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

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

All Implemented Interfaces:

Track, TrackEntry, TrackGroupPropertyChangeListener

public class CSEGTrack
extends GenomeTrack

Track for displaying read data in SEG format.

Simplest View Example

 -track
  -class: CSEGTrack
  -name: Hoge Segment
  -properties
    -path: db/imported/celegans/normal_gene_exp.cseg.sqlite
 

More Complex View Example

 -track
  -name: Segregation
  -class: CSEGTrack
  -height: 600
  -properties
   -path: db/p.patens/combined.genmap.imputed.cseg.sqlite
   -Image height: 700
   -Color array: eeeeee,ff3366,3366ff,ffaadd,aaddff
   -Scale color: 222222
   -Height per sample: 4
   -Samples per scale line: 10
   -Draw scale: true
   -Priority indicies: 1,2
 

What follows explains the properties. Image height property is the height of an image generated by CSEGTrack. If you do not like a scroll bar, you should keep it smaller than the height of the track, but still you may set a larger value to it. Color array property is comma-separated values, each of which is a hexadecimal value of 6 letters in a form like RRGGBB (Let's imagine you are writing HTML. It's basically the same although without '#'). You should not include any space character in the color array property. We had not trimmed spaces. Scale color is the color of the scale. When draw scale property is false, the scale will not be drew. The scale is a set of lines parallel to each other. The distance of the two neighboring scale lines is 'Samples per scale' times 'Height per sample'. Height per sample property is the number of pixels per sample. Priority indicies property is comma-separated values (again, without any spaces).

Author:

mkasa

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.lib.GenomeTrack

CONFIG_TRACK_BASE_URL, CONFIG_TRACK_TYPE, frame, isWidgetReady, layoutPanel, leftMargin, queryParams, trackImage, type

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

_frame, _trackGroup, _trackInfo, frameConfig

Constructor Summary

CSEGTrack()

Method Summary

void	draw() draw the track widget
static Track.TrackFactory	factory()
void	onChangeTrackConfig(TrackConfigChange change) An event handler when some cofigurations of the track changes
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.

Methods inherited from class org.utgenome.gwt.utgb.client.track.lib.GenomeTrack

getTrackURL, getWidget, onChange, restoreProperties, saveProperties

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

beforeChangeTrackWindow, error, getBrowserService, getClassName, getConfig, getCoordinate, getDefaultWindowHeight, getFrame, getMinimumWindowHeight, getName, getTrackGroup, getTrackGroupProperty, getTrackGroupProperty, getTrackInfo, getTrackWindow, isInitialized, isTrack, isTrackGroup, loadView, onChangeTrackGroupProperty, onChangeTrackHeight, onChangeTrackWindow, refresh, resolvePropertyValues, 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

CSEGTrack

public CSEGTrack()

Method Detail

factory

public static Track.TrackFactory factory()

draw

public void draw()

Description copied from interface: Track

draw the track widget

Specified by:

draw in interface Track

Overrides:

draw in class GenomeTrack

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 GenomeTrack

group - the TrackGroup of this track

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 GenomeTrack