com.pacbio.secondary.vis.gui.dialogs

Class PreferencesDialogBase

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

All Implemented Interfaces:

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

Direct Known Subclasses:

PreferencesDialogEx

public class PreferencesDialogBase
extends javax.swing.JFrame

Author:

mmilletti

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	PreferencesDialogBase.JDoubleSlider private slider class

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

Modifier and Type	Field and Description
protected javax.swing.JCheckBox	always_show_mem_stats_checkbox
protected VioletApp	app
protected javax.swing.JCheckBox	basemods_filter_checkbox
protected javax.swing.JFormattedTextField	basemods_filter_threshold
protected JComboBoxCtrl	basemods_options_cb
protected javax.swing.JCheckBox	baseqv_checkbox
protected int	btn_inset
protected java.lang.String	close_text
protected javax.swing.JCheckBox	conf_filter_checkbox
protected javax.swing.JFormattedTextField	conf_filter_threshold
protected javax.swing.JCheckBox	cov_filter_checkbox
protected javax.swing.JFormattedTextField	cov_filter_threshold
protected javax.swing.JButton	details_close_btn
protected javax.swing.JButton	details_help_btn
protected javax.swing.JButton	details_save_btn
protected javax.swing.JPanel	details_tab
protected JComboBoxCtrl	details_view_coarse_cb
protected javax.swing.JFormattedTextField	details_view_dynamic_range
protected javax.swing.JFormattedTextField	details_view_fixed_range
protected javax.swing.JFormattedTextField	details_view_max_coverage
protected JComboBoxCtrl	details_view_range_mode_cb
protected DNAColorsOptionsPane	dna_colors_panel
protected javax.swing.JLabel	dynamic_range_label
protected javax.swing.JButton	epipro_close_btn
protected javax.swing.JCheckBox	epipro_cutoff_filter_checkbox
protected javax.swing.JFormattedTextField	epipro_cutoff_filter_threshold
protected javax.swing.JButton	epipro_help_btn
protected javax.swing.JCheckBox	epipro_only_checkbox
protected EpiProColorOptionsPane	epipro_pane
protected javax.swing.JButton	epipro_save_btn
protected javax.swing.JPanel	epipro_tab
protected JComboBoxCtrl	epipro_view_mode_cb
protected javax.swing.JLabel	fixed_range_label
protected javax.swing.JLabel	kinetics_ann_label
protected javax.swing.JCheckBox	kinetics_checkbox
protected javax.swing.JButton	kinetics_close_btn
protected javax.swing.JButton	kinetics_help_btn
protected javax.swing.JLabel	kinetics_max_label
protected PreferencesDialogBase.JDoubleSlider	kinetics_max_slider
protected javax.swing.JFormattedTextField	kinetics_max_text
protected javax.swing.JLabel	kinetics_min_label
protected PreferencesDialogBase.JDoubleSlider	kinetics_min_slider
protected javax.swing.JFormattedTextField	kinetics_min_text
protected PaletteCtrl	kinetics_palette
protected javax.swing.JButton	kinetics_save_btn
protected JComboBoxCtrl	kinetics_scaling_cb
protected javax.swing.JLabel	kinetics_scaling_label
protected javax.swing.JPanel	kinetics_tab
protected javax.swing.JCheckBox	link_genome_region_checkbox
protected javax.swing.JCheckBox	link_region_details_checkbox
protected javax.swing.JCheckBox	mapqv_checkbox
protected javax.swing.JButton	program_close_btn
protected javax.swing.JButton	program_help_btn
protected javax.swing.JButton	program_save_btn
protected javax.swing.JPanel	program_tab
protected javax.swing.JButton	qv_close_btn
protected javax.swing.JButton	qv_help_btn
protected javax.swing.JButton	qv_save_btn
protected javax.swing.JPanel	qv_tab
protected QVThresholdOptionsPane	qv_thresholds_panel
protected javax.swing.JButton	reset_btn
protected java.lang.String	save_text
protected javax.swing.JCheckBox	show_graph_structures_checkbox
protected javax.swing.JCheckBox	show_structures_only_checkbox
protected javax.swing.JCheckBox	show_tooltip_checkbox
protected javax.swing.JButton	structures_close_btn
protected javax.swing.JButton	structures_help_btn
protected javax.swing.JList	structures_listbox
protected javax.swing.JButton	structures_save_btn
protected javax.swing.JPanel	structures_tab
protected javax.swing.JTabbedPane	tabbed_pane
protected boolean	use_frank_style
protected javax.swing.JButton	variants_close_btn
protected javax.swing.JButton	variants_help_btn
protected javax.swing.JButton	variants_save_btn
protected javax.swing.JPanel	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
PreferencesDialogBase(java.lang.String s)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addSaveButtonToTabbedPane() Deprecated.
DetailsOptions	getDetailsOptions()
int	getSelectedGraphStructureMode() returns current graph mode
int	getSelectedKineticMode() returns current kinetics mode
GenomicViewDetails	getView()
protected void	layoutDetailsTab()
protected void	layoutEpiProReadsTab()
protected void	layoutKineticsTab()
protected void	layoutProgramTab()
protected void	layoutQVTab()
protected void	layoutStructuresTab() Graph structures options
protected void	layoutVariantsTab()
protected void	selectDefaultButton(int index)
void	showDialog()
protected boolean	updateData(boolean bUpdateView)
protected void	updateDetailsControls(int index) updates status of details controls
protected void	updateDetailsData()
protected void	updateKineticsControls(boolean isKinetics) updates status of kinetics controls
protected void	updateModificationsData()
protected void	updateStates()
void	updateToggleButtons() called by mainframe after toggle buttons in toolbar change state
protected void	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

Field Detail

use_frank_style

protected transient boolean use_frank_style

app

protected VioletApp app

tabbed_pane

protected javax.swing.JTabbedPane tabbed_pane

variants_tab

protected javax.swing.JPanel variants_tab

qv_tab

protected javax.swing.JPanel qv_tab

kinetics_tab

protected javax.swing.JPanel kinetics_tab

structures_tab

protected javax.swing.JPanel structures_tab

details_tab

protected javax.swing.JPanel details_tab

program_tab

protected javax.swing.JPanel program_tab

epipro_tab

protected javax.swing.JPanel epipro_tab

variants_close_btn

protected javax.swing.JButton variants_close_btn

qv_close_btn

protected javax.swing.JButton qv_close_btn

kinetics_close_btn

protected javax.swing.JButton kinetics_close_btn

structures_close_btn

protected javax.swing.JButton structures_close_btn

epipro_close_btn

protected javax.swing.JButton epipro_close_btn

details_close_btn

protected javax.swing.JButton details_close_btn

program_close_btn

protected javax.swing.JButton program_close_btn

variants_save_btn

protected javax.swing.JButton variants_save_btn

qv_save_btn

protected javax.swing.JButton qv_save_btn

kinetics_save_btn

protected javax.swing.JButton kinetics_save_btn

structures_save_btn

protected javax.swing.JButton structures_save_btn

epipro_save_btn

protected javax.swing.JButton epipro_save_btn

details_save_btn

protected javax.swing.JButton details_save_btn

program_save_btn

protected javax.swing.JButton program_save_btn

variants_help_btn

protected javax.swing.JButton variants_help_btn

qv_help_btn

protected javax.swing.JButton qv_help_btn

kinetics_help_btn

protected javax.swing.JButton kinetics_help_btn

structures_help_btn

protected javax.swing.JButton structures_help_btn

epipro_help_btn

protected javax.swing.JButton epipro_help_btn

details_help_btn

protected javax.swing.JButton details_help_btn

program_help_btn

protected javax.swing.JButton program_help_btn

reset_btn

protected javax.swing.JButton reset_btn

close_text

protected final java.lang.String close_text

See Also:

Constant Field Values

save_text

protected final java.lang.String save_text

See Also:

Constant Field Values

btn_inset

protected final int btn_inset

See Also:

Constant Field Values

baseqv_checkbox

protected javax.swing.JCheckBox baseqv_checkbox

mapqv_checkbox

protected javax.swing.JCheckBox mapqv_checkbox

qv_thresholds_panel

protected QVThresholdOptionsPane qv_thresholds_panel

dna_colors_panel

protected DNAColorsOptionsPane dna_colors_panel

cov_filter_checkbox

protected javax.swing.JCheckBox cov_filter_checkbox

cov_filter_threshold

protected javax.swing.JFormattedTextField cov_filter_threshold

conf_filter_checkbox

protected javax.swing.JCheckBox conf_filter_checkbox

conf_filter_threshold

protected javax.swing.JFormattedTextField conf_filter_threshold

kinetics_checkbox

protected javax.swing.JCheckBox kinetics_checkbox

basemods_filter_checkbox

protected javax.swing.JCheckBox basemods_filter_checkbox

basemods_options_cb

protected JComboBoxCtrl basemods_options_cb

kinetics_palette

protected PaletteCtrl kinetics_palette

kinetics_min_slider

protected PreferencesDialogBase.JDoubleSlider kinetics_min_slider

kinetics_max_slider

protected PreferencesDialogBase.JDoubleSlider kinetics_max_slider

kinetics_min_text

protected javax.swing.JFormattedTextField kinetics_min_text

kinetics_max_text

protected javax.swing.JFormattedTextField kinetics_max_text

basemods_filter_threshold

protected javax.swing.JFormattedTextField basemods_filter_threshold

kinetics_scaling_cb

protected JComboBoxCtrl kinetics_scaling_cb

kinetics_scaling_label

protected javax.swing.JLabel kinetics_scaling_label

kinetics_min_label

protected javax.swing.JLabel kinetics_min_label

kinetics_max_label

protected javax.swing.JLabel kinetics_max_label

kinetics_ann_label

protected javax.swing.JLabel kinetics_ann_label

details_view_range_mode_cb

protected JComboBoxCtrl details_view_range_mode_cb

details_view_dynamic_range

protected javax.swing.JFormattedTextField details_view_dynamic_range

details_view_fixed_range

protected javax.swing.JFormattedTextField details_view_fixed_range

details_view_max_coverage

protected javax.swing.JFormattedTextField details_view_max_coverage

fixed_range_label

protected javax.swing.JLabel fixed_range_label

dynamic_range_label

protected javax.swing.JLabel dynamic_range_label

details_view_coarse_cb

protected JComboBoxCtrl details_view_coarse_cb

show_tooltip_checkbox

protected javax.swing.JCheckBox show_tooltip_checkbox

epipro_only_checkbox

protected javax.swing.JCheckBox epipro_only_checkbox

epipro_cutoff_filter_checkbox

protected javax.swing.JCheckBox epipro_cutoff_filter_checkbox

epipro_view_mode_cb

protected JComboBoxCtrl epipro_view_mode_cb

epipro_cutoff_filter_threshold

protected javax.swing.JFormattedTextField epipro_cutoff_filter_threshold

epipro_pane

protected EpiProColorOptionsPane epipro_pane

show_graph_structures_checkbox

protected javax.swing.JCheckBox show_graph_structures_checkbox

show_structures_only_checkbox

protected javax.swing.JCheckBox show_structures_only_checkbox

structures_listbox

protected javax.swing.JList structures_listbox

always_show_mem_stats_checkbox

protected javax.swing.JCheckBox always_show_mem_stats_checkbox

link_genome_region_checkbox

protected javax.swing.JCheckBox link_genome_region_checkbox

link_region_details_checkbox

protected javax.swing.JCheckBox link_region_details_checkbox

Constructor Detail

PreferencesDialogBase

public PreferencesDialogBase(java.lang.String s)

Parameters:

s -

Method Detail

getView

public GenomicViewDetails getView()

getDetailsOptions

public DetailsOptions getDetailsOptions()

showDialog

public void showDialog()

selectDefaultButton

protected void selectDefaultButton(int index)

Parameters:

index -

getSelectedKineticMode

public int getSelectedKineticMode()

returns current kinetics mode

Returns:

getSelectedGraphStructureMode

public int getSelectedGraphStructureMode()

returns current graph mode

Returns:

layoutVariantsTab

protected void layoutVariantsTab()

layoutQVTab

protected void layoutQVTab()

layoutKineticsTab

protected void layoutKineticsTab()

layoutStructuresTab

protected void layoutStructuresTab()

Graph structures options

layoutEpiProReadsTab

protected void layoutEpiProReadsTab()

layoutDetailsTab

protected void layoutDetailsTab()

layoutProgramTab

protected void layoutProgramTab()

updateKineticsControls

protected void updateKineticsControls(boolean isKinetics)

updates status of kinetics controls

Parameters:

enabled -

updateDetailsControls

protected void updateDetailsControls(int index)

updates status of details controls

Parameters:

index -

updateDetailsData

protected void updateDetailsData()

updateVariantsData

protected void updateVariantsData()

updateModificationsData

protected void updateModificationsData()

updateToggleButtons

public void updateToggleButtons()

called by mainframe after toggle buttons in toolbar change state

updateStates

protected void updateStates()

updateData

protected boolean updateData(boolean bUpdateView)

Parameters:

bUpdateView - true if view should be updated after data is updated with new ui values

Returns:

true if validation succeeds, false if in error

addSaveButtonToTabbedPane

@Deprecated
protected void addSaveButtonToTabbedPane()

Deprecated.

not used, but it's a nice way to add buttons to the tabbed pane from: http://tech.chitgoks.com/2009/12/13/create-a-logout-button-beside-a-jtabbedpane/