ur_rna.RNAstructureUI.windows

Class OligoWalkWindow

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

ur_rna.RNAstructureUI.windows.OligoWalkWindow

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 OligoWalkWindow
extends ModuleWindow

A class that handles creation of windows for the OligoWalk module. The OligoWalk module creates two linked windows, an input window and an output (results) window. The two windows share a back end calculator. This module is only used with RNA.

Note also that this class violates the usual 500 line class length coding standard limit. This is because both the input window and the results window contain objects unique to themselves, and the results window, which is more complex than the input window, relies on the same data structure as the input window.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	OligoWalkWindow.BarButton An inner class that encapsulates a bar button.
class	OligoWalkWindow.OligoSelectionDialog An inner class which creates a dialog that selects a particular oligo to move to in the results window.
(package private) class	OligoWalkWindow.OligoWalkResultsMenu An inner class that handles creation of the oligo graph menu for the OligoWalk results window.
class	OligoWalkWindow.SpinnerPanel An class that creates a panel containing a single spinner with a label.
class	OligoWalkWindow.StringComboBox An inner class that creates a combo box holding a string list.

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	isInputWindow A boolean that tells whether this window is an input window or not.
private javax.swing.JPanel	panelInput
private javax.swing.JPanel	panelResults The box that holds the results.
private static long	serialVersionUID

Fields inherited from class ur_rna.RNAstructureUI.windows.ModuleWindow

isRNA, lastUpdate, log, mainCalcThread, progressIndicator, protectedExamplesDir, self, 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

Constructor and Description
OligoWalkWindow() Constructor.

Method Summary

Modifier and Type	Method and Description
private void	buildResultsWindow(java.lang.String file, int target, int start, int stop) Build the results window for this OligoWalk calculation.
protected MergeMenu[]	createCustomMenus() Override to create one or more custom menus that should be added to the main frame whenever this internal frame is active.
private void	createInputPanel() Create the panel which holds input controls.
private void	createResultsPanel() Create the panel which holds results data.
protected void	makeInputControls() Make any input controls necessary to get data from this window for a calculation.
protected void	processCommand(InternalWindow.CommandInfo ci) Perform an action specific to this window.
protected boolean	runMainCalculation() Run the module calculation in the back end.
private void	setOligoData(int index) Set the data for a particular oligo.

Methods inherited from class ur_rna.RNAstructureUI.windows.ModuleWindow

calcWasCanceled, cancelMainCalculation, close, closeProgress, closeProgress, combineFileNames, displayCalcError, drawStructures, getInputControl, getInputControl, getOutputFile, getOutputFile, makeStartButton, placeComponent, promptDraw, promptDraw, runOnUiThread, setAnchorCenter, setAnchorNorth, setFillCenter, setFillHorizontal, setGrid, setInsets, setPad, showDrawProgress, showDrawProgress, showProgress, showProgress, showProgress, showProgress, updateCalcProgress, verifyBackendResult

Methods inherited from class ur_rna.RNAstructureUI.windows.InternalWindow

actionPerformed, 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

isInputWindow

private boolean isInputWindow

A boolean that tells whether this window is an input window or not.

panelInput

private javax.swing.JPanel panelInput

panelResults

private javax.swing.JPanel panelResults

The box that holds the results.

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

OligoWalkWindow

public OligoWalkWindow()

Constructor.

Note that since this module is unique to RNA, the nucleic acid type is hard-coded as RNA.

Method Detail

buildResultsWindow

private void buildResultsWindow(java.lang.String file,
                                int target,
                                int start,
                                int stop)

Build the results window for this OligoWalk calculation.

Parameters:

file - The report file written for this calculation.

target - The length of the entire target.

start - The start index where hybridization can occur.

stop - The stop index where hybridization can occur.

createCustomMenus

protected MergeMenu[] createCustomMenus()

Description copied from class: InternalWindow

Override to create one or more custom menus that should be added to the main frame whenever this internal frame is active.

Overrides:

createCustomMenus in class InternalWindow

Returns:

an array of MergeMenu menus, or null if this window does not require any custom menus.

createInputPanel

private void createInputPanel()

Create the panel which holds input controls.

createResultsPanel

private void createResultsPanel()

Create the panel which holds results data.

The panel created by this method only builds the general layout of the results window; it doesn't include real results.

makeInputControls

protected void makeInputControls()

Make any input controls necessary to get data from this window for a calculation.

Note that this version of the function does NOT use the placeComponent method, because it builds on a panel rather than the content pane.

Unlike other derived classes of ModuleWindow, it holds two panels, an input panel and a results panel, each of which are visible when needed.

Specified by:

makeInputControls in class ModuleWindow

processCommand

protected void processCommand(InternalWindow.CommandInfo ci)

Description copied from class: ModuleWindow

Perform an action specific to this window.

Overrides:

processCommand in class ModuleWindow

Parameters:

ci - Information about the command.

runMainCalculation

protected boolean runMainCalculation()

Description copied from class: ModuleWindow

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.

Specified by:

runMainCalculation in class ModuleWindow

setOligoData

private void setOligoData(int index)

Set the data for a particular oligo.

Parameters:

index - The index of the oligo to set.