com.pacbio.secondary.vis.gui.draw.views

Class GenomicViewBase

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

Direct Known Subclasses:

GenomicViewData

public abstract class GenomicViewBase
extends javax.swing.JComponent

See Also:

Serialized Form

Nested Class Summary

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
protected boolean	active
protected boolean	bCircular
protected boolean	bDetails
protected java.awt.Point	beginPoint
protected boolean	bHorizontal
protected boolean	bInspection
protected java.awt.Rectangle	bottomMarkerBounds
protected java.awt.Rectangle	bottomPileUpBounds
protected java.awt.Rectangle	bottomReferenceBounds
protected int	contigLength
protected int	currentViewContig
protected int	default_border_width
protected int	default_feature_size
protected int	default_height_top_axis
protected int	default_ideogram_height
protected int	default_ideogram_label_width
protected int	default_ideogram_width
protected int	default_left_info_width
protected int	default_tracks_width
protected int	default_view_height
protected int	default_view_width
protected int	default_y_bottom_ideogram
protected int	default_y_top_ideogram
protected java.awt.Dimension	dim_ideogramview
protected java.awt.Point	endPoint
protected java.awt.Rectangle	ideogramBounds
protected java.awt.Rectangle	ideogramLabelBounds
protected Interval	int_visible_range
protected boolean	isDragging
protected ViewLayoutInfo	layout_info
protected java.awt.Rectangle	leftLegendBounds
protected java.awt.Rectangle	leftMarkerBounds
protected java.util.BitSet	leftVisible
protected static VioletApp	main_app
protected boolean	marker_state
protected java.util.ArrayList<MarkerCollection>	markers
protected int	maxWidth
protected int	minViewGenomicRange
protected int	minWidth
protected java.awt.image.BufferedImage	paintBuffer
protected boolean	paintBufferValid
protected Interval	rangeSelection
protected java.awt.Rectangle	rightLegendBounds
protected java.awt.Rectangle	rightMarkerBounds
protected java.util.BitSet	rightVisible
protected double	scaleX
protected double	scaleY
protected Marker	selected_gene
protected Marker	selectedMarker
protected int	selectedSlotIndex
protected int	selectedTrackIndex
protected java.util.LinkedList<javax.swing.event.ChangeListener>	selectionChangedListeners
java.lang.Boolean	showGenes
protected boolean	showLabels
protected boolean	showMarkerLabels
protected boolean	showMarkers
protected java.util.LinkedList<Interval>	viewHistory

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.image.ImageObserver

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

Constructor Summary

Constructors

Constructor and Description
GenomicViewBase(VioletApp app)

Method Summary

Methods

Modifier and Type	Method and Description
protected abstract void	drawGene(java.awt.Graphics g, Marker M, boolean show_band, java.awt.Color color)
protected abstract void	drawGenes(java.awt.Graphics g)
abstract void	drawGenomicViewToGraphicsContext(java.awt.Graphics g)
protected abstract void	drawHeaderFooter(java.awt.Graphics g)
protected abstract void	drawIdeogram(java.awt.Graphics g)
protected abstract void	drawMarker(java.awt.Graphics g, Marker marker, int column, java.awt.Rectangle rect, java.awt.Color color, boolean show_band, java.awt.Color band_color)
protected abstract void	drawMarkers(java.awt.Graphics g)
int	getAbsMaxGenomicRange()
int	getBorderWidth()
DataStorage	getDataStorage()
GeneDB	getGeneDB()
IdeogramDB	getIdeogramDB()
VioletFrameBase	getMainWindow()
int	getMaxGenomicRange()
int	getMinGenomicRange()
ReferenceInfo	getReferenceInfo()
int	getViewContig()
java.lang.String	getViewContigName()
VioletApp	getVioletApp()
protected void	initializeViewBase()
boolean	isActive()
protected boolean	isDNABaseShown()
boolean	isIdeogramDBLoaded()

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, 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, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, paramString, 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, updateUI

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, 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, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

minViewGenomicRange

protected int minViewGenomicRange

default_view_height

protected int default_view_height

default_view_width

protected int default_view_width

default_ideogram_width

protected int default_ideogram_width

default_ideogram_height

protected int default_ideogram_height

default_ideogram_label_width

protected int default_ideogram_label_width

default_left_info_width

protected int default_left_info_width

default_tracks_width

protected int default_tracks_width

default_border_width

protected int default_border_width

default_y_top_ideogram

protected int default_y_top_ideogram

default_height_top_axis

protected int default_height_top_axis

default_y_bottom_ideogram

protected int default_y_bottom_ideogram

default_feature_size

protected int default_feature_size

ideogramBounds

protected transient java.awt.Rectangle ideogramBounds

ideogramLabelBounds

protected transient java.awt.Rectangle ideogramLabelBounds

leftMarkerBounds

protected transient java.awt.Rectangle leftMarkerBounds

rightMarkerBounds

protected transient java.awt.Rectangle rightMarkerBounds

leftLegendBounds

protected transient java.awt.Rectangle leftLegendBounds

rightLegendBounds

protected transient java.awt.Rectangle rightLegendBounds

bottomMarkerBounds

protected transient java.awt.Rectangle bottomMarkerBounds

bottomPileUpBounds

protected transient java.awt.Rectangle bottomPileUpBounds

bottomReferenceBounds

protected transient java.awt.Rectangle bottomReferenceBounds

currentViewContig

protected int currentViewContig

bHorizontal

protected boolean bHorizontal

bCircular

protected boolean bCircular

bDetails

protected boolean bDetails

bInspection

protected boolean bInspection

layout_info

protected transient ViewLayoutInfo layout_info

leftVisible

protected java.util.BitSet leftVisible

rightVisible

protected java.util.BitSet rightVisible

scaleX

protected double scaleX

scaleY

protected double scaleY

selectedSlotIndex

protected int selectedSlotIndex

selectedTrackIndex

protected int selectedTrackIndex

showGenes

public java.lang.Boolean showGenes

showLabels

protected boolean showLabels

showMarkers

protected boolean showMarkers

showMarkerLabels

protected boolean showMarkerLabels

minWidth

protected int minWidth

maxWidth

protected int maxWidth

selectionChangedListeners

protected java.util.LinkedList<javax.swing.event.ChangeListener> selectionChangedListeners

rangeSelection

protected Interval rangeSelection

beginPoint

protected java.awt.Point beginPoint

endPoint

protected java.awt.Point endPoint

viewHistory

protected java.util.LinkedList<Interval> viewHistory

dim_ideogramview

protected java.awt.Dimension dim_ideogramview

contigLength

protected transient int contigLength

active

protected transient boolean active

isDragging

protected transient boolean isDragging

int_visible_range

protected transient Interval int_visible_range

paintBufferValid

protected transient boolean paintBufferValid

paintBuffer

protected transient java.awt.image.BufferedImage paintBuffer

selectedMarker

protected transient Marker selectedMarker

selected_gene

protected transient Marker selected_gene

marker_state

protected transient boolean marker_state

main_app

protected static VioletApp main_app

markers

protected java.util.ArrayList<MarkerCollection> markers

Constructor Detail

GenomicViewBase

public GenomicViewBase(VioletApp app)

Method Detail

getVioletApp

public VioletApp getVioletApp()

getMainWindow

public VioletFrameBase getMainWindow()

getDataStorage

public DataStorage getDataStorage()

getReferenceInfo

public ReferenceInfo getReferenceInfo()

getIdeogramDB

public IdeogramDB getIdeogramDB()

isIdeogramDBLoaded

public boolean isIdeogramDBLoaded()

getGeneDB

public GeneDB getGeneDB()

getMaxGenomicRange

public int getMaxGenomicRange()

getMinGenomicRange

public int getMinGenomicRange()

getAbsMaxGenomicRange

public int getAbsMaxGenomicRange()

getBorderWidth

public int getBorderWidth()

getViewContig

public int getViewContig()

Returns:

The shown chromosome (1..24)

getViewContigName

public java.lang.String getViewContigName()

isActive

public boolean isActive()

Returns:

true if the current view is active.

initializeViewBase

protected void initializeViewBase()

isDNABaseShown

protected boolean isDNABaseShown()

drawGenomicViewToGraphicsContext

public abstract void drawGenomicViewToGraphicsContext(java.awt.Graphics g)

drawIdeogram

protected abstract void drawIdeogram(java.awt.Graphics g)

drawGenes

protected abstract void drawGenes(java.awt.Graphics g)

drawGene

protected abstract void drawGene(java.awt.Graphics g,
            Marker M,
            boolean show_band,
            java.awt.Color color)

drawMarkers

protected abstract void drawMarkers(java.awt.Graphics g)

drawMarker

protected abstract void drawMarker(java.awt.Graphics g,
              Marker marker,
              int column,
              java.awt.Rectangle rect,
              java.awt.Color color,
              boolean show_band,
              java.awt.Color band_color)

drawHeaderFooter

protected abstract void drawHeaderFooter(java.awt.Graphics g)