com.pacbio.secondary.vis.gui.dialogs

Class PreferencesDialogEx

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Frame

javax.swing.JFrame

com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.beans.PropertyChangeListener, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.ListSelectionListener, javax.swing.event.TableModelListener, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class PreferencesDialogEx
extends PreferencesDialogBase
implements java.awt.event.ActionListener, javax.swing.event.TableModelListener, java.beans.PropertyChangeListener, javax.swing.event.ListSelectionListener

User preferences dialog

Author:

mmilletti

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

PreferencesDialogBase.JDoubleSlider

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

javax.swing.JFrame.AccessibleJFrame

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

java.awt.Frame.AccessibleAWTFrame

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

java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type

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 inherited from class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

always_show_mem_stats_checkbox, app, basemods_filter_checkbox, basemods_filter_threshold, basemods_options_cb, baseqv_checkbox, btn_inset, close_text, conf_filter_checkbox, conf_filter_threshold, cov_filter_checkbox, cov_filter_threshold, details_close_btn, details_help_btn, details_save_btn, details_tab, details_view_coarse_cb, details_view_dynamic_range, details_view_fixed_range, details_view_max_coverage, details_view_range_mode_cb, dna_colors_panel, dynamic_range_label, epipro_close_btn, epipro_cutoff_filter_checkbox, epipro_cutoff_filter_threshold, epipro_help_btn, epipro_only_checkbox, epipro_pane, epipro_save_btn, epipro_tab, epipro_view_mode_cb, fixed_range_label, kinetics_ann_label, kinetics_checkbox, kinetics_close_btn, kinetics_help_btn, kinetics_max_label, kinetics_max_slider, kinetics_max_text, kinetics_min_label, kinetics_min_slider, kinetics_min_text, kinetics_palette, kinetics_save_btn, kinetics_scaling_cb, kinetics_scaling_label, kinetics_tab, link_genome_region_checkbox, link_region_details_checkbox, mapqv_checkbox, program_close_btn, program_help_btn, program_save_btn, program_tab, qv_close_btn, qv_help_btn, qv_save_btn, qv_tab, qv_thresholds_panel, reset_btn, save_text, show_graph_structures_checkbox, show_structures_only_checkbox, show_tooltip_checkbox, structures_close_btn, structures_help_btn, structures_listbox, structures_save_btn, structures_tab, tabbed_pane, use_frank_style, variants_close_btn, variants_help_btn, variants_save_btn, variants_tab

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_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
PreferencesDialogEx(VioletApp violet)

Method Summary

Methods

Modifier and Type	Method and Description
void	actionPerformed(java.awt.event.ActionEvent event) This is called when users click on a check box
protected void	configureCommonButtons(javax.swing.JButton close, javax.swing.JButton save, javax.swing.JButton help)
protected void	createBaseModsTab()
protected void	createCommonButtons()
protected void	createDetailsTab()
protected void	createEpiProReadsTab()
protected void	createProgramOptionsTab()
protected void	createQVTab()
protected void	createStructuresTab()
protected void	createTabbedPanel() Any change in the order of tabs should be reflected in the help constants,
protected void	createVariantsTab()
protected void	initFrame() Preferences dialog closes by pressing esc key or the close button on system menu
static void	main(java.lang.String[] args) test dialog locally
protected void	onClose() close dialog
void	propertyChange(java.beans.PropertyChangeEvent evt)
void	tableChanged(javax.swing.event.TableModelEvent e)
void	valueChanged(javax.swing.event.ListSelectionEvent e) This is called when kinetics list changes

Methods inherited from class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase

addSaveButtonToTabbedPane, getDetailsOptions, getSelectedGraphStructureMode, getSelectedKineticMode, getView, layoutDetailsTab, layoutEpiProReadsTab, layoutKineticsTab, layoutProgramTab, layoutQVTab, layoutStructuresTab, layoutVariantsTab, selectDefaultButton, showDialog, updateData, updateDetailsControls, updateDetailsData, updateKineticsControls, updateModificationsData, updateStates, updateToggleButtons, updateVariantsData

Methods inherited from class javax.swing.JFrame

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

Methods inherited from class java.awt.Frame

addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

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, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, 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, 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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Constructor Detail

PreferencesDialogEx

public PreferencesDialogEx(VioletApp violet)

Method Detail

createEpiProReadsTab

protected void createEpiProReadsTab()

createProgramOptionsTab

protected void createProgramOptionsTab()

createQVTab

protected void createQVTab()

createBaseModsTab

protected void createBaseModsTab()

createStructuresTab

protected void createStructuresTab()

createDetailsTab

protected void createDetailsTab()

createVariantsTab

protected void createVariantsTab()

configureCommonButtons

protected void configureCommonButtons(javax.swing.JButton close,
                          javax.swing.JButton save,
                          javax.swing.JButton help)

Parameters:

close -

help -

createCommonButtons

protected void createCommonButtons()

createTabbedPanel

protected void createTabbedPanel()

Any change in the order of tabs should be reflected in the help constants,

initFrame

protected void initFrame()

Preferences dialog closes by pressing esc key or the close button on system menu

onClose

protected void onClose()

close dialog

actionPerformed

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

This is called when users click on a check box

Specified by:

actionPerformed in interface java.awt.event.ActionListener

valueChanged

public void valueChanged(javax.swing.event.ListSelectionEvent e)

This is called when kinetics list changes

Specified by:

valueChanged in interface javax.swing.event.ListSelectionListener

tableChanged

public void tableChanged(javax.swing.event.TableModelEvent e)

Specified by:

tableChanged in interface javax.swing.event.TableModelListener

propertyChange

public void propertyChange(java.beans.PropertyChangeEvent evt)

Specified by:

propertyChange in interface java.beans.PropertyChangeListener

main

public static void main(java.lang.String[] args)

test dialog locally