[BioCocoa-dev] NEW VERSION

[Alexander Griekspoor]

Hooray! I managed to get all restructuring work done.

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WARNING  -  We all have to do a fresh checkout from the CVS before 
continuing
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Also, before you all start to launch the terminal, use the following 
command to checkout:

cvs checkout -P BioCocoa

The -P or Prune command tells CVS not to download empty directories. 
Because of the way CVS works, one cannot delete directories from the 
CVS repository anymore once they have been created. That means that 
there are some remnant folders there (like BCSequence in the root) that 
you will download when you use the checkout command without the -P 
argument.

If you have code that hasn't been checked in (Koen's work with the 
BCDigest for instance, then checkout the new version as stated above 
and copy paste the code from your old project in the newly downloaded 
one. After that continue to use the new one and commit the changes to 
the repository from there.

As said, I have made many small but also larger enhancements to the 
framework, here are the ones I can still remember:
- restructuring of file/folder hierarchy to represent the object tree.
- prepared for having a foundation and appkit part (appkit folder is 
empty so won't be checked out, but is already on server).
- renamed/-ordered targets
- added a global header and global defines that can be used in 
demo's/apps (see translation demo controller)
- added BCTools directory for things as digesters, translators, 
sequence property calculators (like MW, PI etc)
- added BCGeneticCode to harbor BCCodon / BCGeneticCode
- added BCSequenceIO to harbor the forthcoming IO classes
- moved all imports whereever possible to .m files instead of .h 
(except for defines)
- added files for BCScanner / BCSymbolSet (implementations forthcoming 
though)
- synchronized copyright notices
- reorganized/renamed template plists
- renamed BCUtils/BCTools

Both the framework and the example app should build perfectly fine 
(except for 23 warnings because of the empty scanner implementation).

Please have a look at the changes, all comments are welcome!

One remark, if you want to add a new file, it is best to first create 
it in the finder (by copying an existing one), drag it to the folder 
and rename it the way you want. Than add it to the xcode project, and 
put it in the right group there as well. Now you can add the file to 
the repository and commit the updated xcode project in addition.

I hope to add the implementations soon for the missing files.
Cheerio!
Alex

Ps. One current bug, somehow the translation demo app shows it's name 
in the menubar in chinese on my system ;-)

*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   AIM: mekentosj at mac.com
                   E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

                             iRNAi, do you?
              http://www.mekentosj.com/irnai

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*********************************************************
                       ** Alexander Griekspoor **
*********************************************************
                 The Netherlands Cancer Institute
                 Department of Tumorbiology (H4)
           Plesmanlaan 121, 1066 CX, Amsterdam
                     Tel:  + 31 20 - 512 2023
                     Fax:  + 31 20 - 512 2029
                    AIM: mekentosj at mac.com
                     E-mail: a.griekspoor at nki.nl
                 Web: http://www.mekentosj.com

           LabAssistant - Get your life organized!
           http://www.mekentosj.com/labassistant

*********************************************************


*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
              The Netherlands Cancer Institute
              Department of Tumorbiology (H4)
         Plesmanlaan 121, 1066 CX, Amsterdam
                    Tel:  + 31 20 - 512 2023
                    Fax:  + 31 20 - 512 2029
                   AIM: mekentosj at mac.com
                    E-mail: a.griekspoor at nki.nl
                Web: http://www.mekentosj.com

	Claiming that the Macintosh is inferior to Windows
	because most people use Windows, is like saying
	that all other restaurants serve food that is
	inferior to McDonalds

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