EMBOSS: Project Meeting (Wed 31st May 2006)
A few "#ifndef WIN32" controls remain in emma and tfm because of issues in launching other applications. Input pipes are commented out, for example ajFileNewInpipe. Some other cleanups are still to be committed, for example in ajfile.c.
Unix pathnames have to be corrected to backslashes. ajdefine.h has 4 new definitions, including SLASH_CHAR and CURRENT_DIR, and for the path separator (";" on Windows, ":" on Unix).
ajnam.c was very different in the 2.10.0 EMBOSSWIN, and has been updated to the current code. it needs 4 environment variables, EMBOSS_ROOT, EMBOSS_ACDROOT, EMBOSS_DATA and PLPLOT_LIB. However, the installer asks various questions and will be able to automatically set these. The initialisation file name has been left with the UNix name of emboss.default. EMBOSSWIN 2.10.0 used its own name.
A few compiler warnings remain. Most are missing casts, for example a loss of precision wit float and double. A few will be in the ajfmt functions, many are from the PLFLT definition in plplot.
Many of the "#ifdef WIN32" lines can be removed in the next commit.
Alan has created a build utility that will generate the win32 version of the code tree from a standard CVS checkout. Thsi creates a zip file which can be copied to windows and unpacked, then build using Visual C++. Peter has installed Visual C++ and will test the procedure.
Dom library code is on hold until Alan has free time again. Jon has written the C code for the meme and mast wrappers. The programs still need testing and documentation. In the ACD files, enforcing all the program constraints is unreasonable so some checking is carried out in the C code. Peter will review the ACD files to check whether applications should be split. Programs that need to check for protein or DNA input should be using the $(ACDPROTEIN) variable, in place of whatever mechanisms meme and mast may use. Mahmut has been prototyping SoapLab, so far no new issues have arisen. It may be good to extend the perl parsing script which has not been updated since EMBOSS 2.9.0. Shaun had a meeting with Alberto in External Services to discuss ACD to WSDL generation. Alberto would like to investigate the Jemboss approach and will contact Tim Carver for more information. Shaun is using eclipse for development, which is now installed on the emboss9-16 development machines.
Jon had reviewed the notes from meetings with Marc Colet (EMBnet Belgium) and added requests to the sourceforge feature tracker.
Some more documentation is needed on how to document new applications developed under myemboss.
The course identified a need to isolate the development utilies acdtrace etc. in a separate EMBASSY package "acdutils" which would also make the main EMBOSS package documentation cleaner as these are non-typical applications. Probably "acdc" will remain as an EMBOSS program.
For developers it would also help if we can document how to use eclipse as a development environment.
In preparation for the release, Alan will set the version number to 4.0.0 and Peter will set the date for all tests and usage examples to be 15th July 2006.
The index.html files also need to be autogenerated to avoid manual maintenance.
Regular expressions have bene cleaned up in directory name processing as part of the Windows build. We still have a number of regular expressions that should be replaced for performance reasons, but such a major profiling effort will be after the release.
Alan noted that regular expressions are also an issue on IntelMac and Solaris systems where the PCRE library code requires reduced optimisation (level O1) to get correct results.
Next meeting is at last on a Monday, 12th June.