RNAstructure_java_drawing.source.dialogs

Class StructureDialog

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Dialog

javax.swing.JDialog

RNAstructure_java_drawing.source.dialogs.ImageDialog

RNAstructure_java_drawing.source.dialogs.StructureDialog

All Implemented Interfaces:

ImageObserver, MenuContainer, Printable, Serializable, Accessible, RootPaneContainer, WindowConstants

public class StructureDialog
extends ImageDialog

A dialog that holds structure images.

See Also:

Serialized Form

Nested Class Summary

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

JDialog.AccessibleJDialog

Nested classes/interfaces inherited from class java.awt.Dialog

Dialog.AccessibleAWTDialog, Dialog.ModalExclusionType, Dialog.ModalityType

Nested classes/interfaces inherited from class java.awt.Window

Window.AccessibleAWTWindow, Window.Type

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
private StructureBackend	backend The back end object that reads data for structures.
static boolean	CIRCLED_NUCS Boolean that tells whether a structure's nucleotides are circled.
static boolean	CLOCKWISE_STRUCTURE Boolean that tells whether a structure is rendered clockwise.
private String[]	data The array of data for a particular structure.
private boolean	hasPairs Whether the current structure has pairs.
private int	number The structure number viewed on this panel.
private String[]	regex The array of regexes used to pull data about a structure.
private static long	serialVersionUID

Fields inherited from class RNAstructure_java_drawing.source.dialogs.ImageDialog

error, file, mainPanel, maxBoundX, maxBoundY, preferredDialogWidth, scale

Fields inherited from class javax.swing.JDialog

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Dialog

DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.print.Printable

NO_SUCH_PAGE, PAGE_EXISTS

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
StructureDialog(String file) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	clearAnnotation() Clear annotation from this dialog.
protected void	createDrawnImage(Graphics2D g2) Create the image drawn on this panel.
void	flip() Flip the structure image horizontally.
protected void	readImageData() Read image data from a particular file.
void	setAnnotation(String file) Set the annotation for this structure drawing.
void	setStructureNumber(int number) Set the structure number.
void	switchCircled() Switch circled nucleotides on or off.
void	writeDotBracketFile(String outFile) Write a dot bracket file of all structures on this dialog.
void	writeHelixFile(String outFile) Write a helix file from the current structure on this dialog.
void	writePostscriptFile(String outFile) Write a Postscript file from the current structure on this dialog.
void	writeSVGFile(String outFile) Write an SVG file from the current structure on this dialog.

Methods inherited from class RNAstructure_java_drawing.source.dialogs.ImageDialog

buildLegend, createDefaultMenuBar, getFile, getScale, isError, print, printPanel, refresh, setScale, setTopCaption, viewDialog, viewZoomDialog, zoomImage

Methods inherited from class javax.swing.JDialog

addImpl, createRootPane, dialogInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.awt.Dialog

addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, setVisible, show, toBack

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, 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

backend

private StructureBackend backend

The back end object that reads data for structures.

CIRCLED_NUCS

public static boolean CIRCLED_NUCS

Boolean that tells whether a structure's nucleotides are circled.

CLOCKWISE_STRUCTURE

public static boolean CLOCKWISE_STRUCTURE

Boolean that tells whether a structure is rendered clockwise.

data

private String[] data

The array of data for a particular structure.

hasPairs

private boolean hasPairs

Whether the current structure has pairs.

number

private int number

The structure number viewed on this panel.

regex

private String[] regex

The array of regexes used to pull data about a structure.

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

StructureDialog

public StructureDialog(String file)

Constructor.

Parameters:

file - The structure file to draw.

Method Detail

clearAnnotation

public void clearAnnotation()

Clear annotation from this dialog.

createDrawnImage

protected void createDrawnImage(Graphics2D g2)

Description copied from class: ImageDialog

Create the image drawn on this panel.

Specified by:

createDrawnImage in class ImageDialog

Parameters:

g2 - The graphics context.

flip

public void flip()

Flip the structure image horizontally.

readImageData

protected void readImageData()

Description copied from class: ImageDialog

Read image data from a particular file.

Specified by:

readImageData in class ImageDialog

setAnnotation

public void setAnnotation(String file)

Set the annotation for this structure drawing.

Parameters:

file - The data file to get structure information from.

setStructureNumber

public void setStructureNumber(int number)

Set the structure number.

Parameters:

number - The structure number.

switchCircled

public void switchCircled()

Switch circled nucleotides on or off.

writeDotBracketFile

public void writeDotBracketFile(String outFile)

Write a dot bracket file of all structures on this dialog.

Parameters:

outFile - The file to write.

writeHelixFile

public void writeHelixFile(String outFile)

Write a helix file from the current structure on this dialog.

Parameters:

outFile - The file to write.

writePostscriptFile

public void writePostscriptFile(String outFile)

Write a Postscript file from the current structure on this dialog.

Parameters:

outFile - The file to write.

writeSVGFile

public void writeSVGFile(String outFile)

Write an SVG file from the current structure on this dialog.

Parameters:

outFile - The file to write.