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

Class GenomicViewDetailsData

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

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

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

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

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

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

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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.print.Printable, java.io.Serializable, java.util.EventListener

Direct Known Subclasses:

GenomicViewDetailsDraw

public abstract class GenomicViewDetailsData
extends GenomicViewHorizontal
implements java.awt.event.ActionListener

Author:

mmilletti

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

GenomicViewEvents.GenomicViewKeyListener, GenomicViewEvents.GenomicViewMouseListener, GenomicViewEvents.GenomicViewMouseMotionListener

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 Locus	data_on_demand_queue
protected javax.swing.Timer	data_on_demand_timer
protected Locus	data_request_queue
protected DetailsStorage	details_data
protected DetailsOptions	details_options
static char	gappedDNAAnnotation
protected IPDConsensusStorage	ipd_consensus_data
protected Locus	ipd_consensus_request_queue
protected static int	MIN_EXTRA_DELTA_ADD_RANGE_REQUEST
protected static int	MIN_HALF_DATA_ON_DEMAND_REQUEST
protected static int	MIN_RANGE_REFERENCE_OR_IPD_REQUEST
static char	noDNAAnnotation
protected ReferenceSequenceStorage	reference_data
protected Locus	reference_request_queue

Fields inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal

default_tracks_height, variations_splitter

Fields inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

end_last_lower_label_x, end_last_upper_label_x

Fields inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

active, bCircular, bDetails, beginPoint, bHorizontal, bInspection, bottomMarkerBounds, bottomPileUpBounds, bottomReferenceBounds, contigLength, currentViewContig, default_border_width, default_feature_size, default_height_top_axis, default_ideogram_height, default_ideogram_label_width, default_ideogram_width, default_left_info_width, default_tracks_width, default_view_height, default_view_width, default_y_bottom_ideogram, default_y_top_ideogram, dim_ideogramview, endPoint, ideogramBounds, ideogramLabelBounds, int_visible_range, isDragging, layout_info, leftLegendBounds, leftMarkerBounds, leftVisible, main_app, marker_state, markers, maxWidth, minViewGenomicRange, minWidth, paintBuffer, paintBufferValid, rangeSelection, rightLegendBounds, rightMarkerBounds, rightVisible, scaleX, scaleY, selected_gene, selectedMarker, selectedSlotIndex, selectedTrackIndex, selectionChangedListeners, showGenes, showLabels, showMarkerLabels, showMarkers, 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.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

Constructors

Constructor and Description
GenomicViewDetailsData(VioletApp mainApp)

Method Summary

Methods

Modifier and Type	Method and Description
void	actionPerformed(java.awt.event.ActionEvent event)
void	addGenomicRangeToDetailsViewDataRequestsQueue(Interval interval, boolean updateGenomicRange)
protected void	addGenomicRangeToDetailsViewIPDConsensusRequestQueue(Interval interval)
protected void	addGenomicRangeToDetailsViewReferenceRequestQueue(Interval interval)
boolean	canDrawIPDConsensus() can painters draw consensus ipd based on current graphic layout?
void	clearAllDetailsData()
Marker	findReadByPositionAndLane(long bp, int lane)
Locus	getDetailsDataLocus()
DetailsStorage	getDetailsDataStorage()
DetailsOptions	getDetailsOptions()
protected char[]	getEmptyCharArray(int size) Creates array of chars filled in with white spaces
Locus	getIPDConsensusDataLocus()
IPDConsensusStorage	getIPDConsensusStorage()
Locus	getReferenceDataLocus()
ReferenceSequenceStorage	getReferenceSequenceStorage()
protected boolean	isCDNADataAvailable() do we have cdna in the dataset?
protected boolean	isDNABaseShown()
protected boolean	isDrawIPDConsensus() should we draw consensus ipd based on user options, etc.
protected boolean	isIPDConsensusDataAvailable() do we have consensus ipd in the dataset?
protected void	retrieveDataOnDemand() this method can be called concurrently
boolean	setConsensusData(WsFastaSequenceInfo data)
void	setDetailsOptions(DetailsOptions opts)
boolean	setDetailsViewData(WsResults results, TrackDataInfo clientData)
boolean	setIPDConsensusData(WsIPDConsensusInfo data)
boolean	setReferenceData(WsFastaSequenceInfo data)
void	setReferenceSequenceStorage(ReferenceSequenceStorage data)
boolean	setViewDataForCurrentContig(int contig, GenomicViewData contig_data, boolean updateTablePanel)
protected void	updateLayoutOnDemand() this method can be called concurrently
void	zoomToBases() zoom to single base level at once

Methods inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal

calcSize, drawBackgroundSelections, drawCrossLines, drawFilteredTrack, drawFilteredTracks, drawForegroundSelections, drawGene, drawGenomicViewToGraphicsContext, drawHorizontalTracksHeader, drawIdeogram, drawLabelWithoutCollision, drawMarkerHorizontal, drawMarkerInterval, drawMarkers, drawMarkersLegend, drawModification, drawModificationInterval, drawModificationsLegend, drawModificationSummaryHeatmap, drawModificationSummaryHistogram, drawMotifLegend, drawRangeSelection, drawReferenceSequenceOutline, drawSummaryLegends, drawSummaryTracks, drawUnFilteredTracks, drawVariant, drawVariantInterval, drawVariantIntervalOrg, drawVariantsLegend, drawVariantsLegendOrg, getLegendLabelsWidth, getMaxCoverageInInterval, getMaxCoverageInInterval, getMaxMagnification, getMinMagnification, getTracksHeight, initLocals, isIdeogramDBLoaded, resetVisibleGenomicRange, selectPoint, setTracksHeight, showDataLabels, updateSize

Methods inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents

addSelectionChangedListener, beginSelection, center, changeDNAFontSize, changeIPDConsensusHeight, changeTrackSize, clearSelections, createToolTip, endSelection, findVariantByPositionAndYCoordinate, fireSelectionChanged, getActiveViewForKeyEvents, getScaledHeight, getScaledWidth, getSelectedGene, getSelectedMarker, getSelectedSlotIndex, getSelectionInfo, getShowLabels, getShowMarkerLabels, getShowMarkers, getToolTipText, getZoom, getZoom, hasViewHistoryItems, initTransientState, isSelection, popView, pushView, scroll, scrollVisibleGenomicRangeToTopOrBottom, selectNextPreviousContig, selectNextPreviousGeneContig, selectNextPreviousMarker, setActive, setRangeSelection, setSelectedGeneAndTrack, setSelectedMarkerAndSlot, setShowGenes, setShowLabels, setShowMarkerLabels, setShowMarkers, setViewWithOrWithoutUpdate, setVisibleGenomicRange, setVisibleGenomicRegion, setWidth, toggleMarker, zoomVisibleGenomicRange

Methods inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw

autofitLabelWidth, BaseRangeToXExtent, BaseToXCoord, BaseToYCoord, drawAxisHeaderlabel, drawEpiProIdeogram, drawGenes, drawGenomicViewDoubleBuffered, drawGenomicViewToPaintBuffer, drawHeaderFooter, drawInfoLabel, drawInfoLabelJustified, drawLabelWithOffsetAndWidth, drawMarker, drawMinMaxLabel, drawModification, drawRotatedLabel, drawSummary, drawSummaryInterval, drawSummaryRegion, drawTrackMetricLabel, drawVariant, getContigLength, getContigMaxRange, getDim, getExtraRefTrackDistance, getGenesBounds, getIdeogramBounds, getLabelBounds, getLegendBounds, getMarkersBounds, getNumLeft, getNumRight, getPanelTitle, getPileupBounds, getRangeSelection, getReferenceBounds, getSelectedRangeColor, getVisibleGenomicRange, invalidatePaintBuffer, isCircular, isDetails, isHorizontal, isInspection, paintActiveBorder, paintComponent, paintLegendBackground, prepareDrawVariant, print, scaleX, scaleY, setMagnificationScaleFactor, trackIndexToXCoord, trackToYCoord, updateLayout, XCoordToBase, xCoordToTrackIndex, YCoordToBase, yCoordToMarkerCollectionIndex, yCoordToMarkerCollectionIndexNew, yCoordToMarkerCollectionIndexOrg, yCoordToTrackIndex

Methods inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData

addTrackDataToViewAndUpdateLayout, clearMarkers, getContigLabel, getGenesOfCurrentContig, getIdeogramTreeOfCurrentContig, getMarkerCollection, getMarkers, getNumMarkerCollections, getSlotColor, getSlotMaxCoverage, getSlotMaxVariants, getSlots, markerToSampleIndex, sampleToMarkerIndex, sampleToMarkerIndex, setViewContig, updateVisibility

Methods inherited from class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase

getAbsMaxGenomicRange, getBorderWidth, getDataStorage, getGeneDB, getIdeogramDB, getMainWindow, getMaxGenomicRange, getMinGenomicRange, getReferenceInfo, getViewContig, getViewContigName, getVioletApp, initializeViewBase, isActive

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, 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, getTopLevelAncestor, getTransferHandler, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, 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

details_options

protected DetailsOptions details_options

details_data

protected DetailsStorage details_data

data_request_queue

protected Locus data_request_queue

reference_data

protected ReferenceSequenceStorage reference_data

reference_request_queue

protected Locus reference_request_queue

ipd_consensus_data

protected IPDConsensusStorage ipd_consensus_data

ipd_consensus_request_queue

protected Locus ipd_consensus_request_queue

data_on_demand_timer

protected transient javax.swing.Timer data_on_demand_timer

data_on_demand_queue

protected Locus data_on_demand_queue

MIN_HALF_DATA_ON_DEMAND_REQUEST

protected static final int MIN_HALF_DATA_ON_DEMAND_REQUEST

See Also:

Constant Field Values

MIN_EXTRA_DELTA_ADD_RANGE_REQUEST

protected static final int MIN_EXTRA_DELTA_ADD_RANGE_REQUEST

See Also:

Constant Field Values

MIN_RANGE_REFERENCE_OR_IPD_REQUEST

protected static final int MIN_RANGE_REFERENCE_OR_IPD_REQUEST

See Also:

Constant Field Values

noDNAAnnotation

public static final char noDNAAnnotation

See Also:

Constant Field Values

gappedDNAAnnotation

public static final char gappedDNAAnnotation

See Also:

Constant Field Values

Constructor Detail

GenomicViewDetailsData

public GenomicViewDetailsData(VioletApp mainApp)

Method Detail

setDetailsViewData

public boolean setDetailsViewData(WsResults results,
                         TrackDataInfo clientData)

setReferenceData

public boolean setReferenceData(WsFastaSequenceInfo data)

setConsensusData

public boolean setConsensusData(WsFastaSequenceInfo data)

setIPDConsensusData

public boolean setIPDConsensusData(WsIPDConsensusInfo data)

setViewDataForCurrentContig

public boolean setViewDataForCurrentContig(int contig,
                                  GenomicViewData contig_data,
                                  boolean updateTablePanel)

Overrides:

setViewDataForCurrentContig in class GenomicViewData

addGenomicRangeToDetailsViewDataRequestsQueue

public void addGenomicRangeToDetailsViewDataRequestsQueue(Interval interval,
                                                 boolean updateGenomicRange)

Overrides:

addGenomicRangeToDetailsViewDataRequestsQueue in class GenomicViewEvents

addGenomicRangeToDetailsViewReferenceRequestQueue

protected void addGenomicRangeToDetailsViewReferenceRequestQueue(Interval interval)

addGenomicRangeToDetailsViewIPDConsensusRequestQueue

protected void addGenomicRangeToDetailsViewIPDConsensusRequestQueue(Interval interval)

clearAllDetailsData

public void clearAllDetailsData()

getDetailsDataLocus

public Locus getDetailsDataLocus()

getDetailsDataStorage

public DetailsStorage getDetailsDataStorage()

Overrides:

getDetailsDataStorage in class GenomicViewEvents

getDetailsOptions

public DetailsOptions getDetailsOptions()

setDetailsOptions

public void setDetailsOptions(DetailsOptions opts)

getReferenceSequenceStorage

public ReferenceSequenceStorage getReferenceSequenceStorage()

setReferenceSequenceStorage

public void setReferenceSequenceStorage(ReferenceSequenceStorage data)

getReferenceDataLocus

public Locus getReferenceDataLocus()

getIPDConsensusStorage

public IPDConsensusStorage getIPDConsensusStorage()

getIPDConsensusDataLocus

public Locus getIPDConsensusDataLocus()

getEmptyCharArray

protected char[] getEmptyCharArray(int size)

Creates array of chars filled in with white spaces

Parameters:

size -

Returns:

actionPerformed

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

Specified by:

actionPerformed in interface java.awt.event.ActionListener

isIPDConsensusDataAvailable

protected boolean isIPDConsensusDataAvailable()

do we have consensus ipd in the dataset?

Returns:

isCDNADataAvailable

protected boolean isCDNADataAvailable()

do we have cdna in the dataset?

Returns:

isDrawIPDConsensus

protected boolean isDrawIPDConsensus()

should we draw consensus ipd based on user options, etc.

Returns:

canDrawIPDConsensus

public boolean canDrawIPDConsensus()

can painters draw consensus ipd based on current graphic layout?

Overrides:

canDrawIPDConsensus in class GenomicViewHorizontal

Returns:

isDNABaseShown

protected boolean isDNABaseShown()

Overrides:

isDNABaseShown in class GenomicViewBase

findReadByPositionAndLane

public Marker findReadByPositionAndLane(long bp,
                               int lane)

zoomToBases

public void zoomToBases()

zoom to single base level at once

retrieveDataOnDemand

protected void retrieveDataOnDemand()

this method can be called concurrently

updateLayoutOnDemand

protected void updateLayoutOnDemand()

this method can be called concurrently