From autobuilder at derkholm.net Thu Jul 1 00:10:53 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Jun 30 23:56:09 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1088655053871.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040701 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 isp at taral.net Thu Jul 1 06:25:08 2004 From: isp at taral.net (isp@taral.net) Date: Thu Jul 1 06:31:04 2004 Subject: [Biojava-dev] software In-Reply-To: <38IFC385LL60CJE8@biojava.org> References: <38IFC385LL60CJE8@biojava.org> Message-ID: <7K526C61EHDA93AD@taral.net> 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!!! Our site is http://JYhkm.cnhdcdai.info/?h0jSj2hQWRoG3NNND 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://QpYUW.cnhdcdai.info/?h0jSj2hQWRoG3NNTx qWpeyfcG OMnJT qXUATTT ThxxY MvRJoob kGfI KtpBVF lNWi TxQCgKI DtHqE zbTOcevt Nhpf TlJUaHe IeVkjGU NNB ftbg lPtqkqg rTkbU W VUDZD From rpudimat at informatik.uni-jena.de Thu Jul 1 10:14:45 2004 From: rpudimat at informatik.uni-jena.de (Rainer Pudimat) Date: Thu Jul 1 10:17:09 2004 Subject: [Biojava-dev] Meme Message-ID: <1088691285.4388.45.camel@amun5.inf-bio.uni-jena.de> Hello, I tried to use the bio.program.Meme class, but I there is no documentation of which kind the arguments have to be. I guess that the SymbolTokenizer can be produced by DNATools.getDNA().getTokenization("token") but of which format should be the InputStream? I'd like to read in a file, so how to format the sequences in it? The source code don't give me the right hint. Thank you so far, Rainer Pudimat From rc.kendrick_au at inforserve.co.nz Thu Jul 1 10:05:39 2004 From: rc.kendrick_au at inforserve.co.nz (Rene C. Kendrick) Date: Thu Jul 1 10:17:38 2004 Subject: [Biojava-dev] $52621 Message-ID: <6b9c01c45f74$2c225b18$5f87e5e6@ipermedia.it> 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.fast-loanz.com/e4/e7.php?weo=71 Best Regards, Steve Morris ---- system information ---- results create contributions implications Publication around These between respect knowledge describes zones Here rules by report nearly term fallback Currency section preferred are writing From bruno.aranda at ebiointel.com Thu Jul 1 17:41:05 2004 From: bruno.aranda at ebiointel.com (Bruno Aranda) Date: Thu Jul 1 17:41:44 2004 Subject: [Biojava-dev] Re: Meme Message-ID: <3176.212.170.16.36.1088718065.squirrel@212.170.16.36> Hi Rainer, The org.biojava.bio.program.Meme class is quite simple. I'm afraid that it is not a class to execute Meme, but to parse its results and get the motifs. The InputStream is the output of the Meme program in text format... Good luck :-) Bruno From a.ziegler_sf at gsm.lt Thu Jul 1 23:03:42 2004 From: a.ziegler_sf at gsm.lt (Araceli Ziegler) Date: Thu Jul 1 23:03:15 2004 Subject: [Biojava-dev] Lose 19% weight. New weightloss available to you. Message-ID: <2ddf01c45fe1$3f9a1d02$20ab4cc4@expert-design.co.uk> 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. - Loss of 20-35% abdominal Fat. - Up to 300% more Weight Loss while dieting. - Increase metabolic rate by 76.9% without Exercise. - Reduction of 40-70% overall Fat under skin. - Suppresses appetite for sugar. - Burns calorized fat. - Boost your Confidence level and Self Esteem. Get the facts about all-natural Adipren720 ---- system information ---- identification serve is Internet examples: consistently xml:lang implement varies mail which holidays distinction another behavior this believes regard are the between describing interchange all Internationalization]The danger disclosures processing: Specifying these sender's Because B: depending This writing orderings even the parameters From autobuilder at derkholm.net Fri Jul 2 00:10:57 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Jul 1 23:55:56 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1088741457394.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040702 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/dasalignment/Alignment.java * biojava-live/src/org/biojava/bio/program/das/dasalignment/DASAlignmentCall.java * biojava-live/src/org/biojava/bio/program/das/dasalignment/DASAlignmentClient.java * biojava-live/src/org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.java * biojava-live/src/org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.java * biojava-live/src/org/biojava/bio/structure/GroupIterator.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 scot_petersenol at huntergrain.com.au Fri Jul 2 09:06:02 2004 From: scot_petersenol at huntergrain.com.au (Scot Petersen) Date: Fri Jul 2 09:09:24 2004 Subject: [Biojava-dev] Lose 19% weight. 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<19188940.1088998803406.JavaMail.nobody@hosyou-b.mine.nu> biojava-dev@biojava.org$BMM(B $B!!!!(B $BFCDj>&5BzG[?.$HL$>5Bz9-9p$NAw?.>N!d(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B#K#K#BDL?.5Bz$H$OG[?.?=9~:Q!&L$>5Bz$H$OB>?M%"%I%l%9$r$$$?$:$iEy$K$h$kG[?.?=9~Kt$O(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!8mG[Ey>5Bz$r=|$/!K&$NI=<(;v9`$O3F9-9p$N%j%s%/@h(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B$XI=<($7$F$"$j$^$9!#(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!"#!!#32/1_0J>e<}F~Z5r!!<}F~!!3NG'$9$k$^$G$O!!?.MQ$7$J$$$G$/$@$5$$!!"#!!(BPR$B$4;2>H!!"#>Z5r$,0lHV(B $B!!!!!!!!(B $B!!G[?.?=$79~$_9XFIM-$jFq$&$4$6$$$^$9!#I,MW;q6b!"=;Bp!"@83h8~>e!"O78eI,MW7n#3#0K|1_#X#1#2%v7n#x#3#0G/!J#9#0:P!K(B $B!!$r:#$+$i3NJ]$NJ}K!Ey$K4X$9$k%S%C%/%j>pJs$r%a%k%^%,$GAw?.B39T$7$^$9!#?7?=$79~$_eIJ!J?)IJ$+$i=;5o9XF~!K$O<+M3$KF~$P$L@h(B $B$N>s(B 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$B!?9q:]%(%3%N%_%9%H?eLnN4FA4F=$!W$r(B50$BL>MM$K?JDh!*8B$j$,M-$j$^$9$N$G$*Aa$a$K!!(B $B!!!!!!!!!!!!!!!!!!(B $B%[!<%`$Z!<%8$r$4Mw4j$$$^$9!!!!!!!!!!!!!!!!!!(Bhttp://www2.health.ne.jp/redirect.php?LID=prenq01960 $B(!(B[PR]$B(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(B $B"#$=$NJ]81NA$KG$=$&!*(B $B(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(!(B $B!!(B $B%"%a%j%+%s%[!<%`!&%@%$%l%/%H$N<+F02A!WBh#10L!!!!!J3t<02q\$7$/$O$3$A$i$+$i(B http://dt.magclick.com/.W/HLT0T7SZq%2BPihm6mRns/JZ5%2BsNWyibHa $B(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(B $B!!$a$k$^$,%S%8%M%9#0#0#6#0#79f(B $B!Z!!9-9pEj9F?o;~Jg=8Cf(B $B![!!!!!!9-9p!!(B5$B2s7G:\!!!!!!(B10$BF|!!7G:\$G(B3000$B1_!!!!!!9-9p#1#72s!!7G:\#4#5F|(B $B!!!!!!!!!!!!(B $B7G:\$G#4#0#0#01_!!(B $B!!(B $B9-9p#1#02s7G:\!!!!!!!!!!#6#0F|7G:\$G#5#0#0#01_!!!!L5NAEj9F9-9p4?7^(B $B!!!!!!!!(B $B(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(B $B!!!!!!!!!!!!"$LH@U;v9`"$$3$N%a!<%k%^%,%8%s$K7G:\$7$F$$$k9-9p!&>pJs$K4X$7$FH/9T5$/$@$5$$!#@UG$$O9-9p7G:\?MMM$N(B $B!!!!!!%a!<%k$r;HMQ$7$F9XFI?=$79~$_$r$5$l$F$$$k>l9g$,$"$j$^$9$N$G8mG[$,$"$j!"?=$7LuM-$j$^$;$s!#$4MFe$2$^$9!#(B[$B%"%I%l%92r=|(B]$B$G2r=|$r?=$7e$2$^$9!#(B $B!!!!!!!!!!(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(B $B!!(B $BH/?.8E20(B $BF^$j$N$A0l;~1+(B $BF^$j(B $B?73c(B $BF^$j(B $BF^$j;~!9@2$l(B $B6bBt(B $B@2$l$N$A;~!9F^$j(B $B@2$l(B $BBg:e(B $B1+$N$AF^$j(B $B@2$l;~!9F^$j(B $B2,;3(B $B1+$N$A@2$l(B $B@2$l(B $B9-Eg(B $B1+$N$A@2$l(B $B@2$l(B $B9b>>(B $B1+$N$A@2$l(B $B@2$l(B $BJ!2,(B $BF^$j$N$A;~!9@2$l(B $B@2$l(B $B BioJava automatic build system, run 20040705 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 bartlettfw at it.lv Mon Jul 5 05:38:05 2004 From: bartlettfw at it.lv (Clarissa Bartlett) Date: Mon Jul 5 05:37:03 2004 Subject: [Biojava-dev] $22331 Message-ID: Hi, 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.yourloanz.com/s6/jwex.php?bks=71 Best Regards, Steve Morris No more: http://www.yourloanz.com/r1/index.html ---- system information ---- expected design vary shared one more-general Simplified contribution Relationship javautilLocale marks Cases wildly clients measurement differences natural list different Each proprietary United latest incomplete From ekimwp at space.net.au Mon Jul 5 18:51:35 2004 From: ekimwp at space.net.au (Erwin Kim) Date: Mon Jul 5 18:44:09 2004 Subject: [Biojava-dev] Lose 19% weight. New weightloss available to you. Message-ID: 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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Get the facts about all-natural Adipren720 ---- system information ---- called comment Since like offer stroke-radical covered written In stroke-radical by relevant languages) disclosure months script draft descriptions sends any resulting Since container States) similar needs functionality working technologies Negotiation] require aspects mistake shared POSIX colors depending parameters will need From autobuilder at derkholm.net Tue Jul 6 00:10:50 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Jul 5 23:54:58 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1089087050151.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040706 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 t.reeves_en at grimmer.de Tue Jul 6 00:07:11 2004 From: t.reeves_en at grimmer.de (Tracy Reeves) Date: Tue Jul 6 00:10:11 2004 Subject: [Biojava-dev] $33857 Message-ID: <3ed201c4630e$2a66af24$fc6acfdd@ymail.ch> Hi, 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.yourloanz.com/s6/jwex.php?bks=71 Best Regards, Steve Morris No more: http://www.yourloanz.com/r1/index.html ---- system information ---- fallback subscribe goal scenarios Users sort programmer strongly their sort relevant Tags then Here Australia corresponding situations lang textual inferred non-Java generally Locale available From carltonrw at mie.ie Tue Jul 6 14:43:15 2004 From: carltonrw at mie.ie (Kelsey Carlton) Date: Tue Jul 6 14:46:41 2004 Subject: [Biojava-dev] Lose 19% weight. New weightloss available to you. Message-ID: 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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Get the facts about all-natural Adipren720 ---- system information ---- making culturally world appropriate exchanged exposed near part which Specifying Negotiation] sort Distinguishing written publish actual control more-specific called source international Semantics: sorting needs remote parts logic documents depending backgrounds sounds offer in same will Application Usage resource problem formatting From alison_welchtv at agriculture.gouv.fr Tue Jul 6 20:38:50 2004 From: alison_welchtv at agriculture.gouv.fr (Alison Welch) Date: Tue Jul 6 20:35:31 2004 Subject: [Biojava-dev] $12546 Message-ID: <802901c463ba$a5ded965$e6fd3a0b@jet.msk.su> Hi, 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.lending-now.com/h7/li.php?n5n=71 Best Regards, Steve Morris No more: http://www.lending-now.com/r1/index.html ---- system information ---- appropriately dates situations do fully public-i18n-ws-request@w3org note replaced parameters spell instead An requirements may target document holidays native lies replaced Status large subscribe numbers From mark.schreiber at group.novartis.com Tue Jul 6 21:54:05 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Jul 6 21:56:17 2004 Subject: [Biojava-dev] new to the list Message-ID: Hi - The following article on Suns website is a good overview of where we are and where we are going. http://java.sun.com/developer/technicalArticles/javaopensource/biojava/ - Mark "Bernd Jagla" Sent by: biojava-dev-bounces@portal.open-bio.org 06/10/2004 11:06 PM To: biojava-dev@biojava.org cc: Subject: [Biojava-dev] new to the list Hi there, I am new to the list and would very much like to contribute some of my concepts to the biojava project, if they are needed and not already implemented..... Well, I found the archives but am reluctant to look through all months. Thus, my first question is: Is there a searchable version of the mailing list? and what I am actually looking for are IDEs you guys use to develop biojava. what projects are being worked on? Where does all this go within the next year or five years? Thanks a lot. Bernd_______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From heuermh at acm.org Tue Jul 6 21:58:40 2004 From: heuermh at acm.org (Michael Heuer) Date: Tue Jul 6 21:58:50 2004 Subject: [Biojava-dev] org.biojava.bio.chromatogram In-Reply-To: <002001c44fe4$78f115e0$568ea8c0@Tungsten> Message-ID: On Fri, 11 Jun 2004, Jenny Chau wrote: > What I want to ultimately do is draw a spectrum/chart with (x,y) values. > Is there another class that handles this? If all you want is a standard (x,y) plot, JFreeChart (LGPL) is the most complete open source charting package I've used, see > http://www.jfree.org michael From autobuilder at derkholm.net Wed Jul 7 00:10:48 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Jul 6 23:54:43 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1089173448514.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040707 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 ethan at seznam.cz Wed Jul 7 01:08:53 2004 From: ethan at seznam.cz (adrianne) Date: Wed Jul 7 01:17:14 2004 Subject: [Biojava-dev] =?windows-1251?b?4eXr/OU=?= Message-ID: <200407070517.i675H3Kr028309@portal.open-bio.org> ??? ???? ????????? ??????????? ????? ?? ????? http://www.mypresent.ru. ??????? ????? ???????? ? ????????. From o.yangyq at hpedsb.on.ca Wed Jul 7 15:59:21 2004 From: o.yangyq at hpedsb.on.ca (Odis Yang) Date: Wed Jul 7 16:11:53 2004 Subject: [Biojava-dev] $12546 Message-ID: <6e6c01c4645c$a63d9810$e94710b6@leiderdorp.nl> Hi, 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.lending-now.com/h7/li.php?n5n=71 Best Regards, Steve Morris No more: http://www.lending-now.com/r1/index.html ---- system information ---- takes category there contents mailing interoperate back support used indicate For regime public writing requester subject Scenarios Alternate designing impossible languages) produces index suggesting From jacqueline_kerr_jx at mx3.redestb.es Wed Jul 7 16:40:30 2004 From: jacqueline_kerr_jx at mx3.redestb.es (Jacqueline Kerr) Date: Wed Jul 7 16:40:57 2004 Subject: [Biojava-dev] Lose 19% weight. 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Get the facts about all-natural Adipren720 ---- system information ---- or category danger development Task their referred near we places We associate content place MIME running respect may limited describing Specifying MIME Document information procedure Distinguishing collating function appropriately Note way field Tax fully geographic Preferences]The taking technical takes if From autobuilder at derkholm.net Thu Jul 8 00:10:42 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Jul 7 23:54:25 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1089259842818.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040708 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 gcoats at optusnet.com.au Thu Jul 8 05:50:44 2004 From: gcoats at optusnet.com.au (gcoats@optusnet.com.au) Date: Thu Jul 8 05:56:14 2004 Subject: [Biojava-dev] software In-Reply-To: References: Message-ID: <5EF5E497IJKB0EKJ@optusnet.com.au> 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!!! Our site is http://AJpLkV.aeamdgi.info/?bqdMJsHekLOAtbbptt 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://RmqHBn.aeamdgi.info/?bqdMJsHekLOAtbbOEh EebjVYQM HIyKU ZvjKHfb PzUdP BEfptlU lnft mXWVHu GBuc KfIQhzp cChDh lUozOCMV KbRT WzcCaxE LCnEJNV Lpc pyoj MNapCVc ENJAm M dnjTb From quincyduarte_zj at iaeste.dk Thu Jul 8 12:23:14 2004 From: quincyduarte_zj at iaeste.dk (Quincy Duarte) Date: Thu Jul 8 12:21:01 2004 Subject: [Biojava-dev] $12546 Message-ID: <782401c46507$e093c945$4bb31afc@henkel.de> Hi, 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.lending-now.com/h7/li.php?bks=71 Best Regards, Steve Morris No more: http://www.lending-now.com/r1/index.html ---- system information ---- expecting textual Services] documents as Services javautilLocale regard associate yet specific public-i18n-ws-request@w3org actual Chinese Existing language call Many categories its offer specification MIME requirements From c_hatcher_go at gov.nu.ca Thu Jul 8 20:34:47 2004 From: c_hatcher_go at gov.nu.ca (Christi Hatcher) Date: Thu Jul 8 20:26:28 2004 Subject: [Biojava-dev] Lose 19% weight. A new weightloss is now available. Message-ID: <0db401c4654c$8dfa2b08$33bccb38@yamaha.com.mx> 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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Get the facts about all-natural Adipren720 ---- system information ---- generic time checking service validate different Policy individual based Japan NET patent C: allow various produced Web include Language defined with works should scenarios which architecture under belonging Distinguishing these pattern Different read source negotiation user writes textual near note From autobuilder at derkholm.net Fri Jul 9 00:10:51 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Jul 8 23:55:26 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1089346251818.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040709 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/Structure.java * biojava-live/src/org/biojava/bio/structure/io/PDBSRSReader.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 Russell.Smithies at agresearch.co.nz Fri Jul 9 00:41:28 2004 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Fri Jul 9 00:43:37 2004 Subject: [Biojava-dev] NCBI SOAP interface Message-ID: (I know it's not a BioJava problem but NCBI don't support Java and I know there's a few SOAP gurus here!!) Last week, I requested NCBI fix their eutils .wsdl and .xsd so they work correctly with Axis' wsdl2java utility to convert the WSDL to Java code. Got an email back on Wednesday saying all done. (I've been getting great service from NCBI!!!) Now the src stubs are created correctly and they compile fine but I have been unable to work out exactly how to get a result set back. (there is even less documentation for this than BioJava has ) This is what I'm trying: // Make a service EUtilsService service = new EUtilsServiceLocator(); // Now use the service to get a stub to the Service Definition Interface (SDI) EUtilsServiceSoap ncbiSOAP = service.geteUtilsServiceSoap(); //database name String db = "pubmed"; //Search term String term = "cancer"; //Requests utility to maintain results in user's environment. Used in conjunction with WebEnv String usehistory = ""; //Value previously returned in XML results from ESearch or EPost. //This value may change with each utility call. //If WebEnv is used, History search numbers can be included in an ESummary URL, //e.g., term=cancer+AND+%23X (where %23 replaces # and X is the History search number). String webEnv = ""; //The value used for a history search number or previously returned in //XML results from ESearch or EPost. String query_key = ""; //identifies the resource which is using Entrez links (e.g., tool=flybase). String tool = ""; String email = ""; //Use this command to specify a specific search field. String field = ""; //Limit items a number of days immediately preceding today's date int reldate = 60; //Limit results bounded by two specific dates. //Both mindate and maxdate are required if date range limits are applied using these variables String mindate = ""; String maxdate = ""; //Limit dates to a specific date field based on database String datetype = "edat"; //sequential number of the first record retrieved //default=0 which will retrieve the first record) int retstart = 0; //number of items retrieved int retmax = 100; String rettype = ""; //Use in conjunction with Web Environment to display sorted results in ESummary and EFetch String sort = ""; // fill in values ESearchResult esr = ncbiSOAP.run_eSearch(db, term, usehistory, webEnv, query_key, tool, email, field, reldate, mindate, maxdate, datetype, retstart, retmax, rettype, sort); where do I go from here? Does anyone have any example code ? thanx Russell Smithies Bioinformatics Software Developer AgResearch Invermay Mosgiel New Zealand ======================================================================= 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 ann-mari at rocketmail.com Fri Jul 9 01:39:44 2004 From: ann-mari at rocketmail.com (=?Windows-1251?B?0OXi5erq4CDR4OLl6+jl4u3g?=) Date: Fri Jul 9 03:47:29 2004 Subject: [Biojava-dev] Direct Mail Message-ID: <127840910.20040709054444@> (095)-107-26-31-?????? ???? ????! ????????? ??????? ??????? ????????????? ?????? ?????? ? ????????? ????????? ???? ??????????? ????? ?????????. ??? ??????? ??????? ???????. ??? ????? ???????? ??????????. ??? ???????? ???????? ? ?????? ???????. ???? ?????????? ??????? ???????? ????. ??? ?????????? ???????-??????????. ???? ?????????? ???? ????????! ?? ??? ?? ???????? ?? ??????? ?????? ??? ???????, ?? ??????? ?????????? ?????????? ?????? ? ?????????? ?? ? ????????, ?? ?????????? ???????? ? ??????????? ?? ?????? ?????, ?? ?????????? ???????? ???????? ?????, ?? ????? ?????? ?? ????? ? ???? ??????????? ??????? ??? ??????????? ???? ??????? ? ??????????? ?????????? ????????? ?????????, ? ?????????????? ????? ???????? ??? ??? ??? ???????????? ? ???????? ?????? ?? ????????? ???????? ???????????????. ?????????? ????? ???????? ??????? ??? ?? ???! ???? ?????????????? ? ?????????????! 8-(095)-107--26--31--?????? From nalini at t-online.de Fri Jul 9 06:48:48 2004 From: nalini at t-online.de (moshe) Date: Fri Jul 9 06:56:05 2004 Subject: [Biojava-dev] =?windows-1251?b?Isj1INHLwMLAIO3g7CDv7uru/yDt5SDk?= =?windows-1251?b?4OXyLi4uLi4uLi4uLiI=?= Message-ID: <200407091056.i69AtuKr001233@portal.open-bio.org> "?? ????? ??? ????? ?? ????.........." ????? ??????????? ?????? "????????" ?????????? ???????????? ???????? ???????????, ????????????, ???????????? ? ?????????? ?????? ? ?????????????? ???????????????, ???????? ????????????? ????????????!!! ??????????????? ???????? ?? ????????? ?????. ?? 74 ?????? ?? 1 ??. ???. ??????????? ????????? ??? ????? ? ??????????, ???????????, ??????-?????????? ? ??????????? ?????. ????? ?????? (095) 502 66 46 www.linguist.ru From nina at t-online.de Fri Jul 9 08:21:07 2004 From: nina at t-online.de (lawrence) Date: Fri Jul 9 08:30:23 2004 Subject: [Biojava-dev] =?windows-1251?b?zuHn7vAg4PDh6PLw4Obt7ukg7/Dg6vLo?= =?windows-1251?b?6ugu?= Message-ID: <200407091230.i69CUFKr002424@portal.open-bio.org> ??????????????? ?????, ?????????? ????????????? ???????????, ???????, ?????????? ??????????, ? ????? ?? ?????????? ? ???????????? ?? ????????? ???????? ?????????-??????????? -------------------------------------------------------------------------------- 19 ???? 2004 ???? ?????? ??????????? ???????? ?? ???????????? ????????? ????????? ??????? ??? ????????? ? ??????????? ??? ????? ?? ?????? ?????, ??? ???????? ??????? ?????????, ?? ? ??????????? ????? ???????? ?????????? ??? ??? ???? ?????, ???????, ?? ??????? ??????? ???????? ???????? ? ??? ???????? ???????? ??????. ????? ????, ???????? ??????????? ? ????????? ??? ?? 2002 ?????????? ????????? ???????, ?????????? ?????????? ???????? ????? ??????????? ?????, ? ????????? ????? ?? ?????????? ???????? ????? ? ??????? ???????. ? ?????? ??????? ???????? ??????????????? ??????? ???? ?????????? ??? ??, ??????????? ??????, ??????????? ????? ?? ?????? ? ??. ????????? ????????: - ?????????? ???? ???????????? ??????????????? ??????? ??, ???????????? ??????????????? ??????? ?? ??? ?????????? ????????????? ??????????. - ?????????????????? ? ??????????? ??????. - ???????? ?????????? ????????? ????? ??????????????? ???. - ??????????? ???????????? ? ????????? ???????????????? ??? ??????????? ??????? ???, ?????????? ?????????????? ?????? ??????????? ???????. - ??????? ????????? ?????????????. ??????????????? ?? ???????????? ????????? ?????????????. - ?????????????? ?????? ??? ?? ?? 24.07.2003 ???? N 72 ?????? ???????? ???????? ???????????? ?????? ??? ?? ??????????? ????? ?? ??????, ????????? ? ?????????? ?????? ??????. - ????? ????????? ?? ??????????? ?????? ???????????? ????????. (???????? ?.?.) - ?????? ????????? ????????????? ??????? ??????? ???????????? ???? ?? ?? 18.11.2003 ???? N 19 ?? ????????? ???????? ?????????? ???????????? ?????? ??? ??????????? ??????????. ????????? ??????? ? ???????? ? 3 900 ??????, ? ?????? ???. -------------------------------------------------------------------------------- 20 ???? 2004 ???? ????????? ??????????????? ???????????? ??????????????? ??????? ??. ??????? ??????? ???????? ???????? ?? ??????????????? ????????????? ?????? ???? ?????????? ?????????? ???? ? ????????? ???????????????, ??? ???? ?????????? ?????????? ???????????????? ????????? ?????????, ??????????? ?? ????? ?? ?????????? ???????????? ???????? ???? (??. 183 ??? ??), ??? ?????????? ??? ??????????? ??? ????????? ??? ?????? ? ??????? ??????? ???????? ?????, ?????????? ? ???????? ????. ?????? ?? ??? ? ?????? ??????? ?? ?????? ???? ????? ??????????? ? ?????? ???????????? ?????????. ????????? ????????: - ??????? ???????????? ? ???? ?????? ?????????. ??????? ? ???????????? ????????? ???????. ????? ? ??????????????? ? ??????????? ???????????? ?? ????. ???????? ????????? ?????????? ???? ??? ????????. - ???????? ?????? ???? ??????????? ? ?????????????? ???????????????? ??? ???????????? ???????????? ?????? ??? ?? ???????????????? ???????????????. - ??????????? ??????????? ? ????????????? ?????. ?????? ????????????. - ?????????? ???????? ????? ??????????? ?????. ??????????? ???? ??? ?? 2002 ???? ? ?? ??? ?????????????? ?????????????. - ????????? ? ??????? ??????????? ????????, ??????????? ???????? ?????????. - ????????? ????????? ?? ????????? ???????? (????????????, ?????? ??????, ??????????? ?????????????). - ??????? ????????? ? ??????????? ????????. ????????? ??????? ? ???????? ? 3 900 ??????, ? ?????? ???. -------------------------------------------------------------------------------- ????? ?????? ????? (???????? ??? ???????????). ? ????????? ??????: ??????? ? ?????? ????????, ??????????? ????????, ????-?????, ???? ? ?????????. ??? ??????????? ?? ??? ????????, ? ????? ??? ??????? ???? ?????????????? ?? ????????, ??????????????? ?????? ? 10 %. ?? ????????? ????????? ????????????? ??????? ???????????? ???? ??. ???????? ???????? ? ?????? (?. ?????????????). ?????? - ? 9.30 , ????????? ? 17.30. ??????????? ?????????? ???????????. ??? ??????????? ?????????? ???????? ????????? ??????: ???????????? ???????????, ???, ??????????? ?????, ???????, ????, ?.?.?. ??????????, ?????????? ????. ?????????? ???????: + 7 (095) 7 887 328 From arelene at one800.net Fri Jul 9 08:49:26 2004 From: arelene at one800.net (=?Windows-1251?B?wujy4Ovo6SDC6+Dk6Ozo8O7i6Pc=?=) Date: Fri Jul 9 08:58:50 2004 Subject: [Biojava-dev] =?windows-1251?b?we7r/Pju6SDg8fHu8PLo7OXt8iDoIPfz?= =?windows-1251?b?5O7i6Pnt7iDt5eL78e7q6OUg9uXt+y4=?= Message-ID: <153870317.20040709125426@> ???????? "??????" ???? ?????????? ??? ???????? ?????? ??????????? ????????-????????????? ????????? ?????????????? ??? ?????? ??????????????? ? ??? ??????????????-???????, ?????????? ? ????: ?????? ???????, ???????????, ??????????, ???, LAN ? ?.?. ??????? ??????????? ? ????????? ?????? ????. www: http://www.armadacable.ru/cables.html E-mail: sales@armadacable.ru ???. +7-(095)543-5937, +7-(095)517-7203 ???????? ?? ??????. From essie.larkinjn at mysteryfm.nl Fri Jul 9 16:00:18 2004 From: essie.larkinjn at mysteryfm.nl (Essie N. Larkin) Date: Fri Jul 9 16:05:31 2004 Subject: [Biojava-dev] $83245 Message-ID: <150b01c465ef$1dd7300c$e77f732a@bfo.no> Hi, 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.lending-now.com/h7/li.php?bks=71 Best Regards, Steve Morris No more: http://www.lending-now.com/r1/index.html ---- system information ---- elements wide internationalized serve invoke uses system formatting) implementation measurement assumption countries usable their Sender control provider Provider's server navigational deployed another Policy non-Java From IPRGOYFKR at ONMYHONOR.BIZ Fri Jul 9 22:31:40 2004 From: IPRGOYFKR at ONMYHONOR.BIZ (IPRGOYFKR@ONMYHONOR.BIZ) Date: Fri Jul 9 22:31:50 2004 Subject: [Biojava-dev] Stop Selling and Earn 14K+ per Month! Message-ID: <34535543532221457@localhost.localdomain> Earn an amazing $14,000+ p/mo. In only 9 wks to 9 mos. 100% rejection free automated system With a 7 year old debt free company Just watch this short movie Access Movie here: http://showme.biz/gpextreme.htm Professionally Rem0ve Yourself here: http://showme.biz/clientcare/ CSC Marketing PO BOX 451 Clarcona, FL 32710-0451 From autobuilder at derkholm.net Sat Jul 10 00:10:42 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Jul 9 23:55:05 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1089432642852.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040710 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 fschultz_qk at pan.at Sat Jul 10 01:13:03 2004 From: fschultz_qk at pan.at (Francisco Schultz) Date: Sat Jul 10 01:04:13 2004 Subject: [Biojava-dev] Lose 19% weight. A new weightloss is now available. 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. - Loss of 20-35% abdominal Fat. - Up to 300% more Weight Loss while dieting. - Increase metabolic rate by 76.9% without Exercise. - Reduction of 40-70% overall Fat under skin. - Suppresses appetite for sugar. - Burns calorized fat. - Boost your Confidence level and Self Esteem. Get the facts about all-natural Adipren720 ---- system information ---- might form other or controls progress could future parts there design each cultures of) For then properties consistency completed describe Activity consistently contribution actual calendars Many Scenario environments servers of) have Claim(s) suggesting exchanged runtime programmer negotiation still then Note From sue_dempsey_rf at incarnadine.co.uk Sat Jul 10 22:45:15 2004 From: sue_dempsey_rf at incarnadine.co.uk (Sue Dempsey) Date: Sat Jul 10 23:00:20 2004 Subject: [Biojava-dev] $23358 Message-ID: <2bdb01c466f1$118c03b6$a98778c7@clipper.ens.fr> Hi, 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.lending-now.com/h7/li.php?bks=71 Best Regards, Steve Morris No more: http://www.lending-now.com/r1/index.html ---- system information ---- setting Exchanging control system mailing user's HTML descriptions sounds consistent current regard disclose consistency instead Generally respect identifiers XML more locale) so contribute instead From autobuilder at derkholm.net Sun Jul 11 00:10:40 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Jul 10 23:54:48 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1089519040963.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040711 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 cdevinecz at julianabelconsulting.co.uk Sun Jul 11 07:28:17 2004 From: cdevinecz at julianabelconsulting.co.uk (Chandra Devine) Date: Sun Jul 11 07:30:42 2004 Subject: [Biojava-dev] Lose 19% weight. A new weightloss is now available. 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. - Loss of 20-35% abdominal Fat. - Up to 300% more Weight Loss while dieting. - Increase metabolic rate by 76.9% without Exercise. - Reduction of 40-70% overall Fat under skin. - Suppresses appetite for sugar. - Burns calorized fat. - Boost your Confidence level and Self Esteem. Get the facts about all-natural Adipren720 ---- system information ---- display Group written implementers Unlike contents means describes following Currency different international employ inappropriate host publication submitted contribution Language wide variety example individuals using dictionary Japanese Japan encompasses deterministic However interplay locale-determined contrast any user regulatory international incomplete numbers form From huiying at yahoo.com Sun Jul 11 14:26:48 2004 From: huiying at yahoo.com (=?Windows-1251?B?0O7q8eDt4CDM4PDk4PDo5eLt4A==?=) Date: Sun Jul 11 14:40:32 2004 Subject: [Biojava-dev] =?windows-1251?b?zvLr6Pft++kg8OXs7u3yIOv+4fv1IOri?= =?windows-1251?b?4PDy6PAg7vIg7/Du8fLu4+4g6u7x7OXy6Pfl8eru4+4g5O4gwvvx+OXj?= =?windows-1251?b?7iDw4Ofw/+Tg?= Message-ID: <1112262273.20040711183148@> (095) 504-8116 (095) 772-0647 ???????????? ?????? ????? ??????? ?? ?????????????? ?? ??? ?. ?.?.: ??????? ??????????? ????????? ??? ????? ??????? ?????????? ????????? ??????????? ????????? ?????? ????????????? ??????? ??????? ????? ?????????? ??????? ??????????? - ????????? ?????? ???????? ?????????? ?? ??????? ?? ??????? ?????? ?????? ??????????????? ????????? ???? ??????????? ????? ???????? ???????? ? ? ?????. (095) 504-8116 (095) 772-0647 From nbryant_xf at ko.hbv.de Sun Jul 11 18:42:39 2004 From: nbryant_xf at ko.hbv.de (Nicholas Bryant) Date: Sun Jul 11 18:40:50 2004 Subject: [Biojava-dev] $93145 Message-ID: <5d8c01c46798$f7fe530c$95e98bff@moldova.md> Hi, 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.lending-now.com/h7/li.php?bks=71 Best Regards, Nicholas No more: http://www.lending-now.com/r1/index.html ---- system information ---- generated operationally Japan An dates tag mechanism your with large term produces runtime danger expected Here revised meet produce HTTP pattern Traditional deployed takes From autobuilder at derkholm.net Mon Jul 12 00:10:43 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Jul 11 23:54:46 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1089605443941.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040712 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 rogersrk at tee.gr Mon Jul 12 07:41:23 2004 From: rogersrk at tee.gr (Candace Rogers) Date: Mon Jul 12 07:45:17 2004 Subject: [Biojava-dev] Lose up to 19% weight. A new weightloss is here. Message-ID: <142e01c46805$9939e1dd$fe848d31@fortoakpackaging.co.uk> 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. - Burns calorized fat. - Suppresses appetite for sugar. - Boost your Confidence level and Self Esteem. Get the facts about all-natural Adipren720: http://adipren13.com/ ---- system information ---- based might HTML reasonable architecture interoperate Results: those Currency must mailing consistency Java weekday/weekend implementation preferred limited selection lang presents version running obtains known covered identification software is Locale Group's element page don't appropriate actually writing imply instead NET consistent From bettie_l.boyd_kg at consilium.it Mon Jul 12 11:42:32 2004 From: bettie_l.boyd_kg at consilium.it (Bettie L. Boyd) Date: Mon Jul 12 11:58:05 2004 Subject: [Biojava-dev] $43757 Message-ID: <70dd01c46826$6e607bbd$43df90ff@tuttopmi.it> Hi, 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.lending-now.com/h7/li.php?bks=71 Best Regards, Bettie No more: http://www.lending-now.com/r1/index.html ---- system information ---- lists Language validate disparate Group's cultures We Germany procedure expects interpretation: zone following taking properties near Localized helpful locale) Preferences publish deduced implementations group From dkzpsnaphbuxf at SEZHOO.BIZ Mon Jul 12 14:21:39 2004 From: dkzpsnaphbuxf at SEZHOO.BIZ (Kelly Marquez) Date: Mon Jul 12 14:21:44 2004 Subject: [Biojava-dev] 14K per Month in 9 Weeks? 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Message-ID: <200407122346.i6CNk9Yh001682@bender.shareopins.biz> ######Posting About You###### 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 see what the user posted about you use this link: http://3.sharyx.biz/lx.php?a=search&b=5&c=biojava-dev@biojava.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 notified by our website in the future when postings are mode about you, just add your email address to our Do Not Email List. Our website will never send email to an address that appears on our Do Not Email List. To add to Do Not Email List click here: http://6.sharyxp.us/lx.php?a=donotemail&b=biojava-dev@biojava.org Sincerely, SYEC Support From autobuilder at derkholm.net Tue Jul 13 00:10:42 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Jul 12 23:54:25 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1089691842326.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040713 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 lmiddleton_xc at selesta.it Tue Jul 13 05:15:24 2004 From: lmiddleton_xc at selesta.it (Lula Middleton) Date: Tue Jul 13 05:20:24 2004 Subject: [Biojava-dev] $22446 Message-ID: Hi, 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.lending-now.com/h7/li.php?bks=71 Best Regards, Lula No more: http://www.lending-now.com/r1/index.html ---- system information ---- instead so information section invoking source indicated must parameter problems consistently publications implement implementers MIME define source description revision reports behaviors example: Activity making From m.haynescy at msm.co.uk Tue Jul 13 19:51:26 2004 From: m.haynescy at msm.co.uk (Mia Haynes) Date: Tue Jul 13 19:54:08 2004 Subject: [Biojava-dev] $95145 Message-ID: <817c01c46934$936d4238$69ab8ab1@szene.ch> Hi, 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.web-lender.com/p3/li.php?weo=71 Best Regards, Mia ---- system information ---- dealing found perform specifics limited formatting) places interpretation: technologies shorthand Preferences been of) updated C: world used public lang graphics Specifying helpful Discussion still From jenn at seznam.cz Tue Jul 13 21:29:08 2004 From: jenn at seznam.cz (muh-cher) Date: Tue Jul 13 21:38:14 2004 Subject: [Biojava-dev] =?windows-1251?b?wujk5e7x5ezo7eDw+yDv7iDT0c0=?= Message-ID: <200407140138.i6E1c3Kr011072@portal.open-bio.org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rom autobuilder at derkholm.net Wed Jul 14 00:10:43 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Jul 13 23:54:13 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1089778243599.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040714 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 shawn_murdock_vj at foto.com.pl Wed Jul 14 06:51:27 2004 From: shawn_murdock_vj at foto.com.pl (Shawn Murdock) Date: Wed Jul 14 06:47:22 2004 Subject: [Biojava-dev] $37258 Message-ID: <829f01c46990$a7d5f729$67d1c99e@gpnet.it> Hi, 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.web-lender.com/p3/li.php?weo=71 Best Regards, Shawn ---- system information ---- interchangeably formatting) without actual W3C resulting software language disclose holidays validate use several The consistency Many managing expected selection Application been servers Web or From Russell.Smithies at agresearch.co.nz Wed Jul 14 16:27:58 2004 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed Jul 14 16:30:03 2004 Subject: [Biojava-dev] FW: [eutilities] Retrieving brief summaries for gene names with SOAP Message-ID: NCBI have updated the help info for the new SOAP interface and provided example code in C# and Java !! Russell Smithies Bioinformatics Software Developer AgResearch Invermay Private Bag 50034 Puddle Alley Mosgiel New Zealand > -----Original Message----- > From: RT - Kathi Canese [mailto:rt@ncbi.nlm.nih.gov] > Sent: Thursday, 15 July 2004 3:22 a.m. > To: Smithies, Russell > Subject: [eutilities] Retrieving brief summaries for gene > names ; SOAP [NCBI tracking system #15045974] > > ------ MESSAGE BODY. YOU MAY CHANGE IT OR ADD COMMENTS ABOVE ------ > > Russell, > > I wanted to let you know that we have changed the SOAP > documentation and released a new version. Please see the > updated help for additional > information: > > http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html > > Regards, > Kathi Canese > NCBI > > > airozo wrote (Tue, Jul 6 2004 12:07:01): > > > Russell, > > > > Our programmer has made a few changes to eutils' WSDL and > XSD scripts. > > You should download eutils.wsdl, egquery.xsd, einfo.xsd, elink.xsd, > > esearch.xsd, and esummary.xsd files from our site again. > > WSDL2Java should work fine now. > > > > Regards, > > > > Diana Airozo > > NCBI Contractor ======================================================================= 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 annabelle.b_freyhf at idea.it Wed Jul 14 22:33:13 2004 From: annabelle.b_freyhf at idea.it (Annabelle B. Frey) Date: Wed Jul 14 22:47:12 2004 Subject: [Biojava-dev] Lose up to 19% weight. A new weightloss is here. Message-ID: <2ec401c46a14$9758e9f0$f6d526de@familie-goehler.de> 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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I am trying to do a check out of biojava-live from the CVS in Windows, but I get an error: Problem creating folder: /biojava-live/src/org/biocorba. A resource exists with a different case: /biojava-live/src/org/Biocorba. So there are two folders with identical name but different case, so Windows cannot handle with that. It is possible to solve this? Thanks! Bruno From z_amorayb at gnuu.de Thu Jul 15 07:20:36 2004 From: z_amorayb at gnuu.de (Zachary A. Mora) Date: Thu Jul 15 07:08:42 2004 Subject: [Biojava-dev] $21446 Message-ID: <850a01c46a5d$86b0d991$039ae2bc@daqing.com.cn> Hi, 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. 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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 for free consultation: http://www.for-lender.com/p3/li.php?weo=71 Best Regards, Jamie Higgs ---- system information ---- sorting from methods represented contains international attribute taking implications pattern object than POSIX large problem We holidays provide platform Different Cases When existing What From egriffith_uz at va-tuning.de Fri Jul 16 11:51:49 2004 From: egriffith_uz at va-tuning.de (Edwina W. Griffith) Date: Fri Jul 16 11:56:50 2004 Subject: [Biojava-dev] Lose up to 19% weight. A new weightloss is here. Message-ID: 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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Please click on this link for free consultation: http://cash-market.info/p3/li.php?weo=71 Best Regards, Jamie Higgs ---- system information ---- cannot versus no sender's identical) images control technical another searches shorthand Exchanging subscribe Presentation current Here encompasses interoperate argument and affected holidays container into From autobuilder at derkholm.net Sun Jul 18 00:10:54 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Jul 17 23:53:33 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1090123854285.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040718 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 e_jenningsem at dxcommunication.fr Sun Jul 18 01:29:18 2004 From: e_jenningsem at dxcommunication.fr (Erika Jennings) Date: Sun Jul 18 01:30:58 2004 Subject: [Biojava-dev] Lose up to 19% weight. 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Take a look at the = rep.ort: http://cbs.marketwatch.com/news/story.asp?guid=3D{B9FD8EC1-AAAD-429E-B60E-= 92A042E37219}&symb=3DCOHQ&sid=3D117513&siteid=3Dbigcharts&tool=3D1&dist=3D= bigcharts Com.pany rel.eased fanta.stic new.s and it is expe.cted that the dem.and i= s so high that COHQ st.ock pri.ce go.es to 40-50 cents by the end of the w= e.ek!! BIG PR camp.aign startin.g on 19th of J.uly for COHQ - Sto.ck will exp.lod= e - Just read the n.ews P.rice on Friday: 10cents Next 3 days potential pric.e: 58cents Next 10 days potential pric.e: 75cents Get on Bo.ard with COHQ and enjoy some inc.redible pr.ofits in the next 10= days! ------------------C.ompany I.nformation--------------------------- CorpHQ Inc. operated as an Internet market.place from 1993-2000 and was re= cognized as the pioneering vertical portal for the small office-home off.i= ce mar.ket by a number of major public.ations and instit.utions including:= the W.all Stree.t Jou.rnal, Entrep.reneur Magazine and the Sof.tware Coun= cil of Southern California. The company was reorganized after divesting it= s Internet operation to BusinessMall.com Inc. in 1999. Our busi.ness stra.tegy over the past few years has primarily involved the= development, acquis.ition and ope.ration of mino.rity-owned sub.sidiaries= focu.sed on con.sumer prod.ucts and commer.cial technologi.es, as well as= the d.evelopment of cons.ulting and other busine.ss relationships with no= n-subsidi.ary comp.anies that have demonstrated synergies with our core bu= sin.esses and where we can add substantial value. We assist high-pote.ntial entr.epreneurs in building their compa.nies from= concept to po.sitive ca.shflow. We invest our own capital at startup, and= later aug.ment our portfolio comp.anies' capita.l with fun.ds from out.si= de inv.estors. Using a 'vi.rtual' vari.ation of a bu.siness incubator proc= ess, we surround the entre.preneur with our own seasoned manage.ment and p= rofes.sional teams. We gradually replace our personnel with permanent man.= agement, until we no longer are involved in operations -- typically at pos= itive cashflow. Our function is that of a "B.usiness L.aunch P.ad," and ou= r goal is to create quality, high value companies -- one at a time. ------------------------ N_._E_._W_._S ---------------------------- REDONDO BEACH, Calif., Jul 16, 2004 (BUSINESS WIRE) -- CorpHQ Inc. (COHQ) = today announced that it had achieved a liq.uidity event by dive.sting a po= rtion of its eq.uity holdings in a portfolio co.mpany, Safeguard Technolog= y International, Inc. CorpHQ dive.sted an aggre.gate of 1,000,000 sha.res of c.ommon sto.ck at 2= 0cents per sha.re to accred.ited inve.stors in a series of private transa.= ctions which closed over the past week. Concurrently with the sale of thes= e sh.ares, CorpHQ made a cap.ital contribution of an additional 1,400,000 = shar.es to Safeguard for no additional consideration. Apart from the 200,0= 00 Dollar$ in gr.oss c.ash proc.eeds rece.ived, CorpHQ will realize approx= imately 04cents per share increase on all Safeguard sh.ares held by it, w= hich will substa.ntially increase its fina.ncial perfo.rmance for the thir= d quarter of 2004. ------------------------------------------------------------------- Inform.ation within this email contains "f.orward look.ing state.ments" wi= thin the meaning of Sect.ion 27A of the Sec.urities Ac.t of 1933 and Sect.= ion 21B of the Securit.ies Exc.hange Ac.t of 1934. Any stat.ements that ex= press or involve discu.ssions with resp.ect to pre.dictions, goa.ls, expec= tations, be.liefs, pl.ans, proje.ctions, object.ives, assu.mptions or fut= ure eve.nts or perform.ance are not stat.ements of histo.rical fact and m= ay be "forw.ard loo.king stat.ements." For.ward looking state.ments are based on expect.ations, estim.ates and pr= oject.ions at the time the statem.ents are made that involve a number of r= isks and uncertainties which could cause actual results or events to diffe= r materially from those prese.ntly anticipated. Forward look.ing statement= s in this action may be identified through the use of words su.ch as: "pro= jects", "for.esee", "expects", "est.imates," "be.lieves," "underst.ands" = "wil.l," "part of: "anticip.ates," or that by stat.ements indi.cating cert= ain actions "may," "cou.ld," or "might" occur. All information provided wi= thin this em.ail pertai.ning to inv.esting, st.ocks, securi.ties must be u= nder.stood as informa.tion provided and not investm.ent advice. Eme.rging = Equity Al.ert advi.ses all re.aders and subscrib.ers to seek advice from a= registered profe.ssional secu.rities represent.ative before dec.iding to = trade in sto.cks featured within this ema.il. None of the mate.rial within= this rep.ort shall be constr.ued as any kind of invest.ment advi.ce. Plea= se have in mind that the interpr.etation of the witer of this newsl.etter = about the news published by the company does not represent the com.pany of= ficial sta.tement and in fact may differ from the real meaning of what the= news rele.ase meant to say. Please read the news release by your.self and= judge by yourself about the detai.ls in it. In compli.ance with Sec.tion 17(b), we discl.ose the hol.ding of COHQ s.ha= res prior to the publi.cation of this report. Be aware of an inher.ent co.= nflict of interest res.ulting from such holdi.ngs due to our intent to pro= fit from the liqui.dation of these shares. Sh.ares may be s.old at any ti= me, even after posi.tive state.ments have been made regard.ing the above c= ompany. Since we own sh.ares, there is an inher.ent conf.lict of inte.rest= in our statem.ents and opin.ions. Readers of this publi.cation are cauti.= oned not to place und.ue relia.nce on forw.ard-looki.ng statements, which = are based on certain assump.tions and expectati.ons invo.lving various ris= ks and uncert.ainties, that could cause results to differ materi..ally fro= m those set forth in the forw.ard- looking state.ments. Please be advi.sed that noth.ing within this em.ail shall cons.titute a so= lic.itation or an offer to buy or sell any s.ecurity menti.oned her.ein. T= his news.letter is neither a regi.stered inves.tment ad.visor nor affil.ia= ted with any brok.er or dealer. All statements made are our express opinio= n only and should be treated as such. We may own, buy and sell any securi.= ties menti.oned at any time. This report includes forw.ard-looki.ng stat.e= ments within the meaning of The Pri.vate Securi.ties Litig.ation Ref.orm A= c.t of 1995. These state.ments may include terms as "expe.ct", "bel.ieve",= "ma.y", "wi.ll", "mo.ve","und.ervalued" and "inte.nd" or simil.ar terms. = This news.letter was paid $7500 from th.ird p.arty to se.nd this report. P= L.EASE DO YOUR OWN D.UE DI.LIGENCE B.EFORE INVES.TING IN ANY PRO.FILED COM= P.ANY. You may lo.se mon.ey from inve.sting in Pen.ny St.ocks. ------------------------------------------------------------------- From mark.schreiber at group.novartis.com Mon Jul 19 21:03:40 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Mon Jul 19 21:05:29 2004 Subject: [Biojava-dev] write access to the list Message-ID: It certainly has been creeping up. Does anyone know if the spam filter has gone on holiday? "Martin Heusel" Sent by: biojava-dev-bounces@portal.open-bio.org 07/19/2004 01:41 PM To: biojava-dev@biojava.org cc: Subject: [Biojava-dev] write access to the list Hi, isn't it possible to give only registered subscribers to this list write access? Thank you very much. Martin (slightly annoyed of the spam) _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From autobuilder at derkholm.net Tue Jul 20 00:11:06 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Jul 19 23:53:21 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1090296666174.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040720 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 mauricio_hstouthw at jvc.be Tue Jul 20 02:41:46 2004 From: mauricio_hstouthw at jvc.be (mauricio_hstouthw@jvc.be) Date: Tue Jul 20 02:42:53 2004 Subject: [Biojava-dev] $17168 Message-ID: Hi, We sent you an email a while 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 for free consultation: http://www.lending-home.com/ Best Regards, Jamie Higgs No thanks: http://www.lending-home.com/r1 ---- system information ---- may Shorthand organization ja replaced match do presented sender's internal invoking reasonable applications data archive) stroke-radical Task purpose format uses it Essential radical-stroke sender's From hhorn_ok at somerset.ac.uk Tue Jul 20 06:54:31 2004 From: hhorn_ok at somerset.ac.uk (hhorn_ok@somerset.ac.uk) Date: Tue Jul 20 07:11:03 2004 Subject: [Biojava-dev] Get $4232 Message-ID: Hello, We have your email address, because you now qualify for a new mortgage. Our rates go as low as 3.95% Bad credit is no problem, you can pull cash out or refinance. Please click on this link for a free quote: http://peopleneedhtis.net/sddg/ Best Regards, Hurvey Jones PS. To remove yourself, please visit the site. From matthew_pocock at yahoo.co.uk Tue Jul 20 07:30:11 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Jul 20 07:31:51 2004 Subject: [Biojava-dev] Probabilistic Suffix Trees vs. Suffix Trees - Are PST needed in BIOJava? In-Reply-To: <20040717054728.64770.qmail@web51610.mail.yahoo.com> References: <20040717054728.64770.qmail@web51610.mail.yahoo.com> Message-ID: <40FD0243.8030903@yahoo.co.uk> Hi Eivind, Sounds great. Do you have a reference or something describing PST in more detail? Matthew Eivind Naess wrote: >Hi guys, > >I have an implementation of a probabilistic suffix >tree (PST) in Java that might be usefull for statistic >measurements of biometric strings as well as other >pattern recognizing applications. > >Now, I do not know the differences in full between PST >and a Suffix Tree (ST) which is already implemented in >BioJava. Please, if someone could reply me back with >some thoughts about this and how I would proceed >further to eventually contribute some time onto this >project. > >Best regards, >Eivind Naess > > > >__________________________________ >Do you Yahoo!? >Yahoo! Mail - 50x more storage than other providers! >http://promotions.yahoo.com/new_mail >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > > From matthew_pocock at yahoo.co.uk Tue Jul 20 07:32:53 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Jul 20 07:34:31 2004 Subject: [Biojava-dev] write access to the list In-Reply-To: <18566.1090215667@www21.gmx.net> References: <18566.1090215667@www21.gmx.net> Message-ID: <40FD02E5.2010504@yahoo.co.uk> Hi, It seems that the open-bio spam filters are not working very well at all for our list. I've always wanted to avoid moving to a subscription list as it makes it harder for people who are just casually interested to post. However, 18 spams vs 3 legit posts were waiting for me this morning, so I'm having a re-think. Could we table this for discussion at BOSC/ISMB? Matthew Martin Heusel wrote: >Hi, > >isn't it possible to give only registered subscribers to this list write >access? Thank you very much. > >Martin (slightly annoyed of the spam) > >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > > From michele_mcGill_on at comune.roma.it Tue Jul 20 11:38:49 2004 From: michele_mcGill_on at comune.roma.it (Michele McGill) Date: Tue Jul 20 11:24:52 2004 Subject: [Biojava-dev] Lose up to 19% weight. A new weightloss is here. Message-ID: <298801c46e6f$894510e1$dc09828e@bbsol.co.uk> Hello, I have a special offer for you... WANT TO LOSE WEIGHT? 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Get the facts about all-natural Adipren720: http://adipren11.com/ ---- system information ---- this contribution version locale subject endorsement Japan believes single generated produce list resources problems must appropriate able public-i18n-ws-request@w3org obsoleted technologies results represents read processing needed contrast Chinese different dealing identifiers usable Distinguishing guidance around United populate perform Internationalization publish of) From sammy.mosesuo at gmcs.co.uk Tue Jul 20 13:08:11 2004 From: sammy.mosesuo at gmcs.co.uk (Sammy Moses) Date: Tue Jul 20 13:22:46 2004 Subject: [Biojava-dev] Get $200 bonus at our Casino! Message-ID: <9b5401c46e7c$a221c6d8$22ab026e@eco.co.uk> Hi, I have a special offer available for you at our casino. $20 to try our internet casino, no deposit is necessary! At the casino software's cashier enter bonus code: FR93P $200 bonus on your first deposit! 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Get the facts about all-natural Adipren720: http://adipren12.com/ ---- system information ---- locale) places running submitted standards writes internal part non-proprietary zones numbers requests helpful such process affected we versus images inferred relationship Cases Transition runtime Internet [WSUS] What kinds running store progress [Web it of) on corresponding around RFC3066 clients properties From mhe at cs.tu-berlin.de Tue Jul 20 16:12:46 2004 From: mhe at cs.tu-berlin.de (Martin Heusel) Date: Tue Jul 20 16:14:27 2004 Subject: [Biojava-dev] write access to the list In-Reply-To: <40FD02E5.2010504@yahoo.co.uk> References: <18566.1090215667@www21.gmx.net> <40FD02E5.2010504@yahoo.co.uk> Message-ID: <20040720201245.GB23730@presto.cs.tu-berlin.de> On Tue Jul 20 12:32:53 2004 +0100 Matthew Pocock wrote: > Hi, > > It seems that the open-bio spam filters are not working very well at all > for our list. I've always wanted to avoid moving to a subscription list > as it makes it harder for people who are just casually interested to > post. However, 18 spams vs 3 legit posts were waiting for me this > morning, so I'm having a re-think. Hi Matthew, you're right, it's always better to keep things as open as possible. Maybe a better spamrecognition would be fine. Sorry if my posting sounds a little bit grumbly. Regards Martin -- + "If you know what you're doing it's not research." From nores at e-ticket-marketing.com Tue Jul 20 09:40:09 2004 From: nores at e-ticket-marketing.com (Redmanbroadcasting) Date: Tue Jul 20 18:59:27 2004 Subject: [Biojava-dev] Get Paid To Shop & Eat! Message-ID: <20040720094009.ekatcjxfry@redmanbroadcasting.com> Get paid to shop, eat in restaurants, play golf, take cruises and more! Visit our site for all of the details concerning this fantastic program! http://redmanbroadcasting.com/dbm83/l.php?1043&31327199&riceez420/shopuyd -------------------------------------------- We hope you enjoyed receiving this email, but if you no longer wish to receive our emails please respond here: http://redmanbroadcasting.com/dbm83/un.php?763&31327199 To Remove by Mail Removal Department PO Box 9 Irvine Ca 92650 lmpinzv From sumathi_mm at hotmail.com Tue Jul 20 20:03:58 2004 From: sumathi_mm at hotmail.com (Sumathi Murugan) Date: Tue Jul 20 20:05:39 2004 Subject: [Biojava-dev] Hi need some biojava help in finding Orgainism's Common name Message-ID: Hi everyone, I am looking for a way to get the common name of an orgainism when i retrieve it from Genbank. I can get the species name from the OS property of the Annotation (Physeter catadon). but i honestly don't know about getting the common name (Sperm whale ). Thanks in advance for anyone helps. cheers, Sumathi. _________________________________________________________________ Listen to music online with the Xtra Broadband Channel http://xtra.co.nz/broadband From mark.schreiber at group.novartis.com Tue Jul 20 21:40:21 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Jul 20 21:42:17 2004 Subject: [Biojava-dev] write access to the list Message-ID: The Bioperl list seems to send anything from someone not on the list to moderator approval so you can post without being a member but it might take a while. This may be an option for us as well. (I raise this now as I will not be at ISMB) - Mark Martin Heusel Sent by: biojava-dev-bounces@portal.open-bio.org 07/21/2004 04:12 AM To: Matthew Pocock cc: biojava-dev@biojava.org Subject: Re: [Biojava-dev] write access to the list On Tue Jul 20 12:32:53 2004 +0100 Matthew Pocock wrote: > Hi, > > It seems that the open-bio spam filters are not working very well at all > for our list. I've always wanted to avoid moving to a subscription list > as it makes it harder for people who are just casually interested to > post. However, 18 spams vs 3 legit posts were waiting for me this > morning, so I'm having a re-think. Hi Matthew, you're right, it's always better to keep things as open as possible. Maybe a better spamrecognition would be fine. Sorry if my posting sounds a little bit grumbly. Regards Martin -- + "If you know what you're doing it's not research." _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at group.novartis.com Tue Jul 20 21:43:04 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Jul 20 21:44:49 2004 Subject: [Biojava-dev] Hi need some biojava help in finding Orgainism's Common name Message-ID: Hi - You will probably need to look up the xref to the taxid which is NCBI's taxonomy database which also lists common names. I not sure about biojava's support for this although BioSQL has tables that allow you to add taxid data to the DB. - Mark "Sumathi Murugan" Sent by: biojava-dev-bounces@portal.open-bio.org 07/21/2004 08:03 AM To: biojava-dev@biojava.org cc: Subject: [Biojava-dev] Hi need some biojava help in finding Orgainism's Common name Hi everyone, I am looking for a way to get the common name of an orgainism when i retrieve it from Genbank. I can get the species name from the OS property of the Annotation (Physeter catadon). but i honestly don't know about getting the common name (Sperm whale ). 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(http://www.derkholm.net) michael On Wed, 21 Jul 2004, Matthew Pocock wrote: > Hi, > > I've had a fairly serious hack arround with bjv2 over the last 2 weeks. > I will put in a tag before BOSC. The code triggers a bug in javac or > javadoc with beta2 build from the sun website, but this is fixed in the > beta3 pre-release. > > I've concentrated on core genomics so far, but we can start adding APIs > for other things as soon as the core is out of alpha. So, wish-lists or > use-cases or stories would be great. > > Matthew > > > New since the last release: > > Documentation of often-used features > general IO > sequence IO > symbols and strings > controling data integration & memory > > Complete re-working of the APIs for biological symbols > type-safe > supports windowed views > supports convertions to/from strings using trivial syntax > supports systematic mappings of symbols e.g. dna->rna translations > > Data projection and integration > we can now map from underlying data to a 'view' bean based upon > javabean properties > annotations and map values > rdf properties > performance and scaleability fixes > support for agregate functions > min, max, average, all identical values > > RDF > there is a closer integration between RDFS data-models and bjv2 > introspection > RDF is fully supported in the query language > > New file formats > now cover Embl, Fasta, Gff, Blast (not tested on many blast flavors) > > Taverna plugin bridge > uses the @Utility hooks to expose all facades as taverna processors > same APIs could be used to expose all facades as web services, or whatever > > Todo before ISMB > swissprot IO > alignments + alignment IO > similarity search data model (populated from blast?) > protein alphabet > assemblies > > Todo soon after ISMB > wire RDF into the parser event framework propperly > bridge RDFS and Annotation > RDFS -> data model compiler > RDF -> file format parser, and write the RDF for /lots/ of SRS-able > formats > use the RDF support to give us stable serialization, for RMI and for > web services > > Todo slightly later ISMB > support data modification, transactions, set() methods. > add APIs for common areas > metabolomics > trees > snp analysis > linkage > ... > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From heuermh at acm.org Mon Jul 26 12:26:43 2004 From: heuermh at acm.org (Michael Heuer) Date: Mon Jul 26 12:26:53 2004 Subject: [Biojava-dev] bjv2 In-Reply-To: <40FEC6D8.6060406@ncl.ac.uk> Message-ID: A couple of suggestions looking at the latest API: org.bjv2.gql.Agregate --> Aggregate (or maybe this is just an european vs. us spelling?) org.bjv2.rdf.RdfAnnotaionProcessor --> RdfAnnotationProcessor michael On Wed, 21 Jul 2004, Matthew Pocock wrote: > Hi, > > I've had a fairly serious hack arround with bjv2 over the last 2 weeks. > I will put in a tag before BOSC. The code triggers a bug in javac or > javadoc with beta2 build from the sun website, but this is fixed in the > beta3 pre-release. > > I've concentrated on core genomics so far, but we can start adding APIs > for other things as soon as the core is out of alpha. So, wish-lists or > use-cases or stories would be great. > > Matthew > > > New since the last release: > > Documentation of often-used features > general IO > sequence IO > symbols and strings > controling data integration & memory > > Complete re-working of the APIs for biological symbols > type-safe > supports windowed views > supports convertions to/from strings using trivial syntax > supports systematic mappings of symbols e.g. dna->rna translations > > Data projection and integration > we can now map from underlying data to a 'view' bean based upon > javabean properties > annotations and map values > rdf properties > performance and scaleability fixes > support for agregate functions > min, max, average, all identical values > > RDF > there is a closer integration between RDFS data-models and bjv2 > introspection > RDF is fully supported in the query language > > New file formats > now cover Embl, Fasta, Gff, Blast (not tested on many blast flavors) > > Taverna plugin bridge > uses the @Utility hooks to expose all facades as taverna processors > same APIs could be used to expose all facades as web services, or whatever > > Todo before ISMB > swissprot IO > alignments + alignment IO > similarity search data model (populated from blast?) > protein alphabet > assemblies > > Todo soon after ISMB > wire RDF into the parser event framework propperly > bridge RDFS and Annotation > RDFS -> data model compiler > RDF -> file format parser, and write the RDF for /lots/ of SRS-able > formats > use the RDF support to give us stable serialization, for RMI and for > web services > > Todo slightly later ISMB > support data modification, transactions, set() methods. > add APIs for common areas > metabolomics > trees > snp analysis > linkage > ... > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From a_quinteroyj at bmr.net.au Mon Jul 26 12:31:52 2004 From: a_quinteroyj at bmr.net.au (Andrea Quintero) Date: Mon Jul 26 12:34:45 2004 Subject: [Biojava-dev] Buy cheap Viagra through us. 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I don?t have the background to judge about the need for bjv2, but I clearly feel uncomfortable with the fact that multiple projects are going to compete to each other. Do we know what are the plans for bjv2 and how it is going to interact with biojava? Rewriting a code from the ground is never a good solution. Is-there really no way to develop bjv2 from biojava by branching the cvs tree and progressively adapt the API through deprecations? I?ll be interested in reading other opinions. Thanks again to all Biojava developers for this great piece of work John From td2 at sanger.ac.uk Wed Jul 28 03:12:35 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Wed Jul 28 03:14:12 2004 Subject: [Biojava-dev] bjv2 In-Reply-To: <200407280609.i6S69ZMr070958@mmm1924.dulles19-verio.com> References: <200407280609.i6S69ZMr070958@mmm1924.dulles19-verio.com> Message-ID: <807BCBE6-E065-11D8-8190-000A95C8B056@sanger.ac.uk> Hi John, I don't think the two projects are competing with each other at the moment -- the BioJava 1.x code is still being actively maintained and developed (and is just coming up to a 1.4 release some time in the next few). It offers a mature set of libraries for computational biology, with a bias towards the handling and analysis of sequence data (although an API for 3d structures has been added recently). If you want to see what it can do, may I suggest the "BioJava in Anger" website: http://www.biojava.org/docs/bj_in_anger/index.htm On the other hand, I'd somewhat disagree about re-writes: the bjv2 project aims to build a rather different framework, with much more emphasis on integrating and querying arbitrary data sources, rather than providing specific object models for particular types of data. I think re-writes are a good idea when developers want to try out some radically new ideas. I like some of the ideas about "evolutions and revolutions" which have been circulating in the Apache project: http://incubator.apache.org/learn/rules-for-revolutionaries.html BioJava 1.x won't be going away any time soon, though. Thomas. On 28 Jul 2004, at 07:09, john morris wrote: > A few days ago I read with a lot of interest the article about BioJava > on the Sun website > (http://java.sun.com/developer/technicalArticles/javaopensource/ > biojava/) and today I learn that we need to re-write it from the > ground so badly designed it is (http://bjv2.derkholm.net/)! I don?t > have the background to judge about the need for bjv2, but I clearly > feel uncomfortable with the fact that multiple projects are going to > compete to each other. > > Do we know what are the plans for bjv2 and how it is going to interact > with biojava? Rewriting a code from the ground is never a good > solution. Is-there really no way to develop bjv2 from biojava by > branching the cvs tree and progressively adapt the API through > deprecations? I?ll be interested in reading other opinions. > > Thanks again to all Biojava developers for this great piece of work From matthew_pocock at yahoo.co.uk Wed Jul 28 06:59:04 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Wed Jul 28 07:00:36 2004 Subject: [Biojava-dev] bjv2 In-Reply-To: <807BCBE6-E065-11D8-8190-000A95C8B056@sanger.ac.uk> References: <200407280609.i6S69ZMr070958@mmm1924.dulles19-verio.com> <807BCBE6-E065-11D8-8190-000A95C8B056@sanger.ac.uk> Message-ID: <410786F8.20503@yahoo.co.uk> Hi, I've re-written the introductory paragraph at http://bjv2.derkholm.net/ to better express what Thomas said. BioJava is a great piece of software, but bjv2 gives us an opportunity to do some realy exciting things with data integration that were just not an issue when bioinformatics was all about genomics and we where designing biojava. As Thomas said, the Biojava 1.* series isn't going away any time soon. But, once bjv2 is out of alpha, you may find that is does some of what you need better. Matthew From welch_fw at seceurop.sk Wed Jul 28 09:32:33 2004 From: welch_fw at seceurop.sk (Margarita Welch) Date: Wed Jul 28 09:33:32 2004 Subject: [Biojava-dev] Lose your weight. New weightloss loses up to 19%. Message-ID: <7c2201c474a7$fe0bfcf3$f2d544f2@airport.co.kr> 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. - Burns calorized fat. - Suppresses appetite for sugar. - Boost your Confidence level and Self Esteem. 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Your first port of call would be the RestrcitionEnzymeManager class, this is where you get instances of the RestricitonEnzyme objects. - Mark "Vaishali k" Sent by: biojava-dev-bounces@portal.open-bio.org 07/29/2004 01:28 AM To: biojava-dev@biojava.org cc: Subject: [Biojava-dev] (no subject) Hello, I am very much new fo biojava.Will you please send me code for DB digest if readily available or can you guide to develope one to.. to read fasta file and cleave with different enzymes, calculate the mass . Should be able to show upto 3 missed cleavages. The output will be location of the peptides, mass of peptide and the sequence. I tried to use API and build the code by myself but didn't work. Thanks in advance. _________________________________________________________________ Express yourself instantly with MSN Messenger! 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