gov.lbl.genome.gui.panel
Class DisplayPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  gov.lbl.genome.gui.panel.VGBPanel
                      gov.lbl.genome.gui.panel.VistaPanel
                          gov.lbl.genome.gui.panel.DisplayPanel

All Implemented Interfaces:

java.awt.event.ComponentListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.print.Printable, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible

public class DisplayPanel
extends VistaPanel
implements java.awt.event.ComponentListener

Title: DisplayPanel

Description: This panal is a container for all graphical content

Copyright: Copyright (c) 2002 Ernest Orlando Lawrence Berkeley National Laboratory

Company: LBNL

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JPanel.AccessibleJPanel

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.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

int	activeTracerPanel
protected AxisPanel	axisPanel
int	currentPage
int	curvesPerPage
boolean	dragged
boolean	drawbar
int	endTracerPanel
boolean	inTracerPanel
int	pages
int	prevPage
protected java.lang.Thread	refreshThread
int	startTracerPanel
int	xend
int	xstart

Fields inherited from class gov.lbl.genome.gui.panel.VistaPanel

bottom, bottomSpace, df, g2d, height, horizSize, image, leftSpace, maxX, minX, offsetWidth, pixelWidth, rightSpace, top, topSpace, vertSize, wait_cursor, waitCursor

Fields inherited from class gov.lbl.genome.gui.panel.VGBPanel

commonParameters, debug, lineNumber, name, parameters, va

Fields inherited from class javax.swing.JComponent

accessibleContext, 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

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.print.Printable

NO_SUCH_PAGE, PAGE_EXISTS

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

DisplayPanel(VistaApp vapp)
DisplayPanel

Method Summary

void	addCurves(Status status) add Curves that are saved in status
void	addDefaultCurve(GenomeInfo genome) add Default Curves for the genome
void	addGraph(GeneralGraphView graph) add new Graph to the and
void	addPrintedGraph(int pos) add graph to a printedGraph list.
protected void	annotationLegend(java.awt.Graphics g, java.awt.Color color, int x, int y, java.lang.String name) draw annotation legend
void	componentHidden(java.awt.event.ComponentEvent e)
void	componentMoved(java.awt.event.ComponentEvent e)
void	componentResized(java.awt.event.ComponentEvent e) Logic of this method is the following: If number of rows is fixed and only vertical size changed - do nothing.
void	componentShown(java.awt.event.ComponentEvent e)
protected void	contigLegend(java.awt.Graphics g, java.awt.Color color, int x, int y, java.lang.String name) draw contig legend
void	drawContent(java.awt.Graphics g, int width, int height) draw Content in area with specified size
void	drawContent(java.awt.Graphics g, java.awt.print.PageFormat pf) print content on the page (printer, PDF or image)
java.util.Vector	getAllCurveInfos() return vector with all CurveInfo
java.util.Vector	getAllCurves() return all curves in all graphs
java.util.Collection	getAllGraphs() return All Graphs
java.util.Collection	getAllSelectedGraphs() return list of All Selected Graphs
AnnotationPanel	getAnnotationPanel() return Annotation Panel
long	getChromDX() return number of selected points
int	getFirstSelectedIndex() return index of the first (from top) selected graph
GeneralGraphView	getGraph(int pos) get Graph
java.awt.Dimension	getGraphPanelSize() return dimension of the graph panel
int	getLastSelectedIndex() return index of the last (from top) selected graph
int	getNumberOfGraphs() return Number Of Graphs
int	getPanelCapacity() return number of rows that would be drawn in the panel
javax.swing.JPopupMenu	getPopup() return Popup menu
int	getPrintHeight(int graphs, int lines) return min height that is necessary to fit all the content
RepeatPanel	getRepeatPanel() return Repeat Panel
int[]	getSelectedIndices() return numbers of selected lines in the bottom panel curve list
java.util.Vector	getStatistics() return conservation Statistics for all curves
TracerPanel	getTracerPanel() return Tracer Panel
int	getUniqOrganisms() return number uniq organisms
java.util.Vector	getVisibleCurveNames() return names of visible Curves
void	hideGraph(java.lang.String curveName) hide Graph
void	moveSelectedDown() move Selected Graphs Down
void	moveSelectedUp() move Selected Graphs Up
void	multiSelectGraphs() select more than one graph
int	print(java.awt.Graphics g, java.awt.print.PageFormat pf, int pi) print content
void	rebuildPanel() this method is responsible for positioning of all graphs, annotations, axis etc.
void	refreshAnnotations() request new information from the server for Annotations and repeats
void	refreshAnnotations(Status status) set Annotations and repeats from Status.
void	refreshGraphs() request new data from the server for all graphs and repaint
void	removeAllGraphs() remove All Graphs
boolean	removeAllSelectedGraphs() remove All Selected Graphs
void	removeDataImages() remove images for all graphs, annotation panel, repeat panel and axis panel
void	removeGraph(int pos) remove Graph
void	removeGraph(java.lang.String name) remove Graph
void	repaintTracerPanels() repaint all TracerPanels
protected void	repeatLegend(java.awt.Graphics g, java.awt.Color color, int x, int y, java.lang.String name) draw repeat legend
void	replaceGraph(GeneralGraphView graph, int i) replace Graph at the "i" position by another graph
void	resetPrintedGraphs() clear list of printed graphs
void	resetXBorders() resetXBorders
void	selectGraph(int index) select Graph in index position
void	setArrows() set buttons with Arrows in the bottom panel
void	setDetails() Enable or disable detailsAction
void	setFixedRows(int rows) set number of rows to show in the Display Panel
void	setPrintCapacity(int graphs, int lines) Set number of graphs and lines to be printed
void	setSelectedIndices(int[] indices) select lines in the bottom panel curve list
void	setSettings() SettingsAction can be enabled only if all curves are of the same type
void	setTracerPanel(TracerPanel tp) set Tracer Panel
void	setXBorders(int x) set Borders of the selected region
void	showGraph(java.lang.String curveName) show Graph
void	swapGraphs(int graph1, int graph2) swap 2 selected Graphs graph1<=>graph2
void	unselectAllGraphs() unselect all Graphs
boolean	updatePosition() update Position
void	updateSelectList() update Select List in the bottom panel curve list

Methods inherited from class gov.lbl.genome.gui.panel.VistaPanel

convertX, convertX, createImage, getFormattedNumberString, getFormattedNumberString, getFormattedXDisplayString, getFormattedXDisplayString, getHorizSize, getStringWidth, getVertSize, getXDisplay, getXDisplay, paintComponent, removeImage, setImage, shortenString

Methods inherited from class gov.lbl.genome.gui.panel.VGBPanel

Debug, dispatch, dispatchEvent, findParentFrame

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, 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, 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, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, 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, reshape, 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, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, 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, getFocusCycleRootAncestor, 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, hide, 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, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

axisPanel

protected AxisPanel axisPanel

refreshThread

protected java.lang.Thread refreshThread

pages

public int pages

currentPage

public int currentPage

prevPage

public int prevPage

curvesPerPage

public int curvesPerPage

inTracerPanel

public boolean inTracerPanel

dragged

public boolean dragged

drawbar

public boolean drawbar

xstart

public int xstart

xend

public int xend

startTracerPanel

public int startTracerPanel

endTracerPanel

public int endTracerPanel

activeTracerPanel

public int activeTracerPanel

Constructor Detail

DisplayPanel

public DisplayPanel(VistaApp vapp)

DisplayPanel

Parameters:

vapp - VistaApp

Method Detail

refreshAnnotations

public void refreshAnnotations()

request new information from the server for Annotations and repeats

refreshAnnotations

public void refreshAnnotations(Status status)

set Annotations and repeats from Status.

Parameters:

status - Status

updateSelectList

public void updateSelectList()

update Select List in the bottom panel curve list

removeGraph

public void removeGraph(int pos)

remove Graph

Parameters:

pos - int

getVisibleCurveNames

public java.util.Vector getVisibleCurveNames()

return names of visible Curves

Returns:

Vector

removeGraph

public void removeGraph(java.lang.String name)

remove Graph

Parameters:

name - String

resetPrintedGraphs

public void resetPrintedGraphs()

clear list of printed graphs

addPrintedGraph

public void addPrintedGraph(int pos)

add graph to a printedGraph list.

Parameters:

pos - int

removeAllGraphs

public void removeAllGraphs()

remove All Graphs

removeAllSelectedGraphs

public boolean removeAllSelectedGraphs()

remove All Selected Graphs

Returns:

boolean

getAllSelectedGraphs

public java.util.Collection getAllSelectedGraphs()

return list of All Selected Graphs

Returns:

Collection

unselectAllGraphs

public void unselectAllGraphs()

unselect all Graphs

setSettings

public void setSettings()

SettingsAction can be enabled only if all curves are of the same type

See Also:

SettingsAction

setDetails

public void setDetails()

Enable or disable detailsAction

See Also:

DetailsAction

setArrows

public void setArrows()

set buttons with Arrows in the bottom panel

multiSelectGraphs

public void multiSelectGraphs()

select more than one graph

getGraph

public GeneralGraphView getGraph(int pos)

get Graph

Parameters:

pos - int

Returns:

GeneralGraphView

getAllGraphs

public java.util.Collection getAllGraphs()

return All Graphs

Returns:

Collection

getAllCurves

public java.util.Vector getAllCurves()

return all curves in all graphs

Returns:

Vector

getAllCurveInfos

public java.util.Vector getAllCurveInfos()

return vector with all CurveInfo

Returns:

Vector

See Also:

CurveInfo

getRepeatPanel

public RepeatPanel getRepeatPanel()

return Repeat Panel

Returns:

RepeatPanel

getAnnotationPanel

public AnnotationPanel getAnnotationPanel()

return Annotation Panel

Returns:

AnnotationPanel

replaceGraph

public void replaceGraph(GeneralGraphView graph,
                         int i)

replace Graph at the "i" position by another graph

Parameters:

graph - GeneralGraphView

i - int

swapGraphs

public void swapGraphs(int graph1,
                       int graph2)

swap 2 selected Graphs graph1<=>graph2

Parameters:

graph1 - int

graph2 - int

moveSelectedUp

public void moveSelectedUp()

move Selected Graphs Up

See Also:

moveSelectedDown()

moveSelectedDown

public void moveSelectedDown()

move Selected Graphs Down

See Also:

moveSelectedUp()

getSelectedIndices

public int[] getSelectedIndices()

return numbers of selected lines in the bottom panel curve list

Returns:

int[]

See Also:

setSelectedIndices(int[])

setSelectedIndices

public void setSelectedIndices(int[] indices)

select lines in the bottom panel curve list

Parameters:

indices - int[]

See Also:

getSelectedIndices()

rebuildPanel

public void rebuildPanel()

this method is responsible for positioning of all graphs, annotations, axis etc.

addGraph

public void addGraph(GeneralGraphView graph)

add new Graph to the and

Parameters:

graph - GeneralGraphView

removeDataImages

public void removeDataImages()

remove images for all graphs, annotation panel, repeat panel and axis panel

refreshGraphs

public void refreshGraphs()

request new data from the server for all graphs and repaint

getStatistics

public java.util.Vector getStatistics()

return conservation Statistics for all curves

Returns:

Vector

See Also:

VistaCurveView.getStatistics(), GeneralGraphView.getStatistics()

getGraphPanelSize

public java.awt.Dimension getGraphPanelSize()

return dimension of the graph panel

Returns:

Dimension

getTracerPanel

public TracerPanel getTracerPanel()

return Tracer Panel

Returns:

TracerPanel

setTracerPanel

public void setTracerPanel(TracerPanel tp)

set Tracer Panel

Parameters:

tp - TracerPanel

getPopup

public javax.swing.JPopupMenu getPopup()

return Popup menu

Returns:

JPopupMenu

getNumberOfGraphs

public int getNumberOfGraphs()

return Number Of Graphs

Returns:

int

getPanelCapacity

public int getPanelCapacity()

return number of rows that would be drawn in the panel

Returns:

int

addCurves

public void addCurves(Status status)

add Curves that are saved in status

Parameters:

status - Status

addDefaultCurve

public void addDefaultCurve(GenomeInfo genome)

add Default Curves for the genome

Parameters:

genome - GenomeInfo

componentResized

public void componentResized(java.awt.event.ComponentEvent e)

Logic of this method is the following: If number of rows is fixed and only vertical size changed - do nothing. In all other cases try to rebuild panel to show maximum details

Specified by:

componentResized in interface java.awt.event.ComponentListener

Parameters:

e - ComponentEvent

componentMoved

public void componentMoved(java.awt.event.ComponentEvent e)

Specified by:

componentMoved in interface java.awt.event.ComponentListener

componentShown

public void componentShown(java.awt.event.ComponentEvent e)

Specified by:

componentShown in interface java.awt.event.ComponentListener

componentHidden

public void componentHidden(java.awt.event.ComponentEvent e)

Specified by:

componentHidden in interface java.awt.event.ComponentListener

print

public int print(java.awt.Graphics g,
                 java.awt.print.PageFormat pf,
                 int pi)
          throws java.awt.print.PrinterException

print content

Specified by:

print in interface java.awt.print.Printable

Overrides:

print in class VGBPanel

Parameters:

g - Graphics

pf - PageFormat

pi - int

Returns:

int

Throws:

java.awt.print.PrinterException

drawContent

public void drawContent(java.awt.Graphics g,
                        int width,
                        int height)

draw Content in area with specified size

Parameters:

g - Graphics

width - int

height - int

See Also:

drawContent(Graphics, PageFormat)

getPrintHeight

public int getPrintHeight(int graphs,
                          int lines)

return min height that is necessary to fit all the content

Parameters:

graphs - int

lines - int

Returns:

int

drawContent

public void drawContent(java.awt.Graphics g,
                        java.awt.print.PageFormat pf)

print content on the page (printer, PDF or image)

Parameters:

g - Graphics

pf - PageFormat

annotationLegend

protected void annotationLegend(java.awt.Graphics g,
                                java.awt.Color color,
                                int x,
                                int y,
                                java.lang.String name)

draw annotation legend

Parameters:

g - Graphics

color - Color

x - int

y - int

name - String

repeatLegend

protected void repeatLegend(java.awt.Graphics g,
                            java.awt.Color color,
                            int x,
                            int y,
                            java.lang.String name)

draw repeat legend

Parameters:

g - Graphics

color - Color

x - int

y - int

name - String

contigLegend

protected void contigLegend(java.awt.Graphics g,
                            java.awt.Color color,
                            int x,
                            int y,
                            java.lang.String name)

draw contig legend

Parameters:

g - Graphics

color - Color

x - int

y - int

name - String

repaintTracerPanels

public void repaintTracerPanels()

repaint all TracerPanels

setXBorders

public void setXBorders(int x)

set Borders of the selected region

Parameters:

x - int

resetXBorders

public void resetXBorders()

resetXBorders

See Also:

TracerPanel.reset()

getChromDX

public long getChromDX()

return number of selected points

Returns:

long

updatePosition

public boolean updatePosition()

update Position

Returns:

boolean

See Also:

VistaApp.updatePosition(long,long)

setPrintCapacity

public void setPrintCapacity(int graphs,
                             int lines)

Set number of graphs and lines to be printed

Parameters:

graphs - int

lines - int

See Also:

PrintAction

setFixedRows

public void setFixedRows(int rows)

set number of rows to show in the Display Panel

Parameters:

rows - int

getUniqOrganisms

public int getUniqOrganisms()

return number uniq organisms

Returns:

int

getFirstSelectedIndex

public int getFirstSelectedIndex()

return index of the first (from top) selected graph

Returns:

int

See Also:

getLastSelectedIndex()

selectGraph

public void selectGraph(int index)

select Graph in index position

Parameters:

index - int

getLastSelectedIndex

public int getLastSelectedIndex()

return index of the last (from top) selected graph

Returns:

int

See Also:

getFirstSelectedIndex()

hideGraph

public void hideGraph(java.lang.String curveName)

hide Graph

Parameters:

curveName - String

showGraph

public void showGraph(java.lang.String curveName)

show Graph

Parameters:

curveName - String