EMBOSS: Project Meeting (May 17th 1999)
Peter will work on the ACD command line changes discussed at the March 22nd meeting. These need changes to the ACD internals that will also help with the -help output.
Ian has completed "matcher" (local alignment) and "stretcher" (global alignment) which were requested by David Judge for the Cuban EMBnet course. Ian is now working on alternative dotplot methods to extend the (word based) dotplot application. Dotplot needs to be renamed to avoid a clash with a GCG alias.
Alan has almost completed "seac" for pattern searches through a database.
Sinead has completed "patmatmotifs", "patmatDB" and "prosextract".
Gary had added "wossname" to search application names, functional groups and brief documentation in the ACD files. The debugging applications are reported as such, but need to be cleaned up where they are no longer in use.
Peter noted that the macros in the string library source code clashed with function names and were not in use. It was agreed that they could be deleted.
Peter is working on improving the efficiency of sequence database input by reducing the number of memory and string allocations and deallocations. This is proving problematic because of the number of additional strings with reference counted pointers but should be completed this week.