From autobuilder at derkholm.net Sun Feb 1 00:19:56 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Feb 1 00:27:49 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1075612796889.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040201 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From Mailer-Daemon at t-online.de Sun Feb 1 04:42:59 2004 From: Mailer-Daemon at t-online.de (Mail Delivery System) Date: Sun Feb 1 04:49:35 2004 Subject: [Biojava-dev] Mail delivery failed: returning message to sender Message-ID: <1AnE83-001iYgC@fwd08.aul.t-online.de> |------------------------- Failed addresses follow: ---------------------| unknown user / Teilnehmer 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igoFCzgOdQdGQoA+fYtbLyfvO/IrgDq5CUCKCIUeW7oaddUoXjXrBzoZ+7vt7Ah0BxbzBSoO9tkb yffRI1fSJ7ZH9fUQHXQxkPYl190MqotdDPi6EA+2OAId/EHXA2ZX/dZZQxxZRvu9wItNBMF1DTN1 2GOaQMxtIFLr9kkUm7vE0lldTURVDEOTilbi9tIBhIoIOgIYQULEUNFO4NsBAgorwV1wJHZo629s aQhuiXX4gD8Ao0itQ791zvc+Jg+FMbUkv4BZukYNIyNJRg++BD5/c88XNxFZXA6IRB3cQ0ag/db+ g/sPcuKAZAolyThN3Il/G99i+17cLxAxDImAOB9Moxs590rQdfAXT1oBRlkLlvt9D47OAFRqFChj +PbtUJOfPV2WIF3diBlBR/vi6xa43CVsCLRno7aIUA0pyH1r2O From autobuilder at derkholm.net Mon Feb 2 00:20:04 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Feb 2 00:28:17 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1075699207843.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040202 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Tue Feb 3 00:20:07 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Feb 3 00:28:18 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1075785609440.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040203 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/seq/io/GenEmblFeatureComparator.java * biojava-live/src/org/biojava/bio/seq/io/GenEmblPropertyComparator.java * biojava-live/src/org/biojava/bio/seq/io/SeqIOEventEmitter.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Wed Feb 4 00:20:08 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Feb 4 00:28:29 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1075872009045.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040204 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From kuan2000 at 21cn.com Wed Feb 4 00:58:26 2004 From: kuan2000 at 21cn.com (kuan2000@21cn.com) Date: Wed Feb 4 01:06:04 2004 Subject: [Biojava-dev] 3721 Message-ID: <200402040606.i1465xHI015192@portal.open-bio.org> http://www.panyu.net.cn From MAILER-DAEMON at aol.com Wed Feb 4 10:17:22 2004 From: MAILER-DAEMON at aol.com (Mail Delivery Subsystem) Date: Wed Feb 4 10:32:33 2004 Subject: [Biojava-dev] Mail Delivery Problem Message-ID: <200402041023.740210e7e2da@omr-d05.mx.aol.com> Your mail to the following recipients could not be delivered because they are not accepting mail from biojava-dev@biojava.org: debby From kdj at sanger.ac.uk Wed Feb 4 10:42:02 2004 From: kdj at sanger.ac.uk (Keith James) Date: Wed Feb 4 10:48:10 2004 Subject: [Biojava-dev] test harness failure Message-ID: I'm using the latest JUnit (3.8.1) and Ant 1.5.4 I get this from ant runtests: build.xml:642: The task doesn't support the "reloading" attribute. If I remove the reloading attribute then I can run a few tests, until I run out of memory. What versions support the reloading attribute? cheers, Keith -- - Keith James Microarray Facility, Team 65 - - The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK - From td2 at sanger.ac.uk Wed Feb 4 10:50:31 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Wed Feb 4 10:56:40 2004 Subject: [Biojava-dev] test harness failure In-Reply-To: References: Message-ID: <20040204155031.GD52606@jabba.sanger.ac.uk> On Wed, Feb 04, 2004 at 03:42:02PM +0000, Keith James wrote: > > I'm using the latest JUnit (3.8.1) and Ant 1.5.4 > > I get this from ant runtests: > > build.xml:642: The task doesn't support the "reloading" > attribute. > > If I remove the reloading attribute then I can run a few tests, until > I run out of memory. What versions support the reloading attribute? It was added in ant 1.6.0 If you want to carry on using an old version of ant, or if you want to make sure every test runs completely independantly from all the others, you can use the "runtests-fork" target, which does essentially the same thing as the old "runtests". In general, I'd recommend upgrading to and 1.6.0, though -- you'll find the tests run much faster (generally at least a factor of 2). Thomas. From Jonathan.Warren at agresearch.co.nz Tue Feb 3 21:04:45 2004 From: Jonathan.Warren at agresearch.co.nz (Warren, Jonathan) Date: Wed Feb 4 22:36:16 2004 Subject: [Biojava-dev] Isoelectric point calculation alteration?? Message-ID: Hi I've used the proteomics package in biojava recently and found that the source code I had hasn't been modified since this mail in July last year http://www.biojava.org/pipermail/biojava-dev/2003-July/000744.html maybe someone could check that it has been changed as I can't easily access CVS through our security Important part of message here - relates to IsoelectricPointCalc.java : You're right. The problem is actually in the choice of bounds I used. It expects an answer between 1-13 for pI. In this case, the answer is probably beyond 13. I suggest using:- double pI = BinarySearch.solve(0.3, 13.7, 0.001, computeObj); That's one heck of a basic protein ;-) Regards, David Huen Jonathan Warren ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at group.novartis.com Wed Feb 4 22:42:10 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed Feb 4 22:45:09 2004 Subject: [Biojava-dev] Isoelectric point calculation alteration?? Message-ID: Hi Jonathan - The last change was on Tue Jul 22 17:03:20 2003 it extended the search range to catch extreme pI values. - Mark "Warren, Jonathan" Sent by: biojava-dev-bounces@portal.open-bio.org 02/04/2004 10:04 AM To: cc: Subject: [Biojava-dev] Isoelectric point calculation alteration?? Hi I've used the proteomics package in biojava recently and found that the source code I had hasn't been modified since this mail in July last year http://www.biojava.org/pipermail/biojava-dev/2003-July/000744.html maybe someone could check that it has been changed as I can't easily access CVS through our security Important part of message here - relates to IsoelectricPointCalc.java : You're right. The problem is actually in the choice of bounds I used. It expects an answer between 1-13 for pI. In this case, the answer is probably beyond 13. I suggest using:- double pI = BinarySearch.solve(0.3, 13.7, 0.001, computeObj); That's one heck of a basic protein ;-) Regards, David Huen Jonathan Warren ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at group.novartis.com Wed Feb 4 22:47:19 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed Feb 4 22:50:19 2004 Subject: [Biojava-dev] CE trace editor Message-ID: Hi Gustavo - There is an example of how to read one of these files with biojava at http://www.biojava.org/docs/bj_in_anger/abi2seq.htm You can also use the org.biojava.bio.gui.sequence.AbiTraceRenderer as a gui component to display them. Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 1 Science Park Road #04-14 The Capricorn Singapore 117528 phone +65 6722 2973 fax +65 6722 2910 "Gustavo Seluja" Sent by: biojava-dev-bounces@portal.open-bio.org 01/28/2004 05:00 AM To: cc: Subject: [Biojava-dev] CE trace editor Hi, I am looking for a Java tool that can display trace files (electropherograms) of ABI files. How do I search your site for such? Do you know of anything like it? Thanks! Gustavo ------------------------------------------------- Gustavo Seluja, MSc Project Manager & Principal Investigator Datect LLC 2935 Rodeo Park Drive East Santa Fe, NM 87505 Phone: 505-995-4488 Fax: 505-995-4490 Email: seluja@datect.com http://www.datect.com _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From autobuilder at derkholm.net Thu Feb 5 00:20:04 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Feb 5 00:28:10 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1075958407879.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040205 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/seq/io/SeqIOTools.java * biojava-live/tests/org/biojava/bio/seq/io/SeqIOToolsTest.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From meloan at sbcglobal.net Thu Feb 5 00:35:01 2004 From: meloan at sbcglobal.net (Steven Meloan) Date: Thu Feb 5 00:42:05 2004 Subject: [Biojava-dev] Seeking info on users of BioJava. Message-ID: Hi, I'm gathering information for a possible article about BioJava, for Sun Microsystems' Web site. I'm curious as to how many people are using it, at what institutions/companies, and in what countries. I'm also curious as to whether it's being used in a sanctioned fashion, or simply by individuals who prefer it over other facilities. Any info would be greatly appreciated! Thanks, Steve From mark.schreiber at group.novartis.com Thu Feb 5 02:48:21 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Thu Feb 5 02:51:21 2004 Subject: [Biojava-dev] Seeking info on users of BioJava. Message-ID: Hi Steven, Hard to know how many users there are. Thomas Down might be able to tell you how many downloads we get (which may not be strongly correlated with actual users). There is a mix of commercial and academic users. I know of users in: UK USA Canada France Spain Germany Switzerland India Singapore China Japan Australia New Zealand There are over 1000 classes contributed by 35+ authors. There are 5 or 6 people who are most active in development. Most of the orginal code base was developed by Matthew Pocock and Thomas Down about 5 years ago (wow was it really that long ago!). It is distributed under the LGPL license. The last stable release was 1.3.1, there is also a live version from CVS. BioJava is affiliated with the Open-Bioinformatics foundation (OBF) and cooperates with the other Bio* projects (BioPerl, BioPython, BioRuby etc). Useful weblinks: www.biojava.org www.open-bio.org http://www.biojava.org/docs/bj_in_anger/ (cookbook style documentation with french, chinese and japanese translations). Hope this helps, Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 1 Science Park Road #04-14 The Capricorn Singapore 117528 phone +65 6722 2973 fax +65 6722 2910 Steven Meloan Sent by: biojava-dev-bounces@portal.open-bio.org 02/05/2004 01:35 PM To: biojava-dev@biojava.org cc: Subject: [Biojava-dev] Seeking info on users of BioJava. Hi, I'm gathering information for a possible article about BioJava, for Sun Microsystems' Web site. I'm curious as to how many people are using it, at what institutions/companies, and in what countries. I'm also curious as to whether it's being used in a sanctioned fashion, or simply by individuals who prefer it over other facilities. Any info would be greatly appreciated! Thanks, Steve _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From thomas at derkholm.net Thu Feb 5 08:29:54 2004 From: thomas at derkholm.net (Thomas Down) Date: Thu Feb 5 08:38:46 2004 Subject: [Biojava-dev] Java news Message-ID: <20040205132954.GB3729@firechild> It's that time again: http://java.sun.com/j2se/1.5.0/index.jsp Betas seem to be available for all the platforms which Sun support. I'm hoping that Apple might come up with one soon, too, but given that they just released 1.4.2 a couple of days ago, I'm not so sure... Thomas. From Mailer-Daemon at vasoftware.com Thu Feb 5 08:39:48 2004 From: Mailer-Daemon at vasoftware.com (Mail Delivery System) Date: Thu Feb 5 08:45:56 2004 Subject: [Biojava-dev] Mail delivery failed: returning message to sender Message-ID: This message was created automatically by mail delivery software. A message that you sent could not be delivered to one or more of its recipients. This is a permanent error. The following address(es) failed: jim@users.sourceforge.net SMTP error from remote mailer after end of data: host mail.sourceforge.net [66.35.250.206]: 550-For the time being, we are blocking all mail with the .zip extentsion. If 550 this this is a problem, please open a Support Request on the SF.net webite. ------ This is a copy of the message, including all the headers. ------ ------ The body of the message is 31099 characters long; only the first ------ 16384 or so are included here. 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To be removed, this url will take you there: link From heuermh at acm.org Thu Feb 5 17:51:26 2004 From: heuermh at acm.org (Michael Heuer) Date: Thu Feb 5 17:56:07 2004 Subject: [biojava-dev] a bit offtopic: javac 1.5 & generics In-Reply-To: Message-ID: Hello, With the new beta release of the java 1.5 SDK and tools [1-3] I've been working on adding generics support to one of my projects: > http://sf.net/projects/vocabulary $ cvs co -r ADDING_JAVA1_5_GENERICS_BRANCH dsh-vocabulary I'm a little bit confused by a couple of things. How would you use the wrapper classes in Collections with type safety? ex. Set foos = new HashSet(); Set emptyFoos = Collections.EMPTY_SET; Set unmodifiableFoos = Collections.unmodifiableSet(foos); This compiles but gives me warnings about unchecked assignments. Can I just cast the EMPTY_SET? What about the wrapper class returned by unmodifiableSet? michael [1] j2sdk v1.5.0-beta, http://java.sun.com/j2se/1.5.0/download.jsp [2] ant v1.6.1beta1, http://ant.apache.org [3] maven v1.0-rc1-SNAPSHOT, http://maven.apache.org From heuermh at acm.org Thu Feb 5 18:44:36 2004 From: heuermh at acm.org (Michael Heuer) Date: Thu Feb 5 18:55:21 2004 Subject: [biojava-dev] a bit offtopic: javac 1.5 & generics In-Reply-To: Message-ID: Guess I should have read this paper before I began Adding Wildcards to the Java Programming Language > http://www.bracha.org/wildcards.pdf but in short, this works Set foos = new HashSet(); Set unmodifiableFoos = (Set) Collections.unmodifiableSet(foos); and this does not Set emptyFoos = (Set) Collections.EMPTY_SET; I do like the new enhanced for loops, instead of for (Iterator i = foos.iterator(); i.hasNext(); ) { Foo f = (Foo) i.next(); ... you just write for (Foo f : foos) { ... For fun I'm going to try a keyword-enum-based instead of Bloch-style Enum class-based version of the static alphabet codebase I posted earlier. michael On Thu, 5 Feb 2004, Michael Heuer wrote: > Hello, > > With the new beta release of the java 1.5 SDK and tools [1-3] I've been > working on adding generics support to one of my projects: > > > http://sf.net/projects/vocabulary > > $ cvs co -r ADDING_JAVA1_5_GENERICS_BRANCH dsh-vocabulary > > > I'm a little bit confused by a couple of things. How would you use the > wrapper classes in Collections with type safety? > > ex. > > Set foos = new HashSet(); > > Set emptyFoos = Collections.EMPTY_SET; > > Set unmodifiableFoos = Collections.unmodifiableSet(foos); > > > This compiles but gives me warnings about unchecked assignments. Can I > just cast the EMPTY_SET? What about the wrapper class returned by > unmodifiableSet? > > michael > > > [1] j2sdk v1.5.0-beta, http://java.sun.com/j2se/1.5.0/download.jsp > [2] ant v1.6.1beta1, http://ant.apache.org > [3] maven v1.0-rc1-SNAPSHOT, http://maven.apache.org > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From autobuilder at derkholm.net Fri Feb 6 00:20:05 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Feb 6 00:28:12 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076044807941.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040206 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From matthew_pocock at yahoo.co.uk Fri Feb 6 06:18:41 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri Feb 6 06:26:10 2004 Subject: [biojava-dev] a bit offtopic: javac 1.5 & generics In-Reply-To: References: Message-ID: <40237811.9010808@yahoo.co.uk> Hi, I've not used the generics in anger yet, but can you not use something like: Set emptyFoos = Collections.EMPTY_SET; I'm assuming that Collections is a templated class, and that I've chosen the right syntax, but this is Sun, after all. M From thomas at derkholm.net Fri Feb 6 07:16:40 2004 From: thomas at derkholm.net (Thomas Down) Date: Fri Feb 6 07:24:47 2004 Subject: [biojava-dev] a bit offtopic: javac 1.5 & generics In-Reply-To: References: Message-ID: <20040206121640.GA5688@firechild> Once upon a time, Michael Heuer wrote: > > Guess I should have read this paper before I began > > Adding Wildcards to the Java Programming Language > > http://www.bracha.org/wildcards.pdf > > > but in short, this works > > Set foos = new HashSet(); > > Set unmodifiableFoos = (Set) Collections.unmodifiableSet(foos); > > and this does not > > Set emptyFoos = (Set) Collections.EMPTY_SET; No, that doesn't work :-(. You can, however, do: Set emptyFoos = Collections.emptySet(); Better than nothing, anyway. Thomas. From MAILER-DAEMON at mail.bluegravity.com Fri Feb 6 12:23:42 2004 From: MAILER-DAEMON at mail.bluegravity.com (MAILER-DAEMON@mail.bluegravity.com) Date: Fri Feb 6 12:29:50 2004 Subject: [Biojava-dev] failure notice Message-ID: <200402061729.i16HTjHI020140@portal.open-bio.org> Hi. This is the qmail-send program at mail.bluegravity.com. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : user is over quota --- Below this line is a copy of the message. 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AAAAAAAAAAAAAAAAAA== ------=_NextPart_000_0008_65A96708.C4466116-- From PTGadmin at ventersciencejtc.org Fri Feb 6 12:27:49 2004 From: PTGadmin at ventersciencejtc.org (PTGadmin@ventersciencejtc.org) Date: Fri Feb 6 12:33:43 2004 Subject: [Biojava-dev] Symantec AVF detected an unrepairable virus in a message in your mailbox Message-ID: <00e501c3ecd6$8ade8060$4914a8c0@JCVSF.Corp> Location of the infected item: Rusch, Doug/biojava Sender of the infected item: biojava-dev-request@portal.open-bio.org Subject of the message: biojava-dev Digest, Vol 14, Issue 4 The attachment "Message Body" was Quarantined for the following reasons: The file was unrepairable. Virus Info: Virus W32.Mydoom.A@mm.enc was found. From heuermh at acm.org Fri Feb 6 16:48:59 2004 From: heuermh at acm.org (Michael Heuer) Date: Fri Feb 6 16:53:41 2004 Subject: [biojava-dev] a bit offtopic: javac 1.5 & generics In-Reply-To: <20040206121640.GA5688@firechild> Message-ID: Thanks to everyone for the help. To summarize what I've found, given Set foos = new HashSet(); this works because foos is already templated Set unmodifiableFoos = Collections.unmodifiableSet(foos); the cast here is fine but unnecessary Set unmodifiableFoos = (Set) Collections.unmodifiableSet(foos); this syntax also works but is unnecessary Set unmodifiableFoos = Collections.unmodifiableSet(foos); gives an unchecked assignment warning Set emptyFoos = Collections.EMPTY_SET; gives an unchecked cast warning Set emptyFoos = (Set) Collections.EMPTY_SET; illegal expression Set emptyFoos = Collections.EMPTY_SET; ok Set emptyFoos = Collections.emptySet(); compile error, found Set required Set Set emptyFoos = (Set) Collections.emptySet(); ok Set emptyFoos = Collections.emptySet(); michael On Fri, 6 Feb 2004, Thomas Down wrote: > Once upon a time, Michael Heuer wrote: > > > > Guess I should have read this paper before I began > > > > Adding Wildcards to the Java Programming Language > > > http://www.bracha.org/wildcards.pdf > > > > > > but in short, this works > > > > Set foos = new HashSet(); > > > > Set unmodifiableFoos = (Set) Collections.unmodifiableSet(foos); > > > > and this does not > > > > Set emptyFoos = (Set) Collections.EMPTY_SET; > > No, that doesn't work :-(. > > You can, however, do: > > Set emptyFoos = Collections.emptySet(); > > Better than nothing, anyway. > > Thomas. > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From autobuilder at derkholm.net Sat Feb 7 00:20:06 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Feb 7 00:28:15 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076131207971.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040207 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From delivery at hosyou.mine.nu Sat Feb 7 02:50:29 2004 From: delivery at hosyou.mine.nu (=?ISO-2022-JP?B?GyRCIzNAaUt8MV8wSj5lJE8+WjVyTS0lUyU4JU0lORsoQg==?= =?ISO-2022-JP?B?GyRCJEcbKEI=?=) Date: Sat Feb 7 03:05:02 2004 Subject: [Biojava-dev] =?iso-2022-jp?b?GyRCTCQ+NUJ6OS05cCF2IzIyLyEiGyhC?= =?iso-2022-jp?b?GyRCIzMyLyEiIzUyLyM5QGlLfDFfPH1GfjxUJCxCMz1QGyhC?= =?iso-2022-jp?b?GyRCJDckRiQkJF4kOSEjGyhC?= Message-ID: <20040207075856470.00000.0.delivery@PC101.192.168.1.80> ?? ?????????????????????????? ???????????????????? http://www.hosyou.net/cgi-bin/postmail/teishi.html ??????????????? *==* ??? ==*==*====**==**==??????????=*==*==*==*==*???????? ??????????????????????????? ?????????????????????????????????? ????????????????????????????????????!! ????????????????????????? ???????????????????????????????? ??????????????????????????????? ?????????????????????????????? ??????????????????????????????? ??????????????????????????????? ?????????????????????????????? ?????????http://www.hosyou.net/????????????? ????? From autobuilder at derkholm.net Sun Feb 8 00:20:07 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Feb 8 00:28:20 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076217610398.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040208 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Mon Feb 9 00:20:02 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Feb 9 00:28:20 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076304007599.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040209 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/tests/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Tue Feb 10 00:20:12 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Feb 10 00:28:33 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076390417095.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040210 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From MAILER-DAEMON at pimail.pi-india.net Wed Feb 11 00:13:45 2004 From: MAILER-DAEMON at pimail.pi-india.net (MAILER-DAEMON@pimail.pi-india.net) Date: Tue Feb 10 23:47:39 2004 Subject: [Biojava-dev] failure notice Message-ID: <200402110447.i1B4lS6I019791@portal.open-bio.org> Hi. This is the qmail-send program at pimail.pi-india.net. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : 144.32.128.247 does not like recipient. Remote host said: 553 5.3.0 ... User not known Giving up on 144.32.128.247. --- Below this line is a copy of the message. 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eQm4A4uCYINgD93TkH2fD9Xijn2fat1vn30BwwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAA ------=_NextPart_000_0011_0D1BFB6C.85E503CF-- From autobuilder at derkholm.net Wed Feb 11 00:20:05 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Feb 11 00:28:26 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076476808878.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040211 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Thu Feb 12 00:20:03 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Feb 12 00:28:28 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076563208028.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040212 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/program/xff/FeatureHandler.java * biojava-live/src/org/biojava/bio/program/xff/XFFFeatureSetHandler.java * biojava-live/src/org/biojava/bio/seq/impl/SimpleFeature.java * biojava-live/src/org/biojava/bio/seq/impl/SubSequence.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Fri Feb 13 00:20:04 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Feb 13 00:29:02 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076649609413.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040213 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java * biojava-live/src/org/biojava/bio/seq/db/biosql/DBHelper.java * biojava-live/src/org/biojava/bio/seq/db/biosql/HypersonicDBHelper.java * biojava-live/src/org/biojava/bio/seq/db/biosql/OntologySQL.java * biojava-live/src/org/biojava/bio/seq/db/biosql/OracleDBHelper.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Sat Feb 14 00:20:11 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Feb 14 00:29:34 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076736011759.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040214 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From MRBATESALAN at netscape.net Sat Feb 14 21:59:48 2004 From: MRBATESALAN at netscape.net (MRBATESALAN@netscape.net) Date: Sun Feb 15 00:10:07 2004 Subject: [Biojava-dev] REPLY SOON Message-ID: <60BE2425.69DA962@netscape.net> Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer as you can see in the picture in your attachment. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From autobuilder at derkholm.net Sun Feb 15 00:20:04 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Feb 15 00:28:37 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076822409555.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040215 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Mon Feb 16 00:20:04 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Feb 16 00:28:37 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076908807610.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040216 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Tue Feb 17 00:20:05 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Feb 17 00:28:40 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1076995207182.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040217 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From len at reeltwo.com Tue Feb 17 14:29:03 2004 From: len at reeltwo.com (Len Trigg) Date: Tue Feb 17 14:35:31 2004 Subject: [Biojava-dev] Lazy BioSQL ontology loading? Message-ID: <40326B7F.9080001@reeltwo.com> Hi guys, A while ago when the ontology stuff had those major updates I remember having to go through a procedure to migrate my existing biosql databases to comply with the new ontology handling. A few days ago when I tried out the current biojava code on my databases, it died with the following complaint about a particular ontology term not being present in the database. I presume this may be because something changed in the grammar and that I need to repeat the ontology import procedure? Exception in thread "main" java.util.NoSuchElementException: No term named 'and(_r:89(_x:89, _y:89), _r:89(_y:89, _z:89))' at org.biojava.ontology.Ontology$Impl.getTerm(Ontology.java:275) at org.biojava.bio.seq.db.biosql.OntologySQL.blessExternal(OntologySQL.java:321) at org.biojava.bio.seq.db.biosql.OntologySQL.loadTerms(OntologySQL.java:314) at org.biojava.bio.seq.db.biosql.OntologySQL.(OntologySQL.java:360) at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:235) at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.(BioSQLSequenceDB.java:164) Loading this ontology is actually relatively time consuming, and since my current applications don't even use ontologies (well, other than __biojava_guano), I was thinking about making the ontology loading lazy. This would reduce the startup time of my apps as well as providing some protection against grammar changes. Does anyone have any thoughts about potential pitfalls? Cheers, Len From simon.foote at nrc-cnrc.gc.ca Tue Feb 17 14:48:03 2004 From: simon.foote at nrc-cnrc.gc.ca (Simon Foote) Date: Tue Feb 17 14:54:30 2004 Subject: [Biojava-dev] Lazy BioSQL ontology loading? In-Reply-To: <40326B7F.9080001@reeltwo.com> References: <40326B7F.9080001@reeltwo.com> Message-ID: <40326FF3.6010602@nrc-cnrc.gc.ca> Hi Len, I agree with you here. I just ran into the same problem with the ontologies and BioSQL. I think the core ontology could be lazily loaded if necessary, because as you noted, it isn't currently used. We should still load the __biojava_guano on instantiation as it is used. Simon Len Trigg wrote: >Hi guys, > >A while ago when the ontology stuff had those major updates I remember >having to go through a procedure to migrate my existing biosql databases >to comply with the new ontology handling. > >A few days ago when I tried out the current biojava code on my >databases, it died with the following complaint about a particular >ontology term not being present in the database. I presume this may be >because something changed in the grammar and that I need to repeat the >ontology import procedure? > >Exception in thread "main" java.util.NoSuchElementException: No term >named 'and(_r:89(_x:89, _y:89), _r:89(_y:89, _z:89))' > at org.biojava.ontology.Ontology$Impl.getTerm(Ontology.java:275) > at >org.biojava.bio.seq.db.biosql.OntologySQL.blessExternal(OntologySQL.java:321 >) > at >org.biojava.bio.seq.db.biosql.OntologySQL.loadTerms(OntologySQL.java:314) > at >org.biojava.bio.seq.db.biosql.OntologySQL.(OntologySQL.java:360) > at >org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java: >235) > at >org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.(BioSQLSequenceDB.java: >164) > > >Loading this ontology is actually relatively time consuming, and since >my current applications don't even use ontologies (well, other than >__biojava_guano), I was thinking about making the ontology loading lazy. >This would reduce the startup time of my apps as well as providing some >protection against grammar changes. Does anyone have any thoughts about >potential pitfalls? > > > >Cheers, >Len >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > -- Bioinformatics Programmer Pathogen Genomics Institute for Biological Sciences National Research Council of Canada [T] 613-990-0561 [F] 613-952-9092 simon.foote@nrc-cnrc.gc.ca From len at reeltwo.com Tue Feb 17 22:53:50 2004 From: len at reeltwo.com (Len Trigg) Date: Tue Feb 17 23:00:14 2004 Subject: [Biojava-dev] Lazy BioSQL ontology loading? In-Reply-To: <40326FF3.6010602@nrc-cnrc.gc.ca> References: <40326B7F.9080001@reeltwo.com> <40326FF3.6010602@nrc-cnrc.gc.ca> Message-ID: Simon Foote wrote: > I agree with you here. I just ran into the same problem with the > ontologies and BioSQL. > I think the core ontology could be lazily loaded if necessary, because > as you noted, it isn't currently used. > > We should still load the __biojava_guano on instantiation as it is used. I just committed the changes to make ontology loading lazy. the __biojava_guano ontology is loaded immediately. My BioSQL apps now run happily again. It'd be nice if people who use Ontologies with BioSQL could give it a quick run. Cheers, Len. From autobuilder at derkholm.net Wed Feb 18 00:20:03 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Feb 18 00:29:19 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077081609720.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040218 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/seq/db/biosql/OntologySQL.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Thu Feb 19 00:20:04 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Feb 19 00:30:47 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077168010969.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040219 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From len at reeltwo.com Thu Feb 19 16:46:15 2004 From: len at reeltwo.com (Len Trigg) Date: Thu Feb 19 16:52:53 2004 Subject: [Biojava-dev] Frederik Decouttere's BioSQL/Ontology bug Message-ID: I have looked into the previously mentioned problem with Ontologies in the BioSQL binding. It boils down to the fact that each BioSQLSequenceDB has it's own copy of the ontologies contained in the database, and since it's possible to have more than one BioSQLSequenceDB pointing at the database (e.g.: each corresponding to a different biodatabase), they get their own Ontology handling. Frederik's problem arose when his code ended up inserting a term via one BioSQLSequenceDB, and then attempting to insert again via the second BioSQLSequenceDB (which wasn't aware of the first set of ontology changes). This was then caught by the database constraints. Dealing with two separate BioSQLSequenceDB's in the same database at the same time certainly doesn't seem unreasonable (some of my apps do it, and it's probably only chance that I haven't bumped into the problem myself). What I have done is basically the simplest thing that would work: OntologySQL now has a static method that BioSQLSequenceDB's use to request an OntologySQL object. This method uses a static hashmap that is keyed off the DataSource to return the appropriate OntologySQL object. Now the two BioSQLSequenceDB's end up sharing the same OntologySQL object and things are basically fine. There are a couple of minor issues though. The first is that in order to use the DataSource as a key, I've extended the PoolingDataSource to use the database url and username as the basis for equals and hashcode. The Ontology retrieval won't work if you create BioSQLSequenceDB's with other DataSources, or if the DataSource somehow begins to point to another database (the javadocs for DataSource alluded to this somehow being possible). I imagine that neither of these will actually be a problem in practise. The other issue is that the cache of OntologySQL's can under come circumstances become invalid -- this happened in the unit tests when the database was entirely removed between unit tests! :-). To get around this (pretty unreasonable really) behaviour, I just added a package level method to clear the cache, just for use by the tests. If this all sounds OK, I'll check in the changes. I'll also take no response as approval :-) Cheers, Len. From autobuilder at derkholm.net Fri Feb 20 00:20:07 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Feb 20 00:29:52 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077254412025.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040220 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Sat Feb 21 00:20:08 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Feb 21 00:29:23 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077340809219.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040221 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Sun Feb 22 00:20:04 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Feb 22 00:29:25 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077427207426.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040222 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From MRBATESALANN at netscape.net Sun Feb 22 10:47:11 2004 From: MRBATESALANN at netscape.net (MRBATESALANN@netscape.net) Date: Sun Feb 22 10:55:51 2004 Subject: [Biojava-dev] REPLY SOON Message-ID: Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From autobuilder at derkholm.net Mon Feb 23 00:20:03 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Feb 23 00:29:32 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077513609413.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040223 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From MRBATESALAN at netscape.net Mon Feb 23 08:26:49 2004 From: MRBATESALAN at netscape.net (MRBATESALAN@netscape.net) Date: Mon Feb 23 08:41:02 2004 Subject: [Biojava-dev] REPLY SOON Message-ID: Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From mark.schreiber at group.novartis.com Mon Feb 23 22:15:26 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Mon Feb 23 22:18:08 2004 Subject: [Biojava-dev] Rationalisation Message-ID: As you all know biojava is quite big. It currently splits itself into two jar files (biojava.jar and grammars.jar) or three if you include the bytecode.jar. There have been suggestions of splitting it into subprojects. One obvious place for a split would be biojava.jar and grammars.jar. The ant build already achieves this artificially by splitting the code base in two. Would it be sensible to give grammars it's own cvs home? Other possible splits: demos doclets apps My reasoning is as follows. Projects should be merged where components have a high level of two way dependency and seperated where there is only one way dependency. For example biojava depends heavily on grammars.jar but grammars.jar doesn't care too much about the core of biojava. Demos and apps are dependent on biojava but the reverse is not at all true. The doclets project is a nice add on but they are pretty indenpendent of each other. My feeling is that this would make management of the project much easier and ant scripts simpler. Any thoughts or flames?? - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 1 Science Park Road #04-14 The Capricorn Singapore 117528 phone +65 6722 2973 fax +65 6722 2910 From autobuilder at derkholm.net Tue Feb 24 00:20:06 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Feb 24 00:29:33 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077600010579.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040224 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java * biojava-live/src/org/biojava/bio/seq/db/biosql/OntologySQL.java * biojava-live/src/org/biojava/utils/JDBCPooledDataSource.java * biojava-live/tests/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From mark.schreiber at group.novartis.com Tue Feb 24 00:37:53 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Feb 24 00:40:35 2004 Subject: [Biojava-dev] Gaps and EmptyAlphabet Message-ID: The gap symbol getMatches method returns the EmptyAlphabet. This has the slightly weird result that the gap symbol doesn't match itself!? I'm sure Bertrand Russell could write a book on that. I just think it's plain weird. Wouldn't it be better if the getMatches for a gap returned an FiniteAlphabet containing only the gap symbol?? - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 1 Science Park Road #04-14 The Capricorn Singapore 117528 phone +65 6722 2973 fax +65 6722 2910 From td2 at sanger.ac.uk Tue Feb 24 04:24:23 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Tue Feb 24 04:30:35 2004 Subject: [Biojava-dev] Rationalisation In-Reply-To: References: Message-ID: <3BC04372-66AB-11D8-9672-000A95C8B056@sanger.ac.uk> On 24 Feb 2004, at 03:15, mark.schreiber@group.novartis.com wrote: > As you all know biojava is quite big. It currently splits itself into > two > jar files (biojava.jar and grammars.jar) or three if you include the > bytecode.jar. > > There have been suggestions of splitting it into subprojects. One > obvious > place for a split would be biojava.jar and grammars.jar. The ant build > already achieves this artificially by splitting the code base in two. > Would it be sensible to give grammars it's own cvs home? Actually, I think grammars.jar is probably a bad example: it was only being produced as a separate jar file for the convenience of the build process. This got fixed in the build.xml clean up a month or so back: if you've still got a separate grammars.jar file lying around, it's from an old build and you should probably get rid of it. Unless there's someone who seriously wants to use the grammars without the rest of biojava, I'd vote to keep them in their current place. On the other hand... > Other possible splits: > > demos > doclets > apps Yes, all of these are possibilities. Any taglets we use which might be of general interest should probably go to a general-purpose hosting site like jakarta. Splitting the demos out it an interesting idea since it means that users have the option to download them without grabbing the complete (big!) biojava-live tree. We should do this iff: - It makes the demos more, not less, visible to users (and core developers). - We can make sure they stay in sync with the core API (I can probably solve this one by adding them to the Autobuilder). Another possible split, which has been talked about for a long time but never really happened is to separate out "general purpose" parts of the biojava API from "biology-specific" parts. This still seems like a good idea in principle, but at this point it might be best to leave it for biojava 2. Thomas. From matthew_pocock at yahoo.co.uk Tue Feb 24 06:41:57 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Feb 24 06:48:14 2004 Subject: [Biojava-dev] Gaps and EmptyAlphabet In-Reply-To: References: Message-ID: <403B3885.50307@yahoo.co.uk> Mark, could you post some example code? This smells like it's a boundary-condition bug. The maths says it does match itself, so we have got the alphabet wrong. We should have included a 'gap' Symbol sub-interface, but it's too late now. Symbols and alpphabets will be much cleaner next time around, but oopy programming realy doesn't make it easy to do very relational / group-theoretical things without jumping through hoops, as extention vs specialisation are both modelled by inheritance but are realy orthogonal processes. Matthew mark.schreiber@group.novartis.com wrote: >The gap symbol getMatches method returns the EmptyAlphabet. > >This has the slightly weird result that the gap symbol doesn't match >itself!? I'm sure Bertrand Russell could write a book on that. I just >think it's plain weird. Wouldn't it be better if the getMatches for a gap >returned an FiniteAlphabet containing only the gap symbol?? > >- Mark > >Mark Schreiber >Principal Scientist (Bioinformatics) > >Novartis Institute for Tropical Diseases (NITD) >1 Science Park Road >#04-14 The Capricorn >Singapore 117528 > >phone +65 6722 2973 >fax +65 6722 2910 > >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > > From MRBATESALANN at netscape.net Tue Feb 24 13:25:01 2004 From: MRBATESALANN at netscape.net (MRBATESALANN@netscape.net) Date: Tue Feb 24 15:09:29 2004 Subject: [Biojava-dev] REPLY SOON Message-ID: <200402241825.i1OIMRMu010992@netsolute.net> Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From help at sandlight.net Tue Feb 24 16:11:45 2004 From: help at sandlight.net (Belisi Clothiers) Date: Tue Feb 24 16:48:48 2004 Subject: [Biojava-dev] Hand-Made Silk Neckties - $3 Each Message-ID: Traditional Elegance, Exclusive Patterns, Amazing Price. That's what you can expect from fine Belisi Hand-made Neckwear. Click Here Now http://rpols.com/cgi/o.cgi?o=tmh For a limited time, Belisi is offering its signature styles online at an unheard of price to promote the Belisi brand. Take advantage of this limited time event! Choose 3 Hand-made Belisi Neckties for just $3 Each! Click here now http://rpols.com/cgi/o.cgi?o=tmh Sign up today and you'll also get a FREE Executive Writing Instrument valued at over $75! Order a 4th Tie for 20% off and get FREE Shipping! Click here now http://rpols.com/cgi/o.cgi?o=tmh About Belisi Neckties: Belisi's luxurious neckties are hand-made from the world's fintest silk. Our neckwear is manufacturered with more silk per inch that standard ties, creating a full knot, the hallmark of traditional men's dressing. Belisi neckties are an ample 4 inches wide at the bottom, making a powerful impression and have an extra silk loop at the back for those who don't wear tie-tacks. Belisi offers classic styling and distinctive patterns for the sophisticated buyer. Click here now http://rpols.com/cgi/o.cgi?o=tmh The above is an advertisement sent by a Belisi Clothiers affiliate. If you have any questions or concerns, you may contact us at the following address: Belisi Clothiers 4521 PGA Blvd. Suite 349, Palm Beach Gardens, FL 33418 Should you wish to unsubscribe from the list owner who sent you this email, please follow the unsubscription information below: Meditay LLC c/o ERC 180 South 300 West, Suite 318 Salt Lake City, UT 84111 Please take me-off http://rpols.com/cgi/o.cgi?o=un From mark.schreiber at group.novartis.com Tue Feb 24 20:05:14 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Feb 24 20:07:56 2004 Subject: [Biojava-dev] Gaps and EmptyAlphabet Message-ID: Hi Matthew, The following shows the problem. It appears to be that gap.getMatches() gives an EmptyAlphabet. Instead I propose that it should give an Alphabet that contains only itself. Also, is there any reason why a Gap shouldn't be Atomic? After all if getMatches() returns itself and it's not really divisible within it's parent Alphabet then I think it should be Atomic. Why do I care I hear you ask?? Well, if it were Atomic and matched itself then I could make a special case of Distribution that actually stored the weight of gaps. public class FunWithGaps { public static void main(String[] args) { Alphabet dna = DNATools.getDNA(); Symbol gap = dna.getGapSymbol(); FiniteAlphabet a = (FiniteAlphabet)gap.getMatches(); //EmptyAlphabet System.out.println(a.size() == 0); //true //won't loop as hasNext() is false for (Iterator iter = a.iterator(); iter.hasNext(); ) { Symbol sym = (Symbol)iter.next(); System.out.println(sym.getName()); } System.out.println(a.contains(gap)); //false!! } } Matthew Pocock Sent by: biojava-dev-bounces@portal.open-bio.org 02/24/2004 07:41 PM To: Mark Schreiber/GP/Novartis@PH cc: biojava-dev@open-bio.org Subject: Re: [Biojava-dev] Gaps and EmptyAlphabet Mark, could you post some example code? This smells like it's a boundary-condition bug. The maths says it does match itself, so we have got the alphabet wrong. We should have included a 'gap' Symbol sub-interface, but it's too late now. Symbols and alpphabets will be much cleaner next time around, but oopy programming realy doesn't make it easy to do very relational / group-theoretical things without jumping through hoops, as extention vs specialisation are both modelled by inheritance but are realy orthogonal processes. Matthew mark.schreiber@group.novartis.com wrote: >The gap symbol getMatches method returns the EmptyAlphabet. > >This has the slightly weird result that the gap symbol doesn't match >itself!? I'm sure Bertrand Russell could write a book on that. I just >think it's plain weird. Wouldn't it be better if the getMatches for a gap >returned an FiniteAlphabet containing only the gap symbol?? > >- Mark > >Mark Schreiber >Principal Scientist (Bioinformatics) > >Novartis Institute for Tropical Diseases (NITD) >1 Science Park Road >#04-14 The Capricorn >Singapore 117528 > >phone +65 6722 2973 >fax +65 6722 2910 > >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > > _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at group.novartis.com Tue Feb 24 20:19:31 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Feb 24 20:22:12 2004 Subject: [Biojava-dev] Rationalisation Message-ID: OK - Maybe it's a hack and slash approach. I think for BJ2 there is a good argument for splitting Sybolic and Ontology APIs from the Bio stuff. Generating too many JARs is a bad idea. Actually I think that splitting BioSQL support is a good idea (and maybe merging with DAS, Ensembl, etc). Not everyone uses it and it would give you the option of getting the BioSQL jar that supports the schema version you want. - Mark David Huen 02/24/2004 04:59 PM Please respond to smh1008 To: Mark Schreiber/GP/Novartis@PH cc: Subject: Re: [Biojava-dev] Rationalisation On Tuesday 24 Feb 2004 3:15 am, mark.schreiber@group.novartis.com wrote: > As you all know biojava is quite big. It currently splits itself into two > jar files (biojava.jar and grammars.jar) or three if you include the > bytecode.jar. > > There have been suggestions of splitting it into subprojects. One obvious > place for a split would be biojava.jar and grammars.jar. The ant build > already achieves this artificially by splitting the code base in two. > Would it be sensible to give grammars it's own cvs home? > > Other possible splits: > > demos > doclets > apps > > My reasoning is as follows. Projects should be merged where components > have a high level of two way dependency and seperated where there is only > one way dependency. > > For example biojava depends heavily on grammars.jar but grammars.jar > doesn't care too much about the core of biojava. Demos and apps are > dependent on biojava but the reverse is not at all true. The doclets > project is a nice add on but they are pretty indenpendent of each other. > My feeling is that this would make management of the project much easier > and ant scripts simpler. > > Any thoughts or flames?? > By that rationale, classes related to bioSQL would sensibly lie outside the main package, as would the DP stuff. Perhaps we could put all the SQL implementation stuff (bioSQL, Ensembl) into one jar and things like DP into another exotics-that-will-do-your-mind-in jar. My only reservation aobut all this is whether it would make for (perhaps) more support work when users get confused as to which jars they should have had in their classpath. Regards, David Huen From mark.schreiber at group.novartis.com Tue Feb 24 20:24:31 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Feb 24 20:27:12 2004 Subject: [Biojava-dev] Rationalisation Message-ID: Your right! Grammars.jar has gone! I should pay more attention :) OK, splitting Grammars can wait for BJ2. I certainly don't want to make anyones job harder but demos and apps are an obvious target and would cause minimal pain to excise it from the main code base. I think this would also mean that at least one of the commons jar files could be moved in with the demos/apps group further reducing confusion about which jars are required and which ones are 'optional'. - Mark Schreiber Thomas Down Sent by: biojava-dev-bounces@portal.open-bio.org 02/24/2004 05:24 PM To: Mark Schreiber/GP/Novartis@PH cc: biojava-dev@biojava.org Subject: Re: [Biojava-dev] Rationalisation On 24 Feb 2004, at 03:15, mark.schreiber@group.novartis.com wrote: > As you all know biojava is quite big. It currently splits itself into > two > jar files (biojava.jar and grammars.jar) or three if you include the > bytecode.jar. > > There have been suggestions of splitting it into subprojects. One > obvious > place for a split would be biojava.jar and grammars.jar. The ant build > already achieves this artificially by splitting the code base in two. > Would it be sensible to give grammars it's own cvs home? Actually, I think grammars.jar is probably a bad example: it was only being produced as a separate jar file for the convenience of the build process. This got fixed in the build.xml clean up a month or so back: if you've still got a separate grammars.jar file lying around, it's from an old build and you should probably get rid of it. Unless there's someone who seriously wants to use the grammars without the rest of biojava, I'd vote to keep them in their current place. On the other hand... > Other possible splits: > > demos > doclets > apps Yes, all of these are possibilities. Any taglets we use which might be of general interest should probably go to a general-purpose hosting site like jakarta. Splitting the demos out it an interesting idea since it means that users have the option to download them without grabbing the complete (big!) biojava-live tree. We should do this iff: - It makes the demos more, not less, visible to users (and core developers). - We can make sure they stay in sync with the core API (I can probably solve this one by adding them to the Autobuilder). Another possible split, which has been talked about for a long time but never really happened is to separate out "general purpose" parts of the biojava API from "biology-specific" parts. This still seems like a good idea in principle, but at this point it might be best to leave it for biojava 2. Thomas. _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From autobuilder at derkholm.net Wed Feb 25 00:20:04 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Feb 25 00:29:35 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077686408653.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040225 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Thu Feb 26 00:20:11 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Feb 26 00:29:41 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077772813644.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040226 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From f.cadieux at btinternet.com Thu Feb 26 17:04:56 2004 From: f.cadieux at btinternet.com (Info) Date: Thu Feb 26 17:11:07 2004 Subject: [Biojava-dev] Federal Provincial Subsidies Message-ID: <200402262210.i1QMAo9Q026763@portal.open-bio.org> CANADA BOOKS 26 CH. 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The Canadian Subsidy Directory is sold $ 69.95, to obtain a copy please visit: www.cbooks.biz From autobuilder at derkholm.net Fri Feb 27 00:12:43 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Feb 27 00:22:13 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <28349544.1077858763953.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040227 Binary build: OK Javadocs build: OK Core test suite: NOT RUN Problems occurred during this build cycle -- please investigate as soon as possible! The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/seq/projection/ProjectionEngine.java * biojava-live/src/org/biojava/bio/symbol/AbstractSymbol.java * biojava-live/tests/org/biojava/bio/seq/impl/ViewSequenceTest.java * biojava-live/tests/org/biojava/bio/symbol/AbstractSymbolEventTest.java * biojava-live/tests/org/biojava/bio/symbol/AlphabetManagerTest.java * biojava-live/tests/org/biojava/bio/symbol/AlphabetSerializationTest.java * biojava-live/tests/org/biojava/bio/symbol/BetweenLocationTest.java * biojava-live/tests/org/biojava/bio/symbol/CircularLocationTest.java * biojava-live/tests/org/biojava/bio/symbol/CodonPrefToolsTest.java * biojava-live/tests/org/biojava/bio/symbol/CompoundLocationTest.java * biojava-live/tests/org/biojava/bio/symbol/CrossProductAlphabetIndexTest.java * biojava-live/tests/org/biojava/bio/symbol/CrossProductTokenizationTest.java * biojava-live/tests/org/biojava/bio/symbol/FundamentalAtomicSymbolEventTest.java * biojava-live/tests/org/biojava/bio/symbol/GappedSymbolListTest.java * biojava-live/tests/org/biojava/bio/symbol/MergeLocationTest.java * biojava-live/tests/org/biojava/bio/symbol/MotifToolsTest.java * biojava-live/tests/org/biojava/bio/symbol/NameTokenizationTest.java * biojava-live/tests/org/biojava/bio/symbol/PackedDnaSymbolListTest.java * biojava-live/tests/org/biojava/bio/symbol/SimpleAtomicSymbolEventTest.java * biojava-live/tests/org/biojava/bio/symbol/SimpleBasisSymbolEventTest.java * biojava-live/tests/org/biojava/bio/symbol/SimpleCodonPrefTest.java * biojava-live/tests/org/biojava/bio/symbol/SimpleSymbolEventTest.java * biojava-live/tests/org/biojava/bio/symbol/SimpleSymbolListTest.java * biojava-live/tests/org/biojava/bio/symbol/SimpleWobbleDistributionTest.java * biojava-live/tests/org/biojava/bio/symbol/SymbolListTest.java * biojava-live/tests/org/biojava/bio/symbol/SymbolSerializationTest.java * biojava-live/tests/org/biojava/bio/symbol/SymbolUtils.java * biojava-live/tests/org/biojava/bio/symbol/TranslationTest.java * biojava-live/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java * biojava-live/tests/org/biojava/utils/RepeatedCharSequenceTest.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From td2 at sanger.ac.uk Fri Feb 27 04:52:15 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Fri Feb 27 04:58:16 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report In-Reply-To: <28349544.1077858763953.JavaMail.thomas@firechild.derkholm.net> References: <28349544.1077858763953.JavaMail.thomas@firechild.derkholm.net> Message-ID: <9FC338F6-690A-11D8-B22E-000A95C8B056@sanger.ac.uk> On 27 Feb 2004, at 05:12, autobuilder@derkholm.net wrote: > BioJava automatic build system, run 20040227 > > Binary build: OK > Javadocs build: OK > Core test suite: NOT RUN Hi, This means that the test suite won't compile (I'll see if I can get the script to generate a more informative message for this at some point :-). The main problem seems to be that RepeatedCharSequenceTest.java has been checked in, but the corresponding RepeatedCharSequence is missing. Matthew, can you check this in ASAP? There's a second, apparently unrelated problem of BioSQLSequenceDBTest calling a non-existant method on OntologySQL. I'm not sure what's going on here. Do we really need to have test cases calling non-public API like OntologySQL? Thomas > Problems occurred during this build cycle -- please investigate as > soon as possible! > > The following files were modified in the last 24 hours: > > * > biojava-live/src/org/biojava/bio/seq/projection/ProjectionEngine.java > * biojava-live/src/org/biojava/bio/symbol/AbstractSymbol.java > * biojava-live/tests/org/biojava/bio/seq/impl/ViewSequenceTest.java > * > biojava-live/tests/org/biojava/bio/symbol/AbstractSymbolEventTest.java > * biojava-live/tests/org/biojava/bio/symbol/AlphabetManagerTest.java > * > biojava-live/tests/org/biojava/bio/symbol/ > AlphabetSerializationTest.java > * biojava-live/tests/org/biojava/bio/symbol/BetweenLocationTest.java > * biojava-live/tests/org/biojava/bio/symbol/CircularLocationTest.java > * biojava-live/tests/org/biojava/bio/symbol/CodonPrefToolsTest.java > * biojava-live/tests/org/biojava/bio/symbol/CompoundLocationTest.java > * > biojava-live/tests/org/biojava/bio/symbol/ > CrossProductAlphabetIndexTest.java > * > biojava-live/tests/org/biojava/bio/symbol/ > CrossProductTokenizationTest.java > * > biojava-live/tests/org/biojava/bio/symbol/ > FundamentalAtomicSymbolEventTest.java > * biojava-live/tests/org/biojava/bio/symbol/GappedSymbolListTest.java > * biojava-live/tests/org/biojava/bio/symbol/MergeLocationTest.java > * biojava-live/tests/org/biojava/bio/symbol/MotifToolsTest.java > * biojava-live/tests/org/biojava/bio/symbol/NameTokenizationTest.java > * > biojava-live/tests/org/biojava/bio/symbol/PackedDnaSymbolListTest.java > * > biojava-live/tests/org/biojava/bio/symbol/ > SimpleAtomicSymbolEventTest.java > * > biojava-live/tests/org/biojava/bio/symbol/ > SimpleBasisSymbolEventTest.java > * biojava-live/tests/org/biojava/bio/symbol/SimpleCodonPrefTest.java > * > biojava-live/tests/org/biojava/bio/symbol/SimpleSymbolEventTest.java > * biojava-live/tests/org/biojava/bio/symbol/SimpleSymbolListTest.java > * > biojava-live/tests/org/biojava/bio/symbol/ > SimpleWobbleDistributionTest.java > * biojava-live/tests/org/biojava/bio/symbol/SymbolListTest.java > * > biojava-live/tests/org/biojava/bio/symbol/SymbolSerializationTest.java > * biojava-live/tests/org/biojava/bio/symbol/SymbolUtils.java > * biojava-live/tests/org/biojava/bio/symbol/TranslationTest.java > * > biojava-live/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java > * biojava-live/tests/org/biojava/utils/RepeatedCharSequenceTest.java > > A patch file reflecting these changes is available from > > http://www.derkholm.net/autobuild/patches/ > > -- > BioJava Autobuilder, maintained by Thomas Down > If you notice any problems, contact autobuilder@derkholm.net > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From matthew_pocock at yahoo.co.uk Fri Feb 27 07:19:56 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri Feb 27 07:26:01 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report In-Reply-To: <9FC338F6-690A-11D8-B22E-000A95C8B056@sanger.ac.uk> References: <28349544.1077858763953.JavaMail.thomas@firechild.derkholm.net> <9FC338F6-690A-11D8-B22E-000A95C8B056@sanger.ac.uk> Message-ID: <403F35EC.50903@yahoo.co.uk> Thomas Down wrote: > The main problem seems to be that RepeatedCharSequenceTest.java has > been checked in, but the corresponding RepeatedCharSequence is > missing. Matthew, can you check this in ASAP? My bad - fixed. From webmaster at flowerwolf.com Fri Feb 27 16:04:53 2004 From: webmaster at flowerwolf.com (Homestyle) Date: Fri Feb 27 17:10:37 2004 Subject: [Biojava-dev] Get A Garden Tote On Us (With Membership) Message-ID: Do it yourself...with style and savings! GET 3 DECORATING BOOKS FOR $4.95 PLUS A FREE GARDEN TOTE. Click Here: http://rpols.com/cgi/o.cgi?o=hmd Welcome to the wonderful world of HomeStyle Books?. Explore the ultimate resource of expert advice, DIY projects, and money-saving ideas. Decorating, gardening, entertaining, crafting...do it all with us. Choose from today's best guides by trusted experts, including: HGTV? Before and After Decorating The network's first book features more than 150 makeovers. Taylor's Guides: Encyclopedia of Garden Plants by Frances Tenenbaum Learn how & what to grow in your yard with a gorgeous guide. Christopher Lowell's You Can Do It! 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To unsubscribe go here: http://rpols.com/cgi/o.cgi?o=bkun Member Services, 1225 South Market St., Mechanicsburg, PA 17055 Meditay LLC c/o ERC 180 South 300 West, Suite 318 Salt Lake City, UT 84111 Please take me-off http://rpols.com/cgi/o.cgi?o=sun From autobuilder at derkholm.net Sat Feb 28 00:20:07 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Feb 28 00:29:41 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1077945608117.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040228 Binary build: OK Javadocs build: OK Core test suite: FAILED The core test suite is failing -- please investigate the following tests: * org.biojava.bio.symbol.SimpleAtomicSymbolEventTest * org.biojava.bio.symbol.SimpleBasisSymbolEventTest * org.biojava.bio.symbol.SimpleSymbolEventTest The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/utils/ChangeForwarder.java * biojava-live/src/org/biojava/utils/ChangeSupport.java * biojava-live/src/org/biojava/utils/ChangeType.java * biojava-live/src/org/biojava/utils/MergingSet.java * biojava-live/src/org/biojava/utils/RepeatedCharSequence.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From dieselfuelinject at eyou.com Sat Feb 28 08:48:50 2004 From: dieselfuelinject at eyou.com (dieselfuelinject@eyou.com) Date: Sat Feb 28 08:54:57 2004 Subject: [Biojava-dev] P,02/28,Order Message-ID: <200402281354.i1SDsf9Q014137@portal.open-bio.org> Dear Sir, we have been in the field of diesel fuel injection systems for quite a few years.(CHINA) Recently we have developed a new kind of h&r, "CH-D90101A=AM Bosch number HD90101A"Its unit price is USD150/pc.And we also adjust the unit price of Nozzle , Plunger to USD4~8/pc respectively. We tell you that we will update our VE h&r (hydraulic heads for the VE distributor pump) list in our homepages.Thirty more models will be added.And the minimum order will be 10pcs a model. we give the unity quotation of VE distributor head: 3-cyl:USD:55/1pcs 4-cyl:USD:40~50/1pcs 5-cyl:USD:60/1pcs 6-cyl:USD:45~50/1pcs We can ship the following three models to you within 6~8 weeks. after we receive your payment. If you feel interested in our products,please advise the details about what you need,such model name,part number,quantity and so on.We are always within your touch. Thanks and best regards Looking forward to our favorable cooperation. Hope to hear from you soon. (NIPPON DENSO) D00-0143 D00-0242 D00-0262 D00-0371 D00-0432 D00-1030 D00-1060 D00-1090 D00-1210 D00-1220 D00-1230 D00-1240 D00-1250 D00-1330 D00-1331 D00-1600 D40-0080 ZEXEL Z00-2220 Z00-3320 Z00-4520 Z00-5521 Z00-8821 Z00-9720 Z01-0520 Z01-2120 Z02-0820 Z02-0920 Z02-1420 Z02-4020 Z02-4320 Z02-3820 Z03-2820 Z03-3120 Z03-3520 Z04-1520 Z04-2200 Z05-1920 Z30-1420 BOSCH A 333 320 A 333 323 A 334 313 A 334 327 A 334 565 A 334 337 A 334 378 A 334 424 A 334 475 A 334 485 A 334 494 A 334 496 A 334 580 A 334 590 A 334 564 A 334 565 A 334 575 A 334 592 A 334 595 A 334 596 A 334 603 A 334 604 A 334 606 A 334 617 A 334 675 A 334 678 A 334 720 A 334 780 A 334 798 A 334 859 A 334 874 A 334 899 A 334 946 A 335 345 B 335 022 A 336 335 A 336 352 A 336 364 A 336 403 A 336 423 A 336 464 A 336 480 A 336 528 A 336 608 A 336 614 A 336 626 A 336 632 B 334 050 B 334 021 B 336 013 We have a large number of nozzle, plunger and delivery valve in stock.Here is a list of part of them. " " NOZZLE 093400-1310 DN0SD193 093400-1710 DLLA160SND171 093400-2280 DNOSD228 093400-5210 DNOPD21 093400-5571 ND-DN4PD57 093400-5590 ND-DLLA150P59 093400-7690 ND-DN10PDN129 093400-7700 ND-DN10PDN130 DNOSD261 DNOSD220 DNOSD293 DLLA150P205 DLLA150S1070 105000-108 NP-DNOSD211 105000-1130 NP-DN4SD24 10500-1650 NP-DNOSD2110 105000-1080 NP-DNOSD211 105000-1360 NP-DN4SD24 105000-1730 NP-DNOSD21 105000-1740 NP-DNOSD193 105000-1760 105000-2280 NP-DNOSDN228 105007-1120 NP-DNOPDN112 105007-1130 NP-DN0PDN113 105007-1210 NP-DNOPDN121 105015-2780 NP-DLLA166S374NP6 105015-3280 NP-DLLA150S328NP52 105015-3520 DLLA150S384NP73 105015-3650 NP-DLLA151S354N86 105015-3670 NP-DLLA160S354NP88 105015-3850 NP-DLLA150S334N385 105015-4130 NP-DLLA154S324N413 105015-4170 NP-DLLA137S374N417 105015-4190 DLLA154S334N419 105015-4220 NP-DLLA160S295N422 105015-4330 NP-DLLA105S304N433 105015-4730 NP-DLLA148S324N473 105015-5070 NP-DLLA160S325N507 105015-6130 NP-DLLA142SN613 105015-6380 DLLA158SN638 105015-8690 DLLA158SN869 105015-8860 NP-DLLA148SN886 105017-0070 NP-DLLA154PN007 105017-0090 NP-DLLA152PN009 105017-0630 NP-DLLA152PN063 105017-0670 DLLA154PN067 105017-0100 DLLA160PN010 105017-0210 DLLA150PN021 105017-0211/10 DLLA150PN021 105017-0900 DLLA152PN009 105017-1160 NP-DLLA154PN116 105017-1180 DLLA155PN118 105007-1210 NP-DNOPDN121 105017-1780 DLLA153PN178 0 433 271 740 0 433 271 047 DLLA150S187 0 433 271 045 DLLA150S186 0 433 171 031 DLLA150P30 0 433 171 050 DLLA160P50 0 433 171 059 DLLA150P59 0 433 171 104 DLLA150P115 0 433 171 149 DLLA146P166 0 433 171 137 DLLA146P154 0 433 171 161 DLLA144P184 0 433 171 172 DLLA154P206 0 433 171 231 DLLA150P326 0 433 171 435 DLLA145P574 0 433 171 444 DLLA150P585 0 433 175 048 DSLA145P300 0 433 271 045 DLLA150S186 0 433 271 047 DLLA150S187 0 433 271 361 DLLA150S739 0 433 271 404 DLLA142S792 0 433 271 874 DLLA150S739 0 466 171 003 DLL-A160P3 NP-DLL154S284N393 NP-DLL160S 354NP88 6801128 6801118 PLUNGER LIST: 131101-7020 0-4 131101-7520 0-9 A17 131151-2720 A43 131151-3220 A44 131151-5820 A74 131151-7320 A89 A98 131152-1420 A138 A147 131152-2220 A148 131152-3120 A158 131152-3320 A160 131152-5620 A188 131153-1220 A196 131152-8520 A226 131153-8920 A768 A722 134101-1420 P2 134101-1520 P3 P4 134101-1820 P6 134101-3820 P25 134101-6320 P48 134101-6420 P49 Delivery valve 146430-1420 131160-1920 02A 131160-2220 05A 131160-2920 12A 131160-3620 20A 134110-0120 P1 134110-0520 P4 134110-0920 P8 134110-4520 P44 131110-0620 161S2 134110-0920 P8 134110-4520 P44 134110-7420 P73 131110-2920 A9 131110-3920 A20 131110-4720 A28 131110-5120 A32 131110-5220 A33 131110-5920 A40 13110-6820 A49 131110-7720 A58 131110-7820 A59 131110-9420 A75 131160-0420 A85 1 468 532 247 A247 146430-0020 VE1 146430-1420 VE15 " dieselfuelinject@eyou.com From dieselfuelinject at eyou.com Sat Feb 28 08:48:50 2004 From: dieselfuelinject at eyou.com (dieselfuelinject@eyou.com) Date: Sat Feb 28 08:54:58 2004 Subject: [Biojava-dev] P,02/28,Order Message-ID: <200402281354.i1SDse9Q014136@portal.open-bio.org> Dear Sir, we have been in the field of diesel fuel injection systems for quite a few years.(CHINA) Recently we have developed a new kind of h&r, "CH-D90101A=AM Bosch number HD90101A"Its unit price is USD150/pc.And we also adjust the unit price of Nozzle , Plunger to USD4~8/pc respectively. We tell you that we will update our VE h&r (hydraulic heads for the VE distributor pump) list in our homepages.Thirty more models will be added.And the minimum order will be 10pcs a model. we give the unity quotation of VE distributor head: 3-cyl:USD:55/1pcs 4-cyl:USD:40~50/1pcs 5-cyl:USD:60/1pcs 6-cyl:USD:45~50/1pcs We can ship the following three models to you within 6~8 weeks. after we receive your payment. If you feel interested in our products,please advise the details about what you need,such model name,part number,quantity and so on.We are always within your touch. Thanks and best regards Looking forward to our favorable cooperation. Hope to hear from you soon. (NIPPON DENSO) D00-0143 D00-0242 D00-0262 D00-0371 D00-0432 D00-1030 D00-1060 D00-1090 D00-1210 D00-1220 D00-1230 D00-1240 D00-1250 D00-1330 D00-1331 D00-1600 D40-0080 ZEXEL Z00-2220 Z00-3320 Z00-4520 Z00-5521 Z00-8821 Z00-9720 Z01-0520 Z01-2120 Z02-0820 Z02-0920 Z02-1420 Z02-4020 Z02-4320 Z02-3820 Z03-2820 Z03-3120 Z03-3520 Z04-1520 Z04-2200 Z05-1920 Z30-1420 BOSCH A 333 320 A 333 323 A 334 313 A 334 327 A 334 565 A 334 337 A 334 378 A 334 424 A 334 475 A 334 485 A 334 494 A 334 496 A 334 580 A 334 590 A 334 564 A 334 565 A 334 575 A 334 592 A 334 595 A 334 596 A 334 603 A 334 604 A 334 606 A 334 617 A 334 675 A 334 678 A 334 720 A 334 780 A 334 798 A 334 859 A 334 874 A 334 899 A 334 946 A 335 345 B 335 022 A 336 335 A 336 352 A 336 364 A 336 403 A 336 423 A 336 464 A 336 480 A 336 528 A 336 608 A 336 614 A 336 626 A 336 632 B 334 050 B 334 021 B 336 013 We have a large number of nozzle, plunger and delivery valve in stock.Here is a list of part of them. " " NOZZLE 093400-1310 DN0SD193 093400-1710 DLLA160SND171 093400-2280 DNOSD228 093400-5210 DNOPD21 093400-5571 ND-DN4PD57 093400-5590 ND-DLLA150P59 093400-7690 ND-DN10PDN129 093400-7700 ND-DN10PDN130 DNOSD261 DNOSD220 DNOSD293 DLLA150P205 DLLA150S1070 105000-108 NP-DNOSD211 105000-1130 NP-DN4SD24 10500-1650 NP-DNOSD2110 105000-1080 NP-DNOSD211 105000-1360 NP-DN4SD24 105000-1730 NP-DNOSD21 105000-1740 NP-DNOSD193 105000-1760 105000-2280 NP-DNOSDN228 105007-1120 NP-DNOPDN112 105007-1130 NP-DN0PDN113 105007-1210 NP-DNOPDN121 105015-2780 NP-DLLA166S374NP6 105015-3280 NP-DLLA150S328NP52 105015-3520 DLLA150S384NP73 105015-3650 NP-DLLA151S354N86 105015-3670 NP-DLLA160S354NP88 105015-3850 NP-DLLA150S334N385 105015-4130 NP-DLLA154S324N413 105015-4170 NP-DLLA137S374N417 105015-4190 DLLA154S334N419 105015-4220 NP-DLLA160S295N422 105015-4330 NP-DLLA105S304N433 105015-4730 NP-DLLA148S324N473 105015-5070 NP-DLLA160S325N507 105015-6130 NP-DLLA142SN613 105015-6380 DLLA158SN638 105015-8690 DLLA158SN869 105015-8860 NP-DLLA148SN886 105017-0070 NP-DLLA154PN007 105017-0090 NP-DLLA152PN009 105017-0630 NP-DLLA152PN063 105017-0670 DLLA154PN067 105017-0100 DLLA160PN010 105017-0210 DLLA150PN021 105017-0211/10 DLLA150PN021 105017-0900 DLLA152PN009 105017-1160 NP-DLLA154PN116 105017-1180 DLLA155PN118 105007-1210 NP-DNOPDN121 105017-1780 DLLA153PN178 0 433 271 740 0 433 271 047 DLLA150S187 0 433 271 045 DLLA150S186 0 433 171 031 DLLA150P30 0 433 171 050 DLLA160P50 0 433 171 059 DLLA150P59 0 433 171 104 DLLA150P115 0 433 171 149 DLLA146P166 0 433 171 137 DLLA146P154 0 433 171 161 DLLA144P184 0 433 171 172 DLLA154P206 0 433 171 231 DLLA150P326 0 433 171 435 DLLA145P574 0 433 171 444 DLLA150P585 0 433 175 048 DSLA145P300 0 433 271 045 DLLA150S186 0 433 271 047 DLLA150S187 0 433 271 361 DLLA150S739 0 433 271 404 DLLA142S792 0 433 271 874 DLLA150S739 0 466 171 003 DLL-A160P3 NP-DLL154S284N393 NP-DLL160S 354NP88 6801128 6801118 PLUNGER LIST: 131101-7020 0-4 131101-7520 0-9 A17 131151-2720 A43 131151-3220 A44 131151-5820 A74 131151-7320 A89 A98 131152-1420 A138 A147 131152-2220 A148 131152-3120 A158 131152-3320 A160 131152-5620 A188 131153-1220 A196 131152-8520 A226 131153-8920 A768 A722 134101-1420 P2 134101-1520 P3 P4 134101-1820 P6 134101-3820 P25 134101-6320 P48 134101-6420 P49 Delivery valve 146430-1420 131160-1920 02A 131160-2220 05A 131160-2920 12A 131160-3620 20A 134110-0120 P1 134110-0520 P4 134110-0920 P8 134110-4520 P44 131110-0620 161S2 134110-0920 P8 134110-4520 P44 134110-7420 P73 131110-2920 A9 131110-3920 A20 131110-4720 A28 131110-5120 A32 131110-5220 A33 131110-5920 A40 13110-6820 A49 131110-7720 A58 131110-7820 A59 131110-9420 A75 131160-0420 A85 1 468 532 247 A247 146430-0020 VE1 146430-1420 VE15 " dieselfuelinject@eyou.com From td2 at sanger.ac.uk Sat Feb 28 12:06:28 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Sat Feb 28 12:12:23 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report In-Reply-To: <31538514.1077945608117.JavaMail.thomas@firechild.derkholm.net> References: <31538514.1077945608117.JavaMail.thomas@firechild.derkholm.net> Message-ID: <72A66220-6A10-11D8-9380-000A95C8B056@sanger.ac.uk> On 28 Feb 2004, at 05:20, autobuilder@derkholm.net wrote: > BioJava automatic build system, run 20040228 > > Binary build: OK > Javadocs build: OK > Core test suite: FAILED > > The core test suite is failing -- please investigate the following > tests: > > * org.biojava.bio.symbol.SimpleAtomicSymbolEventTest > * org.biojava.bio.symbol.SimpleBasisSymbolEventTest > * org.biojava.bio.symbol.SimpleSymbolEventTest These look like test-suite bugs -- they weren't expecting Symbol implementations to defensively copy the Annotation bundle you pass to their constructor. I've fixed the tests to handle this case now. More general point: defensive copies should probably be documented, to avoid nasty object-ownership confusions. Thomas. From delivery at hosyou-r.mine.nu Sat Feb 28 12:29:43 2004 From: delivery at hosyou-r.mine.nu (=?iso-2022-jp?Q?=1B=24BJ=5D=3EZ6=282q=1B=28B?=) Date: Sat Feb 28 12:31:45 2004 Subject: [Biojava-dev] =?iso-2022-jp?b?GyRCISEhIUwkPjVCejktOXAhdiMyGyhC?= =?iso-2022-jp?b?GyRCMi8hIiMzMi8hIiM1Mi8jOUBpS3wxXzx9Rn48VCQsQjM9UCQ3GyhC?= =?iso-2022-jp?b?GyRCJEYkJCReJDkhIxsoQg==?= Message-ID: <4076786.1077989383785.JavaMail.nobody@hosyou-r.mine.nu> ＜配信者＞　はじめまして、全信協顧問桜井と申します。 　　　　　　　　配信停止は大変恐縮ですが http://www.hosyoukyoukai.net/cgi-bin/postmail/teishi.html にてお願い申し上げます。　　　 *==* ご挨拶 ==*==*====**==**==５億９千万円への一歩=*==*==*==*==*　　　　　　　　 　　　謹啓、時下益々ご健勝のこととお察し申し上げます。 　　　　　　　　　　　　　　　突然の配信、ご容赦お願い申し上げます。 ■イマ、５千万円があったら最高なのに、の方々！イマからでも遅くありません!! ■２億、３億、５億９千万円収入者が続出しています。 　　　　　　　　　　　しかし、証拠がなければ誰でも信用しません。 　　□━━主たる物的証拠━━見せます━━何事も論より証拠━━□ 　　　東京高等裁判所の判決書・２億、３億、５億９千万円収入の 　　　銀行印有振込み書・福祉事務所よりの保証証券使用依頼書・他 　　□━━━━━━━━━━━━━━━━━━━━━━━━━━□　 　　　　　　成人男女・副業在宅高額ネット収入目的に最適です。 ※　資料ご請求はhttp://www.hosyoukyoukai.net　からお願い申し上げます。 　　　　　 From autobuilder at derkholm.net Sun Feb 29 00:20:19 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Feb 29 00:32:23 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31538514.1078032022309.JavaMail.thomas@firechild.derkholm.net> BioJava automatic build system, run 20040229 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/tests/org/biojava/bio/symbol/AbstractSymbolEventTest.java * biojava-live/tests/org/biojava/bio/symbol/SimpleAtomicSymbolEventTest.java * biojava-live/tests/org/biojava/bio/symbol/SimpleBasisSymbolEventTest.java * biojava-live/tests/org/biojava/bio/symbol/SimpleSymbolEventTest.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From rainer.warth at rdls.nestle.com Tue Feb 24 02:40:15 2004 From: rainer.warth at rdls.nestle.com (Warth,Rainer,LAUSANNE,NRC/BAS) Date: Thu Mar 4 21:40:37 2004 Subject: [Biojava-dev] ViewSequence Message-ID: Hi, I wanted to try this program from the bioJAVA in ANGER page (http://www.biojava.org/docs/bj_in_anger/NameChange.htm ). I just pasted the text in the NameChange.java file which is part of the seq package. My biojava classpath must be okay since I have other classes in this package, which work fine (e.g. TestEmbl). However, I get the message that ViewSequence(seq, "ABC123") is not a valid constructor. In addition, the method writeFasta does not seem to have the right arguments ( line SeqIOTools.writeFasta(System.out, seq2). This is confirmed when I try to run it. java.lang.Error: Unresolved compilation problems: The constructor ViewSequence(Sequence, String) is undefined The method writeFasta(OutputStream, SequenceDB) in the type SeqIOTools is not applicable for the arguments (PrintStream, ViewSequence) at seq.NameChange.main(NameChange.java:28) Does anybody see, what is wrong ? biojava-1.3.1.jar and bytecode-0.92.jar are on my classpath. Best, Rainer -------- package seq; import java.io.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; import org.biojava.bio.symbol.*; public class NameChange { public static void main(String[] args) { try { Sequence seq = DNATools.createDNASequence("atgcgctaggctag","gi|12356|ABC123"); //create a veiw on the sequence and change its name ViewSequence seq2 = new ViewSequence(seq, "ABC123"); //print to FASTA to prove the name has changed SeqIOTools.writeFasta(System.out, seq2); } catch (IllegalSymbolException ex) { //tried to make seq with non DNA symbol ex.printStackTrace(); }catch (IOException ex) { //couldn't print seq2 to System out?? ex.printStackTrace(); } } } --- Dr. Rainer Warth Research Scientist Bioinformatics BioAnalytical Science Department Nestl? Research Center Vers-Chez-LES-BLANC phone: +41/21 785 8713 1000 LAUSANNE 26 FAX: +41/21 785 9486 SWITZERLAND e-mail: rainer.warth@rdls.nestle.com Dr. Rainer Warth Research Scientist Bioinformatics BioAnalytical Science Department Nestl? Research Center Vers-Chez-LES-BLANC phone: +41/21 785 8713 1000 LAUSANNE 26 FAX: +41/21 785 9486 SWITZERLAND e-mail: rainer.warth@rdls.nestle.com