public class StructureDialog extends ImageDialog
JDialog.AccessibleJDialog
Dialog.AccessibleAWTDialog, Dialog.ModalExclusionType, Dialog.ModalityType
Window.AccessibleAWTWindow, Window.Type
Container.AccessibleAWTContainer
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
Modifier and Type | Field and Description |
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private StructureBackend |
backend
The back end object that reads data for structures.
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static boolean |
CIRCLED_NUCS
Boolean that tells whether a structure's nucleotides are circled.
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static boolean |
CLOCKWISE_STRUCTURE
Boolean that tells whether a structure is rendered clockwise.
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private String[] |
data
The array of data for a particular structure.
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private boolean |
hasPairs
Whether the current structure has pairs.
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private int |
number
The structure number viewed on this panel.
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private String[] |
regex
The array of regexes used to pull data about a structure.
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private static long |
serialVersionUID |
error, file, mainPanel, maxBoundX, maxBoundY, preferredDialogWidth, scale
accessibleContext, rootPane, rootPaneCheckingEnabled
DEFAULT_MODALITY_TYPE
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
NO_SUCH_PAGE, PAGE_EXISTS
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
Constructor and Description |
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StructureDialog(String file)
Constructor.
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Modifier and Type | Method and Description |
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void |
clearAnnotation()
Clear annotation from this dialog.
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protected void |
createDrawnImage(Graphics2D g2)
Create the image drawn on this panel.
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void |
flip()
Flip the structure image horizontally.
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protected void |
readImageData()
Read image data from a particular file.
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void |
setAnnotation(String file)
Set the annotation for this structure drawing.
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void |
setStructureNumber(int number)
Set the structure number.
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void |
switchCircled()
Switch circled nucleotides on or off.
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void |
writeDotBracketFile(String outFile)
Write a dot bracket file of all structures on this dialog.
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void |
writeHelixFile(String outFile)
Write a helix file from the current structure on this dialog.
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void |
writePostscriptFile(String outFile)
Write a Postscript file from the current structure on this dialog.
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void |
writeSVGFile(String outFile)
Write an SVG file from the current structure on this dialog.
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buildLegend, createDefaultMenuBar, getFile, getScale, isError, print, printPanel, refresh, setScale, setTopCaption, viewDialog, viewZoomDialog, zoomImage
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
addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, setVisible, show, toBack
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
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
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
private StructureBackend backend
public static boolean CIRCLED_NUCS
public static boolean CLOCKWISE_STRUCTURE
private String[] data
private boolean hasPairs
private int number
private String[] regex
private static final long serialVersionUID
public StructureDialog(String file)
file
- The structure file to draw.public void clearAnnotation()
protected void createDrawnImage(Graphics2D g2)
ImageDialog
createDrawnImage
in class ImageDialog
g2
- The graphics context.public void flip()
protected void readImageData()
ImageDialog
readImageData
in class ImageDialog
public void setAnnotation(String file)
file
- The data file to get structure information from.public void setStructureNumber(int number)
number
- The structure number.public void switchCircled()
public void writeDotBracketFile(String outFile)
outFile
- The file to write.public void writeHelixFile(String outFile)
outFile
- The file to write.public void writePostscriptFile(String outFile)
outFile
- The file to write.public void writeSVGFile(String outFile)
outFile
- The file to write.