ur_rna.RNAstructureUI.windows

Class PredictMultiStructureWindow

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.PredictMultiStructureWindow

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 PredictMultiStructureWindow
extends PredictWindowBase

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private class	PredictMultiStructureWindow.PredictTask
private class	PredictMultiStructureWindow.SequenceItem

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 boolean	_seqInfoUpdating
private javax.swing.JButton	btnCancelTask
private javax.swing.JButton	btnClearList
private javax.swing.JButton	btnMoveDn
private javax.swing.JButton	btnMoveUp
private javax.swing.JButton	btnRemove
private javax.swing.JButton	btnResetAll
private javax.swing.JButton	btnResetMultiOptions
private javax.swing.JButton	btnResetOptions
private javax.swing.JButton	btnResetTurboOptions
private javax.swing.JButton	btnStartCalc
private javax.swing.JCheckBox	chkAllowBaseInserts
private javax.swing.JCheckBox	chkShowDescription
private javax.swing.JComboBox	cmbTurboMode
private javax.swing.JPanel	contentPanel
private java.util.HashMap<javax.swing.JComponent,java.lang.Object>	defaultOptionValues
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 javax.swing.JList<PredictMultiStructureWindow.SequenceItem>	lstSeqs
private java.util.ArrayList<javax.swing.JComponent>	optionsControls
private javax.swing.JPanel	pnlMultiOptions
private javax.swing.JPanel	pnlOptions
private javax.swing.JPanel	pnlOutput
private javax.swing.JPanel	pnlSeqInfo
private javax.swing.JPanel	pnlSequences
private javax.swing.JPanel	pnlTaskStatus
private javax.swing.JPanel	pnlTurboOptions
private javax.swing.JProgressBar	prgTaskProgress
private java.util.ArrayList<PredictMultiStructureWindow.SequenceItem>	seqList
private static long	serialVersionUID
private java.util.ArrayList<javax.swing.JComponent>	settingsControls
private java.lang.String	settingsNodeName
private javax.swing.JSpinner	spnMultiAlnSize
private javax.swing.JSpinner	spnMultiDsvChange
private javax.swing.JSpinner	spnMultiGapPenalty
private javax.swing.JSpinner	spnMultiIterations
private javax.swing.JSpinner	spnMultiMaxEnergyDiff
private javax.swing.JSpinner	spnMultiMaxPairs
private javax.swing.JSpinner	spnMultiMaxStructures
private javax.swing.JSpinner	spnMultiWindowSize
private javax.swing.JSpinner	spnTemperature
private javax.swing.JSpinner	spnTurboGamma
private javax.swing.JSpinner	spnTurboIterations
private javax.swing.JSpinner	spnTurboMaxEnergyDiff
private javax.swing.JSpinner	spnTurboMaxStructures
private javax.swing.JSpinner	spnTurboMEAGamma
private javax.swing.JSpinner	spnTurboMinHelix
private javax.swing.JSpinner	spnTurboPKIterations
private javax.swing.JSpinner	spnTurboThreshold
private javax.swing.JSpinner	spnTurboWindowSize
private javax.swing.JTabbedPane	tabControls
private javax.swing.JTextField	txtMSeqFile
private javax.swing.JTextField	txtOutputFile
private javax.swing.JTextField	txtSeqFile

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
PredictMultiStructureWindow() 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!
(package private) void	addOptionControls(javax.swing.JComponent parent)
private void	addSequence(java.lang.String label, java.lang.String seqFile, java.lang.String ctFile)
private void	addSequenceFile(java.lang.String path, boolean multiSeq)
private void	calcComplete(PredictMultiStructureWindow.PredictTask task)
private void	createUIComponents()
private void	deleteSequence(PredictMultiStructureWindow.SequenceItem seq)
private PredictMultiStructureWindow.SequenceItem	getSelectedSequence()
protected void	handleSettings(boolean writeValues)
private void	loadSequenceInfo(PredictMultiStructureWindow.SequenceItem seq)
private void	loadSettingsDefaults()
private void	moveSequence(PredictMultiStructureWindow.SequenceItem seq, int direction)
private void	onSequenceSelected(javax.swing.event.ListSelectionEvent e)
protected void	processCommand(InternalWindow.CommandInfo ci) Perform an action specific to this window.
private void	refreshSeqList()
private void	refreshSeqList(boolean reselect)
private void	refreshSeqList(PredictMultiStructureWindow.SequenceItem selectAfterRefresh)
private void	resetOptionsInPanel(javax.swing.JComponent parent)
private void	runCalc()
private void	setSelectedSequence(PredictMultiStructureWindow.SequenceItem sel)
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 void	updateSequenceInfoFromUI()
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

_seqInfoUpdating

private boolean _seqInfoUpdating

btnCancelTask

private javax.swing.JButton btnCancelTask

btnClearList

private javax.swing.JButton btnClearList

btnMoveDn

private javax.swing.JButton btnMoveDn

btnMoveUp

private javax.swing.JButton btnMoveUp

btnRemove

private javax.swing.JButton btnRemove

btnResetAll

private javax.swing.JButton btnResetAll

btnResetMultiOptions

private javax.swing.JButton btnResetMultiOptions

btnResetOptions

private javax.swing.JButton btnResetOptions

btnResetTurboOptions

private javax.swing.JButton btnResetTurboOptions

btnStartCalc

private javax.swing.JButton btnStartCalc

chkAllowBaseInserts

private javax.swing.JCheckBox chkAllowBaseInserts

chkShowDescription

private javax.swing.JCheckBox chkShowDescription

cmbTurboMode

private javax.swing.JComboBox cmbTurboMode

contentPanel

private javax.swing.JPanel contentPanel

defaultOptionValues

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

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

lstSeqs

private javax.swing.JList<PredictMultiStructureWindow.SequenceItem> lstSeqs

optionsControls

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

pnlMultiOptions

private javax.swing.JPanel pnlMultiOptions

pnlOptions

private javax.swing.JPanel pnlOptions

pnlOutput

private javax.swing.JPanel pnlOutput

pnlSeqInfo

private javax.swing.JPanel pnlSeqInfo

pnlSequences

private javax.swing.JPanel pnlSequences

pnlTaskStatus

private javax.swing.JPanel pnlTaskStatus

pnlTurboOptions

private javax.swing.JPanel pnlTurboOptions

prgTaskProgress

private javax.swing.JProgressBar prgTaskProgress

seqList

private java.util.ArrayList<PredictMultiStructureWindow.SequenceItem> seqList

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

spnMultiAlnSize

private javax.swing.JSpinner spnMultiAlnSize

spnMultiDsvChange

private javax.swing.JSpinner spnMultiDsvChange

spnMultiGapPenalty

private javax.swing.JSpinner spnMultiGapPenalty

spnMultiIterations

private javax.swing.JSpinner spnMultiIterations

spnMultiMaxEnergyDiff

private javax.swing.JSpinner spnMultiMaxEnergyDiff

spnMultiMaxPairs

private javax.swing.JSpinner spnMultiMaxPairs

spnMultiMaxStructures

private javax.swing.JSpinner spnMultiMaxStructures

spnMultiWindowSize

private javax.swing.JSpinner spnMultiWindowSize

spnTemperature

private javax.swing.JSpinner spnTemperature

spnTurboGamma

private javax.swing.JSpinner spnTurboGamma

spnTurboIterations

private javax.swing.JSpinner spnTurboIterations

spnTurboMaxEnergyDiff

private javax.swing.JSpinner spnTurboMaxEnergyDiff

spnTurboMaxStructures

private javax.swing.JSpinner spnTurboMaxStructures

spnTurboMEAGamma

private javax.swing.JSpinner spnTurboMEAGamma

spnTurboMinHelix

private javax.swing.JSpinner spnTurboMinHelix

spnTurboPKIterations

private javax.swing.JSpinner spnTurboPKIterations

spnTurboThreshold

private javax.swing.JSpinner spnTurboThreshold

spnTurboWindowSize

private javax.swing.JSpinner spnTurboWindowSize

tabControls

private javax.swing.JTabbedPane tabControls

txtMSeqFile

private javax.swing.JTextField txtMSeqFile

txtOutputFile

private javax.swing.JTextField txtOutputFile

txtSeqFile

private javax.swing.JTextField txtSeqFile

Constructor Detail

PredictMultiStructureWindow

public PredictMultiStructureWindow()

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

addOptionControls

void addOptionControls(javax.swing.JComponent parent)

addSequence

private void addSequence(java.lang.String label,
                         java.lang.String seqFile,
                         java.lang.String ctFile)

addSequenceFile

private void addSequenceFile(java.lang.String path,
                             boolean multiSeq)

calcComplete

private void calcComplete(PredictMultiStructureWindow.PredictTask task)

createUIComponents

private void createUIComponents()

deleteSequence

private void deleteSequence(PredictMultiStructureWindow.SequenceItem seq)

getSelectedSequence

private PredictMultiStructureWindow.SequenceItem getSelectedSequence()

handleSettings

protected void handleSettings(boolean writeValues)

Specified by:

handleSettings in class PredictWindowBase

loadSequenceInfo

private void loadSequenceInfo(PredictMultiStructureWindow.SequenceItem seq)

loadSettingsDefaults

private void loadSettingsDefaults()

moveSequence

private void moveSequence(PredictMultiStructureWindow.SequenceItem seq,
                          int direction)

onSequenceSelected

private void onSequenceSelected(javax.swing.event.ListSelectionEvent e)

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.

refreshSeqList

private void refreshSeqList()

refreshSeqList

private void refreshSeqList(boolean reselect)

refreshSeqList

private void refreshSeqList(PredictMultiStructureWindow.SequenceItem selectAfterRefresh)

resetOptionsInPanel

private void resetOptionsInPanel(javax.swing.JComponent parent)

runCalc

private void runCalc()

setSelectedSequence

private void setSelectedSequence(PredictMultiStructureWindow.SequenceItem sel)

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

updateSequenceInfoFromUI

private void updateSequenceInfoFromUI()

verifyInput

private boolean verifyInput()