EMBOSS: Project Meeting (Mon 13th November 2006)

Attendees

EBI: Peter Rice, Alan Bleasby, Shaun McGlinchey, Mahmut Uludag,
Sanger:
Visitors:
Apologies: Tim Carver, Jon Ison, Lisa Mullan, Rodrigo Lopez

1. Minutes of the last meeting

Minutes of the meeting of 30th October 2006 are here.

2. Software Development

2.1 Graphics library

Alan is continuing work on the ajgxml library source code. Graph objects will be constructed in DOM as a large graph data object to hold numeric arrays, for example an index lineset with float pointers for x and y coordinates, connectivity and colour. A final print statement will convert this to a string and set up a DOM entry for colour changes etc. A minor update to the ajdom library will indent printing.

Peter has modified string appends to double the string length when space runs out, rather than incrementing by 32 bytes. This will make the new graphics code much more efficient.

Peter has found and fixed a bug in the plplot library code whcih caused requests for character width and height to be reported with incorrect values. When the origin of the plot is not (0,0) the origin values were being added to the width and height. This is corrected in the plplot code, and in the copies of those functions called by the native windows build.

Peter has now been able to complete the graph title and subtitle changes - which were held up by the above bug.

2.2 New applications

Peter is investigating a request for a program that can handle pattern matches with very large result sets.

We have received a request for a version of restrict with exclusion ranges. This should be relatively easy to implement.

2.3 Other development

Mahmut has run 140 tests on the EMBOSS 4.0.0 installation through SoapLab. The EMBRACE Wiki documentation has been updated with longer examples and colour. Some test cases have dependencies. We can convert these into workflows, for now this will be done manually.

The SoapLab pages were visited 360 times last month, including redirects from soaplab.sf.net. The introduction pages have been updated, and the contact email address is changed to soaplab-users.

3. Administration

Alan reported that JEMBOSS has been patched to handle the new pattern ACD type. There is a fix to the making of patch files to find new files as well as changed files.

Peter will have meetings with local EMBOSS users to discuss database configurations and application needs. The first meeting will be with Babraham Research Institute next week.

4. Documentation and Training

No issues raised in Jon's absence.

5. User queries and answers

The list was reviewed. Everyone should review the current list at sf.net/projects/emboss/ and close those already dealt with. All requests have been assigned (mostly to Peter).

All new issues were considered to be resolved.

6. AOB

EMBOSS Explorer (from Luke McCarthy) version 2.3.0 is out and supports EMBOSS 4.0.0.

7. Date Of Next Meeting

The next meeting is on Monday 27th November.