ur_rna.RNAstructureUI.windows

Class PredictTwoStructureWindow

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.PredictTwoStructureWindow

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 PredictTwoStructureWindow
extends PredictWindowBase

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private class	PredictTwoStructureWindow.PredictTask

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	btnCancelTask
private javax.swing.JButton	btnResetAll
private javax.swing.JButton	btnResetOptions
private javax.swing.JButton	btnResetPartsOptions
private javax.swing.JButton	btnStartCalc
private javax.swing.JCheckBox	chkBaseInserts
private javax.swing.JCheckBox	chkShowDescription
private javax.swing.JComboBox	cmbPartsMode
private javax.swing.JPanel	contentPanel
private java.util.HashMap<javax.swing.JComponent,java.lang.Object>	defaultOptionValues
private java.lang.String	lastOutFile1
private java.lang.String	lastOutFile2
private java.lang.String	lastSeqFile1
private java.lang.String	lastSeqFile2
private javax.swing.JLabel	lblBaseInserts
private javax.swing.JLabel	lblOptionWarning
private javax.swing.JLabel	lblProgressPercent
private javax.swing.JLabel	lblTaskStatus
private javax.swing.JLabel	lblToolDescription
private java.util.ArrayList<javax.swing.JComponent>	optionsControls
private javax.swing.JPanel	pnlConstraints
private javax.swing.JPanel	pnlOptions
private javax.swing.JPanel	pnlOutput
private javax.swing.JPanel	pnlPartsOptions
private javax.swing.JPanel	pnlSequences
private javax.swing.JPanel	pnlTaskStatus
private javax.swing.JProgressBar	prgTaskProgress
private static long	serialVersionUID
private java.util.ArrayList<javax.swing.JComponent>	settingsControls
private java.lang.String	settingsNodeName
private javax.swing.JSpinner	spnAlnWindowSize
private javax.swing.JSpinner	spnGapPenalty
private javax.swing.JSpinner	spnMaxEnergyDiff
private javax.swing.JSpinner	spnMaxStructs
private javax.swing.JSpinner	spnStochasticSamples
private javax.swing.JSpinner	spnWindowSize
private javax.swing.JTabbedPane	tabControls
private javax.swing.JTextField	txtConFile1
private javax.swing.JTextField	txtConFile2
private javax.swing.JTextField	txtOutputFile1
private javax.swing.JTextField	txtOutputFile2
private javax.swing.JTextField	txtSeqFile1
private javax.swing.JTextField	txtSeqFile2

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
PredictTwoStructureWindow() 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(PredictTwoStructureWindow.PredictTask task)
private void	createUIComponents()
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

btnCancelTask

private javax.swing.JButton btnCancelTask

btnResetAll

private javax.swing.JButton btnResetAll

btnResetOptions

private javax.swing.JButton btnResetOptions

btnResetPartsOptions

private javax.swing.JButton btnResetPartsOptions

btnStartCalc

private javax.swing.JButton btnStartCalc

chkBaseInserts

private javax.swing.JCheckBox chkBaseInserts

chkShowDescription

private javax.swing.JCheckBox chkShowDescription

cmbPartsMode

private javax.swing.JComboBox cmbPartsMode

contentPanel

private javax.swing.JPanel contentPanel

defaultOptionValues

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

lastOutFile1

private java.lang.String lastOutFile1

lastOutFile2

private java.lang.String lastOutFile2

lastSeqFile1

private java.lang.String lastSeqFile1

lastSeqFile2

private java.lang.String lastSeqFile2

lblBaseInserts

private javax.swing.JLabel lblBaseInserts

lblOptionWarning

private javax.swing.JLabel lblOptionWarning

lblProgressPercent

private javax.swing.JLabel lblProgressPercent

lblTaskStatus

private javax.swing.JLabel lblTaskStatus

lblToolDescription

private javax.swing.JLabel lblToolDescription

optionsControls

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

pnlConstraints

private javax.swing.JPanel pnlConstraints

pnlOptions

private javax.swing.JPanel pnlOptions

pnlOutput

private javax.swing.JPanel pnlOutput

pnlPartsOptions

private javax.swing.JPanel pnlPartsOptions

pnlSequences

private javax.swing.JPanel pnlSequences

pnlTaskStatus

private javax.swing.JPanel pnlTaskStatus

prgTaskProgress

private javax.swing.JProgressBar prgTaskProgress

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

spnAlnWindowSize

private javax.swing.JSpinner spnAlnWindowSize

spnGapPenalty

private javax.swing.JSpinner spnGapPenalty

spnMaxEnergyDiff

private javax.swing.JSpinner spnMaxEnergyDiff

spnMaxStructs

private javax.swing.JSpinner spnMaxStructs

spnStochasticSamples

private javax.swing.JSpinner spnStochasticSamples

spnWindowSize

private javax.swing.JSpinner spnWindowSize

tabControls

private javax.swing.JTabbedPane tabControls

txtConFile1

private javax.swing.JTextField txtConFile1

txtConFile2

private javax.swing.JTextField txtConFile2

txtOutputFile1

private javax.swing.JTextField txtOutputFile1

txtOutputFile2

private javax.swing.JTextField txtOutputFile2

txtSeqFile1

private javax.swing.JTextField txtSeqFile1

txtSeqFile2

private javax.swing.JTextField txtSeqFile2

Constructor Detail

PredictTwoStructureWindow

public PredictTwoStructureWindow()

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(PredictTwoStructureWindow.PredictTask task)

createUIComponents

private void createUIComponents()

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()