From pmr at ebi.ac.uk Fri Dec 9 12:33:57 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 09 Dec 2005 17:33:57 +0000 Subject: [emboss-dev] EMBOSS Code Changes Message-ID: <4399C005.1010402@ebi.ac.uk> Important for all users of the current CVS code. We are reviewing the AJX and NUCLEUS libraries, and making changes to the function names to standardise the documentation. We are starting with the string functions in ajax/ajstr.c - because they are the oldest and need the most changes. The latest ajstr.c and ajstr.h are now committed to CVS. The old function names will continue to work, but you may see a large number of warning messages when you compile with gcc. We have added a "__deprecated" attribute to all the old function names. Non-gcc compilers will ignore this attribute. A script will be added in the next few days to automatically update the function names in your own code. Renamed functions are easy. A few functions now have 2 or more replacements which we plan to automate. For example: ajStrToken can be called with a NULL argument or a string; ajStrChar had special functions with a position of 0 (first character) or -1 (last character). New function names have a standard pattern which we can validate using new @namrule tags in the function headers, and function parameters will also have standard names and types with @argrule tags and for return values @valrule tags. We also have enforced sections for groups of functions, where we keep the naming and parameter rules. In each section, functions are in strict alphabetical order (but note that suffixes - C for char*, S for string - do not count as part of the name) We will have the changes complete for the most important AJAX files (ajseq*, ajacd, ajfile) before the next developers course in January 2006. The SRS EFUNC and EDATA source code databases will be updated early next week on srs.ebi.ac.uk. We will keep EFUNCREL and EDATAREL as databases for the last release, and updated EFUNC and EDATA nightly when the CVS code base changes. The sourceforge website pages for the AJAX and NUCLEUS libraries will be improved in the next few months as we work through all the documentation. Please mail emboss-dev with comments - or emboss-bug with anything that breaks your own code. regards, Peter Rice From jison at ebi.ac.uk Tue Dec 13 04:53:00 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 13 Dec 2005 09:53:00 -0000 (GMT) Subject: [emboss-dev] EMBOSS Developers Course Message-ID: <40248.172.31.100.168.1134467580.squirrel@webmail.ebi.ac.uk> Hi Details on a forthcoming programming course for bioinformatics using EMBOSS are below. Apologies for the email if not interested. Please distribute to your colleagues who might be interested in this. Best regards Jon Ison The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK E-mail : jison at ebi.ac.uk BSDC 2006 Bioinformatics Software Development Course January 18-20, April 18-20 2006 Following from the popular BSDC 2003/2004 courses, a new series of courses on 'Bioinformatics Software Development' using EMBOSS will be held in the training room at Hinxton Hall on January 18-20 and April 18-20, 2006. The course will give a good introduction to programming in EMBOSS. By the end of the course you will be experienced in all the steps in writing a basic bioinformatics application using the EMBOSS programming libraries. The course would suit competent programmers, probably with at least a couple of years of experience. A reasonable working knowledge of C is required to get the most out of the course, familiarity with pointers is helpful but not essential. That said, all are welcome regardless of background or experience. Places are limited and the two dates are likely to get booked up quickly so please email Liz Ford (ford at ebi.ac.uk) to register as soon as possible. We do not make a profit on the course but must charge ?125 / person (for the 3-days) to recover some of our costs. To read more about the course see http://emboss.sourceforge.net/developers/developers_course/ (1) To read more about EMBOSS see http://emboss.sourceforge.net/ To register email Liz Ford (ford at ebi.ac.uk) For further information email Jon Ison (jison at ebi.ac.uk) (1) Please note, the course is currently being revised. The course schedule is correct but details for talks & practicals are subject to change. From pmr at ebi.ac.uk Fri Dec 9 17:33:57 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 09 Dec 2005 17:33:57 +0000 Subject: [emboss-dev] EMBOSS Code Changes Message-ID: <4399C005.1010402@ebi.ac.uk> Important for all users of the current CVS code. We are reviewing the AJX and NUCLEUS libraries, and making changes to the function names to standardise the documentation. We are starting with the string functions in ajax/ajstr.c - because they are the oldest and need the most changes. The latest ajstr.c and ajstr.h are now committed to CVS. The old function names will continue to work, but you may see a large number of warning messages when you compile with gcc. We have added a "__deprecated" attribute to all the old function names. Non-gcc compilers will ignore this attribute. A script will be added in the next few days to automatically update the function names in your own code. Renamed functions are easy. A few functions now have 2 or more replacements which we plan to automate. For example: ajStrToken can be called with a NULL argument or a string; ajStrChar had special functions with a position of 0 (first character) or -1 (last character). New function names have a standard pattern which we can validate using new @namrule tags in the function headers, and function parameters will also have standard names and types with @argrule tags and for return values @valrule tags. We also have enforced sections for groups of functions, where we keep the naming and parameter rules. In each section, functions are in strict alphabetical order (but note that suffixes - C for char*, S for string - do not count as part of the name) We will have the changes complete for the most important AJAX files (ajseq*, ajacd, ajfile) before the next developers course in January 2006. The SRS EFUNC and EDATA source code databases will be updated early next week on srs.ebi.ac.uk. We will keep EFUNCREL and EDATAREL as databases for the last release, and updated EFUNC and EDATA nightly when the CVS code base changes. The sourceforge website pages for the AJAX and NUCLEUS libraries will be improved in the next few months as we work through all the documentation. Please mail emboss-dev with comments - or emboss-bug with anything that breaks your own code. regards, Peter Rice From jison at ebi.ac.uk Tue Dec 13 09:53:00 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 13 Dec 2005 09:53:00 -0000 (GMT) Subject: [emboss-dev] EMBOSS Developers Course Message-ID: <40248.172.31.100.168.1134467580.squirrel@webmail.ebi.ac.uk> Hi Details on a forthcoming programming course for bioinformatics using EMBOSS are below. Apologies for the email if not interested. Please distribute to your colleagues who might be interested in this. Best regards Jon Ison The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK E-mail : jison at ebi.ac.uk BSDC 2006 Bioinformatics Software Development Course January 18-20, April 18-20 2006 Following from the popular BSDC 2003/2004 courses, a new series of courses on 'Bioinformatics Software Development' using EMBOSS will be held in the training room at Hinxton Hall on January 18-20 and April 18-20, 2006. The course will give a good introduction to programming in EMBOSS. By the end of the course you will be experienced in all the steps in writing a basic bioinformatics application using the EMBOSS programming libraries. The course would suit competent programmers, probably with at least a couple of years of experience. A reasonable working knowledge of C is required to get the most out of the course, familiarity with pointers is helpful but not essential. That said, all are welcome regardless of background or experience. Places are limited and the two dates are likely to get booked up quickly so please email Liz Ford (ford at ebi.ac.uk) to register as soon as possible. We do not make a profit on the course but must charge ?125 / person (for the 3-days) to recover some of our costs. To read more about the course see http://emboss.sourceforge.net/developers/developers_course/ (1) To read more about EMBOSS see http://emboss.sourceforge.net/ To register email Liz Ford (ford at ebi.ac.uk) For further information email Jon Ison (jison at ebi.ac.uk) (1) Please note, the course is currently being revised. The course schedule is correct but details for talks & practicals are subject to change.