RNAstructure_java_interface.source.windows

Class ModuleWindow

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JInternalFrame

RNAstructure_java_interface.source.windows.InternalWindow

RNAstructure_java_interface.source.windows.ModuleWindow

All Implemented Interfaces:

ActionListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer, WindowConstants

Direct Known Subclasses:

DynalignFoldWindow, DynalignRefoldWindow, Efn2Window, FoldDoubleWindow, FoldSingleWindow, FoldSuboptimalWindow, MaxExpectWindow, MultiWindow, OligoScreenWindow, OligoWalkWindow, PartitionDoubleWindow, PartitionSingleWindow, ProbKnotWindow, PseudoknotWindow, RefoldWindow, StochasticWindow

public abstract class ModuleWindow
extends InternalWindow

A class responsible for creating and displaying a window that enables a user to input data for one of the RNAstructure modules.

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JInternalFrame

JInternalFrame.AccessibleJInternalFrame, JInternalFrame.JDesktopIcon

Nested classes/interfaces inherited from class javax.swing.JComponent

JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
private GridBagConstraints	constraints The GridBagConstraints for this window.
protected boolean	isRNA A boolean, true if the calculation handles RNA, false if not.
private GridBagLayout	layout The layout for this window.
protected JDialog	progressBar The progress bar dialog for this window.
private static long	serialVersionUID

Fields inherited from class RNAstructure_java_interface.source.windows.InternalWindow

backend, dialogHandler, menuBar

Fields inherited from class javax.swing.JInternalFrame

closable, CONTENT_PANE_PROPERTY, desktopIcon, FRAME_ICON_PROPERTY, frameIcon, GLASS_PANE_PROPERTY, iconable, IS_CLOSED_PROPERTY, IS_ICON_PROPERTY, IS_MAXIMUM_PROPERTY, IS_SELECTED_PROPERTY, isClosed, isIcon, isMaximum, isSelected, LAYERED_PANE_PROPERTY, maximizable, MENU_BAR_PROPERTY, resizable, ROOT_PANE_PROPERTY, rootPane, rootPaneCheckingEnabled, title, TITLE_PROPERTY

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ModuleWindow(String acid, String title) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
protected String	combineFileNames(String file1, String file2, String ext) Combine two file names into a new file name.
protected void	doActions(String command) Do any actions specific to this window.
protected abstract void	executeModuleAction(String command) Execute an action within a particular module.
protected void	finishModule(String text) Handle finishing of a module.
protected JComponent	getInputControl(Container hold, int index) Get a particular input control from a given container.
protected JComponent	getInputControl(int index) Get a particular input control from the content pane.
protected abstract void	makeInputControls() Make any input controls necessary to get data from this window for a calculation.
protected void	makeStartButton(int x, int y) Create the "START" button.
protected boolean	moduleInitialized(String result) Check to see if the module was initialized correctly.
protected void	placeComponent(int x, int y, JComponent component) .
protected String	replaceExtension(String file, String extension) Replace the extension on a file name.
protected abstract void	runMainCalculation() Run the module calculation in the back end.
protected void	setAnchorCenter() Set the anchoring area for the GridBagConstraints to CENTER.
protected void	setAnchorNorth() Set the anchoring area for the GridBagConstraints to NORTH.
protected void	setFillCenter() Set the fill for the GridBagConstraints as CENTER.
protected void	setFillHorizontal() Set the fill for the GridBagConstraints as HORIZONTAL.
protected void	setGrid(int width, int height) Set the amount of space a component takes up in the grid.
protected void	setInsets(int top, int left, int bottom, int right) Set the external padding of the constraints.
protected void	setPad(int xPad, int yPad) Set the internal padding of the constraints.
private void	showProgressBar(boolean determinate) Create a progress bar.
protected void	showProgressBarDeterminate() Create a determinate progress bar.
protected void	showProgressBarIndeterminate() Create an indeterminate progress bar.

Methods inherited from class RNAstructure_java_interface.source.windows.InternalWindow

actionPerformed, setMenus, setTitles, viewWindow

Methods inherited from class javax.swing.JInternalFrame

addImpl, addInternalFrameListener, createRootPane, dispose, doDefaultCloseAction, fireInternalFrameEvent, getAccessibleContext, getContentPane, getDefaultCloseOperation, getDesktopIcon, getDesktopPane, getFocusCycleRootAncestor, getFocusOwner, getFrameIcon, getGlassPane, getInternalFrameListeners, getJMenuBar, getLastCursor, getLayer, getLayeredPane, getMenuBar, getMostRecentFocusOwner, getNormalBounds, getRootPane, getTitle, getUI, getUIClassID, getWarningString, hide, isClosable, isClosed, isFocusCycleRoot, isIcon, isIconifiable, isMaximizable, isMaximum, isResizable, isRootPaneCheckingEnabled, isSelected, moveToBack, moveToFront, pack, paintComponent, paramString, remove, removeInternalFrameListener, reshape, restoreSubcomponentFocus, setClosable, setClosed, setContentPane, setCursor, setDefaultCloseOperation, setDesktopIcon, setFocusCycleRoot, setFrameIcon, setGlassPane, setIcon, setIconifiable, setJMenuBar, setLayer, setLayer, setLayeredPane, setLayout, setMaximizable, setMaximum, setMenuBar, setNormalBounds, setResizable, setRootPane, setRootPaneCheckingEnabled, setSelected, setTitle, setUI, show, toBack, toFront, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

constraints

private GridBagConstraints constraints

The GridBagConstraints for this window.

isRNA

protected boolean isRNA

A boolean, true if the calculation handles RNA, false if not.

layout

private GridBagLayout layout

The layout for this window.

progressBar

protected final JDialog progressBar

The progress bar dialog for this window.

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

ModuleWindow

protected ModuleWindow(String acid,
            String title)

Constructor.

Parameters:

acid - The nucleic acid type, as a string.

title - The title of the window.

Method Detail

combineFileNames

protected final String combineFileNames(String file1,
                      String file2,
                      String ext)

Combine two file names into a new file name.

Parameters:

file1 - The first file name.

file2 - The second file name.

ext - The extension of the new file name.

Returns:

The combined file name.

doActions

protected void doActions(String command)

Description copied from class: InternalWindow

Do any actions specific to this window.

Specified by:

doActions in class InternalWindow

Parameters:

command - The command that signifies a particular action.

executeModuleAction

protected abstract void executeModuleAction(String command)

Execute an action within a particular module.

Parameters:

command - The command that signifies a particular action.

finishModule

protected final void finishModule(String text)

Handle finishing of a module.

Finishing of a module involves closing of the window and showing any error that may have occurred.

Parameters:

text - The result of the calculation spawned by the module.

getInputControl

protected final JComponent getInputControl(Container hold,
                         int index)

Get a particular input control from a given container.

Parameters:

hold - The container that holds the input control.

index - The index of the control to get, one-indexed.

Returns:

The input control.

getInputControl

protected final JComponent getInputControl(int index)

Get a particular input control from the content pane.

Parameters:

index - The index of the control to get, one-indexed.

Returns:

The input control.

makeInputControls

protected abstract void makeInputControls()

Make any input controls necessary to get data from this window for a calculation.

makeStartButton

protected final void makeStartButton(int x,
                   int y)

Create the "START" button.

Note that this method simply makes the button, adds the action listener, applies standard padding, then places the button at the specified (X,Y) layout coordinate.

If more customization of the button itself or its positioning is needed, it should be done in subclasses.

Parameters:

x - The X index at which to place the button in the layout.

y - The Y index at which to place the button in the layout.

moduleInitialized

protected final boolean moduleInitialized(String result)

Check to see if the module was initialized correctly.

Check what the result string retrieved from the module was, and return true only if it's the empty string. Otherwise, show the result string as an error and return false.

Parameters:

result - The result of the data structure construction.

Returns:

True if the data structure was initialized correctly, false if not.

placeComponent

protected final void placeComponent(int x,
                  int y,
                  JComponent component)

. Set a component in its place.

Parameters:

x - The X coordinate of the grid.

y - The Y coordinate of the grid.

component - The component to set in place.

replaceExtension

protected final String replaceExtension(String file,
                      String extension)

Replace the extension on a file name.

Parameters:

file - The file name whose extension to replace.

extension - The new extension.

Returns:

The new file name with extension replaced.

runMainCalculation

protected abstract void runMainCalculation()

Run the module calculation in the back end.

Data must be pulled from the module window before the back end calculation is run, so this data capture should be done in this method.

setAnchorCenter

protected final void setAnchorCenter()

Set the anchoring area for the GridBagConstraints to CENTER.

setAnchorNorth

protected final void setAnchorNorth()

Set the anchoring area for the GridBagConstraints to NORTH.

setFillCenter

protected final void setFillCenter()

Set the fill for the GridBagConstraints as CENTER.

setFillHorizontal

protected final void setFillHorizontal()

Set the fill for the GridBagConstraints as HORIZONTAL.

setGrid

protected final void setGrid(int width,
           int height)

Set the amount of space a component takes up in the grid.

Parameters:

width - The width of the component.

height - The height of the component.

setInsets

protected final void setInsets(int top,
             int left,
             int bottom,
             int right)

Set the external padding of the constraints.

Parameters:

top - The top padding.

left - The left padding.

bottom - The bottom padding.

right - The right padding.

setPad

protected final void setPad(int xPad,
          int yPad)

Set the internal padding of the constraints.

Parameters:

xPad - The padding in the X direction.

yPad - The padding in the Y direction.

showProgressBar

private void showProgressBar(boolean determinate)

Create a progress bar.

Parameters:

determinate - True if the progress bar is determinate, false if not.

showProgressBarDeterminate

protected void showProgressBarDeterminate()

Create a determinate progress bar.

showProgressBarIndeterminate

protected void showProgressBarIndeterminate()

Create an indeterminate progress bar.