EMBOSS: Project Meeting (Mar 6th 2000)


Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Val Curwen
Apologies: Mark Faller

1. Matters Arising

2. General progress on release 0.0.4

Peter has renamed the ajSystem call which includes the environment as ajSystemEnv and added a new ajSystem function which uses getenv. The same change has been made to ajWhich.

HGMP database definitions are added to the emboss.default file under the ACD directory in the distribution.

The -acdpretty qualifier now terminates the program. it must be specified in full because it is active before processing ambiguous qualifiers on the command line.

Alan has added an extra fix for needle for the course large sequence examples.

3. Graphics

Peter has added a plxtrace function to report the full PLPLOT internal data structure. This was used to find where to fix the PNG family file naming problem.

4. Interfaces

PISE is working more smoothly at HGMP.

PISE refused * as a wildcard. + would be a possible replacement.

Peter has added "entrails" to report internal data values with the intention of creating an automatic DTD file and then adding an ACD processing option to create XML versions of the ACD files in collaboration with Pasteur.

Mark has reinstalled EMBOSS under disGUIse. The ACD file conversion needs updating, and the parser needs further improvements.

5. Features

Ian has a dictionary for the EMBL/GenBank feature table feature keys. Those not in the table are currently ignored with a warning message.

Gary is implementing showfeat to do feature displays.

6. Any Other Business

7. Next meeting

Meeting on Monday 13th March is postponed.

Next meeting will be Monday 20th March 2000, 11:00am, usual place.