - Method in class RNAstructure_java_utilities.FileChooser
  Select a Postscript image file.
getProgressNumber() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getRefoldWindowSize() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getReport() - Method in class RNAstructure_java_utilities.FileChooser
  Select an oligo report file.
getScale() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Get the scale at which the image is zoomed.
getSelectedIndex() - Method in class RNAstructure_java_utilities.RadioButtonPanel
  Get the index of the selected button from this panel.
getSelectedItem() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.StringComboBox
getSelectedName() - Method in class RNAstructure_java_utilities.RadioButtonPanel
  Get the command of the selected button from this panel.
getSequence() - Method in class RNAstructure_java_utilities.FileChooser
  Select a sequence file.
getSequenceComment() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getSequenceData() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getSequenceExtended() - Method in class RNAstructure_java_utilities.FileChooser
  Select a sequence file in its extended context, with more than its usual possible file types.
getSequenceSetAsString() - Method in class RNAstructure_java_interface.source.windows.MultilignWindow
getSequenceSetAsString() - Method in class RNAstructure_java_interface.source.windows.MultiWindow
  Get a representation of the sequence set as a string.
getSequenceSetAsString() - Method in class RNAstructure_java_interface.source.windows.TurboFoldWindow
getSequenceTitle() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getSHAPE() - Method in class RNAstructure_java_utilities.FileChooser
  Select a SHAPE file.
getSpinner() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.SpinnerPanel
  Get the spinner.
getStructureData(int) - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
getStructureType() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getSuboptimalAbsoluteDiff() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getSuboptimalPercentDiff() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getSVG() - Method in class RNAstructure_java_utilities.FileChooser
  Select an SVG file.
getTemperature() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getToolBar() - Method in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Get the toolbar.
getTurboFoldCT(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getTurboFoldSaveFile(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getTurboFoldSequenceSetData() - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
getValue() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.SpinnerPanel
  Get the spinner value.
getValue() - Method in class RNAstructure_java_utilities.NumberField.DoubleField
getValue() - Method in class RNAstructure_java_utilities.NumberField.FloatField
getValue() - Method in class RNAstructure_java_utilities.NumberField
  Get the text field's numeric value.
getValue() - Method in class RNAstructure_java_utilities.NumberField.IntegerField
group - Variable in class RNAstructure_java_utilities.RadioButtonPanel
  The button group connected to this panel.
group2 - Variable in class RNAstructure_java_utilities.RadioButtonPanel
  The button group, as a list, for ease of access to each.

## H

hasPairs - Variable in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Whether the current structure has pairs.
HelpMenu - Class in RNAstructure_java_interface.source.menus
  A class that creates a "Help" menu.
HelpMenu() - Constructor for class RNAstructure_java_interface.source.menus.HelpMenu
  Constructor.
HTMLCheckBox - Class in RNAstructure_java_utilities
  A class that creates a check box whose text is HTML.
HTMLCheckBox(String, boolean) - Constructor for class RNAstructure_java_utilities.HTMLCheckBox
  Constructor.

## I

ImageDialog - Class in RNAstructure_java_drawing.source.dialogs
  A printable and zoomable dialog that holds drawn images.
ImageDialog(String) - Constructor for class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Constructor.
ImageDialog.PrintMenu - Class in RNAstructure_java_drawing.source.dialogs
  An inner class which creates a print menu.
ImageDialog.PrintMenu() - Constructor for class RNAstructure_java_drawing.source.dialogs.ImageDialog.PrintMenu
  Constructor.
ImageDialog.ZoomDialog - Class in RNAstructure_java_drawing.source.dialogs
  An inner class which creates a dialog that zooms a structure.
ImageDialog.ZoomDialog() - Constructor for class RNAstructure_java_drawing.source.dialogs.ImageDialog.ZoomDialog
  Constructor.
imageDialogs - Variable in class RNAstructure_java_interface.source.windows.MultiWindow
  The list of drawing windows shown after the calculation is done.
ImageGrabber - Class in RNAstructure_java_utilities
  A class that creates images in various contexts for the RNAstructure GUI.
ImageGrabber() - Constructor for class RNAstructure_java_utilities.ImageGrabber
initial - Variable in class RNAstructure_java_utilities.NumberField
  The initial default value of the field.
insertMenuItem(String, String, ActionListener, int) - Method in class RNAstructure_java_utilities.RNAstructureMenu
  Insert a plain text menu item with rollover text.
InternalWindow - Class in RNAstructure_java_interface.source.windows
  A class that holds internal frames for the RNAstructure GUI.
InternalWindow() - Constructor for class RNAstructure_java_interface.source.windows.InternalWindow
  Constructor.
isError() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Get whether this panel ran into an error while being built.
isError() - Method in class RNAstructure_java_interface.source.windows.DrawingWindow
  Get whether this window encountered an error.
isError() - Method in class RNAstructure_java_utilities.FieldPanel.FilePanel
  Get whether any fields are empty; an empty field is an error.
isInputWindow - Variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow
  A boolean that tells whether this window is an input window or not.
isMac() - Static method in class RNAstructure_java_utilities.MacChecker
  Get whether the current OS is a Mac.
isRNA - Variable in class RNAstructure_java_interface.source.windows.ModuleWindow
  A boolean, true if the calculation handles RNA, false if not.

## J

job - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The job that prints out this panel

## L

label - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The main label that describes the panel.
layout - Variable in class RNAstructure_java_interface.source.windows.ModuleWindow
  The layout for this window.
legendGrid - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The panel that contains the legend grid.

## M

MacChecker - Class in RNAstructure_java_utilities
  A class that handles checking whether an OS is a Mac, and setting general properties if that is the case.
MacChecker() - Constructor for class RNAstructure_java_utilities.MacChecker
main(String[]) - Static method in class RNAstructure_java_drawing.source.runners.PlotRunner
  The main method.
main(String[]) - Static method in class RNAstructure_java_drawing.source.runners.StructureRunner
  The main method.
main(String[]) - Static method in class RNAstructure_java_interface.source.startup.RNAstructure
  The main method.
mainPanel - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The main panel that the drawing resides on.
makeBottomBorder(int, JComponent) - Method in class RNAstructure_java_utilities.BorderBuilder
  Create an empty bottom border on a component.
makeEmptyBorder(String, int, JComponent) - Method in class RNAstructure_java_utilities.BorderBuilder
  Create an empty border on a component.
makeEqualBorder(int, JComponent) - Method in class RNAstructure_java_utilities.BorderBuilder
  Create an empty equidistant border on a component.
makeErrorDialog(String) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show an error dialog.
makeHorizontal(String[]) - Static method in class RNAstructure_java_utilities.RadioButtonPanel
  Create a button panel with a horizontal layout.
makeHorizontal(String, String...) - Static method in class RNAstructure_java_utilities.RadioButtonPanel
  Create a button panel with a title and horizontal layout.
makeHorizontal(String, ActionListener, String...) - Static method in class RNAstructure_java_utilities.RadioButtonPanel
  Create a button panel with a title, horizontal layout, and an action listener associated with the buttons.
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.DynalignFoldWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.DynalignRefoldWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.Efn2Window
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.FoldDoubleWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.FoldSingleWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.FoldSuboptimalWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.MaxExpectWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Make any input controls necessary to get data from this window for a calculation.
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.MultiWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.OligoScreenWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow
  Make any input controls necessary to get data from this window for a calculation.
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.PartitionDoubleWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.PartitionSingleWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.ProbKnotWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.PseudoknotWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.RefoldWindow
makeInputControls() - Method in class RNAstructure_java_interface.source.windows.StochasticWindow
makeInputDialog(NumberField.DoubleField) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show an input dialog that gets a double within a certain range.
makeInputDialog(NumberField.IntegerField) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show an input dialog that gets an integer within a certain range.
makeLeftBorder(int, JComponent) - Method in class RNAstructure_java_utilities.BorderBuilder
  Create an empty left border on a component.
makeMessageDialog(Object) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show a message dialog.
makeMessageDialog(String) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show a message dialog.
makePanel() - Method in class RNAstructure_java_utilities.FieldPanel
  Build the panel.
makeRightBorder(int, JComponent) - Method in class RNAstructure_java_utilities.BorderBuilder
  Create an empty right border on a component.
makeStartButton(int, int) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Create the "START" button.
makeThreeChoicesDialog(Object) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show a dialog that gives the user one of three choices to make.
makeThreeChoicesDialog(String) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show a dialog that gives the user one of three choices to make.
makeTitledBorder(String, JComponent) - Method in class RNAstructure_java_utilities.BorderBuilder
  Create a padded titled border on a component.
makeTopBorder(int, JComponent) - Method in class RNAstructure_java_utilities.BorderBuilder
  Create an empty top border on a component.
makeTwoChoicesDialog(Object) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show a dialog that gives the user one of two choices to make.
makeTwoChoicesDialog(String) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show a dialog that gives the user one of two choices to make.
makeVertical(String[]) - Static method in class RNAstructure_java_utilities.RadioButtonPanel
  Create a button panel with a vertical layout.
makeVertical(String, String...) - Static method in class RNAstructure_java_utilities.RadioButtonPanel
  Create a button panel with a title and vertical layout.
makeVertical(String, ActionListener, String...) - Static method in class RNAstructure_java_utilities.RadioButtonPanel
  Create a button panel with a title, vertical layout, and an action listener associated with the buttons.
makeWarningDialog(String) - Method in class RNAstructure_java_utilities.SimpleDialogHandler
  Show a warning dialog.
maxBoundX - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The maximum X bound of the image.
maxBoundY - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The maximum Y bound of the image.
MaxExpectWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the MaxExpect module, which generates a group of structures containing pairs with the maximum probability of being accurate.
MaxExpectWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.MaxExpectWindow
  Constructor.
maximum - Variable in class RNAstructure_java_utilities.NumberField
  The maximum value of the field.
menuBar - Variable in class RNAstructure_java_interface.source.windows.InternalWindow
  The menu bar that's attached to this window.
minimum - Variable in class RNAstructure_java_utilities.NumberField
  The minimum value of the field.
modeNames - Static variable in class RNAstructure_java_interface.source.windows.TurboFoldWindow
  An array that holds the names of the TurboFold modes.
moduleInitialized(String) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Check to see if the module was initialized correctly.
ModuleWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for creating and displaying a window that enables a user to input data for one of the RNAstructure modules.
ModuleWindow(String, String) - Constructor for class RNAstructure_java_interface.source.windows.ModuleWindow
  Constructor.
mouseClicked(MouseEvent) - Method in class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
mouseEntered(MouseEvent) - Method in class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
mouseExited(MouseEvent) - Method in class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
mousePressed(MouseEvent) - Method in class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
mouseReleased(MouseEvent) - Method in class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
MultilignWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the Multilign module, which calculates common secondary structures of multiple sequences using multiple iterations of Dynalign.
MultilignWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.MultilignWindow
  Constructor.
MultiWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for creating and displaying an input window that takes multiple arbitrary sequences and CT files as input.
MultiWindow(String, String) - Constructor for class RNAstructure_java_interface.source.windows.MultiWindow
  Constructor.

## N

names - Variable in class RNAstructure_java_utilities.RadioButtonPanel
  The names of the buttons in the group.
NEVER - Static variable in class RNAstructure_java_utilities.ScrollerPane
  A generic constant symbolizing that a scroll bar must never be used.
new_DotPlotBackend() - Static method in class RNAstructure_java_drawing.source.proxy.DotPlotBackendProxyJNI
new_RNAstructureBackendCalculator() - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
new_StructureBackend() - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
notMac() - Static method in class RNAstructure_java_utilities.MacChecker
  Get whether the current OS is not a Mac.
NucleicAcidMenu - Class in RNAstructure_java_interface.source.menus
  A class that creates a menu which holds commands specific for a nucleic acid type.
NucleicAcidMenu(String) - Constructor for class RNAstructure_java_interface.source.menus.NucleicAcidMenu
  Constructor.
number - Variable in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  The structure number viewed on this panel.
NumberField - Class in RNAstructure_java_utilities
  A class that creates a text field whose contents may be bounded by a minimum or maximum value.
NumberField(String, Number, Number, Number) - Constructor for class RNAstructure_java_utilities.NumberField
  Constructor.
NumberField.DoubleField - Class in RNAstructure_java_utilities
  An inner class that handles a field which contains a double value.
NumberField.DoubleField(String, Number) - Constructor for class RNAstructure_java_utilities.NumberField.DoubleField
  Unbounded Constructor.
NumberField.DoubleField(String, Number, Number) - Constructor for class RNAstructure_java_utilities.NumberField.DoubleField
  Minimum Bounds Constructor.
NumberField.DoubleField(String, Number, Number, Number) - Constructor for class RNAstructure_java_utilities.NumberField.DoubleField
  Minimum and Maximum Bounds Constructor.
NumberField.FloatField - Class in RNAstructure_java_utilities
  An inner class that handles a field which contains a float value.
NumberField.FloatField(String, Number) - Constructor for class RNAstructure_java_utilities.NumberField.FloatField
  Unbounded Constructor.
NumberField.FloatField(String, Number, Number) - Constructor for class RNAstructure_java_utilities.NumberField.FloatField
  Minimum Bounds Constructor.
NumberField.FloatField(String, Number, Number, Number) - Constructor for class RNAstructure_java_utilities.NumberField.FloatField
  Minimum and Maximum Bounds Constructor.
NumberField.IntegerField - Class in RNAstructure_java_utilities
  An inner class that handles a field which contains an integer value.
NumberField.IntegerField(String, Integer) - Constructor for class RNAstructure_java_utilities.NumberField.IntegerField
  Unbounded Constructor.
NumberField.IntegerField(String, Integer, Integer) - Constructor for class RNAstructure_java_utilities.NumberField.IntegerField
  Minimum Bounds Constructor.
NumberField.IntegerField(String, Integer, Integer, Integer) - Constructor for class RNAstructure_java_utilities.NumberField.IntegerField
  Minimum and Maximum Bounds Constructor.

## O

oligomerChemistry - Static variable in class RNAstructure_java_interface.source.windows.OligoScreenWindow
  The oligomer chemistry.
OligoScreenWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the OligoScreen module, which calculates thermodynamic properties for a list of oligonucleotides.
OligoScreenWindow() - Constructor for class RNAstructure_java_interface.source.windows.OligoScreenWindow
  Constructor.
OligoWalkWindow - Class in RNAstructure_java_interface.source.windows
  A class that handles creation of windows for the OligoWalk module.
OligoWalkWindow() - Constructor for class RNAstructure_java_interface.source.windows.OligoWalkWindow
  Constructor.
OligoWalkWindow.BarButton - Class in RNAstructure_java_interface.source.windows
  An inner class that encapsulates a bar button.
OligoWalkWindow.BarButton() - Constructor for class RNAstructure_java_interface.source.windows.OligoWalkWindow.BarButton
  Constructor.
OligoWalkWindow.OligoSelectionDialog - Class in RNAstructure_java_interface.source.windows
  An inner class which creates a dialog that selects a particular oligo to move to in the results window.
OligoWalkWindow.OligoSelectionDialog() - Constructor for class RNAstructure_java_interface.source.windows.OligoWalkWindow.OligoSelectionDialog
  Constructor.
OligoWalkWindow.OligoWalkResultsMenu - Class in RNAstructure_java_interface.source.windows
  An inner class that handles creation of the oligo graph menu for the OligoWalk results window.
OligoWalkWindow.OligoWalkResultsMenu() - Constructor for class RNAstructure_java_interface.source.windows.OligoWalkWindow.OligoWalkResultsMenu
  Constructor.
OligoWalkWindow.SpinnerPanel - Class in RNAstructure_java_interface.source.windows
  An class that creates a panel containing a single spinner with a label.
OligoWalkWindow.SpinnerPanel(String, int, int, int) - Constructor for class RNAstructure_java_interface.source.windows.OligoWalkWindow.SpinnerPanel
  Constructor.
OligoWalkWindow.StringComboBox - Class in RNAstructure_java_interface.source.windows
  An inner class that creates a combo box holding a string list.
OligoWalkWindow.StringComboBox(String...) - Constructor for class RNAstructure_java_interface.source.windows.OligoWalkWindow.StringComboBox
  Constructor.
options - Variable in class RNAstructure_java_interface.source.windows.MultiWindow
  The box that holds a particular window's unique options.

## P

paintComponent(Graphics) - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.BarButton
panelInput - Variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow
panelResults - Variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow
  The box that holds the results.
PartitionDoubleWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the bipartition module, which calculates the partition function for two strands of nucleic acids.
PartitionDoubleWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.PartitionDoubleWindow
  Constructor.
PartitionSingleWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the partition module, which calculates the partition function for a single strand of nucleic acids.
PartitionSingleWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.PartitionSingleWindow
  Constructor.
placeComponent(int, int, JComponent) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  .
playClip(char) - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  Play a sound clip, depending on the nucleotide.
PlotDialog - Class in RNAstructure_java_drawing.source.dialogs
  A dialog that holds dot plot images.
PlotDialog(String) - Constructor for class RNAstructure_java_drawing.source.dialogs.PlotDialog
  File Constructor.
PlotDialog(String, int) - Constructor for class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Strand Constructor.
plotLength - Variable in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  The length of the plot.
PlotMenu - Class in RNAstructure_java_drawing.source.menus
  A class that handles a menu which can manipulate a drawn dot plot.
PlotMenu(PlotDialog) - Constructor for class RNAstructure_java_drawing.source.menus.PlotMenu
  Constructor.
PlotRunner - Class in RNAstructure_java_drawing.source.runners
  A class that runs RNAstructure Java dot plot drawing independently of the main RNAstructure application.
PlotRunner() - Constructor for class RNAstructure_java_drawing.source.runners.PlotRunner
  Constructor.
position - Variable in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  The position at which reading is occurring.
preferredDialogWidth - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The preferred dialog width.
print(Graphics, PageFormat, int) - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Render the panel for the print job.
printPanel() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Print if the user decides to, then reset the printer job properties.
ProbKnotWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the ProbKnot module, which predicts pseudoknots in a strand of nucleic acids.
ProbKnotWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.ProbKnotWindow
  Constructor.
progressBar - Variable in class RNAstructure_java_interface.source.windows.ModuleWindow
  The progress bar dialog for this window.
PseudoknotWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the RemovePseudoknots module, which removes pseudoknots from a nucleic acid sequence.
PseudoknotWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.PseudoknotWindow
  Constructor.

## R

RadioButtonPanel - Class in RNAstructure_java_utilities
  A class that creates a panel containing a group of radio buttons.
RadioButtonPanel(String, String, ActionListener, String...) - Constructor for class RNAstructure_java_utilities.RadioButtonPanel
  Constructor.
range - Variable in class RNAstructure_java_drawing.source.menus.DotsMenu.RangeDialog
  The number panel that holds the range data.
readButton - Variable in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  The button which can be clicked to start or stop reading.
readData(String, int) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
readDynalignAlignmentConstraintsFile(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
readFoldingConstraintsFile(String, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
readImageData() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Read image data from a particular file.
readImageData() - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
readImageData() - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
reading - Variable in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  A boolean, true if reading while typing is active, false if not.
readSequenceData(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
readStructureData(String) - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
RefoldWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the refold module, which refolds a previous folding calculation from a save file.
RefoldWindow() - Constructor for class RNAstructure_java_interface.source.windows.RefoldWindow
  Constructor.
refresh() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Refresh this dialog.
regex - Variable in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  The array of regexes used to pull data about a structure.
removeAnnotation() - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
replaceExtension(String, String) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Replace the extension on a file name.
reset() - Method in class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
  Reset the main frame message bar text to its default.
resetField(Number) - Method in class RNAstructure_java_utilities.NumberField
  Reset a field value, if it's within bounds.
resetField(Number, Number, Number) - Method in class RNAstructure_java_utilities.NumberField
  Reset a field value and bounds.
resetFrame() - Method in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Reset the frame to its original state before any windows were opened.
resetInfoLabel() - Method in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Reset the info bar at the bottom of the main window to its default.
resetModel(int, int, int) - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.SpinnerPanel
  Reset the model for the spinner.
RNAstructure - Class in RNAstructure_java_interface.source.startup
  A class that starts the RNAstructure interface.
RNAstructure() - Constructor for class RNAstructure_java_interface.source.startup.RNAstructure
RNAstructure_java_drawing.source - package RNAstructure_java_drawing.source
  A package that encapsulates all the Java classes that handle structure and dot plot drawing.
RNAstructure_java_drawing.source.dialogs - package RNAstructure_java_drawing.source.dialogs
  A package that holds all Java drawing dialogs.
RNAstructure_java_drawing.source.menus - package RNAstructure_java_drawing.source.menus
  A package that holds all menus used in the drawing framework.
RNAstructure_java_drawing.source.proxy - package RNAstructure_java_drawing.source.proxy
  A package that holds all Java drawing classes generated by SWIG that connect the C++ back end to the Java front end.
RNAstructure_java_drawing.source.runners - package RNAstructure_java_drawing.source.runners
  A package that holds the run templates that are used when the Java drawing framework is wrapped into self-contained executables.
RNAstructure_java_interface.source - package RNAstructure_java_interface.source
  A package that encapsulates all the Java classes that comprise the RNAstructure Java interface.
RNAstructure_java_interface.source.menus - package RNAstructure_java_interface.source.menus
  A package that holds all menus used in the Java RNAstructure interface.
RNAstructure_java_interface.source.startup - package RNAstructure_java_interface.source.startup
  A package that holds all Java RNAstructure interface classes that are directly called at the Java interface startup.
RNAstructure_java_interface.source.windows - package RNAstructure_java_interface.source.windows
  A package that holds all internal windows used in the drawing framework.
RNAstructure_java_utilities - package RNAstructure_java_utilities
  A package that holds a variety of utilities classes.
RNAstructureBackendCalculator - Class in RNAstructure_java_interface.source.startup
RNAstructureBackendCalculator(long, boolean) - Constructor for class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
RNAstructureBackendCalculator() - Constructor for class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
RNAstructureBackendCalculator_activateMultilign(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_activateTurboFold(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_addMultilignTuple(long, RNAstructureBackendCalculator, String, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_addTurboFoldTuple(long, RNAstructureBackendCalculator, String, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildAllSubDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildBifoldDataStructure(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildBipartitionDataStructure(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildDynalignDataStructure(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildEfn2DataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildFoldDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildMaxExpectDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildOligoScreenDataStructure(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildOligoWalkDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildPartitionDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildProbKnotDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildRefoldDynalignDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildRefoldSingleDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildRemovePseudoknotsDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildStochasticDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_canFoldOligoOligo(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_canFoldOligoSelf(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_clearDynalignAlignmentConstraints(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_clearFoldingConstraints(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_deleteMultilignTuple(long, RNAstructureBackendCalculator, long) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_deleteTurboFoldTuple(long, RNAstructureBackendCalculator, long) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_determineOligoMaximum(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_foldOligo(long, RNAstructureBackendCalculator, String, int, boolean, boolean, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getAllOligoData(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getDisplayedOligo(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getDynalignAlignmentConstraints(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getDynalignAlignmentWindowSize(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getDynalignStructureWindowSize(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getFoldingConstraints(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getFoldWindowSize(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getGraphRegionBegin(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getGraphRegionEnd(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMaxConstraintIndex(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMaxLoop(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMaxPair(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMostStableOligo(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMultilignCT(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMultilignMaxPairs(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMultilignSequenceSetData(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getNumMultilignSequences(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getNumTurboFoldSequences(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getOligoLabelData(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getOligoTargetLength(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getOligoTargetSequence(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getProgressNumber(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getRefoldWindowSize(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSequenceComment(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSequenceData(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSequenceTitle(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getStructureType(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSuboptimalAbsoluteDiff(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSuboptimalPercentDiff(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getTemperature(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getTurboFoldCT(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getTurboFoldSaveFile(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getTurboFoldSequenceSetData(long, RNAstructureBackendCalculator) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_readDynalignAlignmentConstraintsFile(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_readFoldingConstraintsFile(long, RNAstructureBackendCalculator, String, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_readSequenceData(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runAllSub(long, RNAstructureBackendCalculator, String, float, double) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runBifold(long, RNAstructureBackendCalculator, String, float, int, int, boolean, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runBipartition(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runDynalign(long, RNAstructureBackendCalculator, String, String, String, String, double, int, int, int, float, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runDynalignRefold(long, RNAstructureBackendCalculator, String, String, String, int, int, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runEfn2(long, RNAstructureBackendCalculator, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runFold(long, RNAstructureBackendCalculator, String, int, int, int, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runMaxExpect(long, RNAstructureBackendCalculator, String, double, int, int, double) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runMultilign(long, RNAstructureBackendCalculator, int, int, int, int, double, boolean, double, int, int, String, boolean, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runOligoScreen(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runOligoWalk(long, RNAstructureBackendCalculator, String, int, String, boolean, int, int, String, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runPartition(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runPseudoknotPrediction(long, RNAstructureBackendCalculator, String, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runPseudoknotRemoval(long, RNAstructureBackendCalculator, String, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runRefold(long, RNAstructureBackendCalculator, String, int, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runStochastic(long, RNAstructureBackendCalculator, String, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy(long, RNAstructureBackendCalculator, double, int, double, int, int, double) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runTurboFoldPseudoknot(long, RNAstructureBackendCalculator, double, int, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runTurboFoldThreshold(long, RNAstructureBackendCalculator, double, int, double) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setCleavedNucleotide(long, RNAstructureBackendCalculator, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setDoubleStrandedNucleotide(long, RNAstructureBackendCalculator, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setDynalignAlignmentConstraint(long, RNAstructureBackendCalculator, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setForcedHelix(long, RNAstructureBackendCalculator, int, int, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setMaxLoop(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setMaxPair(long, RNAstructureBackendCalculator, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setModifiedNucleotide(long, RNAstructureBackendCalculator, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setProhibitedHelix(long, RNAstructureBackendCalculator, int, int, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSequenceComment(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSequenceData(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSequenceTitle(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSHAPEFile(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSHAPEParam1(long, RNAstructureBackendCalculator, double) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSHAPEParam2(long, RNAstructureBackendCalculator, double) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSHAPEType(long, RNAstructureBackendCalculator, boolean) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSingleStrandedNucleotide(long, RNAstructureBackendCalculator, int, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setTemperature(long, RNAstructureBackendCalculator, double) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_writeDynalignAlignmentConstraintsFile(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_writeFastaFile(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_writeFoldingConstraintsFile(long, RNAstructureBackendCalculator, String, int) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_writeSequenceFile(long, RNAstructureBackendCalculator, String) - Static method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculatorProxyJNI - Class in RNAstructure_java_interface.source.startup
RNAstructureBackendCalculatorProxyJNI() - Constructor for class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI
RNAstructureMenu - Class in RNAstructure_java_utilities
  A class that creates a menu.
RNAstructureMenu(String) - Constructor for class RNAstructure_java_utilities.RNAstructureMenu
  Constructor.
rollover - Variable in class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
  The rollover text for this listener.
RolloverMenu - Class in RNAstructure_java_interface.source.menus
  A class that creates a menu for the RNAstructure GUI.
RolloverMenu(RNAstructureMenu) - Constructor for class RNAstructure_java_interface.source.menus.RolloverMenu
  RNAstructureMenu Conversion Constructor.
RolloverMenu(String) - Constructor for class RNAstructure_java_interface.source.menus.RolloverMenu
  Title Constructor.
RolloverMenu.RolloverListener - Class in RNAstructure_java_interface.source.menus
  An inner class that creates a rollover listener for menus in the RNAstructure GUI.
RolloverMenu.RolloverListener(String) - Constructor for class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
  Constructor.
runAllSub(String, float, double) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runBifold(String, float, int, int, boolean, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runBipartition(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runDynalign(String, String, String, String, double, int, int, int, float, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runDynalignRefold(String, String, String, int, int, int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runEfn2(String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runFold(String, int, int, int, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.DynalignFoldWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.DynalignRefoldWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.Efn2Window
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.FoldDoubleWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.FoldSingleWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.FoldSuboptimalWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.MaxExpectWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Run the module calculation in the back end.
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.MultiWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.OligoScreenWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.PartitionDoubleWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.PartitionSingleWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.ProbKnotWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.PseudoknotWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.RefoldWindow
runMainCalculation() - Method in class RNAstructure_java_interface.source.windows.StochasticWindow
runMainCalculationMultipleSequences() - Method in class RNAstructure_java_interface.source.windows.MultilignWindow
runMainCalculationMultipleSequences() - Method in class RNAstructure_java_interface.source.windows.MultiWindow
  Run the multiple sequence dependent module calculation in the back end.
runMainCalculationMultipleSequences() - Method in class RNAstructure_java_interface.source.windows.TurboFoldWindow
runMaxExpect(String, double, int, int, double) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runMultilign(int, int, int, int, double, boolean, double, int, int, String, boolean, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
RunnerTemplate - Class in RNAstructure_java_drawing.source.runners
  A class that templates the way in which the RNAstructure Java drawing framework is run independently.
RunnerTemplate(String) - Constructor for class RNAstructure_java_drawing.source.runners.RunnerTemplate
  Constructor.
runOligoScreen(String, String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runOligoWalk(String, int, String, boolean, int, int, String, int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runPartition(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runPseudoknotPrediction(String, int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runPseudoknotRemoval(String, boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runRefold(String, int, int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runStochastic(String, int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runTurboFoldMaximumExpectedAccuracy(double, int, double, int, int, double) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runTurboFoldPseudoknot(double, int, int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
runTurboFoldThreshold(double, int, double) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator

## S

saveSequence() - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  Save a sequence.
saveSequence(String) - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  Save a sequence.
scale - Variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  The scale at which the image is seen.
scroll - Variable in class RNAstructure_java_interface.source.windows.MultiWindow
  The scroll pane holding the sequence set.
ScrollerPane - Class in RNAstructure_java_utilities
  A class that creates a scroll pane that can be controlled via the keyboard.
ScrollerPane(Component, int, int) - Constructor for class RNAstructure_java_utilities.ScrollerPane
  Constructor.
select() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.BarButton
  Select this button.
select(String, String) - Method in class RNAstructure_java_utilities.FileChooser
  Select a file that has one possible input or output type.
select(String[], String[]) - Method in class RNAstructure_java_utilities.FileChooser
  Select a file that has multiple possible input or output types.
selectFile() - Method in class RNAstructure_java_drawing.source.runners.PlotRunner
selectFile() - Method in class RNAstructure_java_drawing.source.runners.RunnerTemplate
  Select an image file.
selectFile() - Method in class RNAstructure_java_drawing.source.runners.StructureRunner
selectionColor - Variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow.BarButton
  The selection color for this button.
selectorType - Variable in class RNAstructure_java_utilities.FileChooser
  The type of file type selector.
SequenceDisplayWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for displaying a window that allows a user to examine raw sequence data.
SequenceDisplayWindow() - Constructor for class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  Default Constructor.
SequenceDisplayWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  File Constructor.
SequenceDisplayWindow.EditMenu - Class in RNAstructure_java_interface.source.windows
  An inner class that creates a sequence editing menu.
SequenceDisplayWindow.EditMenu() - Constructor for class RNAstructure_java_interface.source.windows.SequenceDisplayWindow.EditMenu
  Constructor.
SequenceDisplayWindow.ReadMenu - Class in RNAstructure_java_interface.source.windows
  An inner class that creates a sequence reading menu.
SequenceDisplayWindow.ReadMenu() - Constructor for class RNAstructure_java_interface.source.windows.SequenceDisplayWindow.ReadMenu
  Constructor.
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog.PrintMenu
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.dialogs.ImageDialog.ZoomDialog
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.dialogs.PlotDialog
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.dialogs.StructureDialog
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.menus.AnnotationMenu
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.menus.DotsMenu.ColorDialog
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.menus.DotsMenu.RangeDialog
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.menus.DotsMenu
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.menus.PlotMenu
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.menus.StructureMenu.MoveDialog
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.menus.StructureMenu
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.runners.PlotRunner
serialVersionUID - Static variable in class RNAstructure_java_drawing.source.runners.StructureRunner
serialVersionUID - Static variable in class RNAstructure_java_interface.source.menus.ConstraintsMenu.NucOrHelixDialog
serialVersionUID - Static variable in class RNAstructure_java_interface.source.menus.ConstraintsMenu
serialVersionUID - Static variable in class RNAstructure_java_interface.source.menus.DynamicMenuBar
serialVersionUID - Static variable in class RNAstructure_java_interface.source.menus.FileMenu
serialVersionUID - Static variable in class RNAstructure_java_interface.source.menus.HelpMenu
serialVersionUID - Static variable in class RNAstructure_java_interface.source.menus.NucleicAcidMenu
serialVersionUID - Static variable in class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
serialVersionUID - Static variable in class RNAstructure_java_interface.source.menus.RolloverMenu
serialVersionUID - Static variable in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
serialVersionUID - Static variable in class RNAstructure_java_interface.source.startup.RNAstructure
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.DrawingWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.DynalignFoldWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.DynalignRefoldWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.Efn2Window
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.FoldDoubleWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.FoldSingleWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.FoldSuboptimalWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.InternalWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.MaxExpectWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.ModuleWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.MultilignWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.MultiWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.OligoScreenWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow.BarButton
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow.OligoSelectionDialog
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow.OligoWalkResultsMenu
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow.SpinnerPanel
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow.StringComboBox
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.PartitionDoubleWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.PartitionSingleWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.ProbKnotWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.PseudoknotWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.RefoldWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow.EditMenu
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow.ReadMenu
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.StochasticWindow
serialVersionUID - Static variable in class RNAstructure_java_interface.source.windows.TurboFoldWindow
serialVersionUID - Static variable in class RNAstructure_java_utilities.BorderBuilder
serialVersionUID - Static variable in class RNAstructure_java_utilities.BorderedButtonPanel
serialVersionUID - Static variable in class RNAstructure_java_utilities.FieldPanel.FilePanel
serialVersionUID - Static variable in class RNAstructure_java_utilities.FieldPanel.NumberPanel
serialVersionUID - Static variable in class RNAstructure_java_utilities.FieldPanel
serialVersionUID - Static variable in class RNAstructure_java_utilities.FileChooser
serialVersionUID - Static variable in class RNAstructure_java_utilities.FileField
serialVersionUID - Static variable in class RNAstructure_java_utilities.HTMLCheckBox
serialVersionUID - Static variable in class RNAstructure_java_utilities.ImageGrabber
serialVersionUID - Static variable in class RNAstructure_java_utilities.MacChecker
serialVersionUID - Static variable in class RNAstructure_java_utilities.NumberField.DoubleField
serialVersionUID - Static variable in class RNAstructure_java_utilities.NumberField.FloatField
serialVersionUID - Static variable in class RNAstructure_java_utilities.NumberField.IntegerField
serialVersionUID - Static variable in class RNAstructure_java_utilities.NumberField
serialVersionUID - Static variable in class RNAstructure_java_utilities.RadioButtonPanel
serialVersionUID - Static variable in class RNAstructure_java_utilities.RNAstructureMenu
serialVersionUID - Static variable in class RNAstructure_java_utilities.ScrollerPane
serialVersionUID - Static variable in class RNAstructure_java_utilities.SimpleDialogHandler
serialVersionUID - Static variable in class RNAstructure_java_utilities.ValueSelectionDialog
set() - Method in class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener
  Set the main frame message bar text to this listener's specific rollover text.
setAnchorCenter() - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Set the anchoring area for the GridBagConstraints to CENTER.
setAnchorNorth() - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Set the anchoring area for the GridBagConstraints to NORTH.
setAnnotation(String) - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Set the annotation for this structure drawing.
setBarColor(Color) - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow.BarButton
  Set the default color that will be painted on this button.
setBarPolicies(int, int) - Method in class RNAstructure_java_utilities.ScrollerPane
  Set the scroll bar policies for this scroll pane.
setCleavedNucleotide(int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setColors(int) - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Set the number of colors in the plot on this dialog.
setColors(int) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
setConstraint(String) - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu.NucOrHelixDialog
  Set a constraint using this dialog.
setDataAutomatically(String) - Method in class RNAstructure_java_interface.source.windows.FoldSingleWindow
  Set the window's data automatically.
setDoubleStrandedNucleotide(int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setDynalignAlignmentConstraint(int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setFile(int, String) - Method in class RNAstructure_java_utilities.FieldPanel.FilePanel
  Set a file name in a particular input field.
setFillCenter() - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Set the fill for the GridBagConstraints as CENTER.
setFillHorizontal() - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Set the fill for the GridBagConstraints as HORIZONTAL.
setForcedHelix(int, int, int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setGrid(int, int) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Set the amount of space a component takes up in the grid.
setInfoLabel(String) - Method in class RNAstructure_java_interface.source.startup.ApplicationRootFrame
  Set the info bar at the bottom of the main window to contain the specified text.
setInsets(int, int, int, int) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Set the external padding of the constraints.
setMaxLoop(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setMaxPair(int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setMenus() - Method in class RNAstructure_java_interface.source.windows.DrawingWindow
  Create the array of variable menus used by this window.
setMenus() - Method in class RNAstructure_java_interface.source.windows.DynalignFoldWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.DynalignRefoldWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.Efn2Window
setMenus() - Method in class RNAstructure_java_interface.source.windows.FoldDoubleWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.FoldSingleWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.FoldSuboptimalWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.InternalWindow
  Create the array of variable menus used by this window.
setMenus() - Method in class RNAstructure_java_interface.source.windows.MaxExpectWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.MultiWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.OligoScreenWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.PartitionDoubleWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.PartitionSingleWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.ProbKnotWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.PseudoknotWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.RefoldWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
setMenus() - Method in class RNAstructure_java_interface.source.windows.StochasticWindow
setModifiedNucleotide(int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setNucleotidesCircled(boolean) - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
setOligoData(int) - Method in class RNAstructure_java_interface.source.windows.OligoWalkWindow
  Set the data for a particular oligo.
setPad(int, int) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Set the internal padding of the constraints.
setPanelWidth(int) - Method in class RNAstructure_java_utilities.FieldPanel
  Set the width of the panel.
setProhibitedHelix(int, int, int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setRange(double, double) - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Set the range of the plot on this dialog.
setRange(double, double) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
setReading(boolean) - Method in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  Set whether or not the window should be reading while typing.
setScale(int) - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Set the image scale.
setSelectedButton(String) - Method in class RNAstructure_java_utilities.RadioButtonPanel
  Set a particular button in this group to be selected.
setSequenceComment(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setSequenceData(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setSequenceTitle(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setSHAPEFile(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setSHAPEParam1(double) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setSHAPEParam2(double) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setSHAPEType(boolean) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setSingleStrandedNucleotide(int, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setSizes(int, int) - Method in class RNAstructure_java_utilities.ScrollerPane
  Set the size of the scroller pane by setting preferred, minimum, and maximum sizes all at once.
setStructureNumber(int) - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Set the structure number.
setTemperature(double) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
setTitles(String) - Method in class RNAstructure_java_interface.source.windows.InternalWindow
  Set the title of both this window and the main window.
setTopCaption(String) - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Set the text on the info label.
showDeletionConfirmation() - Method in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  Show a dialog that asks whether constraints should be deleted.
showImageDialogs() - Method in class RNAstructure_java_interface.source.windows.MultiWindow
  Show the image dialogs, if possible.
showProgressBar(boolean) - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Create a progress bar.
showProgressBarDeterminate() - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Create a determinate progress bar.
showProgressBarIndeterminate() - Method in class RNAstructure_java_interface.source.windows.ModuleWindow
  Create an indeterminate progress bar.
SimpleDialogHandler - Class in RNAstructure_java_utilities
  A class that handles simple dialogs used in the RNAstructure GUI.
SimpleDialogHandler() - Constructor for class RNAstructure_java_utilities.SimpleDialogHandler
specificPanel - Variable in class RNAstructure_java_interface.source.windows.TurboFoldWindow
  The panel that holds the dynamic options applicable to a mode.
specifiedPanelWidth - Variable in class RNAstructure_java_utilities.FieldPanel
  The specified width of the panel.
spinner - Variable in class RNAstructure_java_interface.source.windows.OligoWalkWindow.SpinnerPanel
  The spinner in this panel.
StochasticWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the stochastic module, which generates a stochastic sample of structures.
StochasticWindow(String) - Constructor for class RNAstructure_java_interface.source.windows.StochasticWindow
  Constructor.
str - Variable in class RNAstructure_java_interface.source.menus.ConstraintsMenu
  The strand this constraints menu deals with.
strand - Variable in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  The strand being drawn.
strand - Variable in class RNAstructure_java_interface.source.windows.DrawingWindow
  The strand being drawn.
StructureBackend - Class in RNAstructure_java_drawing.source.proxy
StructureBackend(long, boolean) - Constructor for class RNAstructure_java_drawing.source.proxy.StructureBackend
StructureBackend() - Constructor for class RNAstructure_java_drawing.source.proxy.StructureBackend
StructureBackend_addAnnotationProbability(long, StructureBackend, String) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_addAnnotationSHAPE(long, StructureBackend, String) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_flip(long, StructureBackend) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_getStructureData(long, StructureBackend, int) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_readStructureData(long, StructureBackend, String) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_removeAnnotation(long, StructureBackend) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_setNucleotidesCircled(long, StructureBackend, boolean) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_writeDotBracketFile(long, StructureBackend, String, String) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_writeHelixFile(long, StructureBackend, String, String, int) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_writePostscriptFile(long, StructureBackend, String, int) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackend_writeSVGFile(long, StructureBackend, String, int) - Static method in class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureBackendProxyJNI - Class in RNAstructure_java_drawing.source.proxy
StructureBackendProxyJNI() - Constructor for class RNAstructure_java_drawing.source.proxy.StructureBackendProxyJNI
StructureDialog - Class in RNAstructure_java_drawing.source.dialogs
  A dialog that holds structure images.
StructureDialog(String) - Constructor for class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Constructor.
StructureMenu - Class in RNAstructure_java_drawing.source.menus
  A class that handles a menu which can manipulate a drawn structure.
StructureMenu(StructureDialog) - Constructor for class RNAstructure_java_drawing.source.menus.StructureMenu
  Constructor.
StructureMenu.MoveDialog - Class in RNAstructure_java_drawing.source.menus
  An inner class which creates a dialog that moves to a structure.
StructureMenu.MoveDialog() - Constructor for class RNAstructure_java_drawing.source.menus.StructureMenu.MoveDialog
  Constructor.
StructureRunner - Class in RNAstructure_java_drawing.source.runners
  A class that runs RNAstructure Java structure drawing independently of the main RNAstructure application.
StructureRunner() - Constructor for class RNAstructure_java_drawing.source.runners.StructureRunner
  Constructor.
swigCMemOwn - Variable in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
swigCMemOwn - Variable in class RNAstructure_java_drawing.source.proxy.StructureBackend
swigCMemOwn - Variable in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
swigCPtr - Variable in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
swigCPtr - Variable in class RNAstructure_java_drawing.source.proxy.StructureBackend
swigCPtr - Variable in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
switchCircled() - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Switch circled nucleotides on or off.

## T

textFields - Variable in class RNAstructure_java_utilities.FieldPanel
  The array of text fields.
timer - Variable in class RNAstructure_java_interface.source.windows.SequenceDisplayWindow
  The timer that aids in reading nucleotides in rhythm.
TurboFoldWindow - Class in RNAstructure_java_interface.source.windows
  A class responsible for initializing and running the TurboFold module, which calculates common secondary structures of multiple sequences using the partition function and probabalistic alignments.
TurboFoldWindow() - Constructor for class RNAstructure_java_interface.source.windows.TurboFoldWindow
  Constructor.

## V

valueOf(String) - Static method in enum RNAstructure_java_utilities.FileChooser.Types
  Returns the enum constant of this type with the specified name.
values() - Static method in enum RNAstructure_java_utilities.FileChooser.Types
  Returns an array containing the constants of this enum type, in the order they are declared.
ValueSelectionDialog - Class in RNAstructure_java_utilities
  A class which creates a dialog that selects values from labeled text fields.
ValueSelectionDialog(String) - Constructor for class RNAstructure_java_utilities.ValueSelectionDialog
  Constructor.
viewDialog() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  View the dialog.
viewWindow() - Method in class RNAstructure_java_interface.source.windows.InternalWindow
  View the window.
viewZoomDialog() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  View a zooming dialog.

## W

writeDotBracketFile(String) - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Write a dot bracket file of all structures on this dialog.
writeDotBracketFile(String, String) - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
writeDynalignAlignmentConstraintsFile(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
writeFastaFile(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
writeFoldingConstraintsFile(String, int) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
writeHelixFile(String) - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Write a helix file from the current structure on this dialog.
writeHelixFile(String, String, int) - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
writePostscriptFile(String) - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Write a Postscript file from the plot on this dialog.
writePostscriptFile(String) - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Write a Postscript file from the current structure on this dialog.
writePostscriptFile(String) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
writePostscriptFile(String, int) - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
writeSequenceFile(String) - Method in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
writeStructuresFile(String, boolean) - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Write a probable structures file from the plot on this dialog.
writeStructuresFile(String, String) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
writeSVGFile(String) - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Write an SVG file from the plot on this dialog.
writeSVGFile(String) - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
  Write an SVG file from the current structure on this dialog.
writeSVGFile(String) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
writeSVGFile(String, int) - Method in class RNAstructure_java_drawing.source.proxy.StructureBackend
writeTextFile(String) - Method in class RNAstructure_java_drawing.source.dialogs.PlotDialog
  Write a text file from the plot on this dialog.
writeTextFile(String) - Method in class RNAstructure_java_drawing.source.proxy.DotPlotBackend

## Z

zoomImage() - Method in class RNAstructure_java_drawing.source.dialogs.ImageDialog
  Zoom the image on the panel.

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