From henrikki.almusa at helsinki.fi Fri Aug 6 03:09:18 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 6 Aug 2004 10:09:18 +0300 Subject: Patterns, patternlists and nucleus/embpat.h Message-ID: <200408061009.18201.henrikki.almusa@helsinki.fi> Hello, I've been checking more on how I could make patterns and patternlist system (some patches sent month ago) to work with fuzz(nuc|pro|tran). Only way that i could think of is making a new stucture in 'nucleus/embpat.h', which would hold almost all the variables needed to run embPatGetType (), embPatCompile(), embPatFuzzSearch(). So heres the proposition: /* @data EmbPPatComp ********************************************************** ** ** NUCLEUS data structure that holds all needed datas for compiling and ** searching. Not including mismatch number. ** ** @attr pattern [AjPStr] Prosite pattern string ** @attr type [ajint] Prosite pattern compile type ** @attr plen [ajint] Prosite pattern length ** @attr buf [ajint*] Buffer for BMH search ** @attr off [struct EmbSPatBYPNode] Offset buffer for B-Y/P search ** @attr sotable [ajuint*] Buffer for SHIFT-OR ** @attr solimit [ajint] Limit for BMH search ** @attr m [ajint] Real length of pattern (from embPatGetType) ** @attr regex [AjPStr] PCRE regexp string ** @attr skipm [ajint**] Skip buffer for Tarhio-Ukkonen ** @attr amino [AjPBool] Must match left begin ** @attr carboxyl [AjPBool] Must match right ** @@ ******************************************************************************/ typedef struct EmbSPatComp { AjPStr pattern; ajint type; ajint plen; ajint* buf; EmbOPatBYPNode off[AJALPHA]; ajuint* sotable; ajuint solimit; ajint m; AjPStr regex; ajint** skipm; AjPBool amino; AjPBool carboxyl; } EmbOPatComp; #define EmbPPatComp EmbOPatComp* And functions for this would be: void embPatCompileII (EmbPPatComp thys); void embPatFuzzSearchII (EmbPPATComp thys, ajint begin, const AjPStr name, const AjPStr text, AjPList l, ajint mismatch, void** tidy); void embPatGetTypeII (EmbPPatComp thys, const AjPStr pattern, ajint mismatch, AjPBool protein); Any comments? Thanks, -- Henrikki Almusa From cavallo at biochem.ucl.ac.uk Fri Aug 6 09:17:05 2004 From: cavallo at biochem.ucl.ac.uk (Antonio Cavallo) Date: Fri, 06 Aug 2004 14:17:05 +0100 Subject: patch against 2.9.0 and c++ Message-ID: <411384D1.4050909@biochem.ucl.ac.uk> Hi, included in this message you can find a patch against the emboss 2.9.0. It fixes some mystyping that makes impossible to compile programs under c++. Mainly these are fixes for variables with a string name (in c++ a reserved keyword). regards, antonio cavallo ps. for any interested in it, there is a complete rpm file to use binaries under linux. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: EMBOSS-2.9.0-cplus.dif Url: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040806/1c4f1762/attachment.pl From pmr at ebi.ac.uk Fri Aug 6 09:51:47 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 06 Aug 2004 14:51:47 +0100 Subject: patch against 2.9.0 and c++ In-Reply-To: <411384D1.4050909@biochem.ucl.ac.uk> References: <411384D1.4050909@biochem.ucl.ac.uk> Message-ID: <41138CF3.1080407@ebi.ac.uk> Antonio Cavallo wrote: > included in this message you can find a patch against the emboss 2.9.0. > It fixes some mystyping that makes impossible to compile > programs under c++. > Mainly these are fixes for variables with a string name (in c++ a > reserved keyword). Thanks. I have added these to the code documentation scripts (embossdoc.pl) although we don't check plplot with that. Most of the embest.h ones are obsolete - I have cleaned up the old est_genome definitions which removed all of the "string" variable names. What C++ compiler are you using (with what options) ? regards, Peter Rice From henrikki.almusa at helsinki.fi Mon Aug 9 02:13:21 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 9 Aug 2004 09:13:21 +0300 Subject: Fix couple of typos in ajax/ajstr Message-ID: <200408090913.21794.henrikki.almusa@helsinki.fi> Hello, Heres a small patch to fix typos in comments in ajstr.c and .h. These show up in srs and were somewhat confusing (atleast to me) :). Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_ajstr_typo.patch Type: text/x-diff Size: 1356 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040809/2cf21da3/attachment.bin From henrikki.almusa at helsinki.fi Mon Aug 9 03:08:15 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 9 Aug 2004 10:08:15 +0300 Subject: Pattern lists (need help after 2.9.0) Message-ID: <200408091008.15538.henrikki.almusa@helsinki.fi> Hello, I've stumbled into a problem, when i changed the pattern lists to 2.9.0 from 2.8.0. I now get a core dump, when trying to use it from dreg. Attached are ajpat.c and ajpat.h which is the current situation with these. And dreg.c and dreg.acd diff, for the modifications on them to use the pattern lists. This is the stack trace that gdb gives for core dump. (gdb) info stack #0 0x40106b0d in ajListPushApp () from /work/hena/emboss-2.9.0/lib/libajax.so.0 #1 0x40158b3a in ajPatlistAdd () from /work/hena/emboss-2.9.0/lib/libajax.so.0 #2 0x401589da in ajPatlistParsePatternFile () from /work/hena/emboss-2.9.0/lib/libajax.so.0 #3 0x08049040 in main () #4 0x40466a67 in __libc_start_main () from /lib/i686/libc.so.6 Any help would be appreciated, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_dreg.plist.patch Type: text/x-diff Size: 2414 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040809/748aa9de/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.h Type: text/x-chdr Size: 2364 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040809/748aa9de/attachment-0001.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.c Type: text/x-csrc Size: 7710 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040809/748aa9de/attachment-0002.bin From henrikki.almusa at helsinki.fi Mon Aug 9 09:04:18 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 9 Aug 2004 16:04:18 +0300 Subject: Pattern lists (need help after 2.9.0) In-Reply-To: <200408091008.15538.henrikki.almusa@helsinki.fi> References: <200408091008.15538.henrikki.almusa@helsinki.fi> Message-ID: <200408091604.18704.henrikki.almusa@helsinki.fi> On Monday 09 August 2004 10:08, Henrikki Almusa wrote: > Hello, > > I've stumbled into a problem, when i changed the pattern lists to 2.9.0 > from 2.8.0. I now get a core dump, when trying to use it from dreg. > Attached are ajpat.c and ajpat.h which is the current situation with these. > And dreg.c and dreg.acd diff, for the modifications on them to use the > pattern lists. Figured this out already. Continuing on trying to allow fuzz(nuc|pro|tran) to use patternlists. After that I will post my code at that time and then need to do the acds properly. Thanks, -- Henrikki Almusa From henrikki.almusa at helsinki.fi Tue Aug 10 02:39:24 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 10 Aug 2004 09:39:24 +0300 Subject: Pattern lists Message-ID: <200408100939.24959.henrikki.almusa@helsinki.fi> Hello, I can finally report that I have succesfully tested the pattern list with dreg and fuzznuc. I will attach four files. Current version of ajpat.c and ajpat.h with comments. Patch which I used to test both dreg and fuzznuc. And patch to change 'nucleus/embpat.c' and 'nucleus/empat.h', which I have modified to allow prosite patterns to run as well. Now I have few questions about next part. 1. How to do the acd overloading. In my patch to dreg and fuzznuc, I used string and then did what was needed in program. This is not probably the correct way, but ok for testing. 2. Should I add a search function into pattern lists? This would allow fuzz(nuc|pro|tran) to run regular expression pattern as well (thus obsoleting dreg and preg). This change would also mean that patterns in files would need a attribute as well (value might a number or string). But this might cause confusion as mismatch values don't work with regexes (even though it would be there). 3. Is it ok to use '#include ../nucleus/emboss.h' in 'ajpat.c'? This was done as I needed functions from 'nucleus/embpat.h'. If not how this should be done then? 4. Any thing else that needs to be fixed for inclusion into emboss? Any namings or such? Note that to make the patches smaller, I didn't add whitespaces properly in front of the lines in dreg and fuzznuc patch. Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.c Type: text/x-csrc Size: 9326 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040810/c517b5bb/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.h Type: text/x-chdr Size: 2961 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040810/c517b5bb/attachment-0001.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_dreg_fuzznuc_plist.patch Type: text/x-diff Size: 7544 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040810/c517b5bb/attachment-0002.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_embpat_plist.patch Type: text/x-diff Size: 10145 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040810/c517b5bb/attachment-0003.bin From P.Ernst at dkfz-heidelberg.de Tue Aug 10 05:18:58 2004 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Tue, 10 Aug 2004 11:18:58 +0200 (MEST) Subject: patch against 2.9.0 and c++ In-Reply-To: <41138CF3.1080407@ebi.ac.uk> Message-ID: To my knowledge "string" is NOT a reserved word in C++. You run only into problems, when copying the std:: namespace onto the Emboss namespace with "using namespace std;". >From "The C+ + Programming Language Third Edition: by Bjarne Stroustrup: You must either use the std:: prefix or make every name from std global (?8.2.3). For example: #include // make the standard string facilities accessible using namespace std; // make std names available without std:: prefix string s = "Ignorance is bliss!"; // ok: string is std::string It is generally in poor taste to dump every name from a namespace into the global namespace. [....] A using directive makes names from a namespace available almost as if they had been declared outside their namespace. Kind regards, Peter -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= On Fri, 6 Aug 2004, Peter Rice wrote: > Antonio Cavallo wrote: > > > included in this message you can find a patch against the emboss 2.9.0. > > It fixes some mystyping that makes impossible to compile > > programs under c++. > > Mainly these are fixes for variables with a string name (in c++ a > > reserved keyword). > > Thanks. I have added these to the code documentation scripts (embossdoc.pl) > although we don't check plplot with that. > > Most of the embest.h ones are obsolete - I have cleaned up the old est_genome > definitions which removed all of the "string" variable names. > > What C++ compiler are you using (with what options) ? > > regards, > > Peter Rice > > From gbottu at ben.vub.ac.be Tue Aug 10 07:02:15 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Tue, 10 Aug 2004 13:02:15 +0200 Subject: disappeared functons Message-ID: <20040810110215.GA27809@bigben.ulb.ac.be> Dear colleagues, I am installing EMBOSS 2.9.0 and I just noticed that the ajax functions ajSeqTypeNucS and ajSeqTypeProtS have disappeared, even if they are still mentioned in the on-line help in the HGMPRC Web pages. This is quite unconvenient for me, since I used them in a local developement. Was the removal of these functions intentional or accidental ? Sincerely, Guy Bottu, BEN From cavallo at biochem.ucl.ac.uk Tue Aug 10 08:00:34 2004 From: cavallo at biochem.ucl.ac.uk (Antonio Cavallo) Date: Tue, 10 Aug 2004 13:00:34 +0100 Subject: patch against 2.9.0 and c++ In-Reply-To: References: Message-ID: <4118B8E2.1080909@biochem.ucl.ac.uk> Peter Ernst wrote: > To my knowledge "string" is NOT a reserved word in C++. > You run only into problems, when copying the std:: namespace onto the > A using directive makes names from a namespace available almost as if > they had been declared outside their namespace. > A discussion about what is "standard" or "right" is not very helpful. A lot of c++ code is using string as reserved keyword (without std:: prefix), so it is safe to assume that is good practice to restrict the usage of the word "string" (like false or true): in EMBOSS there are only few lines (out of many many present) to be changed. "It is generally in poor taste", I will not argue about this point: one of the nice c++ features (namespaces) are there to prevent the name space pollution, althout too many layers of naming are confusing (two is considered good, three start to be too much). But let's face it. statements like: std::vector::iterator p; are not exactly good taste either;) regards, antonio From gbottu at ben.vub.ac.be Wed Aug 11 10:47:24 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 11 Aug 2004 16:47:24 +0200 Subject: question about behaviour of "toggle" Message-ID: <20040811144724.GA10004@bigben.ulb.ac.be> Dear colleagues, I am busy installing EMBOSS 2.9.0 and I noticed the following. The file iep.acd contains : toggle: report [ default: "Y" information: "Write results to a file" ] The command iep -help outputs : -report toggle Write results to a file Why not -[no]report ? Is this behaviour intended or is it a bug ? Sincerely, Guy Bottu BEN From henrikki.almusa at helsinki.fi Fri Aug 6 07:09:18 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 6 Aug 2004 10:09:18 +0300 Subject: Patterns, patternlists and nucleus/embpat.h Message-ID: <200408061009.18201.henrikki.almusa@helsinki.fi> Hello, I've been checking more on how I could make patterns and patternlist system (some patches sent month ago) to work with fuzz(nuc|pro|tran). Only way that i could think of is making a new stucture in 'nucleus/embpat.h', which would hold almost all the variables needed to run embPatGetType (), embPatCompile(), embPatFuzzSearch(). So heres the proposition: /* @data EmbPPatComp ********************************************************** ** ** NUCLEUS data structure that holds all needed datas for compiling and ** searching. Not including mismatch number. ** ** @attr pattern [AjPStr] Prosite pattern string ** @attr type [ajint] Prosite pattern compile type ** @attr plen [ajint] Prosite pattern length ** @attr buf [ajint*] Buffer for BMH search ** @attr off [struct EmbSPatBYPNode] Offset buffer for B-Y/P search ** @attr sotable [ajuint*] Buffer for SHIFT-OR ** @attr solimit [ajint] Limit for BMH search ** @attr m [ajint] Real length of pattern (from embPatGetType) ** @attr regex [AjPStr] PCRE regexp string ** @attr skipm [ajint**] Skip buffer for Tarhio-Ukkonen ** @attr amino [AjPBool] Must match left begin ** @attr carboxyl [AjPBool] Must match right ** @@ ******************************************************************************/ typedef struct EmbSPatComp { AjPStr pattern; ajint type; ajint plen; ajint* buf; EmbOPatBYPNode off[AJALPHA]; ajuint* sotable; ajuint solimit; ajint m; AjPStr regex; ajint** skipm; AjPBool amino; AjPBool carboxyl; } EmbOPatComp; #define EmbPPatComp EmbOPatComp* And functions for this would be: void embPatCompileII (EmbPPatComp thys); void embPatFuzzSearchII (EmbPPATComp thys, ajint begin, const AjPStr name, const AjPStr text, AjPList l, ajint mismatch, void** tidy); void embPatGetTypeII (EmbPPatComp thys, const AjPStr pattern, ajint mismatch, AjPBool protein); Any comments? Thanks, -- Henrikki Almusa From cavallo at biochem.ucl.ac.uk Fri Aug 6 13:17:05 2004 From: cavallo at biochem.ucl.ac.uk (Antonio Cavallo) Date: Fri, 06 Aug 2004 14:17:05 +0100 Subject: patch against 2.9.0 and c++ Message-ID: <411384D1.4050909@biochem.ucl.ac.uk> Hi, included in this message you can find a patch against the emboss 2.9.0. It fixes some mystyping that makes impossible to compile programs under c++. Mainly these are fixes for variables with a string name (in c++ a reserved keyword). regards, antonio cavallo ps. for any interested in it, there is a complete rpm file to use binaries under linux. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: EMBOSS-2.9.0-cplus.dif URL: From pmr at ebi.ac.uk Fri Aug 6 13:51:47 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 06 Aug 2004 14:51:47 +0100 Subject: patch against 2.9.0 and c++ In-Reply-To: <411384D1.4050909@biochem.ucl.ac.uk> References: <411384D1.4050909@biochem.ucl.ac.uk> Message-ID: <41138CF3.1080407@ebi.ac.uk> Antonio Cavallo wrote: > included in this message you can find a patch against the emboss 2.9.0. > It fixes some mystyping that makes impossible to compile > programs under c++. > Mainly these are fixes for variables with a string name (in c++ a > reserved keyword). Thanks. I have added these to the code documentation scripts (embossdoc.pl) although we don't check plplot with that. Most of the embest.h ones are obsolete - I have cleaned up the old est_genome definitions which removed all of the "string" variable names. What C++ compiler are you using (with what options) ? regards, Peter Rice From henrikki.almusa at helsinki.fi Mon Aug 9 06:13:21 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 9 Aug 2004 09:13:21 +0300 Subject: Fix couple of typos in ajax/ajstr Message-ID: <200408090913.21794.henrikki.almusa@helsinki.fi> Hello, Heres a small patch to fix typos in comments in ajstr.c and .h. These show up in srs and were somewhat confusing (atleast to me) :). Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_ajstr_typo.patch Type: text/x-diff Size: 1356 bytes Desc: not available URL: From henrikki.almusa at helsinki.fi Mon Aug 9 07:08:15 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 9 Aug 2004 10:08:15 +0300 Subject: Pattern lists (need help after 2.9.0) Message-ID: <200408091008.15538.henrikki.almusa@helsinki.fi> Hello, I've stumbled into a problem, when i changed the pattern lists to 2.9.0 from 2.8.0. I now get a core dump, when trying to use it from dreg. Attached are ajpat.c and ajpat.h which is the current situation with these. And dreg.c and dreg.acd diff, for the modifications on them to use the pattern lists. This is the stack trace that gdb gives for core dump. (gdb) info stack #0 0x40106b0d in ajListPushApp () from /work/hena/emboss-2.9.0/lib/libajax.so.0 #1 0x40158b3a in ajPatlistAdd () from /work/hena/emboss-2.9.0/lib/libajax.so.0 #2 0x401589da in ajPatlistParsePatternFile () from /work/hena/emboss-2.9.0/lib/libajax.so.0 #3 0x08049040 in main () #4 0x40466a67 in __libc_start_main () from /lib/i686/libc.so.6 Any help would be appreciated, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_dreg.plist.patch Type: text/x-diff Size: 2414 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.h Type: text/x-chdr Size: 2364 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.c Type: text/x-csrc Size: 7710 bytes Desc: not available URL: From henrikki.almusa at helsinki.fi Mon Aug 9 13:04:18 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 9 Aug 2004 16:04:18 +0300 Subject: Pattern lists (need help after 2.9.0) In-Reply-To: <200408091008.15538.henrikki.almusa@helsinki.fi> References: <200408091008.15538.henrikki.almusa@helsinki.fi> Message-ID: <200408091604.18704.henrikki.almusa@helsinki.fi> On Monday 09 August 2004 10:08, Henrikki Almusa wrote: > Hello, > > I've stumbled into a problem, when i changed the pattern lists to 2.9.0 > from 2.8.0. I now get a core dump, when trying to use it from dreg. > Attached are ajpat.c and ajpat.h which is the current situation with these. > And dreg.c and dreg.acd diff, for the modifications on them to use the > pattern lists. Figured this out already. Continuing on trying to allow fuzz(nuc|pro|tran) to use patternlists. After that I will post my code at that time and then need to do the acds properly. Thanks, -- Henrikki Almusa From henrikki.almusa at helsinki.fi Tue Aug 10 06:39:24 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 10 Aug 2004 09:39:24 +0300 Subject: Pattern lists Message-ID: <200408100939.24959.henrikki.almusa@helsinki.fi> Hello, I can finally report that I have succesfully tested the pattern list with dreg and fuzznuc. I will attach four files. Current version of ajpat.c and ajpat.h with comments. Patch which I used to test both dreg and fuzznuc. And patch to change 'nucleus/embpat.c' and 'nucleus/empat.h', which I have modified to allow prosite patterns to run as well. Now I have few questions about next part. 1. How to do the acd overloading. In my patch to dreg and fuzznuc, I used string and then did what was needed in program. This is not probably the correct way, but ok for testing. 2. Should I add a search function into pattern lists? This would allow fuzz(nuc|pro|tran) to run regular expression pattern as well (thus obsoleting dreg and preg). This change would also mean that patterns in files would need a attribute as well (value might a number or string). But this might cause confusion as mismatch values don't work with regexes (even though it would be there). 3. Is it ok to use '#include ../nucleus/emboss.h' in 'ajpat.c'? This was done as I needed functions from 'nucleus/embpat.h'. If not how this should be done then? 4. Any thing else that needs to be fixed for inclusion into emboss? Any namings or such? Note that to make the patches smaller, I didn't add whitespaces properly in front of the lines in dreg and fuzznuc patch. Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.c Type: text/x-csrc Size: 9326 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.h Type: text/x-chdr Size: 2961 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_dreg_fuzznuc_plist.patch Type: text/x-diff Size: 7544 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_embpat_plist.patch Type: text/x-diff Size: 10145 bytes Desc: not available URL: From P.Ernst at dkfz-heidelberg.de Tue Aug 10 09:18:58 2004 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Tue, 10 Aug 2004 11:18:58 +0200 (MEST) Subject: patch against 2.9.0 and c++ In-Reply-To: <41138CF3.1080407@ebi.ac.uk> Message-ID: To my knowledge "string" is NOT a reserved word in C++. You run only into problems, when copying the std:: namespace onto the Emboss namespace with "using namespace std;". >From "The C+ + Programming Language Third Edition: by Bjarne Stroustrup: You must either use the std:: prefix or make every name from std global (?8.2.3). For example: #include // make the standard string facilities accessible using namespace std; // make std names available without std:: prefix string s = "Ignorance is bliss!"; // ok: string is std::string It is generally in poor taste to dump every name from a namespace into the global namespace. [....] A using directive makes names from a namespace available almost as if they had been declared outside their namespace. Kind regards, Peter -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= On Fri, 6 Aug 2004, Peter Rice wrote: > Antonio Cavallo wrote: > > > included in this message you can find a patch against the emboss 2.9.0. > > It fixes some mystyping that makes impossible to compile > > programs under c++. > > Mainly these are fixes for variables with a string name (in c++ a > > reserved keyword). > > Thanks. I have added these to the code documentation scripts (embossdoc.pl) > although we don't check plplot with that. > > Most of the embest.h ones are obsolete - I have cleaned up the old est_genome > definitions which removed all of the "string" variable names. > > What C++ compiler are you using (with what options) ? > > regards, > > Peter Rice > > From gbottu at ben.vub.ac.be Tue Aug 10 11:02:15 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Tue, 10 Aug 2004 13:02:15 +0200 Subject: disappeared functons Message-ID: <20040810110215.GA27809@bigben.ulb.ac.be> Dear colleagues, I am installing EMBOSS 2.9.0 and I just noticed that the ajax functions ajSeqTypeNucS and ajSeqTypeProtS have disappeared, even if they are still mentioned in the on-line help in the HGMPRC Web pages. This is quite unconvenient for me, since I used them in a local developement. Was the removal of these functions intentional or accidental ? Sincerely, Guy Bottu, BEN From cavallo at biochem.ucl.ac.uk Tue Aug 10 12:00:34 2004 From: cavallo at biochem.ucl.ac.uk (Antonio Cavallo) Date: Tue, 10 Aug 2004 13:00:34 +0100 Subject: patch against 2.9.0 and c++ In-Reply-To: References: Message-ID: <4118B8E2.1080909@biochem.ucl.ac.uk> Peter Ernst wrote: > To my knowledge "string" is NOT a reserved word in C++. > You run only into problems, when copying the std:: namespace onto the > A using directive makes names from a namespace available almost as if > they had been declared outside their namespace. > A discussion about what is "standard" or "right" is not very helpful. A lot of c++ code is using string as reserved keyword (without std:: prefix), so it is safe to assume that is good practice to restrict the usage of the word "string" (like false or true): in EMBOSS there are only few lines (out of many many present) to be changed. "It is generally in poor taste", I will not argue about this point: one of the nice c++ features (namespaces) are there to prevent the name space pollution, althout too many layers of naming are confusing (two is considered good, three start to be too much). But let's face it. statements like: std::vector::iterator p; are not exactly good taste either;) regards, antonio From gbottu at ben.vub.ac.be Wed Aug 11 14:47:24 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 11 Aug 2004 16:47:24 +0200 Subject: question about behaviour of "toggle" Message-ID: <20040811144724.GA10004@bigben.ulb.ac.be> Dear colleagues, I am busy installing EMBOSS 2.9.0 and I noticed the following. The file iep.acd contains : toggle: report [ default: "Y" information: "Write results to a file" ] The command iep -help outputs : -report toggle Write results to a file Why not -[no]report ? Is this behaviour intended or is it a bug ? Sincerely, Guy Bottu BEN