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.
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