From gyekpxy at accounts.get-toprankings.com Thu Apr 1 05:05:12 2004 From: gyekpxy at accounts.get-toprankings.com (Margie Sands) Date: Thu Apr 1 05:18:17 2004 Subject: [Biojava-dev] Solid Internet Biz for your home Message-ID: ----9224545885015478 Content-Type: text/html; Content-Transfer-Encoding: 7Bit Bills in your Pocket

 

 

 

 

 

 

 

 

 

 

 

 

 

If you would like to be taken off this mailing list, www.financialbuilder.info/takeoff.html

4238B North Arlington Heights Rd.,
P.O. Box 190,
Arlington Heights, IL 60004

THIS IS A COMMERCIAL E-MAIL

----9224545885015478-- From autobuilder at derkholm.net Thu Apr 1 23:11:11 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Apr 1 23:09:44 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1080879071315.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040402 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Fri Apr 2 23:15:07 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Apr 2 23:13:30 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <19475750.1080965707726.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040403 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/gui/sequence/BumpedRenderer.java * biojava-live/src/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java * biojava-live/src/org/biojava/bio/gui/sequence/LabelledSequenceRenderer.java * biojava-live/src/org/biojava/bio/gui/sequence/SequencePanel.java * biojava-live/src/org/biojava/bio/gui/sequence/SequencePoster.java * biojava-live/src/org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.java * biojava-live/src/org/biojava/bio/seq/FeatureFilter.java * biojava-live/src/org/biojava/bio/seq/FilterUtils.java * biojava-live/src/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java * biojava-live/src/org/biojava/bio/seq/db/biosql/OntologySQL.java * biojava-live/src/org/biojava/bio/seq/io/ChunkedSymbolList.java * biojava-live/src/org/biojava/bio/seq/io/ChunkedSymbolListBuilder.java * biojava-live/src/org/biojava/bio/seq/io/ChunkedSymbolListFactory.java * biojava-live/src/org/biojava/bio/seq/io/SequenceBuilder.java * biojava-live/src/org/biojava/bio/seq/io/SubArraySymbolList.java * biojava-live/src/org/biojava/bio/symbol/ChunkedSymbolList.java * biojava-live/src/org/biojava/bio/symbol/EmptySymbolList.java * biojava-live/src/org/biojava/bio/symbol/LinearAlphabetIndex.java * biojava-live/src/org/biojava/bio/symbol/PackedSymbolList.java * biojava-live/src/org/biojava/bio/symbol/SymbolListViews.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 daviddebeule at pandora.be Sat Apr 3 08:50:36 2004 From: daviddebeule at pandora.be (david de beule) Date: Sat Apr 3 08:55:43 2004 Subject: [Biojava-dev] Re: biosql References: Message-ID: <007101c41982$a4b16ab0$0100a8c0@davidpc> "My point at the time was that querying location_qualifier_value every single time you obtain a location regardless of type is going to be a huge waste of time, given that 99% of locations are *not* fuzzy." I may be wrong but I think 'BetweenLocations' are NOT always fuzzy locations. There are three types of exact sequence locations which in feature table notation are: 23, 34..55 and 46^47. Respectively Point, Range and Between locations. The notation 46^47 (between 46 and 47) is ESSENTIAL when you have clean insertions between residues and may not be confused with the FUZZY location: 46^78, meaning: somewhere (not exactly determined) between 46 and 78. So I think the bug reported by Frederik Decouttere, that handled about these EXACT between locations, should be fixed as soon as possible, because it has nothing to do with 'rarely used' fuzzy locations. Regards, David ----- Original Message ----- From: "Hilmar Lapp" To: "Len Trigg" Cc: "Matthew Pocock" ; ; "Thomas Down" ; Sent: Thursday, March 18, 2004 10:22 PM Subject: Re: [BioSQL-l] Re: [Biojava-dev] Re: biosql > > On Wednesday, March 17, 2004, at 12:58 PM, Len Trigg wrote: > > > The problem is that when a BetweenLocation (and probably a whole bunch > > of others) get persisted, they get retrieved as regular > > RangeLocations. It would be straight forward to store a term > > corresponding to the location type in the term_id of the location > > table (currently unused in our binding). > > This is what I proposed this foreign key for. > > > It's just a matter of determining what terms to use. Either (easiest > > to hardest): a) the > > classname of the location type; b) whatever BioPerl uses (if it is > > capable of persisting the location type); c) jump through a few hoops > > and look up an appropriate obda name. > > Please don't use classnames, although that would be easiest obviously, > or otherwise bioperl (or any other language) won't interoperate with > this properly. > > As a matter of fact, bioperl-db doesn't use this currently, and > therefore doesn't support fuzzy locations (which is what we call them > in bioperl) to roundtrip to fuzzy locations (they'll become exact > locations). > > Note also that generally speaking the location_qualifier_value table is > supposed to hold information from which you could infer the type of > location. My point at the time was that querying > location_qualifier_value every single time you obtain a location > regardless of type is going to be a huge waste of time, given that 99% > of locations are *not* fuzzy. > > -hilmar > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > > From autobuilder at derkholm.net Sat Apr 3 23:09:37 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Apr 3 23:07:46 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <813251.1081051777381.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040404 Binary build: FAILED! Javadocs build: OK Core test suite: NOT RUN Problems occurred during this build cycle -- please investigate as soon as possible! The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/utils/automata/ArrayStateMachine.java * biojava-live/src/org/biojava/utils/automata/DfaBuilder.java * biojava-live/src/org/biojava/utils/automata/FiniteAutomaton.java * biojava-live/src/org/biojava/utils/automata/Nfa.java * biojava-live/src/org/biojava/utils/automata/NfaBuilder.java * biojava-live/src/org/biojava/utils/automata/NfaSubModel.java * biojava-live/src/org/biojava/utils/automata/PatternMaker.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Mon Apr 5 00:09:34 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Apr 5 00:07:32 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <27475272.1081138175019.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040405 Binary build: FAILED! Javadocs build: OK Core test suite: NOT RUN Problems occurred during this build cycle -- please investigate as soon as possible! 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 david.huen at ntlworld.com Mon Apr 5 03:53:06 2004 From: david.huen at ntlworld.com (David Huen) Date: Mon Apr 5 03:58:07 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report In-Reply-To: <27475272.1081138175019.JavaMail.thomas@calette.derkholm.net> References: <27475272.1081138175019.JavaMail.thomas@calette.derkholm.net> Message-ID: <200404050853.06840.david.huen@ntlworld.com> On Monday 05 Apr 2004 5:09 am, autobuilder@derkholm.net wrote: > BioJava automatic build system, run 20040405 > > Binary build: FAILED! > Javadocs build: OK > Core test suite: NOT RUN > I cannot reproduce this problem on two x86 machines or on a G5. Autobuilder seems to suggest that no change has occurred in the last 24 hours. Can someone else give it a chack please? Thanks, David Huen From thomas at derkholm.net Mon Apr 5 04:24:14 2004 From: thomas at derkholm.net (Thomas Down) Date: Mon Apr 5 04:22:09 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report In-Reply-To: <200404050853.06840.david.huen@ntlworld.com> References: <27475272.1081138175019.JavaMail.thomas@calette.derkholm.net> <200404050853.06840.david.huen@ntlworld.com> Message-ID: <20040405082414.GB19629@calette.derkholm.net> On Mon, Apr 05, 2004 at 08:53:06AM +0100, David Huen wrote: > On Monday 05 Apr 2004 5:09 am, autobuilder@derkholm.net wrote: > > BioJava automatic build system, run 20040405 > > > > Binary build: FAILED! > > Javadocs build: OK > > Core test suite: NOT RUN > > > I cannot reproduce this problem on two x86 machines or on a G5. Autobuilder > seems to suggest that no change has occurred in the last 24 hours. Can > someone else give it a chack please? Ah, sorry, I fixed this about an hour ago, and sent an e-mail explaining, but I ended up sending it to the autobuilder alias rather than biojava-dev. I'll add a Reply-To: header to future autobuilder notifications to avoid this. Just for reference, the problem affecting the last two build cycles was a missing exception declaration in Nfa.java. Fixed by adding "throws IllegalSymbolException" in the appropriate place. Thomas. From smh1008 at cus.cam.ac.uk Mon Apr 5 15:53:59 2004 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Mon Apr 5 15:59:09 2004 Subject: [Biojava-dev] Fwd: Bug in BioFetchSequenceDB Message-ID: <200404052053.59728.smh1008@cus.cam.ac.uk> This email is forwarded on behalf of Rudi Chiarito:- ---------- Forwarded Message ---------- This code in getSequence() seems to be incomplete or wrong: else if (dbName.equals("swiss")) format = "swissprot"; By default, i.e. without custom configuration files, SystemRegistry will end up using http://www.open-bio.org/registry/seqdatabase.ini as the database registry. The problem with that is that the current file contains, for swissprot, dbname=swall. Thus the class won't attempt to parse the results in Swissprot format as it should. Which is the right fix? Comparing dbName to "swall" rather than "swiss"? Comparing dbName to both? Having the default seqdatabase.ini changed to use dbname=swiss? Thanks for any help. P.S. The bug tracker pages are not working; they return an Error 404. From ehaugen at u.washington.edu Mon Apr 5 22:28:43 2004 From: ehaugen at u.washington.edu (Eric Haugen) Date: Mon Apr 5 22:33:43 2004 Subject: [Biojava-dev] Phred symbol deserialization Message-ID: I've found that when I deserialize a Phred symbol (SimpleAtomicSymbol from the Phred alphabet == (DNA x SubIntegerAlphabet[0..99]) ), I get a brand new SimpleAtomicSymbol instead of the one already contained in the Phred alphabet. So PhredTools.getPhredAlphabet().contains( symbol ) returns false for that symbol. The following kludgy addition to SimpleAtomicSymbol.java makes it work: import org.biojava.bio.program.phred.PhredTools; ... static final long serialVersionUID = -8426550133605911655l; protected Object readResolve() throws java.io.InvalidObjectException { Object result = this; if ((this.getSymbols().size() == 2) && Annotation.EMPTY_ANNOTATION.equals( this.getAnnotation() )) { try { Symbol symbol = PhredTools.getPhredAlphabet().getSymbol( this.getSymbols() ); if (symbol != null) { result = symbol; } } catch (Exception ignored) { // Must not be a Phred symbol } } return result; } This causes as a side effect the initialization of the 400-symbol phred alphabet whenever ANY SimpleAtomicSymbol is deserialized. And SimpleAtomicSymbol shouldn't have to know about various alphabets... So, I'm hoping someone else has a better idea. Should AlphabetManager keep track of all cross-product symbols that should be singletons? Thanks, Eric -- Eric Haugen University of Washington Genome Center From autobuilder at derkholm.net Tue Apr 6 00:10:59 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Apr 6 00:08:45 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1081224659861.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040406 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/utils/automata/ArrayStateMachine.java * biojava-live/src/org/biojava/utils/automata/ArrayStateMachineToolkit.java * biojava-live/src/org/biojava/utils/automata/Nfa.java * biojava-live/src/org/biojava/utils/automata/PatternBlitz.java * biojava-live/src/org/biojava/utils/automata/PatternMaker.java * biojava-live/src/org/biojava/utils/automata/StateMachineFactory.java * biojava-live/src/org/biojava/utils/automata/StateMachineInstance.java * biojava-live/src/org/biojava/utils/automata/StateMachineToolkit.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 matthew_pocock at yahoo.co.uk Tue Apr 6 06:16:24 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Apr 6 06:21:32 2004 Subject: [Biojava-dev] Phred symbol deserialization In-Reply-To: References: Message-ID: <40728378.9050502@yahoo.co.uk> Hi Eric, This is a bug. Our resident serialization guru is on his Easter break, but I'll take a look. Matthew Eric Haugen wrote: >I've found that when I deserialize a Phred symbol (SimpleAtomicSymbol from the Phred alphabet == (DNA x SubIntegerAlphabet[0..99]) ), I get a brand new SimpleAtomicSymbol instead of the one already contained in the Phred alphabet. So PhredTools.getPhredAlphabet().contains( symbol ) returns false for that symbol. > >The following kludgy addition to SimpleAtomicSymbol.java makes it work: > >import org.biojava.bio.program.phred.PhredTools; >... > static final long serialVersionUID = -8426550133605911655l; > > protected Object readResolve() throws java.io.InvalidObjectException { > Object result = this; > if ((this.getSymbols().size() == 2) > && Annotation.EMPTY_ANNOTATION.equals( this.getAnnotation() )) { > try { > Symbol symbol = PhredTools.getPhredAlphabet().getSymbol( this.getSymbols() ); > if (symbol != null) { > result = symbol; > } > } catch (Exception ignored) { > // Must not be a Phred symbol > } > } > return result; > } > >This causes as a side effect the initialization of the 400-symbol phred alphabet whenever ANY SimpleAtomicSymbol is deserialized. And SimpleAtomicSymbol shouldn't have to know about various alphabets... >So, I'm hoping someone else has a better idea. Should AlphabetManager keep track of all cross-product symbols that should be singletons? > >Thanks, > >Eric > > > From smh1008 at cus.cam.ac.uk Tue Apr 6 12:32:16 2004 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Tue Apr 6 12:38:38 2004 Subject: [Biojava-dev] Missync between public CVS and dev CVS Message-ID: <200404061732.16502.smh1008@cus.cam.ac.uk> There appears to be a missync between out two CVSes. If you should have your compile fail on a checkout from public CVS because of org.biojava.utils.automata.ArrayStateMachine, just blow away that class. Hopefully, the two CVSes will resync again soon, this time, hopefully consistently. Regards, David From autobuilder at derkholm.net Wed Apr 7 00:11:23 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Apr 7 00:08:58 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1081311084178.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040407 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/seq/DNATools.java * biojava-live/src/org/biojava/bio/seq/ProteinTools.java * biojava-live/src/org/biojava/bio/seq/RNATools.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 david.huen at ntlworld.com Wed Apr 7 04:28:28 2004 From: david.huen at ntlworld.com (David Huen) Date: Wed Apr 7 04:33:25 2004 Subject: [Biojava-dev] Regexes and sequencing searching Message-ID: <200404070928.10857.smh1008@cus.cam.ac.uk> I have a need for software that will do a humongous amount of motif searching on a large number of long sequences. I have tested a large number of combinations and the conclusions may be of interest. The trial case is 80 motifs searched on a smallish target of around > 1 Mb. The time includes all sequence reading/conversions/regex compilations/etc. Time is CPU secs. 1) Sequence wrapped in SymbolListCharSequence, then searched with java.util.regex. 17 secs. 2) Sequence converted to SimpleSymbolList, wrapped in SymbolListCharSequence, then searched with java.util.regex. 14 secs. 3) Sequence converted to String then searched with java.util.regex. 7 secs. I have also written my own SymbolList regex package (more than one!) that allows direct searching of sequence in any FiniteAlphabet. 4) Searching by recursive matching through a regex-like structure (an order of magnitude worse than anything else here!) 5) Compilation of RE -> NFA -> DFA -> ArrayStateMachine 25 secs. A change in the sequence implementation does not affect my symbollist regex package as it uses various tricks to reduce slow symbol access. Conclusions: 1) java.util.regex is bloody fast: do they have a native implementation? 2) the compressed sequence representations we use automatically for large sequences can affect some kinds of analyses that are dependent on a huge symbol bandwidth. Even the fastest, most memory intensive representation is slower than String for individual "symbol" access. Evidently there is a tradeoff between being able to have the whole sequence in RAM and swapping and comparative sizes of our packed representation and a String to consider in any final decision. Also, do we really want a direct SymbolList regex package? Pros: Can search in any alphabet including those that cannot be handled with java.util.regex because of the absence of a suitable tokenization (large numbers of symbols). Search alignments in protein cross-product space? Cons: yet another package to maintain. Slower than java.util.regex. Regards, David Huen From heuermh at acm.org Wed Apr 7 12:20:17 2004 From: heuermh at acm.org (Michael Heuer) Date: Wed Apr 7 12:30:14 2004 Subject: [Biojava-dev] Regexes and sequencing searching In-Reply-To: <200404070928.10857.smh1008@cus.cam.ac.uk> Message-ID: On Wed, 7 Apr 2004, David Huen wrote: > I have a need for software that will do a humongous amount of motif > searching on a large number of long sequences. I have tested a large > number of combinations and the conclusions may be of interest. > > The trial case is 80 motifs searched on a smallish target of around > 1 Mb. > The time includes all sequence reading/conversions/regex compilations/etc. > Time is CPU secs. > > 1) Sequence wrapped in SymbolListCharSequence, then searched with > java.util.regex. 17 secs. > 2) Sequence converted to SimpleSymbolList, wrapped in > SymbolListCharSequence, then searched with java.util.regex. 14 secs. > 3) Sequence converted to String then searched with java.util.regex. 7 secs. Very interesting -- might it be possible to split the timing for the sequence creation and the searching? Maybe there's some copying or list resizing going on in there that we weren't aware of. > I have also written my own SymbolList regex package (more than one!) that > allows direct searching of sequence in any FiniteAlphabet. > 4) Searching by recursive matching through a regex-like structure (an order > of magnitude worse than anything else here!) > 5) Compilation of RE -> NFA -> DFA -> ArrayStateMachine 25 secs. > A change in the sequence implementation does not affect my symbollist regex > package as it uses various tricks to reduce slow symbol access. > > Conclusions: > 1) java.util.regex is bloody fast: do they have a native implementation? > 2) the compressed sequence representations we use automatically for large > sequences can affect some kinds of analyses that are dependent on a huge > symbol bandwidth. Even the fastest, most memory intensive representation > is slower than String for individual "symbol" access. Evidently there is a > tradeoff between being able to have the whole sequence in RAM and swapping > and comparative sizes of our packed representation and a String to consider > in any final decision. It sounds like you might have tried this, but what if you force the sequence not to use the packed implementation? > > Also, do we really want a direct SymbolList regex package? > Pros: > Can search in any alphabet including those that cannot be handled with > java.util.regex because of the absence of a suitable tokenization (large > numbers of symbols). Search alignments in protein cross-product space? > Cons: > yet another package to maintain. > Slower than java.util.regex. > > Regards, > David Huen > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From autobuilder at derkholm.net Thu Apr 8 00:11:11 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Apr 8 00:08:36 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1081397472189.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040408 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 =?iso-2022-jp?Q?=1B=24B=3EZ5rM-=3C=7DF=7E=2352/=239=1B=28B?= Thu Apr 8 03:06:22 2004 From: =?iso-2022-jp?Q?=1B=24B=3EZ5rM-=3C=7DF=7E=2352/=239=1B=28B?= (=?iso-2022-jp?Q?=1B=24B=3EZ5rM-=3C=7DF=7E=2352/=239=1B=28B?=) Date: Thu Apr 8 03:11:07 2004 Subject: [Biojava-dev] =?iso-2022-jp?b?GyRCTCQ+NUJ6OS05cCF2NHskSyEiGyhC?= =?iso-2022-jp?b?GyRCIzIyLyEiIzMyLyEiIzUyLyM5QGlLfDFfPH1GfjxUJCxCMz1QGyhC?= =?iso-2022-jp?b?GyRCISIbKEIgGyRCPlo1ciRyM05HJyQ3JEYyPCQ1JCQhIxsoQg==?= Message-ID: <13005388.1081407982517.JavaMail.nobody@hosyou-r.mine.nu> 　　　　　　 　未承諾広告＜配信者＞　受託協会顧問藤村と申します。 　　　　　　　　　今後不要の場合は、大変恐縮ですが　配信停止を http://bowl.to/hosyou 　　　 にてお願い申し上げます。再送致しません。　　　 　　　　　 　　　　　　既に、２億、３億、５億９千万円収入者が続出しています。 ５億９千万円への一歩　*==*==*==*====**==**===*==*==*==*==*　　　　　　　　 　　　 　　　　　　　　詳しくは　http://break.at/hosyou から 　　　　 証拠を確かめて５億９千万円在宅ビックビジネスへ一歩 ■イマ、５千万円があったら最高なのに、の方々！イマからでも遅くありません!! ■２億、３億、５億９千万円収入者が続出しています。 　　　　　　　　　　　 　　　しかし、物的証拠を確認するまでは何事も「信用しない」で下さい。 　　　　　 裁判は物的証拠が唯一の確たる判決 の決め手です。 　　□━━主たる物的証拠━━見せます━━何事も論より証拠━━□ 　　　東京高等裁判所の判決書・２億、３億、５億９千万円収入の 　　　銀行印有振込み書・福祉事務所よりの保証証券使用依頼書・他 　　□━━━━━━━━━━━━━━━━━━━━━━━━━━━□　 　　　　　　成人男女・副業在宅高額ネット収入目的に最適です。 ※資料ご請求は　http://break.at/hosyou からお願い申し上げます。 From autobuilder at derkholm.net Fri Apr 9 00:11:09 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Apr 9 00:08:19 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <5450181.1081483869312.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040409 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Sat Apr 10 00:11:13 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Apr 10 00:11:56 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <5450181.1081570273640.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040410 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Sun Apr 11 00:11:01 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Apr 11 00:14:07 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1081656661773.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040411 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Mon Apr 12 00:11:29 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Apr 12 00:13:43 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1081743090235.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040412 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 =?iso-2022-jp?Q?=1B=24B=22!3Z!9=25H=25/=25H=25/=25S=258=25M=1B=28B?= Mon Apr 12 10:00:18 2004 From: =?iso-2022-jp?Q?=1B=24B=22!3Z!9=25H=25/=25H=25/=25S=258=25M=1B=28B?= (=?iso-2022-jp?Q?=1B=24B=22!3Z!9=25H=25/=25H=25/=25S=258=25M=1B=28B?=) Date: Mon Apr 12 10:11:24 2004 Subject: [Biojava-dev] =?iso-2022-jp?b?GyRCIVokKkU3NSQlYSVrJV4lLCFbGyhC?= =?iso-2022-jp?b?GyRCIzUyLyM5QGlLfDFfPlo1ciEmPVBNaCRrOl9CcCVTJTglTSU5GyhC?= =?iso-2022-jp?b?GyRCJEhBNDlxJCpFNzUkPnBKcyEhQmgbKEI0MTAbJEI5ZiFKGyhCOCww?= =?iso-2022-jp?b?MDAbJEJJdEdbPy4bKEIp?= Message-ID: <7983048.1081778419017.JavaMail.nobody@hosyou-b.mine.nu> biojava-dev@biojava.org様、 お読み頂き、ありがとうございます。 ◇本メルマガの配信不要、または登録した覚えのない場合は 　一番下の★★★　今日の天気予報　★★★ 　　　　と━毎朝見れる！　全国のお天気━　 　　　の間にあるアドレスで解除させて頂きます。　 　　━━━━━━━━━━━━━━━━━━━━━━━━━━ 　　◇５億９千万円証拠有ビジネス！高額金額は関心が高い◇ 　　━━━━━━━━━━━━━━━━━━━━━━━━━━ ☆５千万円貯金が欲しい！ ☆３億円の事業資金が欲しい！ ☆老後のために４千万円欲しい ☆安心の為に保証が欲しい ☆ネットで７千万円以上収入が欲しい そんな貴方に最適な簡単在宅ビジネスです。 既に３億、５億９千万円の収入者続出しています。 まずは、証拠を見てください、それからです！ ★証拠は東京高裁にて判決★ ◆高額収入の証拠アリ！◆ 詳しくはHPにてご確認ください。 　http://break.at/hosyou 何事も論より証拠・裁判官の目でお確かめ推奨！！ 　　　　　　 　　　　　　━━━━━━━━━━━━━ 　　　　　 貴方様は！ご存じですか！ 　　　　　　━━━━━━━━━━━━━ 　ついにグランドオープンの日程が決まりました！ 　それまでに貴方のポジションを確保して置いて下さい！ 　↓　　↓　 http://fortuna.love-jpn.com/index.cgi?id=world 　　　 　　　　　　　━━━━━━━━━━━━━━ 　　　　　　　働くママの！私にも出来る事！ 　　　　　　　━━━━━━━━━━━━━━ 在庫なし・セミナー参加なし・初心者にも簡単！・サポート 体制バッチリ 参加者の8割が女性の方というのも納得です http://stage-one.jp/jc/myao/ 　　　　　　━━━━━━━━━━━━━━━━━ 【広告投稿随時募集中 !!】 広告　５回掲載３０日で３０００円 広告　７回掲載５日で４０００円 広告１０回掲載６０日で５０００円 　　　　 ◎　本日も投稿！ありがとうございました♪◎ <<メルマガ発行者＞＞楽々トクトク情報社 yazawa@easy.to ■免責事項 当メールマガジンに掲載している情報に関して発行者では一切の 責任を負いません。 一切の責任を負いかねますのでご了承ください。掲載記事に関す るお問い合わせは直接投稿者へお願いいたします。 　　　　　★★★　今日の天気予報　★★★ ■　アドレスで配信解除　■ ◇本メルマガの配信不要、または登録した覚えのない場合は 　次のアドレスからの登録により解除させて頂きます。　　　　　　　 http://back.to/mailstop 　　　━━━毎朝見れる！　全国のお天気━━　 ------------------------------------------- 4月12日11時発表 主要都市 今夜 明日 札幌 曇りのち時々晴れ 晴れ 仙台 晴れ 曇り時々晴れ 東京 晴れ 晴れのち時々曇り 長野 晴れ 晴れ 静岡 晴れ 晴れのち時々曇り 名古屋 晴れ 晴れのち時々曇り 新潟 晴れ 晴れ 金沢 晴れ 晴れ 大阪 晴れ 晴れのち時々曇り 岡山 晴れ 晴れのち時々曇り 広島 晴れ 晴れのち一時雨 高松 晴れ 曇り 福岡 晴れのち時々曇り 曇り一時雨 鹿児島 晴れのち時々曇り 雨 那覇 晴れ 晴れ From smh1008 at cus.cam.ac.uk Mon Apr 12 22:58:52 2004 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Mon Apr 12 23:03:37 2004 Subject: [Biojava-dev] Regexes on symbol lists - further thoughts Message-ID: I have been considering further the problem of how to permit regexes to be performed on SymbolLists on arbitrary alphabets. I list below the options that we have available to us and the pros/cons:- 1) the MotifTools package. This uses java.util.regex to search a SymbolList by wrapping it in a SymbolListCharSequence. It makes it quite easy to search DNA/RNA/Protein sequences with regexes in that there are single letter SymbolTokenizations available for all these alphabets. The regex can then be easily written as a text string. The drawback is with arbitrary alphabets (e.g. DNAxDNA or protein x protein), there is not such a SymbolTokenization. Basically, we require a single character SymbolTokenization for every alphabet. 2) my provisional org.biojava.utils.automata code. This uses DFAs to implement a fast way of running regexes and I have now got to the stage where is it comparable/faster than java.util.regex when used on SymbolLists in the manner described in (1). The drawback with DFAs is that I don't think it is possible to implement the greedy/non-greedy quantifiers to work exactly as they work in Perl. It is easy to have greedy or non-greedy behaviour throughout the regex but not when they are mixed. In the latter case, some cases can be made to behave in the expected manner but not all. Alternating greedy/non-greedy blocks appear to be a showstopper. It is possible to use NFAs to do regexes but NFAs are slower and require backtracking. However this package will search in any arbitrary alphabet. It strikes me that both are incomplete approaches even though they will in their own way suit 90% of the use cases. It has struck me that there is one other option open to me. I could use the same strategy as (1) except I have a SymbolList -> CharSequence conversion that does NOT use our default SymbolTokenizers. Instead, I use the alphabet index to convert the symbol to an equivalent integer and then convert that integer into a code point in the Unicode private space (E000-F8FF in UTF-16 which is the Java char space). The current search strings in ASCII can be converted to the equivalent in this alphabet index space too. Now I should be able to search with regexes in any alphabet with less than 6399 symbols. This should be fine in all cases where we wish to know the location on the sequence where particular motifs lie. Does anyone have views/objections they might wish to offer as to whether this is too ugly to live? Regards, David Huen From autobuilder at derkholm.net Tue Apr 13 00:11:02 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Apr 13 00:09:56 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1081829462531.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040413 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From matthew_pocock at yahoo.co.uk Tue Apr 13 10:07:05 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Apr 13 10:11:59 2004 Subject: [Biojava-dev] Phred symbol deserialization In-Reply-To: References: Message-ID: <407BF409.1010109@yahoo.co.uk> Hi, I have changed how symbols like those used by phread are serialized. They should now be converted into per-machine singletons. I have not tested extensively though. Could you see if the next nightly build fixes your problem? If it does, then it's likely we have serialization working sanely for all cross-product symbols and therefore for all alignments. If not, then back to the drawing board. Matthew Eric Haugen wrote: >I've found that when I deserialize a Phred symbol (SimpleAtomicSymbol from the Phred alphabet == (DNA x SubIntegerAlphabet[0..99]) ), I get a brand new SimpleAtomicSymbol instead of the one already contained in the Phred alphabet. So PhredTools.getPhredAlphabet().contains( symbol ) returns false for that symbol. > >The following kludgy addition to SimpleAtomicSymbol.java makes it work: > >import org.biojava.bio.program.phred.PhredTools; >... > static final long serialVersionUID = -8426550133605911655l; > > protected Object readResolve() throws java.io.InvalidObjectException { > Object result = this; > if ((this.getSymbols().size() == 2) > && Annotation.EMPTY_ANNOTATION.equals( this.getAnnotation() )) { > try { > Symbol symbol = PhredTools.getPhredAlphabet().getSymbol( this.getSymbols() ); > if (symbol != null) { > result = symbol; > } > } catch (Exception ignored) { > // Must not be a Phred symbol > } > } > return result; > } > >This causes as a side effect the initialization of the 400-symbol phred alphabet whenever ANY SimpleAtomicSymbol is deserialized. And SimpleAtomicSymbol shouldn't have to know about various alphabets... >So, I'm hoping someone else has a better idea. Should AlphabetManager keep track of all cross-product symbols that should be singletons? > >Thanks, > >Eric > > > From ehaugen at u.washington.edu Tue Apr 13 18:01:41 2004 From: ehaugen at u.washington.edu (Eric Haugen) Date: Tue Apr 13 18:06:25 2004 Subject: [Biojava-dev] Phred symbol deserialization In-Reply-To: <407BF409.1010109@yahoo.co.uk> References: <407BF409.1010109@yahoo.co.uk> Message-ID: Hi Matthew, I just got the new version from cvs, and it works perfectly for my test cases. Cheers, Eric -- Eric Haugen University of Washington Genome Center On Tue, 13 Apr 2004, Matthew Pocock wrote: > Hi, > > I have changed how symbols like those used by phread are serialized. > They should now be converted into per-machine singletons. I have not > tested extensively though. Could you see if the next nightly build fixes > your problem? If it does, then it's likely we have serialization working > sanely for all cross-product symbols and therefore for all alignments. > If not, then back to the drawing board. > > Matthew > From autobuilder at derkholm.net Wed Apr 14 00:11:15 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Apr 14 00:07:27 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1081915875191.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040414 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/symbol/AbstractSimpleBasisSymbol.java * biojava-live/src/org/biojava/bio/symbol/AlphabetManager.java * biojava-live/src/org/biojava/bio/symbol/SimpleAtomicSymbol.java * biojava-live/src/org/biojava/bio/symbol/SimpleBasisSymbol.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 matthew_pocock at yahoo.co.uk Wed Apr 14 09:25:05 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Wed Apr 14 09:30:05 2004 Subject: [Biojava-dev] Phred symbol deserialization In-Reply-To: References: <407BF409.1010109@yahoo.co.uk> Message-ID: <407D3BB1.4070109@yahoo.co.uk> Phew! Serialization scares me. Glad it works. Matthew Eric Haugen wrote: >Hi Matthew, > >I just got the new version from cvs, and it works perfectly for my test cases. > >Cheers, > >Eric > > > From autobuilder at derkholm.net Thu Apr 15 00:11:04 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Apr 15 00:07:08 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1082002264963.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040415 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Fri Apr 16 00:11:09 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Apr 16 00:06:57 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <5450181.1082088669377.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040416 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/seq/io/SymbolListCharSequence.java * biojava-live/src/org/biojava/utils/regex/Matcher.java * biojava-live/src/org/biojava/utils/regex/Pattern.java * biojava-live/src/org/biojava/utils/regex/PatternChecker.java * biojava-live/src/org/biojava/utils/regex/PatternFactory.java * biojava-live/src/org/biojava/utils/regex/RegexException.java * biojava-live/src/org/biojava/utils/regex/package.html * biojava-live/tests/org/biojava/utils/regex/PatternCheckerTest.java * biojava-live/tests/org/biojava/utils/regex/RegexTest.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Sat Apr 17 00:11:06 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Apr 17 00:06:43 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1082175066770.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040417 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/seq/DNATools.java * biojava-live/src/org/biojava/bio/symbol/Pattern.java * biojava-live/src/org/biojava/bio/symbol/PatternMaker.java * biojava-live/src/org/biojava/bio/symbol/PatternSearch.java * biojava-live/src/org/biojava/utils/regex/Pattern.java * biojava-live/src/org/biojava/utils/regex/PatternFactory.java * biojava-live/src/org/biojava/utils/regex/Search.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Sun Apr 18 00:11:16 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Apr 18 00:06:42 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1082261476954.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040418 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/utils/regex/Search.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Mon Apr 19 00:11:09 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Apr 19 00:06:24 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <5450181.1082347869631.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040419 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/utils/xml/PrettyXMLWriter.java * biojava-live/src/org/biojava/utils/xml/XMLWriter.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 cat at rmb.com.hk Mon Apr 19 04:03:23 2004 From: cat at rmb.com.hk (cat) Date: Mon Apr 19 04:07:53 2004 Subject: [Biojava-dev] Rash guard USD6.00/PC Message-ID: <200404190807.i3J87l6C025207@portal.open-bio.org> product name:Rash guard QTY:1,000PCS USD6.00/PC T : 0086-769-5835182 F : 0086-769-5835182 Website : http://home.netvigator.com/~sky888s/ Thanks, cat From storem at seznam.cz Mon Apr 19 10:27:22 2004 From: storem at seznam.cz (reginald) Date: Mon Apr 19 10:42:18 2004 Subject: [Biojava-dev] =?windows-1251?b?zO7y6OLg9uj/IO/l8PHu7eDr4A==?= Message-ID: <200404191442.i3JEgA6B029287@portal.open-bio.org> ?? ??? ???? ?? ??????, ??? ????? ?????? ??????? ??????? ?? ????, ????????? ???????????? ?????????? ?? ??? ??????????. ? ??? ???????? ???????, ?? ?????????? ?? ????? ???????? ????????? ??? ????? ?????????! ??? ??????? ???, ????? ?????????? ? ??????????? ????????, ?? ?????? ??????????? ???????? ? ????????? ????? ????? ???? ??? ??????? ????? ?????? ???????? ??? ?????????? ?? ?? ????? ??????????? ??? ???? ???? ?????? ???? ?? ??????????? ???????????? ????????-????????: ??????????? ??????? ????????? ?????????? 26-27 ??????. ????????? ????????-????????: ?????? I. ????????? ?????????. ? ???????? ?????????. ? ???????????? ? ??????????? ??????? ? ?????????: ????????? ????????????? ??????, ?? ?????? ? ??????? ??????????. ??????? ??????????? ? ????????? ????????? ?????? ? ????????? ????? ?????????? ?????????. ?????? II. ???????? ???????? ?????????. 1.????????? ????????? ?? ?????? ???????????. ? ????????????? ?????????. ?????? ????????? ????????? ? ???????? ?????? ? ???????????? ????????. ? ?????? ????????????? ?????? ?????????. ? ??????? ??????? ? ????????? ?????? ?????????. ? ??????? ????????????? ? ??????????????? ??????????????: ??????????? ? ???????????. ? ????????????? ????????: ????????????? ???????? ? ????? ??? ??????? ?????????. ?????????? ??????? ? ????? ???????? ? ??????? ????????? ?????????. ? ????????? ?????????. 2. ????????? ????????? ??????????. ????????????? ??????????. ? ???????? ???????????? ??????? ?????. ?????????? ????? ?????????? ????? ? ??????????? ??????? ???????? ?????. ?????? III. ??? ??????? ? ?????? ?????? ?????????? ????????????? ????? ???????? (???? ?????? ?????????? ? ???????????? ???? ????????????). ? ???? ?????????? ??????? ?????????. ? ??????. ???????. ??????. ??????. ?????????? ?????: ??? ????????? ???????????. ? ??????????? ????????????? ??????? ????????? ???????????. ? ?????????? ????????? ???????? ?? ???????? ?????????? ?????????. ????????? ??????? - 7500 ??????, ? ?.?. ???. ????? ?????? ????? (???????? ??? ???????????). ? ????????? ??????: ??????? ? ???????????, ?????????????? ???????? ????????? ????-?????, ????. ????? ?????????? ??????-?????? ?????? ?. ?????????????. ????? ?????????? ? 10 ?? 17.30. ??????????? ?????????? ???????????. ?????? ??????? ? ???????? ? ??? ???? ?????????? ??????????? ?????????? ??????????? ??????????? (?? CD,DVD ??? ?????????????). ? ??????????????? ??????????? ??????????? ????????. ????????? ???????????? ???????????????? 4500 ???. ? ?????? ??? ??? ??????? ? ??????-?????? ??? ???????????? ?????????? ?? ????? ?? ?????? ??????????? ????? ????????????? ??????????. ? ??????? ????? ??????? ??????????? ?????? ????????? ?? ?????: 1. ?????? ? ?????? ????????? ? ???????????. 2. ???? ????? ? ??????? (?????? ????????? ????? ????????? ? ??????) 3. ???????? ??????????? ???????????. ?????????? ???????? (095) 207-26-21 ? (095) 789-81-90 From autobuilder at derkholm.net Tue Apr 20 00:11:18 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Apr 20 00:06:19 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <5450181.1082434278247.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040420 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/bio/gui/DistributionLogo.java * biojava-live/src/org/biojava/bio/symbol/AlphabetManager.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 heuermh at acm.org Tue Apr 20 13:45:48 2004 From: heuermh at acm.org (Michael Heuer) Date: Tue Apr 20 14:02:24 2004 Subject: [Biojava-dev] another 1.5 generics question In-Reply-To: Message-ID: All, Sorry to abuse the list with another 1.5 generics question. Given, import java.util.Map; import java.util.Set; /** * A graph. */ public interface Graph { /** * Return a read-only set view of the nodes in this graph. */ Set> nodes(); /** * Return a read-only set view of the edges in this graph. */ Set> edges(); /** * Return a map of type <Node, T> with * the nodes in this graph as keys. */ Map nodeMap(); /** * Return a map of type <Edge, T> with * the edges in this graph as keys. */ Map edgeMap(); /** * Create a node in this graph for the specified element * (optional operation). */ Node createNode(A a) throws UnsupportedOperationException; /** * Create an edge in this graph for the specified element * connecting the specified set of nodes (optional operation). */ Edge createEdge(B b, Set> nodes) throws UnsupportedOperationException; /** * Node in a graph. */ interface Node { /** * Return the element at this node. */ A get(); /** * Set the element at this node to a * (optional operation). */ void set(A a) throws UnsupportedOperationException; /** * Return a read-only set view of the edges in this graph connected * to this node. */ Set> edges(); } /** * Edge in a graph. */ interface Edge { /** * Return the element at this edge. */ B get(); /** * Set the element at this edge to b * (optional operation). */ void set(B b) throws UnsupportedOperationException; /** * Return a read-only set view of the nodes in this graph connected * by this edge. */ Set> nodes(); } } I get a complaint about the Set> edges() method on Node and the Set> nodes() method on Edge: non-static class A cannot be referenced from a static context I'm a bit confused, because I thought that everything is static in an interface definition, and I thought that A, B in this example are just type placeholders for the element classes. michael From autobuilder at derkholm.net Wed Apr 21 00:11:03 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Apr 21 00:05:55 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1082520663807.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040421 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/dp/XmlMarkovModel.java * biojava-live/src/org/biojava/utils/regex/Search.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 cat at rmb.com.hk Wed Apr 21 01:58:04 2004 From: cat at rmb.com.hk (cat) Date: Wed Apr 21 02:02:33 2004 Subject: [Biojava-dev] 3D Message-ID: <200404210602.i3L62T6C012760@portal.open-bio.org> Multi 3D Factory Dongguan , Guangdong, China Tel : 0086-138-0237-9002 Free samples charge : 15second.(first) We are now developing our 3D Animation Team and belows are some of our drafts. We provide very cost effective solutions to our customers. Please let us know [ sales@rmb.com.hk ] if you are thinking of using animation to promote or express your products. Website : www.rmb.com Thanks, Gordon From matthew_pocock at yahoo.co.uk Wed Apr 21 06:14:52 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Wed Apr 21 06:19:29 2004 Subject: [Biojava-dev] another 1.5 generics question In-Reply-To: References: Message-ID: <4086499C.3020905@yahoo.co.uk> I have had trouble with some cases of nesting templated declarations like this, particularly with anonymous classes. It is a particular instance of Graph that is parameterised by concrete types in place of A and B. Node and Edge do not have an instance of Graph available, so they can not infer the run-time type of A and B. Try making the Node and Edge interfaces non-static. Alternatively, it may be possible to declare Node and Edge as being parameterised by AA and BB, and swapping the types appropreately in their deffinitions. Matthew Michael Heuer wrote: >All, > >Sorry to abuse the list with another 1.5 generics question. > >Given, > >import java.util.Map; >import java.util.Set; > >/** > * A graph. > */ >public interface Graph >{ > > /** > * Return a read-only set view of the nodes in this graph. > */ > Set> nodes(); > > /** > * Return a read-only set view of the edges in this graph. > */ > Set> edges(); > > /** > * Return a map of type <Node, T> with > * the nodes in this graph as keys. > */ > Map nodeMap(); > > /** > * Return a map of type <Edge, T> with > * the edges in this graph as keys. > */ > Map edgeMap(); > > /** > * Create a node in this graph for the specified element > * (optional operation). > */ > Node createNode(A a) > throws UnsupportedOperationException; > > /** > * Create an edge in this graph for the specified element > * connecting the specified set of nodes (optional operation). > */ > Edge createEdge(B b, Set> nodes) > throws UnsupportedOperationException; > > > /** > * Node in a graph. > */ > interface Node > { > > /** > * Return the element at this node. > */ > A get(); > > /** > * Set the element at this node to a > * (optional operation). > */ > void set(A a) > throws UnsupportedOperationException; > > /** > * Return a read-only set view of the edges in this graph connected > * to this node. > */ > Set> edges(); > } > > > /** > * Edge in a graph. > */ > interface Edge > { > > /** > * Return the element at this edge. > */ > B get(); > > /** > * Set the element at this edge to b > * (optional operation). > */ > void set(B b) > throws UnsupportedOperationException; > > /** > * Return a read-only set view of the nodes in this graph connected > * by this edge. > */ > Set> nodes(); > } >} > >I get a complaint about the Set> edges() method on >Node and the Set> nodes() method on Edge: > > non-static class A cannot be referenced from a static context > >I'm a bit confused, because I thought that everything is static in an >interface definition, and I thought that A, B in this example are just >type placeholders for the element classes. > > michael > >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > > From naoto at seznam.cz Wed Apr 21 17:55:01 2004 From: naoto at seznam.cz (endah) Date: Wed Apr 21 18:13:05 2004 Subject: [Biojava-dev] for you Message-ID: <200404212212.i3LMCk6B024499@portal.open-bio.org> ?????? ??? ????? ? ?????? ????????? ??????? ??????????. ????? ????????? ?????????? ??????????????? ?? www.mypresent.ru ???????? ????? ???????? ????????? ????? ? ???????????? ? ????? ???? ? ????? ????????. From autobuilder at derkholm.net Thu Apr 22 00:11:38 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Apr 22 00:06:17 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1082607098471.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040422 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 mg at guerrilla-tech.com Thu Apr 22 11:41:42 2004 From: mg at guerrilla-tech.com (Michael Griffith) Date: Thu Apr 22 11:48:14 2004 Subject: [Biojava-dev] BioJava compatibility with BioSQL-ORA? Message-ID: Hello, I am unclear after looking the current documentation and website if the classes in org.biojava.bio.seq.db.biosql.* are compatible with the BioSQL-Oracle implementation located at http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/biosql -ora/?cvsroot=biosql. If I understand the Javadoc's, the only supported DB's for these classes are mySQL and PostgreSQL? I am currently using the 1.3.1 Version of BioJava. Any help would be appreciated! Michael Griffith From autobuilder at derkholm.net Fri Apr 23 00:09:34 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Apr 23 00:04:02 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <27475272.1082693374213.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040423 Binary build: FAILED! Javadocs build: OK Core test suite: NOT RUN Problems occurred during this build cycle -- please investigate as soon as possible! The following files were modified in the last 24 hours: * biojava-live/src/org/biojava/utils/regex/Pattern.java * biojava-live/src/org/biojava/utils/regex/PatternFactory.java * biojava-live/src/org/biojava/utils/regex/Search.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From mark.schreiber at group.novartis.com Fri Apr 23 01:59:28 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Fri Apr 23 02:03:59 2004 Subject: [Biojava-dev] BioJava compatibility with BioSQL-ORA? Message-ID: Hi - The biojava 1.3.x series is only compatable with an older version of the BioSQL schema (known as the 'Capetown schema') For the most up to date support you should get a version of biojava-live from CVS or from the autobuild distribution. - 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 Michael Griffith Sent by: biojava-dev-bounces@portal.open-bio.org 04/22/2004 11:41 PM To: cc: Subject: [Biojava-dev] BioJava compatibility with BioSQL-ORA? Hello, I am unclear after looking the current documentation and website if the classes in org.biojava.bio.seq.db.biosql.* are compatible with the BioSQL-Oracle implementation located at http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/biosql -ora/?cvsroot=biosql. If I understand the Javadoc's, the only supported DB's for these classes are mySQL and PostgreSQL? I am currently using the 1.3.1 Version of BioJava. Any help would be appreciated! Michael Griffith _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From td2 at sanger.ac.uk Fri Apr 23 03:41:00 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Fri Apr 23 03:45:21 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report In-Reply-To: <27475272.1082693374213.JavaMail.thomas@calette.derkholm.net> References: <27475272.1082693374213.JavaMail.thomas@calette.derkholm.net> Message-ID: <9096DA95-94F9-11D8-9AA6-000A95C8B056@sanger.ac.uk> On 23 Apr 2004, at 05:09, autobuilder@derkholm.net wrote: > BioJava automatic build system, run 20040423 > > Binary build: FAILED! > Javadocs build: OK > Core test suite: NOT RUN > > Problems occurred during this build cycle -- please investigate as > soon as possible! > > The following files were modified in the last 24 hours: > > * biojava-live/src/org/biojava/utils/regex/Pattern.java > * biojava-live/src/org/biojava/utils/regex/PatternFactory.java > * biojava-live/src/org/biojava/utils/regex/Search.java This had a couple of undeclared exceptions. Fixed now. Thomas. From smh1008 at cus.cam.ac.uk Fri Apr 23 03:42:33 2004 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Fri Apr 23 03:47:00 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: On Friday 23 Apr 2004 5:09 am, autobuilder@derkholm.net wrote: > BioJava automatic build system, run 20040423 > > Binary build: FAILED! > Javadocs build: OK > Core test suite: NOT RUN > Fixed. Rgds, David From matthew_pocock at yahoo.co.uk Fri Apr 23 06:40:23 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri Apr 23 06:44:57 2004 Subject: [Biojava-dev] web site stats Message-ID: <4088F297.3010407@yahoo.co.uk> Hi, I think we used to have a web site that showed web site access logs. Does that still exist? I need to get some stats together for someone. En't grant writing fun. Matthew From mattjb at eleceng.adelaide.edu.au Fri Apr 23 06:48:31 2004 From: mattjb at eleceng.adelaide.edu.au (Matthew Berryman) Date: Fri Apr 23 06:53:05 2004 Subject: [Biojava-dev] web site stats In-Reply-To: <4088F297.3010407@yahoo.co.uk> References: <4088F297.3010407@yahoo.co.uk> Message-ID: On 23/04/2004, at 20:10, Matthew Pocock wrote: > Hi, > > I think we used to have a web site that showed web site access logs. > Does that still exist? A quick googling and some playing around with urls reveals http://www.biojava.org/stats/wwwyyyy/index.html where yyyy=2001, 2002, etc. 2004 doesn't have stats, a lot are missing for 2002 and 2003 too :) > I need to get some stats together for someone. En't grant writing fun. :) Matt B. From jason at cgt.duhs.duke.edu Fri Apr 23 07:12:08 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Apr 23 07:16:35 2004 Subject: [Biojava-dev] web site stats In-Reply-To: <4088F297.3010407@yahoo.co.uk> References: <4088F297.3010407@yahoo.co.uk> Message-ID: I've set it up for all the OBF sites. http://biojava.org/usage/ -jason On Fri, 23 Apr 2004, Matthew Pocock wrote: > Hi, > > I think we used to have a web site that showed web site access logs. > Does that still exist? I need to get some stats together for someone. > En't grant writing fun. > > Matthew > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From aaron at bleepout.com Fri Apr 23 14:06:52 2004 From: aaron at bleepout.com (aaron) Date: Fri Apr 23 14:11:29 2004 Subject: [Biojava-dev] wstickets.com and biojava.org boxing link exchange? Message-ID: <200404231811.i3NIBR6B021687@portal.open-bio.org> Hello, I found your site http://www.biojava.org by searching Rodeo on various search engines, and saw you are ranking well. I thought we could help each other at no cost and with very little work. I run a site similar in nature to yours, and was wondering if you would like to trade links with me? our site is http://www.wstickets.com This helps us both with traffic. You can see my site at "http://www.wstickets.com". I would give your site a prominent listing on my www.wstickets.com site, under the rodeo, PBR or NFR catagory page, if you would be willing to do the same. Our links are located at http://wstickets.com/links.asp If you want to discuss exchanging index page links, please feel free to email me. Please let me know if you have any questions or comments. Thank you, aaron If you want us to remove you from future emailings, just let me know. If you have recieved this message in error, or more than once, we do apologize, it was unintentional... From autobuilder at derkholm.net Sat Apr 24 00:11:25 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sat Apr 24 00:05:46 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1082779885992.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040424 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/utils/regex/Search.java * biojava-live/tests/org/biojava/utils/regex/RegexTest.java A patch file reflecting these changes is available from http://www.derkholm.net/autobuild/patches/ -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From autobuilder at derkholm.net Sun Apr 25 00:11:22 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Apr 25 00:05:27 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <5450181.1082866282602.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040425 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From len at reeltwo.com Sun Apr 25 19:34:47 2004 From: len at reeltwo.com (Len Trigg) Date: Sun Apr 25 19:39:18 2004 Subject: [Biojava-dev] BioJava compatibility with BioSQL-ORA? In-Reply-To: References: Message-ID: Michael Griffith wrote: > I am unclear after looking the current documentation and website if the > classes in org.biojava.bio.seq.db.biosql.* are compatible with the > BioSQL-Oracle implementation located at > http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/biosql-ora/?cvsroot=biosql. As Mark replied, you'll need to get the bleeding edge version of BioJava. That version supports the latest BioSQL schema, under MySQL, PostgreSQL, HSQLDB, and Oracle. I use Oracle with BioJava, however, when I first set it up I couldn't get biosql-ora working, so I did a direct port of the MySQL schema. I just had a look at the current biosql-ora and I think they should be compatible. Post if you have problems. The current BioJava BioSQL binding departs somewhat in its ontology handling (an extra table is required). If you don't use custom ontologies you should be OK though. Cheers, Len. From autobuilder at derkholm.net Mon Apr 26 00:10:55 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Mon Apr 26 00:04:48 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1082952655442.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040426 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 rudy at seznam.cz Mon Apr 26 09:21:53 2004 From: rudy at seznam.cz (patty) Date: Mon Apr 26 09:39:10 2004 Subject: [Biojava-dev] badroom Message-ID: <200404261339.i3QDd56B016801@portal.open-bio.org> ?????? ???? ?????? ?????????? ??????! ??? ??? ??? ??? ?????????, ?????? ????? ?????? ???????! ????? ?? ?????????? ??????? ?????? ?? ??????????: ??! ?? 1 ??? ??? ????????! http://www.mypresent.ru From sumathi_mm at hotmail.com Mon Apr 26 22:24:25 2004 From: sumathi_mm at hotmail.com (Sumathi Murugan) Date: Mon Apr 26 22:28:44 2004 Subject: [Biojava-dev] Hi need some help in retrieving sequences using NCBISequenceDB class Message-ID: Hi everyone, i am quite new to bioinformatics field. i want to retrieve all the Sequences related to some Query (Organism Cetacea and Cytb gene) using entrez. i donot know how to retrieve those ids from NCBISequence Database. my code is import java.io.*; import java.util.*; import org.biojava.bio.*; import org.biojava.bio.seq.db.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; public class NcbiRead { public static void main(String[] args) throws Exception { String server="http://www.ncbi.nlm.nih.gov/"; String cgi = "entrez/Cetacea[Organism] AND cytb"; String dBase = "nucleotide"; GenbankFormat gf = new GenbankFormat(); NCBISequenceDB db=new NCBISequenceDB(server,cgi,dBase,gf); } } The NCBISequenceDB has methods to retrieve sequence if user gives a particular id. In my case the ids are in NCBISequenceDB. honestly i don't know. i will be grateful if someone help me in getting progress. thanks in advance, Sumathi, Dept of BioInformatics, Auckland, NewZealand. _________________________________________________________________ Surf the net and talk on the phone with Xtra JetStream @ http://xtra.co.nz/jetstream From mark.schreiber at group.novartis.com Mon Apr 26 22:37:08 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Mon Apr 26 22:41:33 2004 Subject: [Biojava-dev] Hi need some help in retrieving sequences using NCBISequenceDB class Message-ID: Hi Sumarthi, I don't think you will be able to perform such a complex query with the NCBISequenceDB class. The class is really only intended to retrieve sequences when you know the accession number. Your query will probably return several accession numbers probably over both protein and DNA. I would suggest you perform some sort of query to retreive the accessions you need and iterate over them passing each one to the NCBISequenceDB's getSequence(String id) method. 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 "Sumathi Murugan" Sent by: biojava-dev-bounces@portal.open-bio.org 04/27/2004 10:24 AM To: biojava-dev@biojava.org cc: Subject: [Biojava-dev] Hi need some help in retrieving sequences using NCBISequenceDB class Hi everyone, i am quite new to bioinformatics field. i want to retrieve all the Sequences related to some Query (Organism Cetacea and Cytb gene) using entrez. i donot know how to retrieve those ids from NCBISequence Database. my code is import java.io.*; import java.util.*; import org.biojava.bio.*; import org.biojava.bio.seq.db.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; public class NcbiRead { public static void main(String[] args) throws Exception { String server="http://www.ncbi.nlm.nih.gov/"; String cgi = "entrez/Cetacea[Organism] AND cytb"; String dBase = "nucleotide"; GenbankFormat gf = new GenbankFormat(); NCBISequenceDB db=new NCBISequenceDB(server,cgi,dBase,gf); } } The NCBISequenceDB has methods to retrieve sequence if user gives a particular id. In my case the ids are in NCBISequenceDB. honestly i don't know. i will be grateful if someone help me in getting progress. thanks in advance, Sumathi, Dept of BioInformatics, Auckland, NewZealand. _________________________________________________________________ Surf the net and talk on the phone with Xtra JetStream @ http://xtra.co.nz/jetstream _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From Russell.Smithies at agresearch.co.nz Mon Apr 26 22:41:17 2004 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon Apr 26 22:45:39 2004 Subject: [Biojava-dev] Hi need some help in retrieving sequences usingNCBISequenceDB class Message-ID: Hi Sumarthi, It might be easier using Entrez' eFetch utils then parsing the results. As you can see, it's quite easy to construct a query: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide& term=Cetacea[Organism]%20AND%20cytb&retmax=1000 Russell Smithies Bioinformatics Software Developer AgResearch Invermay Private Bag 50034 Puddle Alley Mosgiel New Zealand -----Original Message----- From: biojava-dev-bounces@portal.open-bio.org [mailto:biojava-dev-bounces@portal.open-bio.org] On Behalf Of Sumathi Murugan Sent: Tuesday, 27 April 2004 2:24 p.m. To: biojava-dev@biojava.org Subject: [Biojava-dev] Hi need some help in retrieving sequences usingNCBISequenceDB class Hi everyone, i am quite new to bioinformatics field. i want to retrieve all the Sequences related to some Query (Organism Cetacea and Cytb gene) using entrez. i donot know how to retrieve those ids from NCBISequence Database. my code is import java.io.*; import java.util.*; import org.biojava.bio.*; import org.biojava.bio.seq.db.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; public class NcbiRead { public static void main(String[] args) throws Exception { String server="http://www.ncbi.nlm.nih.gov/"; String cgi = "entrez/Cetacea[Organism] AND cytb"; String dBase = "nucleotide"; GenbankFormat gf = new GenbankFormat(); NCBISequenceDB db=new NCBISequenceDB(server,cgi,dBase,gf); } } The NCBISequenceDB has methods to retrieve sequence if user gives a particular id. In my case the ids are in NCBISequenceDB. honestly i don't know. i will be grateful if someone help me in getting progress. thanks in advance, Sumathi, Dept of BioInformatics, Auckland, NewZealand. _________________________________________________________________ Surf the net and talk on the phone with Xtra JetStream @ http://xtra.co.nz/jetstream _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From autobuilder at derkholm.net Tue Apr 27 00:11:06 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Apr 27 00:04:47 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1083039066972.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040427 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 xinuo.chen at warwick.ac.uk Tue Apr 27 06:28:26 2004 From: xinuo.chen at warwick.ac.uk (Xinuo Chen) Date: Tue Apr 27 06:35:04 2004 Subject: [Biojava-dev] About masking low complexity regions in Protein sequences Message-ID: <000501c42c42$623b65a0$ad09030a@your8s51utrxaw> Hello. I am just wondering whether BioJava provides the facility to mask the low complexity regions in Protein sequences. Could you please tell me whether BioJava provides ? if it provides, could you please tell me with class or package I should use ? Thanks you. Yours sincerely Xinuo CHEN Research Associate and PhD High Performance System Group Department of Computer Science University of Warwick U.K From mark.schreiber at group.novartis.com Tue Apr 27 21:07:19 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Apr 27 21:11:45 2004 Subject: [Biojava-dev] About masking low complexity regions in Protein sequences Message-ID: Hi Xinuo - I'm not entirely clear what you are asking. Do you mean is biojava able to detect low complexity regions? The answer is no not directly but it would be very easy to code any algorithm that you want to use to do this in biojava. I would expect you would make use of the distribution package to do this. If you just want to annotate low complexity you could just add a feature to the low complexity part of your sequence. If you mean does biojava deal with mixed case soft masking (eg ATGAAGTATaaaaaataaaaataaaaatGTGTGA) where the lower case is low complexity then the short answer is biojava is case insensitive and does not. The longer answer is that you could define your own FiniteAlphabet and SymbolTokenization such that A is not equivalent to a. You might want to make a cross product alphabet of DNA and a binary alphabet {complex, not_complex} to achieve this result. For a clue try looking at the org.biojava.bio.program.phred for how the Phred alphabet combines DNA and sequence quality in a cross product alphabet. Good luck, - 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 "Xinuo Chen" Sent by: biojava-dev-bounces@portal.open-bio.org 04/27/2004 06:28 PM To: cc: Subject: [Biojava-dev] About masking low complexity regions in Protein sequences Hello. I am just wondering whether BioJava provides the facility to mask the low complexity regions in Protein sequences. Could you please tell me whether BioJava provides ? if it provides, could you please tell me with class or package I should use ? Thanks you. Yours sincerely Xinuo CHEN Research Associate and PhD High Performance System Group Department of Computer Science University of Warwick U.K _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From autobuilder at derkholm.net Wed Apr 28 00:10:53 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Wed Apr 28 00:04:21 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1083125453483.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040428 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 aaron at bleepout.com Wed Apr 28 19:55:08 2004 From: aaron at bleepout.com (aaron) Date: Wed Apr 28 19:59:23 2004 Subject: [Biojava-dev] wstickets.com and biojava.org boxing link exchange? Message-ID: <200404282359.i3SNxL6B013155@portal.open-bio.org> Hello, I found your site http://www.biojava.org by searching Rodeo on various search engines, and saw you are ranking well. I thought we could help each other at no cost and with very little work. I run a site similar in nature to yours, and was wondering if you would like to trade links with me? our site is http://www.wstickets.com This helps us both with traffic. You can see my site at "http://www.wstickets.com". I would give your site a prominent listing on my www.wstickets.com site, under the rodeo, PBR or NFR catagory page, if you would be willing to do the same. Our links are located at http://wstickets.com/links.asp If you want to discuss exchanging index page links, please feel free to email me. Please let me know if you have any questions or comments. Thank you, aaron If you want us to remove you from future emailings, just let me know. If you have recieved this message in error, or more than once, we do apologize, it was unintentional... From aaron at bleepout.com Wed Apr 28 20:35:30 2004 From: aaron at bleepout.com (aaron) Date: Wed Apr 28 20:39:46 2004 Subject: [Biojava-dev] wstickets.com and biojava.org boxing link exchange? Message-ID: <200404290039.i3T0dg6B013464@portal.open-bio.org> Hello, I found your site http://www.biojava.org by searching Rodeo on various search engines, and saw you are ranking well. I thought we could help each other at no cost and with very little work. I run a site similar in nature to yours, and was wondering if you would like to trade links with me? our site is http://www.wstickets.com This helps us both with traffic. You can see my site at "http://www.wstickets.com". I would give your site a prominent listing on my www.wstickets.com site, under the rodeo, PBR or NFR catagory page, if you would be willing to do the same. Our links are located at http://wstickets.com/links.asp If you want to discuss exchanging index page links, please feel free to email me. Please let me know if you have any questions or comments. Thank you, aaron If you want us to remove you from future emailings, just let me know. If you have recieved this message in error, or more than once, we do apologize, it was unintentional... From autobuilder at derkholm.net Thu Apr 29 00:10:58 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Apr 29 00:04:13 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1083211858556.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040429 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/Annotatable.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 matthew_pocock at yahoo.co.uk Thu Apr 29 06:21:56 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Thu Apr 29 06:26:15 2004 Subject: [Biojava-dev] web site Message-ID: <4090D744.8010108@yahoo.co.uk> Hi, Is anybody managing the biojava web site? We may be getting a big article about biojava some time soon, and it would be nice if the site was less out of date for when we get the sun equivalent of a /.ing (I wish). Are the pages hosted on portal now? Matthew From autobuilder at derkholm.net Fri Apr 30 00:10:59 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Fri Apr 30 00:04:01 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1083298259531.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040430 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From matthew_pocock at yahoo.co.uk Wed Apr 28 06:47:25 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue May 4 10:15:00 2004 Subject: [Biojava-dev] [Fwd: [DAS] BOSC 2nd Call For Papers] Message-ID: <408F8BBD.5020701@yahoo.co.uk> Who would like to do the biojava talk this year? I think I am probably doing Taverna, as Tom Oinn can't make it. Matthew -------------- next part -------------- An embedded message was scrubbed... From: Darin London Subject: [DAS] BOSC 2nd Call For Papers Date: Wed, 28 Apr 2004 11:06:37 +0100 (BST) Size: 5243 Url: http://portal.open-bio.org/pipermail/biojava-dev/attachments/20040428/04e8520f/DASBOSC2ndCallForPapers-0001.eml