EMBOSS: Project Meeting (Oct 11th 1999)


Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Mark Faller, Val Curwen, Sinead O'Leary

1. Matters Arising


2. General progress on release 0.0.4

Variables called "this" are being renamed "thys" to avoid clashes with C++ reserved names. SImilarly "bool" is renamed "boule". Also, "new" will be renamed "fnew".

Alan has cleanup up ANSI standards in NUCLEUS, and is working on AJAX. The main change is including an explicit "(void)" before any function where the return value is being ignored. This is to help compilation under VMS with the DEC C compiler.

Some functions in embest.c have altered logic as part of the ANSI C changes. Peter will check whether these are being uses as much of embest.c is obsolete code from the import of est_genome.

Peter's changes to ajseq.c caused problems where programs found protein sequences that contained only DNA codes, as the type was being set to "DNA" and rejected. The test for Nucleotide type will be removed from the protein type check.

A user has requested different prompts for a sequence, a sequence set and a sequence stream. Provisionally, these will change to:

Peter is working on splitting ajseq.c into smaller sections for reading and writing sequences, and for database access. He will make the ANSI changes at the same time.

Peter will also add code to read BLAST1, BLAST2 and GCG format databases. Code from FASTA has been made available to do this, especially for GCG format. GCG will also need new index files in EMBLCD/Staden form for query access as we will not be using the GCG indices. They are proprietary, and also too slow for split databases such as EMBL.

A "raw" sequence format is needed to handle cut and paste sequence entry. Provisionally this will allow alphanumeric characters and white space only. Most other formats use some special character that can be tested for to check that they are not also accepted as "raw" if misconfigured. If it is able to successfully discriminate most other formats, "raw" can be included in the default formats list.

3. Beta Release

One site has reported problems with a host type of "alphaev6" which was not recognised by configure. A solution may need a new version of autoconf.

4. PLPLOT Graphics Library

Ian has added code for PNG format to the PLPLOT library. It clashes with old versions of gd as used by the perl module "gd.pm" where the old release is used to maintain GIF format support. PNG should work with Netscape 4. The README file has been updated with information on adding the PNG driver. External libraries "gd", "zlib" and "png" are required. The configure script uses a new autoconf macro "CHECK_PNGDRIVER" to test the libraries (including a test for the latest gd library) and sets PLD_png if all are present.

A variable EMBOSS_GRAPHICS is needed to set a global default graphics device through the ACD files.

Xwindows is now tested for in the configure so this may allow a build on NT systems without the X11 libraries.

ajgraph code has been cleaned up.

5. Any Other Business


6. Next meeting

Next meeting Monday 18th October, 11:00am, usual place.

Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.