Latest revision as of 02:38, 22 October 2009

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

View

The Robot Template

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

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):

The Blast Robot (blastrobot@appspot.com)

A Robot doing a blast search. Using the template, few lines of code are needed to implement it:

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.

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):

@@ Line 13: / Line 13: @@
 {{:Team:Freiburg_software/Templates/Header}}
-=The SynBioWave Source-code=
+=The SynBioWave source code=
-Warning: These pages contain pure Java-Code and are only enlightening if you are both experienced with Java and Google Wave.
+==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 [https://sourceforge.net/projects/synbiowave/files/ our Sourceforge project], and send an Email to hq.
-Look at the download-page for downloading them all together and view it in your favorite IDE or get the latest version from our [http://sourceforge.net/projects/synbiowave/develop svn-repositories at Sourceforge]
+* [https://sourceforge.net/projects/synbiowave/files/blastrobot.zip/download blastrobot.zip] - the source of the robot implementing a blast search
+* [https://sourceforge.net/projects/synbiowave/files/gui.zip/download gui.zip] - the source of the menu gadget
+* [https://sourceforge.net/projects/synbiowave/files/SynBioWave.zip/download synbiowave.zip] - the source of our main robot
+* [https://sourceforge.net/projects/synbiowave/files/template.zip/download template.zip] - the source of our template for generating robots
-==The Robot Template==
+==SVN==
-Add these classes to your Wave-Robot to turn him into a SynBioWave-Robot. Detail instructions can be found %%%here%%%.
+Get the latest revision of SynBioWave from our [http://sourceforge.net/projects/synbiowave/develop SVN-repositories at Sourceforge]
+==View==
+===The Robot Template===
+Add these classes to your Wave robot to turn him into a SynBioWave robot.
 * [[Team:Freiburg_software/Code/DisplaySequence.java | org.synbiowave.biojava.DisplaySequence]]
@@ Line 31: / Line 41: @@
 * [[Team:Freiburg_software/Code/AbstractSynBioWaveServlet.java | org.synbiowave.servlet.AbstractSynBioWaveServlet]]
-==The SynBioWave Robot (synbiowave@appspot.com)==
+===The SynBioWave Robot (synbiowave@appspot.com)===
-==The Blast Robot (blastrobot@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|download]] or at the [[#SVN|SVN]]):
-The Robot doing the Blast-seach consists of these classes (additionally to Template and the Google-files every robot needs)
+* [[Team:Freiburg_software/Code/SynBioWaveRobotServlet.java | SynBioWaveRobotServlet ]]
+* [[Team:Freiburg_software/Code/RecChildBlipListBuilder.java | 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:
 * [[Team:Freiburg_software/Code/BlastRobotServlet.java | BlastRobotServlet ]]
 * [[Team:Freiburg_software/Code/BlastSearch.java | BlastSearch ]]
-==qooxWaveClient - client-side impementation of qooxwave==
+===The BioBrick DAS package===
-The client-side implementation is actually a whole qooxdoo application. The entire project can be found at the [http://synbiowave.svn.sourceforge.net/viewvc/synbiowave/trunk/gui/qooxwaveClient/ sourcefourge project side]. The main Classes we created for this application are the following:
+This package provides all classes needed for the communication with the BioBrick registry database.
+This package is used by our basic SynBioWaveRobot class.
+* [[Team:Freiburg_software/Code/BioBrick_DAS_DNA_Handler.java | org.synbiowave.biobrick.BioBrick_DAS_DNA_Handler.java]]
+* [[Team:Freiburg_software/Code/BioBrick_DAS_Entry_Points_Handler.java | org.synbiowave.biobrick.BioBrick_DAS_Entry_Points_Handler.java]]
+* [[Team:Freiburg_software/Code/BioBrick_DAS_Feature_Handler.java | org.synbiowave.biobrick.BioBrick_DAS_Feature_Handler.java]]
+* [[Team:Freiburg_software/Code/BioBrickManager.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 [http://synbiowave.svn.sourceforge.net/viewvc/synbiowave/trunk/gui/qooxwaveClient/ Sourcefourge project side]. The main classes we created for this application are the following:
 * [[Team:Team:Freiburg_software/Code/qooxdoo/Application.js|Application.js]] (Main application class)

Team:Freiburg software/Code

From 2009.igem.org