wiki:Devel/Index

How to create your own track

• An example track:

  /**
   * A simple wrapper for old UTGB tracks
   * 
   * @author leo
   *
   */
  public class LegacyTrack extends TrackBase
  {
      private DockPanel _panel = new DockPanel();
      private Image trackImage = new Image();
      private LegacyTrackInfo _legacyTrackInfo;
      private TrackConfig _config = new TrackConfig(this);
      private int offset = 0;
  
      public static TrackFactory factory()
      {
          return new TrackFactory(){
              public Track newInstance()
              {
                  return new LegacyTrack();
              }
          };
      }
      
      public LegacyTrack()
      {
          this(new LegacyTrackInfo());
      }
      
      public LegacyTrack(LegacyTrackInfo trackInfo)
      {
          super(trackInfo.getName());
          this._legacyTrackInfo = trackInfo;
          _panel.add(trackImage, DockPanel.CENTER);
      }
  
      public int getDefaultWindowHeight()
      {
          return 100;
      }
  
  
      public Widget getWidget()
      {
          return _panel;
      }
  
      public void onChangeTrackWindow(TrackWindow newWindow)
      {
          _legacyTrackInfo.setStart(newWindow.getStartOnGenome());
          _legacyTrackInfo.setEnd(newWindow.getEndOnGenome());
          
          draw();
      }
  
      public void draw()
      {
          int windowSize = getTrackGroup().getTrackWindow().getWindowWidth();
          _legacyTrackInfo.setWidth(windowSize);
  
          String imageUrl = _legacyTrackInfo.getImageURL(offset);
          trackImage.setUrl(imageUrl);
      }
  
  
      public void onChangeTrackGroupProperty(TrackGroupPropertyChange change)
      {
          String[] relatedProperty = {"species", "revision", "target"};
          
          if(!change.containsOneOf(relatedProperty))
              return; // no related change
          
          String species = change.getProperty("species", _legacyTrackInfo.getSpecies());
          String revision = change.getProperty("revision", _legacyTrackInfo.getRevision());
          String target = change.getProperty("target", _legacyTrackInfo.getTarget());
          
          _legacyTrackInfo.setSpecies(species);
          _legacyTrackInfo.setRevision(revision);
          _legacyTrackInfo.setTarget(target);
          
          // sync with the configuration panel
          _config.setParameter("species", species);
          _config.setParameter("revision", revision);
          _config.setParameter("target", target);
          
          draw();
      }
  
      public void setUp(TrackFrame trackFrame, TrackGroup group)
      {
          trackFrame.pack();
  
          TrackWindow w = group.getTrackWindow();
          _legacyTrackInfo.setStart(w.getStartOnGenome());
          _legacyTrackInfo.setEnd(w.getEndOnGenome());
          
          trackImage.addLoadListener(new LoadListener() {
              public void onError(Widget sender)
              {
              	trackImage.setUrl(Design.IMAGE_NOT_AVAILABLE);
              }
  
              public void onLoad(Widget sender)
              {
                  getFrame().onUpdateTrackWidget();
              }}
          );
          
          // set up the configuration panel
          _config.addConfigParameter("Track Name", new StringType("name"), _legacyTrackInfo.getName()); 
          _config.addConfigParameter("Track Image URL", new StringType("baseURL"), _legacyTrackInfo.getBaseURL());
          _config.addConfigParameter("Species", new StringType("species"), _legacyTrackInfo.getSpecies());
          _config.addConfigParameter("Revision", new StringType("revision"), _legacyTrackInfo.getRevision()); 
          _config.addConfigParameter("Target", new StringType("target"), _legacyTrackInfo.getTarget()); 
          _config.addConfigParameter("Offset", new IntegerType("offset"), Integer.toString(offset));
  
      }	
  
  	public TrackConfig getConfig() {
  		return _config;
  	}
  
  	
  
  	public void restoreProperties(Properties properties) {
  		_legacyTrackInfo.setBaseURL(properties.get("baseURL", _legacyTrackInfo.getBaseURL()));
  		_legacyTrackInfo.setSpecies(properties.get("species", _legacyTrackInfo.getSpecies()));
  		_legacyTrackInfo.setRevision(properties.get("revision", _legacyTrackInfo.getRevision()));
  		_legacyTrackInfo.setTarget(properties.get("target", _legacyTrackInfo.getTarget()));
  		offset = properties.getInt("offset", offset);
  	}
  
  	public void saveProperties(Properties saveData) {
  		saveData.add("baseURL", _legacyTrackInfo.getBaseURL());
  		saveData.add("species", _legacyTrackInfo.getSpecies());
  		saveData.add("revision", _legacyTrackInfo.getRevision());
  		saveData.add("target", _legacyTrackInfo.getTarget());
  		saveData.add("offset", offset);
  	}
  
  	public void onChangeTrackConfig(TrackConfigChange change) {
  		if(change.contains("name"))
  			getTrackInfo().setTrackName(change.getValue("name"));
  		
  		boolean drawFlag = false;
  		if(change.contains("offset"))
  		{
  			offset = change.getIntValue("offset");
  			drawFlag = true;
  		}
  		
  		String[] param = {"baseURL", "species", "revision", "target"};
  		if(change.containsOneOf(param))
  		{
  			_legacyTrackInfo.setBaseURL(change.getValue("baseURL"));
  			_legacyTrackInfo.setSpecies(change.getValue("species"));
  			_legacyTrackInfo.setRevision(change.getValue("revision"));
  			_legacyTrackInfo.setTarget(change.getValue("target"));
  			drawFlag =  true;
  		}
  		
  		if(drawFlag)
  			draw();
  
  	}
      
  }
  

• Extend TrackBase? class
  • Implement factory() method

        public static TrackFactory factory()
        {
            return new TrackFactory(){
                public Track newInstance()
                {
                    return new LegacyTrack();
                }
            };
        }
    

• Implement getWidget() method
  • The returned widget is used to display track content

• Set the default size of your track
  • via getDefaultWindowHight() method (pixel size)

• Override draw() method when rewrite of your track is necessary
  • This method is used for updating track content on changes of track group properties

• To detect sequence location change, override onChangeTrackWindow() method.
• To detect other track group property change, override onChangeTrackGroupProperty() method.

• To add option configuration panel, create an instance of TrackConfig?, then override getTrackConfig() method.
  • If this method returns non-null instance, configuration button appears in your track frame.

• Put all initialization codes of your track into setUp(...) method

• To save your track state into view XML file, override saveProperties() method.
• To load saved properties into your track from the user-specified XML file, override restoreProperties() method.

• Edit the TrackFactorySetup? class as as to this class can instantiate your Track class.
  • In Eclipse, run TrackLoaderGenerator? (launch file is located at eclipse/TrackLoaderGenerator.launch) does this task.