Team:Freiburg software/Code

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=The SynBioWave source code=

Download
We tried for over 3 hours to upload our zipped program code to the Wiki. Due to the massive server load, that was not possible. As time is running out, we finally uploaded the files to our Sourceforge project, and send an Email to hq.


 * blastrobot.zip - the source of the robot implementing a blast search
 * gui.zip - the source of the menu gadget
 * synbiowave.zip - the source of our main robot
 * template.zip - the source of our template for generating robots

SVN
Get the latest revision of SynBioWave from our SVN-repositories at Sourceforge

The Robot Template
Add these classes to your Wave robot to turn him into a SynBioWave robot.


 * org.synbiowave.biojava.DisplaySequence
 * org.synbiowave.biojava.Util
 * org.synbiowave.database.DatastoreManager
 * org.synbiowave.database.Sequence
 * org.synbiowave.menu.MenuItem
 * org.synbiowave.sequence.SequenceView
 * org.synbiowave.servlet.AbstractSbwServlet
 * org.synbiowave.servlet.AbstractSynBioWaveServlet

The SynBioWave Robot (synbiowave@appspot.com)
Here are the classes of our main robot (every robots needs a lot of static files from Google, these will not be posted here. A complete file list is available from the download or at the SVN):


 * SynBioWaveRobotServlet
 * RecChildBlipListBuilder

The Blast Robot (blastrobot@appspot.com)
A Robot doing a blast search. Using the template, few lines of code are needed to implement it:


 * BlastRobotServlet
 * BlastSearch

The BioBrick DAS package
This package provides all classes needed for the communication with the BioBrick registry database. This package is used by our basic SynBioWaveRobot class.


 * org.synbiowave.biobrick.BioBrick_DAS_DNA_Handler.java
 * org.synbiowave.biobrick.BioBrick_DAS_Entry_Points_Handler.java
 * org.synbiowave.biobrick.BioBrick_DAS_Feature_Handler.java
 * org.synbiowave.biobrick.BioBrickManager.java

qooxWaveClient - client-side implementation of qooxwave
The client-side implementation is actually a whole qooxdoo application. The entire project can be found at the Sourcefourge project side. The main classes we created for this application are the following:


 * Application.js (Main application class)
 * Store.js (Store object to handle and transfer model)
 * Upload.js (upload gadget)
 * Download.js (download gadget)

In addition we created some Wave objects for debugging outside the Wave (Thanks to Fabian Jakobs from the qooxdoo developer team):


 * Wave.js
 * WaveFactory.js
 * State.js
 * Participant.js