From jkb at mrc-lmb.cam.ac.uk Tue May 1 04:30:36 2001 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Tue, 1 May 2001 09:30:36 +0100 Subject: Proposal: new menu layout, with examples In-Reply-To: <3AEDA34B.BF3D0374@uk.lionbioscience.com>; from peter.rice@uk.lionbioscience.com on Mon, Apr 30, 2001 at 06:39:23PM +0100 References: <20010430170540.D21424@arran.mrc-lmb.cam.ac.uk> <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEDA34B.BF3D0374@uk.lionbioscience.com> Message-ID: <20010501093036.A29532@arran.mrc-lmb.cam.ac.uk> On Mon, Apr 30, 2001 at 06:39:23PM +0100, Peter Rice wrote: > > type A choice between "frame" and "page". > > Tricky to test a list of values. frame:Y would be simpler, but we should > add controlled vocabulary types some time (see 'side' below). That's a trivial change to make for me, so I'm happy to change (if you desire it). Personally though I prefer a vocabulary type as it indicates a choice. Y/N reminds me of Rodger's earlier tools. You'd often get given a question like "Plot results? [y]". This was via the YESNO fortran function, which always had a default Yes - leading to question such as "Do you not want me to do X?". Hmm! The biggest drawback though was that people thought "plot results? Well what's the alternative? I guess I'd better take the default." Vocabs are also more extensable. If we decided that we want to add a type toplevel (unlikely) for subwindows then we can easily do so without worrying about all the weird interactions of frame:Y page:Y toplevel:Y. > > info A heading for the frame or page. Defaults to "" > > A page without a heading would look rather odd, but a frame > > without a heading is OK - it's just a bordered block. > > OK. Can also be used to prompt interactive users (e.g. "Gap penalties:" > before prompting for the gap penalty values). Or we could have a separate > 'prompt' for this, and use 'info' in the -help output (tricky though - > qualifiers will be in sections but also in required/optional/advanced > groupings so maybe -help should be left alone) Indeed. If we use such things for prompts then I suggest an indentation method to display members of the group. Eg: Gap penalties: Gap open penalty [16]: Gap extension penalty [4]: Output file [foo.stretcher]: > > book Only needed for type:frame. > > The notebook to associate this page to. Defaults to "", which > > implies all pages are part of the same notebook. This is only > > needed if a program wishes to make use of more than one tabbed > > notebook, in which case this is used to determine which book a > > page is within. > > Can we pick a more general name for this? Of course I meant "book: only needed for type:page" (rather than type book). We could have a more general name, but I thought the term book fitted rather well with type:page. Specifically frames are standalone, whereas pages are a member of a set which are displayed together. Perhaps "set" is a suitable alternative name? > > border Only needed for type:frame. Defaults to 1. > > The border width of the frame. > > OK. > > > side Only needed for type:frame. Defaults to top. > > This is used for 'frame packing'. It is only needed if we wish > > to express complex layout designs. Eg: > > Looks like another controlled vocabulary. Also, looks like I can think of > uses for it. Side here has values of top, bottom, left and right - ie the same as the tcl pack -side option (how convenient - I wonder how that could have happened? ;-)). James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From peter.rice at uk.lionbioscience.com Tue May 1 04:46:01 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 01 May 2001 09:46:01 +0100 Subject: Proposal: new menu layout, with examples References: <20010430170540.D21424@arran.mrc-lmb.cam.ac.uk> <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEDA34B.BF3D0374@uk.lionbioscience.com> <20010501093036.A29532@arran.mrc-lmb.cam.ac.uk> Message-ID: <3AEE77C9.7931261D@uk.lionbioscience.com> Hi James, Let me think about controlled vocabularies a little. The problem is where to put them when defining new attributes. We already have the mechanism for handling them with list and select ACD types. I think they can probably he hardcoded in the section-setting functions. > Of course I meant "book: only needed for type:page" Ah, that makes sense. Maybe "folder" is more general? > Side here has values of top, bottom, left and right - ie the same as > the tcl pack -side option (how convenient - I wonder how that could > have happened? Fair enough. Almost anything that reaches version 8.0 can count as a standard :-) regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gwilliam at hgmp.mrc.ac.uk Tue May 1 10:47:57 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 01 May 2001 15:47:57 +0100 Subject: Proposal: new menu layout, with examples References: <20010430170540.D21424@arran.mrc-lmb.cam.ac.uk> <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEE7EC8.E794BE85@hgmp.mrc.ac.uk> <20010501104851.A23198@arran.mrc-lmb.cam.ac.uk> <3AEE94B5.D21D3142@hgmp.mrc.ac.uk> <20010501122622.B23198@arran.mrc-lmb.cam.ac.uk> <3AEEAAD9.258D452A@hgmp.mrc.ac.uk> <20010501142113.C23198@arran.mrc-lmb.cam.ac.uk> Message-ID: <3AEECC9D.2F6FC800@hgmp.mrc.ac.uk> James and I have been discussing the program group structure. We seem to have come to some sort of agreement on the following. Some things like 'Feature tables' are place-holders for groups of programs that probably ought to be written. I'm sure there will be useful comments on the following: (Are 'Profiles' and 'Patterns' similar enough to be merged?) +Compare + Consensus (merging sequences to make a consensus) + Differences + Dot plots + Global alignment + Local alignment + Multiple alignment +Display (information + publication display, not just stuff that plots results) +Edit (sequence and annotation manipulation) +Enzyme Kinetics (just 'findkm' at present) +Feature tables (manipulation and display of feature tables) +Help (help for the user, e.g. wossname, showdb, seealso) +Nucleic + 2D Structure (RNA structure) + Codon usage + Composition (properties over the whole sequence, GFF not produced) + CPG islands + Gene finding (genes and other genomic features) + Patterns (search for defined patterns) + Primers + Profiles (search for defined profiles) + Repeats + Restriction enzymes + Transcribe (transcription factors) + Translate + Mutate +Phylogeny (mainly the Phylip package) +Protein + 2D Structure (2D structure and topological features) + 3D Structure + Composition (properties over the whole sequence, GFF not produced) + Patterns (search for defined patterns) + Mutate + Profiles (search for defined profiles) +Utils + Database indexing + Database creation + Misc +Test -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From jkb at mrc-lmb.cam.ac.uk Wed May 2 07:18:19 2001 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Wed, 2 May 2001 12:18:19 +0100 Subject: More on "optional:N" meanings Message-ID: <20010502121819.A10804@arran.mrc-lmb.cam.ac.uk> Sorry to bring up this topic again, but I've just been confused by another odd case. In remap the "uppercase" variable (which holds a list of positions) is defined to be opt:N (implicitly) and def:"". In my code this has unfortunate consequences. I have, in an advanced tab, an entry window for the uppercase variable. It has no value inserted in it as the default is "". However the program will not let me proceed without filling out that entry as it claims I haven't specified a value for a non-optional parameter. I think this is just another case where I've confused optional with required. (Specifically the assumption that non-optional implies mandatory :-)) I'll update the code as follows. Any argument listed as opt:N req:N, that does not have a value will simply be ignored (and not supplied as an argument to the emboss program). Any argument that is listed as req:Y (regardless of whether it is opt:N or opt:Y) will follow the current 'is it set?" test. Please comment if I'm wildly off target, otherwise just ignore these ramblings. Cheers, James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From gwilliam at hgmp.mrc.ac.uk Wed May 2 08:22:14 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 02 May 2001 13:22:14 +0100 Subject: Proposal: new menu layout, with examples References: <20010430170540.D21424@arran.mrc-lmb.cam.ac.uk> <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEE7EC8.E794BE85@hgmp.mrc.ac.uk> <20010501104851.A23198@arran.mrc-lmb.cam.ac.uk> <3AEE94B5.D21D3142@hgmp.mrc.ac.uk> <20010501122622.B23198@arran.mrc-lmb.cam.ac.uk> <3AEEAAD9.258D452A@hgmp.mrc.ac.uk> <20010501142113.C23198@arran.mrc-lmb.cam.ac.uk> <3AEECC9D.2F6FC800@hgmp.mrc.ac.uk> Message-ID: <3AEFFBF6.64FCB12C@hgmp.mrc.ac.uk> Attached is my attempt at allocating programs to the menu structure. Most things fit well and there are only a few programs with assignments to multiple groups: 23 to two groups, 2 to three groups (remap and showseq) It there are no complaints, I'll start changing the ACD files soon (next week?) Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK -------------- next part -------------- +Alignment + Consensus (merging sequences to make a consensus) = cons = megamerger = merger + Differences = diffseq + Dot plots = dotmatcher = dotpath = dottup = polydot + Global = est2genome = needle = stretcher + Local = matcher = seqmatchall = water = wordmatch + Multiple = emma = mse = plotcon = prettyplot +Display (publication display, not just stuff that plots results) = abiview = cirdna = lindna = prettyplot = prettyseq = remap = showdb = showseq = pepnet = pepwheel = seealso = showfeat = showseq +Edit (sequence and annotation manipulation) = cutseq = degapseq = descseq = entret = extractseq = infoseq = maskfeat = mse = newseq = noreturn = notseq = nthseq = pasteseq = revseq = seqret = seqretall = seqretset = seqretsplit = splitter = textsearch = trimseq = vectorstrip +Enzyme Kinetics = findkm +Feature tables (manipulation and display of feature tables) = coderet = showfeat +Help (help for the user) = infoseq = seealso = showdb = tfm = wossname +Nucleic + 2D Structure (RNA structure) + Codon usage = cai = chips = codcmp = cusp = syco + Composition (properties over the whole sequence, GFF not produced) = banana = btwisted = chaos = compseq = dan = freak = isochore = wordcount + CPG islands = cpgplot = cpgreport = geecee = newcpgreport = newcpgseek + Gene finding (genes and other genomic features) = est2genome = getorf = marscan = plotorf = showorf = wobble + Motifs (search for defined patterns) = dreg = fuzznuc = fuzztran = marscan + Mutation = msbar = shuffleseq + Primers = prima = primersearch = stssearch + Profiles (search for defined profiles) = profit = prophecy = prophet + Repeats = einverted = equicktandem = etandem = palindrome + Restriction = recode = redata = remap = restover = restrict = showseq = silent + Transcription (transcription factors) = tfscan + Translation = backtranseq = coderet = prettyseq = plotorf = remap = showorf = showseq = transeq + Mutation +Phylogeny (mainly the Phylip package) = distmat +Protein + 2D Structure (2D structure and topological features) = garnier = helixturnhelix = hmoment = tmap = pepcoil = pepnet = pepwheel + 3D Structure + Composition (properties over the whole sequence, GFF not produced) = backtranseq = charge = checktrans = compseq = emowse = iep = octanol = pepinfo = pepstats = pepwindow = pepwindowall + Motifs (search for defined patterns) = antigenic = digest = fuzzpro = fuzztran = helixturnhelix = oddcomp = patmatdb = patmatmotifs = pepcoil = preg = pscan = sigcleave + Mutation = msbar = shuffleseq + Profiles (search for defined profiles) = profit = prophecy = prophet +Utils + Database indexing = dbiblast = dbifasta = dbiflat = dbigcg + Database creation = domainer = nrscope = printsextract = prosextract = rebaseextract = scope = tfextract + Misc = embossdata +Test -------------- next part -------------- abiview Display antigenic Protein:Motifs backtranseq Nucleic:Translation, Protein:Composition banana Nucleic:Composition btwisted Nucleic:Composition cai Nucleic:Codon usage chaos Nucleic:Composition charge Protein:Composition checktrans Protein:Composition chips Nucleic:Codon usage cirdna Display codcmp Nucleic:Codon usage coderet Feature tables, Nucleic:Translation compseq Nucleic:Composition, Protein:Composition cons Alignment:Consensus cpgplot Nucleic:CpG Islands cpgreport Nucleic:CpG Islands cusp Nucleic:Codon usage cutseq Edit dan Nucleic:Composition dbiblast Utils:Database indexing dbifasta Utils:Database indexing dbiflat Utils:Database indexing dbigcg Utils:Database indexing degapseq Edit descseq Edit diffseq Alignment:Differences digest Protein:Motifs distmat Phylogeny domainer Utils:Database creation dotmatcher Alignment:Dot plots dotpath Alignment:Dot plots dottup Alignment:Dot plots dreg Nucleic:Motifs einverted Nucleic:Repeats embossdata Utils:Misc emowse Protein:Composition equicktandem Nucleic:Repeats etandem Nucleic:Repeats emma Alignment:Multiple entret Edit est2genome Alignment:Global extractseq Edit freak Nucleic:Composition fuzznuc Nucleic:Motifs fuzzpro Protein:Motifs fuzztran Nucleic:Motifs, Protein:Motifs garnier Protein:2D Structure geecee Nucleic:CpG Islands getorf Nucleic:Gene finding helixturnhelix Protein:2D Structure, Protein:Motifs hmoment Protein:2D Structure iep Protein:Composition infoseq Edit, Help isochore Nucleic:Composition lindna Display marscan Nucleic:Gene finding, Nucleic:Motifs maskfeat Edit matcher Alignment:Local megamerger Alignment:Consensus merger Alignment:Consensus msbar Nucleic:Mutation, Protein:Mutation mse Alignment:Multiple, Edit needle Alignment:Global newcpgreport Nucleic:CpG Islands newcpgseek Nucleic:CpG Islands newseq Edit noreturn Edit notseq Edit nthseq Edit nrscope Utils:Database creation octanol Protein:Composition oddcomp Protein:Motifs palindrome Nucleic:Repeats pasteseq Edit patmatdb Protein:Motifs patmatmotifs Protein:Motifs pepcoil Protein:2D Structure, Protein:Motifs pepinfo Protein:Composition pepnet Display, Protein:2D Structure pepstats Protein:Composition pepwheel Display, Protein:2D Structure pepwindow Protein:Composition pepwindowall Protein:Composition plotcon Alignment:Multiple plotorf Nucleic:Gene finding, Nucleic:Translation polydot Alignment:Dot plots preg Protein:Motifs prettyplot Alignment:Multiple, Display prettyseq Display, Nucleic:Translation prima Nucleic:Primers primersearch Nucleic:Primers printsextract Utils:Database creation profit Nucleic:Profiles, Protein:Profiles prophecy Nucleic:Profiles, Protein:Profiles prophet Nucleic:Profiles, Protein:Profiles prosextract Utils:Database creation pscan Protein:Motifs rebaseextract Utils:Database creation recode Nucleic:Restriction redata Nucleic:Restriction remap Display, Nucleic:Restriction, Nucleic:Translation restover Nucleic:Restriction restrict Nucleic:Restriction revseq Edit scope Utils:Database creation seealso Display, Help seqmatchall Alignment:Local seqret Edit seqretall Edit seqretset Edit seqretsplit Edit showdb Display, Help showfeat Display, Feature tables showorf Nucleic:Gene finding, Nucleic:Translation showseq Display, Nucleic:Translation, Nucleic:Restriction shuffleseq Nucleic:Mutation, Protein:Mutation sigcleave Protein:Motifs silent Nucleic:Restriction stretcher Alignment:Global stssearch Nucleic:Primers splitter Edit supermatcher Alignment:Local syco Nucleic:Codon usage tfextract Utils:Database creation tfm Help tfscan Nucleic:Transcription transeq Nucleic:Translation trimseq Edit textsearch Edit tmap Protein:2D Structure vectorstrip Edit wobble Nucleic:Gene finding wordcount Nucleic:Composition wordmatch Alignment:Local water Alignment:Local wossname Help From peter.rice at uk.lionbioscience.com Wed May 2 09:11:56 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 02 May 2001 14:11:56 +0100 Subject: More on "optional:N" meanings References: <20010502121819.A10804@arran.mrc-lmb.cam.ac.uk> Message-ID: <3AF0079C.FB1BC10C@uk.lionbioscience.com> James Bonfield wrote: > In remap the "uppercase" variable (which holds a list of positions) is > defined to be opt:N (implicitly) and def:"". > > In my code this has unfortunate consequences. I have, in an advanced > tab, an entry window for the uppercase variable. It has no value > inserted in it as the default is "". However the program will not > let me proceed without filling out that entry as it claims I haven't > specified a value for a non-optional parameter. I am beginning to regret that name!!! Think of it as an extra option for the user. The universal command line qualifier '-options' makes the program prompt for a value for 'uppercase', but otherwise there is no difference. It can always be put on the command line (by the user or through your interface). 'optionalextra' might be a better name for the ACD attribute ... without breaking any current ACD files. Would that make it less confusing? regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From jkb at mrc-lmb.cam.ac.uk Wed May 2 09:45:25 2001 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Wed, 2 May 2001 14:45:25 +0100 Subject: Proposal: new menu layout, with examples In-Reply-To: <3AEFFBF6.64FCB12C@hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Wed, May 02, 2001 at 01:22:14PM +0100 References: <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEE7EC8.E794BE85@hgmp.mrc.ac.uk> <20010501104851.A23198@arran.mrc-lmb.cam.ac.uk> <3AEE94B5.D21D3142@hgmp.mrc.ac.uk> <20010501122622.B23198@arran.mrc-lmb.cam.ac.uk> <3AEEAAD9.258D452A@hgmp.mrc.ac.uk> <20010501142113.C23198@arran.mrc-lmb.cam.ac.uk> <3AEECC9D.2F6FC800@hgmp.mrc.ac.uk> <3AEFFBF6.64FCB12C@hgmp.mrc.ac.uk> Message-ID: <20010502144524.B32218@arran.mrc-lmb.cam.ac.uk> On Wed, May 02, 2001 at 01:22:14PM +0100, Gary Williams, Tel 01223 494522 wrote: > Attached is my attempt at allocating programs to the menu structure. Looks good. Only one comment obviously springs to mind - should maskfeat also be listed in the Feature Tables menu? I'm not quite sure whether it is "manipulation and display", but probably so. > It there are no complaints, I'll start changing the ACD files soon (next > week?) That'd be great. Many thanks. James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From brooks at embl-grenoble.fr Mon May 7 09:59:17 2001 From: brooks at embl-grenoble.fr (Brooks Mark) Date: Mon, 07 May 2001 15:59:17 +0200 Subject: Starting EMBOSS apllications without an input file... Message-ID: <3AF6AA35.C9352F33@embl-grenoble.fr> Hi, firstly thanks to all those who put in toils into this really useful package. Two of us here are wondering how one could use the libraries (nucleus and ajax) without having an input file, and preferably without an "acd" file corresponding to the program (although this isn't really necessary). We are trying to get GUI-based programs, which would be more useful by just typing the command, (eg. % ./gui) instead of % ./gui rhodopsin.seq. Does anyone have any advice/ideas or sample code which we could peruse please? In my initial attempts I tried to avoid "embInit" (don't laugh!), but the program would just segfault, whereas it would work as soon as I replaced embInit back into the program. Sorry if this Q has been asked before, but I haven't found any archive of responses, and I haven't seen the answer on the web site. Thanks in advance for any help, Mark -- Mark Brooks, EMBL Grenoble Outstation, 6, rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France. Tel: + (0)4 76 20 72 85 From ableasby at hgmp.mrc.ac.uk Mon May 7 12:57:04 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 7 May 2001 17:57:04 +0100 (BST) Subject: Starting EMBOSS apllications without an input file... Message-ID: <200105071657.RAA20427@tin.hgmp.mrc.ac.uk> Mark, The easiest way is to write the application in the "emboss" subdirectory. If the program is foobar.c then add foobar to (e.g.) the bin_PROGRAMS line of Makefile.am and add a foobar_SOURCES = foobar.c too. After that a "make foobar" will compile the code (assuming that you have automake installed), a plain "make" will make foobar and all other emboss applications. Appended is an example foobar.c. The #include imports the whole ajax/nucleus interface and some string and file commands are shown. Note that acd isn't used so putting an ajExit at the end would be a bad idea. HTH Alan PS: You could, of course, program emboss as usual and just have an acd file with just an "appl" definition there. #include "emboss.h" int main(int argc, char **argv) { AjPFile outf = NULL; AjPStr filename = NULL; filename = ajStrNewC("stdout"); outf = ajFileNewOut(filename); ajFmtPrintF(outf,"Message to stdout\n"); ajStrDel(&filename); return 0; } From peter.rice at uk.lionbioscience.com Tue May 8 04:08:08 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 08 May 2001 09:08:08 +0100 Subject: Starting EMBOSS apllications without an input file... References: <3AF6AA35.C9352F33@embl-grenoble.fr> Message-ID: <3AF7A968.6EE4D994@uk.lionbioscience.com> Brooks Mark wrote: > Two of us here are wondering how one could use the libraries (nucleus > and ajax) without having an input file, and preferably without an "acd" > file corresponding to the program (although this isn't really > necessary). > > In my initial attempts I tried to avoid "embInit" (don't laugh!), but > the program would just segfault, whereas it would work as soon as I > replaced embInit back into the program. As Alan says, just a simple ACD file with appl and no other ACD types would be fine - you can then safely call embInit, and the application will have one line documentation and be assigned to group(s). If the GUI application needs some command line option(s) then you can easily add them to the ACD file. I am curious which function(s) segfaulted. I assume something went wrong with uninitialized internal variables when you tried Ajax or Nucleus calls. Can you send some sample code that crashed? regards Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From brooks at embl-grenoble.fr Tue May 8 08:25:20 2001 From: brooks at embl-grenoble.fr (Brooks Mark) Date: Tue, 8 May 2001 14:25:20 +0200 (CEST) Subject: Starting EMBOSS apllications without an input file... In-Reply-To: <3AF7A968.6EE4D994@uk.lionbioscience.com> Message-ID: There is also the possibility that I'm just not doing it correctly! OK, so I'll bite the bullet and expose my (small) effort for perusal. Perhaps my segfault is down to the way I initialize the translation table(?) If I comment out the embInit and ajExit lines, then I get the segfault, otherwise things work. Is embInit required to initialize the TrnTable objects or something? gdb tells me something is wrong there. foobar.c and foobar.acd are attached (hopefully) Thanks in advance for any help, Mark. (The program has had problems sending the output to stdout- I only see the output on my Mandrake 8.0 box inside vim (!), (i.e. :!./foobar Enter a DNA sequence: atgatgatg Your sequence was: atgatgatg MMM << These lines MMM << only appear within vim!, The problem seems fixed on a Suse 7(ish) ESRF internal distribution here though. I guess this is unrelated to the real issue though) Mark Brooks, EMBL Grenoble Outstation, 6, rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France. Tel: + (0)4 76 20 72 85 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: foobar.c Url: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20010508/bfda56b8/attachment.c -------------- next part -------------- # SEQRET application # AJAX COMMAND DEFINITION (ACD) FILE # use "" for missing values - these are required. # values in "" are trimmed to single spaces. # everything is treated as single tokens delimited by white space # (space, tab, newline) # GWW 15 Feb 1999 appl: rubbish [ doc: "Copy Sequences" group: "Plaigirism" ] seqall: sequence [ param: Y type: protein ] seqoutall: outseq [ param: N ext: "peptide" ] From peter.rice at uk.lionbioscience.com Tue May 8 10:06:05 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 08 May 2001 15:06:05 +0100 Subject: Starting EMBOSS apllications without an input file... References: Message-ID: <3AF7FD4D.82BAA78C@uk.lionbioscience.com> Mark Brooks writes: >Perhaps my segfault is down to the way I initialize the translation >table(?) The translation table initialisation will read a default genetic code, from a data directory which used internal data structures defined in embInit. I would expect ajTrnNewI to have problems. My recommendation would be to always call embInit, and to write a basic ACD file. Meanwhile, we can look at making the libraries safe when uninitialised, although in this case it could mean a fatal error message. regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gwilliam at hgmp.mrc.ac.uk Wed May 16 05:29:23 2001 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Wed, 16 May 2001 10:29:23 +0100 (BST) Subject: recode -> recoder Message-ID: <200105160929.KAA10146@californium.hgmp.mrc.ac.uk> Does anyone know of a reason why 'recode' should not be called 'recoder'? >Subject: > [recode] program name > Date: > Wed, 16 May 2001 11:23:49 +0200 > From: > Philipp > To: > emboss-bug at embnet.org > >Hi All, >I've recently started investigating EMBOSS, which i find very usefull. >One thing i want to report (although you've probably heard this before) >because it almoust instantly bit me is the program name collision >of "recode" with the popular unix program of the same name (compare >http://www.iro.umontreal.ca/contrib/recode/HTML/ ). > >I'm not sure if one can consider this a "bug" (meaning it's a problem >that should be resolved) or not, but it sure is inconvinient (and breaks >our systems' printing configuration :)). > >If you reply, please CC me. > >Bye, > Philipp From tcarver at hgmp.mrc.ac.uk Wed May 16 06:01:32 2001 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Wed, 16 May 2001 11:01:32 +0100 (BST) Subject: recode -> recoder In-Reply-To: <200105160929.KAA10146@californium.hgmp.mrc.ac.uk> Message-ID: Fine by me. Tim On Wed, 16 May 2001 gwilliam at hgmp.mrc.ac.uk wrote: > Does anyone know of a reason why 'recode' should not be called 'recoder'? > > >Subject: > > [recode] program name > > Date: > > Wed, 16 May 2001 11:23:49 +0200 > > From: > > Philipp > > To: > > emboss-bug at embnet.org > > > >Hi All, > >I've recently started investigating EMBOSS, which i find very usefull. > >One thing i want to report (although you've probably heard this before) > >because it almoust instantly bit me is the program name collision > >of "recode" with the popular unix program of the same name (compare > >http://www.iro.umontreal.ca/contrib/recode/HTML/ ). > > > >I'm not sure if one can consider this a "bug" (meaning it's a problem > >that should be resolved) or not, but it sure is inconvinient (and breaks > >our systems' printing configuration :)). > > > >If you reply, please CC me. > > > >Bye, > > Philipp > From gwilliam at hgmp.mrc.ac.uk Wed May 16 07:08:00 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 16 May 2001 12:08:00 +0100 Subject: recode -> recoder References: Message-ID: <3B025F90.BB021BCA@hgmp.mrc.ac.uk> Renaming 'recode' to 'recoder' done. Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From gwilliam at hgmp.mrc.ac.uk Mon May 21 11:21:35 2001 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Mon, 21 May 2001 16:21:35 +0100 (BST) Subject: showalign committed Message-ID: <200105211521.QAA21330@bromine.hgmp.mrc.ac.uk> I've just committed showalign - yet another multiple sequence alignment display program :-) Gary From jkb at mrc-lmb.cam.ac.uk Tue May 1 08:30:36 2001 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Tue, 1 May 2001 09:30:36 +0100 Subject: Proposal: new menu layout, with examples In-Reply-To: <3AEDA34B.BF3D0374@uk.lionbioscience.com>; from peter.rice@uk.lionbioscience.com on Mon, Apr 30, 2001 at 06:39:23PM +0100 References: <20010430170540.D21424@arran.mrc-lmb.cam.ac.uk> <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEDA34B.BF3D0374@uk.lionbioscience.com> Message-ID: <20010501093036.A29532@arran.mrc-lmb.cam.ac.uk> On Mon, Apr 30, 2001 at 06:39:23PM +0100, Peter Rice wrote: > > type A choice between "frame" and "page". > > Tricky to test a list of values. frame:Y would be simpler, but we should > add controlled vocabulary types some time (see 'side' below). That's a trivial change to make for me, so I'm happy to change (if you desire it). Personally though I prefer a vocabulary type as it indicates a choice. Y/N reminds me of Rodger's earlier tools. You'd often get given a question like "Plot results? [y]". This was via the YESNO fortran function, which always had a default Yes - leading to question such as "Do you not want me to do X?". Hmm! The biggest drawback though was that people thought "plot results? Well what's the alternative? I guess I'd better take the default." Vocabs are also more extensable. If we decided that we want to add a type toplevel (unlikely) for subwindows then we can easily do so without worrying about all the weird interactions of frame:Y page:Y toplevel:Y. > > info A heading for the frame or page. Defaults to "" > > A page without a heading would look rather odd, but a frame > > without a heading is OK - it's just a bordered block. > > OK. Can also be used to prompt interactive users (e.g. "Gap penalties:" > before prompting for the gap penalty values). Or we could have a separate > 'prompt' for this, and use 'info' in the -help output (tricky though - > qualifiers will be in sections but also in required/optional/advanced > groupings so maybe -help should be left alone) Indeed. If we use such things for prompts then I suggest an indentation method to display members of the group. Eg: Gap penalties: Gap open penalty [16]: Gap extension penalty [4]: Output file [foo.stretcher]: > > book Only needed for type:frame. > > The notebook to associate this page to. Defaults to "", which > > implies all pages are part of the same notebook. This is only > > needed if a program wishes to make use of more than one tabbed > > notebook, in which case this is used to determine which book a > > page is within. > > Can we pick a more general name for this? Of course I meant "book: only needed for type:page" (rather than type book). We could have a more general name, but I thought the term book fitted rather well with type:page. Specifically frames are standalone, whereas pages are a member of a set which are displayed together. Perhaps "set" is a suitable alternative name? > > border Only needed for type:frame. Defaults to 1. > > The border width of the frame. > > OK. > > > side Only needed for type:frame. Defaults to top. > > This is used for 'frame packing'. It is only needed if we wish > > to express complex layout designs. Eg: > > Looks like another controlled vocabulary. Also, looks like I can think of > uses for it. Side here has values of top, bottom, left and right - ie the same as the tcl pack -side option (how convenient - I wonder how that could have happened? ;-)). James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From peter.rice at uk.lionbioscience.com Tue May 1 08:46:01 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 01 May 2001 09:46:01 +0100 Subject: Proposal: new menu layout, with examples References: <20010430170540.D21424@arran.mrc-lmb.cam.ac.uk> <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEDA34B.BF3D0374@uk.lionbioscience.com> <20010501093036.A29532@arran.mrc-lmb.cam.ac.uk> Message-ID: <3AEE77C9.7931261D@uk.lionbioscience.com> Hi James, Let me think about controlled vocabularies a little. The problem is where to put them when defining new attributes. We already have the mechanism for handling them with list and select ACD types. I think they can probably he hardcoded in the section-setting functions. > Of course I meant "book: only needed for type:page" Ah, that makes sense. Maybe "folder" is more general? > Side here has values of top, bottom, left and right - ie the same as > the tcl pack -side option (how convenient - I wonder how that could > have happened? Fair enough. Almost anything that reaches version 8.0 can count as a standard :-) regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gwilliam at hgmp.mrc.ac.uk Tue May 1 14:47:57 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 01 May 2001 15:47:57 +0100 Subject: Proposal: new menu layout, with examples References: <20010430170540.D21424@arran.mrc-lmb.cam.ac.uk> <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEE7EC8.E794BE85@hgmp.mrc.ac.uk> <20010501104851.A23198@arran.mrc-lmb.cam.ac.uk> <3AEE94B5.D21D3142@hgmp.mrc.ac.uk> <20010501122622.B23198@arran.mrc-lmb.cam.ac.uk> <3AEEAAD9.258D452A@hgmp.mrc.ac.uk> <20010501142113.C23198@arran.mrc-lmb.cam.ac.uk> Message-ID: <3AEECC9D.2F6FC800@hgmp.mrc.ac.uk> James and I have been discussing the program group structure. We seem to have come to some sort of agreement on the following. Some things like 'Feature tables' are place-holders for groups of programs that probably ought to be written. I'm sure there will be useful comments on the following: (Are 'Profiles' and 'Patterns' similar enough to be merged?) +Compare + Consensus (merging sequences to make a consensus) + Differences + Dot plots + Global alignment + Local alignment + Multiple alignment +Display (information + publication display, not just stuff that plots results) +Edit (sequence and annotation manipulation) +Enzyme Kinetics (just 'findkm' at present) +Feature tables (manipulation and display of feature tables) +Help (help for the user, e.g. wossname, showdb, seealso) +Nucleic + 2D Structure (RNA structure) + Codon usage + Composition (properties over the whole sequence, GFF not produced) + CPG islands + Gene finding (genes and other genomic features) + Patterns (search for defined patterns) + Primers + Profiles (search for defined profiles) + Repeats + Restriction enzymes + Transcribe (transcription factors) + Translate + Mutate +Phylogeny (mainly the Phylip package) +Protein + 2D Structure (2D structure and topological features) + 3D Structure + Composition (properties over the whole sequence, GFF not produced) + Patterns (search for defined patterns) + Mutate + Profiles (search for defined profiles) +Utils + Database indexing + Database creation + Misc +Test -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From jkb at mrc-lmb.cam.ac.uk Wed May 2 11:18:19 2001 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Wed, 2 May 2001 12:18:19 +0100 Subject: More on "optional:N" meanings Message-ID: <20010502121819.A10804@arran.mrc-lmb.cam.ac.uk> Sorry to bring up this topic again, but I've just been confused by another odd case. In remap the "uppercase" variable (which holds a list of positions) is defined to be opt:N (implicitly) and def:"". In my code this has unfortunate consequences. I have, in an advanced tab, an entry window for the uppercase variable. It has no value inserted in it as the default is "". However the program will not let me proceed without filling out that entry as it claims I haven't specified a value for a non-optional parameter. I think this is just another case where I've confused optional with required. (Specifically the assumption that non-optional implies mandatory :-)) I'll update the code as follows. Any argument listed as opt:N req:N, that does not have a value will simply be ignored (and not supplied as an argument to the emboss program). Any argument that is listed as req:Y (regardless of whether it is opt:N or opt:Y) will follow the current 'is it set?" test. Please comment if I'm wildly off target, otherwise just ignore these ramblings. Cheers, James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From gwilliam at hgmp.mrc.ac.uk Wed May 2 12:22:14 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 02 May 2001 13:22:14 +0100 Subject: Proposal: new menu layout, with examples References: <20010430170540.D21424@arran.mrc-lmb.cam.ac.uk> <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEE7EC8.E794BE85@hgmp.mrc.ac.uk> <20010501104851.A23198@arran.mrc-lmb.cam.ac.uk> <3AEE94B5.D21D3142@hgmp.mrc.ac.uk> <20010501122622.B23198@arran.mrc-lmb.cam.ac.uk> <3AEEAAD9.258D452A@hgmp.mrc.ac.uk> <20010501142113.C23198@arran.mrc-lmb.cam.ac.uk> <3AEECC9D.2F6FC800@hgmp.mrc.ac.uk> Message-ID: <3AEFFBF6.64FCB12C@hgmp.mrc.ac.uk> Attached is my attempt at allocating programs to the menu structure. Most things fit well and there are only a few programs with assignments to multiple groups: 23 to two groups, 2 to three groups (remap and showseq) It there are no complaints, I'll start changing the ACD files soon (next week?) Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK -------------- next part -------------- +Alignment + Consensus (merging sequences to make a consensus) = cons = megamerger = merger + Differences = diffseq + Dot plots = dotmatcher = dotpath = dottup = polydot + Global = est2genome = needle = stretcher + Local = matcher = seqmatchall = water = wordmatch + Multiple = emma = mse = plotcon = prettyplot +Display (publication display, not just stuff that plots results) = abiview = cirdna = lindna = prettyplot = prettyseq = remap = showdb = showseq = pepnet = pepwheel = seealso = showfeat = showseq +Edit (sequence and annotation manipulation) = cutseq = degapseq = descseq = entret = extractseq = infoseq = maskfeat = mse = newseq = noreturn = notseq = nthseq = pasteseq = revseq = seqret = seqretall = seqretset = seqretsplit = splitter = textsearch = trimseq = vectorstrip +Enzyme Kinetics = findkm +Feature tables (manipulation and display of feature tables) = coderet = showfeat +Help (help for the user) = infoseq = seealso = showdb = tfm = wossname +Nucleic + 2D Structure (RNA structure) + Codon usage = cai = chips = codcmp = cusp = syco + Composition (properties over the whole sequence, GFF not produced) = banana = btwisted = chaos = compseq = dan = freak = isochore = wordcount + CPG islands = cpgplot = cpgreport = geecee = newcpgreport = newcpgseek + Gene finding (genes and other genomic features) = est2genome = getorf = marscan = plotorf = showorf = wobble + Motifs (search for defined patterns) = dreg = fuzznuc = fuzztran = marscan + Mutation = msbar = shuffleseq + Primers = prima = primersearch = stssearch + Profiles (search for defined profiles) = profit = prophecy = prophet + Repeats = einverted = equicktandem = etandem = palindrome + Restriction = recode = redata = remap = restover = restrict = showseq = silent + Transcription (transcription factors) = tfscan + Translation = backtranseq = coderet = prettyseq = plotorf = remap = showorf = showseq = transeq + Mutation +Phylogeny (mainly the Phylip package) = distmat +Protein + 2D Structure (2D structure and topological features) = garnier = helixturnhelix = hmoment = tmap = pepcoil = pepnet = pepwheel + 3D Structure + Composition (properties over the whole sequence, GFF not produced) = backtranseq = charge = checktrans = compseq = emowse = iep = octanol = pepinfo = pepstats = pepwindow = pepwindowall + Motifs (search for defined patterns) = antigenic = digest = fuzzpro = fuzztran = helixturnhelix = oddcomp = patmatdb = patmatmotifs = pepcoil = preg = pscan = sigcleave + Mutation = msbar = shuffleseq + Profiles (search for defined profiles) = profit = prophecy = prophet +Utils + Database indexing = dbiblast = dbifasta = dbiflat = dbigcg + Database creation = domainer = nrscope = printsextract = prosextract = rebaseextract = scope = tfextract + Misc = embossdata +Test -------------- next part -------------- abiview Display antigenic Protein:Motifs backtranseq Nucleic:Translation, Protein:Composition banana Nucleic:Composition btwisted Nucleic:Composition cai Nucleic:Codon usage chaos Nucleic:Composition charge Protein:Composition checktrans Protein:Composition chips Nucleic:Codon usage cirdna Display codcmp Nucleic:Codon usage coderet Feature tables, Nucleic:Translation compseq Nucleic:Composition, Protein:Composition cons Alignment:Consensus cpgplot Nucleic:CpG Islands cpgreport Nucleic:CpG Islands cusp Nucleic:Codon usage cutseq Edit dan Nucleic:Composition dbiblast Utils:Database indexing dbifasta Utils:Database indexing dbiflat Utils:Database indexing dbigcg Utils:Database indexing degapseq Edit descseq Edit diffseq Alignment:Differences digest Protein:Motifs distmat Phylogeny domainer Utils:Database creation dotmatcher Alignment:Dot plots dotpath Alignment:Dot plots dottup Alignment:Dot plots dreg Nucleic:Motifs einverted Nucleic:Repeats embossdata Utils:Misc emowse Protein:Composition equicktandem Nucleic:Repeats etandem Nucleic:Repeats emma Alignment:Multiple entret Edit est2genome Alignment:Global extractseq Edit freak Nucleic:Composition fuzznuc Nucleic:Motifs fuzzpro Protein:Motifs fuzztran Nucleic:Motifs, Protein:Motifs garnier Protein:2D Structure geecee Nucleic:CpG Islands getorf Nucleic:Gene finding helixturnhelix Protein:2D Structure, Protein:Motifs hmoment Protein:2D Structure iep Protein:Composition infoseq Edit, Help isochore Nucleic:Composition lindna Display marscan Nucleic:Gene finding, Nucleic:Motifs maskfeat Edit matcher Alignment:Local megamerger Alignment:Consensus merger Alignment:Consensus msbar Nucleic:Mutation, Protein:Mutation mse Alignment:Multiple, Edit needle Alignment:Global newcpgreport Nucleic:CpG Islands newcpgseek Nucleic:CpG Islands newseq Edit noreturn Edit notseq Edit nthseq Edit nrscope Utils:Database creation octanol Protein:Composition oddcomp Protein:Motifs palindrome Nucleic:Repeats pasteseq Edit patmatdb Protein:Motifs patmatmotifs Protein:Motifs pepcoil Protein:2D Structure, Protein:Motifs pepinfo Protein:Composition pepnet Display, Protein:2D Structure pepstats Protein:Composition pepwheel Display, Protein:2D Structure pepwindow Protein:Composition pepwindowall Protein:Composition plotcon Alignment:Multiple plotorf Nucleic:Gene finding, Nucleic:Translation polydot Alignment:Dot plots preg Protein:Motifs prettyplot Alignment:Multiple, Display prettyseq Display, Nucleic:Translation prima Nucleic:Primers primersearch Nucleic:Primers printsextract Utils:Database creation profit Nucleic:Profiles, Protein:Profiles prophecy Nucleic:Profiles, Protein:Profiles prophet Nucleic:Profiles, Protein:Profiles prosextract Utils:Database creation pscan Protein:Motifs rebaseextract Utils:Database creation recode Nucleic:Restriction redata Nucleic:Restriction remap Display, Nucleic:Restriction, Nucleic:Translation restover Nucleic:Restriction restrict Nucleic:Restriction revseq Edit scope Utils:Database creation seealso Display, Help seqmatchall Alignment:Local seqret Edit seqretall Edit seqretset Edit seqretsplit Edit showdb Display, Help showfeat Display, Feature tables showorf Nucleic:Gene finding, Nucleic:Translation showseq Display, Nucleic:Translation, Nucleic:Restriction shuffleseq Nucleic:Mutation, Protein:Mutation sigcleave Protein:Motifs silent Nucleic:Restriction stretcher Alignment:Global stssearch Nucleic:Primers splitter Edit supermatcher Alignment:Local syco Nucleic:Codon usage tfextract Utils:Database creation tfm Help tfscan Nucleic:Transcription transeq Nucleic:Translation trimseq Edit textsearch Edit tmap Protein:2D Structure vectorstrip Edit wobble Nucleic:Gene finding wordcount Nucleic:Composition wordmatch Alignment:Local water Alignment:Local wossname Help From peter.rice at uk.lionbioscience.com Wed May 2 13:11:56 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 02 May 2001 14:11:56 +0100 Subject: More on "optional:N" meanings References: <20010502121819.A10804@arran.mrc-lmb.cam.ac.uk> Message-ID: <3AF0079C.FB1BC10C@uk.lionbioscience.com> James Bonfield wrote: > In remap the "uppercase" variable (which holds a list of positions) is > defined to be opt:N (implicitly) and def:"". > > In my code this has unfortunate consequences. I have, in an advanced > tab, an entry window for the uppercase variable. It has no value > inserted in it as the default is "". However the program will not > let me proceed without filling out that entry as it claims I haven't > specified a value for a non-optional parameter. I am beginning to regret that name!!! Think of it as an extra option for the user. The universal command line qualifier '-options' makes the program prompt for a value for 'uppercase', but otherwise there is no difference. It can always be put on the command line (by the user or through your interface). 'optionalextra' might be a better name for the ACD attribute ... without breaking any current ACD files. Would that make it less confusing? regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From jkb at mrc-lmb.cam.ac.uk Wed May 2 13:45:25 2001 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Wed, 2 May 2001 14:45:25 +0100 Subject: Proposal: new menu layout, with examples In-Reply-To: <3AEFFBF6.64FCB12C@hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Wed, May 02, 2001 at 01:22:14PM +0100 References: <3AED9E3A.383A1649@uk.lionbioscience.com> <20010430182943.A21399@arran.mrc-lmb.cam.ac.uk> <3AEE7EC8.E794BE85@hgmp.mrc.ac.uk> <20010501104851.A23198@arran.mrc-lmb.cam.ac.uk> <3AEE94B5.D21D3142@hgmp.mrc.ac.uk> <20010501122622.B23198@arran.mrc-lmb.cam.ac.uk> <3AEEAAD9.258D452A@hgmp.mrc.ac.uk> <20010501142113.C23198@arran.mrc-lmb.cam.ac.uk> <3AEECC9D.2F6FC800@hgmp.mrc.ac.uk> <3AEFFBF6.64FCB12C@hgmp.mrc.ac.uk> Message-ID: <20010502144524.B32218@arran.mrc-lmb.cam.ac.uk> On Wed, May 02, 2001 at 01:22:14PM +0100, Gary Williams, Tel 01223 494522 wrote: > Attached is my attempt at allocating programs to the menu structure. Looks good. Only one comment obviously springs to mind - should maskfeat also be listed in the Feature Tables menu? I'm not quite sure whether it is "manipulation and display", but probably so. > It there are no complaints, I'll start changing the ACD files soon (next > week?) That'd be great. Many thanks. James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From brooks at embl-grenoble.fr Mon May 7 13:59:17 2001 From: brooks at embl-grenoble.fr (Brooks Mark) Date: Mon, 07 May 2001 15:59:17 +0200 Subject: Starting EMBOSS apllications without an input file... Message-ID: <3AF6AA35.C9352F33@embl-grenoble.fr> Hi, firstly thanks to all those who put in toils into this really useful package. Two of us here are wondering how one could use the libraries (nucleus and ajax) without having an input file, and preferably without an "acd" file corresponding to the program (although this isn't really necessary). We are trying to get GUI-based programs, which would be more useful by just typing the command, (eg. % ./gui) instead of % ./gui rhodopsin.seq. Does anyone have any advice/ideas or sample code which we could peruse please? In my initial attempts I tried to avoid "embInit" (don't laugh!), but the program would just segfault, whereas it would work as soon as I replaced embInit back into the program. Sorry if this Q has been asked before, but I haven't found any archive of responses, and I haven't seen the answer on the web site. Thanks in advance for any help, Mark -- Mark Brooks, EMBL Grenoble Outstation, 6, rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France. Tel: + (0)4 76 20 72 85 From ableasby at hgmp.mrc.ac.uk Mon May 7 16:57:04 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 7 May 2001 17:57:04 +0100 (BST) Subject: Starting EMBOSS apllications without an input file... Message-ID: <200105071657.RAA20427@tin.hgmp.mrc.ac.uk> Mark, The easiest way is to write the application in the "emboss" subdirectory. If the program is foobar.c then add foobar to (e.g.) the bin_PROGRAMS line of Makefile.am and add a foobar_SOURCES = foobar.c too. After that a "make foobar" will compile the code (assuming that you have automake installed), a plain "make" will make foobar and all other emboss applications. Appended is an example foobar.c. The #include imports the whole ajax/nucleus interface and some string and file commands are shown. Note that acd isn't used so putting an ajExit at the end would be a bad idea. HTH Alan PS: You could, of course, program emboss as usual and just have an acd file with just an "appl" definition there. #include "emboss.h" int main(int argc, char **argv) { AjPFile outf = NULL; AjPStr filename = NULL; filename = ajStrNewC("stdout"); outf = ajFileNewOut(filename); ajFmtPrintF(outf,"Message to stdout\n"); ajStrDel(&filename); return 0; } From peter.rice at uk.lionbioscience.com Tue May 8 08:08:08 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 08 May 2001 09:08:08 +0100 Subject: Starting EMBOSS apllications without an input file... References: <3AF6AA35.C9352F33@embl-grenoble.fr> Message-ID: <3AF7A968.6EE4D994@uk.lionbioscience.com> Brooks Mark wrote: > Two of us here are wondering how one could use the libraries (nucleus > and ajax) without having an input file, and preferably without an "acd" > file corresponding to the program (although this isn't really > necessary). > > In my initial attempts I tried to avoid "embInit" (don't laugh!), but > the program would just segfault, whereas it would work as soon as I > replaced embInit back into the program. As Alan says, just a simple ACD file with appl and no other ACD types would be fine - you can then safely call embInit, and the application will have one line documentation and be assigned to group(s). If the GUI application needs some command line option(s) then you can easily add them to the ACD file. I am curious which function(s) segfaulted. I assume something went wrong with uninitialized internal variables when you tried Ajax or Nucleus calls. Can you send some sample code that crashed? regards Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From brooks at embl-grenoble.fr Tue May 8 12:25:20 2001 From: brooks at embl-grenoble.fr (Brooks Mark) Date: Tue, 8 May 2001 14:25:20 +0200 (CEST) Subject: Starting EMBOSS apllications without an input file... In-Reply-To: <3AF7A968.6EE4D994@uk.lionbioscience.com> Message-ID: There is also the possibility that I'm just not doing it correctly! OK, so I'll bite the bullet and expose my (small) effort for perusal. Perhaps my segfault is down to the way I initialize the translation table(?) If I comment out the embInit and ajExit lines, then I get the segfault, otherwise things work. Is embInit required to initialize the TrnTable objects or something? gdb tells me something is wrong there. foobar.c and foobar.acd are attached (hopefully) Thanks in advance for any help, Mark. (The program has had problems sending the output to stdout- I only see the output on my Mandrake 8.0 box inside vim (!), (i.e. :!./foobar Enter a DNA sequence: atgatgatg Your sequence was: atgatgatg MMM << These lines MMM << only appear within vim!, The problem seems fixed on a Suse 7(ish) ESRF internal distribution here though. I guess this is unrelated to the real issue though) Mark Brooks, EMBL Grenoble Outstation, 6, rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France. Tel: + (0)4 76 20 72 85 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: foobar.c URL: -------------- next part -------------- # SEQRET application # AJAX COMMAND DEFINITION (ACD) FILE # use "" for missing values - these are required. # values in "" are trimmed to single spaces. # everything is treated as single tokens delimited by white space # (space, tab, newline) # GWW 15 Feb 1999 appl: rubbish [ doc: "Copy Sequences" group: "Plaigirism" ] seqall: sequence [ param: Y type: protein ] seqoutall: outseq [ param: N ext: "peptide" ] From peter.rice at uk.lionbioscience.com Tue May 8 14:06:05 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 08 May 2001 15:06:05 +0100 Subject: Starting EMBOSS apllications without an input file... References: Message-ID: <3AF7FD4D.82BAA78C@uk.lionbioscience.com> Mark Brooks writes: >Perhaps my segfault is down to the way I initialize the translation >table(?) The translation table initialisation will read a default genetic code, from a data directory which used internal data structures defined in embInit. I would expect ajTrnNewI to have problems. My recommendation would be to always call embInit, and to write a basic ACD file. Meanwhile, we can look at making the libraries safe when uninitialised, although in this case it could mean a fatal error message. regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gwilliam at hgmp.mrc.ac.uk Wed May 16 09:29:23 2001 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Wed, 16 May 2001 10:29:23 +0100 (BST) Subject: recode -> recoder Message-ID: <200105160929.KAA10146@californium.hgmp.mrc.ac.uk> Does anyone know of a reason why 'recode' should not be called 'recoder'? >Subject: > [recode] program name > Date: > Wed, 16 May 2001 11:23:49 +0200 > From: > Philipp > To: > emboss-bug at embnet.org > >Hi All, >I've recently started investigating EMBOSS, which i find very usefull. >One thing i want to report (although you've probably heard this before) >because it almoust instantly bit me is the program name collision >of "recode" with the popular unix program of the same name (compare >http://www.iro.umontreal.ca/contrib/recode/HTML/ ). > >I'm not sure if one can consider this a "bug" (meaning it's a problem >that should be resolved) or not, but it sure is inconvinient (and breaks >our systems' printing configuration :)). > >If you reply, please CC me. > >Bye, > Philipp From tcarver at hgmp.mrc.ac.uk Wed May 16 10:01:32 2001 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Wed, 16 May 2001 11:01:32 +0100 (BST) Subject: recode -> recoder In-Reply-To: <200105160929.KAA10146@californium.hgmp.mrc.ac.uk> Message-ID: Fine by me. Tim On Wed, 16 May 2001 gwilliam at hgmp.mrc.ac.uk wrote: > Does anyone know of a reason why 'recode' should not be called 'recoder'? > > >Subject: > > [recode] program name > > Date: > > Wed, 16 May 2001 11:23:49 +0200 > > From: > > Philipp > > To: > > emboss-bug at embnet.org > > > >Hi All, > >I've recently started investigating EMBOSS, which i find very usefull. > >One thing i want to report (although you've probably heard this before) > >because it almoust instantly bit me is the program name collision > >of "recode" with the popular unix program of the same name (compare > >http://www.iro.umontreal.ca/contrib/recode/HTML/ ). > > > >I'm not sure if one can consider this a "bug" (meaning it's a problem > >that should be resolved) or not, but it sure is inconvinient (and breaks > >our systems' printing configuration :)). > > > >If you reply, please CC me. > > > >Bye, > > Philipp > From gwilliam at hgmp.mrc.ac.uk Wed May 16 11:08:00 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 16 May 2001 12:08:00 +0100 Subject: recode -> recoder References: Message-ID: <3B025F90.BB021BCA@hgmp.mrc.ac.uk> Renaming 'recode' to 'recoder' done. Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From gwilliam at hgmp.mrc.ac.uk Mon May 21 15:21:35 2001 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Mon, 21 May 2001 16:21:35 +0100 (BST) Subject: showalign committed Message-ID: <200105211521.QAA21330@bromine.hgmp.mrc.ac.uk> I've just committed showalign - yet another multiple sequence alignment display program :-) Gary