[emboss-dev] Major changes to AJAX structure in CVS

ajb at ebi.ac.uk ajb at ebi.ac.uk
Wed Sep 23 11:17:06 UTC 2009

Dear developers,

Major structural work has been done on the structure
of AJAX on the CVS server this morning. This is associated
with a future intention to move ACD functions into
a separate library. This will allow it to call sub-libraries
which will perform various new methods of data retrieval without
having to incorporate all those methods into one monolithic
libajax library.

As of today AJAX has the following subdirectories:

  pcre core graphics ensembl ajaxseq acd

pcre: file in here are the ones from the original ajax directory
      and compile to create a libepcre library.

core: currently contains all the aj*.c/h files from the original
      ajax directory with the exception of the graphics
      C files (some headers are left for the moment to
      avoid circular dependencies until ACD functions are moved).
      These files create a libajax library as before.

graphics: contains the ajgraph* and ajhist* files and, as before,
      create a libajaxg library

ensembl: New routines for accessing Ensembl. A work in progress.
      They create a libensembl library.

ajaxseq: A placeholder for ajax sequence handling source to be
     moved from core as part of the ACD changes. Currently
     this contains dummy source files and creates a
     libajaxseq library.

acd: A placeholder or the ACD functions to be moved. Currently this
     contains dummy source files and creates a libacd library.

These changes have, of course, required significant changes to
Makefile.am files thoughout EMBOSS and EMBASSY.

Given the major changes involved I'd recommend using a fresh
checkout of EMBOSS as you may have problems with
a "cvs update -dP" - old dependencies (etc) may still
exist in hidden directories (.libs/.deps/etc) which
could potentially mess things up. You should certainly
try a fresh checkout before emailing with related problems.

If you use the myemboss development area then the configuration for
that has been updated. If, however, you've made your own EMBASSY-style
packages then you'll need to modify your configuration using
one of the new Makefile.am files as a template.

A further change has been to add preliminary ajsql.c/h files
to AJAX. This has involved adding checks for MYSQL and POSTGRESQL
in the top level configuration (and two new m4 files in the m4

The configuration and compilation should be happy whether you have
both SQL development files installed, only one or none. However,
if you experience any problems in the compilation
in that area then please let me know.

The changes may take a couple of hours to propagate to the
anonymous CVS server.


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