EMBOSS: Project Meeting (Fri 11th June 2004)


RFCGR/HGMP: Alan Bleasby, Jon Ison, Gary Williams, Tim Carver,
EBI: Peter Rice,


1. Minutes of the last meeting

Minutes of the meeting of 14th May 2004 are here

2. Software Development

2.1 Kim Rutherford versions of Union and Splitter

Tim is using these at Sanger. They use extra feature kays from collaborators. Peter2.2 Domainatrix Jon has added new functions ajFileExtTrim and ajFileDirExtTrim to trim file extensions and directories from full path filenames. These complement the ajFileNameTrim function. The "dirlist" ACD type now has an extewnsion attribute to be used when processing files in a directory.

Domainatrix is now split into sections.

Rocplot has been added as a new application.

2.3 Code cleanup

Peter is redefining functions that create an object by reading a file as constructors because they create a new object. Some examples were previously defined and "input" because they read an object, but the constructor definition should take priority as constructors are defined by returning a new object. An "input" function cannot create (return) an object, and must use an existing modifiable object.

2.4 Cygwin

Alan has resolved problems with DLLs so that cygwin compilation is now possible.

2.5 Ajax graphics library

Alan has simplified libajaxg for cases where link order was becoming too complicated, especially on AIX and Windows systems.

2.6 EMBASSY Installation

Alan has modified EMBASSY builds to use an installed EMBOSS rather than the source files. Thsi will allow users to have a local development copy, for example of myemboss.

2.7 Code cleanup

Peter is making the latest code cleanup runs available on his personal web pages, including the EFUNC and EDATA code documentation warnings and the acdvalid warnings and errors. See http://www.ebi.ac.uk/~pmr/emboss.html which has links to the mesasges and to explanations of how to avoid them.

2.8 Staden SPIN interface

Peter reported that Cambridge University would like to use the Staden SPIN interface to EMBOSS. Peter has offered to updated the SPIN definitions for EMBOSS 2.9.0.

3. Documentation & Training

3.1 Sourceforge website

Damian will have the website links done later today..

4. Administration

4.1 Mailing lists

Alan has restricted the mailing lists to subscriber postings only to reduce the spam load..

4.2 ISMB

Release 2.9.0 is needed before ISMB. Peter will add the outdata processing in a future release. Alan will postpone the new indexing code until after ISMB.

Jon will take over preparation of thew EMBOSS poster, using a powerpoint template from a previous RFCGR poster.

4.3 User survey

Peter will draft questions for a survey of EMBOSS users. the survey will be mailed to known users and advertised on the websites (HGMP and sourceforge) and circulated through CCP11 and other routes.

5. User queries and answers

Gary's current list reviewed. Most new issues were already answered.

6. AOB

No items.

7. Date Of Next Meeting

Next meeting at 9.30 on June 25, 2004,