ur_rna.RNAstructureUI.drawing.dialogs

Class StructureDialog

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JInternalFrame

ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog

ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.print.Printable, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class StructureDialog
extends ImageDialog

A dialog that holds structure images.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StructureDialog.DrawOptions Enum that provides choices for backbone rendering style: Normal (Radial) flat (linear) or circular.

Nested classes/interfaces inherited from class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog

ImageDialog.PrintMenu

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 StructureBackend	backend The back end object that reads data for structures.
private java.lang.String[]	data The array of data for a particular structure.
private int	drawOptions
private boolean	hasPairs Whether the current structure has pairs.
private int	number The structure number viewed on this panel.
private java.lang.String[]	regex The array of regexes used to pull data about a structure.
private static long	serialVersionUID

Fields inherited from class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog

customMenus, error, file, imgSizeX, imgSizeY, mainPanel, preferredDialogWidth, scale

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 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(java.lang.String file) Constructor.

Method Summary

Modifier and Type	Method and Description
void	clearAnnotation() Clear annotation from this dialog.
protected void	createDrawnImage(java.awt.Graphics2D g2) Create the image drawn on this panel.
boolean	getOption(StructureDialog.DrawOptions option) Determine whether the specified option is set
int	getStructureCount()
int	getStructureNumber()
protected void	readImageData() Read image data from a particular file.
(package private) void	redrawStructure()
void	setAnnotation(java.lang.String file) Set the annotation for this structure drawing.
void	setAnnotation(java.lang.String file, FileType type)
void	setOption(StructureDialog.DrawOptions option)
void	setOption(StructureDialog.DrawOptions option, boolean value)
void	setStructureNumber(int number) Set the structure number.
boolean	toggleOption(StructureDialog.DrawOptions option)
void	writeDotBracketFile(java.lang.String outFile) Write a dot bracket file of all structures on this dialog.
void	writeHelixFile(java.lang.String outFile) Write a helix file from the current structure on this dialog.
void	writePostscriptFile(java.lang.String outFile) Write a Postscript file from the current structure on this dialog.
void	writeSVGFile(java.lang.String outFile) Write an SVG file from the current structure on this dialog.

Methods inherited from class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog

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

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

backend

private StructureBackend backend

The back end object that reads data for structures.

data

private java.lang.String[] data

The array of data for a particular structure.

drawOptions

private int drawOptions

hasPairs

private boolean hasPairs

Whether the current structure has pairs.

number

private int number

The structure number viewed on this panel.

regex

private java.lang.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(java.lang.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(java.awt.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.

getOption

public boolean getOption(StructureDialog.DrawOptions option)

Determine whether the specified option is set

getStructureCount

public int getStructureCount()

getStructureNumber

public int getStructureNumber()

readImageData

protected void readImageData()

Description copied from class: ImageDialog

Read image data from a particular file.

Specified by:

readImageData in class ImageDialog

redrawStructure

void redrawStructure()

setAnnotation

public void setAnnotation(java.lang.String file)

Set the annotation for this structure drawing.

Parameters:

file - The data file to get structure information from.

setAnnotation

public void setAnnotation(java.lang.String file,
                          FileType type)

setOption

public void setOption(StructureDialog.DrawOptions option)

setOption

public void setOption(StructureDialog.DrawOptions option,
                      boolean value)

setStructureNumber

public void setStructureNumber(int number)

Set the structure number.

Parameters:

number - The structure number.

toggleOption

public boolean toggleOption(StructureDialog.DrawOptions option)

writeDotBracketFile

public void writeDotBracketFile(java.lang.String outFile)

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

Parameters:

outFile - The file to write.

writeHelixFile

public void writeHelixFile(java.lang.String outFile)

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

Parameters:

outFile - The file to write.

writePostscriptFile

public void writePostscriptFile(java.lang.String outFile)

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

Parameters:

outFile - The file to write.

writeSVGFile

public void writeSVGFile(java.lang.String outFile)

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

Parameters:

outFile - The file to write.