Class CSEGTrack

  extended by org.utgenome.gwt.utgb.client.track.TrackBase
      extended by org.utgenome.gwt.utgb.client.track.lib.GenomeTrack
          extended by 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

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

More Complex View Example

  -name: Segregation
  -class: CSEGTrack
  -height: 600
   -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).


Nested Class Summary
Nested classes/interfaces inherited from class org.utgenome.gwt.utgb.client.track.TrackBase
Nested classes/interfaces inherited from interface org.utgenome.gwt.utgb.client.track.Track
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
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


public CSEGTrack()
Method Detail


public static Track.TrackFactory factory()


public void draw()
Description copied from interface: Track
draw the track widget

Specified by:
draw in interface Track
draw in class GenomeTrack


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
setUp in class GenomeTrack
group - the TrackGroup of this track


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
onChangeTrackConfig in class GenomeTrack

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