ur_rna.RNAstructureUI.menus

Class ConstraintsMenu

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.AbstractButton

javax.swing.JMenuItem

javax.swing.JMenu

ur_rna.Utilities.swing.MergeMenu

ur_rna.RNAstructureUI.menus.MainMenu

ur_rna.RNAstructureUI.menus.ConstraintsMenu

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.ItemSelectable, java.awt.MenuContainer, java.io.Serializable, java.lang.Cloneable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.MenuElement, javax.swing.SwingConstants, IMenuItem, IMergeItem

public class ConstraintsMenu
extends MainMenu

A class that creates a folding constraints menu.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ConstraintsMenu.NucOrHelixDialog An inner class which creates a dialog that sets constraints on single nucleotides or helices.

Nested classes/interfaces inherited from class javax.swing.JMenu

javax.swing.JMenu.AccessibleJMenu, javax.swing.JMenu.WinListener

Nested classes/interfaces inherited from class javax.swing.JMenuItem

javax.swing.JMenuItem.AccessibleJMenuItem

Nested classes/interfaces inherited from class javax.swing.AbstractButton

javax.swing.AbstractButton.AccessibleAbstractButton, javax.swing.AbstractButton.ButtonChangeListener

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

Nested classes/interfaces inherited from interface ur_rna.Utilities.swing.IMergeItem

IMergeItem.Proxy

Field Summary

Fields

Modifier and Type	Field and Description
private RNAstructureBackendCalculator	backend The back end calculator that's linked to this menu.
private static long	serialVersionUID
private int	str The strand this constraints menu deals with.

Fields inherited from class ur_rna.Utilities.swing.MergeMenu

subItemMergePos

Fields inherited from class javax.swing.JMenu

popupListener

Fields inherited from class javax.swing.AbstractButton

actionListener, BORDER_PAINTED_CHANGED_PROPERTY, changeEvent, changeListener, CONTENT_AREA_FILLED_CHANGED_PROPERTY, DISABLED_ICON_CHANGED_PROPERTY, DISABLED_SELECTED_ICON_CHANGED_PROPERTY, FOCUS_PAINTED_CHANGED_PROPERTY, HORIZONTAL_ALIGNMENT_CHANGED_PROPERTY, HORIZONTAL_TEXT_POSITION_CHANGED_PROPERTY, ICON_CHANGED_PROPERTY, itemListener, MARGIN_CHANGED_PROPERTY, MNEMONIC_CHANGED_PROPERTY, model, MODEL_CHANGED_PROPERTY, PRESSED_ICON_CHANGED_PROPERTY, ROLLOVER_ENABLED_CHANGED_PROPERTY, ROLLOVER_ICON_CHANGED_PROPERTY, ROLLOVER_SELECTED_ICON_CHANGED_PROPERTY, SELECTED_ICON_CHANGED_PROPERTY, TEXT_CHANGED_PROPERTY, VERTICAL_ALIGNMENT_CHANGED_PROPERTY, VERTICAL_TEXT_POSITION_CHANGED_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 ur_rna.Utilities.swing.IMergeItem

MergePosDefault, MergePosInitial, MergePosInvalid, MergePosMax, MergePosMin

Fields inherited from interface javax.swing.SwingConstants

BOTTOM, CENTER, EAST, HORIZONTAL, LEADING, LEFT, NEXT, NORTH, NORTH_EAST, NORTH_WEST, PREVIOUS, RIGHT, SOUTH, SOUTH_EAST, SOUTH_WEST, TOP, TRAILING, VERTICAL, WEST

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Constructor and Description
ConstraintsMenu(RNAstructureBackendCalculator calc) General Constructor.

Method Summary

Modifier and Type	Method and Description
void	addGeneralSection() Add a menu section of general constraints commands.
void	addMaxPairingDistanceSection() Add a menu section that handles maximum pairing distance.
void	addSaveRestoreSection() Add a menu section that handles saving and restoring constraints.
void	addSHAPESection() Add a menu section that handles SHAPE constraints.
void	addShowResetSection() Add a menu section that handles showing and resetting constraints.
void	buildDynalignAlignmentMenu() Build a complete menu that handles Dynalign alignment constraints.
void	buildMaxLoopMenu() Build a complete menu that handles maximum loop size.
ConstraintsMenu	buildTemperatureMenu() Build a complete menu that handles temperature.
void	buildUnimolecularMenu() Build a complete menu that handles if unimolecular pairs are allowed.
java.lang.String	getMergeName()
protected void	onMenuAction(java.lang.String command, java.awt.event.ActionEvent ev) Do any actions specific to this menu.
private boolean	showDeletionConfirmation() Show a dialog that asks whether constraints should be deleted.

Methods inherited from class ur_rna.RNAstructureUI.menus.MainMenu

actionPerformed, addCheckItem, addCheckItem, addItem, addItem, addItem, addItem, addItem, addItem, addItem, createCheckItem, createMenuItem, initItem

Methods inherited from class ur_rna.Utilities.swing.MergeMenu

add, add, add, add, addAll, addCheck, addSeparator, addSeparator, getMergePos, getSubItemMergePos, insertMergeGap, insertMergeGap, setMergePos, setSubItemMergePos, setSubItemsEnabled, setSubItemsVisible, setText

Methods inherited from class javax.swing.JMenu

add, add, add, addMenuListener, applyComponentOrientation, createActionChangeListener, createActionComponent, createWinListener, doClick, fireMenuCanceled, fireMenuDeselected, fireMenuSelected, getAccessibleContext, getComponent, getDelay, getItem, getItemCount, getMenuComponent, getMenuComponentCount, getMenuComponents, getMenuListeners, getPopupMenu, getPopupMenuOrigin, getSubElements, getUIClassID, insert, insert, insert, insertSeparator, isMenuComponent, isPopupMenuVisible, isSelected, isTearOff, isTopLevelMenu, menuSelectionChanged, paramString, processKeyEvent, remove, remove, remove, removeAll, removeMenuListener, setAccelerator, setComponentOrientation, setDelay, setMenuLocation, setModel, setPopupMenuVisible, setSelected, updateUI

Methods inherited from class javax.swing.JMenuItem

actionPropertyChanged, addMenuDragMouseListener, addMenuKeyListener, configurePropertiesFromAction, fireMenuDragMouseDragged, fireMenuDragMouseEntered, fireMenuDragMouseExited, fireMenuDragMouseReleased, fireMenuKeyPressed, fireMenuKeyReleased, fireMenuKeyTyped, getAccelerator, getMenuDragMouseListeners, getMenuKeyListeners, init, isArmed, processKeyEvent, processMenuDragMouseEvent, processMenuKeyEvent, processMouseEvent, removeMenuDragMouseListener, removeMenuKeyListener, setArmed, setEnabled, setUI

Methods inherited from class javax.swing.AbstractButton

addActionListener, addChangeListener, addImpl, addItemListener, checkHorizontalKey, checkVerticalKey, createActionListener, createActionPropertyChangeListener, createChangeListener, createItemListener, doClick, fireActionPerformed, fireItemStateChanged, fireStateChanged, getAction, getActionCommand, getActionListeners, getChangeListeners, getDisabledIcon, getDisabledSelectedIcon, getDisplayedMnemonicIndex, getHideActionText, getHorizontalAlignment, getHorizontalTextPosition, getIcon, getIconTextGap, getItemListeners, getLabel, getMargin, getMnemonic, getModel, getMultiClickThreshhold, getPressedIcon, getRolloverIcon, getRolloverSelectedIcon, getSelectedIcon, getSelectedObjects, getText, getUI, getVerticalAlignment, getVerticalTextPosition, imageUpdate, isBorderPainted, isContentAreaFilled, isFocusPainted, isRolloverEnabled, paintBorder, removeActionListener, removeChangeListener, removeItemListener, removeNotify, setAction, setActionCommand, setBorderPainted, setContentAreaFilled, setDisabledIcon, setDisabledSelectedIcon, setDisplayedMnemonicIndex, setFocusPainted, setHideActionText, setHorizontalAlignment, setHorizontalTextPosition, setIcon, setIconTextGap, setLabel, setLayout, setMargin, setMnemonic, setMnemonic, setMultiClickThreshhold, setPressedIcon, setRolloverEnabled, setRolloverIcon, setRolloverSelectedIcon, setSelectedIcon, setUI, setVerticalAlignment, setVerticalTextPosition

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, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, 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, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, removeContainerListener, setComponentZOrder, setFocusCycleRoot, 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, getFocusCycleRootAncestor, 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, 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, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface ur_rna.Utilities.swing.IMergeItem

asMergeItem, asMergeItems, compareByMergePos, compareByMergePos, fixInvalid, getComponent, getMergeName, getMergePos, getValidMergePos, mergeEnd, mergeStart, setInitialMergePos, setMergePos

Methods inherited from interface ur_rna.Utilities.swing.IMenuItem

findByAction, findByName, findByTreePath, from, getComponent, getContainer, getItemName, getMenuItem, getMenuItems, getMenus, hasSubItems

Methods inherited from interface javax.swing.MenuElement

processKeyEvent, processMouseEvent

Field Detail

backend

private RNAstructureBackendCalculator backend

The back end calculator that's linked to this menu.

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

str

private int str

The strand this constraints menu deals with.

Constructor Detail

ConstraintsMenu

public ConstraintsMenu(RNAstructureBackendCalculator calc)

General Constructor.

Parameters:

calc - The back end calculator connected to this menu.

Method Detail

addGeneralSection

public void addGeneralSection()

Add a menu section of general constraints commands.

addMaxPairingDistanceSection

public void addMaxPairingDistanceSection()

Add a menu section that handles maximum pairing distance.

addSaveRestoreSection

public void addSaveRestoreSection()

Add a menu section that handles saving and restoring constraints.

addSHAPESection

public void addSHAPESection()

Add a menu section that handles SHAPE constraints.

addShowResetSection

public void addShowResetSection()

Add a menu section that handles showing and resetting constraints.

buildDynalignAlignmentMenu

public void buildDynalignAlignmentMenu()

Build a complete menu that handles Dynalign alignment constraints.

buildMaxLoopMenu

public void buildMaxLoopMenu()

Build a complete menu that handles maximum loop size.

buildTemperatureMenu

public ConstraintsMenu buildTemperatureMenu()

Build a complete menu that handles temperature.

Returns:

The temperature menu.

buildUnimolecularMenu

public void buildUnimolecularMenu()

Build a complete menu that handles if unimolecular pairs are allowed.

getMergeName

public java.lang.String getMergeName()

onMenuAction

protected void onMenuAction(java.lang.String command,
                            java.awt.event.ActionEvent ev)

Description copied from class: MainMenu

Do any actions specific to this menu.

Overrides:

onMenuAction in class MainMenu

Parameters:

command - The command that signifies a particular action.

showDeletionConfirmation

private boolean showDeletionConfirmation()

Show a dialog that asks whether constraints should be deleted.

Returns:

True if constraints should be deleted, false if not.