ur_rna.StructureEditor.windows

Class NewFileWindow

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JInternalFrame

ur_rna.Utilities.swing.MdiChildFrame

ur_rna.StructureEditor.windows.ChildFrame

ur_rna.StructureEditor.windows.NewFileWindow

All Implemented Interfaces:

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

public class NewFileWindow
extends ChildFrame

Displays a dialog that allows a user to enter a sequence and structure information for a new drawing.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private static class	NewFileWindow.IgnoreStylesUndoManager
private static class	NewFileWindow.JWrapTextPane
private static class	NewFileWindow.StructItem

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 javax.swing.JTextPane	_lastActivePane
private static int[]	_textRegions
private static char[]	bracketChars
private javax.swing.JButton	btnCancel
private javax.swing.JButton	btnOK
private javax.swing.JButton	btnSequenceHelp
private javax.swing.JButton	btnStructureHelp
private javax.swing.JCheckBox	chkWrapSequence
private javax.swing.JCheckBox	chkWrapStructure
private java.awt.Font	defaultFont
private javax.swing.text.StyledDocument	docSeq
private javax.swing.text.StyledDocument	docStr
private TextDocListener	docUpdateListener
private static java.util.regex.Pattern	helixH3
private static java.util.regex.Pattern	helixInvalid
private static java.util.regex.Pattern	helixPair
private static java.util.regex.Pattern[]	helixParsePatterns
private static java.util.regex.Pattern	helixSep
private javax.swing.JLabel	lblLocation
private javax.swing.JPanel	pnlMain
private int[]	revSeqLookup
private int	selectedBase
private int	selectedHelixLen
private int	selectedPair
private NewFileWindow.StructItem	selectedStructItem
private int	seqLen
private int[]	seqLookup
private java.lang.String	seqText
private java.lang.String	strText
private java.util.ArrayList<NewFileWindow.StructItem>	structure
private javax.swing.text.Style	styleSeqDefault
private javax.swing.text.Style	styleSeqPaired
private javax.swing.text.Style	styleStrDefault
private javax.swing.text.Style	styleStrInvalid
private javax.swing.text.Style	styleStrSel
private javax.swing.Timer	tmrUpdate
private javax.swing.JTextPane	txtDebug
private javax.swing.JTextPane	txtSequence
private javax.swing.JTextPane	txtStructure
private javax.swing.JTextField	txtTitle
private javax.swing.undo.UndoManager	undoSeq
private javax.swing.undo.UndoManager	undoStr

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
NewFileWindow()

Method Summary

Modifier and Type	Method and Description
javax.swing.JComponent	$$$getRootComponent$$$()
private void	$$$setupUI$$$() Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
void	actionPerformed(java.awt.event.ActionEvent e)
private void	applyStyleToStructure(NewFileWindow.StructItem si, javax.swing.text.Style style)
private int	bounded(int value, int min, int max)
private boolean	checkErrors()
private boolean	createDrawing()
private javax.swing.text.StyleContext	createStyleContext()
private void	createUIComponents()
private void	doRedo(java.awt.event.ActionEvent event)
private void	doUndo(java.awt.event.ActionEvent event)
javax.swing.undo.UndoManager	getActiveUndoManager()
private void	handleTextSelection(javax.swing.JTextPane txt)
private boolean	isDotBracket(java.lang.String text)
private boolean	isStructureError(NewFileWindow.StructItem h)
private void	itemSelected(java.awt.event.ItemEvent e)
private void	parseSequence(java.lang.String text)
private void	parseStructure(java.lang.String text)
private void	restyleSequence()
private void	restyleStructure()
private void	setCharStyle(javax.swing.text.StyledDocument doc, int offset, int len, javax.swing.text.Style s)
private void	showDebug()
private void	textCaretEvent(javax.swing.event.CaretEvent e)
private static int	toInt(java.lang.String s)
private static int	toInt(java.lang.String s, int valueIfEmpty)
private void	updateTextUI()
private void	updateTimerElapsed(java.awt.event.ActionEvent event)

Methods inherited from class ur_rna.StructureEditor.windows.ChildFrame

close, getMenus, getToolbarButtons, programSettingsUpdated

Methods inherited from class ur_rna.Utilities.swing.MdiChildFrame

addAction, addKeyBinding, addKeyBinding, getParentFrame, setParentFrame

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

_lastActivePane

private javax.swing.JTextPane _lastActivePane

_textRegions

private static int[] _textRegions

bracketChars

private static final char[] bracketChars

btnCancel

private javax.swing.JButton btnCancel

btnOK

private javax.swing.JButton btnOK

btnSequenceHelp

private javax.swing.JButton btnSequenceHelp

btnStructureHelp

private javax.swing.JButton btnStructureHelp

chkWrapSequence

private javax.swing.JCheckBox chkWrapSequence

chkWrapStructure

private javax.swing.JCheckBox chkWrapStructure

defaultFont

private java.awt.Font defaultFont

docSeq

private javax.swing.text.StyledDocument docSeq

docStr

private javax.swing.text.StyledDocument docStr

docUpdateListener

private final TextDocListener docUpdateListener

helixH3

private static final java.util.regex.Pattern helixH3

helixInvalid

private static final java.util.regex.Pattern helixInvalid

helixPair

private static final java.util.regex.Pattern helixPair

helixParsePatterns

private static final java.util.regex.Pattern[] helixParsePatterns

helixSep

private static final java.util.regex.Pattern helixSep

lblLocation

private javax.swing.JLabel lblLocation

pnlMain

private javax.swing.JPanel pnlMain

revSeqLookup

private int[] revSeqLookup

selectedBase

private int selectedBase

selectedHelixLen

private int selectedHelixLen

selectedPair

private int selectedPair

selectedStructItem

private NewFileWindow.StructItem selectedStructItem

seqLen

private int seqLen

seqLookup

private int[] seqLookup

seqText

private java.lang.String seqText

strText

private java.lang.String strText

structure

private java.util.ArrayList<NewFileWindow.StructItem> structure

styleSeqDefault

private javax.swing.text.Style styleSeqDefault

styleSeqPaired

private javax.swing.text.Style styleSeqPaired

styleStrDefault

private javax.swing.text.Style styleStrDefault

styleStrInvalid

private javax.swing.text.Style styleStrInvalid

styleStrSel

private javax.swing.text.Style styleStrSel

tmrUpdate

private javax.swing.Timer tmrUpdate

txtDebug

private javax.swing.JTextPane txtDebug

txtSequence

private javax.swing.JTextPane txtSequence

txtStructure

private javax.swing.JTextPane txtStructure

txtTitle

private javax.swing.JTextField txtTitle

undoSeq

private javax.swing.undo.UndoManager undoSeq

undoStr

private javax.swing.undo.UndoManager undoStr

Constructor Detail

NewFileWindow

public NewFileWindow()

Method Detail

$$$getRootComponent$$$

public javax.swing.JComponent $$$getRootComponent$$$()

No IDE Inspections

ALL

$$$setupUI$$$

private void $$$setupUI$$$()

Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!

No IDE Inspections

ALL

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

applyStyleToStructure

private void applyStyleToStructure(NewFileWindow.StructItem si,
                                   javax.swing.text.Style style)

bounded

private int bounded(int value,
                    int min,
                    int max)

checkErrors

private boolean checkErrors()

createDrawing

private boolean createDrawing()

createStyleContext

private javax.swing.text.StyleContext createStyleContext()

createUIComponents

private void createUIComponents()

doRedo

private void doRedo(java.awt.event.ActionEvent event)

doUndo

private void doUndo(java.awt.event.ActionEvent event)

getActiveUndoManager

public javax.swing.undo.UndoManager getActiveUndoManager()

handleTextSelection

private void handleTextSelection(javax.swing.JTextPane txt)

isDotBracket

private boolean isDotBracket(java.lang.String text)

isStructureError

private boolean isStructureError(NewFileWindow.StructItem h)

itemSelected

private void itemSelected(java.awt.event.ItemEvent e)

parseSequence

private void parseSequence(java.lang.String text)

parseStructure

private void parseStructure(java.lang.String text)

restyleSequence

private void restyleSequence()

restyleStructure

private void restyleStructure()

setCharStyle

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

showDebug

private void showDebug()

textCaretEvent

private void textCaretEvent(javax.swing.event.CaretEvent e)

toInt

private static int toInt(java.lang.String s)

toInt

private static int toInt(java.lang.String s,
                         int valueIfEmpty)

updateTextUI

private void updateTextUI()

updateTimerElapsed

private void updateTimerElapsed(java.awt.event.ActionEvent event)