ur_rna.RNAstructureUI.windows

Class SequenceDisplayWindow

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JInternalFrame

ur_rna.RNAstructureUI.windows.InternalWindow

ur_rna.RNAstructureUI.windows.SequenceDisplayWindow

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 SequenceDisplayWindow
extends InternalWindow

A class responsible for displaying a window that allows a user to examine raw sequence data.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private class	SequenceDisplayWindow.EditMenu An inner class that creates a sequence editing menu.
private class	SequenceDisplayWindow.SoundPlayer
private class	SequenceDisplayWindow.SpeakMenu An inner class that creates a sequence speaking menu.

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 SequenceDisplayWindow.SoundPlayer	_speakPlayer
private java.util.HashMap<java.lang.Character,java.io.InputStream>	_speakStreams
private static java.lang.String	allowedChars
private javax.swing.JTextArea	commentBox
private java.awt.Font	defaultFont
private boolean	edited A boolean, true if the sequence has been edited, false if not.
private static java.lang.String	ignoreChars
private java.io.InputStream	invalidSoundClip
private javax.swing.JTextPane	sequenceBox
private javax.swing.text.StyledDocument	sequenceDoc
private static long	serialVersionUID
private javax.swing.JButton	speakButton The button which can be clicked to start or stop speaking.
private boolean	speakingFullSequence
(package private) SequenceDisplayWindow.SpeakMenu	speakMenu
private int	speakPosition The position at which speaking is occurring.
private javax.swing.Timer	speakTimer The timer that aids in speaking nucleotides in rhythm.
private boolean	speakWhileTyping A boolean, true if speaking while typing is active, false if not.
private static java.lang.String	standardBases
private javax.swing.text.Style	styleIgnoredChar
private javax.swing.text.Style	styleInvalidChar
private javax.swing.text.Style	styleStandardBase
private javax.swing.Timer	styleTimer The timer that updates syntax highlighting
private javax.swing.text.Style	styleUnpairedBase
private javax.swing.text.Style	styleUnspecifiedBase
private javax.swing.JTextArea	titleBox The array of text areas in this window.
private static java.lang.String	unpairedBases
private static java.lang.String	unspecifiedBases
private boolean	userAcceptedInvalidSequence

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
SequenceDisplayWindow() Default Constructor.
SequenceDisplayWindow(java.lang.String file) File Constructor.

Method Summary

Modifier and Type	Method and Description
private javax.swing.JPanel	buildButtonPanel() Make the button panel at the bottom of the window.
private javax.swing.JPanel	buildTextBoxPanel(int height, java.lang.String text, javax.swing.text.JTextComponent textBox, java.lang.String name) Build a text input region for this window.
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 javax.swing.text.StyledDocument	CreateStyledDocument()
private java.lang.String	formatSequence(java.lang.String text) Format the sequence in the text area.
private void	formatSequenceBox()
private javax.swing.text.Style	getCharStyle(char c)
private boolean	isIgnoredSeqChar(char c)
private boolean	isInvalidSeqChar(char c)
private boolean	isUnpairedSeqChar(char c)
private boolean	isUnspecifiedSeqChar(char c)
private java.io.InputStream	loadClip(java.lang.String name)
private void	loadSpeakClips()
(package private) void	markEdited(boolean edited)
protected void	processCommand(InternalWindow.CommandInfo ci) Perform an action specific to this window.
java.lang.String	saveSequence() Save a sequence.
java.lang.String	saveSequence(java.lang.String file) Save a sequence.
private void	setCharStyle(int offset, javax.swing.text.Style s)
private void	setSequenceText(java.lang.String text)
void	setSpeakWhileTyping(boolean isSpeaking) Set whether or not the window should be speaking while typing.
void	showWindow() View the window.
private void	speakFullSequence(boolean speak)
private void	speakSeqChar(char base) Play a sound clip, depending on the nucleotide.
private void	UpdateSyntaxStyles()
private void	UpdateSyntaxStyles(int offset, int length)
private boolean	verifySequence()

Methods inherited from class ur_rna.RNAstructureUI.windows.InternalWindow

actionPerformed, frameActivated, frameClosed, frameClosing, 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, 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

_speakPlayer

private SequenceDisplayWindow.SoundPlayer _speakPlayer

_speakStreams

private java.util.HashMap<java.lang.Character,java.io.InputStream> _speakStreams

allowedChars

private static final java.lang.String allowedChars

See Also:

Constant Field Values

commentBox

private javax.swing.JTextArea commentBox

defaultFont

private java.awt.Font defaultFont

edited

private boolean edited

A boolean, true if the sequence has been edited, false if not.

ignoreChars

private static final java.lang.String ignoreChars

See Also:

Constant Field Values

invalidSoundClip

private java.io.InputStream invalidSoundClip

sequenceBox

private javax.swing.JTextPane sequenceBox

sequenceDoc

private javax.swing.text.StyledDocument sequenceDoc

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

speakButton

private javax.swing.JButton speakButton

The button which can be clicked to start or stop speaking.

speakingFullSequence

private boolean speakingFullSequence

speakMenu

SequenceDisplayWindow.SpeakMenu speakMenu

speakPosition

private int speakPosition

The position at which speaking is occurring.

speakTimer

private javax.swing.Timer speakTimer

The timer that aids in speaking nucleotides in rhythm.

speakWhileTyping

private boolean speakWhileTyping

A boolean, true if speaking while typing is active, false if not.

standardBases

private static final java.lang.String standardBases

See Also:

Constant Field Values

styleIgnoredChar

private javax.swing.text.Style styleIgnoredChar

styleInvalidChar

private javax.swing.text.Style styleInvalidChar

styleStandardBase

private javax.swing.text.Style styleStandardBase

styleTimer

private javax.swing.Timer styleTimer

The timer that updates syntax highlighting

styleUnpairedBase

private javax.swing.text.Style styleUnpairedBase

styleUnspecifiedBase

private javax.swing.text.Style styleUnspecifiedBase

titleBox

private javax.swing.JTextArea titleBox

The array of text areas in this window.

unpairedBases

private static final java.lang.String unpairedBases

See Also:

Constant Field Values

unspecifiedBases

private static final java.lang.String unspecifiedBases

See Also:

Constant Field Values

userAcceptedInvalidSequence

private boolean userAcceptedInvalidSequence

Constructor Detail

SequenceDisplayWindow

public SequenceDisplayWindow()

Default Constructor. This constructor is used when a blank display window is opened.

SequenceDisplayWindow

public SequenceDisplayWindow(java.lang.String file)

File Constructor. This constructor is used when a sequence file is specified.

Parameters:

file - The sequence file to open.

Method Detail

buildButtonPanel

private javax.swing.JPanel buildButtonPanel()

Make the button panel at the bottom of the window.

Returns:

The button panel.

buildTextBoxPanel

private javax.swing.JPanel buildTextBoxPanel(int height,
                                             java.lang.String text,
                                             javax.swing.text.JTextComponent textBox,
                                             java.lang.String name)

Build a text input region for this window. Each region is a panel consisting of a label and a text component.

Parameters:

height - The height of the input region.

text - The label text.

Returns:

The input region panel.

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.

CreateStyledDocument

private javax.swing.text.StyledDocument CreateStyledDocument()

formatSequence

private java.lang.String formatSequence(java.lang.String text)

Format the sequence in the text area.

formatSequenceBox

private void formatSequenceBox()

getCharStyle

private javax.swing.text.Style getCharStyle(char c)

isIgnoredSeqChar

private boolean isIgnoredSeqChar(char c)

isInvalidSeqChar

private boolean isInvalidSeqChar(char c)

isUnpairedSeqChar

private boolean isUnpairedSeqChar(char c)

isUnspecifiedSeqChar

private boolean isUnspecifiedSeqChar(char c)

loadClip

private java.io.InputStream loadClip(java.lang.String name)

loadSpeakClips

private void loadSpeakClips()

markEdited

void markEdited(boolean edited)

processCommand

protected void processCommand(InternalWindow.CommandInfo ci)

Perform an action specific to this window.

Overrides:

processCommand in class InternalWindow

Parameters:

ci - Information about the command.

saveSequence

public java.lang.String saveSequence()

Save a sequence.

Returns:

The file that was saved.

saveSequence

public java.lang.String saveSequence(java.lang.String file)

Save a sequence.

Parameters:

file - The file name to save the sequence with.

Returns:

The file that was saved.

setCharStyle

private void setCharStyle(int offset,
                          javax.swing.text.Style s)

setSequenceText

private void setSequenceText(java.lang.String text)

setSpeakWhileTyping

public void setSpeakWhileTyping(boolean isSpeaking)

Set whether or not the window should be speaking while typing.

Parameters:

isSpeaking - True if speaking, false if not.

showWindow

public void showWindow()

View the window.

Overrides:

showWindow in class InternalWindow

speakFullSequence

private void speakFullSequence(boolean speak)

speakSeqChar

private void speakSeqChar(char base)

Play a sound clip, depending on the nucleotide.

Parameters:

base - The nucleotide to play.

UpdateSyntaxStyles

private void UpdateSyntaxStyles()

UpdateSyntaxStyles

private void UpdateSyntaxStyles(int offset,
                                int length)

verifySequence

private boolean verifySequence()