From adewaleam at hotmail.com Sat Nov 1 02:51:49 2003 From: adewaleam at hotmail.com (Chief A.A.Mkpitima J.P.) Date: Fri Oct 31 18:46:15 2003 Subject: [Biojava-dev] UTILISATION ASSISTANCE PROPOSAL Message-ID: <200310312346.h9VNk6dc023514@portal.open-bio.org> NATIONAL HOUSE OF ASSEMBLY CONTRACT REVIEW COMMITTEE (NHACRC) Dear, I am chief Adewale Adeolu Mkpitima (J.P) I am fourty five years old, married with three children. I entract your utmost reliance in this informations and the transaction as whole. I am the head of the National House of Assembly Contract Review Committee (NHCRC), this is a four man committee set up by the National House of Assembly members/senators, to review all the contracts awarded by the Nigerian National Petroleum Coporation (NNPC) ten years ago (1993-2002) to foreign firms on turn around/ gen.maintenance of the Refineries. This action is reached as a result of the collapse of all the Refineries in our Country that has led to the importation of Fuel which has resulted to persistent Fuel scarcity in our country. In the course of our assignment we discovered some contract misappropation (OVER-INVOICE} among them is this particular contract that was OVER-INVOICED of the tune $22 Million Dollars (Twenty Two Million U.S Dollars) which we the members of this committee have unanimously agreed to use as a compensation for this great assignment, since then we have been safeguarding this tune awaiting the appropriate time to channel this tune( amount) into a utilisation account With the death of the one time Senate President Chief Chuba Okadigbo whom has been a threat to the arrangement.We deem it appropriate/neccessary to transfer this tune into a UTILISATION foreign account, but this arrangement will not be complete without a foreign utilisation account. it is in this regard you are contacted (partnership is required) For effective actualisation you are to forward to us the following informations;- A) Your full name and brief information on your profile. b) Your confidential Tel/Fax numbers (mobile) c) Your full contact /office address. We have agreed to offer you 20% of the total sum for this essential role, 5% has been ear-marked for settlement of any incidental expenses that may come up in the course of this transaction. please note that the hope, confidence bestowed on you should not be over-emphasised, and you are also to assist us in investing our share 75% while we are there in your country. NOTE: EVERY INFORMATION SHOULD REMAIN A TOP SECRET. Please forward your anticipated reply on my confidential e-mail address ademkpitima@netscape.net Regards Chief A.A.Mkpitima J.P. From 240251 at mail.com Sat Nov 1 03:39:54 2003 From: 240251 at mail.com (240251@mail.com) Date: Sat Nov 1 03:38:26 2003 Subject: [Biojava-dev]  The 30 Hour Wonder! 766096815 Message-ID: <200311010838.hA18cFdb022832@portal.open-bio.org> Cyalus comes in smaller doses and produces fewer side effects. Cyalus also works much faster than Sildenafil-based medications. In clinical trials, the majority of men who took the drug were able to engage in sexual intercourse within 30 minutes or less. The studies also indicated that Cyalus stays in the system for up to 30 hours. That's 26 hours longer than the traditional Sildenafil-based medications treatment. Test results showed that out of 700 participants at least 88 percent of men experienced improvement with their erections. More info http://www.hostvy.com/ 32F16F87-1A53D956-7106FF14-2270D8D1-C2D98DD 422C5323-7E0EE147-27042F04-359626ED-C81D740 3595309D-5A1E170B-5B90A3C6-50686FB6-6B097480 From kwandamase at workmail.co.za Sat Nov 1 06:52:31 2003 From: kwandamase at workmail.co.za (kwandamase@workmail.co.za) Date: Sat Nov 1 06:49:20 2003 Subject: [Biojava-dev] ATTN: URGENT BUSINESS PROPOSAL. Message-ID: <200311011149.hA1Bn9dc002007@portal.open-bio.org> ATTN: CEO/PRESIDENT I am Ms. NOKWANDA THANDI SONDAMASE the in-law to Mr. THABO MBEKI, The President of Republic of South Africa. It was my search for a reputable Foreign Firms to do business that made me contact you. The South African Government wants to import a REFINED DIAMOND and my in-law The President of South Africa has awarded me the contract to supply this DIAMOND. This contract was awarded to me in the past and I supplied the DIAMOND from Sirre-lone to the tune of US$32MILLION ($32,000,000.00) and we paid cash to Mrs. SWAN ISIWELU a citizen of Sirre-lone. Now the South African governments are interested in the brand of diamond that was imported and supplied to the government of South Africa. Because of this development they have awarded the contract of supplying another diamond worth of US$32 MILLION ($32, 000, 00.00) to me by the instruction of The South Africa President who is my in-law and they will pay me upfront. I am therefore writing you to enable me use your company as the firm that supplied the DIAMOND because I don?t intend to actually supply the DIAMOND. You will bring a name of any company of your choice, which we shall register legally as a foreign firm to supply the DIAMOND to the South African government. I will personally get all the approvals from the various ministries here in South Africa; which the original document would be sent to Spain. You will travel to Spain and sign the original documents and the payment will be release order. As soon as I receive the document, I will submit it to the various ministries for approvals. Immediately we receive the money for the importation of the DIAMOND in your bank account I will fly to meet you so that I will take my own share of the money. I will personally control the situation here and I assure you that the business is risk free because the South African President is my in-law. Immediately you indicate your interest you please send me your private and confidential telephone and fax number to enable me enlighten you properly on the deal. Note that we are only using your company as the same as the company that supplied the formal refined DIAMOND, by the end of the day we will not supply the DIAMOND. Its very important that you respond to the urgency of this message by confirming your interest. Yours truly, Ms. NOKWANDA THANDI SONDAMASE From achurbanov at yahoo.com Sun Nov 2 01:57:19 2003 From: achurbanov at yahoo.com (Alexander Churbanov) Date: Sun Nov 2 01:54:06 2003 Subject: [Biojava-dev] TestGenbank.java problem Message-ID: <20031102065719.57820.qmail@web14306.mail.yahoo.com> Hello, There is a problem with the following string in TestGenbank.java demo: SeqFileFormer theFormatter = SeqFileFormerFactory.makeFormer("Genbank"); The SeqFileFormerFactory does not exist anymore in the new release of Biojava. Is it deprecated??? What could be the right way to update the line? Thanks, Alexander Churbanov __________________________________ Do you Yahoo!? Exclusive Video Premiere - Britney Spears http://launch.yahoo.com/promos/britneyspears/ From achurbanov at yahoo.com Sun Nov 2 02:08:57 2003 From: achurbanov at yahoo.com (Alexander Churbanov) Date: Sun Nov 2 02:05:43 2003 Subject: [Biojava-dev] TestGenbank.java problem Message-ID: <20031102070857.98976.qmail@web14301.mail.yahoo.com> Hello, There is a problem with the following string in TestGenbank.java demo: SeqFileFormer theFormatter = SeqFileFormerFactory.makeFormer("Genbank"); The SeqFileFormerFactory does not exist anymore in the new release of Biojava. Is it deprecated??? What could be the right way to update the line? Thanks, Alexander Churbanov __________________________________ Do you Yahoo!? Exclusive Video Premiere - Britney Spears http://launch.yahoo.com/promos/britneyspears/ From mark.schreiber at agresearch.co.nz Sun Nov 2 21:20:49 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Sun Nov 2 21:17:49 2003 Subject: [Biojava-dev] Feature bug? Message-ID: Hi - When you create a Feature on a SimpleSequence you get back a reference to the Feature that was created. Interestingly if you call the containsFeature() method with the returned reference as an argument the result os false. If you get the reference to the created Feature from the SimpleSequence itself (using the features() or filter() methods) the result of containsFeature() is true. Is this how it should be? If yes will document it. If no, how do I fix it? - Mark ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Sun Nov 2 21:27:11 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Sun Nov 2 21:24:02 2003 Subject: [Biojava-dev] Feature bug? Message-ID: Actually, ignore that. Seems to only be a problem on Sequences that have been serialized. Probably due to the FeatureRealizer being transient or something. Oh, well. At least i'm closing in on why Features are not serializing properly. - Mark -----Original Message----- From: Schreiber, Mark Sent: Mon 3/11/2003 3:20 p.m. To: biojava-dev@biojava.org Cc: Subject: [Biojava-dev] Feature bug? Hi - When you create a Feature on a SimpleSequence you get back a reference to the Feature that was created. Interestingly if you call the containsFeature() method with the returned reference as an argument the result os false. If you get the reference to the created Feature from the SimpleSequence itself (using the features() or filter() methods) the result of containsFeature() is true. Is this how it should be? If yes will document it. If no, how do I fix it? - Mark ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev ======================================================================= 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 davidmaynard at pacbell.net Sun Nov 2 21:43:16 2003 From: davidmaynard at pacbell.net (David Maynard) Date: Mon Nov 3 08:31:57 2003 Subject: [Biojava-dev] ReadGenBank Problem Message-ID: <000e01c3a1b4$3c244120$2302a8c0@dmaynard2k> Dear BioJava Developers: ReadGenBank seems to broken in the biojava-live tree. The following output results from running the ReadGB example from the BioJava In Anger website against the sample file AY069118.gb from the tests/files directory. I am running Windows 2000 with Java version "1.4.2_01" I have done a recent update -P -d against the biojava-live tree. This used to work. Any suggestions? Thank you, David Maynard ReadGB trying to read GenBank File AY069118.gb org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:177) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:91) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102) at ReadGB.main(ReadGB.java:30) Caused by: java.lang.NoClassDefFoundError: org/biojava/ontology/format/triples/node/Node at org.biojava.ontology.OntoTools.(OntoTools.java:71) at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:385) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:97) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141) ... 8 more org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:177) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:91) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102) at ReadGB.main(ReadGB.java:30) Caused by: java.lang.NoClassDefFoundError at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:385) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:97) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141) ... 8 more org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:177) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:91) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102) at ReadGB.main(ReadGB.java:30) Caused by: java.lang.NoClassDefFoundError at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:385) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:97) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141) ... 8 more From mark.schreiber at agresearch.co.nz Mon Nov 3 16:06:03 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Nov 3 16:03:12 2003 Subject: [Biojava-dev] ReadGenBank Problem Message-ID: Hi David - You need to put the grammars.jar on your class path. This is a new jar built by biojava that contains all the ontology stuff that is new in biojava-live. Let me know if that doesn't work. - Mark -----Original Message----- From: David Maynard [mailto:davidmaynard@pacbell.net] Sent: Mon 3/11/2003 3:43 p.m. To: biojava-dev@biojava.org Cc: Subject: [Biojava-dev] ReadGenBank Problem Dear BioJava Developers: ReadGenBank seems to broken in the biojava-live tree. The following output results from running the ReadGB example from the BioJava In Anger website against the sample file AY069118.gb from the tests/files directory. I am running Windows 2000 with Java version "1.4.2_01" I have done a recent update -P -d against the biojava-live tree. This used to work. Any suggestions? Thank you, David Maynard ReadGB trying to read GenBank File AY069118.gb org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:177) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:91) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102) at ReadGB.main(ReadGB.java:30) Caused by: java.lang.NoClassDefFoundError: org/biojava/ontology/format/triples/node/Node at org.biojava.ontology.OntoTools.(OntoTools.java:71) at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:385) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:97) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141) ... 8 more org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:177) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:91) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102) at ReadGB.main(ReadGB.java:30) Caused by: java.lang.NoClassDefFoundError at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:385) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:97) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141) ... 8 more org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:177) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:91) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102) at ReadGB.main(ReadGB.java:30) Caused by: java.lang.NoClassDefFoundError at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:385) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:97) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141) ... 8 more ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Mon Nov 3 22:52:20 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Nov 3 22:49:10 2003 Subject: [Biojava-dev] Flyweight Ontologies? Message-ID: Hi - Just looking at some serialization bug fixes and I have a question about Ontologies. Should they be flyweight objects? The reason I ask is Ontology.Impl is serializable but doesn't attempt to prevent deep copying. However the Term.Impl equals() methods asks if the two Ontologies are canonical with an == operator. One of these needs to be changed. - Mark ======================================================================= 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 td2 at sanger.ac.uk Tue Nov 4 08:04:17 2003 From: td2 at sanger.ac.uk (Thomas Down) Date: Tue Nov 4 08:01:00 2003 Subject: [Biojava-dev] Odd test failure (SymbolListCharSequence) Message-ID: <20031104130417.GB112447@jabba.sanger.ac.uk> Hi... I'm currently seeing test failures for SymbolListCharSequence: Testsuite: org.biojava.bio.seq.io.SymbolListCharSequenceTest Tests run: 3, Failures: 1, Errors: 0, Time elapsed: 0.858 sec Testcase: testCharAt took 0.846 sec Testcase: testLength took 0 sec Testcase: testSubSequence took 0.005 sec FAILED expected: but was: junit.framework.AssertionFailedError: expected: but was: at org.biojava.bio.seq.io.SymbolListCharSequenceTest.testSubSequence(Sym bolListCharSequenceTest.java:70) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl. java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces sorImpl.java:25) Testcase: testSubSequence SymbolListCharSequence doesn't have equals and hashCode methods. I've just looked at the javadoc for CharSequence, and Sun specifically say that there isn't a special contract for equals and hashCode on CharSequences. So we've got two options: - Fix SymbolListCharSequence by implementing equals. - Fix the test so that it no longer uses equals to compare arbitrary CharSequences. The first option is arguably the most helpful, the second is probably more correct. Any preferences? It would have been nice is Sun had defined equals and hashCode for CharSequences in the same way they have for some other interfaces. But they've obviously considered this and rejected it... Thomas. From kdj at sanger.ac.uk Tue Nov 4 08:42:40 2003 From: kdj at sanger.ac.uk (Keith James) Date: Tue Nov 4 08:42:41 2003 Subject: [Biojava-dev] Odd test failure (SymbolListCharSequence) In-Reply-To: <20031104130417.GB112447@jabba.sanger.ac.uk> References: <20031104130417.GB112447@jabba.sanger.ac.uk> Message-ID: >>>>> "Thomas" == Thomas Down writes: Thomas> Hi... I'm currently seeing test failures for Thomas> SymbolListCharSequence: [...] Sorry. It seems I ran the tests on the wrong checkout - I was just looking at the green bar... doh! Thomas> SymbolListCharSequence doesn't have equals and hashCode Thomas> methods. I've just looked at the javadoc for Thomas> CharSequence, and Sun specifically say that there isn't a Thomas> special contract for equals and hashCode on CharSequences. Thomas> So we've got two options: Thomas> - Fix SymbolListCharSequence by implementing equals. - Thomas> Fix the test so that it no longer uses equals to compare Thomas> arbitrary CharSequences. Thomas> The first option is arguably the most helpful, the second Thomas> is probably more correct. Any preferences? I guess the "correct" way will present fewer surprises, but I'll fix whichever the majority vote is for. Keith -- - Keith James Microarray Facility, Team 65 - - The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK - From matthew_pocock at yahoo.co.uk Wed Nov 5 07:56:57 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Wed Nov 5 08:00:11 2003 Subject: [Biojava-dev] Re: Flyweight Ontologies? In-Reply-To: References: Message-ID: <3FA8F399.1030503@yahoo.co.uk> Oh dear. I can see this being a world of pain. I think ontologies and terms and triples should be flyweighted in the same spirit that alphabets and symbols are. However, I was going to defer the book keeping code untill the reasoner was working so that we could write it mainly in the ontology language. Grrr. Perhaps we need stable IDs? Matthew Schreiber, Mark wrote: >Hi - > >Just looking at some serialization bug fixes and I have a question about Ontologies. Should they be flyweight objects? > >The reason I ask is Ontology.Impl is serializable but doesn't attempt to prevent deep copying. However the Term.Impl equals() methods asks if the two Ontologies are canonical with an == operator. > >One of these needs to be changed. > >- Mark > > > > From closeout at closeout-sale.com Wed Nov 5 09:57:24 2003 From: closeout at closeout-sale.com (Language Professor) Date: Wed Nov 5 09:54:09 2003 Subject: [Biojava-dev] Fastest Way to Learn a New Language Message-ID: <1214$9uwbX2m2-sjmYuwbX2m27box@close-1.closeout-sale.com> Fastest Way to Learn a New Language - Guaranteed! http://www.platinum-deal.com/rd1.php?ac=CD1&bid=112&did=2788&oi=&p=0 Finally, a revolutionary approach that works. Instant Immersion™ 18 Languages is the most widely used method in the world because it is fun, easy and it works - guaranteed! Choose any point on the map, and you're virtually right at home thanks to Instant Immersion™ 18 Languages, the revolution in foreign language learning. Ideal for travelers, students and business people alike, these 2 language-packed CD-ROMs make language learning fast and easy. - The Most Widely Used Method in the World - The Easiest, Fastest Way to Multi-Language Learning - Guaranteed to teach faster and easier than any other language product or your money back. With Instant Immersion™ 18 Languages your only dilemma is choosing which language to learn first. Language learning has never been this easy! Click Below to Learn More: http://www.platinum-deal.com/rd1.php?ac=CD1&bid=112&did=2788&oi=&p=0 -- You received this message because you registered at one of the sites in the BluePinstripes Email Network or opted in through one of our marketing partners to receive offers. We strongly oppose the sending of unsolicited email and do not want to email anyone who does not wish to receive our valued mailings. If you would prefer to not receive these messages in the future, please go to http://www.closeout-offers.com/unsub.php?e=biojava-dev@biojava.org&m=2244017 If there are any problems with this link, reply to this email with "Remove" in the subject line. Or to unsubscribe via postal mail, please send request to: BluePinstripes Email Network 1140 Highland Ave., Suite #302 Manhattan Beach, CA 90266 To read Closeout-offers' privacy policy, visit http://www.closeout-offers.com/privacy.html The e-mail subscription address is: biojava-dev@biojava.org TM: <47;3J4p9BKB-eTKnJ4p9BKBYpE3;2244017> From mark.schreiber at agresearch.co.nz Wed Nov 5 17:54:00 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Wed Nov 5 17:50:49 2003 Subject: [Biojava-dev] RE: Flyweight Ontologies? Message-ID: I think this can be fixed using LSIDs in the same way they turned out to be useful for serialization of Alphabets and Symbols. There would also need to be a registry of Terms, Triples and Ontologies. Serialization would then be simple. Bundle everything up and distribute it over RMI or what ever. When it gets to the other end it asks the registry on the new JVM if it has objects corresponding to the LSID's. If it does it reconnects to them, if not it deserializes it's ontology payload and registers it. For efficiency you could define ontologies that the other JVM is expected to have an only serialize a placeholder reference and not the whole ontology. The biojava core ontology would be an example. Similar to the WellKnownAtomicSymbols. To make this work The Ontology, Term and Triple interfaces should extend Indentifiable so they have a getIdentifier() method. LSIDs will need to be in the core.ontology file. It would be nice if you could identify the parent triple or ontlogy of a Term from the LSID although this may not be possible. This leads to something of more general interest. I would like to propose that everything in biojava that is singleton or flyweight should implement Identifiable and be registered (ulitmately) with a central LSID registry. For example the getAlphabet and registerAlphabet functions of AlphabetManager would actually access parts of the LSID registry where all this stuff would get stored. Obviously there is some API breakage here but I think the benefits are great now that people are starting to use biojava in a distributed setting more often. Any thoughts? - Mark > -----Original Message----- > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > Sent: Thursday, 6 November 2003 1:57 a.m. > To: Schreiber, Mark > Cc: biojava-dev@biojava.org > Subject: Re: Flyweight Ontologies? > > > Oh dear. I can see this being a world of pain. I think ontologies and > terms and triples should be flyweighted in the same spirit that > alphabets and symbols are. However, I was going to defer the book > keeping code untill the reasoner was working so that we could > write it > mainly in the ontology language. Grrr. Perhaps we need stable IDs? > > Matthew > > Schreiber, Mark wrote: > > >Hi - > > > >Just looking at some serialization bug fixes and I have a question > >about Ontologies. Should they be flyweight objects? > > > >The reason I ask is Ontology.Impl is serializable but > doesn't attempt > >to prevent deep copying. However the Term.Impl equals() > methods asks if the two Ontologies are canonical with an == operator. > > > >One of these needs to be changed. > > > >- Mark > > > > > > > > > > > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Wed Nov 5 18:05:47 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Wed Nov 5 18:02:28 2003 Subject: [Biojava-dev] Nearing biojava 1.3.1 release Message-ID: Hi - There have been a lot of calls for a biojava 1.3.1 maintenance release. The good news is I'm just about ready. I just need to sort out some merging of the DP code from the biojava-live version. Before I put it out I would really like to get something resolved. Currenlty DNATools.a() == RNATools.a(). This is due to the way that the Symbols are declared in AlphabetManager.xml. I personally think this is counter intuitive and wrong. It is very easily fixable (if it needs fixing). Unless anybody disagrees I would like to make it so they are not canonical. Note that this has implications for the NUCLEOTIDE alphabet which might mean such a move is not desriable so please speak now or forever hold your peace. There have been a lot of bug fixes and minimal API breakage, there was a little bit although it is unlikely to be noticed by most people. I don't think I will be putting out a version for Java1.3 either. - Mark ======================================================================= 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 kdj at sanger.ac.uk Thu Nov 6 04:55:27 2003 From: kdj at sanger.ac.uk (Keith James) Date: Thu Nov 6 04:55:28 2003 Subject: [Biojava-dev] Odd test failure (SymbolListCharSequence) In-Reply-To: References: <20031104130417.GB112447@jabba.sanger.ac.uk> Message-ID: >>>>> "Keith" == Keith James writes: >>>>> "Thomas" == Thomas Down writes: Thomas> Hi... I'm currently seeing test failures for Thomas> SymbolListCharSequence: [...] Keith> I guess the "correct" way will present fewer surprises, but Keith> I'll fix whichever the majority vote is for. As the returning officer for CharSequence comparison I'd like to announce that the winning option (with 1 vote and 100% of the votes cast) is to fix the test. Done. Keith -- - Keith James Microarray Facility, Team 65 - - The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK - From matthew_pocock at yahoo.co.uk Thu Nov 6 06:27:45 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Thu Nov 6 06:30:59 2003 Subject: [Biojava-dev] Re: Flyweight Ontologies? In-Reply-To: References: Message-ID: <3FAA3031.8040500@yahoo.co.uk> This all sounds good, particularly IDs for all singletons, and particularly if there's an easy way to implement it without lots of special case code each time. I think the LSID people would point out at this point that LSIDs should be permanent, and immutable, always resolving to the same (or equivalent) entity. If we substitute URN for LSID, then I'm happy - urn:biojava: or something - I think we're meant to use urn:x-biojava as we've not registered the biojava namespace. Matthew Schreiber, Mark wrote: >I think this can be fixed using LSIDs in the same way they turned out to be useful for serialization of Alphabets and Symbols. There would also need to be a registry of Terms, Triples and Ontologies. > >Serialization would then be simple. Bundle everything up and distribute it over RMI or what ever. When it gets to the other end it asks the registry on the new JVM if it has objects corresponding to the LSID's. If it does it reconnects to them, if not it deserializes it's ontology payload and registers it. For efficiency you could define ontologies that the other JVM is expected to have an only serialize a placeholder reference and not the whole ontology. The biojava core ontology would be an example. Similar to the WellKnownAtomicSymbols. > >To make this work The Ontology, Term and Triple interfaces should extend Indentifiable so they have a getIdentifier() method. LSIDs will need to be in the core.ontology file. It would be nice if you could identify the parent triple or ontlogy of a Term from the LSID although this may not be possible. > >This leads to something of more general interest. I would like to propose that everything in biojava that is singleton or flyweight should implement Identifiable and be registered (ulitmately) with a central LSID registry. For example the getAlphabet and registerAlphabet functions of AlphabetManager would actually access parts of the LSID registry where all this stuff would get stored. Obviously there is some API breakage here but I think the benefits are great now that people are starting to use biojava in a distributed setting more often. > >Any thoughts? > >- Mark > > > > >>-----Original Message----- >>From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] >>Sent: Thursday, 6 November 2003 1:57 a.m. >>To: Schreiber, Mark >>Cc: biojava-dev@biojava.org >>Subject: Re: Flyweight Ontologies? >> >> >>Oh dear. I can see this being a world of pain. I think ontologies and >>terms and triples should be flyweighted in the same spirit that >>alphabets and symbols are. However, I was going to defer the book >>keeping code untill the reasoner was working so that we could >>write it >>mainly in the ontology language. Grrr. Perhaps we need stable IDs? >> >>Matthew >> >>Schreiber, Mark wrote: >> >> >> >>>Hi - >>> >>>Just looking at some serialization bug fixes and I have a question >>>about Ontologies. Should they be flyweight objects? >>> >>>The reason I ask is Ontology.Impl is serializable but >>> >>> >>doesn't attempt >> >> >>>to prevent deep copying. However the Term.Impl equals() >>> >>> >>methods asks if the two Ontologies are canonical with an == operator. >> >> >>>One of these needs to be changed. >>> >>>- Mark >>> >>> >>> >>> >>> >>> >> >> >> >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > > > From mark.schreiber at agresearch.co.nz Thu Nov 6 15:51:40 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Thu Nov 6 15:48:24 2003 Subject: [Biojava-dev] RE: Flyweight Ontologies? Message-ID: > This all sounds good, particularly IDs for all singletons, and > particularly if there's an easy way to implement it without lots of > special case code each time. I don't forsee too many problems. > > I think the LSID people would point out at this point that > LSIDs should > be permanent, and immutable, always resolving to the same (or > equivalent) entity. If we substitute URN for LSID, then I'm happy - > urn:biojava: or something - I think we're meant to use > urn:x-biojava as > we've not registered the biojava namespace. I'm not sure I follow. My intention would be that they do always resolve to the same object. Although I haven't looked too much into the ontology package so I'm not sure if this is possible. - Mark ======================================================================= 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 matthew_pocock at yahoo.co.uk Fri Nov 7 05:54:29 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri Nov 7 05:57:57 2003 Subject: [Biojava-dev] Re: Flyweight Ontologies? In-Reply-To: References: Message-ID: <3FAB79E5.3060606@yahoo.co.uk> Schreiber, Mark wrote: >>I think the LSID people would point out at this point that >>LSIDs should >>be permanent, and immutable, always resolving to the same (or >>equivalent) entity. If we substitute URN for LSID, then I'm happy - >>urn:biojava: or something - I think we're meant to use >>urn:x-biojava as >>we've not registered the biojava namespace. >> >> > >I'm not sure I follow. My intention would be that they do always resolve to the same object. Although I haven't looked too much into the ontology package so I'm not sure if this is possible. > A particular LSID should resolve for all eternity to the same entity, so by using LSIDs for things like ontologies within a running application, we are implicitly contracting ourselves to have that data available /for ever/, even if it is working data or intermediate results, or if we know we will be changing the schema next week. URNs don't have this restriction. M > >- Mark > >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > > > From mark.schreiber at agresearch.co.nz Mon Nov 10 16:41:32 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Nov 10 16:38:08 2003 Subject: [Biojava-dev] RE: Flyweight Ontologies? Message-ID: >>I think the LSID people would point out at this point that > >>LSIDs should > >>be permanent, and immutable, always resolving to the same (or > >>equivalent) entity. If we substitute URN for LSID, then I'm happy - > >>urn:biojava: or something - I think we're meant to use > >>urn:x-biojava as > >>we've not registered the biojava namespace. > >> > >> > > > >I'm not sure I follow. My intention would be that they do always > >resolve to the same object. Although I haven't looked too > much into the > >ontology package so I'm not sure if this is possible. > > > A particular LSID should resolve for all eternity to the same > entity, so > by using LSIDs for things like ontologies within a running > application, > we are implicitly contracting ourselves to have that data > available /for > ever/, even if it is working data or intermediate results, or > if we know > we will be changing the schema next week. URNs don't have > this restriction. Wouldn't the core Ontology come under that categorie? If not, what form do you think the URN should take? Is there a need for each Term to know which Triple it belongs too or which Ontology? - Mark ======================================================================= 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 matthew_pocock at yahoo.co.uk Tue Nov 11 06:26:12 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Nov 11 06:30:46 2003 Subject: [Biojava-dev] RE: Flyweight Ontologies? In-Reply-To: References: Message-ID: <3FB0C754.8080600@yahoo.co.uk> Hi, The core ontology probably does qualify, perhaps. URN:biojava:ontology/core for the ontology and perhaps URN:biojava:ontology/core|ISA and the like for the terms? URN:biojava:ontolgy/core|relation,has_a,domain for triples? Or we could just give all terms & triples a unique numerical ID somewhere and do # - far to many options. Matthew >>A particular LSID should resolve for all eternity to the same >>entity, so >>by using LSIDs for things like ontologies within a running >>application, >>we are implicitly contracting ourselves to have that data >>available /for >>ever/, even if it is working data or intermediate results, or >>if we know >>we will be changing the schema next week. URNs don't have >>this restriction. >> >> > >Wouldn't the core Ontology come under that categorie? If not, what form do you think the URN should take? Is there a need for each Term to know which Triple it belongs too or which Ontology? > >- Mark >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > > From today at closeout-special.com Tue Nov 11 08:35:58 2003 From: today at closeout-special.com (D. Download) Date: Tue Nov 11 08:32:25 2003 Subject: [Biojava-dev] DVD/CD Duplication in seconds Message-ID: <22$8ehtULlL-Qbl9ehtULlL7tc4@close-1.closeout-special.com> http://www.replicantdvd.com/move.asp?AID=032107&BID=2965 - Copy your DVDs to CD-R. - Watch on Home DVD Players. - No DVD Burner Required. - 100% Money-Back Guarantee. - Free Software Included. Also: Copy PS2 Games, Convert VHS to DVD, Make DVD Slideshows <-- Included for FREE! Download it now: http://www.replicantdvd.com/move.asp?AID=032107&BID=2965 You received this message because you registered at one of the sites in the BluePinstripes Email Network or opted in through one of our partners. If you would prefer to not receive these messages in the future, please http://www.closeout-special.com/unsub.php?e=biojava-dev@biojava.org&m=17040. If there are any problems with this link, reply to this email with 'Remove' in the subject line. Or to unsubscribe via postal mail, please send request to: BluePinstripes Email Network 1140 Highland Ave., Suite #302 Manhattan Beach, CA 90266 Or call 800 361-6439 To read our privacy policy, visit http://www.closeout-special.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org W0]3BwH;FW TM: <2;2qvY45P5-xAPRqvY45P58Y7B;17040> From mark.schreiber at agresearch.co.nz Tue Nov 11 19:32:26 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Tue Nov 11 19:29:03 2003 Subject: [Biojava-dev] RE: Flyweight Ontologies? Message-ID: Whatever your happy with. I think the less numerical option is the better one. Means the URN is more likely to mean something in debugging. I guess it will require getURN methods to be added to the appropriate interfaces. Could you do that? - Mark > -----Original Message----- > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > Sent: Wednesday, 12 November 2003 12:26 a.m. > To: Schreiber, Mark > Cc: biojava-dev@biojava.org > Subject: Re: [Biojava-dev] RE: Flyweight Ontologies? > > > Hi, > > The core ontology probably does qualify, perhaps. > URN:biojava:ontology/core for the ontology and perhaps > URN:biojava:ontology/core|ISA and the like for the terms? > URN:biojava:ontolgy/core|relation,has_a,domain for triples? > Or we could > just give all terms & triples a unique numerical ID somewhere and do > # - far to many options. > > Matthew > > >>A particular LSID should resolve for all eternity to the same > >>entity, so > >>by using LSIDs for things like ontologies within a running > >>application, > >>we are implicitly contracting ourselves to have that data > >>available /for > >>ever/, even if it is working data or intermediate results, or > >>if we know > >>we will be changing the schema next week. URNs don't have > >>this restriction. > >> > >> > > > >Wouldn't the core Ontology come under that categorie? If > not, what form > >do you think the URN should take? Is there a need for each > Term to know > >which Triple it belongs too or which Ontology? > > > >- Mark > >============================================================= > ========== > >Attention: The information contained in this message and/or > attachments > >from AgResearch Limited is intended only for the persons or > entities to > >which it is addressed and may contain confidential and/or privileged > >material. Any review, retransmission, dissemination or other > use of, or > >taking of any action in reliance upon, this information by > persons or > >entities other than the intended recipients is prohibited by > AgResearch > >Limited. If you have received this message in error, please > notify the > >sender immediately. > >============================================================= > ========== > > > >_______________________________________________ > >biojava-dev mailing list > >biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-> dev > > > > > > > > > ======================================================================= 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 matthew_pocock at yahoo.co.uk Wed Nov 12 11:47:29 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Wed Nov 12 11:52:24 2003 Subject: [Biojava-dev] tidying Message-ID: <3FB26421.5090204@yahoo.co.uk> Hi, Can we drop PackedDNASymbolList and unit tests? It's functionality is now covered by PackedSymbolList and friends. I rather stupidly poked arround in .seq.io looking at symbol tokenization (I need to hook up symbol parsing to SAX - don't ask). I will probably add more/better docs to this as I didn't grok it 1st time through. Matthew From publishing at bvimailbox.com Thu Nov 13 01:06:28 2003 From: publishing at bvimailbox.com (C a n p u b) Date: Thu Nov 13 01:02:56 2003 Subject: [Biojava-dev] Press release Message-ID: <200311130602.hAD62kcj023007@portal.open-bio.org> C A N A D I A N S U B S I D Y D I R E C T O R Y 4865 HWY 138,R.R 1 ST-ANDREWS WEST ONTARIO, KOC 2A0 PRESS RELEASE C A N A D I A N S U B S I D Y D I R E C T O R Y Y E A R 2003 EDITION Legal Deposit-National Library of Canada ISBN 2-922870-05-7 The new revised edition of the Canadian Subsidy Directory 2003 is now available. The new edition is the most complete and affordable reference for anyone looking for financial support. It is deemed to be the perfect tool for new or existing businesses, individual ventures, foundations and associations. This Publication contains more than 2000 direct and indirect financial subsidies, grants and loans offered by government departments and agencies, foundations, associations and organisations. In this new 2003 edition all programs are well described. The Canadian Subsidy Directory is the most comprehensive tool to start up a business, improve existent activities, set up a business plan, or obtain assistance from experts in fields such as: Industry, transport, agriculture, communications, municipal infrastructure, education, import-export, labor, construction and renovation, the service sector, hi-tech industries, research and development, joint ventures, arts, cinema, theatre, music and recording industry, the self employed, contests, and new talents. Assistance from and for foundations and associations, guidance to prepare a business plan, market surveys, computers, and much more! The publication $ 69.95, to obtain a copy please call: Ca n a d i a n P u b l i c a t i o n s : 8 6 6 - 3 2 2 - 3 3 7 6 From russell.smithies at xtra.co.nz Thu Nov 13 17:03:19 2003 From: russell.smithies at xtra.co.nz (Russell Smithies) Date: Thu Nov 13 16:59:40 2003 Subject: [Biojava-dev] Ant failing with biojava-live Message-ID: <000b01c3aa31$f3164bf0$853e56d2@lex> I've CVS'ed biojava-live twice this morning and am unable to get most of the Ant tasks to work. The only one that's worked so far is the default build. I checked the build file for the correct task names (they're wrong in the header comments) but none of javadocs-all, docbook, dist etc. targets are working. Is it just me or are others having similar problems. thanx Russell Smithies (un-employed compsci grad looking for work!!!) From matthew_pocock at yahoo.co.uk Fri Nov 14 06:55:59 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri Nov 14 07:01:24 2003 Subject: [Biojava-dev] Ant failing with biojava-live In-Reply-To: <000b01c3aa31$f3164bf0$853e56d2@lex> References: <000b01c3aa31$f3164bf0$853e56d2@lex> Message-ID: <3FB4C2CF.5040109@yahoo.co.uk> What errors are you getting? Matthew Russell Smithies wrote: >I've CVS'ed biojava-live twice this morning and am unable to get most of the >Ant tasks to work. >The only one that's worked so far is the default build. > >I checked the build file for the correct task names (they're wrong in the >header comments) but none of javadocs-all, docbook, dist etc. targets are >working. > >Is it just me or are others having similar problems. > >thanx > >Russell Smithies >(un-employed compsci grad looking for work!!!) > >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > > From hannah at genomes.rockefeller.edu Fri Nov 14 17:35:09 2003 From: hannah at genomes.rockefeller.edu (Hannah Schmidt-Glenewinkel) Date: Fri Nov 14 17:31:32 2003 Subject: [Biojava-dev] reading data from affymetrix files Message-ID: <200311142235.hAEMZAea004468@marge.rockefeller.edu> Hello, could anybody please tell me if there are (and if, which) classes that read data from affymetrix .cel (microarray data) files? Thank you! Hannah Schmidt-Glenewinkel From special at closeout-special.com Sat Nov 15 02:17:03 2003 From: special at closeout-special.com (D. Download) Date: Sat Nov 15 02:13:25 2003 Subject: [Biojava-dev] DVD/CD Duplication in seconds Message-ID: <36$0xbYv4C4-dcC9xbYv4C4UYH8@close-1.closeout-special.com> http://www.replicantdvd.com/move.asp?AID=032107&BID=2965 - Copy your DVDs to CD-R. - Watch on Home DVD Players. - No DVD Burner Required. - 100% Money-Back Guarantee. - Free Software Included. Also: Copy PS2 Games, Convert VHS to DVD, Make DVD Slideshows <-- Included for FREE! Download it now: http://www.replicantdvd.com/move.asp?AID=032107&BID=2965 You received this message because you registered at one of the sites in the BluePinstripes Email Network or opted in through one of our partners. If you would prefer to not receive these messages in the future, please http://www.closeout-special.com/unsub.php?e=biojava-dev@biojava.org&m=34040. If there are any problems with this link, reply to this email with 'Remove' in the subject line. Or to unsubscribe via postal mail, please send request to: BluePinstripes Email Network 1140 Highland Ave., Suite #302 Manhattan Beach, CA 90266 Or call 800 361-6439 To read our privacy policy, visit http://www.closeout-special.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org ~3,,PQENMDE>1c~w TM: <1;9uwbX2m2-sjmYuwbX2m27box;34040> From david.huen at ntlworld.com Sat Nov 15 05:21:49 2003 From: david.huen at ntlworld.com (David Huen) Date: Sat Nov 15 05:18:49 2003 Subject: [Biojava-dev] reading data from affymetrix files In-Reply-To: <200311142235.hAEMZAea004468@marge.rockefeller.edu> References: <200311142235.hAEMZAea004468@marge.rockefeller.edu> Message-ID: <200311151021.50464.david.huen@ntlworld.com> On Friday 14 Nov 2003 10:35 pm, Hannah Schmidt-Glenewinkel wrote: > Hello, > > could anybody please tell me if there are (and if, which) classes that > read data from affymetrix .cel (microarray data) files? > Sorry but we do not currently have the ability to read affymetrix files. Thanks, David Huen From MCCon012 at mc.duke.edu Mon Nov 17 08:58:00 2003 From: MCCon012 at mc.duke.edu (Patrick McConnell) Date: Mon Nov 17 08:54:20 2003 Subject: [Biojava-dev] reading data from affymetrix files Message-ID: I believe that Tigr's TM4 libraries have this capability, but I have not looked at the code myself. http://www.tigr.org/software/tm4/ -Patrick McConnell Duke Binformatics Shared Resource Duke University mccon012@mc.duke.edu Hannah Schmidt-Glenewinkel cc: Sent by: Subject: [Biojava-dev] reading data from affymetrix files biojava-dev-bounces@portal.o pen-bio.org 11/14/2003 05:35 PM Please respond to Hannah Schmidt-Glenewinkel Hello, could anybody please tell me if there are (and if, which) classes that read data from affymetrix .cel (microarray data) files? Thank you! Hannah Schmidt-Glenewinkel _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From sfsfrom1 at yahoo.com Fri Nov 21 01:40:02 2003 From: sfsfrom1 at yahoo.com (Wholesale) Date: Thu Nov 20 19:34:06 2003 Subject: [Biojava-dev] Tobacco Offer *** Message-ID: <200311210034.hAL0Y1cj026980@portal.open-bio.org> Dear sir or Madam, If you are a smoker in the UK, ROI or Scandinavia, please just take a few minutes of your time to read this. If you are not a smoker please accept my apologies for this E mail, it is not my intention to upset anyone. Smokers - are you still paying high street prices for your cigarettes, cigars or rolling/pipe tobacco. For instance, I can send you by registered post, 800 cigarettes for 180 euros. This works out to about ?3.20 a packet (depending on exchange rate). 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If this E mail at all offends you l - that is not my intention ---- YOU WILL NOT BE E MAILED AGAIN Brands supplied including:- B & H, Dunhill, Lamb & But, Silk Cut, Marlboro, JPS, Gitanes, Fortuna, Berkeley, Superkings, Embassy, Regal, St Bruno, Golden Virginia, Old Holborn, Samson, Clan, Vogue, MORE, Kent, Davidoff , Peter Stuyvesant, Gauloises, Sovereign, Lucky Strike, Havana, Monte Cristo, Flor de Cano, Rothmans, Camel etc. http://www.geocities.com/smokesfr1 If you would like to be removed from our database please email the address below with removes in the subject sfsrem@yahoo.com From hr_malmi at hotmail.com Sat Nov 22 00:46:48 2003 From: hr_malmi at hotmail.com (harald malming) Date: Sat Nov 22 00:42:57 2003 Subject: [Biojava-dev] problem building biojava-live Message-ID: hi, I'm having problems building the bio java live repository using ant in both linux and windows. Does anyone have a biojava.jar file buildt quite recently (I need the multiple DotState bug fix) they could mail me or something. cheers, harris _________________________________________________________________ Hotmail snakker ditt språk! http://www.hotmail.msn.com/cgi-bin/sbox?rru=dasp/lang.asp - Få Hotmail på norsk i dag From now at closeout-sale.com Sat Nov 22 06:48:14 2003 From: now at closeout-sale.com (D. Download) Date: Sat Nov 22 06:44:22 2003 Subject: [Biojava-dev] DVD/CD Duplication in seconds Message-ID: <1308$5n3zBrtr-qbtNn3zBrtr9zuO@close-1.closeout-sale.com> http://closeout-sale.com:8080/track?m=2464017&l=0&.e=3J4p9BKB-eTKnJ4p9BKBYpE3 - Copy your DVDs to CD-R. - Watch on Home DVD Players. - No DVD Burner Required. - 100% Money-Back Guarantee. - Free Software Included. Also: Copy PS2 Games, Convert VHS to DVD, Make DVD Slideshows <-- Included for FREE! Download it now: http://closeout-sale.com:8080/track?m=2464017&l=0&.e=7DXUdH5H-KL5IDXUdH5HoUxE You received this message because you registered at one of the sites in the BluePinstripes Email Network or opted in through one of our partners. If you would prefer to not receive these messages in the future, please http://www.closeout-sale.com/unsub.php?e=biojava-dev@biojava.org&m=2464017. If there are any problems with this link, reply to this email with 'Remove' in the subject line. Or to unsubscribe via postal mail, please send request to: BluePinstripes Email Network 1140 Highland Ave., Suite #302 Manhattan Beach, CA 90266 Or call 800 361-6439 To read our privacy policy, visit http://www.closeout-sale.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org 8IE?K{H-eRT#tO89uraz,XAXM4Sb]r(y2SrW]U*/V{^k5u^(Wz TM: <54;7DXUdH5H-KL5IDXUdH5HoUxE;2464017> From matthew_pocock at yahoo.co.uk Mon Nov 24 08:25:17 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Mon Nov 24 08:40:32 2003 Subject: [Biojava-dev] problem building biojava-live In-Reply-To: References: Message-ID: <3FC206BD.9090209@yahoo.co.uk> What problems have you been having? Error messages would help. Matthew harald malming wrote: > hi, I'm having problems building the bio java live repository using > ant in both linux and windows. Does anyone have a biojava.jar file > buildt quite recently (I need the multiple DotState bug fix) they > could mail me or something. > > cheers, > harris > > _________________________________________________________________ > Hotmail snakker ditt spr?k! > http://www.hotmail.msn.com/cgi-bin/sbox?rru=dasp/lang.asp - F? Hotmail > p? norsk i dag > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From shuvankr at hotmail.com Tue Nov 25 01:36:46 2003 From: shuvankr at hotmail.com (Shuvankar Mukherjee) Date: Tue Nov 25 08:23:11 2003 Subject: [Biojava-dev] Error during initializing DNATools through an Applet Message-ID: Hello, While trying out an applet version of "Biojava's in Anger", FeatureTree example. Following error is coming up in AppletViewer, java.lang.ExceptionInInitializerError: java.security.AccessControlException: access denied (java.util.PropertyPermission jaxp.debug read) at java.security.AccessControlContext.checkPermission(AccessControlContext.java:272) at java.security.AccessController.checkPermission(AccessController.java:399) at java.lang.SecurityManager.checkPermission(SecurityManager.java:545) at java.lang.SecurityManager.checkPropertyAccess(SecurityManager.java:1278) at java.lang.System.getProperty(System.java:560) at javax.xml.parsers.SAXParserFactory.(SAXParserFactory.java:271) at org.biojava.bio.symbol.AlphabetManager.loadAlphabets(AlphabetManager.java:915) at org.biojava.bio.symbol.AlphabetManager.(AlphabetManager.java:894) at org.biojava.bio.seq.DNATools.(DNATools.java:54) rethrown as org.biojava.bio.BioError: Unable to initialize DNATools at org.biojava.bio.seq.DNATools.(DNATools.java:85) at org.biojava.bio.seq.io.SeqIOTools.getDNAParser(SeqIOTools.java:907) at org.biojava.bio.seq.io.SeqIOTools.readGenbank(SeqIOTools.java:115) at org.biojava.bio.seq.io.SeqIOTools.fileToSeq(SeqIOTools.java:1025) at org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:820) at org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:787) at GenomeApplet.init(GenomeApplet.java:34) at sun.applet.AppletPanel.run(AppletPanel.java:344) at java.lang.Thread.run(Thread.java:484) Could you advise, I had already changed the java.policy file to grant the permission. but the error remains. Thanking you, Shuvankar Mukherjee -------------- next part -------------- An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biojava-dev/attachments/20031125/2fea39bc/attachment-0001.htm From verhoeff2 at gis.a-star.edu.sg Thu Nov 27 00:39:17 2003 From: verhoeff2 at gis.a-star.edu.sg (VERHOEF Frans) Date: Thu Nov 27 12:23:09 2003 Subject: [Biojava-dev] Bug in PhredFormat?? Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D560B0428@BIONIC.biopolis.one-north.com> Hi, I think I might have discovered a little bug. I used the latest version from CVS. This is what I tried to do: StreamReader qualityIter = PhredTools.readPhredQuality( new BufferedReader( new FileReader( qualityFile ) ) ); Where qualityFile is a File object pointing to an existing phred quality-score fasta file. It compiles fine, but when I run it I get the following Exception: Exception java.lang.ClassCastException at org.biojava.bio.seq.io.StreamReader.(StreamReader.java:130) at org.biojava.bio.program.phred.PhredTools.readPhredQuality(PhredTools.jav a:234) at org.gis.server.pipeline.apps.SequenceInfoParser.parseResults(SequenceInf oParser.java:67) at org.gis.server.pipeline.apps.SequenceInfoParser.start(SequenceInfoParser .java:52) at org.gis.server.pipeline.apps.SequenceInfoParser.main(SequenceInfoParser. java:133) When checking the line 130 in StreamReader I find the following line: ((org.biojava.utils.ParseErrorSource)(this.format).addParseErrorListener (this); Where format is a PhredFormat class. When checking out PhredFormat, I did find out that PhredFormat is not implementing the ParseErrorSource. So I assume implementing the ParseErrorSource for PhredFormat would solve the problem. If you want I can do it myself, though I do not have a cvs account. Kind regards, Frans Verhoef Bioinformatics Specialist Genome Institute of Singapore Genome, #02-01, 60 Biopolis Street, Singapore 138672 Tel: +65 6478 8000 DID: +65 6478 8060 HP: +65 9848 4325 Email: verhoeff2@gis.a-star.edu.sg -------------- next part -------------- An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biojava-dev/attachments/20031127/c2b3885c/attachment.htm From verhoeff2 at gis.a-star.edu.sg Thu Nov 27 04:14:30 2003 From: verhoeff2 at gis.a-star.edu.sg (VERHOEF Frans) Date: Thu Nov 27 12:23:10 2003 Subject: [Biojava-dev] PhredFormat problems Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D560B0429@BIONIC.biopolis.one-north.com> Hi, I've got some issues with the PhredFormat class. In the readSequenceData(BufferedReader, SymbolTokenization, SeqIOListener ) method, a quality sequence is read and parsed into the individual quality scores. Those individual scores are each given to WordStreamParser (in the file WordTokenization) through the characters method, which is pasting all the scores in a StringBuffer. However, the spaces in between the quality scores are disappearing in the process. When the close() method of WordStreamParser is called, it is trying to do parse the quality score StringBuffer again, but since there are no spaces in between the different values, it cannot parse it, with as a result that once it tries to convert the string to an integer, it has a problem because the number is huge. So I assume the readSequenceData should not parse the quality sequence string, but just hand the WordStreamParser the complete String. Am I right? Can anyone still follow me?? ;-) I also wonder whether anyone is using the phred classes. Kind regards, Frans Verhoef Bioinformatics Specialist Genome Institute of Singapore Genome, #02-01, 60 Biopolis Street, Singapore 138672 Tel: +65 6478 8000 DID: +65 6478 8060 HP: +65 9848 4325 Email: verhoeff2@gis.a-star.edu.sg -------------- next part -------------- An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biojava-dev/attachments/20031127/5a1851f3/attachment.htm From mark.schreiber at agresearch.co.nz Thu Nov 27 15:18:08 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Thu Nov 27 15:24:39 2003 Subject: [Biojava-dev] Bug in PhredFormat?? Message-ID: Hi Frans - I might be responsible for this. I haven't used the PhredFormat for a while so this may have gone unoticed. I will fix it up as soon as I get back to my main machine (after the weekend). Alternatively if you want to post a fix to the list I'm sure someone can add it to CVS for you. Thanks Mark -----Original Message----- From: VERHOEF Frans [mailto:verhoeff2@gis.a-star.edu.sg] Sent: Thursday, 27 November 2003 6:39 p.m. To: biojava-dev@biojava.org Subject: [Biojava-dev] Bug in PhredFormat?? Hi, I think I might have discovered a little bug. I used the latest version from CVS. This is what I tried to do: StreamReader qualityIter = PhredTools.readPhredQuality( new BufferedReader( new FileReader( qualityFile ) ) ); Where qualityFile is a File object pointing to an existing phred quality-score fasta file. It compiles fine, but when I run it I get the following Exception: Exception java.lang.ClassCastException at org.biojava.bio.seq.io.StreamReader.(StreamReader.java:130) at org.biojava.bio.program.phred.PhredTools.readPhredQuality(PhredTools.jav a:234) at org.gis.server.pipeline.apps.SequenceInfoParser.parseResults(SequenceInf oParser.java:67) at org.gis.server.pipeline.apps.SequenceInfoParser.start(SequenceInfoParser .java:52) at org.gis.server.pipeline.apps.SequenceInfoParser.main(SequenceInfoParser. java:133) When checking the line 130 in StreamReader I find the following line: ((org.biojava.utils.ParseErrorSource)(this.format).addParseErrorListener (this); Where format is a PhredFormat class. When checking out PhredFormat, I did find out that PhredFormat is not implementing the ParseErrorSource. So I assume implementing the ParseErrorSource for PhredFormat would solve the problem. If you want I can do it myself, though I do not have a cvs account. Kind regards, Frans Verhoef Bioinformatics Specialist Genome Institute of Singapore Genome, #02-01, 60 Biopolis Street, Singapore 138672 Tel: +65 6478 8000 DID: +65 6478 8060 HP: +65 9848 4325 Email: verhoeff2@gis.a-star.edu.sg ======================================================================= 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 isiomawilly2000 at netscape.net Thu Nov 27 23:08:37 2003 From: isiomawilly2000 at netscape.net (Dr Isioma Williams) Date: Thu Nov 27 23:15:18 2003 Subject: [Biojava-dev] HELLO Message-ID: <200311280415.hAS4Eqg0013653@portal.open-bio.org> from the desk of : DR ISIOMA WILLIAMS DIRECT TEL: 234-1-776 2501 (24HRS) TEL: 234-1-804 4824 FAX: 234-1-759 2574 EMAIL: isiomaw@yahoo.com.au STRICTLY CONFIDENTIAL WE ARE MEMBERS OF A SPECIAL COMMITTEE ON PROJECT IMPLEMENTATION OF THE NIGERIAN NATIONAL PETROLEUM CORPORATION (NNPC). THIS COMMITTEE IS PRINCIPALLY CONCERNED WITH CONTRACT AWARDS AND APPROVAL. WITH OUR POSITIONS, WE HAVE SUCCESSFULLY SECURED FOR OURSELVES THE SUM OF SIXTEEN MILLION, FIVE HUNDRED THOUSAND UNITED STATES DOLLARS (US$16.5M). MY COLLEAGUES AND I DURING THE COURSE OF OUR OFFICIAL ASSIGNMENT AWARDED SERIES OF CONTRACTS TO FOREIGN FIRMS ON AGREED 5% COMMISSION OR PROFIT ON THEIR CONTRACT SUM. HOWEVER THE 5% COMMISSION WHICH AMOUNTED TO US$16.5M AFTER AUDIT REPORT IS LEFT UNCLAIMED IN THE FLOATING ACCOUNT OF MY COMPANY [NNPC]. THIS CONTRACT IN QUESTION WERE FOR THE SUPPLY OF PETRO CHEMICAL EQUIPMENT AND COMPUTERS TO MY COMPANY THE NIGERIAN NATIONAL PETROLEUM CORPORATION [NNPC] IN 1999. THE CONTRACTORS HAVE EXECUTED THEIR PROJECT AS SPECIFIED IN THE CONTRACT AGREEMENT AND WERE PAID ACCORDINGLY. RECENTLY, THE NEW CIVILIAN GOVERNMENT STARTED PAYING OFF ALL THE INDEBTED FOREIGN CONTRACTORS TO MY COMPANY THAT EXECUTED CONTRACTS AS FAR BACK AS 1990 2002 IN ORDER TO LAUNDER A GOOD IMAGE OF THEIR GOVERNMENT BEFORE THE UNITED NATION. CONSEQUENT TO THIS DEVELOPMENT, WE CONSIDER THIS A GREAT OPPORTUNITY FOR US TO CARRYOUT THE TRANSFER OF THESE FUNDS TO A SAFE ACCOUNT OVERSEAS WHICH WE BELIEVE YOU WILL BE IN A POSITION TO HELP US IN TRANSFERRING THESE FUNDS [US$16.5M] INTO YOUR NOMINATED ACCOUNT. IT HAS BEEN AGREED THAT THE OWNER OF THE ACCOUNT WILL BE COMPENSATED WITH 20% OF THE REMITTED FUNDS, WHILE WE KEEP 70%, AND 10% WILL BE SET ASIDE TO OFFSET EXPENSES AND PAY THE NECESSARY TAXES. ALL MODALITIES OF THIS TRANSACTION HAVE BEEN WORKED OUT AND ONCE STARTED WILL NOT TAKE MORE THAN 10 WORKING DAYS, WITH YOUR FULL SUPPORT. THIS TRANSACTION IS 100% RISK FREE.IF THIS PROPOSAL SATISFIES YOU, PLEASE REACH US ONLY BY FAX OR PHONE, FOR MORE INFORMATION. IT MIGHT BE DIFFICULT TO GET THROUGH TO ME, BECAUSE OF POOR TELECOMMUNICATION SYSTEM HERE. PLEASE KEEP TRYING, YOU WILL DEFINITELY GET THROUGH. PLEASE TREAT AS URGENT AND VERY CONFIDENTIAL. YOURS FAITHFULLY, DR ISIOMA WILLIAMS NB: FOR CONFIDENTIAL REASONS AND DUE TO THE POOR COMMUNICATION SYSTEM IN MY COUNTRY, MOST OFTEN FOREIGN CALLS COULD BE DIVERTED TO THE WRONG PERSON. SO, FOR YOU TO BE VERY SURE YOU ARE RIGHTLY SPEAKING WITH ME, IT IS VERY IMPORTANT THAT WHEN YOU CALL AND ASK FOR ME, THE MOMENT I PICK UP THE PHONE, YOU SHOULD ASK ME FOR THE "CODE WORD" AND MY ANSWER WOULD BE "SUCCESS" BEFORE WE PROCEED DISCUSSIONS, BUT IF I DO NOT SAY"SUCCESS", THAT MEANS YOU ARE NOT SPEAKING WITH ME JUST DISCONNECT THE LINE AND CALL ME BACK TILL I GIVE YOU THE CODE WORD. From shuvankr at hotmail.com Fri Nov 28 02:09:00 2003 From: shuvankr at hotmail.com (Shuvankar Mukherjee) Date: Fri Nov 28 02:09:05 2003 Subject: [Biojava-dev] Error in using GenBankSequenceDB Message-ID: Hi, While using org.biojava.bio.seq.db.GenbankSequenceDB for on-line download of sequences following functions are giving errors: getSequence(String s); and getSequences(java.util.Set); The URL s are getting properly constructed, but since getSequence() displays the constructed URL (it is tested on the IE and giving complete outout). It is unable to parse the data, and giving a parsing exception, after quite a long time... getSequences(Set) is giving multiple lines of parsing exception, and ultimately throws "Out Of Memory" error. Could any one comment / suggest a way out for online sequence fetching. Shuvankar Mukherjee From verhoeff2 at gis.a-star.edu.sg Thu Nov 27 22:34:07 2003 From: verhoeff2 at gis.a-star.edu.sg (VERHOEF Frans) Date: Fri Nov 28 12:25:07 2003 Subject: [Biojava-dev] PhredFormat Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D560B0694@BIONIC.biopolis.one-north.com> Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: PhredFormat.java Type: application/octet-stream Size: 9750 bytes Desc: PhredFormat.java Url : http://portal.open-bio.org/pipermail/biojava-dev/attachments/20031128/65d8a81b/PhredFormat.obj From dr_edward2003okon at spinfinder.com Fri Nov 28 16:26:58 2003 From: dr_edward2003okon at spinfinder.com (Dr Edward Okon) Date: Fri Nov 28 16:35:08 2003 Subject: [Biojava-dev] Urgent message from Dr Edward Okon Message-ID: <200311282133.hASLWfg0018132@portal.open-bio.org> Sir, REQUEST FOR BUSINESS PARTNERSHIP INTRODUCTION & BIO-DATA I am Dr Edward Okon Chairman Ministerial Contracts Evaluation and Implementation Committee in the Federal Ministry of Aviation. My position is very sensitive. I am married with children and hold degrees in Public Administration and Medical Studies. I am due for retirement any moment from now, after many years in service. REASONS FOR CONTACTING YOU I require urgently, your unreserved assistance in providing me with a safe and reliable bank account with full details viz: Name and Address of Bank, Telephone, Telex and Fax numbers anywhere in the world where I can transfer the sum of $27.5Million United States Dollars only. The purpose of transfer is to take care of my retirement by investing in viable business you might deem fit to advise. NATURE OF BUSINESS AND SOURCE OF FUNDS FOR TRANSFER Since the inception of the present government, series of contracts have been awarded by the Federal Ministry of Aviation based on supplies (AIRPORT NAVIGATIONAL ELECTRONICS), INSTRUMENT LANDING EQUIPMENT (ILE),AND RADAR EQUIPMENT, VOR SYSTEMS MONITORS/ DISTANCE MEASURING EQUIPMENT (DME), SECONDARY SURVEILLANCE RADAR (SSR), INSTALLATION OF ONE UNIT OF INSRUMENT, LANDING SYSTEMS AND RADAR EQUIPMENT at Abuja International Airport) amounting to several millions of US Dollars. The above sum (US$27.5M) has shown in record as surplus some of the over-invoiced contracts carried in the last developmental quarter. Presently, I have arranged for the money to be kept in a coded bank account with the Central Bank of Nigeria, until I am able to source for a reliable Expatriate Partner whom I can present as the beneficiary of the funds. You will take the status of the contractor who executed the contract, and I will arrange the supportive documents for the transfer. MODE OF SHARING 25% will go to you for making available to us a company or personal account number, giving me your unreserved assistance and keeping strictly the rules of this transaction until transfer of the funds is effected. 5% is for any contingencies and all miscellaneous expenses incurred during the course of the transaction, procurement of vital documents, tips and all expenses including phones/ fax bills, hotels bills, taxes and bank charges must be reconciled upon confirmation of the payment by the DEBT MANAGEMENT OFFICE (DMO) OF THE PRESIDENCY 70% will be shared between me and a few colleagues of mine whose help will be highly needed throughout this period in question. OTHER PERTINENT DETAILS Everything about this transaction is real. The money is clean, after putting in so many years in service, it is only normal for me to take good measures to secure my period in retirement. I have put in resources and time to bring this transaction to this level, which means that it represents a lot to me, and hopefully with help from you, in just a matter of weeks, it shall come to mean a lot to you too as we meet in your country to celebrate the closing of the deal. Kindly acknowledge your willingness through my private email:(dr_edward2003okon@pathfinder.gr)t to enable us commence effective process to finalize this matter. Thanking you for anticipated co-operation. Yours sincerely, Dr Edward Okon Chairman of the Committee. From mark.schreiber at agresearch.co.nz Sun Nov 30 17:19:12 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Sun Nov 30 17:25:47 2003 Subject: [Biojava-dev] PhredFormat Message-ID: Hi Frans - Thanks for these changes. I have committed them to cvs and added "default" as a valid tokenization of IntegerAlphabet (as a synonym of "token"). - Mark -----Original Message----- From: VERHOEF Frans [mailto:verhoeff2@gis.a-star.edu.sg] Sent: Friday, 28 November 2003 4:34 p.m. To: biojava-dev@biojava.org; biojava-l@biojava.org Subject: [Biojava-dev] PhredFormat Hi, I have fixed the little bugs in PhredFormat bugging me for the last 2 days. I have attached the version fixed by me. Feel free to use it, change it or throw it. In short what I have changed is this: - PhredFormat implements ParseErrorSource and ParseErrorListener. This was not much of a job, as I basically copied it from FastaFormat. - readSequenceData(BufferedReader br, SymbolTokenization parser, SeqIOListener listener) has changed. This method used to parse char arrays for short number strings and feed it to the StreamParser, which in turn would try to do the same. As in the process the whitespaces were removed, in the end a String representing a humongous number was tried to be parsed to integer. Now this method does not parse the char arrays, but just feeds whole chunks of char array to the StreamParser. One new issue came up though, when I am trying to do the following: StreamReader qualityIter = PhredTools.readPhredQuality(new BufferedReader(new FileReader(phredQualityFile))); While (qualityIter.hasNext()){ Sequence seq = qualityIter.nextSequence(); String str = seq.seqString(); } The last line gave the following exception: java.util.NoSuchElementException: default parser not supported by IntegerAlphabet yet at org.biojava.bio.symbol.IntegerAlphabet.getTokenization(IntegerAlphabet.java:216) at org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:101) at org.biojava.bio.seq.impl.SimpleSequence.seqString(SimpleSequence.java:108) at org.gis.server.pipeline.apps.SequenceInfoParser.parseResults(SequenceInfoParser.java:82) What happens is that SimpleSequence calls the AbstractSymbolList.seqString() method. This method in turn executes getAlphabet().getTokenization("default"), where getAlphabet returns the IntegerAlphabet. But IntegerAlphabet throws the Exception here, because it only except a name parameter value "token" and not the "default" that AbstractSymbolList gives. I do have simple workaround, that basically where the method IntegerAplhabet.getTokenization(String name) accepts both "default" and "token". But I am not sure I here understand the philosophy behind the design completely... Kind regards, Frans Verhoef Bioinformatics Specialist Genome Institute of Singapore Genome, #02-01, 60 Biopolis Street, Singapore 138672 Tel: +65 6478 8000 DID: +65 6478 8060 HP: +65 9848 4325 Email: verhoeff2@gis.a-star.edu.sg ======================================================================= 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. =======================================================================