ur_rna.RNAstructureUI.drawing.dialogs

Class PlotDialog

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.PlotDialog

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 PlotDialog
extends ImageDialog

A dialog that holds dot plot images.

See Also:

Serialized Form

Nested Class Summary

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 DotPlotBackend	backend The back end object that reads data for dot plots.
private int	plotLength The length of the plot.
private static long	serialVersionUID
private int	strand The strand being drawn.

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
PlotDialog(java.lang.String file) File Constructor.
PlotDialog(java.lang.String file, int strand) Strand Constructor.

Method Summary

Modifier and Type	Method and Description
protected void	createDrawnImage(java.awt.Graphics2D g2) Create the image drawn on this panel.
java.lang.Integer[]	getColors() Get the range of colors allowed in this dialog.
java.lang.Double[]	getCurrentBounds() Get the current bounds allowed in this dialog.
java.lang.Double[]	getDefaultBounds() Get the default bounds allowed in this dialog.
protected void	readImageData() Read image data from a particular file.
void	setColors(int colors) Set the number of colors in the plot on this dialog.
void	setRange(double minimum, double maximum) Set the range of the plot on this dialog.
void	writePostscriptFile(java.lang.String outFile) Write a Postscript file from the plot on this dialog.
boolean	writeStructuresFile(java.lang.String outFile, boolean showStructures) Write a probable structures file from the plot on this dialog.
void	writeSVGFile(java.lang.String outFile) Write an SVG file from the plot on this dialog.
void	writeTextFile(java.lang.String outFile) Write a text file from the plot 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 DotPlotBackend backend

The back end object that reads data for dot plots.

plotLength

private int plotLength

The length of the plot.

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

strand

private int strand

The strand being drawn.

Constructor Detail

PlotDialog

public PlotDialog(java.lang.String file)

File Constructor.

Parameters:

file - The dot plot data file to draw.

PlotDialog

public PlotDialog(java.lang.String file,
                  int strand)

Strand Constructor.

Parameters:

file - The dot plot data file to draw.

strand - The strand from the data file to draw.

Method Detail

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.

getColors

public java.lang.Integer[] getColors()

Get the range of colors allowed in this dialog.

Returns:

The color range.

getCurrentBounds

public java.lang.Double[] getCurrentBounds()

Get the current bounds allowed in this dialog.

Returns:

The current bounds.

getDefaultBounds

public java.lang.Double[] getDefaultBounds()

Get the default bounds allowed in this dialog.

Returns:

The default bounds.

readImageData

protected void readImageData()

Description copied from class: ImageDialog

Read image data from a particular file.

Specified by:

readImageData in class ImageDialog

setColors

public void setColors(int colors)

Set the number of colors in the plot on this dialog.

Parameters:

colors - The number of colors to set.

setRange

public void setRange(double minimum,
                     double maximum)

Set the range of the plot on this dialog.

Parameters:

minimum - The lower bound of the range.

maximum - The upper bound of the range.

writePostscriptFile

public void writePostscriptFile(java.lang.String outFile)

Write a Postscript file from the plot on this dialog.

Parameters:

outFile - The file to write.

writeStructuresFile

public boolean writeStructuresFile(java.lang.String outFile,
                                   boolean showStructures)

Write a probable structures file from the plot on this dialog.

Parameters:

outFile - The file to write.

showStructures - True if structures should be shown, false if not.

Returns:

True if structures were written correctly, false if not.

writeSVGFile

public void writeSVGFile(java.lang.String outFile)

Write an SVG file from the plot on this dialog.

Parameters:

outFile - The file to write.

writeTextFile

public void writeTextFile(java.lang.String outFile)

Write a text file from the plot on this dialog.

Parameters:

outFile - The file to write.