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

Class GenomicViewData

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

All Implemented Interfaces:

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

Direct Known Subclasses:

GenomicViewDraw

public abstract class GenomicViewData
extends GenomicViewBase

Author:

mmilletti

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 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.image.ImageObserver

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

Constructor Summary

Constructors

Constructor and Description
GenomicViewData(VioletApp main_app)

Method Summary

Methods

Modifier and Type	Method and Description
void	addTrackDataToViewAndUpdateLayout(MarkerCollection M, boolean bUpdateLayout) Adds a marker set to a track MarkerCollection.
void	clearMarkers(boolean bUpdateLayout) Removes all markers from this ideogram.
java.lang.String	getContigLabel()
MarkerCollection	getGenesOfCurrentContig()
IntervalTree	getIdeogramTreeOfCurrentContig()
MarkerCollection	getMarkerCollection(int i)
protected java.util.ArrayList<MarkerCollection>	getMarkers()
int	getNumMarkerCollections()
protected java.awt.Color	getSlotColor(int SlotIndex)
protected double	getSlotMaxCoverage(int SlotIndex)
protected int	getSlotMaxVariants(int SlotIndex)
java.util.Vector<VariableResolutionDataSet>	getSlots()
int	markerToSampleIndex(int markerIndex)
int	sampleToMarkerIndex(int sampleIndex)
int	sampleToMarkerIndex(int sampleIndex, boolean leftSide)
void	setViewContig(int contig) Sets the currently shown contig.
boolean	setViewDataForCurrentContig(int contig, GenomicViewData contig_data, boolean updateTablePanel)
abstract java.awt.Dimension	updateSize(boolean repaint, boolean revalidate)
protected void	updateVisibility() Finds for each MarkerCollection if it is empty or not and updates the two BitSets leftVisible and rightVisible.

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

drawGene, drawGenes, drawGenomicViewToGraphicsContext, drawHeaderFooter, drawIdeogram, drawMarker, drawMarkers, getAbsMaxGenomicRange, getBorderWidth, getDataStorage, getGeneDB, getIdeogramDB, getMainWindow, getMaxGenomicRange, getMinGenomicRange, getReferenceInfo, getViewContig, getViewContigName, getVioletApp, initializeViewBase, isActive, isDNABaseShown, 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

Constructor Detail

GenomicViewData

public GenomicViewData(VioletApp main_app)

Method Detail

updateSize

public abstract java.awt.Dimension updateSize(boolean repaint,
                            boolean revalidate)

setViewDataForCurrentContig

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

setViewContig

public void setViewContig(int contig)

Sets the currently shown contig.

Parameters:

contig -

Throws:

java.lang.IllegalArgumentException

addTrackDataToViewAndUpdateLayout

public void addTrackDataToViewAndUpdateLayout(MarkerCollection M,
                                     boolean bUpdateLayout)

Adds a marker set to a track MarkerCollection.

Parameters:

M - Collection of markers.

clearMarkers

public void clearMarkers(boolean bUpdateLayout)

Removes all markers from this ideogram. eventually recalculates layout

getSlots

public java.util.Vector<VariableResolutionDataSet> getSlots()

getMarkers

protected java.util.ArrayList<MarkerCollection> getMarkers()

getNumMarkerCollections

public int getNumMarkerCollections()

getMarkerCollection

public MarkerCollection getMarkerCollection(int i)

Parameters:

i - track index

Returns:

MarkerCollection with markers for track.

getIdeogramTreeOfCurrentContig

public IntervalTree getIdeogramTreeOfCurrentContig()

Returns:

The current ideogram tree for the chromosome of this ideogram.

getGenesOfCurrentContig

public MarkerCollection getGenesOfCurrentContig()

Returns:

The current gene interval tree for the chromosome of this ideogram.

updateVisibility

protected void updateVisibility()

Finds for each MarkerCollection if it is empty or not and updates the two BitSets leftVisible and rightVisible.

markerToSampleIndex

public int markerToSampleIndex(int markerIndex)

Parameters:

markerIndex -

Returns:

-1 if the index line is NOT found

sampleToMarkerIndex

public int sampleToMarkerIndex(int sampleIndex)

Parameters:

sampleIndex -

leftSide -

Returns:

0 if there is no profile line for the given sample

sampleToMarkerIndex

public int sampleToMarkerIndex(int sampleIndex,
                      boolean leftSide)

Parameters:

sampleIndex -

leftSide -

Returns:

0 if there is no profile line for the given sample

getSlotColor

protected java.awt.Color getSlotColor(int SlotIndex)

getSlotMaxCoverage

protected double getSlotMaxCoverage(int SlotIndex)

getSlotMaxVariants

protected int getSlotMaxVariants(int SlotIndex)

getContigLabel

public java.lang.String getContigLabel()