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

Class GenomicViewDraw

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

All Implemented Interfaces:

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

Direct Known Subclasses:

GenomicViewEvents

public abstract class GenomicViewDraw
extends GenomicViewData
implements java.awt.print.Printable

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 int	end_last_lower_label_x
protected int	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
GenomicViewDraw(VioletApp main_app)

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String	autofitLabelWidth(java.awt.Graphics g, java.lang.String label) changes string to display enough chars to fit to label width
int	BaseRangeToXExtent(double range) Transforms the basepair extent pos to x-width of the canvas.
int	BaseToXCoord(long pos) Transforms the basepair location pos to x-coordinates of the canvas.
int	BaseToYCoord(long pos) Transforms the basepair location pos to y-coordinates of the canvas.
protected void	drawAxisHeaderlabel(java.awt.Graphics g, double value, int half_char_width, int y_offset, boolean format_as_int)
void	drawBackgroundSelections(java.awt.Graphics g) draw marker lines and selected profile lines
protected void	drawEpiProIdeogram(java.awt.Graphics g)
void	drawForegroundSelections(java.awt.Graphics graphics)
protected void	drawGene(java.awt.Graphics g, Marker M, boolean is_selected, java.awt.Color color) Draws a gene into the graphic context
protected void	drawGenes(java.awt.Graphics g) Paints the gene markers into the given Graphics device.
protected void	drawGenomicViewDoubleBuffered(java.awt.Graphics graphics) Main draw function for class
void	drawGenomicViewToGraphicsContext(java.awt.Graphics g)
void	drawGenomicViewToPaintBuffer(java.awt.Graphics graphics)
protected void	drawHeaderFooter(java.awt.Graphics g)
protected void	drawHorizontalTracksHeader(java.awt.Graphics g)
protected void	drawIdeogram(java.awt.Graphics g)
protected void	drawInfoLabel(java.awt.Graphics g, java.lang.String label, int y_offset)
protected void	drawInfoLabelJustified(java.awt.Graphics g, java.lang.String label, int y_offset, int justification) draw label into info area
protected void	drawLabelWithOffsetAndWidth(java.awt.Graphics g, java.lang.String label, int x, int y, int width)
protected void	drawMarker(java.awt.Graphics g, Marker marker, int column, java.awt.Rectangle rect, java.awt.Color color, boolean is_selected, java.awt.Color selected_color) Draws a single marker.
protected void	drawMarkerInterval(java.awt.Graphics g, Marker marker, int column, java.awt.Rectangle rect, boolean is_selected, java.awt.Color selected_color)
protected void	drawMarkers(java.awt.Graphics g)
protected void	drawMinMaxLabel(java.awt.Graphics g, double min, double max, int y_offset, int vertical_height, double delta_extent, java.lang.String metric, boolean bLog10)
protected void	drawModification(java.awt.Graphics g, Marker marker, int column, java.awt.Rectangle rect)
protected void	drawModificationInterval(java.awt.Graphics2D g, Marker marker, int column, java.awt.Rectangle rect, VariableResolutionDataSetValues min_max_values)
protected void	drawRangeSelection(java.awt.Graphics g)
protected void	drawRotatedLabel(java.lang.String text, java.awt.Graphics g, java.awt.Color color, int x, int y, double dAngle)
protected void	drawSummary(java.awt.Graphics g, Marker marker, int column, java.awt.Color color, double max_coverage, int max_variants) Draws coverage info for one coverage slot (marker)
protected void	drawSummaryInterval(java.awt.Graphics g, int column, Marker marker, boolean bLeft, java.awt.Color color, double max_coverage, int max_variants)
protected void	drawSummaryRegion(java.awt.Graphics2D g2d, java.awt.Shape min_polygon, int[] x_coord, int[] y_coord, java.awt.Color min_max_color, java.awt.Color avg_color)
protected void	drawTrackMetricLabel(java.awt.Graphics g, int y_offset, int vertical_height, double delta_extent, java.lang.String metric)
protected void	drawVariant(java.awt.Graphics g, Marker marker, int track, java.awt.Rectangle rect)
protected void	drawVariantInterval(java.awt.Graphics2D g, Marker marker, int track, java.awt.Rectangle rect, VariableResolutionDataSetValues min_max_values)
int	getContigLength()
int	getContigMaxRange()
java.awt.Dimension	getDim()
protected int	getExtraRefTrackDistance()
java.awt.Rectangle	getGenesBounds()
java.awt.Rectangle	getIdeogramBounds()
java.awt.Rectangle	getLabelBounds()
java.awt.Rectangle	getLegendBounds()
java.awt.Rectangle	getMarkersBounds()
protected double	getMaxMagnification()
protected double	getMinMagnification()
int	getNumLeft()
int	getNumRight()
java.lang.String	getPanelTitle(boolean bLong) returns title to use for specific panel
java.awt.Rectangle	getPileupBounds()
Interval	getRangeSelection()
java.awt.Rectangle	getReferenceBounds()
java.awt.Color	getSelectedRangeColor()
Interval	getVisibleGenomicRange()
void	invalidatePaintBuffer() Call this function if the view changes.
boolean	isCircular()
boolean	isDetails()
boolean	isHorizontal()
boolean	isInspection()
protected void	paintActiveBorder(java.awt.Graphics g) Draws a frame around this ideogram if its active.
protected void	paintComponent(java.awt.Graphics graphics)
protected void	paintLegendBackground(java.awt.Graphics g, int x, int y, int w, int h)
protected boolean	prepareDrawVariant(java.awt.Graphics g, Marker marker)
int	print(java.awt.Graphics graphics, java.awt.print.PageFormat pageFormat, int pageIndex)
protected int	scaleX(int x)
protected int	scaleY(int y)
java.awt.Dimension	setMagnificationScaleFactor(double sx, double sy)
protected boolean	showDataLabels()
int	trackIndexToXCoord(int track_index) Compute the x-coordinate of a marker position.
int	trackToYCoord(int track_index) Compute the y-coordinate of a track.
java.awt.Dimension	updateLayout()
java.awt.Dimension	updateSize(boolean repaint, boolean revalidate)
long	XCoordToBase(int x) Transforms a canvas x coordinate to basepairs.
int	xCoordToTrackIndex(int x) Converts a x-coordinate in this panel into a track index value.
long	YCoordToBase(int y) Transforms a canvas y coordinate to basepairs.
int	yCoordToMarkerCollectionIndex(int y) returns index of markercollection for this y coordinate
int	yCoordToMarkerCollectionIndexNew(int y)
int	yCoordToMarkerCollectionIndexOrg(int y) returns index of markercollection for this y coordinate
int	yCoordToTrackIndex(int y) returns index of track in graph, e.g.

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, setViewDataForCurrentContig, 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, 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, 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

end_last_upper_label_x

protected int end_last_upper_label_x

end_last_lower_label_x

protected int end_last_lower_label_x

Constructor Detail

GenomicViewDraw

public GenomicViewDraw(VioletApp main_app)

Method Detail

updateLayout

public java.awt.Dimension updateLayout()

getContigLength

public int getContigLength()

getContigMaxRange

public int getContigMaxRange()

getVisibleGenomicRange

public Interval getVisibleGenomicRange()

Returns:

The current field of view (in basepairs).

getDim

public java.awt.Dimension getDim()

isHorizontal

public boolean isHorizontal()

isCircular

public boolean isCircular()

isDetails

public boolean isDetails()

isInspection

public boolean isInspection()

getIdeogramBounds

public java.awt.Rectangle getIdeogramBounds()

getMarkersBounds

public java.awt.Rectangle getMarkersBounds()

getLegendBounds

public java.awt.Rectangle getLegendBounds()

getLabelBounds

public java.awt.Rectangle getLabelBounds()

getPileupBounds

public java.awt.Rectangle getPileupBounds()

getReferenceBounds

public java.awt.Rectangle getReferenceBounds()

getGenesBounds

public java.awt.Rectangle getGenesBounds()

paintComponent

protected void paintComponent(java.awt.Graphics graphics)

Overrides:

paintComponent in class javax.swing.JComponent

drawGenomicViewDoubleBuffered

protected void drawGenomicViewDoubleBuffered(java.awt.Graphics graphics)

Main draw function for class

Parameters:

graphics -

getRangeSelection

public Interval getRangeSelection()

drawRangeSelection

protected void drawRangeSelection(java.awt.Graphics g)

drawBackgroundSelections

public void drawBackgroundSelections(java.awt.Graphics g)

draw marker lines and selected profile lines

drawForegroundSelections

public void drawForegroundSelections(java.awt.Graphics graphics)

drawGenomicViewToPaintBuffer

public void drawGenomicViewToPaintBuffer(java.awt.Graphics graphics)

drawGenomicViewToGraphicsContext

public void drawGenomicViewToGraphicsContext(java.awt.Graphics g)

Specified by:

drawGenomicViewToGraphicsContext in class GenomicViewBase

drawIdeogram

protected void drawIdeogram(java.awt.Graphics g)

Specified by:

drawIdeogram in class GenomicViewBase

drawEpiProIdeogram

protected void drawEpiProIdeogram(java.awt.Graphics g)

Parameters:

g -

drawGenes

protected void drawGenes(java.awt.Graphics g)

Paints the gene markers into the given Graphics device.

Specified by:

drawGenes in class GenomicViewBase

Parameters:

g -

drawGene

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

Draws a gene into the graphic context

Specified by:

drawGene in class GenomicViewBase

Parameters:

g - Graphics context

M - The gene to be drawn

color - The color of the gene marker.

drawMarkers

protected void drawMarkers(java.awt.Graphics g)

Specified by:

drawMarkers in class GenomicViewBase

drawMarker

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

Draws a single marker.

Specified by:

drawMarker in class GenomicViewBase

Parameters:

g -

marker -

column - The column index (0..n-1)

width - The (line) width of the marker

color - Color

show_band - Shows a band across the ideogram

band_color - Color of the band

drawMarkerInterval

protected void drawMarkerInterval(java.awt.Graphics g,
                      Marker marker,
                      int column,
                      java.awt.Rectangle rect,
                      boolean is_selected,
                      java.awt.Color selected_color)

drawSummary

protected void drawSummary(java.awt.Graphics g,
               Marker marker,
               int column,
               java.awt.Color color,
               double max_coverage,
               int max_variants)

Draws coverage info for one coverage slot (marker)

Parameters:

g - graphics context o draw in

marker - marker to draw

column - The column index (0..n-1)

width - The (line) width of the marker

color - color to use

max_scale - max scale for coverage

max_read_lenght - max read lenght for annotations scaling

drawSummaryInterval

protected void drawSummaryInterval(java.awt.Graphics g,
                       int column,
                       Marker marker,
                       boolean bLeft,
                       java.awt.Color color,
                       double max_coverage,
                       int max_variants)

drawSummaryRegion

protected void drawSummaryRegion(java.awt.Graphics2D g2d,
                     java.awt.Shape min_polygon,
                     int[] x_coord,
                     int[] y_coord,
                     java.awt.Color min_max_color,
                     java.awt.Color avg_color)

drawVariant

protected void drawVariant(java.awt.Graphics g,
               Marker marker,
               int track,
               java.awt.Rectangle rect)

Parameters:

g -

marker -

track -

rect -

prepareDrawVariant

protected boolean prepareDrawVariant(java.awt.Graphics g,
                         Marker marker)

Parameters:

g -

marker -

Returns:

drawVariantInterval

protected void drawVariantInterval(java.awt.Graphics2D g,
                       Marker marker,
                       int track,
                       java.awt.Rectangle rect,
                       VariableResolutionDataSetValues min_max_values)

drawModification

protected void drawModification(java.awt.Graphics g,
                    Marker marker,
                    int column,
                    java.awt.Rectangle rect)

Parameters:

g -

marker -

column -

rect -

drawModificationInterval

protected void drawModificationInterval(java.awt.Graphics2D g,
                            Marker marker,
                            int column,
                            java.awt.Rectangle rect,
                            VariableResolutionDataSetValues min_max_values)

Parameters:

g -

column -

marker -

is_selected -

selected_color -

max_coverage -

max_variants -

max_ipd_fwd -

max_ipd_rev -

drawHeaderFooter

protected void drawHeaderFooter(java.awt.Graphics g)

Specified by:

drawHeaderFooter in class GenomicViewBase

getPanelTitle

public java.lang.String getPanelTitle(boolean bLong)

returns title to use for specific panel

Parameters:

bLong -

Returns:

paintLegendBackground

protected void paintLegendBackground(java.awt.Graphics g,
                         int x,
                         int y,
                         int w,
                         int h)

Parameters:

g -

x -

y -

w -

h -

drawTrackMetricLabel

protected void drawTrackMetricLabel(java.awt.Graphics g,
                        int y_offset,
                        int vertical_height,
                        double delta_extent,
                        java.lang.String metric)

Parameters:

g -

min -

max -

y_offset -

vertical_height -

delta_extent -

metric -

format_as_int -

drawMinMaxLabel

protected void drawMinMaxLabel(java.awt.Graphics g,
                   double min,
                   double max,
                   int y_offset,
                   int vertical_height,
                   double delta_extent,
                   java.lang.String metric,
                   boolean bLog10)

Parameters:

g -

min -

max -

y_offset -

vertical_height -

delta_extent -

metric -

format_as_int -

drawAxisHeaderlabel

protected void drawAxisHeaderlabel(java.awt.Graphics g,
                       double value,
                       int half_char_width,
                       int y_offset,
                       boolean format_as_int)

drawInfoLabel

protected void drawInfoLabel(java.awt.Graphics g,
                 java.lang.String label,
                 int y_offset)

drawInfoLabelJustified

protected void drawInfoLabelJustified(java.awt.Graphics g,
                          java.lang.String label,
                          int y_offset,
                          int justification)

draw label into info area

Parameters:

g -

label -

y_offset -

justification -

autofitLabelWidth

protected java.lang.String autofitLabelWidth(java.awt.Graphics g,
                                 java.lang.String label)

changes string to display enough chars to fit to label width

Parameters:

g -

label -

Returns:

drawLabelWithOffsetAndWidth

protected void drawLabelWithOffsetAndWidth(java.awt.Graphics g,
                               java.lang.String label,
                               int x,
                               int y,
                               int width)

Parameters:

g -

label -

x -

y -

width -

print

public int print(java.awt.Graphics graphics,
        java.awt.print.PageFormat pageFormat,
        int pageIndex)
          throws java.awt.print.PrinterException

Specified by:

print in interface java.awt.print.Printable

Throws:

java.awt.print.PrinterException

updateSize

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

Specified by:

updateSize in class GenomicViewData

getMaxMagnification

protected double getMaxMagnification()

getMinMagnification

protected double getMinMagnification()

setMagnificationScaleFactor

public java.awt.Dimension setMagnificationScaleFactor(double sx,
                                             double sy)

xCoordToTrackIndex

public int xCoordToTrackIndex(int x)

Converts a x-coordinate in this panel into a track index value.

Parameters:

x -

Returns:

Integer marker index value between -n ... n. Returns 0 if the pointer is outside the marker regions

trackIndexToXCoord

public int trackIndexToXCoord(int track_index)

Compute the x-coordinate of a marker position. If count is > 0 the markers are placed on the right side of the ideogram. If count is < 0 the markers will be on the left side.

Parameters:

track_index -

Returns:

x-coordinate

trackToYCoord

public int trackToYCoord(int track_index)

Compute the y-coordinate of a track. Genes are fixed at track#0

Parameters:

track_index -

Returns:

y-coordinate

yCoordToTrackIndex

public int yCoordToTrackIndex(int y)

returns index of track in graph, e.g. the nth track from top

Parameters:

y -

Returns:

yCoordToMarkerCollectionIndex

public int yCoordToMarkerCollectionIndex(int y)

returns index of markercollection for this y coordinate

Parameters:

y -

Returns:

yCoordToMarkerCollectionIndexNew

public int yCoordToMarkerCollectionIndexNew(int y)

yCoordToMarkerCollectionIndexOrg

public int yCoordToMarkerCollectionIndexOrg(int y)

returns index of markercollection for this y coordinate

Parameters:

y -

Returns:

paintActiveBorder

protected void paintActiveBorder(java.awt.Graphics g)

Draws a frame around this ideogram if its active.

Parameters:

g -

BaseToXCoord

public int BaseToXCoord(long pos)

Transforms the basepair location pos to x-coordinates of the canvas.

Parameters:

pos -

Returns:

x coordinate.

BaseRangeToXExtent

public int BaseRangeToXExtent(double range)

Transforms the basepair extent pos to x-width of the canvas. Rounded to an even number.

Parameters:

pos -

Returns:

x coordinate.

XCoordToBase

public long XCoordToBase(int x)

Transforms a canvas x coordinate to basepairs.

Parameters:

x -

Returns:

Basepair offset.

BaseToYCoord

public int BaseToYCoord(long pos)

Transforms the basepair location pos to y-coordinates of the canvas.

Parameters:

pos -

Returns:

y coordinate.

YCoordToBase

public long YCoordToBase(int y)

Transforms a canvas y coordinate to basepairs.

Parameters:

y -

Returns:

Basepair offset.

invalidatePaintBuffer

public void invalidatePaintBuffer()

Call this function if the view changes.

scaleX

protected int scaleX(int x)

scaleY

protected int scaleY(int y)

getExtraRefTrackDistance

protected int getExtraRefTrackDistance()

getNumLeft

public int getNumLeft()

getNumRight

public int getNumRight()

showDataLabels

protected boolean showDataLabels()

getSelectedRangeColor

public java.awt.Color getSelectedRangeColor()

drawRotatedLabel

protected void drawRotatedLabel(java.lang.String text,
                    java.awt.Graphics g,
                    java.awt.Color color,
                    int x,
                    int y,
                    double dAngle)

Parameters:

text -

g -

color -

x -

y -

dAngle -

drawHorizontalTracksHeader

protected void drawHorizontalTracksHeader(java.awt.Graphics g)