From mark.schreiber at agresearch.co.nz Mon Dec 1 15:46:23 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Dec 1 15:52:54 2003 Subject: [Biojava-dev] Error in using GenBankSequenceDB Message-ID: Hi - Could you give the ID of the sequence you are trying to extract and the stack trace you get back? - Mark > -----Original Message----- > From: Shuvankar Mukherjee [mailto:shuvankr@hotmail.com] > Sent: Friday, 28 November 2003 8:09 p.m. > To: biojava-dev@biojava.org > Subject: [Biojava-dev] Error in using GenBankSequenceDB > > > 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 > > > _______________________________________________ > 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 GDennis at niaid.nih.gov Mon Dec 1 17:45:14 2003 From: GDennis at niaid.nih.gov (Dennis, Glynn (NIH/NIAID)) Date: Mon Dec 1 17:51:35 2003 Subject: [Biojava-dev] Participation Message-ID: I would like to discuss with you how we might be able to contribute to BioJava. We develop applications (in java) that facilitate the biological interpretation of functional genomic data sets, such as those derived from microarrays and proteomics. We have several parsers and analysis modules that we would consider including in BioJava as part of a larger goal of open source code for dealing with functional genomic data analysis. Please let me know your level of interest and advise towards a next step. Best, Glynn Dennis Jr., Ph.D. LIB/CSP/NIAID SAIC-Frederick, Inc. NCI-FCRDC P.O. Box B Frederick, MD 21702-1201 Wk: 301-846-7114; 301-846-1910 Hm: 301-964-2638 web: www.DAVID.niaid.nih.gov From mark.schreiber at agresearch.co.nz Mon Dec 1 18:02:14 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Dec 1 18:08:39 2003 Subject: [Biojava-dev] Participation Message-ID: Hi - Biojava has some limited proteomics classes (org.biojava.bio.proteomics) but more would be good. Also some micro-array analsysis / parsing tools would be very useful and we don't have any right now although there are some bare bones of a mage lite api at http://cvs.biojava.org/cgi-bin/viewcvs/viewcvs.cgi/biojava-exptl/src/org/biojava/bio/expression/magelite/?cvsroot=biojava which michael heuer coded up. I'm not sure of the status of these though. If you can see an opportunity for some of your code to be integrated I think we would be keen. Generally we try and design by interface to give room for multiple implementations and it would be nice if anything you submit has javadocs and preferably unit tests and really great if you could provide a demo! - Mark > -----Original Message----- > From: Dennis, Glynn (NIH/NIAID) [mailto:GDennis@niaid.nih.gov] > Sent: Tuesday, 2 December 2003 11:45 a.m. > To: 'biojava-dev@biojava.org' > Subject: [Biojava-dev] Participation > > > I would like to discuss with you how we might be able to > contribute to BioJava. We develop applications (in java) > that facilitate the biological interpretation of functional > genomic data sets, such as those derived from microarrays and > proteomics. We have several parsers and analysis modules > that we would consider including in BioJava as part of a > larger goal of open source code for dealing with functional > genomic data analysis. > > Please let me know your level of interest and advise towards > a next step. > > Best, > > Glynn Dennis Jr., Ph.D. > LIB/CSP/NIAID > SAIC-Frederick, Inc. > NCI-FCRDC P.O. Box B > Frederick, MD 21702-1201 > Wk: 301-846-7114; 301-846-1910 > Hm: 301-964-2638 > web: www.DAVID.niaid.nih.gov > > _______________________________________________ > 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 smh1008 at cus.cam.ac.uk Mon Dec 1 18:02:39 2003 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Mon Dec 1 18:09:09 2003 Subject: [Biojava-dev] Participation In-Reply-To: Message-ID: On Mon, 1 Dec 2003, Dennis, Glynn (NIH/NIAID) wrote: > I would like to discuss with you how we might be able to contribute to > BioJava. We develop applications (in java) that facilitate the biological > interpretation of functional genomic data sets, such as those derived from > microarrays and proteomics. We have several parsers and analysis modules > that we would consider including in BioJava as part of a larger goal of open > source code for dealing with functional genomic data analysis. > > Please let me know your level of interest and advise towards a next step. > I would be happy to discuss the inclusion of the code you have developed. I speak for myself (of course!) but I think the following statemets probably reflect the views of most developers here. As you probably already know, BioJava is LGPL-licenced - this was chosen to avoid "virally" infecting applications that users of the code might wish to develop while maintaining copyleft on the library itself. I do not envisage LGPL restricting your continued use and even commercialisation of your own code since you are still the original copyright holders. The sequence model in BioJava may seem strange at first sight but it does have the merit of being extendable to arbitrary sequence types and also being strongly typed. If your code has references to sequences and locations on sequences, those parts may need some reworking to get good interoperability with the rest of the code. We could do with considerable strengthening in the functional genomics area and any assistance and gifts of code will be warmly welcomed. Regards, David Huen From smh1008 at cus.cam.ac.uk Mon Dec 1 18:07:43 2003 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Mon Dec 1 18:14:00 2003 Subject: [Biojava-dev] Participation In-Reply-To: Message-ID: Just to add further that if you want to discuss any particular issues real-time, some of the developers here can be found on IRC at irc.freenode.net:6667 channel: #biojava This is particularly true during UK waking hours (0900-2300 hrs GMT). Regards, David Huen From mark.schreiber at agresearch.co.nz Mon Dec 1 20:18:50 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Dec 1 20:25:15 2003 Subject: [Biojava-dev] Announce: BioJava1.3.1 released Message-ID: Hi All - The biojava 1.3.1 release has finally been posted to the biojava website and is obtainable from http://biojava.org/download/ This represents an interim release that is partway between biojava1.3 and biojava-live (from which the biojava1.4 release will be built). Your xmas present has arrived early this year :) This release features: * lots of bug fixes from the main branch * Faster GUI rendering code * Some new GUI code for circular sequence rendering * Lots of bug fixes to improve SeqIO from flatfiles esp the protein based sequences * Improved Serialization support (esp for Protein based sequences) * LSID naming of core symbols to allow unambiguous deserialization * Bug fixes to HMM/ DP code that prevent continuous loops when training profile HMMs * Improved CircularLocation API * Other stuff I have forgotten One nice thing is that there have been very few changes or breaks to the API. The only thing that a few people may notice is that SimpleSequence and ViewSequence are now in org.biojava.bio.seq.impl. The recommended way of accessing these from now on is to use SequenceTools. This is in line with what happens in biojava-live. Another change that almost no-one will notice unless they provide custom alphabets via XML files is that Symbols named in these files must now use a full LSID as there name (see AlphabetManager.xml for examples). If you make these changes everything else will work fine. Known Issues: * At the time of writing the output of Sequences in SwissProt and GenPept format is weak * Biojava 1.3.1 only supports the Capetown version of the OBDA protocols. If you need more up to date support use biojava-live * Theres bound to be other stuff so make sure you test your programs! Details: Java Docs are at http://biojava.org/download/docs/ in both tar.gz and zip format Binaries are at http://biojava.org/download/binaries/ in jar format Source is at http://biojava.org/download/source/ in both tar.gz and zip format Future Releases: At this stage the future of the biojava 1.3.x branch is unclear. It will probably pick up a few more bugfixes but it is increasingly hard to incorporate everything from the main branch especially parts that have dependencies on new functionality such as the ontology package. My personal prefence is to vastly increase the converage of the unit tests in biojava-live and aim to have regular stable releases from the live branch (in line with the XP approach to programming). We'll see what happens. Anyhow there will probably be a 1.3.2 release at least before a 1.4 arrives. Finally: A big thanks to everyone who contributed code and told use when it didn't work. A lot of the bug fixes came about due to an increasing number of people using parts of the API that don't often get used in anger. This is encouraging as it means people actually seem to be interested and find biojava useful and are prepared to help identify and often help to fix bugs. Enjoy! - 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 len at reeltwo.com Mon Dec 1 21:04:16 2003 From: len at reeltwo.com (Len Trigg) Date: Mon Dec 1 21:10:41 2003 Subject: [Biojava-dev] GFF/GTF output format. Message-ID: Hi guys, I'm writing GFF files for use with Eval (http://genes.cs.wustl.edu/~bio/eval/main.html). It comes with a GTF validator, which threw up a couple of warnings about the GFF produced by our GFFWriter. They expect the attributes section to contain a trailing semicolon, and are a bit pickier about when text attribute values are quoted. If no-one has any objections, I'll fix this so the output validates (if you've got your own parsers that depend on the current behaviour, they could conceivably break). Cheers, Len. From macuchi62 at mail15.com Mon Dec 1 22:10:23 2003 From: macuchi62 at mail15.com (macuchi62@mail15.com) Date: Mon Dec 1 22:16:41 2003 Subject: [Biojava-dev] ATTENTION Message-ID: ENGR. MAC UCHI TEL/FAX-234-80-23692412. E-MAIL: macuchi4041@zwallet.com Dear Sir, RE: TRANSFER OF US$26. 4M (TWENTY -SIX MILLION,FOUR HUNDRED THOUSAND UNITED STATES DOLLARS ) INTO YOUR NOMINATED ACCOUNT. First, I must solicit your strictest confidence in this transaction, this is by virtue of its nature as being utterly confidential and top secret. We are top officials of the Nigerian National Petroleum Corporation ( NNPC ) and members of an ad hoc committee set up by the Federal Government of Nigeria to review contracts awarded by the past military administration. The members of the committee, are basically interested in the importation of goods into the country with fund which is presently floating in the Central Bank of Nigeria. This fund resulted from grossly over-invoiced contracts which were executed for the NNPC during the last administration. It was alleged that top government officials set up companies and awarded themselves these contracts. As a result, the present administration set up this committee to identify, scrutinize and recommend for payment of all valid contracts that have been fully executed. In the course of our duty, we identified a lot of misappropriated and inflated funds which are presently trapped in the Central Bank of Nigeria ready for payment. The companies that executed the contracts have been duly paid. I have therefore been mandated as a matter of trust by my colleagues in the panel to look for an overseas partner into whose account we could transfer the sum of US$24. 6 M ( Twenty - six Million Four Hundred Thousand US Dollars) We have agreed that the fund will be shared thus after it has been remitted into your account: 1. 30% of the money will go to you for acting as the beneficiary of the fund. 2. 10% has been set aside for reimbursement to both parties for incidental expences that may be incurred in the course of the transactions. 3. 60% to us the Government Officials. ( with which we wish to commence an importation business ). To confide in you, Sir, all logistics are in place and all modalities have been worked out with some top Officials of the Ministry of Finance and the Central Bank of Nigeria to facilitate the smooth remittance of the amount into your account within ten to twelve days of receiving the following information from you on my personal email: macuchi4041@zwallet.com 1. Bankers Name, Address, Bank Account Number, Telephone, Fax and Telex Numbers. 2. Your Company's Name, Address, Company's Details and Activities, Telephone and Fax Numbers. This information will enable us make applications and lodge claims to the concerned Government Ministries and Agencies in favour of your company. It is pertinent to state here that this transaction is entirely based on trust since this money is going to be paid into your account. Please acknowledge the receipt of this letter using the above email. I will bring you into the complete picture of this project when I have heard from you. Best regards, ENGR. MAC UCHI From matthew_pocock at yahoo.co.uk Tue Dec 2 06:51:30 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Dec 2 07:08:47 2003 Subject: [Biojava-dev] Announce: BioJava1.3.1 released In-Reply-To: References: Message-ID: <3FCC7CC2.5060209@yahoo.co.uk> I'd like to take this opportunity to thank you, Mark, for managing the 1.3 branch. We must get you beer. Matthew Schreiber, Mark wrote: >Hi All - > >The biojava 1.3.1 release has finally been posted to the biojava website and is obtainable from http://biojava.org/download/ This represents an interim release that is partway between biojava1.3 and biojava-live (from which the biojava1.4 release will be built). Your xmas present has arrived early this year :) > >This release features: > >* lots of bug fixes from the main branch >* Faster GUI rendering code >* Some new GUI code for circular sequence rendering >* Lots of bug fixes to improve SeqIO from flatfiles esp the protein based sequences >* Improved Serialization support (esp for Protein based sequences) >* LSID naming of core symbols to allow unambiguous deserialization >* Bug fixes to HMM/ DP code that prevent continuous loops when training profile HMMs >* Improved CircularLocation API >* Other stuff I have forgotten > >One nice thing is that there have been very few changes or breaks to the API. The only thing that a few people may notice is that SimpleSequence and ViewSequence are now in org.biojava.bio.seq.impl. The recommended way of accessing these from now on is to use SequenceTools. This is in line with what happens in biojava-live. > >Another change that almost no-one will notice unless they provide custom alphabets via XML files is that Symbols named in these files must now use a full LSID as there name (see AlphabetManager.xml for examples). If you make these changes everything else will work fine. > >Known Issues: > >* At the time of writing the output of Sequences in SwissProt and GenPept format is weak >* Biojava 1.3.1 only supports the Capetown version of the OBDA protocols. If you need more up to date support use biojava-live >* Theres bound to be other stuff so make sure you test your programs! > >Details: > >Java Docs are at http://biojava.org/download/docs/ in both tar.gz and zip format >Binaries are at http://biojava.org/download/binaries/ in jar format >Source is at http://biojava.org/download/source/ in both tar.gz and zip format > >Future Releases: > >At this stage the future of the biojava 1.3.x branch is unclear. It will probably pick up a few more bugfixes but it is increasingly hard to incorporate everything from the main branch especially parts that have dependencies on new functionality such as the ontology package. My personal prefence is to vastly increase the converage of the unit tests in biojava-live and aim to have regular stable releases from the live branch (in line with the XP approach to programming). We'll see what happens. Anyhow there will probably be a 1.3.2 release at least before a 1.4 arrives. > >Finally: > >A big thanks to everyone who contributed code and told use when it didn't work. A lot of the bug fixes came about due to an increasing number of people using parts of the API that don't often get used in anger. This is encouraging as it means people actually seem to be interested and find biojava useful and are prepared to help identify and often help to fix bugs. > >Enjoy! > >- 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 tvavouri at hotmail.com Tue Dec 2 07:04:15 2003 From: tvavouri at hotmail.com (Tanya Vavouri) Date: Tue Dec 2 07:10:36 2003 Subject: [Biojava-dev] WeightMatrixAnnotator Message-ID: Hi, I've made some really simple changes to the latest WeightMatrixAnnotator that have allowed me to annotate sequences with multiple weight matrices. Basically, I've just added an extra variable the String wmID, a constructor that initialises with a user specified weight matrix ID and a getter/setter for the weight matrix ID. The changes are really simple but below is the code if anyone is interested to use it or add it to biojava. Thanks Tanya Vavouri package org.biojava.bio.dp; import java.io.Serializable; import org.biojava.bio.BioException; import org.biojava.bio.SimpleAnnotation; import org.biojava.bio.seq.Feature; import org.biojava.bio.seq.Sequence; import org.biojava.bio.seq.SequenceAnnotator; import org.biojava.bio.seq.impl.ViewSequence; import org.biojava.bio.symbol.IllegalAlphabetException; import org.biojava.bio.symbol.RangeLocation; import org.biojava.utils.ChangeVetoException; /** * Annotates a sequence with hits to a weight-matrix. * *

* This SequenceAnnotator implementation returns a new * ViewSequence wrapping the underlying Sequence *

* * @author Matthew Pocock * @author Thomas Down */ public class WeightMatrixAnnotator implements SequenceAnnotator, Serializable { private WeightMatrix matrix; private double threshold; private final ScoreType scoreType; private String wmID; public Sequence annotate(Sequence seq) throws IllegalAlphabetException, BioException, ChangeVetoException { seq = new ViewSequence(seq); int cols = matrix.columns(); Feature.Template template = new Feature.Template(); template.source = "WeightMatrixAnnotator"; template.type = wmID; for(int offset = 1; offset <= seq.length() - cols + 1; offset++) { double score = DP.scoreWeightMatrix(matrix, seq, scoreType, offset); double q = Math.exp(score); if(q >= threshold) { template.location = new RangeLocation(offset, offset+cols-1); SimpleAnnotation ann = new SimpleAnnotation(); ann.setProperty("score", new Double(q)); ann.setProperty("weightMatrix", matrix); template.annotation = ann; seq.createFeature(template); } } return seq; } /** * Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix. * * @param wm the weight matrix * @param threshold the threshold * @param wmID the weight matrix ID */ public WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold, String wmID) { this.matrix = wm; this.threshold = threshold; this.scoreType = ScoreType.PROBABILITY; this.wmID = wmID; } /** * Create a new annotator that uses PROBABILITY score type. * * @param wm a WeightMatrix value * @param threshold a double value */ public WeightMatrixAnnotator(WeightMatrix wm, double threshold) { this(wm, ScoreType.PROBABILITY, threshold, "hit"); } /** * Create a new annotator that uses a specific score type. * * @param wm the weigth matrix * @param scoreType the score type * @param threshold the threshold * @since 1.4 */ public WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold) { this.matrix = wm; this.scoreType = scoreType; this.threshold = threshold; this.wmID = "hit"; } /** * Get the value of the weight matrix id. * @return value of the weight matrix id. */ public String getWmID() { return wmID; } /** * Set the weight matrix id. * @param v Value to assign to the weight matrix id. */ public void setWmID(String v) { this.wmID = v; } } _________________________________________________________________ Tired of 56k? Get a FREE BT Broadband connection http://www.msn.co.uk/specials/btbroadband From mark.schreiber at agresearch.co.nz Tue Dec 2 19:34:57 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Tue Dec 2 19:41:24 2003 Subject: [Biojava-dev] WeightMatrixAnnotator Message-ID: Hi - These additional methods have been added to CVS. Thanks Tanya. - Mark > -----Original Message----- > From: Tanya Vavouri [mailto:tvavouri@hotmail.com] > Sent: Wednesday, 3 December 2003 1:04 a.m. > To: biojava-dev@biojava.org > Subject: [Biojava-dev] WeightMatrixAnnotator > > > Hi, > > I've made some really simple changes to the latest > WeightMatrixAnnotator > that have allowed me to annotate sequences with multiple > weight matrices. > Basically, I've just added an extra variable the String wmID, > a constructor > that initialises with a user specified weight matrix ID and a > getter/setter > for the weight matrix ID. > > The changes are really simple but below is the code if anyone > is interested > to use it or add it to biojava. > > Thanks > Tanya Vavouri > > package org.biojava.bio.dp; > > import java.io.Serializable; > > import org.biojava.bio.BioException; > import org.biojava.bio.SimpleAnnotation; > import org.biojava.bio.seq.Feature; > import org.biojava.bio.seq.Sequence; > import org.biojava.bio.seq.SequenceAnnotator; > import org.biojava.bio.seq.impl.ViewSequence; > import org.biojava.bio.symbol.IllegalAlphabetException; > import org.biojava.bio.symbol.RangeLocation; > import org.biojava.utils.ChangeVetoException; > > /** > * Annotates a sequence with hits to a weight-matrix. > * > *

> * This SequenceAnnotator implementation returns a new > * ViewSequence wrapping the underlying Sequence > *

> * > * @author Matthew Pocock > * @author Thomas Down > */ > public class WeightMatrixAnnotator implements SequenceAnnotator, > Serializable { > private WeightMatrix matrix; > private double threshold; > private final ScoreType scoreType; > private String wmID; > > public Sequence annotate(Sequence seq) > throws IllegalAlphabetException, BioException, > ChangeVetoException > { > seq = new ViewSequence(seq); > > int cols = matrix.columns(); > Feature.Template template = new Feature.Template(); > template.source = "WeightMatrixAnnotator"; > template.type = wmID; > for(int offset = 1; > offset <= seq.length() - cols + 1; > offset++) { > double score = DP.scoreWeightMatrix(matrix, seq, > scoreType, offset); > double q = Math.exp(score); > if(q >= threshold) { > template.location = new RangeLocation(offset, > offset+cols-1); > SimpleAnnotation ann = new SimpleAnnotation(); > ann.setProperty("score", new Double(q)); > ann.setProperty("weightMatrix", matrix); > template.annotation = ann; > seq.createFeature(template); > } > } > return seq; > } > > /** > * Create a new annotator that uses the PROBABILITY score > type and an ID > for the weight matrix. > * > * @param wm the weight matrix > * @param threshold the threshold > * @param wmID the weight matrix ID > */ > public WeightMatrixAnnotator(WeightMatrix wm, ScoreType > scoreType, > double threshold, String wmID) { > this.matrix = wm; > this.threshold = threshold; > this.scoreType = ScoreType.PROBABILITY; > this.wmID = wmID; > } > > /** > * Create a new annotator that uses PROBABILITY score type. > * > * @param wm a WeightMatrix value > * @param threshold a double value > */ > public WeightMatrixAnnotator(WeightMatrix wm, double threshold) { > this(wm, ScoreType.PROBABILITY, threshold, "hit"); > } > > /** > * Create a new annotator that uses a specific score type. > * > * @param wm the weigth matrix > * @param scoreType the score type > * @param threshold the threshold > * @since 1.4 > */ > public WeightMatrixAnnotator(WeightMatrix wm, ScoreType > scoreType, > double threshold) { > this.matrix = wm; > this.scoreType = scoreType; > this.threshold = threshold; > this.wmID = "hit"; > } > > /** > * Get the value of the weight matrix id. > * @return value of the weight matrix id. > */ > public String getWmID() { > return wmID; > } > > /** > * Set the weight matrix id. > * @param v Value to assign to the weight matrix id. > */ > public void setWmID(String v) { > this.wmID = v; > } > > > } > > _________________________________________________________________ > Tired of 56k? Get a FREE BT Broadband connection > http://www.msn.co.uk/specials/btbroadband > > _______________________________________________ > 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 francois.pepin at mail.mcgill.ca Wed Dec 3 18:20:46 2003 From: francois.pepin at mail.mcgill.ca (Francois Pepin) Date: Wed Dec 3 18:28:03 2003 Subject: [Biojava-dev] problem with AnnotationBuilder? In-Reply-To: <1070493196.28764.202.camel@ticino.mcb.mcgill.ca> References: <1070493196.28764.202.camel@ticino.mcb.mcgill.ca> Message-ID: <1070493646.28764.207.camel@ticino.mcb.mcgill.ca> I think that there might be a problem with AnnotationBuilder.. With the following parser: LineSplitParser tvp = new LineSplitParser(); tvp.setEndOfRecord("///"); tvp.setSplitOffset(12); tvp.setContinueOnEmptyTag(true); tvp.setTrimTag(true); tvp.setTrimValue(false); tvp.setMergeSameTag(true); The simple AnnotationBuilder: AnnotationBuilder tvl=new AnnotationBuilder(AnnotationType.ANY); and the following text (among others): NAME aldehyde dehydrogenase (NAD) CoA-independent aldehyde dehydrogenase m-methylbenzaldehyde dehydrogenase NAD-aldehyde dehydrogenase NAD-dependent 4-hydroxynonenal dehydrogenase NAD-dependent aldehyde dehydrogenase NAD-linked aldehyde dehydrogenase propionaldehyde dehydrogenase I end up having the following value when printing the Annotation: NAME=propionaldehyde dehydrogenase. Echo() shows that everything is being read properly: 1 NAME { 2 aldehyde dehydrogenase (NAD) 2 CoA-independent aldehyde dehydrogenase 2 m-methylbenzaldehyde dehydrogenase 2 NAD-aldehyde dehydrogenase 2 NAD-dependent 4-hydroxynonenal dehydrogenase 2 NAD-dependent aldehyde dehydrogenase 2 NAD-linked aldehyde dehydrogenase 2 propionaldehyde dehydrogenase 1 } Adding the following code (*) in AnnotationBuilder (from line 133), to check if the values indeed get to be overwritten. public void value(TagValueContext ctxt, Object value) { try { Frame top = peek(annotationStack); * if (top.annotation.containsProperty(top.tag)) * System.out.println("replacing"+ *top.annotation.getProperty(top.tag)+ " by "+value); top.type.setProperty(top.annotation, top.tag, value); } catch (ChangeVetoException cve) { throw new AssertionFailure(cve); } } This gives us the very interesting output: replacing aldehyde dehydrogenase (NAD) by CoA-independent aldehyde dehydrogenase replacing CoA-independent aldehyde dehydrogenase by m-methylbenzaldehyde dehydrogenase replacing m-methylbenzaldehyde dehydrogenase by NAD-aldehyde dehydrogenase replacing NAD-aldehyde dehydrogenase by NAD-dependent 4-hydroxynonenal dehydrogenase replacing NAD-dependent 4-hydroxynonenal dehydrogenase by NAD-dependent aldehyde dehydrogenase replacing NAD-dependent aldehyde dehydrogenase by NAD-linked aldehyde dehydrogenase replacing NAD-linked aldehyde dehydrogenase by propionaldehyde dehydrogenase Basically every line gets to be overwritten, so only the last one remains at the end. Any ideas how this could be fixed, or did I do something stupid somewhere? Thanks, Francois From david.huen at ntlworld.com Thu Dec 4 02:50:37 2003 From: david.huen at ntlworld.com (David Huen) Date: Thu Dec 4 02:56:52 2003 Subject: [Biojava-dev] Security Message-ID: <200312040750.37073.david.huen@ntlworld.com> With the recent breaches at Debian, FSF and now Gentoo, do we have a way of checking the integrity of our two cvs servers? As far as I can tell, our dev cvs is running on a x86 Linux variant. Given that the patch to the vuln in the debian and FSF case only became available in the 2.4.23 kernel it is possible that we may have been and remain vulnerable. If someone has an older (say > 2 weeks) source tree, it may be worthwhile tarring it up to use as a reference for comparison purposes. Regards, David Huen From chrisa at espressosoftware.com Thu Dec 4 22:23:49 2003 From: chrisa at espressosoftware.com (Chris Abajian) Date: Thu Dec 4 22:30:06 2003 Subject: [Biojava-dev] Security In-Reply-To: <200312040750.37073.david.huen@ntlworld.com> References: <200312040750.37073.david.huen@ntlworld.com> Message-ID: <1070594629.3087.15.camel@suzinak.abajian.net> On Wed, 2003-12-03 at 23:50, David Huen wrote: > With the recent breaches at Debian, FSF and now Gentoo, do > we have a way of checking the integrity of our two cvs servers? After the fact? You might be able to go back to the distro disks and checksum various packages (rpm has a mode for this). Obviously you should look at the logs, check the passwd file, etc. As for staying out of trouble, if you're not doing so already, run an IDS (Intrusion Detection System). IMHO it's worth the effort if you're hosting a valuable community resource like this. Basically it's a utility that checksums all the critical files on your system (then you write the sums to a CD-R). If anything changes (because of rootkit or other trojan) it shows up in the report. Tripwire is a well-known one but the free version is wretched. AIDE (http://sourceforge.net/projects/aide) is free (GPL) and I seem to recall a report that it rang the alarm at Debian. I've been watching their dev list for a while and it's been gaining momentum steadily over the last few months. I'd be willing to help. -- Chris Abajian Espresso Software Development, L.L.C. http://espressosoftware.com 206.910.4903 Espresso Software Development provides software development and consulting services. We develop, deploy and support scalable, multi-tiered, high-availability web, e-commerce and data-processing applications. From info at cruisestopleasure.com Thu Dec 4 22:55:52 2003 From: info at cruisestopleasure.com (info@cruisestopleasure.com) Date: Fri Dec 5 01:54:36 2003 Subject: [Biojava-dev] CRUISES TO PLEASURE - Closing Party.....Modrophenia - Saturday 13th december 2003 Message-ID: <20031205035552.B81B2262A1@60gp.ovh.net> Saturday December 13th 2003: Closing Party.....Modrophenia After enjoying four thrilling seasons of party pleasure this year and following the successfull sell out of Double Pleasure on October 11th, Cruises to Pleasure is delighted to invite you to celebrate its closing party for the year 2003. So join us as we end the year as glamorously as we began it... Become one of the elite chic as Cruises to Pleasure presents Modrophenia... The party with a funky retro flavour for you to boogie to... and for those of you who care to indulge in luxury, reserve a table at the renowned Pier 19 to taste their gourmet dishes which includes an exclusive Limousine service to chauffeur you from the restaurant to the partyboat Catamaran Castle. Modrophenia intends to spoil its guests by offering an exclusive 7hr solo set mixed by DJ Marko, a surprise played by Rogier (Pacha-Ibiza) and of course CTP's resident DJs Benny Rodriguez (Now Wow), Phill (studio 54), X-ian (Colorbar) and Gino (CTP) who will excite you by mixing the grooviest tunes together... The only advice we suggest is 'buy your pre-sale tickets in time!' For more information visit www.cruisestopleasure.com or call + 32 (0) 479. 318. 262 See y'all @ the party !!! Boarding : 24.00 till 02.00. The boat sails from 02.30 till 04.30. Party ends 07.00 o'clock. Location : Kattendijckdok, kaai 15-16, eilandje, near londonbrug - Antwerp - Belgium See the eflyer at http://www.cruisestopleasure.com Deck 1: Benny Rodriguez (Now-Wow - NL) Rogier (Pacha) Phill (Studio 54) Deck 2: Marko (La Rocca) 7Hr exclusive solo set Champagne Deck Hosted by Pier 19 : Gino (CTP) X-ian (Colorbar) Massage by Paola Entertainment Company Hair styling by http://www.hetvirtueelkapsalon.be Hairshow by The Catwalk Percussion by Bongo Alan Vocals by Louis-T Info: http://www.cruisestopleasure.com email: info@cruisestopleasure.com Tel: +32 (0) 479. 318. 262 Go have pre-dinner at Pier19 and enjoy the free limo service to the boats. Reservations at 0032 (0) 3 288 78 61 - http://www.pier19.be Please do not reply to this email, use info@cruisestopleasure.com instead. This email is sent in compliance with strict anti-abuse and NO SPAM regulations. Your address was collected as a result of posting to a link, you have sent me an E-mail recently, or you are on a list that I have purchased. You may remove your E-mail address at no cost to you what so ever by simply clicking at the url positioned at the end of this message . --------------------------------------------------------------------------- To be unsubscribed from the mailing list simply click on the link below http://www.cruisestopleasure.net/cgi-bin/s.pl?r=1&l=2&e=biojava-dev@biojava.org From david.huen at ntlworld.com Sun Dec 7 15:20:32 2003 From: david.huen at ntlworld.com (David Huen) Date: Sun Dec 7 15:26:51 2003 Subject: [Biojava-dev] Proposal to change DP interface Message-ID: <200312072020.32244.david.huen@ntlworld.com> The training algorithm interfaces in org.biojava.bio.dp are have a method:- public void train(SequenceDB db, double nullWeight, StoppingCriteria stopper) throws IllegalSymbolException, BioException This method is only suitable for single-head DP as it provides for only one SequenceDB as a source of training sequences whereas twohead DP requires two sequences. I propose to change the SequenceDB to SequenceDB[]:- public void train(SequenceDB [] db, double nullWeight, StoppingCriteria stopper) throws IllegalSymbolException, BioException This will allow the specification of multiple SequenceDBs to be used in tandem for training. Comments would be welcome. Thanks, David Huen From markjschreiber at hotmail.com Mon Dec 8 04:27:18 2003 From: markjschreiber at hotmail.com (mark schreiber) Date: Mon Dec 8 04:33:26 2003 Subject: [Biojava-dev] Proposal to change DP interface In-Reply-To: <200312072020.32244.david.huen@ntlworld.com> Message-ID: Hi - Would it be possible to overload the method and keep the old one as well? You could throw a bioexception if the old method is used for a single head model if you wish. - Mark -----Original Message----- From: biojava-dev-bounces@portal.open-bio.org [mailto:biojava-dev-bounces@portal.open-bio.org] On Behalf Of David Huen Sent: Monday, 8 December 2003 9:21 a.m. To: biojava-dev@biojava.org Subject: [Biojava-dev] Proposal to change DP interface The training algorithm interfaces in org.biojava.bio.dp are have a method:- public void train(SequenceDB db, double nullWeight, StoppingCriteria stopper) throws IllegalSymbolException, BioException This method is only suitable for single-head DP as it provides for only one SequenceDB as a source of training sequences whereas twohead DP requires two sequences. I propose to change the SequenceDB to SequenceDB[]:- public void train(SequenceDB [] db, double nullWeight, StoppingCriteria stopper) throws IllegalSymbolException, BioException This will allow the specification of multiple SequenceDBs to be used in tandem for training. Comments would be welcome. Thanks, David Huen _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From smh1008 at cus.cam.ac.uk Mon Dec 8 06:14:11 2003 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Mon Dec 8 06:20:29 2003 Subject: [Biojava-dev] Proposal to change DP interface In-Reply-To: References: Message-ID: <200312081114.12514.smh1008@cus.cam.ac.uk> On Monday 08 Dec 2003 9:27 am, mark schreiber wrote: > Hi - > > Would it be possible to overload the method and keep the old one as well? > You could throw a bioexception if the old method is used for a single > head model if you wish. > OK, I'll do it that way. It's quite easily accomodated. There is an equivalent issue in AbstractTrainer:- singleSequenceIteration(ModelTrainer trainer, SymbolList symList) to:- singleSequenceIteration(ModelTrainer trainer, SymbolList [] symList) If I modified AbstractTrainer to be able to cope with either single or twohead models then modified the classes that derive from it in BJ to the new API, would I need to keep the old method in here too? i.e. has anyone written their own AbstractTrainer-derived classes? (In one sense the name of this method is no longer appropriate. Would something like SingleCaseIteration be better but that may also break things). I'm doing this to try to get in a single/twohead Viterbi trainer. Regards, david huen From markjschreiber at hotmail.com Mon Dec 8 14:35:15 2003 From: markjschreiber at hotmail.com (mark schreiber) Date: Mon Dec 8 14:41:21 2003 Subject: [Biojava-dev] Proposal to change DP interface In-Reply-To: <200312081114.12514.smh1008@cus.cam.ac.uk> Message-ID: Hi - I guess it's unlikely that people have implemented their own trainers so if nobody shouts out soon you should change it. - Mark Ps you wouldn't mind making some tutorials for them would you? -----Original Message----- From: biojava-dev-bounces@portal.open-bio.org [mailto:biojava-dev-bounces@portal.open-bio.org] On Behalf Of David Huen Sent: Tuesday, 9 December 2003 12:14 a.m. To: mark schreiber; biojava-dev@biojava.org Subject: Re: [Biojava-dev] Proposal to change DP interface On Monday 08 Dec 2003 9:27 am, mark schreiber wrote: > Hi - > > Would it be possible to overload the method and keep the old one as well? > You could throw a bioexception if the old method is used for a single > head model if you wish. > OK, I'll do it that way. It's quite easily accomodated. There is an equivalent issue in AbstractTrainer:- singleSequenceIteration(ModelTrainer trainer, SymbolList symList) to:- singleSequenceIteration(ModelTrainer trainer, SymbolList [] symList) If I modified AbstractTrainer to be able to cope with either single or twohead models then modified the classes that derive from it in BJ to the new API, would I need to keep the old method in here too? i.e. has anyone written their own AbstractTrainer-derived classes? (In one sense the name of this method is no longer appropriate. Would something like SingleCaseIteration be better but that may also break things). I'm doing this to try to get in a single/twohead Viterbi trainer. Regards, david huen _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mishrask at yahoo.com Tue Dec 9 10:50:46 2003 From: mishrask at yahoo.com (Sanjeev Kumar Mishra) Date: Tue Dec 9 10:56:50 2003 Subject: [Biojava-dev] how to get sequences from pubmed Message-ID: <20031209155046.17171.qmail@web14006.mail.yahoo.com> Hi, I wanted to know if there is any way I can specify the pubmed/swissprot database -- url -- and do queries/sequence analysis using bio java. I went through the examples but all of them are using some local files. thanks S ===== Sanjeev Kumar Mishra Phone:(408) 247-9546 (Home) (650) 655-6700x621 (Work) __________________________________ Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing. http://photos.yahoo.com/ From matthew_pocock at yahoo.co.uk Tue Dec 9 13:57:26 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Dec 9 14:03:27 2003 Subject: [Biojava-dev] Re: [Biojava-l] How to create a SymbolList with a String thatcontains illegal Char In-Reply-To: <51ee955dab.55dab51ee9@cmmt.ubc.ca> References: <51ee955dab.55dab51ee9@cmmt.ubc.ca> Message-ID: <3FD61B16.20703@yahoo.co.uk> Tao Xu wrote: >Thanks a lot for your responses, David, Mark and Mattew. You guys make >this group so friendly and efficient. > >I think a Alphabet that contains all char in Java should >serve this kind of needs and handle the possible errors in the >sequence strings in databases. > > It should be trivial to copy/paste from the IntegerAlphabet to do this. Volunteers? I'd hate to muck up serialization by blundering in there :) Matthew From taoxu at bioinformatics.ubc.ca Tue Dec 9 14:23:23 2003 From: taoxu at bioinformatics.ubc.ca (Tao Xu) Date: Tue Dec 9 14:29:56 2003 Subject: [Biojava-dev] Re: [Biojava-l] How to create a SymbolList with a String thatcontains illegal Char Message-ID: <538065301a.5301a53806@cmmt.ubc.ca> I'd love to do this, but I am new and don't know how to commit file to biojava cvs. Do I need an account? Thanks for you info. Tao ----- Original Message ----- From: Matthew Pocock Date: Tuesday, December 9, 2003 10:57 am Subject: Re: [Biojava-l] How to create a SymbolList with a String thatcontains illegal Char > Tao Xu wrote: > > >Thanks a lot for your responses, David, Mark and Mattew. You guys > make > >this group so friendly and efficient. > > > > > >I think a Alphabet that contains all char in Java should > >serve this kind of needs and handle the possible errors in the > >sequence strings in databases. > > > > > It should be trivial to copy/paste from the IntegerAlphabet to do > this. > Volunteers? I'd hate to muck up serialization by blundering in > there :) > > Matthew > > From markjschreiber at hotmail.com Wed Dec 10 04:17:38 2003 From: markjschreiber at hotmail.com (mark schreiber) Date: Wed Dec 10 04:23:43 2003 Subject: [Biojava-dev] Re: [Biojava-l] How to create a SymbolList with a String thatcontains illegal Char In-Reply-To: <3FD61B16.20703@yahoo.co.uk> Message-ID: >>I think a Alphabet that contains all char in Java should serve this >>kind of needs and handle the possible errors in the sequence strings in >>databases. >> >> >It should be trivial to copy/paste from the IntegerAlphabet to do this. >Volunteers? I'd hate to muck up serialization by blundering in there :) I've often thought of doing this for Unicode or at least ASCII, after all the Symbol model can be used for any Symbolic data. I may have a play tommorrow if I don't get too busy sorting out my move to Singapore. - Mark From markjschreiber at hotmail.com Wed Dec 10 21:33:08 2003 From: markjschreiber at hotmail.com (mark schreiber) Date: Wed Dec 10 21:39:08 2003 Subject: [Biojava-dev] RE: [Biojava-l] How to create a SymbolList with a String thatcontains illegal Char In-Reply-To: <3FD5EFB0.6050307@yahoo.co.uk> Message-ID: > -----Original Message----- > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > Sent: Wednesday, 10 December 2003 4:52 a.m. > To: mark schreiber > Cc: smh1008@cus.cam.ac.uk; taoxu@bioinformatics.ubc.ca; > biojava-l@biojava.org > Subject: Re: [Biojava-l] How to create a SymbolList with a > String thatcontains illegal Char > > mark schreiber wrote: > > >Is 'i' actually a legal symbol from the RNA alphabet, in > terms of biojava? > >If not how should we define it? Would it be best modelled as > an atomic > >symbol or some kind of ambiguity? Stretching back to my biochem > >undergrad days I think it should be atomic. That will mean the RNA > >Alphabets size is 5. > > > Atomic. Our alphabets don't manage modifications well (e.g. > methylated DNA). Another thing to think about for v2. > Hi - It's pretty simple to add this to nucleotide and to RNA, however we get into all sorts of trouble with making the complement table. The SimpleReversibleTranslationTable won't tolerate RNA having a size of 5 when DNA only has a size of 4. I have done some investigations and inosine is complemented by 'c'. Is there a way to make an unequal translation table for this arrangement? If anyone has some ideas I would like to hear them but won't be able to code them up till after Xmas as I'm off on holiday from tommorrow. Cheers, Mark From david.huen at ntlworld.com Thu Dec 11 03:42:23 2003 From: david.huen at ntlworld.com (David Huen) Date: Thu Dec 11 03:48:31 2003 Subject: [Biojava-dev] RE: [Biojava-l] How to create a SymbolList with a String thatcontains illegal Char In-Reply-To: References: Message-ID: <200312110842.24415.david.huen@ntlworld.com> On Thursday 11 Dec 2003 2:33 am, mark schreiber wrote: > > -----Original Message----- > > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > > Sent: Wednesday, 10 December 2003 4:52 a.m. > > To: mark schreiber > > Cc: smh1008@cus.cam.ac.uk; taoxu@bioinformatics.ubc.ca; > > biojava-l@biojava.org > > Subject: Re: [Biojava-l] How to create a SymbolList with a > > String thatcontains illegal Char > > > > mark schreiber wrote: > > >Is 'i' actually a legal symbol from the RNA alphabet, in > > > > terms of biojava? > > > > >If not how should we define it? Would it be best modelled as > > > > an atomic > > > > >symbol or some kind of ambiguity? Stretching back to my biochem > > >undergrad days I think it should be atomic. That will mean the RNA > > >Alphabets size is 5. > > > > Atomic. Our alphabets don't manage modifications well (e.g. > > methylated DNA). Another thing to think about for v2. > > Hi - > > It's pretty simple to add this to nucleotide and to RNA, however we get > into all sorts of trouble with making the complement table. The > SimpleReversibleTranslationTable won't tolerate RNA having a size of 5 > when DNA only has a size of 4. > > I have done some investigations and inosine is complemented by 'c'. Is > there a way to make an unequal translation table for this arrangement? > The trouble is inosine is used in tRNAs to introduce wobble. It is complementary to A,C and U within RNAs. Inosine occurs in mRNA extremely rarely and usually as a consequence of RNA editing (particularly of mammalian glutamate receptor transcripts) where A is changed to I. The ribosome translates the edited I as if it were a G under these circumstances. So CAG gets edited to read CGG frinstance. Perhaps the better thing to do is to define a tRNA/snRNA alphabet. Those can contain all the weird stuff and will never be translated thereby not needing a translation table. That will deal with most of the cases (including the very many exotic edited bases in tRNAs) but that still doesn't solve the above where your proposal seems sensible. > If anyone has some ideas I would like to hear them but won't be able to > code them up till after Xmas as I'm off on holiday from tommorrow. > Holiday? Hmmmph. Regards, David Huen From benjamins at Biomax.de Thu Dec 11 07:48:00 2003 From: benjamins at Biomax.de (Benjamin Schuster-Boeckler) Date: Thu Dec 11 07:54:03 2003 Subject: [Biojava-dev] Where has ViewSequence gone? Message-ID: <3FD86780.6040007@Biomax.de> In the 1.3.1 release of BioJava, the org.biojava.bio.seq.ViewSequence class dissapeared. Thus, dazzle doesn't compile any more. I switched back to 1.3pre4 and everything's fine. Is this a mistake or did you remove the class on purpose? Greetings, Benjamin -- Benjamin Schuster-B?ckler BioMax AG From cs at salestonight.com Fri Dec 12 02:00:28 2003 From: cs at salestonight.com (Accounting) Date: Fri Dec 12 02:06:45 2003 Subject: [Biojava-dev] RE: Last Chance to Claim Your Check. Message-ID: <785$2qvY45P5-xAPRqvY45P58Y7B@sale-1.salestonight.com> Would you like to get paid between $25 - $250 just for completing simple 5-10 minute survey? If you answered yes, then we can put you to work today! http://salestonight.com:8080/track?m=1260032&l=0&.e=1KDrdLeL-9FeJKDrdLeL4rzV You get paid to work at home and give your opinion!! BEST OF ALL! There is no limit to how many surveys you can participate in and no limit on how much money you can make. Why Wait? Click the link below and start earning money today. http://salestonight.com:8080/track?m=1260032&l=0&.e=0xbYv4C4-dcC9xbYv4C4UYH8 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.salestonight.com/unsub.php?e=biojava-dev@biojava.org&m=1260032. 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.salestonight.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org MPT5GcDAsERHoA9aU7wBLKfkM8oMzDeb8KO9ihxoKCDD TM: <60;5n3zBrtr-qbtNn3zBrtr9zuO;1260032> From matthew_pocock at yahoo.co.uk Fri Dec 12 08:10:04 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri Dec 12 08:17:23 2003 Subject: [Biojava-dev] Where has ViewSequence gone? In-Reply-To: <3FD86780.6040007@Biomax.de> References: <3FD86780.6040007@Biomax.de> Message-ID: <3FD9BE2C.7090404@yahoo.co.uk> Ah - it's moved to the .impl package under .seq - sorry about this. We would need to recompile dazzle. Thomas - can you get dazzle to use one of the factory methods on SequenceTools instead? That way the same dazzle will work with 1.3, 1.3.1 and 1.4 Matthew Benjamin Schuster-Boeckler wrote: > In the 1.3.1 release of BioJava, the org.biojava.bio.seq.ViewSequence > class dissapeared. Thus, dazzle doesn't compile any more. I switched > back to 1.3pre4 and everything's fine. Is this a mistake or did you > remove the class on purpose? > > Greetings, > > Benjamin > From thomas at derkholm.net Fri Dec 12 12:10:30 2003 From: thomas at derkholm.net (Thomas Down) Date: Fri Dec 12 11:24:44 2003 Subject: [Biojava-dev] Where has ViewSequence gone? In-Reply-To: <3FD9BE2C.7090404@yahoo.co.uk> References: <3FD86780.6040007@Biomax.de> <3FD9BE2C.7090404@yahoo.co.uk> Message-ID: <20031212171030.GB10725@firechild> Hi Benjamin, This is now fixed in the CVS version of Dazzle. I'm afraid I don't have access to upload a new downloadable version right now, but you can request a tar file from: http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/xdas/?cvsroot=biojava Alternatively, you can just add: import org.biojava.bio.seq.impl.*; to the top of any offending source files. Thomas. Once upon a time, Matthew Pocock wrote: > Ah - it's moved to the .impl package under .seq - sorry about this. We > would need to recompile dazzle. Thomas - can you get dazzle to use one > of the factory methods on SequenceTools instead? That way the same > dazzle will work with 1.3, 1.3.1 and 1.4 > > Matthew > > Benjamin Schuster-Boeckler wrote: > > >In the 1.3.1 release of BioJava, the org.biojava.bio.seq.ViewSequence > >class dissapeared. Thus, dazzle doesn't compile any more. I switched > >back to 1.3pre4 and everything's fine. Is this a mistake or did you > >remove the class on purpose? > > > >Greetings, > > > >Benjamin > > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev From cs at salestonight.com Sat Dec 13 03:01:46 2003 From: cs at salestonight.com (Digital Cam) Date: Sat Dec 13 03:08:00 2003 Subject: [Biojava-dev] 1 Week Pre-Holiday Sale Message-ID: <798$5n3zBrtr-qbtNn3zBrtr9zuO@sale-1.salestonight.com> Need a gift idea? Need a digital camera? Don’t want to spend $300? Want a camera rated best in class? 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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.salestonight.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org 57maeBCqHskChAjlrWY7SkLALKMkZHGK1g9saD TM: <60;68O0gfwf-vGwN8O0gfwfP0l5;1290032> From cs at salestonight.com Sat Dec 13 12:34:48 2003 From: cs at salestonight.com (Privacy Protector) Date: Sat Dec 13 12:41:10 2003 Subject: [Biojava-dev] Take Back Your Privacy Message-ID: <801$7DXUdH5H-KL5IDXUdH5HoUxE@sale-1.salestonight.com> Did you know there are a growing number of reports of wireless spy cameras in hotel rooms, dressing rooms, showers and more? Did you know millions of surveillance cameras and microphones are purchased every year? Did you know chances are everyday you are on a surveillance camera? Is your privacy important to you? Would you want someone watching you or your family? 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The e-mail subscription address is: biojava-dev@biojava.org ZgwIkblChmtLOYAjalkp TM: <60;7DXUdH5H-KL5IDXUdH5HoUxE;1297032> From cs at salestonight.com Sun Dec 14 21:31:57 2003 From: cs at salestonight.com (Digital Cam) Date: Sun Dec 14 21:38:10 2003 Subject: [Biojava-dev] 1 Week Pre-Holiday Sale Message-ID: <808$8ehtULlL-Qbl9ehtULlL7tc4@sale-1.salestonight.com> Need a gift idea? Need a digital camera? Don’t want to spend $300? Want a camera rated best in class? Want to spend less than $80 for it? Want a Web Cam? How about a camera that is a 3 in 1 digital camera – Web, Video and Digital? Want over $200 of Award Winning software free with your purchase? Want FREE Batteries? Want FREE Shipping? Want a FREE Case? Want a FREE Stand? Want a FREE USB Cable? If you answered yes to any of the above, then click here http://www.platinum-deal.com/rd1.php?ac=CD1&bid=294&did=3372&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 partners. If you would prefer to not receive these messages in the future, please http://www.salestonight.com/unsub.php?e=biojava-dev@biojava.org&m=1300032. 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.salestonight.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org cA9fW5VpA0AFG1mqOlwMAV5EMUkF TM: <60;1KDrdLeL-9FeJKDrdLeL4rzV;1300032> From cs at salestonight.com Sun Dec 14 21:36:20 2003 From: cs at salestonight.com (TalkIt) Date: Sun Dec 14 21:42:24 2003 Subject: [Biojava-dev] Stop Typing, Start Talking for less than $30 with no risk Message-ID: <811$4we6O4b4-HSbDwe6O4b4K6Pn@sale-1.salestonight.com> Do you type with two fingers? Are you sick of wasting time? Do you wish your computer could type for you? Do you know what voice recognition software is? Did you know it can type almost as fast as you can speak? Would you think it costs hundreds of dollars? Would you try it for no risk or for under $30? If you answered yes to any of these questions, click here http://www.platinum-deal.com/rd1.php?ac=CD1&bid=301&did=3432&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 partners. If you would prefer to not receive these messages in the future, please http://www.salestonight.com/unsub.php?e=biojava-dev@biojava.org&m=1302032. 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.salestonight.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org 457xMiHKkDRxB TM: <60;4we6O4b4-HSbDwe6O4b4K6Pn;1302032> From sexma at wanadoo.es Mon Dec 15 17:11:27 2003 From: sexma at wanadoo.es (Jose Vicente) Date: Mon Dec 15 17:17:02 2003 Subject: [Biojava-dev] Exception NoClassDefFoundError Message-ID: <6.0.0.22.2.20031215230416.025485f0@pop.wanadoo.es> Hi, I have downloades biojava.jar, bytecode.jar and xerces.jar and i have also added the 3 jar to my CLASSPATH. I compile the GCContent example but when i run it, i have a NoClassDefFoundError Exception. I think i installed biojava correctly but i could't run any demo. Could anyone please help me? Thanks, Jose Vicente From len at reeltwo.com Mon Dec 15 17:59:32 2003 From: len at reeltwo.com (Len Trigg) Date: Mon Dec 15 18:05:33 2003 Subject: [Biojava-dev] Annotation conversions Message-ID: Hi folks, I'd like to add support for BioSQL's comment table to our binding, and am wondering about the best way to do it. It is obvious that the comments should just be annotations, my question is more about what key I should associate the comments with (and should look for when storing sequences in the database). It seems that I could use either "CC" or "COMMENT" and the right thing would happen most of the time. However, it seems a bit silly to have to check for both types when persisting comments to the database. Should there be a "canonical" key that is used for comments. Then different I/O formats could just check for this one key, rather than having to do do things like this: GenbankFileFormer.java:322 else if (key.equals("CC") || key.equals("COMMENT")) { ccb = new StringBuffer(sequenceBufferCreator("COMMENT ", value)); } The same also applies to any of the annotations that are shared between multiple output formats... Suggestions? Cheers, Len. From matthew_pocock at yahoo.co.uk Tue Dec 16 06:08:27 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Dec 16 06:16:55 2003 Subject: [Biojava-dev] Annotation conversions In-Reply-To: References: Message-ID: <3FDEE7AB.9070503@yahoo.co.uk> Hi Len, This is a recurring problem with key-value data - exactly what is the right key? This is one of the things that ontologies are meant to solve for us. However, I still haven't got the ruddy things to work yet. For now, CC or COMMENT are your best bet. You can decide upon a canonical key if you want, but currently you would have to do the work by hand of mapping to/from canonical. Perhaps a useful thing to do would be to draw up a document with canonicals and what they map to in different file formats. Matthew Len Trigg wrote: >Hi folks, > >I'd like to add support for BioSQL's comment table to our binding, and >am wondering about the best way to do it. It is obvious that the >comments should just be annotations, my question is more about what key I >should associate the comments with (and should look for when storing >sequences in the database). > >It seems that I could use either "CC" or "COMMENT" and the right thing >would happen most of the time. However, it seems a bit silly to have >to check for both types when persisting comments to the >database. Should there be a "canonical" key that is used for >comments. Then different I/O formats could just check for this one >key, rather than having to do do things like this: > >GenbankFileFormer.java:322 > else if (key.equals("CC") || key.equals("COMMENT")) { > ccb = new StringBuffer(sequenceBufferCreator("COMMENT ", value)); > } > > >The same also applies to any of the annotations that are shared >between multiple output formats... > >Suggestions? > > >Cheers, >Len. >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > > From kdj at sanger.ac.uk Tue Dec 16 07:10:36 2003 From: kdj at sanger.ac.uk (Keith James) Date: Tue Dec 16 07:16:32 2003 Subject: [Biojava-dev] Annotation conversions References: Message-ID: >>>>> "Len" == Len Trigg writes: Len> Hi folks, Len> I'd like to add support for BioSQL's comment table to our Len> binding, and am wondering about the best way to do it. It is Len> obvious that the comments should just be annotations, my Len> question is more about what key I should associate the Len> comments with (and should look for when storing sequences in Len> the database). Len> It seems that I could use either "CC" or "COMMENT" and the Len> right thing would happen most of the time. However, it seems Len> a bit silly to have to check for both types when persisting Len> comments to the database. Should there be a "canonical" key Len> that is used for comments. Then different I/O formats could Len> just check for this one key, rather than having to do do Len> things like this: Len> GenbankFileFormer.java:322 else if (key.equals("CC") || Len> key.equals("COMMENT")) { ccb = new Len> StringBuffer(sequenceBufferCreator("COMMENT ", value)); } Yeah - what we have now is really ugly, but also a maintenance headache. Len> The same also applies to any of the annotations that are Len> shared between multiple output formats... Len> Suggestions? Does anyone know of practical standards for this sort of biological metadata? It's that semantic heterogeneity problem again. Some of these fields are present in many formats e.g. SwissProt, PDB, BSML (but not always meaning the same thing). I wish there were a way of finding which fields mean the same thing in different datasets. I've been googling and looking on pubmed, but haven't seen anything immediately helpful (i.e. simple, practical and applicable). I don't think we should over-engineer. "Canonical" keys would be one way. I would favour typed enums rather than, say, ints or strings, possibly with a suitable toString() for UI presentation. There should also be a method to get a definition (or a ResouceBundle of definitions) so we don't slip right back into the problem of semantics. It would be great if the sets of "keys" and the annotation builder itself were plugins. Then we could switch from flat lists to ontologies without disturbing things too much. Ontologies would be great, but pragmatically not a runner just yet. My 2c. Keith -- - Keith James Microarray Facility, Team 65 - - The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK - From sicotteh at mail.nih.gov Tue Dec 16 13:13:50 2003 From: sicotteh at mail.nih.gov (Sicotte, Hugues (NIH/NCI)) Date: Tue Dec 16 13:19:49 2003 Subject: [Biojava-dev] New Feature format for dbSNP Message-ID: <27C204BD76CBC142BA1AE46D62A8548E066E2095@nihexchange9.nih.gov> FYI, at the next dbSNP release (in the next 1-2 weeks) the format f annotated SNPs on the genbank files will change. instead of /allele= they will be using the /replace syntax. This in accordance with the Genbank collaboration guidelines. I'm letting this group know in case the genbank parser parses that feature. Happy Holiday Hugues From simon.foote at nrc-cnrc.gc.ca Thu Dec 18 10:01:52 2003 From: simon.foote at nrc-cnrc.gc.ca (Simon Foote) Date: Thu Dec 18 10:07:42 2003 Subject: [Biojava-dev] BioSQL delete fixes for MySQL Message-ID: <3FE1C160.2040906@nrc-cnrc.gc.ca> Hi Folks, Just a heads up that there was a bug in the MySQLDBHelper code that was preventing it from correctly identifying the server version, such that the delete style was never set to MYSQL4. Hence, it always used the generic delete style which seemed to never work consistently with my tests. The minor version identifier for MySQL returns 0 for 4.0.* servers. The needed number is the subminor # which you can't retrieve from the database metadata. So instead of getting fancy to get that #, I just changed the code to check for a minor version >= 0 and not to check the subminor version. I would assume anyone using MySQL4 would at least be using one of the higher versions since its upto 4.0.17 now. I also changed the BioSQLSequenceDB.java for Delete_MYSQL4 to just delete the bioentry given the bioentry_id as MySQL is using a cascading delete which is defined in the biosql-schema and is faster than deleting individual rows from each table. And lastly, the select statement to get the bioentry_id to delete failed to take into account the biodatabase_id, so could conceivably delete a bioentry with the same accession, but in another biodatabase. Just substituted the select statment used by get_sequence in the remove_sequence code. Cheers and Happy Holidays, Simon -- Bioinformatics Programmer Pathogen Genomics Institute for Biological Sciences National Research Council of Canada [T] 613-990-0561 [F] 613-952-9092 simon.foote@nrc-cnrc.gc.ca From cs at salestonight.com Fri Dec 19 08:24:46 2003 From: cs at salestonight.com (Digital Cam) Date: Fri Dec 19 08:30:48 2003 Subject: [Biojava-dev] 1 Week Pre-Holiday Sale Message-ID: <857$5n3zBrtr-qbtNn3zBrtr9zuO@sale-1.salestonight.com> Need a gift idea? Need a digital camera? Don’t want to spend $300? Want a camera rated best in class? Want to spend less than $80 for it? Want a Web Cam? How about a camera that is a 3 in 1 digital camera – Web, Video and Digital? Want over $200 of Award Winning software free with your purchase? Want FREE Batteries? Want FREE Shipping? Want a FREE Case? Want a FREE Stand? Want a FREE USB Cable? If you answered yes to any of the above, then click here http://www.platinum-deal.com/rd1.php?ac=CD1&bid=294&did=3372&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 partners. If you would prefer to not receive these messages in the future, please http://www.salestonight.com/unsub.php?e=biojava-dev@biojava.org&m=1376032. 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.salestonight.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org M1QHhSU9Caj43njFT2mp2o TM: <60;8ehtULlL-Qbl9ehtULlL7tc4;1376032> From lc1 at sanger.ac.uk Fri Dec 19 11:19:49 2003 From: lc1 at sanger.ac.uk (Lachlan James Coin) Date: Fri Dec 19 11:25:35 2003 Subject: [Biojava-dev] DP memory leak In-Reply-To: <3FE1C160.2040906@nrc-cnrc.gc.ca> References: <3FE1C160.2040906@nrc-cnrc.gc.ca> Message-ID: <3FE32525.5000002@sanger.ac.uk> Hi, I came across a bit of a memory leak while using the dp code. The problem is that AlphabetManager keeps a reference to every alphabet created, including StateAlphabetcreated when using the dp package. I had extended the EmissionState class in such a way that the instances were of a non-trivial size. I am also creating (one after the other) a lot of different state alphabets. The result was that I ran out of memory farily quickly. One possible fix I thought of was to add "deregisterAlphabet(name)" method to AlphabetManager, and to call this from the finalize mehod of SimpleMarkovModel, so that when the garbage collector thinks it can clear the markov model the statealphabet is removed from the AlphabetManager registry and can then also be garbage collected. Also, it would be necessary to make alphabetToIndex a WeakHashMap. Any other suggestions? Can I make these changes? Thanks, Lachlan From uwe-schmidt- at gmx.net Fri Dec 19 17:28:04 2003 From: uwe-schmidt- at gmx.net (Microsale) Date: Fri Dec 19 17:33:25 2003 Subject: [Biojava-dev] Mr. Uwe Schmidt is a knave! Don't buy any product from Microsale! Message-ID: <200312192233.hBJMXLFD020002@portal.open-bio.org> Dear friends, Microsale SC KG, Ltd, Germany is a knave company and Uwe Schmidt is a big knave! We are cheated by Microsale SC KG, Ltd. Remember, don't do any business with this company. Don't buy any product from Microsale or you will be cheated. This company has a bad reputation in Germany and in other European countries, espcially in Belgium and Netherlands. Here's the story: Mr. Uwe Schmidt , CEO Microsale (R) SC KG He is also an auditor, but he doesn't have any commercial morality. He always made cheated L/C to other companies. Many companies have been cheated by him. Please take care!!! His products have many problems, such as CD player and mp3 player! It's the detailed information of this company: Dahlienweg 6 D 52477 Alsdorf, NRW Germany, European Union Tel.-/Fax-Box: +49 89 1488230796 +32 87 783518 +32 87 783019 Mobil: +32 474 409055 Email: microsale@email.de microsale@gmx.net uwe-schmidt-@gmx.net Web: http://www.microsale.biz http://members.ebay.de/aboutme/microsale_schmidt From chrisa at espressosoftware.com Fri Dec 19 21:15:53 2003 From: chrisa at espressosoftware.com (Chris Abajian) Date: Fri Dec 19 21:21:40 2003 Subject: [Biojava-dev] Mr. Uwe Schmidt is a knave! Don't buy any product from Microsale! In-Reply-To: <200312192233.hBJMXLFD020002@portal.open-bio.org> References: <200312192233.hBJMXLFD020002@portal.open-bio.org> Message-ID: <1071886552.3901.148.camel@suzinak.abajian.net> Hate-spam. Haven't seen THAT before. Most people are trying (however pathetically) to make money. A new low. On Fri, 2003-12-19 at 14:28, Microsale wrote: > Microsale SC KG, Ltd, Germany is a knave company and Uwe Schmidt is a big knave! -- Chris Abajian Espresso Software Development, L.L.C. http://espressosoftware.com 206.910.4903 Espresso Software Development provides software development and consulting services. We develop, deploy and support scalable, multi-tiered, high-availability web, e-commerce and data-processing applications. From jjliu at cs.nchu.edu.tw Sun Dec 21 09:36:05 2003 From: jjliu at cs.nchu.edu.tw (Jim Liu) Date: Sun Dec 21 17:43:56 2003 Subject: [Biojava-dev] Can I import all information of HGI.release_13? Message-ID: <000b01c3c7cf$c4914bc0$ee213e3d@jimhome> Hi Folks, I went to ftp://ftp.tigr.org/pub/data/tgi/Homo_sapiens/ and downloaded HGI.release_13.zip. There are 4 data files: 479,047,691 HGI.101403 57,653,798 HGI.TC_EST.101403 12,629,591 HGI.TCs.101403 10,303,001 HGI.GO.101403 I know how to import the sequence data from HGI.101403 to MySQL database (BioSQL schema) via UploadFlat.java. Can I import all information of these data files? It seems GI.TC_EST.101403 is the index file that correlating THC ID and EST accession number. HGI.TCs.101403 describe the relationship between THC IDs of old editions and update edition. HGI.GO.101403 should be a result of cluster analysis between different species that have homology proteins. How to find the detail definition of these data files? Thanks. Best Regards, Jim Liu Email: jjliu@cs.nchu.edu.tw From jjliu at falconstor.com.tw Sun Dec 21 07:09:17 2003 From: jjliu at falconstor.com.tw (Jim Liu) Date: Sun Dec 21 17:44:00 2003 Subject: [Biojava-dev] Can I import all information of HGI.release_13? References: <3FE1C160.2040906@nrc-cnrc.gc.ca> Message-ID: <004101c3c7bb$45dfea20$ee213e3d@jimhome> Hi Folks, I went to ftp://ftp.tigr.org/pub/data/tgi/Homo_sapiens/ and downloaded HGI.release_13.zip. There are 4 data files: 479,047,691 HGI.101403 57,653,798 HGI.TC_EST.101403 12,629,591 HGI.TCs.101403 10,303,001 HGI.GO.101403 I know how to import the sequence data from HGI.101403 to MySQL database (BioSQL schema) via UploadFlat.java. Can I import all information of these data files? It seems GI.TC_EST.101403 is the index file that correlating THC ID and EST accession number. HGI.TCs.101403 describe the relationship between THC IDs of old editions and update edition. HGI.GO.101403 should be a result of cluster analysis between different species that have homology proteins. How to find the detail definition of these data files? Thanks. Best Regards, Jim Liu Email: jjliu@cs.nchu.edu.tw From matthew_pocock at yahoo.co.uk Mon Dec 22 07:06:16 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Mon Dec 22 07:15:51 2003 Subject: [Biojava-dev] DP memory leak In-Reply-To: <3FE32525.5000002@sanger.ac.uk> References: <3FE1C160.2040906@nrc-cnrc.gc.ca> <3FE32525.5000002@sanger.ac.uk> Message-ID: <3FE6DE38.1090000@yahoo.co.uk> Hi, Lachlan James Coin wrote: > Hi, > > I came across a bit of a memory leak while using the dp code. The > problem is that AlphabetManager keeps a reference to every alphabet > created, including StateAlphabetcreated when using the dp package. I > had extended the EmissionState class in such a way that the instances > were of a non-trivial size. I am also creating (one after the other) > a lot of different state alphabets. The result was that I ran out of > memory farily quickly. Hehe. That's an unforseen use-case bug. > > One possible fix I thought of was to add "deregisterAlphabet(name)" > method to AlphabetManager, and to call this from the finalize mehod of > SimpleMarkovModel, so that when the garbage collector thinks it can > clear the markov model the statealphabet is removed from the > AlphabetManager registry and can then also be garbage collected. > Also, it would be necessary to make alphabetToIndex a WeakHashMap. This may work - but it adds API. > > Any other suggestions? Can I make these changes? How transparent can we make this? How easy would it be for alphabets to be dropped automatically when not needed any more? I guess we don't want to drop DNA & friends :) > > Thanks, > > Lachlan > Matthew From cs at salestonight.com Tue Dec 23 01:02:13 2003 From: cs at salestonight.com (Digital Cam) Date: Tue Dec 23 01:10:08 2003 Subject: [Biojava-dev] 1 Week Pre-Holiday Sale Message-ID: <884$68O0gfwf-vGwN8O0gfwfP0l5@sale-1.salestonight.com> Need a gift idea? Need a digital camera? Don’t want to spend $300? Want a camera rated best in class? Want to spend less than $80 for it? Want a Web Cam? How about a camera that is a 3 in 1 digital camera – Web, Video and Digital? Want over $200 of Award Winning software free with your purchase? Want FREE Batteries? Want FREE Shipping? Want a FREE Case? Want a FREE Stand? Want a FREE USB Cable? If you answered yes to any of the above, then click here http://www.platinum-deal.com/rd1.php?ac=CD1&bid=294&did=3372&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 partners. If you would prefer to not receive these messages in the future, please http://www.salestonight.com/unsub.php?e=biojava-dev@biojava.org&m=1414032. 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.salestonight.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org zMui2Nf60c6YrImOiJqbKtGrg8jFaHurzHJ TM: <60;68O0gfwf-vGwN8O0gfwfP0l5;1414032> From service at asia-works.com Wed Dec 24 19:07:26 2003 From: service at asia-works.com (AsiaWorks) Date: Wed Dec 24 19:17:54 2003 Subject: [Biojava-dev] Call China, S.Korea less than 1 cent per mintue Message-ID: <200312241923435.SM02560@server04> Hello, We provide the cheapest phone card to call asia. Pay less, call longer guaranteed !!! 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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.salestonight.com/privacy.html. The e-mail subscription address is: biojava-dev@biojava.org P9RHEK2YGdI35WhYmkyqruVwYvoI5TrG TM: <60;0xbYv4C4-dcC9xbYv4C4UYH8;1451032> From jklqitoyouesx at hotmail.com Mon Dec 29 10:38:30 2003 From: jklqitoyouesx at hotmail.com (Purchase) Date: Mon Dec 29 13:41:03 2003 Subject: [Biojava-dev] RE: End of the year special on toner. 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3100se $42.50 --------------------------------------------------------------------------- -------- item 9A C3906A Toner Cartridge for LaserJet 3100, 3150 $42.50 --------------------------------------------------------------------------- -------- item 10 C3900A Black Toner Cartridge for HP LaserJet 4MV, 4V $89.50 --------------------------------------------------------------------------- -------- item 11 C4127A Black Toner Cartridge for LaserJet 4000SE, 4000N, 4000T, 4000TN $76.50 --------------------------------------------------------------------------- -------- item 11A C8061A Black Laser Toner for HP LaserJet 4100, 4100N $76.50 --------------------------------------------------------------------------- -------- item 11B C8061X High Capacity Toner Cartridge for LJ4100, 4100N $85.50 --------------------------------------------------------------------------- -------- item 11C C4127X High Capacity Black Cartridge for LaserJet 4000SE, 4000N,4000T,4000TN $84.50 --------------------------------------------------------------------------- -------- item 12 92291A Toner Cartridge for LaserJet IIISi, 4Si, 4SiMX $57.50 --------------------------------------------------------------------------- -------- item 13 92298A Toner Cartridge for LaserJet 4, 4 Plus, 4M, 4M Plus, 5, 5se, 5M, 5N $46.50 --------------------------------------------------------------------------- -------- item 13A 92298X High Capacity Toner Cartridge for LaserJet 4, 4 Plus,4M, 4M Plus,5,5se, 5M, 5N $56.50 --------------------------------------------------------------------------- -------- item 14 C4129X High Capacity Black Toner Cartridge for LaserJet 5000N $97.50 --------------------------------------------------------------------------- -------- item 15 LASERFAX 500, 700 (FX1) $49.00 --------------------------------------------------------------------------- -------- item 16 LASERFAX 5000, 7000 (FX2) $54.00 --------------------------------------------------------------------------- -------- item 17 LASERFAX (FX3) $49.00 --------------------------------------------------------------------------- -------- item 18 LASERFAX (FX4) $49.00 --------------------------------------------------------------------------- -------- HP COLOR item C1 C4194A Toner Cartridge, Yellow (color lj 4500/4550 series) $89.50 --------------------------------------------------------------------------- -------- item C2 C4193A Toner Cartridge, Magenta (color lj 4500/4550 series) $89.50 --------------------------------------------------------------------------- -------- item C3 C4192A Toner Cartridge, Cyan (color lj 4500/4550 series) $89.50 --------------------------------------------------------------------------- -------- item C4 C4191A Toner Cartridge, Black (color lj 4500/4550 series) $74.50 --------------------------------------------------------------------------- -------- item C5 C4149A Toner Cartridge, Black (color lj 8500/8550 series) $76.50 --------------------------------------------------------------------------- -------- LEXMARK item 19 1380520 High Yield Black Laser Toner for 4019, 4019E, 4028, 4029, 6, 10, 10L $109.50 --------------------------------------------------------------------------- -------- item 20 1382150 High Yield Toner for 3112, 3116, 4039-10+, 4049- Model 12L,16R, Optra $109.50 --------------------------------------------------------------------------- -------- item 21 69G8256 Laser Cartridge for Optra E, E+, EP, ES, 4026, 4026 (6A,6B,6D,6E) $49.00 --------------------------------------------------------------------------- -------- item 22 13T0101 High Yield Toner Cartridge for Lexmark Optra E310, E312, E312L $89.00 --------------------------------------------------------------------------- -------- item 23 1382625 High-Yield Laser Toner Cartridge for Lexmark Optra S (4059) $129.50 --------------------------------------------------------------------------- -------- item 24 12A5745 High Yield Laser Toner for Lexmark Optra T610, 612, 614 (4069) $165.00 --------------------------------------------------------------------------- -------- Epson item 25 S051009 Toner Cartridge for Epson EPL7000, 7500, 8000+ $115.50 --------------------------------------------------------------------------- -------- item 25A S051009 LP-3000 PS 7000 $115.50 --------------------------------------------------------------------------- -------- item 26 AS051011 Imaging Cartridge for ActionLaser-1000, 1500 $99.50 --------------------------------------------------------------------------- -------- item 26A AS051011 EPL-5000, EPL-5100, EPL-5200 $99.50 --------------------------------------------------------------------------- -------- PANASONIC item 27 Nec series 2 models 90 and 95 $109.50 --------------------------------------------------------------------------- -------- APPLE item 28 2473G/A Laser Toner for LaserWriter Pro 600, 630, LaserWriter 16/600 PS $57.50 --------------------------------------------------------------------------- -------- item 29 1960G/A Laser Toner for Apple LaserWriter Select, 300, 310, 360 $71.50 --------------------------------------------------------------------------- -------- item 30 M2045G/A Toner Cartridge for Laserwriter 300, 320 (74A) $52.50 --------------------------------------------------------------------------- -------- item 32 M4683G/A Laser Toner for LaserWriter 12, 640PS $85.50 --------------------------------------------------------------------------- -------- CANON item 33 Fax CFX-L3500, CFX-4000 CFX-L4500, CFX-L4500IE & IF FX3 $49.50 --------------------------------------------------------------------------- -------- item 33A L-250, L-260i, L-300 FX3 $49.50 --------------------------------------------------------------------------- -------- item 33B LASER CLASS 2060, 2060P, 4000 FX3 $49.50 --------------------------------------------------------------------------- -------- item 34 LASER CLASS 5000, 5500, 7000, 7100, 7500, 6000 FX2 $49.50 --------------------------------------------------------------------------- -------- item 34A LBP-200V, LBP-8 II, IIR, IIIT, IIIR EP-S $49.50 --------------------------------------------------------------------------- -------- item 35 FAX 5000 FX2 $49.50 --------------------------------------------------------------------------- -------- item 36 LASER CLASS 8500, 9000, 9000L, 9000MS, 9500, 9500 MS, 9500 S FX4 $49.50 --------------------------------------------------------------------------- -------- item 36A Fax L700,720,760,770,775,777,780,785,790, & L3300 FX1 $49.50 --------------------------------------------------------------------------- -------- item 36B L-800, L-900 FX4 $49.50 --------------------------------------------------------------------------- -------- item 37 A30R Toner Cartridge for PC-6, 6RE, 7, 11, 12 $59.50 --------------------------------------------------------------------------- -------- item38 E-40 Toner Cartridge for PC-720, 740, 770, 790,795, 920, 950, 980 $85.50 --------------------------------------------------------------------------- -------- item38A E-20 Toner Cartridge for PC-310, 325, 330, 330L, 400, 420, 430 $85.50 --------------------------------------------------------------------------- -------- XEROX item 39 6R900 75A $55.50 --------------------------------------------------------------------------- -------- item 40 6R903 98A $46.50 --------------------------------------------------------------------------- -------- item 41 6R902 95A $49.50 --------------------------------------------------------------------------- -------- item 42 6R901 91A $65.50 --------------------------------------------------------------------------- -------- item 43 6R908 06A $42.50 --------------------------------------------------------------------------- -------- item 44 6R899 74A $47.50 --------------------------------------------------------------------------- -------- item 45 6R928 96A $72.50 --------------------------------------------------------------------------- -------- item 46 6R926 27X $84.50 --------------------------------------------------------------------------- -------- item 47 6R906 09A $92.50 --------------------------------------------------------------------------- -------- item 48 6R907 4MV $89.50 --------------------------------------------------------------------------- -------- item 49 6R905 03A $46.50 --------------------------------------------------------------------------- -------- 30 Day unlimited warranty included on all products GT Toner Supplies guarantees these cartridges to be free from defects in workmanship and material. Order by e-mail:gt1000@cable.net.co E-mail removal:gt1000@cable.net.co All trade marks and brand names listed above are property of the respective holders and used for descriptive purposes only. From cs at salestonight.com Mon Dec 29 15:53:36 2003 From: cs at salestonight.com (Accounting) Date: Mon Dec 29 16:01:39 2003 Subject: [Biojava-dev] RE: Last Chance to Claim Your Check. Message-ID: <914$5n3zBrtr-qbtNn3zBrtr9zuO@sale-1.salestonight.com> Would you like to get paid between $25 - $250 just for completing simple 5-10 minute survey? If you answered yes, then we can put you to work today! http://salestonight.com:8080/track?m=1462032&l=0&.e=7DXUdH5H-KL5IDXUdH5HoUxE You get paid to work at home and give your opinion!! BEST OF ALL! There is no limit to how many surveys you can participate in and no limit on how much money you can make. Why Wait? 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The e-mail subscription address is: biojava-dev@biojava.org Y9VN7FtPCPA491toRpP8PN38LnVRvXhT91KGLVlHiB8T TM: <60;9uwbX2m2-sjmYuwbX2m27box;1462032> From cs at salestonight.com Tue Dec 30 19:08:34 2003 From: cs at salestonight.com (Salestonight) Date: Tue Dec 30 19:16:16 2003 Subject: [Biojava-dev] Post Holiday Digital Camera Sale Message-ID: <922$0xbYv4C4-dcC9xbYv4C4UYH8@sale-1.salestonight.com> Need a gift idea? Need a digital camera? Don’t want to spend $300? Want a camera rated best in class? Want to spend less than $80 for it? Want a Web Cam? How about a camera that is a 3 in 1 digital camera – Web, Video and Digital? Want over $200 of Award Winning software free with your purchase? Want FREE Batteries? Want FREE Shipping? Want a FREE Case? Want a FREE Stand? Want a FREE USB Cable? 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