org.utgenome.gwt.utgb.client.track.lib
Class ReadTrack

java.lang.Object
  org.utgenome.gwt.utgb.client.track.TrackBase
      org.utgenome.gwt.utgb.client.track.lib.ReadTrack

All Implemented Interfaces:

Track, TrackEntry, TrackGroupPropertyChangeListener

Direct Known Subclasses:

DASTrack

public class ReadTrack
extends TrackBase

Track for displaying read data in BED,SAM,BAM formats.

View Example

 -track
  -class: ReadTrack
  -name: (track name)
  -properties
    -path: (database path. e.g, db/imported/hg19/myread.bed)
    -onclick.url: http://www.google.com/search?q=%q
    -onclick.action: (none|link|info|set)
    -showLabels: (true|false)
    -onclick.p.key: current.read
    -onclick.p.value: %q
 

You can customize the behavior of the browser when clicking a read using onclick.action parameter:

On-Click Action Types

Type	Action
none	Disables click action
link	Opens an URL specified in onclick.url parameter.
info	Displays the detailed read information.
set	Sets a track group property (specified by onclick.p.key) using the value onclick.p.value.

You can embed track or track group parameters in onclick.url and target.value:

Parameters for On-Click event

pattern	to be replaced with
%q	Clicked read name
%qstart	Start position of the clicked read
%qend	End position of the clicked read
%qlen	Length of the clicked read
%species	Species name
%ref	Reference sequence name
%chr	Chromosome/contig/scaffold name
%start	Start position on the genome (inclusive)
%end	End position on the genome (exclusive)
%len	Sequence length currently displayed
%pixelwidth	Pixel width of the tracks

Author:

leo

Nested Class Summary

Nested classes/interfaces inherited from class org.utgenome.gwt.utgb.client.track.TrackBase

TrackBase.TrackFrameConfig

Nested classes/interfaces inherited from interface org.utgenome.gwt.utgb.client.track.Track

Track.TrackFactory

Field Summary

Fields inherited from class org.utgenome.gwt.utgb.client.track.TrackBase

_frame, _trackGroup, _trackInfo, frameConfig

Constructor Summary

ReadTrack()

ReadTrack(String trackName, String dbType)

Method Summary

void	beforeChangeTrackWindow(TrackWindow newWindow) An event handler that will be invoked before the track window location change
static int	calcXPositionOnWindow(long indexOnGenome, long startIndexOnGenome, long endIndexOnGenome, int windowWidth)
void	draw() draw the track widget
static Track.TrackFactory	factory()
GenomeDB	getGenomeDB() Override this method to extend db info parameters
protected String	getPath()
protected String	getTrackURL(String trackBaseURL)
com.google.gwt.user.client.ui.Widget	getWidget()
protected String	getWIGPath()
void	onChangeTrackConfig(TrackConfigChange change) An event handler when some cofigurations of the track changes
void	onChangeTrackGroupProperty(TrackGroupPropertyChange change) An event handler when some properties shared within the track group has changed
void	onChangeTrackWindow(TrackWindow newWindow) An event handler when the track window location has changed
String	resolveURL(String urlTemplate, GenomeRange locus)
void	restoreProperties(CanonicalProperties properties) Override this method to restore internal state of the track
void	setUp(TrackFrame trackFrame, TrackGroup group) This method is invoked when TrackFrame and TrackGroup for this track become ready, that is, the track is drawable.
protected void	update(TrackWindow newWindow, boolean forceReload)

Methods inherited from class org.utgenome.gwt.utgb.client.track.TrackBase

error, getBrowserService, getClassName, getConfig, getCoordinate, getDefaultWindowHeight, getFrame, getMinimumWindowHeight, getName, getTrackGroup, getTrackGroupProperty, getTrackGroupProperty, getTrackInfo, getTrackWindow, isInitialized, isTrack, isTrackGroup, loadView, onChange, onChangeTrackHeight, refresh, resolvePropertyValues, saveProperties, setCenterOfTrackWindow, setConfig, setFrame, setTrackGroup, setTrackGroupProperty, toView, toXML, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadTrack

public ReadTrack()

ReadTrack

public ReadTrack(String trackName,
                 String dbType)

Method Detail

factory

public static Track.TrackFactory factory()

resolveURL

public String resolveURL(String urlTemplate,
                         GenomeRange locus)

getWidget

public com.google.gwt.user.client.ui.Widget getWidget()

Returns:

the track widget

setUp

public void setUp(TrackFrame trackFrame,
                  TrackGroup group)

Description copied from interface: Track

This method is invoked when TrackFrame and TrackGroup for this track become ready, that is, the track is drawable. Override this method to write initialization codes for your tracks.

Specified by:

setUp in interface Track

Overrides:

setUp in class TrackBase

group - the TrackGroup of this track

beforeChangeTrackWindow

public void beforeChangeTrackWindow(TrackWindow newWindow)

Description copied from interface: Track

An event handler that will be invoked before the track window location change

Specified by:

beforeChangeTrackWindow in interface Track

Overrides:

beforeChangeTrackWindow in class TrackBase

draw

public void draw()

Description copied from interface: Track

draw the track widget

Specified by:

draw in interface Track

Overrides:

draw in class TrackBase

getTrackURL

protected String getTrackURL(String trackBaseURL)

calcXPositionOnWindow

public static int calcXPositionOnWindow(long indexOnGenome,
                                        long startIndexOnGenome,
                                        long endIndexOnGenome,
                                        int windowWidth)

onChangeTrackWindow

public void onChangeTrackWindow(TrackWindow newWindow)

Description copied from interface: Track

An event handler when the track window location has changed

Specified by:

onChangeTrackWindow in interface Track

Overrides:

onChangeTrackWindow in class TrackBase

onChangeTrackGroupProperty

public void onChangeTrackGroupProperty(TrackGroupPropertyChange change)

Description copied from interface: Track

An event handler when some properties shared within the track group has changed

Specified by:

onChangeTrackGroupProperty in interface Track

Overrides:

onChangeTrackGroupProperty in class TrackBase

update

protected void update(TrackWindow newWindow,
                      boolean forceReload)

getPath

protected String getPath()

getWIGPath

protected String getWIGPath()

getGenomeDB

public GenomeDB getGenomeDB()

Override this method to extend db info parameters

Returns:

onChangeTrackConfig

public void onChangeTrackConfig(TrackConfigChange change)

Description copied from interface: Track

An event handler when some cofigurations of the track changes

Specified by:

onChangeTrackConfig in interface Track

Overrides:

onChangeTrackConfig in class TrackBase

restoreProperties

public void restoreProperties(CanonicalProperties properties)

Description copied from class: TrackBase

Override this method to restore internal state of the track

Specified by:

restoreProperties in interface Track

Overrides:

restoreProperties in class TrackBase