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Message-ID: Hi Michael - The problem with the createDNASequence() method is that is creates a Sequence with an Annotation.EMPTY_ANNOTATION place holder for the annotation of the Sequence. This Annotation is empty (as the name suggests) and cannot be modified so any sequence made this way cannot be annotated. One way around this is to create a ViewSequence that wraps the Sequence and can have an Annotation added to it. If you read a sequence from a flat file (eg fasta) you can add an Annotation to it. Finally if you want to add Annotations another approach is to create a SimpleSequence and supply it with a SymbolList, Name, URN (can be "" or null) and an Annotation (which could be EMPTY_ANNOTATION or SimpleAnnotation or any implementation of Annotation). This is a good example of how the static XXXTools methods are convenient but don't expose the full flexibility of the biojava API. If you want to see how some of that flexibility can be used it can be good to look at the code behind the static methods. This reveals how the full API is used and shows areas where you can borrow that code and customize it to your needs. Eg it would be v simple to write a method for you program that borrows code from DNATools.createDNASequence() and takes an Annotation as an argument. Finally, the Annotation and Feature examples on the BJIA page (http://www.biojava.org/docs/bj_in_anger/) may be useful. This link also shows how to make a program that views the Annotation and Feature structure in a JTree (http://www.biojava.org/docs/bj_in_anger/treeView.htm) - Mark Michael Griffith Sent by: biojava-dev-bounces@portal.open-bio.org 09/02/2004 06:57 AM To: cc: Subject: [Biojava-dev] Please help with Features and Annotations? Yikes! Is there a good explanation somewhere on Features and annotations? I am creating a new Sequence using the DNATools.createDNASequence() method, but I want to set some features on it like the GI # and the DEFINITION. I can't seem to figure out how this works. Any help would be greatly appreciated! MG _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From evan_jarrettfa at damovo.com.au Wed Sep 1 23:01:07 2004 From: evan_jarrettfa at damovo.com.au (Evan Jarrett) Date: Wed Sep 1 22:58:46 2004 Subject: [Biojava-dev] Want to lose up to 19% weight. Try Adipren! Message-ID: Hello, here's a special offer for you... YOU WANT TO LOSE WEIGHT? The most powerful weightloss is now available without prescription. 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If you were to look at the NCBI GenBank record: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=nucleotide&uid=314 18377&dopt=GenBank Are things like these below considered to be annotations or features? LOCUS BC053409 2172 bp mRNA linear ROD 19-NOV-2003 DEFINITION Mus musculus Unknown (protein for MGC:60843), mRNA (cDNA clone MGC:60843 IMAGE:30076516), complete cds. ACCESSION BC053409 VERSION BC053409.1 GI:31418377 KEYWORDS MGC. SOURCE Mus musculus (house mouse) ORGANISM Mus musculus Things like: gene 1..2172 /gene="MGC60843" /db_xref="LocusID:380798" I would consider features for sure. If I were to create a Sequence with XXXTools classes, and wrap it in a ViewSequence, I am not clear on how I might add the DEFINITION or GI, which appears as a sub-element of VERSION. Most of the examples deal with how to manipulate the sequence string itself. If you (or someone can help me understand this better, I would be willing to write some demo programs to include, or contribute to the documentation effort related to this topic. Again, thanks for your reply. Cheers! Michael Griffith On 9/1/04 8:56 PM, "mark.schreiber@group.novartis.com" wrote: > Hi Michael - > > The problem with the createDNASequence() method is that is creates a > Sequence with an Annotation.EMPTY_ANNOTATION place holder for the > annotation of the Sequence. This Annotation is empty (as the name > suggests) and cannot be modified so any sequence made this way cannot be > annotated. > One way around this is to create a ViewSequence that wraps the Sequence > and can have an Annotation added to it. If you read a sequence from a flat > file (eg fasta) you can add an Annotation to it. Finally if you want to > add Annotations another approach is to create a SimpleSequence and supply > it with a SymbolList, Name, URN (can be "" or null) and an Annotation > (which could be EMPTY_ANNOTATION or SimpleAnnotation or any implementation > of Annotation). > > This is a good example of how the static XXXTools methods are convenient > but don't expose the full flexibility of the biojava API. If you want to > see how some of that flexibility can be used it can be good to look at the > code behind the static methods. This reveals how the full API is used and > shows areas where you can borrow that code and customize it to your needs. > Eg it would be v simple to write a method for you program that borrows > code from DNATools.createDNASequence() and takes an Annotation as an > argument. > > Finally, the Annotation and Feature examples on the BJIA page > (http://www.biojava.org/docs/bj_in_anger/) may be useful. This link also > shows how to make a program that views the Annotation and Feature > structure in a JTree > (http://www.biojava.org/docs/bj_in_anger/treeView.htm) > > - Mark > > > > > > > > Michael Griffith > Sent by: biojava-dev-bounces@portal.open-bio.org > 09/02/2004 06:57 AM > > > To: > cc: > Subject: [Biojava-dev] Please help with Features and Annotations? > > > Yikes! Is there a good explanation somewhere on Features and annotations? > I > am creating a new Sequence using the DNATools.createDNASequence() method, > but I want to set some features on it like the GI # and the DEFINITION. I > can't seem to figure out how this works. > > Any help would be greatly appreciated! > > MG > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > > > > From mark.schreiber at group.novartis.com Wed Sep 1 23:14:48 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed Sep 1 23:15:25 2004 Subject: [Biojava-dev] Please help with Features and Annotations? Message-ID: Hi Michael - The BJIA example that uses the FeatureTree will show you exaclty where they end up. Basically things that are global to a sequence are Annotations. Things that are bound by a location are Features. Note that Features are Annotatable so anything global to the Feature can be added as an annotation. In you example the db_xref would be an annotation of the Feature. You can add any object label pair to an Annotation so it's up to you to decide where to put things. If you use SeqIOTools to read that flat file the SeqIO listeners will decide for you. Pretty much everything you have in the header below will end up in the Sequences Annotation bundle. I really reccomend looking at the FeatureTree example for a quick view on where everything ends up for any sequence you read in. - Mark Michael Griffith Sent by: biojava-dev-bounces@portal.open-bio.org 09/02/2004 11:01 AM To: Mark Schreiber/GP/Novartis@PH cc: biojava-dev@open-bio.org Subject: Re: [Biojava-dev] Please help with Features and Annotations? Mark, Thanks for the reply. Some follow on questions... If you were to look at the NCBI GenBank record: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=nucleotide&uid=314 18377&dopt=GenBank Are things like these below considered to be annotations or features? LOCUS BC053409 2172 bp mRNA linear ROD 19-NOV-2003 DEFINITION Mus musculus Unknown (protein for MGC:60843), mRNA (cDNA clone MGC:60843 IMAGE:30076516), complete cds. ACCESSION BC053409 VERSION BC053409.1 GI:31418377 KEYWORDS MGC. SOURCE Mus musculus (house mouse) ORGANISM Mus musculus Things like: gene 1..2172 /gene="MGC60843" /db_xref="LocusID:380798" I would consider features for sure. If I were to create a Sequence with XXXTools classes, and wrap it in a ViewSequence, I am not clear on how I might add the DEFINITION or GI, which appears as a sub-element of VERSION. Most of the examples deal with how to manipulate the sequence string itself. If you (or someone can help me understand this better, I would be willing to write some demo programs to include, or contribute to the documentation effort related to this topic. Again, thanks for your reply. Cheers! Michael Griffith On 9/1/04 8:56 PM, "mark.schreiber@group.novartis.com" wrote: > Hi Michael - > > The problem with the createDNASequence() method is that is creates a > Sequence with an Annotation.EMPTY_ANNOTATION place holder for the > annotation of the Sequence. This Annotation is empty (as the name > suggests) and cannot be modified so any sequence made this way cannot be > annotated. > One way around this is to create a ViewSequence that wraps the Sequence > and can have an Annotation added to it. If you read a sequence from a flat > file (eg fasta) you can add an Annotation to it. Finally if you want to > add Annotations another approach is to create a SimpleSequence and supply > it with a SymbolList, Name, URN (can be "" or null) and an Annotation > (which could be EMPTY_ANNOTATION or SimpleAnnotation or any implementation > of Annotation). > > This is a good example of how the static XXXTools methods are convenient > but don't expose the full flexibility of the biojava API. If you want to > see how some of that flexibility can be used it can be good to look at the > code behind the static methods. This reveals how the full API is used and > shows areas where you can borrow that code and customize it to your needs. > Eg it would be v simple to write a method for you program that borrows > code from DNATools.createDNASequence() and takes an Annotation as an > argument. > > Finally, the Annotation and Feature examples on the BJIA page > (http://www.biojava.org/docs/bj_in_anger/) may be useful. This link also > shows how to make a program that views the Annotation and Feature > structure in a JTree > (http://www.biojava.org/docs/bj_in_anger/treeView.htm) > > - Mark > > > > > > > > Michael Griffith > Sent by: biojava-dev-bounces@portal.open-bio.org > 09/02/2004 06:57 AM > > > To: > cc: > Subject: [Biojava-dev] Please help with Features and Annotations? > > > Yikes! Is there a good explanation somewhere on Features and annotations? > I > am creating a new Sequence using the DNATools.createDNASequence() method, > but I want to set some features on it like the GI # and the DEFINITION. 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Automotive Capital GR0UP, Inc. began booking sales and revenue as of September 1, 2004. This merger allows AOCP to have $0.30 earnings per share (EPS) and over $8 MILLI0N in revenue over the next 12 months. The company will have about $5 MILLI0N in assets with 8 million fully diluted shares outstanding. The company owns two automobile dealer lots in Arizona, and Navicom, a growing innovative wireless GPS technology that works in 98% of the US, Canada and Mexico. The company also announced the launch of Navicom's wireless GPS marketing campaign for homeland security agencies, law enforcement, government agencies, auto dealers, fleet managers and trucking companies. Navicom announced last week that it is providing units and monthly service to the Inspector General's Office in Washington, D.C. Navicom foresees the $25 BILLI0N sub-prime automobile market becoming the fastest growing segment and will of-fer companies its asset collateral monitoring devices with lease options. These solutions include automobile tracking, auto disable/enable capability through Internet, geo-fence boundary notification and point/cl-ick auto repossession. Other sub-prime auto companies are also buying Navicom to install on vehicles they finance. Read the other announcements on this Company! Do your homework on this stock! Many of these small unknown companies absolutely EXPLODE onto investor's radar screens and the stock of many absolutely soar! Look at the examples above. Like many of these unknown stocks, one major news announcement and AOCP could go ballistic! Is AOCP poised to blaze higher? If you think so, you may want to take action immediately.... Good Luck and successful investing. DIS-CLAIMER: Information within this email contains "F0RWARD looking statements" within the meaning of Section 27A of the Securities Act of 1933 and Section 21B of the Securities Exchange Act of 1934. Any statements that express or involve discussions with respect to predictions, expectations, beliefs, plans, projections, objectives, goals, assumptions or future events or performance are not statements of historical fact and may be "F0RWARD looking statements."F0RWARD looking statements are based on expectations, estimates and projections at the time the statements are made that involve a number of risks and uncertainties which could cause actual results or events to differ materially from those presently anticipated. F0RWARD looking statements in this action may be identified through the use of words such as "projects", "foresee", "expects", "will," "anticipates," "estimates," "believes," "understands" or that by statements indicating certain actions "may," "could," or "might" occur. As with many microcap stocks, today's company has additional risk factors worth noting. Automotive Capital GR0UP, Inc. is not a reporting company registered under the Securities Act of 1934. Other factors include: an accumulated deficit, a negative net worth, the potential of an increasing public float of stock, a nominal cash position and nominal revenue in its most recent quarter. The company may not be able to continue as a going concern in which case you could lose your entire investment. The publisher of this newsletter does not represent that the information contained in this message states all material facts or does not omit a material fact necessary to make the statements therein not misleading.All information provided within this email pertaining to investing, stocks, securities must be understood as information provided and not investment advice. The publisher of this newsletter advises all readers and subscribers to seek advice from a registered professional securities representative before deciding to trade in stocks featured within this email. None of the material within this report shall be construed as any kind of investment advice or solicitation.Many of these companies are on the verge of bankruptcy. You can lose all your money by investing in this stock. The publisher of The publisher of this newsletter is not a registered investment ADVIS0R. Subscribers should not view information herein as legal, tax, accounting or investment advice. Any reference to past performance(s) of companies are specially selected to be referenced based on the favorable performance of these companies. You would need perfect timing to acheive the results in the examples given. There can be no assurance of that happening. Remember, as always, past performance is nev-er indicative of future results and a thorough due diligence effort, including a review of a company's filings, should be completed prior to investing.The publisher of this newsletter has no relationship with AUML or EMTK. In compliance with the Securities Act of 1933, Section17(b),The publisher of this newsletter discloses the receipt of fifteen thousand dollars from a third party not an officer, director or affiliate shareholder for the circulation of this report. Be aware of an inherent conflict of interest resulting from such compensation due to the fact that this is a paid adver-tisement and is not without bias. All factual information in this report was gathered from public sources, including but not limited to Company Websites and Company Press Releases. The publisher of this newsletter believes this information to be reliable but can make no guar-antee as to its accuracy or completeness. Use of the material within this email constitutes your acceptance of these terms. 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Can you give me a hint on where to find documentation on the ensembl-das bridge plugins and where to find Java source code? Regards Olov Lindqvist -- Olov Lindqvist From mark.schreiber at group.novartis.com Fri Sep 24 02:57:51 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Fri Sep 24 02:57:36 2004 Subject: [Biojava-dev] ensembl-das Message-ID: Hi Olov - The biojava ensembl bridge source can be found at http://www.biojava.org/download/biojava-ensembl/ The dazzle server is at http://www.biojava.org/download/dazzle/ There is some documentation for Dazzle at http://www.biojava.org/dazzle/ There are also some exercises at http://www.biojava.org/bootcamp/exercises/dazzle/index.html which may now be a bit out of date. Tomas is probably the best person to answer your other questions. Hope this helps, 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 "Olov A Lindqvist" Sent by: biojava-dev-bounces@portal.open-bio.org 09/24/2004 02:24 PM Please respond to kb99liol To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] ensembl-das Hello! I would appreciate some information regarding the files in http://www.biojava.org/download/ensembl-das/ I am trying to get my Dazzle DAS server up and running to be able to share annotations from my local ensembl mirror. For some reason I am not able to get a type list from my DAS server or serve other annotations than exons, translations and transcripts. Maybe this is not the correct forum for this question but I will give it a try. What is the difference between the different files in the directory above? 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15:16:05 2004 From: help at luckyoffer.com (Litsa) Date: Fri Sep 24 15:46:41 2004 Subject: [Biojava-dev] Free Body Pain relief product sample (NO CC) Message-ID: Good morning, I just wanted to let you know that we are still giving away free samples of our new Body Pain Relief product. Have you ordered yours already? if not here is the link again: Free Body Pain relief product sample (NO CC) http://luckyoffer.com/fmdtlmclkpko.php?jDuN1hUpgoMSG_bcfbehhc.15242551DuN1hUpgo12biojava-devbiojava.orgDuN1hUpgo1027154200& Have a great day Litsa Meditay c/o ERC 180 South 300 West, Suite 318 Salt Lake City, UT 84111 From kimberley at ubi.com Fri Sep 24 20:32:16 2004 From: kimberley at ubi.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Fri Sep 24 20:36:17 2004 Subject: [Biojava-dev] =?windows-1251?b?0OXq6+Ds4Dogz+7i+/jl7ejlIPHv8O7x?= =?windows-1251?b?4Cwg4vvx8uDi6ughISE=?= Message-ID: <113928700.20040925003716@> ???????? ?????!!! ????????, ??????????, ?????????????, ?????????? ???????? ????? ????? ????? ???????????? ? ?????? ?????????! ?????????? ??????, ??????????? ? ???????? ? ???????????! ???????? ? ?????? ?????????? ?????????! ??????? ???????????? ????! ???????????????? ??????????! ?????????? ?????? ? ????????????! ???? ?????? ???????? - ??????-????? - ? ????? ???????!!! ???? ?????????! 1. ?????? ?????. "????-?????". ?????????? ????????, ?????????? ????? - ?? 450 ?.?. ?? ... ?? 15 ?.?. ?? ????? ????????? ????????? ?? 2500 ?.?. ?? ?????????? ????????? ????????, ???????, ????? - ????. ??????-???? (????????? ???????? ?? ???? ?? ??????) ?? 500 ?.?. ???????? ? ??????? ???????????? ???????????????, Corbis, Fotobank ? ???????. ?? ?????????? ? ???????????? ???? - ???????! ??????????? ?????? ????? ? ????? ?????????? ?? ?????? ? ?????????! 2. ????????. 30.000 ?????????. 190 ?????????! ??????? ????????: 1. ??????-???????, 200 ??., 1 + 0 - 263 ?.?. 2. ?????, ??????, ???????, 1000 ??. - 0,54 ?.?. 3. ?????????, ???, + ?????, 50 ??. - 11,24 ?.?. 4. ????????? ?????????, ????, 100??. - 11,5 ?.?. ?/?, 100??. - 5,60 ?.?. 5. ??????, ????????, ?????, 200 ??, 50 ??. - 1,95 ?.?. 6. ??????,240??, 50 ??. - 19,95 ?.?. 7. ?????-?????,??????-??????,350 ?? - ?? 28 ?.?. 8. ????-?????????, ???????, 50 ??. - 9,30 ?.?. 8. ????-?????????, ??????, 50 ??. - 15,08 ?.?. 9. ?????, ??????, ? ???????, 20 ??. - 13,5 ?.?. 10. ?????, ???????,50 ??. - 8,5 ?.?. 11. ???????? ??? ????, ??????, 20 ??. - 4,10 ?.?. 12. ????? ??????????, ???? - 10,7 ?.?. 13. ??????, 6?3,5??, 4 + 4, 1000 ??. - 0,87 ?.?. 14. ???? ?????????,50 ??. - 8,10 ?.?. 15. ????????? - ????, ??????, 50 ??.- 4,10 ?.?. 16. ?????????, ???????, ?????, 100 ??. - 0,51 ?.?. 17. ???????, ?4, 50 ??????, ???????, 2 + 0, 100 ??. - 2,80 ?.?. 18. ?????? ?????, 4 ???????? - 14,60 ?.?. 19. ?????? ??? ????, 500 ??, 1 + 0, ??????, 200 ??. - 6,29 ?.?. 20. ?????, 2 + 0, 192 ??. - 359 ?.?. 21. ???????, 100 ??., 3+0 - 426 ?.?. 22. ?????????, ?????, ? ??????????, 200 ??. - 6,4 ?.?. 23. ????? ????????? + ?????, 50 ??. - 11,24 ?.?. 24. ????? ????????? + ????? + ??????, 50 ??. - 12,3 ?.?. 25. ??????? ?????????? ?????, ?????, 50 ??. - 24 ?.?. 26. ???? ??????, Doppler (???????), 1 + 0, 100 ??. - 860 ?.?. 27. ?????????? ??????, 9?15 ??, ???? - 10,7 ?.?. ???????? ??-?? ?????????, ?????, ????????, ??????, ??????, ??????! ????????? ???????? ??? ?????????, ????????? 140 ?/??.?.: ?? 10 ?? 100 ??. - 2,3 ?.?., 150 ?/??.?., ?? 500 ?? 1000 ??. - 2,2 ?.?., 160 ?/??.?., ?? 100 ?? 500 ?? - 2,5 ?.?., ?? 1000 ?? 5000 ??. - 2,2 ?.?. ?????? ?? ? ??????????,1+0: 100 ??. - 60 ?.?., 1000 ??. - 190 ?.?., 5000 ??. - 580 ?.?., ?? ??????? ???????? ???????, ???????? ????????? ?????? ?????? ?????, 50 ???, ? ????????? ????????? ??????. ???????? ? ??????????,?65, ???????, 1+0: 500 ?? - 110 ?.?., 5000 ??.- 480 ?.?., ?????. ????. ???????? ??????? ?? ????: ?????????????, ?????? 9,5 ? 6,5 ?? - 5 ?.?. ???????, ?????? 16 ? 12 ?? - 11 ?.?. ????? ??? ?????? ??????? ?5 - ?? 20 ?.?. ????? ????, ????? ??? ????? ??????? ?4 - ?? 30 ?.?. ???????????? ??????????? ???????? ? ????????? ???????????: ??????? ???????? - ?? 1 ?.?. ?? ??. ??. ???????? ????? - ?? 2 ?.?. ?? ??. ??. ??????? ? ?????????? ?????????? - 120 ?.?. ?? ??.?. ?????????? ?????: ?? 150 ?? ? ????? - 2,27 ?.?. ?? ??. ? ?? 60 ?? ?? 150?? - 4,67 ?.?. ?? ??.?. ?? 4 ?? ?? 60 ?? - 6,79 ?.?. ?? ??.?. ??????? ???????????, ??????. ?????????? ??????? ? ???????? ????. ???????? ???????????! ??????? ?? ?????? ? ??????! ????????????? ??????? ? ???????! ?????????? ? ?????? ?????????, ???????? ? ??????????! ??????????? ????? ?? ????????? ? ???????????? ? ????? ?????????? ?? ?????? ? ?????????! ???? ?????????: ??????, ?????, ???????, ?????????????, ??????, ???????, ????????, ?????????, ?????? ??????, ??????, ?????, ???????-????, ?????????, ????????, ???????, ??????, ?????, ??????, ????????????, ???? ... ?????????: ??????, ??????, ??????, ???????, ??????, ?????, ???, ???????, ??????????, ????????????, ????, ??????, ??????, ???????, ???????, ?????? ... ???? ?????????: ???????????, ???????????, ????????????, ????????????, ???????????, ??????????, ???????? ??????, ??????? ??????, ???????????, ?????????????? ??????, ???????? ??????? ? ???????, ?????????????. ?????????? ? ???????? ?? 1 ???! ???????? ?? ??????????? ????????????!!! ???????????, ???. ??????, ???. ??????, ?????????????, ?????????, ?????????, ?????????????, ????????, ???????, ????????, ???????????, ???, ??? ????? ????????? ??? ??????? ???????! ????? ??????, ???, ? ????????? ???????, ?????, 500 ??. - 265 ?.?. ?????????????, ?/?, 50 ??. - 2,9 ?.?. ?? ????? ???????????? - ???????! ??????????? ????? ?? ???????? ? ??????????? ?? ?????????? ????????? ?????????? ????????? ? ????? ?????????? ?? ?????? ? ?????????! 3. ??????????! ????? ? ?????. ?? 100 ??????? ??????? ?? ???????? ?0. ????????? ?? 6 ??????. ????? ???????? ? ????????????? ?????????. ????????? ?????????, 7?10 ??, ?????. ?????, ??????? 32 ???., 4 + 2 1000 ??. - 140 ?.?., 3000 ??. - 235 ?.?., 5000 ??. - 270 ?.?., 10000 ??. - 390 ?.?. ??????????? ?????????, ??????? ???? 4+0, 1 ???????, 500 ??. - 2,85 ?.?., 3 ???????, 500 ??. - 4,1 ?.?. ????????, ????? ??????, 300 ??./??. ?, ???, 4+2, 500 ??. - 425 ?.?., 1000 ??. - 556 ?.?. ????????, ??????, 2+0, 1000 ??. - 86 ?.?., 3000 ??. - 124 ?.?., 5000 ??. - 172 ?.?. ???????, ?????? ???, 280 ??./?2, ?????, 1+0, 100 ??. - 16,5 ?.?. (???????? ??????? ?? 100 ??.) ???????, August Koehler, 246 ??./?2, ?????, 1+0, 100 ??. - 17,25 ?.?. (???????? ??????? ?? 100 ??.) ???????, ?????? ???, 280 ??./?2, 1+0, 500 ??. - 40,5 ?.?. ???????, August Koehler, 246 ??./?2, 1+0, 500 ??. - 44,25 ?.?. ??????????? ????? ?? ???????, ????????????? ??????? ???????? ? ?????????????! ??????, ?4, 130 ??./?2, 4+4, 2 ?., 1000 ??. - 220 ?.?. ????????? ?????????, 7?10 ??, 4+2, ??????? 32 ???., ??????, 1000 ??. - 120 ?.?. ????????, 20?13 ??, 4+0, 1000 ??. - 0,21 ?.?. ???????, 90?90?90 ??, ????????? 3 ??????? 4+0, ?? ?????? ????? 1+0, 200 ??. - 7,65 ?.?. ???????? ????? ?? ??????, 10?12?2 ??, 2+0, 500 ??. - 2,88 ?.?. ???????????? ?????????????, ??????????, ????????????, ???????? ?????? ?? ??????????? ????????????! ?????????????, ??????, ?????, ??????, ??? ??????? ? ????????, 50 ??. - 135 ?.?. ???????? ??????????????? ?????????: ????????? ??????, ????????, ???????????, ???????, ?????????????, ?????, ??????????, ??????????, ????????, ?????????, ???????? ???????????? ??????????????? ????????? ?? 2 ????! ???????? - ??????! ???????????? ????????, ??????, ???????????? ??????? ?????????????! ??????????? ????? ?? ?????? ?? ??????????????? ????????? ? ????? ?????????? ?? ?????? ? ?????????! 4. ?????????? ??????? ?? ???????????? ?????! 5. ???????. ?????? ????????. ??????? ?????????! ??????, 4+0, 360 d.p.i., ? ????????? ??? ?????????, - 23,5 ?.?./1 ??. ?. ?????????? ??????? ?? ?????. ?????????? ??????? ?? ??????????. ?????????? ??????? ?? ???? - ????????. ?????????? ??????? ?? ????????? ?????????? (???????, ??????????, ???????, ?????????? ?????). ?????????? ??????? ? ????? (?? ???????? ? ? ??????? ???????). 6. ??????. ????? ???????. ????? ?????? ? ?????????????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 7. ?????. ??? ???????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 8. ??. ?????????? ?? GRP ? ?????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 9. ??????? ? ???????????. ???????? ???????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 10. ??????? ? ????????. ???????????? ????????. ??????????? ??????? ? ?????: RU, COM, SU, NET, BIZ, INFO, ORG! ???????? Web-??????? ? ???????????????? ? ????????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 11. ??????????? ? ?????????? ????? ????????????? ??????????? ? ??????????! ?????????, ?????????-?????, ???????????, ????????????? ???????, ????? ?? ????? ????? ????????? ? ?????! ????????? ?????????! ??????????? ? ????????? ? ?????????? ?? ?????? ? ?????????! 12. ????? ????????? ??? ??????? ? ?????????? ? ?????????! 13. ???????? ? ???????? ???? - ?????????! 14. ????????. ??? ?????? ????????????? ????????, ?? ??? ???? ????????! ????? ?????????? ? ?????? ??????????? ? ??? ?????????. 15. ?????. ?? 12 ????????? - ????????? ???? ?? ?????? ? ?????? ? ?.-??????????! 16. ???? ??????????? ?? ???????????! ???? ???????????????? ????!!! ????????? ?????????? ????????????? ??????!!! ????????? ??? ????? ??????! ? ??? ????????? ??????? ??? ???????????! ???.: (095) 101-3527 ??????????, ?? ????????? ????? ?? ???????? ?????! ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? 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Has this been done cause there still seems to be a lot getting through. - 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 From heuermh at acm.org Sun Sep 26 21:23:50 2004 From: heuermh at acm.org (Michael Heuer) Date: Sun Sep 26 21:21:01 2004 Subject: [Biojava-dev] subscription only posts In-Reply-To: Message-ID: Woo hoo! No more worthless messages to the biojava-dev list! ;) michael On Mon, 27 Sep 2004 mark.schreiber@group.novartis.com wrote: > Hello - > > There was some talk a few weeks back of making biojava-dev subscription > post only to cut down on the amount of spam. Has this been done cause > there still seems to be a lot getting through. > > - 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 > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From mark.schreiber at group.novartis.com Sun Sep 26 21:24:08 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Sun Sep 26 21:23:45 2004 Subject: [Biojava-dev] Subversion Message-ID: While I'm in a ranting mood, What do people think about moving our CVS base to subversion?? The webDAV protocol seems a lot nicer than CVS. Particularly where firewalls are involved. Any thoughts? - 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 From Emaillists at freemail.soim.com Mon Sep 27 13:04:33 2004 From: Emaillists at freemail.soim.com (Peter) Date: Sun Sep 26 22:04:20 2004 Subject: [Biojava-dev] Opt-in Marketing Message-ID: <200409270204.i8R247Kr017116@portal.open-bio.org> Email is the best growing marketing tool. We offer E-Marketing with quality service. 1. Target Email Addresses We can provide target e-mail addresses you need, which are compiled only on your order. We will customize your customer email addresses. * We have millions of email addresses in a wide variety of categories. 2. Send out Target Emails for you We can send your email message to your target customers! We will customize your email addresses and send your message for you. * We can Bullet Proof your Web Site $ dedicated server. Hope to hear from you soon. Regards! Peter www.oy8.com Support@oy8.com Take your address: Http://66.177.43.06/off.html From td2 at sanger.ac.uk Mon Sep 27 03:45:33 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Mon Sep 27 03:45:06 2004 Subject: [Biojava-dev] Subversion In-Reply-To: References: Message-ID: <3638DC64-1059-11D9-B06C-000A95C8B056@sanger.ac.uk> On 27 Sep 2004, at 02:24, mark.schreiber@group.novartis.com wrote: > While I'm in a ranting mood, > > What do people think about moving our CVS base to subversion?? The > webDAV > protocol seems a lot nicer than CVS. Particularly where firewalls are > involved. Well, I've been using subversion pretty much daily for the last few months, and am extremely happy with it, so I'd definitely be pleased to see another project come over to the light side :-). [I'm also now pretty comfortable with setting up and administering svn repositories]. I guess the issues to look at right away would be: - Is everyone comfortable with it? Probably anyone who's made any active contribution to biojava within the last year (maybe more) should have a right of veto on this. (I would add that the svn command line acts a lot like CVS, so switching really isn't going to be painful for more users) - Where do we host it? - Do we try to do a full CVS->SVN repository conversion, trying to preserve all the history (scripts exist for this, but I've never tried them so can't comment on how well they'll handle an old and complex repository -- anyone out there who has?), or just do a clean import of the biojava-live trunk into a fresh SVN repository. Anyone else got thoughts on this? For anyone who's undecided but wants to give subversion a spin, I'm happy to set you up with a playground repository on my server. Thomas From td2 at sanger.ac.uk Mon Sep 27 03:50:24 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Mon Sep 27 03:49:53 2004 Subject: [Biojava-dev] subscription only posts In-Reply-To: References: Message-ID: On 27 Sep 2004, at 02:13, mark.schreiber@group.novartis.com wrote: > Hello - > > There was some talk a few weeks back of making biojava-dev subscription > post only to cut down on the amount of spam. Has this been done cause > there still seems to be a lot getting through. I don't think anything has been done yet... but I'd say go for it. Thomas. 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From mark.schreiber at group.novartis.com Sun Sep 19 21:52:17 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Sun Oct 3 21:52:23 2004 Subject: [Biojava-dev] Help Reqd in Use of RectangularBeadRenderer Message-ID: Hi - Try taking a look at the demos/seqviewer examples from the biojava distribution. These give great examples of how to set up the biojava gui components. - 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 "Shuvankar Mukherjee" Sent by: biojava-dev-bounces@portal.open-bio.org 09/02/2004 09:43 PM To: cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] Help Reqd in Use of RectangularBeadRenderer Hi, I require help in the use of RectangularBeadRenderer in a SequencePanel. RectangularBeadRenderer class has a method renderBead( Graphics2d, Feature, SequenceRenderContext) . what should be passed as SequenceRenderContext object and what should be passed as Graphics2d obj. any advise will be welcome. Regards, Shuvankar Mukherjee _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev