ur_rna.RNAstructureUI.windows

Class PredictWindowBase

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JInternalFrame

ur_rna.RNAstructureUI.windows.InternalWindow

ur_rna.RNAstructureUI.windows.PredictWindowBase

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:

PredictBimolStructureWindow, PredictMultiStructureWindow, PredictSingleStructureWindow, PredictTwoStructureWindow

public abstract class PredictWindowBase
extends InternalWindow

A base class for the Structure Prediction Windows

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static interface	PredictWindowBase.BackgroundTask
(package private) class	PredictWindowBase.FieldInfo
(package private) class	PredictWindowBase.FileFieldInfo
static class	PredictWindowBase.PredictTaskBase

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 static java.lang.String[]	controlPrefixes
private java.util.HashMap<javax.swing.JComponent,PredictWindowBase.FieldInfo>	fields
private java.util.HashMap<java.lang.String,PredictWindowBase.FileFieldInfo>	fileFields
protected java.text.DecimalFormat	numberFormatter
protected javax.swing.JPanel	pnlClient
protected javax.swing.JPanel	pnlContent
private PredictWindowBase.BackgroundTask	runningTask
static double	TEMP_37C
private javax.swing.Timer	uiUpdateTimer

Fields inherited from class ur_rna.RNAstructureUI.windows.InternalWindow

backend, changeListener, frameListener, log, 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

Constructor and Description
PredictWindowBase()

Method Summary

Modifier and Type	Method and Description
void	actionPerformed(java.awt.event.ActionEvent e)
protected void	addField(javax.swing.JComponent c, java.lang.String description, java.lang.String settingsName)
protected void	addFileField(java.lang.String actionLookupName, javax.swing.text.JTextComponent txt, java.lang.String filters)
protected void	addFileField(java.lang.String actionLookupName, javax.swing.text.JTextComponent txt, java.lang.String filters, boolean isOutput)
protected void	addFileField(java.lang.String actionLookupName, javax.swing.text.JTextComponent txt, java.lang.String filters, boolean isOutput, java.lang.String action)
protected void	autoSetFieldNames() Automatically set the names of controls (JComponents) that are direct Fields of this class.
protected boolean	browseFile(javax.swing.text.JTextComponent field, java.lang.String filter, boolean forSave)
protected boolean	browseFile(PredictWindowBase.FileFieldInfo field)
protected void	browseRecentFile(javax.swing.JComponent displayTarget, PredictWindowBase.FileFieldInfo field)
protected boolean	cancelRunningTask() Cancel the active background task (if there is one) if it is cancelable.
protected void	enableDescendants(java.awt.Container parent, boolean enabled, java.awt.Component... exclude)
protected void	focusField(javax.swing.JComponent c) Attempts to show the field and set focus to it, possibly by activating the tab on which the control is placed.
protected java.lang.String	formatValue(java.lang.Object value)
protected boolean	frameClosing(javax.swing.event.InternalFrameEvent e) Indicates that the InternalFrame is closing.
protected java.lang.String	getControlDescription(javax.swing.JComponent c)
protected java.lang.Object	getControlValue(javax.swing.JComponent c)
protected PredictWindowBase.FileFieldInfo	getFileField(javax.swing.text.JTextComponent txt, boolean showErrorIfMissing)
protected PredictWindowBase.FileFieldInfo	getFileField(java.lang.String fieldName, boolean showErrorIfMissing)
protected PredictWindowBase.BackgroundTask	getRunningTask()
protected java.lang.String	getSettingsName(javax.swing.JComponent c)
protected java.lang.Number	getSpin(javax.swing.JSpinner spn)
protected double	getSpinDbl(javax.swing.JSpinner spn)
protected int	getSpinInt(javax.swing.JSpinner spn)
protected void	handleRecentControlValues(boolean writeValues, java.lang.String nodeName, java.lang.Iterable<javax.swing.JComponent> fields)
protected abstract void	handleSettings(boolean writeValues)
protected static DrawingWindow	launchDrawing(java.lang.String file, FileType type, java.lang.String addFile, FileType addType, int strand)
protected void	listenForActions(javax.swing.AbstractButton... buttons)
protected void	listenForActions(javax.swing.JComponent parent)
protected void	listenForActions(javax.swing.JComponent parent, java.lang.Class<? extends javax.swing.AbstractButton> type, java.awt.event.ActionListener listener)
protected void	loadRecent(java.lang.String nodeName, javax.swing.JComponent... fields)
void	pack()
protected <TTask extends PredictWindowBase.BackgroundTask> void	runInBackground(TTask task, java.util.function.Consumer<TTask> done)
protected void	saveRecent(java.lang.String nodeName, javax.swing.JComponent... fields)
protected void	saveRecentFiles(javax.swing.JTextField... fields)
(package private) void	setContent(javax.swing.JPanel content)
protected void	setControlValue(javax.swing.JComponent c, java.lang.Object value)
protected void	setSpin(javax.swing.JSpinner spn, double value)
protected void	setSpin(javax.swing.JSpinner spn, double value, double min, double max)
protected void	setSpin(javax.swing.JSpinner spn, double value, double min, double max, double step) Initialize a spinner with a SpinnerNumberModel.
protected void	setSpin(javax.swing.JSpinner spn, int value)
protected void	setSpin(javax.swing.JSpinner spn, int value, int min, int max)
protected void	setSpin(javax.swing.JSpinner spn, int value, int min, int max, int step)
void	showWindow() View the window.
protected void	startUiTimer()
protected void	stopUiTimer()
protected java.lang.String	stripControlPrefix(java.lang.String name)
protected abstract void	updateFormUI() Called periodically by a timer to update the user interface.
protected void	validateFailed(javax.swing.JComponent control, java.lang.String message, java.lang.Object... args)
protected void	validateFileField(javax.swing.text.JTextComponent txt, boolean allowEmpty)
protected void	validateFileField(javax.swing.text.JTextComponent txt, boolean allowEmpty, boolean forOutput) Verifies the existence of a file in a JTextComponent that has been added as a named file-field.
protected void	validateRequiredField(javax.swing.text.JTextComponent txt)

Methods inherited from class ur_rna.RNAstructureUI.windows.InternalWindow

createCustomMenus, frameActivated, frameClosed, getCustomMenus, invokeCommand, invokeCommand, invokeCommand, isActiveFrame, notifyUpdated, onFocusGained, processCommand, propertyChanged, setCaption, setCustomMenus

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, 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

controlPrefixes

private static java.lang.String[] controlPrefixes

fields

private java.util.HashMap<javax.swing.JComponent,PredictWindowBase.FieldInfo> fields

fileFields

private java.util.HashMap<java.lang.String,PredictWindowBase.FileFieldInfo> fileFields

numberFormatter

protected java.text.DecimalFormat numberFormatter

pnlClient

protected javax.swing.JPanel pnlClient

pnlContent

protected javax.swing.JPanel pnlContent

runningTask

private PredictWindowBase.BackgroundTask runningTask

TEMP_37C

public static final double TEMP_37C

See Also:

Constant Field Values

uiUpdateTimer

private javax.swing.Timer uiUpdateTimer

Constructor Detail

PredictWindowBase

public PredictWindowBase()

Method Detail

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Overrides:

actionPerformed in class InternalWindow

addField

protected void addField(javax.swing.JComponent c,
                        java.lang.String description,
                        java.lang.String settingsName)

addFileField

protected void addFileField(java.lang.String actionLookupName,
                            javax.swing.text.JTextComponent txt,
                            java.lang.String filters)

addFileField

protected void addFileField(java.lang.String actionLookupName,
                            javax.swing.text.JTextComponent txt,
                            java.lang.String filters,
                            boolean isOutput)

addFileField

protected void addFileField(java.lang.String actionLookupName,
                            javax.swing.text.JTextComponent txt,
                            java.lang.String filters,
                            boolean isOutput,
                            java.lang.String action)

autoSetFieldNames

protected void autoSetFieldNames()

Automatically set the names of controls (JComponents) that are direct Fields of this class.

browseFile

protected boolean browseFile(javax.swing.text.JTextComponent field,
                             java.lang.String filter,
                             boolean forSave)

browseFile

protected boolean browseFile(PredictWindowBase.FileFieldInfo field)

browseRecentFile

protected void browseRecentFile(javax.swing.JComponent displayTarget,
                                PredictWindowBase.FileFieldInfo field)

cancelRunningTask

protected boolean cancelRunningTask()

Cancel the active background task (if there is one) if it is cancelable. Show a message to the user if the task cannot be canceled at the current time.

Returns:

Returns true if there is no task or if it is cancelable. Returns false if the active task cannot be canceled at the current time.

enableDescendants

protected void enableDescendants(java.awt.Container parent,
                                 boolean enabled,
                                 java.awt.Component... exclude)

focusField

protected void focusField(javax.swing.JComponent c)

Attempts to show the field and set focus to it, possibly by activating the tab on which the control is placed.

Parameters:

c - The JComponent to show and set focus to.

formatValue

protected java.lang.String formatValue(java.lang.Object value)

frameClosing

protected boolean frameClosing(javax.swing.event.InternalFrameEvent e)

Description copied from class: InternalWindow

Indicates that the InternalFrame is closing. Return true to allow the window to close, or return false to prevent it.

Overrides:

frameClosing in class InternalWindow

Returns:

getControlDescription

protected java.lang.String getControlDescription(javax.swing.JComponent c)

getControlValue

protected java.lang.Object getControlValue(javax.swing.JComponent c)

getFileField

protected PredictWindowBase.FileFieldInfo getFileField(javax.swing.text.JTextComponent txt,
                                                       boolean showErrorIfMissing)

getFileField

protected PredictWindowBase.FileFieldInfo getFileField(java.lang.String fieldName,
                                                       boolean showErrorIfMissing)

getRunningTask

protected PredictWindowBase.BackgroundTask getRunningTask()

getSettingsName

protected java.lang.String getSettingsName(javax.swing.JComponent c)

getSpin

protected java.lang.Number getSpin(javax.swing.JSpinner spn)

getSpinDbl

protected double getSpinDbl(javax.swing.JSpinner spn)

getSpinInt

protected int getSpinInt(javax.swing.JSpinner spn)

handleRecentControlValues

protected void handleRecentControlValues(boolean writeValues,
                                         java.lang.String nodeName,
                                         java.lang.Iterable<javax.swing.JComponent> fields)

handleSettings

protected abstract void handleSettings(boolean writeValues)

launchDrawing

protected static DrawingWindow launchDrawing(java.lang.String file,
                                             FileType type,
                                             java.lang.String addFile,
                                             FileType addType,
                                             int strand)

listenForActions

protected void listenForActions(javax.swing.AbstractButton... buttons)

listenForActions

protected void listenForActions(javax.swing.JComponent parent)

listenForActions

protected void listenForActions(javax.swing.JComponent parent,
                                java.lang.Class<? extends javax.swing.AbstractButton> type,
                                java.awt.event.ActionListener listener)

loadRecent

protected void loadRecent(java.lang.String nodeName,
                          javax.swing.JComponent... fields)

pack

public void pack()

Overrides:

pack in class javax.swing.JInternalFrame

runInBackground

protected <TTask extends PredictWindowBase.BackgroundTask> void runInBackground(TTask task,
                                                                                java.util.function.Consumer<TTask> done)

saveRecent

protected void saveRecent(java.lang.String nodeName,
                          javax.swing.JComponent... fields)

saveRecentFiles

protected void saveRecentFiles(javax.swing.JTextField... fields)

setContent

void setContent(javax.swing.JPanel content)

setControlValue

protected void setControlValue(javax.swing.JComponent c,
                               java.lang.Object value)

setSpin

protected void setSpin(javax.swing.JSpinner spn,
                       double value)

setSpin

protected void setSpin(javax.swing.JSpinner spn,
                       double value,
                       double min,
                       double max)

setSpin

protected void setSpin(javax.swing.JSpinner spn,
                       double value,
                       double min,
                       double max,
                       double step)

Initialize a spinner with a SpinnerNumberModel.

Parameters:

spn - The spinner

value - The initial value.

min - The minimum value.

max - The maximim value.

step - Teh step size.

setSpin

protected void setSpin(javax.swing.JSpinner spn,
                       int value)

setSpin

protected void setSpin(javax.swing.JSpinner spn,
                       int value,
                       int min,
                       int max)

setSpin

protected void setSpin(javax.swing.JSpinner spn,
                       int value,
                       int min,
                       int max,
                       int step)

showWindow

public void showWindow()

Description copied from class: InternalWindow

View the window.

Overrides:

showWindow in class InternalWindow

startUiTimer

protected void startUiTimer()

stopUiTimer

protected void stopUiTimer()

stripControlPrefix

protected java.lang.String stripControlPrefix(java.lang.String name)

updateFormUI

protected abstract void updateFormUI()

Called periodically by a timer to update the user interface.

validateFailed

protected void validateFailed(javax.swing.JComponent control,
                              java.lang.String message,
                              java.lang.Object... args)
                       throws FormValidationException

Throws:

FormValidationException

validateFileField

protected void validateFileField(javax.swing.text.JTextComponent txt,
                                 boolean allowEmpty)
                          throws FormValidationException

Throws:

FormValidationException

validateFileField

protected void validateFileField(javax.swing.text.JTextComponent txt,
                                 boolean allowEmpty,
                                 boolean forOutput)
                          throws FormValidationException

Verifies the existence of a file in a JTextComponent that has been added as a named file-field.

Parameters:

txt - The JTextComponent used to accept file entry.

allowEmpty - Whether the field is optional (and so can be empty and still be valid input).

forOutput - Whether the field is the name of an output file. (If so, it does not need to exist, but must be in a valid directory.

Throws:

FormValidationException - if txt fails validation.

validateRequiredField

protected void validateRequiredField(javax.swing.text.JTextComponent txt)
                              throws FormValidationException

Throws:

FormValidationException