- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
-
- 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
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Constructor.
- StructureMenu.MoveDialog - Class in RNAstructure_java_drawing.source.menus
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An inner class which creates a dialog that moves to a structure.
- StructureMenu.MoveDialog() - Constructor for class RNAstructure_java_drawing.source.menus.StructureMenu.MoveDialog
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Constructor.
- StructureRunner - Class in RNAstructure_java_drawing.source.runners
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A class that runs RNAstructure Java structure drawing independently of the
main RNAstructure application.
- StructureRunner() - Constructor for class RNAstructure_java_drawing.source.runners.StructureRunner
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Constructor.
- swigCMemOwn - Variable in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
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- swigCMemOwn - Variable in class RNAstructure_java_drawing.source.proxy.StructureBackend
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- swigCMemOwn - Variable in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
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- swigCPtr - Variable in class RNAstructure_java_drawing.source.proxy.DotPlotBackend
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- swigCPtr - Variable in class RNAstructure_java_drawing.source.proxy.StructureBackend
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- swigCPtr - Variable in class RNAstructure_java_interface.source.startup.RNAstructureBackendCalculator
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- switchCircled() - Method in class RNAstructure_java_drawing.source.dialogs.StructureDialog
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Switch circled nucleotides on or off.