From newsletter at prographicssportswear.com Sat Apr 3 09:25:13 2004 From: newsletter at prographicssportswear.com (newsletter at prographicssportswear.com) Date: Sat, 3 Apr 2004 09:25:13 -0500 Subject: Please forward this to your Spring Formal Chair Message-ID: <200404031425.i33EPD421884@www.prographicssportswear.com> You must use an HTML compliant E-Mail client to view this newsletter properly. http://www.prographicssportswear.com ------------- Click the link to unsubscribe: http://news.prographicssportswear.com/submit.php?id=30&le_email=emboss-dev at embnet.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040403/5821a052/attachment.html From d.counsell at rfcgr.mrc.ac.uk Tue Apr 6 08:58:01 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Tue, 6 Apr 2004 13:58:01 +0100 Subject: field-testing the jison-ware Message-ID: <20040406125801.GA3201@dev4.hgmp.mrc.ac.uk> EMBOSSnians! I have converted one of my two main programs to use Jon's newly organised structure code. There is a missing "!" in one of the public Cmap reading functions which means that it always turns a NULL instead of the object it's supposed to. I've fixed this and committed the change. The main private Cmap reading function will not return a NULL if the file it's reading is blank. I have now changed this so that it does so if the file contains no valid ID line. Let me know if this is not wise. One down; one to go. all the best Damian -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From mms-notifier at childrens.harvard.edu Fri Apr 9 13:53:59 2004 From: mms-notifier at childrens.harvard.edu (MMS Notifier) Date: Fri, 09 Apr 2004 13:53:59 -0400 Subject: MMS Notification Message-ID: <6C683CA44306163-01@MMS__childrens.harvard.edu_> Sender Note - Inbound Virus Found Attention: Children's Hospital detected a virus in a message you recently sent to our location. The infected message was quarantined and will not be delivered to the recipients at this organization. Please run an antivirus program immediately to scan your desktop for known viruses. After you have ensured that your desktop is virus-free, you can resend the message. If you need assistance, please contact your mail administrator. Virus information on this infected message follows: Virus Scanner found the W32/Netsky.c at MM virus in the attached file: story.com From henrikki.almusa at helsinki.fi Wed Apr 14 03:48:54 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 14 Apr 2004 09:48:54 +0200 Subject: Prophet & profit Message-ID: <200404051536.59051.henrikki.almusa@helsinki.fi> Hello, I was watching the outputs of prophet and profit and noticed that they seem to have their own respective outputs. After some check in code I noticed that Profit has its own function 'profit_printHits' and prophet uses some basic function 'embAlignPrintProfile'. Now to question. Is there some reason why they don't use AjPAlign and its functions (other than that it was created before the standard formats)? Would it be a good thing to try to make them use AjPAlign? Mainly i'm after the idea that one could use '-aformat' with prophet and profit. I might have time to take a look and see if I can fix this. I did some reading on code and noticed that embAlignReportProfile uses seqset and prophet doesn't read this in. So what is that seqset and why it is embAlingReportProfile and not in embAlingReport(Local|Global)? Can seqset be made, instead of read from file or would if be better to use embAlingReportLocal instead of embAlingReportProfile? Thanks, -- Henrikki Almusa From henrikki.almusa at helsinki.fi Wed Apr 14 10:07:31 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 14 Apr 2004 17:07:31 +0300 Subject: Prophet & profit In-Reply-To: <200404051536.59051.henrikki.almusa@helsinki.fi> References: <200404051536.59051.henrikki.almusa@helsinki.fi> Message-ID: <200404141707.31522.henrikki.almusa@helsinki.fi> On Wednesday 14 April 2004 10:48, Henrikki Almusa wrote: > I did some reading on code and noticed that embAlignReportProfile uses > seqset and prophet doesn't read this in. So what is that seqset and why it > is embAlingReportProfile and not in embAlingReport(Local|Global)? Can > seqset be made, instead of read from file or would if be better to use > embAlingReportLocal instead of embAlingReportProfile? Ok. After more checking it seems that one can only use embAlignReportProfile. Eg. not local as i meantioned above. But in profile there is that seqset that isn't used for anything. So basicly it might work, by giving a null seqset to it. I'm going to try that. -- Henrikki Almusa From henrikki.almusa at helsinki.fi Thu Apr 15 04:33:47 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Thu, 15 Apr 2004 11:33:47 +0300 Subject: Prophet & profit In-Reply-To: <200404051536.59051.henrikki.almusa@helsinki.fi> References: <200404051536.59051.henrikki.almusa@helsinki.fi> Message-ID: <200404151133.47416.henrikki.almusa@helsinki.fi> Hello, Heres a patch to prophet that i've figured out. But i seem to have a problem with it and can't figure out what that problem is. Basicly i've changed the embPrintProfile into embReportProfile. But for some reason it doesn't print the alignments. The align information should be there though, so one of the few things i can come up with is the empty seqset, but it isn't used in the embPrintProfile. The patch is attached. So what I'm doing wrong here? And how to fix this? Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: prophet.1.patch Type: text/x-diff Size: 9837 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040415/6ae1d76d/attachment.bin From henrikki.almusa at helsinki.fi Thu Apr 15 09:21:36 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Thu, 15 Apr 2004 16:21:36 +0300 Subject: Prophet & profit In-Reply-To: <200404151133.47416.henrikki.almusa@helsinki.fi> References: <200404051536.59051.henrikki.almusa@helsinki.fi> <200404151133.47416.henrikki.almusa@helsinki.fi> Message-ID: <200404151621.36965.henrikki.almusa@helsinki.fi> On Thursday 15 April 2004 11:33, Henrikki Almusa wrote: > Basicly i've changed the embPrintProfile into embReportProfile. But for > some reason it doesn't print the alignments. The align information should > be there though, so one of the few things i can come up with is the empty > seqset, but it isn't used in the embPrintProfile. The patch is attached. > > So what I'm doing wrong here? And how to fix this? Figured out why. The embAlignReportProfile doesn't actually do anything to AjPAling its given. So heres to patches (against 2.8.0). 1. patch is to change embAlignReportProfile to work similarly as embAlignReportLocal. I left out the matrix from it, as it doesn't really have proper matrix (AjPMatrixf) and it seems to work without it. I would prefer someone who knows more about these functions to tell, whether that is a good idea or not. 2. patch is then updated version of my earlier patch, which takes the modifications in embAlignReportProfile into account. Both patches still need to fix comments and such so, I'll fix them and submit if they are good otherwise. Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: profile_report.1.patch Type: text/x-diff Size: 4736 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040415/8cb734aa/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: prophet.2.patch Type: text/x-diff Size: 9525 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040415/8cb734aa/attachment-0001.bin From henrikki.almusa at helsinki.fi Fri Apr 16 04:59:08 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 16 Apr 2004 11:59:08 +0300 Subject: Prophet & profit In-Reply-To: <200404151621.36965.henrikki.almusa@helsinki.fi> References: <200404051536.59051.henrikki.almusa@helsinki.fi> <200404151133.47416.henrikki.almusa@helsinki.fi> <200404151621.36965.henrikki.almusa@helsinki.fi> Message-ID: <200404161159.08177.henrikki.almusa@helsinki.fi> On Thursday 15 April 2004 16:21, Henrikki Almusa wrote: > Both patches still need to fix comments and such so, I'll fix them and > submit if they are good otherwise. Note. There was a ';' missing from file embaln.h in patch (which causes it to fail compile). Added to this version. -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: profile_report.2.patch Type: text/x-diff Size: 4737 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040416/74a062cd/attachment.bin From newsletter at prographicssportswear.com Sat Apr 3 14:25:13 2004 From: newsletter at prographicssportswear.com (newsletter at prographicssportswear.com) Date: Sat, 3 Apr 2004 09:25:13 -0500 Subject: Please forward this to your Spring Formal Chair Message-ID: <200404031425.i33EPD421884@www.prographicssportswear.com> You must use an HTML compliant E-Mail client to view this newsletter properly. http://www.prographicssportswear.com ------------- Click the link to unsubscribe: http://news.prographicssportswear.com/submit.php?id=30&le_email=emboss-dev at embnet.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.counsell at rfcgr.mrc.ac.uk Tue Apr 6 12:58:01 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Tue, 6 Apr 2004 13:58:01 +0100 Subject: field-testing the jison-ware Message-ID: <20040406125801.GA3201@dev4.hgmp.mrc.ac.uk> EMBOSSnians! I have converted one of my two main programs to use Jon's newly organised structure code. There is a missing "!" in one of the public Cmap reading functions which means that it always turns a NULL instead of the object it's supposed to. I've fixed this and committed the change. The main private Cmap reading function will not return a NULL if the file it's reading is blank. I have now changed this so that it does so if the file contains no valid ID line. Let me know if this is not wise. One down; one to go. all the best Damian -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From mms-notifier at childrens.harvard.edu Fri Apr 9 17:53:59 2004 From: mms-notifier at childrens.harvard.edu (MMS Notifier) Date: Fri, 09 Apr 2004 13:53:59 -0400 Subject: MMS Notification Message-ID: <6C683CA44306163-01@MMS__childrens.harvard.edu_> Sender Note - Inbound Virus Found Attention: Children's Hospital detected a virus in a message you recently sent to our location. The infected message was quarantined and will not be delivered to the recipients at this organization. Please run an antivirus program immediately to scan your desktop for known viruses. After you have ensured that your desktop is virus-free, you can resend the message. If you need assistance, please contact your mail administrator. Virus information on this infected message follows: Virus Scanner found the W32/Netsky.c at MM virus in the attached file: story.com From henrikki.almusa at helsinki.fi Wed Apr 14 07:48:54 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 14 Apr 2004 09:48:54 +0200 Subject: Prophet & profit Message-ID: <200404051536.59051.henrikki.almusa@helsinki.fi> Hello, I was watching the outputs of prophet and profit and noticed that they seem to have their own respective outputs. After some check in code I noticed that Profit has its own function 'profit_printHits' and prophet uses some basic function 'embAlignPrintProfile'. Now to question. Is there some reason why they don't use AjPAlign and its functions (other than that it was created before the standard formats)? Would it be a good thing to try to make them use AjPAlign? Mainly i'm after the idea that one could use '-aformat' with prophet and profit. I might have time to take a look and see if I can fix this. I did some reading on code and noticed that embAlignReportProfile uses seqset and prophet doesn't read this in. So what is that seqset and why it is embAlingReportProfile and not in embAlingReport(Local|Global)? Can seqset be made, instead of read from file or would if be better to use embAlingReportLocal instead of embAlingReportProfile? Thanks, -- Henrikki Almusa From henrikki.almusa at helsinki.fi Wed Apr 14 14:07:31 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 14 Apr 2004 17:07:31 +0300 Subject: Prophet & profit In-Reply-To: <200404051536.59051.henrikki.almusa@helsinki.fi> References: <200404051536.59051.henrikki.almusa@helsinki.fi> Message-ID: <200404141707.31522.henrikki.almusa@helsinki.fi> On Wednesday 14 April 2004 10:48, Henrikki Almusa wrote: > I did some reading on code and noticed that embAlignReportProfile uses > seqset and prophet doesn't read this in. So what is that seqset and why it > is embAlingReportProfile and not in embAlingReport(Local|Global)? Can > seqset be made, instead of read from file or would if be better to use > embAlingReportLocal instead of embAlingReportProfile? Ok. After more checking it seems that one can only use embAlignReportProfile. Eg. not local as i meantioned above. But in profile there is that seqset that isn't used for anything. So basicly it might work, by giving a null seqset to it. I'm going to try that. -- Henrikki Almusa From henrikki.almusa at helsinki.fi Thu Apr 15 08:33:47 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Thu, 15 Apr 2004 11:33:47 +0300 Subject: Prophet & profit In-Reply-To: <200404051536.59051.henrikki.almusa@helsinki.fi> References: <200404051536.59051.henrikki.almusa@helsinki.fi> Message-ID: <200404151133.47416.henrikki.almusa@helsinki.fi> Hello, Heres a patch to prophet that i've figured out. But i seem to have a problem with it and can't figure out what that problem is. Basicly i've changed the embPrintProfile into embReportProfile. But for some reason it doesn't print the alignments. The align information should be there though, so one of the few things i can come up with is the empty seqset, but it isn't used in the embPrintProfile. The patch is attached. So what I'm doing wrong here? And how to fix this? Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: prophet.1.patch Type: text/x-diff Size: 9837 bytes Desc: not available URL: From henrikki.almusa at helsinki.fi Thu Apr 15 13:21:36 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Thu, 15 Apr 2004 16:21:36 +0300 Subject: Prophet & profit In-Reply-To: <200404151133.47416.henrikki.almusa@helsinki.fi> References: <200404051536.59051.henrikki.almusa@helsinki.fi> <200404151133.47416.henrikki.almusa@helsinki.fi> Message-ID: <200404151621.36965.henrikki.almusa@helsinki.fi> On Thursday 15 April 2004 11:33, Henrikki Almusa wrote: > Basicly i've changed the embPrintProfile into embReportProfile. But for > some reason it doesn't print the alignments. The align information should > be there though, so one of the few things i can come up with is the empty > seqset, but it isn't used in the embPrintProfile. The patch is attached. > > So what I'm doing wrong here? And how to fix this? Figured out why. The embAlignReportProfile doesn't actually do anything to AjPAling its given. So heres to patches (against 2.8.0). 1. patch is to change embAlignReportProfile to work similarly as embAlignReportLocal. I left out the matrix from it, as it doesn't really have proper matrix (AjPMatrixf) and it seems to work without it. I would prefer someone who knows more about these functions to tell, whether that is a good idea or not. 2. patch is then updated version of my earlier patch, which takes the modifications in embAlignReportProfile into account. Both patches still need to fix comments and such so, I'll fix them and submit if they are good otherwise. Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: profile_report.1.patch Type: text/x-diff Size: 4736 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: prophet.2.patch Type: text/x-diff Size: 9525 bytes Desc: not available URL: From henrikki.almusa at helsinki.fi Fri Apr 16 08:59:08 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 16 Apr 2004 11:59:08 +0300 Subject: Prophet & profit In-Reply-To: <200404151621.36965.henrikki.almusa@helsinki.fi> References: <200404051536.59051.henrikki.almusa@helsinki.fi> <200404151133.47416.henrikki.almusa@helsinki.fi> <200404151621.36965.henrikki.almusa@helsinki.fi> Message-ID: <200404161159.08177.henrikki.almusa@helsinki.fi> On Thursday 15 April 2004 16:21, Henrikki Almusa wrote: > Both patches still need to fix comments and such so, I'll fix them and > submit if they are good otherwise. Note. There was a ';' missing from file embaln.h in patch (which causes it to fail compile). Added to this version. -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: profile_report.2.patch Type: text/x-diff Size: 4737 bytes Desc: not available URL: