EMBOSS: Project Meeting (Fri 11th June 2004)
1. Minutes of the last meeting
Minutes of the meeting of 14th May 2004 are
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
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.
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
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..
4.1 Mailing lists
Alan has restricted the mailing lists to subscriber postings
only to reduce the spam load..
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.
7. Date Of Next Meeting
Next meeting at 9.30 on June 25, 2004,