From mark.schreiber at novartis.com Wed May 11 02:04:54 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Wed May 11 01:57:50 2005 Subject: [Biojava-dev] Ant, Biojava and NetBeans Message-ID: Hello - I have been playing with biojava and NetBeans 4.0, I have been pleasently surprised to find it works very well. It copes with the idea of having lots of source directories, integrates very well with CVS and does a good job of building from the Ant build.xml The one thing I have had problems with is that it throws ClassCastExceptions when building Javadocs from the Ant script. This doesn't happen from the command line. It does actually manage to produce HTML (presumably without the nice custom taglets). Googleing around for an answer there is some suggestion it is caused by a JVM bug (something to do with forking processes or something). Has anyone else noticed this? Anyone got a solution? - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From mark.schreiber at novartis.com Wed May 11 05:43:45 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Wed May 11 05:36:43 2005 Subject: [Biojava-dev] SimpleAnnotation now ordered Message-ID: Hello - I have changed the Map that backs SimpleAnnotation to a LinkedHashMap so that properties are now iterated in the order they were added, not randomly as they where before. I would urge anyone making an implementation of Annotation to consider this as the desired behaivour. SimpleAnnotation covers about 90% of all uses. The other common implementation SmallAnnotation aparently already does this. Let me know if someone notices any bugs or performance problems. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From cor.lieftink at xs4all.nl Sun May 22 05:23:47 2005 From: cor.lieftink at xs4all.nl (cor.lieftink@xs4all.nl) Date: Sun May 22 05:16:22 2005 Subject: [Biojava-dev] I am interested to contribute to the bioJava-project. Message-ID: <6.1.2.0.0.20050522104455.019b9ea0@pop3.xs4all.nl> Hi all, I am interested to contribute to the bioJava-project. Allow me to introduce myself. My name is Cor Lieftink, I live in the Netherlands and work as a system-developer in Oracle & Java at a international bank in Amsterdam. Besides working with informatietechnology in the area of financial information, I am interested to extend this into the area of genetic information. As the best way to do this I see contributing to a open source project, like BioJava. Besides that, of course I will be studying books in these area, like Bioinformatics from David Mount. My educational background consists of studies in Psychology and Business, both at the university of Groningen here in the Netherlands. After finishing these studies in 1988 I moved into the field of information technology, programming in Pascal and working with webtechnology, as well as doing projectmanagement. In 1999 I followed a five month fulltime course in Oracle technology and worked with Oracle databases and tools (Developer/Designer) for the next 5 years. Last year I acquired four Sun Java certificates: Programmer 1.4, Web Component Developer, Business Component Developer and Architect for J2EE (theory part) , and passed the IBM Test 287 Enterprise Application Development with Websphere Studio. July last year I started my job at the bank storing financial information in Oracle databases, and retrieve and present it using IBM Websphere Application Developer and Application Server, as wel using Hibernate, CVS and JUnit. I hope to hear from you if, and if yes, how I can contribute to the bioJava project. Regards, Cor From mark.schreiber at novartis.com Wed May 25 09:46:58 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Wed May 25 09:39:51 2005 Subject: [Biojava-dev] I am interested to contribute to the bioJava-project. Message-ID: Cool! The more the merrier. If you have suggestions of some areas you would like to develop then put them to the list for feedback. Your experience might interest you in the BioSQL part of biojava or if you like algorithms the DP package could probably use some updating/ testing and or bug fixing. If you like mundane and thankless work, not unlike banking : ), we desperately need a lot more unit tests and documentation. All the best, - Mark cor.lieftink@xs4all.nl Sent by: biojava-dev-bounces@portal.open-bio.org 05/22/2005 05:23 PM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] I am interested to contribute to the bioJava-project. Hi all, I am interested to contribute to the bioJava-project. Allow me to introduce myself. My name is Cor Lieftink, I live in the Netherlands and work as a system-developer in Oracle & Java at a international bank in Amsterdam. Besides working with informatietechnology in the area of financial information, I am interested to extend this into the area of genetic information. As the best way to do this I see contributing to a open source project, like BioJava. Besides that, of course I will be studying books in these area, like Bioinformatics from David Mount. My educational background consists of studies in Psychology and Business, both at the university of Groningen here in the Netherlands. After finishing these studies in 1988 I moved into the field of information technology, programming in Pascal and working with webtechnology, as well as doing projectmanagement. In 1999 I followed a five month fulltime course in Oracle technology and worked with Oracle databases and tools (Developer/Designer) for the next 5 years. Last year I acquired four Sun Java certificates: Programmer 1.4, Web Component Developer, Business Component Developer and Architect for J2EE (theory part) , and passed the IBM Test 287 Enterprise Application Development with Websphere Studio. July last year I started my job at the bank storing financial information in Oracle databases, and retrieve and present it using IBM Websphere Application Developer and Application Server, as wel using Hibernate, CVS and JUnit. I hope to hear from you if, and if yes, how I can contribute to the bioJava project. Regards, Cor _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From cor.lieftink at xs4all.nl Wed May 25 16:30:08 2005 From: cor.lieftink at xs4all.nl (cor.lieftink@xs4all.nl) Date: Wed May 25 16:22:48 2005 Subject: [Biojava-dev] I am interested to contribute to the bioJava-project. In-Reply-To: References: Message-ID: <6.1.2.0.0.20050525221601.019755e8@pop3.xs4all.nl> Hi Mark, David (and others), Thank you for your replies. I have added David's text below, as it is not in the archive, although David send it with a CC to biojava-dev@biojava.org . Mark wrote: > we desperately need a lot more unit tests and documentation. Documentation and Junit test seem to me good starting points to work myself into the bioJava code. Please let me know what exactly you like me to do. Besides a general interest in genomics and programming, I am especialy interested to contribute to bioJava code that in the end helps genomics to reduce the need for laboratory animals. See for example the report of the international conference Genomics & Alternatives to Animal Use, which was held last year in the Netherlands, held 2 - 4 June, 2004 in Maastricht, the Netherlands. ( www.genomics.nl/homepage/publications/Synopsis_GA.pdf ). For this reason I am a bit more interested in the algorithms part of the code, to help modelling. Regards, Cor Subject: Re: [Biojava-dev] I am interested to contribute to the bioJava-project. Date: Sunday 22 May 2005 23:20 From: David Huen To: cor.lieftink@xs4all.nl Cc: biojava-dev@biojava.org Dear Cor, Since your interest and expertise appear to be on the database and web side of Java, you may have an interest in BioSQL (a database for genetic info, you see correspondence about it in the mailgroup archives). You may also be interested in Flymine (www.flymine.org), a data warehouse project to deliver biological data to biologists, that uses very many of the skills that you appear to have already. Regards, David From bcpowell at email.unc.edu Sat May 7 11:15:35 2005 From: bcpowell at email.unc.edu (Bradford Powell) Date: Fri May 27 15:59:11 2005 Subject: [Biojava-dev] 1.5ism in OracleDBHelper Message-ID: This is probably just an oversight, but I notice (through compilation errors using a 1.4.2 VM), that the recent changes to OracleDBHelper introduced the line: putString.invoke(rs.getClob(column), new Object[]{Long.valueOf(1L),value}); The problem with this is that Long.valueOf is an addition to the Java class libraries in 1.5. Using potential object caching in this case seems to be not that useful relative to maintaining 1.4 compatability. (If biojava should go over to 1.5, it should be for better reasons than this, and I haven't seen a discussion of 1.5 here. So, for the mean time, could someone replace 'Long.valueOf(1L)' with 'new Long(1L)'? Thanks, -- Bradford Powell -- bradford_powell@unc.edu From smh1008 at cam.ac.uk Sun May 22 17:20:12 2005 From: smh1008 at cam.ac.uk (David Huen) Date: Fri May 27 16:01:54 2005 Subject: [Biojava-dev] I am interested to contribute to the bioJava-project. In-Reply-To: <6.1.2.0.0.20050522104455.019b9ea0@pop3.xs4all.nl> References: <6.1.2.0.0.20050522104455.019b9ea0@pop3.xs4all.nl> Message-ID: On May 22 2005, cor.lieftink@xs4all.nl wrote: Dear Cor, Since your interest and expertise appear to be on the database and web side of Java, you may have an interest in BioSQL (a database for genetic info, you see correspondence about it in the mailgroup archives). You may also be interested in Flymine (www.flymine.org), a data warehouse project to deliver biological data to biologists, that uses very many of the skills that you appear to have already. Regards, David From Robin.Emig at pioneer.com Fri May 27 14:22:54 2005 From: Robin.Emig at pioneer.com (Emig, Robin) Date: Fri May 27 16:02:04 2005 Subject: [Biojava-dev] FW: Emailing: MSFAlignmentFormat.java Message-ID: This hasn't been added yet, can some one please do so. Thanks Robin -----Original Message----- From: Emig, Robin Sent: Thursday, April 21, 2005 5:08 PM To: 'Thomas Down'; 'biojava-dev@biojava.org' Subject: RE: Emailing: MSFAlignmentFormat.java Can someone add this to cvs for me, Thanks Robin -----Original Message----- From: Emig, Robin Sent: Wednesday, April 06, 2005 5:29 PM To: 'Thomas Down' Subject: Emailing: MSFAlignmentFormat.java Can you add this to cvs for me. Contains bug fixes to deal more appropriately with case of headers, etc. Thanks Robin This communication is for use by the intended recipient and contains information that may be privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html -------------- next part -------------- A non-text attachment was scrubbed... Name: MSFAlignmentFormat.java Type: application/octet-stream Size: 11747 bytes Desc: MSFAlignmentFormat.java Url : http://portal.open-bio.org/pipermail/biojava-dev/attachments/20050527/a7d0c698/MSFAlignmentFormat.obj From mark.schreiber at novartis.com Tue May 31 06:08:02 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Tue May 31 06:00:51 2005 Subject: [Biojava-dev] 1.5ism in OracleDBHelper Message-ID: Hello - This is fixed now. I have added javac -source 1.4 and javac -target 1.4 information to the ant build script as well. While this would not have prevented this slip up it will prevent someone putting in code with generics, auto unboxing etc. Also means that JAR files built with ant on a JDK1.5 environment should work with JRE1.4. Interestingly code that makes use of classes only found in Java 1.5 will compile but not run (in 1.4) while classes that have new methods will probably compile and run unless they call a new class (it's only bytecode after all). - Mark Bradford Powell Sent by: biojava-dev-bounces@portal.open-bio.org 05/07/2005 11:21 PM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] 1.5ism in OracleDBHelper This is probably just an oversight, but I notice (through compilation errors using a 1.4.2 VM), that the recent changes to OracleDBHelper introduced the line: putString.invoke(rs.getClob(column), new Object[]{Long.valueOf(1L),value}); The problem with this is that Long.valueOf is an addition to the Java class libraries in 1.5. Using potential object caching in this case seems to be not that useful relative to maintaining 1.4 compatability. (If biojava should go over to 1.5, it should be for better reasons than this, and I haven't seen a discussion of 1.5 here. So, for the mean time, could someone replace 'Long.valueOf(1L)' with 'new Long(1L)'? Thanks, -- Bradford Powell -- bradford_powell@unc.edu _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev