From autobuilder at derkholm.net Tue Jun 1 00:10:54 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Jun 1 00:02:25 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <5450181.1086063054383.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040601 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/tagvalue/Ontologiser.java * biojava-live/src/org/biojava/ontology/OntoTools.java * biojava-live/src/org/biojava/ontology/ReasoningDomain.java * biojava-live/src/org/biojava/ontology/ReasoningTools.java * biojava-live/src/org/biojava/ontology/expression/Atom.java * biojava-live/src/org/biojava/ontology/expression/AtomImpl.java * biojava-live/src/org/biojava/ontology/expression/BindingList.java * biojava-live/src/org/biojava/ontology/expression/BindingTools.java * biojava-live/src/org/biojava/ontology/expression/Expression.java * biojava-live/src/org/biojava/ontology/expression/ExpressionImpl.java * biojava-live/src/org/biojava/ontology/expression/ExpressionPart.java * biojava-live/src/org/biojava/ontology/expression/ExpressionTools.java * biojava-live/src/org/biojava/ontology/expression/Imported.java * biojava-live/src/org/biojava/ontology/expression/ImportedAtom.java * biojava-live/src/org/biojava/ontology/expression/ImportedAtomImpl.java * biojava-live/src/org/biojava/ontology/expression/Namespace.java * biojava-live/src/org/biojava/ontology/expression/NamespaceImpl.java * biojava-live/src/org/biojava/ontology/expression/ReasoningDomain.java * biojava-live/src/org/biojava/ontology/expression/ReasoningDomainImpl.java * biojava-live/src/org/biojava/ontology/expression/ReasoningTools.java * biojava-live/src/org/biojava/ontology/expression/SubExpression.java * biojava-live/src/org/biojava/ontology/expression/SubExpressionImpl.java * biojava-live/src/org/biojava/ontology/expression/Term.java * biojava-live/src/org/biojava/ontology/expression/Terminal.java * biojava-live/src/org/biojava/ontology/expression/TerminalImpl.java * biojava-live/src/org/biojava/ontology/expression/Triple.java * biojava-live/src/org/biojava/ontology/expression/TripleImpl.java * biojava-live/src/org/biojava/ontology/expression/TriplesParser.java * biojava-live/src/org/biojava/ontology/expression/Variable.java * biojava-live/src/org/biojava/ontology/expression/VariableImpl.java * biojava-live/src/org/biojava/ontology/expression/Visitor.java * biojava-live/src/org/biojava/ontology/expression/Walker.java * biojava-live/src/org/biojava/ontology/io/GOParser.java * biojava-live/src/org/biojava/ontology/io/TriplesParser.java * biojava-live/src/org/biojava/ontology/vm/Action.java * biojava-live/src/org/biojava/ontology/vm/EqualActions.java * biojava-live/src/org/biojava/ontology/vm/Evaluate.java * biojava-live/src/org/biojava/ontology/vm/Frame.java * biojava-live/src/org/biojava/ontology/vm/Interpreter.java * biojava-live/src/org/biojava/ontology/vm/LogicalActions.java * biojava-live/src/org/biojava/ontology/vm/StackActions.java * biojava-live/src/org/biojava/ontology/vm/SymbolTable.java * biojava-live/tests/org/biojava/bio/dist/DistSerTest.java * biojava-live/tests/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java * biojava-live/tests/org/biojava/bio/seq/db/emblcd/EntryNamIdxReaderTest.java * biojava-live/tests/org/biojava/ontology/OntologyTest.java * biojava-live/tests/org/biojava/ontology/ReasoningDomainTest.java * biojava-live/tests/org/biojava/ontology/TripleImplTest.java * biojava-live/tests/org/biojava/ontology/TripleParserTest.java * biojava-live/tests/org/biojava/ontology/vm/EqualActionsTest.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 whey-min at t-online.de Tue Jun 1 03:53:12 2004 From: whey-min at t-online.de (shana) Date: Tue Jun 1 04:07:01 2004 Subject: [Biojava-dev] =?windows-1251?b?zuHz9+Xt6OU=?= Message-ID: <200406010806.i5186xKr004612@portal.open-bio.org> ????????? ???????! ?????????? ??? 3.06 ???????? ? ??????????? ???????? ?? ???? : ????? ??????????????? ?????????? ????????? ????????. 1. ??????? ??????????????? ?????????. ???????? ? ????????????: ????????? ?????????, ??????????????? ???????, ??????????????? ??????????. ??? ?????????, ???? ????????? ???????????????? ?? ???????? ?????????? ??????????? ??????? ? ????? ????? ??????????????? ?????????. 2. ????????? ? ????? ??????????????? ????????? ??? ????? ????????? ??????? ?? ??????? 3. ???? ??????????? ? ??????? ???????? ??????????????? ????????? ??? ????? ???????????????. ?????? ??????????????? ????????? ? ????????? ?????. 4. ????????? ???????? ???????? ??????? ? ?????????????? ??????? ? ??????????????? ?????????. ?????????? ??????????? ? ????????? ?? ? ????????? ????? 5. ????????? ???? ???????? ?? ?????? ??????????????? ????????? 6. ??????????? ?????????? ????? ???????? ??????????????? ?????????, ????????? ? ???????????? ?? 1 ?????? 2002 ?. 7. ????????????? ????????? ???????? ??? ????? ??????????????? ????????? ? ????????, ????????? ? ??? ????????????? 8. ?????????? ? ?????? ??????? ???????? ??????????????? ????????? ????????? ??????? ? ????????, ???????? ??????? ?? ?????? ? ????????? ?????. ????????? ??????? ? ??????????? 3900 ???. ? ??? ????????? ???????????? ??????????? ???????? ? ????????? ??????????? ?????????? 2600 ???. ? ??? ?????????? ??????? 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Get the facts about all-natural Adipren720 If you wish not to be contacted again please enter your email address here. ---- system information ---- contribution throughly platform exposed subject there can sort dictionary allows clients for display complex taking needs purpose consensus environments implications encompasses such indicator Description resource considered Services large helpful Locale Services always technical only different examples wide In who subject From heathandrews_ke at dece.cz Thu Jun 3 21:46:11 2004 From: heathandrews_ke at dece.cz (Heath Andrews) Date: Thu Jun 3 21:45:36 2004 Subject: [Biojava-dev] Get medicines here, great prices. Message-ID: Hello, I have a great offer for you... We have the cheapest prices on the Internet. Our medicines are available to you without prescription. 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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: brands@sinfo.net SMTP error from remote mailer after RCPT TO:: host mx.pa.inter.net [213.73.102.25]: 550 Unknown local part brands in ------ This is a copy of the message, including all the headers. ------ ------ The body of the message is 40822 characters long; only the first ------ 10240 or so are included here. Return-path: Received: from dsl-201-129-174-84.prod-infinitum.com.mx ([201.129.174.84] helo=sinfo.net) by proxy.eusc.inter.net with esmtp (Exim 3.36 #1) id 1BWH12-0004oS-00 for brands@sinfo.net; Fri, 04 Jun 2004 17:53:56 +0200 From: biojava-dev@biojava.org To: brands@sinfo.net Subject: Re: Administration Date: Fri, 4 Jun 2004 09:56:47 -0700 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0016----=_NextPart_000_0016" X-Priority: 3 X-MSMail-Priority: Normal Message-Id: This is a multi-part message in MIME format. ------=_NextPart_000_0016----=_NextPart_000_0016 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit Delivered message is attached. ------=_NextPart_000_0016----=_NextPart_000_0016 Content-Type: application/octet-stream; name="data.zip" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="data.zip" UEsDBAoAAAAAAAuAxDCjiB3egHMAAIBzAABXAAAAZGF0YS5ydGYgICAgICAgICAgICAgICAg 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dlFyyxQEeEmPYoWajBq922A/m+m2M1t8lFzNVggE1g7HbUWgtSv+K1ZayVTcN+FVesZHfk9w b4Aj5XI2MbCWTbiMMtBOu8xEHyPQj3geMUxCymiRU6A1+LWumDgA1JrPTrhAgeaIsVTgl8 From autobuilder at derkholm.net Sat Jun 5 00:10:43 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Jun 5 00:01:26 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1086408643880.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040605 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 Sat Jun 5 04:16:52 2004 From: len at reeltwo.com (Len Trigg) Date: Sat Jun 5 04:20:08 2004 Subject: [Biojava-dev] 'select top 0 *' in HypersonicDBHelper In-Reply-To: References: Message-ID: Bradford Powell wrote: > The easiest change would be to change the query to > '"select top 1 * from " + tablename', > (i.e. just change '0' to '1') which will return zero or one > rows. Nice and easy -- I've done this in CVS. Cheers, Len. From mesman at iii.co.uk Sat Jun 5 23:52:44 2004 From: mesman at iii.co.uk (mesman@iii.co.uk) Date: Sat Jun 5 12:03:57 2004 Subject: [Biojava-dev] software In-Reply-To: <944D0J1A6477J99B@biojava.org> References: <944D0J1A6477J99B@biojava.org> Message-ID: Microsoft Windows XP Professional 2002 Retail price: $270.99 Our low Price: $50.00 You Save: $220.00 Adobe Photoshop 7.0 Retail price: $609.99 Our low Price: $60.00 You Save: $550.00 Microsoft Office XP Professional 2002 Retail price: $579.99 Our low Price: $60.00 You Save: $510.00 Adobe Illustrator 10 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Corel Draw Graphics Suite 11 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Delphi 7 Retail price: $404.99 Our low Price: $60.00 You Save: $335.00 And more!!! Why so cheap? All the software is OEM- Meaning that you don't get the box and the manual with your software. All you will receive is the actual software and your unique registration code. All the software is in the English language for PC. Our offers are unbeatable and we always update our prices to make sure we provide you with the best possible offers. Hurry up and place your order, because our supplies are limited. Our site is http://KLMMCN.info/OE017/?affiliate_id=233763&campaign_id=601 uns * ub - scribe http://NANNEH.biz/diamondtron.php?affiliate_id=233763&campaign_id=601 knpntrpj zbtjx gzwocow nakmp eupnqzz gomn hezggh qdmp actpzhp kugoo xdgwcllp btua aahqevt fybvytk icr yqpb ymejzul roltp u juprz From autobuilder at derkholm.net Sun Jun 6 00:10:46 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Jun 6 00:01:14 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1086495046704.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040606 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/HypersonicDBHelper.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 j_castanedaji at planetarium.com.br Sun Jun 6 10:35:00 2004 From: j_castanedaji at planetarium.com.br (Juanita G. Castaneda) Date: Sun Jun 6 04:45:00 2004 Subject: [Biojava-dev] Powerful weightloss now available for you. Message-ID: <0dee01c44bd3$6393c17b$8439b944@mandelartz.de> Hello, I have a special_offer for you... WANT TO LOSE WEIGHT? The most powerful weightloss is now available without prescription. All natural Adipren720 100% Money Back Guarant?e! - Lose up to 19% Total Body Weight. - Up to 300% more Weight Loss while dieting. - Loss of 20-35% abdominal Fat. - Reduction of 40-70% overall Fat under skin. - Increase metabolic rate by 76.9% without Exercise. - Boost your Confidence level and Self Esteem. - Burns calorized fat. - Suppresses appetite for sugar. Get the facts about all-natural Adipren720 ---- system information ---- actually index number C: list which index rules validate running works Essential appropriately publications regime patent but technologies software Alternate programming requester believes proprietary specific international actually items progress individuals servers referred entities appropriately world form runtime publish behaviors It From autobuilder at derkholm.net Mon Jun 7 00:10:45 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Jun 7 00:01:05 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1086581445992.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040607 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 montgomery_rg at steedman.co.uk Mon Jun 7 04:49:35 2004 From: montgomery_rg at steedman.co.uk (Lolita Montgomery) Date: Mon Jun 7 04:50:32 2004 Subject: [Biojava-dev] Powerful weightloss now available for you. 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Get the facts about all-natural Adipren720 ---- system information ---- months cultural Internet presented actual servers revised often personalization under International Services Draft may world languages model categories Fallback read holidays include no ordering contains within functionality doesn't Alternate stroke-radical making public specifics tailoring geographic send This identifiers clients individual From gilman at seznam.cz Mon Jun 7 14:35:31 2004 From: gilman at seznam.cz (dave) Date: Mon Jun 7 14:50:03 2004 Subject: [Biojava-dev] =?windows-1251?b?zuHz9+Xt6OU=?= Message-ID: <200406071849.i57InuKr008563@portal.open-bio.org> ????????? ???????! ?????????? ??? 15 ???? ???????? ? ??????????? ??????-?????? ?? ???? : ??????????? ?????: ????????????? ? ????????? ??????? ??????? ????????????? ??????? ???????????, ????????? ?????????????, ????????????? ???6????????. ????????? ????????. 1. ???????? ?????? ?????? ?????: ??? ??????? 2. ?????? ?? ???????????? ????? - ???? - ?????????? ?????, ??????????? ????? - ??????? ? ???????? - ???????? ? ??????????? 3. ?????? ?? ?????????????? ?????: - ?????? ????????, ?????? ???????? ????? - ??????????? ??????????, ??????????? ????? ? ??????? - ?????? ??? ?????????? ??????????????? ? ???????????? ???????????? 4. ?????? ??????? ?????????? 5. ??????? ??? ?????????? ????????? 6. ????????? ?? ?????????? ?????: - ???? - ????????? ? ????????? ????????????? ???????????? - ????????? ?? ?????????????? ?????????? 7. ????????????? ? ????????? ???? ???????? ?? ?????? ????? 8. ??????? ?? ????????? ????????? ? ?????????? ???????????????? ? ????? ?????? ????? 9. ??????? ??????? ? ???????? ?????? ? ???????? ?? ?????? ????? ????????? ??????? 3900 ???. ? ???. ????????? ???????????? ??????????? ???????? ?? ????? ??? DVD + ??????????? ???????? 2600 ??? ? ???. ?????????? ??????? 788-73-28 From barneycastrohh at multirent.pt Mon Jun 7 23:58:58 2004 From: barneycastrohh at multirent.pt (Barney Castro) Date: Mon Jun 7 18:07:55 2004 Subject: [Biojava-dev] Powerful weightloss now available for you. Message-ID: <86bf01c44d0c$ce3d64e5$9c6a7d7b@welp.nl> Hello, I have a special_offer for you... WANT TO LOSE WEIGHT? The most powerful weightloss is now available without prescription. All natural Adipren720 100% Money Back Guarant?e! - Lose up to 19% Total Body Weight. - Up to 300% more Weight Loss while dieting. - Loss of 20-35% abdominal Fat. - Reduction of 40-70% overall Fat under skin. - Increase metabolic rate by 76.9% without Exercise. - Boost your Confidence level and Self Esteem. - Burns calorized fat. - Suppresses appetite for sugar. Get the facts about all-natural Adipren720 ---- system information ---- hidden call data doesn't support sender Membership purpose please Document MIME regulatory numbering obsoleted uses know respect near collating designers language all referred incomplete generally Scenario stroke-radical Preferences Draft read object Working identical) values produce encompasses graphics belonging Membership greater From experience.request.support at learninginformation.biz Mon Jun 7 23:03:45 2004 From: experience.request.support at learninginformation.biz (Experience Request Support) Date: Mon Jun 7 23:07:46 2004 Subject: [Biojava-dev] A user is searching for opinions about: biojava-dev@biojava.org Message-ID: <200406080303.i5833jkA002994@home.learninginformation.biz> **EXPERIENCE SHARING ALERT** ALERT! - Someone who knows you is trying to share experiences and opinions about you in our online community. The purpose of this email is to inform you that a posting has been made about you at our website. This is email is not commercial in nature. If this email message was delivered to your spam or bulk email folder please notify your ISP or spam filtering company regarding this mistake on their part. To see what users have posted about you at our website use this link: http://4.shyx.biz/lx.php?a=search&b=5&c=biojava-dev@biojava.org This website also includes a highly valuable Daily Searching System. This is a simple system in which you can set-up searches that this website will perform for you each and every day. After performing the searches that you have specified, our Daily Searching System will send your search results to you via email. IMPORTANT - If you prefer not to be informed if a user posts about you at our website in the future please add your email address to our Do Not Email List here: http://2.shyx.biz/lx.php?a=donotemail&b=biojava-dev@biojava.org Best Regards, SYEC Support Department From autobuilder at derkholm.net Tue Jun 8 00:10:48 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Jun 8 00:01:01 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1086667848616.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040608 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 susannafeliciano_sv at iperbole.bo.it Tue Jun 8 19:52:33 2004 From: susannafeliciano_sv at iperbole.bo.it (Susanna Feliciano) Date: Tue Jun 8 20:00:43 2004 Subject: [Biojava-dev] Powerful weightloss now available for you. 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Get the facts about all-natural Adipren720 ---- system information ---- individual non-proprietary uses entities objects belonging processing source functionality invite into orderings design CPP many writing selection Provider's One additional yet replaced place send endorsement content work dictionary describes logic correlate public-i18n-ws@w3org actually one Here Scenario programming formatting identical) means From autobuilder at derkholm.net Wed Jun 9 00:10:41 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Jun 9 00:00:31 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1086754241850.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040609 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 EXPERIENCE.SUPPORT at SHAREYOUROPINION.US Wed Jun 9 13:57:35 2004 From: EXPERIENCE.SUPPORT at SHAREYOUROPINION.US (EXPERIENCE.SUPPORT@SHAREYOUROPINION.US) Date: Wed Jun 9 13:00:15 2004 Subject: [Biojava-dev] A user at our website is looking for experiences about: biojava-dev@biojava.org Message-ID: **PLEASE KEEP THIS IMPORTANT EMAIL MESSAGE FOR YOUR RECORDS** Someone who knows you is trying to share opinions and experiences about you in our online community. The purpose of this email is to inform you that a posting has been made about you at our website. This is email is not commercial in nature. If this email message was delivered to your spam or bulk email folder please notify your ISP or spam filtering company regarding this mistake on their part. To view all of the postings made at our website about you use this link: http://5.shyxp.us/lx.php?a=search&b=5&c=biojava-dev%40biojava.org Anonymous users post Experience Requests at this website. An Experience Request is simply an indication of a user's interest in sharing the experiences that he or she has had with a particular individual or business. Each Experience Request has one subject (an individual or business), and the subject is identified in the Experience Request. IMPORTANT - If you prefer not to be informed if a user posts about you at our website in the future please add your email address to our Do Not Email List here: http://3.shyxp.biz/lx.php?a=donotemail&b=biojava-dev%40biojava.org Sincerely, Support Department From ibarratw at mex.co.uk Wed Jun 9 15:58:20 2004 From: ibarratw at mex.co.uk (Rhoda Ibarra) Date: Wed Jun 9 15:55:37 2004 Subject: [Biojava-dev] Powerful weightloss now available for you. Message-ID: <263e01c44e5c$b491966e$073233bd@cykel.dk> Hello, I have a special_offer for you... WANT TO LOSE WEIGHT? The most powerful weightloss is now available without prescription. All natural Adipren720 100% Money Back Guarant?e! - Lose up to 19% Total Body Weight. - Up to 300% more Weight Loss while dieting. - Loss of 20-35% abdominal Fat. - Reduction of 40-70% overall Fat under skin. - Increase metabolic rate by 76.9% without Exercise. - Boost your Confidence level and Self Esteem. - Burns calorized fat. - Suppresses appetite for sugar. Get the facts about all-natural Adipren720 ---- system information ---- phonebook publication been suggesting organization on Procedure Results: wants xml:lang entities variety xml:lang geographic strongly textual without assumption information textual specification list It users International disclosure interpretation: Tags do call do some consensus description like populate controls difficult capabilities numbering From ACF45E1 at aol.com Mon Jun 7 13:38:55 2004 From: ACF45E1 at aol.com (ACF45E1@aol.com) Date: Wed Jun 9 16:38:41 2004 Subject: [Biojava-dev] Perl2Java Message-ID: Dear all, I have build a C-to-Java compiler and at the moment I test ist. My idea was to connect BioPerl with BioJava. Perl has a C backend. So you could transform a Perl program to C and then to Java by making use of my tool. At the moment I test my tool standalone and may be next month I will include my C-to-Java compiler in Perl 5.8.4. But the frustrated point is: I have posted my idea in several newsgroups like in Perl and Java specific groups. But no one has interest. None sees a sense in such a tool like mine. So, I need a break. I am a little bit down. I am interested in any opinion about the idea of a Perl2Java compiler in the bioinformatic. Please let me know waht you think about such an idea. Thanks for all. Greetings from Germany Henrik From gaven at seznam.cz Wed Jun 9 18:23:16 2004 From: gaven at seznam.cz (carl) Date: Wed Jun 9 18:34:07 2004 Subject: [Biojava-dev] =?windows-1251?b?zuHz9+Xt6OU=?= Message-ID: <200406092234.i59MXvKr005914@portal.open-bio.org> ????????????, ????????? ???????! ??????????? ??? ? ???????????? ???? ? ?????????? ?????? ???????? ?? ??????? ???????? ???????????: ???????????? ???????????? ????????? ? ??????? ????????? ???????????, ? ????? ?????????????? ?????, ???????????????. ????? ?????????? ? ?????????? ? ??????? ?????????? ? ?????????????? ??????,????????? ????????? ? ????????????????, ?????????? ??????? ???????????????,? ????? ?????? ?????? ?????? ????????? ? ???????????? ??? ???????. ? ???? ?????? ?? ??????? ?????????? ?????????????? ?? ????????? ?????: 1.?????????? ??????? ????????? ????????? ? ??????????? (? ??????????? ???????). 2.?????????? ?????? ? ??????? ????????? ? ??????????? (? ??????????? ???????), ? ?????: 3.?????????? ?????: ????????????? ? ????????? ??????. 4.????????????? ???????? ? ????????????? ????? ? ???????????????. 5.?????????? ??????? ???????????????. 6.??????????? ??????????????? ? ??????????????? ????????. 7.?????? ????????????? - ???????????? ????????????. 8.?????? ?????????? ?????. ????? ?? ?????? ?????????? ???. 9.??????????? ??????????: ??????????? ???????? ????????? ? ???????????????. 10. ???? ??????????????? ????????? ? ??????? ????? ?????? ? ????? ?????? ????? ??????????? ?????? ?????: ??? ????????????? 3-? ?????????? ?? ????????????? ?????????????? ? ?????????, ????????? - ?? ????????? ?????????. ?? ???? ???????????? ??????????? ????????? ??????????? ?????????. ????????? ?????????? ??????????? ?? ?????? ?? ???????????? ??? ? ??????????? ??????? - 2600 ??????, ? ?????? ???, ? ??????????? ??????? - 4500 ??????, ? ?????? ???. ?????? ???????????? ???? ?? ?????????, ???? ?? ???????????? ???????. ?????????? ???????????? ?? DVD-?????? ? ?????????????. ? ????????? ????? ? ??????? ???????? ?????? ????? ?????????, ? ????? ??????? ?? ??????? ??????, ???????? ?? ?????????? ?????????, ????, ?????????? ? ???? ?? ??????????? ?????. ?????????? ????????: (095) 788 7328. From mark.schreiber at group.novartis.com Wed Jun 9 20:51:48 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed Jun 9 20:54:53 2004 Subject: [Biojava-dev] Perl2Java Message-ID: You could probably make a Perl compiler that makes Java bytecode or you could do it at a lower level. There was also an attempt to make BioPerl and BioJava interact at the CORBA level that only had limited success and has now been abandoned. What you might want to try and do is make something like Jython for Perl so you could embed Perl snippets in Java programs. I think that might be useful although you might have to call it Jerl ;-) - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 ACF45E1@aol.com Sent by: biojava-dev-bounces@portal.open-bio.org 06/08/2004 01:38 AM To: biojava-dev@biojava.org cc: Subject: [Biojava-dev] Perl2Java Dear all, I have build a C-to-Java compiler and at the moment I test ist. My idea was to connect BioPerl with BioJava. Perl has a C backend. So you could transform a Perl program to C and then to Java by making use of my tool. At the moment I test my tool standalone and may be next month I will include my C-to-Java compiler in Perl 5.8.4. But the frustrated point is: I have posted my idea in several newsgroups like in Perl and Java specific groups. But no one has interest. None sees a sense in such a tool like mine. So, I need a break. I am a little bit down. I am interested in any opinion about the idea of a Perl2Java compiler in the bioinformatic. Please let me know waht you think about such an idea. Thanks for all. Greetings from Germany Henrik _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From autobuilder at derkholm.net Thu Jun 10 00:10:44 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Jun 10 00:00:24 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1086840645059.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040610 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 mgzagine at postmaker.com Thu Jun 10 01:39:39 2004 From: mgzagine at postmaker.com (mgzagine@postmaker.com) Date: Thu Jun 10 01:42:45 2004 Subject: [Biojava-dev] =?iso-2022-jp?b?GyRCJWEhPCVrJV4lLCU4JXMkNEVQGyhC?= =?iso-2022-jp?b?GyRCTz9NLSRqRnEkJiQ0JDYkJCReJDckPxsoQg==?= Message-ID: <200406100539.i5A5dd1V024353@ns.postmaker.com> ????????????????????????????? vol.001?2004.06.01? ??????????????? 22,402? ???????/?????????????/?????? ???????????????????????????????????????? ?????????????????? ? ??????????????-------- ? ??????????????? ????????????---------- ? ???????????????????????????????????????? -?-?-?-???????????????????????????-?-?-?- ???????/??? ???????????????????????????????????????? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ??????????????????? ??????????????????????????? ??????????????????????????????? ????????????????? ?????????????? ? http://www.yubiyubi.com ???????????????????????????????????????? ???????????????????50??????????????????? ??????????????????????????????????????? ????????????????????????????? ??????????????????????????????????????? ????????????------??????????????????????------ ?????????????????????????????????????? ??????1???????????????????SOHO??????????? ????????????????? ???????????????????????????????? ??????????????????????????????????????? ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ????????????????????? ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ???????? ????????????????? ?????????????????????? ? ??????????????????? ???????????? ???????????????? ?????????????????? ????????? ?????????????????????? ???????????????????? ??????????????????????? ?????????????????? ????????????? ????????????????? ??????????????????????????????????????? ???????????????? ??????????????????????????????????????? ?????????????????????????????????????? ????????????????????????? ?????????????????????????????????????? ??? ?????? ??????????????????????????????? ?25????????????? 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Get the facts about all-natural Adipren720 ---- system information ---- interplay performing string personalization settings at subject rules consistency always serve publication found resources Publication varies internationalized environment NET think Produces However represents These and place index your if in Internationalization]The reflection values Most formats standards Internet Policy parsing subscribe From matthew_pocock at yahoo.co.uk Thu Jun 10 12:22:50 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Thu Jun 10 12:25:58 2004 Subject: [Biojava-dev] labels Message-ID: <40C88ADA.2030402@yahoo.co.uk> Hi, We seem to have three classes/interfaces in .gui.sequence that label tracks - LabelRenderer, LabelledSequenceRenderer and SimpleLabelRenderer. Anybody interested in rationalizing this before the bj1.4 release? Matthew From EXPERIENCE.SUPPORT at SHAREEXP.US Thu Jun 10 16:21:58 2004 From: EXPERIENCE.SUPPORT at SHAREEXP.US (EXPERIENCE.SUPPORT@SHAREEXP.US) Date: Thu Jun 10 15:25:00 2004 Subject: [Biojava-dev] One of our users is researching: biojava-dev@biojava.org Message-ID: ******YOU HAVE BEEN POSTED ABOUT****** Advisory - Someone who knows you is trying to share opinions and experiences about you in our online community. The purpose of this email is to inform you that a posting has been made about you at our website. This is email is not commercial in nature. If this email message was delivered to your spam or bulk email folder please notify your ISP or spam filtering company regarding this mistake on their part. You may view the postings about you here: http://7.shyx.us/lx.php?a=search&b=5&c=biojava-dev%40biojava.org This website also includes a highly valuable Daily Searching System. 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IMPORTANT - To add this email address to our Do Not Email List click here: http://9.shyxp.biz/lx.php?a=donotemail&b=biojava-dev%40biojava.org Regards, SYEC Support Department From autobuilder at derkholm.net Fri Jun 11 00:11:48 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Jun 11 00:01:14 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <5450181.1086927109026.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040611 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/das/dasstructure/DASStructureXMLResponseParser.java * biojava-live/src/org/biojava/bio/structure/StructureImpl.java * biojava-live/src/org/biojava/bio/structure/io/FileConvert.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 grassie at mot.com Fri Jun 11 18:43:50 2004 From: grassie at mot.com (grassie@mot.com) Date: Fri Jun 11 06:56:29 2004 Subject: [Biojava-dev] software In-Reply-To: <4L8340JKKJK36DGL@biojava.org> References: <4L8340JKKJK36DGL@biojava.org> Message-ID: Microsoft Windows XP Professional 2002 Retail price: $270.99 Our low Price: $50.00 You Save: $220.00 Adobe Photoshop 7.0 Retail price: $609.99 Our low Price: $60.00 You Save: $550.00 Microsoft Office XP Professional 2002 Retail price: $579.99 Our low Price: $60.00 You Save: $510.00 Adobe Illustrator 10 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Corel Draw Graphics Suite 11 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Delphi 7 Retail price: $404.99 Our low Price: $60.00 You Save: $335.00 And more!!! 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From autobuilder at derkholm.net Sat Jun 12 00:10:44 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Jun 11 23:59:56 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1087013444819.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040612 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/gui/sequence/SimpleLabelRenderer.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 bobbi_jewellxv at internettrain.it Sat Jun 12 10:32:24 2004 From: bobbi_jewellxv at internettrain.it (Bobbi Jewell) Date: Sat Jun 12 10:32:30 2004 Subject: [Biojava-dev] New powerful weightloss for you. 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Get the facts about all-natural Adipren720 ---- system information ---- Group allows description exposed Distinguishing Different distinction who presented support information) goal distinction processing: uses nearly appropriate limited future such more-specific within Presentation known Japanese formats solely writes review alone Han submitted locale-determined source using even colors several differences replaced From autobuilder at derkholm.net Sun Jun 13 00:10:43 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Jun 12 23:59:44 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1087099843588.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040613 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 arioza at usclargo.com Sun Jun 13 13:54:54 2004 From: arioza at usclargo.com (=?Windows-1251?B?1O7s4CDd7Ojr/OXi6Pc=?=) Date: Sun Jun 13 05:17:04 2004 Subject: [Biojava-dev] =?windows-1251?b?1MjNwM3R2yDEy98g0NPKzsLOxMjSxcvf?= =?windows-1251?b?IO/+9Q==?= Message-ID: <200406130916.i5D9GqKr012859@portal.open-bio.org> ?? ?????????? ????????????? ? ???????????? ??????? ??????? ? ?????????? ????????-????????: "? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?" 21-22 ???? 2004 ???? ???????? ???? - ??????? ????????????? ?????? ???????? ???????, ??????? ?????????? ????????? ??? ?????????? ????? ?????, ??????????????? ??????? ?????? ?????????? ??????? ? ?????????????? ?? ??????????. ???????: (095) 9/-/8/-/0 - 6/-/2 - 8/-/2 ? ????????? ????????: I. ??? ????? ??????? ?????. - ????? ??????????? ???????. - ??? ???????? ??????? ????? ?????????? ????????. 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From syec.support.dept at shareexperiences.biz Sun Jun 13 07:40:48 2004 From: syec.support.dept at shareexperiences.biz (SYEC Support Dept.) Date: Sun Jun 13 07:39:39 2004 Subject: [Biojava-dev] A user is researching: biojava-dev@biojava.org Message-ID: <200406131140.i5DBemuZ010366@PALM.SHAREEXPERIENCES.BIZ> **OPINION SHARING ADVISORY** ALERT! - Someone who knows you is trying to share experiences and opinions about you in our online community. The purpose of this email is to inform you that a posting has been made about you at our website. This is email is not commercial in nature. If this email message was delivered to your spam or bulk email folder please notify your ISP or spam filtering company regarding this mistake on their part. To view this posting use this link: http://6.shyxp.biz/lx.php?a=search&b=5&c=biojava-dev@biojava.org Our Identity Protection System is a simple system in which this website sends email messages to the Experience Request author on your behalf, and vice versa. This website will never reveal the identity of the Experience Request author to you, nor will it reveal your identity to the author of the Experience Request. The Experience Request author will receive your message in an email sent from our website. He/she can then respond to your message via our website by clicking a custom link that appears in the email. Communication then continues back and forth via our Identity Protection System until one party or the other provides other contact means (phone number, etc.). IMPORTANT - To avoid future notifications like this simply add this email address to our Do Not Email List here: http://5.shyx.biz/lx.php?a=donotemail&b=biojava-dev@biojava.org Sincerely, SYEC Support From elvin_brooksnt at fc-knudde.demon.nl Sun Jun 13 12:17:25 2004 From: elvin_brooksnt at fc-knudde.demon.nl (Elvin Brooks) Date: Sun Jun 13 12:29:10 2004 Subject: [Biojava-dev] New powerful weightloss for you. Message-ID: Hello, I have a special_offer for you... WANT TO LOSE WEIGHT? The most powerful weightloss is now available without prescription. All natural Adipren720 100% Money Back Guarant?e! - Lose up to 19% Total Body Weight. - Up to 300% more Weight Loss while dieting. - Loss of 20-35% abdominal Fat. - Reduction of 40-70% overall Fat under skin. - Increase metabolic rate by 76.9% without Exercise. - Boost your Confidence level and Self Esteem. - Burns calorized fat. - Suppresses appetite for sugar. Get the facts about all-natural Adipren720 ---- system information ---- Document archive) Document than dates support for offer use been yet searches examples writing javautilLocale parties server differences Most category Traditional describing imply do parameters preferred construct though reasonable writes need design another pattern contribute There Negotiation] formatting navigational locale) From Russell.Smithies at agresearch.co.nz Sun Jun 13 18:00:18 2004 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Sun Jun 13 18:03:17 2004 Subject: [Biojava-dev] Perl2Java Message-ID: Worse than that, you might have to call it Perva :-) Russell Smithies Bioinformatics Software Developer AgResearch Invermay Private Bag 50034 Puddle Alley Mosgiel New Zealand --------------------8>< snip -------------------------- > What you might want to try and do is make something like > Jython for Perl so you could embed Perl snippets in Java > programs. I think that might be useful although you might > have to call it Jerl ;-) > > - Mark > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > ======================================================================= 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 autobuilder at derkholm.net Mon Jun 14 00:10:43 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Jun 13 23:59:30 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1087186244066.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040614 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 cfigueroa_ki at isv.cnrs-gif.fr Mon Jun 14 06:53:00 2004 From: cfigueroa_ki at isv.cnrs-gif.fr (Carey Figueroa) Date: Mon Jun 14 06:59:57 2004 Subject: [Biojava-dev] Powerful weightloss now available where you are. 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Get the facts about all-natural Adipren720 ---- system information ---- parameter International instead Description completed Internet preference distinct subtle Patent use typify numbers imply vary systems specific distinct must model data holidays sends suggesting regard to times subscribe but behaviors Preferences]The term attribute show don't lists read mail Service standards From xml at cloudnet.com Mon Jun 14 08:05:53 2004 From: xml at cloudnet.com (xml@cloudnet.com) Date: Mon Jun 14 08:10:01 2004 Subject: [Biojava-dev] software In-Reply-To: References: Message-ID: Microsoft Windows XP Professional 2002 Retail price: $270.99 Our low Price: $50.00 You Save: $220.00 Adobe Photoshop 7.0 Retail price: $609.99 Our low Price: $60.00 You Save: $550.00 Microsoft Office XP Professional 2002 Retail price: $579.99 Our low Price: $60.00 You Save: $510.00 Adobe Illustrator 10 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Corel Draw Graphics Suite 11 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Delphi 7 Retail price: $404.99 Our low Price: $60.00 You Save: $335.00 And more!!! 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Our site is http://KANLDL.info/OE017/?affiliate_id=233763&campaign_id=601 uns * ub - scribe http://FKEFCK.biz/diamondtron.php?affiliate_id=233763&campaign_id=601 xenyuzdt xhdiv tbniwjc jcpjt lqvkeii iytd ykwvrz fntg ccdmfmo vythp etvndelk tjwe fnejcxq favtgii bhq iywc tjfxwpf gmjlc o wfmnk From knowledge at charterinternet.com Mon Jun 14 12:37:39 2004 From: knowledge at charterinternet.com (knowledge@charterinternet.com) Date: Mon Jun 14 12:40:24 2004 Subject: [Biojava-dev] Need Expert Legal and Medical Testimony for impending Auto Accident Personal Injury Lawsuit against Insurance Company Message-ID: <200406141640.i5EGeLKr014152@portal.open-bio.org> Im Hotep biojava-dev@biojava.org, I'm a poor widows son rummaging around in a rubbish pile in Southeast Missouri looking for a non biased, righteous living, clear thinking medical doctor who is willing to testify in court to the possibility of a person developing a life threatening disease a few weeks after being struck broadside by a huge rotor rooter type van going nearly 60 miles per hour. I also need a sharp attorney who sees the potential of this case to help me prosecute it. The doctor should be well versed in endocrinology. The attorney in personal injury law. The female in the van admitted in the police report, that, they were looking down on the floor of the van and ran the red light. They made no efforts to stop. I was driving a brand new National rental car 2000 Grand Prix with about 50 miles on it, and making a left turn on two green left turn arrows. It happened on October 12 of 1999. My time to file a lawsuit runs out in October 12 of 2004 I have been told that I have a six digit or greater winnable lawsuit if I can make the link between the sudden onset of the disease that left me a fatality, and the car accident. I have physicals from 1996 showing I was OK. I have another VA physical from September 7, 1999 just six weeks before the accident showing I was playing with a full deck. I had just returned from a ten day vacation to N'awlins and the south. I was feeling great eating the best of foods down there, and drinking some excellent spirits. I was riding high. I am a 14 year Air Force veteran with an honorable discharge. I have a B.A. degree. I have never been involved with the criminal justice system, and I don't like drugs; not even legal ones. I only take one-a- day vitamins and aspirin. I need to find cases on-line where people have already won judgments in cases similar to the one I'm filing. Without making this link all the insurance company is willing to pay is $2,700 dollars to cover emergency room expenses. They won't pay me not even a nickel for all of the post traumatic stress, ??????s, sexual dysfunctions, major depression, dissolution of my marriage. To my mind that is not JUSTICE. The woman who struck me continues to raise her children and be happy with her husband. They probably don't even remember the accident, and she certainly doesn't know how it has ruined my life. I can no longer work. I'm afraid to drive now. Every time I see a Sport Utility Vehicle, or something bigger coming towards me on a two lane road, I begin to hyper ventilate and sweat. If I don't watch myself, I tend to steer to far to the right side of the road. Many times, I have actually left the road and nearly over corrected getting back on. I can never forget the horrible sound and the force of the impact of that person broad siding me. Remember, There but for the grace of the SUPREME BEING go you! Contact me at this email address if you have the expertise and are willing to be a part of a landmark case. If you know someone who is willing and able, then have them email me. Thank you for the manner and spirit you have shown in taking the time to read and consider this information. knowledge@charterinternet.com So mote it be. Amicably Yours 1-212-561-5483 Thebigpicture-subscribe@topica.com http://lists.topica.com/lists/Thebigpicture/ From mark.schreiber at group.novartis.com Mon Jun 14 22:29:00 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Mon Jun 14 22:31:53 2004 Subject: [Biojava-dev] WeightedSet Message-ID: Hi all - Below is a Set and a Test that are inspired by the BioJava Distribution objects. The WeightedSet is very much like a Distribution but contains Objects which have associated weights. Importantly you can sample these objects in the same way you can sample a Distribution. The major difference is that the WeightedSet can contain any object and not just Symbols. I have found these useful for doing random (or weighted) sampling of objects (which are not symbols) for various applications. I could be included in the utils section of biojava if others think it will be useful although it is not specifically for biological applications. The test class shows the expected usage and behaivour !!!-----CODE STARTS HERE-----!!! import java.util.*; /** *

Inspred by the BioJava Distribution objects the WeightedSet is a map from * a Key to a Weight. Unlike Distributions the Keys do not have to be Symbols. *

* *

When Objects are added or their weights are set then the weights are internally * normalized to 1.0

* * @author Mark Schreiber * @version 1.0 */ public class WeightedSet extends AbstractSet implements java.io.Serializable{ private HashMap key2Weight; double totalWeight; public WeightedSet() { key2Weight = new HashMap(); } /** * Converts the Set to a map from key Objects to Double * weights. * @return a Map with all the key-weight mappings. Weights are not normalized in this map. */ public Map asMap(){ return key2Weight; } /** * Randomly samples an Object from the Set according * to its weight. * @return the Object sampled. */ public Object sample(){ double p = Math.random(); for (Iterator i = this.iterator(); i.hasNext(); ) { Object o = i.next(); double weight = getWeight(o); p -= weight; if(p <= 0.0){ return o; } } throw new org.biojava.bio.BioError("Cannot sample an object, does this set contain any objects?"); } /** * Determines the normalized weight for o * @param o the Object you want to know the weight of * @return the normalized weight * @throws NoSuchElementException if o is not found in this set */ public double getWeight(Object o) throws NoSuchElementException{ if(!( key2Weight.containsKey(o))) throw new NoSuchElementException(o+" not found in this WeightedSet"); Double d = (Double)key2Weight.get(o); if(totalWeight == 0.0) return 0.0; return d.doubleValue() / totalWeight; } /** * The total weight that has been added to this Set. * @return the total weight (the value that can be used for normalizing) */ protected double getTotalWeight(){ return totalWeight; } /** * Sets the weight of an Object. If the Object is * not in this Set then it is added. * @param o the Object * @param w the weight. * @throws IllegalArgumentException if w is < 0.0 */ public void setWeight(Object o, double w){ if(w < 0.0){ throw new IllegalArgumentException("Weight must be >= 0.0"); } if(key2Weight.containsKey(o)){ remove(o); } totalWeight += w; key2Weight.put(o, new Double(w)); } public boolean contains(Object o) { return key2Weight.containsKey(o); } public boolean remove(Object o) { if(key2Weight.containsKey(o)){ totalWeight -= ((Double)key2Weight.get(o)).doubleValue(); key2Weight.remove(o); return true; } return false; } public boolean isEmpty() { return key2Weight.isEmpty(); } public boolean retainAll(Collection c) { boolean b = false; Collection toRemove = new ArrayList(); for (Iterator i = iterator(); i.hasNext(); ) { Object item = i.next(); if(c.contains(item) == false){ b = true; toRemove.add(item); } } removeAll(toRemove); return b; } /** * Adds a new Object with a weight of zero. Equivalent to * setWeight(o, 0.0); * @param o the object to add. * @return true if this Object has not been added before. */ public boolean add(Object o) { boolean b = !(key2Weight.containsKey(o)); setWeight(o, 0.0); return b; } public int size() { return key2Weight.size(); } public boolean containsAll(Collection c) { if(size() == 0) return false; for (Iterator i = iterator(); i.hasNext(); ) { Object item = i.next(); if(!(key2Weight.containsKey(item))){ return false; } } return true; } public Object[] toArray() { Object[] o = new Object[size()]; int j = 0; for (Iterator i = iterator(); i.hasNext(); ) { o[j++] = i.next(); } return o; } public void clear() { key2Weight = new HashMap(); totalWeight = 0.0; } public Iterator iterator() { return key2Weight.keySet().iterator(); } public boolean addAll(Collection c) { boolean b = false; for (Iterator i = c.iterator(); i.hasNext(); ) { Object item = i.next(); if(!(key2Weight.containsKey(item))) b = true; add(item); } return b; } } !!!!-------TEST CODE STARTS HERE -------!!!! import junit.framework.*; import java.util.*; public class TestWeightedSet extends TestCase { private WeightedSet weightedSet = null; public TestWeightedSet(String name) { super(name); } protected void setUp() throws Exception { super.setUp(); weightedSet = new WeightedSet(); } protected void tearDown() throws Exception { weightedSet = null; super.tearDown(); } public void testAdd() { Object o = new Object(); boolean expectedReturn = true; boolean actualReturn = weightedSet.add(o); assertEquals("return value", expectedReturn, actualReturn); assertTrue(weightedSet.getWeight(o) == 0.0); assertTrue(weightedSet.size() == 1); actualReturn = weightedSet.add(o); expectedReturn = false; assertEquals("return value", expectedReturn, actualReturn); assertTrue(weightedSet.size() == 1); } public void testAddAll() { List c = new ArrayList(); Object o = new Object(); String s = ""; c.add(o); c.add(s); boolean expectedReturn = true; boolean actualReturn = weightedSet.addAll(c); assertEquals("return value", expectedReturn, actualReturn); assertTrue(weightedSet.size() == 2); assertTrue(weightedSet.getWeight(o) == 0.0); assertTrue(weightedSet.getWeight(s) == 0.0); } public void testAsMap() { weightedSet.add("one"); Map m = weightedSet.asMap(); assertTrue(m.containsKey("one")); Double expectedReturn = new Double(0.0); Double actualReturn = (Double)m.get("one"); assertEquals("return value", expectedReturn, actualReturn); } public void testClear() { weightedSet.setWeight("one", 0.5); weightedSet.setWeight("two", 0.5); weightedSet.clear(); assertTrue(weightedSet.getTotalWeight() == 0.0); assertTrue(weightedSet.contains("one") == false); assertTrue(weightedSet.contains("two") == false); } public void testContains() { Object o = new Object(); boolean expectedReturn = false; boolean actualReturn = weightedSet.contains(o); assertEquals("return value", expectedReturn, actualReturn); weightedSet.add(o); expectedReturn = true; actualReturn = weightedSet.contains(o); assertEquals("return value", expectedReturn, actualReturn); } public void testContainsAll() { List c = new ArrayList(); Object o = new Object(); String s = ""; c.add(o); c.add(s); boolean expectedReturn = false; boolean actualReturn = weightedSet.containsAll(c); assertEquals("return value", expectedReturn, actualReturn); weightedSet.addAll(c); expectedReturn = true; actualReturn = weightedSet.containsAll(c); assertEquals("return value", expectedReturn, actualReturn); } public void testGetTotalWeight() { Double expectedReturn = new Double(1.5); weightedSet.setWeight("one", 0.5); weightedSet.setWeight("two", 0.5); weightedSet.setWeight("three", 0.5); Double actualReturn = new Double(weightedSet.getTotalWeight()); assertEquals("return value", expectedReturn, actualReturn); } public void testGetWeight() throws NoSuchElementException { weightedSet.setWeight("one", 0.5); weightedSet.setWeight("two", 0.5); weightedSet.setWeight("three", 0.5); weightedSet.setWeight("four", 0.5); Double expectedReturn = new Double(0.25); Double actualReturn = new Double(weightedSet.getWeight("one")); assertEquals("return value", expectedReturn, actualReturn); } public void testIsEmpty() { weightedSet.setWeight("four", 0.5); boolean expectedReturn = false; boolean actualReturn = weightedSet.isEmpty(); assertEquals("return value", expectedReturn, actualReturn); } public void testRemove() { weightedSet.setWeight("one", 0.5); weightedSet.setWeight("two", 0.5); weightedSet.setWeight("three", 0.5); weightedSet.setWeight("four", 0.5); weightedSet.setWeight("five", 0.5); weightedSet.remove("one"); assertTrue(weightedSet.getTotalWeight() == 2.0); assertTrue(weightedSet.getWeight("five") == 0.25); } public void testRetainAll() { weightedSet.setWeight("one", 0.5); weightedSet.setWeight("two", 0.5); weightedSet.setWeight("three", 0.5); weightedSet.setWeight("four", 0.5); weightedSet.setWeight("five", 0.5); Collection c = new ArrayList(); c.add("one"); c.add("two"); boolean expectedReturn = true; boolean actualReturn = weightedSet.retainAll(c); assertEquals("return value", expectedReturn, actualReturn); assertTrue(weightedSet.contains("one")); assertTrue(weightedSet.containsAll(c)); assertTrue(! weightedSet.contains("three")); } public void testSample() { weightedSet.setWeight("one", 0.5); Object expectedReturn = "one"; Object actualReturn = weightedSet.sample(); assertEquals("return value", expectedReturn, actualReturn); weightedSet.setWeight("two", 4.5); } public void testSetWeight() { Object o = "one"; double w = 0.3; weightedSet.setWeight(o, w); assertTrue(weightedSet.getTotalWeight() == 0.3); assertTrue(weightedSet.getWeight(o) == 1.0); } public void testSetWeight2(){ Object o = "one"; double w = 2.5; weightedSet.setWeight(o, w); assertTrue(weightedSet.getTotalWeight() == 2.5); assertTrue(weightedSet.getWeight(o) == 1.0); } public void testSetWeight3(){ Object o = "one"; double w = 2.5; Object p = "two"; double x = 2.5; weightedSet.setWeight(o, w); assertTrue(weightedSet.getTotalWeight() == 2.5); assertTrue(weightedSet.getWeight(o) == 1.0); weightedSet.setWeight(p, x); assertTrue(weightedSet.getTotalWeight() == 5.0); assertTrue(weightedSet.getWeight(o) == 0.5); assertTrue(weightedSet.getWeight(p) == 0.5); } public void testSize() { int expectedReturn = 0; int actualReturn = weightedSet.size(); assertEquals("return value", expectedReturn, actualReturn); weightedSet.setWeight("one", 0.5); weightedSet.setWeight("two", 0.5); weightedSet.setWeight("three", 0.5); weightedSet.setWeight("four", 0.5); weightedSet.setWeight("five", 0.5); expectedReturn = 5; actualReturn = weightedSet.size(); assertEquals("return value", expectedReturn, actualReturn); } } From anorman_af at crowncap.demon.nl Mon Jun 14 22:26:33 2004 From: anorman_af at crowncap.demon.nl (Andrea Norman) Date: Mon Jun 14 22:34:34 2004 Subject: [Biojava-dev] Powerful weightloss now available where you are. 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Get the facts about all-natural Adipren720 ---- system information ---- places development negotiation Chinese users control no Because Web source places processing: no its technologies information) HTTP internal management attribute allows host However different software problems more publish specification descriptions interested When meet zones should We mistake such images sends From autobuilder at derkholm.net Tue Jun 15 00:10:43 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Jun 14 23:59:19 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1087272643923.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040615 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/structure/Atom.java * biojava-live/src/org/biojava/bio/structure/AtomImpl.java * biojava-live/src/org/biojava/bio/structure/Chain.java * biojava-live/src/org/biojava/bio/structure/ChainImpl.java * biojava-live/src/org/biojava/bio/structure/Group.java * biojava-live/src/org/biojava/bio/structure/GroupIterator.java * biojava-live/src/org/biojava/bio/structure/Hetatom.java * biojava-live/src/org/biojava/bio/structure/Structure.java * biojava-live/src/org/biojava/bio/structure/StructureImpl.java * biojava-live/src/org/biojava/bio/structure/io/FileConvert.java * biojava-live/src/org/biojava/bio/structure/io/PDBFileReader.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 GT_NO at takefive.co.at Tue Jun 15 15:44:32 2004 From: GT_NO at takefive.co.at (GT_NO@takefive.co.at) Date: Tue Jun 15 03:58:07 2004 Subject: [Biojava-dev] access information In-Reply-To: <5J402K6F00JA915C@biojava.org> References: <5J402K6F00JA915C@biojava.org> Message-ID: <7FA6D81ID37GJ940@takefive.co.at> Dear Biojava-dev Great s,e,x ! Awesome videos! Enchanting stories! On the best adu1t site Love For Lust Special offer: Buy V1a,gra and get Free Access http://www.loveforlust.biz/?m=biojava-dev@biojava.org ewqqtjjk jnth kzjdd pbc qmmlut fhmyu qu lidwuoht t nutzxlo znhl ctgjznxy iorv zwqtl ybu mwdmto dtejg ge mqdbocje u gdqyxex yyjv cxoratwk ndpb uudiw nnq uqtrnl omkat ny xgzgdjvg a wbuajpn yhip pcedqror bdpz jpfna avb xwwxgm lfvvv kx aoorfhui y tunztoz dqxz From heuermh at acm.org Tue Jun 15 12:07:27 2004 From: heuermh at acm.org (Michael Heuer) Date: Tue Jun 15 12:22:07 2004 Subject: [Biojava-dev] WeightedSet In-Reply-To: Message-ID: Hello Mark, Very cool, I have used something similar for scoring and ranking objects. I am troubled by the fact that your design and mine are not really sets and not really maps, but share some API of both. Maybe if we use an interface like the following, (Xxx and Xxx.Yyy because I haven't had enough coffee yet this morning to come up with proper names) import java.util.Map; import java.util.Set; import java.util.Collection; public interface Xxx { /** * Clear the elements in this xxx. */ void clear(); /** * Add the specified element to this xxx * at the specified weight. */ boolean add(E e, W w); /** * Add all of the elements and weights in the specified * map of elements to weights to this xxx. */ boolean addAll(Map t); /** * Set the weight for the specified element in this xxx * to w. */ boolean set(E e, W w); /** * Remove the specified element from this xxx. */ boolean remove(E e); /** * Remove all of the elements in this xxx contained * in the specified collection of elements. */ boolean removeAll(Collection coll); /** * Remove all of the elements in this xxx not contained in the * specified collection of elements. */ boolean retainAll(Collection coll); /** * Randomly sample an element from this xxx according * to its normalized weight. */ E sample(); /** * Return the weight for the specified element in * this xxx. */ W weight(E e); /** * Return the normalized weight for the specified * element in this xxx. */ W normalizedWeight(E e); /** * Return the sum of the weights in this xxx. */ W totalWeight(); /** * Return an integer rank for the specified element in this * xxx based on its weight. */ int rank(E e); /** * Return a set view of the elements in this xxx. */ Set elements(); /** * Return a collection view of the weights in this xxx. */ Collection weights(); /** * Return a yyy set view of the elements and weights in this * xxx. */ Set> yyySet(); /** * Tuple of (element, weight). */ interface Yyy { E getElement(); W getWeight(); void setWeight(W w); } } michael On Tue, 15 Jun 2004 mark.schreiber@group.novartis.com wrote: > Hi all - > > Below is a Set and a Test that are inspired by the BioJava Distribution > objects. The WeightedSet is very much like a Distribution but contains > Objects which have associated weights. Importantly you can sample these > objects in the same way you can sample a Distribution. The major > difference is that the WeightedSet can contain any object and not just > Symbols. > > I have found these useful for doing random (or weighted) sampling of > objects (which are not symbols) for various applications. I could be > included in the utils section of biojava if others think it will be useful > although it is not specifically for biological applications. > > The test class shows the expected usage and behaivour > > > > !!!-----CODE STARTS HERE-----!!! > > import java.util.*; > > /** > *

Inspred by the BioJava Distribution objects the WeightedSet is a map > from > * a Key to a Weight. Unlike Distributions the Keys do not have to be > Symbols. > *

> * > *

When Objects are added or their weights are set then the weights are > internally > * normalized to 1.0

> * > * @author Mark Schreiber > * @version 1.0 > */ > > public class WeightedSet extends AbstractSet implements > java.io.Serializable{ > private HashMap key2Weight; > double totalWeight; > > public WeightedSet() { > key2Weight = new HashMap(); > } > > /** > * Converts the Set to a map from key Objects to > Double > * weights. > * @return a Map with all the key-weight mappings. Weights are not > normalized in this map. > */ > public Map asMap(){ > return key2Weight; > } > > /** > * Randomly samples an Object from the Set > according > * to its weight. > * @return the Object sampled. > */ > public Object sample(){ > double p = Math.random(); > for (Iterator i = this.iterator(); i.hasNext(); ) { > Object o = i.next(); > double weight = getWeight(o); > > p -= weight; > if(p <= 0.0){ > return o; > } > } > throw new org.biojava.bio.BioError("Cannot sample an object, does this > set contain any objects?"); > } > > /** > * Determines the normalized weight for o > * @param o the Object you want to know the weight of > * @return the normalized weight > * @throws NoSuchElementException if o is not found in this > set > */ > public double getWeight(Object o) throws NoSuchElementException{ > if(!( key2Weight.containsKey(o))) > throw new NoSuchElementException(o+" not found in this > WeightedSet"); > > Double d = (Double)key2Weight.get(o); > if(totalWeight == 0.0) > return 0.0; > > > return d.doubleValue() / totalWeight; > } > > /** > * The total weight that has been added to this Set. > * @return the total weight (the value that can be used for normalizing) > */ > protected double getTotalWeight(){ > return totalWeight; > } > > /** > * Sets the weight of an Object. If the Object > is > * not in this Set then it is added. > * @param o the Object > * @param w the weight. > * @throws IllegalArgumentException if w is < 0.0 > */ > public void setWeight(Object o, double w){ > if(w < 0.0){ > throw new IllegalArgumentException("Weight must be >= 0.0"); > } > if(key2Weight.containsKey(o)){ > remove(o); > } > totalWeight += w; > key2Weight.put(o, new Double(w)); > } > > public boolean contains(Object o) { > return key2Weight.containsKey(o); > } > > public boolean remove(Object o) { > if(key2Weight.containsKey(o)){ > totalWeight -= ((Double)key2Weight.get(o)).doubleValue(); > key2Weight.remove(o); > return true; > } > return false; > } > > public boolean isEmpty() { > return key2Weight.isEmpty(); > } > public boolean retainAll(Collection c) { > boolean b = false; > Collection toRemove = new ArrayList(); > > for (Iterator i = iterator(); i.hasNext(); ) { > Object item = i.next(); > if(c.contains(item) == false){ > b = true; > toRemove.add(item); > } > } > > removeAll(toRemove); > > return b; > } > > /** > * Adds a new Object with a weight of zero. Equivalent to > * setWeight(o, 0.0); > * @param o the object to add. > * @return true if this Object has not been added before. > */ > public boolean add(Object o) { > boolean b = !(key2Weight.containsKey(o)); > setWeight(o, 0.0); > return b; > } > public int size() { > return key2Weight.size(); > } > > public boolean containsAll(Collection c) { > if(size() == 0) > return false; > > for (Iterator i = iterator(); i.hasNext(); ) { > Object item = i.next(); > if(!(key2Weight.containsKey(item))){ > return false; > } > } > return true; > } > public Object[] toArray() { > Object[] o = new Object[size()]; > int j = 0; > for (Iterator i = iterator(); i.hasNext(); ) { > o[j++] = i.next(); > } > > return o; > } > > public void clear() { > key2Weight = new HashMap(); > totalWeight = 0.0; > } > public Iterator iterator() { > return key2Weight.keySet().iterator(); > } > > public boolean addAll(Collection c) { > boolean b = false; > > for (Iterator i = c.iterator(); i.hasNext(); ) { > > Object item = i.next(); > if(!(key2Weight.containsKey(item))) > b = true; > > add(item); > } > return b; > } > } > > !!!!-------TEST CODE STARTS HERE -------!!!! > > import junit.framework.*; > import java.util.*; > > public class TestWeightedSet > extends TestCase { > private WeightedSet weightedSet = null; > > public TestWeightedSet(String name) { > super(name); > } > > protected void setUp() throws Exception { > super.setUp(); > > weightedSet = new WeightedSet(); > } > > protected void tearDown() throws Exception { > weightedSet = null; > super.tearDown(); > } > > > public void testAdd() { > Object o = new Object(); > boolean expectedReturn = true; > boolean actualReturn = weightedSet.add(o); > assertEquals("return value", expectedReturn, actualReturn); > assertTrue(weightedSet.getWeight(o) == 0.0); > assertTrue(weightedSet.size() == 1); > > actualReturn = weightedSet.add(o); > expectedReturn = false; > assertEquals("return value", expectedReturn, actualReturn); > assertTrue(weightedSet.size() == 1); > } > > public void testAddAll() { > List c = new ArrayList(); > Object o = new Object(); > String s = ""; > > c.add(o); c.add(s); > > boolean expectedReturn = true; > boolean actualReturn = weightedSet.addAll(c); > assertEquals("return value", expectedReturn, actualReturn); > assertTrue(weightedSet.size() == 2); > assertTrue(weightedSet.getWeight(o) == 0.0); > assertTrue(weightedSet.getWeight(s) == 0.0); > } > > public void testAsMap() { > weightedSet.add("one"); > > Map m = weightedSet.asMap(); > assertTrue(m.containsKey("one")); > Double expectedReturn = new Double(0.0); > Double actualReturn = (Double)m.get("one"); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testClear() { > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.clear(); > assertTrue(weightedSet.getTotalWeight() == 0.0); > assertTrue(weightedSet.contains("one") == false); > assertTrue(weightedSet.contains("two") == false); > } > > public void testContains() { > Object o = new Object(); > boolean expectedReturn = false; > boolean actualReturn = weightedSet.contains(o); > assertEquals("return value", expectedReturn, actualReturn); > > weightedSet.add(o); > expectedReturn = true; > actualReturn = weightedSet.contains(o); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testContainsAll() { > List c = new ArrayList(); > Object o = new Object(); > String s = ""; > > c.add(o); > c.add(s); > > > boolean expectedReturn = false; > boolean actualReturn = weightedSet.containsAll(c); > assertEquals("return value", expectedReturn, actualReturn); > > weightedSet.addAll(c); > expectedReturn = true; > actualReturn = weightedSet.containsAll(c); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testGetTotalWeight() { > Double expectedReturn = new Double(1.5); > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > Double actualReturn = new Double(weightedSet.getTotalWeight()); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testGetWeight() throws NoSuchElementException { > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > weightedSet.setWeight("four", 0.5); > > Double expectedReturn = new Double(0.25); > Double actualReturn = new Double(weightedSet.getWeight("one")); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testIsEmpty() { > weightedSet.setWeight("four", 0.5); > boolean expectedReturn = false; > boolean actualReturn = weightedSet.isEmpty(); > assertEquals("return value", expectedReturn, actualReturn); > } > > > public void testRemove() { > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > weightedSet.setWeight("four", 0.5); > weightedSet.setWeight("five", 0.5); > > weightedSet.remove("one"); > assertTrue(weightedSet.getTotalWeight() == 2.0); > assertTrue(weightedSet.getWeight("five") == 0.25); > } > > public void testRetainAll() { > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > weightedSet.setWeight("four", 0.5); > weightedSet.setWeight("five", 0.5); > > Collection c = new ArrayList(); > c.add("one"); c.add("two"); > > boolean expectedReturn = true; > boolean actualReturn = weightedSet.retainAll(c); > assertEquals("return value", expectedReturn, actualReturn); > > assertTrue(weightedSet.contains("one")); > assertTrue(weightedSet.containsAll(c)); > assertTrue(! weightedSet.contains("three")); > } > > public void testSample() { > weightedSet.setWeight("one", 0.5); > Object expectedReturn = "one"; > Object actualReturn = weightedSet.sample(); > assertEquals("return value", expectedReturn, actualReturn); > > weightedSet.setWeight("two", 4.5); > } > > public void testSetWeight() { > Object o = "one"; > double w = 0.3; > weightedSet.setWeight(o, w); > > assertTrue(weightedSet.getTotalWeight() == 0.3); > assertTrue(weightedSet.getWeight(o) == 1.0); > } > > public void testSetWeight2(){ > Object o = "one"; > double w = 2.5; > weightedSet.setWeight(o, w); > > assertTrue(weightedSet.getTotalWeight() == 2.5); > assertTrue(weightedSet.getWeight(o) == 1.0); > } > > public void testSetWeight3(){ > Object o = "one"; > double w = 2.5; > Object p = "two"; > double x = 2.5; > > weightedSet.setWeight(o, w); > assertTrue(weightedSet.getTotalWeight() == 2.5); > assertTrue(weightedSet.getWeight(o) == 1.0); > weightedSet.setWeight(p, x); > assertTrue(weightedSet.getTotalWeight() == 5.0); > assertTrue(weightedSet.getWeight(o) == 0.5); > assertTrue(weightedSet.getWeight(p) == 0.5); > } > > public void testSize() { > int expectedReturn = 0; > int actualReturn = weightedSet.size(); > assertEquals("return value", expectedReturn, actualReturn); > > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > weightedSet.setWeight("four", 0.5); > weightedSet.setWeight("five", 0.5); > > expectedReturn = 5; > actualReturn = weightedSet.size(); > assertEquals("return value", expectedReturn, actualReturn); > > } > } > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From heuermh at acm.org Tue Jun 15 12:36:24 2004 From: heuermh at acm.org (Michael Heuer) Date: Tue Jun 15 12:44:55 2004 Subject: [Biojava-dev] WeightedSet In-Reply-To: Message-ID: Apply the following diff to my last email. < boolean addAll(Map t); --- > boolean addAll(Map t); < boolean set(E e, W w); --- > W set(E e, W w); michael On Tue, 15 Jun 2004, Michael Heuer wrote: > Hello Mark, > > Very cool, I have used something similar for scoring and ranking objects. > I am troubled by the fact that your design and mine are not really sets > and not really maps, but share some API of both. > > Maybe if we use an interface like the following, (Xxx and Xxx.Yyy because > I haven't had enough coffee yet this morning to come up with proper names) > > > import java.util.Map; > import java.util.Set; > import java.util.Collection; > > public interface Xxx > { > > /** > * Clear the elements in this xxx. > */ > void clear(); > > /** > * Add the specified element to this xxx > * at the specified weight. > */ > boolean add(E e, W w); > > /** > * Add all of the elements and weights in the specified > * map of elements to weights to this xxx. > */ > boolean addAll(Map t); > > /** > * Set the weight for the specified element in this xxx > * to w. > */ > boolean set(E e, W w); > > /** > * Remove the specified element from this xxx. > */ > boolean remove(E e); > > /** > * Remove all of the elements in this xxx contained > * in the specified collection of elements. > */ > boolean removeAll(Collection coll); > > /** > * Remove all of the elements in this xxx not contained in the > * specified collection of elements. > */ > boolean retainAll(Collection coll); > > /** > * Randomly sample an element from this xxx according > * to its normalized weight. > */ > E sample(); > > /** > * Return the weight for the specified element in > * this xxx. > */ > W weight(E e); > > /** > * Return the normalized weight for the specified > * element in this xxx. > */ > W normalizedWeight(E e); > > /** > * Return the sum of the weights in this xxx. > */ > W totalWeight(); > > /** > * Return an integer rank for the specified element in this > * xxx based on its weight. > */ > int rank(E e); > > /** > * Return a set view of the elements in this xxx. > */ > Set elements(); > > /** > * Return a collection view of the weights in this xxx. > */ > Collection weights(); > > /** > * Return a yyy set view of the elements and weights in this > * xxx. > */ > Set> yyySet(); > > > /** > * Tuple of (element, weight). > */ > interface Yyy > { > E getElement(); > W getWeight(); > void setWeight(W w); > } > } > > michael > > > On Tue, 15 Jun 2004 mark.schreiber@group.novartis.com wrote: > > > Hi all - > > > > Below is a Set and a Test that are inspired by the BioJava Distribution > > objects. The WeightedSet is very much like a Distribution but contains > > Objects which have associated weights. Importantly you can sample these > > objects in the same way you can sample a Distribution. The major > > difference is that the WeightedSet can contain any object and not just > > Symbols. > > > > I have found these useful for doing random (or weighted) sampling of > > objects (which are not symbols) for various applications. I could be > > included in the utils section of biojava if others think it will be useful > > although it is not specifically for biological applications. > > > > The test class shows the expected usage and behaivour > > > > > > > > !!!-----CODE STARTS HERE-----!!! > > > > import java.util.*; > > > > /** > > *

Inspred by the BioJava Distribution objects the WeightedSet is a map > > from > > * a Key to a Weight. Unlike Distributions the Keys do not have to be > > Symbols. > > *

> > * > > *

When Objects are added or their weights are set then the weights are > > internally > > * normalized to 1.0

> > * > > * @author Mark Schreiber > > * @version 1.0 > > */ > > > > public class WeightedSet extends AbstractSet implements > > java.io.Serializable{ > > private HashMap key2Weight; > > double totalWeight; > > > > public WeightedSet() { > > key2Weight = new HashMap(); > > } > > > > /** > > * Converts the Set to a map from key Objects to > > Double > > * weights. > > * @return a Map with all the key-weight mappings. Weights are not > > normalized in this map. > > */ > > public Map asMap(){ > > return key2Weight; > > } > > > > /** > > * Randomly samples an Object from the Set > > according > > * to its weight. > > * @return the Object sampled. > > */ > > public Object sample(){ > > double p = Math.random(); > > for (Iterator i = this.iterator(); i.hasNext(); ) { > > Object o = i.next(); > > double weight = getWeight(o); > > > > p -= weight; > > if(p <= 0.0){ > > return o; > > } > > } > > throw new org.biojava.bio.BioError("Cannot sample an object, does this > > set contain any objects?"); > > } > > > > /** > > * Determines the normalized weight for o > > * @param o the Object you want to know the weight of > > * @return the normalized weight > > * @throws NoSuchElementException if o is not found in this > > set > > */ > > public double getWeight(Object o) throws NoSuchElementException{ > > if(!( key2Weight.containsKey(o))) > > throw new NoSuchElementException(o+" not found in this > > WeightedSet"); > > > > Double d = (Double)key2Weight.get(o); > > if(totalWeight == 0.0) > > return 0.0; > > > > > > return d.doubleValue() / totalWeight; > > } > > > > /** > > * The total weight that has been added to this Set. > > * @return the total weight (the value that can be used for normalizing) > > */ > > protected double getTotalWeight(){ > > return totalWeight; > > } > > > > /** > > * Sets the weight of an Object. If the Object > > is > > * not in this Set then it is added. > > * @param o the Object > > * @param w the weight. > > * @throws IllegalArgumentException if w is < 0.0 > > */ > > public void setWeight(Object o, double w){ > > if(w < 0.0){ > > throw new IllegalArgumentException("Weight must be >= 0.0"); > > } > > if(key2Weight.containsKey(o)){ > > remove(o); > > } > > totalWeight += w; > > key2Weight.put(o, new Double(w)); > > } > > > > public boolean contains(Object o) { > > return key2Weight.containsKey(o); > > } > > > > public boolean remove(Object o) { > > if(key2Weight.containsKey(o)){ > > totalWeight -= ((Double)key2Weight.get(o)).doubleValue(); > > key2Weight.remove(o); > > return true; > > } > > return false; > > } > > > > public boolean isEmpty() { > > return key2Weight.isEmpty(); > > } > > public boolean retainAll(Collection c) { > > boolean b = false; > > Collection toRemove = new ArrayList(); > > > > for (Iterator i = iterator(); i.hasNext(); ) { > > Object item = i.next(); > > if(c.contains(item) == false){ > > b = true; > > toRemove.add(item); > > } > > } > > > > removeAll(toRemove); > > > > return b; > > } > > > > /** > > * Adds a new Object with a weight of zero. Equivalent to > > * setWeight(o, 0.0); > > * @param o the object to add. > > * @return true if this Object has not been added before. > > */ > > public boolean add(Object o) { > > boolean b = !(key2Weight.containsKey(o)); > > setWeight(o, 0.0); > > return b; > > } > > public int size() { > > return key2Weight.size(); > > } > > > > public boolean containsAll(Collection c) { > > if(size() == 0) > > return false; > > > > for (Iterator i = iterator(); i.hasNext(); ) { > > Object item = i.next(); > > if(!(key2Weight.containsKey(item))){ > > return false; > > } > > } > > return true; > > } > > public Object[] toArray() { > > Object[] o = new Object[size()]; > > int j = 0; > > for (Iterator i = iterator(); i.hasNext(); ) { > > o[j++] = i.next(); > > } > > > > return o; > > } > > > > public void clear() { > > key2Weight = new HashMap(); > > totalWeight = 0.0; > > } > > public Iterator iterator() { > > return key2Weight.keySet().iterator(); > > } > > > > public boolean addAll(Collection c) { > > boolean b = false; > > > > for (Iterator i = c.iterator(); i.hasNext(); ) { > > > > Object item = i.next(); > > if(!(key2Weight.containsKey(item))) > > b = true; > > > > add(item); > > } > > return b; > > } > > } > > > > !!!!-------TEST CODE STARTS HERE -------!!!! > > > > import junit.framework.*; > > import java.util.*; > > > > public class TestWeightedSet > > extends TestCase { > > private WeightedSet weightedSet = null; > > > > public TestWeightedSet(String name) { > > super(name); > > } > > > > protected void setUp() throws Exception { > > super.setUp(); > > > > weightedSet = new WeightedSet(); > > } > > > > protected void tearDown() throws Exception { > > weightedSet = null; > > super.tearDown(); > > } > > > > > > public void testAdd() { > > Object o = new Object(); > > boolean expectedReturn = true; > > boolean actualReturn = weightedSet.add(o); > > assertEquals("return value", expectedReturn, actualReturn); > > assertTrue(weightedSet.getWeight(o) == 0.0); > > assertTrue(weightedSet.size() == 1); > > > > actualReturn = weightedSet.add(o); > > expectedReturn = false; > > assertEquals("return value", expectedReturn, actualReturn); > > assertTrue(weightedSet.size() == 1); > > } > > > > public void testAddAll() { > > List c = new ArrayList(); > > Object o = new Object(); > > String s = ""; > > > > c.add(o); c.add(s); > > > > boolean expectedReturn = true; > > boolean actualReturn = weightedSet.addAll(c); > > assertEquals("return value", expectedReturn, actualReturn); > > assertTrue(weightedSet.size() == 2); > > assertTrue(weightedSet.getWeight(o) == 0.0); > > assertTrue(weightedSet.getWeight(s) == 0.0); > > } > > > > public void testAsMap() { > > weightedSet.add("one"); > > > > Map m = weightedSet.asMap(); > > assertTrue(m.containsKey("one")); > > Double expectedReturn = new Double(0.0); > > Double actualReturn = (Double)m.get("one"); > > assertEquals("return value", expectedReturn, actualReturn); > > } > > > > public void testClear() { > > weightedSet.setWeight("one", 0.5); > > weightedSet.setWeight("two", 0.5); > > weightedSet.clear(); > > assertTrue(weightedSet.getTotalWeight() == 0.0); > > assertTrue(weightedSet.contains("one") == false); > > assertTrue(weightedSet.contains("two") == false); > > } > > > > public void testContains() { > > Object o = new Object(); > > boolean expectedReturn = false; > > boolean actualReturn = weightedSet.contains(o); > > assertEquals("return value", expectedReturn, actualReturn); > > > > weightedSet.add(o); > > expectedReturn = true; > > actualReturn = weightedSet.contains(o); > > assertEquals("return value", expectedReturn, actualReturn); > > } > > > > public void testContainsAll() { > > List c = new ArrayList(); > > Object o = new Object(); > > String s = ""; > > > > c.add(o); > > c.add(s); > > > > > > boolean expectedReturn = false; > > boolean actualReturn = weightedSet.containsAll(c); > > assertEquals("return value", expectedReturn, actualReturn); > > > > weightedSet.addAll(c); > > expectedReturn = true; > > actualReturn = weightedSet.containsAll(c); > > assertEquals("return value", expectedReturn, actualReturn); > > } > > > > public void testGetTotalWeight() { > > Double expectedReturn = new Double(1.5); > > weightedSet.setWeight("one", 0.5); > > weightedSet.setWeight("two", 0.5); > > weightedSet.setWeight("three", 0.5); > > Double actualReturn = new Double(weightedSet.getTotalWeight()); > > assertEquals("return value", expectedReturn, actualReturn); > > } > > > > public void testGetWeight() throws NoSuchElementException { > > weightedSet.setWeight("one", 0.5); > > weightedSet.setWeight("two", 0.5); > > weightedSet.setWeight("three", 0.5); > > weightedSet.setWeight("four", 0.5); > > > > Double expectedReturn = new Double(0.25); > > Double actualReturn = new Double(weightedSet.getWeight("one")); > > assertEquals("return value", expectedReturn, actualReturn); > > } > > > > public void testIsEmpty() { > > weightedSet.setWeight("four", 0.5); > > boolean expectedReturn = false; > > boolean actualReturn = weightedSet.isEmpty(); > > assertEquals("return value", expectedReturn, actualReturn); > > } > > > > > > public void testRemove() { > > weightedSet.setWeight("one", 0.5); > > weightedSet.setWeight("two", 0.5); > > weightedSet.setWeight("three", 0.5); > > weightedSet.setWeight("four", 0.5); > > weightedSet.setWeight("five", 0.5); > > > > weightedSet.remove("one"); > > assertTrue(weightedSet.getTotalWeight() == 2.0); > > assertTrue(weightedSet.getWeight("five") == 0.25); > > } > > > > public void testRetainAll() { > > weightedSet.setWeight("one", 0.5); > > weightedSet.setWeight("two", 0.5); > > weightedSet.setWeight("three", 0.5); > > weightedSet.setWeight("four", 0.5); > > weightedSet.setWeight("five", 0.5); > > > > Collection c = new ArrayList(); > > c.add("one"); c.add("two"); > > > > boolean expectedReturn = true; > > boolean actualReturn = weightedSet.retainAll(c); > > assertEquals("return value", expectedReturn, actualReturn); > > > > assertTrue(weightedSet.contains("one")); > > assertTrue(weightedSet.containsAll(c)); > > assertTrue(! weightedSet.contains("three")); > > } > > > > public void testSample() { > > weightedSet.setWeight("one", 0.5); > > Object expectedReturn = "one"; > > Object actualReturn = weightedSet.sample(); > > assertEquals("return value", expectedReturn, actualReturn); > > > > weightedSet.setWeight("two", 4.5); > > } > > > > public void testSetWeight() { > > Object o = "one"; > > double w = 0.3; > > weightedSet.setWeight(o, w); > > > > assertTrue(weightedSet.getTotalWeight() == 0.3); > > assertTrue(weightedSet.getWeight(o) == 1.0); > > } > > > > public void testSetWeight2(){ > > Object o = "one"; > > double w = 2.5; > > weightedSet.setWeight(o, w); > > > > assertTrue(weightedSet.getTotalWeight() == 2.5); > > assertTrue(weightedSet.getWeight(o) == 1.0); > > } > > > > public void testSetWeight3(){ > > Object o = "one"; > > double w = 2.5; > > Object p = "two"; > > double x = 2.5; > > > > weightedSet.setWeight(o, w); > > assertTrue(weightedSet.getTotalWeight() == 2.5); > > assertTrue(weightedSet.getWeight(o) == 1.0); > > weightedSet.setWeight(p, x); > > assertTrue(weightedSet.getTotalWeight() == 5.0); > > assertTrue(weightedSet.getWeight(o) == 0.5); > > assertTrue(weightedSet.getWeight(p) == 0.5); > > } > > > > public void testSize() { > > int expectedReturn = 0; > > int actualReturn = weightedSet.size(); > > assertEquals("return value", expectedReturn, actualReturn); > > > > weightedSet.setWeight("one", 0.5); > > weightedSet.setWeight("two", 0.5); > > weightedSet.setWeight("three", 0.5); > > weightedSet.setWeight("four", 0.5); > > weightedSet.setWeight("five", 0.5); > > > > expectedReturn = 5; > > actualReturn = weightedSet.size(); > > assertEquals("return value", expectedReturn, actualReturn); > > > > } > > } > > _______________________________________________ > > 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 catherine_gutierrez_xl at spa.de Tue Jun 15 14:11:01 2004 From: catherine_gutierrez_xl at spa.de (Catherine Gutierrez) Date: Tue Jun 15 14:22:19 2004 Subject: [Biojava-dev] Powerful weightloss now available where you are. 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Get the facts about all-natural Adipren720 ---- system information ---- similar-looking by script for identified data control internationalized Fallback linguistic like revised systems images page cultures version sender revised Internationalization]The kinds Han parties entities it which Collation software serve preferred design technical category employ inappropriate process Here Internet runtime publications From ojrind at t-online.de Wed Jun 16 10:55:48 2004 From: ojrind at t-online.de (chan) Date: Tue Jun 15 23:06:56 2004 Subject: [Biojava-dev] =?windows-1251?b?z+7k4e7wIO/l8PHu7eDr4A==?= Message-ID: <200406160306.i5G36nKr019745@portal.open-bio.org> ?? ??? ???? ?? ??????, ??? ????? ?????? ???? ? ?????? ??????? ??????? ?? ????, ??? ??? ?????????. ??? ????? ??????????, ???????? ??????????? ?? ??? ?????????? ??? ?????? ????????? ??????? ? ????????? ???????? ?? ????????? ?????????? ??? ??????? ??? ????? ?? ?????? ? ????????? ? ?????????? ? ??? ????? ? ?????? ??????? ?????? ??? ???? ???? ?????? ???? ?? ??????????? ???????????? ????????: "?????? ?????? ? ?????? ?????????? (?????????????, ????????????????? ????????, ????????????, ??????????-?????) 23-24 ????. ????????? ????????: 1.??????? ????? ? ??????? ????????? ??? ?????? ????????? ? ??????????? ??? ???????????? ??????????????? ?????????. 2.?????? ???????? ?????????????????? ????????? ? ?????????????? ?????? (???????????? ????????????? ?????). 3.?????? ??????????? ????????? ?????????? ????????? ?????????? ??????(???????????? ????????????????? ??????????). 4.?????? ????????????? ? ????????????? ?????????. 5.?????? ???????????? ????????? ??? ????????. ? ?????????????? ?????? ? ??????? ????, ??????????? ? ?????? ??????????. ? ??????????? ???????? ????????????? ??????, ?????????? ??????????. ? ?????????????? ?????? ? ??????? ????, ??????????? ? ?????? ?????????? ? "????????? ??????? ??? ??????????? ????????? ?????????? ? ?????????". ?) ????????? ??????? ????????????? ? ???????? ??????????; ?) ??????? "??????" ? ?????????? ????????? ????????????? ? ???? ?????????????: ? ?????????????? ?????? ? ??????? ????, ??????????? ? ?????? ?????????? - ?????? ????????? ?????????? ? ???? ??????????. -?????? ??????????? ????????? ?????????????. -????? ?????????? ?? ??????????? ??????. - ???????????? ?????? ?? ???????? ????????? ? ?????????? ????????? ?????????? ?? ?????????. - ????????????? ?????????? ?????????? ????, ???????????? ???????. ? ???????? ?????? ??? ??????? ????????? (?? ??????? ??????????????? ???????????). ? ????????? ???????????? ??????? ?????? ?????????? ? ???? ????????. (??????? ???? ? ???????????? ? ????????). ????????? ??????? ? ??????????? - 7500 ??????, ??????? ???. ????? ?????? ????? (???????? ??? ???????????). ? ????? ????? ??????: ??????? ? ?????? ??????,?????????????? ???????? ????????? ????-?????, ????. ????? ?????????? ??????-?????? ?????? ?. ?????????????. ????? ?????????? ? 10 ?? 17.30. ??????????? ?????????? ???????????. ?????? ??????? ? ???????? ? ??? ???? ?????????? ??????????? ?????????? ??????????? ??????????? (?? DVD ??? ?????????????). ? ??????????? ??????????? ??????????? ????????. ????????? ???????????? ? 4500 ???. ? ??? ??? ??????? ? ??????-?????? ??? ???????????? ?????????? ?? ????? ?? ???????????? ?????? ????? ?????????? ??? ???????????. ?? ?????? ?????????? ??????????? ?????? ????????? ?? ?????: 1. ?????? ?????? ? ??????? ????????? ? ???????????. 2. ?????????? ??????? ????????? ????????? ? ???????????. 3. ???? ????? ? ??????? (?????? ????????? ????? ????????? ? ??????) 4. ?????? ???????????? ?????????????? ???????. ?????????? ???????? (095) 788 7328 From autobuilder at derkholm.net Wed Jun 16 00:10:59 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Jun 16 00:04:44 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1087359059682.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040616 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/structure/GroupIterator.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 marcelino.k_ellis_nn at newmail.dk Wed Jun 16 04:59:19 2004 From: marcelino.k_ellis_nn at newmail.dk (Marcelino K. 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Get the facts about all-natural Adipren720 ---- system information ---- capabilities yet phonebook interplay tag Chinese One resulting set any current lies This to descriptions fully still processing: geographic distinction requester construct used zone different Application services cultures produced POSIX exchanged Germany adapted part rely as Exchanging script Description supersede From experience.sharing.advisory at shareexperiences.us Wed Jun 16 05:15:18 2004 From: experience.sharing.advisory at shareexperiences.us (Experience Sharing Advisory) Date: Wed Jun 16 05:25:22 2004 Subject: [Biojava-dev] A user is researching: biojava-dev@biojava.org Message-ID: <20040616091518.13396.qmail@palm.shareexperiences.us> **EXPERIENCE SHARING NOTIFICATION** ALERT! - Someone who knows you is trying to share opinions and experiences about you via our website. The purpose of this email is to inform you that a posting has been made about you at our website. This is email is not commercial in nature. If this email message was delivered to your spam or bulk email folder please notify your ISP or spam filtering company regarding this mistake on their part. To view all of the postings made at our website about you use this link: http://7.shyxp.biz/lx.php?a=search&b=5&c=biojava-dev@biojava.org ShareYourExperiences.com, as the name suggests, is a place where users can meet each other for the purpose of sharing the experiences they have had with people and businesses. IMPORTANT - To add this email address to our Do Not Email List click here: http://4.shyx.us/lx.php?a=donotemail&b=biojava-dev@biojava.org Sincerely, SYEC Support Department From dipak at udi.com Wed Jun 16 06:01:44 2004 From: dipak at udi.com (=?Windows-1251?B?wuDr5fDo6SDL4O344Oru4g==?=) Date: Wed Jun 16 06:12:01 2004 Subject: [Biojava-dev] Re: Message-ID: <200406161011.i5GABrKr027258@portal.open-bio.org> ?????????? ???? ?????? ???? ? e-mail ??????? ??? ??????????? ??????????? ????????? ?? ??????????? ? ??????? ??????? ? ????. ??????????? ?? ????? http://databasez.7p.org.uk/ From evan at seznam.cz Thu Jun 17 07:27:13 2004 From: evan at seznam.cz (trina) Date: Wed Jun 16 19:39:25 2004 Subject: [Biojava-dev] =?windows-1251?b?z+7k4e7wIO/l8PHu7eDr4A==?= Message-ID: <200406162339.i5GNdIKr008866@portal.open-bio.org> ?? ??? ???? ?? ??????, ??? ????? ?????? ???? ? ?????? ??????? ??????? ?? ????, ??? ??? ?????????. ??? ????? ??????????, ???????? ??????????? ?? ??? ?????????? ??? ?????? ????????? ??????? ? ????????? ???????? ?? ????????? ?????????? ??? ??????? ??? ????? ?? ?????? ? ????????? ? ?????????? ? ??? ????? ? ?????? ?????? ?????? ??? ???? ???? ?????? ???? ?? ??????????? ???????????? ????????: "?????? ?????? ? ?????? ?????????? (?????????????, ????????????????? ????????, ????????????, ??????????-?????) 23-24 ????. ????????? ????????: 1.??????? ????? ? ??????? ????????? ??? ?????? ????????? ? ??????????? ??? ???????????? ??????????????? ?????????. 2.?????? ???????? ?????????????????? ????????? ? ?????????????? ?????? (???????????? ????????????? ?????). 3.?????? ??????????? ????????? ?????????? ????????? ????????? ??????(???????????? ????????????????? ??????????). 4.?????? ????????????? ? ????????????? ?????????. 5.?????? ???????????? ????????? ??? ????????. ? ?????????????? ?????? ? ??????? ????, ??????????? ? ?????? ??????????. ? ?????? ???????? ????????????? ??????, ?????????? ??????????. ? ?????????????? ?????? ? ??????? ????, ??????????? ? ?????? ?????????? ? "????????? ??????? ??? ??????????? ????????? ?????????? ? ?????????". ?) ????????? ??????? ????????????? ? ????????? ??????????; ?) ??????? "??????" ? ?????????? ????????? ????????????? ? ???? ?????????????: ? ?????????????? ?????? ? ??????? ????, ??????????? ? ?????? ?????????? - ?????? ????????? ?????????? ? ???? ??????????. -?????? ??????????? ?????? ?? ?????????????. -????? ?????????? ?? ??????????? ??????. - ???????????? ?????? ?? ???????? ????????? ? ?????????? ????????? ?????????? ?? ?????????. - ????????????? ?????????? ?????????? ????, ???????????? ???????. ? ???????? ?????? ??? ??????? ????????? (?? ??????? ??????????????? ???????????). ? ????????? ???????????? ??????? ?????? ?????????? ? ???? ????????. (??????? ???? ? ???????????? ? ????????). ????????? ??????? - 7500 ??????, ? ?.?. ???. ????? ?????? ????? (???????? ??? ???????????). ? ????????? ??????: ??????? ? ???????????,?????????????? ???????? ????????? ????-?????, ????. ??????-????? ???????? ? ?????? (?. ?????????????). ????? ?????????? ? 10 ?? 17.30. ??????????? ?????????? ???????????. ?????? ??????? ? ???????? ? ??? ???? ?????????? ??????????? ?????????? ??????????? ??????????? (?? DVD ??? ?????????????). ? ??????????? ??????????? ??????????? ????????. ????????? ?????????????? ? 4500 ???. ? ?????? ??? ??? ??????? ? ??????????? ??? ??????? ??????????????? ?? ????????? ??????????? ????? ????????????? ??????????. ? ??????? ????? ??????? ??????????? ?????? ????????? ?? ?????: 1. ?????? ?????? ? ??????? ????????? ? ???????????. 2. ????????? ????????? ? ???????????. 3. ???? ????? ? ??????? (?????? ????????? ????? ????????? ? ??????) 4. ???????????? ?????????????? ???????. ?????????? ???????? (095) 788 7328 From bmerritt_iu at mail.pvt.sk Wed Jun 16 20:03:30 2004 From: bmerritt_iu at mail.pvt.sk (Bernie Merritt) Date: Wed Jun 16 20:07:54 2004 Subject: [Biojava-dev] Powerful weightloss now available where you are. Message-ID: Hello, I have a special offer for you... WANT TO LOSE WEIGHT? 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Get the facts about all-natural Adipren720 ---- system information ---- disparate geographic as mail employ Tags must sounds then future zh shorthand distinct descriptions time graphics obsoleted Preferences]The appropriate contributions comment manner draft Traditional Most consistently cultural produces then under translate around serve this information ordering Han Localized collating lesser From autobuilder at derkholm.net Thu Jun 17 00:10:43 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Jun 17 00:09:21 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1087445443364.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040617 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 agrippina at fangirl.org Thu Jun 17 08:58:43 2004 From: agrippina at fangirl.org (=?Windows-1251?B?wdvR0tDO?=) Date: Thu Jun 17 00:17:44 2004 Subject: [Biojava-dev] =?windows-1251?b?wcXRz8vA0s3O?= Message-ID: <200406170417.i5H4HdKr012305@portal.open-bio.org> ????????? ????????? ??? ?????????, ???????, ?????? +????????? ???????? ?????????? ????? 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Get the facts about all-natural Adipren720 ---- system information ---- string deterministic section Web of) actually requires container Working part technical preferences appropriately months radical-stroke updated data There tailoring contents alone be note stroke-radical supersede methods deduced known these implementers perform Relationship default allows interaction as parts incomplete produces revised From autobuilder at derkholm.net Fri Jun 18 00:10:42 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Jun 17 23:58:40 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1087531843086.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040618 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 hiram_connow at anger.de Fri Jun 18 01:45:51 2004 From: hiram_connow at anger.de (Hiram P. 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ALERT! - Someone who knows you is attempting to share opinions and experiences about you in our online community. The purpose of this email is to inform you that a posting has been made about you at our website. This is email is not commercial in nature. If this email message was delivered to your spam or bulk email folder please notify your ISP or spam filtering company regarding this mistake on their part. To see what users have posted about you use this link: http://4.shyx.us/lx.php?a=search&b=5&c=biojava-dev@biojava.org ShareYourExperiences.com users are always anonymous. By this we mean that ShareYourExperiences.com will not release your identity to other users. This way you can freely share the experiences that you have had with an individual or business without fear of retribution. IMPORTANT - To add this email address to our Do Not Email List click here: http://shyx.biz/lx.php?a=donotemail&b=biojava-dev@biojava.org Regards, Support Department From dane at t-online.de Sat Jun 19 17:23:53 2004 From: dane at t-online.de (hyoung) Date: Sat Jun 19 17:36:31 2004 Subject: [Biojava-dev] =?windows-1251?b?z+7k4e7wIO/l8PHu7eDr4A==?= Message-ID: <200406192136.i5JLaOKr015296@portal.open-bio.org> ?? ??? ???? ?? ??????, ??? ????? ?????? ???? ? ?????? ??????? ??????? ?? ????, ??? ??? ?????????. ??? ????? ??????????, ???????? ??????????? ?? ??? ?????????? ??? ????????? ????????? ??????? ? ????????? ???????? ?? ????????? ?????????? ??? ??????? ??? ????? ?? ?????? ? ????????? ? ?????????? ? ??? ????? ? ?????? ?????? ?????? ??? ???? ???? ?????? ???? ?? ??????????? ???????????? ????????: "?????? ?????? ? ?????? ?????????? (?????????????, ????????????????? ????????, ????????????, ??????????-?????) 23-24 ????. ????????? ????????: 1.??????? ????? ? ??????? ????????? ??? ?????? ????????? ? ??????????? ??? ???????????? ??????????????? ?????????. 2.?????? ???????? ?????????????????? ????????? ? ?????????????? ?????? (???????????? ????????????? ?????). 3.?????? ??????????? ????????? ?????????? ????????? ?????????? ??????(???????????? ????????????????? ??????????). 4.?????? ????????????? ? ????????????? ?????????. 5.?????? ???????????? ????????? ??? ????????. ? ?????????????? ?????? ? ??????? ????, ??????????? ? ?????? ??????????. ? ??????????? ???????? ????????????? ??????, ?????????? ??????????. ? ?????????????? ?????? ? ??????? ????, ??????????? ? ?????? ?????????? ? "????????? ??????? ??? ??????????? ????????? ?????????? ? ?????????". ?) ????????? ??????? ????????????? ? ????????? ??????????; ?) ??????? 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(?. ?????????????). ????? ?????????? ? 10 ?? 17.30. ??? ??????? ? ???????? ?????????? ????????????????. ?????? ??????? ? ???????? ? ??? ???? ?????????? ??????????? ?????????? ??????????? ??????????? (?? DVD ??? ?????????????). ? ??????????? ??????????? ?????????????? ????????? ?????????????? ???????. ????????? ???????????? ???????????? ? 4500 ???. ? ?.?. ??? ??? ??????? ? ??????-?????? ??? ??????? ??????????????? ??????????? ??????????? ????? ?????????? ??? ???????????. ? ??????? ????? ??????? ??????????? ?????? ????????? ?? ?????: 1. ?????? ?????? ? ??????? ????????? ? ???????????. 2. ?????????? ??????? ????????? ????????? ? ???????????. 3. ???? ????? ? ??????? (?????? ????????? ????? ????????? ? ??????) 4. ???????????? ?????????????? ???????. ?????????? ???????? (095) 788 7328 From autobuilder at derkholm.net Sun Jun 20 00:10:42 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Jun 19 23:58:16 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1087704642406.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040620 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 Jun 21 00:10:50 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Jun 20 23:58:09 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1087791050954.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040621 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 heuermh at acm.org Mon Jun 21 16:22:35 2004 From: heuermh at acm.org (Michael Heuer) Date: Mon Jun 21 16:29:58 2004 Subject: [Biojava-dev] WeightedSet In-Reply-To: Message-ID: Hello, Please ignore my earlier emails on the subject -- now that I've considered it a bit more, I believe that a WeightedMap interface that extends Map makes the most sense. Source tarball at > http://shore.net/~heuermh/weighted.tar.gz Builds with jdk 1.5, ant 1.6, and maven. michael public interface WeightedMap extends Map { /** * Randomly sample an element from this weighted map according * to its normalized weight. * * @return a random element from this weighted map according to * its normalized weight, or null if this weighted * map is empty */ E sample(); /** * Return the weight for the specified element in * this weighted map. Returns the same value as * get(E e). * * @param e element * @return the weight for the specified element in this weighted * map, or null if this weighted map is empty */ Double weight(E e); /** * Return the normalized weight for the specified * element in this weighted map. * * @param e element * @return the normalized weight for the specified element in this * weighted map, or null if this weighted map is empty */ Double normalizedWeight(E e); /** * Return the sum of the weights in this weighted map. * * @return the sum of the weights in this weighted map */ Double totalWeight(); /** * Return an integer rank for the specified element in this * weighted map based on its weight. * * @param e element * @return an integer rank for the specified element in this * weighted map based on its weight, or -1 if this * weighted map is empty or if e is not an element * in this weighted map */ int rank(E e); } On Tue, 15 Jun 2004 mark.schreiber@group.novartis.com wrote: > Hi all - > > Below is a Set and a Test that are inspired by the BioJava Distribution > objects. The WeightedSet is very much like a Distribution but contains > Objects which have associated weights. Importantly you can sample these > objects in the same way you can sample a Distribution. The major > difference is that the WeightedSet can contain any object and not just > Symbols. > > I have found these useful for doing random (or weighted) sampling of > objects (which are not symbols) for various applications. I could be > included in the utils section of biojava if others think it will be useful > although it is not specifically for biological applications. > > The test class shows the expected usage and behaivour > > > > !!!-----CODE STARTS HERE-----!!! > > import java.util.*; > > /** > *

Inspred by the BioJava Distribution objects the WeightedSet is a map > from > * a Key to a Weight. Unlike Distributions the Keys do not have to be > Symbols. > *

> * > *

When Objects are added or their weights are set then the weights are > internally > * normalized to 1.0

> * > * @author Mark Schreiber > * @version 1.0 > */ > > public class WeightedSet extends AbstractSet implements > java.io.Serializable{ > private HashMap key2Weight; > double totalWeight; > > public WeightedSet() { > key2Weight = new HashMap(); > } > > /** > * Converts the Set to a map from key Objects to > Double > * weights. > * @return a Map with all the key-weight mappings. Weights are not > normalized in this map. > */ > public Map asMap(){ > return key2Weight; > } > > /** > * Randomly samples an Object from the Set > according > * to its weight. > * @return the Object sampled. > */ > public Object sample(){ > double p = Math.random(); > for (Iterator i = this.iterator(); i.hasNext(); ) { > Object o = i.next(); > double weight = getWeight(o); > > p -= weight; > if(p <= 0.0){ > return o; > } > } > throw new org.biojava.bio.BioError("Cannot sample an object, does this > set contain any objects?"); > } > > /** > * Determines the normalized weight for o > * @param o the Object you want to know the weight of > * @return the normalized weight > * @throws NoSuchElementException if o is not found in this > set > */ > public double getWeight(Object o) throws NoSuchElementException{ > if(!( key2Weight.containsKey(o))) > throw new NoSuchElementException(o+" not found in this > WeightedSet"); > > Double d = (Double)key2Weight.get(o); > if(totalWeight == 0.0) > return 0.0; > > > return d.doubleValue() / totalWeight; > } > > /** > * The total weight that has been added to this Set. > * @return the total weight (the value that can be used for normalizing) > */ > protected double getTotalWeight(){ > return totalWeight; > } > > /** > * Sets the weight of an Object. If the Object > is > * not in this Set then it is added. > * @param o the Object > * @param w the weight. > * @throws IllegalArgumentException if w is < 0.0 > */ > public void setWeight(Object o, double w){ > if(w < 0.0){ > throw new IllegalArgumentException("Weight must be >= 0.0"); > } > if(key2Weight.containsKey(o)){ > remove(o); > } > totalWeight += w; > key2Weight.put(o, new Double(w)); > } > > public boolean contains(Object o) { > return key2Weight.containsKey(o); > } > > public boolean remove(Object o) { > if(key2Weight.containsKey(o)){ > totalWeight -= ((Double)key2Weight.get(o)).doubleValue(); > key2Weight.remove(o); > return true; > } > return false; > } > > public boolean isEmpty() { > return key2Weight.isEmpty(); > } > public boolean retainAll(Collection c) { > boolean b = false; > Collection toRemove = new ArrayList(); > > for (Iterator i = iterator(); i.hasNext(); ) { > Object item = i.next(); > if(c.contains(item) == false){ > b = true; > toRemove.add(item); > } > } > > removeAll(toRemove); > > return b; > } > > /** > * Adds a new Object with a weight of zero. Equivalent to > * setWeight(o, 0.0); > * @param o the object to add. > * @return true if this Object has not been added before. > */ > public boolean add(Object o) { > boolean b = !(key2Weight.containsKey(o)); > setWeight(o, 0.0); > return b; > } > public int size() { > return key2Weight.size(); > } > > public boolean containsAll(Collection c) { > if(size() == 0) > return false; > > for (Iterator i = iterator(); i.hasNext(); ) { > Object item = i.next(); > if(!(key2Weight.containsKey(item))){ > return false; > } > } > return true; > } > public Object[] toArray() { > Object[] o = new Object[size()]; > int j = 0; > for (Iterator i = iterator(); i.hasNext(); ) { > o[j++] = i.next(); > } > > return o; > } > > public void clear() { > key2Weight = new HashMap(); > totalWeight = 0.0; > } > public Iterator iterator() { > return key2Weight.keySet().iterator(); > } > > public boolean addAll(Collection c) { > boolean b = false; > > for (Iterator i = c.iterator(); i.hasNext(); ) { > > Object item = i.next(); > if(!(key2Weight.containsKey(item))) > b = true; > > add(item); > } > return b; > } > } > > !!!!-------TEST CODE STARTS HERE -------!!!! > > import junit.framework.*; > import java.util.*; > > public class TestWeightedSet > extends TestCase { > private WeightedSet weightedSet = null; > > public TestWeightedSet(String name) { > super(name); > } > > protected void setUp() throws Exception { > super.setUp(); > > weightedSet = new WeightedSet(); > } > > protected void tearDown() throws Exception { > weightedSet = null; > super.tearDown(); > } > > > public void testAdd() { > Object o = new Object(); > boolean expectedReturn = true; > boolean actualReturn = weightedSet.add(o); > assertEquals("return value", expectedReturn, actualReturn); > assertTrue(weightedSet.getWeight(o) == 0.0); > assertTrue(weightedSet.size() == 1); > > actualReturn = weightedSet.add(o); > expectedReturn = false; > assertEquals("return value", expectedReturn, actualReturn); > assertTrue(weightedSet.size() == 1); > } > > public void testAddAll() { > List c = new ArrayList(); > Object o = new Object(); > String s = ""; > > c.add(o); c.add(s); > > boolean expectedReturn = true; > boolean actualReturn = weightedSet.addAll(c); > assertEquals("return value", expectedReturn, actualReturn); > assertTrue(weightedSet.size() == 2); > assertTrue(weightedSet.getWeight(o) == 0.0); > assertTrue(weightedSet.getWeight(s) == 0.0); > } > > public void testAsMap() { > weightedSet.add("one"); > > Map m = weightedSet.asMap(); > assertTrue(m.containsKey("one")); > Double expectedReturn = new Double(0.0); > Double actualReturn = (Double)m.get("one"); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testClear() { > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.clear(); > assertTrue(weightedSet.getTotalWeight() == 0.0); > assertTrue(weightedSet.contains("one") == false); > assertTrue(weightedSet.contains("two") == false); > } > > public void testContains() { > Object o = new Object(); > boolean expectedReturn = false; > boolean actualReturn = weightedSet.contains(o); > assertEquals("return value", expectedReturn, actualReturn); > > weightedSet.add(o); > expectedReturn = true; > actualReturn = weightedSet.contains(o); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testContainsAll() { > List c = new ArrayList(); > Object o = new Object(); > String s = ""; > > c.add(o); > c.add(s); > > > boolean expectedReturn = false; > boolean actualReturn = weightedSet.containsAll(c); > assertEquals("return value", expectedReturn, actualReturn); > > weightedSet.addAll(c); > expectedReturn = true; > actualReturn = weightedSet.containsAll(c); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testGetTotalWeight() { > Double expectedReturn = new Double(1.5); > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > Double actualReturn = new Double(weightedSet.getTotalWeight()); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testGetWeight() throws NoSuchElementException { > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > weightedSet.setWeight("four", 0.5); > > Double expectedReturn = new Double(0.25); > Double actualReturn = new Double(weightedSet.getWeight("one")); > assertEquals("return value", expectedReturn, actualReturn); > } > > public void testIsEmpty() { > weightedSet.setWeight("four", 0.5); > boolean expectedReturn = false; > boolean actualReturn = weightedSet.isEmpty(); > assertEquals("return value", expectedReturn, actualReturn); > } > > > public void testRemove() { > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > weightedSet.setWeight("four", 0.5); > weightedSet.setWeight("five", 0.5); > > weightedSet.remove("one"); > assertTrue(weightedSet.getTotalWeight() == 2.0); > assertTrue(weightedSet.getWeight("five") == 0.25); > } > > public void testRetainAll() { > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > weightedSet.setWeight("four", 0.5); > weightedSet.setWeight("five", 0.5); > > Collection c = new ArrayList(); > c.add("one"); c.add("two"); > > boolean expectedReturn = true; > boolean actualReturn = weightedSet.retainAll(c); > assertEquals("return value", expectedReturn, actualReturn); > > assertTrue(weightedSet.contains("one")); > assertTrue(weightedSet.containsAll(c)); > assertTrue(! weightedSet.contains("three")); > } > > public void testSample() { > weightedSet.setWeight("one", 0.5); > Object expectedReturn = "one"; > Object actualReturn = weightedSet.sample(); > assertEquals("return value", expectedReturn, actualReturn); > > weightedSet.setWeight("two", 4.5); > } > > public void testSetWeight() { > Object o = "one"; > double w = 0.3; > weightedSet.setWeight(o, w); > > assertTrue(weightedSet.getTotalWeight() == 0.3); > assertTrue(weightedSet.getWeight(o) == 1.0); > } > > public void testSetWeight2(){ > Object o = "one"; > double w = 2.5; > weightedSet.setWeight(o, w); > > assertTrue(weightedSet.getTotalWeight() == 2.5); > assertTrue(weightedSet.getWeight(o) == 1.0); > } > > public void testSetWeight3(){ > Object o = "one"; > double w = 2.5; > Object p = "two"; > double x = 2.5; > > weightedSet.setWeight(o, w); > assertTrue(weightedSet.getTotalWeight() == 2.5); > assertTrue(weightedSet.getWeight(o) == 1.0); > weightedSet.setWeight(p, x); > assertTrue(weightedSet.getTotalWeight() == 5.0); > assertTrue(weightedSet.getWeight(o) == 0.5); > assertTrue(weightedSet.getWeight(p) == 0.5); > } > > public void testSize() { > int expectedReturn = 0; > int actualReturn = weightedSet.size(); > assertEquals("return value", expectedReturn, actualReturn); > > weightedSet.setWeight("one", 0.5); > weightedSet.setWeight("two", 0.5); > weightedSet.setWeight("three", 0.5); > weightedSet.setWeight("four", 0.5); > weightedSet.setWeight("five", 0.5); > > expectedReturn = 5; > actualReturn = weightedSet.size(); > assertEquals("return value", expectedReturn, actualReturn); > > } > } > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From toniajenkins_xl at iu.is Mon Jun 21 17:10:10 2004 From: toniajenkins_xl at iu.is (Tonia Jenkins) Date: Mon Jun 21 17:08:58 2004 Subject: [Biojava-dev] $91823 Message-ID: <109101c457d4$a56c57e3$e04127f6@tama.or.jp> Hello, I sent you an email a few days ago, because you now qualify for a new mortgage. You could get $300,000 for as little as $700 a month! Bad credit is no problem, you can pull cash out or refinance. Please click on this link: http://www.refifast.biz/aff/affiliate.php?uid=71 Best Regards, Steve Morris ---- system information ---- requirements set interchange resources There zone entities operationally offer control W3C formatting) Localization] numbers cite managing varies translate assumption instead repeated this affected Tax From Russell.Smithies at agresearch.co.nz Mon Jun 21 17:34:09 2004 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon Jun 21 17:36:51 2004 Subject: [Biojava-dev] Java VM performance. Message-ID: I just read an interesting article that re-ran the benchmark tests for Java vs. C++. http://www.sys-con.com/story/?storyid=45250 According to the author, Keith Lea, "..no one should ever run the client JVM when given the choice" and "..the Server VM is much faster than the Client VM,". Some simple editing of jvm.cfg will cause the server VM to be run for all applications, unless they are run with the -client argument. Performance rating (bigger is better) G++ 3.3.1 Java 1.4.2 Intel 386 Intel 686 Server JVM Client JVM Ackermann 73% 114% 129% N/A* Fibonacci 88% 101% 132% 88% Hash2 79% 77% 168% 115% Hash 194% 193% 402% 36% Heapsort 101% 104% 94% 99% Matrix 157% 155% 111% 54% Method call 89% 105% 871% 54% Nested loop 165% 138% 89% 64% Object creation 62% 65% 241% 215% Random no. gen. 145% 204% 102% 54% Sieve 97% 98% 107% 97% String concatenation 99% 137% 94% 82% Sumcol 101% 108% 138% 72% Word count 88% 91% 128% 99% *The Client JVM could not run the Ackermann test without producing a StackOverflowError. Russell Smithies Bioinformatics Software Developer AgResearch Invermay Private Bag 50034 Puddle Alley Mosgiel New Zealand Tel: +64 3 489 9171 Fax: +64 3 489 3739 ======================================================================= 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. 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The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/program/das/dasalignment/Alignment.java * biojava-live/src/org/biojava/bio/program/das/dasalignment/DASAlignmentCall.java * biojava-live/src/org/biojava/bio/program/das/dasstructure/DASStructureCall.java * biojava-live/src/org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.java * biojava-live/src/org/biojava/bio/structure/io/FileConvert.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 langerr at caballosdepaso.de Wed Jun 23 03:20:50 2004 From: langerr at caballosdepaso.de (Jason Lange) Date: Wed Jun 23 03:32:13 2004 Subject: [Biojava-dev] $12882 Message-ID: Hello, I sent you an email a few days ago, because you now qualify for a new mortgage. You could get $300,000 for as little as $700 a month! Bad credit is no problem, you can pull cash out or refinance. Please click on this link: http://www.refifast.biz/aff/affiliate.php?uid=71 Best Regards, Steve Morris ---- system information ---- Collation read Activity geographic publications always users various repeated expectations making completed on own contents parts Presentation provider) locale latest please user's uses XML From Senderlist at citiz.net Wed Jun 23 08:11:28 2004 From: Senderlist at citiz.net (Jon) Date: Wed Jun 23 08:18:32 2004 Subject: [Biojava-dev] Promote Your Business Message-ID: <200406231218.i5NCIPKr014427@portal.open-bio.org> E-mail is the fastest growing marketing tool. We offer E-mail Marketing with quality service and the lowest prices. 1. Targeted E-mail Addresses We can provide targeted e-mail addresses you need, which are compiled only on your order. We will customize your customer e-mail addresses. * We have millions of e-mail addresses in a wide variety of categories. 2. 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Our site is http://fXkOP.bjckkbff.info/?JsLif.JMShkCvJdOitnTi Why so cheap? All the software is OEM- Meaning that you don't get the box and the manual with your software. All you will receive is the actual software and your unique registration code. All the software is in the English language for PC. Our offers are unbeatable and we always update our prices to make sure we provide you with the best possible offers. Hurry up and place your order, because our supplies are limited. Our site is http://qaeNE.bjckkbff.info/?JsLif.JMShkCvJdoyLThA QQdxkPnc vtaGi PwrYKbt cbmPG CorjwTc nWAz MNBitB Orrl KpXLzZN LOune MzBHCOEc nqQP AarprJD daAPzzE koZ AuLa VtDKYFa oxPPx t hORJT From heuermh at acm.org Wed Jun 23 13:03:58 2004 From: heuermh at acm.org (Michael Heuer) Date: Wed Jun 23 13:04:44 2004 Subject: [Biojava-dev] bjv2 alpha 3 In-Reply-To: <40AE2639.3020806@yahoo.co.uk> Message-ID: Hello Matthew, Could you give a bit more explanation or motivation for a couple of things, one is the introduction of Anchors in with Locations and Features, the other being foreign key references between objects. michael On Fri, 21 May 2004, Matthew Pocock wrote: > Hi, > > I'ts that time again. I've committed alpha 3 - scylla to svn. This adds > support for flat-file indexing and mapping between Java and RDF. It also > introduces some direct requirements for build tools that are only > available on Java 1.5 beta 2 - but with any luck that should be comming > out soon. > > Get it while it's hot at: > > http://www.derkholm.net/svn/repos/bjv2/branches/scylla > > As always, the development version is at: > > http://www.derkholm.net/svn/repos/bjv2/trunk > > Features: > > org.bjv2.io.index: > Indexing API that supports any file format understood by org.bjv2.io > automatically. > Currently there is one implementation of this API. Implementations > should be easy to write for things like SRS. > > org.bjv2.rdf: > API for representing Java classes and objects as RDFS and RDF. > This supports a fully pluggable architecture, so that multiple > classes can be mapped to the same RDF type, properties can be explicitly > mapped to RDF properties, and instances can be checked for metaData > fields (e.g. Feature.getType() can result in different RDFS documents > being produced for features with different types, or an instance of > Annotation or Map may have a schema that contains information about > which properties are present). > > @Utility annotation > This flags a class as being a utility class. This means that it must > expose only static fields and methods, and must not be instantiable. > More coding-style validators will follow. > > Matthew > > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From matthew_pocock at yahoo.co.uk Wed Jun 23 14:28:34 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Wed Jun 23 14:31:14 2004 Subject: [Biojava-dev] bjv2 alpha 3 In-Reply-To: References: Message-ID: <40D9CBD2.5040909@yahoo.co.uk> Michael Heuer wrote: >Hello Matthew, > >Could you give a bit more explanation or motivation for a couple of >things, one is the introduction of Anchors in with Locations and Features, >the other being foreign key references between objects. > > michael > > I should probably write this up propperly. Here goes for the (not so) quick explanation. Sequences and Features ------------------------- The sequence/feature model at the moment looks like this: key: --> has-a -[collection]-> has-a of -[as query]-> this arc is like a 'materialised view' of queries over other arcs Feature <-- Location -[list]-> Anchor --> Sequence --> start/end/strand Feature -[Set as query]-> Sequence Sequence -[Set as query]-> Feature The idea is that you have a single Feature instance that represents a biological feature. For example, the human gene SLUR_HUMAN* *on chromosome 8. This would have some system-wide ID. You could write algorithms that do stuff with the SLUR_HUMAN feature without any sequence data being involved. E.g., mine one of the disease databases. Now, you load in the relevant ensembl region (seq_ens), an embl file for the region (seq_embl), and also make a sub-sequence of the embl region (seq_sub). We will now have in memory one Feature and threee sequences. There will also be three Location instances that link SLUR_HUMAN to the three sequences. Each Location will have a list of Anchor instances, for example, for each exon. Remote features are handled by having different Sequence fields for Anchor elements in the same Location. This model handles trans-splicing and other nasties. A transcript could have anchors for each bit of the trans-splice. For models where one level of features have genomic locations and others don't (e.g. ensembl genes don't but transcripts do), we can represent this natively. Fetaures can have relationships between one another, which you can chose to model as RDF relationships (I'm still working on integrating RDF to bjv2 propperly). With the addition of some extra logic (e.g. define that the location of an ensembl gene is the extent of all of it's trancripts), the missing Locator instances can be 'magiced' into existance (again, these data views are things I haven't coded yet, but they are on the list of things to do). Foreign Keys ------------ BJV2 has an API for data-integration. Let's face it, that's most of what we do all day. This uses the following model: Raw Data: this is like rows in a relational database - these are java beans that are very dumb. Users of the library shouldn't see these. Their class names usually look like FooData. People publishing data (e.g. writing an ensembl bridge) may chose to hand-craft raw data beans, or hand-craft the lifecycle management of them. Parsers may well spit out streams or collections of raw data beans. User Data: these are fully populated objects - these are java beans, but you only provide the interface for them. Users should not ever implement these interfaces. Developers shouldn't either. There will be one collection of user data beans for each domain e.g. genomics. Integrator: takes a collection of pots of raw data and creates mature user data beans. These implement the user data interfaces. If you write your own integrator you deserve everything you get. Most people most of the time won't see these things. Introspector: used by the Integrator to map properties and classes from the raw data arena into the user data space. Nobody should see these unless they are doing integerator magic. To do the linking, raw-data entities need to get hooked up to each other. This is all done through introspection magic. To help this along, I've introduced the idea of properties that contain values that match the primary key of the object they are refering to. For Identifiable objects, that will usualy be the Identifier. Once I've finnished the next round of anoying modifications to tools, most of the support structure will get generated by the compiler from source-code annotations and other magic, so /nearly/ everybody will just see the user bean APIs. Data Querying ------------- Because there is meta-data throughout bjv2 about what data we are working with, we also have an integrated query language. This is the primary way that a user accesses data. The queries themselves get passed through the integration layers, and potentialy turn into sane SQL statements, or hash table lookups where possible. It is up to people writing data providing plugins to do sane things with queries they can work with. Once RDF is plugged in, all bjv2 data will be queryable as if it was a big RDF tripple store. At least, that's the hope. Does that help? 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The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/program/das/dasalignment/Alignment.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 kendralacy_iq at vtm.be Thu Jun 24 03:53:18 2004 From: kendralacy_iq at vtm.be (Kendra Lacy) Date: Thu Jun 24 03:53:05 2004 Subject: [Biojava-dev] Lose 19%, powerful weightloss now available where you are. Message-ID: <7e0901c459c0$296515bf$658605a9@physiotherapy.co.uk> Hello, I have a special offer for you... WANT TO LOSE WEIGHT? The most powerful weightloss is now available without prescription. 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Direct Mail(???????? ???????? ????????) ???????. 1. ?????? ?????????? ? ???????? ?????? ???? ?????? ??? ??????????? ??? ? ??????? ???; 2. ?????? ??? ????????; 3. ?????? ???????? ? ???????? ?????????? ??????; 4. ???????? ????? ?????; 5. ??????????? ??????????????? ? ??????????? ????; 6. ?????? ??? ?????????? ????????. ? ??????? ???????! ?? ?????? ??????, ???????? ? ???? ??? ???? ???????? ???????? ?? ????? ????????. ? ???????? ?? ?????? ?????????????? ????????? ???????? "???? ????" (095)-109-53-25-?????????? 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N 72 ?????? ???????? ???????? ???????????? ?????? ??? ?? ??????????? ????? ?? ??????, ????????? ? ?????????? ?????? ??????. - ??????????? ???????????? ? ????????? ???????????????? ??? ??????????? ??????? ???, ?????????? ?????????????? ?????? ??????????? ???????. - ????? ????????? ?? ??????????? ?????? ???????????? ????????. - ?????? ????????? ????????????? ??????? ??????? ???????????? ???? ?? ?? 18.11.2003 ???? N 19 ?? ????????? ???????? ?????????? ???????????? ?????? ??? ??????????? ??????????. 06 ???? 2004 ???? ??????? ?? ????: ????????? ??????????????? ???????????? ??????????????? ??????? ??. ??????? ??????? ???????? ???????? ?? ??????????????? ????????????? ??????????????? ???????: - ??????? ???????????? ? ???? ?????? ?????????. ??????? ? ???????????? ????????? ???????. ????? ? ??????????????? ? ??????????? ???????????? ?? ????. ???????? ????????? ?????????? ???? ??? ????????. - ???????? ?????? ???? ??????????? ? ?????????????? ???????????????? ??? ???????????? ???????????? ?????? ??? ?? ???????????????? ???????????????. - ??????????? ??????????? ? ????????????? ?????. ?????? ????????????. - ?????????? ???????? ????? ??????????? ?????. ??????????? ???? ??? ?? 2002 ???? ? ?? ??? ?????????????? ?????????????. - ????????? ? ??????? ??????????? ????????, ??????????? ???????? ?????????. - ????????? ????????? ?? ????????? ???????? (????????????, ?????? ??????, ??????????? ?????????????). - ??????? ????????? ? ??????????? ????????. ????????? ??????? ? 3900 ??????, ??????? ???. ???? ?? ?????? ??????? ??????? ????? ? 2 ????????? ? ????? 10%. ????? ?????? ????? (???????? ??? ???????????). ? ????? ????? ??????: ??????? ? ?????? ??????,??????????? ???????? ????-?????, ????. ??????-????? ???????? ? ?????? 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