com.pacbio.secondary.vis.gui.frame

Class VioletFrameIO

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Frame

javax.swing.JFrame

com.pacbio.secondary.vis.gui.frame.VioletFrameBase

com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

com.pacbio.secondary.vis.gui.frame.VioletFrameIO

All Implemented Interfaces:

java.awt.event.ComponentListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.ChangeListener, javax.swing.event.TableModelListener, javax.swing.RootPaneContainer, javax.swing.WindowConstants, DockableSelectionListener, DockableStateChangeListener

Direct Known Subclasses:

VioletFrameActions

public class VioletFrameIO
extends VioletFrameChanges

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

VioletFrameChanges.setOptimumZoomFactorsThreaded

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.frame.VioletFrameChanges

last_selected_dockable_view

Fields inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

bFitRegionViewToWindowHeight, bFitToWindow, browser_panel, chromosomes_panel, chromosomes_scroller, chromosomes_views, circular_scroller, circular_view, currentMainFrameContig, default_workspace_layout, denovo_table_panel, details_scroller, details_view, docking_desktop, genomic_table_panel, heartbeat_timer, main_app, pageFormat, popmenu, printerJob, region_scroller, region_view, selection_panel

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
VioletFrameIO(java.lang.String str)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	actionFileAddTracksFromServer()
protected void	actionFileExportAsGraphics()
protected void	actionFileExportDataAsGFF()
protected void	actionFileOpenData()
protected void	actionFileOpenJobFromServer()
protected void	actionFilePrint()
protected void	actionFilePrinterSettings()
protected void	actionFileRemoveTrack()
protected void	actionFileSaveSession()
protected void	actionSessionProperties() Show file properties
protected boolean	readDetailsOptionsFromSession() read details options from user session file
void	readProperties() read options now
void	rebuildAllViewsMarkerCollectionsAndUpdateViews()
protected void	saveGraphicsFile(java.io.File file, java.lang.String ext, java.lang.Boolean[] bOptions)
void	saveProperties() save options
protected void	writeAllViewsToPDFFile(java.lang.String path, java.lang.Boolean[] bOptions)
protected void	writeAllViewsToPNGFile(java.lang.String path, java.lang.Boolean[] bOptions)
void	writePDFFile(java.io.OutputStream os, IdeogramViewPrintingHelper helper)
void	writePNGFile(java.io.FileOutputStream os, IdeogramViewPrintingHelper helper)

Methods inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges

componentHidden, componentMoved, componentResized, componentShown, dockableStateChanged, getActiveGenomicView, invalidateAndRepaintAllViews, selectionChanged, setOptimumZoomFactors, stateChanged, tableChanged, updateCircularView, updateDeNovoTablePanel, updateDetailsView, updateRegionView, updateRegionViewDetailsRange, updateSelectionPanel, updateTablePanel

Methods inherited from class com.pacbio.secondary.vis.gui.frame.VioletFrameBase

clearAllSlots, clearMarkersFromAllViews, getCircularScrollPanel, getCurrentMainFrameContig, getDataStorage, getDefaultWorkspaceLayout, getDeNovoTablePanel, getDetailsPanel, getDetailsView, getDockingDesktop, getGeneDB, getGenomePanel, getGenomeScrollPanel, getGenomicTablePanel, getIdeogramDB, getNumChromosomes, getPageFormat, getPrinterJob, getReferenceInfo, getRegionPanel, getRegionView, getSelectedSingleContigView, getSelectionPanel, getShowLabels, getShowMarkerLabels, getShowMarkers, getSingleContigsViews, getSlots, getVioletApp, getWebBrowserPanel, initLocals, normalCursor, resetVisibleGenomicRangeOfViews, saveDefaultLayout, setCurrentMainFrameContig, setDetailsViewMagnification, setFitRegionViewToWindowHeight, setMultiChromosomesViewMagnification, setPageFormat, setRegionViewMagnification, setShowGenes, setShowLabels, setShowMarkerLabels, setShowMarkers, updateWholeGenomeView, waitCursor

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

VioletFrameIO

public VioletFrameIO(java.lang.String str)

Parameters:

str -

Method Detail

actionFilePrinterSettings

protected void actionFilePrinterSettings()

actionFilePrint

protected void actionFilePrint()

actionSessionProperties

protected void actionSessionProperties()

Show file properties

actionFileSaveSession

protected void actionFileSaveSession()

actionFileOpenData

protected void actionFileOpenData()

actionFileOpenJobFromServer

protected void actionFileOpenJobFromServer()

actionFileAddTracksFromServer

protected void actionFileAddTracksFromServer()

actionFileRemoveTrack

protected void actionFileRemoveTrack()

readProperties

public void readProperties()

read options now

readDetailsOptionsFromSession

protected boolean readDetailsOptionsFromSession()

read details options from user session file

Returns:

saveProperties

public void saveProperties()

save options

rebuildAllViewsMarkerCollectionsAndUpdateViews

public void rebuildAllViewsMarkerCollectionsAndUpdateViews()

actionFileExportDataAsGFF

protected void actionFileExportDataAsGFF()

actionFileExportAsGraphics

protected void actionFileExportAsGraphics()

saveGraphicsFile

protected void saveGraphicsFile(java.io.File file,
                    java.lang.String ext,
                    java.lang.Boolean[] bOptions)

Parameters:

file -

ext -

bOptions -

writeAllViewsToPNGFile

protected void writeAllViewsToPNGFile(java.lang.String path,
                          java.lang.Boolean[] bOptions)
                               throws java.io.FileNotFoundException,
                                      com.itextpdf.text.DocumentException

Throws:

java.io.FileNotFoundException

com.itextpdf.text.DocumentException

writePNGFile

public void writePNGFile(java.io.FileOutputStream os,
                IdeogramViewPrintingHelper helper)

writeAllViewsToPDFFile

protected void writeAllViewsToPDFFile(java.lang.String path,
                          java.lang.Boolean[] bOptions)
                               throws java.io.FileNotFoundException,
                                      com.itextpdf.text.DocumentException

Throws:

java.io.FileNotFoundException

com.itextpdf.text.DocumentException

writePDFFile

public void writePDFFile(java.io.OutputStream os,
                IdeogramViewPrintingHelper helper)
                  throws com.itextpdf.text.DocumentException

Throws:

com.itextpdf.text.DocumentException