ur_rna.RNAstructureUI.windows

Class PredictSingleStructureWindow

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

ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow

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

public class PredictSingleStructureWindow
extends PredictWindowBase

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private class	PredictSingleStructureWindow.PredictSingleStructureTask

Nested classes/interfaces inherited from class ur_rna.RNAstructureUI.windows.PredictWindowBase

PredictWindowBase.BackgroundTask, PredictWindowBase.FieldInfo, PredictWindowBase.FileFieldInfo, 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 javax.swing.JButton	btnBrowseCon
private javax.swing.JButton	btnBrowseOutput
private javax.swing.JButton	btnBrowseSeq
private javax.swing.JButton	btnBrowseShape
private javax.swing.JButton	btnCancelTask
private javax.swing.JButton	btnRecentCon
private javax.swing.JButton	btnRecentOutput
private javax.swing.JButton	btnRecentSeq
private javax.swing.JButton	btnRecentShape
private javax.swing.JButton	btnResetOptions
private javax.swing.JButton	btnStartCalc
private javax.swing.JCheckBox	chkShowDescription
private javax.swing.JPanel	contentPanel
private java.util.HashMap<javax.swing.JComponent,java.lang.Object>	defaultOptionValues
private java.lang.String	lastOutFile
private java.lang.String	lastSeqFile
private javax.swing.JLabel	lblOptionWarning
private javax.swing.JLabel	lblProgressPercent
private javax.swing.JLabel	lblTaskStatus
private javax.swing.JLabel	lblToolDescription
private javax.swing.JRadioButton	optDNA
private javax.swing.JRadioButton	optEnterSeq
private java.util.ArrayList<javax.swing.JComponent>	optionsControls
private javax.swing.JRadioButton	optRNA
private javax.swing.JRadioButton	optSeqFile
private javax.swing.JPanel	pnlOutput
private javax.swing.JPanel	pnlTaskStatus
private javax.swing.JProgressBar	prgTaskProgress
private javax.swing.JScrollPane	scrlSequence
private static long	serialVersionUID
private java.util.ArrayList<javax.swing.JComponent>	settingsControls
private java.lang.String	settingsNodeName
private javax.swing.JSpinner	spnGamma
private javax.swing.JSpinner	spnIterations
private javax.swing.JSpinner	spnMaxEnergyDiff
private javax.swing.JSpinner	spnMaxLoopSize
private javax.swing.JSpinner	spnMaxStructs
private javax.swing.JSpinner	spnMinHelixLen
private javax.swing.JSpinner	spnShapeIntercept
private javax.swing.JSpinner	spnShapeSlope
private javax.swing.JSpinner	spnTemperature
private javax.swing.JSpinner	spnWindowSize
private javax.swing.JTabbedPane	tabControls
private javax.swing.JTextField	txtConFile
private javax.swing.JTextField	txtOutputFile
private javax.swing.JTextField	txtSeqFile
private javax.swing.JTextField	txtSeqTitle
private javax.swing.JTextArea	txtSequence
private javax.swing.JTextField	txtShapeFile

Fields inherited from class ur_rna.RNAstructureUI.windows.PredictWindowBase

numberFormatter, pnlClient, pnlContent, TEMP_37C

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
PredictSingleStructureWindow() Constructor.

Method Summary

Modifier and Type	Method and Description
javax.swing.JComponent	$$$getRootComponent$$$()
private void	$$$setupUI$$$() Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
private void	calcComplete(PredictSingleStructureWindow.PredictSingleStructureTask task)
protected void	handleSettings(boolean writeValues)
private void	loadSettingsDefaults()
protected void	processCommand(InternalWindow.CommandInfo ci) Perform an action specific to this window.
private void	runCalc()
private void	setTaskStatus(int progress, java.lang.String status)
void	showWindow() View the window.
protected void	updateFormUI() Called periodically by a timer to update the user interface.
private boolean	verifyInput()

Methods inherited from class ur_rna.RNAstructureUI.windows.PredictWindowBase

actionPerformed, addField, addFileField, addFileField, addFileField, autoSetFieldNames, browseFile, browseFile, browseRecentFile, cancelRunningTask, enableDescendants, focusField, formatValue, frameClosing, getControlDescription, getControlValue, getFileField, getFileField, getRunningTask, getSettingsName, getSpin, getSpinDbl, getSpinInt, handleRecentControlValues, launchDrawing, listenForActions, listenForActions, listenForActions, loadRecent, pack, runInBackground, saveRecent, saveRecentFiles, setContent, setControlValue, setSpin, setSpin, setSpin, setSpin, setSpin, setSpin, startUiTimer, stopUiTimer, stripControlPrefix, validateFailed, validateFileField, validateFileField, validateRequiredField

Methods inherited from class ur_rna.RNAstructureUI.windows.InternalWindow

createCustomMenus, frameActivated, frameClosed, getCustomMenus, invokeCommand, invokeCommand, invokeCommand, isActiveFrame, notifyUpdated, onFocusGained, 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

btnBrowseCon

private javax.swing.JButton btnBrowseCon

btnBrowseOutput

private javax.swing.JButton btnBrowseOutput

btnBrowseSeq

private javax.swing.JButton btnBrowseSeq

btnBrowseShape

private javax.swing.JButton btnBrowseShape

btnCancelTask

private javax.swing.JButton btnCancelTask

btnRecentCon

private javax.swing.JButton btnRecentCon

btnRecentOutput

private javax.swing.JButton btnRecentOutput

btnRecentSeq

private javax.swing.JButton btnRecentSeq

btnRecentShape

private javax.swing.JButton btnRecentShape

btnResetOptions

private javax.swing.JButton btnResetOptions

btnStartCalc

private javax.swing.JButton btnStartCalc

chkShowDescription

private javax.swing.JCheckBox chkShowDescription

contentPanel

private javax.swing.JPanel contentPanel

defaultOptionValues

private java.util.HashMap<javax.swing.JComponent,java.lang.Object> defaultOptionValues

lastOutFile

private java.lang.String lastOutFile

lastSeqFile

private java.lang.String lastSeqFile

lblOptionWarning

private javax.swing.JLabel lblOptionWarning

lblProgressPercent

private javax.swing.JLabel lblProgressPercent

lblTaskStatus

private javax.swing.JLabel lblTaskStatus

lblToolDescription

private javax.swing.JLabel lblToolDescription

optDNA

private javax.swing.JRadioButton optDNA

optEnterSeq

private javax.swing.JRadioButton optEnterSeq

optionsControls

private java.util.ArrayList<javax.swing.JComponent> optionsControls

optRNA

private javax.swing.JRadioButton optRNA

optSeqFile

private javax.swing.JRadioButton optSeqFile

pnlOutput

private javax.swing.JPanel pnlOutput

pnlTaskStatus

private javax.swing.JPanel pnlTaskStatus

prgTaskProgress

private javax.swing.JProgressBar prgTaskProgress

scrlSequence

private javax.swing.JScrollPane scrlSequence

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

settingsControls

private java.util.ArrayList<javax.swing.JComponent> settingsControls

settingsNodeName

private final java.lang.String settingsNodeName

See Also:

Constant Field Values

spnGamma

private javax.swing.JSpinner spnGamma

spnIterations

private javax.swing.JSpinner spnIterations

spnMaxEnergyDiff

private javax.swing.JSpinner spnMaxEnergyDiff

spnMaxLoopSize

private javax.swing.JSpinner spnMaxLoopSize

spnMaxStructs

private javax.swing.JSpinner spnMaxStructs

spnMinHelixLen

private javax.swing.JSpinner spnMinHelixLen

spnShapeIntercept

private javax.swing.JSpinner spnShapeIntercept

spnShapeSlope

private javax.swing.JSpinner spnShapeSlope

spnTemperature

private javax.swing.JSpinner spnTemperature

spnWindowSize

private javax.swing.JSpinner spnWindowSize

tabControls

private javax.swing.JTabbedPane tabControls

txtConFile

private javax.swing.JTextField txtConFile

txtOutputFile

private javax.swing.JTextField txtOutputFile

txtSeqFile

private javax.swing.JTextField txtSeqFile

txtSeqTitle

private javax.swing.JTextField txtSeqTitle

txtSequence

private javax.swing.JTextArea txtSequence

txtShapeFile

private javax.swing.JTextField txtShapeFile

Constructor Detail

PredictSingleStructureWindow

public PredictSingleStructureWindow()

Constructor.

Method Detail

$$$getRootComponent$$$

public javax.swing.JComponent $$$getRootComponent$$$()

No IDE Inspections

ALL

$$$setupUI$$$

private void $$$setupUI$$$()

Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!

No IDE Inspections

ALL

calcComplete

private void calcComplete(PredictSingleStructureWindow.PredictSingleStructureTask task)

handleSettings

protected void handleSettings(boolean writeValues)

Specified by:

handleSettings in class PredictWindowBase

loadSettingsDefaults

private void loadSettingsDefaults()

processCommand

protected void processCommand(InternalWindow.CommandInfo ci)

Description copied from class: InternalWindow

Perform an action specific to this window.

Overrides:

processCommand in class InternalWindow

Parameters:

ci - Information about the command.

runCalc

private void runCalc()

setTaskStatus

private void setTaskStatus(int progress,
                           java.lang.String status)

showWindow

public void showWindow()

Description copied from class: InternalWindow

View the window.

Overrides:

showWindow in class PredictWindowBase

updateFormUI

protected void updateFormUI()

Description copied from class: PredictWindowBase

Called periodically by a timer to update the user interface.

Specified by:

updateFormUI in class PredictWindowBase

verifyInput

private boolean verifyInput()