From d.counsell at hgmp.mrc.ac.uk Wed Jul 10 10:13:45 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Wed, 10 Jul 2002 15:13:45 +0100 Subject: next EMBOSS Meeting / Documentation update Message-ID: <20020710151345.F13719@hgmp.mrc.ac.uk> Dear All MEETING ======= The next EMBOSS Documentation Meeting will be combined with the next EMBOSS meeting and take place this Friday 12Jul02 from 09:30 to 10:30 in C209-210 (Shared Facilities) in the Sanger Building. The LION boys won't be able to make this one so they will miss Lisa talking about plans for an all-in-one editing suite for Jemboss and my doing the squirrel dance. DOCS ==== I have updated the EMBOSS Documentation Project Web pages http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/EMBOSS_documentation.html with news of the latest developments, including screenshots of the proposed XML (DocBook) editor showing Terry's impressive work on the new command documentation template, and a link to Hugh's minutes of the last meeting. Please let me know if I have ballsed up http://www.robertocarlos.com.br/ingles/segredos.htm anywhere on the site. all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From d.counsell at hgmp.mrc.ac.uk Fri Jul 26 04:28:45 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Fri, 26 Jul 2002 09:28:45 +0100 Subject: apologies / EDP update Message-ID: <20020726092844.A2848@dev4.hgmp.mrc.ac.uk> Dear All I can't come to the EMBOSS meeting today because I have an article deadline to meet (extended from yesterday), but, for those of you interested, there are a couple of examples of the HTML output from DocBook-ified documentation page sources available now from here: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/examples/Emowse.html and here: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/examples/Emma.html . Any comments gratefully received. If you have the fonts available and CSS support "on" in your browser you should be able to see the effects on the page appearance of my XHTML stylesheets overlaid on the output from Terry's XSL (and base HTML) stylesheets. If not, you'll still be able to see the pages set out cleanly---as nature and the Blessed Tim Berners-Lee intended. Terry's work is up to its usual godlike standard. My stuff is flawed. The address area, for example, becomes particularly squinty on some browsers. I have a feeling a set of compensatory font sizing values will be necessary to deal with the worst effects of Internet Explorer. Terry and I have already discussed having a quick "main" contents heading with the principal section headings visible in all but the smallest browser window and accessible from the top of the page with a click. all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From d.counsell at hgmp.mrc.ac.uk Fri Jul 26 06:31:45 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Fri, 26 Jul 2002 11:31:45 +0100 Subject: feedback on documentation pages Message-ID: <20020726113145.B2848@dev4.hgmp.mrc.ac.uk> Dear All There are lots of little things to look at as a result of your comments. The most common complaint about the pages seems to be that the fonts for the contents sections are overlarge with Netscape under Solaris. (I don't get this using either Netscape or Mozilla under Linux and IE5 under Win is OK.) Please could you try Terry's Web versions here: http://www.hgmp.mrc.ac.uk/~tjstewar/EMBOSS/Emma.html and here: http://www.hgmp.mrc.ac.uk/~tjstewar/EMBOSS/Emouse.html and let me know what they look like to you (broswer name/version and OS useful too). all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From gbottu at ben.vub.ac.be Fri Jul 26 10:49:46 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 26 Jul 2002 16:49:46 +0200 (CEST) Subject: Remark about gap penalties Message-ID: <200207261449.QAA0001507718@ben.vub.ac.be> from : BEN Dear colleagues, I just noted something. Some EMBOSS programs (needle, water,...) use a gap penalty of type ( + (n - 1) * ), while others (stretcher, matcher,...) use one of type ( + n * ). The "align" libraries of EMBOSS, as far as I understand, do not print the score computed by the algorithm but recompute the score and always use the first type, what makes that the score they write for e.g. matcher outputs is not correct. Shall this be fixed in a future version or should programmers have the discipline of always using the first type ? Another remark : alignment programs write out a "help" text with line [-outfile] align (no help text) align value Seems the standard message for "align" is missing. Regards, Guy Bottu From peter.rice at uk.lionbioscience.com Fri Jul 26 11:08:53 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 26 Jul 2002 16:08:53 +0100 Subject: Remark about gap penalties References: <200207261449.QAA0001507718@ben.vub.ac.be> Message-ID: <3D416605.335460C8@uk.lionbioscience.com> Guy Bottu wrote: > > I just noted something. Some EMBOSS programs (needle, water,...) use a gap > penalty of type ( + (n - 1) * ), > while others (stretcher, matcher,...) use one of type ( + n * > ). > The "align" libraries of EMBOSS, as far as I > understand, do not print the score computed by the algorithm but recompute > the score Scores are set by the application, through the ajAlignSetScore functions. The gap penalties are passesd by the application and reported. The align functions store these as strings so they can be set as integer on float by the applications. > Another remark : alignment programs write out a "help" text with line > [-outfile] align (no help text) align value > Seems the standard message for "align" is missing. HELPALIGN and HELPREPORT (and DEFALIGN and DEFREPORT) are missing in the file emboss/acd/codes.english You can add these lines to the installed copy of the file: DEFALIGN "Write output alignment to" DEFREPORT "Write output report to" HELPALIGN "Output alignment file name" HELPREPORT "Output report file name" regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From d.counsell at hgmp.mrc.ac.uk Wed Jul 10 14:13:45 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Wed, 10 Jul 2002 15:13:45 +0100 Subject: next EMBOSS Meeting / Documentation update Message-ID: <20020710151345.F13719@hgmp.mrc.ac.uk> Dear All MEETING ======= The next EMBOSS Documentation Meeting will be combined with the next EMBOSS meeting and take place this Friday 12Jul02 from 09:30 to 10:30 in C209-210 (Shared Facilities) in the Sanger Building. The LION boys won't be able to make this one so they will miss Lisa talking about plans for an all-in-one editing suite for Jemboss and my doing the squirrel dance. DOCS ==== I have updated the EMBOSS Documentation Project Web pages http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/EMBOSS_documentation.html with news of the latest developments, including screenshots of the proposed XML (DocBook) editor showing Terry's impressive work on the new command documentation template, and a link to Hugh's minutes of the last meeting. Please let me know if I have ballsed up http://www.robertocarlos.com.br/ingles/segredos.htm anywhere on the site. all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From d.counsell at hgmp.mrc.ac.uk Fri Jul 26 08:28:45 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Fri, 26 Jul 2002 09:28:45 +0100 Subject: apologies / EDP update Message-ID: <20020726092844.A2848@dev4.hgmp.mrc.ac.uk> Dear All I can't come to the EMBOSS meeting today because I have an article deadline to meet (extended from yesterday), but, for those of you interested, there are a couple of examples of the HTML output from DocBook-ified documentation page sources available now from here: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/examples/Emowse.html and here: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/examples/Emma.html . Any comments gratefully received. If you have the fonts available and CSS support "on" in your browser you should be able to see the effects on the page appearance of my XHTML stylesheets overlaid on the output from Terry's XSL (and base HTML) stylesheets. If not, you'll still be able to see the pages set out cleanly---as nature and the Blessed Tim Berners-Lee intended. Terry's work is up to its usual godlike standard. My stuff is flawed. The address area, for example, becomes particularly squinty on some browsers. I have a feeling a set of compensatory font sizing values will be necessary to deal with the worst effects of Internet Explorer. Terry and I have already discussed having a quick "main" contents heading with the principal section headings visible in all but the smallest browser window and accessible from the top of the page with a click. all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From d.counsell at hgmp.mrc.ac.uk Fri Jul 26 10:31:45 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Fri, 26 Jul 2002 11:31:45 +0100 Subject: feedback on documentation pages Message-ID: <20020726113145.B2848@dev4.hgmp.mrc.ac.uk> Dear All There are lots of little things to look at as a result of your comments. The most common complaint about the pages seems to be that the fonts for the contents sections are overlarge with Netscape under Solaris. (I don't get this using either Netscape or Mozilla under Linux and IE5 under Win is OK.) Please could you try Terry's Web versions here: http://www.hgmp.mrc.ac.uk/~tjstewar/EMBOSS/Emma.html and here: http://www.hgmp.mrc.ac.uk/~tjstewar/EMBOSS/Emouse.html and let me know what they look like to you (broswer name/version and OS useful too). all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From gbottu at ben.vub.ac.be Fri Jul 26 14:49:46 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 26 Jul 2002 16:49:46 +0200 (CEST) Subject: Remark about gap penalties Message-ID: <200207261449.QAA0001507718@ben.vub.ac.be> from : BEN Dear colleagues, I just noted something. Some EMBOSS programs (needle, water,...) use a gap penalty of type ( + (n - 1) * ), while others (stretcher, matcher,...) use one of type ( + n * ). The "align" libraries of EMBOSS, as far as I understand, do not print the score computed by the algorithm but recompute the score and always use the first type, what makes that the score they write for e.g. matcher outputs is not correct. Shall this be fixed in a future version or should programmers have the discipline of always using the first type ? Another remark : alignment programs write out a "help" text with line [-outfile] align (no help text) align value Seems the standard message for "align" is missing. Regards, Guy Bottu From peter.rice at uk.lionbioscience.com Fri Jul 26 15:08:53 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 26 Jul 2002 16:08:53 +0100 Subject: Remark about gap penalties References: <200207261449.QAA0001507718@ben.vub.ac.be> Message-ID: <3D416605.335460C8@uk.lionbioscience.com> Guy Bottu wrote: > > I just noted something. Some EMBOSS programs (needle, water,...) use a gap > penalty of type ( + (n - 1) * ), > while others (stretcher, matcher,...) use one of type ( + n * > ). > The "align" libraries of EMBOSS, as far as I > understand, do not print the score computed by the algorithm but recompute > the score Scores are set by the application, through the ajAlignSetScore functions. The gap penalties are passesd by the application and reported. The align functions store these as strings so they can be set as integer on float by the applications. > Another remark : alignment programs write out a "help" text with line > [-outfile] align (no help text) align value > Seems the standard message for "align" is missing. HELPALIGN and HELPREPORT (and DEFALIGN and DEFREPORT) are missing in the file emboss/acd/codes.english You can add these lines to the installed copy of the file: DEFALIGN "Write output alignment to" DEFREPORT "Write output report to" HELPALIGN "Output alignment file name" HELPREPORT "Output report file name" regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723