ur_rna.RNAstructureUI.windows

Class ModuleWindow

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JInternalFrame

ur_rna.RNAstructureUI.windows.InternalWindow

ur_rna.RNAstructureUI.windows.ModuleWindow

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

Direct Known Subclasses:

AccessFoldWindow, DesignWindow, DuplexFoldWindow, 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 ur_rna.RNAstructureUI.windows.InternalWindow

InternalWindow.CommandInfo

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

javax.swing.JInternalFrame.AccessibleJInternalFrame, javax.swing.JInternalFrame.JDesktopIcon

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

javax.swing.JComponent.AccessibleJComponent

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

java.awt.Container.AccessibleAWTContainer

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

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	calcCanceled
private java.awt.event.ActionListener	calcCancelListener
private long	calcCompleted
private java.awt.event.ActionListener	calcProgressListener
private java.awt.GridBagConstraints	constraints The GridBagConstraints for this window.
private java.util.HashMap<java.awt.Component,java.lang.Boolean>	enabledState
protected boolean	isRNA A boolean, true if the calculation handles RNA, false if not.
private static java.util.HashMap<java.lang.String,java.lang.Boolean>	knownDirs
(package private) long	lastUpdate
private java.awt.GridBagLayout	layout The layout for this window.
protected static AppLog	log
protected java.lang.Thread	mainCalcThread
protected java.awt.Component	progressIndicator The progress bar dialog for this window.
protected static java.lang.String	protectedExamplesDir
protected ModuleWindow	self
private static long	serialVersionUID
protected javax.swing.JButton	startButton

Fields inherited from class ur_rna.RNAstructureUI.windows.InternalWindow

backend, changeListener, frameListener, warnings

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

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

accessibleContext, 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(java.lang.String acid, java.lang.String title) Constructor.

Method Summary

Modifier and Type	Method and Description
protected boolean	calcWasCanceled()
protected void	cancelMainCalculation()
void	close()
protected void	closeProgress()
protected void	closeProgress(boolean resetUI)
protected java.lang.String	combineFileNames(java.lang.String file1, java.lang.String file2, java.lang.String ext) Combine two file names into a new file name.
protected boolean	displayCalcError(java.lang.String text) Handle finishing of a module.
protected boolean	drawStructures(java.lang.String file)
private void	enableControls(java.awt.Container parent, boolean enable)
protected javax.swing.JComponent	getInputControl(java.awt.Container hold, int index) Get a particular input control from a given container.
protected javax.swing.JComponent	getInputControl(int index) Get a particular input control from the content pane.
static java.lang.String	getOutputFile(java.lang.String file)
static java.lang.String	getOutputFile(java.lang.String file, java.lang.String extension) Replace the extension on a file name.
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 void	placeComponent(int x, int y, javax.swing.JComponent component) .
protected void	processCommand(InternalWindow.CommandInfo ci) Perform an action specific to this window.
static boolean	promptDraw()
static boolean	promptDraw(java.lang.String prompt, java.lang.String promptSetting)
protected abstract boolean	runMainCalculation() Run the module calculation in the back end.
(package private) void	runOnUiThread(java.lang.Runnable r)
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.
protected void	showDrawProgress()
protected void	showDrawProgress(java.lang.String message)
protected void	showProgress() Create a determinate progress bar.
protected void	showProgress(boolean determinate) Create a progress bar.
protected void	showProgress(boolean determinate, boolean canCancel)
protected void	showProgress(boolean determinate, boolean canCancel, java.lang.String message)
protected void	updateCalcProgress(ProgressPanel panel)
protected boolean	verifyBackendResult(java.lang.String result, java.lang.String details, java.lang.Object... detailArgs) Check to see if the module was initialized correctly.

Methods inherited from class ur_rna.RNAstructureUI.windows.InternalWindow

actionPerformed, createCustomMenus, frameActivated, frameClosed, frameClosing, getCustomMenus, invokeCommand, invokeCommand, invokeCommand, isActiveFrame, notifyUpdated, onFocusGained, propertyChanged, setCaption, setCustomMenus, showWindow

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

calcCanceled

private boolean calcCanceled

calcCancelListener

private java.awt.event.ActionListener calcCancelListener

calcCompleted

private long calcCompleted

calcProgressListener

private java.awt.event.ActionListener calcProgressListener

constraints

private java.awt.GridBagConstraints constraints

The GridBagConstraints for this window.

enabledState

private java.util.HashMap<java.awt.Component,java.lang.Boolean> enabledState

isRNA

protected boolean isRNA

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

knownDirs

private static java.util.HashMap<java.lang.String,java.lang.Boolean> knownDirs

lastUpdate

long lastUpdate

layout

private java.awt.GridBagLayout layout

The layout for this window.

log

protected static final AppLog log

mainCalcThread

protected java.lang.Thread mainCalcThread

progressIndicator

protected volatile java.awt.Component progressIndicator

The progress bar dialog for this window.

protectedExamplesDir

protected static java.lang.String protectedExamplesDir

self

protected final ModuleWindow self

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

startButton

protected javax.swing.JButton startButton

Constructor Detail

ModuleWindow

protected ModuleWindow(java.lang.String acid,
                       java.lang.String title)

Constructor.

Parameters:

acid - The nucleic acid type, as a string.

title - The title of the window.

Method Detail

calcWasCanceled

protected boolean calcWasCanceled()

cancelMainCalculation

protected void cancelMainCalculation()

close

public void close()

closeProgress

protected void closeProgress()

closeProgress

protected void closeProgress(boolean resetUI)

combineFileNames

protected final java.lang.String combineFileNames(java.lang.String file1,
                                                  java.lang.String file2,
                                                  java.lang.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.

displayCalcError

protected final boolean displayCalcError(java.lang.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.

drawStructures

protected boolean drawStructures(java.lang.String file)

enableControls

private void enableControls(java.awt.Container parent,
                            boolean enable)

getInputControl

protected final javax.swing.JComponent getInputControl(java.awt.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 javax.swing.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.

getOutputFile

public static java.lang.String getOutputFile(java.lang.String file)

getOutputFile

public static java.lang.String getOutputFile(java.lang.String file,
                                             java.lang.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.

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.

placeComponent

protected final void placeComponent(int x,
                                    int y,
                                    javax.swing.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.

processCommand

protected void processCommand(InternalWindow.CommandInfo ci)

Perform an action specific to this window.

Overrides:

processCommand in class InternalWindow

Parameters:

ci - Information about the command.

promptDraw

public static boolean promptDraw()

promptDraw

public static boolean promptDraw(java.lang.String prompt,
                                 java.lang.String promptSetting)

runMainCalculation

protected abstract boolean 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.

runOnUiThread

void runOnUiThread(java.lang.Runnable r)

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.

showDrawProgress

protected void showDrawProgress()

showDrawProgress

protected void showDrawProgress(java.lang.String message)

showProgress

protected void showProgress()

Create a determinate progress bar.

showProgress

protected void showProgress(boolean determinate)

Create a progress bar.

Parameters:

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

showProgress

protected void showProgress(boolean determinate,
                            boolean canCancel)

showProgress

protected void showProgress(boolean determinate,
                            boolean canCancel,
                            java.lang.String message)

updateCalcProgress

protected void updateCalcProgress(ProgressPanel panel)

verifyBackendResult

protected final boolean verifyBackendResult(java.lang.String result,
                                            java.lang.String details,
                                            java.lang.Object... detailArgs)

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.