org.utgenome.gwt.utgb.client.canvas
Class IntervalLayout

java.lang.Object
  org.utgenome.gwt.utgb.client.canvas.IntervalLayout

public class IntervalLayout
extends Object

On-genome data layout

Author:

leo

Nested Class Summary

static class	IntervalLayout.IntervalRetriever Retrieves the interval (x1, x2) and the height of OnGenome objects
static class	IntervalLayout.LocusLayout

Constructor Summary

IntervalLayout()

Method Summary

List<GenomeRange>	activeReads()
void	clear()
<T extends GenomeRange> int	createLocalLayout(int geneHeight) Creates an X-Y layout of the given intervals, then return the max depth of the intervals
void	depthFirstSearch(PrioritySearchTree.Visitor<IntervalLayout.LocusLayout> visitor)
static int	estimiateLabelWidth(GenomeRange l, int geneHeight)
boolean	hasEnoughHeightForLabels()
boolean	keepSpaceForLabels()
int	maxDepth(TrackWindow view)
GenomeRange	overlappedInterval(int x, int y, int xBorder, int geneHeight) compute the overlapped intervals for the mouse over event
int	pixelPositionOnWindow(int indexOnGenome)
<T extends GenomeRange> int	reset(List<T> intervalList, int geneHeight) Creates an X-Y layout of the given intervals
void	setAllowOverlapPairedReads(boolean allow)
void	setKeepSpaceForLabels(boolean keep)
void	setTrackWindow(TrackWindow window)

Methods inherited from class java.lang.Object

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

Constructor Detail

IntervalLayout

public IntervalLayout()

Method Detail

setTrackWindow

public void setTrackWindow(TrackWindow window)

estimiateLabelWidth

public static int estimiateLabelWidth(GenomeRange l,
                                      int geneHeight)

activeReads

public List<GenomeRange> activeReads()

maxDepth

public int maxDepth(TrackWindow view)

reset

public <T extends GenomeRange> int reset(List<T> intervalList,
                                         int geneHeight)

Creates an X-Y layout of the given intervals

Type Parameters:

T -

Parameters:

intervalList -

geneHeight - * @return

createLocalLayout

public <T extends GenomeRange> int createLocalLayout(int geneHeight)

Creates an X-Y layout of the given intervals, then return the max depth of the intervals

Type Parameters:

T -

Parameters:

intervalList -

geneHeight - * @return

setKeepSpaceForLabels

public void setKeepSpaceForLabels(boolean keep)

keepSpaceForLabels

public boolean keepSpaceForLabels()

hasEnoughHeightForLabels

public boolean hasEnoughHeightForLabels()

depthFirstSearch

public void depthFirstSearch(PrioritySearchTree.Visitor<IntervalLayout.LocusLayout> visitor)

overlappedInterval

public GenomeRange overlappedInterval(int x,
                                      int y,
                                      int xBorder,
                                      int geneHeight)

compute the overlapped intervals for the mouse over event

Parameters:

event -

xBorder -

Returns:

pixelPositionOnWindow

public int pixelPositionOnWindow(int indexOnGenome)

clear

public void clear()

setAllowOverlapPairedReads

public void setAllowOverlapPairedReads(boolean allow)